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Investigation of Conservative Genes in 711 Prokaryotes
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  • Journal title : Journal of Life Science
  • Volume 25, Issue 9,  2015, pp.1007-1013
  • Publisher : Korean Society of Life Science
  • DOI : 10.5352/JLS.2015.25.9.1007
 Title & Authors
Investigation of Conservative Genes in 711 Prokaryotes
Lee, Dong-Geun; Lee, Sang-Hyeon;
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A COG (Cluster of Orthologous Groups of proteins) algorithm was applied to detect conserved genes in 711 prokaryotes. Only COG0080 (ribosomal protein L11) was common among all the 711 prokaryotes analyzed and 58 COGs were common in more than 700 prokaryotes. Nine COGs among 58, including COG0197 (endonuclease III) and COG0088 (ribosomal protein L4), were conserved in a form of one gene per one organism. COG0008 represented 1356 genes in 709 of the prokaryotes and this was the highest number of genes among 58 COGs. Twenty-two COGs were conserved in more than 708 prokaryotes. Of these, two were transcription related, four were tRNA synthetases, eight were large ribosomal subunits, seven were small ribosomal subunits, and one was translation elongation factor. Among 58 conserved COGs in more than 700 prokaryotes, 50 (86.2%) were translation related, and four (6.9%) were transcription related, pointing to the importance of protein-synthesis in prokaryotes. Among these 58 COGs, the most conserved COG was COG0060 (isoleucyl tRNA synthetase), and the least conserved was COG0143 (methionyl tRNA synthetase). Archaea and eubacteria were discriminated in the genomic analysis by the average distance and variation in distance of common COGs. The identification of these conserved genes could be useful in basic and applied research, such as antibiotic development and cancer therapeutics.
Conservative gene;COG (cluster of orthologous groups of protein);ortholog;prokaryotic genome;
 Cited by
유전자 보유 계통수를 이용한 원핵생물 680종의 분석,이동근;이상현;

생명과학회지, 2016. vol.26. 6, pp.711-720 crossref(new window)
Phylogenetic Analysis of 680 Prokaryotes by Gene Content, Journal of Life Science, 2016, 26, 6, 711  crossref(new windwow)
Bapteste, E., Boucher, Y., Leigh, J. and Doolittle, W. F. 2004. Phylogenetic reconstruction and lateral gene transfer. Trends Microbiol. 12, 406-411. crossref(new window)

Bhat, K. P., Itahana, K., Jin, A. and Zhang, Y. 2004. Essential role of ribosomal protein L11 in mediating growth inhibition-induced p53 activation. EMBO J. 23, 2402-2412. crossref(new window)


Galperin, M. Y., Makarova, K. S., Wolf, Y. I. and Koonin, E. V. 2015. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 43, D261-D269. crossref(new window)



Kang, H. Y., Shin, C. J., Kang, B. C., Park, J. H., Shin, D. H., Choi, J. H., Cho, H. G., Cha, J. H., Lee, D. G., Lee, J. H., Park, H. K. and Kim, C. M. 2002. Investigation of conserved gene in microbial genomes using in silico analysis. J. Life Sci. 5, 610-621.

Kimura, M. 1983. The neutral theory of molecular evolution. Cambridge University Press.

Kristensen, D. M., Waller, A. S., Yamada, T, Bork, P., Mushegian, A. R. and Koonin, E. V. 2013. Orthologous gene clusters and taxon signature genes for viruses of prokaryotes. J. Bacteriol. 195, 941-950. crossref(new window)

Lee, D. G., Lee, J. H., Lee, S. H., Ha, B. J., Kim, C. M., Shim, D. H., Park, E. K., Kim, J. W., Li, H. Y., Nam, C. S., Kim, N. Y., Lee, E. J., Back, J. W. and Ha, J. M. 2005. Investigation of conserved genes in microorganism. J. Life Sci. 15, 261-266. crossref(new window)

Lee, D. G., Kang, H. Y., Lee, J. H. and Kim, C. M. 2003.Detection of conserved genes in proteobacteria by using a COG algorithm. Kor. J. Biotechnol. Bioeng. 17, 560-565.

Reddy, P. J., Ray, S., Sathe, G. J., Gajbhiye, A., Prasad, T. S., Rapole, S., Panda, D. and Srivastava, S. 2015. A comprehensive proteomic analysis of totarol induced alterations in Bacillus subtilis by multipronged quantitative proteomics. J. Proteomics. 30, 247-262.

Tatusov, R. L., Koonin, E. V. and Lipman, D. L. 1997. A genomic perspective on protein families. Science 278, 631-637. crossref(new window)

Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., Krylov, D. M., Mazumder, R., Mekhedov, S. L., Nikolskaya, A. N., Rao, B. S., Smirnov, S., Sverdlov, A. V., Vasudevan, S., Wolf, Y. I., Yin, J. J. and Natale, D. A. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinf. 4, 41. crossref(new window)

Vishwanath, P., Favaretto, P., Hartman, H., Mohr, S. C. and Smith, T. F. 2004. Ribosomal protein-sequence block structure suggests complex prokaryotic evolution with implications for the origin of eukaryotes. Mol. Phylogenet. Evol. 33, 615-625. crossref(new window)

Wolf, Y. I., Makarova, K. S., Yutin, N. and Koonin, E. V. 2012. Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer. Biol. Direct. 7, 46. crossref(new window)

Zhang, S., Scott, J. M. and Haldenwang, W. G. 2001. Loss of ribosomal protein L11 blocks stress activation of the Bacillus subtilis transcription factor sigma(B). J. Bacteriol. 183, 2316-2321. crossref(new window)

Zhou, X., Liao, W. J., Liao, J. M., Liao, P. and Lu, H. 2015. Ribosomal proteins: functions beyond the ribosome. J. Mol. Cell Biol. 7, 92-104. crossref(new window)