Dataset Information

The Transcription Unit Architecture of Streptomyces lividans TK24.

ABSTRACT: Streptomyces lividans is an attractive host for production of heterologous proteins and secondary metabolites of other Streptomyces species. To fully harness the industrial potential of S. lividans, understanding its metabolism and genetic regulatory elements is essential. This study aimed to determine its transcription unit (TU) architecture and elucidate its diverse regulatory elements, including promoters, ribosome binding sites, 5'-untranslated regions, and transcription terminators. Total 1,978 transcription start sites and 1,640 transcript 3'-end positions were identified, which were integrated to determine 1,300 TUs, consistent with transcriptomic profiles. The conserved promoter sequences were found as 5'-TANNNT and 5'-TGAC, representing the -10 and -35 elements, respectively. Analysis of transcript 3'-end positions revealed the presence of distinctive terminator sequences and the RNA stem structure responsible for the determination of the 3'-boundary of a transcript. Functionally related genes are likely to be regulated simultaneously by using similar promoters and being transcribed as a poly-cistronic TU. Poly-cistronic TUs were further processed or alternatively transcribed into multiple TUs to fine-regulate individual genes in response to environmental conditions. The TU information and regulatory elements identified will serve as invaluable resources for understanding the complex regulatory mechanisms of S. lividans and to elevate its industrial potential.

SUBMITTER: Lee Y

PROVIDER: S-EPMC6742748 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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The Transcription Unit Architecture of Streptomyces lividans TK24.

Lee Yongjae Y Lee Namil N Jeong Yujin Y Hwang Soonkyu S Kim Woori W Cho Suhyung S Palsson Bernhard O BO Cho Byung-Kwan BK

Frontiers in microbiology 20190906

Streptomyces lividans is an attractive host for production of heterologous proteins and secondary metabolites of other Streptomyces species. To fully harness the industrial potential of S. lividans, understanding its metabolism and genetic regulatory elements is essential. This study aimed to determine its transcription unit (TU) architecture and elucidate its diverse regulatory elements, including promoters, ribosome binding sites, 5'-untranslated regions, and transcription ...[more]

PMID: 31555254

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Project description:Streptomyces lividans TK24 is a relevant Gram-positive soil inhabiting bacterium and one of the model organisms of the genus Streptomyces. It is known for its potential to produce secondary metabolites, antibiotics, and other industrially relevant products. S. lividans TK24 is the plasmid-free derivative of S. lividans 66 and a close genetic relative of the strain Streptomyces coelicolor A3(2). In this study, we used transcriptome and proteome data to improve the annotation of the S. lividans TK24 genome. The RNA-seq data of primary 5'-ends of transcripts were used to determine transcription start sites (TSS) in the genome. We identified 5,424 TSS, of which 4,664 were assigned to annotated CDS and ncRNAs, 687 to antisense transcripts distributed between 606 CDS and their UTRs, 67 to tRNAs, and 108 to novel transcripts and CDS. Using the TSS data, the promoter regions and their motifs were analyzed in detail, revealing a conserved -10 (TAnnnT) and a weakly conserved -35 region (nTGACn). The analysis of the 5' untranslated region (UTRs) of S. lividans TK24 revealed 17% leaderless transcripts. Several cis-regulatory elements, like riboswitches or attenuator structures could be detected in the 5'-UTRs. The S. lividans TK24 transcriptome contains at least 929 operons. The genome harbors 27 secondary metabolite gene clusters of which 26 could be shown to be transcribed under at least one of the applied conditions. Comparison of the reannotated genome with that of the strain Streptomyces coelicolor A3(2) revealed a high degree of similarity. This study presents an extensive reannotation of the S. lividans TK24 genome based on transcriptome and proteome analyses. The analysis of TSS data revealed insights into the promoter structure, 5'-UTRs, cis-regulatory elements, attenuator structures and novel transcripts, like small RNAs. Finally, the repertoire of secondary metabolite gene clusters was examined. These data provide a basis for future studies regarding gene characterization, transcriptional regulatory networks, and usage as a secondary metabolite producing strain.

Dataset Information

The Transcription Unit Architecture of Streptomyces lividans TK24.

Publications

The Transcription Unit Architecture of <i>Streptomyces lividans</i> TK24.

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