Identification and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota
[en] A metagenomic library was constructed from microorganisms associated with the brown alga Ascophyllum nodosum. Functional screening of this library revealed 13 novel putative esterase loci and two glycoside hydrolase loci. Sequence and gene cluster analysis showed the wide diversity of the identified enzymes and gave an idea of the microbial populations present during the sample collection period. Lastly, an endo-β-1,4-glucanase having less than 50% identity to sequences of known cellulases was purified and partially characterized, showing activity at low temperature and after prolonged incubation in concentrated salt solutions.
Disciplines :
Microbiology
Author, co-author :
Martin, Marjolaine ; Université de Liège - ULiège > Chimie et bio-industries > Microbiologie et génomique
Biver, Sophie ; Université de Liège - ULiège > Chimie et bio-industries > Microbiologie et génomique
Steels, Sébastien ; Université de Liège - ULiège > Chimie et bio-industries > Microbiologie et génomique
Barbeyron, Tristan
Jam, Murielle
Portetelle, Daniel ; Université de Liège - ULiège > Chimie et bio-industries > Microbiologie et génomique
Michel, Gurvan
Vandenbol, Micheline ; Université de Liège - ULiège > Chimie et bio-industries > Microbiologie et génomique
Language :
English
Title :
Identification and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota
Publication date :
August 2014
Journal title :
Applied and Environmental Microbiology
ISSN :
0099-2240
eISSN :
1098-5336
Publisher :
American Society for Microbiology (ASM), Washington, United States - District of Columbia
Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:1919-1925.
Pace NR. 1997. A molecular view of microbial diversity and the biosphere. Science 276:734-740. http://dx.doi.org/10.1126/science.276.5313.734.
Handelsman J. 2004. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68:669-685. http://dx.doi.org/10.1128/MMBR.68.4.669-685.2004.
Sleator RD, Shortall C, Hill C. 2008. Metagenomics. Lett. Appl. Microbiol. 47:361-366. http://dx.doi.org/10.1111/j.1472-765X.2008.02444.x.
Edwards JL, Smith DL, Connolly J, McDonald JE, Cox MJ, Joint I, Edwards C, McCarthy AJ. 2010. Identification of carbohydrate metabolism genes in the metagenome of a marine biofilm community shown to be dominated by Gammaproteobacteria and Bacteroidetes. Genes (Basel) 1:371-384. http://dx.doi.org/10.3390/genes1030371.
Biver S, Vandenbol M. 2013. Characterization of three new carboxylic ester hydrolases isolated by functional screening of a forest soil metagenomic library. J. Ind. Microbiol. Biotechnol. 40:191-200. http://dx.doi.org/10.1007/s10295-012-1217-7.
Sharma S, Khan FG, Qazi GN. 2010. Molecular cloning and characterization of amylase from soil metagenomic library derived from Northwestern Himalayas. Appl. Microbiol. Biotechnol. 86:1821-1828. http://dx.doi.org/10.1007/s00253-009-2404-y.
Geng A, Zou G, Yan X, Wang Q, Zhang J, Liu F, Zhu B, Zhou Z. 2012. Expression and characterization of a novel metagenome-derived cellulase Exo2b and its application to improve cellulase activity in Trichoderma reesei. Appl. Microbiol. Biotechnol. 96:951-962. http://dx.doi.org/10.1007/s00253-012-3873-y.
Feng Y, Duan C-J, Pang H, Mo X-C, Wu C-F, Yu Y, Hu Y-L, Wei J, Tang J-L, Feng J-X. 2007. Cloning and identification of novel cellulase genes from uncultured microorganisms in rabbit cecum and characterization of the expressed cellulases. Appl. Microbiol. Biotechnol. 75:319-328. http://dx.doi.org/10.1007/s00253-006-0820-9.
Wang T-Y, Chen H-L, Lu M-YJ, Chen Y-C, Sung H-M, Mao C-T, Cho H-Y, Ke H-M, Hwa T-Y, Ruan S-K, Hung K-Y, Chen C-K, Li J-Y, Wu Y-C, Chen Y-H, Chou S-P, Tsai Y-W, Chu T-C, Shih C-C, Li W-H, Shih M-C. 2011. Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses. Biotechnol. Biofuels 4:24. http://dx.doi.org/10.1186/1754-6834-4-24.
Ferrer M, Ghazi A, Beloqui A, Vieites JM, López-Cortés N, Marín-Navarro J, Nechitaylo TY, Guazzaroni M-E, Polaina J, Waliczek A, Chernikova TN, Reva ON, Golyshina OV, Golyshin PN. 2012. Functional metagenomics unveils a multifunctional glycosyl hydrolase from the family 43 catalysing the breakdown of plant polymers in the calf rumen. PLoSOne7:e38134. http://dx.doi.org/10.1371/journal.pone.0038134.
Mattéotti C, Thonart P, Francis F, Haubruge E, Destain J, Brasseur C, Bauwens J, De Pauw E, Portetelle D, Vandenbol M. 2011. New glucosidase activities identified by functional screening of a genomic DNA library from the gut microbiota of the termite Reticulitermes santonensis. Microbiol. Res. 166:629-642. http://dx.doi.org/10.1016/j.micres.2011.01.001.
Tasse L, Bercovici J, Pizzut-Serin S, Robe P, Tap J, Klopp C, Cantarel BL, Coutinho PM, Henrissat B, Leclerc M, Doré J, Monsan P, Remaud-Simeon M, Potocki-Veronese G. 2010. Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res. 20:1605-1612. http://dx.doi.org/10.1101/gr.108332.110.
Kennedy J, O'Leary ND, Kiran GS, Morrissey JP, O'Gara F, Selvin J, Dobson ADW. 2011. Functional metagenomic strategies for the discovery of novel enzymes and biosurfactants with biotechnological applications from marine ecosystems. J. Appl. Microbiol. 111:787-799. http://dx.doi.org/10.1111/j.1365-2672.2011.05106.x.
Lee D-G, Jeon JH, Jang MK, Kim NY, Lee JH, Lee J-H, Kim S-J, Kim G-D, Lee S-H. 2007. Screening and characterization of a novel fibrinolytic metalloprotease from a metagenomic library. Biotechnol. Lett. 29:465-472. http://dx.doi.org/10.1007/s10529-006-9263-8.
Lee M-H, Lee C-H, Oh T-K, Song JK, Yoon J-H. 2006. Isolation and characterization of a novel lipase from a metagenomic library of tidal flat sediments: evidence for a new family of bacterial lipases. Appl. Environ. Microbiol. 72:7406-7409. http://dx.doi.org/10.1128/AEM.01157-06.
Sim S-J, Baik KS, Park SC, Choe HN, Seong CN, Shin T-S, Woo HC, Cho J-Y, Kim D. 2012. Characterization of alginate lyase gene using a metagenomic library constructed from the gut microflora of abalone. J. Ind. Microbiol. Biotechnol. 39:585-593. http://dx.doi.org/10.1007/s10295-011-1054-0.
Martin M, Portetelle D, Michel G, Vandenbol M. 2014. Microorganisms living on macroalgae: diversity, interactions, and biotechnological appli-cations. Appl. Microbiol. Biotechnol. 98:2917-2935. http://dx.doi.org/10.1007/s00253-014-5557-2.
Burke C, Steinberg P, Rusch D, Kjelleberg S, Thomas T. 2011. Bacterial community assembly based on functional genes rather than species. Proc. Natl. Acad. Sci. U. S. A. 108:14288-14293. http://dx.doi.org/10.1073/pnas.1101591108.
Lachnit T, Meske D, Wahl M, Harder T, Schmitz R. 2011. Epibacterial community patterns on marine macroalgae are host-specific but temporally variable. Environ. Microbiol. 13:655-665. http://dx.doi.org/10.1111/j.1462-2920.2010.02371.x.
Fisher MM, Wilcox LW, Graham LE, Wilcox LEEW. 1998. Molecular characterization of epiphytic bacterial communities on charophycean green algae. Appl. Environ. Microbiol. 64:3484-4389.
Debnath M, Paul AK, Bisen PS. 2007. Natural bioactive compounds and biotechnological potential of marine bacteria. Curr. Pharm. Biotechnol. 8:253-260. http://dx.doi.org/10.2174/138920107782109976.
Michel G, Czjzek M. 2013. Polysaccharide-degrading enzymes from marine bacteria, p 429-464. In Trincone A (ed), Marine enzymes for biocatalysis: sources, biocatalytic characteristic and bioprocesses of marine enzymes. Woodhead Publishing Limited, Cambridge, United Kingdom.
Gibbs MD, Saul DJ, Lüthi E, Bergquist PL. 1992. The beta-mannanase from "Caldocellum saccharolyticum" is part of a multidomain enzyme. Appl. Environ. Microbiol. 58:3864-3867.
Fu X, Liu P, Lin L, Hong Y, Huang X, Meng X, Liu Z. 2010. A novel endoglucanase (Cel9P) from a marine bacterium Paenibacillus sp. BME-14. Appl. Biochem. Biotechnol. 160:1627-1636. http://dx.doi.org/10.1007/s12010-009-8648-2.
Dong J, Hong Y, Shao Z, Liu Z. 2010. Molecular cloning, purification, and characterization of a novel, acidic, pH-stable endoglucanase from Martelella mediterranea. J. Microbiol. 48:393-398. http://dx.doi.org/10.1007/s12275-010-9361-0.
Shanmughapriya S, Kiran GS, Selvin J, Thomas TA, Rani C. 2010. Optimization, purification, and characterization of extracellular mesophilic alkaline cellulase from sponge-associated Marinobacter sp. MSI032. Appl. Biochem. Biotechnol. 162:625-640. http://dx.doi.org/10.1007/s12010-009-8747-0.
Kuhad RC, Gupta R, Singh A. 2011. Microbial cellulases and their industrial applications. Enzyme Res. 2011:280696. http://dx.doi.org/10.4061/2011/280696.
Duan C-J, Feng J-X. 2010. Mining metagenomes for novel cellulase genes. Biotechnol. Lett. 32:1765-1775. http://dx.doi.org/10.1007/s10529-010-0356-z.
Lachnit T, Blümel M, Imhoff J, Wahl M. 2009. Specific epibacterial communities on macroalgae: phylogeny matters more than habitat. Aquat. Biol. 5:181-186. http://dx.doi.org/10.3354/ab00149.
Petersen TN, Brunak S, von Heijne G, Nielsen H. 2011. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods 8:785-786. http://dx.doi.org/10.1038/nmeth.1701.
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer ELL, Tate J, Punta M. 2014. Pfam: the protein families database. Nucleic Acids Res. 42:D222-D230. http://dx.doi.org/10.1093/nar/gkt1223.
Biver S, Portetelle D, Vandenbol M. 2013. Characterization of a new oxidant-stable serine protease isolated by functional metagenomics. Springerplus 2:410. http://dx.doi.org/10.1186/2193-1801-2-410.
Miller GL. 1959. Use of dinitrosaIicyIic acid reagent for determination of reducing sugar. Anal. Chem. 31:426-428. http://dx.doi.org/10.1021/ac60147a030.
Burke C, Kjelleberg S, Thomas T. 2009. Selective extraction of bacterial DNA from the surfaces of macroalgae. Appl. Environ. Microbiol. 75:252-256. http://dx.doi.org/10.1128/AEM.01630-08.
Popper ZA, Michel G, Hervé C, Domozych DS, Willats WGT, Tuohy MG, Kloareg B, Stengel DB. 2011. Evolution and diversity of plant cell walls: from algae to flowering plants. Annu. Rev. Plant Biol. 62:567-590. http://dx.doi.org/10.1146/annurev-arplant-042110-103809.
Arpigny JL, Jaeger KE. 1999. Bacterial lipolytic enzymes: classification and properties. Biochem. J. 343:177-183. http://dx.doi.org/10.1042/0264-6021:3430177.
Hausmann S, Jaeger KE. 2010. Lipolytic enzymes of bacteria, p 1099-1126. In Timmis KN (ed), Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, Germany.
Chu X, He H, Guo C, Sun B. 2008. Identification of two novel esterases from a marine metagenomic library derived from South China Sea. Appl. Microbiol. Biotechnol. 80:615-625. http://dx.doi.org/10.1007/s00253-008-1566-3.
Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B. 2009. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37:D233-D238. http://dx.doi.org/10.1093/nar/gkn663.
Aspeborg H, Coutinho PM, Wang Y, Brumer H, Henrissat B. 2012. Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5). BMC Evol. Biol. 12:186. http://dx.doi.org/10.1186/1471-2148-12-186.
Lee K, Lee HK, Choi T-H, Cho J-C. 2007. Robiginitomaculum antarcticum gen. nov., sp. nov., a member of the family Hyphomonadaceae, from Antarctic seawater. Int. J. Syst. Evol. Microbiol. 57:2595-2599. http://dx.doi.org/10.1099/ijs.0.65274-0.
Bengtsson MM, Sjoetun K, Lanzen A, Oevreas L. 2012. Bacterial diversity in relation to secondary production and succession on surfaces of the kelp Laminaria hyperborea. ISME J. 6:2188-2198. http://dx.doi.org/10.1038/ismej.2012.67.
Steele HL, Jaeger K-E, Daniel R, Streit WR. 2009. Advances in recovery of novel biocatalysts from metagenomes. J. Mol. Microbiol. Biotechnol. 16:25-37. http://dx.doi.org/10.1159/000142892.
Fu C, Hu Y, Xie F, Guo H, Ashforth EJ, Polyak SW, Zhu B, Zhang L. 2011. Molecular cloning and characterization of a new cold-active esterase from a deep-sea metagenomic library. Appl. Microbiol. Biotechnol. 90: 961-970. http://dx.doi.org/10.1007/s00253-010-3079-0.
Jeon JH, Kim J-T, Kang SG, Lee J-H, Kim S-J. 2009. Characterization and its potential application of two esterases derived from the arctic sediment metagenome. Mar. Biotechnol. (NY) 11:307-316. http://dx.doi.org/10.1007/s10126-008-9145-2.
Jeon JH, Lee HS, Kim JT, Kim S-J, Choi SH, Kang SG, Lee J-H. 2012. Identification of a new subfamily of salt-tolerant esterases from a metagenomic library of tidal flat sediment. Appl. Microbiol. Biotechnol. 93: 623-631. http://dx.doi.org/10.1007/s00253-011-3433-x.
Hu Y, Fu C, Huang Y, Yin Y, Cheng G, Lei F, Lu N, Li J, Ashforth EJ, Zhang L, Zhu B. 2010. Novel lipolytic genes from the microbial metagenomic library of the South China Sea marine sediment. FEMS Microbiol. Ecol. 72:228-237. http://dx.doi.org/10.1111/j.1574-6941.2010.00851.x.
Jiang X, Xu X, Huo Y, Wu Y, Zhu X, Zhang X, Wu M. 2012. Identification and characterization of novel esterases from a deep-sea sediment metagenome. Arch. Microbiol. 194:207-214. http://dx.doi.org/10.1007/s00203-011-0745-2.
Okamura Y, Kimura T, Yokouchi H, Meneses-Osorio M, Katoh M, Matsunaga T, Takeyama H. 2010. Isolation and characterization of a GDSL esterase from the metagenome of a marine sponge-associated bacteria. Mar. Biotechnol. (NY) 12:395-402. http://dx.doi.org/10.1007/s10126-009-9226-x.
Oh K-H, Nguyen G-S, Kim E-Y, Kourist R, Bornscheuer U, Oh T-K, Yoon J-H. 2012. Characterization of a novel esterase isolated from intertidal flat metagenome and its tertiary alcohols synthesis. J. Mol. Catal. B Enzym. 80:67-73. http://dx.doi.org/10.1016/j.molcatb.2012.04.015.
Akoh CC, Lee G-C, Liaw Y-C, Huang T-H, Shaw J-F. 2004. GDSL family of serine esterases/lipases. Prog. Lipid Res. 43:534-552. http://dx.doi.org/10.1016/j.plipres.2004.09.002.
Nacke H, Engelhaupt M, Brady S, Fischer C, Tautzt J, Rolf D. 2012. Identification and characterization of novel cellulolytic and hemicellulolytic genes and enzymes derived from German grassland soil metagenomes. Biotechnol. Lett. 34:663-675. http://dx.doi.org/10.1007/s10529-011-0830-2.
Voget S, Steele HL, Streit WR. 2006. Characterization of a metagenomederived halotolerant cellulase. J. Biotechnol. 126:26-36. http://dx.doi.org/10.1016/j.jbiotec.2006.02.011.
Pang H, Zhang P, Duan C-J, Mo X-C, Tang J-L, Feng J-X. 2009. Identification of cellulase genes from the metagenomes of compost soils and functional characterization of one novel endoglucanase. Curr. Microbiol. 58:404-408. http://dx.doi.org/10.1007/s00284-008-9346-y.
Kim SJ, Lee CM, Han BR, Kim MY, Yeo YS, Yoon SH, Koo BS, Jun HK. 2008. Characterization of a gene encoding cellulase from uncultured soil bacteria. FEMS Microbiol. Lett. 282:44-51. http://dx.doi.org/10.1111/j.1574-6968.2008.01097.x.
Rashamuse KJ, Visser DF, Hennessy F, Kemp J, Roux-van der Merwe MP, Badenhorst J, Ronneburg T, Francis-Pope R, Brady D. 2013. Characterisation of two bifunctional cellulase-xylanase enzymes isolated from a bovine rumen metagenome library. Curr. Microbiol. 66:145-151. http://dx.doi.org/10.1007/s00284-012-0251-z.
Bao L, Huang Q, Chang L, Zhou J, Lu H. 2011. Screening and characterization of a cellulase with endocellulase and exocellulase activity from yak rumen metagenome. J. Mol. Catal. B Enzym. 73:104-110. http://dx.doi.org/10.1016/j.molcatb.2011.08.006.
Liu J, Liu W, Zhao X, Shen W, Cao H, Cui Z. 2011. Cloning and functional characterization of a novel endo-β-1,4-glucanase gene from a soil-derived metagenomic library. Appl. Microbiol. Biotechnol. 89:1083-1092. http://dx.doi.org/10.1007/s00253-010-2828-4.
Xu Y, Duan C, Zhou Q, Tang J, Feng J. 2006. Cloning and identification of cellulase genes from uncultured microorganisms in pulp sediments from paper mill effluent. Wei Sheng Wu Xue Bao 46:783-788.
Pereira JH, Chen Z, McAndrew RP, Sapra R, Chhabra SR, Sale KL, Simmons BA, Adams PD. 2010. Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima. J. Struct. Biol. 172:372-379. http://dx.doi.org/10.1016/j.jsb.2010.06.018.
Chhabra SR, Shockley KR, Ward DE, Kelly RM. 2002. Regulation of endo-acting glycosyl hydrolases in the hyperthermophilic bacterium Thermotoga maritima grown on glucan-and mannan-based polysaccharides. Appl. Environ. Microbiol. 68:545-554. http://dx.doi.org/10.1128/AEM.68.2.545-554.2002.
Wang Y, Wang X, Tang R, Yu S, Zheng B, Feng Y. 2010. A novel thermostable cellulase from Fervidobacterium nodosum. J. Mol. Catal. B Enzym. 66:294-301. http://dx.doi.org/10.1016/j.molcatb.2010.06.006.
Zeng R, Xiong P, Wen J. 2006. Characterization and gene cloning of a cold-active cellulase from a deep-sea psychrotrophic bacterium Pseudoalteromonas sp. DY3. Extremophiles 10:79-82. http://dx.doi.org/10.1007/s00792-005-0475-y.
Liang C, Xue Y, Fioroni M, Rodríguez-Ropero F, Zhou C, Schwaneberg U, Ma Y. 2011. Cloning and characterization of a thermostable and halotolerant endoglucanase from Thermoanaerobacter tengcongensis MB4. Appl. Microbiol. Biotechnol. 89:315-326. http://dx.doi.org/10.1007/s00253-010-2842-6.
Zheng Y, Pan Z, Zhang R, Wang D, Jenkins B. 2008. Non-ionic surfactants and non-catalytic protein treatment on enzymatic hydrolysis of pretreated creeping wild ryegrass. Appl. Biochem. Biotechnol. 146:231-248. http://dx.doi.org/10.1007/s12010-007-8035-9.
Duan C-J, Xian L, Zhao G-C, Feng Y, Pang H, Bai X-L, Tang J-L, Ma Q-S, Feng J-X. 2009. Isolation and partial characterization of novel genes encoding acidic cellulases from metagenomes of buffalo rumens. J. Appl. Microbiol. 107:245-256. http://dx.doi.org/10.1111/j.1365-2672.2009.04202.x.