Title

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

Authors

Sushanta Deba, Surajit Basak*a,b

Affiliation

aDepartment of Molecular Biology & Bioinformatics, Tripura University, Suryamaninagar, Tripura-799022, India; bBioinformatics Centre, Tripura University, Suryamaninagar, Tripura-799022, India

Email

Surajit Basak – E-mail: basaksurajit@gmail.com; *Corresponding author

Article Type

Hypothesis

Date

Received September 22, 2106; Accepted November 5, 2016; Published December 1, 2016

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.

Keywords:

Variation, synonymous codon usage, Paenibacillus, genome

Citation

Deb & Basak, Bioinformation 12(11): 396-399 (2016)

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.