genetic and bioinformatic analysis of Streptomyces coelicolor genes containing TTA codons, possible targets for regulation by a developmentally significant tRNA

• Published in: FEMS microbiology letters Vol. 266; no. 1; pp. 20 - 28
• Main Authors: Li, Wencheng, Wu, Jing, Tao, Weixin, Zhao, Chunhua, Wang, Yemin, He, Xinyi, Chandra, Govind, Zhou, Xiufen, Deng, Zixin, Chater, Keith F, Tao, Meifeng
• Format: Journal Article
• Language: English
• Published: Oxford, UK Oxford, UK : Blackwell Publishing Ltd 2007; Blackwell Publishing Ltd; Blackwell; Oxford University Press
• Subjects: Bacteriology; bioinformatics; Biological and medical sciences; Biological evolution; bldA; Chromosomes; Codon; codon adaptation index; Codons; Computational Biology; Evolutionary genetics; Fundamental and applied biological sciences. Psychology; Gene expression; Gene Expression Regulation, Bacterial; Genes; Genes, Bacterial; Genetic analysis; Genetics; Genome, Bacterial; Genomes; Microbiology; mRNA; Mutagenesis, Site-Directed; Regulatory Elements, Transcriptional; RNA, Transfer - metabolism; RNA, Transfer - physiology; Sequence Analysis, DNA; Streptomyces; Streptomyces - genetics; Streptomyces avermitilis; Streptomyces coelicolor; Streptomyces coelicolor - genetics; Streptomyces coelicolor - growth & development; tRNA; TTA codon; TTA codon; bioinformatics; codon adaptation index; Streptomycetaceae; tRNA; Streptomyces coelicolor; bldA; Actinomycetales; Codon; Gene; Bacteria; Genetics; Actinomycetes; Adaptation
• ISSN: 0378-1097; 1574-6968
• DOI: 10.1111/j.1574-6968.2006.00494.x

The rarest codon in the high G+C genome of Streptomyces coelicolor is TTA, corresponding in mRNA to the UUA codon that is recognized by a developmentally important tRNA encoded by the bldA gene. There are 145 TTA-containing genes in the chromosome of S. coelicolor. Only 42 of these are represented in the genome of Streptomyces avermitilis, among which only 12 have a TTA codon in both species. The TTA codon is less represented in housekeeping genes and orthologous genes, and is more represented in functional-unknown, extrachromosomal or weakly expressed genes. Twenty one TTA-containing chromosomal genes in S. coelicolor were disrupted, including 12 of the 42 genes that are common to both S. avermitillis and S. coelicolor. None of the mutant strains showed any obvious phenotypic differences from the wild-type strain under tested conditions. Possible reasons for this, and the role and evolution of the observed distribution of TTA codons among Streptomyces genes were discussed.