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Qiu J, Zhai Y, Wei M, Zheng C, Jiao X. Toxin–antitoxin systems: Classification, biological roles, and applications. Microbiol Res 2022; 264:127159. [DOI: 10.1016/j.micres.2022.127159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/28/2022]
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Abstract
Toxin-antitoxin systems are widespread in bacterial genomes. They are usually composed of two elements: a toxin that inhibits an essential cellular process and an antitoxin that counteracts its cognate toxin. In the past decade, a number of new toxin-antitoxin systems have been described, bringing new growth inhibition mechanisms to light as well as novel modes of antitoxicity. However, recent advances in the field profoundly questioned the role of these systems in bacterial physiology, stress response and antimicrobial persistence. This shifted the paradigm of the functions of toxin-antitoxin systems to roles related to interactions between hosts and their mobile genetic elements, such as viral defence or plasmid stability. In this Review, we summarize the recent progress in understanding the biology and evolution of these small genetic elements, and discuss how genomic conflicts could shape the diversification of toxin-antitoxin systems.
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Abstract
Type II toxin-antitoxin (TA) systems are small genetic elements composed of a toxic protein and its cognate antitoxin protein, the latter counteracting the toxicity of the former. While TA systems were initially discovered on plasmids, functioning as addiction modules through a phenomenon called postsegregational killing, they were later shown to be massively present in bacterial chromosomes, often in association with mobile genetic elements. Extensive research has been conducted in recent decades to better understand the physiological roles of these chromosomally encoded modules and to characterize the conditions leading to their activation. Type II toxin-antitoxin (TA) systems are small genetic elements composed of a toxic protein and its cognate antitoxin protein, the latter counteracting the toxicity of the former. While TA systems were initially discovered on plasmids, functioning as addiction modules through a phenomenon called postsegregational killing, they were later shown to be massively present in bacterial chromosomes, often in association with mobile genetic elements. Extensive research has been conducted in recent decades to better understand the physiological roles of these chromosomally encoded modules and to characterize the conditions leading to their activation. The diversity of their proposed roles, ranging from genomic stabilization and abortive phage infection to stress modulation and antibiotic persistence, in conjunction with the poor understanding of TA system regulation, resulted in the generation of simplistic models, often refuted by contradictory results. This review provides an epistemological and critical retrospective on TA modules and highlights fundamental questions concerning their roles and regulations that still remain unanswered.
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Gupta A, Venkataraman B, Vasudevan M, Gopinath Bankar K. Co-expression network analysis of toxin-antitoxin loci in Mycobacterium tuberculosis reveals key modulators of cellular stress. Sci Rep 2017; 7:5868. [PMID: 28724903 PMCID: PMC5517426 DOI: 10.1038/s41598-017-06003-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 06/07/2017] [Indexed: 11/09/2022] Open
Abstract
Research on toxin-antitoxin loci (TA loci) is gaining impetus due to their ubiquitous presence in bacterial genomes and their observed roles in stress survival, persistence and drug tolerance. The present study investigates the expression profile of all the seventy-nine TA loci found in Mycobacterium tuberculosis. The bacterium was subjected to multiple stress conditions to identify key players of cellular stress response and elucidate a TA-coexpression network. This study provides direct experimental evidence for transcriptional activation of each of the seventy-nine TA loci following mycobacterial exposure to growth-limiting environments clearly establishing TA loci as stress-responsive modules in M. tuberculosis. TA locus activation was found to be stress-specific with multiple loci activated in a duration-based response to a particular stress. Conditions resulting in arrest of cellular translation led to greater up-regulation of TA genes suggesting that TA loci have a primary role in arresting translation in the cell. Our study identifed higBA2 and vapBC46 as key loci that were activated in all the conditions tested. Besides, relBE1, higBA3, vapBC35, vapBC22 and higBA1 were also upregulated in multpile stresses. Certain TA modules exhibited co-activation across multiple conditions suggestive of a common regulatory mechanism.
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Affiliation(s)
- Amita Gupta
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India. .,Department of Biochemistry and Centre for Innovation in Infectious Diseases Research, Education and Training (CIIDRET), University of Delhi South Campus, New Delhi, 110021, India.
| | - Balaji Venkataraman
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Madavan Vasudevan
- Genome Informatics Research Group, Bionivid Technology Pvt Ltd, Bengaluru, 560043, India
| | - Kiran Gopinath Bankar
- Genome Informatics Research Group, Bionivid Technology Pvt Ltd, Bengaluru, 560043, India
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Abstract
Persisters are drug-tolerant bacteria that account for the majority of bacterial infections. They are not mutants, rather, they are slow-growing cells in an otherwise normally growing population. It is known that the frequency of persisters in a population is correlated with the number of toxin–antitoxin systems in the organism. Our previous work provided a mechanistic link between the two by showing how multiple toxin–antitoxin systems, which are present in nearly all bacteria, can cooperate to induce bistable toxin concentrations that result in a heterogeneous population of slow- and fast-growing cells. As such, the slow-growing persisters are a bet-hedging subpopulation maintained under normal conditions. For technical reasons, the model assumed that the kinetic parameters of the various toxin–antitoxin systems in the cell are identical, but experimental data indicate that they differ, sometimes dramatically. Thus, a critical question remains: whether toxin–antitoxin systems from the diverse families, often found together in a cell, with significantly different kinetics, can cooperate in a similar manner. Here, we characterize the interaction of toxin–antitoxin systems from many families that are unrelated and kinetically diverse, and identify the essential determinant for their cooperation. The generic architecture of toxin–antitoxin systems provides the potential for bistability, and our results show that even when they do not exhibit bistability alone, unrelated systems can be coupled by the growth rate to create a strongly bistable, hysteretic switch between normal (fast-growing) and persistent (slow-growing) states. Different combinations of kinetic parameters can produce similar toxic switching thresholds, and the proximity of the thresholds is the primary determinant of bistability. Stochastic fluctuations can spontaneously switch all of the toxin–antitoxin systems in a cell at once. The spontaneous switch creates a heterogeneous population of growing and non-growing cells, typical of persisters, that exist under normal conditions, rather than only as an induced response. The frequency of persisters in the population can be tuned for a particular environmental niche by mixing and matching unrelated systems via mutation, horizontal gene transfer and selection.
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Affiliation(s)
- Rick A Fasani
- Department of Biomedical Engineering and Microbiology Graduate Group, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Michael A Savageau
- Department of Biomedical Engineering and Microbiology Graduate Group, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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Abstract
Toxin-antitoxin (TA) systems are small genetic modules formed by a stable toxin and an unstable antitoxin that are widely present in plasmids and in chromosomes of Bacteria and Archaea. Toxins can interfere with cell growth or viability, targeting a variety of key processes. Antitoxin inhibits expression of the toxin, interacts with it, and neutralizes its effect. In a plasmid context, toxins are kept silent by the continuous synthesis of the unstable antitoxins; in plasmid-free cells (segregants), toxins can be activated owing to the faster decay of the antitoxin, and this results in the elimination of these cells from the population (postsegregational killing [PSK]) and in an increase of plasmid-containing cells in a growing culture. Chromosomal TA systems can also be activated in particular circumstances, and the interference with cell growth and viability that ensues contributes in different ways to the physiology of the cell. In this article, we review the conditional activation of TAs in selected plasmidic and chromosomal TA pairs and the implications of this activation. On the whole, the analysis underscores TA interactions involved in PSK and points to the effective contribution of TA systems to the physiology of the cell.
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Hayes F, Kędzierska B. Regulating toxin-antitoxin expression: controlled detonation of intracellular molecular timebombs. Toxins (Basel) 2014; 6:337-58. [PMID: 24434949 PMCID: PMC3920265 DOI: 10.3390/toxins6010337] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 12/20/2013] [Accepted: 01/08/2014] [Indexed: 11/24/2022] Open
Abstract
Genes for toxin-antitoxin (TA) complexes are widely disseminated in bacteria, including in pathogenic and antibiotic resistant species. The toxins are liberated from association with the cognate antitoxins by certain physiological triggers to impair vital cellular functions. TAs also are implicated in antibiotic persistence, biofilm formation, and bacteriophage resistance. Among the ever increasing number of TA modules that have been identified, the most numerous are complexes in which both toxin and antitoxin are proteins. Transcriptional autoregulation of the operons encoding these complexes is key to ensuring balanced TA production and to prevent inadvertent toxin release. Control typically is exerted by binding of the antitoxin to regulatory sequences upstream of the operons. The toxin protein commonly works as a transcriptional corepressor that remodels and stabilizes the antitoxin. However, there are notable exceptions to this paradigm. Moreover, it is becoming clear that TA complexes often form one strand in an interconnected web of stress responses suggesting that their transcriptional regulation may prove to be more intricate than currently understood. Furthermore, interference with TA gene transcriptional autoregulation holds considerable promise as a novel antibacterial strategy: artificial release of the toxin factor using designer drugs is a potential approach to induce bacterial suicide from within.
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Affiliation(s)
- Finbarr Hayes
- Faculty of Life Sciences and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Barbara Kędzierska
- Faculty of Life Sciences and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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Boss L, Labudda Ł, Węgrzyn G, Hayes F, Kędzierska B. The axe-txe complex of Enterococcus faecium presents a multilayered mode of toxin-antitoxin gene expression regulation. PLoS One 2013; 8:e73569. [PMID: 24019928 PMCID: PMC3760812 DOI: 10.1371/journal.pone.0073569] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 07/20/2013] [Indexed: 01/25/2023] Open
Abstract
Multidrug-resistant variants of human pathogens from the genus Enterococcus represent a significant health threat as leading agents of nosocomial infections. The easy acquisition of plasmid-borne genes is intimately involved in the spread of antibiotic resistance in enterococci. Toxin-antitoxin (TA) systems play a major role in both maintenance of mobile genetic elements that specify antibiotic resistance, and in bacterial persistence and virulence. Expression of toxin and antitoxin genes must be in balance as inappropriate levels of toxin can be dangerous to the host. The controlled production of toxin and antitoxin is usually achieved by transcriptional autoregulation of TA operons. One of the most prevalent TA modules in enterococcal species is axe-txe which is detected in a majority of clinical isolates. Here, we demonstrate that the axe-txe cassette presents a complex pattern of gene expression regulation. Axe-Txe cooperatively autorepress expression from a major promoter upstream of the cassette. However, an internal promoter that drives the production of a newly discovered transcript from within axe gene combined with a possible modulation in mRNA stability play important roles in the modulation of Axe:Txe ratio to ensure controlled release of the toxin.
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Affiliation(s)
- Lidia Boss
- Department of Molecular Biology, University of Gdańsk, Gdańsk, Poland
| | - Łukasz Labudda
- Department of Molecular Biology, University of Gdańsk, Gdańsk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdańsk, Gdańsk, Poland
| | - Finbarr Hayes
- Faculty of Life Sciences and Manchester Institute of Biotechnology, the University of Manchester, Manchester, United Kingdom
| | - Barbara Kędzierska
- Department of Molecular Biology, University of Gdańsk, Gdańsk, Poland
- * E-mail:
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Cleavage of the antitoxin of the parD toxin–antitoxin system is determined by the ClpAP protease and is modulated by the relative ratio of the toxin and the antitoxin. Plasmid 2013; 70:78-85. [DOI: 10.1016/j.plasmid.2013.01.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 01/29/2013] [Accepted: 01/30/2013] [Indexed: 11/21/2022]
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Kasari V, Mets T, Tenson T, Kaldalu N. Transcriptional cross-activation between toxin-antitoxin systems of Escherichia coli. BMC Microbiol 2013; 13:45. [PMID: 23432955 PMCID: PMC3598666 DOI: 10.1186/1471-2180-13-45] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 02/18/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacterial toxin-antitoxin (TA) systems are formed by potent regulatory or suicide factors (toxins) and their short-lived inhibitors (antitoxins). Antitoxins are DNA-binding proteins and auto-repress transcription of TA operons. Transcription of multiple TA operons is activated in temporarily non-growing persister cells that can resist killing by antibiotics. Consequently, the antitoxin levels of persisters must have been dropped and toxins are released of inhibition. RESULTS Here, we describe transcriptional cross-activation between different TA systems of Escherichia coli. We find that the chromosomal relBEF operon is activated in response to production of the toxins MazF, MqsR, HicA, and HipA. Expression of the RelE toxin in turn induces transcription of several TA operons. We show that induction of mazEF during amino acid starvation depends on relBE and does not occur in a relBEF deletion mutant. Induction of TA operons has been previously shown to depend on Lon protease which is activated by polyphospate accumulation. We show that transcriptional cross-activation occurs also in strains deficient for Lon, ClpP, and HslV proteases and polyphosphate kinase. Furthermore, we find that toxins cleave the TA mRNA in vivo, which is followed by degradation of the antitoxin-encoding fragments and selective accumulation of the toxin-encoding regions. We show that these accumulating fragments can be translated to produce more toxin. CONCLUSION Transcriptional activation followed by cleavage of the mRNA and disproportionate production of the toxin constitutes a possible positive feedback loop, which can fire other TA systems and cause bistable growth heterogeneity. Cross-interacting TA systems have a potential to form a complex network of mutually activating regulators in bacteria.
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Affiliation(s)
- Villu Kasari
- Institute of Technology, University of Tartu, Nooruse 1, 50411, Tartu, Estonia
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Diago-Navarro E, Hernandez-Arriaga AM, López-Villarejo J, Muñoz-Gómez AJ, Kamphuis MB, Boelens R, Lemonnier M, Díaz-Orejas R. parD toxin-antitoxin system of plasmid R1 - basic contributions, biotechnological applications and relationships with closely-related toxin-antitoxin systems. FEBS J 2010; 277:3097-117. [DOI: 10.1111/j.1742-4658.2010.07722.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
Toxin-antitoxin (TA) systems are plasmid- or chromosome-encoded protein complexes composed of a stable toxin and a short-lived inhibitor of the toxin. In cultures of Escherichia coli, transcription of toxin-antitoxin genes was induced in a nondividing subpopulation of bacteria that was tolerant to bactericidal antibiotics. Along with transcription of known toxin-antitoxin operons, transcription of mqsR and ygiT, two adjacent genes with multiple TA-like features, was induced in this cell population. Here we show that mqsR and ygiT encode a toxin-antitoxin system belonging to a completely new family which is represented in several groups of bacteria. The mqsR gene encodes a toxin, and ectopic expression of this gene inhibits growth and induces rapid shutdown of protein synthesis in vivo. ygiT encodes an antitoxin, which protects cells from the effects of MqsR. These two genes constitute a single operon which is transcriptionally repressed by the product of ygiT. We confirmed that transcription of this operon is induced in the ampicillin-tolerant fraction of a growing population of E. coli and in response to activation of the HipA toxin. Expression of the MqsR toxin does not kill bacteria but causes reversible growth inhibition and elongation of cells.
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Overgaard M, Borch J, Gerdes K. RelB and RelE of Escherichia coli form a tight complex that represses transcription via the ribbon-helix-helix motif in RelB. J Mol Biol 2009; 394:183-96. [PMID: 19747491 PMCID: PMC2812701 DOI: 10.1016/j.jmb.2009.09.006] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 08/31/2009] [Accepted: 09/01/2009] [Indexed: 11/17/2022]
Abstract
RelB, the ribbon–helix–helix (RHH) repressor encoded by the relBE toxin–antitoxin locus of Escherichia coli, interacts with RelE and thereby counteracts the mRNA cleavage activity of RelE. In addition, RelB dimers repress the strong relBE promoter and this repression by RelB is enhanced by RelE; that is, RelE functions as a transcriptional co-repressor. RelB is a Lon protease substrate, and Lon is required both for activation of relBE transcription and for activation of the mRNA cleavage activity of RelE. Here we characterize the molecular interactions important for transcriptional control of the relBE model operon. Using an in vivo screen for relB mutants, we identified multiple nucleotide changes that map to important amino acid positions within the DNA-binding domain formed by the N-terminal RHH motif of RelB. Analysis of DNA binding of a subset of these mutant RHH proteins by gel-shift assays, transcriptional fusion assays and a structure model of RelB–DNA revealed amino acid residues making crucial DNA–backbone contacts within the operator (relO) DNA. Mutational and footprinting analyses of relO showed that RelB dimers bind on the same face of the DNA helix and that the RHH motif recognizes four 6-bp repeats within the bipartite binding site. The spacing between each half-site was found to be essential for cooperative interactions between adjacently bound RelB dimers stabilized by the co-repressor RelE. Kinetic and stoichiometric measurements of the interaction between RelB and RelE confirmed that the proteins form a high-affinity complex with a 2:1 stoichiometry. Lon degraded RelB in vitro and degradation was inhibited by RelE, consistent with the proposal that RelE protects RelB from proteolysis by Lon in vivo.
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Affiliation(s)
- Martin Overgaard
- Department of Biochemistry and Molecular Biology, University of Southern Denmark Odense, Campusvej 55, 5230 Odense M, Denmark
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Diago-Navarro E, Kamphuis MB, Boelens R, Barendregt A, Heck AJ, van den Heuvel RH, Díaz-Orejas R. A mutagenic analysis of the RNase mechanism of the bacterial Kid toxin by mass spectrometry. FEBS J 2009; 276:4973-86. [PMID: 19694809 DOI: 10.1111/j.1742-4658.2009.07199.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Kid, the toxin of the parD (kis, kid) maintenance system of plasmid R1, is an endoribonuclease that preferentially cleaves RNA at the 5' of A in the core sequence 5'-UA(A/C)-3'. A model of the Kid toxin interacting with the uncleavable mimetic 5'-AdUACA-3' is available. To evaluate this model, a significant collection of mutants in some of the key residues proposed to be involved in RNA binding (T46, A55, T69 and R85) or RNA cleavage (R73, D75 and H17) were analysed by mass spectrometry in RNA binding and cleavage assays. A pair of substrates, 5'-AUACA-3', and its uncleavable mimetic 5'-AdUACA-3', used to establish the model and structure of the Kid-RNA complex, were used in both the RNA cleavage and binding assays. A second RNA substrate, 5'-UUACU-3' efficiently cleaved by Kid both in vivo and in vitro, was also used in the cleavage assays. Compared with the wild-type protein, mutations in the residues of the catalytic site abolished RNA cleavage without substantially altering RNA binding. Mutations in residues proposed to be involved in RNA binding show reduced binding efficiency and a corresponding decrease in RNA cleavage efficiency. The cleavage profiles of the different mutants were similar with the two substrates used, but RNA cleavage required much lower protein concentrations when the 5'-UUACU-3' substrate was used. Protein synthesis and growth assays are consistent with there being a correlation between the RNase activity of Kid and its inhibitory potential. These results give important support to the available models of Kid RNase and the Kid-RNA complex.
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Affiliation(s)
- Elizabeth Diago-Navarro
- Centro de Investigaciones Biológicas, Departamento de Microbiología Molecular, Madrid, Spain
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Affiliation(s)
- Roy David Magnuson
- Department of Biological Sciences, University of Alabama in Huntsville, 301 Sparkman Drive, WH 258, Huntsville, AL 35758, USA.
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Monti MC, Hernández-Arriaga AM, Kamphuis MB, López-Villarejo J, Heck AJR, Boelens R, Díaz-Orejas R, van den Heuvel RHH. Interactions of Kid-Kis toxin-antitoxin complexes with the parD operator-promoter region of plasmid R1 are piloted by the Kis antitoxin and tuned by the stoichiometry of Kid-Kis oligomers. Nucleic Acids Res 2007; 35:1737-49. [PMID: 17317682 PMCID: PMC1865072 DOI: 10.1093/nar/gkm073] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The parD operon of Escherichia coli plasmid R1 encodes a toxin–antitoxin system, which is involved in plasmid stabilization. The toxin Kid inhibits cell growth by RNA degradation and its action is neutralized by the formation of a tight complex with the antitoxin Kis. A fascinating but poorly understood aspect of the kid–kis system is its autoregulation at the transcriptional level. Using macromolecular (tandem) mass spectrometry and DNA binding assays, we here demonstrate that Kis pilots the interaction of the Kid–Kis complex in the parD regulatory region and that two discrete Kis-binding regions are present on parD. The data clearly show that only when the Kis concentration equals or exceeds the Kid concentration a strong cooperative effect exists between strong DNA binding and Kid2–Kis2–Kid2–Kis2 complex formation. We propose a model in which transcriptional repression of the parD operon is tuned by the relative molar ratio of the antitoxin and toxin proteins in solution. When the concentration of the toxin exceeds that of the antitoxin tight Kid2–Kis2–Kid2 complexes are formed, which only neutralize the lethal activity of Kid. Upon increasing the Kis concentration, (Kid2–Kis2)n complexes repress the kid–kis operon.
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Affiliation(s)
- Maria C. Monti
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Department of Biomolecular Mass Spectrometry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, Centro de Investigaciones Biológicas, Departamento de Microbiología Molecular, Ramiro de Maeztu 9, E-28040 Madrid, Spain and Bijvoet Center for Biomolecular Research, Department of NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ana M. Hernández-Arriaga
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Department of Biomolecular Mass Spectrometry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, Centro de Investigaciones Biológicas, Departamento de Microbiología Molecular, Ramiro de Maeztu 9, E-28040 Madrid, Spain and Bijvoet Center for Biomolecular Research, Department of NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Monique B. Kamphuis
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Department of Biomolecular Mass Spectrometry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, Centro de Investigaciones Biológicas, Departamento de Microbiología Molecular, Ramiro de Maeztu 9, E-28040 Madrid, Spain and Bijvoet Center for Biomolecular Research, Department of NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Juan López-Villarejo
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Department of Biomolecular Mass Spectrometry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, Centro de Investigaciones Biológicas, Departamento de Microbiología Molecular, Ramiro de Maeztu 9, E-28040 Madrid, Spain and Bijvoet Center for Biomolecular Research, Department of NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Department of Biomolecular Mass Spectrometry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, Centro de Investigaciones Biológicas, Departamento de Microbiología Molecular, Ramiro de Maeztu 9, E-28040 Madrid, Spain and Bijvoet Center for Biomolecular Research, Department of NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Department of Biomolecular Mass Spectrometry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, Centro de Investigaciones Biológicas, Departamento de Microbiología Molecular, Ramiro de Maeztu 9, E-28040 Madrid, Spain and Bijvoet Center for Biomolecular Research, Department of NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ramón Díaz-Orejas
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Department of Biomolecular Mass Spectrometry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, Centro de Investigaciones Biológicas, Departamento de Microbiología Molecular, Ramiro de Maeztu 9, E-28040 Madrid, Spain and Bijvoet Center for Biomolecular Research, Department of NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Robert H. H. van den Heuvel
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Department of Biomolecular Mass Spectrometry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, Centro de Investigaciones Biológicas, Departamento de Microbiología Molecular, Ramiro de Maeztu 9, E-28040 Madrid, Spain and Bijvoet Center for Biomolecular Research, Department of NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- *To whom correspondence should be addressed. +31 302536797+31 302518219 or
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Abstract
Although plasmid-borne and chromosomal toxin-antitoxin (TA) operons have been known for some time, the recent identification of mRNA as the target of at least two different classes of toxins has led to a dramatic renewal of interest in these systems as mediators of stress responses. Members of the MazF/PemK family, the so-called mRNA interferases, are ribonucleases that inhibit translation by destroying cellular mRNAs under stress conditions, while the founder member of the RelE family promotes cleavage of mRNAs through the ribosome. Detailed structures of these enzymes, often in complex with their inhibitors, have provided vital clues to their mechanisms of action. The primary role and regulation of these systems has been the subject of some controversy. One model suggests they play a beneficial role by wiping the slate clean and preventing wasteful energy consumption by the translational apparatus during adaptation to stress conditions, while another favours the idea that their main function is programmed cell death. The two models might not be mutually exclusive if a side-effect of prolonged exposure to toxic RNase activity without de novo synthesis of the inhibitor were a state of dormancy for which we do not yet understand the key to recovery. In this review, I discuss the recent developments in the rapidly expanding field of what I refer to as bacterial shutdown decay.
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Affiliation(s)
- Ciarán Condon
- CNRS UPR 9073 (affiliated with Université de Paris 7 - Denis Diderot), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
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Inouye M. The discovery of mRNA interferases: Implication in bacterial physiology and application to biotechnology. J Cell Physiol 2006; 209:670-6. [PMID: 17001682 DOI: 10.1002/jcp.20801] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Escherichia coli contains a large number of suicide or toxin genes, whose expression leads to cell growth arrest and eventual cell death. This raises intriguing questions as to why E. coli contains so many toxin genes and what are their roles in bacterial physiology. Among these, MazF has been shown to be a sequence-specific endoribonuclease, which cleaves mRNAs at ACA sequences to completely inhibit protein synthesis. MazF is therefore called mRNA interferase. A number of other mRNA interferases with different cleavage specificities have been discovered not only in E. coli, but also in other bacteria including Mycobacterium tuberculosis. Induction of MazF in the cell leads to cellular dormancy termed quasi-dormancy. In spite of complete cell growth inhibition, cells in the quasi-dormant state are fully capable of energy metabolism, amino acids and nucleic acids biosynthesis and RNA and protein synthesis. The quasi-dormancy may be implicated in cell survival under stress conditions and may play a major role in pathogenicity of M. tuberculosis. The quasi-dormant cells provide an intriguing novel biotechnological system producing only a protein of interest in a high yield. MazF causing Bak-dependent programmed cell death in mammalian cells may be used as a tool for gene therapy against cancer and AIDS. The discovery of a novel way to interfere with mRNA function by mRNA interferases opens a wide variety of avenues in basic as well as applied and clinical sciences.
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Affiliation(s)
- Masayori Inouye
- Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA.
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Pimentel B, Madine MA, de la Cueva-Méndez G. Kid cleaves specific mRNAs at UUACU sites to rescue the copy number of plasmid R1. EMBO J 2005; 24:3459-69. [PMID: 16163387 PMCID: PMC1276173 DOI: 10.1038/sj.emboj.7600815] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2005] [Accepted: 08/23/2005] [Indexed: 11/09/2022] Open
Abstract
Stability and copy number of extra-chromosomal elements are tightly regulated in prokaryotes and eukaryotes. Toxin Kid and antitoxin Kis are the components of the parD stability system of prokaryotic plasmid R1 and they can also function in eukaryotes. In bacteria, Kid was thought to become active only in cells that lose plasmid R1 and to cleave exclusively host mRNAs at UA(A/C/U) trinucleotide sites to eliminate plasmid-free cells. Instead, we demonstrate here that Kid becomes active in plasmid-containing cells when plasmid copy number decreases, cleaving not only host- but also a specific plasmid-encoded mRNA at the longer and more specific target sequence UUACU. This specific cleavage by Kid inhibits bacterial growth and, at the same time, helps to restore the plasmid copy number. Kid targets a plasmid RNA that encodes a repressor of the synthesis of an R1 replication protein, resulting in increased plasmid DNA replication. This mechanism resembles that employed by some human herpesviruses to regulate viral amplification during infection.
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Affiliation(s)
- Belén Pimentel
- MRC, Cancer Cell Unit, Hutchison/MRC Research Centre, Hills Road, Cambridge, UK
| | - Mark A Madine
- MRC, Cancer Cell Unit, Hutchison/MRC Research Centre, Hills Road, Cambridge, UK
| | - Guillermo de la Cueva-Méndez
- MRC, Cancer Cell Unit, Hutchison/MRC Research Centre, Hills Road, Cambridge, UK
- MRC, Cancer Cell Unit. Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 2XZ, UK. Tel.: +44 1223 763286; Fax: +44 1223 763241; E-mail:
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21
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Pellegrini O, Mathy N, Gogos A, Shapiro L, Condon C. The Bacillus subtilis ydcDE operon encodes an endoribonuclease of the MazF/PemK family and its inhibitor. Mol Microbiol 2005; 56:1139-48. [PMID: 15882409 DOI: 10.1111/j.1365-2958.2005.04606.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Operons encoding stable toxins and their labile antidote are widespread in prokaryotes and play important roles in plasmid partitioning and cellular responses to stress. One such family of toxins MazF/ChpAK/PemK encodes an endoribonuclease that inactivates cellular mRNAs by cleaving them at specific, but frequently occurring sites. Here we show that the Bacillus subtilis ydcE gene encodes a member of this family of RNases, which we have called EndoA. Overexpression of EndoA is toxic for bacterial cell growth and this toxicity is reversed by coexpression of the gene immediately upstream, ydcD. Furthermore, YdcD inhibits EndoA activity directly in vitro. EndoA has similar cleavage specificity to MazF and PemK and yields cleavage products with 3'-phosphate and 5'-hydroxyl groups, typical of EDTA-resistant degradative RNases. This is the first example of an antitoxin-toxin system in B. subtilis.
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Affiliation(s)
- Olivier Pellegrini
- CNRS UPR 9073 (affiliated with Université de Paris 7 - Denis Diderot), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
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22
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Pandey DP, Gerdes K. Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res 2005; 33:966-76. [PMID: 15718296 PMCID: PMC549392 DOI: 10.1093/nar/gki201] [Citation(s) in RCA: 705] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Prokaryotic chromosomes code for toxin–antitoxin (TA) loci, often in multiple copies. In E.coli, experimental evidence indicates that TA loci are stress-response elements that help cells survive unfavorable growth conditions. The first gene in a TA operon codes for an antitoxin that combines with and neutralizes a regulatory ‘toxin’, encoded by the second gene. RelE and MazF toxins are regulators of translation that cleave mRNA and function, in interplay with tmRNA, in quality control of gene expression. Here, we present the results from an exhaustive search for TA loci in 126 completely sequenced prokaryotic genomes (16 archaea and 110 bacteria). We identified 671 TA loci belonging to the seven known TA gene families. Surprisingly, obligate intracellular organisms were devoid of TA loci, whereas free-living slowly growing prokaryotes had particularly many (38 in Mycobacterium tuberculosis and 43 in Nitrosomonas europaea). In many cases, TA loci were clustered and closely linked to mobile genetic elements. In the most extreme of these cases, all 13 TA loci of Vibrio cholerae were bona fide integron elements located in the V.cholerae mega-integron. These observations strongly suggest that TA loci are mobile cassettes that move frequently within and between chromosomes and also lend support to the hypothesis that TA loci function as stress-response elements beneficial to free-living prokaryotes.
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Affiliation(s)
| | - Kenn Gerdes
- To whom correspondence should be addressed. Tel: +45 6550 2413; Fax: +45 6550 2769;
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Lemonnier M, Santos-Sierra S, Pardo-Abarrio C, Díaz-Orejas R. Identification of residues of the kid toxin involved in autoregulation of the parD system. J Bacteriol 2004; 186:240-3. [PMID: 14679244 PMCID: PMC303459 DOI: 10.1128/jb.186.1.240-243.2004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The toxin-antitoxin system parD (kis kid) of plasmid R1 is coregulated by the coordinated action of its two gene products. Here we describe the isolation and the in vivo characterization of three single-amino-acid changes in the Kid toxin, G4E, C74Y, and E91K, that affect the coregulatory activity but preserve the toxicity of the protein.
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Affiliation(s)
- Marc Lemonnier
- Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain
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de la Cueva-Méndez G, Mills AD, Clay-Farrace L, Díaz-Orejas R, Laskey RA. Regulatable killing of eukaryotic cells by the prokaryotic proteins Kid and Kis. EMBO J 2003; 22:246-51. [PMID: 12514130 PMCID: PMC140101 DOI: 10.1093/emboj/cdg026] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Plasmid R1 inhibits growth of bacteria by synthesizing an inhibitor of cell proliferation, Kid, and a neutralizing antidote, Kis, which binds tightly to the toxin. Here we report that this toxin and antidote, which have evolved to function in bacteria, also function efficiently in a wide range of eukaryotes. Kid inhibits cell proliferation in yeast, Xenopus laevis and human cells, whilst Kis protects. Moreover, we show that Kid triggers apoptosis in human cells. These effects can be regulated in vivo by modulating the relative amounts of antidote and toxin using inducible eukaryotic promoters for independent transcriptional control of their genes. These findings allow highly regulatable, selective killing of eukaryotic cells, and could be applied to eliminate cancer cells or specific cell lineages in development.
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Affiliation(s)
- Guillermo de la Cueva-Méndez
- MRC Cancer Cell Unit, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 2XZ, Wellcome Trust Cancer Research UK Institute, Tennis Court Road, Cambridge CB2 1QR and Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK and
Centro de Investigaciones Biológicas (C.S.I.C.), Department of Molecular Microbiology, Velázquez 144, E-28006 Madrid, Spain Corresponding author e-mail:
| | | | | | - Ramón Díaz-Orejas
- MRC Cancer Cell Unit, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 2XZ, Wellcome Trust Cancer Research UK Institute, Tennis Court Road, Cambridge CB2 1QR and Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK and
Centro de Investigaciones Biológicas (C.S.I.C.), Department of Molecular Microbiology, Velázquez 144, E-28006 Madrid, Spain Corresponding author e-mail:
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Santapaola D, Casalino M, Petrucca A, Presutti C, Zagaglia C, Berlutti F, Colonna B, Nicoletti M. Enteroinvasive Escherichia coli virulence-plasmid-carried apyrase (apy) and ospB genes are organized as a bicistronic operon and are subject to differential expression. MICROBIOLOGY (READING, ENGLAND) 2002; 148:2519-2529. [PMID: 12177345 DOI: 10.1099/00221287-148-8-2519] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In Shigella flexneri and enteroinvasive Escherichia coli (EIEC) the expression of the virulence-plasmid(pINV)-carried potential pathogenesis-associated apy gene, which encodes apyrase (ATP diphosphohydrolase), is regulated by the same regulators that govern the expression of virulence genes. To understand the transcriptional organization of the apy gene, the authors sequenced an 8023 bp PstI fragment of the pINV of EIEC strain HN280, which encompasses apy as well as its adjacent genes. The PstI fragment displays 99% identity with the corresponding fragment of pWR100, the pINV of S. flexneri strain M90T, and contains four genes. One of these genes, ospB, encodes a secreted protein of unknown activity and is located immediately upstream of apy. Analyses of sequence, Northern hybridization, RT-PCR and primer extension data and transcriptional fusions indicated that ospB and apy are co-transcribed as a 2 kb bicistronic, temperature-regulated mRNA from an upstream promoter that precedes ospB. The 2 kb mRNA is post-transcriptionally processed in the intercistronic ospB-apy region, leading to the considerable accumulation of a more stable 1 kb apy-specific mRNA (half-life of 2.2+/-0.3 min, versus 27+/-4 s for the 2 kb transcript). Upon temperature induction, peak expression of the ospB-apy operon occurs when bacteria enter into the late phases of bacterial growth, where the apy-specific transcript was found to be much more prevalent if compared to the ospB-apy transcript.
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Affiliation(s)
- Daniela Santapaola
- Dipartimento di Scienze Biomediche, Sezione di Microbiologia, Università G. D'Annunzio, 66100 Chieti, Italy1
| | | | | | - Carlo Presutti
- Dipartimento di Genitica e Biologia Molecolare4, Dipartimento di Scienze di Sanità Pubblica, Sezione di Microbiologia5 and Dipartimento di Biologia Cellulare e dello Sviluppo, Sezione di Scienze Microbiologiche6, Università di Roma La Sapienza, 00185 Rome, Italy
| | - Carlo Zagaglia
- Dipartimento di Genitica e Biologia Molecolare4, Dipartimento di Scienze di Sanità Pubblica, Sezione di Microbiologia5 and Dipartimento di Biologia Cellulare e dello Sviluppo, Sezione di Scienze Microbiologiche6, Università di Roma La Sapienza, 00185 Rome, Italy
| | - Francesca Berlutti
- Dipartimento di Genitica e Biologia Molecolare4, Dipartimento di Scienze di Sanità Pubblica, Sezione di Microbiologia5 and Dipartimento di Biologia Cellulare e dello Sviluppo, Sezione di Scienze Microbiologiche6, Università di Roma La Sapienza, 00185 Rome, Italy
| | - Bianca Colonna
- Dipartimento di Genitica e Biologia Molecolare4, Dipartimento di Scienze di Sanità Pubblica, Sezione di Microbiologia5 and Dipartimento di Biologia Cellulare e dello Sviluppo, Sezione di Scienze Microbiologiche6, Università di Roma La Sapienza, 00185 Rome, Italy
| | - Mauro Nicoletti
- Dipartimento di Scienze Biomediche, Sezione di Microbiologia, Università G. D'Annunzio, 66100 Chieti, Italy1
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Thies FL, Karch H, Hartung HP, Giegerich G. Cloning and expression of the dnaK gene of Campylobacter jejuni and antigenicity of heat shock protein 70. Infect Immun 1999; 67:1194-200. [PMID: 10024560 PMCID: PMC96446 DOI: 10.1128/iai.67.3.1194-1200.1999] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Campylobacter jejuni is a leading cause of infectious diarrhea throughout the world. In addition, there is growing evidence that Guillain-Barré syndrome, an inflammatory demyelinating disease of the peripheral nervous system, is frequently preceded by C. jejuni infection. In the present study, the hrcA-grpE-dnaK gene cluster of C. jejuni was cloned and sequenced. The dnaK gene consists of an open reading frame of 1,869 bp and encodes a protein with a high degree of homology to other bacterial 70-kDa heat shock proteins (HSPs). The overall percentages of identity to the HSP70 proteins of Helicobacter pylori, Borrelia burgdorferi, Chlamydia trachomatis, and Bacillus subtilis were calculated to be 78.1, 60.5, 57.2, and 53. 8%, respectively. Regions similar to the Escherichia coli sigma70 promoter consensus sequence and to a cis-acting regulatory element (CIRCE) are located upstream of the hrcA gene. Following heat shock, a rapid increase of dnaK mRNA was detectable, which reached its maximum after 20 to 30 min. A 6-His-tagged recombinant DnaK protein (rCjDnaK-His) was generated in E. coli, after cloning of the dnaK coding region into pET-22b(+), and purified by affinity and gel filtration chromatography. Antibody responses to rCjDnaK-His were significantly elevated, compared to those of healthy individuals, in about one-third of the serum specimens obtained from C. jejuni enteritis patients.
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Affiliation(s)
- F L Thies
- Department of Neurology, Julius-Maximilians-Universität, D-97080 Würzburg, Germany
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Abstract
The P1 plasmid addiction operon encodes Doc, a toxin that kills plasmid-free segregants, and Phd, an unstable antidote that neutralizes the toxin. Additionally, these products repress transcription of the operon. The antidote binds to two adjacent sites in the promoter. Here we present evidence concerning the regulatory role of the toxin, which we studied with the aid of a mutation, docH66Y. The DocH66Y protein retained the regulatory properties of the wild-type protein, but not its toxicity. In vivo, DocH66Y enhanced repression by Phd but failed to affect repression in the absence of Phd, suggesting that DocH66Y contacts Phd. In vitro, a MalE-DocH66Y fusion protein was found to bind Phd. Binding of toxin to antidote may be the physical basis for the neutralization of toxin. DocH66Y failed to bind DNA in vitro yet enhanced the affinity, cooperativity, and specificity with which Phd bound the operator. Although DocH66Y enhanced the binding of Phd to two adjacent Phd-binding sites, DocH66Y had relatively little effect on the binding of Phd to a single Phd-binding site, indicating that DocH66Y mediates cooperative interactions between adjacent Phd-binding sites. Several electrophoretically distinct protein-DNA complexes were observed with different amounts of DocH66Y relative to Phd. Maximal repression and specificity of DNA binding were observed with subsaturating amounts of DocH66Y relative to Phd. Analogous antidote-toxin pairs appear to have similar autoregulatory circuits. Autoregulation, by dampening fluctuations in the levels of toxin and antidote, may prevent the inappropriate activation of the toxin.
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Affiliation(s)
- R Magnuson
- Laboratory of Biochemistry, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4225, USA.
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Holčík M, Iyer VM. Conditionally lethal genes associated with bacterial plasmids. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 11):3403-3416. [PMID: 9387219 DOI: 10.1099/00221287-143-11-3403] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Martin Holčík
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa Ontario Canada K1S5B6
| | - V M Iyer
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa Ontario Canada K1S5B6
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