Comparative evolutionary genomics of Corynebacterium with special reference to codon and amino acid usage diversities

Abstract

The present study has been aimed to the comparative analysis of high GC composition containing Corynebacterium genomes and their evolutionary study by exploring codon and amino acid usage patterns. Phylogenetic study by MLSA approach, indel analysis and BLAST matrix differentiated Corynebacterium species in pathogenic and non-pathogenic clusters. Correspondence analysis on synonymous codon usage reveals that, gene length, optimal codon frequencies and tRNA abundance affect the gene expression of Corynebacterium. Most of the optimal codons as well as translationally optimal codons are C ending i.e. RNY (R-purine, N-any nucleotide base, and Y-pyrimidine) and reveal translational selection pressure on codon bias of Corynebacterium. Amino acid usage is affected by hydrophobicity, aromaticity, protein energy cost, etc. Highly expressed genes followed the cost minimization hypothesis and are less diverged at their synonymous positions of codons. Functional analysis of core genes shows significant difference in pathogenic and non-pathogenic Corynebacterium. The study reveals close relationship between non-pathogenic and opportunistic pathogenic Corynebaterium as well as between molecular evolution and survival niches of the organism.

Biosynthetic energy cost of potentially highly expressed proteins vary with niche in selected actinobacteria

“…UUC, UAC, AUC, AAG were more used for phynylalanine, tyrosine, isoleucine, and lysine, respectively and they are C or G ending codons. Since, actinobacteria is well‐known for their GC enrichment, a direct relation between the codon usage and compositional constrain is revealed which may have an implication on their niche adaptability .…”

Comprehensive analysis of genomic variation, pan-genome and biosynthetic potential of Corynebacterium glutamicum strains

“…casei LMG S-19264 (3.11 Mbp) and C . efficiens YS-314 (3.15 Mbp) [ 66 ]. Moreover, the average number of genes (3197) was also higher than C .…”

“…casei LMG S-19264 (2872) and C . efficiens YS-314 (3064) [ 66 ]. On the other hand, the average GC content was lower among C .…”

The Genus Corynebacterium in the Genomic Era

“…The pan-genome is constituted by the core genome, which configures the genes present among all analyzed strains; the accessory genome that shares genes between two or more, but not all, strains and includes the genes the bacteria needs to survive in a specific environment, in addition to species-specific genes belonging to a single lineage, which can be acquired via horizontal transfer [37,39]. The representatives of the genus Corynebacterium become an interesting object of studies of comparative genomics and evolution, due to its diverse lifestyles [40].…”

“…These factors reveal the type of selective pressure in eukaryotic and prokaryotic genes. In order to understand the molecular evolution of the genus Corynebacterium, comparative analyzes of G + C content and codon use were carried out relating different species, revealing evolutionary relationships that allowed divergence between the groups of pathogenic and nonpathogenic corynebacteria [40].…”