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http://dx.doi.org/10.4014/jmb.0905.05017

Elucidation of Multifaceted Evolutionary Processes of Microorganisms by Comparative Genome-Based Analysis  

Nguyen, Thuy Vu An (School of Chemical Engineering and Bioengineering, University of Ulsan)
Hong, Soon-Ho (School of Chemical Engineering and Bioengineering, University of Ulsan)
Lee, Sang-Yup (Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering(BK21 Program), Korea Advanced Institute of Science and Technology)
Publication Information
Journal of Microbiology and Biotechnology / v.19, no.11, 2009 , pp. 1301-1305 More about this Journal
Abstract
The evolution of living organisms occurs via a combination of highly complicated processes that involve modification of various features such as appearance, metabolism and sensing systems. To understand the evolution of life, it is necessary to understand how each biological feature has been optimized in response to new environmental conditions and interrelated with other features through evolution. To accomplish this, we constructed contents-based trees for a two-component system (TCS) and metabolic network to determine how the environmental communication mechanism and the intracellular metabolism have evolved, respectively. We then conducted a comparative analysis of the two trees using ARACNE to evaluate the evolutionary and functional relationship between TCS and metabolism. The results showed that such integrated analysis can give new insight into the study of bacterial evolution.
Keywords
Integrated evolutionary analysis; genome sequences; metabolic networks; two-component systems; ARACNE;
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Times Cited By Web Of Science : 0  (Related Records In Web of Science)
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1 Daubin, V., M. Gouy, and G. Perriere. 2002. A phylogenie approach to bacterial phylogeny: Evidence of core genes sharing a common history. Genome Res. 12: 1080-1090   DOI   ScienceOn
2 Franckea, C., R. J. Siezena, and B. Teusink. 2005. Reconstructing the metabolic network of a bacterium from its genome. Trends Microbiol. 13: 550-558   DOI   ScienceOn
3 Ribeiro, S. and G. B. Golding. 1998. The mosaic nature of the eukaryotic nucleus. Mol. Biol. Evol. 15: 779-788   DOI   PUBMED   ScienceOn
4 Hong, S. H. 2007. Systems approaches to succinic acid-producing microorganisms. Biotechnol. Bioprocess Eng. 12: 73-79   과학기술학회마을   DOI   ScienceOn
5 Snel, B., P. Bork, and M. A. Huynen. 1999. Genome phylogeny based on gene content. Nat. Genet. 21: 108-110   DOI   ScienceOn
6 Kim, T. Y. and S. Y. Lee. 2006. Accurate metabolic flux analysis through data reconciliation of isotope balance-based data. J. Microbiol. Biotechnol. 16: 1139-1143   ScienceOn
7 Zuckerkandl, E. and L. Pauling. 1965. Molecules as documents of evolutionary history. J. Theor. Biol. 8: 357-366   DOI   ScienceOn
8 Eisen, M. B., P. T. Spellman, P. O. Brown, and D. Botstein. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA. 95: 14863-14868   DOI   ScienceOn
9 Kitano, H. 2002. Systems biology: A brief overview. Science 295: 1662-1664   DOI   PUBMED   ScienceOn
10 Olsen, G. J., C. R. Woese, and R. Overbeek. 1994. The wind of (evolutionary) change: Breathing new life into microbiology. J. Bacteriol. 176: 1-6   PUBMED   ScienceOn
11 Butte, A. J. and I. S. Kohane. 2000. Mutual information relevance networks: Functional genomic clustering using pairwise entropy measurements. Pac. Symp. Biocomput. 5: 418-429
12 Lee, S. Y., H. M. Woo, D-Y. Lee, H. S. Choi, T. Y. Kim, and H. Yun. 2005. Systems-level analysis of genome-scale in silico metabolic models using MetaFluxNet. Biotechnol. Bioprocess Eng. 10: 425-431   과학기술학회마을   DOI   ScienceOn
13 Hong, S. H., T. Y. Kim, and S. Y. Lee. 2004. Phylogenetic analysis based on genome-scale metabolic pathway reaction content. Appl. Microbiol. Biotechnol. 65: 203-210   PUBMED   ScienceOn
14 Asenjo, J. A., P. Ramirez, I. Rapaport, J. Aracena, E. Goles, and B. A. Andrews. 2007. A discrete mathematical model applied to genetic regulation and metabolic networks. J. Microbiol. Biotechnol. 17: 496-510   PUBMED   ScienceOn
15 Feng, D. F., G. Cho, and R. F. Doolittle. 1997. Determining divergence times with a protein clock: Update and reevaluation. Proc. Natl. Acad. Sci. USA. 94: 13028-13033   DOI   ScienceOn
16 Nguyen, T. V. A. and S. H. Hong. 2008. Whole genome-based phylogenetic analysis of bacterial two-component systems. Biotechnol. Bioprocess Eng. 13: 288-292   DOI   ScienceOn
17 Tekaia, F., A. Lazcano, and B. Dujon. 1999. The genomic tree as revealed from whole proteome comparisons. Genome Res. 9: 550-557   PUBMED   ScienceOn
18 Margolin, A. A., K. Wang, W. K. Lim, M. Kustagi, I. Nemenman, and A. Califano. 2006. Reverse engineering cellular networks. Nat. Protocol 1: 663-672
19 Ideker, T., T. Galitski, and L. Hood. 2001. A new approach to decoding life: Systems biology. Annu. Rev. Genomics Hum. Genet. 2: 343-372   DOI   ScienceOn
20 Kanehisa, M., S. Goto, S. Kawashima, and A. Nakaya. 2002. The KEGG databases at GenomeNet. Nucleic Acids Res. 30: 42-46   DOI   ScienceOn
21 Kim, J. S. and S. Y. Lee. 2006. Genomic tree of gene contents based on the functional groups of KEGG orthology. J. Microbiol. Biotechnol. 16: 748-756   ScienceOn
22 Fitch, W. M. and E. Margoliash. 1967. Construction of phylogenetic trees. Science 155: 279-284   DOI   PUBMED   ScienceOn
23 Rivera, M. C., R. Jain, J. E. Moore, and J. A. Lake. 1998. Genomic evidence for two functionally distinct gene classes. Proc. Natl. Acad. Sci. USA. 95: 6239-6244   DOI   ScienceOn
24 Bansal, A. K. 1999. An automated comparative analysis of 17 complete microbial genomes. Bioirfomatics 15: 900-908   DOI
25 Brown, J. R., C. J. Douady, M. J. ltalia, W. E. Marshall, and M. J. Stanhope. 2001. Universal trees based on large combined protein sequence data sets. Nat. Genet. 28: 281-285   DOI   ScienceOn
26 Duarte, N. C., S. A. Becker, N. Jamshidi, I. Thiele, M. I. Mo, T. D. Vo, R. Srivas, and B. O. Palsson. 2007. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc. Natl. Acad. Sci. U.S.A. 104: 1777-1782   DOI   ScienceOn
27 Meyer, T. E., M. A. Cusanovich, and M. D. Kamen. 1986. Evidence against use of bacterial amino acid sequence data for construction of all-inclusive phylogenetic trees. Proc. Natl. Acad. Sci. U.S.A. 83: 217-220   DOI   ScienceOn
28 Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51: 221-271   PUBMED   ScienceOn
29 Ma, H. W. and A. P. Zeng. 2004. Phylogenetic comparison of metabolic capacities of organisms at genome level. Mol. Phylogenet Evol. 31: 204-213   DOI   ScienceOn
30 Fitz-Gibbon, S. T. and C. H. House. 1999. Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res. 27: 4218-4222   DOI   ScienceOn