Variation in synonymous codon usage in Paenibacillus sp. 32O-W genome.

Sushanta Deba,Surajit Basak

doi:10.6026/97320630012396

Abstract

Paenibacillus sp. 32O-W, which is attributed for biodesulfurization of petroleum, has 56.34% genomic G+C content. Correspondence analysis on Relative Synonymous Codon Usage (RSCU) of the Paenibacillus sp. 32O-W genome has revealed the two different trends of codon usage variation. Two sets of genes have been identified representing the two distinct pattern of codon usage in this bacterial genome. We have measured several codon usage indices to understand the influencing factors governing the differential pattern of codon usage variation in this bacterial genome. We also observed significant differences in many protein properties between the two gene sets (e.g., hydrophobicity, protein biosynthetic cost, protein aggregation propensity). The compositional difference between the two sets of genes and the difference in their potential gene expressivity are the driving force for the differences in protein biosynthetic cost and aggregation propensity. Based on our results we argue that codon usage variation in Paenibacillus sp. 32O-W genome is actually influenced by both mutational bias and translational selection.

Highlights

Though Paenibacillus sp. 32O-W, cannot metabolize derivatives of dibenzothiophene but surprisingly together with Paenibacillus napthalenovorans 32O-Y, able to metabolize derivatives of dibenzothiophene even in a advanced speed than that of Paenibacillus napthalenovorans 32O-Y alone [1]
Gene sequences Complete coding sequences (CDS) of Paenibacillus sp. 32O-W genome were retrieved from Gene bank (CP013653)
Indices of codon usage The extent of codon bias of an individual gene were measured by obtaining the values of effective number of codon (NC) providing the values ranging from 20 for the gene with extreme bias using only one codon per amino acid, to 61 for a gene using all the codons allotted for each amino acid randomly with no bias

Summary

Introduction

Though Paenibacillus sp. 32O-W, cannot metabolize derivatives of dibenzothiophene but surprisingly together with Paenibacillus napthalenovorans 32O-Y, able to metabolize derivatives of dibenzothiophene even in a advanced speed than that of Paenibacillus napthalenovorans 32O-Y alone [1]. Research on synonymous codon usage gives the information about the molecular evolution of individual gene, data obtained from the research are being utilized to develop algorithms for gene recognition, to design DNA primers and discern the events of Horizontal gene transfer [2]. Several earlier studies suggested those different varieties of factors contributing to the biased usage of synonymous codons such as gene length, proteins secondary structure and gene density, CpG islands, gene expression level and other things. To date studies revealed that the two major phenomena determine the codon usage was mutational bias or natural selection there is no any unified theory describing codon usage. Varying strength of selection acting on evolutionarily conserved amino acid residues exhibits stronger bias. Weaker codon usage bias observed in evolutionary variable residues [3,4]

Methods

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Discussion

Conclusion