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

Gatewood, Marcha L.; Bralley, Patricia; Weil, M. Ryan; Jones, George H.

doi:10.1128/jb.06541-11

Cited by 33 publications

(40 citation statements)

References 47 publications

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“…RNase III was also reported to cleave the mRNA for AdpA, a pleiotropic transcription factor affecting both differentiation and antibiotic production (see below) (152). Recently, RNA-Seq showed that depletion of RNase III resulted in increased levels of many transcripts, including some (SCO5608, SCO0168, and SCO0864) thought to be involved in antibiotic production (153). An alternative explanation of the effect of RNase III on antibiotic production is that RNase III is responsible for rRNA maturation, which is important for the translation of long mRNA (149,154).…”

Section: Rna Regulation Of Antibiotic Productionmentioning

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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Section: Rna Regulation Of Antibiotic Productionmentioning

confidence: 99%

Molecular Regulation of Antibiotic Biosynthesis in Streptomyces

Liu

Chater

Chandra

et al. 2013

Microbiol Mol Biol Rev

592

536

View full text Add to dashboard Cite

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“…RNase III has been reasonably well studied in S. coelicolor (20)(21)(22)36), and given the extensive sequence similarity shared with RNase III in S. venezuelae, these proteins are expected to function in a similar manner. For all Streptomyces species in the StrepDB database (http://strepdb.streptomyces.org.uk/), rnc appears to be the third gene in an operon that includes genes encoding a conserved, hypothetical protein and the large ribosomal subunit protein L32 (rpmF) (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The mechanism underlying this observation is not immediately obvious, but previous RNA-seq and chromatin immunoprecipitation analyses in S. coelicolor revealed a number of membrane proteins, lipoproteins, and other secreted protein-encoding genes to be affected by the loss of RNase III (22), and it is conceivable that one or more of these contribute to increased vancomycin sensitivity or, indeed, general antibiotic sensitivity through enhanced uptake/ reduced efflux.…”

Section: Figmentioning

confidence: 99%

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Development, Antibiotic Production, and Ribosome Assembly in Streptomyces venezuelae Are Impacted by RNase J and RNase III Deletion

2014

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b RNA metabolism is a critical but frequently overlooked control element affecting virtually every cellular process in bacteria. RNA processing and degradation is mediated by a suite of ribonucleases having distinct cleavage and substrate specificity. Here, we probe the role of two ribonucleases (RNase III and RNase J) in the emerging model system Streptomyces venezuelae. We show that each enzyme makes a unique contribution to the growth and development of S. venezuelae and further affects the secondary metabolism and antibiotic production of this bacterium. We demonstrate a connection between the action of these ribonucleases and translation, with both enzymes being required for the formation of functional ribosomes. RNase III mutants in particular fail to properly process 23S rRNA, form fewer 70S ribosomes, and show reduced translational processivity. The loss of either RNase III or RNase J additionally led to the appearance of a new ribosomal species (the 100S ribosome dimer) during exponential growth and dramatically sensitized these mutants to a range of antibiotics. R ibonucleases (RNases) are enzymes that process and degrade RNA molecules; consequently, they are critical for RNA maturation, RNA stability, and posttranscriptional regulation (1). In bacterial cells, the finely tuned balance between RNA synthesis and RNA degradation allows for rapid adaptation to changing environments, proper processing of noncoding RNAs, and efficient recycling of ribonucleotides (2).Our understanding of RNA metabolism to date is based largely on studies of Escherichia coli and Bacillus subtilis, which employ distinct enzymes for RNA processing and degradation. In E. coli, RNase E is the central component of the RNA degradosome; as such, it is responsible for much of the RNA decay in this organism. B. subtilis lacks this enzyme, and acting in its place are three other nucleases: RNase J1/J2 and RNase Y (3, 4). Virtually all bacteria contain at least one of RNase E (or its paralog, RNase G), RNase J, or RNase Y (5). These RNases are unrelated in primary sequence and mechanism of catalysis but have similar substrate specificity: they all have single-strand-specific endonuclease activity and preferentially cleave AU-rich regions (4, 6, 7). Unlike RNase E and Y, however, RNase J has the capacity to act both as an endonuclease and as a 5= exonuclease (8, 9). The analysis of available genome sequences suggests that more than half of all bacteria, and over two-thirds of Archaea, possess an RNase J homologue (6,8). In addition to these diverse single-strand-specific RNases, most bacteria also encode the double-strand-specific RNase III (10). This enzyme is highly conserved in bacteria and eukaryotes and has a critical role in posttranscriptional regulation, where it cleaves double-stranded substrates, such as those resulting from the base pairing of an mRNA and noncoding RNA (11), or those associated with highly structured RNAs, such as ribosomal RNAs (rRNAs) (12, 13). There can be considerable functional interplay between RNases, ...

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“…In a recent study, we have identified a number of genes whose expression is affected by the absence of RNase III. We have proposed a model in which antibiotic production in S. coelicolor is affected because of the sheer number of transcripts that are cleaved by RNase III (26). A similar situation may obtain in S. antibioticus.…”

Section: Fig 3 Growth and Actinomycin Production Of S Antibioticus Cmentioning

confidence: 99%

RNase III Is Required for Actinomycin Production in Streptomyces antibioticus

Lee

Gatewood

Jones

2013

Appl Environ Microbiol

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Using insertional mutagenesis, we have disrupted the RNase III gene, rnc, of the actinomycin-producing streptomycete, Streptomyces antibioticus. Disruption was verified by Southern blotting. The resulting strain grows more vigorously than its parent on actinomycin production medium but produces significantly lower levels of actinomycin. Complementation of the rnc disruption with the wild-type rnc gene from S. antibioticus restored actinomycin production to nearly wild-type levels. Western blotting experiments demonstrated that the disruptant did not produce full-length or truncated forms of RNase III. Thus, as is the case in Streptomyces coelicolor, RNase III is required for antibiotic production in S. antibioticus. No differences in the chemical halflives of bulk mRNA were observed in a comparison of the S. antibioticus rnc mutant and its parental strain. RNase III is a double-strand-specific endonuclease that is found in bacteria and eukaryotes (1-3). 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 by cleaving an untranslated leader in its mRNA. This cleavage leads to an increased rate of decay of the RNase III mRNA, downregulating expression of the RNase III gene, rnc (4-6). RNase III is also involved in the regulation of the expression of the polynucleotide phosphorylase (PNPase) gene, pnp, in bacteria. RNase III cleaves a stem-loop structure in the 5= leader of the pnp transcripts in E. coli. The 3= ends produced by this cleavage then serve as targets for polyadenylation by poly(A) polymerase I, and the polyadenylated 3= ends are degraded by PNPase itself (7,8). Thus, RNase III cleavage, polyadenylation, and PNPase action on its own mRNA lead to instability of that mRNA, resulting in decreased synthesis of PNPase (7-9). 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 1, 2, and 3).RNase III also plays an important role in the regulation of antibiotic synthesis in Streptomyces coelicolor. Some years ago, Champness and coworkers identified an S. coelicolor locus, which they designated absB (10). The synthesis of all four antibiotics normally produced by S. coelicolor was severely reduced in an absB mutant, C120. Specifically, they reported that the production of actinorhodin (encoded by the act gene cluster) by the C120 mutant was reduced to only 2% of the normally observed level and that the level of undecylprodigiosin (encoded by the red gene cluster) was only 15% of that normally observed (10). Production of the calcium-dependent antibiotic and of methylenomycin was also reduced. Champness and coworkers subsequently demonstrated that the absB locus encoded a homolog of RNase III, the double-strand-specific endoribonuclease discussed above, and the C120 absB mutant was shown to contain a point mutation that resulted in a change of leucine to proline in the R...

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

Cited by 33 publications

References 47 publications

Molecular Regulation of Antibiotic Biosynthesis in Streptomyces

Molecular Regulation of Antibiotic Biosynthesis in Streptomyces

Development, Antibiotic Production, and Ribosome Assembly in Streptomyces venezuelae Are Impacted by RNase J and RNase III Deletion

RNase III Is Required for Actinomycin Production in Streptomyces antibioticus

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