Extensive Reannotation of the Genome of the Model Streptomycete Streptomyces lividans TK24 Based on Transcriptome and Proteome Information

Droste J, Rückert C, Kalinowski J, Hamed MB, Anné J, Simoens K, Bernaerts K, Economou A, Busche T (2021)
Frontiers in Microbiology 12: 604034.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Droste, JulianUniBi; Rückert, ChristianUniBi ; Kalinowski, JörnUniBi; Hamed, Mohamed Belal; Anné, Jozef; Simoens, Kenneth; Bernaerts, Kristel; Economou, Anastassios; Busche, TobiasUniBi
Abstract / Bemerkung
Streptomyces lividansTK24 is a relevant Gram-positive soil inhabiting bacterium and one of the model organisms of the genusStreptomyces. It is known for its potential to produce secondary metabolites, antibiotics, and other industrially relevant products.S. lividansTK24 is the plasmid-free derivative ofS. lividans66 and a close genetic relative of the strainStreptomyces coelicolorA3(2). In this study, we used transcriptome and proteome data to improve the annotation of theS. lividansTK24 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) ofS. lividansTK24 revealed 17% leaderless transcripts. Severalcis-regulatory elements, like riboswitches or attenuator structures could be detected in the 5′-UTRs. TheS. lividansTK24 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 strainStreptomyces coelicolorA3(2) revealed a high degree of similarity. This study presents an extensive reannotation of theS. lividansTK24 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.
Stichworte
Streptomyces lividans TK24; reannotation; promoter; RNA sequencing (RNA-seq); cis-regulatory elements; attenuation; secondary metabolite gene clusters
Erscheinungsjahr
2021
Zeitschriftentitel
Frontiers in Microbiology
Band
12
Art.-Nr.
604034
eISSN
1664-302X
Finanzierungs-Informationen
Open-Access-Publikationskosten wurden durch die Universität Bielefeld gefördert.
Page URI
https://pub.uni-bielefeld.de/record/2954272

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Droste J, Rückert C, Kalinowski J, et al. Extensive Reannotation of the Genome of the Model Streptomycete Streptomyces lividans TK24 Based on Transcriptome and Proteome Information. Frontiers in Microbiology. 2021;12: 604034.
Droste, J., Rückert, C., Kalinowski, J., Hamed, M. B., Anné, J., Simoens, K., Bernaerts, K., et al. (2021). Extensive Reannotation of the Genome of the Model Streptomycete Streptomyces lividans TK24 Based on Transcriptome and Proteome Information. Frontiers in Microbiology, 12, 604034. https://doi.org/10.3389/fmicb.2021.604034
Droste, J., Rückert, C., Kalinowski, J., Hamed, M. B., Anné, J., Simoens, K., Bernaerts, K., Economou, A., and Busche, T. (2021). Extensive Reannotation of the Genome of the Model Streptomycete Streptomyces lividans TK24 Based on Transcriptome and Proteome Information. Frontiers in Microbiology 12:604034.
Droste, J., et al., 2021. Extensive Reannotation of the Genome of the Model Streptomycete Streptomyces lividans TK24 Based on Transcriptome and Proteome Information. Frontiers in Microbiology, 12: 604034.
J. Droste, et al., “Extensive Reannotation of the Genome of the Model Streptomycete Streptomyces lividans TK24 Based on Transcriptome and Proteome Information”, Frontiers in Microbiology, vol. 12, 2021, : 604034.
Droste, J., Rückert, C., Kalinowski, J., Hamed, M.B., Anné, J., Simoens, K., Bernaerts, K., Economou, A., Busche, T.: Extensive Reannotation of the Genome of the Model Streptomycete Streptomyces lividans TK24 Based on Transcriptome and Proteome Information. Frontiers in Microbiology. 12, : 604034 (2021).
Droste, Julian, Rückert, Christian, Kalinowski, Jörn, Hamed, Mohamed Belal, Anné, Jozef, Simoens, Kenneth, Bernaerts, Kristel, Economou, Anastassios, and Busche, Tobias. “Extensive Reannotation of the Genome of the Model Streptomycete Streptomyces lividans TK24 Based on Transcriptome and Proteome Information”. Frontiers in Microbiology 12 (2021): 604034.
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2021-04-27T11:52:48Z
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