Metagenomic approaches to the discovery of cellulases

Methods in Enzymology

Volumn 510, Issue , 2012, Pages 375-394

  Rooks, David J ^a   McDonald, James E ^b   McCarthy, Alan J ^a  

^a UNIVERSITY OF LIVERPOOL   (United Kingdom)

^b BANGOR UNIVERSITY   (United Kingdom)

Author keywords

Endoglucanases; Environmental DNA; Fosmids; Metagenomics; Metatranscriptomics; mRNA enrichment; Pyrosequencing

Indexed keywords

CELLULASE; COMPLEMENTARY DNA; DNA; MESSENGER RNA; NUCLEIC ACID; RNA;

AMINO ACID SEQUENCE; ARTICLE; BIOMICS; DNA EXTRACTION; EXTRACTION; GENE AMPLIFICATION; GENE EXPRESSION; METAGENOME; METAGENOMICS; METATRANSCRIPTOMICS; MOLECULAR CLONING; NUCLEIC ACID EXTRACTION; PRIORITY JOURNAL;

EID: 84861144903     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-415931-0.00020-3     Document Type: Chapter

References (66)

1. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402
2. J.S. Ammiraju, Y. Yu, M. Luo, D. Kudrna, H. Kim, J.L. Goicoechea, Y. Katayose, T. Matsumoto, J. Wu, T. Sasaki, and R.A. Wing Random sheared fosmid library as a new genomic tool to accelerate complete finishing of rice (Oryza sativa spp. Nipponbare) genome sequence: Sequencing of gap-specific fosmid clones uncovers new euchromatic portions of the genome Theor. Appl. Genet. 111 2005 1596 1607
3. A. Beloqui, T.Y. Nechitaylo, N. Lopez-Cortes, A. Ghazi, M.E. Guazzaroni, J. Polaina, A.W. Strittmatter, O. Reva, A. Waliczek, M.M. Yakimov, O.V. Golyshina, and M. Ferrer Diversity of glycosyl hydrolases from cellulose-depleting communities enriched from casts of two earthworm species Appl. Environ. Microbiol. 76 2010 5934 5946
4. B.L. Cantarel, P.M. Coutinho, C. Rancurel, T. Bernard, V. Lombard, and B. Henrissat The Carbohydrate-Active EnZymes database (CAZy): An expert resource for glycogenomics Nucleic Acids Res. 37 2009 D233 D238
5. J.R. Cole, B. Chai, R.J. Farris, Q. Wang, A.S. Kulam-Syed-Mohideen, D.M. McGarrell, A.M. Bandela, E. Cardenas, G.M. Garrity, and J.M. Tiedje The ribosomal database project (RDP-II): Introducing myRDP space and quality controlled public data Nucleic Acids Res. 35 2007 D169 D172
6. E.F. DeLong, L.T. Taylor, T.L. Marsh, and C.M. Preston Visualisation and enumeration of marine planktonic archaea and bacteria by using polyribonucleotide probes and fluorescent in situ hybridization Appl. Environ. Microbiol. 65 1999 5554 5563
7. T.Z. DeSantis, P. Hugenholtz, N. Larsen, M. Rojas, E.L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu, and G.L. Andersen Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB Appl. Environ. Microbiol. 72 2006 5069 5072
8. C.J. Duan, L. Xian, G.C. Zhao, Y. Feng, H. Pang, X.L. Bai, J.L. Tang, Q.S. Ma, and J.X. Feng Isolation and partial characterization of novel genes encoding acidic cellulases from metagenomes of buffalo rumens J. Appl. Microbiol. 107 2009 245 256
9. P.M. Dunman, E. Murphy, S. Haney, D. Palacios, G. Tucker-Kellogg, S. Wu, E.L. Brown, R.J. Zagursky, D. Shlaes, and S.J. Projan Transcription profiling-based identification of Staphylococcus aureus genes regulated by the agr and/or sarA loci J. Bacteriol. 183 2001 7341 7353
10. J.L. Edwards, D.L. Smith, J. Connolly, J.E. McDonald, M.J. Cox, I. Joint, C. Edwards, and A.J. McCarthy Identification of carbohydrate metabolism genes in the metagenome of a marine biofilm community shown to be dominated by gammaproteobacteria and bacteroidetes Genes 1 2010 371 384
11. Y. Feng, C.J. Duan, H. Pang, X.C. Mo, C.F. Wu, Y. Yu, Y.L. Hu, J. Wei, J.L. Tang, and J.X. Feng Cloning and identification of novel cellulase genes from uncultured microorganisms in rabbit cecum and characterization of the expressed cellulases Appl. Microbiol. Biotechnol. 75 2007 319 328
12. M. Ferrer, O.V. Golyshina, T.N. Chernikova, A.N. Khachane, D. Reyes-Duarte, V.A. Santos, C. Strompl, K. Elborough, G. Jarvis, A. Neef, M.M. Yakimov, and K.N. Timmis Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora Environ. Microbiol. 7 2005 1996 2010
13. S.D. Foster, and P.K. Dunstan The analysis of biodiversity using rank abundance distributions Biometrics 66 2010 186 195
14. J. Frias-Lopez, Y. Shi, G.W. Tyson, M.L. Coleman, S.C. Schuster, S.W. Chisholm, and E.F. Delong Microbial community gene expression in ocean surface waters Proc. Natl. Acad. Sci. USA 105 2008 3805 3810
15. E.M. Gabor, E.J. de Vries, and D.B. Janssen Construction, characterization, and use of small-insert gene banks of DNA isolated from soil and enrichment cultures for the recovery of novel amidases Environ. Microbiol. 6 2004 948 958
16. B. Garcia-Alvarez, R. Melero, F.M.V. Dias, J.A.M. Prates, C.M.G.A. Fontes, S.P. Smith, M.J. Romao, A.L. Carvalho, and O. Llorca Molecular architecture and structural transitions of a Clostridium thermocellum mini-cellulosome J. Mol. Biol. 407 2011 571 580
17. J.A. Gilbert, D. Field, Y. Huang, R. Edwards, W. Li, P. Gilna, and I. Joint Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities PLoS One 3 2008 e3042
18. J.E. Graham, M.E. Clark, D.C. Nadler, S. Huffer, H.A. Chokhawala, S.E. Rowland, H.W. Blanch, D.S. Clark, and F.T. Robb Identification and characterization of a multidomain hyperthermophilic cellulase from an archaeal enrichment Nat. Commun. 2 2011 375 Doi: 10.1038/ncomms1373
19. R.I. Griffiths, A.S. Whiteley, A.G. O'Donnell, and M.J. Bailey Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition Appl. Environ. Microbiol. 66 2000 5488 5491
20. Y. Hu, G.M. Zhang, A.Y. Li, J. Chen, and L.X. Ma Cloning and enzymatic characterization of a xylanase gene from a soil-derived metagenomic library with an efficient approach Appl. Microbiol. Biotechnol. 80 2008 823 830
21. D.E. Hunt, V. Klepac-Ceraj, S.G. Acinas, C. Gautier, S. Bertilsson, and M.F. Polz Evaluation of 23S rRNA primers for use in phylogenetic studies of bacterial diversity Appl. Environ. Microbiol. 72 2006 2221 2225
22. D.H. Huson, A.F. Auch, J. Qi, and S.C. Schuster MEGAN analysis of metagenomic data Genome Res. 17 2007 377 386
23. T.V. Karpinets, D.J. Greenwood, C.E. Sams, and J.T. Ammons RNA: protein ratio of the unicellular organism as a characteristic of phosphorous and nitrogen stoichiometry and of the cellular requirement of ribosomes for protein synthesis BMC Biol. 4 2006 30
24. I. Kataeva, X.L. Li, H. Chen, S.K. Choi, and L.G. Ljungdahl Cloning and sequence analysis of a new cellulase gene encoding CelK, a major cellulosome component of Clostridium thermocellum: Evidence for gene duplication and recombination J. Bacteriol. 181 1999 5288 5295
25. S.J. Kim, C.M. Lee, B.R. Han, M.Y. Kim, Y.S. Yeo, S.H. Yoon, B.S. Koo, and H.K. Jun Characterization of a gene encoding cellulase from uncultured soil bacteria FEMS Microbiol. Lett. 282 2008 44 51
26. D. Kim, S.N. Kim, K.S. Baik, S.C. Park, C.H. Lim, J.O. Kim, T.S. Shin, M.J. Oh, and C.N. Seong Screening and characterization of a cellulase gene from the gut microflora of abalone using metagenomic library J. Microbiol. 49 2011 141 145
27. T. Kong, Y. Xia, R. Seviour, M. He, T. McAllister, and R. Forster In situ identification of carboxymethyl cellulose-digesting bacteria in the rumen of cattle fed alfalfa or triticale FEMS Microbiol. Ecol. 80 2011 159 167
28. M. Langer, E.M. Gabor, K. Liebeton, G. Meurer, F. Niehaus, R. Schulze, J. Eck, and P. Lorenz Metagenomics: An inexhaustible access to nature's diversity Biotechnol. J. 1 2006 815 821
29. S. Leininger, T. Urich, M. Schloter, L. Schwark, J. Qi, G.W. Nicol, J.I. Prosser, S.C. Schuster, and C. Schleper Archaea predominate among ammonia-oxidizing prokaryotes in soils Nature 442 2006 806 809
30. J. Liu, W.D. Liu, X.L. Zhao, W.J. Shen, H. Cao, and Z.L. Cui Cloning and functional characterization of a novel endo-beta-1,4-glucanase gene from a soil-derived metagenomic library Appl. Microbiol. Biotechnol. 89 2011 1083 1092
31. R.J. Lockhart, M.I. Van Dyke, I.R. Beadle, P. Humphreys, and A.J. McCarthy Molecular biological detection of anaerobic gut fungi (Neocallimastigales) from landfill sites Appl. Environ. Microbiol. 72 2006 5659 5661
32. D. Martinez, R.M. Berka, B. Henrissat, M. Saloheimo, M. Arvas, S.E. Baker, J. Chapman, O. Chertkov, P.M. Coutinho, D. Cullen, E.G. Danchin, and I.V. Grigoriev Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina) Nat. Biotechnol. 26 2008 553 560
33. W.E. Mayer, L.N. Schuster, G. Bartelmes, C. Dieterich, and R.J. Sommer Horizontal gene transfer of microbial cellulases into nematode genomes is associated with functional assimilation and gene turnover BMC Evol. Biol. 11 2011 13
34. J.E. McDonald, R.J. Lockhart, M.J. Cox, H.E. Allison, and A.J. McCarthy Detection of novel Fibrobacter populations in landfill sites and determination of their relative abundance via quantitative PCR Environ. Microbiol. 10 2008 1310 1319
35. J.E. McDonald, A.B. de Menezes, H.E. Allison, and A.J. McCarthy Molecular biological detection and quantification of novel Fibrobacter populations in freshwater lakes Appl. Environ. Microbiol. 75 2009 5148 5152
36. J.E. McDonald, J.N.I. Houghton, D.J. Rooks, H.E. Allison, and A.J. McCarthy The microbial ecology of anaerobic cellulose degradation in municipal waste landfill sites: Evidence of a role for fibrobacters Environ. Microbiol 2012 10.1111/j.1462-2920.2011.02688.x
37. D. Medini, D. Serruto, J. Parkhill, D.A. Relman, C. Donati, R. Moxon, S. Falkow, and R. Rappuoli Microbiology in the post-genomic era Nat. Rev. Microbiol. 6 2008 419 430
38. L.V. Mello, X. Chen, and D.J. Rigden Mining metagenomic data for novel domains: BACON, a new carbohydrate-binding module FEBS Lett. 584 2010 2421 2426
39. F. Meyer, D. Paarmann, M. D'Souza, R. Olson, E.M. Glass, M. Kubal, T. Paczian, A. Rodriguez, R. Stevens, A. Wilke, J. Wilkening, and R.A. Edwards The metagenomics RAST server - A public resource for the automatic phylogenetic and functional analysis of metagenomes BMC Bioinformatics 9 2008 386
40. S. Mitra, P. Rupek, D.C. Richter, T. Urich, J.A. Gilbert, F. Meyer, A. Wilke, and D.H. Huson Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG BMC Bioinformatics 12 Suppl 1 2011 S21
41. J.D. Neufeld, H. Schafer, M.J. Cox, R. Boden, I.R. McDonald, and J.C. Murrell Stable-isotope probing implicates Methylophaga spp. and novel Gammaproteobacteria in marine methanol and methylamine metabolism ISME J. 1 2007 480 491
42. T.P. Niedringhaus, D. Milanova, M.B. Kerby, M.P. Snyder, and A.E. Barron Landscape of next-generation sequencing technologies Anal. Chem. 83 2011 4327 4341
43. R. Overbeek, T. Begley, R.M. Butler, J.V. Choudhuri, H.Y. Chuang, M. Cohoon, V. de Crecy-Lagard, N. Diaz, T. Disz, R. Edwards, M. Fonstein, and E.D. Frank The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes Nucleic Acids Res. 33 2005 5691 5702
44. H. Pang, P. Zhang, C.J. Duan, X.C. Mo, J.L. Tang, and J.X. Feng Identification of cellulase genes from the metagenomes of compost soils and functional characterization of one novel endoglucanase Curr. Microbiol. 58 2009 404 408
45. K.J. Purdy Nucleic acid recovery from complex environmental samples Methods Enzymol. 397 2005 271 292
46. D.E. Robertson, J.A. Chaplin, G. DeSantis, M. Podar, M. Madden, E. Chi, T. Richardson, A. Milan, M. Miller, D.P. Weiner, K. Wong, and J. McQuaid Exploring nitrilase sequence space for enantioselective catalysis Appl. Environ. Microbiol. 70 2004 2429 2436
47. S. Rodrigue, A.C. Materna, S.C. Timberlake, M.C. Blackburn, R.R. Malmstrom, E.J. Alm, and S.W. Chisholm Unlocking short read sequencing for metagenomics PLoS One 5 2010 e11840
48. D.J. Rooks, D.L. Smith, J.E. McDonald, M.J. Woodward, A.J. McCarthy, and H.E. Allison 454-Pyrosequencing: A molecular battiscope for freshwater viral ecology Genes 1 2010 210 226
49. E.E. Schadt, S. Turner, and A. Kasarskis A window into third-generation sequencing Hum. Mol. Genet. 19 2010 R227 R240
50. Y. Shi, G.W. Tyson, and E.F. DeLong Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column Nature 459 2009 266 269
51. C. Simon, and R. Daniel Construction of small-insert and large-insert metagenomic libraries Methods Mol. Biol. 668 2010 39 50
52. H.L. Steele, K.E. Jaeger, R. Daniel, and W.R. Streit Advances in recovery of novel biocatalysts from metagenomes J. Mol. Microbiol. Biotechnol. 16 2009 25 37
53. F.J. Stewart, E.A. Ottesen, and E.F. DeLong Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics ISME J. 4 2010 896 907
54. H. Suenaga, T. Ohnuki, and K. Miyazaki Functional screening of a metagenomic library for genes involved in microbial degradation of aromatic compounds Environ. Microbiol. 9 2007 2289 2297
55. L.O. Sukharnikov, B.J. Cantwell, M. Podar, and I.B. Zhulin Cellulases: Ambiguous nonhomologous enzymes in a genomic perspective Trends Biotechnol. 29 2011 473 479
56. L. Tasse, J. Bercovici, S. Pizzut-Serin, P. Robe, J. Tap, C. Klopp, B.L. Cantarel, P.M. Coutinho, B. Henrissat, M. Leclerc, J. Dore, and P. Monsan Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes Genome Res. 20 2010 1605 1612
57. R.M. Teather, and P.J. Wood Use of Congo red polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from the bovine rumen Appl. Environ. Microbiol. 43 1982 777 780
58. T. Uchiyama, and K. Miyazaki Functional metagenomics for enzyme discovery: Challenges to efficient screening Curr. Opin. Biotechnol. 20 2009 616 622
59. M.I. Van Dyke, and A.J. McCarthy Molecular biological detection and characterization of Clostridium populations in municipal landfill sites Appl. Environ. Microbiol. 68 2002 2049 2053
60. S. van Sint Fiet, J.B. van Beilen, and B. Witholt Selection of biocatalysts for chemical synthesis Proc. Natl. Acad. Sci. USA 103 2006 1693 1698
61. J.C. Venter, K. Remington, J.F. Heidelberg, A.L. Halpern, D. Rusch, J.A. Eisen, D. Wu, I. Paulsen, K.E. Nelson, W. Nelson, D.E. Fouts, and S. Levy Environmental genome shotgun sequencing of the Sargasso Sea Science 304 2004 66 74
62. S. Voget, H.L. Steele, and W.R. Streit Characterization of a metagenome-derived halotolerant cellulase J. Biotechnol. 126 2006 26 36
63. F. Wang, F. Li, G. Chen, and W. Liu Isolation and characterization of novel cellulase genes from uncultured microorganisms in different environmental niches Microbiol. Res. 164 2009 650 657
64. F. Warnecke, and M. Hess A perspective: Metatranscriptomics as a tool for the discovery of novel biocatalysts J. Biotechnol. 142 2009 91 95
65. Y.H.P. Zhang, M.E. Himmel, and J.R. Mielenz Outlook for cellulase improvement: Screening and selection strategies Biotechnol. Adv. 24 2006 452 481
66. J. Zhao, L. Hyman, and C. Moore Formation of mRNA 3′ ends in eukaryotes: Mechanism, regulation, and interrelationships with other steps in mRNA synthesis Microbiol. Mol. Biol. Rev. 63 1999 405 445