ArticleJournal of bacteriology2012
RNA-Seq and RNA immunoprecipitation analyses of the transcriptome of Streptomyces coelicolor identify substrates for RNase III.
Article in Journal of bacteriology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 35 citations in OpenAlex.
- Antisense RNA controls the degradation of phycobilisomes in heterocyst-forming cyanobacteria by a transcriptional interference mechanism.Nucleic acids research · 2026Article
- Methodologies for bacterial ribonuclease characterization using RNA-seq.FEMS microbiology reviews · 2023Review
- Review
- RNase III, Ribosome Biogenesis and Beyond.Microorganisms · 2021Review
- Bacterial 3'UTRs: A Useful Resource in Post-transcriptional Regulation.Frontiers in molecular biosciences · 2020Review
- Multi-level regulation of coelimycin synthesis in Streptomyces coelicolor A3(2).Applied microbiology and biotechnology · 2019Review
- Bacterial ribonucleases and their roles in RNA metabolism.Critical reviews in biochemistry and molecular biology · 2019Review
- Widespread Antisense Transcription in Prokaryotes.Microbiology spectrum · 2018Review
- RNase III-Binding-mRNAs Revealed Novel Complementary Transcripts inFrontiers in microbiology · 2017Article
- The dynamic transcriptional and translational landscape of the model antibiotic producer Streptomyces coelicolor A3(2).Nature communications · 2016Article
- Mapping of internal monophosphate 5' ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains.Nucleic acids research · 2016Article
- Combined computational and experimental analysis of a complex of ribonuclease III and the regulatory macrodomain protein, YmdB.Proteins · 2015Article
- Development, antibiotic production, and ribosome assembly in Streptomyces venezuelae are impacted by RNase J and RNase III deletion.Journal of bacteriology · 2014Article
- Temporal dynamics of the Saccharopolyspora erythraea phosphoproteome.Molecular & cellular proteomics : MCP · 2014Article
- Actinomycetes biosynthetic potential: how to bridge in silico and in vivo?Journal of industrial microbiology & biotechnology · 2014Review
- Article
- Article
- Small non-coding RNAs in streptomycetes.RNA biology · 2014Review
- RNase III is required for actinomycin production in Streptomyces antibioticus.Applied and environmental microbiology · 2013Article
- Comparative analysis of non-coding RNAs in the antibiotic-producing Streptomyces bacteria.BMC genomics · 2013Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 protein-coding 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.
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