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.
Saubashya Sur, Asim K Bothra, Manprit Bajwa, Louis S. Tisa and Arnab Sen, 2008. In silico Analysis of Chlorobium Genomes Divulge Insights into the Lifestyle of the Bacteria. Research Journal of Microbiology, 3: 600-613.