In silico Analysis of Chlorobium Genomes Divulge Insights into the Lifestyle of the Bacteria
The finished sequences of three Chlorobium genomes were examined and compared to each other for their synonymous codon usage. Codon usage by Chlorobium was moderately biased but a considerable amount of variation was observed. GC3 composition plays an important role in the codon usage variation among the genes in the studied genomes. Similar homologs of horizontally transferred nitrogen fixing and photosynthesis related genes having high identity levels indicated their co-evolution within the genus. Correlation of codon usage bias with tRNA content in Chlorobium genomes revealed the inability of the translation machinery in these bacteria to co-evolve with higher codon usage resulting in moderate bias. Arrangement of the genes in leading strand and lagging strand of replication had virtually no role in influencing synonymous codon usage variation in these bacteria. Whole genome alignment revealed the conserved nature of the genomes. Using codon adaptation index, a set of potentially highly expressed genes in Chlorobium was determined taking ribosomal protein genes as a reference. A sizeable fraction of the potentially highly expressed (PHX) genes in the COG categories were related to metabolism. Quite fascinatingly, some of the genes associated with nitrogen fixation and photosynthesis like hydrogenases, nitrogenase iron protein complexes, bacteriochlorophylls, chlorosomes etc. were also PHX. These results offer insights into the survival patterns of these bacteria thriving under stressed conditions and efficiently carrying out two important metabolic processes especially under reduced light and anoxic environments.
Research Journal of Microbiology
Academic Journals Inc., USA
Digital Object Identifier (DOI)
Sur, S., A. K. Bothra, M. Bajwa, L. S. Tisa, and A. Sen. 2008. In silico analysis of the Chlorobium genomes divulge insight on the lifestyle of the bacteria. Res. J. of Microbiol. 3:600-613