1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Grohmann E, Goessweiner-Mohr N, Brantl S. DNA-Binding Proteins Regulating pIP501 Transfer and Replication. Front Mol Biosci 2016; 3:42. [PMID: 27563645 PMCID: PMC4981023 DOI: 10.3389/fmolb.2016.00042] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 07/29/2016] [Indexed: 12/21/2022] Open
Abstract
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 detected in clinical Enterococcus faecalis and Enterococcus faecium strains. 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 function: It acts as transcriptional repressor at the repR promoter and, in addition, prevents convergent transcription of RNAIII and repR mRNA (RNAII), which indirectly increases 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 Streptomyces 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 overlapping 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.
Collapse
Affiliation(s)
- Elisabeth Grohmann
- Division of Infectious Diseases, University Medical Center FreiburgFreiburg im Breisgau, Germany; Life Sciences and Technology, Beuth University of Applied Sciences BerlinBerlin, Germany
| | - Nikolaus Goessweiner-Mohr
- Center for Structural System Biology, University Medical Center Hamburg-EppendorfHamburg, Germany; Deutsches Elektronen-SynchrotronHamburg, Germany; Institute of Molecular Biotechnology, Austrian Academy of SciencesVienna, Austria; Research Institute of Molecular PathologyVienna, Austria
| | - Sabine Brantl
- Lehrstuhl für Genetik, Biologisch-Pharmazeutische Fakultät, AG Bakteriengenetik, Friedrich-Schiller-Universität Jena Jena, Germany
| |
Collapse
|
3
|
Müller P, Jahn N, Ring C, Maiwald C, Neubert R, Meißner C, Brantl S. A multistress responsive type I toxin-antitoxin system: bsrE/SR5 from the B. subtilis chromosome. RNA Biol 2016; 13:511-23. [PMID: 26940229 DOI: 10.1080/15476286.2016.1156288] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Peter Müller
- a Friedrich-Schiller-Universität Jena , Lehrstuhl für Genetik , AG Bakteriengenetik, Philosophenweg, Jena , Germany
| | - Natalie Jahn
- a Friedrich-Schiller-Universität Jena , Lehrstuhl für Genetik , AG Bakteriengenetik, Philosophenweg, Jena , Germany
| | - Christiane Ring
- a Friedrich-Schiller-Universität Jena , Lehrstuhl für Genetik , AG Bakteriengenetik, Philosophenweg, Jena , Germany
| | - Caroline Maiwald
- a Friedrich-Schiller-Universität Jena , Lehrstuhl für Genetik , AG Bakteriengenetik, Philosophenweg, Jena , Germany
| | - Robert Neubert
- a Friedrich-Schiller-Universität Jena , Lehrstuhl für Genetik , AG Bakteriengenetik, Philosophenweg, Jena , Germany
| | - Christin Meißner
- a Friedrich-Schiller-Universität Jena , Lehrstuhl für Genetik , AG Bakteriengenetik, Philosophenweg, Jena , Germany
| | - Sabine Brantl
- a Friedrich-Schiller-Universität Jena , Lehrstuhl für Genetik , AG Bakteriengenetik, Philosophenweg, Jena , Germany
| |
Collapse
|
4
|
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.
Collapse
|
5
|
Construction of an environmental safe Bacillus thuringiensis engineered strain against Coleoptera. Appl Microbiol Biotechnol 2016; 100:4027-34. [DOI: 10.1007/s00253-015-7250-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 11/24/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
|
6
|
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.
Collapse
Affiliation(s)
- Sabine Brantl
- Friedrich-Schiller-Universität Jena, Lehrstuhl für Genetik, AG Bakteriengenetik, Philosophenweg 12, D-07743 Jena, Germany.
| |
Collapse
|
7
|
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.
Collapse
Affiliation(s)
- Andreas Licht
- AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Philosophenweg 12, D-07743 Jena, Germany.
| | | | | |
Collapse
|
8
|
Dmowski M, Sitkiewicz I, Ceglowski P. Characterization of a novel partition system encoded by the delta and omega genes from the streptococcal plasmid pSM19035. J Bacteriol 2006; 188:4362-72. [PMID: 16740943 PMCID: PMC1482978 DOI: 10.1128/jb.01922-05] [Citation(s) in RCA: 25] [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
High segregational stability of the streptococcal plasmid pSM19035 is achieved by the concerted action of systems involved in plasmid copy number control, multimer resolution, and postsegregational killing. In this study, we demonstrate the role of two genes, delta and omega, in plasmid stabilization by a partition mechanism. We show that these two genes can stabilize the native pSM19035 replicon as well as other theta- and sigma-type plasmids in Bacillus subtilis. In contrast to other known partition systems, in this case the two genes are transcribed separately; however, they are coregulated by the product of the parB-like gene omega. Analysis of mutants of the parA-like gene delta showed that the Walker A ATPase motif is necessary for plasmid stabilization. The ParB-like product of the omega gene binds to three regions containing repeated WATCACW heptamers, localized in the copS (regulation of plasmid copy number), delta, and omega promoter regions. We demonstrate that all three of these regions can cause partition-mediated incompatibility. Moreover, our data suggest that each of these could play the role of a centromere-like sequence. We conclude that delta and omega constitute a novel type of plasmid stabilization system.
Collapse
Affiliation(s)
- Michal Dmowski
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawiskiego 5A, 02-106 Warsaw, Poland.
| | | | | |
Collapse
|
9
|
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.
Collapse
Affiliation(s)
- Sabine Brantl
- Institut für Molekularbiologie, Friedrich-Schiller-Universität Jena, Winzerlaer Strasse 10, Jena D-07745, Germany.
| | | |
Collapse
|
10
|
Abstract
We studied DNA binding of a transcriptional repressor, CopF, displayed on a filamentous phage. Mutagenesis of a putative helix-turn-helix motif of CopF and of certain bases of the operator abolished the protein-DNA interaction, establishing the elements involved in CopF function and showing that phage display can be used to study repressor proteins.
Collapse
Affiliation(s)
- E d'Alençon
- Génétique Microbienne, INRA, Domaine de Vilvert, 78352 Jouy en Josas Cedex, France
| | | |
Collapse
|
11
|
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.
Collapse
Affiliation(s)
- A Wilcks
- National Institute of Occupational Health, Copenhagen, Denmark
| | | | | | | | | | | |
Collapse
|
12
|
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.
Collapse
Affiliation(s)
- C Bruand
- Laboratoire de Génétique Microbienne, INRA, Jouy-en-Josas, France.
| | | |
Collapse
|
13
|
Pujol C, Chédin F, Ehrlich SD, Jannière L. Inhibition of a naturally occurring rolling-circle replicon in derivatives of the theta-replicating plasmid pIP501. Mol Microbiol 1998; 29:709-18. [PMID: 9723911 DOI: 10.1046/j.1365-2958.1998.00940.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The mechanisms ensuring regulation of DNA replication in genomes containing multiple replicons are poorly understood. In this report, we addressed this question by analysing in Bacillus subtilis the replication of a derivative of the promiscuous plasmid pIP501 that carries a rolling-circle and a theta replicon. Genetic analyses revealed that the rolling-circle replicon is strongly inhibited in the derivative and that inhibition requires three elements involved in theta replication: the replication origin, the initiator RepR protein and strong transcription of the repR gene. Inhibition is, however, independent of DNA synthesis at the theta origin. We conclude that rolling-circle inhibition is caused by an inhibitory signal encoded by the theta replicon and propose that the signal is composed, at least, of the RepR protein bound to its cognate origin.
Collapse
Affiliation(s)
- C Pujol
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | | | | |
Collapse
|
14
|
Abstract
Replication of plasmid pIP501 is regulated at a step subsequent to transcription initiation by an antisense RNA (RNAIII) and transcriptionally by a repressor protein, CopR. Previously, it had been shown that CopR binds to a 44-bp DNA fragment upstream of and overlapping the repR promoter pII. Subsequently, we found that high-copy-number pIP501 derivatives lacking copR and low-copy-number derivatives containing copR produced the same intracellular amounts of RNAIII. This suggested a second, hitherto-unknown function of CopR. In this report, we show that CopR does not affect the half-life of RNAIII. Instead, we demonstrate in vivo that, in the presence of both pII and pIII, CopR provided in cis or in trans causes an increase in the intracellular concentration of RNAIII and that this effect is due to the function of the protein rather than its mRNA. We suggest that, in the absence of CopR, the increased (derepressed) RNAII transcription interferes, in cis, with initiation of transcription of RNAIII (convergent transcription), resulting in a lower RNAIII/plasmid ratio. When CopR is present, the pII promoter is repressed to >90%, so that convergent transcription is mostly abolished and RNAIII/plasmid ratios are high. The hypothesis that RNAII transcription influences promoter pIII through induced changes in DNA supercoiling is supported by the finding that the gyrase inhibitor novobiocin affects the accumulation of both sense and antisense RNA. The dual role of CopR in repression of RNAII transcription and in prevention of convergent transcription is discussed in the context of replication control of pIP501.
Collapse
MESH Headings
- Bacillus subtilis/genetics
- Bacterial Proteins
- Blotting, Northern
- Cloning, Molecular
- DNA, Superhelical/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/physiology
- Escherichia coli/genetics
- Escherichia coli Proteins
- Gene Expression Regulation, Bacterial
- Novobiocin/pharmacology
- Plasmids/genetics
- Promoter Regions, Genetic
- RNA/analysis
- RNA/metabolism
- RNA, Antisense/analysis
- RNA, Antisense/drug effects
- RNA, Antisense/metabolism
- Recombination, Genetic
- Trans-Activators/genetics
- Trans-Activators/physiology
- Transcription, Genetic
- Transformation, Genetic
Collapse
Affiliation(s)
- S Brantl
- Institut für Molekularbiologie, Friedrich-Schiller-Universität Jena, Germany.
| | | |
Collapse
|
15
|
Steinmetzer K, Brantl S. Plasmid pIP501 encoded transcriptional repressor CopR binds asymmetrically at two consecutive major grooves of the DNA. J Mol Biol 1997; 269:684-93. [PMID: 9223633 DOI: 10.1006/jmbi.1997.1083] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Replication of the streptococcal plasmid pIP501 is regulated by the CopR protein and an antisense-RNA (RNAIII). CopR acts as transcriptional repressor at the essential repR promoter pII by binding to inverted repeat IR1 upstream of pII. To further characterize the interaction of CopR with its target, footprinting studies were performed. Methylation interference identified three guanine bases (G240, G242 and G251) in the top strand and two (G252 and G254) in the bottom strand contacted by CopR in the major groove of the DNA. Missing base interference revealed the contribution of the bases in the neighbourhood of these guanine bases to the specific DNA-protein contacts. Phosphate residues essential for CopR binding were determined by ethylation interference. The recognition sequence was localized at the centre of inverted repeat IR1. CopR contacts two consecutive major grooves (site I and II) on the same face of the DNA. Although the two sites share a common sequence motif, neighbouring bases are contacted differently. DNA fragments carrying single mutations in site I or II were analysed by band shift assays. Gel filtration and native gel electrophoresis demonstrated that CopR exists only as a dimer. A sigmoidal binding curve of CopR to its DNA target was observed and allowed the determination of the apparent dissociation constant K(D). The significance of the relatively high apparent K(D) for the role of CopR in pIP501 copy number regulation is discussed.
Collapse
Affiliation(s)
- K Steinmetzer
- Institut für Molekularbiologie, Friedrich-Schiller-Universität Jena, Germany
| | | |
Collapse
|
16
|
Burian J, Guller L, Macor M, Kay WW. Small cryptic plasmids of multiplasmid, clinical Escherichia coli. Plasmid 1997; 37:2-14. [PMID: 9073577 DOI: 10.1006/plas.1996.1273] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Clinical isolates of Escherichia coli were found to host a multiplicity of plasmids. These were resolved from plasmid gel profiles, from the properties of various transconjugants and transformants of E. coli DH1, by the topoisomerase I relaxation of covalently closed circle plasmid DNA, by electron microscopy, and by the determination of their compatibilities. The majority of these were unusually small, cryptic plasmids (SCPs). From one strain, KL4, 13 electrophoretic bands were resolved to five plasmids, three of which were SCPs. SCPs were phenotypically barren, and the smallest of these, pKL1, contained barely enough information for self-replication. A derivative of pKL1, pKL1Km, in which the transposon was restricted to a small 350-bp region, was stably maintained in Shigella, Salmonella, Serratia, and Citrobacter species and its replication was polA independent. pKL1 encoded only a single protein, RepA (Mr 17960), which specifically bound to pKL1 DNA. No apparent homologies with other RepA protein sequences could be detected. Thus the SCP, pKL1, is a novel minimal plasmid replicon encoding only enough information to ensure perpetuation. A hypothesis is presented describing SCPs as a class of selfish DNA that persists simply due to its ability to replicate and to its stability based on high copy number.
Collapse
Affiliation(s)
- J Burian
- Faculty of Natural Sciences, Comenius University, Mlynská dolina B-2, Bratislava, Slovakia
| | | | | | | |
Collapse
|
17
|
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.
Collapse
Affiliation(s)
- E Le Chatelier
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | | |
Collapse
|
18
|
Ramesh A, Panda AK, Maiti BR, Mukhopadhyay A. Studies on plasmid stability and LTB production by recombinant Vibrio cholerae in batch and chemostat cultures: a lesson for optimizing conditions for chemical induction. J Biotechnol 1995; 43:45-51. [PMID: 8573322 DOI: 10.1016/0168-1656(95)00121-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Plasmid content, its stability and the expression of B-subunit of Escherichia coli heat-labile enterotoxin (LTB) in Vibrio cholerae/r-pMMB68 system have been studied in batch as well as in chemostat cultures. Upon induction with isopropyl-beta-D-thiogalactopyranoside (IPTG), cultures secreted LTB into the extracellular milieu. Highest specific LTB production rate of 7.3 mg mg-1h-1 was achieved in batch culture induced at the late exponential growth phase. The plasmid pMMB68 was fairly stable up to 20 generations, even in the absence of selection pressure. Instability of the plasmid was accelerated in the presence of IPTG and at higher dilution rates. Maximum productivity of 2.1 mg l-1 h-1 was achieved in continuous culture, which remained constant at a range of dilution rates from 0.20 to 0.35 h-1.
Collapse
Affiliation(s)
- A Ramesh
- Department of Chemical Engineering, Indian Institute of Technology, Kharagpur, West Bengal, India
| | | | | | | |
Collapse
|
19
|
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.
Collapse
Affiliation(s)
- E Le Chatelier
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | | |
Collapse
|
20
|
Frère J, Benachour A, Novel M, Novel G. Identification of the theta-type minimal replicon of theLactococcus lactis subsp.lactis CNRZ270 lactose protease plasmid pUCL22. Curr Microbiol 1993. [DOI: 10.1007/bf01570865] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
21
|
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.
Collapse
Affiliation(s)
- S Brantl
- Institut für Molekularbiologie, Jena, Germany
| | | | | |
Collapse
|
22
|
Ceglowski P, Lurz R, Alonso JC. Functional analysis of pSM19035-derived replicons in Bacillus subtilis. FEMS Microbiol Lett 1993. [DOI: 10.1111/j.1574-6968.1993.tb06159.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
23
|
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.
Collapse
Affiliation(s)
- S Brantl
- Institute for Molecular Biology, Jena, Germany
| | | |
Collapse
|