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Research Article Volume 8 Issue 2
Codon usage bias and peptide properties of Pseudomonas Balearica DSM 6083T
Maurice HT Ling, Argho Maitra
Department of Applied Sciences, Northumbria University, UK
School of Life Sciences, Management Development Institute of Singapore, Singapore
HOHY PTE LTD, Singapore
Received: March 25, 2019 | Published: April 15, 2019
Citation: Maitra A, Ling MHT. Codon usage bias and peptide properties of Pseudomonas Balearica DSM 6083T . MOJ Proteomics Bioinform. 2019;8(2):27-36. DOI: 10.15406/mojpb.2019.08.00263
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
©2019 Maitra, et al. This is an open access article distributed under the terms of the, which permits unrestricted use, distribution, and build upon your work non-commercially.