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

Ayon Pal,Subhasis Mukhopadhyay,Uttam Kumar Mondal,Asim Kumar Bothra

doi:10.6026/97320630005446

Abstract

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.

Highlights

Arthrobacter is a ubiquitous soil-dwelling eubacterium [1]
The depth and width of pathway molecular network interaction data made available through pathway informatics databases like KEGG [3], BioCyc, MetaCyc [4] and other such endeavours have paved the way for comparing organisms, at the whole genome level and across the core biochemical and biophysical metabolic pathways
The nucleotide sequences encoding the information for the production of proteins and enzymes involved in amino acid metabolism pathways and hexose degradation by EMP pathway of glycolysis were sorted out using references from pathway metabolic information database KEGG [3] and MetaCyc [4]

Summary

Background

Arthrobacter is a ubiquitous soil-dwelling eubacterium [1]. They are found in extreme environments, such as deep subsurface soils, arctic sea and radioactive waste tanks. A comparative genomic study of these three species at the level of metabolic pathways was performed to obtain a better insight about the similarities and dissimilarities in characteristics such as codon usage, gene expression, evolutionary divergence and nature of selection in these closely related species of Arthrobacter. In order to obtain an insight about the evolutionary divergence of the gene sequences of the three different Arthrobacter species together with the nature of the selection forces acting on them, we calculated the synonymous and non-synonymous substitution rates of the glycolysis and amino acid metabolism pathway gene sequences. Multiple sequence alignment was carried out using ClustalX [18] for all the genes involved in glycolysis, together with a number of genes involved in amino acid metabolism and a few randomly selected genes from the genome of the three different species of Arthrobacter. The curated alignment data files were used as input for the program DnaSP [19] to calculate the DNA sequence variation at synonymous (Ks) and nonsynonymous sites (Ka) [20]

Results and Discussion

Conclusion:

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