501
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Kirkpatrick CL, Viollier PH. Decoding Caulobacter development. FEMS Microbiol Rev 2011; 36:193-205. [PMID: 22091823 DOI: 10.1111/j.1574-6976.2011.00309.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 09/15/2011] [Accepted: 09/15/2011] [Indexed: 11/27/2022] Open
Abstract
Caulobacter crescentus uses a multi-layered system of oscillating regulators to program different developmental fates into each daughter cell at division. This is achieved by superimposing gene expression, subcellular localization, phosphorylation, and regulated proteolysis to form a complex regulatory network that integrates chromosome replication, segregation, polar differentiation, and cytokinesis. In this review, we outline the current state of research in the field of Caulobacter development, emphasizing new findings that elaborate how the developmental program is modulated by factors such as the environment or the metabolic state of the cell.
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Affiliation(s)
- Clare L Kirkpatrick
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
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502
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Crystal structure of the VapBC toxin-antitoxin complex from Shigella flexneri reveals a hetero-octameric DNA-binding assembly. J Mol Biol 2011; 414:713-22. [PMID: 22037005 PMCID: PMC3384007 DOI: 10.1016/j.jmb.2011.10.024] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 10/06/2011] [Accepted: 10/12/2011] [Indexed: 12/20/2022]
Abstract
Toxin–antitoxin (TA) loci are common in archaea and prokaryotes and allow cells to rapidly adapt to changing environmental conditions through release of active regulators of metabolism. Many toxins are endonucleases that target cellular mRNA and tRNAs, while the antitoxins tightly wrap around the toxins to inhibit them under normal circumstances. The antitoxins also bind to operators in the promoter regions of the cognate TA operon and thereby regulate transcription. For enteric vapBC TA loci, the VapC toxins specifically cleave tRNAfMet and thus down-regulate protein synthesis. Here, we describe the crystal structure of the intact Shigella flexneri VapBC TA complex, determined to 2.7 Å resolution. Both in solution and in the crystal structure, four molecules of each protein combine to form a large and globular hetero-octameric assembly with SpoVT/AbrB-type DNA-binding domains at each end and a total molecular mass of about 100 kDa. The structure gives new insights into the inhibition of VapC toxins by VapB and provides the molecular basis for understanding transcriptional regulation through VapB dimerization.
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503
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Zorzini V, Haesaerts S, Cheung A, Loris R, van Nuland NAJ. 1H, 13C, and 15N backbone and side-chain chemical shift assignment of the staphylococcal MazF mRNA interferase. BIOMOLECULAR NMR ASSIGNMENTS 2011; 5:157-160. [PMID: 21213075 DOI: 10.1007/s12104-010-9290-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Accepted: 12/27/2010] [Indexed: 05/30/2023]
Abstract
MazF proteins are ribonucleases that cleave mRNA with high sequence-specificity as part of bacterial stress response and that are neutralized by the action of the corresponding antitoxin MazE. Prolonged activation of the toxin MazF leads to cell death. Several mazEF modules from gram-negative bacteria have been characterized in terms of catalytic activity, auto-regulation mechanism and structure, but less is known about their distant relatives found in gram-positive organisms. Currently, no solution NMR structure is available for any wild-type MazF toxin. Here we report the (1)H, (15)N and (13)C backbone and side-chain chemical shift assignments of this toxin from the pathogen bacterium Staphylococcus aureus. The BMRB accession number is 17288.
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Affiliation(s)
- Valentina Zorzini
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
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504
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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: 16.2] [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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505
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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: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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506
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The Proteolytic Activation of the relNEs (ssr1114/slr0664) Toxin–Antitoxin System by Both Proteases Lons and ClpP2s/Xs of Synechocystis sp. PCC 6803. Curr Microbiol 2011; 63:496-502. [DOI: 10.1007/s00284-011-0011-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 08/25/2011] [Indexed: 10/17/2022]
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507
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Williams JJ, Halvorsen EM, Dwyer EM, DiFazio RM, Hergenrother PJ. Toxin-antitoxin (TA) systems are prevalent and transcribed in clinical isolates of Pseudomonas aeruginosa and methicillin-resistant Staphylococcus aureus. FEMS Microbiol Lett 2011; 322:41-50. [PMID: 21658105 PMCID: PMC3184004 DOI: 10.1111/j.1574-6968.2011.02330.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The percentage of bacterial infections refractory to standard antibiotic treatments is steadily increasing. Among the most problematic hospital and community-acquired pathogens are methicillin-resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa (PA). One novel strategy proposed for treating infections of multidrug-resistant bacteria is the activation of latent toxins of toxin-antitoxin (TA) protein complexes residing within bacteria; however, the prevalence and identity of TA systems in clinical isolates of MRSA and PA has not been defined. We isolated DNA from 78 MRSA and 42 PA clinical isolates and used PCR to probe for the presence of various TA loci. Our results showed that the genes for homologs of the mazEF TA system in MRSA and the relBE and higBA TA systems in PA were present in 100% of the respective strains. Additionally, reverse transcriptase PCR analysis revealed that these transcripts are produced in the clinical isolates. These results indicate that TA genes are prevalent and transcribed within MRSA and PA and suggest that activation of the toxin proteins could be an effective antibacterial strategy for these pathogens.
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Affiliation(s)
- Julia J. Williams
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Elizabeth M. Halvorsen
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Ellen M. Dwyer
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Robert M. DiFazio
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Paul J. Hergenrother
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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508
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Wu X, Wang X, Drlica K, Zhao X. A toxin-antitoxin module in Bacillus subtilis can both mitigate and amplify effects of lethal stress. PLoS One 2011; 6:e23909. [PMID: 21897862 PMCID: PMC3163665 DOI: 10.1371/journal.pone.0023909] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Accepted: 07/31/2011] [Indexed: 11/26/2022] Open
Abstract
Background Bacterial type-2 (protein-protein) toxin-antitoxin (TA) modules are two-gene operons that are thought to participate in the response to stress. Previous work with Escherichia coli has led to a debate in which some investigators conclude that the modules protect from stress, while others argue that they amplify lethal stress and lead to programmed cell death. To avoid ambiguity arising from the presence of multiple TA modules in E. coli, the effect of the sole type-2 toxin-antitoxin module of Bacillus subtilis was examined for several types of lethal stress. Methodology/Principal Findings Genetic knockout of the toxin gene, ndoA (ydcE), conferred protection to lethal stressors that included kanamycin, moxifloxacin, hydrogen peroxide, and UV irradiation. However, at low doses of UV irradiation the ndoA deficiency increased lethality. Indeed, gradually increasing UV dose with the ndoA mutant revealed a crossover response – from the mutant being more sensitive than wild-type cells to being less sensitive. For high temperature and nutrient starvation, the toxin deficiency rendered cells hypersensitive. The ndoA deficiency also reduced sporulation frequency, indicating a role for toxin-antitoxin modules in this developmental process. In the case of lethal antimicrobial treatment, deletion of the toxin eliminated a surge in hydrogen peroxide accumulation observed in wild-type cells. Conclusions A single toxin-antitoxin module can mediate two opposing effects of stress, one that lowers lethality and another that raises it. Protective effects are thought to arise from toxin-mediated inhibition of translation based on published work. The enhanced, stress-mediated killing probably involves toxin-dependent accumulation of reactive oxygen species, since a deficiency in the NdoA toxin suppressed peroxide accumulation following antimicrobial treatment. The type and perhaps the level of stress appear to be important for determining whether this toxin will have a protective or detrimental effect.
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Affiliation(s)
- Xiangli Wu
- Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, United States of America
- State Key Laboratory for Agrobiotechnology and Department of Microbiology, China Agricultural University, Beijing, China
| | - Xiuhong Wang
- Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, United States of America
- Department of Biochemistry, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Karl Drlica
- Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, United States of America
- Department of Microbiology & Molecular Genetics, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, United States of America
| | - Xilin Zhao
- Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, United States of America
- Department of Microbiology & Molecular Genetics, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, United States of America
- * E-mail:
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509
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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: 320] [Impact Index Per Article: 22.9] [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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510
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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: 205] [Impact Index Per Article: 14.6] [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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511
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Zhabokritsky A, Kutky M, Burns LA, Karran RA, Hudak KA. RNA toxins: mediators of stress adaptation and pathogen defense. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:890-903. [PMID: 21809449 DOI: 10.1002/wrna.99] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
RNA toxins are a group of enzymes primarily synthesized by bacteria, fungi, and plants that either cleave or depurinate RNA molecules. These proteins may be divided according to their RNA substrates: ribotoxins are nucleases that cleave ribosomal RNA (rRNA), ribosome inactivating proteins are glycosidases that remove a base from rRNA, messenger RNA (mRNA) interferases are nucleases that cleave mRNAs, and anticodon nucleases cleave transfer RNAs (tRNAs). These modifications to the RNAs may substantially alter gene expression and translation rates. Given that some of these enzymes cause cell death, it has been suggested that they function mainly in defense, either to kill competing cells or to elicit suicide and thereby limit pathogen spread from infected cells. Although good correlations have been drawn between their enzymatic functions and toxicity, recent work has shown that some RNA toxins cause apoptosis in the absence of damage to RNA and that defense against pathogens can be achieved without host cell death. Moreover, a decrease in cellular translation rate, insufficient to cause cell death, allows some organisms to adapt to stress and environmental change. Although ascribing effects observed in vitro to the roles of these toxins in nature has been challenging, recent results have expanded our understanding of their modes of action, and emphasized the importance of these toxins in development, adaptation to stress and defense against pathogens.
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512
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Abstract
Bacteria form persisters, individual cells that are highly tolerant to different types of antibiotics. Persister cells are genetically identical to nontolerant kin but have entered a dormant state in which they are recalcitrant to the killing activity of the antibiotics. The molecular mechanisms underlying bacterial persistence are unknown. Here, we show that the ubiquitous Lon (Long Form Filament) protease and mRNA endonucleases (mRNases) encoded by toxin-antitoxin (TA) loci are required for persistence in Escherichia coli. Successive deletion of the 10 mRNase-encoding TA loci of E. coli progressively reduced the level of persisters, showing that persistence is a phenotype common to TA loci. In all cases tested, the antitoxins, which control the activities of the mRNases, are Lon substrates. Consistently, cells lacking lon generated a highly reduced level of persisters. Moreover, Lon overproduction dramatically increased the levels of persisters in wild-type cells but not in cells lacking the 10 mRNases. These results support a simple model according to which mRNases encoded by TA loci are activated in a small fraction of growing cells by Lon-mediated degradation of the antitoxins. Activation of the mRNases, in turn, inhibits global cellular translation, and thereby induces dormancy and persistence. Many pathogenic bacteria known to enter dormant states have a plethora of TA genes. Therefore, in the future, the discoveries described here may lead to a mechanistic understanding of the persistence phenomenon in pathogenic bacteria.
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513
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Genetic regulation of the yefM-yoeB toxin-antitoxin locus of Streptococcus pneumoniae. J Bacteriol 2011; 193:4612-25. [PMID: 21764929 DOI: 10.1128/jb.05187-11] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Type II (proteic) toxin-antitoxin systems (TAS) are ubiquitous among bacteria. In the chromosome of the pathogenic bacterium Streptococcus pneumoniae, there are at least eight putative TAS, one of them being the yefM-yoeB(Spn) operon studied here. Through footprinting analyses, we showed that purified YefM(Spn) antitoxin and the YefM-YoeB(Spn) TA protein complex bind to a palindrome sequence encompassing the -35 region of the main promoter (P(yefM2)) of the operon. Thus, the locus appeared to be negatively autoregulated with respect to P(yefM2), since YefM(Spn) behaved as a weak repressor with YoeB(Spn) as a corepressor. Interestingly, a BOX element, composed of a single copy (each) of the boxA and boxC subelements, was found upstream of promoter P(yefM2). BOX sequences are pneumococcal, perhaps mobile, genetic elements that have been associated with bacterial processes such as phase variation, virulence regulation, and genetic competence. In the yefM-yoeB(Spn) locus, the boxAC element provided an additional weak promoter, P(yefM1), upstream of P(yefM2) which was not regulated by the TA proteins. In addition, transcriptional fusions with a lacZ reporter gene showed that P(yefM1) was constitutive albeit weaker than P(yefM2). Intriguingly, the coupling of the boxAC element to P(yefM1) and yefM(Spn) in cis (but not in trans) led to transcriptional activation, indicating that the regulation of the yefM-yoeB(Spn) locus differs somewhat from that of other TA loci and may involve as yet unidentified elements. Conservation of the boxAC sequences in all available sequenced genomes of S. pneumoniae which contained the yefM-yoeB(Spn) locus suggested that its presence may provide a selective advantage to the bacterium.
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514
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Engelberg-Kulka H, Yelin I, Kolodkin-Gal I. Activation of a built-in bacterial programmed cell death system as a novel mechanism of action of some antibiotics. Commun Integr Biol 2011; 2:211-2. [PMID: 19641731 DOI: 10.4161/cib.2.3.7876] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Accepted: 01/19/2009] [Indexed: 11/19/2022] Open
Abstract
The modes of action of antibiotics are mainly characterized by their effects on their targets. Previously,1,2 and in a recent paper,3 we have reported our discovery of a new mechanism for the action of some antibiotics. Rather than directly interfering with a vital bacterial pathway, these antibiotics act by triggering the bacterial toxin-antitoxin chromosomal module mazEF, thereby causing the bacteria to commit suicide. We also showed that antibiotics that inhibit transcription and/or translation cause mazEF-mediated cell death by forming Reactive Oxygen Species (ROS).3 Moreover, we found that after treatment by such antibiotics, the mazEF system cannot be activated, and thus ROS cannot be formed, without the presence of communication signaling peptide called the Extracellular Death Factor (EDF). Our results challenge the classical division between bacteriostatic and bactericidal antibiotics. Our study further provides evidence that mode of action of antibiotics may also be determined by the ability of the bacteria to communicate through the signaling peptide EDF. In this Addendum article we present a model of how the presence of some antibiotics may result in this novel downstream pathway.
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Affiliation(s)
- Hanna Engelberg-Kulka
- Department of Molecular Biology; The Hebrew University-Hadassah Medical School; Jerusalem, Israel
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515
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Maezato Y, Daugherty A, Dana K, Soo E, Cooper C, Tachdjian S, Kelly RM, Blum P. VapC6, a ribonucleolytic toxin regulates thermophilicity in the crenarchaeote Sulfolobus solfataricus. RNA (NEW YORK, N.Y.) 2011; 17:1381-1392. [PMID: 21622901 PMCID: PMC3138573 DOI: 10.1261/rna.2679911] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 04/15/2011] [Indexed: 05/30/2023]
Abstract
The phylum Crenarchaeota includes hyperthermophilic micro-organisms subjected to dynamic thermal conditions. Previous transcriptomic studies of Sulfolobus solfataricus identified vapBC6 as a heat-shock (HS)-inducible member of the Vap toxin-antitoxin gene family. In this study, the inactivation of the vapBC6 operon by targeted gene disruption produced two recessive phenotypes related to fitness, HS sensitivity and a heat-dependent reduction in the rate of growth. In-frame vapBC6 deletion mutants were analyzed to examine the respective roles of each protein. Since vapB6 transcript abundance was elevated in the vapC6 deletion, the VapC6 toxin appears to regulate abundance of its cognate antitoxin. In contrast, vapC6 transcript abundance was reduced in the vapB6 deletion. A putative intergenic terminator may underlie these observations by coordinating vapBC6 expression. As predicted by structural modeling, recombinant VapC6 produced using chaperone cosynthesis exhibited heat-dependent ribonucleolytic activity toward S. solfataricus total RNA. This activity could be blocked by addition of preheated recombinant VapB6. In vivo transcript targets were identified by assessing the relative expression of genes that naturally respond to thermal stress in VapBC6-deficient cells. Preferential increases were observed for dppB-1 and tetR, and preferential decreases were observed for rpoD and eIF2 gamma. Specific VapC6 ribonucleolytic action could also be demonstrated in vitro toward RNAs whose expression increased in the VapBC6-deficient strain during heat shock. These findings provide a biochemical mechanism and identify cellular targets underlying VapBC6-mediated control over microbial growth and survival at temperature extremes.
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Affiliation(s)
- Yukari Maezato
- Beadle Center for Genetics, School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588-0666, USA
| | - Amanda Daugherty
- Beadle Center for Genetics, School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588-0666, USA
| | - Karl Dana
- Beadle Center for Genetics, School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588-0666, USA
| | - Edith Soo
- Beadle Center for Genetics, School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588-0666, USA
| | - Charlotte Cooper
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, USA
| | - Sabrina Tachdjian
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, USA
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, USA
| | - Paul Blum
- Beadle Center for Genetics, School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588-0666, USA
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516
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VapC toxins from Mycobacterium tuberculosis are ribonucleases that differentially inhibit growth and are neutralized by cognate VapB antitoxins. PLoS One 2011; 6:e21738. [PMID: 21738782 PMCID: PMC3126847 DOI: 10.1371/journal.pone.0021738] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 06/09/2011] [Indexed: 12/18/2022] Open
Abstract
The chromosome of Mycobacterium tuberculosis (Mtb) encodes forty seven toxin-antitoxin modules belonging to the VapBC family. The role of these modules in the physiology of Mtb and the function(s) served by their expansion are unknown. We investigated ten vapBC modules from Mtb and the single vapBC from M. smegmatis. Of the Mtb vapCs assessed, only Rv0549c, Rv0595c, Rv2549c and Rv2829c were toxic when expressed from a tetracycline-regulated promoter in M. smegmatis. The same genes displayed toxicity when conditionally expressed in Mtb. Toxicity of Rv2549c in M. smegmatis correlated with the level of protein expressed, suggesting that the VapC level must exceed a threshold for toxicity to be observed. In addition, the level of Rv2456 protein induced in M. smegmatis was markedly lower than Rv2549c, which may account for the lack of toxicity of this and other VapCs scored as ‘non-toxic’. The growth inhibitory effects of toxic VapCs were neutralized by expression of the cognate VapB as part of a vapBC operon or from a different chromosomal locus, while that of non-cognate antitoxins did not. These results demonstrated a specificity of interaction between VapCs and their cognate VapBs, a finding corroborated by yeast two-hybrid analyses. Deletion of selected vapC or vapBC genes did not affect mycobacterial growth in vitro, but rendered the organisms more susceptible to growth inhibition following toxic VapC expression. However, toxicity of ‘non-toxic’ VapCs was not unveiled in deletion mutant strains, even when the mutation eliminated the corresponding cognate VapB, presumably due to insufficient levels of VapC protein. Together with the ribonuclease (RNase) activity demonstrated for Rv0065 and Rv0617 – VapC proteins with similarity to Rv0549c and Rv3320c, respectively – these results suggest that the VapBC family potentially provides an abundant source of RNase activity in Mtb, which may profoundly impact the physiology of the organism.
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517
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Abstract
Tuberculosis continues to be a major public health problem in many parts of the world. Significant obstacles in controlling the epidemic are the length of treatment and the large reservoir of latently infected people. Bacteria form dormant, drug-tolerant persister cells, which may be responsible for the difficulty in treating both acute and latent infections. We find that in Mycobacterium tuberculosis, low numbers of drug-tolerant persisters are present in lag and early exponential phases, increasing sharply at late exponential and stationary phases to make up ~1% of the population. This suggests that persister formation is governed by both stochastic and deterministic mechanisms. In order to isolate persisters, an exponentially growing population was treated with d-cycloserine, and cells surviving lysis were collected by centrifugation. A transcriptome of persisters was obtained by using hybridization to an Affymetrix array. The transcriptome shows downregulation of metabolic and biosynthetic pathways, consistent with a certain degree of dormancy. A set of genes was upregulated in persisters, and these are likely involved in persister formation and maintenance. A comparison of the persister transcriptome with transcriptomes obtained for several in vitro dormancy models identified a small number of genes upregulated in all cases, which may represent a core dormancy response. It is estimated that every third person on the planet is infected with Mycobacterium tuberculosis. The two major problems in controlling M. tuberculosis are the length of the treatment and the large reservoir of latently infected people. Dormant persister cells may be responsible for both problems. We find that M. tuberculosis produces persisters in vitro in a growth phase-dependent manner. Persisters were isolated from an exponentially growing population, and their transcriptome shows a distinct pattern of dormancy. These results give the first insight into M. tuberculosis persisters and point to possible mechanisms responsible for their formation.
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518
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Botelho-Nevers E, Rovery C, Richet H, Raoult D. Analysis of risk factors for malignant Mediterranean spotted fever indicates that fluoroquinolone treatment has a deleterious effect. J Antimicrob Chemother 2011; 66:1821-30. [DOI: 10.1093/jac/dkr218] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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519
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You XY, Liu C, Wang SY, Jiang CY, Shah SA, Prangishvili D, She Q, Liu SJ, Garrett RA. Genomic analysis of Acidianus hospitalis W1 a host for studying crenarchaeal virus and plasmid life cycles. Extremophiles 2011; 15:487-97. [PMID: 21607549 PMCID: PMC3119797 DOI: 10.1007/s00792-011-0379-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 04/26/2011] [Indexed: 11/29/2022]
Abstract
The Acidianus hospitalis W1 genome consists of a minimally sized chromosome of about 2.13 Mb and a conjugative plasmid pAH1 and it is a host for the model filamentous lipothrixvirus AFV1. The chromosome carries three putative replication origins in conserved genomic regions and two large regions where non-essential genes are clustered. Within these variable regions, a few orphan orfB and other elements of the IS200/607/605 family are concentrated with a novel class of MITE-like repeat elements. There are also 26 highly diverse vapBC antitoxin–toxin gene pairs proposed to facilitate maintenance of local chromosomal regions and to minimise the impact of environmental stress. Complex and partially defective CRISPR/Cas/Cmr immune systems are present and interspersed with five vapBC gene pairs. Remnants of integrated viral genomes and plasmids are located at five intron-less tRNA genes and several non-coding RNA genes are predicted that are conserved in other Sulfolobus genomes. The putative metabolic pathways for sulphur metabolism show some significant differences from those proposed for other Acidianus and Sulfolobus species. The small and relatively stable genome of A. hospitalis W1 renders it a promising candidate for developing the first Acidianus genetic systems.
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Affiliation(s)
- Xiao-Yan You
- State Key Laboratory of Microbial Resources and Center for Environmental Microbiology, Institute of Microbiology, Chinese Academy of Sciences, Bei-Chen-Xi-Lu No. Chao-Yang District, Beijing, People's Republic of China
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520
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Enteric virulence associated protein VapC inhibits translation by cleavage of initiator tRNA. Proc Natl Acad Sci U S A 2011; 108:7403-7. [PMID: 21502523 DOI: 10.1073/pnas.1019587108] [Citation(s) in RCA: 210] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eukaryotic PIN (PilT N-terminal) domain proteins are ribonucleases involved in quality control, metabolism and maturation of mRNA and rRNA. The majority of prokaryotic PIN-domain proteins are encoded by the abundant vapBC toxin--antitoxin loci and inhibit translation by an unknown mechanism. Here we show that enteric VapCs are site-specific endonucleases that cleave tRNA(fMet) in the anticodon stem-loop between nucleotides +38 and +39 in vivo and in vitro. Consistently, VapC inhibited translation in vivo and in vitro. Translation-reactions could be reactivated by the addition of VapB and extra charged tRNA(fMet). Similarly, ectopic production of tRNA(fMet) counteracted VapC in vivo. Thus, tRNA(fMet) is the only cellular target of VapC. Depletion of tRNA(fMet) by vapC induction was bacteriostatic and stimulated ectopic translation initiation at elongator codons. Moreover, addition of chloramphenicol to cells carrying vapBC induced VapC activity. Thus, by cleavage of tRNA(fMet), VapC simultaneously may regulate global cellular translation and reprogram translation initiation.
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521
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Mutschler H, Gebhardt M, Shoeman RL, Meinhart A. A novel mechanism of programmed cell death in bacteria by toxin-antitoxin systems corrupts peptidoglycan synthesis. PLoS Biol 2011; 9:e1001033. [PMID: 21445328 PMCID: PMC3062530 DOI: 10.1371/journal.pbio.1001033] [Citation(s) in RCA: 174] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Accepted: 02/09/2011] [Indexed: 12/30/2022] Open
Abstract
Most genomes of bacteria contain toxin-antitoxin (TA) systems. These gene systems encode a toxic protein and its cognate antitoxin. Upon antitoxin degradation, the toxin induces cell stasis or death. TA systems have been linked with numerous functions, including growth modulation, genome maintenance, and stress response. Members of the epsilon/zeta TA family are found throughout the genomes of pathogenic bacteria and were shown not only to stabilize resistance plasmids but also to promote virulence. The broad distribution of epsilon/zeta systems implies that zeta toxins utilize a ubiquitous bacteriotoxic mechanism. However, whereas all other TA families known to date poison macromolecules involved in translation or replication, the target of zeta toxins remained inscrutable. We used in vivo techniques such as microscropy and permeability assays to show that pneumococcal zeta toxin PezT impairs cell wall synthesis and triggers autolysis in Escherichia coli. Subsequently, we demonstrated in vitro that zeta toxins in general phosphorylate the ubiquitous peptidoglycan precursor uridine diphosphate-N-acetylglucosamine (UNAG) and that this activity is counteracted by binding of antitoxin. After identification of the product we verified the kinase activity in vivo by analyzing metabolite extracts of cells poisoned by PezT using high pressure liquid chromatograpy (HPLC). We further show that phosphorylated UNAG inhibitis MurA, the enzyme catalyzing the initial step in bacterial peptidoglycan biosynthesis. Additionally, we provide what is to our knowledge the first crystal structure of a zeta toxin bound to its substrate. We show that zeta toxins are novel kinases that poison bacteria through global inhibition of peptidoglycan synthesis. This provides a fundamental understanding of how epsilon/zeta TA systems stabilize mobile genetic elements. Additionally, our results imply a mechanism that connects activity of zeta toxin PezT to virulence of pneumococcal infections. Finally, we discuss how phosphorylated UNAG likely poisons additional pathways of bacterial cell wall synthesis, making it an attractive lead compound for development of new antibiotics.
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Affiliation(s)
- Hannes Mutschler
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Maike Gebhardt
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Robert L. Shoeman
- 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
- * E-mail:
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522
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Leplae R, Geeraerts D, Hallez R, Guglielmini J, Drèze P, Van Melderen L. Diversity of bacterial type II toxin-antitoxin systems: a comprehensive search and functional analysis of novel families. Nucleic Acids Res 2011; 39:5513-25. [PMID: 21422074 PMCID: PMC3141249 DOI: 10.1093/nar/gkr131] [Citation(s) in RCA: 320] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Type II toxin–antitoxin (TA) systems are generally composed of two genes organized in an operon, encoding a labile antitoxin and a stable toxin. They were first discovered on plasmids where they contribute to plasmid stability by a phenomenon denoted as ‘addiction’, and subsequently in bacterial chromosomes. To discover novel families of antitoxins and toxins, we developed a bioinformatics approach based on the ‘guilt by association’ principle. Extensive experimental validation in Escherichia coli of predicted antitoxins and toxins increased significantly the number of validated systems and defined novel toxin and antitoxin families. Our data suggest that toxin families as well as antitoxin families originate from distinct ancestors that were assembled multiple times during evolution. Toxin and antitoxin families found on plasmids tend to be promiscuous and widespread, indicating that TA systems move through horizontal gene transfer. We propose that due to their addictive properties, TA systems are likely to be maintained in chromosomes even though they do not necessarily confer an advantage to their bacterial hosts. Therefore, addiction might play a major role in the evolutionary success of TA systems both on mobile genetic elements and in bacterial chromosomes.
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Affiliation(s)
- Raphaël Leplae
- Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Faculté des Sciences, Université Libre de Bruxelles, Bld du Triomphe, 1050 Bruxelles, Belgium and Laboratoire de Génétique et Physiologie Bactérienne, Institut de Biologie et de Médecine Moléculaires, Faculté des Sciences, Université Libre de Bruxelles, 12 rue des Professeurs Jeener et Brachet, 6041 Gosselies, Belgium
| | - Damien Geeraerts
- Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Faculté des Sciences, Université Libre de Bruxelles, Bld du Triomphe, 1050 Bruxelles, Belgium and Laboratoire de Génétique et Physiologie Bactérienne, Institut de Biologie et de Médecine Moléculaires, Faculté des Sciences, Université Libre de Bruxelles, 12 rue des Professeurs Jeener et Brachet, 6041 Gosselies, Belgium
| | - Régis Hallez
- Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Faculté des Sciences, Université Libre de Bruxelles, Bld du Triomphe, 1050 Bruxelles, Belgium and Laboratoire de Génétique et Physiologie Bactérienne, Institut de Biologie et de Médecine Moléculaires, Faculté des Sciences, Université Libre de Bruxelles, 12 rue des Professeurs Jeener et Brachet, 6041 Gosselies, Belgium
| | - Julien Guglielmini
- Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Faculté des Sciences, Université Libre de Bruxelles, Bld du Triomphe, 1050 Bruxelles, Belgium and Laboratoire de Génétique et Physiologie Bactérienne, Institut de Biologie et de Médecine Moléculaires, Faculté des Sciences, Université Libre de Bruxelles, 12 rue des Professeurs Jeener et Brachet, 6041 Gosselies, Belgium
| | - Pierre Drèze
- Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Faculté des Sciences, Université Libre de Bruxelles, Bld du Triomphe, 1050 Bruxelles, Belgium and Laboratoire de Génétique et Physiologie Bactérienne, Institut de Biologie et de Médecine Moléculaires, Faculté des Sciences, Université Libre de Bruxelles, 12 rue des Professeurs Jeener et Brachet, 6041 Gosselies, Belgium
| | - Laurence Van Melderen
- Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Faculté des Sciences, Université Libre de Bruxelles, Bld du Triomphe, 1050 Bruxelles, Belgium and Laboratoire de Génétique et Physiologie Bactérienne, Institut de Biologie et de Médecine Moléculaires, Faculté des Sciences, Université Libre de Bruxelles, 12 rue des Professeurs Jeener et Brachet, 6041 Gosselies, Belgium
- *To whom correspondence should be addressed. Tel: +32 2 650 97 78; Fax: +32 2 650 97 70;
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Genomes of the most dangerous epidemic bacteria have a virulence repertoire characterized by fewer genes but more toxin-antitoxin modules. PLoS One 2011; 6:e17962. [PMID: 21437250 PMCID: PMC3060909 DOI: 10.1371/journal.pone.0017962] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 02/22/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND We conducted a comparative genomic study based on a neutral approach to identify genome specificities associated with the virulence capacity of pathogenic bacteria. We also determined whether virulence is dictated by rules, or if it is the result of individual evolutionary histories. We systematically compared the genomes of the 12 most dangerous pandemic bacteria for humans ("bad bugs") to their closest non-epidemic related species ("controls"). METHODOLOGY/PRINCIPAL FINDINGS We found several significantly different features in the "bad bugs", one of which was a smaller genome that likely resulted from a degraded recombination and repair system. The 10 Cluster of Orthologous Group (COG) functional categories revealed a significantly smaller number of genes in the "bad bugs", which lacked mostly transcription, signal transduction mechanisms, cell motility, energy production and conversion, and metabolic and regulatory functions. A few genes were identified as virulence factors, including secretion system proteins. Five "bad bugs" showed a greater number of poly (A) tails compared to the controls, whereas an elevated number of poly (A) tails was found to be strongly correlated to a low GC% content. The "bad bugs" had fewer tandem repeat sequences compared to controls. Moreover, the results obtained from a principal component analysis (PCA) showed that the "bad bugs" had surprisingly more toxin-antitoxin modules than did the controls. CONCLUSIONS/SIGNIFICANCE We conclude that pathogenic capacity is not the result of "virulence factors" but is the outcome of a virulent gene repertoire resulting from reduced genome repertoires. Toxin-antitoxin systems could participate in the virulence repertoire, but they may have developed independently of selfish evolution.
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524
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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: 73] [Impact Index Per Article: 5.2] [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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525
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Chim N, Habel JE, Johnston JM, Krieger I, Miallau L, Sankaranarayanan R, Morse RP, Bruning J, Swanson S, Kim H, Kim CY, Li H, Bulloch EM, Payne RJ, Manos-Turvey A, Hung LW, Baker EN, Lott JS, James MN, Terwilliger TC, Eisenberg DS, Sacchettini JC, Goulding CW. The TB Structural Genomics Consortium: a decade of progress. Tuberculosis (Edinb) 2011; 91:155-72. [PMID: 21247804 PMCID: PMC3310434 DOI: 10.1016/j.tube.2010.11.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 11/19/2010] [Accepted: 11/26/2010] [Indexed: 01/03/2023]
Abstract
The TB Structural Genomics Consortium is a worldwide organization of collaborators whose mission is the comprehensive structural determination and analyses of Mycobacterium tuberculosis proteins to ultimately aid in tuberculosis diagnosis and treatment. Congruent to the overall vision, Consortium members have additionally established an integrated facilities core to streamline M. tuberculosis structural biology and developed bioinformatics resources for data mining. This review aims to share the latest Consortium developments with the TB community, including recent structures of proteins that play significant roles within M. tuberculosis. Atomic resolution details may unravel mechanistic insights and reveal unique and novel protein features, as well as important protein-protein and protein-ligand interactions, which ultimately lead to a better understanding of M. tuberculosis biology and may be exploited for rational, structure-based therapeutics design.
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Affiliation(s)
- Nicholas Chim
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Jeff E. Habel
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jodie M. Johnston
- School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1142, New Zealand
| | - Inna Krieger
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Linda Miallau
- UCLA-DOE Lab of Structural Biology, Howard Hughes Medical Institute, Molecular Biology Institute, University of California, UCLA Box 951570, Los Angeles, CA 90095, USA
| | - Ramasamy Sankaranarayanan
- Group in Protein Structure and Function, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G2H7
| | - Robert P. Morse
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - John Bruning
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Stephanie Swanson
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Haelee Kim
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Chang-Yub Kim
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Hongye Li
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Esther M. Bulloch
- School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1142, New Zealand
| | - Richard J. Payne
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Li-Wei Hung
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Edward N. Baker
- School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1142, New Zealand
| | - J. Shaun Lott
- School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1142, New Zealand
| | - Michael N.G. James
- Group in Protein Structure and Function, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G2H7
| | | | - David S. Eisenberg
- UCLA-DOE Lab of Structural Biology, Howard Hughes Medical Institute, Molecular Biology Institute, University of California, UCLA Box 951570, Los Angeles, CA 90095, USA
| | - James C. Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Celia W. Goulding
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
- Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
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526
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Zorzini V, Haesaerts S, Donegan NP, Fu Z, Cheung AL, van Nuland NAJ, Loris R. Crystallization of the Staphylococcus aureus MazF mRNA interferase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:386-9. [PMID: 21393849 PMCID: PMC3053169 DOI: 10.1107/s1744309111000571] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Accepted: 01/05/2011] [Indexed: 11/11/2022]
Abstract
mazEF modules encode toxin-antitoxin pairs that are involved in the bacterial stress response through controlled and specific degradation of mRNA. Staphylococcus aureus MazF and MazE constitute a unique toxin-antitoxin module under regulation of the sigB operon. A MazF-type mRNA interferase is combined with an antitoxin of unknown fold. Crystals of S. aureus MazF (SaMazF) were grown in space group P2(1)2(1)2(1). The crystals diffracted to 2.1 Å resolution and are likely to contain two SaMazF dimers in the asymmetric unit.
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Affiliation(s)
- Valentina Zorzini
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
- Department of Molecular and Cellular Interactions, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Sarah Haesaerts
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
- Department of Molecular and Cellular Interactions, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Niles P. Donegan
- Department of Microbiology and Immunology, Dartmouth Medical School, Hanover, NH 03755, USA
| | - Zhibiao Fu
- Department of Microbiology and Immunology, Dartmouth Medical School, Hanover, NH 03755, USA
| | - Ambrose L. Cheung
- Department of Microbiology and Immunology, Dartmouth Medical School, Hanover, NH 03755, USA
| | - Nico A. J. van Nuland
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
- Department of Molecular and Cellular Interactions, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Remy Loris
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
- Department of Molecular and Cellular Interactions, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
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527
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Gómez FA, Cárdenas C, Henríquez V, Marshall SH. Characterization of a functional toxin-antitoxin module in the genome of the fish pathogen Piscirickettsia salmonis. FEMS Microbiol Lett 2011; 317:83-92. [PMID: 21241361 DOI: 10.1111/j.1574-6968.2011.02218.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
This is the first report of a functional toxin-antitoxin (TA) locus in Piscirickettsia salmonis. The P. salmonis TA operon (ps-Tox-Antox) is an autonomous genetic unit containing two genes, a regulatory promoter site and an overlapping putative operator region. The ORFs consist of a toxic ps-Tox gene (P. salmonis toxin) and its upstream partner ps-Antox (P. salmonis antitoxin). The regulatory promoter site contains two inverted repeat motifs between the -10 and -35 regions, which may represent an overlapping operator site, known to mediate transcriptional auto-repression in most TA complexes. The Ps-Tox protein contains a PIN domain, normally found in prokaryote TA operons, especially those of the VapBC and ChpK families. The expression in Escherichia coli of the ps-Tox gene results in growth inhibition of the bacterial host confirming its toxicity, which is neutralized by coexpression of the ps-Antox gene. Additionally, ps-Tox is an endoribonuclease whose activity is inhibited by the antitoxin. The bioinformatic modelling of the two putative novel proteins from P. salmonis matches with their predicted functional activity and confirms that the active site of the Ps-Tox PIN domain is conserved.
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Affiliation(s)
- Fernando A Gómez
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
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528
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Hurley JM, Cruz JW, Ouyang M, Woychik NA. Bacterial toxin RelE mediates frequent codon-independent mRNA cleavage from the 5' end of coding regions in vivo. J Biol Chem 2011; 286:14770-8. [PMID: 21324908 DOI: 10.1074/jbc.m110.108969] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The enzymatic activity of the RelE bacterial toxin component of the Escherichia coli RelBE toxin-antitoxin system has been extensively studied in vitro and to a lesser extent in vivo. These earlier reports revealed that 1) RelE alone does not exhibit mRNA cleavage activity, 2) RelE mediates mRNA cleavage through its association with the ribosome, 3) RelE-mediated mRNA cleavage occurs at the ribosomal A site and, 4) Cleavage of mRNA by RelE exhibits high codon specificity. More specifically, RelE exhibits a preference for the stop codons UAG and UGA and sense codons CAG and UCG in vitro. In this study, we used a comprehensive primer extension approach to map the frequency and codon specificity of RelE cleavage activity in vivo. We found extensive cleavage at the beginning of the coding region of five transcripts, ompA, lpp, ompF, rpsA, and tufA. We then mapped RelE cleavage sites across one short transcript (lpp) and two long transcripts (ompF and ompA). RelE cut all of these transcripts frequently and efficiently within the first ∼100 codons, only occasionally cut beyond this point, and rarely cut at sites in proximity to the 3' end. Among 196 RelE sites in these five transcripts, there was no preference for CAG or UCG sense codons. In fact, bioinformatic analysis of the RelE cleavage sites failed to identify any sequence preferences. These results suggest a model of RelE function distinct from those proposed previously, because RelE directed frequent codon-independent mRNA cleavage coincident with the commencement of translation elongation.
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Affiliation(s)
- Jennifer M Hurley
- Department of Molecular Genetics, Microbiology, and Immunology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
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529
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Blower TR, Pei XY, Short FL, Fineran PC, Humphreys DP, Luisi BF, Salmond GPC. A processed noncoding RNA regulates an altruistic bacterial antiviral system. Nat Struct Mol Biol 2011; 18:185-90. [PMID: 21240270 PMCID: PMC4612426 DOI: 10.1038/nsmb.1981] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 11/08/2010] [Indexed: 01/21/2023]
Abstract
The ≥ 10³⁰ bacteriophages on Earth relentlessly drive adaptive coevolution, forcing the generation of protective mechanisms in their bacterial hosts. One such bacterial phage-resistance system, ToxIN, consists of a protein toxin (ToxN) that is inhibited in vivo by a specific RNA antitoxin (ToxI); however, the mechanisms for this toxicity and inhibition have not been defined. Here we present the crystal structure of the ToxN-ToxI complex from Pectobacterium atrosepticum, determined to 2.75-Å resolution. ToxI is a 36-nucleotide noncoding RNA pseudoknot, and three ToxI monomers bind to three ToxN monomers to generate a trimeric ToxN-ToxI complex. Assembly of this complex is mediated entirely through extensive RNA-protein interactions. Furthermore, a 2'-3' cyclic phosphate at the 3' end of ToxI, and catalytic residues, identify ToxN as an endoRNase that processes ToxI from a repetitive precursor but is regulated by its own catalytic product.
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Affiliation(s)
- Tim R Blower
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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531
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Blower TR, Salmond GPC, Luisi BF. Balancing at survival's edge: the structure and adaptive benefits of prokaryotic toxin-antitoxin partners. Curr Opin Struct Biol 2011; 21:109-18. [PMID: 21315267 DOI: 10.1016/j.sbi.2010.10.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Accepted: 10/31/2010] [Indexed: 01/21/2023]
Abstract
Many prokaryotes express toxin-antitoxin (TA) pairs that are harmful to their hosts if not maintained in delicate balance. The maintenance of potentially lethal toxin-antitoxin pairs could be viewed as a high-risk strategy. However, accumulating evidence suggests that toxin-antitoxin pairs can confer selective evolutionary benefits such as adaptive stress responses, starvation recovery and herd immunity to predation. Many of the known TA pairs interact as proteins, but recent work has identified a new class of antitoxins that are RNA cleavage products. Structural studies have revealed common folds for diverse toxins, highlighting unexpected evolutionary relationships within different toxin classes. TA pairs appear to have diverged in function considerably, to meet the specialised requirements of their varied prokaryotic hosts.
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Affiliation(s)
- Tim R Blower
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, United Kingdom.
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532
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Abstract
Potential mobility of restriction-modification systems has been suggested by evolutionary/bioinformatic analysis of prokaryotic genomes. Here we demonstrate in vivo movement of a restriction-modification system within a genome under a laboratory condition. After blocking replication of a temperature-sensitive plasmid carrying a PaeR7I restriction-modification system in Escherichia coli cells, the plasmid was found integrated into the chromosome of the surviving cells. Sequence analysis revealed that, in the majority of products, the restriction-modification system was linked to chromosomal insertion sequences (ISs). Three types of products were: (I) apparent co-integration of the plasmid and the chromosome at a chromosomal IS1 or IS5 copy (24/28 analyzed); (II) de novo insertion of IS1 with the entire plasmid except for a 1–3 bp terminal deletion (2/28); and (III) reciprocal crossing-over between the plasmid and the chromosome involving 1–3 bp of sequence identity (2/28). An R-negative mutation apparently decreased the efficiency of successful integration by two orders of magnitude. Reconstruction experiments demonstrated that the restriction-dependence was mainly due to selection against cells without proper integration: their growth was inhibited by the restriction enzyme action. These results demonstrate collaboration of a mobile element and a restriction-modification system for successful joint migration. This collaboration may have promoted the spread and, therefore, the long-term persistence of these complexes and restriction-modification systems in a wide range of prokaryotes.
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533
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Genome analyses of Icelandic strains of Sulfolobus islandicus, model organisms for genetic and virus-host interaction studies. J Bacteriol 2011; 193:1672-80. [PMID: 21278296 DOI: 10.1128/jb.01487-10] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genomes of two Sulfolobus islandicus strains obtained from Icelandic solfataras were sequenced and analyzed. Strain REY15A is a host for a versatile genetic toolbox. It exhibits a genome of minimal size, is stable genetically, and is easy to grow and manipulate. Strain HVE10/4 shows a broad host range for exceptional crenarchaeal viruses and conjugative plasmids and was selected for studying their life cycles and host interactions. The genomes of strains REY15A and HVE10/4 are 2.5 and 2.7 Mb, respectively, and each genome carries a variable region of 0.5 to 0.7 Mb where major differences in gene content and gene order occur. These include gene clusters involved in specific metabolic pathways, multiple copies of VapBC antitoxin-toxin gene pairs, and in strain HVE10/4, a 50-kb region rich in glycosyl transferase genes. The variable region also contains most of the insertion sequence (IS) elements and high proportions of the orphan orfB elements and SMN1 miniature inverted-repeat transposable elements (MITEs), as well as the clustered regular interspaced short palindromic repeat (CRISPR)-based immune systems, which are complex and diverse in both strains, consistent with them having been mobilized both intra- and intercellularly. In contrast, the remainder of the genomes are highly conserved in their protein and RNA gene syntenies, closely resembling those of other S. islandicus and Sulfolobus solfataricus strains, and they exhibit only minor remnants of a few genetic elements, mainly conjugative plasmids, which have integrated at a few tRNA genes lacking introns. This provides a possible rationale for the presence of the introns.
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534
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Zhong C, Peng D, Ye W, Chai L, Qi J, Yu Z, Ruan L, Sun M. Determination of plasmid copy number reveals the total plasmid DNA amount is greater than the chromosomal DNA amount in Bacillus thuringiensis YBT-1520. PLoS One 2011; 6:e16025. [PMID: 21283584 PMCID: PMC3026805 DOI: 10.1371/journal.pone.0016025] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 12/03/2010] [Indexed: 11/30/2022] Open
Abstract
Bacillus thuringiensis is the most widely used bacterial bio-insecticide, and most insecticidal crystal protein-coding genes are located on plasmids. Most strains of B. thuringiensis harbor numerous diverse plasmids, although the plasmid copy numbers (PCNs) of all native plasmids in this host and the corresponding total plasmid DNA amount remains unknown. In this study, we determined the PCNs of 11 plasmids (ranging from 2 kb to 416 kb) in a sequenced B. thuringiensis subsp. kurstaki strain YBT-1520 using real-time qPCR. PCNs were found to range from 1.38 to 172, and were negatively correlated to plasmid size. The amount of total plasmid DNA (∼8.7 Mbp) was 1.62-fold greater than the amount of chromosomal DNA (∼5.4 Mbp) at the mid-exponential growth stage (OD(600) = 2.0) of the organism. Furthermore, we selected three plasmids with different sizes and replication mechanisms to determine the PCNs over the entire life cycle. We found that the PCNs dynamically shifted at different stages, reaching their maximum during the mid-exponential growth or stationary phases and remaining stable and close to their minimum after the prespore formation stage. The PCN of pBMB2062, which is the smallest plasmid (2062 bp) and has the highest PCN of those tested, varied in strain YBT-1520, HD-1, and HD-136 (172, 115, and 94, respectively). These findings provide insight into both the total plasmid DNA amount of B. thuringiensis and the strong ability of the species to harbor plasmids.
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Affiliation(s)
- Chunying Zhong
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Donghai Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Weixing Ye
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lujun Chai
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Junliang Qi
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ziniu Yu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lifang Ruan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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535
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Tan Q, Awano N, Inouye M. YeeV is an Escherichia coli toxin that inhibits cell division by targeting the cytoskeleton proteins, FtsZ and MreB. Mol Microbiol 2011; 79:109-18. [PMID: 21166897 PMCID: PMC3021753 DOI: 10.1111/j.1365-2958.2010.07433.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Toxin-antitoxin (TA) systems of free-living bacteria have recently demonstrated that these toxins inhibit cell growth by targeting essential functions of cellular metabolism. Here we show that YeeV toxin inhibits cell division, leads to a change in morphology and lysis of Escherichia coli cells. YeeV interacts with two essential cytoskeleton proteins, FtsZ and MreB. Purified YeeV inhibits both the GTPase activity and the GTP-dependent polymerization of FtsZ. YeeV also inhibits ATP-dependent polymerization of MreB. Truncated C-terminal deletions of YeeV result in elongation of cells, and a deletion of the first 15 amino acids from the N-terminus of YeeV caused lemon-shaped cell formation. The YeeV toxin is distinct from other well-studied toxins: it directs the binding of two cytoskeletal proteins and inhibits FtsZ and MreB simultaneously.
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Affiliation(s)
| | | | - Masayori Inouye
- Department of Biochemistry, Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, 679 Hoes lane, Piscataway, NJ 08854
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536
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Abstract
Bacteria, the most abundant organisms on the planet, are outnumbered by a factor of 10 to 1 by phages that infect them. Faced with the rapid evolution and turnover of phage particles, bacteria have evolved various mechanisms to evade phage infection and killing, leading to an evolutionary arms race. The extensive co-evolution of both phage and host has resulted in considerable diversity on the part of both bacterial and phage defensive and offensive strategies. Here, we discuss the unique and common features of phage resistance mechanisms and their role in global biodiversity. The commonalities between defense mechanisms suggest avenues for the discovery of novel forms of these mechanisms based on their evolutionary traits.
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Affiliation(s)
- Adi Stern
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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537
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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: 1.3] [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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538
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The chromosomal mazEF locus of Streptococcus mutans encodes a functional type II toxin-antitoxin addiction system. J Bacteriol 2010; 193:1122-30. [PMID: 21183668 DOI: 10.1128/jb.01114-10] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Type II chromosomal toxin-antitoxin (TA) modules consist of a pair of genes that encode two components: a stable toxin and a labile antitoxin interfering with the lethal action of the toxin through protein complex formation. Bioinformatic analysis of Streptococcus mutans UA159 genome identified a pair of linked genes encoding a MazEF-like TA. Our results show that S. mutans mazEF genes form a bicistronic operon that is cotranscribed from a σ70-like promoter. Overproduction of S. mutans MazF toxin had a toxic effect on S. mutans which can be neutralized by coexpression of its cognate antitoxin, S. mutans MazE. Although mazF expression inhibited cell growth, no cell lysis of S. mutans cultures was observed under the conditions tested. The MazEF TA is also functional in E. coli, where S. mutans MazF did not kill the cells but rather caused reversible cell growth arrest. Recombinant S. mutans MazE and MazF proteins were purified and were shown to interact with each other in vivo, confirming the nature of this TA as a type II addiction system. Our data indicate that MazF is a toxic nuclease arresting cell growth through the mechanism of RNA cleavage and that MazE inhibits the RNase activity of MazF by forming a complex. Our results suggest that the MazEF TA module might represent a cell growth modulator facilitating the persistence of S. mutans under the harsh conditions of the oral cavity.
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539
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Yuan J, Sterckx Y, Mitchenall LA, Maxwell A, Loris R, Waldor MK. Vibrio cholerae ParE2 poisons DNA gyrase via a mechanism distinct from other gyrase inhibitors. J Biol Chem 2010; 285:40397-408. [PMID: 20952390 PMCID: PMC3001019 DOI: 10.1074/jbc.m110.138776] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 09/23/2010] [Indexed: 01/21/2023] Open
Abstract
DNA gyrase is an essential bacterial enzyme required for the maintenance of chromosomal DNA topology. This enzyme is the target of several protein toxins encoded in toxin-antitoxin (TA) loci as well as of man-made antibiotics such as quinolones. The genome of Vibrio cholerae, the cause of cholera, contains three putative TA loci that exhibit modest similarity to the RK2 plasmid-borne parDE TA locus, which is thought to target gyrase although its mechanism of action is uncharacterized. Here we investigated the V. cholerae parDE2 locus. We found that this locus encodes a functional proteic TA pair that is active in Escherichia coli as well as V. cholerae. ParD2 co-purified with ParE2 and interacted with it directly. Unlike many other antitoxins, ParD2 could prevent but not reverse ParE2 toxicity. ParE2, like the unrelated F-encoded toxin CcdB and quinolones, targeted the GyrA subunit and stalled the DNA-gyrase cleavage complex. However, in contrast to other gyrase poisons, ParE2 toxicity required ATP, and it interfered with gyrase-dependent DNA supercoiling but not DNA relaxation. ParE2 did not bind GyrA fragments bound by CcdB and quinolones, and a set of strains resistant to a variety of known gyrase inhibitors all exhibited sensitivity to ParE2. Together, our findings suggest that ParE2 and presumably its many plasmid- and chromosome-encoded homologues inhibit gyrase in a different manner than previously described agents.
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Affiliation(s)
- Jie Yuan
- From the Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School
- the Howard Hughes Medical Institute, and
- the Program in Immunology, Tufts University School of Medicine, Boston, Massachusetts 02115
| | - Yann Sterckx
- Structural Biology Brussels, Vrije Universiteit Brussel Pleinlaan 2, Brussels 1050, Belgium
- the Department of Molecular and Cellular Interactions, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, Brussels 1050, Belgium, and
| | - Lesley A. Mitchenall
- the Department of Biological Chemistry, John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom
| | - Anthony Maxwell
- the Department of Biological Chemistry, John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom
| | - Remy Loris
- Structural Biology Brussels, Vrije Universiteit Brussel Pleinlaan 2, Brussels 1050, Belgium
- the Department of Molecular and Cellular Interactions, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, Brussels 1050, Belgium, and
| | - Matthew K. Waldor
- From the Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School
- the Howard Hughes Medical Institute, and
- the Program in Immunology, Tufts University School of Medicine, Boston, Massachusetts 02115
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540
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Abstract
Persisters are dormant variants of regular cells that form stochastically in microbial populations and are highly tolerant to antibiotics. High persister (hip) mutants of Pseudomonas aeruginosa are selected in patients with cystic fibrosis. Similarly, hip mutants of Candida albicans are selected in patients with an oral thrush biofilm. These observations suggest that persisters may be the main culprit responsible for the recalcitrance of chronic infectious disease to antimicrobial therapy. Screening knockout libraries has not produced mutants lacking persisters, indicating that dormancy mechanisms are redundant. Toxin/antitoxin (TA) modules are involved in persister formation in Escherichia coli. The SOS response leads to overexpression of the TisB toxin and persister formation. TisB is a membrane-acting peptide that apparently sends cells into dormancy by decreasing the proton motive force and ATP levels. Stress responses may act as general activators of persister formation. Proteins required for maintaining persisters may represent realistic targets for discovery of drugs capable of effectively treating chronic infections.
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Affiliation(s)
- Kim Lewis
- Department of Biology and Antimicrobial Discovery Center, Northeastern University, Boston, Massachusetts 02115, USA.
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541
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Affiliation(s)
- Guillaume Cambray,
- Institut Pasteur, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, F-75015 Paris, France;
- CNRS, URA2171, F-75015 Paris, France
| | - Anne-Marie Guerout,
- Institut Pasteur, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, F-75015 Paris, France;
- CNRS, URA2171, F-75015 Paris, France
| | - Didier Mazel
- Institut Pasteur, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, F-75015 Paris, France;
- CNRS, URA2171, F-75015 Paris, France
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542
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Huang F, He ZG. Characterization of an interplay between a Mycobacterium tuberculosis MazF homolog, Rv1495 and its sole DNA topoisomerase I. Nucleic Acids Res 2010; 38:8219-30. [PMID: 20724443 PMCID: PMC3001090 DOI: 10.1093/nar/gkq737] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Revised: 07/26/2010] [Accepted: 08/04/2010] [Indexed: 11/14/2022] Open
Abstract
The MazEF systems are thought to contribute to the capacity for long-term dormancy observed in the human pathogen, Mycobacterium tuberculosis. However, except for their functions as mRNA interferases, little is known regarding any additional cellular functions of these systems in the pathogen. In the present study, we observed a negative interplay between MazF protein Rv1495 and the sole M. tuberculosis DNA topoisomerase I (MtbTopA) with respect to protein functions. Through its C-terminal domain, MtbTopA physically interacted with and inhibited the mRNA cleavage activity of Rv1495. Rv1495, in turn, inhibited the DNA cleavage activity of MtbTopA as well as its function of relaxation of supercoiled DNA. An N-terminus fragment of Rv1495, designated Rv1495-N(29-56), lost mRNA cleavage activity, but retained a significant physical interaction and inhibitory effect on TopA proteins from both M. tuberculosis and M. smegmatis. This fragment, although less effective than the full-length protein, was able to inhibit mycobacterial growth when expressed through a recombinant plasmid in M. smegmatis. The Rv1495 physically interacted with the M. smegmatis TopA both in vitro and in vivo. Our findings imply that MazEF systems can affect bacterial survival by a novel mechanism that allows direct modulation of M. tuberculosis topoisomerase I.
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Affiliation(s)
| | - Zheng-Guo He
- National Key Laboratory of Agricultural Microbiology, Center for Proteomics Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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543
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Arbing MA, Handelman SK, Kuzin AP, Verdon G, Wang C, Su M, Rothenbacher FP, Abashidze M, Liu M, Hurley JM, Xiao R, Acton T, Inouye M, Montelione GT, Woychik NA, Hunt JF. Crystal structures of Phd-Doc, HigA, and YeeU establish multiple evolutionary links between microbial growth-regulating toxin-antitoxin systems. Structure 2010; 18:996-1010. [PMID: 20696400 DOI: 10.1016/j.str.2010.04.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2009] [Revised: 03/22/2010] [Accepted: 04/21/2010] [Indexed: 10/19/2022]
Abstract
Bacterial toxin-antitoxin (TA) systems serve a variety of physiological functions including regulation of cell growth and maintenance of foreign genetic elements. Sequence analyses suggest that TA families are linked by complex evolutionary relationships reflecting likely swapping of functional domains between different TA families. Our crystal structures of Phd-Doc from bacteriophage P1, the HigA antitoxin from Escherichia coli CFT073, and YeeU of the YeeUWV systems from E. coli K12 and Shigella flexneri confirm this inference and reveal additional, unanticipated structural relationships. The growth-regulating Doc toxin exhibits structural similarity to secreted virulence factors that are toxic for eukaryotic target cells. The Phd antitoxin possesses the same fold as both the YefM and NE2111 antitoxins that inhibit structurally unrelated toxins. YeeU, which has an antitoxin-like activity that represses toxin expression, is structurally similar to the ribosome-interacting toxins YoeB and RelE. These observations suggest extensive functional exchanges have occurred between TA systems during bacterial evolution.
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Affiliation(s)
- Mark A Arbing
- Department of Biological Sciences, Columbia University, 702 Fairchild Center, MC2434, New York, NY 10027, USA
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544
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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: 47] [Impact Index Per Article: 3.1] [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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545
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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: 5.7] [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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546
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Van Melderen L. Toxin-antitoxin systems: why so many, what for? Curr Opin Microbiol 2010; 13:781-5. [PMID: 21041110 DOI: 10.1016/j.mib.2010.10.006] [Citation(s) in RCA: 237] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 09/29/2010] [Accepted: 10/07/2010] [Indexed: 01/04/2023]
Abstract
Toxin-antitoxin (TA) systems are small genetic modules that are abundant in bacterial genomes. Three types have been described so far, depending on the nature and mode of action of the antitoxin component. While type II systems are surprisingly highly represented because of their capacity to move by horizontal gene transfer, type I systems appear to have evolved by gene duplication and are more constrained. Type III is represented by a unique example located on a plasmid. Type II systems promote stability of mobile genetic elements and might act at the selfish level. Conflicting hypotheses about chromosomally encoded systems, from programmed cell death and starvation-induced stasis to protection against invading DNA and stabilization of large genomic fragments have been proposed.
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Affiliation(s)
- Laurence Van Melderen
- Laboratoire de Génétique et Physiologie Bactérienne, Faculté des Sciences, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, Belgium.
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547
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Arcus VL, McKenzie JL, Robson J, Cook GM. The PIN-domain ribonucleases and the prokaryotic VapBC toxin-antitoxin array. Protein Eng Des Sel 2010; 24:33-40. [PMID: 21036780 DOI: 10.1093/protein/gzq081] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The PIN-domains are small proteins of ~130 amino acids that are found in bacteria, archaea and eukaryotes and are defined by a group of three strictly conserved acidic amino acids. The conserved three-dimensional structures of the PIN-domains cluster these acidic residues in an enzymatic active site. PIN-domains cleave single-stranded RNA in a sequence-specific, Mg²+- or Mn²+-dependent manner. These ribonucleases are toxic to the cells which express them and to offset this toxicity, they are co-expressed with tight binding protein inhibitors. The genes encoding these two proteins are adjacent in the genome of all prokaryotic organisms where they are found. This sequential arrangement of inhibitor-RNAse genes conforms to that of the so-called toxin-antitoxin (TA) modules and the PIN-domain TAs have been named VapBC TAs (virulence associated proteins, VapB is the inhibitor which contains a transcription factor domain and VapC is the PIN-domain ribonuclease). The presence of large numbers of vapBC loci in disparate prokaryotes has motivated many researchers to investigate their biochemical and biological functions. For example, the devastating human pathogen Mycobacterium tuberculosis has 45 vapBC loci encoded in its genome whereas its non-pathogenic relative, Mycobacterium smegmatis has just one vapBC operon. On another branch of the prokaryotic tree, the nitrogen-fixing symbiont of legumes, Sinorhizobium meliloti has 21 vapBC loci and at least one of these loci have been implicated in the regulation of growth in the plant nodule. A range of biological functions has been suggested for these operons and this review sets out to survey the PIN-domains and summarise the current knowledge about the vapBC TA systems and their roles in diverse bacteria.
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Affiliation(s)
- Vickery L Arcus
- Department of Biological Sciences, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.
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548
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Halvorsen EM, Williams JJ, Bhimani AJ, Billings EA, Hergenrother PJ. Txe, an endoribonuclease of the enterococcal Axe-Txe toxin-antitoxin system, cleaves mRNA and inhibits protein synthesis. MICROBIOLOGY-SGM 2010; 157:387-397. [PMID: 21030436 PMCID: PMC3090131 DOI: 10.1099/mic.0.045492-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The axe-txe operon encodes a toxin-antitoxin (TA) pair, Axe-Txe, that was initially identified on the multidrug-resistance plasmid pRUM in Enterococcus faecium. In Escherichia coli, expression of the Txe toxin is known to inhibit cell growth, and co-expression of the antitoxin, Axe, counteracts the toxic effect of Txe. Here, we report the nucleotide sequence of pS177, a 39 kb multidrug-resistant plasmid isolated from vancomycin-resistant Ent. faecium, which harbours the axe-txe operon and the vanA gene cluster. RT-PCR analysis revealed that the axe-txe transcript is produced by strain S177 as well as by other vancomycin-resistant enteroccoci. Moreover, we determine the mechanism by which the Txe protein exerts its toxic activity. Txe inhibits protein synthesis in E. coli without affecting DNA or RNA synthesis, and inhibits protein synthesis in a cell-free system. Using in vivo primer extension analysis, we demonstrate that Txe preferentially cleaves single-stranded mRNA at the first base after an AUG start codon. We conclude that Txe is an endoribonuclease which cleaves mRNA and inhibits protein synthesis.
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Affiliation(s)
- Elizabeth M Halvorsen
- Department of Microbiology, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA
| | - Julia J Williams
- Department of Microbiology, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA
| | - Azra J Bhimani
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA
| | - Emily A Billings
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA
| | - Paul J Hergenrother
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA.,Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA
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549
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Lew JM, Kapopoulou A, Jones LM, Cole ST. TubercuList--10 years after. Tuberculosis (Edinb) 2010; 91:1-7. [PMID: 20980199 DOI: 10.1016/j.tube.2010.09.008] [Citation(s) in RCA: 310] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 09/06/2010] [Accepted: 09/30/2010] [Indexed: 01/10/2023]
Abstract
TubercuList (http://tuberculist.epfl.ch/), the relational database that presents genome-derived information about H37Rv, the paradigm strain of Mycobacterium tuberculosis, has been active for ten years and now presents its twentieth release. Here, we describe some of the recent changes that have resulted from manual annotation with information from the scientific literature. Through manual curation, TubercuList strives to provide current gene-based information and is thus distinguished from other online sources of genome sequence data for M. tuberculosis. New, mostly small, genes have been discovered and the coordinates of some existing coding sequences have been changed when bioinformatics or experimental data suggest that this is required. Nucleotides that are polymorphic between different sources of H37Rv are annotated and gene essentiality data have been updated. A host of functional information has been gleaned from the literature and many new activities of proteins and RNAs have been included. To facilitate basic and translational research, TubercuList also provides links to other specialized databases that present diverse datasets such as 3D-structures, expression profiles, drug development criteria and drug resistance information, in addition to direct access to PubMed articles pertinent to particular genes. TubercuList has been and remains a highly valuable tool for the tuberculosis research community with >75,000 visitors per month.
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Affiliation(s)
- Jocelyne M Lew
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Station 19, CH-1015 Lausanne, Switzerland.
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Shao Y, Harrison EM, Bi D, Tai C, He X, Ou HY, Rajakumar K, Deng Z. TADB: a web-based resource for Type 2 toxin-antitoxin loci in bacteria and archaea. Nucleic Acids Res 2010; 39:D606-11. [PMID: 20929871 PMCID: PMC3013778 DOI: 10.1093/nar/gkq908] [Citation(s) in RCA: 209] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
TADB (http://bioinfo-mml.sjtu.edu.cn/TADB/) is an integrated database that provides comprehensive information about Type 2 toxin-antitoxin (TA) loci, genetic features that are richly distributed throughout bacterial and archaeal genomes. Two-gene and much less frequently three-gene Type 2 TA loci code for cognate partners that have been hypothesized or demonstrated to play key roles in stress response, bacterial physiology and stabilization of horizontally acquired genetic elements. TADB offers a unique compilation of both predicted and experimentally supported Type 2 TA loci-relevant data and currently contains 10,753 Type 2 TA gene pairs identified within 1240 prokaryotic genomes, and details of over 240 directly relevant scientific publications. A broad range of similarity search, sequence alignment, genome context browser and phylogenetic tools are readily accessible via TADB. We propose that TADB will facilitate efficient, multi-disciplinary and innovative exploration of the bacteria and archaea Type 2 TA space, better defining presently recognized TA-related phenomena and potentially even leading to yet-to-be envisaged frontiers. The TADB database, envisaged as a one-stop shop for Type 2 TA-related research, will be maintained, updated and improved regularly to ensure its ongoing maximum utility to the research community.
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Affiliation(s)
- Yucheng Shao
- Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai 200030, PR China
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