Comparative analysis of codon usage patterns and identification of predicted highly expressed genes in fiveSalmonellagenomes

Abstract

Purpose: To anlyse codon usage patterns of Þ ve complete genomes of Salmonella, predict highly expressed genes, examine horizontally transferred pathogenicity-related genes to detect their presence in the strains, and scrutinize the nature of highly expressed genes to infer upon their lifestyle. Methods: Protein coding genes, ribosomal protein genes, and pathogenicity-related genes were analysed with Codon W and CAI (codon adaptation index) Calculator. Results: Translational efÞ ciency plays a role in codon usage variation in Salmonella genes. Low bias was noticed in most of the genes. GC3 (guanine cytosine at third position) composition does not inß uence codon usage variation in the genes of these Salmonella strains. Among the cluster of orthologous groups (COGs), translation, ribosomal structure biogenesis [J], and energy production and conversion [C] contained the highest number of potentially highly expressed (PHX) genes. Correspondence analysis reveals the conserved nature of the genes. Highly expressed genes were detected. Conclusions: Selection for translational efÞ ciency is the major source of variation of codon usage in the genes of Salmonella. Evolution of pathogenicity-related genes as a unit suggests their ability to infect and exist as a pathogen. Presence of a lot of PHX genes in the information and storage-processing category of COGs indicated their lifestyle and revealed that they were not subjected to genome reduction.

Sequence variability of Rhizobiales orthologs and relationship with physico-chemical characteristics of proteins

“…The differences in evolutionary rates of genes have been adscribed to functional constraints, but a debate is open to clarify the importance of translational costs, reflected in misfolding [47], structural factors [48,49], and even pleiotropy [50], as the factors influencing the evolution of proteins. The compositional and adaptation codon bias in genes are important characteristics of GC-rich organisms, such as the Rhizobiales, because these traits are related to increased expressivity [51-53]. We found that low dN genes had high CAI values (not shown) showing, as others have, that codon bias is a selective force in these genes and a negative correlation of expressivity and evolutionary rates exists [54-56].…”