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

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.

Microparticles enhance the formation of seven major classes of natural products in native and metabolically engineered actinobacteria through accelerated morphological development

“…Total RNA was isolated using the Quick-RNA Miniprep Plus kit (Zymo Research). After DNase treatment, the obtained RNA was The obtained reads were mapped to the S. lividans D/G2 genome sequence (CP071123), which is based on the re-annotated S. lividans TK24 genome (Droste et al, 2021), using BOWTIE2 under standard settings (Langmead & Salzberg, 2012), except for increasing the maximally allowed distance for paired reads to 600 bases. To visualize read alignments, the software READXPLORER 2.2.3 (Hilker et al, 2016) was used.…”

Identification and characterization of a strong constitutive promoter stnYp for activating biosynthetic genes and producing natural products in streptomyces

“…The promoter sequence plays a critical role in promoter activity [ 26 ]. The structure of the promoter stnYp 339 was analyzed based on the TSS and translation start sites (TLSs) in the genome sequence of S. coelicolor A3 and S. lividans TK24 [ 27 , 28 ]. The results revealed conserved − 10 (TAnnnT) and weakly conserved − 35 motifs (nTGACn) in the promoter region of the stnY gene.…”

“…The σ factor recognizes the core promoter region, which typically consists of two conserved motifs at nucleotide positions − 35 and − 10 relative to the TSS [ 37 ]. Based on the analysis of the TSS and TLS in the genome of S. coelicolor A3 and S. lividans TK24, the sequence of conserved − 10 motifs is TAnnnT, and the sequence of weakly conserved − 35 motifs is nTGACn [ 27 , 28 ]. The core promoter region of stnYp is TAGCAT in the − 10 motifs and TTGGCG in the − 35 motifs, which is quite similar to the consensus sequence recognized by the σ factor HrdB in Streptomyces [ 30 ].…”

Enhanced protein secretion in reduced genome strains ofStreptomyces lividans

“…The number of secondary metabolic gene clusters varies between Streptomyces species, e.g. 37 in S. avermitilis (22), 29 in S. lividans TK24 and S. coelicolor A3 (2) (22)(23)(24). The chemical structure of <30% of the synthesized compounds has been elucidated (25).…”