Asian-Australasian Journal of Animal Sciences

  • 제26권8호
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  • Pages.1144-1151
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  • 2013
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  • 1011-2367(pISSN)
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  • 1976-5517(eISSN)
아세아태평양축산학회 (Asian Australasian Association of Animal Production Societies)
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Metagenome Analysis of Protein Domain Collocation within Cellulase Genes of Goat Rumen Microbes

  • Lim, SooYeon (Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University) ;
  • Seo, Jaehyun (Department of Agricultural Science, Korea National Open University) ;
  • Choi, Hyunbong (Department of Agricultural Science, Korea National Open University) ;
  • Yoon, Duhak (Department of Animal Science, Kyungpook National University) ;
  • Nam, Jungrye (Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University) ;
  • Kim, Heebal (Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University) ;
  • Cho, Seoae (C&K genomics Inc. 514 Main Bldg., Seoul National University Research Park) ;
  • Chang, Jongsoo (Department of Agricultural Science, Korea National Open University)
  • 투고 : 2013.04.16
  • 심사 : 2013.04.29
  • 발행 : 2013.08.01
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초록

In this study, protein domains with cellulase activity in goat rumen microbes were investigated using metagenomic and bioinformatic analyses. After the complete genome of goat rumen microbes was obtained using a shotgun sequencing method, 217,892,109 pair reads were filtered, including only those with 70% identity, 100-bp matches, and thresholds below $E^{-10}$ using METAIDBA. These filtered contigs were assembled and annotated using blastN against the NCBI nucleotide database. As a result, a microbial community structure with 1431 species was analyzed, among which Prevotella ruminicola 23 bacteria and Butyrivibrio proteoclasticus B316 were the dominant groups. In parallel, 201 sequences related with cellulase activities (EC.3.2.1.4) were obtained through blast searches using the enzyme.dat file provided by the NCBI database. After translating the nucleotide sequence into a protein sequence using Interproscan, 28 protein domains with cellulase activity were identified using the HMMER package with threshold E values below $10^{-5}$. Cellulase activity protein domain profiling showed that the major protein domains such as lipase GDSL, cellulase, and Glyco hydro 10 were present in bacterial species with strong cellulase activities. Furthermore, correlation plots clearly displayed the strong positive correlation between some protein domain groups, which was indicative of microbial adaption in the goat rumen based on feeding habits. This is the first metagenomic analysis of cellulase activity protein domains using bioinformatics from the goat rumen.

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참고문헌

  1. Alzari, P. M., and R. Dominguez. 1996. The crystal structure of endoglucanase CelA, a family 8 glycosyl hydrolase from Clostridium thermocellum. Structure 4:265-275. https://doi.org/10.1016/S0969-2126(96)00031-7
  2. Bazan, J. F. 1990. Structural design and molecular evolution of a cytokine receptor superfamily. Proc. Natl. Acad. Sci. USA 87: 6934-6938. https://doi.org/10.1073/pnas.87.18.6934
  3. Brick, D. J., M. J. Brumlik, J. T. Buckley, J.-X. Cao, P. C. Davies, S. Misra, T. J. Tranbarger, and C. Upton. 1995. A new family of lipolytic plant enzymes with members in rice, arabidopsis and maize. FEBS Lett. 377:475-480. https://doi.org/10.1016/0014-5793(95)01405-5
  4. Bryant, M. P., and N. Small. 1956. The anaerobic monotrichous butyric acid-producing curved rod-shaped bacteria of the rumen. J. Bacteriol. 72:16-21.
  5. Castillo, R. M., K. Mizuguchi, V. Dhanaraj, A. Albert, T. L. Blundell, and A. G. Murzin. 1999. A six-stranded double-psi ${\beta}$ barrel is shared by several protein superfamilies. Structure 7: 227-236. https://doi.org/10.1016/S0969-2126(99)80028-8
  6. Chow, J. M., and J. B. Russell. 1992. Effect of pH and monensin on glucose transport by Fibrobacter succinogenes, a cellulolytic ruminal bacterium. Appl. Environ. Microbiol. 58: 1115-1120.
  7. Dominguez, R., H. Souchon, M.-B. Lascombe, and P. M. Alzari. 1996. The crystal structure of a family 5 endoglucanase mutant in complexed and uncomplexed forms reveals an induced fit activation mechanism. J. Mol. Biol. 257:1042-1051. https://doi.org/10.1006/jmbi.1996.0222
  8. Ferrer, M., Olga V. Golyshina, Tatyana N. Chernikova, Amit N. Khachane, Dolores Reyes-Duarte, Vitor A. P. Martins Dos Santos, Carsten Strompl, Kieran Elborough, Graeme Jarvis, Alexander Neef, Michail M. Yakimov, Kenneth N. Timmis, and Peter N. Golyshin. 2005. Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora. Environ. Microbiol. 7:1996-2010. https://doi.org/10.1111/j.1462-2920.2005.00920.x
  9. Galagan, J. E., S. E. Calvo, C. Cuomo, L.-J. Ma, J. R. Wortman, S. Batzoglou, S.-I. Lee, M. Bastuerkmen, C. C. Spevak, J. Clutterbuck, V. Kapitonov, J. Jurka, C. Scazzocchio, M. L. Farman, J. Butler, S. Purcell, S. Harris, G. H. Braus, and B. W. Birren. 2005. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature. 438:1105-1115. https://doi.org/10.1038/nature04341
  10. Guan, L. L., J. D. Nkrumah, J. A. Basarab, and S. S. Moore. 2008. Linkage of microbial ecology to phenotype: correlation of rumen microbial ecology to cattle's feed efficiency. FEMS Microbiol. Lett. 288:85-91. https://doi.org/10.1111/j.1574-6968.2008.01343.x
  11. Hegarty, R. S. 1999. Reducing rumen methane emissions through elimination of rumen protozoa. Aust. J. Agric. Res. 50:1321-1328. https://doi.org/10.1071/AR99008
  12. Heinrichova, K., M. Wojciechowicz, and A. Ziolecki. 1989. The pectinolytic enzyme of Selenomonas ruminantium. J. Appl. Microbiol. 66:169-174. https://doi.org/10.1111/j.1365-2672.1989.tb02466.x
  13. Hess, M., A. Sczyrba, R. Egan, T. W. Kim, H. Chokhawala, G. Schroth, S. Luo, D. S. Clark, F. Chen, T. Zhang, R. I. Mackie, L. A. Pennacchio, S. G. Tringe, A. Visel, T. Woyke, Z. Wang, and E. M. Rubin. 2011. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science (New York, NY) 331:463-467. https://doi.org/10.1126/science.1200387
  14. Janssen, R., J. Smeitink, R. Smeets, and L. van den Heuvel. 2002. CIA30 complex I assembly factor: a candidate for human complex I deficiency? Hum. Genet. 110:264-270. https://doi.org/10.1007/s00439-001-0673-3
  15. Johnson, P. E., M. D. Joshi, P. Tomme, D. G. Kilburn, and L. P. McIntosh. 1996. Structure of the N-terminal cellulose-binding domain of Cellulomonas fimi CenC determined by nuclear magnetic resonance spectroscopy. Biochemistry 35:14381-14394. https://doi.org/10.1021/bi961612s
  16. Kitago, Y., S. Karita, N. Watanabe, M. Kamiya, T. Aizawa, K. Sakka, and I. Tanaka. 2007. Crystal structure of Cel44A, a glycoside hydrolase family 44 endoglucanase from Clostridium thermocellum. J. Biol. Chem. 282:35703-35711. https://doi.org/10.1074/jbc.M706835200
  17. Kornblihtt, A. R., K. Umezawa, K. Vibe-Pedersen, and F. Baralle. 1985. Primary structure of human fibronectin: differential splicing may generate at least 10 polypeptides from a single gene. EMBO J. 4:1755-1759.
  18. Kosugi, A., Y. Amano, K. Murashima, and R. H. Doi. 2004. Hydrophilic domains of scaffolding protein CbpA promote glycosyl hydrolase activity and localization of cellulosomes to the cell surface of Clostridium cellulovorans. J. Bacteriol. 186: 6351-6359. https://doi.org/10.1128/JB.186.19.6351-6359.2004
  19. Krause, D. O., T. G. Nagaraja, A. D. G. Wright, and T. R. Callaway. 2013. Board-invited review: Rumen microbiology: Leading the way in microbial ecology. J. Anim. Sci. 91:331-341. https://doi.org/10.2527/jas.2012-5567
  20. Little, E., P. Bork, and R. F. Doolittle. 1994. Tracing the spread of fibronectin type III domains in bacterial glycohydrolases. J. Mol. Evol. 39:631-643. https://doi.org/10.1007/BF00160409
  21. Lytle, B. L., B. F. Volkman, W. M. Westler, and J. Wu. 2000. Secondary structure and calcium-induced folding of the Clostridium thermocellum dockerin domain determined by NMR spectroscopy. Arch. Biochem. Biophys. 379:237-244. https://doi.org/10.1006/abbi.2000.1882
  22. McAllister, T. A., H. D. Bae, G. A. Jones, and K-J. Cheng. 1994. Microbial attachment and feed digestion in the rumen. J. Anim. Sci. 72:3004-3018.
  23. Molgaard, A., S. Kauppinen, and S. Larsen. 2000. Rhamnogalacturonan acetylesterase elucidates the structure and function of a new family of hydrolases. Structure 8:373-383. https://doi.org/10.1016/S0969-2126(00)00118-0
  24. McKain, N., R. J. Wallace, and N. D. Watt. 1992. Selective isolation of bacteria with dipeptidyl aminopeptidase type I activity from the sheep rumen. FEMS Microbiol. Lett. 95:169-173. https://doi.org/10.1111/j.1574-6968.1992.tb05361.x
  25. Mesnage, S., T. Fontaine, T. Mignot, M. Delepierre, M. Mock, and A. Fouet. 2000. Bacterial SLH domain proteins are non-covalently anchored to the cell surface via a conserved mechanism involving wall polysaccharide pyruvylation. EMBO J. 19:4473-4484. https://doi.org/10.1093/emboj/19.17.4473
  26. Mizuguchi, K., V. Dhanaraj, T. L. Blundell, and A. G. Murzin. 1999. N-ethylmaleimide-sensitive fusion protein (NSF) and CDC48 confirmed as members of the double-psi beta-barrel aspartate decarboxylase/formate dehydrogenase family. Structure (London, England: 1993) 7:R215-R216. https://doi.org/10.1016/S0969-2126(99)80169-5
  27. Moon, C. D., D. M. Pacheco, W. J. Kelly, S. C. Leahy, D. Li, J. Kopecny, and G. T. Attwood. 2008. Reclassification of Clostridium proteoclasticum as Butyrivibrio proteoclasticus comb. nov., a butyrate-producing ruminal bacterium. Intl J. Syst. Evol. Microbiol. 58:2041-2045. https://doi.org/10.1099/ijs.0.65845-0
  28. Mosbah, A., A. Bela ch, O. Bornet, J.-P. Belaich, B. Henrissat, and H. Darbon. 2000. Solution structure of the module X2_1 of unknown function of the cellulosomal scaffolding protein CipC of Clostridium cellulolyticum. J. Mol. Biol. 304:201-217. https://doi.org/10.1006/jmbi.2000.4192
  29. Peng, Y., Henry C. M. Leung, S. M. Yiu, and Francis Y. L. Chin. 2011. Meta-IDBA: a de Novo assembler for metagenomic data. Bioinformatics 27:i94-i101. https://doi.org/10.1093/bioinformatics/btr216
  30. Poole, D. M., E. Morag, R. Lamed, E. A. Bayer, G. P. Hazlewood, and H. J. Gilbert. 1992. Identification of the cellulose-binding domain of the cellulosome subunit S1 from Clostridium thermocellum YS. FEMS Microbiol. Lett. 99:181-186. https://doi.org/10.1111/j.1574-6968.1992.tb05563.x
  31. Ross, E. M., P. J. Moate, C. R. Bath, S. E. Davidson, T. I. Sawbridge, K. M. Guthridge, B. G. Cocks, and B. J. Hayes. 2012. High throughput whole rumen metagenome profiling using untargeted massively parallel sequencing. BMC Genet. 13:53.
  32. Shoham, Y., R. Lamed, and E. A. Bayer. 1999. The cellulosome concept as an efficient microbial strategy for the degradation of insoluble polysaccharides. Trends Microbiol. 7:275-281. https://doi.org/10.1016/S0966-842X(99)01533-4
  33. Takase, I., F. Ishino, M. Wachi, H. Kamata, M. Doi, S. Asoh, H. Matsuzawa, T. Ohta, and M. Matsuhashi. 1987. Genes encoding two lipoproteins in the leuS-dacA region of the Escherichia coli chromosome. J. Bacteriol. 169:5692-5699.
  34. Tews, I., A. Perrakis, A. Oppenheim, Z. Dauter, K. S. Wilson, and C. E. Vorgias. 1996. Bacterial chitobiase structure provides insight into catalytic mechanism and the basis of Tay-Sachs disease. Nat. Struct. Biol. 3:638-648. https://doi.org/10.1038/nsb0796-638
  35. Tormo, J., R. Lamed, A. J. Chirino, E. Morag, E. A. Bayer, Y. Shoham, and T. A. Steitz. 1996. Crystal structure of a bacterial family-III cellulose-binding domain: a general mechanism for attachment to cellulose. EMBO J. 15:5739-5751.
  36. Toyoda, A., W. Iio, M. Mitsumori, and H. Minato. 2009. Isolation and identification of cellulose-binding proteins from sheep rumen contents. Appl. Environ. Microbiol. 75:1667-1673. https://doi.org/10.1128/AEM.01838-08
  37. Van Gylswyk, N., and J. Van Der Toorn. 1986. Enumeration of Bacteroides succinogenes in the rumen of sheep fed maize-straw diets. FEMS Microbiol. Lett. 38:205-209.
  38. Walker, J. E., J. M. Arizmendi, A. Dupuis, I. M. Fearnley, M. Finel, S. M. Medd, S. J. Pilkington, M. J. Runswick, and J. M. Skehel. 1992. Sequences of 20 subunits of NADH: ubiquinone oxidoreductase from bovine heart mitochondria: Application of a novel strategy for sequencing proteins using the polymerase chain reaction. J. Mol. Biol. 226:1051-1072. https://doi.org/10.1016/0022-2836(92)91052-Q
  39. Wortman, J. R., J. M. Gilsenan, V. Joardar, J. Deegan, J. Clutterbuck, M. R. Andersen, D. Archer, M. Bencina, G. Braus, P. Coutinho, H. von Dohren, J. Doonan, A. J. Driessen, P. Durek, E. Espeso, E. Fekete, M. Flipphi, C. G. Estrada and G. Turner. 2009. The 2008 update of the Aspergillus nidulans genome annotation: a community effort. Fungal Genet. Biol. 46:S2-13. https://doi.org/10.1016/j.fgb.2008.12.003
  40. Xu, G.-Y., E. Ong, N. R. Gilkes, D. G. Kilburn, D. Muhandiram, M. Harris-Brandts, J. P. Carver, L. E. Kay, and T. S. Harvey. 1995. Solution structure of a cellulose-binding domain from Cellulomonas fimi by nuclear magnetic resonance spectroscopy. Biochemistry 34:6993-7009. https://doi.org/10.1021/bi00021a011
  41. Zhou, J., B. Copeland, C. Zhang, Z. Liu, S. Bhatti, R. Sauve, and S. Zhou. 2011. Identification of prokaryotic organisms in goat rumen based on metagenomic DNA sequences. J. Res. Biol. 6: 451-455.

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