Deep sequencing-based identification of small non-coding RNAs in<i>Streptomyces coelicolor</i>

Vockenhuber, Michael-Paul; Sharma, Cynthia M.; Statt, Michaela G.; Schmidt, Denis; Xu, Zhenjiang Zech; Dietrich, Sascha; Liesegang, Heiko; Mathews, David H.; Suess, Beatrix

doi:10.4161/rna.8.3.14421

Cited by 82 publications

(111 citation statements)

References 50 publications

(64 reference statements)

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“…3,100 genes may be transcribed at low levels during exponential growth, perhaps from leaky promoters. Antisense transcripts, which have been identified in S. coelicolor and other bacteria (39,41,42), may also contribute to the low-abundance category.…”

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

“…These studies include the use of proteome analysis to examine the response of S. coelicolor to phosphate limitation (37) and to examine overall levels of gene expression in that organism (43) and the use of microarrays to examine the expression of genes involved in differentiation and antibiotic production under various conditions (17, 18, 22-24, 27, 37, 43). Recently, high-throughput cDNA sequencing (RNA-Seq) was used to examine the expression of small noncoding RNAs in S. coelicolor (42).To facilitate the analysis of genes that serve as targets for RNase III regulation of antibiotic production and to obtain more general information about the role of RNase III in the control of gene expression in S. coelicolor, we have performed an RNA-Seq analysis of the transcriptomes of S. coelicolor M145, a parental strain, and JSE1880 (16), an S. coelicolor mutant lacking RNase III. This analysis was extended by using RNA immunoprecipitation to identify specific transcripts that are cleaved by RNase III and to which RNase III may bind without cleavage.…”

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RNA-Seq and RNA Immunoprecipitation Analyses of the Transcriptome of Streptomyces coelicolor Identify Substrates for RNase III

et al. 2012

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RNase III is a key enzyme in the pathways of RNA degradation and processing in bacteria and has been suggested as a global regulator of antibiotic production in Streptomyces coelicolor. Using RNA-Seq, we have examined the transcriptomes of S. coelicolor M145 and an RNase III (rnc)-null mutant of that strain. RNA preparations with reduced levels of structural RNAs were prepared by subtractive hybridization prior to RNA-Seq analysis. We initially identified 7,800 transcripts of known and putative proteincoding genes in M145 and the null mutant, JSE1880, along with transcripts of 21 rRNA genes and 65 tRNA genes. Approximately 3,100 of the protein-coding transcripts were categorized as low-abundance transcripts. For further analysis, we selected those transcripts of known and putative protein-coding genes whose levels changed by >2-fold between the two S. coelicolor strains and organized those transcripts into 16 functional categories. We refined our analysis by performing RNA immunoprecipitation of the mRNA preparation from JSE1880 using a mutant RNase III protein that binds to transcripts but does not cleave them. This analysis identified ca. 800 transcripts that were enriched in the RNA immunoprecipitates, including 28 transcripts whose levels also changed by >2-fold in the RNA-Seq analysis. We compare our results with those obtained by microarray analysis of the S. coelicolor transcriptome and with studies describing the characterization of small noncoding RNAs. We have also used the RNA immunoprecipitation results to identify new substrates for RNase III cleavage.T he double-strand-specific endonuclease RNase III is found in bacteria and eukaryotes (12,25,33). In addition to its general role in RNA processing, RNase III is involved in the regulation of gene expression in Escherichia coli and other bacteria. Thus, RNase III autoregulates its own expression in E. coli and is also involved in the regulation of the expression of the polynucleotide phosphorylase (PNPase) gene, pnp (3, 40). There are a number of other examples of the regulation of gene expression by RNase III in E. coli and other bacteria (reviewed in references 12, 25, and 33).Streptomyces are Gram-positive soil bacteria notable for their ability to sporulate and for the production of antibiotics (6,7,11). Members of the genus Streptomyces produce nearly 70% of all antibiotics used in clinical and veterinary medicine worldwide (5). Much is known about the regulation of antibiotic production in the paradigm for the study of antibiotic production in streptomycetes, Streptomyces coelicolor (6, 7). Of particular relevance to the present report are the studies of Champness and coworkers (1, 2) on the absB locus of S. coelicolor. absB was shown to encode a homolog of E. coli RNase III, and the function of the absB product as a double-strand-specific endoribonuclease has been subsequently verified (1, 2, 10). Mutations in the absB locus reduce or abolish the production of all four of the antibiotics normally synthesized by S. coelicolor (2). Moreover, Acet...

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Section: Resultsmentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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RNA-Seq and RNA Immunoprecipitation Analyses of the Transcriptome of Streptomyces coelicolor Identify Substrates for RNase III

et al. 2012

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“…Also shown are binding sites inferred by coupling of experimental evidence of interaction with the promoter region and the presence of matches to known consensus binding sites. of RED and the possibility that it might interact with target DNA rather than the ScbR2 protein hamper unambiguous interpretation of the RED effect (52). Although RED and ACT are very different molecules, ScbR2 structural predictions revealed that its ligand-binding pocket had features reminiscent of QacR and TtgR, other members of the TetR superfamily that possess large helix-rich cavities capable of binding structurally diverse drugs (51,53,54).…”

Section: Regulation Of the "Cryptic Polyketide" Gene Clustermentioning

confidence: 99%

“…Combinations of bioinformatic predictions and experimental approaches have facilitated the identification of many sRNAs in S. coelicolor and other species (52,(269)(270)(271), and what little is known about their functions points to a boost in the perceived importance of sRNA-mediated regulation of antibiotic production in the near future. Thus, the overexpression of scr5239, an sRNA recently identified in S. coelicolor, decreased ACT production, whereas depletion of scr5239 increased production (272), and overexpression of cnc2198.1as significantly decreased RED production (273).…”

Section: Srnasmentioning

confidence: 99%

Molecular Regulation of Antibiotic Biosynthesis in Streptomyces

Liu

Chater

Chandra

et al. 2013

Microbiol Mol Biol Rev

592

536

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SUMMARY Streptomycetes are the most abundant source of antibiotics. Typically, each species produces several antibiotics, with the profile being species specific. Streptomyces coelicolor , the model species, produces at least five different antibiotics. We review the regulation of antibiotic biosynthesis in S. coelicolor and other, nonmodel streptomycetes in the light of recent studies. The biosynthesis of each antibiotic is specified by a large gene cluster, usually including regulatory genes (cluster-situated regulators [CSRs]). These are the main point of connection with a plethora of generally conserved regulatory systems that monitor the organism's physiology, developmental state, population density, and environment to determine the onset and level of production of each antibiotic. Some CSRs may also be sensitive to the levels of different kinds of ligands, including products of the pathway itself, products of other antibiotic pathways in the same organism, and specialized regulatory small molecules such as gamma-butyrolactones. These interactions can result in self-reinforcing feed-forward circuitry and complex cross talk between pathways. The physiological signals and regulatory mechanisms may be of practical importance for the activation of the many cryptic secondary metabolic gene cluster pathways revealed by recent sequencing of numerous Streptomyces genomes.

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Methods for Bioinformatic Prediction of Genuine sRNAs from Outer Membrane Vesicles

Ali,

Salem

2024

Methods in Molecular Biology

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Deep sequencing-based identification of small non-coding RNAs inStreptomyces coelicolor

Cited by 82 publications

References 50 publications

RNA-Seq and RNA Immunoprecipitation Analyses of the Transcriptome of Streptomyces coelicolor Identify Substrates for RNase III

RNA-Seq and RNA Immunoprecipitation Analyses of the Transcriptome of Streptomyces coelicolor Identify Substrates for RNase III

Molecular Regulation of Antibiotic Biosynthesis in Streptomyces

Methods for Bioinformatic Prediction of Genuine sRNAs from Outer Membrane Vesicles

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