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Codon usage bias and peptide properties of Pseudomonas Balearica DSM 6083T


MOJ Proteomics & Bioinformatics
Argho Maitra,1,2 Maurice HT Ling1,2,3

Abstract

Pseudomonas balearica DSM 6083T has potential applications in bioremediation and its genome is recently sequenced. Codon usage bias is important in the study of evolutionary pressures on the organism and physical properties of peptides may elucidate functional peptides. However, both have not been studied for P. balearica DSM 6083T. Here, we investigated the codon usage bias and peptide properties of the 4,050 coding sequences in P. balearica. Codon usage analysis suggests that all preferred codons were either G or C ending. There is a skew towards smaller peptides and all peptide properties (pI, aromaticity, hydropathy, and instability) are correlated (|r| >0.102, p-value <7 x 10-11). %GC is correlated (|r| >0.122, p-value <6 x 10-15) to peptide length, aromaticity, hydropathy, and instability. Peptide length is correlated (|r| <0.057, p-value <0.0003) to pI, aromaticity, and instability. Codon usage is correlated (r<-0.042, p-value <0.0075) with all peptide properties while amino acid usage is correlated (r<-0.084, p-value <8 x 10-8) to all peptide properties except instability. A substantial proportion (26.9%) of genes show significantly different codon and amino acid ratios compared to the genomic and proteomic averages respectively (p-value <1.2 x 10-5), suggesting potential exogenous origins. These results suggest a complex interplay of metagenomic environment and various genomic/proteomic properties in shaping the evolution of P. balearica DSM 6083T.

Keywords

Pseudomonas balearica, aromaticity, hydropathy,bioremediation, genomics, genomics, codon usage bias, guanine-cytosine, tryptophan, Bonferroni correction, physical properties of peptides, RNAs

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