Strategies for Genome Reduction in Microbial Genomes
Niche dependent differential gene loss and overlapping genes have been proposed as means of achieving genome reduction by retaining indispensable genes and compressing maximum amount of information in available sequence space. Herein, we analyzed the differential gene loss and overlapping genes in b...
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| Published in | Genome Informatics Vol. 16; no. 2; pp. 69 - 75 |
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| Main Authors | , |
| Format | Journal Article |
| Language | English |
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Japan
Japanese Society for Bioinformatics
2005
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| Abstract | Niche dependent differential gene loss and overlapping genes have been proposed as means of achieving genome reduction by retaining indispensable genes and compressing maximum amount of information in available sequence space. Herein, we analyzed the differential gene loss and overlapping genes in bacterial genomes with different lifestyles. Our results clearly suggest that gene loss and overlapping genes could be a result of evolutionary pressure to minimize genome size. Comparative analysis of the genomes shows that the genomes display marked similarities in patterns of protein length and frequency. It is clear from our analysis that habitat is a major factor contributing to genome reduction. These comparisons increase our knowledge of the forces that drive the extreme specialization of the bacteria and its association to the host. |
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| AbstractList | Niche dependent differential gene loss and overlapping genes have been proposed as means of achieving genome reduction by retaining indispensable genes and compressing maximum amount of information in available sequence space. Herein, we analyzed the differential gene loss and overlapping genes in bacterial genomes with different lifestyles. Our results clearly suggest that gene loss and overlapping genes could be a result of evolutionary pressure to minimize genome size. Comparative analysis of the genomes shows that the genomes display marked similarities in patterns of protein length and frequency. It is clear from our analysis that habitat is a major factor contributing to genome reduction. These comparisons increase our knowledge of the forces that drive the extreme specialization of the bacteria and its association to the host. |
| Author | Sakharkar, Kishore R. Chow, Vincent T.K. |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/16901090$$D View this record in MEDLINE/PubMed |
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| References | [12] Sakharkar, K. R., Dhar, P. K., and Chow, V. T., Genome reduction in prokaryotic obligatory intracellular parasites of humans: a comparative analysis, Int. J. Syst. Evol. Microbiol., 54: 1937-1941, 2004. [2] Andersson, J. O. and Andersson, S. G., Pseudogenes, junk DNA, and the dynamics of Rickettsia genomes, Mol. Biol. Evol., 18: 829-839, 2001. [1] Andersson, J. O. and Andersson, S. G., Insights into the evolutionary process of genome degradation, Curr. Opin. Genet. Dev., 9: 664 671, 1999. [9] Norinark, S., Bergstrom, S., Edlund, T., Grundstrom, T., Jaurin, B., Lindberg, F. P., and Olsson, O., Overlapping genes, Annu. Rev. Genet., 17: 499-525, 1983. [8] Natale, D. A., Galperin, M. Y., Tatusov, R. L., and Koonin, E. V., Using the COG database to improve gene recognition in complete genomes, Genetica, 108: 9-17, 2000. [10] Ochrnan, H. and Moran, N., Genes lost and genes found: Evolution of bacterial pathogenesis and symbiosis, Science, 292: 1096-1098, 2001. [4] Andersson, S. G., Zomorodipour, A., Andersson, J. O., Sicheritz-Ponten, T., Alsmark, U. C., Podowski, R. M., Naslund, A. K., Eriksson, A. S., Winkler, H. H., and Kurland, C. G., The genome sequence of Rickettsia prowazekii and the origin of mitochondria, Nature, 396: 133-140, 1998. [6] Fukuda, Y., Nakayama, Y. and Tomita, M., On dynamics of overlapping genes in bacterial genomes, Gene, 323: 181-187, 2003. [7] Inokuchi, Y., Hirashima, A., Sekine, Y., Janosi, L., and Kaji, A., Role of ribosome recycling factor (RRF) in translational coupling, EMBO J., 19: 3788-3798, 2000. [15] Zomorodipour, A. and Andersson, S. G., Obligate intracellular parasites: Rickettsia prowazekii and Chlamydia trachomatis, FEBS Lett., 452: 11-15, 1999. [14] Tamas, I., Klasson, L. M., Callback, B., Naslund, A. K., Eriksson, A., Wernegreen, J. J., Sandstorm, J. P., Moran, N. A., and Andersson, S. G., 50 Million years of genomic stasis in endosymbiotic bacteria, Science, 296: 2376-2379, 2002. [3] Andersson, S. G. and Kurland, C. G., Reductive evolution of resident genomes, Trends Microbiol., 6: 263-268, 1998. [11] Rogozin, I. B., Spiridonov, A. N., Sorokin, A. V., Wolf, Y. I., Jordan, I. K., Tatusov, R. L. and Koonin, E. V., Purifying and directional selection in overlapping prokaryotic genes, Trends Genet., 18: 228-232, 2002. [5] Chen, S. M., Takiff, H. E., Barber, A. M., Dubois, G. C., Bardwell, J. C., and Court, D. L., Expression and characterization of RNase III and Era proteins. Products of the rne operon of Escherichia coli, J. Biol. Chem., 265: 2888-2895, 1990. [13] Sakharkar, K. R., Sakharkar, M. K., Verma, C., and Chow, V. T., Comparative study of overlapping genes in bacteria, with special reference to Rickettsia prowazekii and Rickettsia conorii, Int. J. Syst. Evol. Microbiol., 55: 1205-1209, 2005. |
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| SubjectTerms | Bacteria - genetics Computational Biology - methods Evolution, Molecular Gene Deletion Genes, Overlapping genome reduction Genome, Bacterial minimal genomes obligatory intracellular parasites overlapping genes overprinting Structural Homology, Protein |
| Title | Strategies for Genome Reduction in Microbial Genomes |
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