Title

Genomic heterogeneity within conserved metabolic pathways of Arthrobacter species - a bioinformatic approach

Authors

Ayon Pal¹, Uttam Kumar Mondal², Subhasis Mukhopadhyay³, Asim Kumar Bothra²*

Affiliation

¹Department of Botany, Raiganj College (University College), Raiganj-733134, Uttar Dinajpur, West Bengal, India; ²Cheminformatics Bioinformatics Laboratory, Department of Chemistry, Raiganj College (University College), Raiganj-733134, Uttar Dinajpur, West Bengal, India; ³Department of Bio-Physics, Molecular Biology and Bioinformatics, University of Calcutta, 92, APC Road, Kolkata-700009, West Bengal, India;

Email

asimbothra@gmail.com; *Corresponding author

Article Type

Hypothesis

Date

Received November 11, 2010; Accepted January 05, 2011; Published February 15, 2011

A comparative genomic analysis of three species of the soil bacterium Arthrobacter was undertaken with specific emphasis on genes involved in important and core energy metabolism pathways like glycolysis and amino acid metabolism. During the course of this study, it was revealed that codon bias of a particular species, namely Arthrobacter aurescens TC1, is significantly lower than that of the other two species A. chlorophenolicus A6 and Arthrobacter sp. FB24. The codon bias was also found to be negatively correlated with gene expression level which is determined by computing codon adaptation index of the genes. Uniformity in codon usage pattern among three species is evident in terms of genes which has high codon bias and multifunctional nature. Further, it was observed that this trend is present amongst the genes of important metabolic pathways, such as glycolysis and amino acid metabolism. The evolutionary divergence of the pathway gene sequences was calculated and was found to be equivalent in nature in the case of Arthrobacter sp. FB24 and Arthrobacter chlorophenolicus A6, but turned out to be dissimilar in the case of Arthrobacter aurescens TC1. A strong correlation between synonymous substitution rate and effective codon number or Nc was also observed. These observations clearly point out that the genes having low bias, in Arthrobacter aurescens TC1, and even of those that are part of highly conserved metabolic pathways like glycolysis and amino acid ensemble pathways have undergone a different type of evolution and might be subjected to positive selection pressure in comparison with Arthrobacter sp. FB24 and Arthrobacter chlorophenolicus A6. 

Citation

Pal et al. Bioinformation 5(10): 446-454 (2011)

Edited by

N Srinivasan

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.