Evolutionary Forces in Shaping the Codon and Amino Acid Usages inBlochmannia floridanus

Abstract

Endosymbiotic relationship has great effect on ecological system. Codon and amino acid usages bias of endosymbiotic bacteria Blochmannia floridanus (whose host is an ant Camponotus floridanus) was investigated using experimentally known genes of this organism. Correspondence Analysis on RSCU values show that there exists only one single explanatory major axis that is linked to the strand specific mutational biases. Majority of the genes have a tendency to concentrate on the leading strand, which may be related to the adaptive property related to the replication mechanisms. Amino acid usages were markedly different between the highly and lowly expressed genes in this organism and in particular, GC rich amino acids were found to occur significantly higher in highly expressed genes than the lowly expressed genes. Comparative analyses of the orthologous genes of Escherichia coli and Blochmannia floridanus show that highly expressed genes are significantly more conserved than lowly expressed genes. Based on our results we concluded that strand specific mutational bias is strongly operational in selecting the codon usage in this organism. Replicational-transcriptional selection can be invoked from the presence of majority of highly expressed genes in the leading strand. Conservation of GC rich amino acids in the highly expressed genes to its ancestor is the major source of variation in amino acid usages in the organism. Hydrophobicity of the genes is the second major source in differentiating the genes according to their amino acid usages in this organism.

Gene expression levels influence amino acid usage and evolutionary rates in endosymbiotic bacteria

“…c) AT-enrichment is mitigated in a fraction of genes thought to be under greater selective constraint. This pattern seems to reflect greater conservation of these genes since divergence from free-living relatives (Herbeck et al, 2003;Rispe et al, 2004;Banerjee et al, 2004). The alternative explanation, i.e.…”

“…While the overall frequency of amino acid changes is known to be lower at PHEG because these genes are more conserved, it remains unclear whether PHEG and PLEG have the same configuration of changes (Herbeck et al, 2003;Banerjee et al, 2004). To more clearly distinguish the effects of conservation and selection on particular amino acids, we extended the previous analyses to include additional loci, other endosymbiont genomes, and amino acids that are AT-rich in EK12 as well and for HEG and LEG.…”

“…a) The strand specific mutational bias is the dominant source of codon usage variation in Buchnera (Rispe et al, 2004) and Bfl (Banerjee et al, 2004). b) The majority of putatively highly expressed genes are situated on the leading strand in Buchnera (Rispe et al, 2004) and Bfl (Banerjee et al, 2004).…”

“…b) The majority of putatively highly expressed genes are situated on the leading strand in Buchnera (Rispe et al, 2004) and Bfl (Banerjee et al, 2004). Thus, a residual effect of replicational or translational selection can be hypothesized.…”

“…Analysis of amino acids substitutions between endosymbionts and an inferred ancestor can shed light on selective processes that shape these genomes, and has been performed for Wgl (Herbeck et al, 2003) and Bfl (Banerjee et al, 2004). However, in these studies, only few genes were used possibly lacking statistical power.…”