pubmed.ncbi.nlm.nih.gov

Genomic heterogeneity within conservedmetabolic pathways of Arthrobacter species - a bioinformatic approach - PubMed

  • ️Sat Jan 01 2011

Genomic heterogeneity within conservedmetabolic pathways of Arthrobacter species - a bioinformatic approach

Ayon Pal et al. Bioinformation. 2011.

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.

Keywords: Actinomycetales; Amino acid metabolism; Arthrobacter aurescensTC1; Arthrobacter chlorophenolicusA6; Arthrobactersp. FB24; Atrazine; Codon adaptation index; Correspondence analysis; Effective codon number; GC3; Glycolysis; KEGG; Ka; Ks; MetaCyc; Metabolic pathways; Nc; Positive selection; RSCU.

PubMed Disclaimer

Figures

Figure 1
Figure 1

Nc plot of amino acid metabolism pathway (AAM) and glycolysis pathway (Gly) genes of Arthrobacter aurescens TC1 (􀂋), A. chlorophenolicus A6 (􀂄) and Arthrobacter sp. FB24 (􀁓).

Figure 2
Figure 2

Correspondence analysis on RSCU of glycolysis of three species of Arthrobacter. TC1= A. aurescens TC1; A6 = A. chlorophenolicus A6; FB24 = Arthrobacter sp. FB24.

Figure 3
Figure 3

Correspondence analysis on RSCU of amino acid metabolism of three species of Arthrobacter. TC1= A. aurescens TC1; A6 = A. chlorophenolicus A6; FB24 = Arthrobacter sp. FB24.

Figure 4
Figure 4

The rate of synonymous nucleotide substitution (Ks) of selected genes from the whole genome (Genome) [4a], glycolysis (Gly) [4b] and amino acid metabolism (AAM) [4c] of Arthrobacter sp. FB24 (=FB24), A. chlorophenolicus A6 (=A6) and A. aurescens TC1 (=TC1) plotted against the mean Nc of the respective pathways.

Figure 5
Figure 5

The rate of non-synonymous nucleotide substitution (Ka) of selected genes from the whole genome (Genome) [5a], glycolysis (Gly) [5b] and amino acid metabolism (AAM) [5c] of Arthrobacter sp. FB24 (=FB24), A. chlorophenolicus A6 (=A6) and A. aurescens TC1 (=TC1) plotted against the mean Nc of the respective pathways.

Similar articles

Cited by

References

    1. http://genome.jgi-psf.org/art_f/art_f.home.html.
    1. Mongodin E, et al. PLoS Genet. 2006;2:2094. - PMC - PubMed
    1. Kanehisa M, et al. Nucleic Acids Res. 2008;36:D480. - PMC - PubMed
    1. Karp P, et al. Nucleic Acids Res. 2002;30:59. - PMC - PubMed
    1. Ashida Y, et al. IPSJ Digit Cour. 2008;4:228.

LinkOut - more resources