RNA processing in <i>Bacillus subtilis</i>: identification of targets of the essential RNase Y

Lehnik-Habrink, Martin; Schaffer, Marc; Mäder, Ulrike; Diethmaier, Christine; Herzberg, Christina; Stülke, Jörg

doi:10.1111/j.1365-2958.2011.07777.x

Cited by 95 publications

(135 citation statements)

References 64 publications

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“…Thus, it is possible that the three strong stem-loops in the predicted S1228 structure are responsible for controlling the dhbA mRNA levels, and it would be interesting to study the role of RNase Y in this process. Likewise, the yhrE gene, encoding formate dehydrogenase, is also stabilized upon RNase Y depletion (88), and its 5=UTR S1031 (21/62 genomes, MFE Z-score Ϫ4.3) also contains three strong stem-loops. S1031 is in fact the seventh segment in the top-10 list of predicted 5=UTRs and was also identified by termSeq (57).…”

Section: = Untranslated Regions With Other or Unknown Functionsmentioning

confidence: 99%

Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression

Mars

Nicolas

Denham

et al. 2016

Microbiol Mol Biol Rev

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SUMMARY Bacteria can employ widely diverse RNA molecules to regulate their gene expression. Such molecules include trans -acting small regulatory RNAs, antisense RNAs, and a variety of transcriptional attenuation mechanisms in the 5′ untranslated region. Thus far, most regulatory RNA research has focused on Gram-negative bacteria, such as Escherichia coli and Salmonella . Hence, there is uncertainty about whether the resulting insights can be extrapolated directly to other bacteria, such as the Gram-positive soil bacterium Bacillus subtilis . A recent study identified 1,583 putative regulatory RNAs in B. subtilis , whose expression was assessed across 104 conditions. Here, we review the current understanding of RNA-based regulation in B. subtilis , and we categorize the newly identified putative regulatory RNAs on the basis of their conservation in other bacilli and the stability of their predicted secondary structures. Our present evaluation of the publicly available data indicates that RNA-mediated gene regulation in B. subtilis mostly involves elements at the 5′ ends of mRNA molecules. These can include 5′ secondary structure elements and metabolite-, tRNA-, or protein-binding sites. Importantly, sense-independent segments are identified as the most conserved and structured potential regulatory RNAs in B. subtilis . Altogether, the present survey provides many leads for the identification of new regulatory RNA functions in B. subtilis .

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Section: = Untranslated Regions With Other or Unknown Functionsmentioning

confidence: 99%

Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression

Mars

Nicolas

Denham

et al. 2016

Microbiol Mol Biol Rev

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“…Northern Blot Analysis-Preparation of total RNA and Northern blot analysis were carried out as described previously (26). Digoxigenin RNA probes were obtained by in vitro transcription with T7 RNA polymerase (Roche Diagnostics) using PCR-generated DNA fragments as templates.…”

Section: Construction Of Integrative Vectors That Allow the Ectopic Ementioning

confidence: 99%

Cyclic Di-AMP Homeostasis in Bacillus subtilis

Mehne

Gunka

Eilers

et al. 2013

Journal of Biological Chemistry

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“…The resulting cell powder was used to extract the metabolites, and the dried metabolite extracts were dissolved with 200 l of H 2 O. After repeated centrifugation and addition of internal standards ([ 13 C, 15 N]cdi-GMP and [ 13 C, 15 N]c-di-AMP), part of the extracts was analyzed by LC-MS/MS.…”

Section: Methodsmentioning

confidence: 99%

“…In vitro RNA labeling, hybridization, and signal detection were carried out according to the instructions of the manufacturer (DIG RNA labeling kit and detection chemicals; Roche Diagnostics). RNA stability was analyzed as described previously (15). Briefly, rifampin was added to stationary growing cultures (final concentration, 100 g/ml), and samples were taken at the time points indicated.…”

Section: Methodsmentioning

confidence: 99%

“…The SinI-SinR complex is no longer able to bind to DNA (12,13). Although sinI and sinR are adjacent on the chromosome, the transcription profile of the sin operon is under complex regulation to result in an unequal expression profile of the two genes (14,15). Two additional proteins, SlrR and SlrA, that also influence this switch were discovered recently, and these proteins are homologues of SinR and SinI, respectively (16)(17)(18).…”

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confidence: 99%

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The YmdB Phosphodiesterase Is a Global Regulator of Late Adaptive Responses in Bacillus subtilis

Diethmaier

Newman

Kovács³

et al. 2013

Journal of Bacteriology

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dBacillus subtilis mutants lacking ymdB are unable to form biofilms, exhibit a strong overexpression of the flagellin gene hag, and are deficient in SlrR, a SinR antagonist. Here, we report the functional and structural characterization of YmdB, and we find that YmdB is a phosphodiesterase with activity against 2=,3=-and 3=,5=-cyclic nucleotide monophosphates. The structure of YmdB reveals that the enzyme adopts a conserved phosphodiesterase fold with a binuclear metal center. Mutagenesis of a catalytically crucial residue demonstrates that the enzymatic activity of YmdB is essential for biofilm formation. The deletion of ymdB affects the expression of more than 800 genes; the levels of the D -dependent motility regulon and several sporulation genes are increased, and the levels of the SinR-repressed biofilm genes are decreased, confirming the role of YmdB in regulating late adaptive responses of B. subtilis.

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RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y

Cited by 95 publications

References 64 publications

Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression

Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression

Cyclic Di-AMP Homeostasis in Bacillus subtilis

The YmdB Phosphodiesterase Is a Global Regulator of Late Adaptive Responses in Bacillus subtilis

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