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Klimina KM, Kjasova DK, Poluektova EU, Krügel H, Leuschner Y, Saluz HP, Danilenko VN. Identification and characterization of toxin-antitoxin systems in strains of Lactobacillus rhamnosus isolated from humans. Anaerobe 2013; 22:82-9. [PMID: 23727113 DOI: 10.1016/j.anaerobe.2013.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 05/16/2013] [Accepted: 05/20/2013] [Indexed: 12/19/2022]
Abstract
The toxin-antitoxin gene systems (TASs) are present in the genomes of the overwhelming majority of bacteria and archaea. These systems are involved in various cellular regulatory processes (including stress response), and have not been previously investigated in Lactobacilli. We identified 6 putative TASs with toxins belonging to the MazE and RelE superfamilies (PemK1-А1Lrh, PemK2-А2Lrh, PemK3-RelB2Lrh, RelE1Lrh, RelB3-RelE3Lrh, and YefM-YoeBLrh) in the genomes of annotated strains of Lactobacillus rhamnosus. PCR analyses revealed that all systems were found in the genomes of 15 strains of L. rhamnosus isolated from humans in central Russia. These strains were highly heterogeneous with respect to the presence of TASs, as well as their nucleotide and amino acid sequences. In three cases, the relE1 genes contained IS3 elements. TAS heterogeneity may be used to reveal inter-genus differences between strains. Cloning of the toxin genes of 3 TASs inhibited Escherichia coli growth, thus confirming their functionality. Cell growth arrest caused by expression of the toxin genes could be reverted by the expression of a cognate antitoxins. Transcription of toxin-antitoxin loci in L. rhamnosus was shown by RT-PCR.
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Affiliation(s)
- K M Klimina
- Laboratory of Genetics of Microorganisms, Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin Street, 119991 GSP-1 Moscow, Russian Federation
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Identification and characterization of type II toxin-antitoxin systems in the opportunistic pathogen Acinetobacter baumannii. J Bacteriol 2013; 195:3165-72. [PMID: 23667234 DOI: 10.1128/jb.00237-13] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Acinetobacter baumannii is an opportunistic pathogen that causes nosocomial infections. Due to the ability to persist in the clinical environment and rapidly acquire antibiotic resistance, multidrug-resistant A. baumannii clones have spread in medical units in many countries in the last decade. The molecular basis of the emergence and spread of the successful multidrug-resistant A. baumannii clones is not understood. Bacterial toxin-antitoxin (TA) systems are abundant genetic loci harbored in low-copy-number plasmids and chromosomes and have been proposed to fulfill numerous functions, from plasmid stabilization to regulation of growth and death under stress conditions. In this study, we have performed a thorough bioinformatic search for type II TA systems in genomes of A. baumannii strains and estimated at least 15 possible TA gene pairs, 5 of which have been shown to be functional TA systems. Three of them were orthologs of bacterial and archaeal RelB/RelE, HicA/HicB, and HigB/HigA systems, and others were the unique SplT/SplA and CheT/CheA TA modules. The toxins of all five TA systems, when expressed in Escherichia coli, inhibited translation, causing RNA degradation. The HigB/HigA and SplT/SplA TA pairs of plasmid origin were highly prevalent in clinical multidrug-resistant A. baumannii isolates from Lithuanian hospitals belonging to the international clonal lineages known as European clone I (ECI) and ECII.
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Zhao J, Wang Q, Li M, Heijstra BD, Wang S, Liang Q, Qi Q. Escherichia coli toxin gene hipA affects biofilm formation and DNA release. Microbiology (Reading) 2013; 159:633-640. [DOI: 10.1099/mic.0.063784-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Junqiao Zhao
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
| | - Qian Wang
- National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
| | - Mingji Li
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
| | - Björn D. Heijstra
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Shengjun Wang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
| | - Quanfeng Liang
- National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
| | - Qingsheng Qi
- National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
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Ning D, Jiang Y, Liu Z, Xu Q. Characterization of a chromosomal type II toxin-antitoxin system mazEaFa in the Cyanobacterium Anabaena sp. PCC 7120. PLoS One 2013; 8:e56035. [PMID: 23451033 PMCID: PMC3581536 DOI: 10.1371/journal.pone.0056035] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 01/04/2013] [Indexed: 01/04/2023] Open
Abstract
Cyanobacteria have evolved to survive stressful environmental changes by regulating growth, however, the underlying mechanism for this is obscure. The ability of chromosomal type II toxin-antitoxin (TA) systems to modulate growth or cell death has been documented in a variety of prokaryotes. A chromosomal mazEaFa locus of Anabaena sp. PCC 7120 has been predicted as a putative mazEF TA system. Here we demonstrate that mazEaFa form a bicistronic operon that is co-transcribed under normal growth conditions. Overproduction of MazFa induced Anabaena growth arrest which could be neutralized by co-expression of MazEa. MazFa also inhibited the growth of Escherichia coli cells, and this effect could be overcome by simultaneous or subsequent expression of MazEa via formation of the MazEa-MazFa complex in vivo, further confirming the nature of the mazEaFa locus as a type II TA system. Interestingly, like most TA systems, deletion of mazEaFa had no effect on the growth of Anabaena during the tested stresses. Our data suggest that mazEaFa, or together with other chromosomal type II TA systems, may promote cells to cope with particular stresses by inducing reversible growth arrest of Anabaena.
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Affiliation(s)
- Degang Ning
- Department of Environment Sciences, School of the Environment, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yan Jiang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Zhaoying Liu
- Department of Environment Sciences, School of the Environment, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Qinggang Xu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
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Yan X, Gurtler JB, Fratamico PM, Hu J, Juneja VK. Phylogenetic identification of bacterial MazF toxin protein motifs among probiotic strains and foodborne pathogens and potential implications of engineered probiotic intervention in food. Cell Biosci 2012. [PMID: 23186337 PMCID: PMC3519753 DOI: 10.1186/2045-3701-2-39] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
UNLABELLED BACKGROUND Toxin-antitoxin (TA) systems are commonly found in bacteria and Archaea, and it is the most common mechanism involved in bacterial programmed cell death or apoptosis. Recently, MazF, the toxin component of the toxin-antitoxin module, has been categorized as an endoribonuclease, or it may have a function similar to that of a RNA interference enzyme. RESULTS In this paper, with comparative data and phylogenetic analyses, we are able to identify several potential MazF-conserved motifs in limited subsets of foodborne pathogens and probiotic strains and further provide a molecular basis for the development of engineered/synthetic probiotic strains for the mitigation of foodborne illnesses. Our findings also show that some probiotic strains, as fit as many bacterial foodborne pathogens, can be genetically categorized into three major groups based on phylogenetic analysis of MazF. In each group, potential functional motifs are conserved in phylogenetically distant species, including foodborne pathogens and probiotic strains. CONCLUSION These data provide important knowledge for the identification and computational prediction of functional motifs related to programmed cell death. Potential implications of these findings include the use of engineered probiotic interventions in food or use of a natural probiotic cocktail with specificity for controlling targeted foodborne pathogens.
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Affiliation(s)
- Xianghe Yan
- Eastern Regional Research Center, Agricultural Research Service, U,S, Department of Agriculture, 600 E, Mermaid Lane, Wyndmoor, PA, 19038, USA.
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Rankin DJ, Turner LA, Heinemann JA, Brown SP. The coevolution of toxin and antitoxin genes drives the dynamics of bacterial addiction complexes and intragenomic conflict. Proc Biol Sci 2012; 279:3706-15. [PMID: 22787022 PMCID: PMC3415908 DOI: 10.1098/rspb.2012.0942] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 06/20/2012] [Indexed: 12/12/2022] Open
Abstract
Bacterial genomes commonly contain 'addiction' gene complexes that code for both a toxin and a corresponding antitoxin. As long as both genes are expressed, cells carrying the complex can remain healthy. However, loss of the complex (including segregational loss in daughter cells) can entail death of the cell. We develop a theoretical model to explore a number of evolutionary puzzles posed by toxin-antitoxin (TA) population biology. We first extend earlier results demonstrating that TA complexes can spread on plasmids, as an adaptation to plasmid competition in spatially structured environments, and highlight the role of kin selection. We then considered the emergence of TA complexes on plasmids from previously unlinked toxin and antitoxin genes. We find that one of these traits must offer at least initially a direct advantage in some but not all environments encountered by the evolving plasmid population. Finally, our study predicts non-transitive 'rock-paper-scissors' dynamics to be a feature of intragenomic conflict mediated by TA complexes. Intragenomic conflict could be sufficient to select deleterious genes on chromosomes and helps to explain the previously perplexing observation that many TA genes are found on bacterial chromosomes.
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Affiliation(s)
- Daniel J. Rankin
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Building Y27, Winterthurerstrasse 190, 8057 Zürich, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge Bâtiment Génopode, 1015 Lausanne, Switzerland
| | - Leighton A. Turner
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jack A. Heinemann
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Sam P. Brown
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
- Centre for Immunity, Infection and Evolution, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
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Marshall SH, Gómez FA, Ramírez R, Nilo L, Henríquez V. Biofilm generation by Piscirickettsia salmonis under growth stress conditions: a putative in vivo survival/persistence strategy in marine environments. Res Microbiol 2012; 163:557-66. [DOI: 10.1016/j.resmic.2012.08.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 07/28/2012] [Indexed: 10/28/2022]
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Benz J, Sendlmeier C, Barends TRM, Meinhart A. Structural insights into the effector-immunity system Tse1/Tsi1 from Pseudomonas aeruginosa. PLoS One 2012; 7:e40453. [PMID: 22792331 PMCID: PMC3391265 DOI: 10.1371/journal.pone.0040453] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 06/07/2012] [Indexed: 11/19/2022] Open
Abstract
During an interbacterial battle, the type-6-secretion-system (T6SS) of the human pathogen Pseudomonas aeruginosa injects the peptidoglycan(PG)-hydrolase Tse1 into the periplasm of gram-negative enemy cells and induces their lysis. However, for its own benefit, P. aeruginosa produces and transports the immunity-protein Tsi1 into its own periplasm where in prevents accidental exo- and endogenous intoxication. Here we present the high-resolution X-ray crystal structure of the lytic enzyme Tse1 and describe the mechanism by which Tse1 cleaves the γ-D-glutamyl-l-meso-diaminopimelic acid amide bond of crosslinked PG. Tse1 belongs to the superfamily of N1pC/P60 peptidases but is unique among described members of this family of which the structure was described, since it is a single domain protein without any putative localization domain. Most importantly, we present the crystal structure of Tse1 bound to its immunity-protein Tsi1 as well and describe the mechanism of enzyme inhibition. Tsi1 occludes the active site of Tse1 and abolishes its enzyme activity by forming a hydrogen bond to a catalytically important histidine residue in Tse1. Based on our structural findings in combination with a bioinfomatic approach we also identified a related system in Burkholderia phytofirmans. Not only do our findings point to a common catalytic mechanism of the Tse1 PG-hydrolases, but we can also show that it is distinct from other members of this superfamily. Furthermore, we provide strong evidence that the mechanism of enzyme inhibition between Tsi1 orthologues is conserved. This work is the first structural description of an entire effector/immunity pair injected by the T6SS system. Moreover, it is also the first example of a member of the N1pC/P60 superfamily which becomes inhibited upon binding to its cognate immunity protein.
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Affiliation(s)
- Juliane Benz
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Christina Sendlmeier
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Thomas R. M. Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Anton Meinhart
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
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Sterckx YGJ, Garcia-Pino A, Haesaerts S, Jové T, Geerts L, Sakellaris V, Van Melderen L, Loris R. The ParE2-PaaA2 toxin-antitoxin complex from Escherichia coli O157 forms a heterodocecamer in solution and in the crystal. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:724-9. [PMID: 22684081 PMCID: PMC3370921 DOI: 10.1107/s1744309112015230] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 04/06/2012] [Indexed: 11/10/2022]
Abstract
Escherichia coli O157 paaR2-paaA2-parE2 constitutes a unique three-component toxin-antitoxin (TA) module encoding a toxin (ParE2) related to the classic parDE family but with an unrelated antitoxin called PaaA2. The complex between PaaA2 and ParE2 was purified and characterized by analytical gel filtration, dynamic light scattering and small-angle X-ray scattering. It consists of a particle with a radius of gyration of 3.95 nm and is likely to form a heterododecamer. Crystals of the ParE2-PaaA2 complex diffract to 3.8 Å resolution and belong to space group P3(1)21 or P3(2)21, with unit-cell parameters a = b = 142.9, c = 87.5 Å. The asymmetric unit is consistent with a particle of around 125 kDa, which is compatible with the solution data. Therefore, the ParE2-PaaA2 complex is the largest toxin-antitoxin complex identified to date and its quaternary arrangement is likely to be of biological significance.
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Affiliation(s)
- Yann G. J. Sterckx
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
- Molecular Recognition Unit, Department of Structural Biology, VIB, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Abel Garcia-Pino
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
- Molecular Recognition Unit, Department of Structural Biology, VIB, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Sarah Haesaerts
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
- Molecular Recognition Unit, Department of Structural Biology, VIB, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Thomas Jové
- Génétique et Physiologie Bactérienne, Université Libre de Bruxelles, 12 Rue des Professeurs Geener et Brachet, B-6041 Gosselies, Belgium
| | - Lieselotte Geerts
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Viktor Sakellaris
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Laurence Van Melderen
- Génétique et Physiologie Bactérienne, Université Libre de Bruxelles, 12 Rue des Professeurs Geener et Brachet, B-6041 Gosselies, Belgium
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
- Molecular Recognition Unit, Department of Structural Biology, VIB, Pleinlaan 2, B-1050 Brussel, Belgium
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Two programmed cell death systems in Escherichia coli: an apoptotic-like death is inhibited by the mazEF-mediated death pathway. PLoS Biol 2012; 10:e1001281. [PMID: 22412352 PMCID: PMC3295820 DOI: 10.1371/journal.pbio.1001281] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 01/26/2012] [Indexed: 12/17/2022] Open
Abstract
A newly discovered apoptotic-like death is inhibited by the previously described mazEF-mediated death pathway, revealing two programmed cell death systems in Escherichia coli. In eukaryotes, the classical form of programmed cell death (PCD) is apoptosis, which has as its specific characteristics DNA fragmentation and membrane depolarization. In Escherichia coli a different PCD system has been reported. It is mediated by the toxin–antitoxin system module mazEF. The E. coli mazEF module is one of the most thoroughly studied toxin–antitoxin systems. mazF encodes a stable toxin, MazF, and mazE encodes a labile antitoxin, MazE, which prevents the lethal effect of MazF. mazEF-mediated cell death is a population phenomenon requiring the quorum-sensing pentapeptide NNWNN designated Extracellular Death Factor (EDF). mazEF is triggered by several stressful conditions, including severe damage to the DNA. Here, using confocal microscopy and FACS analysis, we show that under conditions of severe DNA damage, the triggered mazEF-mediated cell death pathway leads to the inhibition of a second cell death pathway. The latter is an apoptotic-like death (ALD); ALD is mediated by recA and lexA. The mazEF-mediated pathway reduces recA mRNA levels. Based on these results, we offer a molecular model for the maintenance of an altruistic characteristic in cell populations. In our model, the ALD pathway is inhibited by the altruistic EDF-mazEF-mediated death pathway. The enteric bacterium Escherichia coli, like most other bacteria, carries on its chromosome a pair of genes, mazE and mazF (mazEF): mazF specifies a toxin, and mazE specifies an antitoxin. Previously, we have shown that E. coli mazEF is responsible for bacterial programmed cell death in response to stressors such as DNA damage. Here, we report that extensive DNA damage can induce a second mode of cell death, which we call apoptotic-like death (ALD). ALD is like apoptosis—a mode of cell death that has previously been recorded only in eukaryotes. During ALD, the cell membrane is depolarized, and the DNA is fragmented and can be detected using the classical TUNEL assay. The MazEF death pathway, however, shows neither of those features, yet also kills the cell. We show that ALD is mediated by two proteins, RecA and LexA, which are noteworthy because LexA is an inhibitor of the SOS response (which is a global response to DNA damage in which the cell cycle is arrested and DNA repair is induced). This defines ALD as a form of SOS response. Furthermore, MazEF and its downstream components cause reduction of recA mRNA levels, which could explain how the MazEF pathway inhibits the ALD pathway. We conclude that the E. coli ALD pathway is a back-up system for the traditional mazEF cell death pathway. Should one of the components of the mazEF pathway be inactivated, bacterial cell death would occur through ALD. These findings also have implications for the mechanisms of “altruistic” cell death among bacterial populations.
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Characterization of Escherichia coli dinJ-yafQ toxin-antitoxin system using insights from mutagenesis data. J Bacteriol 2012; 194:1523-32. [PMID: 22247505 DOI: 10.1128/jb.06104-11] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli dinJ-yafQ operon codes for a functional toxin-antitoxin (TA) system. YafQ toxin is an RNase which, upon overproduction, specifically inhibits the translation process by cleaving cellular mRNA at specific sequences. DinJ is an antitoxin and counteracts YafQ-mediated toxicity by forming a strong protein complex. In the present study we used site-directed mutagenesis of YafQ to determine the amino acids important for its catalytic activity. His50Ala, His63Ala, Asp67Ala, Trp68Ala, Trp68Phe, Arg83Ala, His87Ala, and Phe91Ala substitutions of the predicted active-site residues of YafQ abolished mRNA cleavage in vivo, whereas Asp61Ala and Phe91Tyr mutations inhibited YafQ RNase activity only moderately. We show that YafQ, upon overexpression, cleaved mRNAs preferably 5' to A between the second and third nucleotides in the codon in vivo. YafQ also showed RNase activity against mRNA, tRNA, and 5S rRNA molecules in vitro, albeit with no strong specificity. The endoribonuclease activity of YafQ was inhibited in the complex with DinJ antitoxin in vitro. DinJ-YafQ protein complex and DinJ antitoxin alone selectively bind to one of the two palindromic sequences present in the intergenic region upstream of the dinJ-yafQ operon, suggesting the autoregulation mode of this TA system.
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62
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Lee MW, Rogers EE, Stenger DC. Xylella fastidiosa plasmid-encoded PemK toxin is an endoribonuclease. PHYTOPATHOLOGY 2012; 102:32-40. [PMID: 21864087 DOI: 10.1094/phyto-05-11-0150] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Stable inheritance of pXF-RIV11 in Xylella fastidiosa is conferred by the pemI/pemK toxin-antitoxin (TA) system. PemK toxin inhibits bacterial growth; PemI is the corresponding antitoxin that blocks activity of PemK by direct binding. PemK and PemI were overexpressed in Escherichia coli and activities of each were assessed. Purified PemK toxin specifically degraded single-stranded RNA but not double-stranded RNA, double-stranded DNA, or single-stranded DNA. Addition of PemI antitoxin inhibited nuclease activity of PemK toxin. Purified complexes of PemI bound to PemK exhibited minimal nuclease activity; removal of PemI antitoxin from the complex restored nuclease activity of PemK toxin. Sequencing of 5' rapid amplification of cDNA ends products of RNA targets digested with PemK revealed a preference for cleavage between U and A residues of the sequence UACU and UACG. Nine single amino-acid substitution mutants of PemK toxin were constructed and evaluated for growth inhibition, ribonuclease activity, and PemI binding. Three PemK point-substitution mutants (R3A, G16E, and D79V) that lacked nuclease activity did not inhibit growth. All nine PemK mutants retained the ability to bind PemI. Collectively, the results indicate that the mechanism of stable inheritance conferred by pXF-RIV11 pemI/pemK is similar to that of the R100 pemI/pemK TA system of E. coli.
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Affiliation(s)
- Min Woo Lee
- San Joaquin Agricultural Sciences Center, United States Department of Agriculture, Parlier, CA, USA
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63
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Frampton R, Aggio RBM, Villas-Bôas SG, Arcus VL, Cook GM. Toxin-antitoxin systems of Mycobacterium smegmatis are essential for cell survival. J Biol Chem 2011; 287:5340-56. [PMID: 22199354 DOI: 10.1074/jbc.m111.286856] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The role of chromosomal toxin-antitoxin (TA) modules in bacterial physiology remains enigmatic despite their abundance in the genomes of many bacteria. Mycobacterium smegmatis contains three putative TA systems, VapBC, MazEF, and Phd/Doc, and previous work from our group has shown VapBC to be a bona fide TA system. In this study, we show that MazEF and Phd/Doc are also TA systems that are constitutively expressed, transcribed as leaderless transcripts, and subject to autoregulation, and expression of the toxin component leads to growth inhibition that can be rescued by the cognate antitoxin. No phenotype was identified for deletions of the individual TA systems, but a triple deletion strain (ΔvapBC, mazEF, phd/doc), designated ΔTA(triple), exhibited a survival defect in complex growth medium demonstrating an essential role for these TA modules in mycobacterial survival. Transcriptomic analysis revealed no significant differences in gene expression between wild type and the ΔTA(triple) mutant under these conditions suggesting that the growth defect was not at a transcriptional level. Metabolomic analysis demonstrated that in response to starvation in complex medium, both the wild type and ΔTA(triple) mutant consumed a wide range of amino acids from the external milieu. Analysis of intracellular metabolites revealed a significant difference in the levels of branched-chain amino acids between the wild type and ΔTA(triple) mutant, which are proposed to play essential roles in monitoring the nutritional supply and physiological state of the cell and linking catabolic with anabolic reactions. Disruption of this balance in the ΔTA(triple) mutant may explain the survival defect in complex growth medium.
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Affiliation(s)
- Rebekah Frampton
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand
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64
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Balaban NQ. Persistence: mechanisms for triggering and enhancing phenotypic variability. Curr Opin Genet Dev 2011; 21:768-75. [DOI: 10.1016/j.gde.2011.10.001] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 09/19/2011] [Accepted: 10/04/2011] [Indexed: 11/28/2022]
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65
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Vesper O, Amitai S, Belitsky M, Byrgazov K, Kaberdina AC, Engelberg-Kulka H, Moll I. Selective translation of leaderless mRNAs by specialized ribosomes generated by MazF in Escherichia coli. Cell 2011; 147:147-57. [PMID: 21944167 DOI: 10.1016/j.cell.2011.07.047] [Citation(s) in RCA: 227] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 03/11/2011] [Accepted: 07/21/2011] [Indexed: 01/17/2023]
Abstract
Escherichia coli (E. coli) mazEF is a stress-induced toxin-antitoxin (TA) module. The toxin MazF is an endoribonuclease that cleaves single-stranded mRNAs at ACA sequences. Here, we show that MazF cleaves at ACA sites at or closely upstream of the AUG start codon of some specific mRNAs and thereby generates leaderless mRNAs. Moreover, we provide evidence that MazF also targets 16S rRNA within 30S ribosomal subunits at the decoding center, thereby removing 43 nucleotides from the 3' terminus. As this region comprises the anti-Shine-Dalgarno (aSD) sequence that is required for translation initiation on canonical mRNAs, a subpopulation of ribosomes is formed that selectively translates the described leaderless mRNAs both in vivo and in vitro. Thus, we have discovered a modified translation machinery that is generated in response to MazF induction and that probably serves for stress adaptation in Escherichia coli.
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Affiliation(s)
- Oliver Vesper
- Max F. Perutz Laboratories, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Dr. Bohrgasse 9/4, 1030 Vienna, Austria
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66
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Yamaguchi Y, Inouye M. Regulation of growth and death in Escherichia coli by toxin–antitoxin systems. Nat Rev Microbiol 2011; 9:779-90. [DOI: 10.1038/nrmicro2651] [Citation(s) in RCA: 299] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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67
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Wang X, Wood TK. Toxin-antitoxin systems influence biofilm and persister cell formation and the general stress response. Appl Environ Microbiol 2011; 77:5577-83. [PMID: 21685157 PMCID: PMC3165247 DOI: 10.1128/aem.05068-11] [Citation(s) in RCA: 314] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
In many genomes, toxin-antitoxin (TA) systems have been identified; however, their role in cell physiology has been unclear. Here we examine the evidence that TA systems are involved in biofilm formation and persister cell formation and that these systems may be important regulators of the switch from the planktonic to the biofilm lifestyle as a stress response by their control of secondary messenger 3',5'-cyclic diguanylic acid. Specifically, upon stress, the sequence-specific mRNA interferases MqsR and MazF mediate cell survival. In addition, we propose that TA systems are not redundant, as they may have developed to respond to specific stresses.
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Affiliation(s)
- Xiaoxue Wang
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122
- Key Laboratory of Marine Bio-Resource Sustainable Utilization, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, People's Republic of China
| | - Thomas K. Wood
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122
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68
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Hayes F, Van Melderen L. Toxins-antitoxins: diversity, evolution and function. Crit Rev Biochem Mol Biol 2011; 46:386-408. [PMID: 21819231 DOI: 10.3109/10409238.2011.600437] [Citation(s) in RCA: 196] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Genes for toxin-antitoxin (TA) complexes are widespread in prokaryote genomes, and species frequently possess tens of plasmid and chromosomal TA loci. The complexes are categorized into three types based on genetic organization and mode of action. The toxins universally are proteins directed against specific intracellular targets, whereas the antitoxins are either proteins or small RNAs that neutralize the toxin or inhibit toxin synthesis. Within the three types of complex, there has been extensive evolutionary shuffling of toxin and antitoxin genes leading to considerable diversity in TA combinations. The intracellular targets of the protein toxins similarly are varied. Numerous toxins, many of which are sequence-specific endoribonucleases, dampen protein synthesis levels in response to a range of stress and nutritional stimuli. Key resources are conserved as a result ensuring the survival of individual cells and therefore the bacterial population. The toxin effects generally are transient and reversible permitting a set of dynamic, tunable responses that reflect environmental conditions. Moreover, by harboring multiple toxins that intercede in protein synthesis in response to different physiological cues, bacteria potentially sense an assortment of metabolic perturbations that are channeled through different TA complexes. Other toxins interfere with the action of topoisomersases, cell wall assembly, or cytoskeletal structures. TAs also play important roles in bacterial persistence, biofilm formation and multidrug tolerance, and have considerable potential both as new components of the genetic toolbox and as targets for novel antibacterial drugs.
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Affiliation(s)
- Finbarr Hayes
- Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester, UK.
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69
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Wang X, Kim Y, Hong SH, Ma Q, Brown BL, Pu M, Tarone AM, Benedik MJ, Peti W, Page R, Wood TK. Antitoxin MqsA helps mediate the bacterial general stress response. Nat Chem Biol 2011; 7:359-66. [PMID: 21516113 PMCID: PMC3097263 DOI: 10.1038/nchembio.560] [Citation(s) in RCA: 174] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 02/10/2011] [Indexed: 01/19/2023]
Abstract
Although it is well-recognized that bacteria respond to environmental stress via global networks, the mechanism by which stress is relayed to the interior of the cell is poorly understood. Here we show that enigmatic toxin/antitoxin systems play a vital role in mediating the environmental stress response. Specifically, the antitoxin MqsA represses rpoS, which encodes the master regulator of stress. Repression of rpoS by MqsA reduces the concentration of the internal messenger 3,5-cyclic diguanylic acid, leading to increased motility and decreased biofilm formation. Furthermore, the repression of rpoS by MqsA decreases oxidative stress resistance via catalase activity. Upon oxidative stress, MqsA is rapidly degraded by Lon protease resulting in induction of rpoS. Hence, we show that external stress alters gene regulation controlled by toxin/antitoxin systems, such that the degradation of antitoxins during stress leads to a switch from the planktonic state (high motility) to the biofilm state (low motility).
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Affiliation(s)
- Xiaoxue Wang
- Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA
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70
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The Escherichia coli Extracellular Death Factor EDF Induces the Endoribonucleolytic Activities of the Toxins MazF and ChpBK. Mol Cell 2011; 41:625-35. [DOI: 10.1016/j.molcel.2011.02.023] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 10/17/2010] [Accepted: 12/24/2010] [Indexed: 01/15/2023]
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71
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Recent advancements in toxin and antitoxin systems involved in bacterial programmed cell death. Int J Microbiol 2010; 2010:781430. [PMID: 21253538 PMCID: PMC3021852 DOI: 10.1155/2010/781430] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 10/14/2010] [Accepted: 11/21/2010] [Indexed: 01/22/2023] Open
Abstract
Programmed cell death (PCD) systems have been extensively studied for their significant role in a variety of biological processes in eukaryotic organisms. Recently, more and more researches have revealed the existence of similar systems employed by bacteria in response to various environmental stresses. This paper summarized the recent researching advancements in toxin/antitoxin systems located on plasmids or chromosomes and their regulatory roles in bacterial PCD. The most studied yet disputed mazEF system was discussed in depth, and possible roles and status of such a special bacterial death and TA systems were also reviewed from the ecological and evolutionary perspectives.
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72
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Polyethyleneimine nanoparticles incorporated into resin composite cause cell death and trigger biofilm stress in vivo. Proc Natl Acad Sci U S A 2010; 107:22038-43. [PMID: 21131569 DOI: 10.1073/pnas.1010341107] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Incorporation of cross-linked quaternary ammonium polyethylenimine (QPEI) nanoparticles in dental resin composite has a long-lasting and wide antimicrobial effect with no measured impact on biocompatibility in vitro. We hypothesized that QPEI nanoparticles incorporated into a resin composite have a potent antibacterial effect in vivo and that this stress condition triggers a suicide module in the bacterial biofilm. Ten volunteers wore a removable acrylic appliance, in which two control resin composite specimens and two resin composite specimens incorporating 1% wt/wt QPEI nanoparticles were inserted to allow the buildup of intraoral biofilms. After 4 h, the specimens were removed and tested for bacterial vitality and biofilm thickness, using confocal laser scanning microscopy. The vitality rate in specimens incorporating QPEI was reduced by > 50% (p < 0.00001), whereas biofilm thickness was increased (p < 0.05). The ability of the biofilm supernatant to restore bacterial death was tested in vitro. The in vitro tests showed a 70% decrease in viable bacteria (p < 0.05). Biofilm morphological differences were also observed in the scanning electron microscope micrographs of the resin composite versus the resin composite incorporating QPEI. These results strongly suggest that QPEI nanoparticles incorporated at a low concentration in resin composite exert a significant in vivo antibiofilm activity and exhibit a potent broad spectrum antibacterial activity against salivary bacteria.
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73
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The three vibrio cholerae chromosome II-encoded ParE toxins degrade chromosome I following loss of chromosome II. J Bacteriol 2010; 193:611-9. [PMID: 21115657 DOI: 10.1128/jb.01185-10] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Three homologues of the plasmid RK2 ParDE toxin-antitoxin system are present in the Vibrio cholerae genome within the superintegron on chromosome II. Here we found that these three loci-two of which have identical open reading frames and regulatory sequences-encode functional toxin-antitoxin systems. The ParE toxins inhibit bacterial division and reduce viability, presumably due to their capacity to damage DNA. The in vivo effects of ParE1/3 mimic those of ParE2, which we have previously demonstrated to be a DNA gyrase inhibitor in vitro, suggesting that ParE1/3 is likewise a gyrase inhibitor, despite its relatively low degree of sequence identity. ParE-mediated DNA damage activates the V. cholerae SOS response, which in turn likely accounts for ParE's inhibition of cell division. Each toxin's effects can be prevented by the expression of its cognate ParD antitoxin, which acts in a toxin-specific fashion both to block toxicity and to repress the expression of its parDE operon. Derepression of ParE activity in ΔparAB2 mutant V. cholerae cells that have lost chromosome II contributes to the prominent DNA degradation that accompanies the death of these cells. Overall, our findings suggest that the ParE toxins lead to the postsegregational killing of cells missing chromosome II in a manner that closely mimics postsegregational killing mediated by plasmid-encoded homologs. Thus, the parDE loci aid in the maintenance of the integrity of the V. cholerae superintegron and in ensuring the inheritance of chromosome II.
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Kroll J, Klinter S, Schneider C, Voss I, Steinbüchel A. Plasmid addiction systems: perspectives and applications in biotechnology. Microb Biotechnol 2010; 3:634-57. [PMID: 21255361 PMCID: PMC3815339 DOI: 10.1111/j.1751-7915.2010.00170.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Accepted: 02/17/2010] [Indexed: 11/26/2022] Open
Abstract
Biotechnical production processes often operate with plasmid-based expression systems in well-established prokaryotic and eukaryotic hosts such as Escherichia coli or Saccharomyces cerevisiae, respectively. Genetically engineered organisms produce important chemicals, biopolymers, biofuels and high-value proteins like insulin. In those bioprocesses plasmids in recombinant hosts have an essential impact on productivity. Plasmid-free cells lead to losses in the entire product recovery and decrease the profitability of the whole process. Use of antibiotics in industrial fermentations is not an applicable option to maintain plasmid stability. Especially in pharmaceutical or GMP-based fermentation processes, deployed antibiotics must be inactivated and removed. Several plasmid addiction systems (PAS) were described in the literature. However, not every system has reached a full applicable state. This review compares most known addiction systems and is focusing on biotechnical applications.
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Affiliation(s)
- Jens Kroll
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, D-48149 Münster, Germany
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75
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Gao Y, Chen K, Zhang B, Li X, Chen L, Li Y, Jia X, Lei Y, Yan Z, Kong L, Wang N, Liu W, Qi Y. Antioxidant and free radical-scavenging activity of the extracellular death factor in Escherichia coli. Peptides 2010; 31:1821-5. [PMID: 20621143 DOI: 10.1016/j.peptides.2010.06.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 06/30/2010] [Accepted: 06/30/2010] [Indexed: 11/19/2022]
Abstract
The extracellular death factor (EDF) is a newly discovered linear pentapeptide with the sequence of H-Asn-Asn-Trp-Asn-Asn-OH (NNWNN). It could act as a quorum-sensing molecule and participate in the mazEF-mediated cell death in Escherichia coli. In the present study, we firstly studied the antioxidant and free radical-scavenging activities of EDF. EDF could scavenge hydroxyl radicals in vitro and protect protein, lipid and DNA from being damaged by hydroxyl radicals. Our results indicated that this extracellular death factor might have dual effects during the programmed cell death process of Escherichia coli.
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Affiliation(s)
- Yanfeng Gao
- Department of Bioengineering, Zhengzhou University, Zhengzhou 450001, China.
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Nieto C, Sadowy E, de la Campa AG, Hryniewicz W, Espinosa M. The relBE2Spn toxin-antitoxin system of Streptococcus pneumoniae: role in antibiotic tolerance and functional conservation in clinical isolates. PLoS One 2010; 5:e11289. [PMID: 20585658 PMCID: PMC2890582 DOI: 10.1371/journal.pone.0011289] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Accepted: 05/21/2010] [Indexed: 01/24/2023] Open
Abstract
Type II (proteic) chromosomal toxin-antitoxin systems (TAS) are widespread in Bacteria and Archaea but their precise function is known only for a limited number of them. Out of the many TAS described, the relBE family is one of the most abundant, being present in the three first sequenced strains of Streptococcus pneumoniae (D39, TIGR4 and R6). To address the function of the pneumococcal relBE2Spn TAS in the bacterial physiology, we have compared the response of the R6-relBE2Spn wild type strain with that of an isogenic derivative, Delta relB2Spn under different stress conditions such as carbon and amino acid starvation and antibiotic exposure. Differences on viability between the wild type and mutant strains were found only when treatment directly impaired protein synthesis. As a criterion for the permanence of this locus in a variety of clinical strains, we checked whether the relBE2Spn locus was conserved in around 100 pneumococcal strains, including clinical isolates and strains with known genomes. All strains, although having various types of polymorphisms at the vicinity of the TA region, contained a functional relBE2Spn locus and the type of its structure correlated with the multilocus sequence type. Functionality of this TAS was maintained even in cases where severe rearrangements around the relBE2Spn region were found. We conclude that even though the relBE2Spn TAS is not essential for pneumococcus, it may provide additional advantages to the bacteria for colonization and/or infection.
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Affiliation(s)
- Concha Nieto
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Ewa Sadowy
- National Medicines Institute, Warsaw, Poland
| | - Adela G. de la Campa
- Centro Nacional de Microbiología and CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Majadahonda, Spain
| | | | - Manuel Espinosa
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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Mutschler H, Reinstein J, Meinhart A. Assembly dynamics and stability of the pneumococcal epsilon zeta antitoxin toxin (PezAT) system from Streptococcus pneumoniae. J Biol Chem 2010; 285:21797-806. [PMID: 20442221 DOI: 10.1074/jbc.m110.126250] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The pneumococcal epsilon zeta antitoxin toxin (PezAT) system is a chromosomally encoded, class II toxin antitoxin system from the human pathogen Streptococcus pneumnoniae. Neutralization of the bacteriotoxic protein PezT is carried out by complex formation with its cognate antitoxin PezA. Here we study the stability of the inhibitory complex in vivo and in vitro. We found that toxin release is impeded in Escherichia coli and Bacillus subtilis due to the proteolytic resistance of PezA once bound to PezT. These findings are supported by in vitro experiments demonstrating a strong thermodynamic stabilization of both proteins upon binding. A detailed kinetic analysis of PezAT assembly revealed that these particular features of PezAT are based on a strong, electrostatically guided binding mechanism leading to a stable toxin antitoxin complex with femtomolar affinity. Our data show that PezAT complex formation is distinct to all other conventional toxin antitoxin modules and a controlled mode of toxin release is required for activation.
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Affiliation(s)
- Hannes Mutschler
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
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78
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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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