title: Codon usage bias in phylum Actinobacteria: relevance to environmental adaptation and host pathogenicity.
abstract: Actinobacteria are Gram-positive bacteria commonly found in soil, freshwater and marine ecosystems. In this investigation, bias in codon usages of ninety actinobacterial genomes was analyzed by estimating different indices of codon bias such as Nc (effective number of codons), SCUO (synonymous codon usage order), RSCU (relative synonymous codon usage), as well as sequence patterns of codon contexts. The results revealed several characteristic features of codon usage in Actinobacteria, as follows: 1) C- or G-ending codons are used frequently in comparison with A- and U ending codons; 2) there is a direct relationship of GC content with use of specific amino acids such as alanine, proline and glycine; 3) there is an inverse relationship between GC content and Nc estimates, 4) there is low SCUO value (<0.5) for most genes; and 5) GCC-GCC, GCC-GGC, GCC-GAG and CUC-GAC are the frequent context sequences among codons. This study highlights the fact that: 1) in Actinobacteria, extreme GC content and codon bias are driven by mutation rather than natural selection; (2) traits like aerobicity are associated with effective natural selection and therefore low GC content and low codon bias, demonstrating the role of both mutational bias and translational selection in shaping the habitat and phenotype of actinobacterial species.
authors.affiliation: Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India; Department of Zoology, Ramjas College, University of Delhi, Delhi 110 007, India. Electronic address: dev83.sharma@gmail.com.
authors.forename: Devi
authors.initials: D
authors.lastname: Lal
authors.affiliation: Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India; Department of Zoology, Sri Venkateswara College, University of Delhi South Campus, New Delhi 110 021, India. Electronic address: mansiverma20@gmail.com.
authors.forename: Mansi
authors.initials: M
authors.lastname: Verma
authors.affiliation: ARSC, Division of Animal Sciences, Room # S128, University of Missouri, Columbia, MO 65211, USA. Electronic address: behuras@missouri.edu.
authors.forename: Susanta K
authors.initials: SK
authors.lastname: Behura
authors.affiliation: Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India. Electronic address: ruplal@gmail.com.
authors.forename: Rup
authors.initials: R
authors.lastname: Lal
mesh_terms: D039903:Actinobacteria / Q000235:genetics*; D000220:Adaptation, Biological; D001482:Base Composition; D003062:Codon; D009154:Mutation; D014176:Protein Biosynthesis
chemical_list: D003062:Codon
keywords: Actinobacteria; Codon adaptation index; Codon usage; Effective number of codons; Highly expressed genes; Pathogenicity