Abstract
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.
Highlights
The genus Streptomyces includes Gram-positive filamentous growing soil bacteria with an extraordinarily high G + C content (Bentley et al, 2002)
7,472 CDS were annotated in the S. lividans TK24 genome (Table 1), compared to 7,361 predicted CDS in the previous annotation (Rückert et al, 2015)
Bioreactor experiments are performed in minimal medium (10 g L1 glucose, 3 g L1 (NH4)2SO4, 2.6 g L1 K2HPO4, 1.8 g L1 NaH2PO4, 0.6 g L1 MgSO4 x 7H2O, 1 mg L1 ZnSO4 x 7H2O, 1 mg L1 FeSO4 x 7H2O, 1 mg L1 CaCl2, 1 mg L1 MnCl2 x 4H2O) and minimal medium supplemented with casamino acids (5 g.L-1 Casamino Acids Technical)
Summary
The genus Streptomyces includes Gram-positive filamentous growing soil bacteria with an extraordinarily high G + C content (Bentley et al, 2002). Streptomyces spp. are well known for their potential to produce secondary metabolites such as antibiotics. Important representatives of this genus are Streptomyces coelicolor A3(2) and Streptomyces lividans. They are the best-characterized Streptomyces strains and serve as model organisms (Hopwood, 1999). S. lividans TK24 is a plasmid-free, streptomycin-resistant derivative of the strain S. lividans 66 (Hopwood et al, 1983) and is often used as a host for cloning or heterologous expression and secretion of proteins or production of enzymes involved in antibiotic production (Hopwood et al, 1995; Bibb, 2005; Hamed et al, 2018)
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