title: A genetic and bioinformatic analysis of Streptomyces coelicolor genes containing TTA codons, possible targets for regulation by a developmentally significant tRNA.
abstract: 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.
authors.affiliation: State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
authors.forename: Wencheng
authors.initials: W
authors.lastname: Li
authors.forename: Jing
authors.initials: J
authors.lastname: Wu
authors.forename: Weixin
authors.initials: W
authors.lastname: Tao
authors.forename: Chunhua
authors.initials: C
authors.lastname: Zhao
authors.forename: Yemin
authors.initials: Y
authors.lastname: Wang
authors.forename: Xinyi
authors.initials: X
authors.lastname: He
authors.forename: Govind
authors.initials: G
authors.lastname: Chandra
authors.forename: Xiufen
authors.initials: X
authors.lastname: Zhou
authors.forename: Zixin
authors.initials: Z
authors.lastname: Deng
authors.forename: Keith F
authors.initials: KF
authors.lastname: Chater
authors.forename: Meifeng
authors.initials: M
authors.lastname: Tao
mesh_terms: D003062:Codon; D019295:Computational Biology; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D016297:Mutagenesis, Site-Directed; D012343:RNA, Transfer / Q000378:metabolism* / Q000502:physiology; D050436:Regulatory Elements, Transcriptional; D017422:Sequence Analysis, DNA; D013302:Streptomyces / Q000235:genetics; D048372:Streptomyces coelicolor / Q000235:genetics* / Q000254:growth & development
chemical_list: D003062:Codon; D012343:RNA, Transfer