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Sabine Brantl
Friedrich-Schiller-Universität Jena, Matthias-Schleiden-Institut, AG Bakteriengenetik, D-07743 Jena, Germany

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Short Biography

1. PD Dr. Sabine Brantl, leader of workgroup Bacterial Genetics at the Friedrich-Schiller University (FSU) Jena 2. Study of Biology/Genetics at Martin-Luther University Halle 1978-1983, PhD (1988) at the Academy of Science of the G.D.R., Central Institute of Microbiology and Experimental Therapy in Jena; habilitation (1998) in Genetics, Friedrich-Schiller University (FSU) Jena, Heisenberg fellow of the German Research Council 1998-2000, lecturer at the FSU Jena 2000-2007 3. Group leader since 1995, university teaching in Genetics and Biochemistry since 1996 (FSU) Visiting scientist at Institute of Molecular Biology in Moscow (1985 and1986, 4 months each), Max-Planck-Institut in Berlin (1989, 3 months), Centro de Biología Molecular in Madrid (1990, 2 months), Institute for Microbiology in Uppsala, Sweden (1994, 3 months, with EMBO short-term fellowship) 4. Research interests: Bacterial gene regulation by sRNAs and small proteins, RNA degradation, RNA chaperones 5. Member of the German Society of General and Applied Microbiology

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Review
Published: 12 May 2021 in Microorganisms
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Moonlighting proteins are proteins with more than one function. During the past 25 years, they have been found to be rather widespread in bacteria. In Bacillus subtilis, moonlighting has been disclosed to occur via DNA, protein or RNA binding or protein phosphorylation. In addition, two metabolic enzymes, enolase and phosphofructokinase, were localized in the degradosome-like network (DLN) where they were thought to be scaffolding components. The DLN comprises the major endoribonuclease RNase Y, 3′-5′ exoribonuclease PnpA, endo/5′-3′ exoribonucleases J1/J2 and helicase CshA. We have ascertained that the metabolic enzyme GapA is an additional component of the DLN. In addition, we identified two small proteins that bind scaffolding components of the degradosome: SR1P encoded by the dual-function sRNA SR1 binds GapA, promotes the GapA-RNase J1 interaction and increases the RNase J1 activity. SR7P encoded by the dual-function antisense RNA SR7 binds to enolase thereby enhancing the enzymatic activity of enolase bound RNase Y. We discuss the role of small proteins in modulating the activity of two moonlighting proteins.

ACS Style

Inam Ul Haq; Sabine Brantl. Moonlighting in Bacillus subtilis: The Small Proteins SR1P and SR7P Regulate the Moonlighting Activity of Glyceraldehyde 3-Phosphate Dehydrogenase A (GapA) and Enolase in RNA Degradation. Microorganisms 2021, 9, 1046 .

AMA Style

Inam Ul Haq, Sabine Brantl. Moonlighting in Bacillus subtilis: The Small Proteins SR1P and SR7P Regulate the Moonlighting Activity of Glyceraldehyde 3-Phosphate Dehydrogenase A (GapA) and Enolase in RNA Degradation. Microorganisms. 2021; 9 (5):1046.

Chicago/Turabian Style

Inam Ul Haq; Sabine Brantl. 2021. "Moonlighting in Bacillus subtilis: The Small Proteins SR1P and SR7P Regulate the Moonlighting Activity of Glyceraldehyde 3-Phosphate Dehydrogenase A (GapA) and Enolase in RNA Degradation." Microorganisms 9, no. 5: 1046.

Review article
Published: 07 August 2020 in Frontiers in Molecular Biosciences
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In bacterial cells we find a variety of interacting macromolecules, among them RNAs and proteins. Not only small regulatory RNAs (sRNAs), but also small proteins have been increasingly recognized as regulators of bacterial gene expression. An average bacterial genome encodes between 200 and 300 sRNAs, but an unknown number of small proteins. sRNAs can be cis- or trans-encoded. Whereas cis-encoded sRNAs interact only with their single completely complementary mRNA target transcribed from the opposite DNA strand, trans-encoded sRNAs are only partially complementary to their numerous mRNA targets, resulting in huge regulatory networks. In addition to sRNAs, uncharged tRNAs can interact with mRNAs in T-box attenuation mechanisms. For a number of sRNA-mRNA interactions, the stability of sRNAs or translatability of mRNAs, RNA chaperones are required. In Gram-negative bacteria, the well-studied abundant RNA-chaperone Hfq fulfils this role, and recently another chaperone, ProQ, has been discovered and analyzed in this respect. By contrast, evidence for RNA chaperones or their role in Gram-positive bacteria is still scarce, but CsrA might be such a candidate. Other RNA-protein interactions involve tmRNA/SmpB, 6S RNA/RNA polymerase, the dual-function aconitase and protein-bound transcriptional terminators and antiterminators. Furthermore, small proteins, often missed in genome annotations and long ignored as potential regulators, can interact with individual regulatory proteins, large protein complexes, RNA or the membrane. Here, we review recent advances on biological role and regulatory principles of the currently known sRNA-mRNA interactions, sRNA-protein interactions and small protein-protein interactions in the Gram-positive model organism Bacillus subtilis. We do not discuss RNases, ribosomal proteins, RNA helicases or riboswitches.

ACS Style

Inam Ul Haq; Peter Müller; Sabine Brantl. Intermolecular Communication in Bacillus subtilis: RNA-RNA, RNA-Protein and Small Protein-Protein Interactions. Frontiers in Molecular Biosciences 2020, 7, 178 .

AMA Style

Inam Ul Haq, Peter Müller, Sabine Brantl. Intermolecular Communication in Bacillus subtilis: RNA-RNA, RNA-Protein and Small Protein-Protein Interactions. Frontiers in Molecular Biosciences. 2020; 7 ():178.

Chicago/Turabian Style

Inam Ul Haq; Peter Müller; Sabine Brantl. 2020. "Intermolecular Communication in Bacillus subtilis: RNA-RNA, RNA-Protein and Small Protein-Protein Interactions." Frontiers in Molecular Biosciences 7, no. : 178.

Research paper
Published: 05 August 2020 in RNA Biology
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Here, we describe SR7, a dual-function antisense RNA encoded on the Bacillus subtilis chromosome. This RNA was earlier described as SigB-dependent regulatory RNA S1136 and reported to reduce the amount of the small ribosomal subunit under ethanol stress. We found that the 5ʹ portion of SR7 encodes a small protein composed of 39 amino acids which we designated SR7P. It is translated from a 185 nt SigB-dependent mRNA under five different stress conditions and a longer SigB-independent RNA constitutively. About three-fold higher amounts of SR7P were detected in B. subtilis cells exposed to salt, ethanol, acid or heat stress. Co-elution experiments with SR7PC-FLAG and Far-Western blotting demonstrated that SR7P interacts with the glycolytic enzyme enolase. Enolase is a scaffolding component of the B. subtilis degradosome where it interacts with RNase Y and phosphofructokinase PfkA. We found that SR7P increases the amount of RNase Y bound to enolase without affecting PfkA. RNA does not bridge the SR7P-enolase-RNase Y interaction. In vitro-degradation assays with the known RNase Y substrates yitJ and rpsO mRNA revealed enhanced enzymatic activity of enolase-bound RNase Y in the presence of SR7P. Northern blots showed a major effect of enolase and a minor effect of SR7P on the half-life of rpsO mRNA indicating a fine-tuning role of SR7P in RNA degradation.

ACS Style

Inam Ul Haq; Peter Müller; Sabine Brantl. SR7 – a dual-function antisense RNA from Bacillus subtilis. RNA Biology 2020, 18, 104 -117.

AMA Style

Inam Ul Haq, Peter Müller, Sabine Brantl. SR7 – a dual-function antisense RNA from Bacillus subtilis. RNA Biology. 2020; 18 (1):104-117.

Chicago/Turabian Style

Inam Ul Haq; Peter Müller; Sabine Brantl. 2020. "SR7 – a dual-function antisense RNA from Bacillus subtilis." RNA Biology 18, no. 1: 104-117.

Preprint content
Published: 15 May 2020
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SummaryHere, we describe SR7, a dual-function antisense RNA from the Bacillus subtilis chromosome. This RNA was earlier published as the SigB-dependent regulatory RNA S1136 and reported to reduce the amount of the small ribosomal subunit under ethanol stress. We found that the 5’ portion of SR7 encodes a small protein composed of 39 amino acids which we designated SR7P. It is translated from a 185 nt SigB-dependent mRNA under five different stress conditions and a longer SigB-independent RNA constitutively. Two- to three-fold higher amounts of SR7P were detected in B. subtilis cells exposed to salt, ethanol or heat stress. Co-elution experiments with SR7PC-FLAG and Far-Western blotting demonstrated that SR7P interacts with the glycolytic enzyme enolase. Enolase is a scaffolding component of the B. subtilis degradosome where it interacts with RNase Y and phosphofructokinase PfkA. We found that SR7P increases the amount of RNase Y bound to enolase without affecting PfkA. RNA does not bridge the SR7P-enolase-RNase Y interaction. In vitro-degradation assays with the known RNase Y substrates yitJ and rpsO mRNA revealed enhanced enzymatic activity of enolase-bound RNase Y in the presence of SR7P. Northern blots showed a major effect of enolase and a minor effect of SR7P on the half-life of rpsO mRNA indicating a fine-tuning role of SR7P in RNA degradation. Moreover, SR7P impacts survival of B. subtilis under stress conditions. We suggest that the SR7P-dependent modification of the degradosome affects targets in different physiological pathways.

ACS Style

Inam Ul Haq; Peter Müller; Sabine Brantl. SR7 - a dual function antisense RNA from Bacillus subtilis. 2020, 1 .

AMA Style

Inam Ul Haq, Peter Müller, Sabine Brantl. SR7 - a dual function antisense RNA from Bacillus subtilis. . 2020; ():1.

Chicago/Turabian Style

Inam Ul Haq; Peter Müller; Sabine Brantl. 2020. "SR7 - a dual function antisense RNA from Bacillus subtilis." , no. : 1.

Review
Published: 09 May 2019 in Toxins
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Toxin–antitoxin (TA) systems were originally discovered as plasmid maintenance systems in a multitude of free-living bacteria, but were afterwards found to also be widespread in bacterial chromosomes. TA loci comprise two genes, one coding for a stable toxin whose overexpression kills the cell or causes growth stasis, and the other coding for an unstable antitoxin that counteracts toxin action. Of the currently known six types of TA systems, in Bacillus subtilis, so far only type I and type II TA systems were found, all encoded on the chromosome. Here, we review our present knowledge of these systems, the mechanisms of antitoxin and toxin action, and the regulation of their expression, and we discuss their evolution and possible physiological role.

ACS Style

Sabine Brantl; Peter Müller. Toxin–Antitoxin Systems in Bacillus subtilis. Toxins 2019, 11, 262 .

AMA Style

Sabine Brantl, Peter Müller. Toxin–Antitoxin Systems in Bacillus subtilis. Toxins. 2019; 11 (5):262.

Chicago/Turabian Style

Sabine Brantl; Peter Müller. 2019. "Toxin–Antitoxin Systems in Bacillus subtilis." Toxins 11, no. 5: 262.

Research paper
Published: 01 May 2019 in RNA Biology
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CsrA is a widely conserved, abundant small RNA binding protein that has been found in E. coli and other Gram-negative bacteria where it is involved in the regulation of carbon metabolism, biofilm formation and virulence. CsrA binds to single-stranded GGA motifs around the SD sequence of target mRNAs where it inhibits or activates translation or influences RNA processing. Small RNAs like CsrB or CsrC containing 13–22 GGA motifs can sequester CsrA, thereby abrogating the effect of CsrA on its target mRNAs. In B. subtilis, CsrA has so far only been found to regulate one target, hag mRNA and to be sequestered by a protein (FliW) and not by an sRNA. Here, we employ a combination of in vitro and in vivo methods to investigate the effect of CsrA on the small regulatory RNA SR1 from B. subtilis, its primary target ahrC mRNA and its downstream targets, the rocABC and rocDEF operons. We demonstrate that CsrA can promote the base-pairing interactions between SR1 and ahrC mRNA, a function that has so far only been found for Hfq or ProQ.

ACS Style

Peter Müller; Matthias Gimpel; Theresa Wildenhain; Sabine Brantl. A new role for CsrA: promotion of complex formation between an sRNA and its mRNA target in Bacillus subtilis. RNA Biology 2019, 16, 972 -987.

AMA Style

Peter Müller, Matthias Gimpel, Theresa Wildenhain, Sabine Brantl. A new role for CsrA: promotion of complex formation between an sRNA and its mRNA target in Bacillus subtilis. RNA Biology. 2019; 16 (7):972-987.

Chicago/Turabian Style

Peter Müller; Matthias Gimpel; Theresa Wildenhain; Sabine Brantl. 2019. "A new role for CsrA: promotion of complex formation between an sRNA and its mRNA target in Bacillus subtilis." RNA Biology 16, no. 7: 972-987.

Wissenschaft
Published: 13 November 2018 in BIOspektrum
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Although short open reading frames (sORFs) are present in all genomes, they have often been missed in annotations. Nevertheless, a small variety of peptides involved in different pathways were identified serendipitously and investigated in more detail. Among them are type I toxins, nucleic acid and metal chaperones, membrane components, stabilizing factors of large protein complexes, and regulatory peptides.

ACS Style

Matthias Gimpel; Inam Ul Haq; Sabine Brantl. Peptid-codierende kleine RNAs in Bakterien. BIOspektrum 2018, 24, 684 -687.

AMA Style

Matthias Gimpel, Inam Ul Haq, Sabine Brantl. Peptid-codierende kleine RNAs in Bakterien. BIOspektrum. 2018; 24 (7):684-687.

Chicago/Turabian Style

Matthias Gimpel; Inam Ul Haq; Sabine Brantl. 2018. "Peptid-codierende kleine RNAs in Bakterien." BIOspektrum 24, no. 7: 684-687.

Journal article
Published: 07 February 2018 in Toxins
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YonT/SR6 is the second type I toxin-antitoxin (TA) system encoded on prophage SPβ in the B. subtilis chromosome. The yonT ORF specifying a 58 aa toxin is transcribed on a polycistronic mRNA under control of the yonT promoter. The antitoxin SR6 is a 100 nt antisense RNA that overlaps yonT at its 3′ end and the downstream gene yoyJ encoding a second, much weaker, toxin at its 5′ end. SR6 displays a half-life of >60 min, whereas yonT mRNA is less stable with a half-life of ≈8 min. SR6 is in significant excess over yonT mRNA except in minimal medium with glucose. It interacts with the 3′ UTR of yonT mRNA, thereby promoting its degradation by RNase III. By contrast, SR6 does not affect the amount or half-life of yoyJ mRNA. However, in its absence, a yoyJ overexpression plasmid could not be established in Bacillus subtilis suggesting that SR6 inhibits yoyJ translation by directly binding to its ribosome-binding site. While the amounts of both yonT RNA and SR6 were affected by vancomycin, manganese, heat-shock and ethanol stress as well as iron limitation, oxygen stress decreased only the amount of SR6.

ACS Style

Celine Reif; Charlotte Löser; Sabine Brantl. Bacillus subtilis Type I antitoxin SR6 Promotes Degradation of Toxin yonT mRNA and Is Required to Prevent Toxic yoyJ Overexpression. Toxins 2018, 10, 74 .

AMA Style

Celine Reif, Charlotte Löser, Sabine Brantl. Bacillus subtilis Type I antitoxin SR6 Promotes Degradation of Toxin yonT mRNA and Is Required to Prevent Toxic yoyJ Overexpression. Toxins. 2018; 10 (2):74.

Chicago/Turabian Style

Celine Reif; Charlotte Löser; Sabine Brantl. 2018. "Bacillus subtilis Type I antitoxin SR6 Promotes Degradation of Toxin yonT mRNA and Is Required to Prevent Toxic yoyJ Overexpression." Toxins 10, no. 2: 74.

Journal article
Published: 01 August 2017 in Microbiology
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Small regulatory RNAs (sRNAs) are the most prominent post-transcriptional regulators in all kingdoms of life. A few of them, e.g. SR1 from Bacillus subtilis, are dual-function sRNAs. SR1 acts as a base-pairing sRNA in arginine catabolism and as an mRNA encoding the small peptide SR1P in RNA degradation. Both functions of SR1 are highly conserved among 23 species of Bacillales. Here, we investigate the interaction between SR1P and GapA by a combination of in vivo and in vitro methods. De novo prediction of the structure of SR1P yielded five models, one of which was consistent with experimental circular dichroism spectroscopy data of a purified, synthetic peptide. Based on this model structure and a comparison between the 23 SR1P homologues, a series of SR1P mutants was constructed and analysed by Northern blotting and co-elution experiments. The known crystal structure of Geobacillus stearothermophilus GapA was used to model SR1P onto this structure. The hypothetical SR1P binding pocket, composed of two α-helices at both termini of GapA, was investigated by constructing and assaying a number of GapA mutants in the presence and absence of wild-type or mutated SR1P. Almost all residues of SR1P located in the two highly conserved motifs are implicated in the interaction with GapA. A critical lysine residue (K332) in the C-terminal α-helix 14 of GapA corroborated the predicted binding pocket.

ACS Style

Matthias Gimpel; Caroline Maiwald; Christoph Wiedemann; Matthias Görlach; Sabine Brantl. Characterization of the interaction between the small RNA-encoded peptide SR1P and GapA from Bacillus subtilis. Microbiology 2017, 163, 1248 -1259.

AMA Style

Matthias Gimpel, Caroline Maiwald, Christoph Wiedemann, Matthias Görlach, Sabine Brantl. Characterization of the interaction between the small RNA-encoded peptide SR1P and GapA from Bacillus subtilis. Microbiology. 2017; 163 (8):1248-1259.

Chicago/Turabian Style

Matthias Gimpel; Caroline Maiwald; Christoph Wiedemann; Matthias Görlach; Sabine Brantl. 2017. "Characterization of the interaction between the small RNA-encoded peptide SR1P and GapA from Bacillus subtilis." Microbiology 163, no. 8: 1248-1259.

Review
Published: 14 November 2016 in Molecular Microbiology
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Dual-function sRNAs are a subgroup of small regulatory RNAs that act on the one hand as base-pairing sRNAs to inhibit or activate target gene expression and on the other hand as peptide-encoding mRNAs that function either in the same or in another metabolic pathway. Here, we review and compare the five currently known and intensively characterized dual-function sRNAs with regard to their two functions, their biological role, their evolutionary conservation and their requirements for RNA chaperones. Furthermore, we summarize the data available on five potential dual-function sRNAs, whose base-pairing function is well established whereas the role of their encoded peptides has not yet been elucidated. In addition, we provide three examples for RNAs with more than one function that do not fall into the above-mentioned category. With the application of RNAseq, peptidomics and transcriptomics it can be expected that the number of dual-function sRNAs will considerably increase within the next years, thus enhancing our knowledge on the regulatory potential of these RNAs.

ACS Style

Matthias Gimpel; Sabine Brantl. Dual‐function small regulatory RNAs in bacteria. Molecular Microbiology 2016, 103, 387 -397.

AMA Style

Matthias Gimpel, Sabine Brantl. Dual‐function small regulatory RNAs in bacteria. Molecular Microbiology. 2016; 103 (3):387-397.

Chicago/Turabian Style

Matthias Gimpel; Sabine Brantl. 2016. "Dual‐function small regulatory RNAs in bacteria." Molecular Microbiology 103, no. 3: 387-397.

Review article
Published: 11 August 2016 in Frontiers in Molecular Biosciences
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PIP501 is a Gram-positive broad-host-range model plasmid intensively used for studying plasmid replication and conjugative transfer. It is a multiple antibiotic resistance plasmid frequently found in clinical Enterococcus faecalis and Enterococcus faecium isolates. Replication of pIP501 proceeds unidirectionally by a theta mechanism. The minimal replicon of pIP501 is composed of the repR gene encoding the essential rate-limiting replication initiator protein RepR and the origin of replication, oriR, located downstream of repR. RepR is similar to RepE of related streptococcal plasmid pAMβ1, which has been shown to possess RNase activity cleaving free RNA molecules in close proximity of the initiation site of DNA synthesis. Replication of pIP501 is controlled by the concerted action of a small protein, CopR, and an antisense RNA, RNAIII. CopR has a dual role: It acts as transcriptional repressor at the repR promoter and prevents convergent transcription of RNAIII and repR mRNA (RNAII), thereby indirectly increasing RNAIII synthesis. CopR binds asymmetrically as a dimer at two consecutive binding sites upstream of and overlapping with the repR promoter. RNAIII induces transcriptional attenuation within the leader region of the repR mRNA (RNAII). Deletion of either control component causes a 10- to 20-fold increase of plasmid copy number, while simultaneous deletions have no additional effect. Conjugative transfer of pIP501 depends on a type IV secretion system (T4SS) encoded in a single operon. Its transfer host-range is considerably broad, as it has been transferred to virtually all Gram-positive bacteria including filamentous streptomycetes and even the Gram-negative Escherichia coli. Expression of the 15 genes encoding the T4SS is tightly controlled by binding of the relaxase TraA, the transfer initiator protein, to the operon promoter, which overlaps with the origin of transfer (oriT). The T4SS operon encodes the DNA-binding proteins TraJ (VirD4-like coupling protein) and the VirB4-like ATPase, TraE. Both proteins are actively involved in conjugative DNA transport. Moreover, the operon encodes TraN, a small cytoplasmic protein, whose specific binding to a sequence upstream of the oriT nic-site was demonstrated. TraN seems to be an effective repressor of pIP501 transfer, as conjugative transfer rates were significantly increased in an E. faecalis pIP501ΔtraN mutant.

ACS Style

Elisabeth Grohmann; Nikolaus Gössweiner-Mohr; Sabine Brantl. DNA-Binding Proteins Regulating pIP501 Transfer and Replication. Frontiers in Molecular Biosciences 2016, 3, 42 .

AMA Style

Elisabeth Grohmann, Nikolaus Gössweiner-Mohr, Sabine Brantl. DNA-Binding Proteins Regulating pIP501 Transfer and Replication. Frontiers in Molecular Biosciences. 2016; 3 ():42.

Chicago/Turabian Style

Elisabeth Grohmann; Nikolaus Gössweiner-Mohr; Sabine Brantl. 2016. "DNA-Binding Proteins Regulating pIP501 Transfer and Replication." Frontiers in Molecular Biosciences 3, no. : 42.

Research paper
Published: 05 August 2016 in RNA Biology
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SR1 is a dual-function sRNA from B. subtilis that acts as a base-pairing regulatory RNA and as a peptide-encoding mRNA. Both functions of SR1 are highly conserved. Previously, we uncovered that the SR1 encoded peptide SR1P binds the glycolytic enzyme GapA resulting in stabilization of gapA mRNA. Here, we demonstrate that GapA interacts with RNases Y and J1, and this interaction was RNA-independent. About 1% of GapA molecules purified from B. subtilis carry RNase J1 and about 2% RNase Y. In contrast to the GapA/RNase Y interaction, the GapA/RNaseJ1 interaction was stronger in the presence of SR1P. GapA/SR1P-J1/Y displayed in vitro RNase activity on known RNase J1 substrates. Moreover, the RNase J1 substrate SR5 has altered half-lives in a ΔgapA strain and a Δsr1 strain, suggesting in vivo functions of the GapA/SR1P/J1 interaction. Our results demonstrate that the metabolic enzyme GapA moonlights in recruiting RNases while GapA bound SR1P promotes binding of RNase J1 and enhances its activity.

ACS Style

Matthias Gimpel; Sabine Brantl. Dual-function sRNA encoded peptide SR1P modulates moonlighting activity of B. subtilis GapA. RNA Biology 2016, 13, 916 -926.

AMA Style

Matthias Gimpel, Sabine Brantl. Dual-function sRNA encoded peptide SR1P modulates moonlighting activity of B. subtilis GapA. RNA Biology. 2016; 13 (9):916-926.

Chicago/Turabian Style

Matthias Gimpel; Sabine Brantl. 2016. "Dual-function sRNA encoded peptide SR1P modulates moonlighting activity of B. subtilis GapA." RNA Biology 13, no. 9: 916-926.

Research paper
Published: 20 November 2015 in RNA Biology
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BsrE/SR5 is a type I TA system from prophage-like element P6 of the B. subtilis chromosome. The 256 nt bsrE RNA encodes a 30 aa toxin. The antitoxin SR5 is a 163 nt antisense RNA. Both genes overlap at their 3′ ends. Overexpression of bsrE causes cell lysis on agar plates, which can be neutralized by sr5 overexpression, whereas deletion of the chromosomal sr5 copy has no effect. SR5 is short-lived with a half-life of ≈7 min, whereas bsrE RNA is stable with a half-life of >80 min. The sr5 promoter is 10-fold stronger than the bsrE promoter. SR5 interacts with the 3′ UTR of bsrE RNA, thereby promoting its degradation by recruiting RNase III. RNase J1 is the main RNase responsible for SR5 and bsrE RNA degradation, and PnpA processes an SR5 precursor to the mature RNA. Hfq stabilizes SR5, but is not required for its inhibitory function. While bsrE RNA is affected by temperature shock and alkaline stress, the amount of SR5 is significantly influenced by various stresses, among them pH, anoxia and iron limitation. Only the latter one is dependent on sigB. Both RNAs are extremely unstable upon ethanol stress due to rapid degradation by RNase Y.

ACS Style

Peter Müller; Natalie Jahn; Christiane Ring; Caroline Maiwald; Robert Neubert; Christin Meißner; Sabine Brantl. A multistress responsive type I toxin-antitoxin system:bsrE/SR5 from theB. subtilischromosome. RNA Biology 2015, 13, 511 -523.

AMA Style

Peter Müller, Natalie Jahn, Christiane Ring, Caroline Maiwald, Robert Neubert, Christin Meißner, Sabine Brantl. A multistress responsive type I toxin-antitoxin system:bsrE/SR5 from theB. subtilischromosome. RNA Biology. 2015; 13 (5):511-523.

Chicago/Turabian Style

Peter Müller; Natalie Jahn; Christiane Ring; Caroline Maiwald; Robert Neubert; Christin Meißner; Sabine Brantl. 2015. "A multistress responsive type I toxin-antitoxin system:bsrE/SR5 from theB. subtilischromosome." RNA Biology 13, no. 5: 511-523.

Review
Published: 01 March 2015 in Plasmid
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Over the past decade, a wealth of small noncoding RNAs (sRNAs) have been discovered in the genomes of almost all bacterial species, where they constitute the most abundant class of posttranscriptional regulators. These sRNAs are key-players in prokaryotic metabolism, stress response and virulence. However, the first bona-fide antisense RNAs had been found already in 1981 in plasmids, where they regulate replication or maintenance. Antisense RNAs involved in plasmid replication control - meanwhile investigated in depth for almost 35 years - employ a variety of mechanisms of action: They regulate primer maturation, inhibit translation of essential replication initiator proteins (Rep proteins) as well as leader peptides or the formation of activator pseudoknots required for efficient rep translation. Alternatively they attenuate transcription or translation of rep mRNAs. Some antisense RNAs collaborate with transcriptional repressors to ensure proper copy-number control. Here, I summarize our knowledge on replication control of the broad-host range plasmid pIP501 that was originally isolated from Streptococcus agalactiae. Plasmid pIP501 uses two copy number-control elements, RNAIII, a cis-encoded antisense RNA, and transcriptional repressor CopR. RNA III mediates transcription attenuation, a rather widespread concept that found its culmination in the recent discovery of riboswitches. A peculiarity of pIP501 is the unusual stability of RNA III, which requires a second function of CopR: CopR does not only repress transcription from the essential repR promoter, but also prevents convergent transcription between rep mRNA and RNAIII, thereby indirectly increasing the amount of RNAIII. The concerted action of these two control elements is necessary to prevent plasmid loss at dangerously low copy numbers.

ACS Style

Sabine Brantl. Antisense-RNA mediated control of plasmid replication – pIP501 revisited. Plasmid 2015, 78, 4 -16.

AMA Style

Sabine Brantl. Antisense-RNA mediated control of plasmid replication – pIP501 revisited. Plasmid. 2015; 78 ():4-16.

Chicago/Turabian Style

Sabine Brantl. 2015. "Antisense-RNA mediated control of plasmid replication – pIP501 revisited." Plasmid 78, no. : 4-16.

Review
Published: 15 August 2014 in Microbiology Spectrum
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Plasmids are selfish genetic elements that normally constitute a burden for the bacterial host cell. This burden is expected to favor plasmid loss. Therefore, plasmids have evolved mechanisms to control their replication and ensure their stable maintenance. Replication control can be either mediated by iterons or by antisense RNAs. Antisense RNAs work through a negative control circuit. They are constitutively synthesized and metabolically unstable. They act both as a measuring device and a regulator, and regulation occurs by inhibition. Increased plasmid copy numbers lead to increasing antisense-RNA concentrations, which, in turn, result in the inhibition of a function essential for replication. On the other hand, decreased plasmid copy numbers entail decreasing concentrations of the inhibiting antisense RNA, thereby increasing the replication frequency. Inhibition is achieved by a variety of mechanisms, which are discussed in detail. The most trivial case is the inhibition of translation of an essential replication initiator protein (Rep) by blockage of the rep -ribosome binding site. Alternatively, ribosome binding to a leader peptide mRNA whose translation is required for efficient Rep translation can be prevented by antisense-RNA binding. In 2004, translational attenuation was discovered. Antisense-RNA-mediated transcriptional attenuation is another mechanism that has, so far, only been detected in plasmids of Gram-positive bacteria. ColE1, a plasmid that does not need a plasmid-encoded replication initiator protein, uses the inhibition of primer formation. In other cases, antisense RNAs inhibit the formation of an activator pseudoknot that is required for efficient Rep translation.

ACS Style

Sabine Brantl. Plasmid Replication Control by Antisense RNAs. Microbiology Spectrum 2014, 2, 1 -0001.

AMA Style

Sabine Brantl. Plasmid Replication Control by Antisense RNAs. Microbiology Spectrum. 2014; 2 (4):1-0001.

Chicago/Turabian Style

Sabine Brantl. 2014. "Plasmid Replication Control by Antisense RNAs." Microbiology Spectrum 2, no. 4: 1-0001.

Review
Published: 10 February 2014 in RNA Biology
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Small regulatory RNAs (sRNAs) that act by base-pairing were first discovered in so-called accessory DNA elements—plasmids, phages, and transposons—where they control replication, maintenance, and transposition. Since 2001, a huge body of work has been performed to predict and identify sRNAs in a multitude of bacterial genomes. The majority of chromosome-encoded sRNAs have been investigated in E. coli and other Gram-negative bacteria. However, during the past five years an increasing number of sRNAs were found in Gram-positive bacteria. Here, we outline our current knowledge on chromosome-encoded sRNAs from low-GC Gram-positive species that act by base-pairing, i.e., an antisense mechanism. We will focus on sRNAs with known targets and defined regulatory mechanisms with special emphasis on Bacillus subtilis.

ACS Style

Sabine Brantl; Reinhold Brückner. Small regulatory RNAs from low-GC Gram-positive bacteria. RNA Biology 2014, 11, 443 -456.

AMA Style

Sabine Brantl, Reinhold Brückner. Small regulatory RNAs from low-GC Gram-positive bacteria. RNA Biology. 2014; 11 (5):443-456.

Chicago/Turabian Style

Sabine Brantl; Reinhold Brückner. 2014. "Small regulatory RNAs from low-GC Gram-positive bacteria." RNA Biology 11, no. 5: 443-456.

Review
Published: 01 July 2012 in Future Microbiology
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SRNAs that act by base pairing were first discovered in plasmids, phages and transposons, where they control replication, maintenance and transposition. Since 2001, however, computational searches were applied that led to the discovery of a plethora of sRNAs in bacterial chromosomes. Whereas the majority of these chromsome-encoded sRNAs have been investigated in Escherichia coli, Salmonella and other Gram-negative bacteria, only a few well-studied examples are known from Gram-positive bacteria. Here, the author summarizes our current knowledge on plasmid- and chromosome-encoded sRNAs from Gram-positive species, thereby focusing on regulatory mechanisms used by these RNAs and their biological role in complex networks. Furthermore, regulatory factors that control the expression of these RNAs will be discussed and differences between sRNAs from Gram-positive and Gram-negative bacteria highlighted. The main emphasis of this review is on sRNAs that act by base pairing (i.e., by an antisense mechanism). Thereby, both plasmid-encoded and chromosome-encoded sRNAs will be considered.

ACS Style

Sabine Brantl. Acting antisense: plasmid- and chromosome-encoded sRNAs from Gram-positive bacteria. Future Microbiology 2012, 7, 853 -871.

AMA Style

Sabine Brantl. Acting antisense: plasmid- and chromosome-encoded sRNAs from Gram-positive bacteria. Future Microbiology. 2012; 7 (7):853-871.

Chicago/Turabian Style

Sabine Brantl. 2012. "Acting antisense: plasmid- and chromosome-encoded sRNAs from Gram-positive bacteria." Future Microbiology 7, no. 7: 853-871.

Journal article
Published: 09 January 2012 in Molecular Microbiology
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Here, we describe bsrG/SR4, a novel type I toxin–antitoxin system from the SPβ prophage region of the Bacillus subtilis chromosome. The 294‐nucleotide bsrG RNA encodes a 38‐amino‐acid toxin, whereas SR4 is a 180‐nucleotide antisense RNA that acts as the antitoxin. Both genes overlap by 123 nucleotides. BsrG expression increases at the onset of stationary phase. The sr4 promoter is 6‐ to 10‐fold stronger than the bsrG promoter. Deletion of sr4 stabilizes bsrG mRNA and causes cell lysis on agar plates, which is due to the BsrG peptide and not the bsrG mRNA. SR4 overexpression could compensate cell lysis caused by overexpression of bsrG. SR4 interacts with the 3′ UTR of bsrG RNA, thereby promoting its degradation. RNase III cleaves the bsrG RNA/SR4 duplex at position 185 of bsrG RNA, but is not essential for the function of the toxin–antitoxin system. Endoribonuclease Y and 3′‐5′ exoribonuclease R participate in the degradation of both bsrG RNA and SR4, whereas PnpA processes three SR4 precursors to the mature RNA. A heat shock at 48°C results in faster degradation and, therefore, significantly decreased amounts of bsrG RNA.

ACS Style

Natalie Jahn; Heike Preis; Christoph Wiedemann; Sabine Brantl. BsrG/SR4 from Bacillus subtilis- the first temperature-dependent type I toxin-antitoxin system. Molecular Microbiology 2012, 83, 579 -598.

AMA Style

Natalie Jahn, Heike Preis, Christoph Wiedemann, Sabine Brantl. BsrG/SR4 from Bacillus subtilis- the first temperature-dependent type I toxin-antitoxin system. Molecular Microbiology. 2012; 83 (3):579-598.

Chicago/Turabian Style

Natalie Jahn; Heike Preis; Christoph Wiedemann; Sabine Brantl. 2012. "BsrG/SR4 from Bacillus subtilis- the first temperature-dependent type I toxin-antitoxin system." Molecular Microbiology 83, no. 3: 579-598.

Book chapter
Published: 28 November 2011 in Regulatory RNAs
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Small RNAs (sRNAs) gained worldwide attention in the late 2002, when the journal Science published a special issue entitled “Small RNAs – Breakthrough of the Year.” However, small antisense RNAs in bacteria involved in the regulation of plasmid replication and maintenance, phage life cycles, and transposition had been investigated in great depth for more than 20 years. Whereas these sRNAs were discovered only fortuitously, systematic computer-based searches have only been used since 2001. Currently, it is estimated that a bacterial genome encodes ∼200–300 sRNAs with diverse functions. To date (2011), about 140 sRNAs are known in Escherichia coli and Salmonella. However, only about 25 of these have been assigned a biological function, indicating that defining their functions continues to be a challenging issue. Systematic searches have also been performed for a few Gram-positive bacterial species. sRNAs in bacteria can be divided into two major groups: The first group regulates gene expression by a base-pairing mechanism with target mRNA, whereas the second group acts by binding of small proteins. This chapter covers mechanisms of action, biological functions, integration in regulatory circuits, and evolutionary aspects of base-pairing and protein-binding sRNAs.

ACS Style

Sabine Brantl. Small Regulatory RNAs (sRNAs): Key Players in Prokaryotic Metabolism, Stress Response, and Virulence. Regulatory RNAs 2011, 73 -109.

AMA Style

Sabine Brantl. Small Regulatory RNAs (sRNAs): Key Players in Prokaryotic Metabolism, Stress Response, and Virulence. Regulatory RNAs. 2011; ():73-109.

Chicago/Turabian Style

Sabine Brantl. 2011. "Small Regulatory RNAs (sRNAs): Key Players in Prokaryotic Metabolism, Stress Response, and Virulence." Regulatory RNAs , no. : 73-109.

Journal article
Published: 01 April 2011 in Microbiology
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CopR is a transcriptional repressor encoded by the broad-host-range streptococcal plasmid pIP501, which also replicates in Bacillus subtilis. It acts in concert with the antisense RNA, RNAIII, to control pIP501 replication. CopR represses transcription of the essential repR mRNA about 10- to 20-fold. In previous work, DNA binding and dimerization constants were determined and the motifs responsible localized. The C terminus of CopR was shown to be required for stability. Furthermore, SELEX of the copR operator revealed that in vivo evolution was for maximal binding affinity. Here, we elucidate the repression mechanism of CopR. Competition assays showed that CopR–operator complexes are 18-fold less stable than RNA polymerase (RNAP)–pII complexes. DNase I footprinting revealed that the binding sites for CopR and RNAP overlap. Gel-shift assays demonstrated that CopR and B. subtilis RNAP cannot bind simultaneously, but compete for binding at promoter pII. Due to its higher intracellular concentration CopR inhibits RNAP binding. Additionally, KMnO4 footprinting experiments indicated that prevention of open complex formation at pII does not further contribute to the repression effect of CopR.

ACS Style

Andreas Licht; Peggy Freede; Sabine Brantl. Transcriptional repressor CopR acts by inhibiting RNA polymerase binding. Microbiology 2011, 157, 1000 -1008.

AMA Style

Andreas Licht, Peggy Freede, Sabine Brantl. Transcriptional repressor CopR acts by inhibiting RNA polymerase binding. Microbiology. 2011; 157 (4):1000-1008.

Chicago/Turabian Style

Andreas Licht; Peggy Freede; Sabine Brantl. 2011. "Transcriptional repressor CopR acts by inhibiting RNA polymerase binding." Microbiology 157, no. 4: 1000-1008.