1
|
Figueroa-Bossi N, Fernández-Fernández R, Kerboriou P, Bouloc P, Casadesús J, Sánchez-Romero MA, Bossi L. Transcription-driven DNA supercoiling counteracts H-NS-mediated gene silencing in bacterial chromatin. Nat Commun 2024; 15:2787. [PMID: 38555352 PMCID: PMC10981669 DOI: 10.1038/s41467-024-47114-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/19/2024] [Indexed: 04/02/2024] Open
Abstract
In all living cells, genomic DNA is compacted through interactions with dedicated proteins and/or the formation of plectonemic coils. In bacteria, DNA compaction is achieved dynamically, coordinated with dense and constantly changing transcriptional activity. H-NS, a major bacterial nucleoid structuring protein, is of special interest due to its interplay with RNA polymerase. H-NS:DNA nucleoprotein filaments inhibit transcription initiation by RNA polymerase. However, the discovery that genes silenced by H-NS can be activated by transcription originating from neighboring regions has suggested that elongating RNA polymerases can disassemble H-NS:DNA filaments. In this study, we present evidence that transcription-induced counter-silencing does not require transcription to reach the silenced gene; rather, it exerts its effect at a distance. Counter-silencing is suppressed by introducing a DNA gyrase binding site within the intervening segment, suggesting that the long-range effect results from transcription-driven positive DNA supercoils diffusing toward the silenced gene. We propose a model wherein H-NS:DNA complexes form in vivo on negatively supercoiled DNA, with H-NS bridging the two arms of the plectoneme. Rotational diffusion of positive supercoils generated by neighboring transcription will cause the H-NS-bound negatively-supercoiled plectoneme to "unroll" disrupting the H-NS bridges and releasing H-NS.
Collapse
Affiliation(s)
- Nara Figueroa-Bossi
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France
| | - Rocío Fernández-Fernández
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Sevilla, Spain
| | - Patricia Kerboriou
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France
| | - Philippe Bouloc
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France
| | - Josep Casadesús
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | | | - Lionello Bossi
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France.
| |
Collapse
|
2
|
Colgan AM, Quinn HJ, Kary SC, Mitchenall LA, Maxwell A, Cameron ADS, Dorman CJ. Negative supercoiling of DNA by gyrase is inhibited in Salmonella enterica serovar Typhimurium during adaptation to acid stress. Mol Microbiol 2018; 107:734-746. [PMID: 29352745 DOI: 10.1111/mmi.13911] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 01/15/2018] [Accepted: 01/16/2018] [Indexed: 12/26/2022]
Abstract
DNA in intracellular Salmonella enterica serovar Typhimurium relaxes during growth in the acidified (pH 4-5) macrophage vacuole and DNA relaxation correlates with the upregulation of Salmonella genes involved in adaptation to the macrophage environment. Bacterial ATP levels did not increase during adaptation to acid pH unless the bacterium was deficient in MgtC, a cytoplasmic-membrane-located inhibitor of proton-driven F1 F0 ATP synthase activity. Inhibiting ATP binding by DNA gyrase and topo IV with novobiocin enhanced the effect of low pH on DNA relaxation. Bacteria expressing novobiocin-resistant (NovR ) derivatives of gyrase or topo IV also exhibited DNA relaxation at acid pH, although further relaxation with novobiocin was not seen in the strain with NovR gyrase. Thus, inhibition of the negative supercoiling activity of gyrase was the primary cause of enhanced DNA relaxation in drug-treated bacteria. The Salmonella cytosol reaches pH 5-6 in response to an external pH of 4-5: the ATP-dependent DNA supercoiling activity of purified gyrase was progressively inhibited by lowering the pH in this range, as was the ATP-dependent DNA relaxation activity of topo IV. We propose that DNA relaxation in Salmonella within macrophage is due to acid-mediated impairment of the negative supercoiling activity of gyrase.
Collapse
Affiliation(s)
- Aoife M Colgan
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Heather J Quinn
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Stefani C Kary
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland.,Department of Biology, Institute for Microbial Systems and Society, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Lesley A Mitchenall
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Andrew D S Cameron
- Department of Biology, Institute for Microbial Systems and Society, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Charles J Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| |
Collapse
|
3
|
Higgins NP, Vologodskii AV. Topological Behavior of Plasmid DNA. Microbiol Spectr 2015; 3:10.1128/microbiolspec.PLAS-0036-2014. [PMID: 26104708 PMCID: PMC4480603 DOI: 10.1128/microbiolspec.plas-0036-2014] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Indexed: 11/20/2022] Open
Abstract
The discovery of the B-form structure of DNA by Watson and Crick led to an explosion of research on nucleic acids in the fields of biochemistry, biophysics, and genetics. Powerful techniques were developed to reveal a myriad of different structural conformations that change B-DNA as it is transcribed, replicated, and recombined and as sister chromosomes are moved into new daughter cell compartments during cell division. This article links the original discoveries of superhelical structure and molecular topology to non-B form DNA structure and contemporary biochemical and biophysical techniques. The emphasis is on the power of plasmids for studying DNA structure and function. The conditions that trigger the formation of alternative DNA structures such as left-handed Z-DNA, inter- and intra-molecular triplexes, triple-stranded DNA, and linked catenanes and hemicatenanes are explained. The DNA dynamics and topological issues are detailed for stalled replication forks and for torsional and structural changes on DNA in front of and behind a transcription complex and a replisome. The complex and interconnected roles of topoisomerases and abundant small nucleoid association proteins are explained. And methods are described for comparing in vivo and in vitro reactions to probe and understand the temporal pathways of DNA and chromosome chemistry that occur inside living cells.
Collapse
Affiliation(s)
- N Patrick Higgins
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
| | | |
Collapse
|
4
|
Rovinskiy N, Agbleke AA, Chesnokova O, Pang Z, Higgins NP. Rates of gyrase supercoiling and transcription elongation control supercoil density in a bacterial chromosome. PLoS Genet 2012; 8:e1002845. [PMID: 22916023 PMCID: PMC3420936 DOI: 10.1371/journal.pgen.1002845] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 06/07/2012] [Indexed: 12/23/2022] Open
Abstract
Gyrase catalyzes negative supercoiling of DNA in an ATP-dependent reaction that helps condense bacterial chromosomes into a compact interwound "nucleoid." The supercoil density (σ) of prokaryotic DNA occurs in two forms. Diffusible supercoil density (σ(D)) moves freely around the chromosome in 10 kb domains, and constrained supercoil density (σ(C)) results from binding abundant proteins that bend, loop, or unwind DNA at many sites. Diffusible and constrained supercoils contribute roughly equally to the total in vivo negative supercoil density of WT cells, so σ = σ(C)+σ(D). Unexpectedly, Escherichia coli chromosomes have a 15% higher level of σ compared to Salmonella enterica. To decipher critical mechanisms that can change diffusible supercoil density of chromosomes, we analyzed strains of Salmonella using a 9 kb "supercoil sensor" inserted at ten positions around the genome. The sensor contains a complete Lac operon flanked by directly repeated resolvase binding sites, and the sensor can monitor both supercoil density and transcription elongation rates in WT and mutant strains. RNA transcription caused (-) supercoiling to increase upstream and decrease downstream of highly expressed genes. Excess upstream supercoiling was relaxed by Topo I, and gyrase replenished downstream supercoil losses to maintain an equilibrium state. Strains with TS gyrase mutations growing at permissive temperature exhibited significant supercoil losses varying from 30% of WT levels to a total loss of σ(D) at most chromosome locations. Supercoil losses were influenced by transcription because addition of rifampicin (Rif) caused supercoil density to rebound throughout the chromosome. Gyrase mutants that caused dramatic supercoil losses also reduced the transcription elongation rates throughout the genome. The observed link between RNA polymerase elongation speed and gyrase turnover suggests that bacteria with fast growth rates may generate higher supercoil densities than slow growing species.
Collapse
Affiliation(s)
- Nikolay Rovinskiy
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Andrews Akwasi Agbleke
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Olga Chesnokova
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Zhenhua Pang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Cathay Industrial Biotech, Shanghai, China
| | - N. Patrick Higgins
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
| |
Collapse
|
5
|
Booker BM, Deng S, Higgins NP. DNA topology of highly transcribed operons in Salmonella enterica serovar Typhimurium. Mol Microbiol 2010; 78:1348-64. [PMID: 21143310 DOI: 10.1111/j.1365-2958.2010.07394.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Bacteria differ from eukaryotes by having the enzyme DNA gyrase, which catalyses the ATP-dependent negative supercoiling of DNA. Negative supercoils are essential for condensing chromosomes into an interwound (plectonemic) and branched structure known as the nucleoid. Topo-1 removes excess supercoiling in an ATP-independent reaction and works with gyrase to establish a topological equilibrium where supercoils move within 10 kb domains bounded by stochastic barriers along the sequence. However, transcription changes the stochastic pattern by generating supercoil diffusion barriers near the sites of gene expression. Using supercoil-dependent Tn3 and γδ resolution assays, we studied DNA topology upstream, downstream and across highly transcribed operons. Whenever two Res sites flanked efficiently transcribed genes, resolution was inhibited and the loss in recombination efficiency was proportional to transcription level. Ribosomal RNA operons have the highest transcription rates, and resolution assays at the rrnG and rrnH operons showed inhibitory levels 40-100 times those measured in low-transcription zones. Yet, immediately upstream and downstream of RNA polymerase (RNAP) initiation and termination sites, supercoiling characteristics were similar to poorly transcribed zones. We present a model that explains why RNAP blocks plectonemic supercoil movement in the transcribed track and suggests how gyrase and TopA control upstream and downstream transcription-driven supercoiling.
Collapse
Affiliation(s)
- Betty M Booker
- Department of Biochemistry and Molecular Genetics, University of Alabama , Birmingham, AL 35294-0024, USA
| | | | | |
Collapse
|
6
|
Samul R, Leng F. Transcription-coupled hypernegative supercoiling of plasmid DNA by T7 RNA polymerase in Escherichia coli topoisomerase I-deficient strains. J Mol Biol 2007; 374:925-35. [PMID: 17980389 DOI: 10.1016/j.jmb.2007.10.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2007] [Revised: 09/08/2007] [Accepted: 10/02/2007] [Indexed: 10/22/2022]
Abstract
Transcription by RNA polymerase can stimulate negative DNA supercoiling in Escherichia coli topA strains. This phenomenon has been explained by a "twin-supercoiled-domain" model of transcription in which positive DNA supercoils are generated in front of a translocating RNA polymerase and negative supercoils behind it. However, since there is lack of a specific system to study the factors governing this biologically important process, the parameters regulating transcription-coupled DNA supercoiling (TCDS) in E.coli still remain elusive. Here, we describe our efforts to study TCDS in E.coli using a newly developed system. This system consists of a topA strain, VS111(DE3) or DM800(DE3), in which a lambdaDE3 prophage containing a T7 RNA polymerase gene under the control of lacUV5 promoter has been integrated into the cell chromosome, along with a set of plasmids producing RNA transcripts of various lengths by T7 RNA polymerase. Using this system, we found that transcription by T7 RNA polymerase strikingly induced the formation of hypernegatively supercoiled plasmid DNA. We also discovered, for the first time, that TCDS was dependent on the length of RNA transcripts in vivo, precisely predicted by the twin-supercoiled-domain model of transcription. Furthermore, our results demonstrated that hypernegative supercoiling of plasmid DNA by T7 RNA polymerase did not require anchoring of DNA to the bacterial cytoplasmic membrane. These results indicate that a transcribing RNA polymerase alone is sufficient to cause a change in local DNA superhelicity, which can have a powerful impact on the conformation and function of critical DNA sequence elements such as promoters and DNA replication origins.
Collapse
Affiliation(s)
- Rebecca Samul
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | | |
Collapse
|
7
|
Blanc-Potard AB, Labesse G, Figueroa-Bossi N, Bossi L. Mutation at the "exit gate" of the salmonella gyrase a subunit suppresses a defect in the gyrase B subunit. J Bacteriol 2005; 187:6841-4. [PMID: 16166547 PMCID: PMC1251596 DOI: 10.1128/jb.187.19.6841-6844.2005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Salmonella enterica serovar Typhimurium, an S431P substitution in the B subunit of gyrase (allele gyrB651) confers resistance to nalidixic acid and causes reduced DNA superhelicity and hypersensitivity to novobiocin. Selection for novobiocin resistance allowed isolation of a mutation in the gyrA gene (allele gyrA659), a T467S substitution, which partially suppresses the supercoiling defect of gyrB651. Modeling analysis suggests that this mutation acts by destabilizing the GyrA bottom dimer interface. This is the first example of a gyrA mutation that compensates for a gyrB defect.
Collapse
Affiliation(s)
- Anne-Béatrice Blanc-Potard
- Avenir team Institut National de la Santé et de la Recherche Médicale, Unité 431, Faculté de Médecine, CS 83021, Avenue J. F. Kennedy, 30908 Nîmes Cedex 02, France.
| | | | | | | |
Collapse
|
8
|
Stein RA, Deng S, Higgins NP. Measuring chromosome dynamics on different time scales using resolvases with varying half-lives. Mol Microbiol 2005; 56:1049-61. [PMID: 15853889 PMCID: PMC1373788 DOI: 10.1111/j.1365-2958.2005.04588.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The bacterial chromosome is organized into multiple independent domains, each capable of constraining the plectonemic negative supercoil energy introduced by DNA gyrase. Different experimental approaches have estimated the number of domains to be between 40 and 150. The site-specific resolution systems of closely related transposons Tn3 and gammadelta are valuable tools for measuring supercoil diffusion and analysing bacterial chromosome dynamics in vivo. Once made, the wild-type resolvase persists in cells for time periods greater than the cell doubling time. To examine chromosome dynamics over shorter time frames that are more closely tuned to processes like inducible transcription, we constructed a set of resolvases with cellular half-lives ranging from less than 5 min to 30 min. Analysing chromosomes on different time scales shows domain structure to be dynamic. Rather than the 150 domains detected with the Tn3 resolvase, wild-type cells measured over a 10 min time span have more than 400 domains per genome equivalent, and some gyrase mutants exceed 1000.
Collapse
Affiliation(s)
- Richard A. Stein
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Shuang Deng
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - N. Patrick Higgins
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| |
Collapse
|
9
|
Amzallag GN. Adaptive changes in bacteria: a consequence of nonlinear transitions in chromosome topology? J Theor Biol 2004; 229:361-9. [PMID: 15234203 DOI: 10.1016/j.jtbi.2004.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2003] [Revised: 01/11/2004] [Accepted: 04/06/2004] [Indexed: 10/26/2022]
Abstract
Adaptive changes in bacteria are generally considered to result from random mutations selected by the environment. This interpretation is challenged by the non-randomness of genomic changes observed following ageing or starvation in bacterial colonies. A theory of adaptive targeting of sequences for enzymes involved in DNA transactions is proposed here. It is assumed that the sudden leakage of cAMP consecutive to starvation induces a rapid drop in the ATP/ADP ratio that inactivates the homeostasis in control of the level of DNA supercoiling. This phase change enables the emergence of local modifications in chromosome topology in relation to the missing metabolites, a first stage in expression of an adaptive status in which DNA transactions are induced. The nonlinear perspective proposed here is homologous to that already suggested for adaptation of pluricellular organisms during their development. In both cases, phases of robustness in regulation networks for genetic expression are interspaced by critical periods of breakdown of the homeostatic regulations during which, through isolation of nodes from a whole network, specific changes with adaptive value may locally occur.
Collapse
Affiliation(s)
- G N Amzallag
- The Judea Center for Research and Development, Carmel 90404, Israel.
| |
Collapse
|
10
|
El Hanafi D, Bossi L. Activation and silencing of leu-500 promoter by transcription-induced DNA supercoiling in the Salmonella chromosome. Mol Microbiol 2000; 37:583-94. [PMID: 10931352 DOI: 10.1046/j.1365-2958.2000.02015.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The notion that transcription can generate supercoils in the DNA template largely stems from work with small circular plasmids. In the present work, we tested this model in the bacterial chromosome using a supercoiling-sensitive promoter as a functional sensor of superhelicity changes. The leu-500 promoter of Salmonella typhimurium is a mutant and inactive variant of the leucine operon promoter that regains activity if negative DNA supercoiling rises above normal levels, typically as a result of mutations affecting DNA topoisomerase I (topA mutants). Activation of the leu-500 promoter was analysed in topA mutant cells harbouring transcriptionally inducible tet or cat gene cassettes inserted in the region upstream from the leu operon. Some insertions inhibited leu-500 promoter activation in the absence of inducer. This effect is dramatic in the interval between 1.7 kb and 0.6 kb from the leu operon, suggesting that the insertions physically interfere with the mechanism responsible for activation. Superimposed on these effects, transcription of the inserted gene stimulated or inhibited leu-500 promoter activity depending on whether this gene was oriented divergently from the leu operon or in the same direction respectively. Interestingly, transcription-mediated inhibition of leu-500 promoter was observed with inserts as far as 5 kb from the leu operon, and it could be relieved by the introduction of a strong gyrase site between the inserted element and the leu-500 promoter. These results are consistent with the idea that transcriptionally generated positive and negative supercoils can diffuse along chromosomal DNA and, depending on their topological sign, elicit opposite responses from the leu-500 promoter.
Collapse
Affiliation(s)
- D El Hanafi
- Centre de Génétique Moléculaire, CNRS, 91198 Gif-sur-Yvette, France
| | | |
Collapse
|
11
|
Abstract
Transcription can induce high levels of negative supercoiling into plasmid DNA under some circumstances. This is especially true when the plasmid carries a functional tetracycline-resistance gene tetA, and is borne in a topA strain of Escherichia coli or Salmonella typhimurium. An important mechanism in transcription-induced supercoiling is believed to be the twin supercoiled-domain effect resulting from hindered rotation of the transcriptional complex, and this is very much more efficient where there is coupled transcription, translation and membrane insertion of the gene product. However, we have noted that strong promoters inserted into tetA-carrying plasmids can greatly increase the fraction of hypersupercoiled DNA. We show here that this effect is clearly present when the inserted promoter transcribes a very short segment of DNA (down to transcript lengths of approximately 45 nt), and where there is no possibility of translation of the RNA transcript. We suggest that the repeated helical opening due to transcriptional initiation is a significant contributor to the induction of high levels of supercoiling.
Collapse
Affiliation(s)
- D Chen
- Department of Biochemistry, The University of Dundee, Dundee, DD1 4HN, UK
| | | |
Collapse
|
12
|
Abstract
In bacteria, DNA supercoil movement is restricted to subchromosomal regions or 'domains.' To elucidate the nature of domain boundaries, we analysed reaction kinetics for gammadelta site-specific resolution in six chromosomal intervals ranging in size from 14 to 90 kb. In stationary cultures of Salmonella typhimurium, resolution kinetics were rapid for both short and long intervals, suggesting that random stationary barriers occur with a 30% probability at approximately 80 kb intervals along DNA. To test the biochemical nature of domain barriers, a genetic screen was used to look for mutants with small domains. Rare temperature-sensitive alleles of DNA gyrase and Topo IV (the two essential type II topoisomerases) had more supercoil barriers than wild-type strains in all growth states. The most severe gyrase mutants were found to have twice as many barriers in growing cells as wild type throughout a 90 kb interval of the chromosome. We propose that knots and tangles in duplex DNA restrain supercoil diffusion in living bacteria.
Collapse
MESH Headings
- Chromosomes, Bacterial/chemistry
- Chromosomes, Bacterial/metabolism
- DNA Topoisomerase IV
- DNA Topoisomerases, Type II/genetics
- DNA Topoisomerases, Type II/metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/metabolism
- DNA, Superhelical/chemistry
- DNA, Superhelical/metabolism
- Genes, Bacterial
- Kinetics
- Models, Biological
- Mutation
- Salmonella typhimurium/genetics
- Salmonella typhimurium/metabolism
Collapse
Affiliation(s)
- P Staczek
- Department of Biochemistry, University of Alabama at Birmingham, 35294, USA
| | | |
Collapse
|
13
|
Figueroa-Bossi N, Guérin M, Rahmouni R, Leng M, Bossi L. The supercoiling sensitivity of a bacterial tRNA promoter parallels its responsiveness to stringent control. EMBO J 1998; 17:2359-67. [PMID: 9550733 PMCID: PMC1170579 DOI: 10.1093/emboj/17.8.2359] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In Salmonella typhimurium, expression of the hisR locus, a tRNA operon, decreases upon inhibiting DNA gyrase. Here, the hisR promoter dependence on negative DNA supercoiling was examined in vivo and in vitro. Mutant analysis showed the sequence determinants of this dependence to lie in the region between the -10 box and the transcription start site. As with most promoters subject to stringent control, this portion of the hisR promoter is C-G-rich. Replacing a C/G bp with T/A at position -7 partially relieves the supercoiling response while changing the sequence between -5 and + 1 (-CCCCCG-) for -GTTAA- abolishes the response in vitro and in vivo. The relief of the supercoiling dependence closely correlates with increased promoter susceptibility to melting in vivo and a lesser requirement for initiating nucleotides in the formation of stable initiation complexes in vitro. Studies in isoleucine-starved cells showed that such sequence changes mitigate and abolish the hisR promoter response to stringent control, respectively. The data presented suggest that the hisR promoter's sensitivity to stringent regulation arises from the same physical property that confers supercoiling sensitivity, i.e. resistance to melting. We propose that the stringent control mechanism acts by hampering the ability of RNA polymerase to melt the DNA helix.
Collapse
Affiliation(s)
- N Figueroa-Bossi
- Centre de Génétique Moléculaire, CNRS, 91198 Gif-sur-Yvette cédex, France
| | | | | | | | | |
Collapse
|
14
|
Spirito F, Bossi L. Long-distance effect of downstream transcription on activity of the supercoiling-sensitive leu-500 promoter in a topA mutant of Salmonella typhimurium. J Bacteriol 1996; 178:7129-37. [PMID: 8955393 PMCID: PMC178624 DOI: 10.1128/jb.178.24.7129-7137.1996] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Expression of the lacZ gene from the supercoiling-sensitive leu-500 promoter on a plasmid in topA mutant cells was stimulated by activating a divergently oriented Tac promoter, 400 bp upstream from leu-500. The stimulation was approximately threefold regardless of whether the Tac promoter drove the expression of the tet gene, whose product is membrane bound, or of the cat gene, whose product is cytosolic. Putting a second copy of the Tac promoter downstream from lacZ, approximately 3,000 bp from leu-500 in the same orientation as the latter, resulted in 30-fold increase in lacZ expression upon isopropyl-beta-D-thiogalactopyranoside induction. Again, these effects were independent of the nature of the gene upstream from leu-500 (tet or cat). With both tet- and cat-harboring constructs, activation of the two Tac promoter copies caused plasmid DNA to become hypernegatively supercoiled in topA mutant cells. Thus, neither leu-500 activation nor hypernegative plasmid DNA supercoiling appears to require membrane anchoring of DNA in this system. Replacing the downstream copy of Tac with a constitutive promoter resulted in high-level lacZ expression even when the upstream copy was repressed. Under these conditions, no hypernegative DNA supercoiling was observed, indicating that the activity of plasmid-borne leu-500 in topA mutant cells does not necessarily correlate with the linking deficit of plasmid DNA. The response of the leu-500-lacZ fusion to downstream transcription provides a sensitive assay for transcriptional supercoiling in bacteria.
Collapse
Affiliation(s)
- F Spirito
- Centre de Génétique Moléculaire du CNRS, Gif-sur-Yvette, France
| | | |
Collapse
|
15
|
Albert AC, Spirito F, Figueroa-Bossi N, Bossi L, Rahmouni AR. Hyper-negative template DNA supercoiling during transcription of the tetracycline-resistance gene in topA mutants is largely constrained in vivo. Nucleic Acids Res 1996; 24:3093-9. [PMID: 8760899 PMCID: PMC146055 DOI: 10.1093/nar/24.15.3093] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The excess linking deficit of plasmid DNA from topoisomerase I-defective bacteria (topA mutants) results mainly from transcription and is commonly ascribed to unbalanced relaxation of transcription-induced twin-supercoiled domains. This defect is aggravated in genes for membrane-binding proteins (such as the tet gene) where anchoring of the transcription complex to the bacterial membrane is thought to enhance twin-domain partitioning. Thus, it is often assumed that the 'hyper-negative' linking difference of plasmid DNA from topA mutants reflects unconstrained, hyper-negative DNA supercoiling inside the cell. We tested the validity of this assumption in the present study. A DNA sequence that undergoes a gradual B to Z transition under increasing negative superhelical tension was used as a sensor of unconstrained negative supercoiling. Z-DNA formation was probed at a site upstream from the inducible pTac promoter fused either to the tet gene or to the gene for cytosolic chloramphenicol acetyl transferase (cat). Although plasmid DNA linking deficit increased more extensively in topA mutants following tet activation than following cat activation, no significant differences were observed in the extents to which the B to Z DNA transition is stimulated in the two cases. We infer that the excess linking deficit of the tet-containing plasmid DNA reflects constrained negative DNA supercoiling inside the cell.
Collapse
Affiliation(s)
- A C Albert
- Centre de Biophysique Moléculaire, Orléans, France
| | | | | | | | | |
Collapse
|
16
|
Guptasarma P. Cooperative relaxation of supercoils and periodic transcriptional initiation within polymerase batteries. Bioessays 1996; 18:325-32. [PMID: 8967901 DOI: 10.1002/bies.950180411] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Transcription and DNA supercoiling are known to be linked by a cause-effect relationship that operates in both directions. It is proposed here that this two-way relationship may be exploited by the E. coli genome to facilitate constitutive transcription of supercoil-sensitive genes by polymerase batteries made up of uniformly spaces RNA polymerase elongation complexes. Specifically, it is argued that (1) polymerases transcribing DNA in tandem cooperate to relax each other's transcription-driven positive supercoils; and (2) negative supercoils driven upstream by elongation complexes tend to be 'harnessed' and used to cooperatively (and periodically) initiate fresh transcription from promoters. Harnessing of transcription-driven negative supercoils is thought to be achieved through the erection of protein barriers to the rotational upstream propagation of supercoils from transcription events. The possible relevance of such cooperation amongst polymerases to the activation of transcription by DNA-binding protein factors is emphasized. Some testable predictions are made and implications are discussed.
Collapse
Affiliation(s)
- P Guptasarma
- Centre for Cellular and Molecular Biology, Hyderabad, India. . ac.uk
| |
Collapse
|
17
|
Blanc-Potard AB, Gari E, Spirito F, Figueroa-Bossi N, Bossi L. RNA polymerase (rpoB) mutants selected for increased resistance to gyrase inhibitors in Salmonella typhimurium. MOLECULAR & GENERAL GENETICS : MGG 1995; 247:680-92. [PMID: 7616959 DOI: 10.1007/bf00290399] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Some rifampicin-resistance (RifR) mutations make bacteria slightly resistant to the gyrase inhibitors novobiocin (Nov) and nalidixic acid (Nal). This suggested that it might be possible to isolate rpoB mutants using either drug for positive selection. In an initial test, we confirmed the presence of Rif-resistant isolates among clones selected for Nov resistance. These mutants are also more resistant to Nal. In a subsequent experiment, we found that mutants selected for low-level resistance to Nal include isolates harboring mutations genetically linked to the rpoB locus; of two such mutants studied, one is temperature-sensitive for growth. These two mutants, which are only marginally affected in their response to Nov, are normally sensitive to Rif and thus might be representative of a new class of rpoB alleles. The Rif-resistant and Rif-sensitive rpoB alleles that increase resistance to gyrase inhibitors have one property in common: they all suppress, to varying degrees, the defect in his operon regulation (transcriptional deattenuation) caused by a gyrase defect or inhibition by novobiocin. To further analyse the transcription-supercoiling relationships in these mutants, we examined the ability of RNA polymerase to recruit gyrase activity during transcription. This was done by two independent approaches: (i) observing transcription-induced accumulation of hyper-negatively supercoiled plasmid DNA in a topA mutant background and (ii) measuring transcription-induced plasmid DNA cleavage in the presence of oxolinic acid. Results indicate that the rpoB alleles described in this study diminish the recruitment of gyrase activity by the transcription process. This property correlates with a decrease in the rate of transcription initiation.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
Affiliation(s)
- A B Blanc-Potard
- Centre de Génétique Moléculaire du Centre National de la Recherche Scientifique Associé à l'Université P. et M. Curie, Gif-sur-Yvette, France
| | | | | | | | | |
Collapse
|
18
|
Blanc-Potard AB, Bossi L. Phenotypic suppression of DNA gyrase deficiencies by a deletion lowering the gene dosage of a major tRNA in Salmonella typhimurium. J Bacteriol 1994; 176:2216-26. [PMID: 7512550 PMCID: PMC205342 DOI: 10.1128/jb.176.8.2216-2226.1994] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
One of the pleiotropic phenotypes of mutations affecting DNA gyrase activity in Salmonella typhimurium is the constitutive deattenuation of the histidine operon. In the present work, we isolated and characterized a suppressor mutation which restores his attenuation in the presence of a defective gyrase. Such a suppressor, initially named sgdA1 (for suppressor gyrase deficiency), was found to correct additional phenotypes associated with defective gyrase function. These include the aberrant nucleoid partitioning of a gyrB mutant and the conditional lethality of a gyrA mutation. Furthermore, the sgdA1 mutation was found to confer low-level resistance to nalidixic acid. The last phenotype permitted isolation of a number of additional sgdA mutants. Genetic analysis established the recessive character of these alleles as well as the position of the sgdA locus at 57 U on the Salmonella genetic map. All of the sgdA mutants result from the same molecular event: a deletion removing three of the four tandemly repeated copies of argV, the gene which specifies tRNA(2Arg), the major arginine isoacceptor tRNA. These findings, combined with the observation of some Sgd-like phenotypes in a tRNA modification mutant (hisT mutant), lead us to propose that protein synthesis contributes, directly or indirectly, to the pathology of gyrase alterations in growing bacteria. We discuss plausible mechanisms which may be responsible for these effects.
Collapse
MESH Headings
- Base Sequence
- DNA Topoisomerases, Type II/genetics
- Gene Deletion
- Genes, Bacterial/genetics
- Genes, Bacterial/physiology
- Genes, Suppressor/genetics
- Genes, Suppressor/physiology
- Histidine/genetics
- Histidine/metabolism
- Molecular Sequence Data
- Mutation/drug effects
- Mutation/genetics
- Mutation/physiology
- Nalidixic Acid/pharmacology
- Phenotype
- RNA, Bacterial/genetics
- RNA, Bacterial/physiology
- RNA, Transfer, Arg/genetics
- RNA, Transfer, Arg/physiology
- Salmonella typhimurium/drug effects
- Salmonella typhimurium/enzymology
- Salmonella typhimurium/genetics
Collapse
Affiliation(s)
- A B Blanc-Potard
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
| | | |
Collapse
|