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) |
1 | 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. DOI ScienceOn |
2 | 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. |
3 | Castillo, R. M., K. Mizuguchi, V. Dhanaraj, A. Albert, T. L. Blundell, and A. G. Murzin. 1999. A six-stranded double-psi barrel is shared by several protein superfamilies. Structure 7: 227-236. DOI ScienceOn |
4 | 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. |
5 | 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. DOI ScienceOn |
6 | 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. DOI ScienceOn |
7 | 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. DOI ScienceOn |
8 | 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. DOI ScienceOn |
9 | 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. DOI |
10 | 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. DOI ScienceOn |
11 | 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. |
12 | 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. DOI ScienceOn |
13 | 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. DOI ScienceOn |
14 | 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. DOI ScienceOn |
15 | 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. DOI ScienceOn |
16 | 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. DOI ScienceOn |
17 | 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. DOI ScienceOn |
18 | 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. DOI ScienceOn |
19 | 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. |
20 | 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. DOI |
21 | 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. DOI ScienceOn |
22 | 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. |
23 | 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. DOI ScienceOn |
24 | 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. DOI ScienceOn |
25 | Bazan, J. F. 1990. Structural design and molecular evolution of a cytokine receptor superfamily. Proc. Natl. Acad. Sci. USA 87: 6934-6938. DOI |
26 | Hegarty, R. S. 1999. Reducing rumen methane emissions through elimination of rumen protozoa. Aust. J. Agric. Res. 50:1321-1328. DOI |
27 | Heinrichova, K., M. Wojciechowicz, and A. Ziolecki. 1989. The pectinolytic enzyme of Selenomonas ruminantium. J. Appl. Microbiol. 66:169-174. DOI |
28 | 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. DOI ScienceOn |
29 | 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. DOI ScienceOn |
30 | 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. DOI ScienceOn |
31 | 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. |
32 | 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. DOI ScienceOn |
33 | 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. DOI ScienceOn |
34 | 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. |
35 | 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. DOI ScienceOn |
36 | 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. DOI ScienceOn |
37 | 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. DOI ScienceOn |
38 | 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. DOI ScienceOn |
39 | 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. |
40 | 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. DOI ScienceOn |
41 | 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. |