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Ul Haq I, Brantl S, Müller P. A new role for SR1 from Bacillus subtilis: regulation of sporulation by inhibition of kinA translation. Nucleic Acids Res 2021; 49:10589-10603. [PMID: 34478554 PMCID: PMC8501984 DOI: 10.1093/nar/gkab747] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/27/2021] [Accepted: 08/20/2021] [Indexed: 12/25/2022] Open
Abstract
SR1 is a dual-function sRNA from Bacillus subtilis. It inhibits translation initiation of ahrC mRNA encoding the transcription activator of the arginine catabolic operons. Base-pairing is promoted by the RNA chaperone CsrA, which induces a slight structural change in the ahrC mRNA to facilitate SR1 binding. Additionally, SR1 encodes the small protein SR1P that interacts with glyceraldehyde-3P dehydrogenase A to promote binding to RNase J1 and enhancing J1 activity. Here, we describe a new target of SR1, kinA mRNA encoding the major histidine kinase of the sporulation phosphorelay. SR1 and kinA mRNA share 7 complementary regions. Base-pairing between SR1 and kinA mRNA decreases kinA translation without affecting kinA mRNA stability and represses transcription of the KinA/Spo0A downstream targets spoIIE, spoIIGA and cotA. The initial interaction between SR1 and kinA mRNA occurs 10 nt downstream of the kinA start codon and is decisive for inhibition. The sr1 encoded peptide SR1P is dispensable for kinA regulation. Deletion of sr1 accelerates sporulation resulting in low quality spores with reduced stress resistance and altered coat protein composition which can be compensated by sr1 overexpression. Neither CsrA nor Hfq influence sporulation or spore properties.
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Affiliation(s)
- Inam Ul Haq
- Matthias-Schleiden-Institut für Genetik, Bioinformatik und Molekulare Botanik, AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, Jena D-07743, Germany
| | - Sabine Brantl
- Matthias-Schleiden-Institut für Genetik, Bioinformatik und Molekulare Botanik, AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, Jena D-07743, Germany
| | - Peter Müller
- Matthias-Schleiden-Institut für Genetik, Bioinformatik und Molekulare Botanik, AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, Jena D-07743, Germany
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2
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Abstract
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.
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Affiliation(s)
- Inam Ul Haq
- Friedrich-Schiller-Universität Jena, Matthias-Schleiden-Institut , AG Bakteriengenetik, Jena, Germany
| | - Peter Müller
- Friedrich-Schiller-Universität Jena, Matthias-Schleiden-Institut , AG Bakteriengenetik, Jena, Germany
| | - Sabine Brantl
- Friedrich-Schiller-Universität Jena, Matthias-Schleiden-Institut , AG Bakteriengenetik, Jena, Germany
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Müller P, Gimpel M, Wildenhain T, Brantl S. A new role for CsrA: promotion of complex formation between an sRNA and its mRNA target in Bacillus subtilis. RNA Biol 2019; 16:972-987. [PMID: 31043113 PMCID: PMC6546359 DOI: 10.1080/15476286.2019.1605811] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
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. Abbreviations: aa, amino acid; bp, basepair; nt, nucleotide; PAA, polyacrylamide; SD, Shine Dalgarno.
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Affiliation(s)
- Peter Müller
- a Matthias-Schleiden-Institut für Genetik, Bioinformatik und Molekulare Botanik, AG Bakteriengenetik , Friedrich-Schiller-Universität Jena , Jena , Germany
| | - Matthias Gimpel
- a Matthias-Schleiden-Institut für Genetik, Bioinformatik und Molekulare Botanik, AG Bakteriengenetik , Friedrich-Schiller-Universität Jena , Jena , Germany.,b Institut für Biotechnologie , Fachgebiet Bioverfahrenstechnik , Berlin , Germany
| | - Theresa Wildenhain
- a Matthias-Schleiden-Institut für Genetik, Bioinformatik und Molekulare Botanik, AG Bakteriengenetik , Friedrich-Schiller-Universität Jena , Jena , Germany
| | - Sabine Brantl
- a Matthias-Schleiden-Institut für Genetik, Bioinformatik und Molekulare Botanik, AG Bakteriengenetik , Friedrich-Schiller-Universität Jena , Jena , Germany
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Kohler V, Vaishampayan A, Grohmann E. Broad-host-range Inc18 plasmids: Occurrence, spread and transfer mechanisms. Plasmid 2018; 99:11-21. [PMID: 29932966 DOI: 10.1016/j.plasmid.2018.06.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/17/2018] [Accepted: 06/18/2018] [Indexed: 11/18/2022]
Abstract
Conjugative plasmid transfer is one of the major mechanisms responsible for the spread of antibiotic resistance and virulence genes. The incompatibility (Inc) 18 group of plasmids is a family of plasmids replicating by the theta-mechanism, whose members have been detected frequently in enterococci and streptococci. Inc18 plasmids encode a variety of antibiotic resistances, including resistance to vancomycin, chloramphenicol and the macrolide-lincosamide-streptogramine (MLS) group of antibiotics. These plasmids comprising insertions of Tn1546 were demonstrated to be responsible for the transfer of vancomycin resistance encoded by the vanA gene from vancomycin resistant enterococci (VRE) to methicillin resistant Staphylococcus aureus (MRSA). Thereby vancomycin resistant S. aureus (VRSA) were generated, which are serious multi-resistant pathogens challenging the health care system. Inc18 plasmids are widespread in the clinic and frequently have been detected in the environment, especially in domestic animals and wastewater. pIP501 is one of the best-characterized conjugative Inc18 plasmids. It was originally isolated from a clinical Streptococcus agalactiae strain and is, due to its small size and simplicity, a model to study conjugative plasmid transfer in Gram-positive bacteria. Here, we report on the occurrence and spread of Inc18-type plasmids in the clinic and in different environments as well as on the exchange of the plasmids among them. In addition, we discuss molecular details on the transfer mechanism of Inc18 plasmids and its regulation, as exemplified by the model plasmid pIP501. We finish with an outlook on promising approaches on how to reduce the emerging spread of antibiotic resistances.
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Affiliation(s)
- Verena Kohler
- Institute of Molecular Biosciences, University of Graz, A-8010 Graz, Austria
| | - Ankita Vaishampayan
- Life Sciences and Technology, Beuth University of Applied Sciences Berlin, D-13347 Berlin, Germany
| | - Elisabeth Grohmann
- Life Sciences and Technology, Beuth University of Applied Sciences Berlin, D-13347 Berlin, Germany.
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Abstract
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.
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Chromosomally and Extrachromosomally Mediated High-Level Gentamicin Resistance in Streptococcus agalactiae. Antimicrob Agents Chemother 2016; 60:1702-7. [PMID: 26729498 DOI: 10.1128/aac.01933-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 12/09/2015] [Indexed: 11/20/2022] Open
Abstract
Streptococcus agalactiae (group B Streptococcus [GBS]) is a leading cause of sepsis in neonates. The rate of invasive GBS disease in nonpregnant adults also continues to climb. Aminoglycosides alone have little or no effect on GBS, but synergistic killing with penicillin has been shown in vitro. High-level gentamicin resistance (HLGR) in GBS isolates, however, leads to the loss of a synergistic effect. We therefore performed a multicenter study to determine the frequency of HLGR GBS isolates and to elucidate the molecular mechanisms leading to gentamicin resistance. From eight centers in four countries, 1,128 invasive and colonizing GBS isolates were pooled and investigated for the presence of HLGR. We identified two strains that displayed HLGR (BSU1203 and BSU452), both of which carried the aacA-aphD gene, typically conferring HLGR. However, only one strain (BSU1203) also carried the previously described chromosomal gentamicin resistance transposon designated Tn3706. For the other strain (BSU452), plasmid purification and subsequent DNA sequencing resulted in the detection of plasmid pIP501 carrying a remnant of a Tn3 family transposon. Its ability to confer HLGR was proven by transfer into an Enterococcus faecalis isolate. Conversely, loss of HLGR was documented after curing both GBS BSU452 and the transformed E. faecalis strain from the plasmid. This is the first report showing plasmid-mediated HLGR in GBS. Thus, in our clinical GBS isolates, HLGR is mediated both chromosomally and extrachromosomally.
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Brantl S. Antisense-RNA mediated control of plasmid replication - pIP501 revisited. Plasmid 2014; 78:4-16. [PMID: 25108234 DOI: 10.1016/j.plasmid.2014.07.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/24/2014] [Accepted: 07/26/2014] [Indexed: 02/02/2023]
Abstract
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.
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Affiliation(s)
- Sabine Brantl
- Friedrich-Schiller-Universität Jena, Lehrstuhl für Genetik, AG Bakteriengenetik, Philosophenweg 12, D-07743 Jena, Germany.
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8
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Gimpel M, Brantl S. Construction of a modular plasmid family for chromosomal integration in Bacillus subtilis. J Microbiol Methods 2012; 91:312-7. [PMID: 22982324 DOI: 10.1016/j.mimet.2012.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 09/06/2012] [Accepted: 09/06/2012] [Indexed: 10/27/2022]
Abstract
The investigation of molecular processes involves the generation of knockout strains, the determination of promoter strength and protein overexpression. Here, we report the construction of the multifunctional pMG expression vector family for integration into the Bacillus subtilis chromosome that allows gene expression under single copy conditions. The pMG family enables a rapid exchange of all features for integration, selection and gene expression with or without N-terminal strep-tags. This modular architecture increases the applicabilities for these plasmids tremendously, permitting the construction of pMG derivatives for chromosomal integration at versatile loci and in different Bacillus species under control of natural or heterologous constitutive or inducible promoters. Additionally, the possible replacement of the antibiotic resistance cassettes helps circumvent problems that arise when the use of more than three antibiotics is required. Furthermore, the high copy number and structural stability of the pUC19-based pMG vectors in Escherichia coli facilitates template production for target host transformation.
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Affiliation(s)
- Matthias Gimpel
- AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, D-07743 Jena, Germany.
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Jahn N, Preis H, Wiedemann C, Brantl S. BsrG/SR4 from Bacillus subtilis--the first temperature-dependent type I toxin-antitoxin system. Mol Microbiol 2012; 83:579-98. [PMID: 22229825 DOI: 10.1111/j.1365-2958.2011.07952.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
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.
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Affiliation(s)
- Natalie Jahn
- Friedrich-Schiller-Universität Jena, Biologisch-Pharmazeutische Fakultät, AG Bakteriengenetik, Philosophenweg 12, Jena, Germany
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Gimpel M, Heidrich N, Mäder U, Krügel H, Brantl S. A dual-function sRNA from B. subtilis: SR1 acts as a peptide encoding mRNA on the gapA operon. Mol Microbiol 2010; 76:990-1009. [PMID: 20444087 DOI: 10.1111/j.1365-2958.2010.07158.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Small non-coding RNAs (sRNAs) have been found to regulate gene expression in all three kingdoms of life. So far, relatively little is known about sRNAs from Gram-positive bacteria. SR1 is a regulatory sRNA from the Bacillus subtilis chromosome that inhibits by base-pairing translation initiation of ahrC mRNA encoding a transcriptional activator of the arginine catabolic operons. Here we present a novel target of SR1, the glycolytic gapA operon. Both microarray and Northern blot analyses show that the amount of gapA operon mRNA is significantly higher in the presence of SR1 when cells were grown in complex medium until stationary phase. Translational lacZ fusions and toeprinting analyses demonstrate that SR1 does not promote translation of gapA mRNA. By contrast, the half-life of gapA operon mRNA is strongly reduced in the sr1 knockout strain. SR1 does not act as a base-pairing sRNA on gapA operon mRNA. Instead, we demonstrate that the 39 aa peptide encoded by SR1, SR1P, is responsible for the effect of SR1 on the gapA operon. We show that SR1P binds GapA, thereby stabilizing the gapA operon mRNA by a hitherto unknown mechanism. SR1 is the first dual-function sRNA found in B. subtilis.
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Affiliation(s)
- Matthias Gimpel
- AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, Jena D-07743, Germany
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Rosvoll TC, Pedersen T, Sletvold H, Johnsen PJ, Sollid JE, Simonsen GS, Jensen LB, Nielsen KM, Sundsfjord A. PCR-based plasmid typing inEnterococcus faeciumstrains reveals widely distributed pRE25-, pRUM-, pIP501- and pHTβ-related replicons associated with glycopeptide resistance and stabilizing toxin–antitoxin systems. ACTA ACUST UNITED AC 2010; 58:254-68. [DOI: 10.1111/j.1574-695x.2009.00633.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
Regulatory small RNAs (sRNAs) in bacterial genomes have become a focus of research over the past 8 years. Whereas more than 100 such sRNAs have been found in Escherichia coli, relatively little is known about sRNAs in gram-positive bacteria. Using a computational approach, we identified two sRNAs in intergenic regions of the Bacillus subtilis genome, SR1 and SR2 (renamed BsrF). Recently, we demonstrated that SR1 inhibits the translation initiation of the transcriptional activator AhrC. Here, we describe detection of BsrF, its expression profile, and its regulation by CodY. Furthermore, we mapped the secondary structure of BsrF. BsrF is expressed in complex and minimal media in all growth phases in B. subtilis and, with a similar expression profile, also in Bacillus amyloliquefaciens. Neither overexpression nor deletion of bsrF affected the growth of B. subtilis. BsrF was found to be long-lived in complex and minimal media. Analysis of 13 putative transcription factor binding sites upstream of bsrF revealed only an effect for CodY. Here, we showed by using Northern blotting, lacZ reporter gene fusions, in vitro transcription, and DNase I footprinting that the transcription of bsrF is activated by CodY in the presence of branched-chain amino acids and GTP. Furthermore, BsrF transcription was increased 1.5- to 2-fold by glucose in the presence of branched-chain amino acids, and this increase was independent of the known glucose-dependent regulators. BsrF is the second target for which transcriptional activation by CodY has been discovered.
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Licht A, Golbik R, Brantl S. Identification of ligands affecting the activity of the transcriptional repressor CcpN from Bacillus subtilis. J Mol Biol 2008; 380:17-30. [PMID: 18511073 DOI: 10.1016/j.jmb.2008.05.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Revised: 04/29/2008] [Accepted: 05/02/2008] [Indexed: 11/18/2022]
Abstract
Carbon catabolite repression in Bacillus subtilis is mediated primarily by the major regulator CcpA. However, sugar-dependent repression of three genes, sr1 encoding a small nontranslated RNA and two genes coding for gluconeogenic enzymes, gapB and pckA, is carried out by the transcriptional repressor CcpN (control catabolite protein of gluconeogenic genes). It has previously been shown that ccpN is constitutively expressed, which leads to a constant occupation of all operators with CcpN. Since this would not allow for specific regulation, a ligand that modulates CcpN activity is required. In vitro transcription assays demonstrated that CcpN is able to specifically repress transcription to a small extent at the three mentioned promoters in the absence of an activating ligand. Upon testing of several ligands, including nucleotides and glycolysis intermediates, it could be shown that ATP is able to specifically enhance the repressing activity of CcpN, and this effect was more pronounced at a slightly acidic pH. Furthermore, ADP was found to specifically counteract the repressive effect of ATP. Circular dichroism measurements demonstrated a significant alteration of CcpN structure in the presence of ATP at acidic pH and in the presence of ADP. Electrophoretic mobility shift assays revealed that neither ATP nor ADP altered the affinity of CcpN for its operators. Therefore, we hypothesise that the effect of ligand-bound CcpN on the RNA polymerase might be due to a conformational switch that alters the interaction between the two proteins. Based on these results, a working model for CcpN action is discussed.
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Affiliation(s)
- Andreas Licht
- AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, D-07743 Jena, Germany.
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Heidrich N, Brantl S. Antisense-RNA mediated transcriptional attenuation: importance of a U-turn loop structure in the target RNA of plasmid pIP501 for efficient inhibition by the antisense RNA. J Mol Biol 2003; 333:917-29. [PMID: 14583190 DOI: 10.1016/j.jmb.2003.09.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Antisense-RNA mediated gene regulation has been found and studied in detail mainly in prokaryotic accessory DNA elements. In spite of different regulatory mechanisms, in all cases a rapid interaction between antisense and target RNA has been shown to be crucial for efficient regulation. Recently, a sequence comparison revealed in 45 antisense RNA control systems a 5' YUNR motif indicative for the formation of a U-turn structure in either an antisense or a target RNA loop and confirmed in the case of the hok/sok system of plasmid R1 its importance for regulation.Here, we demonstrate the importance of the 5' YUNR motif in the target RNA (RNAII) loop L1 of the replication control system of plasmid pIP501. The effect of four individual mutations in L1 was studied in vivo and in vitro. Mutations that maintained the putative U-turn or swapped it from sense to antisense RNA were silent, whereas mutations that eliminated the 5'-YUNR motif showed two- to threefold elevated copy numbers in vivo in correlation with three- to fourfold reduced inhibition rate constants of the complementary RNAIII species in vitro, whereas the half-lives of all RNAIII species were not affected. ENU probing experiments confirmed the U-turn structure for the silent mutation (N-C) and disruption of this structure upon alteration of the invariant U or inversion of the YUNR motif-containing loop. RNA secondary structure probing excluded loop size alterations as a reason for altered inhibition rates. Implications for the pathway and efficiency of RNAII/RNAIII interaction, and hence, pIP501 copy-number control, are discussed.
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Affiliation(s)
- Nadja Heidrich
- Institut für Molekularbiologie, Friedrich-Schiller-Universität Jena, Winzerlaer Strasse 10, D-07745 Jena, Germany
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15
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Brantl S, Wagner EGH. An antisense RNA-mediated transcriptional attenuation mechanism functions in Escherichia coli. J Bacteriol 2002; 184:2740-7. [PMID: 11976303 PMCID: PMC135013 DOI: 10.1128/jb.184.10.2740-2747.2002] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antisense RNA-mediated transcriptional attenuation is a regulatory mechanism operating in the replication control of two groups of plasmids in gram-positive bacteria, the pT181 group and the inc18 family, represented by pIP501. In contrast, this control mechanism has so far not been identified in gram-negative bacteria or their plasmids. In this work we asked whether such a mechanism can be supported by Escherichia coli. The core replication control regions of plasmids pT181 and pIP501 were transferred into this heterologous host. In vivo lacZ reporter gene assays showed that the antisense RNAs of these plasmids can inhibit lacZ expression and that most of this effect can be accounted for by reduced mRNA readthrough. Northern analyses confirmed that the ratio of attenuated to readthrough target RNA was increased in the presence of the cognate antisense RNA, as expected for this mechanism. Similarly, both antisense RNAs induced premature termination of their cognate target RNAs in an E. coli in vitro transcription system, whereas the noncognate antisense RNAs had no effect. Thus, this report shows that antisense RNA-mediated transcriptional attenuation is supported by at least one gram-negative host, although the data indicate that inhibitory efficiencies are lower than those for, e.g., Bacillus subtilis. Possible explanations for the apparent absence of this control mode in plasmids of gram-negative bacteria are discussed.
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Affiliation(s)
- Sabine Brantl
- Institut für Molekularbiologie, Friedrich-Schiller-Universität Jena, Winzerlaer Strasse 10, Jena D-07745, Germany.
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Schwarz FV, Perreten V, Teuber M. Sequence of the 50-kb conjugative multiresistance plasmid pRE25 from Enterococcus faecalis RE25. Plasmid 2001; 46:170-87. [PMID: 11735367 DOI: 10.1006/plas.2001.1544] [Citation(s) in RCA: 128] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The complete 50,237-bp DNA sequence of the conjugative and mobilizing multiresistance plasmid pRE25 from Enterococcus faecalis RE25 was determined. The plasmid had 58 putative open reading frames, 5 of which encode resistance to 12 antimicrobials. Chloramphenicol acetyltransferase and the 23S RNA methylase are identical to gene products of the broad-host-range plasmid pIP501 from Streptococcus agalactiae. In addition, a 30.5-kb segment is almost identical to pIP501. Genes encoding an aminoglycoside 6-adenylyltransferase, a streptothricin acetyltransferase, and an aminoglycoside phosphotransferase are arranged in tandem on a 7.4-kb fragment as previously reported in Tn5405 from Staphylococcus aureus and in pJH1 from E. faecalis. One interrupted and five complete IS elements as well as three replication genes were also identified. pRE25 was transferred by conjugation to E. faecalis, Listeria innocua, and Lactococcus lactis by means of a transfer region that appears similar to that of pIP501. It is concluded that pRE25 may contribute to the further spread of antibiotic-resistant microorganisms via food into the human community.
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Affiliation(s)
- F V Schwarz
- Laboratory for Food Microbiology, Swiss Federal Institute of Technology of Zurich, Zurich, CH-8092, Switzerland
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Wilcks A, Smidt L, Okstad OA, Kolsto AB, Mahillon J, Andrup L. Replication mechanism and sequence analysis of the replicon of pAW63, a conjugative plasmid from Bacillus thuringiensis. J Bacteriol 1999; 181:3193-200. [PMID: 10322022 PMCID: PMC93776 DOI: 10.1128/jb.181.10.3193-3200.1999] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A 5.8-kb fragment of the large conjugative plasmid pAW63 from Bacillus thuringiensis subsp. kurstaki HD73 containing all the information for autonomous replication was cloned and sequenced. By deletion analysis, the pAW63 replicon was reduced to a 4.1-kb fragment harboring four open reading frames (ORFs). Rep63A (513 amino acids [aa]), encoded by the largest ORF, displayed strong similarity (40% identity) to the replication proteins from plasmids pAMbeta1, pIP501, and pSM19035, indicating that the pAW63 replicon belongs to the pAMbeta1 family of gram-positive theta-replicating plasmids. This was confirmed by the facts that no single-stranded DNA replication intermediates could be detected and that replication was found to be dependent on host-gene-encoded DNA polymerase I. An 85-bp region downstream of Rep63A was also shown to have strong similarity to the origins of replication of pAMbeta1 and pIP501, and it is suggested that this region contains the bona fide pAW63 ori. The protein encoded by the second large ORF, Rep63B (308 aa), was shown to display similarity to RepB (34% identity over 281 aa) and PrgP (32% identity over 310 aa), involved in copy control of the Enterococcus faecalis plasmids pAD1 and pCF10, respectively. No significant similarity to known proteins or DNA sequences could be detected for the two smallest ORFs. However, the location, size, hydrophilicity, and orientation of ORF6 (107 codons) were analogous to those features of the putative genes repC and prgO, which encode stability functions on plasmids pAD1 and pCF10, respectively. The cloned replicon of plasmid pAW63 was stably maintained in Bacillus subtilis and B. thuringiensis and displayed incompatibility with the native pAW63. Hybridization experiments using the cloned replicon as a probe showed that pAW63 has similarity to large plasmids from other B. thuringiensis subsp. kurstaki strains and to a strain of B. thuringiensis subsp. alesti.
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Affiliation(s)
- A Wilcks
- National Institute of Occupational Health, Copenhagen, Denmark
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18
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Abstract
pAMbeta1 is a plasmid isolated from Enterococcus faecalis which replicates in Bacillus subtilis by a unidirectional theta mechanism. It has been shown previously that initiation of pAMbeta1 replication requires a plasmid-encoded protein (RepE) and a short origin and is carried out by the host DNA polymerase I. It is not known which primer is used by this polymerase for initiating replication. Here, we report that a transcription fork passing through the origin is a limiting factor for plasmid replication. Transcription that activates the origin is initiated at the repE promoter and is thus regulated by the plasmid copy-number control system. Two lines of evidence suggest that the transcription generates the primer for the DNA polymerase I. First, the transcription must start upstream from the origin and progress in the direction of replication to be effective. Second, 3' ends of RNA transcripts initiated upstream of the origin map within the origin, provided that the Rep protein and an intact origin are present. This is the first report for simultaneous requirement of a transcription fork, a replication protein and the DNA polymerase I in initiation of DNA replication.
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Affiliation(s)
- C Bruand
- Laboratoire de Génétique Microbienne, INRA, Jouy-en-Josas, France.
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19
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Le Chatelier E, Ehrlich SD, Jannière L. Countertranscript-driven attenuation system of the pAM beta 1 repE gene. Mol Microbiol 1996; 20:1099-112. [PMID: 8809762 DOI: 10.1111/j.1365-2958.1996.tb02550.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The plasmid-encoded RepE protein is absolutely essential and rate-limiting for replication of the promiscuous plasmid pAM beta 1 originating from Enterococcus faecalis. We previously showed that the rep gene is transcribed from a promoter that is negatively regulated (approximately 10-fold reduction) by the CopF repressor. In this report, we show that this transcription is decreased a further approximately 10-times by a countertranscript-driven transcriptional attenuation system. Extensive mutagenesis revealed that this system operates by a mechanism similar to that previously described for the unrelated repC gene of plasmid pT181.
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Affiliation(s)
- E Le Chatelier
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, Jouy en Josas, France
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Brantl S, Wagner EG. An unusually long-lived antisense RNA in plasmid copy number control: in vivo RNAs encoded by the streptococcal plasmid pIP501. J Mol Biol 1996; 255:275-88. [PMID: 8551520 DOI: 10.1006/jmbi.1996.0023] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The main regulator of pIP501 replication is an antisense RNA (RNAIII) that induces transcriptional attenuation of the essential RNAII. Previous studies identified the termination point in vivo and demonstrated attenuation in vitro. This in vivo analysis confirms the appearance of attenuated RNAII dependent on RNAIII. Half-lives and intracellular levels of RNAII and RNAIII were determined: in a Bacillus subtilis cell harboring a wild-type pIP501 plasmid, approximately 50 molecules RNAII and 1000 to 2000 molecules of RNAIII were measured, respectively. The half-life of RNAII was in the range of that of other target RNAs, whereas that of RNAIII (approximately 30 minutes) was unusually long, representing a so far unprecedented case of a metabolically stable antisense RNA regulating plasmid copy number. Long antisense RNA half-life is predicted to yield sluggish control and instability of maintenance. We propose a model for how plasmid pIP501 may avoid this problem by using both the repressor CopR and the antisense RNAIII for control. Four stem-loop mutants of RNAII/RNAIII with elevated copy numbers were characterized for in vitro antisense/target RNA binding, RNAIII half-life, incompatibility, and attenuation in vivo. Two classes were found: interaction mutants and half-life mutants. The former suggest a key function for loop LIII of RNAIII as recognition loop in the primary steps of RNAII/RNAIII interaction.
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Affiliation(s)
- S Brantl
- Institut für Molekularbiologie Friedrich-Schiller-Universität Jena, Germany
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21
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Brantl S. The copR gene product of plasmid pIP501 acts as a transcriptional repressor at the essential repR promoter. Mol Microbiol 1994; 14:473-83. [PMID: 7533881 DOI: 10.1111/j.1365-2958.1994.tb02182.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The amount of the rate-limiting replication initiator protein RepR of plasmid pIP501 is negatively controlled by an antisense RNA (RNAIII) and a dispensable protein (CopR). Deletions or mutations in either component cause a 10-20-fold copy number increase. RNAIII induces transcription attenuation of the repR mRNA; the mode of CopR action remained unclear. To test the function of CopR, transcriptional fusions of promoters pI, pII and pIII with lacZ were integrated into the Bacillus subtilis chromosome. CopR and/or RepR were supplied in trans, and LacZ synthesis measured. The results show that CopR represses the repR promoter pII. Neither CopR nor RepR autoregulate their promoters. Gel mobility shift assays indicate that CopR binds to a 44 bp DNA fragment comprising the inverted repeat upstream of pII.
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Affiliation(s)
- S Brantl
- Friedrich-Schiller-Universität Jena, Institut für Molekularbiologie, Germany
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22
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Le Chatelier E, Ehrlich SD, Jannière L. The pAM beta 1 CopF repressor regulates plasmid copy number by controlling transcription of the repE gene. Mol Microbiol 1994; 14:463-71. [PMID: 7885230 DOI: 10.1111/j.1365-2958.1994.tb02181.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
pAM beta 1 is a low-copy-number, promiscuous plasmid from Gram-positive bacteria that replicates by a unidirectional theta-type mode. Its replication is initiated by an original mechanism, involving the positive rate-limiting RepE protein. Here we show that the pAM beta 1-encoded CopF protein is involved in negative regulation of the plasmid copy number. CopF represses approximately 10-fold the transcription initiated at the promoter of the repE gene and binds to a 31 bp segment which is located immediately upstream of the -35 box of the repE promoter. We propose that CopF inhibits initiation of transcription at the repE promoter by binding to its operator.
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Affiliation(s)
- E Le Chatelier
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, Jouy en Josas, France
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Bruand C, Le Chatelier E, Ehrlich SD, Jannière L. A fourth class of theta-replicating plasmids: the pAM beta 1 family from gram-positive bacteria. Proc Natl Acad Sci U S A 1993; 90:11668-72. [PMID: 8265606 PMCID: PMC48045 DOI: 10.1073/pnas.90.24.11668] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Plasmid pAM beta 1 from Enterococcus faecalis uses a unidirectional theta mode of replication. We show here that this replication (i) is dependent on a plasmid-encoded replication protein (Rep) but not on a DNA structure typical for origins of most Rep-dependent plasmids and (ii) is initiated by DNA polymerase I (PolI). pAM beta 1 minimal replicon shares no homology with highly conserved ColE1-type replicons, which use PolI for initiation but do not encode a Rep, or with ColE2 and ColE3 replicons, which require PolI for replication and encode a Rep. We propose that pAM beta 1 and a number of other naturally occurring and closely related plasmids from a distinct plasmid class.
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Affiliation(s)
- C Bruand
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, Jouy en Josas, France
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Brantl S, Birch-Hirschfeld E, Behnke D. RepR protein expression on plasmid pIP501 is controlled by an antisense RNA-mediated transcription attenuation mechanism. J Bacteriol 1993; 175:4052-61. [PMID: 8320221 PMCID: PMC204834 DOI: 10.1128/jb.175.13.4052-4061.1993] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Expression of the rate-limiting initiator protein RepR of plasmid pIP501 is controlled by the antisense RNAIII. Mutational alteration of individual G residues within the single-stranded loops of RNAIII led to an increase in copy number. In contrast to the G-rich single-stranded loops, two smaller AT-rich loops of RNAIII were found to be dispensable for its inhibitory function. Reciprocal mutations in the same loop compensated for each other's effect, and a destabilization of the major stem structure of RNAIII also resulted in an increased copy number. These data were consistent with the idea that the interaction of RNAIII with its target starts with the formation of a kissing complex between the single-stranded loops of both molecules. The repR mRNA leader sequence, which includes the target of RNAIII, is able to assume two alternative structures due to the presence of two inverted repeats the individual sequences of which are mutually complementary. In the presence of the antisense RNAIII, one of these inverted repeats (IR2) is forced to fold into a transcriptional terminator structure that prevents transcription of the repR gene. In the absence of RNAIII, formation of the transcriptional terminator is prevented and expression of the essential repR gene can proceed normally. This antisense RNA-driven transcriptional attenuation mechanism was supported by extensive deletional analysis and direct evidence that IR2 functions as a transcriptional terminator.
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Affiliation(s)
- S Brantl
- Institut für Molekularbiologie, Jena, Germany
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Brantl S, Behnke D. Characterization of the minimal origin required for replication of the streptococcal plasmid pIP501 in Bacillus subtilis. Mol Microbiol 1992; 6:3501-10. [PMID: 1474894 DOI: 10.1111/j.1365-2958.1992.tb01785.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
By using deletional analysis the origin of replication, oriR, of the streptococcal plasmid pIP501 in Bacillus subtilis has been mapped at a position immediately downstream of the repR gene. Determination of both the right and left border of oriR allowed the definition of a sequence of a maximum of 52 nucleotides which theoretically constitutes the minimal origin of replication. Recently, the start point of leading-strand synthesis of the closely related plasmid pAM beta 1 has been mapped at a position which is located exactly in the middle of this sequence (Bruand et al., 1991). The function of oriR did not depend on its location downstream of the repR gene. Translocation of oriR-containing fragments to other regions of the plasmid proved to be possible. The smallest translocated fragment that still reconstituted autonomous replication was 72bp in size. This fragment was also active in directing the replication of an Escherichia coli plasmid in B. subtilis when the RepR protein was supplied in trans from a repR gene integrated into the host chromosome. The transformation efficiency of plasmids carrying translocated oriR fragments showed a certain dependence on the fragment length and orientation. The DNA sequence of oriR included an inverted repeat, both branches of which appeared to be essential for oriR function. The repeats of oriR shared sequence similarity with a repeat located upstream of promoter pII, which has been suggested to be involved in autoregulation of repR expression.
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Affiliation(s)
- S Brantl
- Institute for Molecular Biology, Jena, Germany
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