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Picker MA, Karney MMA, Gerson TM, Karabachev A, Duhart J, McKenna J, Wing H. Localized modulation of DNA supercoiling, triggered by the Shigella anti-silencer VirB, is sufficient to relieve H-NS-mediated silencing. Nucleic Acids Res 2023; 51:3679-3695. [PMID: 36794722 PMCID: PMC10164555 DOI: 10.1093/nar/gkad088] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/17/2023] Open
Abstract
In Bacteria, nucleoid structuring proteins govern nucleoid dynamics and regulate transcription. In Shigella spp., at ≤30°C, the histone-like nucleoid structuring protein (H-NS) transcriptionally silences many genes on the large virulence plasmid. Upon a switch to 37°C, VirB, a DNA binding protein and key transcriptional regulator of Shigella virulence, is produced. VirB functions to counter H-NS-mediated silencing in a process called transcriptional anti-silencing. Here, we show that VirB mediates a loss of negative DNA supercoils from our plasmid-borne, VirB-regulated PicsP-lacZ reporter in vivo. The changes are not caused by a VirB-dependent increase in transcription, nor do they require the presence of H-NS. Instead, the VirB-dependent change in DNA supercoiling requires the interaction of VirB with its DNA binding site, a critical first step in VirB-dependent gene regulation. Using two complementary approaches, we show that VirB:DNA interactions in vitro introduce positive supercoils in plasmid DNA. Subsequently, by exploiting transcription-coupled DNA supercoiling, we reveal that a localized loss of negative supercoils is sufficient to alleviate H-NS-mediated transcriptional silencing independently of VirB. Together, our findings provide novel insight into VirB, a central regulator of Shigella virulence and, more broadly, a molecular mechanism that offsets H-NS-dependent silencing of transcription in bacteria.
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Affiliation(s)
- Michael A Picker
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Monika M A Karney
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Taylor M Gerson
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
| | | | - Juan C Duhart
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Joy A McKenna
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Helen J Wing
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
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Picker MA, Karney MMA, Gerson TM, Karabachev AD, Duhart JC, McKenna JA, Wing HJ. Localized modulation of DNA supercoiling, triggered by the Shigella anti-silencer VirB, is sufficient to relieve H-NS-mediated silencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523335. [PMID: 36711906 PMCID: PMC9882051 DOI: 10.1101/2023.01.09.523335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In Bacteria, nucleoid structuring proteins govern nucleoid dynamics and regulate transcription. In Shigella spp ., at ≤ 30 °C, the histone-like nucleoid structuring protein (H-NS) transcriptionally silences many genes on the large virulence plasmid. Upon a switch to 37 °C, VirB, a DNA binding protein and key transcriptional regulator of Shigella virulence, is produced. VirB functions to counter H-NS-mediated silencing in a process called transcriptional anti-silencing. Here, we show that VirB mediates a loss of negative DNA supercoils from our plasmid-borne, VirB-regulated PicsP-lacZ reporter, in vivo . The changes are not caused by a VirB-dependent increase in transcription, nor do they require the presence of H-NS. Instead, the VirB-dependent change in DNA supercoiling requires the interaction of VirB with its DNA binding site, a critical first step in VirB-dependent gene regulation. Using two complementary approaches, we show that VirB:DNA interactions in vitro introduce positive supercoils in plasmid DNA. Subsequently, by exploiting transcription-coupled DNA supercoiling, we reveal that a localized loss of negative supercoils is sufficient to alleviate H-NS-mediated transcriptional silencing, independently of VirB. Together, our findings provide novel insight into VirB, a central regulator of Shigella virulence and more broadly, a molecular mechanism that offsets H-NS-dependent silencing of transcription in bacteria.
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Development of TaqMan real-time PCR assays for monitoring Vibrio harveyi infection and a plasmid harbored by virulent strains in European abalone Haliotis tuberculata aquaculture. AQUACULTURE 2013. [DOI: 10.1016/j.aquaculture.2013.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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ParAB-mediated intermolecular association of plasmid P1 parS sites. Virology 2011; 421:192-201. [PMID: 22018490 DOI: 10.1016/j.virol.2011.09.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 08/05/2011] [Accepted: 09/28/2011] [Indexed: 11/20/2022]
Abstract
The P1 plasmid partition system depends on ParA-ParB proteins acting on centromere-like parS sites for a faithful plasmid segregation during the Escherichia coli cell cycle. In vivo we placed parS into host E. coli chromosome and on a Sop(+) F plasmid and found that the stability of a P1 plasmid deleted for parA-parB could be partially restored when parB was expressed in trans. In vitro, parS, conjugated to magnetic beads could capture free parS DNA fragment in presence of ParB. In vitro, ParA stimulated ParB-mediated association of intermolecular parS sites in an ATP-dependent manner. However, in the presence of ADP, ParA reduced ParB-mediated pairing to levels below that seen by ParB alone. ParB of P1 pairs the parS sites of plasmids in vivo and fragments in vitro. Our findings support a model whereby ParB complexes P1 plasmids, ParA-ATP stimulates this interaction and ParA-ADP inhibits ParB pairing activity in a parS-independent manner.
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Leroy Q, Lebrigand K, Armougom F, Barbry P, Thiéry R, Raoult D. Coxiella burnetii transcriptional analysis reveals serendipity clusters of regulation in intracellular bacteria. PLoS One 2010; 5:e15321. [PMID: 21203564 PMCID: PMC3006202 DOI: 10.1371/journal.pone.0015321] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 11/05/2010] [Indexed: 11/19/2022] Open
Abstract
Coxiella burnetii, the causative agent of the zoonotic disease Q
fever, is mainly transmitted to humans through an aerosol route. A spore-like
form allows C. burnetii to resist different environmental
conditions. Because of this, analysis of the survival strategies used by this
bacterium to adapt to new environmental conditions is critical for our
understanding of C. burnetii pathogenicity. Here, we report the
early transcriptional response of C. burnetii under temperature
stresses. Our data show that C. burnetii exhibited minor
changes in gene regulation under short exposure to heat or cold shock. While
small differences were observed, C. burnetii seemed to respond
similarly to cold and heat shock. The expression profiles obtained using
microarrays produced in-house were confirmed by quantitative RT-PCR. Under
temperature stresses, 190 genes were differentially expressed in at least one
condition, with a fold change of up to 4. Globally, the differentially expressed
genes in C. burnetii were associated with bacterial division,
(p)ppGpp synthesis, wall and membrane biogenesis and, especially,
lipopolysaccharide and peptidoglycan synthesis. These findings could be
associated with growth arrest and witnessed transformation of the bacteria to a
spore-like form. Unexpectedly, clusters of neighboring genes were differentially
expressed. These clusters do not belong to operons or genetic networks; they
have no evident associated functions and are not under the control of the same
promoters. We also found undescribed but comparable clusters of regulation in
previously reported transcriptomic analyses of intracellular bacteria, including
Rickettsia sp. and Listeria monocytogenes.
The transcriptomic patterns of C. burnetii observed under
temperature stresses permits the recognition of unpredicted clusters of
regulation for which the trigger mechanism remains unidentified but which may be
the result of a new mechanism of epigenetic regulation.
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Affiliation(s)
- Quentin Leroy
- Unité de Recherche en Maladies Infectieuses et Tropicales
Emergentes, CNRS-IRD, UMR 6236, Faculté de Médecine,
Université de la Méditerranée, Marseille,
France
| | - Kevin Lebrigand
- Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), UMR
6079 CNRS/UNSA, Sophia Antipolis, France
| | - Fabrice Armougom
- Unité de Recherche en Maladies Infectieuses et Tropicales
Emergentes, CNRS-IRD, UMR 6236, Faculté de Médecine,
Université de la Méditerranée, Marseille,
France
| | - Pascal Barbry
- Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), UMR
6079 CNRS/UNSA, Sophia Antipolis, France
| | - Richard Thiéry
- Unité de Pathologie des Ruminants, Agence Française de
Sécurité Sanitaire des Aliments (AFSSA) Sophia Antipolis,
France
| | - Didier Raoult
- Unité de Recherche en Maladies Infectieuses et Tropicales
Emergentes, CNRS-IRD, UMR 6236, Faculté de Médecine,
Université de la Méditerranée, Marseille,
France
- * E-mail:
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Abstract
Non-essential extra-chromosomal DNA elements such as plasmids are responsible for their own propagation in dividing host cells, and one means to ensure this is to carry a miniature active segregation system reminiscent of the mitotic spindle. Plasmids that are maintained at low numbers in prokaryotic cells have developed a range of such active partitioning systems, which are characterized by an impressive simplicity and efficiency and which are united by the use of dynamic, nucleotide-driven filaments to separate and position DNA molecules. A comparison of different plasmid segregation systems reveals (i) how unrelated filament-forming and DNA-binding proteins have been adopted and modified to create a range of simple DNA segregating complexes and (ii) how subtle changes in the few components of these DNA segregation machines has led to a remarkable diversity in the molecular mechanisms of closely related segregation systems. Here, our current understanding of plasmid segregation systems is reviewed and compared with other DNA segregation systems, and this is extended by a discussion of basic principles of plasmid segregation systems, evolutionary implications and the relationship between an autonomous DNA element and its host cell.
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Affiliation(s)
- Jeanne Salje
- MRC Laboratory of Molecular Biology, Cambridge, UK.
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Pratto F, Suzuki Y, Takeyasu K, Alonso JC. Single-molecule analysis of proteinxDNA complexes formed during partition of newly replicated plasmid molecules in Streptococcus pyogenes. J Biol Chem 2009; 284:30298-306. [PMID: 19726689 DOI: 10.1074/jbc.m109.035410] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Streptococcus pyogenes pSM19035 partition locus is ubiquitous among plasmids from vancomycin- or methicillin-resistant bacteria. An increasing understanding of this segregation system may highlight novel protein targets that could be blocked to curb bacterial proliferation. pSM19035 segregation depends on two homodimeric (delta(2) (ParA) and omega(2) (ParB)) proteins and six cis-acting centromeric noncurved parS sites. In the presence of ATPxMg(2+), delta(2) (delta x ATP x Mg(2+))(2) binds DNA in a sequence-independent manner. Protein omega(2) binds with high affinity and cooperatively to B-form parS DNA. Atomic force microscopy experiments indicate that about 10 omega(2) molecules bind parS, consisting of 10 contiguous iterons. Protein (delta x ATP x Mg(2+))(2), by interacting with the N terminus of omega(2) bound to parS, loses its association with DNA and relocalizes with omega(2).parS to form a ternary complex ((deltaxATPxMg(2+))(2) x omega(2) x parS) with the DNA remaining in straight B-form. Then, the interaction of two (delta x ATP x Mg(2+))(2).omega(2).parS complexes via delta(2) promotes pairing of a plasmid subfraction. (deltaD60A x ATP x Mg(2+))(2), which binds but does not hydrolyze ATP, leads to accumulation of pairing intermediates, suggesting that ATP hydrolysis induces plasmid separation. We propose that the molar omega(2):delta(2) ratio regulates the different stages of pSM19035 segregation, pairing, and delta(2) polymerization, before cell division.
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Affiliation(s)
- Florencia Pratto
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
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Abstract
The mitotic apparatus that a plasmid uses to ensure its stable inheritance responds to the appearance of an additional copy of the plasmid's centromere by segregating it from the pre-existing copies: if the new copy arises by replication of the plasmid the result is partition, if it arrives on a different plasmid the result is incompatibility. Incompatibility thus serves as a probe of the partition mechanism. Coupling of distinct plasmids via their shared centromeres to form mixed pairs has been the favoured explanation for centromere-based incompatibility, because it supports a long-standing assumption that pairing of plasmid replicas is a prerequisite for their partition into daughter cells. Recent results from molecular genetic and fluorescence microscopy studies challenge this mixed pairing model. Partition incompatibility is seen to result from various processes, including titration, randomized positioning and a form of mixed pairing that is based on co-activation of the same partition event rather than direct contact between partition complexes. The perspectives thus opened onto the partition mechanism confirm the continuing utility of incompatibility as an approach to understanding bacterial mitosis. The results considered are compatible with the view that direct pairing of plasmids is not essential to plasmid partition.
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Affiliation(s)
- Jean-Yves Bouet
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de Recherche Scientifique, Campus Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France
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Bouet JY, Ah-Seng Y, Benmeradi N, Lane D. Polymerization of SopA partition ATPase: regulation by DNA binding and SopB. Mol Microbiol 2006; 63:468-81. [PMID: 17166176 DOI: 10.1111/j.1365-2958.2006.05537.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In bacteria, mitotic stability of plasmids and many chromosomes depends on replicon-specific systems which comprise a centromere, a centromere-binding protein and an ATPase. Dynamic self-assembly of the ATPase appears to enable active partition of replicon copies into cell-halves, but for most ATPases (the Walker-box type) the mechanism is unknown. Also unknown is how the host cell contributes to partition. We have examined the effects of non-sequence-specific DNA on in vitro self-assembly of the SopA partition ATPase of plasmid F. SopA underwent polymerization provided ATP was present. DNA inhibited this polymerization and caused breakdown of pre-formed polymers. Centromere-binding protein SopB counteracted DNA-mediated inhibition by itself binding to and masking the DNA, as well as by stimulating polymerization directly. The results suggest that in vivo, SopB smothers DNA by spreading from sopC, allowing SopA-ATP polymerization which initiates plasmid displacement. We propose that SopB and nucleoid DNA regulate SopA polymerization and hence partition.
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Affiliation(s)
- Jean-Yves Bouet
- Laboratoire de Microbiologie et de Génétique Moléculaire, UMR5100 CNRS, Toulouse, France.
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