WO2010129940A2 - Archael laccases and multicopper oxidases (mcos) and their uses thereof - Google Patents

Archael laccases and multicopper oxidases (mcos) and their uses thereof Download PDF

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WO2010129940A2
WO2010129940A2 PCT/US2010/034177 US2010034177W WO2010129940A2 WO 2010129940 A2 WO2010129940 A2 WO 2010129940A2 US 2010034177 W US2010034177 W US 2010034177W WO 2010129940 A2 WO2010129940 A2 WO 2010129940A2
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polypeptide
lcca
seq
activity
laccase
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WO2010129940A3 (en
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Julie A. Maupin-Furlow
Sivakumar Uthandi
Boutaiba Saad
Matthew A. Humbard
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University Of Florida Research Foundation, Inc.
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/0004—Oxidoreductases (1.)
    • C12N9/0091—Oxidoreductases (1.) oxidizing metal ions (1.16)
    • C—CHEMISTRY; METALLURGY
    • C02—TREATMENT OF WATER, WASTE WATER, SEWAGE, OR SLUDGE
    • C02F—TREATMENT OF WATER, WASTE WATER, SEWAGE, OR SLUDGE
    • C02F3/00—Biological treatment of water, waste water, or sewage
    • C02F3/34—Biological treatment of water, waste water, or sewage characterised by the microorganisms used
    • C02F3/342—Biological treatment of water, waste water, or sewage characterised by the microorganisms used characterised by the enzymes used
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/0004—Oxidoreductases (1.)
    • C12N9/0055—Oxidoreductases (1.) acting on diphenols and related substances as donors (1.10)
    • C12N9/0057—Oxidoreductases (1.) acting on diphenols and related substances as donors (1.10) with oxygen as acceptor (1.10.3)
    • C12N9/0061—Laccase (1.10.3.2)
    • D—TEXTILES; PAPER
    • D21—PAPER-MAKING; PRODUCTION OF CELLULOSE
    • D21C—PRODUCTION OF CELLULOSE BY REMOVING NON-CELLULOSE SUBSTANCES FROM CELLULOSE-CONTAINING MATERIALS; REGENERATION OF PULPING LIQUORS; APPARATUS THEREFOR
    • D21C5/00—Other processes for obtaining cellulose, e.g. cooking cotton linters ; Processes characterised by the choice of cellulose-containing starting materials
    • D21C5/005—Treatment of cellulose-containing material with microorganisms or enzymes
    • C—CHEMISTRY; METALLURGY
    • C02—TREATMENT OF WATER, WASTE WATER, SEWAGE, OR SLUDGE
    • C02F—TREATMENT OF WATER, WASTE WATER, SEWAGE, OR SLUDGE
    • C02F2101/00—Nature of the contaminant
    • C02F2101/30—Organic compounds
    • C02F2101/308—Dyes; Colorants; Fluorescent agents
    • C—CHEMISTRY; METALLURGY
    • C02—TREATMENT OF WATER, WASTE WATER, SEWAGE, OR SLUDGE
    • C02F—TREATMENT OF WATER, WASTE WATER, SEWAGE, OR SLUDGE
    • C02F2101/00—Nature of the contaminant
    • C02F2101/30—Organic compounds
    • C02F2101/34—Organic compounds containing oxygen
    • C02F2101/345—Phenols
    • C—CHEMISTRY; METALLURGY
    • C02—TREATMENT OF WATER, WASTE WATER, SEWAGE, OR SLUDGE
    • C02F—TREATMENT OF WATER, WASTE WATER, SEWAGE, OR SLUDGE
    • C02F2103/00—Nature of the water, waste water, sewage or sludge to be treated
    • C02F2103/26—Nature of the water, waste water, sewage or sludge to be treated from the processing of plants or parts thereof
    • C02F2103/28—Nature of the water, waste water, sewage or sludge to be treated from the processing of plants or parts thereof from the paper or cellulose industry
    • C—CHEMISTRY; METALLURGY
    • C02—TREATMENT OF WATER, WASTE WATER, SEWAGE, OR SLUDGE
    • C02F—TREATMENT OF WATER, WASTE WATER, SEWAGE, OR SLUDGE
    • C02F2103/00—Nature of the water, waste water, sewage or sludge to be treated
    • C02F2103/30—Nature of the water, waste water, sewage or sludge to be treated from the textile industry
    • C—CHEMISTRY; METALLURGY
    • C02—TREATMENT OF WATER, WASTE WATER, SEWAGE, OR SLUDGE
    • C02F—TREATMENT OF WATER, WASTE WATER, SEWAGE, OR SLUDGE
    • C02F2103/00—Nature of the water, waste water, sewage or sludge to be treated
    • C02F2103/34—Nature of the water, waste water, sewage or sludge to be treated from industrial activities not provided for in groups C02F2103/12 - C02F2103/32
    • C02F2103/343—Nature of the water, waste water, sewage or sludge to be treated from industrial activities not provided for in groups C02F2103/12 - C02F2103/32 from the pharmaceutical industry, e.g. containing antibiotics
    • D—TEXTILES; PAPER
    • D21—PAPER-MAKING; PRODUCTION OF CELLULOSE
    • D21C—PRODUCTION OF CELLULOSE BY REMOVING NON-CELLULOSE SUBSTANCES FROM CELLULOSE-CONTAINING MATERIALS; REGENERATION OF PULPING LIQUORS; APPARATUS THEREFOR
    • D21C11/00—Regeneration of pulp liquors or effluent waste waters
    • D21C11/0057—Oxidation of liquors, e.g. in order to reduce the losses of sulfur compounds, followed by evaporation or combustion if the liquor in question is a black liquor
    • D—TEXTILES; PAPER
    • D21—PAPER-MAKING; PRODUCTION OF CELLULOSE
    • D21C—PRODUCTION OF CELLULOSE BY REMOVING NON-CELLULOSE SUBSTANCES FROM CELLULOSE-CONTAINING MATERIALS; REGENERATION OF PULPING LIQUORS; APPARATUS THEREFOR
    • D21C3/00—Pulping cellulose-containing materials
    • D21C3/04—Pulping cellulose-containing materials with acids, acid salts or acid anhydrides
    • D—TEXTILES; PAPER
    • D21—PAPER-MAKING; PRODUCTION OF CELLULOSE
    • D21C—PRODUCTION OF CELLULOSE BY REMOVING NON-CELLULOSE SUBSTANCES FROM CELLULOSE-CONTAINING MATERIALS; REGENERATION OF PULPING LIQUORS; APPARATUS THEREFOR
    • D21C9/00—After-treatment of cellulose pulp, e.g. of wood pulp, or cotton linters ; Treatment of dilute or dewatered pulp or process improvement taking place after obtaining the raw cellulosic material and not provided for elsewhere
    • D21C9/10—Bleaching ; Apparatus therefor

Definitions

  • Multicopper oxidases are a family of enzymes that include laccascs (p- diphenol: dioxygen oxidoreductases, EC 1.10.3.2), ascorbate oxidases (EC 1.10.3.3), ferroxidascs (EC 1.16.3.1), bilirubin oxidases (EC 1.3.3.5) and other enzyme subfamilies (Solomon et al, 1996; Hoegger et al., 2006). MCOs couple the oxidation of organic and/or inorganic substrates to the four-electron reduction of molecular oxygen to water.
  • Type I Type 1
  • T2 Type 2
  • T3 Type 3
  • a mononuclear Tl center on the surface of the enzyme provides long range intramolecular one-electron transfer from electron-donating substrates to an internal trinuclear T2/T3 center formed by a T2 Cu coordinated to a T3 Cu pair.
  • the T2/T3 cluster subsequently reduces dioxygen to water.
  • Enzymes of the laccase subfamily oxidize a broad range of compounds including phenols, polyphenols, aromatic amines, and non-phenolic substrates by one-electron transfer to molecular oxygen and, thus, have a wide variety of applications spanning from biofuels to human health.
  • a lacquer tree laccase (from Rhus vernicifera) has been used in paint and adhesives in East Asia for more than 6000 years (H ⁇ ttermann et al., 2001).
  • Laccases have also been used in the delignification of pulp, bleaching of textile and carcinogenic dyes, detoxification of water and soils, removal of phenolics from wines, improving adhesive properties of lignocellulosic products, determination of bilirubin levels in serum, and transformation of antibiotics and steroids (Sakurai el al., 2007). Likewise, laccases have demonstrated potential in biosensors, bioreactors and biofuel cells (Shleev et al., 2005).
  • laccases were once thought to be restricted to eukaryotes (fungi, plants, insects), recent evidence suggests their widespread distribution in bacteria (Claus, 2004).
  • laccascs are required for normal cell wall structure and integrity in xylem fibers and apparently involved in lignification (Ranocha et al., 2002).
  • laccases mediate the modification and degradation of complex natural polymers such as lignin and humic acids (Widsten et al, 2008; Claus et al., 1998).
  • the lacasse-like MCOs of insects seem to play an important role in cuticular sclerotization, melanization, iron homeostasis and the oxidation of toxic compounds in the diet (Claus, 2004).
  • laccase- like MCOs of bacteria have a wide variety of biological roles including sporulation, electron transport, pigmentation, metal (copper, iron, manganese) homeostasis, oxidation of phenolate-sidcrophorcs, phcnoxazinone synthesis, cell division and morphorgenesis (Claus, 2003).
  • Martins et al (2002) characterized a laccase enzyme isolated from the endospore coat of Bacillus sublilis.
  • Koschorreck et al. (2008) recently disclosed a laccase isolated from Bacillus licheniformis and found it to catalyze dimerization of phenolic acids.
  • laccases usually have very limited temperature, pIT, and salt range because of the living conditions of the plants and bacteria. Their industrial application, which sometimes requires high laccase activity under extreme conditions, may, thus, be further limited. Therefore, laccases with extreme thermal and salt/solvent stability are highly desired.
  • Archaea one of the three domains of life along with the Bacteria and Eukarya, have evolved to thrive in harsh environmental conditions including high temperature, extreme pH, and/or low water activity. Thus, their systems and enzymes are deemed ideal for a number of industrial processes. In contrast to the widespread occurrence of laccascs in eukaryotes and bacteria, only a few putative MCOs are predicted in genomes of archaea including the hyperthermophilic crenarchaeote Pyrobaculum aerophilum (PAEl 888) (Fitz-Gibbon et al., 2002) and the P ⁇ E1888-encoded enzyme is not likely to catalyze the oxidation of phenolic compounds particularly in the absence of metal supplementation.
  • PAEl 888 hyperthermophilic crenarchaeote Pyrobaculum aerophilum
  • the subject invention provides a novel laccasc that is highly thermostable and salt/solvent tolerant and nucleic acids encoding the laccase.
  • the purified laccase has a molecular weight of about 65 kDa and an amino acid sequence comprising SEQ ID NO: 2.
  • the novel laccase is isolated and purified from strains of Haloferax volcanii species. Examples of some Haloferax volcanii strains are listed in Table 1.
  • the laccase is produced by Hfx. volcanii SBOl and US02. The molecular weight is about 65 kDa, determined by gel-filtration chromatography.
  • the subject invention is a method of producing the above disclosed laccase.
  • the laccase is produced in the culture media of its natural host, for example, Hfx. volcanii SBOl , the method comprising the steps of culturing a Haloferax volcanii strain under conditions suitable to produce the enzyme and then recovering the enzyme from the cells or the culture media.
  • the laccase is produced in a production host, such as E. coli, Bacillus megaterium and Saccharomyces cerevisiae, by means of recombinant technology.
  • the subject invention further relates to the use of the claimed laccase in various industrially important protocols that utilize laccases.
  • Figure IA shows phylogenetic comparison of laccase and related multicopper oxidase protein sequences. Origin of protein sequences used for the analysis with corresponding accession numbers and references to biochemical and/or physiological studies in parenthesis were as follows: Hfx. volcanii DS2 (HvoB0205, LccA this study), Acremonium murorum (polyphenol oxidase or PpoA, Q9P8C3) (Gouka et al, 2001), Anaeromyxobacter sp.
  • Fwl09-5 (A7H7L9), Aquifex aeolicus (McoA, AAC07157.1) (Fernandes et al, 2007), Arabidopsis lhaliana (ABG81319, LPRl) and (NP 565008.1, LPR2) (Svistoonoff et al, 2007), Bacillus amyloliquefaciens FZB42 (A7Z229), Bacillus clausii KSM-Kl 6 (Q5WEM6), Bacillus coagulans 36Dl ( ⁇ 2U4V3), Bacillus licheniformis DSM 13 / ATCC 14580 (Q65MU7) (Koschoor et al , 2008).
  • Bacillus pumilus SAFR-032 (A8F ⁇ G9), Bacillus subtilis (P07788, CotA) (Martins et al, 2002), Bacillus sp. B 14905 (A3I8L4), Carnobacterium sp. AT7 (ZP_02185070.1), Clostridium botulinum ATCC 3502 (A5I081), Cyanoihece sp. PCC 7424 (B2F9S5), Escherichia coli (P36649.2, CueO) (Wang et al, 2004), Exiguobacterium sp. ATIb (ZPJ)2990140.1), Frankia sp.
  • volcanii DS2 HVOJ30205, LccA this study
  • Acremonium murorum polyphenol oxidase or PpoA, Q9P8C3
  • Aquifex aeolicus McoA, AAC07157.1
  • Bacillus amyloliquefaciens FZB42 A7Z229)
  • Bacillus clausii KSM-K16 Q5WEM6
  • Bacillus coagulans 36Dl A2U4V3
  • Bacillus licheniformis DSM 13 / ATCC 14580 Q65MU7
  • Bacillus pumilus SAFR-032 A8FAG9
  • Bacillus subtilis P07788, CotA
  • Figure 2A shows laccase activity of Hfic. volcanii SBOl cultures at various stages of growth.
  • Hfx. volcanii SBOl cells were inoculated to a final OD 6O o of 0.01 in Hv-LMM supplemented with 0.1 ⁇ g per ml novobiocin and 100 ⁇ M copper sulfate.
  • Cells were grown for 120 h at 42°C in an orbital shaker (150 - 200 rpm). Samples were withdrawn at periodical intervals and used for estimation of growth (1 OD OOO unit ⁇ 1 x 10 9 CFU per ml) and laccase activity.
  • cells were pelleted by centrifugation (for 10 min at 10,000 ⁇ g and 4 0 C), washed twice in T buffer supplemented with 2 M NaCl, resuspended in T buffer and lysed by sonication (15 s on. 45 s off at 20 % amplitude for 3 min). Culture broth and cell lysate were assayed for laccase (SGZ oxidizing) activity under standard conditions.
  • Figure 2B shows laccase activity of H. volcanii US02 strains at various stages of growth.
  • H. volcanii US02 and parent H26 were inoculated to a final QD OOO of 0.01 in medium supplemented with novobiocin and 100 ⁇ M copper sulfate.
  • LMM and YPC were optimal for production of laccase activity for US02.
  • cells were harvested by centrifugation (10 min at 10,000 x g and 4 0 C), washed twice in T buffer supplemented with 2 M NaCl, resuspended in T buffer and lysed by sonication (15 s on, 45 s off at 20 % amplitude for 3 min). Culture broth (filtered by 0.4 ⁇ m) and cell lysate were assayed for laccase (SGZ oxidizing) activity under standard conditions.
  • Figures 3A-3B show LccA purified to electrophoretic homogeneity from the culture broth of Hfx. volcanii SBOl .
  • MonoQ 10/10, pH 8.4 fractions (lane 5);
  • FIG. 4 shows LccA purified as an 65.4-kDa monomer from the culture broth of Hfx v ⁇ lcanii SBOl.
  • Native molecular mass of Lcc ⁇ was determined by applying protein fractions eluted at 625 to 650 mM NaCl in 25 mM Tris-HCl buffer at pH 8.4 (T buffer) from MonoQ 5/5 to a Superdex 200 HR 10/30 column calibrated with protein molecular mass standards with elution volumes ( ⁇ ) as indicated.
  • Figure 5 show UV-Visible absorbance spectrum of LccA purified from Hfx. volcanii SBOl .
  • Purified LccA (77 ⁇ g-ml "1 ) was dissolved in T buffer containing 185 mM NaCl.
  • FIGS 6A-6F show temperature (Fig. 6A), salt (Fig. 6B) and pH (Fig. 6C) optima of LccA purified from Hfx volcanii SBOl .
  • Fig. 6A Effect of temperature on the catalytic activity of LccA.
  • LccA (51 ⁇ g-ml " ) activity was assayed at different temperatures (22° to 70 0 C) in T buffer with 185 mM NaCl using SGZ (1 mM) as the substrate. Activity is expressed as percent relative to the optimum at 45 0 C;
  • Fig. 6B Effect of salt on the catalytic activity of LccA.
  • the SGZ oxidizing activity of LccA was measured at different concentrations (up to 1.0 M) of NaCl (•) and KCl (o) in T buffer at 45 0 C. Activity is expressed as percent relative to 185 mM NaCl; Fig. 6C - Effect of pH on the catalytic activity of LccA.
  • LccA activity was assayed with SGZ (•) from pH 6 to 11 and with ABTS (o) from pH 3 to 8 at 45 0 C using following buffers: 100 mM sodium acetate for pH 3 to 6, 25 mM Tris-HCl for pH 7 to 10, and 25 mM glycine-NaOH for pH 11. Activity is expressed as percent relative to oxidation of ABTS at pH 6.
  • Fig. 6D Thermostability of LccA.
  • Purified enzyme (50.6 ⁇ g-ml "1 ) was pre-incubated in T buffer supplemented with 185 mM NaCl at temperatures from 37° to 70 0 C for up to 60 h, as indicated. After incubation, laccase activity was estimated by oxidation of SGZ at standard conditions. Activity is presented as percent relative to incubation on ice (37 0 C (•), 45 0 C ( ⁇ ), 50 0 C (A), 55 0 C ( ⁇ ). 60 0 C (o). 65 0 C (D) and 70 0 C ( ⁇ )); Fig. 6E - Salt tolerance of LccA protein.
  • Enzyme (7.5 ⁇ g-ml "1 ) was incubated in T buffer with 185 mM NaCl in the presence and absence of 25 % (v/v) solvent (DMSO, DMF, ethanol and methanol) at room temperature for 90 min (white bar), 3 h (grey bar) and 24 h (black bar). Enzyme and solvent were diluted 4-fold in T buffer with 185 mM NaCl and residual enzyme activity was estimated under standard conditions using SGZ as the substrate. Activity is calculated as percent relative to incubation without solvent.
  • Figure 7 shows sequence alignment of Hfx. volcanii laccase (LccA. IIvoJ30205, SEQ ID NO: 2) to multicopper oxidases.
  • ) represents cleavage site which has experimental evidence for LccA and Mvcr__Q12737.
  • TAT motifs indicated by a bold double underline, are based on in silico analysis using TATFIND vl .4 server. The one cysteine and 10 histidine residues that bind the four copper atoms to form the Type I. Il and III active sites of known multicopper oxidases are indicated above the amino acid residue (•).
  • Hlac ZP-02016827 SEQ ID NO: 3
  • Halorubrum lacusprofundi putative multicopper oxidase (Copeland el al, 2008); Bsub_BAA22774 (SEQ ID NO: 4), Bacillus subtilis spore coat protein A (CotA) with laccase activity (Martins et al, 2002); Scha_A ⁇ Y23005 (SEQ ID NO: 5), Stachybotrys chartariim phenol oxidase A (Mander et al, 2006); Mver_Q12737 (SEQ ID NO: 6), Myrolhecium verrucaria bilirubrin oxidase (Koikeda et al, 1993).
  • Figure 8 provides various exemplary fragments of the laccase disclosed herein.
  • the numbering of the N- and C-terminal amino acid residue is provided with reference to Figure 7 and SEQ ID NO: 2.
  • Figure 9 shows Gel filtration analysis of LccA.
  • LccA (MonoQ 5/5, pll 8.4, MQl) fractions from H. volcanii SBOl were applied to a calibrated Supcrdex 200 HR 10/30 column as described in methods.
  • the laccase active peak containing LccA protein is indicated by an arrow.
  • FIG. 10 shows MS-analysis of LccA.
  • LccA fractions purified from H. volcanii SBOl (SEQ ID NO: 28) and US02 (SEQ ID NO: 29) were digested with trypsin and analyzed by MS as described in methods. Tryptic peptides identified by MS are underlined and detailed in Table 5.
  • FIG 11 shows LccA purified to electrophoretic homogeneity from the culture broth of //, volcanii US02. Reducing 10 % SDS PAGE of LccA at various stages of purification including ethanol precipitate (lanes 1, EP) and MonoQ 10/10. pll 8.4 (lane 2, MQ) as indicated. Molecular standards on left. Proteins were stained with Coomassie brilliant blue R-
  • Figures 12A-12C show LccA purified from US02 is a glycoprotein.
  • A Native gels of
  • Prestained kaleidoscope and low range protein standards were included for US02 and SBOl, respectively as indicated on left of each gel.
  • B Pro-Q Emerald glycoprotein analysis of US02-purified LccA. Proteins were separated by reducing 10 % SDS-PAGE. Gels were stained for glycosylation by Pro-Q Emerald (left) and total protein by SYPRO-
  • Probes including a mixture of glyosylated (G) and nonglycosylated proteins as indicated (lane 5).
  • C Deglycosylation of LccA.
  • LccA purified from US02 was treated with TFMS on ice for 0 h (lane 1), 1O h (lane 2) and 3 h (lane 3) and separated by reducing 6 and 10 % SDS-
  • Figure 13 shows UV-Visible absorbance spectrum of LccA.
  • Absorbance of LccA 1.5 mg-ml "1 ) purified from H volcanii US02 in T buffer containing 185 mM NaCl was analyzed from 300 to 700 nm.
  • Figure 14 shows laccase activity produced culture broth of //, volcanii strain US02 in accordance with the subject invention.
  • Figure 15 shows ability of LccA to delignify sugarcane bagasse.
  • SEQ ID NO: 1 polynucleotide sequence encoding Hfx. volcanii laccase.
  • SEQ ID NO: 2 polypeptide sequence of ///3c. volcanii laccase. DETAILED DISCLOSURE OF THE INVENTION
  • oligopeptide in natural form, that is to say that they are not in their natural environment but that the polypeptides may have been isolated or obtained by purification from natural sources or obtained from host cells prepared by genetic manipulation (e.g., the polypeptides, or fragments thereof, are recombinantly produced by host cells, or by chemical synthesis).
  • Nucleotide sequence can be used interchangeably and are understood to mean, according to the present invention, either a double-stranded DNA, a single-stranded DNA or products of transcription of the said DNAs (e.g., RNA molecules). It should also be understood that the present invention does not relate to genomic polynucleotide sequences in their natural environment or natural state.
  • nucleic acid, polynucleotide, or nucleotide sequences of the invention can be isolated, purified (or partially purified), by separation methods including, but not limited to, ion- exchange chromatography, molecular size exclusion chromatography, or by genetic engineering methods such as amplification, subtractive hybridization, cloning, subcloning or chemical synthesis, or combinations of these genetic engineering methods.
  • isolated or “biologically pure” refer to material that is substantially or essentially free from components which normally accompany the material as it is found in its native state.
  • isolated requires that the material be removed from its original environment (e.g., the natural environment if it is naturally occurring).
  • a naturally-occurring polynucleotide or polypeptide present in a viable eukaryotic cell or a prokaryotic cell is not isolated, but the same polynucleotide or DNA or polypeptide, separated from some or all of the coexisting materials in the natural system, is isolated.
  • Such polynucleotide could be part of a vector and/or such polynucleotide or polypeptide could be part of a composition, and still be isolated in that the vector or composition is not part of its natural environment.
  • isolated are: nucleic acid sequences found in databases containing the complete genomic sequence of Haloferax volcanii, naturally-occurring chromosomes (such as chromosome spreads of Halqferax volcanii or chromosomes isolated from Haloferax volcanii), artificial chromosomal libraries of Haloferax volcanii.
  • genomic libraries of Haloferax volcanii and cDNA libraries of Haloferax volcanii that exist either as an in vitro nucleic acid preparation or as a transfected/transformed host cell preparation, wherein the host cells are either an in vitro heterogeneous preparation or plated as a heterogeneous population of single colonies.
  • an isolated polynucleotide comprising SEQ ID NO: 1 is specifically defined as excluding those sequences found in a database containing the genomic sequence of Haloferax volcanii, naturally-occurring chromosomes of Haloferax volcanii (e.g., chromosome spreads of Haloferax volcanii or chromosomes isolated from Haloferax volcanii), artificial chromosomal libraries of Haloferax volcanii, genomic libraries of Haloferax volcanii, and/or cDNA libraries of Haloferax volcanii that contain SEQ ID NO: 1 or a polynucleotide encoding SEQ ID NO: 2.
  • whole cell ⁇ Haloferax volcanii genomic DNA or whole cell RNA preparations (including whole cell preparations which are mechanically sheared or enzymatically digested).
  • whole cell Haloferax volcanii preparations as either an in vitro preparation or as a heterogeneous mixture separated by electrophoresis (including blot transfers of the same) wherein the polynucleotide of the invention has not further been separated from the heterologous polynucleotides in the electrophoresis medium ⁇ e.g., further separating by excising a single band from a heterogeneous band population in an agarose gel or nylon blot).
  • antibodies that specifically bind to SEQ ID NO: 2 are provided. In various embodiments, these antibodies do not cross-react with other proteins that are structurally related.
  • One aspect of the subject invention provides isolated, purified, and/or recombinant polypeptides having laccase activity, wherein the polypeptides have a molecular weight of about 65 kDa (using gel-filtration chromatography) and/or comprise the amino acid sequence SEQ ID NO: 2.
  • Another aspect of the invention provides for fragments of the polypeptides disclosed herein, wherein the polypeptide fragments retain laccase activity.
  • Polypeptide fragments, as described herein can be obtained by cleaving the polypeptides of the invention with a proteolytic enzyme (such as trypsin, chymotrypsin, collagenase or other known proteases) or with a chemical reagent, such as cyanogen bromide (CNBr).
  • a proteolytic enzyme such as trypsin, chymotrypsin, collagenase or other known proteases
  • CBr cyanogen bromide
  • polypeptide fragments can be generated in a highly acidic environment, for example at pH 2.5. After cleavage via any of these agents, the polypeptide fragments can be assayed for laccase activity as described herein.
  • compositions comprising SEQ ID NO: 2, or fragments thereof retaining laccase activity and a carrier (e.g., an aqueous or organic liquid).
  • a carrier e.g., an aqueous or organic liquid.
  • fragments having laccase activity such as those disclosed in Figure 8. are provided.
  • fragments of SEQ ID NO: 2 having laccase activity can start at any one of amino acid residues 140, 141, 142, 143. 144 or 145 and the C-terminal amino acid of the fragment can be any amino acid found at positions 524 through 579 of SEQ ID NO: 2.
  • the polypeptides can be obtained from a Hal of er ax volcanii strain, for example, Hfx. volcanii DS2 or a mutant strain thereof. In a preferred embodiment, a mutant strain Hfx. volcanii SBOl is used. In another embodiment, the polypeptide has the amino acid sequence set forth in SEQ ID NO: 2.
  • a "variant polypeptide” (or polypeptide variant) is to be understood to designate polypeptides exhibiting, in relation to SEQ ID NO: 2. certain modifications. These modifications can include a deletion, addition, or substitution of at least one amino acid, a truncation, an extension, a chimeric fusion, a mutation, or polypeptides exhibiting post- translational modifications.
  • homologous variant polypeptides arc those comprising amino acid sequences exhibiting between at least (or at least about) 39.00% to 99.99% (inclusive) identity to the full length, native, or naturally occurring polypeptide are another aspect of the invention.
  • variant polypeptides can have 39, 40, 41, 42, 43, 44, 45. 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66. 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78. 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89. 90,
  • a variant or modified polypeptide exhibits at least 60, 61, 62, 63, 64, 65. 66. 67, 68, 69, 70, 71, 72, 73. 74, 75, 76, 77, 78. 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96. 97, 98, or 99 percent identity to SEQ ID NO: 2.
  • the percent identity is calculated with reference to the full-length, native, and/or naturally occurring polypeptide (e.g., SEQ ID NO: 2). In all instances, variant polypeptides retain the laccase activity associated with SEQ ID NO: 2.
  • variant polypeptides can also comprise one or more heterologous polypeptide sequences (e.g., tags that facilitate purification of the polypeptides of the invention (see, for example, U.S. Patent No. 6.342.362, hereby incorporated by reference in its entirety).
  • the microorganisms can be cultivated on a suitable medium, including, for example, a halobacterium medium ATCC 974.
  • the medium can also include other ingredients, such as salts, buffers, drugs, and nutrients.
  • the strain is grown in complex medium ATCC 974 and lactate-minimal medium (Hv-LMM).
  • the medium can also include other ingredients such as antibiotics, e.g. ampicillin and novobiocin.
  • the culture can be grown in liquid or solid medium.
  • the Hv-LMM is supplemented with CUSO 4 for faster production of the enzyme in Hfx. volcanii, presumably based on a more efficient conversion of the apoenzyme to the mature copper-loaded, active form.
  • the concentration of CuSO 4 can be about 100 ⁇ iM.
  • Various other embodiments utilize less agitated culture conditions over heavily agitated conditions in obtaining greater production of the claimed laccase.
  • the production of the polypeptide can be detected by measuring the laccase activity
  • Suitable substrates for measuring the enzyme activity include 2,2'-azino-bis-3-ethylbenzthiazoline-6-sulphonic acid (ABTS). 2,6-dimethoxyphenol (DMP), 2-methoxyphenol (guaiacol), and 4-hydroxy-3,5-dimethoxybenzaldehyde azine (syringaldazine or SGZ).
  • ABTS 2,2'-azino-bis-3-ethylbenzthiazoline-6-sulphonic acid
  • DMP 2,6-dimethoxyphenol
  • guaiacol 2-methoxyphenol
  • 4-hydroxy-3,5-dimethoxybenzaldehyde azine syringaldazine or SGZ.
  • the polypeptide can be produced in its native host.
  • the native host is Hfx. volcanii DS70.
  • the polypeptide of SEQ ID NO: 2 can also be produced by an engineered host cell expressing a nucleic acid encoding SEQ ID NO: 2.
  • engineered host cells expressing a nucleic acid encoding SEQ ID NO: 2 include E. coli, Bacillus megaterium and Saccharomyces cerevisiae.
  • the subject invention relates to methods of producing a polypeptide comprising cultivating a Haloferax volcanii strain that is able to secrete the polypeptide naturally or a host cell containing the encoding gene, under conditions suitable to produce the polypeptide, and recovering the polypeptide from the culture medium.
  • the recovered polypeptide can then be isolated and purified by using known methods of protein purification, such as precipitation, centrifugation, filtration, anion exchange chromatography, and gel- filtration chromatography.
  • the laccase is purified from a culture broth by filtration.
  • the culture broth is further purified by ethanol precipitation and centrifugation.
  • Anion-exchange chromatography is further used for purification.
  • the purified product can be verified by SDS-PAGE, mass spectroscopy and in gel activity staining. In one embodiment, the purity of the obtained laccase is between 38 to 68% from the above application. In another embodiment, SDS-PAGE gives a molecular weight of 70.7 kDa. In yet another embodiment, the gel filtration chromatography estimates the native molecular mass to be about 65 kDa.
  • the purified and concentrated polypeptide can be characterized for enzyme activity, thermostability, salt/solvent stability, or other properties.
  • the laccase activity of the purified polypeptide at various temperatures, pH, and salt concentrations can be determined using SGZ and/or ABTS as substrates.
  • the thermo, salt or solvent stability can be determined by incubating the purified polypeptide at various temperatures, salt concentrations, or solvent types with the other factors fixed.
  • the polypeptide, and biologically active fragments thereof, disclosed herein exhibits laccase activity at temperatures of about 2O 0 C to about 70 0 C, about 3O 0 C to about 55 0 C (with over 80% laccase activity) or between about 45 0 C to about 50 0 C.
  • the polypeptide is salt resistant exhibits laccase activity at all concentrations between about 100 mM and 300 mM NaCl or KCl ⁇ e.g. , >100 mM NaCl or KCl, between 100-250 mM NaCl or KCl, between about 150-250 mM NaCl or KCl, or about 200 mM NaCl or KCl).
  • the polypeptide displays about 1.5-fold higher activity in KCl than NaCl.
  • the polypeptide of the subject invention is catalytically active under both acidic and alkaline pH conditions while being substrate dependent (Fig. 6C).
  • Most microbial laccases display optimal activity at low pH.
  • the alkalophilic nature of the polypeptide disclosed herein is advantageous in various industrial applications including paper pulp bleaching and wastewater treatment processes. Unlike the subject polypeptide, the few microbial laccases that are active at alkaline pH do not exhibit significant activity below pH 6.0.
  • the subject polypeptide is also thermostable at temperatures from 37 to 70 0 C. In one embodiment, it is fully active after 1 h at 55°C and 5 h at 50 0 C, with a half-live of inactivation at 5O 0 C of 31.5 h ( Figures 6A and 6D).
  • the polypeptide retains nearly all of its original laccase activity at 37 0 C and 35 to 60% of its activity at 45 to 5O 0 C, after incubation for 2 Vi days.
  • the purified polypeptide is stable in a wide range of NaCl concentrations from 100 mM to, at least, 1.4 M, retaining nearly all of its original activity if not higher ( Figures 6B and 6E). Prolonged incubation, from about 90 min to 24 h, of the polypeptide in salt does not alter this activity profile. This is better than a recently analyzed laccase from a bacterium isolated from a mangrove swamp (i.e., Streplomyces psammoticus) which only demonstrated salt tolerance with full activity after incubation for 24 h in 0.8 M NaCl (Niladevi el al., 2008).
  • Salt tolerance is one of the preferred characteristics from an industrial stand-point as laccases are used for effluent treatment including bleaching and decolorization of phenolilc dyes where salt concentration can be a constraint for in situ enzymatic treatment of wastewaters rich in salts.
  • the purified polypeptide is highly solvent tolerant.
  • the polypeptide is relatively stable in all solvents (i.e., methanol, ethanol, dimethyl sulfoxide or DMSO and dimethylformamide or DMF) examined, retaining nearly 75% of its activity after about 24 h incubation in methanol or ethanol and over 50% of its activity after incubation in DMSO or DMF (Fig. 6F).
  • Solvent compatibility of the subject polypeptide from Hfic. volcanii may be used to facilitate transformation of insoluble lignin components and lower the degree of polymerization of phenoxyl radicals originated during lignin oxidation.
  • laccase substrates and mediators are insoluble or poorly soluble in water and the solvent stability of the disclosed polypeptide would be of much interest to change the direction of catalytic reactions and to gain access to insoluble substrates and enhance the solubility of mediators.
  • several potential applications of laccases need to be performed in the presence of significant amounts (in some cases up to 50% v/v) of water-miscible organic cosolvent.
  • the subject invention also provides polynucleotides, vectors, genetic constructs and transformed host cells. These polynucleotides, vectors, genetic constructs, and transformed host cells contain nucleic acids encoding a laccase as described herein. Nucleic acid probes derived from such nucleic acids are also provided by the subject invention.
  • the subject invention also provides isolated, recombinant, and/or purified polynucleotide sequences comprising: a) a polynucleotide sequence encoding a polypeptide comprising SEQ ID NO: 2; b) a homologous polynucleotide sequence having at least about 20% to 99.99% identity to a polynucleotide sequence encoding a polypeptide SEQ ID NO: 2, wherein said polynucleotide encodes a polypeptide having laccase activity; c) a polynucleotide sequence comprising SEQ ID NO: 1 ; d) a homologous polynucleotide sequence having at least about 20% to 99.99% identity to the polynucleotide sequence of SEQ ID NO: 1 and encoding a polypeptide having laccase activity; e) a polynucleotide that is complementary to the polynucleotides set forth in (a), (b), (c), or (d);
  • a vector comprising a polynucleotide or genetic construct as set forth in (a), (b), (c), (d). (e), or (f); h) a host cell comprising a vector as set forth in (g); i) a polynucleotide that hybridizes under low, intermediate or high stringency with a polynucleotide sequence as set forth in (a), (b), (c), (d) or (e); or j) a probe comprising a polynucleotide according to (a), (b), (c), (d), (c), (f), or (g) and, optionally, a label or marker;
  • a homologous polynucleotide sequence for the purposes of the present invention, encompasses a sequence having a percentage identity with the polynucleotide sequences, set forth herein, of between at least (or at least about) 20.00% to 99.99% (inclusive).
  • the aforementioned range of percent identity is to be taken as including, and providing written description and support for, any fractional percentage, in intervals of 0.01 %, between 20.00% and. up to, including 99.99%.
  • These percentages are purely statistical and differences between two nucleic acid sequences can be distributed randomly and over the entire sequence length.
  • homologous sequences can exhibit a percent identity of 20, 21 , 22, 23,
  • the percent identity is calculated with reference to the full length, native, and/or naturally occurring polynucleotide.
  • Both protein and nucleic acid sequence homologies may be evaluated using any of the variety of sequence comparison algorithms and programs known in the art.
  • sequence comparison algorithms and programs include, but are by no means limited to, TBLASTN, BLASTP, FAST ⁇ , TFASTA, and CLUSTALW (Pearson and Lipman, 1988, Proc. Natl. Acad. Sci. USA «5 ⁇ :2444-2448; Altschul et al , 1990, J. MoI. Biol. 275(5/403-410; Thompson et al, 1994; Higgins et al, 1996, Methods Enzymol. 266:383-402; Altschul et al, 1990, J. MoI.
  • a “complementary" polynucleotide sequence generally refers to a sequence arising from the hydrogen bonding between a particular purine and a particular pyrimidine in double-stranded nucleic acid molecules (DNA-DNA, DNA-RNA, or RNA- RNA). The major specific pairings are guanine with cytosine and adenine with thymine or uracil.
  • a ''complementary" polynucleotide sequence may also be referred to as an "antisense' " polynucleotide sequence or an "antisense sequence”.
  • Sequence homology and sequence identity can also be determined by hybridization studies under high stringency, intermediate stringency, and/or low stringency. Various degrees of stringency of hybridization can be employed. The more severe the conditions, the greater the complementarity that is required for duplex formation. Severity of conditions can be controlled by temperature, probe concentration, probe length, ionic strength, time, and the like. Preferably, hybridization is conducted under low, intermediate, or high stringency conditions by techniques well known in the art, as described, for example, in Keller, G.H., MM. Manak [1987] DNA Probes. Stockton Press, New York, NY., pp. 169-170.
  • hybridization of immobilized DNA on Southern blots with 32 P-labeled gene-specific probes can be performed by standard methods (Maniatis et al. [1982] Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York). In general, hybridization and subsequent washes can be carried out under intermediate to high stringency conditions that allow for detection of target sequences with homology to the exemplified polynucleotide sequence.
  • hybridization can be carried out overnight at 20-25 0 C below the melting temperature (T 1n ) of the DNA hybrid in 6X SSPE, 5X Denhardt's solution, 0.1% SDS, 0.1 mg/ml denatured DNA. The melting temperature is described by the following formula (Beltz et al, [1983] Methods of Enzymology, R. Wu, L. Grossman and K. Moldave [eds.J Academic Press, New York 100:266-285).
  • T m melting temperature
  • T m (°C) 2(number T/A base pairs)" 4(number G/C base pairs) (Suggs el al. [19811 ICN-UCLA Symp. Dev. Biol. Using Purified Genes, D. D. Brown [ed.]. Academic Press, New York, 23:683-693).
  • Washes can be carried out as follows:
  • salt and/or temperature can be altered to change stringency.
  • a labeled DNA fragment >70 or so bases in length the following conditions can be used:
  • procedures using conditions of high stringency can also be performed as follows: pre-hybridization of filters containing DNA is carried out for 8 h to overnight at 65°C in buffer composed of 6X SSC, 50 mM Tris-HCl
  • the hybridization step can be performed at 65°C in the presence of SSC buffer, IX SSC corresponding to 0.15 M NaCl and
  • filter washes can be done at 37°C for 1 h in a solution containing 2X SSC, 0.01% PVP, 0.01% Ficoll, and 0.01% BSA, followed by a wash in 0.1X
  • filter washes can be performed in a solution containing 2X SSC and 0.1% SDS, or 0.5X SSC and 0.1% SDS, or 0.1X SSC and 0.1% SDS at 68°C for 15 minute intervals.
  • the hybridized probes are detectable by autoradiography.
  • Other conditions of high stringency which may be used are well known in the art and as cited in Sambrook et al, 1989, Molecular Cloning, A Laboratory Manual, Second Edition, Cold Spring Harbor Press, N. Y., pp. 9.47-9.57; and Ausubel et al, 1989, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N. Y.
  • the probe sequences of the subject invention include mutations (both single and multiple), deletions, insertions of the described sequences, and combinations thereof, wherein said mutations, insertions and deletions permit formation of stable hybrids with the target polynucleotide of interest. Mutations, insertions and deletions can be produced in a given polynucleotide sequence in many ways, and these methods are known to an ordinarily skilled artisan. Other methods may become known in the future.
  • restriction enzymes can be used to obtain functional fragments of the subject DNA sequences.
  • BaB l exonuclease can be conveniently used for time-controlled limited digestion of DNA (commonly referred to as "erase-a-base” procedures). See, for example, Maniatis et al [1982] Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York; Wei et al. [1983] J. Biol. Chem. 258: 13006-13512.
  • the present invention further comprises fragments of the polynucleotide sequences of the instant invention.
  • Representative fragments of the polynucleotide sequences according to the invention will be understood to mean any nucleotide fragment having at least 5 successive nucleotides, preferably at least 12 successive nucleotides, and still more preferably at least 15, 18, or at least 20 successive nucleotides of the sequence from which it is derived.
  • the upper limit for such fragments is the total number of nucleotides found in the full-length sequence encoding a particular polypeptide (e.g., a polypeptide such as that of SRQ ID NO: 2).
  • a polynucleotide fragment may be referred to as "a contiguous span of at least X nucleotides, wherein X is any integer value beginning with 5; the upper limit for such fragments is one nucleotide less than the total number of nucleotides found in the full-length sequence encoding a particular polypeptide ⁇ e.g., a polypeptide comprising SEQ ID NO: 2).
  • the subject invention includes those fragments capable of hybridizing under various conditions of stringency conditions (e.g., high or intermediate or low stringency) with a nucleotide sequence according to the invention; fragments that hybridize with a nucleotide sequence of the subject invention can be, optionally, labeled as set forth below.
  • stringency conditions e.g., high or intermediate or low stringency
  • the subject invention provides, in one embodiment, methods for the identification of the presence of nucleic acids according to the subject invention in transformed host cells or in cells expressing similar laccases.
  • the invention provides for the detection of nucleic acids in a sample (obtained from a cell) comprising contacting a sample with a nucleic acid (polynucleotide) of the subject invention (such as an RNA, mRNA. DNA, cDNA, or other nucleic acid).
  • a nucleic acid polynucleotide
  • the polynucleotide is a probe that is, optionally, labeled and used in the detection system.
  • Many methods for detection of nucleic acids exist and any suitable method for detection is encompassed by the instant invention.
  • Typical assay formats utilizing nucleic acid hybridization includes, and are not limited to, 1) nuclear run-on assay, 2) slot blot assay, 3) northern blot assay (Alwine, el al, Pr ⁇ c. Nail. Acad. Sci. 74:5350), 4) magnetic particle separation, 5) nucleic acid or DN ⁇ chips, 6) reverse Northern blot assay, 7) dot blot assay, 8) in situ hybridization, 9) RNase protection assay (Melton, el al, Nuc. Acids Res.
  • Labels suitable for use in these detection methodologies include, and are not limited to 1) radioactive labels, 2) enzyme labels, 3) chemiluminescent labels, 4) fluorescent labels, 5) magnetic labels, or other suitable labels, including those set forth below. These methodologies and labels are well known in the art and widely available to the skilled artisan. Likewise, methods of incorporating labels into the nucleic acids are also well known to the skilled artisan.
  • the subject invention also provides detection probes (e.g., fragments of the disclosed polynucleotide sequences) for hybridization with a target sequence or the amplicon generated from the target sequence.
  • detection probes e.g., fragments of the disclosed polynucleotide sequences
  • Such a detection probe will comprise a contiguous/consecutive span of at least 8, 9, 10, 1 1 , 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75. 80, 85. 90, 95, or 100 nucleotides.
  • Labeled probes or primers are labeled with a radioactive compound or with another type of label as set forth above (e.g., 1) radioactive labels, 2) enzyme labels, 3) chemiluminescent labels, 4) fluorescent labels, or 5) magnetic labels).
  • non-labeled nucleotide sequences may be used directly as probes or primers; however, the sequences are generally labeled with a radioactive element ( 32 P, 33 S, H, 2S I) or with a molecule such as biotin, acetylaminofluorene, digoxigenin, 5-bromo-deoxyuridine, or fluorescein to provide probes that can be used in numerous applications.
  • Polynucleotides of the subject invention can also be used for the qualitative and quantitative analysis of gene expression using arrays or polynucleotides that are attached to a solid support.
  • array means a one -, two-, or multi-dimensional arrangement of full length polynucleotides or polynucleotides of sufficient length to permit specific detection of gene expression.
  • the fragments are at least 15 nucleotides in length. More preferably, the fragments are at least 100 nucleotides in length. More preferably, the fragments are more than 100 nucleotides in length. In some embodiments the fragments may be more than 500 nucleotides in length.
  • quantitative analysis of gene expression may be performed with full- length polynucleotides of the subject invention, or fragments thereof, in a complementary DNA microarray as described by Schena et al. (Science 270:467-470, 1995; Proc. Natl. Acad.
  • Polynucleotides, or fragments thereof, are amplified by PCR and arrayed onto silylated microscope slides.
  • Printed arrays are incubated in a humid chamber to allow rehydration of the array elements and rinsed, once in 0.2% SDS for 1 min, twice in water for 1 min and once for 5 min in sodium borohydride solution.
  • the arrays are submerged in water for 2 min at 95 0 C, transferred into 0.2% SDS for 1 min, rinsed twice with water, air dried and stored in the dark at 25°C.
  • mRNA is isolated from a biological sample and probes are prepared by a single round of reverse transcription.
  • Probes are hybridized to 1 cm rnicroarrays under a 14 x 14 mm glass coverslip for 6-12 hours at 6O 0 C. Arrays arc washed for 5 min at 25 0 C in low stringency wash buffer (I x SSC/0.2% SDS), then for 10 min at room temperature in high stringency wash buffer (0.1 x SSC/0.2% SDS). Arrays are scanned in 0.1 x SSC using a fluorescence laser scanning device fitted with a custom filter set. Accurate differential expression measurements are obtained by talcing the average of the ratios of two independent hybridizations.
  • Quantitative analysis of the polynucleotides present in a biological sample can also be performed in complementary DNA arrays as described by Pietu et al (Genome Research 6:492-503, 1996).
  • the polynucleotides of the invention, or fragments thereof, are PCR amplified and spotted on membranes. Then, mRNAs originating from biological samples derived from various tissues or cells are labeled with radioactive nucleotides. After hybridization and washing in controlled conditions, the hybridized mRNAs are detected by phospho-imaging or autoradiography. Duplicate experiments are performed and a quantitative analysis of differentially expressed mRNAs is then performed.
  • the polynucleotide sequences of to the invention may also be used in analytical systems, such as DNA chips.
  • DNA chips and their uses are well known in the art and (see for example, U.S. Patent Nos. 5,561,071 ; 5,753,439; 6,214,545; Schena et al, BioEssays, 1996, 18:427-431; Bianchi et al, CUn. Diagn. Virol, 1997, 8:199-208; each of which is hereby incorporated by reference in their entireties) and/or are provided by commercial vendors such as Affymetrix, Inc. (Santa Clara, CA).
  • the nucleic acid sequences of the subject invention can be used as molecular weight markers in nucleic acid analysis procedures.
  • modified nucleotide sequences will be understood to mean any nucleotide sequence that has been modified, according to techniques well known to persons skilled in the art, and exhibiting modifications in relation to the native, naturally occurring nucleotide sequences.
  • the subject invention also provides genetic constructs comprising: a) a polynucleotide sequence encoding a polypeptide comprising SEQ ID No: 2, or a fragment thereof, optionally having laccase activity; b) a polynucleotide sequence having at least about 20% to 99.99% identity to a polynucleotide sequence encoding a polypeptide comprising SEQ ID No: 2 or a fragment of SEQ ID NO: 2, wherein said polynucleotide encodes a polypeptide or fragment thereof has laccase activity; c) a polynucleotide sequence encoding a fragment of a polypeptide comprising SEQ ID No: 2, wherein said fragment has laccase activity; d) a polynucleotide sequence comprising SEQ ID NO: 1; c) a polynucleotide sequence having at least about 20% to 99.99% identity to the polynucleotide sequence of SEQ ID NO: 1) a polynucleotide sequence
  • variant polypeptide of the polypeptide of SEQ ID No: 2. wherein said variant has laccase activity; or f) a polynucleotide sequence encoding a fragment of a variant polypeptide as set forth in (e).
  • Genetic constructs of the subject invention can also contain additional regulatory elements such as promoters and enhancers and, optionally, selectable markers.
  • the genetic construct comprises a promoter operably linked to a polynucleotide sequence encoding SEQ ID NO: 2.
  • the vectors and expression cassettes may contain additional transcriptional control sequences as well.
  • the vectors and expression cassettes may further comprise selectable markers.
  • the expression cassette may contain at least one additional gene, operably linked to control elements, to be co-transformed into the organism.
  • the additional gene(s) and control element(s) can be provided on multiple expression cassettes.
  • Such expression cassettes are provided with a plurality of restriction sites for insertion of the sequences of the invention to be under the transcriptional regulation of the regulatory regions.
  • the expression cassette(s) may additionally contain selectable marker genes operably linked to control elements.
  • the expression cassette will include in the 5'-3' direction of transcription, a transcriptional and translational initiation region, a DNA sequence of the invention, and a transcriptional and translational termination regions.
  • Vectors of this invention can also comprise elements necessary to allow the expression and/or the secretion of the said nucleotide sequences in a given host cell.
  • the vector can contain a promoter, signals for initiation and for termination of translation, as well as appropriate regions for regulation of transcription.
  • the vectors can be stably maintained in the host cell and can, optionally, contain signal sequences directing the secretion of translated protein. These different elements are chosen according to the host cell used.
  • Vectors can integrate into the host genome or. optionally, be autonomously-replicating vectors.
  • the subject invention also provides for the expression of a polypeptide, peptide, fragment, or variant encoded by a polynucleotide sequence disclosed herein comprising the culture of a host cell transformed with a polynucleotide of the subject invention under conditions that allow for the expression of the polypeptide and, optionally, recovering the expressed polypeptide.
  • One aspect of the invention provides for methods of oxidizing a phenolic substrate comprising contacting the polypeptide as described herein, or fragments thereof retaining laccase activity, with a substrate comprising phenolic compounds under conditions that allow for the oxidation of the phenolic compounds.
  • the phenolic substrates include 2,6-dimelhoxyphenol (DMP) and 4-hydroxy-3,5-dimethoxybenzaldehyde azine (syringaldazine or SGZ).
  • DMP 2,6-dimelhoxyphenol
  • syringaldazine or SGZ 4-hydroxy-3,5-dimethoxybenzaldehyde azine
  • Wine is another source of phenolic substrates that can be oxidized by the disclosed laccase.
  • the contacting step can be performed by adding a composition comprising the purified laccase as described herein, or fragments thereof retaining laccase activity, to the phenolic compounds.
  • the contacting step can be performed in the presence of other materials
  • the subject polypeptide, or fragments thereof retaining laccase activity is capable of oxidizing bilirubin to biliverdin and water, which is desirable for a variety of clinical applications.
  • bilirubin interferes with adsorption bands between 400 and 500 nm. Addition of the polypeptide to plasma samples diminishes interference enables quantification of molecules at 400 to 500 nm such as plasma hemoglobin at 415 nm.
  • the polypeptide of SEQ ID NO: 2, or fragments thereof retaining laccase activity is able to mediate the delignification and detoxification of acid- pretreated biomass. Simultaneous saccharification and fermentation of hemicellulosic biomass is limited by the toxic compounds generated during the biomass pretreatment that restrict activity of the saccharifying enzymes and productivity of the microbial biocatalysts. Likewise, steps taken to optimize the modification of lignin by enzymes could bypass the need for harsher pretreatment steps and thereby facilitate bioprocess consolidation.
  • the subject invention provides methods of delignification and detoxification of acid-pretreated biomass comprising contacting acid-pretreated biomass with a laccase comprising SEQ ID NO: 2, or fragments thereof retaining laccase activity.
  • the laccasc of SEQ ID NO: 2. or fragments thereof retaining laccase activity can be used for bleaching of dye in solutions.
  • Such a method comprises contacting the dye with the laccase comprising SEQ ID NO: 2 within the solution.
  • Yet another aspect of the invention provides methods of bleaching pulp for paper production that comprises contacting paper pulp with a laccase comprising SEQ ID NO: 2, or fragments thereof retaining laccase activity.
  • the disclosed laccase can be used in methods of lignin modification (e.g. in the manufacture of wood composites, such as wood fiber materials such as chipboards, fiber boards, or particle boards, or in the manufacture of laminated wood products, such as laminated beams and plywood) comprising contacting a lignin with a laccase comprising SEQ ID NO: 2, or fragments thereof retaining laccase activity.
  • An additional aspect of the invention comprises the treatment of waste water from: chemical or pharmaceutical factories; dye manufacturing facilities or dye-works; textile facilities or pulp production facilities.
  • This aspect of the invention comprises contacting waste water from such facilities with a laccase comprising SEQ ID NO: 2, or fragments thereof retaining laccase activity.
  • Biochemicals were from Sigma-Aldrich (St. Louis, Mo.). Other organic and inorganic analytical grade chemicals were from Fisher Scientific (Atlanta, Ga.). Restriction endonucleases, T4 DNA ligase and Vent DNA polymerase were from New England Biolabs (Ipswich, Mass.). AccuPrime GC -rich DNA polymerase was from Invitrogen (Carlsbad, Calif.). Desalted oligonucleotides were from Integrated DNA Technologies (Coralville, Iowa). Agarose for routine analysis of DNA was from BioRad Laboratories (Hercules. Calif). SeaKem GTG agarose used for separation and isolation of DNA fragments prior to ligation was from FMC Bioproducts (Rockland, ME). Strains, Media and Plasmids
  • E. coli DH5 ⁇ was used for routine recombinant DNA experiments, and E. coli GM2163 was used to generate plasmid DNA for transformation of Hfx. volcanii (Dyall-Smith, 2008).
  • E. coli strains were grown at 37 0 C in Luria-Bertani medium.
  • Hfx. volcanii strains were grown at 42 0 C in complex (ATCC 974 and yeasl-peptone-Casamino Acids) and lactate-minimal medium (Hv- LMM).
  • Hv-LMM included 2.46 M NaCl, 84 niM MgCl 2 -OH 2 O, 84 niM MgSO 4 -7H 2 O. 56 mM KCl, 6 niM CaCl 2 -2H 2 O, 5 mM NII 4 Cl, 4.6 mM NaBr, 1.4 mM NaIICO 3 , 9.75 mM KPO 4 pH 7.5. 30 mM Tris pH 7.5, 0.25% (v/v) DL-lactic acid, 14 mM succinic acid.
  • NCBI Local BlastP (Altschul et al, 1997) with BioEdit sequence editor software v7.0.4.1 (Hall, 1999) was used to compare the theoretical Hfx. volcanii DS2 proteome (http://archaea.ucsc.edu/, April 2007 version) (Hartman et al.. 2009) to fungal and bacterial proteins with known laccase activity.
  • Laccase protein sequences included phenol oxidase A of the ligno-cellulolytic ascomycete Siachybotrys chartarum (Mander et al., 2006), spore coat protein A (CotA) from Bacillus subtilis (Martins et al..
  • TatP vl .O Bose et al , 2005
  • TATHND vl .4 Rose et al, 2002
  • EnsembleGly Caragea et al., 2007
  • PCR was performed with an iCycler (BioRad Laboratories), and sizes of products were analyzed by electrophoresis using 0.8% (w/v) agarose gels in TAE buffer (40 m ⁇ l Tris acetate, 2 mM EDTA, pH 8.5) with Hi-Lo DNA molecular weight markers as standards (Minnesota Molecular, Minneapolis, Minn.). Gels were photographed after staining with ethidium bromide at 0.5 ⁇ g-mF 1 with a Mini visionary imaging system (FOTODYNE, Hartland, Wis.).
  • PCR generated-DNA fragments of appropriate si/e for the lccA gene (1.8 kb) were isolated from 0.8% (w/v) ScaKem GTG agarose (FMC Bioproducts, Rockland, ME) gels in TAE buffer using the QIAquick gel extraction kit (Qiagen) and ligated into the Ndel to HindIII sites of pET24b to generate plasmid pJ ⁇ M821 and pJAM823 for expression of the lccA gene in recombinant E. coli Rosetta (DE3).
  • the lccA gene was excised from plasmids pJAM821 and pJAM823 and ligated into the Ndcl to BIpI sites of a Hfx. volcanii shuttle vector (pJ ⁇ M202) to position the lccA gene downstream of a constitutive ribosomal RNA promoter P2.
  • These expression plasmids (pJAM822 and pJAM824) were transformed into Hfx. volcanii H26 to generate strain SBOl and US02 for high-level synthesis of lccA with and without a C-termianl strepll tag (- WSHPQFEK), respectively.
  • Plasmid DNA was isolated using the QIAprep Spin Miniprep Kit (Qiagen. Valencia, Calif.), and the fidelity of cloned DNA sequences and the 100% identity of lccA genes from DS2 and DS70 strains were confirmed by Sanger DNA Sequencing (ICBR Genomics Facility, University of Florida). Enzyme Purification
  • Hfx. volcanii SBOl and US02 cells were grown in media supplemented with 100 ⁇ M CuSO 4 (LMM or YPC; 25 ml per 125 -ml Erlenmeyer flask) and harvested by centrifugation (15,000 x g; 20 min at 4 0 C). Culture broth was filtered by 3MM Whatman chromato graph ⁇ paper. Protein was concentrated by gradual addition of one volume of cold absolute ethanol, incubation on ice (1 h) and centrifugation (7,000 x g at 4°C, 10 min). The resulting precipitate was suspended in 25 mM Tris-HCl buffer at pH 8.4 (T buffer) to 1/5 original sample volume and recentrifuged to eliminate insoluble material.
  • T buffer Tris-HCl buffer
  • Elution was carried out with a linear NaCl gradient (0 to 1 M in 1 ml T buffer) with fractions containing peak activity at 625 to 675 mM NaCl. Additional steps were included for purification of LccA from SBOl, including application of active fractions (0.25 ml per run) to a Superdex 200 HR 10/30 column (Pharmacia) equilibrated in T buffer with 150 mM NaCl, followed by a MonoQ HR 10/10 column (Pharmacia) equilibrated in T buffer and developed with a linear NaCl gradient (600 to 800 mM in 1 ml T buffer).
  • bovine serum albumin (97.3), ovalbumin (54.1 kDa), carbonic anhydrase (37.6 kDa), soybean trypsin inhibitor (29.2 kDa), lysozyme (20.0 kDa).
  • Native molecular mass was determined by applying samples to a calibrated Superose 200 HR 10/30 column as recommended by supplier (Pharmacia).
  • Molecular mass standards for gel filtration calibration included: cytochrome c (12.4 kDa). carbonic anhydrase (29 kDa).
  • bovine serum albumin 66 kDa
  • alcohol dehydrogenase 150 kDa
  • ⁇ -amylase 200 kDa
  • apoferritin 443 kDa
  • Substrates for enzyme activity assay included 2,2'-azino-bis-3-elhylbenzthiazoline-6- sulphonic acid (ABTS) (Sigma; A1888), 2,6-dimethoxyphenol (DMP) (Sigma; D135550), 2- methoxyphenol (guaiacol) (Sigma; G5502), 4-hydroxy-3.5-dimethoxybenzaldehyde azine (syringaldazine or SGZ) (Sigma; S7896), bilirubin (Sigma; B4126), and ferrous ammonium sulfate.
  • ABTS 2,2'-azino-bis-3-elhylbenzthiazoline-6- sulphonic acid
  • DMP 2,6-dimethoxyphenol
  • D135550 2- methoxyphenol
  • guaiacol Sigma; G5502
  • 4-hydroxy-3.5-dimethoxybenzaldehyde azine syringaldazine
  • Standard assay conditions were 185 mM NaCl at 45 0 C with the following buffers and substrate concentrations: 100 mM sodium acetate buffer at pll 6.0 for ABTS (at 5 mM), DMP (at 2 mM) and guaiacol (at 5 mM); 25 mM Tris-HC) buffer at pH 8.4 for SGZ (at 1 mM); and 200 mM Tris-HCl buffer at pH 8.4 for bilirubin (0.45 mM). Copper sulfate (1 mM) was included for assay of DMP oxidation.
  • MES morpholineethanesulfonic acid
  • Tris-HCl buffer pH 7.0 and 8.4
  • One unit of enzyme activity is defined as the amount of enzyme that oxidizes 1 ⁇ mol of substrate per min at standard conditions.
  • Kinetic studies were conducted using purified Lcc ⁇ at a final concentration of 0.61 ⁇ g-ml "1 with 5 to 160 ⁇ M of SGZ, 50 to 1,250 mM ABTS, and 90 to 540 ⁇ M bilirubin.
  • Kinetic parameters (K 1n , V max and k cat ) were determined using the Michaelis-Menten equation. Protein concentration was determined according to Bradford (1976) using a Bio-Rad protein assay with bovine serum albumin as a standard (BioRad Laboratories). All assays and protein purifications were performed at least in triplicate.
  • LccA was provided for MS analysis as an in-solution sample and as protein bands separated by reducing SDS-PAGE (7.5%). Gels were stained with Biosafc Coomassic (BioRad), and LccA-protein bands (71 IcDa) were excised from the gel and destained with 100 mM NH 4 HCO 3 (pH 7.5) in 50% (v/v) acetonitrile (4 0 C overnight). Protein samples were reduced, alkylated in gel or in solution, digested with a 1 :20 mg ratio of trypsin (Promega) to protein (18 to 24 h, 37 0 C) and desalted with a PepMap Cl 8 cartridge.
  • LccA N-Terminal Sequence Analysis of Protein Purified LccA was separated by reducing 12% SDS PAGE and transferred by electroblotting to Immobilon-P (PVDF) membranes (Amersham Biosciences) at 100 V for 100 min at 4°C. Proteins were stained in membrane with 0.2 % (w/v) Coomassie blue R-250 in 40% acetic acid for 30 sec and rinsed with deionized water. The LccA-specif ⁇ c protein band was excised and subjected to automated Edman degradation for N-terminal sequencing (Edman, 1970). Glycoprotein Analysis
  • LccA was separated by reducing SDS-PAGE and stained in gel for glycosylation using Pro-Q Emerald 300 ( ⁇ nvitrogen P21857) and total protein was separated using Sypro
  • LocA The carbohydrate content of purified LocA was estimated by the colorimetric method of Dubois et al. (Dubois et al., 1956) using glucose as a standard. Pure LccA was deglycosylated by the trifluoromethanesulfonic acid (TFMS) method (Edge et al., 1981) for 0 to 10 hours on ice and analyzed by reducing SDS-PAGE.
  • TFMS trifluoromethanesulfonic acid
  • the Hfx. volcanii LccA was also predicted to be secreted by the twin-arginine translocation (TAT) system, based on a N-terminal twin arginine motif (SRRRFL) preceding a hydrophobic patch.
  • TAT twin-arginine translocation
  • SRRRFL N-terminal twin arginine motif
  • LccA was also predicted to be cleaved between Ala31 and Ala 32 to generate a mature protein of 60.1 kDa and to be glycosylated based on the presence of O- and N-linked glycosylation motifs, Thr-X 5 -Pro-X-Pro and Asn-X- (Thr/Ser) (where X represents any amino acid) (Fig. 7).
  • an ORF closely related to the Hfx. volcanii LccA was present in the draft genome of the haloarchaeon Halorubrum lacusprofundi (HlacDRAFT_2279), LccA homologs were not universal among the haloarchaea and were absent from the genomes of Halobacterium sp.
  • NRC-I Hb. salinarum Rl
  • Haloquadratum walsbyi DSM 16790 (Bolhuis et al, 2006)
  • Haloarcula marismortui ATCC 43049 Baliga et al, 2004
  • Naironomonas pharaonis DSM 2160 FeIb et al, 2005.
  • the Hfic volcanii Lcc ⁇ was closely related to MCO proteins of the gram-positive fimiicutes, including CotA proteins of R. subtilis and Bacillus licheniformis.
  • thermostable laccase activity (Martins et al, 2002; Koschorreck et al, 2008).
  • LccA was closely related (45% identity) only to Hlac_1049, encoded on the main chromosome of IIalorubrum lacuspro fundi.
  • Other archaeal genomes did not encode LccA homologs, including the haloarchaea Halobaclerium sp. NRC-I (JIalohacterium salinarum Rl). Haloquadratum walsbyi DSM 16790. Haloarcula marismortui ATCC 43049.
  • PAEl 888 an uncharacterized protein with enhanced transcript leels under denitrifying conditions in of P. aerophilum (Cozen el al., 2009). PAEl 888 clusters instead with McoA of Aquifex aeolicus, CueO of E. coli and Mco of Staphylococcus aureus. All three of these latter bacterial MCOs have catalytic and/or genetic properties consistent with their proposed role in oxidative stress and/or copper and iron homeostasis (e.g., Singh et al.
  • laccase gene homologs among the archaea and the close relationship of LccA to laccases of the firmicutcs suggest that lccA was acquired by horizontal gene transfer from the Bacteria domain and that it encodes a laccase that oxidizes phenolic compounds.
  • LccA LccA
  • TAT substrates "salt-loving" haloarchaeal proteins, enzymes with elaborate metal clusters, and glycoproteins are all notoriously difficult to produce in an active form at high-levels in conventional expression systems, such as E. coli and Saccharomyces cerevisiae (Connaris el al., 1999; Madzak et al., 2005; Br ⁇ ser,
  • the native host i.e., Hfx. volcanii, known for its halophilic properties and robust TAT system (Rose et al., 2002) was engineered for enhanced expression of Ice A.
  • Multicopy plasmids pJAM822 and pJAM824 with a pHV2 origin of replication, ribosomal RNA P2 promoter and T7 transcriptional terminator were used for this lccA gene-expression.
  • the lccA gene was positioned downstream of a strong rRNA P2 promoter on a multicopy plasmid (pHV2 based) with and without coding sequence for a 1-Da C-terminal Strepll tag (- WSHPQFEK), and the resulting plasmids were transformed into Ii. volcanii H26.
  • the resulting strains, Hfx. volcanii SBOl and US02 (Table 1) were grown in various media supplemented with CuSO 4 (50 to 500 ⁇ M) and compared to their parent (H26) for the production of laccase activity by monitoring the oxidation of SGZ. Using this approach, laccase activity associated with H.
  • volcanii cells was negligible for all three strains examined reaching at most 0.69 ⁇ 0.12 mU-mF 1 after 80 - 12O h of growth (Figs. 2A and 2B). In contrast to these cellular fractions, significant levels of laccase activity were detected in the culture broth of H. volcanii SBOl and US02 with the highest level of activity detected for strain US02 in YPC medium with 100 ⁇ M CuSO 4 (Fig. 2B).
  • EXAMPLE 3 PURIFICATION OF LccA FROM THE CULTURE BROTH OF HFX.
  • Laccase activity was purified 12-fold from the culture broth of Hfx. volcanii SBOl to a specific activity of 1.3 U-mg "1 (SGZ oxidation) as outlined in Table 2.
  • extracellular proteins were precipitated from culture broth and fractionated by a combination of anion exchange and gel-filtration chromatography steps. It is interesting to note that the laccase activity reproducibly increased 1.4-fold after ethanol precipitation (Table 2), most likely due to the removal of inhibitory compounds and/or proteins from the sample by this technique.
  • the final chromatography steps yielded a homogeneous and laccase-active preparation of LccA based on SDS-PAGE, mass spectroscopy and in gel activity staining ( Figure 3).
  • MonoQ 10/10 fraction was composed of a single protein band estimated at 70.7 kDa compared to the migration of molecular mass standards (Figure 3 ⁇ ). This molecular mass was somewhat higher, yet consistent, with the 63,397 Da calculated in silico for the LccA polypeptide.
  • Final MonoQ 10/10 fractions were further analyzed by mass spectrometry, using QSTAR XL hybrid LC/MS/MS, to confirm the protein composition and purity. The MS profiles of tryptic peptide fragments generated from the protein in solution were compared to the fragments generated after excision of the 71 -IcDa protein from the gel.
  • LccA was identified as the protein responsible for the laccase activity with 38 to 68% coverage (Table 5). LccA fractions were further analyzed by native PAGE coupled with in gel activity stain followed by staining for total protein. A single protein band was detected in the Superdex 200 HR 10/30 fractions that was active in the oxidation of both ABTS and SGZ ( Figure 3B). As the mobility in native PAGE gels depends on both the charge and hydrodynamic size of the protein, the low pi of LccA (calculated at 4.34) is likely to account for its rapid migration in the gel compared to proteins of lower molecular mass (e.g.. 54-kDa ovalbumin).
  • LccA LccA protein was applied to a gel filtration chromatography (Superose 200 HR 10/30 column) calibrated with molecular mass standards.
  • the LccA protein was estimated to be 65.4 kDa and, thus, is most likely associated as a monomer ( Figure 4).
  • N-tcrminal sequencing of the LccA protein was unsuccessful suggesting it may be blocked by modifications such as N ⁇ -acetylation which is common to this organism (Kirkland el al., 2008).
  • LccA- StrepII was similarly purified from SBOl with the addition of gel filtration (Fig. 9) and MonoQ chromatography steps at the final stages of purification (Table 2).
  • the specific activity of LccA-StrepII was over 20-fold lower at only 1.3
  • LccA (purified as described above) was separated by native PAGE and stained for SGZ oxidizing activity and total protein.
  • LccA-StrepIT SBOl purified LccA-StrepIT
  • LccA purified from US02 migrated as at least four separate isoforms that were all active in SGZ oxidation (Fig. 12A).
  • LccA was modified post-translational and that addition of a C-terminal StrepII tag abolished this modification.
  • mobility in native gels depends not only on the hydrodynamic size but also the charge of the protein.
  • the LccA polypeptide sequence is predicted to be highly acidic, and this is likely to account for the rapid migration of all of the LccA isoforms compared to protein standards of similar molecular mass.
  • the US02-purified LccA was N- terminal sequenced by Edman degradation and analyzed for glycosylation.
  • Purified LccA was cleaved after Ala31 (Fig. 7) and glycosylated based on a carbohydrate content of 6.9 ⁇ 0.06 % as determined by a phenol-sulfuric acid method (Dyall-Smith et al., 2008) and staining using Pro-Q Emerald 300 (Hoegger et al., 2006) (Fig. 12B).
  • the carbohydrate content of LccA was 2.6-fold lower than observed for the commercial T.
  • TFMS treatment did not shift the migration of non- glycosylated control proteins (e.g., carbonic anhydrase) confirming that polypeptide chains remained intact under these conditions (data not shown). Together these results provide evidence that LccA is secreted, cleaved and glycosylated during its maturation; however, the order of these events remains to be determined.
  • non- glycosylated control proteins e.g., carbonic anhydrase
  • EXAMPLE 6 SPECTROSCOPIC AND CATALYTIC PROPERTIES OF PURIFIED LccA
  • the purified LccA protein (purified from US02) was blue and exhibited an absorbance spectrum typical of blue multicopper oxidases including a peak at approximately 600 nm and shoulder at 330 nm ( Figure 5).
  • Many laccases isolated from fungi and bacteria are blue multicopper oxidases that coordinate four copper atoms into three types of copper- binding sites (Hoegger el al., 2006). All of these 'blue' enzymes produce spectra with a maximum at 605 nm corresponding to the Tl or blue copper atom.
  • the T2 copper site exhibits weakly visible absorbance, and the T3 copper site has two copper centers and is responsible for a shoulder at around 330 nm.
  • the spectrum of LccA is consistent with its clustering to blue laccases including the closely related and structurally characterized B. subtilis CotA (Enguita et ah, 2003).
  • B. subtilis CotA Enguita et ah, 2003.
  • the conserved cysteine and 10 histidinc residues are likely to coordinate the three types of copper sites in LccA.
  • the activity of LccA toward different phenolic and non-phenolic compounds was investigated.
  • LccA did not oxidize Fe H or guaiacol in the presence or absence of copper supplementation, it did oxidize the remaining substrates, i.e., ABTS at 6.1 ⁇ 0.39 U-mg "1 .
  • DMP at 12.6 ⁇ 1.1 U-mg "1
  • SGZ at 29.4 ⁇ 1.4 U-mg "1
  • bilirubin at 25.5 ⁇ 1 U-mg "1 where the values reported are for US02- purified LccA under standard conditions (see methods for details). Note that the oxidation of DMP was highly stable for several hours but, unlike ABTS, SGZ and bilirubin, required addition Of CuSO 4 .
  • LccA presented a higher specificity for SGZ than for ABTS, with k c JK m values of 0.62 and 0.015 S ' VM "1 , respectively (Table 3). While the SGZ specificity of LccA was significantly lower than that of the DUF 152 RL5-laccases, it is comparable to if not higher than that of B. subtilis CotA (Table 3).
  • laccases have been grouped based on their DMP oxidase activity (Solano et ah, 2001).
  • the first group oxidizes DMP without copper supplementation (e.g., laccase of Pyricularia oryzae, PpoA of Marinomonas mediterrane ⁇ )
  • the second group of en/ymes readily oxidize DMP after addition of copper but are also rapidly inactivated (e.g., CucO of E. col ⁇ )
  • the third type shows a very slow rate of DMP oxidation that lasts for hours, but only in the presence of added copper (e.g., CotA of B subtilis).
  • LccA oxidized DMP only in the presence of added CuSO 4 ; hence, it appears most similar to this latter group of laccases.
  • LccA activity was optimum at 45 to 50 0 C ( Figure 6A), consistent with the optimal growth temperature of this organism (42 to 45°C) (Robinson et al, 2005). Relative to this optimum, LccA was -75% active at room temperature (25 0 C) and 15, 35, 48 and 67% active at 70. 65. 60 and 55°C respectively.
  • the temperature optimum of LccA is similar to a number of bacterial MCOs including the 40 to 45 0 C for laccases of Streptomyces sp (Niladevi and Prema.
  • LccA activity was optimal at ⁇ 200 mM salt with 1.5-fold higher activity in KCl than NaCl, and the enzyme displayed reduced activity after removal of the salt by dialysis ( Figure 6B).
  • LccA was also active at relatively high concentrations of salt with 65% relative activity at 1 M NaCl ( Figure 6B). The ability of LccA to rapidly oxidize phenolic substrates at molar concentrations of salt is not surprising as this enzyme is secreted by a microbe isolated from the Dead Sea. Similarly Lbhl from Bacillus halodurans was stimulated by addition of 450 rnM NaCl
  • LccA Unlike LccA, the few microbial laccases that are active at alkaline pH do not exhibit significant activity below pi I 6.0.
  • the alkalophilic nature of LccA might be of interest in paper pulp bleaching, which requires an alkaline pH optimum.
  • LccA IS STABLE AT HIGH TEMPERATURE, SALT AND SOLVENT
  • the purified protein was pre-incubated at various temperatures from 37 to 70 0 C for up to 2 1 A days.
  • LccA was fully active after 1 h at 55 0 C and 5 h at 5O 0 C, with a half-live of inactivation at 5O 0 C of 31.5 h ( Figure 6D).
  • the enzyme retained nearly all of its original activity at 37°C and 35 to 60% of its activity at 45 to 50 0 C, after incubation for 2 Vz days.
  • the multicopper oxidase of Aquifex aeolicus, McoA. has remarkably stable activity, with the ability to oxidize metals after incubation for 5 h at 90 0 C (Fernandes et al., 2007).
  • the recently studied recombinant RL 5 laccase from rumen metagenome has maximal activity at 6O 0 C and is fully stable at this temperature for 200 min (Beloqui el al.. 2006).
  • Cot ⁇ of /?. subtilis is also thermostable, with a half-life of nearly 2 h at 80 0 C (Martins et al, 2002).
  • the purified LccA was also stable in a wide range of NaCl concentrations from 100 mM to. at least, 1.4 M, retaining nearly all of its original activity if not higher (Figure 6E). It is noteworthy that prolonged incubation, from 90 min to 24 h, of LccA in salt did not alter this activity profile (data not shown). Recent analysis of a laccase from a bacterium isolated from a mangrove swamp (i.e., Streptomyces psammoticus) demonstrated this enzyme is also salt tolerant with full activity after incubation for 24 h in 0.8 M NaCl (Niladevi and Prema, 2008).
  • LccA activity A number of compounds were examined for their influence on LccA activity including small ions (sodium azide or NaN 3 ), sulfhydryl-group containing redox reagents (L- cysteine, dithiothreitol or DTT), denaturants (thiourea) and chelators (EDT ⁇ , 1,10- phenanthroline, 2,2-dipyridyl) (Table 4).
  • the most effective laccase inhibitors to date are small anions, especially N 3 " , which often bind to the trinuclear copper center and interfere with electron flow and substrate oxidation (Johnson el al., 2003). Consistent with this, LccA was inhibited nearly 50% by addition of 1 mM NaN 3 .
  • the LccA protein was also susceptible to denaturation by thiourea with 90% inhibition at 10 mM. Although the general chelator EDTA had no inhibitory activity toward LccA at 50 mM, the transition metal chelators 2,2-dipyridyl and 1 , 10-phenanthroline were inhibitory with a 25% and 90% reduction in LccA activity at 10 mM, respectively. These results are consistent with the recalcitrant nature of the copper- containing laccases toward chelation by EDTA ⁇ e.g., (Saito et ah, 2003), yet reveal a likely role of metals in LccA activity, based on inhibition by phenanthroline.
  • EXAMPLE 9 IMPROVED PRODUCTION OF LACCASE ACTIVITY BY Hfx. v ⁇ lcanii Laccasc activity was produced at high-levels (1.65 ⁇ 0.22 U-ml "1 ) in the culture broth of // volcanii strain US02 after 72 h of growth (at 42° C; 150 rpm) in YPC medium supplemented with 100 ⁇ M CuSO 4 (see Fig. 14). Activity was enhanced 10-fold by improved culture and enzyme assay conditions compared to earlier report (Uthandi et al., 2010).
  • EXAMPLE 10 DELIGNIFIC ATION OF SUGARCANE BAGASSE BY LccA
  • sugarcane bagasse was treated with 1% (v/v) phosphoric acid and steam exploded in a shotgun reactor at 190 0 C for 10 min.
  • the resultant bagasse was adjusted to pH 8.4 with 5M NaOH.
  • Stream exploded bagasse was delignified using the laccase, LccA, from H. volcanii
  • EXAMPLE 12 PRODUCTION AND ACTIVATION OF LACCASE (LccA) FROM RECOMBINANT E. coli
  • the Ufa. volcanii lccA gene was altered by site-directed mutagenesis for production of an LccA protein with an altered TAT signalling motif (Arg ⁇ Lys, Arg7Lys and Arg8Lys) (LccA ⁇ TAT).
  • This LccA protein variant was produced in recombinant E. coli Rosetta (DE3) (Table 1) using the pET expression system. Cells were lysed by French press (1,000 lb/in 2 ) in 20 mM Tris buffer at pH 7.5 with 150 mM NaCl. Cell lysate was clarified by centrifugation
  • ⁇ p r ; NV; 11-kb Hfx. volcanii-E. coli shuttle vector derived from pBAP5009 includes Halobacterium (Jolley et al.. pBAP5010 ciitirubrum rRNA P2 promoter (?2 r ⁇ n ), T7 transcription terminator and pHV2 ori for expression of cloned 1997) genes in Hfx volcanii pJAM202 Ap r ; Nv 1 ; pBAP5010 containing ?2 nn -psmB-H6 (Kaczowka et al.,
  • HvoB0205 5'-aaAAGCTTtcaggccacttcgtcgccgcttc-3' (SEQ ID This study
  • HJx. volcanii SBOl and US02 were grown for 60 to 72 h in HvLMM (42 0 C, 200 rpm), respectively.
  • LccA protein was purified from culture broth as indicated. Activity was monitored by oxidation of SGZ under standard assay conditions (see methods).
  • Fl and F2 represents the lower (viscous) and upper fractions generated after concentration by centrifugal filtration using a Centricon PL-30, respectively (see methods).
  • ⁇ LccA was incubated with the various compounds for 10 min at 45 0 C in T buffer with 185 mM NaCl and assayed for SGZ oxidizing activity under standard conditions. ⁇ Values represent the average of at least 3 replicates. c u.d., undetectable.
  • K.FVQPLP1PSVR.E (Ions score 55) (SEQ ID NO' 10) K FVQPLP1PSVREPDGQR.D (Ions score 30) (SEQ ID NO' 10)
  • FaIb M., Pfeiffer, F., Palm, P., Rodewald, K., Hickmann, V., Tittor, J., and Oesterhelt, D. (2005) Genome Res. 15, 1336-1343.
  • Koschorreck K., Richter, S. M., Ene, A. B., Roduner, E., Schmid, R. D., and Urlacher, V. B.
  • Patcl M. A., Ou, M. S., Harbrucker, R., Aldrich, H. C 5 Buszko, M. L., Ingram, L. O., and

Abstract

The subject invention pertains to a novel purified polypeptide having laccase activity and the nucleic acid sequences encoding the polypeptide. The disclosed polypeptide works at moderately high temperatures from below 20°C to about 70°C, both acidic and alkaline pH conditions, high salt concentrations and in the presence of organo solvents. The high stability of the enzyme enables its wide applications under even extreme conditions. The invention also provides methods of producing the laccase enzyme.

Description

DESCRIPTION
ARCHAEL LACCASES AND MULTICOPPER OXIDASES (MCOs)
AND THEIR USES THEREOF
CROSS-REFERENCED TO RELATED APPLICATION
This application claims the benefit of U.S. Provisional Application Serial No. 61/176,587, filed May 8, 2009, the disclosure of which is hereby incorporated by reference in its entirety, including all figures, tables and amino acid or nucleic acid sequences.
BACKGROUND OF THE INVENTION
Multicopper oxidases (MCOs) are a family of enzymes that include laccascs (p- diphenol: dioxygen oxidoreductases, EC 1.10.3.2), ascorbate oxidases (EC 1.10.3.3), ferroxidascs (EC 1.16.3.1), bilirubin oxidases (EC 1.3.3.5) and other enzyme subfamilies (Solomon et al, 1996; Hoegger et al., 2006). MCOs couple the oxidation of organic and/or inorganic substrates to the four-electron reduction of molecular oxygen to water. These enzymes often have four Cu atoms classified into Type I (Tl), Type 2 (T2) and Type 3 (T3) centers, in which a mononuclear Tl center on the surface of the enzyme provides long range intramolecular one-electron transfer from electron-donating substrates to an internal trinuclear T2/T3 center formed by a T2 Cu coordinated to a T3 Cu pair. The T2/T3 cluster subsequently reduces dioxygen to water.
Enzymes of the laccase subfamily oxidize a broad range of compounds including phenols, polyphenols, aromatic amines, and non-phenolic substrates by one-electron transfer to molecular oxygen and, thus, have a wide variety of applications spanning from biofuels to human health. A lacquer tree laccase (from Rhus vernicifera) has been used in paint and adhesives in East Asia for more than 6000 years (Hϋttermann et al., 2001). Laccases have also been used in the delignification of pulp, bleaching of textile and carcinogenic dyes, detoxification of water and soils, removal of phenolics from wines, improving adhesive properties of lignocellulosic products, determination of bilirubin levels in serum, and transformation of antibiotics and steroids (Sakurai el al., 2007). Likewise, laccases have demonstrated potential in biosensors, bioreactors and biofuel cells (Shleev et al., 2005).
Although laccases were once thought to be restricted to eukaryotes (fungi, plants, insects), recent evidence suggests their widespread distribution in bacteria (Claus, 2004). In plants, laccascs are required for normal cell wall structure and integrity in xylem fibers and apparently involved in lignification (Ranocha et al., 2002). In fungi, laccases mediate the modification and degradation of complex natural polymers such as lignin and humic acids (Widsten et al, 2008; Claus et al., 1998). The lacasse-like MCOs of insects seem to play an important role in cuticular sclerotization, melanization, iron homeostasis and the oxidation of toxic compounds in the diet (Claus, 2004). Likewise, the more recently described laccase- like MCOs of bacteria have a wide variety of biological roles including sporulation, electron transport, pigmentation, metal (copper, iron, manganese) homeostasis, oxidation of phenolate-sidcrophorcs, phcnoxazinone synthesis, cell division and morphorgenesis (Claus, 2003). For example, Martins et al (2002) characterized a laccase enzyme isolated from the endospore coat of Bacillus sublilis. Koschorreck et al. (2008) recently disclosed a laccase isolated from Bacillus licheniformis and found it to catalyze dimerization of phenolic acids.
However, these laccases usually have very limited temperature, pIT, and salt range because of the living conditions of the plants and bacteria. Their industrial application, which sometimes requires high laccase activity under extreme conditions, may, thus, be further limited. Therefore, laccases with extreme thermal and salt/solvent stability are highly desired.
Archaea, one of the three domains of life along with the Bacteria and Eukarya, have evolved to thrive in harsh environmental conditions including high temperature, extreme pH, and/or low water activity. Thus, their systems and enzymes are deemed ideal for a number of industrial processes. In contrast to the widespread occurrence of laccascs in eukaryotes and bacteria, only a few putative MCOs are predicted in genomes of archaea including the hyperthermophilic crenarchaeote Pyrobaculum aerophilum (PAEl 888) (Fitz-Gibbon et al., 2002) and the PΛE1888-encoded enzyme is not likely to catalyze the oxidation of phenolic compounds particularly in the absence of metal supplementation. This limitation in PAEl 888 activity is based on the inventors' dendrogram analysis (see report) and transcriptional mapping by Cozen et al. (2009, J. Bacteriol. 191(3): 782-794), both of which suggest PΛE1888 is not a true laccase and instead encodes a metal oxidase and/or NO2 " or N2O reductase. In addition, whereas all of the archaea with identified MCO grow in the presence of oxygen, most archaea with sequcnced genomes are strict anaerobes, likely limiting the distribution of the oxygen-utilizing MCOs among this group. BRIEF SUMMARY OF THE INVENTION
The subject invention provides a novel laccasc that is highly thermostable and salt/solvent tolerant and nucleic acids encoding the laccase. In one embodiment, the purified laccase has a molecular weight of about 65 kDa and an amino acid sequence comprising SEQ ID NO: 2.
In another embodiment, the novel laccase is isolated and purified from strains of Haloferax volcanii species. Examples of some Haloferax volcanii strains are listed in Table 1. Preferably, the laccase is produced by Hfx. volcanii SBOl and US02. The molecular weight is about 65 kDa, determined by gel-filtration chromatography. Also provided by the subject invention is a method of producing the above disclosed laccase. In one embodiment, the laccase is produced in the culture media of its natural host, for example, Hfx. volcanii SBOl , the method comprising the steps of culturing a Haloferax volcanii strain under conditions suitable to produce the enzyme and then recovering the enzyme from the cells or the culture media. In another embodiment, the laccase is produced in a production host, such as E. coli, Bacillus megaterium and Saccharomyces cerevisiae, by means of recombinant technology.
The subject invention further relates to the use of the claimed laccase in various industrially important protocols that utilize laccases.
BRIEF DESCRIPTION OF THE DRAWINGS
Figure IA shows phylogenetic comparison of laccase and related multicopper oxidase protein sequences. Origin of protein sequences used for the analysis with corresponding accession numbers and references to biochemical and/or physiological studies in parenthesis were as follows: Hfx. volcanii DS2 (HvoB0205, LccA this study), Acremonium murorum (polyphenol oxidase or PpoA, Q9P8C3) (Gouka et al, 2001), Anaeromyxobacter sp. Fwl09-5 (A7H7L9), Aquifex aeolicus (McoA, AAC07157.1) (Fernandes et al, 2007), Arabidopsis lhaliana (ABG81319, LPRl) and (NP 565008.1, LPR2) (Svistoonoff et al, 2007), Bacillus amyloliquefaciens FZB42 (A7Z229), Bacillus clausii KSM-Kl 6 (Q5WEM6), Bacillus coagulans 36Dl (Λ2U4V3), Bacillus licheniformis DSM 13 / ATCC 14580 (Q65MU7) (Koschoor et al , 2008). Bacillus pumilus SAFR-032 (A8FΛG9), Bacillus subtilis (P07788, CotA) (Martins et al, 2002), Bacillus sp. B 14905 (A3I8L4), Carnobacterium sp. AT7 (ZP_02185070.1), Clostridium botulinum ATCC 3502 (A5I081), Cyanoihece sp. PCC 7424 (B2F9S5), Escherichia coli (P36649.2, CueO) (Wang et al, 2004), Exiguobacterium sp. ATIb (ZPJ)2990140.1), Frankia sp. EANlpec (A8LFX9), Ganoderma lucidum (Lacl, Q9HG17) (Joo el al, 2008), Geobacter metallireducens GS- 15 (Q39TP0), Geobacter sp. FRC-32 (Q0YK09), Halorubrum lacusprofundi ATCC 49239 (A7D715), Lentinula edodes (Lccl, Q68LM1) (Sakamoto et al, 2008). Listeria monocytogenes (ABV56573.1), Lysinϊbacillus sphaericus C3-41 (B1IIU92), Magnaporthe grisea (A4RGT9), Marinomonas mediterranea MMB-I (PpoA, Q9KJB8) (Sanchez- Amat et al, 2001 ), Melhylobacterium sp. 4-46 (B0U9I8), Monosiga brevicollis (XP_001748107.1 ), Myrothecium verrucaria (Q12737) (Koikeda et al., 1993), Neurospora crassa (Q7RX46), Nitrosospira multiformis ATCC 25196 (Q2Y8L3), Nodularia spumigena CCY 9414 (A0ZH42), Oceanobacillus iheyensis (Q8CXJ7), Phaeosphaeria nodorum (Q0UUB4), Physcomitrella patens (XPJ)01760041), Podospora anserine (B2ANK8), Pyrenophora tritici-repentis Pt-IC-BFP (XPJ)Ol 940237), Pyrobaculum aerophilum (PAE1888, AAL63794.1), Rubrobacter xylanophilus DSM 9941 (NCJ308148), Saccharopolyspora erythraea NRRL 23338 (A4FAR2), Salinispora arenicola CNS-205 (A8M6C1 and A8M7X1), Salinispora tropica CNB-440 (A4X8A2), Sorangium cellulosum So ce56
(A9GCD5), Stachyhoirys chartarum (Q4ZIR9) (Mander el al., 2006), Staphylococcus aureus (Mco, Q69HT9) (Sitthisak et al., 2005), Streptomyces antibioticus (phenoxazinone synthase or PhsA, Q53692) (Choy et al, 1981), Streptomyces coelicolor A3(2) (NP^630785, SLAC) (Machczynski el al.. 2004), Streptomyces echinatus (AlCl 71), Streptomyces griseus (EpoA, Q93IIV5) (Endo et al, 2003), Streptomyces lavendulae REN-7 (laccase, Q8GB87) (Suzuki et al, 2003), Thiobacillus denitrijicans ATCC 25259 (Q3SJX4) and Vitis vinifera (CAO42253.1). Neurospora crassa catalase-3 (Cat-3, Q9C169) served as the outgroup for this analysis. Species with associated biochemical and/or physiological studies of their MCO family member are underlined and in bold. Figure IB. Phylogenetic comparison of H. volcanii LccA to laccases and other multicopper oxidase protein sequences. Proteins with associated biochemical, microarray and/or physiological studies are underlined and in bold. Origin of protein sequences used for the analysis with corresponding accession numbers and references were as follows: H. volcanii DS2 (HVOJ30205, LccA this study), Acremonium murorum (polyphenol oxidase or PpoA, Q9P8C3), Aquifex aeolicus (McoA, AAC07157.1), Bacillus amyloliquefaciens FZB42 (A7Z229), Bacillus clausii KSM-K16 (Q5WEM6), Bacillus coagulans 36Dl (A2U4V3), Bacillus licheniformis DSM 13 / ATCC 14580 (Q65MU7), Bacillus pumilus SAFR-032 (A8FAG9), Bacillus subtilis (P07788, CotA), Bacillus sp. B 14905 (A3Ϊ8L4), Escherichia coll (P36649.2, CueO). Halorubrum lacusprofundi ATCC 49239 (ACM56646. Hlac_1049), Lysinibacillus sphaericus C3-41 (B1HU92), Myroihecium verrucaria (Ql 2737, billirubin oxidase), Oceanobacillus iheyensis (Q8CXJ7), Pyrobaculitm aerophilum (AAL63794.1, PAEl 888), Stachybotrys chartarum (Q4ZIR9), Staphylococcus aureus (Q69HT9, Mco), Streptomyces antihiolicus (Q53692, phenoxazinonc synthase or PhsA) and Slreptomyces lavendulae REN-7 (laccase, Q8GB87). Myxococcus xanthus (Q1D6V6, CuoA; Q1D6V1, CuoB: Q1D6U4, CuoC) served as an outgroup for this analysis.
Figure 2A shows laccase activity of Hfic. volcanii SBOl cultures at various stages of growth. Hfx. volcanii SBOl cells were inoculated to a final OD6Oo of 0.01 in Hv-LMM supplemented with 0.1 μg per ml novobiocin and 100 μM copper sulfate. Cells were grown for 120 h at 42°C in an orbital shaker (150 - 200 rpm). Samples were withdrawn at periodical intervals and used for estimation of growth (1 ODOOO unit ~ 1 x 109 CFU per ml) and laccase activity. For analysis of cell lysate, cells were pelleted by centrifugation (for 10 min at 10,000 χ g and 40C), washed twice in T buffer supplemented with 2 M NaCl, resuspended in T buffer and lysed by sonication (15 s on. 45 s off at 20 % amplitude for 3 min). Culture broth and cell lysate were assayed for laccase (SGZ oxidizing) activity under standard conditions.
Figure 2B shows laccase activity of H. volcanii US02 strains at various stages of growth. H. volcanii US02 and parent H26 (data not shown) were inoculated to a final QDOOO of 0.01 in medium supplemented with novobiocin and 100 μM copper sulfate. LMM and YPC were optimal for production of laccase activity for US02. Cells w-cre grown for up to 120 h at 42 0C in an orbital shaker (150 - 200 rpm). Samples were withdrawn at periodical intervals and used for estimation of growth (1 OD6OO unit ~ 1 x 109 CFU per ml) and assay of laccase activity. For analysis of cell lysate, cells were harvested by centrifugation (10 min at 10,000 x g and 40C), washed twice in T buffer supplemented with 2 M NaCl, resuspended in T buffer and lysed by sonication (15 s on, 45 s off at 20 % amplitude for 3 min). Culture broth (filtered by 0.4 μm) and cell lysate were assayed for laccase (SGZ oxidizing) activity under standard conditions.
Figures 3A-3B show LccA purified to electrophoretic homogeneity from the culture broth of Hfx. volcanii SBOl . a) SDS PAGE gel of LccA at various stages of purification from Hfx. volcanii SBOl . Molecular standards indicated on left. Culture broth (lane 1), ethanol precipitate (lane 2). MonoQ 5/5, pH 8.4 fractions (lane 3), Superdex 200 HR 10/30 fractions (lane 4). MonoQ 10/10, pH 8.4 fractions (lane 5); b) Native gels of LccA fractions stained for laccase activity and total protein. MonoQ 5/5 and Superdex 200 HR 10/30 fractions of LccA stained with SGZ (lanes 1 and 2); ABTS (lanes 3 and 4) and Coomassie brilliant blue R-250 (lanes 5 and 6), respectively. Protein standards (prestained BioRad) on left include: PHO b, phosphorylase b; BSA, bovine serum albumin, OVA, ovalbumin; CA, carbonic anhydrase, TRI, trypsin inhibitor; LYS, lysozyme.
Figure 4 shows LccA purified as an 65.4-kDa monomer from the culture broth of Hfx vυlcanii SBOl. Native molecular mass of LccΛ was determined by applying protein fractions eluted at 625 to 650 mM NaCl in 25 mM Tris-HCl buffer at pH 8.4 (T buffer) from MonoQ 5/5 to a Superdex 200 HR 10/30 column calibrated with protein molecular mass standards with elution volumes (■) as indicated.
Figure 5 show UV-Visible absorbance spectrum of LccA purified from Hfx. volcanii SBOl . Purified LccA (77 μg-ml"1) was dissolved in T buffer containing 185 mM NaCl.
Figures 6A-6F show temperature (Fig. 6A), salt (Fig. 6B) and pH (Fig. 6C) optima of LccA purified from Hfx volcanii SBOl . Fig. 6A - Effect of temperature on the catalytic activity of LccA. LccA (51 μg-ml" ) activity was assayed at different temperatures (22° to 70 0C) in T buffer with 185 mM NaCl using SGZ (1 mM) as the substrate. Activity is expressed as percent relative to the optimum at 45 0C; Fig. 6B - Effect of salt on the catalytic activity of LccA. The SGZ oxidizing activity of LccA was measured at different concentrations (up to 1.0 M) of NaCl (•) and KCl (o) in T buffer at 45 0C. Activity is expressed as percent relative to 185 mM NaCl; Fig. 6C - Effect of pH on the catalytic activity of LccA. LccA activity was assayed with SGZ (•) from pH 6 to 11 and with ABTS (o) from pH 3 to 8 at 45 0C using following buffers: 100 mM sodium acetate for pH 3 to 6, 25 mM Tris-HCl for pH 7 to 10, and 25 mM glycine-NaOH for pH 11. Activity is expressed as percent relative to oxidation of ABTS at pH 6. Fig. 6D -Thermostability of LccA. Purified enzyme (50.6 μg-ml"1) was pre-incubated in T buffer supplemented with 185 mM NaCl at temperatures from 37° to 70 0C for up to 60 h, as indicated. After incubation, laccase activity was estimated by oxidation of SGZ at standard conditions. Activity is presented as percent relative to incubation on ice (37 0C (•), 45 0C (■), 50 0C (A), 55 0C (♦). 60 0C (o). 65 0C (D) and 70 0C (Δ)); Fig. 6E - Salt tolerance of LccA protein. Purified enzyme (16.5 μg-ml"1) was pre-incubated for 30 min in T buffer at pH 8.4 supplemented with different concentrations of NaCl (0 to 1.4 M) as indicated. Samples were diluted to a final concentration 4.12 μg-ml"1 protein and 185 mM NaCl in T buffer and assayed for SGZ oxidizing activity under standard conditions. Residual activity was calculated as percent relative to incubation at 185 mM NaCl. Fig. 6F - Effect of mixed organo-solvents on LccA activity. Enzyme (7.5 μg-ml"1) was incubated in T buffer with 185 mM NaCl in the presence and absence of 25 % (v/v) solvent (DMSO, DMF, ethanol and methanol) at room temperature for 90 min (white bar), 3 h (grey bar) and 24 h (black bar). Enzyme and solvent were diluted 4-fold in T buffer with 185 mM NaCl and residual enzyme activity was estimated under standard conditions using SGZ as the substrate. Activity is calculated as percent relative to incubation without solvent.
Figure 7 shows sequence alignment of Hfx. volcanii laccase (LccA. IIvoJ30205, SEQ ID NO: 2) to multicopper oxidases. Vertical line ( | ) represents cleavage site which has experimental evidence for LccA and Mvcr__Q12737. TAT motifs, indicated by a bold double underline, are based on in silico analysis using TATFIND vl .4 server. The one cysteine and 10 histidine residues that bind the four copper atoms to form the Type I. Il and III active sites of known multicopper oxidases are indicated above the amino acid residue (•). Potential O- and N-linked glycosylation sites with EnsembleGly scores above 0.8 are indicated by respective O* and N* above the residue with the Thr-Xs-P-X-P and N-X-T/S motifs boxed. Amino acid sequences in bold and underlined represent peptides detected by MS/MS analysis of the laccase purified from Hfic. volcanii (details of MS/MS analysis in Table 5). Abbreviation and GenBank accession number: Hlac ZP-02016827 (SEQ ID NO: 3), Halorubrum lacusprofundi putative multicopper oxidase (Copeland el al, 2008); Bsub_BAA22774 (SEQ ID NO: 4), Bacillus subtilis spore coat protein A (CotA) with laccase activity (Martins et al, 2002); Scha_AΛY23005 (SEQ ID NO: 5), Stachybotrys chartariim phenol oxidase A (Mander et al, 2006); Mver_Q12737 (SEQ ID NO: 6), Myrolhecium verrucaria bilirubrin oxidase (Koikeda et al, 1993).
Figure 8 provides various exemplary fragments of the laccase disclosed herein. The numbering of the N- and C-terminal amino acid residue is provided with reference to Figure 7 and SEQ ID NO: 2.
Figure 9 shows Gel filtration analysis of LccA. LccA (MonoQ 5/5, pll 8.4, MQl) fractions from H. volcanii SBOl were applied to a calibrated Supcrdex 200 HR 10/30 column as described in methods. The laccase active peak containing LccA protein is indicated by an arrow.
Figure 10 shows MS-analysis of LccA. LccA fractions purified from H. volcanii SBOl (SEQ ID NO: 28) and US02 (SEQ ID NO: 29) were digested with trypsin and analyzed by MS as described in methods. Tryptic peptides identified by MS are underlined and detailed in Table 5.
Figure 11 shows LccA purified to electrophoretic homogeneity from the culture broth of //, volcanii US02. Reducing 10 % SDS PAGE of LccA at various stages of purification including ethanol precipitate (lanes 1, EP) and MonoQ 10/10. pll 8.4 (lane 2, MQ) as indicated. Molecular standards on left. Proteins were stained with Coomassie brilliant blue R-
250.
Figures 12A-12C show LccA purified from US02 is a glycoprotein. A, Native gels of
LccA at its final stages of purification from US02 (Superdex 200 HR 10/30, lanes 1-2) and SBOl (MonoQ 10/10, pH 8.4, lanes 3-5). Gels were stained for total protein by Coomassie brilliant blue R-250 (CB) and laccase activity by in gel oxidation of SGZ (SGZ) as indicated.
Prestained kaleidoscope and low range protein standards (Bio-Rad) were included for US02 and SBOl, respectively as indicated on left of each gel. B, Pro-Q Emerald glycoprotein analysis of US02-purified LccA. Proteins were separated by reducing 10 % SDS-PAGE. Gels were stained for glycosylation by Pro-Q Emerald (left) and total protein by SYPRO-
Ruby (right) as indicated. Proteins included carbonic anhydrase (lane 1, CA), T. versicolor laccase (lane 2, TvLc), LccA MonoQ 10/10, pH 8.4, fractions (lane 3. HVLCMQ). LCCA ethanol precipitate (lane 4, HVLCEP). CandyCane molecular mass standards (Molecular
Probes) including a mixture of glyosylated (G) and nonglycosylated proteins as indicated (lane 5). C, Deglycosylation of LccA. LccA purified from US02 was treated with TFMS on ice for 0 h (lane 1), 1O h (lane 2) and 3 h (lane 3) and separated by reducing 6 and 10 % SDS-
PAGE as indicated (see methods for details).
Figure 13 shows UV-Visible absorbance spectrum of LccA. Absorbance of LccA (1.5 mg-ml"1) purified from H volcanii US02 in T buffer containing 185 mM NaCl was analyzed from 300 to 700 nm.
Figure 14 shows laccase activity produced culture broth of //, volcanii strain US02 in accordance with the subject invention.
Figure 15 shows ability of LccA to delignify sugarcane bagasse.
BRIEF DESCRIPTION OF THE SEQUENCES
SEQ ID NO: 1 polynucleotide sequence encoding Hfx. volcanii laccase. SEQ ID NO: 2 polypeptide sequence of ///3c. volcanii laccase. DETAILED DISCLOSURE OF THE INVENTION
In the context of the instant invention, the terms "oligopeptide", "polypeptide", "peptide" and "protein" can be used interchangeably; however, it should be understood that the invention does not relate to the polypeptides in natural form, that is to say that they are not in their natural environment but that the polypeptides may have been isolated or obtained by purification from natural sources or obtained from host cells prepared by genetic manipulation (e.g., the polypeptides, or fragments thereof, are recombinantly produced by host cells, or by chemical synthesis).
"Nucleotide sequence", "polynucleotide" or "nucleic acid" can be used interchangeably and are understood to mean, according to the present invention, either a double-stranded DNA, a single-stranded DNA or products of transcription of the said DNAs (e.g., RNA molecules). It should also be understood that the present invention does not relate to genomic polynucleotide sequences in their natural environment or natural state. The nucleic acid, polynucleotide, or nucleotide sequences of the invention can be isolated, purified (or partially purified), by separation methods including, but not limited to, ion- exchange chromatography, molecular size exclusion chromatography, or by genetic engineering methods such as amplification, subtractive hybridization, cloning, subcloning or chemical synthesis, or combinations of these genetic engineering methods.
The terms "comprising", "consisting of and "consisting essentially of' are defined according to their standard meaning. The terms may be substituted for one another throughout the instant application in order to attach the specific meaning associated with each term.
The phrases "isolated" or "biologically pure" refer to material that is substantially or essentially free from components which normally accompany the material as it is found in its native state. The term "isolated" requires that the material be removed from its original environment (e.g., the natural environment if it is naturally occurring). For example, a naturally-occurring polynucleotide or polypeptide present in a viable eukaryotic cell or a prokaryotic cell is not isolated, but the same polynucleotide or DNA or polypeptide, separated from some or all of the coexisting materials in the natural system, is isolated. Such polynucleotide could be part of a vector and/or such polynucleotide or polypeptide could be part of a composition, and still be isolated in that the vector or composition is not part of its natural environment. Specifically excluded from the term "isolated" are: nucleic acid sequences found in databases containing the complete genomic sequence of Haloferax volcanii, naturally-occurring chromosomes (such as chromosome spreads of Halqferax volcanii or chromosomes isolated from Haloferax volcanii), artificial chromosomal libraries of Haloferax volcanii. genomic libraries of Haloferax volcanii, and cDNA libraries of Haloferax volcanii that exist either as an in vitro nucleic acid preparation or as a transfected/transformed host cell preparation, wherein the host cells are either an in vitro heterogeneous preparation or plated as a heterogeneous population of single colonies. Thus, "an isolated polynucleotide comprising SEQ ID NO: 1 is specifically defined as excluding those sequences found in a database containing the genomic sequence of Haloferax volcanii, naturally-occurring chromosomes of Haloferax volcanii (e.g., chromosome spreads of Haloferax volcanii or chromosomes isolated from Haloferax volcanii), artificial chromosomal libraries of Haloferax volcanii, genomic libraries of Haloferax volcanii, and/or cDNA libraries of Haloferax volcanii that contain SEQ ID NO: 1 or a polynucleotide encoding SEQ ID NO: 2. Further specifically excluded are whole cell {Haloferax volcanii) genomic DNA or whole cell RNA preparations (including whole cell preparations which are mechanically sheared or enzymatically digested). Further specifically excluded are the above whole cell Haloferax volcanii preparations as either an in vitro preparation or as a heterogeneous mixture separated by electrophoresis (including blot transfers of the same) wherein the polynucleotide of the invention has not further been separated from the heterologous polynucleotides in the electrophoresis medium {e.g., further separating by excising a single band from a heterogeneous band population in an agarose gel or nylon blot). In one aspect of the invention, antibodies that specifically bind to SEQ ID NO: 2 are provided. In various embodiments, these antibodies do not cross-react with other proteins that are structurally related.
One aspect of the subject invention provides isolated, purified, and/or recombinant polypeptides having laccase activity, wherein the polypeptides have a molecular weight of about 65 kDa (using gel-filtration chromatography) and/or comprise the amino acid sequence SEQ ID NO: 2. Another aspect of the invention provides for fragments of the polypeptides disclosed herein, wherein the polypeptide fragments retain laccase activity. Polypeptide fragments, as described herein, can be obtained by cleaving the polypeptides of the invention with a proteolytic enzyme (such as trypsin, chymotrypsin, collagenase or other known proteases) or with a chemical reagent, such as cyanogen bromide (CNBr). Alternatively, polypeptide fragments can be generated in a highly acidic environment, for example at pH 2.5. After cleavage via any of these agents, the polypeptide fragments can be assayed for laccase activity as described herein. Also provided are compositions comprising SEQ ID NO: 2, or fragments thereof retaining laccase activity and a carrier (e.g., an aqueous or organic liquid). In various aspects of the invention, fragments having laccase activity, such as those disclosed in Figure 8. are provided. Alternatively, fragments of SEQ ID NO: 2 having laccase activity can start at any one of amino acid residues 140, 141, 142, 143. 144 or 145 and the C-terminal amino acid of the fragment can be any amino acid found at positions 524 through 579 of SEQ ID NO: 2.
The polypeptides can be obtained from a Hal of er ax volcanii strain, for example, Hfx. volcanii DS2 or a mutant strain thereof. In a preferred embodiment, a mutant strain Hfx. volcanii SBOl is used. In another embodiment, the polypeptide has the amino acid sequence set forth in SEQ ID NO: 2.
A "variant polypeptide" (or polypeptide variant) is to be understood to designate polypeptides exhibiting, in relation to SEQ ID NO: 2. certain modifications. These modifications can include a deletion, addition, or substitution of at least one amino acid, a truncation, an extension, a chimeric fusion, a mutation, or polypeptides exhibiting post- translational modifications. Among these homologous variant polypeptides, arc those comprising amino acid sequences exhibiting between at least (or at least about) 39.00% to 99.99% (inclusive) identity to the full length, native, or naturally occurring polypeptide are another aspect of the invention. The aforementioned range of percent identity is to be taken as including, and providing written description and support for, any fractional percentage, in intervals of 0.01%, between 20.00% and. up to, including 99.99%. These percentages are purely statistical and differences between two polypeptide sequences can be distributed randomly and over the entire sequence length. Thus, variant polypeptides can have 39, 40, 41, 42, 43, 44, 45. 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66. 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78. 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89. 90,
91, 92, 93, 94, 95, 96, 97, 98, or 99 percent identity with the polypeptide sequences of the instant invention. In a preferred embodiment, a variant or modified polypeptide exhibits at least 60, 61, 62, 63, 64, 65. 66. 67, 68, 69, 70, 71, 72, 73. 74, 75, 76, 77, 78. 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96. 97, 98, or 99 percent identity to SEQ ID NO: 2. Typically, the percent identity is calculated with reference to the full-length, native, and/or naturally occurring polypeptide (e.g., SEQ ID NO: 2). In all instances, variant polypeptides retain the laccase activity associated with SEQ ID NO: 2. Variant polypeptides can also comprise one or more heterologous polypeptide sequences (e.g., tags that facilitate purification of the polypeptides of the invention (see, for example, U.S. Patent No. 6.342.362, hereby incorporated by reference in its entirety).
Strains of Haloferax volcanii are available from various public culture collections, including the American Type Culture Collection (ΛTCC, USA), ATCC 29605; Deutsche Sammlung von Mikroorganismenn und Zellkulturen GmbH (DSMZ, Germany), DSM 3757 and 5716; Czechoslovak Collection of Microorganisms (CCM, Czech Republic), CCM 2852; National Collection of Industrial and Marine Bacteria (NCIMB, Scotland), NCIMB 2012; and Institute for Fermentation (IFO, Japan), IFO 14742. The microorganisms can be cultivated on a suitable medium, including, for example, a halobacterium medium ATCC 974. The medium can also include other ingredients, such as salts, buffers, drugs, and nutrients. In one embodiment, the strain is grown in complex medium ATCC 974 and lactate-minimal medium (Hv-LMM). The medium can also include other ingredients such as antibiotics, e.g. ampicillin and novobiocin. The culture can be grown in liquid or solid medium. In some embodiments, the Hv-LMM is supplemented with CUSO4 for faster production of the enzyme in Hfx. volcanii, presumably based on a more efficient conversion of the apoenzyme to the mature copper-loaded, active form. For example, the concentration of CuSO4 can be about 100 μiM. Various other embodiments utilize less agitated culture conditions over heavily agitated conditions in obtaining greater production of the claimed laccase. The production of the polypeptide can be detected by measuring the laccase activity
(e.g., oxidation of a substrate). Suitable substrates for measuring the enzyme activity include 2,2'-azino-bis-3-ethylbenzthiazoline-6-sulphonic acid (ABTS). 2,6-dimethoxyphenol (DMP), 2-methoxyphenol (guaiacol), and 4-hydroxy-3,5-dimethoxybenzaldehyde azine (syringaldazine or SGZ). Oxidation of the substrate can be determined by absorbance increase or decrease by spectroscopy at certain wavelength, for example, ABTS at 420 nm with ε = 36,000 M"1 cm"1 ; SGZ at 526 nm with ε = 65,000 M"1 cm"1; DMP at 468 nm with ε = 49,000 M"1 cm"1; guaiacol at 436 nm with ε = 26,600 M"1 cm'1; bilirubin at 440 nm with ε = 56,300 M"1 cm"1.
As discussed above, the polypeptide can be produced in its native host. In one embodiment, the native host is Hfx. volcanii DS70. The polypeptide of SEQ ID NO: 2 can also be produced by an engineered host cell expressing a nucleic acid encoding SEQ ID NO: 2. Non-limiting examples of engineered host cells expressing a nucleic acid encoding SEQ ID NO: 2 include E. coli, Bacillus megaterium and Saccharomyces cerevisiae. Therefore, the subject invention relates to methods of producing a polypeptide comprising cultivating a Haloferax volcanii strain that is able to secrete the polypeptide naturally or a host cell containing the encoding gene, under conditions suitable to produce the polypeptide, and recovering the polypeptide from the culture medium. The recovered polypeptide can then be isolated and purified by using known methods of protein purification, such as precipitation, centrifugation, filtration, anion exchange chromatography, and gel- filtration chromatography. In several embodiments, the laccase is purified from a culture broth by filtration. The culture broth is further purified by ethanol precipitation and centrifugation. Anion-exchange chromatography is further used for purification. The purified product can be verified by SDS-PAGE, mass spectroscopy and in gel activity staining. In one embodiment, the purity of the obtained laccase is between 38 to 68% from the above application. In another embodiment, SDS-PAGE gives a molecular weight of 70.7 kDa. In yet another embodiment, the gel filtration chromatography estimates the native molecular mass to be about 65 kDa. The purified and concentrated polypeptide can be characterized for enzyme activity, thermostability, salt/solvent stability, or other properties. The laccase activity of the purified polypeptide at various temperatures, pH, and salt concentrations can be determined using SGZ and/or ABTS as substrates. The thermo, salt or solvent stability can be determined by incubating the purified polypeptide at various temperatures, salt concentrations, or solvent types with the other factors fixed.
The polypeptide, and biologically active fragments thereof, disclosed herein exhibits laccase activity at temperatures of about 2O0C to about 700C, about 3O0C to about 550C (with over 80% laccase activity) or between about 450C to about 500C. In addition, the polypeptide is salt resistant exhibits laccase activity at all concentrations between about 100 mM and 300 mM NaCl or KCl {e.g. , >100 mM NaCl or KCl, between 100-250 mM NaCl or KCl, between about 150-250 mM NaCl or KCl, or about 200 mM NaCl or KCl). In one embodiment, at same protein concentration, the polypeptide displays about 1.5-fold higher activity in KCl than NaCl.
The polypeptide of the subject invention is catalytically active under both acidic and alkaline pH conditions while being substrate dependent (Fig. 6C). In the presence of ABTS, the polypeptide has laccase activity over the range of pH = 3-8, 4-7, or 5-6.5. The activity is at its highest at about pH 6. The subject polypeptide can also oxidize SGZ at pH range of pH = 6-11, 7-10, or 8-9. The optimum pH for SGZ oxidation is about 8.4. Most microbial laccases display optimal activity at low pH. The alkalophilic nature of the polypeptide disclosed herein is advantageous in various industrial applications including paper pulp bleaching and wastewater treatment processes. Unlike the subject polypeptide, the few microbial laccases that are active at alkaline pH do not exhibit significant activity below pH 6.0. These unique catalytic properties of the described polypeptide underline its potential as a source of high- value laccases.
The subject polypeptide is also thermostable at temperatures from 37 to 700C. In one embodiment, it is fully active after 1 h at 55°C and 5 h at 500C, with a half-live of inactivation at 5O0C of 31.5 h (Figures 6A and 6D). The polypeptide retains nearly all of its original laccase activity at 37 0C and 35 to 60% of its activity at 45 to 5O0C, after incubation for 2 Vi days. These results reveal that the polypeptide described herein is highly thermostable, retaining most of its activity after prolonged incubation at moderately high temperatures. Advantageously, most of industrial processes work at optimal temperatures of not more than 500C. Hence the temperature optima and thermal stability of the subject polypeptide are well within the required range for most of the industrial bioprocesses.
Furthermore, the purified polypeptide is stable in a wide range of NaCl concentrations from 100 mM to, at least, 1.4 M, retaining nearly all of its original activity if not higher (Figures 6B and 6E). Prolonged incubation, from about 90 min to 24 h, of the polypeptide in salt does not alter this activity profile. This is better than a recently analyzed laccase from a bacterium isolated from a mangrove swamp (i.e., Streplomyces psammoticus) which only demonstrated salt tolerance with full activity after incubation for 24 h in 0.8 M NaCl (Niladevi el al., 2008). Salt tolerance is one of the preferred characteristics from an industrial stand-point as laccases are used for effluent treatment including bleaching and decolorization of phenolilc dyes where salt concentration can be a constraint for in situ enzymatic treatment of wastewaters rich in salts.
The purified polypeptide is highly solvent tolerant. In the experimental conditions described in Example 5, the polypeptide is relatively stable in all solvents (i.e., methanol, ethanol, dimethyl sulfoxide or DMSO and dimethylformamide or DMF) examined, retaining nearly 75% of its activity after about 24 h incubation in methanol or ethanol and over 50% of its activity after incubation in DMSO or DMF (Fig. 6F). Solvent compatibility of the subject polypeptide from Hfic. volcanii may be used to facilitate transformation of insoluble lignin components and lower the degree of polymerization of phenoxyl radicals originated during lignin oxidation. More importantly, many laccase substrates and mediators are insoluble or poorly soluble in water and the solvent stability of the disclosed polypeptide would be of much interest to change the direction of catalytic reactions and to gain access to insoluble substrates and enhance the solubility of mediators. Additionally, several potential applications of laccases need to be performed in the presence of significant amounts (in some cases up to 50% v/v) of water-miscible organic cosolvent. Therefore, several industrial applications would greatly benefit from the addition of water-miscible organic cosolvents to laccase-mediated reactions, particularly the conversion of insoluble substrates such as lignin and its derivatives to useful products (Barreca et al., 2003; Potthast el ah, 1995; d'Acunzo et al, 2004). The subject invention also provides polynucleotides, vectors, genetic constructs and transformed host cells. These polynucleotides, vectors, genetic constructs, and transformed host cells contain nucleic acids encoding a laccase as described herein. Nucleic acid probes derived from such nucleic acids are also provided by the subject invention. Thus, the subject invention also provides isolated, recombinant, and/or purified polynucleotide sequences comprising: a) a polynucleotide sequence encoding a polypeptide comprising SEQ ID NO: 2; b) a homologous polynucleotide sequence having at least about 20% to 99.99% identity to a polynucleotide sequence encoding a polypeptide SEQ ID NO: 2, wherein said polynucleotide encodes a polypeptide having laccase activity; c) a polynucleotide sequence comprising SEQ ID NO: 1 ; d) a homologous polynucleotide sequence having at least about 20% to 99.99% identity to the polynucleotide sequence of SEQ ID NO: 1 and encoding a polypeptide having laccase activity; e) a polynucleotide that is complementary to the polynucleotides set forth in (a), (b), (c), or (d); f) a genetic construct comprising a polynucleotide sequence as set forth in (a),
(b)5 (c), (d). or (e); g) a vector comprising a polynucleotide or genetic construct as set forth in (a), (b), (c), (d). (e), or (f); h) a host cell comprising a vector as set forth in (g); i) a polynucleotide that hybridizes under low, intermediate or high stringency with a polynucleotide sequence as set forth in (a), (b), (c), (d) or (e); or j) a probe comprising a polynucleotide according to (a), (b), (c), (d), (c), (f), or (g) and, optionally, a label or marker;
A homologous polynucleotide sequence, for the purposes of the present invention, encompasses a sequence having a percentage identity with the polynucleotide sequences, set forth herein, of between at least (or at least about) 20.00% to 99.99% (inclusive). The aforementioned range of percent identity is to be taken as including, and providing written description and support for, any fractional percentage, in intervals of 0.01 %, between 20.00% and. up to, including 99.99%. These percentages are purely statistical and differences between two nucleic acid sequences can be distributed randomly and over the entire sequence length. For example, homologous sequences can exhibit a percent identity of 20, 21 , 22, 23,
24, 25, 26, 27, 28, 29, 30, 31 , 32, 33, 34, 35, 36, 37. 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48. 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62. 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73. 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87. 88, 89. 90, 91, 92, 93, 94, 95, 96, 97, 98. or 99 percent with the sequences of the instant invention. Typically, the percent identity is calculated with reference to the full length, native, and/or naturally occurring polynucleotide. The terms "identical" or percent "identity", in the context of two or more polynucleotide or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues that are the same, when compared and aligned for maximum correspondence over a comparison window, as measured using a sequence comparison algorithm or by manual alignment and visual inspection.
Both protein and nucleic acid sequence homologies may be evaluated using any of the variety of sequence comparison algorithms and programs known in the art. Such algorithms and programs include, but are by no means limited to, TBLASTN, BLASTP, FASTΛ, TFASTA, and CLUSTALW (Pearson and Lipman, 1988, Proc. Natl. Acad. Sci. USA «5^:2444-2448; Altschul et al , 1990, J. MoI. Biol. 275(5/403-410; Thompson et al, 1994; Higgins et al, 1996, Methods Enzymol. 266:383-402; Altschul et al, 1990, J. MoI. Biol 275(5,):403-410; Altschul et al, 1993, Nature Genetics 3:266-272). Sequence comparisons are, typically, conducted using default parameters provided by the vendor or using those parameters set forth in the above-identified references, which are hereby incorporated by reference in their entireties.
A "complementary" polynucleotide sequence, as used herein, generally refers to a sequence arising from the hydrogen bonding between a particular purine and a particular pyrimidine in double-stranded nucleic acid molecules (DNA-DNA, DNA-RNA, or RNA- RNA). The major specific pairings are guanine with cytosine and adenine with thymine or uracil. A ''complementary" polynucleotide sequence may also be referred to as an "antisense'" polynucleotide sequence or an "antisense sequence".
Sequence homology and sequence identity can also be determined by hybridization studies under high stringency, intermediate stringency, and/or low stringency. Various degrees of stringency of hybridization can be employed. The more severe the conditions, the greater the complementarity that is required for duplex formation. Severity of conditions can be controlled by temperature, probe concentration, probe length, ionic strength, time, and the like. Preferably, hybridization is conducted under low, intermediate, or high stringency conditions by techniques well known in the art, as described, for example, in Keller, G.H., MM. Manak [1987] DNA Probes. Stockton Press, New York, NY., pp. 169-170.
For example, hybridization of immobilized DNA on Southern blots with 32P-labeled gene-specific probes can be performed by standard methods (Maniatis et al. [1982] Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York). In general, hybridization and subsequent washes can be carried out under intermediate to high stringency conditions that allow for detection of target sequences with homology to the exemplified polynucleotide sequence. For double-stranded DNA gene probes, hybridization can be carried out overnight at 20-250C below the melting temperature (T1n) of the DNA hybrid in 6X SSPE, 5X Denhardt's solution, 0.1% SDS, 0.1 mg/ml denatured DNA. The melting temperature is described by the following formula (Beltz et al, [1983] Methods of Enzymology, R. Wu, L. Grossman and K. Moldave [eds.J Academic Press, New York 100:266-285).
Tm=81.5°C+16.6 Log[Na+]+0.41(%G+C)-0.61 (%formamide)-600/length of duplex in base pairs. Washes are typically carried out as follows:
(1) twice at room temperature for 15 minutes in IX SSPE, 0.1% SDS (low stringency wash);
(2) once at Tm - 200C for 15 minutes in 0.2X SSPE, 0.1% SDS (intermediate stringency wash). For oligonucleotide probes, hybridization can be carried out overnight at 10-200C below the melting temperature (Tm) of the hybrid in 6X SSPE, 5X Denhardt's solution, 0.1 % SDS, 0.1 mg/ml denatured DNΛ. Tm for oligonucleotide probes can be determined by the following formula:
Tm(°C)=2(number T/A base pairs)" 4(number G/C base pairs) (Suggs el al. [19811 ICN-UCLA Symp. Dev. Biol. Using Purified Genes, D. D. Brown [ed.]. Academic Press, New York, 23:683-693).
Washes can be carried out as follows:
(1) twice at room temperature for 15 minutes IX SSPE, 0.1 % SDS (low stringency wash);
T) once at the hybridization temperature for 15 minutes in IX SSPE. 0.1% SDS (intermediate stringency wash).
In general, salt and/or temperature can be altered to change stringency. With a labeled DNA fragment >70 or so bases in length, the following conditions can be used:
Low: 1 or 2X SSPE, room temperature Low: 1 or 2X SSPE, 420C
Intermediate: 0.2X or IX SSPE, 65°C High: 0.1X SSPE, 65°C.
By way of another non-limiting example, procedures using conditions of high stringency can also be performed as follows: pre-hybridization of filters containing DNA is carried out for 8 h to overnight at 65°C in buffer composed of 6X SSC, 50 mM Tris-HCl
(pH 7.5), 1 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.02% BSA, and 500 μg/ml denatured salmon sperm DNA. Filters are hybridized for 48 h at 65°C, the preferred hybridization temperature, in pre-hybridization mixture containing 100 μg/ml denatured salmon sperm DNΛ and 5-20 x 106 cpm of '2P-labeled probe. Alternatively, the hybridization step can be performed at 65°C in the presence of SSC buffer, IX SSC corresponding to 0.15 M NaCl and
0.05 M Na citrate. Subsequently, filter washes can be done at 37°C for 1 h in a solution containing 2X SSC, 0.01% PVP, 0.01% Ficoll, and 0.01% BSA, followed by a wash in 0.1X
SSC at 50°C for 45 min. Alternatively, filter washes can be performed in a solution containing 2X SSC and 0.1% SDS, or 0.5X SSC and 0.1% SDS, or 0.1X SSC and 0.1% SDS at 68°C for 15 minute intervals. Following the wash steps, the hybridized probes are detectable by autoradiography. Other conditions of high stringency which may be used are well known in the art and as cited in Sambrook et al, 1989, Molecular Cloning, A Laboratory Manual, Second Edition, Cold Spring Harbor Press, N. Y., pp. 9.47-9.57; and Ausubel et al, 1989, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N. Y. are incorporated herein in their entirety. Another non-limiting example of procedures using conditions of intermediate stringency are as follows: Filters containing DNA are pre-hybridized, and then hybridized at a temperature of 6O0C in the presence of a 5X SSC buffer and labeled probe. Subsequently, filters washes are performed in a solution containing 2X SSC at 5O0C and the hybridized probes are detectable by autoradiography. Other conditions of intermediate stringency which may be used are well known in the art and as cited in Sambrook et al, 1989, Molecular Cloning, A Laboratory Manual, Second Edition, Cold Spring Harbor Press, N. Y., pp. 9.47- 9.57; and Ausubel el al, 1989, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N. Y. are incorporated herein in their entirety.
Duplex formation and stability depend on substantial complementarity between the two strands of a hybrid and, as noted above, a certain degree of mismatch can be tolerated. Therefore, the probe sequences of the subject invention include mutations (both single and multiple), deletions, insertions of the described sequences, and combinations thereof, wherein said mutations, insertions and deletions permit formation of stable hybrids with the target polynucleotide of interest. Mutations, insertions and deletions can be produced in a given polynucleotide sequence in many ways, and these methods are known to an ordinarily skilled artisan. Other methods may become known in the future.
It is also well known in the art that restriction enzymes can be used to obtain functional fragments of the subject DNA sequences. For example, BaB l exonuclease can be conveniently used for time-controlled limited digestion of DNA (commonly referred to as "erase-a-base" procedures). See, for example, Maniatis et al [1982] Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York; Wei et al. [1983] J. Biol. Chem. 258: 13006-13512.
The present invention further comprises fragments of the polynucleotide sequences of the instant invention. Representative fragments of the polynucleotide sequences according to the invention will be understood to mean any nucleotide fragment having at least 5 successive nucleotides, preferably at least 12 successive nucleotides, and still more preferably at least 15, 18, or at least 20 successive nucleotides of the sequence from which it is derived. The upper limit for such fragments is the total number of nucleotides found in the full-length sequence encoding a particular polypeptide (e.g., a polypeptide such as that of SRQ ID NO: 2). The term "successive'' can be interchanged with the term "consecutive" or the phrase "contiguous span"'. Thus, in some embodiments, a polynucleotide fragment may be referred to as "a contiguous span of at least X nucleotides, wherein X is any integer value beginning with 5; the upper limit for such fragments is one nucleotide less than the total number of nucleotides found in the full-length sequence encoding a particular polypeptide {e.g., a polypeptide comprising SEQ ID NO: 2).
In some embodiments, the subject invention includes those fragments capable of hybridizing under various conditions of stringency conditions (e.g., high or intermediate or low stringency) with a nucleotide sequence according to the invention; fragments that hybridize with a nucleotide sequence of the subject invention can be, optionally, labeled as set forth below.
The subject invention provides, in one embodiment, methods for the identification of the presence of nucleic acids according to the subject invention in transformed host cells or in cells expressing similar laccases. In these varied embodiments, the invention provides for the detection of nucleic acids in a sample (obtained from a cell) comprising contacting a sample with a nucleic acid (polynucleotide) of the subject invention (such as an RNA, mRNA. DNA, cDNA, or other nucleic acid). In a preferred embodiment, the polynucleotide is a probe that is, optionally, labeled and used in the detection system. Many methods for detection of nucleic acids exist and any suitable method for detection is encompassed by the instant invention. Typical assay formats utilizing nucleic acid hybridization includes, and are not limited to, 1) nuclear run-on assay, 2) slot blot assay, 3) northern blot assay (Alwine, el al, Prυc. Nail. Acad. Sci. 74:5350), 4) magnetic particle separation, 5) nucleic acid or DNΛ chips, 6) reverse Northern blot assay, 7) dot blot assay, 8) in situ hybridization, 9) RNase protection assay (Melton, el al, Nuc. Acids Res. 12:7035 and as described in the 1998 catalog of Ambion, Inc., Austin, Tex.), 10) ligase chain reaction, 11) polymerase chain reaction (PCR), 12) reverse transcriptase (RT)-PCR (Berchtold, et al , Nuc. Acids. Res. 17:453), 13) differential display RT-PCR (DDRT-PCR) or other suitable combinations of techniques and assays. Labels suitable for use in these detection methodologies include, and are not limited to 1) radioactive labels, 2) enzyme labels, 3) chemiluminescent labels, 4) fluorescent labels, 5) magnetic labels, or other suitable labels, including those set forth below. These methodologies and labels are well known in the art and widely available to the skilled artisan. Likewise, methods of incorporating labels into the nucleic acids are also well known to the skilled artisan.
Thus, the subject invention also provides detection probes (e.g., fragments of the disclosed polynucleotide sequences) for hybridization with a target sequence or the amplicon generated from the target sequence. Such a detection probe will comprise a contiguous/consecutive span of at least 8, 9, 10, 1 1 , 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75. 80, 85. 90, 95, or 100 nucleotides. Labeled probes or primers are labeled with a radioactive compound or with another type of label as set forth above (e.g., 1) radioactive labels, 2) enzyme labels, 3) chemiluminescent labels, 4) fluorescent labels, or 5) magnetic labels). Alternatively, non-labeled nucleotide sequences may be used directly as probes or primers; however, the sequences are generally labeled with a radioactive element (32P, 33S, H, 2SI) or with a molecule such as biotin, acetylaminofluorene, digoxigenin, 5-bromo-deoxyuridine, or fluorescein to provide probes that can be used in numerous applications. Polynucleotides of the subject invention can also be used for the qualitative and quantitative analysis of gene expression using arrays or polynucleotides that are attached to a solid support. As used herein, the term array means a one -, two-, or multi-dimensional arrangement of full length polynucleotides or polynucleotides of sufficient length to permit specific detection of gene expression. Preferably, the fragments are at least 15 nucleotides in length. More preferably, the fragments are at least 100 nucleotides in length. More preferably, the fragments are more than 100 nucleotides in length. In some embodiments the fragments may be more than 500 nucleotides in length.
For example, quantitative analysis of gene expression may be performed with full- length polynucleotides of the subject invention, or fragments thereof, in a complementary DNA microarray as described by Schena et al. (Science 270:467-470, 1995; Proc. Natl. Acad.
Sci. U.S.A. 93:10614-10619, 1996). Polynucleotides, or fragments thereof, are amplified by PCR and arrayed onto silylated microscope slides. Printed arrays are incubated in a humid chamber to allow rehydration of the array elements and rinsed, once in 0.2% SDS for 1 min, twice in water for 1 min and once for 5 min in sodium borohydride solution. The arrays are submerged in water for 2 min at 950C, transferred into 0.2% SDS for 1 min, rinsed twice with water, air dried and stored in the dark at 25°C. mRNA is isolated from a biological sample and probes are prepared by a single round of reverse transcription. Probes are hybridized to 1 cm rnicroarrays under a 14 x 14 mm glass coverslip for 6-12 hours at 6O0C. Arrays arc washed for 5 min at 250C in low stringency wash buffer (I x SSC/0.2% SDS), then for 10 min at room temperature in high stringency wash buffer (0.1 x SSC/0.2% SDS). Arrays are scanned in 0.1 x SSC using a fluorescence laser scanning device fitted with a custom filter set. Accurate differential expression measurements are obtained by talcing the average of the ratios of two independent hybridizations.
Quantitative analysis of the polynucleotides present in a biological sample can also be performed in complementary DNA arrays as described by Pietu et al (Genome Research 6:492-503, 1996). The polynucleotides of the invention, or fragments thereof, are PCR amplified and spotted on membranes. Then, mRNAs originating from biological samples derived from various tissues or cells are labeled with radioactive nucleotides. After hybridization and washing in controlled conditions, the hybridized mRNAs are detected by phospho-imaging or autoradiography. Duplicate experiments are performed and a quantitative analysis of differentially expressed mRNAs is then performed. Alternatively, the polynucleotide sequences of to the invention may also be used in analytical systems, such as DNA chips. DNA chips and their uses are well known in the art and (see for example, U.S. Patent Nos. 5,561,071 ; 5,753,439; 6,214,545; Schena et al, BioEssays, 1996, 18:427-431; Bianchi et al, CUn. Diagn. Virol, 1997, 8:199-208; each of which is hereby incorporated by reference in their entireties) and/or are provided by commercial vendors such as Affymetrix, Inc. (Santa Clara, CA). In addition, the nucleic acid sequences of the subject invention can be used as molecular weight markers in nucleic acid analysis procedures.
The subject invention also provides for modified nucleotide sequences. Modified nucleic acid sequences will be understood to mean any nucleotide sequence that has been modified, according to techniques well known to persons skilled in the art, and exhibiting modifications in relation to the native, naturally occurring nucleotide sequences.
The subject invention also provides genetic constructs comprising: a) a polynucleotide sequence encoding a polypeptide comprising SEQ ID No: 2, or a fragment thereof, optionally having laccase activity; b) a polynucleotide sequence having at least about 20% to 99.99% identity to a polynucleotide sequence encoding a polypeptide comprising SEQ ID No: 2 or a fragment of SEQ ID NO: 2, wherein said polynucleotide encodes a polypeptide or fragment thereof has laccase activity; c) a polynucleotide sequence encoding a fragment of a polypeptide comprising SEQ ID No: 2, wherein said fragment has laccase activity; d) a polynucleotide sequence comprising SEQ ID NO: 1; c) a polynucleotide sequence having at least about 20% to 99.99% identity to the polynucleotide sequence of SEQ ID NO: 1) a polynucleotide sequence encoding variant (e g . a variant polypeptide) of the polypeptide of SEQ ID No: 2. wherein said variant has laccase activity; or f) a polynucleotide sequence encoding a fragment of a variant polypeptide as set forth in (e). Genetic constructs of the subject invention can also contain additional regulatory elements such as promoters and enhancers and, optionally, selectable markers. In one aspect of the subject invention, the genetic construct comprises a promoter operably linked to a polynucleotide sequence encoding SEQ ID NO: 2. Also within the scope of the subject instant invention are vectors or expression cassettes containing genetic constructs as set forth herein or polynucleotides encoding the polypeptides, set forth supra, operably linked to regulatory elements. The vectors and expression cassettes may contain additional transcriptional control sequences as well. The vectors and expression cassettes may further comprise selectable markers. The expression cassette may contain at least one additional gene, operably linked to control elements, to be co-transformed into the organism. Alternatively, the additional gene(s) and control element(s) can be provided on multiple expression cassettes. Such expression cassettes are provided with a plurality of restriction sites for insertion of the sequences of the invention to be under the transcriptional regulation of the regulatory regions. The expression cassette(s) may additionally contain selectable marker genes operably linked to control elements.
The expression cassette will include in the 5'-3' direction of transcription, a transcriptional and translational initiation region, a DNA sequence of the invention, and a transcriptional and translational termination regions.
Another aspect of the invention provides vectors for the cloning and/or the expression of a polynucleotide sequence taught herein. Vectors of this invention, including vaccine vectors, can also comprise elements necessary to allow the expression and/or the secretion of the said nucleotide sequences in a given host cell. The vector can contain a promoter, signals for initiation and for termination of translation, as well as appropriate regions for regulation of transcription. In certain embodiments, the vectors can be stably maintained in the host cell and can, optionally, contain signal sequences directing the secretion of translated protein. These different elements are chosen according to the host cell used. Vectors can integrate into the host genome or. optionally, be autonomously-replicating vectors. The subject invention also provides for the expression of a polypeptide, peptide, fragment, or variant encoded by a polynucleotide sequence disclosed herein comprising the culture of a host cell transformed with a polynucleotide of the subject invention under conditions that allow for the expression of the polypeptide and, optionally, recovering the expressed polypeptide.
One aspect of the invention provides for methods of oxidizing a phenolic substrate comprising contacting the polypeptide as described herein, or fragments thereof retaining laccase activity, with a substrate comprising phenolic compounds under conditions that allow for the oxidation of the phenolic compounds. Examples of the phenolic substrates include 2,6-dimelhoxyphenol (DMP) and 4-hydroxy-3,5-dimethoxybenzaldehyde azine (syringaldazine or SGZ). Wine is another source of phenolic substrates that can be oxidized by the disclosed laccase. In one aspect, the contacting step can be performed by adding a composition comprising the purified laccase as described herein, or fragments thereof retaining laccase activity, to the phenolic compounds. The contacting step can be performed in the presence of other materials, such as salts and buffers. Additionally, the oxidation process can be optimized on specific substrate by manipulating the reaction conditions including temperature, pH, salt, and dissolved oxygen.
In another embodiment, the subject polypeptide, or fragments thereof retaining laccase activity, is capable of oxidizing bilirubin to biliverdin and water, which is desirable for a variety of clinical applications. In plasma samples, bilirubin interferes with adsorption bands between 400 and 500 nm. Addition of the polypeptide to plasma samples diminishes interference enables quantification of molecules at 400 to 500 nm such as plasma hemoglobin at 415 nm.
In yet another embodiment, the polypeptide of SEQ ID NO: 2, or fragments thereof retaining laccase activity, is able to mediate the delignification and detoxification of acid- pretreated biomass. Simultaneous saccharification and fermentation of hemicellulosic biomass is limited by the toxic compounds generated during the biomass pretreatment that restrict activity of the saccharifying enzymes and productivity of the microbial biocatalysts. Likewise, steps taken to optimize the modification of lignin by enzymes could bypass the need for harsher pretreatment steps and thereby facilitate bioprocess consolidation. Thus, the subject invention provides methods of delignification and detoxification of acid-pretreated biomass comprising contacting acid-pretreated biomass with a laccase comprising SEQ ID NO: 2, or fragments thereof retaining laccase activity. In another aspect of the invention, the laccasc of SEQ ID NO: 2. or fragments thereof retaining laccase activity, can be used for bleaching of dye in solutions. Such a method comprises contacting the dye with the laccase comprising SEQ ID NO: 2 within the solution.
Yet another aspect of the invention provides methods of bleaching pulp for paper production that comprises contacting paper pulp with a laccase comprising SEQ ID NO: 2, or fragments thereof retaining laccase activity. Alternatively, the disclosed laccase can be used in methods of lignin modification (e.g. in the manufacture of wood composites, such as wood fiber materials such as chipboards, fiber boards, or particle boards, or in the manufacture of laminated wood products, such as laminated beams and plywood) comprising contacting a lignin with a laccase comprising SEQ ID NO: 2, or fragments thereof retaining laccase activity.
An additional aspect of the invention comprises the treatment of waste water from: chemical or pharmaceutical factories; dye manufacturing facilities or dye-works; textile facilities or pulp production facilities. This aspect of the invention comprises contacting waste water from such facilities with a laccase comprising SEQ ID NO: 2, or fragments thereof retaining laccase activity.
All patents, patent applications, provisional applications, and publications referred to or cited herein are incorporated by reference in their entirety, including all figures and tables, to the extent they are not inconsistent with the explicit teachings of this specification. Following are examples which illustrate procedures for practicing the invention.
These examples should not be construed as limiting. All percentages are by weight and all solvent mixture proportions are by volume unless otherwise noted.
MATERIALS AND METHODS Materials
Biochemicals were from Sigma-Aldrich (St. Louis, Mo.). Other organic and inorganic analytical grade chemicals were from Fisher Scientific (Atlanta, Ga.). Restriction endonucleases, T4 DNA ligase and Vent DNA polymerase were from New England Biolabs (Ipswich, Mass.). AccuPrime GC -rich DNA polymerase was from Invitrogen (Carlsbad, Calif.). Desalted oligonucleotides were from Integrated DNA Technologies (Coralville, Iowa). Agarose for routine analysis of DNA was from BioRad Laboratories (Hercules. Calif). SeaKem GTG agarose used for separation and isolation of DNA fragments prior to ligation was from FMC Bioproducts (Rockland, ME). Strains, Media and Plasmids
Strains, primers and plasmids are summarized in Table 1. Escherichia coli DH5α was used for routine recombinant DNA experiments, and E. coli GM2163 was used to generate plasmid DNA for transformation of Hfx. volcanii (Dyall-Smith, 2008). E. coli strains were grown at 37 0C in Luria-Bertani medium. Hfx. volcanii strains were grown at 420C in complex (ATCC 974 and yeasl-peptone-Casamino Acids) and lactate-minimal medium (Hv- LMM). Hv-LMM included 2.46 M NaCl, 84 niM MgCl2-OH2O, 84 niM MgSO4-7H2O. 56 mM KCl, 6 niM CaCl2-2H2O, 5 mM NII4Cl, 4.6 mM NaBr, 1.4 mM NaIICO3, 9.75 mM KPO4 pH 7.5. 30 mM Tris pH 7.5, 0.25% (v/v) DL-lactic acid, 14 mM succinic acid. 0.0255% (v/v) glycerol, 1.8 nM MnCl2-4H2O, 1.5 nM ZnSO4-7H2O, 8.28 nM FeSO4-7H2O. 100 μM CuSO4-5H2O. 66 μg-mT histidine, 51 μg-ml" each of leucine, methionine, tryptophan, glycine. DL-pantothenic acid and uracil, 41 μg-ml"1 each of thymidine and hypoxantine, 800 ng thiamine and 100 ng D-biotin. Ampicillin (0.1 mg-ml"1), novobiocin (0.1 μg-ml"1), and CuSO4 (50 to 500 μM) were included as needed. Cultures were grown in liquid (150 to 200 rpm) and solid medium (15% [w/v] agar plates).
Genome Analysis
NCBI Local BlastP (Altschul et al, 1997) with BioEdit sequence editor software v7.0.4.1 (Hall, 1999) was used to compare the theoretical Hfx. volcanii DS2 proteome (http://archaea.ucsc.edu/, April 2007 version) (Hartman et al.. 2009) to fungal and bacterial proteins with known laccase activity. Laccase protein sequences included phenol oxidase A of the ligno-cellulolytic ascomycete Siachybotrys chartarum (Mander et al., 2006), spore coat protein A (CotA) from Bacillus subtilis (Martins et al.. 2002) and polyphenoloxidase (PPO) from Strepiomyces lavendulae (Suzuki et al.. 2003). Phylogenetic and molecular evolutionary analyses of the primary sequences of proteins were conducted using MEGA v3.1 (Kumar et al, 2004). Pairwise and multiple sequence alignment was performed using Clustal W (Thompson et al., 1994). Non-conserved regions in the N- and C-termini were excluded from the alignment. Evolutionary distances were estimated from the protein sequences using the proportion (p-) distance substitution model. Consensus tree inference was by neighbor-joining with bootstrap phylogeny test (1000 replicates; seed number for bootstrap, 64238) and pairwise gap deletion. TatP vl .O (Bcndtsen et al , 2005), TATHND vl .4 (Rose et al, 2002) and EnsembleGly (Caragea et al., 2007) servers were used for prediction of twin arginine translocation (TAT) and glycosylation motifs in the LccA protein (see Fig. 7).
DNA Isolation, Analysis and Strain Construction Hfic. volcanii DS70 genomic DNA (a strain of DS2 cured of plasmid pIIV2)
(Wendoloski et ah, 2001) was prepared for polymerase chain reaction (PCR) by transfer of isolated colonies to 30 μil deionized H2O using toothpicks. Cells were boiled (5 min), and the resulting lysate was chilled on ice (10 min) and centrifuged (14,000 x g; 10 min at 4 0C). Supernatant (5 - 10 μl) was used as template for PCR with primer pairs specific for the Hfx. volcanii laccase gene (lccA, HvoB0205), as listed in Table 1. A mixture of AccuPrime GC- Rich and Vent DNA polymerase at a 9:1 ratio was used for PCR with buffer and nucleotide concentrations according to Invitrogen. PCR was performed with an iCycler (BioRad Laboratories), and sizes of products were analyzed by electrophoresis using 0.8% (w/v) agarose gels in TAE buffer (40 mλl Tris acetate, 2 mM EDTA, pH 8.5) with Hi-Lo DNA molecular weight markers as standards (Minnesota Molecular, Minneapolis, Minn.). Gels were photographed after staining with ethidium bromide at 0.5 μg-mF1 with a Mini visionary imaging system (FOTODYNE, Hartland, Wis.). PCR generated-DNA fragments of appropriate si/e for the lccA gene (1.8 kb) were isolated from 0.8% (w/v) ScaKem GTG agarose (FMC Bioproducts, Rockland, ME) gels in TAE buffer using the QIAquick gel extraction kit (Qiagen) and ligated into the Ndel to HindIII sites of pET24b to generate plasmid pJΛM821 and pJAM823 for expression of the lccA gene in recombinant E. coli Rosetta (DE3). In addition, the lccA gene was excised from plasmids pJAM821 and pJAM823 and ligated into the Ndcl to BIpI sites of a Hfx. volcanii shuttle vector (pJΛM202) to position the lccA gene downstream of a constitutive ribosomal RNA promoter P2. These expression plasmids (pJAM822 and pJAM824) were transformed into Hfx. volcanii H26 to generate strain SBOl and US02 for high-level synthesis of lccA with and without a C-termianl strepll tag (- WSHPQFEK), respectively. Plasmid DNA was isolated using the QIAprep Spin Miniprep Kit (Qiagen. Valencia, Calif.), and the fidelity of cloned DNA sequences and the 100% identity of lccA genes from DS2 and DS70 strains were confirmed by Sanger DNA Sequencing (ICBR Genomics Facility, University of Florida). Enzyme Purification
Hfx. volcanii SBOl and US02 cells were grown in media supplemented with 100 μM CuSO4 (LMM or YPC; 25 ml per 125 -ml Erlenmeyer flask) and harvested by centrifugation (15,000 x g; 20 min at 40C). Culture broth was filtered by 3MM Whatman chromato graph} paper. Protein was concentrated by gradual addition of one volume of cold absolute ethanol, incubation on ice (1 h) and centrifugation (7,000 x g at 4°C, 10 min). The resulting precipitate was suspended in 25 mM Tris-HCl buffer at pH 8.4 (T buffer) to 1/5 original sample volume and recentrifuged to eliminate insoluble material. US02 precipitate (from an original culture of 360 ml) was concentrated to 3 ml using a Centricon PL-30 centrifugal filter according to the instructions of the supplier (Millipore, Billerica, MA) and separated into two 1.5 -ml fractions (where Fl and F2 represent the more viscous lower and upper fractions, respectively) and diluted 6.7-fold with T buffer. For both SBOl and US02 samples, proteins were filtered (0.20 μm) immediately prior to application to an anion-exchange MonoQ HR 5/5 or 10/10 column (Pharmacia) equilibrated with T buffer, as indicated in Table 1 . Elution was carried out with a linear NaCl gradient (0 to 1 M in 1 ml T buffer) with fractions containing peak activity at 625 to 675 mM NaCl. Additional steps were included for purification of LccA from SBOl, including application of active fractions (0.25 ml per run) to a Superdex 200 HR 10/30 column (Pharmacia) equilibrated in T buffer with 150 mM NaCl, followed by a MonoQ HR 10/10 column (Pharmacia) equilibrated in T buffer and developed with a linear NaCl gradient (600 to 800 mM in 1 ml T buffer). Fractions were monitored for purity by assay with 4-hydroxy-3,5-dimethoxybenzaldehyde azine (syringaldazine [SGZ]) under standard assay conditions (see below for details) and staining with Coomassie blue R-250 after separation by reducing 12% SDS-PAGE according to Laemmli (1970). Prestained SDS-PAGE standards and Kaleidoscope standards (BioRad) were used as protein standards for PAGE. They included: phosphorylase B (100.9 IcDa). bovine serum albumin (97.3), ovalbumin (54.1 kDa), carbonic anhydrase (37.6 kDa), soybean trypsin inhibitor (29.2 kDa), lysozyme (20.0 kDa). Native molecular mass was determined by applying samples to a calibrated Superose 200 HR 10/30 column as recommended by supplier (Pharmacia). Molecular mass standards for gel filtration calibration included: cytochrome c (12.4 kDa). carbonic anhydrase (29 kDa). bovine serum albumin (66 kDa), alcohol dehydrogenase (150 kDa), β-amylase (200 kDa) and apoferritin (443 kDa) (Sigma). Samples were stored in the presence of oxygen at 4°C. Enzyme Activity and Protein Estimation
Substrates for enzyme activity assay included 2,2'-azino-bis-3-elhylbenzthiazoline-6- sulphonic acid (ABTS) (Sigma; A1888), 2,6-dimethoxyphenol (DMP) (Sigma; D135550), 2- methoxyphenol (guaiacol) (Sigma; G5502), 4-hydroxy-3.5-dimethoxybenzaldehyde azine (syringaldazine or SGZ) (Sigma; S7896), bilirubin (Sigma; B4126), and ferrous ammonium sulfate. Enzyme activity was determined by change in absorbance, in triplicate, by UV/Visible-spectroscopy using a BioTek Synergy HT multi-detection microplate reader with a 96-well plate. Oxidation of substrate was monitored by absorbance increase (AB T S at 420 nm with ε = 36.000 M"1 cm"'; SGZ at 526 nm with ε = 65,000 M"1 cm"1; DMP at 468 nni with ε = 49,000 M"1 cm"1; guaiacol at 436 nm with ε = 26,600 M"1 cm"1; ferrous ammonium sulfate at 315 nm with ε = 2,200 M"1 cm"1) or decrease (bilirubin at 440 nm with ε = 56,300 M"1 cm" l). Standard assay conditions were 185 mM NaCl at 450C with the following buffers and substrate concentrations: 100 mM sodium acetate buffer at pll 6.0 for ABTS (at 5 mM), DMP (at 2 mM) and guaiacol (at 5 mM); 25 mM Tris-HC) buffer at pH 8.4 for SGZ (at 1 mM); and 200 mM Tris-HCl buffer at pH 8.4 for bilirubin (0.45 mM). Copper sulfate (1 mM) was included for assay of DMP oxidation. Oxidation of ferrous ammonium sulphate (1 mM) was monitored at 315 nm (ε = 2,200 M"1 cm"1) with and without salt (185 mM NaCl) in 100 mM MES (morpholineethanesulfonic acid) buffer at pH 5 as well as 25 mM Tris-HCl buffer at pH 7.0 and 8.4. One unit of enzyme activity is defined as the amount of enzyme that oxidizes 1 μmol of substrate per min at standard conditions. Kinetic studies were conducted using purified LccΛ at a final concentration of 0.61 μg-ml"1 with 5 to 160 μM of SGZ, 50 to 1,250 mM ABTS, and 90 to 540 μM bilirubin. Kinetic parameters (K1n, Vmax and kcat) were determined using the Michaelis-Menten equation. Protein concentration was determined according to Bradford (1976) using a Bio-Rad protein assay with bovine serum albumin as a standard (BioRad Laboratories). All assays and protein purifications were performed at least in triplicate.
For detection of laccase activity in gel, non-boiled samples were separated by 7.5% PAGE gels devoid of SDS and β-mercaptoelhanol. Gels were immersed in either T buffer containing 1 mM SGZ And activity was rapidly visualized as a pink color. For detection of total protein, gels were counterstained in Coomassie blue R-250 stain and destained according to instructions of the supplier (BioRad). Images of activity and protein staining were acquired using a VersaDoc 1000 imaging system (BioRad). Mass Spectrometry (MS) Analysis
Purified LccA was provided for MS analysis as an in-solution sample and as protein bands separated by reducing SDS-PAGE (7.5%). Gels were stained with Biosafc Coomassic (BioRad), and LccA-protein bands (71 IcDa) were excised from the gel and destained with 100 mM NH4HCO3 (pH 7.5) in 50% (v/v) acetonitrile (40C overnight). Protein samples were reduced, alkylated in gel or in solution, digested with a 1 :20 mg ratio of trypsin (Promega) to protein (18 to 24 h, 370C) and desalted with a PepMap Cl 8 cartridge. Peptides were further separated by capillary reverse-phase high-performance liquid chromatography (RP HPLC) using a PepMap Cj8 column (15 cm x 75 μm inside diameter [i.d.]) and an Ultimate Capillary HPLC System (LC Packings, San Francisco, CA) with a linear gradient of 5% to 40% (v/v) acetonitrile for 25 min at 200 nl/min. Tandem MS (MS-MS) analysis was performed online using a hybrid quadrupole time-of-flight instrument (QSTAR XL hybrid LC/MS/MS) equipped with a nanoelectrospray source (Applied Biosystems, Foster City, CA) and operated with the Analyst QS vl .l data acquisition software. Spectra from all experiments were converted to DTA files and merged to facilitate database searching using the Mascot search algorithm v2.1 (Matrix Science, Boston, MA) against the theoretical Hfx. volcanii proteome (http://archaea.ucsc.edu/, April 2007 version). Search parameters included trypsin as the cleavage enzyme and carbamidomethylation as a fixed modification. Variable modifications included dcamidation of asparagine and glutamine, oxidation of methionine, methyl- esterification of aspartate and glutamate, and N-acetylation and phosphorylation of serine, threonine and tyrosine. Mass tolerances for all QSTAR analyses were 0.3 Da, and peptides with assigned probability-based Mascot ion scores less than 30 were excluded.
N-Terminal Sequence Analysis of Protein Purified LccA was separated by reducing 12% SDS PAGE and transferred by electroblotting to Immobilon-P (PVDF) membranes (Amersham Biosciences) at 100 V for 100 min at 4°C. Proteins were stained in membrane with 0.2 % (w/v) Coomassie blue R-250 in 40% acetic acid for 30 sec and rinsed with deionized water. The LccA-specifϊc protein band was excised and subjected to automated Edman degradation for N-terminal sequencing (Edman, 1970). Glycoprotein Analysis
LccA was separated by reducing SDS-PAGE and stained in gel for glycosylation using Pro-Q Emerald 300 (ϊnvitrogen P21857) and total protein was separated using Sypro
Ruby (BioRad; 1703126) with a VersaDoc 4000 imaging system according to the instructions of the manufacturer (BioRad Laboratories). The carbohydrate content of purified LocA was estimated by the colorimetric method of Dubois et al. (Dubois et al., 1956) using glucose as a standard. Pure LccA was deglycosylated by the trifluoromethanesulfonic acid (TFMS) method (Edge et al., 1981) for 0 to 10 hours on ice and analyzed by reducing SDS-PAGE.
Trametes versicolor laccase (Sigma Fluka; 53739) and bovine carbonic anhydrase (Sigma- Λldrich; C7025) were included for glycoprotein analysis as positive and negative controls, respectively.
EXAMPLE 1— LccA IS RELATED TO LACCASES OF THE MULTICOPPER OXIDASE
FAMILY Basic local alignment search tool (BLAST) analysis of the Hfic. volcanii genome revealed a 63,397 Da-polypeptide of pi 4.34 (Hvo_B0205; designated as LccA in this study) related to laccases of the multicopper oxidase (MCO) family. The gene locus encoding LccA resided on pHV3 (440 kb), one of three large replicons with edeό- and orci-associated replication origins separate from the 2.848-Mb chromosome (Norais et al., 2007). Proteins that cluster to the MCO family are rare in archaea with only a few examples, all of which remain to be characterized. The one cysteine and 10 histidine residues required for coordination of the Type 1. 2 and 3 copper centers of blue copper laccases were highly conserved in the Hfx. volcanii LccA (Fig. 7) suggesting this protein may catalyze the oxidation of phenolic compounds. The Hfx. volcanii LccA was also predicted to be secreted by the twin-arginine translocation (TAT) system, based on a N-terminal twin arginine motif (SRRRFL) preceding a hydrophobic patch. LccA was also predicted to be cleaved between Ala31 and Ala 32 to generate a mature protein of 60.1 kDa and to be glycosylated based on the presence of O- and N-linked glycosylation motifs, Thr-X5-Pro-X-Pro and Asn-X- (Thr/Ser) (where X represents any amino acid) (Fig. 7). Although an ORF closely related to the Hfx. volcanii LccA was present in the draft genome of the haloarchaeon Halorubrum lacusprofundi (HlacDRAFT_2279), LccA homologs were not universal among the haloarchaea and were absent from the genomes of Halobacterium sp. NRC-I (Hb. salinarum Rl) (Ng et al., 2000), Haloquadratum walsbyi DSM 16790 (Bolhuis et al, 2006), Haloarcula marismortui ATCC 43049 (Baliga et al, 2004) and Naironomonas pharaonis DSM 2160 (FaIb et al, 2005). Based on consensus tree inference (Figures IA and I B), the Hfic volcanii LccΛ was closely related to MCO proteins of the gram-positive fimiicutes, including CotA proteins of R. subtilis and Bacillus licheniformis. which have demonstrated thermostable laccase activity (Martins et al, 2002; Koschorreck et al, 2008). Among the archaea, LccA was closely related (45% identity) only to Hlac_1049, encoded on the main chromosome of IIalorubrum lacuspro fundi. Other archaeal genomes (completed as of November 2009) did not encode LccA homologs, including the haloarchaea Halobaclerium sp. NRC-I (JIalohacterium salinarum Rl). Haloquadratum walsbyi DSM 16790. Haloarcula marismortui ATCC 43049. and Natronomonas pharaonis DSM 2160. The Hfic. volcanii LccA was distinct, however, from an MCO of the hyperthermophilic archaeon Pyrobaculum aerophilum. PAEl 888, an uncharacterized protein with enhanced transcript leels under denitrifying conditions in of P. aerophilum (Cozen el al., 2009). PAEl 888 clusters instead with McoA of Aquifex aeolicus, CueO of E. coli and Mco of Staphylococcus aureus. All three of these latter bacterial MCOs have catalytic and/or genetic properties consistent with their proposed role in oxidative stress and/or copper and iron homeostasis (e.g., Singh et al. 2004; Fernandes et al, 2007; Sitthisak et al, 2005). This includes a higher enzyme specificity (kcJKm) for cuprous and ferrous iron than for aromatic substrates and aromatic oxidation activity that requires addition of copper (Solano et al., 2001). Consistent with this, the methionine-rich helix proposed to be involved in metal sequestration that lies over the type 1 sites of the metal -oxidizing MCOs, such as E. coli CueO (Roberts et al., 2002), is not conserved in LccA. The sparse distribution of laccase gene homologs among the archaea and the close relationship of LccA to laccases of the firmicutcs (e.g., B. subtilis CotA), suggest that lccA was acquired by horizontal gene transfer from the Bacteria domain and that it encodes a laccase that oxidizes phenolic compounds.
EXAMPLE 2— LACCASE ACTIVITY IN THE CULTURE BROTII OF HFX. VOLCANII
The initial efforts focused on engineering the Hfic. volcanii lccA gene for production of the LccA protein in recombinant E. coli Rosctta (DE3) with plasmids pJAM821 and pJAM823 (Table 1) using the pET expression system. Although numberous Hfx. volcanii proteins have been successfully produced using this type of bacterial system (Kaczowka et al., 2003; and Reuter et al., 2004), LccA protein and laccase activity, however, were not detected in either the culture broth or cell lysate of this E. coli strain as determined by SDS- PAGE and SGZ oxidation assay, respectively (data not shown). The undetectable levels of LccA may be due to a number of factors. TAT substrates, "salt-loving" haloarchaeal proteins, enzymes with elaborate metal clusters, and glycoproteins are all notoriously difficult to produce in an active form at high-levels in conventional expression systems, such as E. coli and Saccharomyces cerevisiae (Connaris el al., 1999; Madzak et al., 2005; Brϋser,
2007).
To overcome the difficulties of producing LccA in E. coli, the native host (i.e., Hfx. volcanii, known for its halophilic properties and robust TAT system (Rose et al., 2002) was engineered for enhanced expression of Ice A. Multicopy plasmids (pJAM822 and pJAM824) with a pHV2 origin of replication, ribosomal RNA P2 promoter and T7 transcriptional terminator were used for this lccA gene-expression. In particular, the lccA gene was positioned downstream of a strong rRNA P2 promoter on a multicopy plasmid (pHV2 based) with and without coding sequence for a 1-Da C-terminal Strepll tag (- WSHPQFEK), and the resulting plasmids were transformed into Ii. volcanii H26. The resulting strains, Hfx. volcanii SBOl and US02 (Table 1), were grown in various media supplemented with CuSO4 (50 to 500 μM) and compared to their parent (H26) for the production of laccase activity by monitoring the oxidation of SGZ. Using this approach, laccase activity associated with H. volcanii cells was negligible for all three strains examined reaching at most 0.69 ± 0.12 mU-mF1 after 80 - 12O h of growth (Figs. 2A and 2B). In contrast to these cellular fractions, significant levels of laccase activity were detected in the culture broth of H. volcanii SBOl and US02 with the highest level of activity detected for strain US02 in YPC medium with 100 μM CuSO4 (Fig. 2B). Under these conditions, the laccase activity of US02 reached a maximum of 170 ± 10 mU-ml"1 at stationary phase (72 to 80 h); whereas, the level of laccase activity secreted by SBOl was 40-fold lower reaching levels of only 4.3 ± 0.23 mlJ-ml"1 at 54 h. Laccase activity was not detected in the culture broth of US02 and SBOl until stationary phase (Figs. 2A and 2B) and was not detected at significant levels throughout all phases of growth for parent strain Η26 (data not shown). The reason for the lag in laccase productivity for US02 and SBOl remains to be determined; however, a similar time course has been observed for the secretion of the Natrialba magadii subtilisin-like Nep protease from recombinant H. volcanii (De Castro et al., 2008). While the addition of a strong, relatively constitutive promoter upstream of lccA enhanced laccase productivity by over 170-fold, addition of a C-terminal Strepll coding sequence significantly decreased LccA productivity. Thus, enhanced expression of Ice A coding sequence alone was optimum for secretion of laccase activity by H. volcanii.
Although the genetic systems of archaea are not as advanced as those of bacteria or yeast, the productivity of the engineered H. volcanii strain US02 was surprisingly high, with 170 mU'ml"1 laccase activity produced in the medium in less than 3 days. This level of productivity is comparable to that of yeast systems, such as Yarrυwia lipolytica and Pichia methanolica systems, developed for secretion of the laccase of Trametes versicolor (a white- rot fungus). Typically, these yeast systems require 5 to 6 days of cultivation for production of 230 to 1,260 mU-ml"1 of laccase activity (Jolivalt et al, 2005; Guo et at., 2006). Secretion of LccΛ, contrasts with the vast majority of recombinant systems for production of bacterial laccase/MCO enzymes which are based on enzyme purification from the soluble and/or insoluble fractions of recombinant E. coli cells, such as those used for Thermus ihermophilus Tth-laccase (Miyazaki 2005), Bacillus subtilis and Bacillus licheniformis CotA (Martins et al, 2002; Koschorreck et al, 2008), Bacillus halodurans Lbhl (Miyazaki 2005), Staphylococcus aureus Mco (Sitthisak el al., 2005), Aquifex aeolicus McoA (Fernandcs et al., 2007), and Bacteroides RL5 from the rumen metagenome (Beloqui el al., 2006).
EXAMPLE 3— PURIFICATION OF LccA FROM THE CULTURE BROTH OF HFX.
VOLCANII Purification of LccA from culture broth of Hfx. volcanii SBOl
Laccase activity was purified 12-fold from the culture broth of Hfx. volcanii SBOl to a specific activity of 1.3 U-mg"1 (SGZ oxidation) as outlined in Table 2. For purification, extracellular proteins were precipitated from culture broth and fractionated by a combination of anion exchange and gel-filtration chromatography steps. It is interesting to note that the laccase activity reproducibly increased 1.4-fold after ethanol precipitation (Table 2), most likely due to the removal of inhibitory compounds and/or proteins from the sample by this technique. The final chromatography steps yielded a homogeneous and laccase-active preparation of LccA based on SDS-PAGE, mass spectroscopy and in gel activity staining (Figure 3). Separation of protein fractions from the various stages of purification by SDS- PAGE revealed the final MonoQ 10/10 fraction was composed of a single protein band estimated at 70.7 kDa compared to the migration of molecular mass standards (Figure 3Λ). This molecular mass was somewhat higher, yet consistent, with the 63,397 Da calculated in silico for the LccA polypeptide. Final MonoQ 10/10 fractions were further analyzed by mass spectrometry, using QSTAR XL hybrid LC/MS/MS, to confirm the protein composition and purity. The MS profiles of tryptic peptide fragments generated from the protein in solution were compared to the fragments generated after excision of the 71 -IcDa protein from the gel. In all cases, LccA was identified as the protein responsible for the laccase activity with 38 to 68% coverage (Table 5). LccA fractions were further analyzed by native PAGE coupled with in gel activity stain followed by staining for total protein. A single protein band was detected in the Superdex 200 HR 10/30 fractions that was active in the oxidation of both ABTS and SGZ (Figure 3B). As the mobility in native PAGE gels depends on both the charge and hydrodynamic size of the protein, the low pi of LccA (calculated at 4.34) is likely to account for its rapid migration in the gel compared to proteins of lower molecular mass (e.g.. 54-kDa ovalbumin). To estimate the native molecular mass of LccA, the protein was applied to a gel filtration chromatography (Superose 200 HR 10/30 column) calibrated with molecular mass standards. The LccA protein was estimated to be 65.4 kDa and, thus, is most likely associated as a monomer (Figure 4). Unlike other characterized haloarchaeal proteins \e g., (Wilson el a!.. 1999)], N-tcrminal sequencing of the LccA protein was unsuccessful suggesting it may be blocked by modifications such as Nα-acetylation which is common to this organism (Kirkland el al., 2008).
Purification of LccA from culture broth of Hfx. volcanii US02 LccA was purified 13-fold from the culture broth of H. volcanii IJS02 to a specific activity of 29.4 U 'mg'1 by ethanol precipitation, concentration using a Centricon PL-30 centrifugal filter and fractionation by MonoQ chromatography as outlined in Table 2. LccA- StrepII was similarly purified from SBOl with the addition of gel filtration (Fig. 9) and MonoQ chromatography steps at the final stages of purification (Table 2). In contrast to US02 purified LccA, the specific activity of LccA-StrepII was over 20-fold lower at only 1.3
U-mg"1. Thus, addition of a C-terminal StrepII tag not only reduced productivity of the strain but also reduced LccA enzyme activity. Incorporation of StrepTactin chromatography did not improve the overall activity or yield of LccA-StrepII from SBOl and, thus, was not further pursued (data not shown). The LccA protein isolated from US02 (as described above) was analyzed for purity by- reducing SDS-PAGE and mass spectrometry (MS). Purified LccA migrated as a single protein band of 75 - 80 kDa (Fig. 1 1) that was specific for LccA based on MS analysis with 38 to 68 % coverage of the LccA polypeptide sequence (Figs. 7 and 10 and Table 5). The 10 - 20 kDa difference in migration of LccA by SDS-PAGE compared to that calculated from the polypeptide sequence was consistent with its low pi and/or post-translational modification by glycosylation.
EXAMPLE 4— MULTIPLE ISOFORMS OF LccA
LccA (purified as described above) was separated by native PAGE and stained for SGZ oxidizing activity and total protein. In contrast to SBOl purified LccA-StrepIT, for which only a single protein band was detected, LccA purified from US02 migrated as at least four separate isoforms that were all active in SGZ oxidation (Fig. 12A). These results suggested that LccA was modified post-translational and that addition of a C-terminal StrepII tag abolished this modification. It should be noted that mobility in native gels depends not only on the hydrodynamic size but also the charge of the protein. The LccA polypeptide sequence is predicted to be highly acidic, and this is likely to account for the rapid migration of all of the LccA isoforms compared to protein standards of similar molecular mass.
EXAMPLE 5— N-TERMINAL CLEAVAGE AND GLYCOSYLATION OF LccA
Many fungal laccases are modified post-translational Iy including removal of N- tcrminal residues as well as the addition of high-mannose-type glycans to Asn residues (N- glycosylation) [e.g., Bertrand et al , 2002; Giardina et al, 2007; Koikeda et al, 1993; Madzak et al, 2005; Quaratino et al., 2007; and Yavcr et al., 1999J. Based on bio informatics, LccA is predicted to be cleaved between Ala31 and Ala32 and to be N- and/or O- glycosylated (Fig. 7). To investigate these possibilities, the US02-purified LccA was N- terminal sequenced by Edman degradation and analyzed for glycosylation. Purified LccA was cleaved after Ala31 (Fig. 7) and glycosylated based on a carbohydrate content of 6.9 ± 0.06 % as determined by a phenol-sulfuric acid method (Dyall-Smith et al., 2008) and staining using Pro-Q Emerald 300 (Hoegger et al., 2006) (Fig. 12B). Although the carbohydrate content of LccA was 2.6-fold lower than observed for the commercial T. versicolor laccase, it was similar to the 6.9 % previously reported for other fungal laccases (Barreca et al., 2003). To further analyze and confirm LccA glycosylation, the purified protein was treated with trifluoromethanesulfonic acid (TFMS), a strong acid known to remove glycans from polypeptide chains (Edman, P., 1970). A molecular weight shift of 10 - 20 kDa was observed by SDS-PAGE for the TFMS-treated LccA compared to the untreated control and resulted in its migration at ~ 60 kDa consistent with the molecular mass calculated from the deduced amino acid sequence (Fig. 12C). TFMS treatment did not shift the migration of non- glycosylated control proteins (e.g., carbonic anhydrase) confirming that polypeptide chains remained intact under these conditions (data not shown). Together these results provide evidence that LccA is secreted, cleaved and glycosylated during its maturation; however, the order of these events remains to be determined.
Interestingly, the LccA-StrepII variant purified from SBOl was not associated with carbohydrate and did not stain by Pro-Q Emerald (data not shown). Furthermore, the N- terminus of LccA-StrepII was not amendable to sequencing by Edman degradation suggesting it may be blocked by Nα-acetylation. These results are consistent with the native PAGE analysis and suggest that addition of a StrepII tag to the C-terminus of LccA not only reduces its activity but also inhibits its N-terminal cleavage and glycosylation.
EXAMPLE 6—SPECTROSCOPIC AND CATALYTIC PROPERTIES OF PURIFIED LccA The purified LccA protein (purified from US02) was blue and exhibited an absorbance spectrum typical of blue multicopper oxidases including a peak at approximately 600 nm and shoulder at 330 nm (Figure 5). Many laccases isolated from fungi and bacteria are blue multicopper oxidases that coordinate four copper atoms into three types of copper- binding sites (Hoegger el al., 2006). All of these 'blue' enzymes produce spectra with a maximum at 605 nm corresponding to the Tl or blue copper atom. The T2 copper site exhibits weakly visible absorbance, and the T3 copper site has two copper centers and is responsible for a shoulder at around 330 nm. The spectrum of LccA is consistent with its clustering to blue laccases including the closely related and structurally characterized B. subtilis CotA (Enguita et ah, 2003). Thus, the conserved cysteine and 10 histidinc residues are likely to coordinate the three types of copper sites in LccA. The activity of LccA toward different phenolic and non-phenolic compounds was investigated. Four substrates most commonly used for determination of laccase activity were evaluated; 2,2'-azino-bis-3-ethylbenzthia/oline-6-sulphonic acid (ABTS), 2,6- dimethoxyphenol (DMP), 2-methoxyphenol (guaiacol), and 4-hydroxy-3,5- dimethoxybenzaldehyde azine (syringaldazine or SGZ). Oxidation of ferrous (Fe""1") ammonium sulphate and bilirubin was also investigated. Although LccA did not oxidize Fe H or guaiacol in the presence or absence of copper supplementation, it did oxidize the remaining substrates, i.e., ABTS at 6.1 ± 0.39 U-mg"1. DMP at 12.6 ± 1.1 U-mg"1, SGZ at 29.4 ± 1.4 U-mg"1 and bilirubin at 25.5 ± 1 U-mg"1 where the values reported are for US02- purified LccA under standard conditions (see methods for details). Note that the oxidation of DMP was highly stable for several hours but, unlike ABTS, SGZ and bilirubin, required addition Of CuSO4. LccA presented a higher specificity for SGZ than for ABTS, with kcJKm values of 0.62 and 0.015 S'VM"1 , respectively (Table 3). While the SGZ specificity of LccA was significantly lower than that of the DUF 152 RL5-laccases, it is comparable to if not higher than that of B. subtilis CotA (Table 3). Furthermore, the specific activity of LccA for oxidation of bilirubin was comparable (if not higher, with a kcjKm value of 0.12 s"1 μM"1 (kcat, 29 s"1; Km, 236 μM)) than reported for the Amano MvBO-3 enzyme at 1 .2 U mg"1 (Amano Enzyme USA, Product Data Sheet for Bilirubin Oxidase "Amano" 3 [BO-3] (Myrothecium sp.).
Recently, laccases have been grouped based on their DMP oxidase activity (Solano et ah, 2001). The first group oxidizes DMP without copper supplementation (e.g., laccase of Pyricularia oryzae, PpoA of Marinomonas mediterraneά), the second group of en/ymes readily oxidize DMP after addition of copper but are also rapidly inactivated (e.g., CucO of E. colϊ) and the third type shows a very slow rate of DMP oxidation that lasts for hours, but only in the presence of added copper (e.g., CotA of B subtilis). LccA oxidized DMP only in the presence of added CuSO4; hence, it appears most similar to this latter group of laccases.
To further evaluate the catalytic properties of LccA, the temperature, pH and salt optima of the purified enzyme were determined using SGZ and/or ABTS as substrates. LccA activity was optimum at 45 to 500C (Figure 6A), consistent with the optimal growth temperature of this organism (42 to 45°C) (Robinson et al, 2005). Relative to this optimum, LccA was -75% active at room temperature (250C) and 15, 35, 48 and 67% active at 70. 65. 60 and 55°C respectively. The temperature optimum of LccA is similar to a number of bacterial MCOs including the 40 to 450C for laccases of Streptomyces sp (Niladevi and Prema. 2008; Endo et al, 2003), 52°C for Bacteroides thetaiotaomicron BTH4389 and 44 0C for Escherichia coli YifH (Beloqui et ah, 2006). It is also closely related to the temperature optimum for simultaneous saccharification and fermentation (SSF) processes which include fungal cellulases and second generation microbial biocatalysts (Endo el al.. 2003). However, it is significantly lower than the 75°C optimum for Bacillus subtilis CotA (Martins et al, 2002) and 700C optimum for Λquifex aeolicus McoA (Fernandes et al. 2007).
Most extracellular and intracellular enzymes of the haloarchaea. including Hfic volcanii, require salt for activity and stability. Consistent with this. LccA activity was optimal at ~ 200 mM salt with 1.5-fold higher activity in KCl than NaCl, and the enzyme displayed reduced activity after removal of the salt by dialysis (Figure 6B). LccA was also active at relatively high concentrations of salt with 65% relative activity at 1 M NaCl (Figure 6B). The ability of LccA to rapidly oxidize phenolic substrates at molar concentrations of salt is not surprising as this enzyme is secreted by a microbe isolated from the Dead Sea. Similarly Lbhl from Bacillus halodurans was stimulated by addition of 450 rnM NaCl
(Ruijssenaars and Hartmans, 2004).
While the oxidation of ABTS by LccA was optimal at low pi I (pH of 6.0). its optimum for SGZ oxidization was more alkaline (pH of 8.4) (Figure 6C). Most microbial laccases display optimal activity at low pH. Those with alkaline or near neutral pH optima are not as common with examples including those of Acremonium murorum (Gouka et al., 2001), Bacillus halodurans (Ruijssenaars and Hartmans. 2004), Coprinus cinereus (Yaver et al., 1999) and Melanocarpus albomyces (Kiiskinen et al., 2002). Unlike LccA, the few microbial laccases that are active at alkaline pH do not exhibit significant activity below pi I 6.0. The alkalophilic nature of LccA might be of interest in paper pulp bleaching, which requires an alkaline pH optimum. These unique catalytic properties of LccA underline the potential of archaea as a source of high-value laccases.
EXAMPLE 7— LccA IS STABLE AT HIGH TEMPERATURE, SALT AND SOLVENT To assess the thermostability of LccA, the purified protein was pre-incubated at various temperatures from 37 to 700C for up to 2 1A days. LccA was fully active after 1 h at 550C and 5 h at 5O0C, with a half-live of inactivation at 5O0C of 31.5 h (Figure 6D). The enzyme retained nearly all of its original activity at 37°C and 35 to 60% of its activity at 45 to 500C, after incubation for 2 Vz days. These results reveal that LccA is highly thermostable, retaining most of its activity after prolonged incubation at moderately high temperatures. The multicopper oxidase of Aquifex aeolicus, McoA. has remarkably stable activity, with the ability to oxidize metals after incubation for 5 h at 900C (Fernandes et al., 2007). Likewise, the recently studied recombinant RL 5 laccase from rumen metagenome has maximal activity at 6O0C and is fully stable at this temperature for 200 min (Beloqui el al.. 2006). CotΛ of /?. subtilis is also thermostable, with a half-life of nearly 2 h at 800C (Martins et al, 2002). The purified LccA was also stable in a wide range of NaCl concentrations from 100 mM to. at least, 1.4 M, retaining nearly all of its original activity if not higher (Figure 6E). It is noteworthy that prolonged incubation, from 90 min to 24 h, of LccA in salt did not alter this activity profile (data not shown). Recent analysis of a laccase from a bacterium isolated from a mangrove swamp (i.e., Streptomyces psammoticus) demonstrated this enzyme is also salt tolerant with full activity after incubation for 24 h in 0.8 M NaCl (Niladevi and Prema, 2008).
Commonly used water miscible organo- solvents (i.e., methanol, ethanol, dimethyl sulfoxide or DMSO and dimethylibrmamide or DMF) were examined for their compatibility with LccA stability and activity. Purified LccA protein was incubated in T buffer with 25%
(v/v) solvent in the presence of salt (185 mM NaCl) for 90 min to 24 h. The enzyme and solvent mixtures were then diluted 4-fold and assayed for SGZ oxidizing activity under standard conditions (Figure 6F). LccA was relatively stable in all solvents examined, retaining nearly 75% of its activity after 24 h incubation in methanol or ethanol and over 50% of its activity after incubation in DMSO or DMF. The influence of water-miscible cosolvcnts on enzyme activity and stability has been examined for several fungal laccases (Rodakiewicz- Nowak et al, 1999; Robles et al., 2002; Milstein et al., 1993; Luterek et #/.,1998; Cantarella et al., 2003). These prior studies coupled with the current findings reveal a wide-variety of laccases, including LccA, are stable and/or can support catalysis and conversion of phenolic substrates in water-organic mixed solvents. Since most of the substrates and mediators of laccases are insoluble or poorly soluble in water and the degree of polymerization of phenoxyl radicals is higher in aqueous media (Milstein et al., 1993), solvent stability is an important feature to consider in optimizing this group of enzymes. Several industrial applications would greatly benefit from the addition of water-miscible organic cosolvcnts to laccase-mediated reactions, particularly the conversion of insoluble substrates such as lignin and its derivatives to useful products (Barreca et ah, 2003; Potthast et ah, 1995: d'Acunzo et al., 2004). Use of compatible organic solvents would also lower the degree of polymerization of phenoxyl radicals generated during the oxidation of substrates such as lignin (Milstein et al.. 1993).
EXAMPLE 8— EFFECT OF INHIBITORS
A number of compounds were examined for their influence on LccA activity including small ions (sodium azide or NaN3), sulfhydryl-group containing redox reagents (L- cysteine, dithiothreitol or DTT), denaturants (thiourea) and chelators (EDTΛ, 1,10- phenanthroline, 2,2-dipyridyl) (Table 4). The most effective laccase inhibitors to date are small anions, especially N3 ", which often bind to the trinuclear copper center and interfere with electron flow and substrate oxidation (Johnson el al., 2003). Consistent with this, LccA was inhibited nearly 50% by addition of 1 mM NaN3. In contrast, some fungal laccases. such as that reported by Saito et al. (Saito et al., 2003), are relatively unaltered by NaNs (at 10 mM). Of the redox reagents examined, both L-cysteine and DTT were strong inhibitors of the observed LccA activity and were effective at relatively low concentrations {i.e., 0.1 to 1 mM). As has been observed for other laccases, this inhibition is likely caused by reduction of the oxidized substrate by the sulfhydryl-groups of the redox reagents and not by inhibition of the enzyme (Johannes et ah, 2000). The LccA protein was also susceptible to denaturation by thiourea with 90% inhibition at 10 mM. Although the general chelator EDTA had no inhibitory activity toward LccA at 50 mM, the transition metal chelators 2,2-dipyridyl and 1 , 10-phenanthroline were inhibitory with a 25% and 90% reduction in LccA activity at 10 mM, respectively. These results are consistent with the recalcitrant nature of the copper- containing laccases toward chelation by EDTA {e.g., (Saito et ah, 2003), yet reveal a likely role of metals in LccA activity, based on inhibition by phenanthroline.
EXAMPLE 9— IMPROVED PRODUCTION OF LACCASE ACTIVITY BY Hfx. vυlcanii Laccasc activity was produced at high-levels (1.65 ± 0.22 U-ml"1) in the culture broth of // volcanii strain US02 after 72 h of growth (at 42° C; 150 rpm) in YPC medium supplemented with 100 μM CuSO4 (see Fig. 14). Activity was enhanced 10-fold by improved culture and enzyme assay conditions compared to earlier report (Uthandi et al., 2010).
EXAMPLE 10— DELIGNIFIC ATION OF SUGARCANE BAGASSE BY LccA Prior to enzymatic treatment, sugarcane bagasse was treated with 1% (v/v) phosphoric acid and steam exploded in a shotgun reactor at 190 0C for 10 min. The resultant bagasse was adjusted to pH 8.4 with 5M NaOH. Stream exploded bagasse was delignified using the laccase, LccA, from H. volcanii
US02. LccA was prepared for the delignification reaction by concentrating //. volcanii US02 culture supernatant 5-fold with ethanol precipitation and dialyzing the concentrate against 25 mM Tris buffer pH 8.4 supplemented with 200 mM NaCl (T buffer) with regenerated cellulose dialysis tubing (3500 Da molecular weight cut off; Thermo Scientific SnakeSkin Pleated Dialysis Tubing).
Assays were performed with 3.7 g of steam exploded bagasse (~lg dry weight equivalents) dissolved in 15 ml of T buffer in 250 ml Erlenmeyer flasks. Bagasse samples were treated with LccA in a rotary shaker at 150 rpm with similar doses of heat killed LccA enzyme (HKE) as a control. Periodically clear supernatant obtained by centrifugation of small fraction of hydro Iy sate was used for total phenol estimation by Folin-Ciocalteau method (Singleton and Rossi, 1965). Optimal conditions were determined to be treatment with 3 UmI"1 LccA at 37 0C in T buffer at pH 8.4 for 3-6 h. A 21% reduction in the phenol content from 1473 ±10 to 1160 ± 26 mg phenol per liter after 3 h of treatment was reproducibly observed (see Fig. 15). Further dilution of steam exploded bagasse (~l g dry weight equivalents) dissolved in 50 ml of T buffer resulted in a 38 - 43% reduction in the phenol content that was LccA-dependent.
EXAMPLE 11— IMPROVED PURIFICATION OF LACCASE (LccA) FROM Hfx. volcanii
An improved protocol was developed for 22-fold purification of LccA from recombinant H. volcanii US02 to a specific activity of 51.5 U-mg"1. This protocol included ethanol precipitation of LccA from culture broth. The ethanol precipitates were then dialyzed
(50 kDa MWCO) against 25 niM Tris buffer at pH 8.4 supplemented with 185 mM NaCl and concentrated to 15 mg protein per 11 ml with a Centricon PL-30 filter. LccA protein was further purified by MonoQ 10/10 anion exchange chromatography with T buffer and a linear gradient of NaCl. Results are shown in Table 6.
EXAMPLE 12— PRODUCTION AND ACTIVATION OF LACCASE (LccA) FROM RECOMBINANT E. coli
The Ufa. volcanii lccA gene was altered by site-directed mutagenesis for production of an LccA protein with an altered TAT signalling motif (ArgόLys, Arg7Lys and Arg8Lys) (LccAΔTAT). This LccA protein variant was produced in recombinant E. coli Rosetta (DE3) (Table 1) using the pET expression system. Cells were lysed by French press (1,000 lb/in2) in 20 mM Tris buffer at pH 7.5 with 150 mM NaCl. Cell lysate was clarified by centrifugation
(10,000 x g at 4°C for 15 min) and NaCl was added to the supernatant to a final concentration of 2 M NaCl in 20 mM Tris buffer at pFI 7.5. Laccase activity was assayed by the oxidation of SGZ using standard conditions. Specific activity of LccΛΔTAT protein in cell lysate was 0.6 U-mg"1 for a total of 1 ,100 U activity per liter of culture. Table 1. List of strains, plasmids and oligonucleotide primers used in this study.
Strain or Description Source or plasmid reference
Strains
E. coli DH5α F* recAl endAl
Figure imgf000044_0001
supE44 M-I gyrA Life Technologies re IA 1
GM2163 V ara-14 leuB6βιuA31 lacYl isx78 glnV44 galK2 New England galT22 mcrA dcm-6 hisG4 rfl>Dl rpsL 136 daml3::Tn9 Biolabs xylAS mtl-1 thi-1 mcrBl hsdR2
Rosetta F" ompT hsdSφύ mB ") gal dcm (DE3) pRARE (Cam") Novagen
(DE3)
Hfx. volcanii Wild-type isolate DS2 cured of plasmid pHV2 (Wendoloski et
DS70 α/. , 2001)
H26 OS70 pyrE (Allers et al.,
2004)
SBOl H26 carrying plasmid pJAM822 This study
US02 H26 carrying plasmid pJAM824 This study
Plasmids pET24b Km1; E. coli expression vector Nova pen
Λpr; NV; 11-kb Hfx. volcanii-E. coli shuttle vector derived from pBAP5009, includes Halobacterium (Jolley et al.. pBAP5010 ciitirubrum rRNA P2 promoter (?2rιn), T7 transcription terminator and pHV2 ori for expression of cloned 1997) genes in Hfx volcanii pJAM202 Apr; Nv1; pBAP5010 containing ?2nn-psmB-H6 (Kaczowka et al.,
2003) pJAM202c Apr; NV; pJAM202 with V2rrn-psmB-H6 deleted (Zhou et al. ,
2008) pJAM821 Km'; pET24b with lccA-strepII 'for expression of LccA This study
(HvoB0205, laccasc) with a C-terminal Strepll tag in
E. coli Rosetta (DE3) pJAM822 Apr; Nvr; pJAM202 with ?2rrn-IccA-strepII for This study synthesis of LccA (HvoB0205, laccase) with a C- terminal Strepll tag in Hfx. volcanii pJΛM823 Kmr; pET24b with lccA for expression of LccA This study
(HvoB0205, laccase) in E. coli Rosetta (DE3) pJAM824 Apr; Nvr; pJAM202 with ?2nn-lccA for synthesis of This study
LccA (HvoB0205, laccasc) in Hfx. volcanii
Primers
HvoB0205 5 ' -tgggcgtC AT ATGacagactggtctag >cggcgg-3' (SEQ This study (lccA) up ID NO: 7); Table 1. List of strains, plasmids and oligonucleotide primers used in this study.
Strain or Description Source or plasmid reference
Ndel site uppercase
HvoB0205 5 '-aaAAGCTTcacttctcgaactgcgggtgcgaccaA GTACTG This study (lccA) down gcgacttcgtcgccgcttc-3' (SEQ ID NO: 8); HindIII and
Seal site uppercase
HvoB0205 5'-aaAAGCTTtcaggccacttcgtcgccgcttc-3' (SEQ ID This study
(lccA) NO: 9); HindIII site uppercase down 2
Table 2. Purification of LccA from the culture broth of HJx. volcanii SBOl and
US02 cells'.
Fraction Total Protein Yield Specific Purification
Activity (mg) (%) Activity (-fold
(mil) (U • rag 1) enrichment)
HJx. volcanii SBOl
60-h culture broth (130 ml) 740 6.72a 100 0.11 1
60-h culture broth filtered 765 6.43 103 0.12 1.1 ethanol ppt. 1010 6.33 136 0.16 1.5
MonoQ 5/5, pH 8.4 467 0.92 63 0.51 4.6
Superdex 200
HR 10/30 173 0.23 23 0.76 6.9
MonoQ 10/10. pH 8.4 95.3 0.07 13 1.34 12
HJx. volcanii US02
72-h culture broth (360 ml) 57 25 100 1.4 1
Ethanol precipitate 55 13 94 4.3 2
Centricon PL-
30 and Fl,
MonoQ 10/10, Fl, 41.5; Fl, 1.4; 72; Fl 29.4; F1, 13; F2, pH 8.4 F2, 14.2 F2, 2.1 F2, 24 F2, 6.7 2.9
aHJx. volcanii SBOl and US02 were grown for 60 to 72 h in HvLMM (420C, 200 rpm), respectively. LccA protein was purified from culture broth as indicated. Activity was monitored by oxidation of SGZ under standard assay conditions (see methods). Fl and F2 represents the lower (viscous) and upper fractions generated after concentration by centrifugal filtration using a Centricon PL-30, respectively (see methods).
Table 3. Kinetic parameters of Hfx. volcanii LccA compared to select laccase-like enzymes.
ABTS SGZ
Enzyme, Origin of Source of Purified
Kn, l- Encoding Gene Enzyme ^cat 'feat' Λ- w Km Λcat kosJKm Ref. (μM) (S-1) (S"1 μM"1) (μM) (S-1) (s"1 μM"1)
LccA, Hfx. volcanii Culture broth of Hfx. 700 10.0 0.014 67 19.4 0.3 This study volcanii BSOl
Culture broth of Hfx. 671 9.9 0.015 35 21.7 0.62 This study volcanii US02
CotA, Bacillus sublilis Cell lysate of 106 16.8 0.16 26 3.7 0.14 (Martins et al. , recombinant E. coli 2002
CotA, Bacillus Cell lysate of 6.5 83 13 4.3 100 23 (Koschorrcck et al.. licheniformis recombinant E. coli 2008)
McoA, Aquifex Refolded from cell 128 2.1 0.016 38 0.48 0.013 (Fernandes et al. , aeolicus lysate of 2007) recombinant E. coli
LAC2. white-rot Culture supernatant 536 683 1.27 6.8 1.093 160 (Klonowska et al. basidiomycete C30 of C30 2002)
LACl, white -rot Culture supernatant 56 10.7 5.22 1.8 30 17 (Klonowska et al.. basidiomycete C30 of C30 2002)
RL 5, metagenome Cell lysate of 26 18 0.69 0.43 660 1,534 (Beloqui et al. , library of bovine rumen recombinant E. coli 2006)
(tentative Bacterυides origin)
BT4348, Bacteroides Cell lysate of 10 217 21.7 0.83 555 669 (Beloqui et al, thetaiotaom icron recombinant is. coli 2006)
Yiffl, E. coli Cell lysate of 23 24 1.05 1.1 362 329 (Beloqui et al.. recombinant E. coli 2006)
Table 4. Effect of various compounds on activity of
LccA isolated from Hfx. volcanii SBOl .
Compound" Concentration Relative
(mM) Activity (%)*
Control 100.0 ± 0.9
L-Cysteine 0.1 83.0 ± 3.7
1 u.d.c
Sodium azide 1 55.2 ± 2.7
DL-Dilhiothretol 0.01 90.5 ± 5.5
0.1 u.d.
1 u.d.
EDTA 0.1 100.6 ± 1.8
1 106.3 ± 5.8
5 123.6 ± 3.2
50 123.7 ± 3.0
Thiourea 1 96.5 ± 3.9
10 9.5 ± 1.3
1 , 10-Phenantbroline 1 85.3 ± 3.4
10 10.9 ± 3.9
2,2-Dipyridyl 1 86.6 ± 3.3
10 75.2 ± 2.3
αLccA was incubated with the various compounds for 10 min at 450C in T buffer with 185 mM NaCl and assayed for SGZ oxidizing activity under standard conditions. ^Values represent the average of at least 3 replicates. cu.d., undetectable.
Table 5. Peptide summary report of Mascot search results generated from MS analysis of the tryptic peptides generated from LccA purified from H. volcanii SBOl and US02.
LccA from SBOl:
Residue no.
Start - End Observed Mr(expt) Mr(calc) Delta Miss Peptide Sequence
39 - 49 626.79 1251.57 1251.73 -0.16 0 K.FVQPLP1PSVR.E (Ions score 55) (SEQ ID NO' 10) K FVQPLP1PSVREPDGQR.D (Ions score 30) (SEQ ID
39 - 55 645.63 1933.88 1934.04 -0.16 1 NO: 11)
R.FDNSGLPSEHLFPVDDR.L (Ions score 74) (SEQ ID
105 - 121 648.91 1943 7 1943.9 -0.2 0 NO: 13)
R FDNSGLPSEHLFPVDDR. L (Ions score 52) (SEQ ID
105 - 121 648.93 1943.77 1943.9 -0.14 0 NO: 13)
R.LUGTTAENHPGYDGPVPEVR.T (Ions score 85) (SEQ
122 - 141 689.26 2064.75 2064.99 -0.23 0 ID NO- 14)
R.FDSAWQELPMEQGR.T (Ions score 53) (SEQ ID NO'
173 - 186 565.21 1692 61 1692.76 -0 15 0 16)
R.TTSTYHDHTLGI'I R.L (Ions score 103) (SEQ ID NO
187 - 200 801.81 1601.6 1601.78 -0.18 0 17)
R.LNAYAGLLGLYSITTDAER.E (Ions score 97) (SEQ ID
201 - 219 680.96 2039.87 2040.05 -0.19 0 NO: 18)
R.ELGLPSGDYDIPLLLQDK.E (Ions score 60) (SEQ ID
220 - 237 662.63 1984.87 1985.04 -0.17 0 NO: 19) 407 - 415 518.15 1034.28 1034.51 -0.23 0 R.EMTLGTEVR.N (Ions score 44) (SEQ ID NO 21) 455 - 465 457.22 1368 63 1368.78 -0 14 0 R.HPIIILIILVTFR.V (Ions score 55) (SEQ ID NO: 23) R.VIGRGPDGTQPPDPNELGPK.D (Ions score 68) (SEQ
466 - 485 681.96 2042.87 2043.04 -0.17 1 ID NO: 24)
R. VIGRGPDGTQPPDPNELGPKDTVR V (Ions score 66)
466 - 489 629.51 2513.99 2514.28 -0.29 2 (SEQ ID NO: 25) R.GPDGTQPPDPNELGPK.D (Ions score 77) (SEQ ID NO:
470 - 485 809.76 1617.5 1617.76 -0.26 0 26)
R.GPDGTQPPDPNELGPKDTVR.V (Ions score 67) (SKQ
470 - 489 697.29 2088.84 2089.01 -0.17 J ID NO: 27)
LccA from US02:
Observe Mr(expt Mr(calc Mis Start - End d ) ) Delta s Sequence
39 - 49 626.94 1,252.03 1251.88 0.14 0 K.FVQPLPIPSVR.E (Ion score 44) (SEQ ID NO- 10)
39 - 55 968.06 1,934.20 1934.12 0.08 1 K FVQPLPIPSVREPDGQR.D (Ion score 18) (SEQ ID NO. 1 1)
105 - 121 973.01 1,944.14 1944.01 0.1 1 0 R.FDNSGLPSEHLFPVDDR L (Ion score 70) (SEQ ID NO 13) R.LGGTTAENHPGYDGPVPEVR.T (Ion score 45) (SOQ ID
122 - 141 689.41 2,065.43 2065 21 0.22 0 NO: 14)
R.TVTHFHGLELDPΛNDGQSDMWTSPGGVEGPR.F (Ion
142 - 172 1103.22 3,306.77 3306.63 0.13 0 score 51) (SEQ ID NO: 15)
173 - 186 565.37 1 ,693.44 1693.09 0.33 0 R.FDSAWQELPMEQGR.T (Ion score 50 ) (SEQ ID NO: 16)
187 - 200 801.92 1,601.90 1601.83 0.06 0 R.TTSTYIIDIITLGITR.L (Ion score 98 ) (SEQ ID NO: 17) R.LNAYAGLLGLYSITTDAER.E (Ion score 1 10 ) (SEQ ID NO.
201 - 219 1021.07 2,040.20 2040 12 0.074 0 18)
220 - 237 993.58 1,985 28 1985.15 0.12 0 R.ELGLPSGDYD1PLLLQDK E (Ion score 68 ) (SEQ ID NO: 19) K.EFNDDGSLHYPEEFVSAFLGDTA VVNGA VWPYVEVEPR.
238 - 275 1419.1 1 4,254.65 4254.31 0.32 0 R (Ion score 28) (SEQ ID NO: 12)
279 - 288 599.38 1,196.84 1 196 74 0.09 1 R.FRILNGΛNHR.S (Ion score 33) (SEQ ID NO: 20)
R. VSDPSTPPEDASADPTSLSLPTPAS YDESDΛRVTR.E (SEQ
372 - 406 121 1.65 3,633.18 3631.93 1 25 1 ID NO: 22)
407 - 415 518.34 1,034.85 1034.68 0.17 0 R.EMTLGTEVR.N (Ion score 48 ) (SEQ ID NO: 21)
R. V1GRGPDGTQPPDPNELGPK.D (Ion score 47) (SEQ ID NO
466 - 489 1022 59 2,043.31 2043 17 0 13 2 24)
466 - 485 839.16 2,5 14.63 2514.45 0 17 1 R.VIGRGPDGTQPPDPNELGPKDTVR.V (SEQ ID NO' 25) R.GPDGTQPPDPNELGPKDTVR.V (Ion score 31 ) (SEQ ID
470 - 489 697.40 2,089.37 2089.19 0.18 1 NO: 27)
470 - 485 37.25 1,617.92 1617.84 0.07 0 R.GPDGTQPPDPNELGPK.D (Ion score 37 ) (SEQ ID NQ: 26)
Figure imgf000050_0001
It should be understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and the scope of the appended claims. In addition, any elements or limitations of any invention or embodiment thereof disclosed herein can be combined with any and/or all other elements or limitations (individually or in any combination) or any other invention or embodiment thereof disclosed herein, and all such combinations are contemplated with the scope of the invention without limitation thereto.
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Claims

CLAIMS We claim:
1. A purified polypeptide comprising: a) SEQ ID NO: 2 or comprising amino acids 32-579 or SEQ ID NO: 2; b) a polypeptide obtained from a Haloferax volcanii strain that has greater than 65% sequence identity to SEQ ID NO: 2 and has laccase activity; c) a polypeptide having laccase activity and greater than 65% identity to SEQ ID NO: 2; or d) a fragment of the polypeptide set forth in (a) or (b), said fragment having laccase activity or a fragment as set forth in Figure 8.
2. A composition comprising the polypeptide of claim 1 and a carrier.
3. A composition of matter comprising: a) a polynucleotide sequence encoding a polypeptide comprising SEQ ID NO: 2, a fragment of SEQ ID NO: 2, said fragment having laccase activity or a fragment as set forth in Figure 8; b) a homologous polynucleotide sequence having at least about 20% to 99.99% identity to a polynucleotide sequence encoding a polypeptide SEQ ID NO: 2, wherein said polynucleotide encodes a polypeptide having laccase activity; c) a polynucleotide sequence comprising SEQ ID NO: 1; d) a homologous polynucleotide sequence having at least about 20% to 99.99% identity to the polynucleotide sequence of SEQ ID NO: 1 and encoding a polypeptide having laccase activity; e) a polynucleotide that is complementary to the polynucleotides set forth in (a), (b), (c), or (d); f) a genetic construct comprising a polynucleotide sequence as set forth in (a). (b), (c), (d), or (e); g) a vector comprising a polynucleotide or genetic construct as set forth in (a). (b), (c), (d), (e). or (f); h) a host cell comprising a vector as set forth in (g); i) a polynucleotide that hybridizes under low, intermediate or high stringency with a polynucleotide sequence as set forth in (a), (b), (c), (d) or (e); or j) a probe comprising a polynucleotide according to (a), (b), (c), (d), (e), (f), or (g) and, optionally, a label or marker.
4. A method of producing a laccase comprising: a) culturing a Haloferax volcanii strain containing said polypeptide of claim 1, under conditions suitable to produce the polypeptide; and b) recovering the polypeptide.
5. A method of oxidizing a phenolic substrate comprising contacting a polypeptide according to claim 1 with a phenolic substrate under conditions that allow for the oxidation of the phenolic compounds.
6. A method of oxidizing bilirubin to biliverdin and water comprising contacting a polypeptide according to claim 1 with a solution comprising bilirubin under conditions that allow for the oxidation of bilirubin.
7. A method for the delignifϊcation and/or detoxification of acid-pretreated biomass comprising contacting acid-pretreated biomass with a polypeptide according to claim 1 under conditions that allow for the delignifi cation and/or detoxification of acid-pretreated biomass.
8. A method of bleaching dye comprising contacting a solution comprising a dye with a polypeptide according to claim 1 under conditions that allow for the bleaching of said dye.
9. A method of bleaching pulp for paper production comprising contacting paper pulp with a polypeptide according to claim 1 under conditions that allow for the bleaching of said paper pulp.
10. A method of modifying lignin comprising contacting lignin with a polypeptide according to claim 1 under conditions that allow for the modification of said lignin.
11. A method for the treatment of waste water comprising contacting waste water containing a phenolic compound with a polypeptide according to claim 1 under conditions that allow for the oxidation of said phenolic compound.
12. A genetically engineered host cell expressing a polypeptide according to claim 1.
13. A genetically engineered host cell expressing a polypeptide comprising: a) SEQ ID NO: 2; b) amino acids 32-579 or SEQ ID NO: 2; or c) a fragment of the polypeptide set forth in (a) or (b), said fragment having laccase activity or a fragment as set forth in Figure 8 having laccase activity.
14. The genetically engineered host cell according to claims 12 or 13, wherein said host cell is E. coli, Bacillus megaterium or Saccharomyces cerevisiae.
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