Small non-coding RNAs in Streptomyces coelicolor

Swiercz, Julia P.; Hindra, Hindra; Bobek, Jan; Haiser, Henry J.; Berardo, Christina Di; Tjaden, Brian; Elliot, Marie A.

doi:10.1093/nar/gkn898

Cited by 68 publications

(97 citation statements)

References 51 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…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%

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

et al. 2012

View full text Add to dashboard Cite

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...

show abstract

Section: Resultsmentioning

confidence: 99%

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

et al. 2012

View full text Add to dashboard Cite

show abstract

“…Small noncoding RNAs (sRNAs) control a wide variety of cellular processes in bacteria by modulating the stability and/or translation of mRNA targets or by modifying protein activity (269). 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.…”

Section: Srnasmentioning

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

595

536

View full text Add to dashboard Cite

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.

show abstract

“…The complete genome sequences of several species of Actinobacteria, including two Streptomyces species, S. coelicolor A3(2) (3) and Streptomyces avermitilis (11), facilitated bioinformatics prediction of candidate regions for sRNAs in Streptomyces. Recently, two studies (23,27) reported the identification of sRNAs in S. coelicolor A3(2). Panek et al (23) predicted 32 potential sRNAs, and the expression of 20 of them was detected by reverse transcription (RT)-PCR and DNA microarray analyses.…”

mentioning

confidence: 99%

Identification and Gene Disruption of Small Noncoding RNAs in Streptomyces griseus

et al. 2009

View full text Add to dashboard Cite

Small noncoding RNAs (sRNAs) have been shown to control diverse cellular processes in prokaryotes. To identify and characterize novel bacterial sRNAs, a gram-positive, soil-inhabiting, filamentous bacterium, Streptomyces griseus, was examined, on the assumption that Streptomyces should express sRNAs as important regulators of morphological and physiological differentiation. By bioinformatics investigation, 54 sRNA candidates, which were encoded on intergenic regions of the S. griseus chromosome and were highly conserved in those of both Streptomyces coelicolor A3(2) and Streptomyces avermitilis, were selected. Of these 54 sRNA candidates, 17 transcripts were detected by Northern blot analysis of the total RNAs isolated from cells grown on solid medium. Then, the direction of transcription of each sRNA candidate gene was determined by S1 nuclease mapping, followed by exclusion of four sRNA candidates that were considered riboswitches of their downstream open reading frames (ORFs). Finally, a further sRNA candidate was excluded because it was cotranscribed with the upstream ORF determined by reverse transcription-PCR. Thus, 12 sRNAs ranging in size from 40 to 300 nucleotides were identified in S. griseus. Seven of them were apparently transcribed in a growth phase-dependent manner. Furthermore, of the 12 sRNAs, the expression profiles of 7 were significantly influenced by a mutation of adpA, which encodes the central transcriptional regulator of the A-factor regulatory cascade involved in both morphological differentiation and secondary metabolism in S. griseus. However, disruption of all 12 sRNA genes showed no detectable phenotypic changes; all the disruptants grew and formed aerial mycelium and spores with the same time course as the wild-type strain on various media and produced streptomycin similarly to the wild-type strain.

show abstract

Small non-coding RNAs in Streptomyces coelicolor

Cited by 68 publications

References 51 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

Identification and Gene Disruption of Small Noncoding RNAs in Streptomyces griseus

Contact Info

Product

Resources

About