Discovery of (hemi-) cellulase genes in a metagenomic library from a biogas digester using 454 pyrosequencing

Applied Microbiology and Biotechnology

Volumn 97, Issue 18, 2013, Pages 8173-8182

  Yan, Xing ^a   Geng, Alei ^a,b   Zhang, Jun ^a,c   Wei, Yongjun ^a   Zhang, Lei ^a   Qian, Changli ^a   Wang, Qianfu ^a   Wang, Shengyue ^d   Zhou, Zhihua ^a  

^a INSTITUTE OF PLANT PHYSIOLOGY AND ECOLOGY   (China)

^b JIANGSU UNIVERSITY   (China)

^c NORTHWEST UNIVERSITY   (China)

^d CHINESE NATIONAL HUMAN GENOME CENTER AT SHANGHAI   (China)

Author keywords

454 Pyrosequencing; Biogas digester; Fosmid library; Glycosyl hydrolase; Metagenome

Indexed keywords

454-PYROSEQUENCING; BIOGAS DIGESTERS; BIOINFORMATIC ANALYSIS; CARBOXY METHYLCELLULOSE; COST-EFFECTIVE APPROACH; GLYCOSYL HYDROLASES; METAGENOMES; METAGENOMIC LIBRARIES;

BIOGAS; CLONING; GENES; HYDROLASES; INDUSTRIAL APPLICATIONS; LAKES;

BIOINFORMATICS;

BETA GLUCOSIDASE; BIOGAS; CARBOXYMETHYLCELLULOSE; CELLULASE; ENDO 1,4 BETA XYLANASE; GLYCOSIDASE; HEMICELLULOSE; LIGNOCELLULOSE;

BIOGAS; BIOINFORMATICS; ENZYME; GENE; HYDROLYSIS; PH;

454 PYROSEQUENCING; AFFINITY CHROMATOGRAPHY; ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; BIOGAS DIGESTER; BIOINFORMATICS; CLONE; COMPARATIVE STUDY; DNA SEQUENCE; ENZYME ACTIVITY; EXPERIMENTAL PIG; GENE LIBRARY; METAGENOMICS; METHANOGENESIS; NONHUMAN; NUCLEAR ENERGY AND RELATED PHENOMENA; NUCLEOTIDE SEQUENCE; PROTEIN EXPRESSION; PROTEIN PURIFICATION; PYROSEQUENCING; RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

BACTERIA; BACTERIAL PROTEINS; BIOREACTORS; CELLULASE; ENZYME STABILITY; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOMICS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; SUBSTRATE SPECIFICITY;

EID: 84883518652     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-013-4927-5     Document Type: Article

References (39)

1. Bayer EA, Belaich JP, Shoham Y, Lamed R (2004) The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides. Annu Rev Microbiol 58:521-554 (Pubitemid 39551996)
2. Brulc JM, Antonopoulos DA, Miller MEB, Wilson MK, Yannarell AC, Dinsdale EA, Edwards RE, Frank ED, Emerson JB, Wacklin P, Coutinho PM, Henrissat B, Nelson KE, White BA (2009) Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci USA 106:1948-1953
3. Bower BS, Larenas EA, Mitchinson C (2006) Exo-endo cellulase fusion protein. US patent No.: US2006/0057672A1
4. Demain AL, Newcomb M, Wu JHD (2005) Cellulase, clostridia, and ethanol. Microbiol Mol Biol Rev 69:124-154 (Pubitemid 40360711)
5. Duan CJ, Feng JX (2010) Mining metagenomes for novel cellulase genes. Biotechnol Lett 32:1765-1775
6. Duan CJ, Xian L, Zhao GC, Feng Y, Pang H, Bai XL, Tang JL, Ma QS, Feng JX (2009) Isolation and partial characterization of novel genes encoding acidic cellulases from metagenomes of buffalo rumens. J Appl Microbiol 107:245-256
7. Eberhart B, Cross DF, Chase LR (1964) β-Glucosidase system of Neurospora crassa. I. β-Glucosidase and cellulase activities of mutant and wild-type strains. J Bacteriol 87:761-770
8. 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
9. Ghai R, Martin-Cuadrado AB, Molto AG, Heredia IG, Cabrera R, Martin J, Verdú M, Deschamps P, Moreira D, López-García P, Mira A, Rodriguez-Valera F (2010) Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing. ISME J 4:1154-1166
10. Han SO, Yukawa H, Inui M, Doi RH (2004) Isolation and expression of the xynB gene and its product, XynB, a consistent component of the Clostridium cellulovorans cellulosome. J Bacteriol 186:8347-8355 (Pubitemid 39603225)
11. Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5:R245-R249
12. Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, Mackie RI, Pennacchio LA, Tringe SG, Visel A, Woyke T, Wang Z, Rubin EM (2011) Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331:463-467
13. Jiang CJ, Li SX, Luo FF, Jin K, Wang Q, Hao ZY, Wu LL, Zhao GC, Ma GF, Shen PH, Tang XL, Wu B (2011) Biochemical characterization of two novel β-glucosidase genes by metagenome expression cloning. Bioresour Technol 102:3272-3278
14. Katoh K, Toh H (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinformatics 9:286-298 (Pubitemid 351890825)
15. 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 (Pubitemid 351473557)
16. Lee MH, Lee CH, Oh TK, Song JK, Yoon JH (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 (Pubitemid 44748467)
17. Liu J, Liu W, Zhao X, Shen W, Cao H, Cui Z (2011a) 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
18. Liu N, Yan X, Zhang M, Xie L, Wang Q, Huang Y, Zhou X, Wang S, Zhou Z (2011b) Microbiome of fungus-growing termites: a new reservoir for lignocellulase genes. Appl Environ Microbiol 77:48-56
19. Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M (2012) Comparison of next-generation sequencing systems. J Biomed Biotechnol. doi: 10.1155/2012/251364
20. Mardis ER (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24:133-1341
21. Merino ST, Cherry J (2007) Progress and challenges in enzyme development for biomass utilization. Adv Biochem Eng Biot 108:95-120 (Pubitemid 47434544)
22. Miller GL (1959) Use of dinitro-salicylic acid reagent for determination of reducing sugars. Anal Chem 31:426-428
23. Oh JW, Rhee JK, Ahn DG, Kim YG (2005) New thermophilic and thermostable esterase with sequence similarity to the hormone-sensitive lipase family, cloned from a metagenomic library. Appl Environ Microbiol 71:817-825 (Pubitemid 40223568)
24. Pang H, Zhang P, Duan CJ, Mo XC, Tang JL, Feng JX (2009) Identification of cellulase genes from the metagenomes of compost soils and functional characterization of one novel endoglucanase. Curr Microbiol 58:404-408
25. Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil IA, Minor C, Tiong CL, Gilman M, Osburne MS, Clardy J, Handelsman J, Goodman RM (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66:2541-2547 (Pubitemid 30353963)
26. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463-5467
27. Schlüter A, Bekel T, Diaz NN, Dondrup M, Eichenlaub R, Gartemann KH, Krahn I, Krause L, Krömeke H, Kruse O, Mussgnug JH, Neuweger H, Niehaus K, Pühler A, Runte KJ, Szczepanowski R, Tauch A, Tilker A, Viehöver P, Goesmann A (2008) The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology. J Biotechnol 136:77-90
28. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599 (Pubitemid 47236692)
29. Teather RM, Wood PJ (1982) Use of Congo Red polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from the bovine rumen. Appl Environ Microbiol 43:777-780 (Pubitemid 12105973)
30. van den Brink J, de Vries RP (2011) Fungal enzyme sets for plant polysaccharide degradation. Appl Microbiol Biotechnol 91:1477-1492
31. Vlasenko E, Schülein M, Cherry J, Xu F (2010) Substrate specificity of family 5, 6, 7, 9, 12, and 45 endoglucanases. Bioresour Technol 101:2405-2411
32. Voget S, Steele HL, Streit WR (2006) Characterization of a metagenome-derived halotolerant cellulase. J Biotechnol 126:26-36 (Pubitemid 44402764)
33. Warnecke F, Luginbühl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, Cayouette M, McHardy AC, Djordjevic G, Aboushadi N, Sorek R, Tringe SG, Podar M, Martin HG, Kunin V, Dalevi D, Madejska J, Kirton E, Platt D, Szeto E, Salamov A, Barry K, Mikhailova N, Kyrpides NC, Matson EG, Ottesen EA, Zhang XN, Hernández M, Murillo C, Acosta LG, Rigoutsos I, Tamayo G, Green BD, Chang C, Rubin EM, Mathur EJ, Robertson DE, Hugenholtz P, Leadbetter JR (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450:560-565 (Pubitemid 350190243)
34. Wilson RA, Ashton PD, Braschi S, Dillon GP, Berriman M, Ivens A (2007) Oming in on schistosomes: prospects and limitations for post-genomics. Trends Parasitol 23:14-20 (Pubitemid 44969628)
35. Yamada K, Terahara T, Kurata S, Yokomaku T, Tsuneda S, Harayama S (2008) Retrieval of entire genes from environmental DNA by inverse PCR with pre-amplification of target genes using primers containing locked nucleic acids. Environ Microbiol 10:978-987 (Pubitemid 351406096)
36. Yang B, Dai Z, Ding SY, Wyman CE (2011) Enzymatic hydrolysis of cellulosic biomass. Biofuels 2:421-450
37. Yeh Y, Chang SC, Kuo H, Tong C, Yu S, Ho TD (2013) A metagenomic approach for the identification and cloning of an endoglucanase from rice straw compost. Gene. doi: 10.1016/j.gene.2012.07.076
38. Zhou F, Chen H, Xu Y (2010) GASdb: a large-scale and comparative exploration database of glycosyl hydrolysis systems. BMC Microbiol 10:69
39. Zou G, Shi S, Jiang Y, van den Brink J, de Vries RP, Chen L, Zhang J, Ma L, Wang C, Zhou Z (2012) Construction of a cellulase hyper-expression system in Trichoderma reesei by promoter and enzyme engineering. Microb Cell Fact 11:21