Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus.

Gudepalya R Rudramurthy,Manikandan Mohan,Reethu Vivekanandam,Panayampalli S Satheshkumar,Rahul Raveendran Nair

doi:10.3390/pathogens10121649

Abstract

Trends associated with codon usage in molluscum contagiosum virus (MCV) and factors governing the evolution of codon usage have not been investigated so far. In this study, attempts were made to decipher the codon usage trends and discover the major evolutionary forces that influence the patterns of codon usage in MCV with special reference to sub-types 1 and 2, MCV-1 and MCV-2, respectively. Three hypotheses were tested: (1) codon usage patterns of MCV-1 and MCV-2 are identical; (2) SCUB (synonymous codon usage bias) patterns of MCV-1 and MCV-2 slightly deviate from that of human host to avoid affecting the fitness of host; and (3) translational selection predominantly shapes the SCUB of MCV-1 and MCV-2. Various codon usage indices viz. relative codon usage value, effective number of codons and codon adaptation index were calculated to infer the nature of codon usage. Correspondence analysis and correlation analysis were performed to assess the relative contribution of silent base contents and significance of codon usage indices in defining bias in codon usage. Among the tested hypotheses, only the second and third hypotheses were accepted.

Highlights

In universal genetic code, any given amino acid except tryptophan and methionine is encoded by a specific set of multi-fold degenerate codons called synonymous codons [1,2]
The present study focused on the genomes of molluscum contagiosum virus (MCV)-1 and MCV-2 due to their higher rates of infectioncausing capabilities among the four sub-types
In light of the fact that MCV has unique strategies to coexist with natural host [45], the present study is focused on testing the following three hypotheses to obtain insight into the co-evolving trend of the MCV genome with the host genome: (1) codon usage patterns of MCV-1 and MCV-2 are identical, (2) SCUB patterns of MCV-1 and MCV-2 slightly deviate from that of human host to avoid affecting the fitness of host, and (3) translational selection predominantly shapes the SCUB of MCV-1 and MCV-2

Summary

Introduction

Any given amino acid except tryptophan and methionine is encoded by a specific set of multi-fold degenerate codons called synonymous codons [1,2]. As an event of mutation which causes replacement of one synonymous codon with another in a given coding region does not modify the amino acid sequence, these mutations are called ‘silent’ [3]. These synonymous changes are seemingly neutral, selection of synonymous codons occurs during the process of evolution as these ‘silent’ changes have many effects on the functioning of a living cell [3]. Despite the fact that selection and mutation still remain as two major explanations in delineating the origin of SCUB (SCU bias) [5,9], several factors of varying intensities contribute to the origin of distinct patterns of SCU within and between genomes [10], for instance, GC content [11,12], rate of gene expression [13,14], mRNA decoding tempo of ribosomes [13], mRNA secondary structure [15,16], mRNA turnover [17,18], co-translational protein folding and translation elongation [19], gene function [20], rate of recombination [21,22], gene length [23,24], codon position [21], habitat stress [25,26] and population size [21]

Methods

Results

Discussion

Conclusion