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Clarifying the Link between Toxin–Antitoxin Modules and Bacterial Persistence. J Mol Biol 2019; 431:3462-3471. [DOI: 10.1016/j.jmb.2019.03.019] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/05/2019] [Accepted: 03/13/2019] [Indexed: 11/21/2022]
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Chromosomally Encoded hok-sok Toxin-Antitoxin System in the Fire Blight Pathogen Erwinia amylovora: Identification and Functional Characterization. Appl Environ Microbiol 2019; 85:AEM.00724-19. [PMID: 31101613 DOI: 10.1128/aem.00724-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/08/2019] [Indexed: 12/28/2022] Open
Abstract
Toxin-antitoxin (TA) systems are genetic elements composed of a protein toxin and a counteracting antitoxin that is either a noncoding RNA or protein. In type I TA systems, the antitoxin is a noncoding small RNA (sRNA) that base pairs with the cognate toxin mRNA interfering with its translation. Although type I TA systems have been extensively studied in Escherichia coli and a few human or animal bacterial pathogens, they have not been characterized in plant-pathogenic bacteria. In this study, we characterized a chromosomal locus in the plant pathogen Erwinia amylovora Ea1189 that is homologous to the hok-sok type I TA system previously identified in the Enterobacteriaceae-restricted plasmid R1. Phylogenetic analysis indicated that the chromosomal location of the hok-sok locus is, thus far, unique to E. amylovora We demonstrated that ectopic overexpression of hok is highly toxic to E. amylovora and that the sRNA sok reversed the toxicity of hok through mok, a reading frame presumably translationally coupled with hok We also identified the region that is essential for maintenance of the main toxicity of Hok. Through a hok-sok deletion mutant (Ea1189Δhok-sok), we determined the contribution of the hok-sok locus to cellular growth, micromorphology, and catalase activity. Combined, our findings indicate that the hok-sok TA system, besides being potentially self-toxic, provides fitness advantages to E. amylovora IMPORTANCE Bacterial toxin-antitoxin systems have received great attention because of their potential as targets for antimicrobial development and as tools for biotechnology. Erwinia amylovora, the causal agent of fire blight disease on pome fruit trees, is a major plant-pathogenic bacterium. In this study, we identified and functionally characterized a unique chromosomally encoded hok-sok toxin-antitoxin system in E. amylovora that resembles the plasmid-encoded copies of this system in other Enterobacteriaceae This study of a type I toxin-antitoxin system in a plant-pathogenic bacterium provides the basis to further understand the involvement of toxin-antitoxin systems during infection by a plant-pathogenic bacterium. The new linkage between the hok-sok toxin-antitoxin system and the catalase-mediated oxidative stress response leads to additional considerations of targeting this system for antimicrobial development.
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Deep A, Tiwari P, Agarwal S, Kaundal S, Kidwai S, Singh R, Thakur KG. Structural, functional and biological insights into the role of Mycobacterium tuberculosis VapBC11 toxin-antitoxin system: targeting a tRNase to tackle mycobacterial adaptation. Nucleic Acids Res 2019; 46:11639-11655. [PMID: 30329074 PMCID: PMC6265470 DOI: 10.1093/nar/gky924] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/04/2018] [Indexed: 01/10/2023] Open
Abstract
Toxin–antitoxin (TA) systems are involved in diverse physiological processes in prokaryotes, but their exact role in Mycobacterium tuberculosis (Mtb) virulence and in vivo stress adaptation has not been extensively studied. Here, we demonstrate that the VapBC11 TA module is essential for Mtb to establish infection in guinea pigs. RNA-sequencing revealed that overexpression of VapC11 toxin results in metabolic slowdown, suggesting that modulation of the growth rate is an essential strategy for in vivo survival. Interestingly, overexpression of VapC11 resulted in the upregulation of chromosomal TA genes, suggesting the existence of highly coordinated crosstalk among TA systems. In this study, we also present the crystal structure of the VapBC11 heterooctameric complex at 1.67 Å resolution. Binding kinetic studies suggest that the binding affinities of toxin–substrate and toxin–antitoxin interactions are comparable. We used a combination of structural studies, molecular docking, mutational analysis and in vitro ribonuclease assays to enhance our understanding of the mode of substrate recognition by the VapC11 toxin. Furthermore, we have also designed peptide-based inhibitors to target VapC11 ribonuclease activity. Taken together, we propose that the structure-guided design of inhibitors against in vivo essential ribonucleases might be a novel strategy to hasten clearance of intracellular Mtb.
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Affiliation(s)
- Amar Deep
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh 160036, India
| | - Prabhakar Tiwari
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad Gurgaon Expressway, Faridabad 121001, India
| | - Sakshi Agarwal
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad Gurgaon Expressway, Faridabad 121001, India
| | - Soni Kaundal
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh 160036, India
| | - Saqib Kidwai
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad Gurgaon Expressway, Faridabad 121001, India
| | - Ramandeep Singh
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad Gurgaon Expressway, Faridabad 121001, India
| | - Krishan G Thakur
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh 160036, India
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The role of small proteins in Burkholderia cenocepacia J2315 biofilm formation, persistence and intracellular growth. Biofilm 2019; 1:100001. [PMID: 33447789 PMCID: PMC7798474 DOI: 10.1016/j.bioflm.2019.100001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 06/03/2019] [Accepted: 06/05/2019] [Indexed: 01/14/2023] Open
Abstract
Burkholderia cenocepacia infections are difficult to treat due to resistance, biofilm formation and persistence. B. cenocepacia strain J2315 has a large multi-replicon genome (8.06 Mb) and the function of a large fraction of (conserved) hypothetical genes remains elusive. The goal of the present study is to elucidate the role of small proteins in B. cenocepacia, focusing on genes smaller than 300 base pairs of which the function is unknown. Almost 10% (572) of the B. cenocepacia J2315 genes are smaller than 300 base pairs and more than half of these are annotated as coding for hypothetical proteins. For 234 of them no similarity could be found with non-hypothetical genes in other bacteria using BLAST. Using available RNA sequencing data obtained from biofilms, a list of 27 highly expressed B. cenocepacia J2315 genes coding for small proteins was compiled. For nine of them expression in biofilms was also confirmed using LC-MS based proteomics and/or expression was confirmed using eGFP translational fusions. Overexpression of two of these genes negatively impacted growth, whereas for four others overexpression led to an increase in biofilm biomass. Overexpression did not have an influence on the MIC for tobramycin, ciprofloxacin or meropenem but for five small protein encoding genes, overexpression had an effect on the number of persister cells in biofilms. While there were no significant differences in adherence to and invasion of A549 epithelial cells between the overexpression mutants and the WT, significant differences were observed in intracellular growth/survival. Finally, the small protein BCAM0271 was identified as an antitoxin belonging to a toxin-antitoxin module. The toxin was found to encode a tRNA acetylase that inhibits translation. In conclusion, our results confirm that small proteins are present in the genome of B. cenocepacia J2315 and indicate that they are involved in various biological processes, including biofilm formation, persistence and intracellular growth.
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Brown BP, Wernegreen JJ. Genomic erosion and extensive horizontal gene transfer in gut-associated Acetobacteraceae. BMC Genomics 2019; 20:472. [PMID: 31182035 PMCID: PMC6558740 DOI: 10.1186/s12864-019-5844-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 05/24/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Symbiotic relationships between animals and bacteria have profound impacts on the evolutionary trajectories of each partner. Animals and gut bacteria engage in a variety of relationships, occasionally persisting over evolutionary timescales. Ants are a diverse group of animals that engage in many types of associations with taxonomically distinct groups of bacterial associates. Here, we bring into culture and characterize two closely-related strains of gut associated Acetobacteraceae (AAB) of the red carpenter ant, Camponotus chromaiodes. RESULTS Genome sequencing, assembly, and annotation of both strains delineate stark patterns of genomic erosion and sequence divergence in gut associated AAB. We found widespread horizontal gene transfer (HGT) in these bacterial associates and report elevated gene acquisition associated with energy production and conversion, amino acid and coenzyme transport and metabolism, defense mechanisms, and lysine export. Both strains have acquired the complete NADH-quinone oxidoreductase complex, plausibly from an Enterobacteriaceae origin, likely facilitating energy production under diverse conditions. Conservation of several lysine biosynthetic and salvage pathways and accumulation of lysine export genes via HGT implicate L-lysine supplementation by both strains as a potential functional benefit for the host. These trends are contrasted by genome-wide erosion of several amino acid biosynthetic pathways and pathways in central metabolism. We perform phylogenomic analyses on both strains as well as several free living and host associated AAB. Based on their monophyly and deep divergence from other AAB, these C. chromaiodes gut associates may represent a novel genus. Together, our results demonstrate how extensive horizontal transfer between gut associates along with genome-wide deletions leads to mosaic metabolic pathways. More broadly, these patterns demonstrate that HGT and genomic erosion shape metabolic capabilities of persistent gut associates and influence their genomic evolution. CONCLUSIONS Using comparative genomics, our study reveals substantial changes in genomic content in persistent associates of the insect gastrointestinal tract and provides evidence for the evolutionary pressures inherent to this environment. We describe patterns of genomic erosion and horizontal acquisition that result in mosaic metabolic pathways. Accordingly, the phylogenetic position of both strains of these associates form a divergent, monophyletic clade sister to gut associates of honey bees and more distantly to Gluconobacter.
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Affiliation(s)
- Bryan P Brown
- Nicholas School of the Environment, Duke University, 9 Circuit Dr., Durham, NC, 27710, USA. .,Genomic and Computational Biology, Duke University, 101 Science Dr., Durham, NC, 27705, USA. .,Center for Global Infectious Disease Research, Seattle Children's Research Institute, 1900 9 Ave., Seattle, WA, 98101, USA.
| | - Jennifer J Wernegreen
- Nicholas School of the Environment, Duke University, 9 Circuit Dr., Durham, NC, 27710, USA.,Genomic and Computational Biology, Duke University, 101 Science Dr., Durham, NC, 27705, USA
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Long Y, Fu W, Li S, Ren H, Li M, Liu C, Zhang B, Xia Y, Fan Z, Xu C, Liu J, Jin Y, Bai F, Cheng Z, Liu X, Jin S, Wu W. Identification of novel genes that promote persister formation by repressing transcription and cell division in Pseudomonas aeruginosa. J Antimicrob Chemother 2019; 74:2575-2587. [DOI: 10.1093/jac/dkz214] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/14/2019] [Accepted: 04/18/2019] [Indexed: 12/24/2022] Open
Abstract
AbstractObjectivesBacterial persisters are a small subpopulation of cells that are highly tolerant of antibiotics and contribute to chronic and recalcitrant infections. Global gene expression in Pseudomonas aeruginosa persister cells and genes contributing to persister formation remain largely unknown. The objective of this study was to examine the gene expression profiles of the persister cells and those that regained growth in fresh medium, as well as to identify novel genes related to persister formation.MethodsP. aeruginosa persister cells and those that regrew in fresh medium were collected and subjected to RNA sequencing analysis. Genes up-regulated in the persister cells were overexpressed to evaluate their roles in persister formation. The functions of the persister-contributing genes were assessed with pulse–chase assay, affinity chromatography, fluorescence and electron microscopy, as well as a light-scattering assay.ResultsAn operon containing PA2282–PA2287 was up-regulated in the persister cells and down-regulated in the regrowing cells. PA2285 and PA2287 play key roles in persister formation. PA2285 and PA2287 were found to bind to RpoC and FtsZ, which are involved in transcription and cell division, respectively. Pulse–chase assays demonstrated inhibitory effects of PA2285 and PA2287 on the overall transcription. Meanwhile, light-scattering and microscopy assays demonstrated that PA2285 and PA2287 interfere with cell division by inhibiting FtsZ aggregation. PA2285 and PA2287 are conserved in pseudomonads and their homologous genes in Pseudomonas putida contribute to persister formation.ConclusionsPA2285 and PA2287 are novel bifunctional proteins that contribute to persister formation in P. aeruginosa.
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Affiliation(s)
- Yuqing Long
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Weixin Fu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Shouyi Li
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Huan Ren
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Mei Li
- Meishan Product Quality Supervision and Inspection Institute and National Pickle Quality Inspection Center, Meishan, P.R. China
| | - Chang Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Buyu Zhang
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, P.R. China
| | - Yushan Xia
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Zheng Fan
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Chang Xu
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, P.R. China
| | - Jianfeng Liu
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, P.R. China
| | - Yongxin Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Fang Bai
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Zhihui Cheng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Xiaoyun Liu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, P.R. China
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, P.R. China
| | - Shouguang Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, P.R. China
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Identification of a Novel Plasmid Carrying mcr-4.3 in an Acinetobacter baumannii Strain in China. Antimicrob Agents Chemother 2019; 63:AAC.00133-19. [PMID: 30936095 DOI: 10.1128/aac.00133-19] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 03/23/2019] [Indexed: 12/21/2022] Open
Abstract
Here, we identified mcr-4.3 in Acinetobacter baumannii, which had not been previously observed to carry an mcr gene. The mcr-4.3-harboring A. baumannii strain AB18PR065 was isolated from pig feces from a slaughterhouse in Guangdong Province of China. The mcr-4.3-carrying pAB18PR065 is 25,602 bp in size and could not be transferred in conjugation, transformation, and electroporation experiments, as we did not find any conjugation-related genes therein. pAB18PR065 harbors two copies of type II toxin-antitoxin systems, which are functional in plasmid stabilization and maintenance. pAB18PR065 shares similarity only with one recently identified plasmid, pAb-MCR4.3 (35,502 bp), from a clinical A. baumannii strain. It is likely that the emergence of pAb-MCR4.3 was due to the insertion of an 11,386-bp, ISAba19-based, composite transposon into pAB18PR065. These data indicate that mcr-4.3 was captured by an A. baumannii-original plasmid via horizontal gene transfer.
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Srivastava A, Garg S, Jain R, Ayana R, Kaushik H, Garg L, Pati S, Singh S. Identification and functional characterization of a bacterial homologue of Zeta toxin in Leishmania donovani. FEBS Lett 2019; 593:1223-1235. [PMID: 31074836 DOI: 10.1002/1873-3468.13429] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/05/2019] [Accepted: 03/11/2019] [Indexed: 02/04/2023]
Abstract
Zeta-toxin is a cognate toxin of epsilon antitoxin of prokaryotic Type II toxin-antitoxin system (TA) and play an important role in cell death. An orthologue of bacterial-zeta-toxin (BzT) was identified in Leishmania donovani with similar structural and functional features. Leishmania zeta-toxin (named Ld_ζ1) harboring similar UNAG and ATP-binding pockets showed UNAG kinase and ATP-binding activity. An active Ld_ζ1 was found to express in infective extracellular promastigotes stage of L. donovani and episomal overexpression of an active Ld_ζ1domain-triggered cell death. This study demonstrates the presence of prokaryotic-like-zeta-toxin in eukaryotic parasite Leishmania and its association with cell death. Conceivably, phosphorylated UNAG or analogues, the biochemical mimics of zeta-toxin function mediating cell death can act as a novel anti-leishmanial chemotherapeutics.
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Affiliation(s)
- Akriti Srivastava
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, India
| | - Swati Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, India
| | - Ravi Jain
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, India
| | - Rajagopal Ayana
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, India
| | - Himani Kaushik
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India
| | - Lalit Garg
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India
| | - Soumya Pati
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, India
| | - Shailja Singh
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, India.,Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
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Crystal Structure of VapBC-1 from Nontypeable Haemophilus influenzae and the Effect of PIN Domain Mutations on Survival during Infection. J Bacteriol 2019; 201:JB.00026-19. [PMID: 30936373 DOI: 10.1128/jb.00026-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/29/2019] [Indexed: 12/15/2022] Open
Abstract
Toxin-antitoxin (TA) gene pairs have been identified in nearly all bacterial genomes sequenced to date and are thought to facilitate persistence and antibiotic tolerance. TA loci are classified into various types based upon the characteristics of their antitoxins, with those in type II expressing proteic antitoxins. Many toxins from type II modules are ribonucleases that maintain a PilT N-terminal (PIN) domain containing conserved amino acids considered essential for activity. The vapBC (virulence-associated protein) TA system is the largest subfamily in this class and has been linked to pathogenesis of nontypeable Haemophilus influenzae (NTHi). In this study, the crystal structure of the VapBC-1 complex from NTHi was determined to 2.20 Å resolution. Based on this structure, aspartate-to-asparagine and glutamate-to-glutamine mutations of four conserved residues in the PIN domain of the VapC-1 toxin were constructed and the effects of the mutations on protein-protein interactions, growth of Escherichia coli, and pathogenesis ex vivo were tested. Finally, a novel model system was designed and utilized that consists of an NTHi ΔvapBC-1 strain complemented in cis with the TA module containing a mutated or wild-type toxin at an ectopic site on the chromosome. This enabled the analysis of the effect of PIN domain toxin mutants in tandem with their wild-type antitoxin under the control of the vapBC-1 native promoter and in single copy. This is the first report of a system facilitating the study of TA mutant operons in the background of NTHi during infections of primary human tissues ex vivo IMPORTANCE Herein the crystal structure of the VapBC-1 complex from nontypeable Haemophilus influenzae (NTHi) is described. Our results show that some of the mutations in the PIN domain of the VapC-1 toxin were associated with decreased toxicity in E. coli, but the mutants retained the ability to homodimerize and to heterodimerize with the wild-type cognate antitoxin, VapB-1. A new system was designed and constructed to quantify the effects of these mutations on NTHi survival during infections of primary human tissues ex vivo Any mutation to a conserved amino acid in the PIN domain significantly decreased the number of survivors compared to that of the in cis wild-type toxin under the same conditions.
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Barbosa LCB, Dos Santos Carrijo R, da Conceição MB, Campanella JEM, Júnior EC, Secches TO, Bertolini MC, Marchetto R. Characterization of an OrtT-like toxin of Salmonella enterica serovar Houten. Braz J Microbiol 2019; 50:839-848. [PMID: 31055774 DOI: 10.1007/s42770-019-00085-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 04/25/2019] [Indexed: 01/09/2023] Open
Abstract
The Escherichia coli GhoT/GhoS system is a type V toxin-antitoxin system in which the antitoxin GhoS cleaves the GhoT mRNA, controlling its translation. GhoT is a small hydrophobic protein that damages bacterial membranes. OrtT is a GhoT-like toxin, but it apparently lacks a corresponding antitoxin and serves a different physiologic role. Using a profile hidden Markov model approach, a Salmonella enterica serovar Houten genome was screened to obtain homologs of GhoT/OrtT. We only found one protein (referred to here as OrtT-Sal) that shared more sequence identity with OrtT than GhoT. The chromosomal region around the coding sequence of OrtT-Sal suggests that it is an orphan toxin and can be under RpoH activation. To study OrtT-Sal, we chemically synthesized and expressed in E. coli the whole toxin and its N- and C-terminal regions (OrtT-Sal1-29 and OrtT-Sal29-57, respectively). Our findings have shown that the overproduction of the polypeptides resulted in severe growth inhibition and cell lysis. Using circular dichroism, we found that OrtT-Sal, OrtT-Sal1-29, and OrtT-Sal29-57 form an alpha-helical structure in the presence of SDS micelles or TFE. Finally, using carboxyfluorescein-loaded lipid vesicles, we determined that the polypeptides damage lipid membrane directly.
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Affiliation(s)
- Luiz Carlos Bertucci Barbosa
- Institute of Natural Resources, Federal University of Itajubá, BPS, 1303, Bairro Pinheirinho, Itajubá, MG, 37500-903, Brazil.
| | | | | | | | | | - Thais Oliveira Secches
- Institute of Natural Resources, Federal University of Itajubá, BPS, 1303, Bairro Pinheirinho, Itajubá, MG, 37500-903, Brazil
| | | | - Reinaldo Marchetto
- Institute of Chemistry, São Paulo State University, Araraquara, SP, Brazil
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Akarsu H, Bordes P, Mansour M, Bigot DJ, Genevaux P, Falquet L. TASmania: A bacterial Toxin-Antitoxin Systems database. PLoS Comput Biol 2019; 15:e1006946. [PMID: 31022176 PMCID: PMC6504116 DOI: 10.1371/journal.pcbi.1006946] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 05/07/2019] [Accepted: 03/11/2019] [Indexed: 11/30/2022] Open
Abstract
Bacterial Toxin-Antitoxin systems (TAS) are involved in key biological functions including plasmid maintenance, defense against phages, persistence and virulence. They are found in nearly all phyla and classified into 6 different types based on the mode of inactivation of the toxin, with the type II TAS being the best characterized so far. We have herein developed a new in silico discovery pipeline named TASmania, which mines the >41K assemblies of the EnsemblBacteria database for known and uncharacterized protein components of type I to IV TAS loci. Our pipeline annotates the proteins based on a list of curated HMMs, which leads to >2.106 loci candidates, including orphan toxins and antitoxins, and organises the candidates in pseudo-operon structures in order to identify new TAS candidates based on a guilt-by-association strategy. In addition, we classify the two-component TAS with an unsupervised method on top of the pseudo-operon (pop) gene structures, leading to 1567 “popTA” models offering a more robust classification of the TAs families. These results give valuable clues in understanding the toxin/antitoxin modular structures and the TAS phylum specificities. Preliminary in vivo work confirmed six putative new hits in Mycobacterium tuberculosis as promising candidates. The TASmania database is available on the following server https://shiny.bioinformatics.unibe.ch/apps/tasmania/. TASmania offers an extensive annotation of TA loci in a very large database of bacterial genomes, which represents a resource of crucial importance for the microbiology community. TASmania supports i) the discovery of new TA families; ii) the design of a robust experimental strategy by taking into account potential interferences in trans; iii) the comparative analysis between TA loci content, phylogeny and/or phenotypes (pathogenicity, persistence, stress resistance, associated host types) by providing a vast repertoire of annotated assemblies. Our database contains TA annotations of a given strain not only mapped to its core genome but also to its plasmids, whenever applicable.
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Affiliation(s)
- Hatice Akarsu
- Department of Biology, University of Fribourg & Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Patricia Bordes
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Moise Mansour
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Donna-Joe Bigot
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Pierre Genevaux
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Laurent Falquet
- Department of Biology, University of Fribourg & Swiss Institute of Bioinformatics, Fribourg, Switzerland
- * E-mail:
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Tandon H, Sharma A, Wadhwa S, Varadarajan R, Singh R, Srinivasan N, Sandhya S. Bioinformatic and mutational studies of related toxin-antitoxin pairs in Mycobacterium tuberculosis predict and identify key functional residues. J Biol Chem 2019; 294:9048-9063. [PMID: 31018964 DOI: 10.1074/jbc.ra118.006814] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 04/23/2019] [Indexed: 12/17/2022] Open
Abstract
Mycobacterium tuberculosis possesses an unusually large representation of type II toxin-antitoxin (TA) systems, whose functions and targets are mostly unknown. To better understand the basis of their unique expansion and to probe putative functional similarities among these systems, here we computationally and experimentally investigated their sequence relationships. Bioinformatic and phylogenetic investigations revealed that 51 sequences of the VapBC toxin family group into paralogous sub-clusters. On the basis of conserved sequence fingerprints within paralogues, we predicted functional residues and residues at the putative TA interface that are useful to evaluate TA interactions. Substitution of these likely functional residues abolished the toxin's growth-inhibitory activity. Furthermore, conducting similarity searches in 101 mycobacterial and ∼4500 other prokaryotic genomes, we assessed the relative conservation of the M. tuberculosis TA systems and found that most TA orthologues are well-conserved among the members of the M. tuberculosis complex, which cause tuberculosis in animal hosts. We found that soil-inhabiting, free-living Actinobacteria also harbor as many as 12 TA pairs. Finally, we identified five novel putative TA modules in M. tuberculosis. For one of them, we demonstrate that overexpression of the putative toxin, Rv2514c, induces bacteriostasis and that co-expression of the cognate antitoxin Rv2515c restores bacterial growth. Taken together, our findings reveal that toxin sequences are more closely related than antitoxin sequences in M. tuberculosis Furthermore, the identification of additional TA systems reported here expands the known repertoire of TA systems in M. tuberculosis.
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Affiliation(s)
- Himani Tandon
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012 and
| | - Arun Sharma
- the Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, P. O. Box 4, Faridabad, Haryana-121001, India
| | - Saruchi Wadhwa
- the Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, P. O. Box 4, Faridabad, Haryana-121001, India
| | - Raghavan Varadarajan
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012 and
| | - Ramandeep Singh
- the Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, P. O. Box 4, Faridabad, Haryana-121001, India
| | | | - Sankaran Sandhya
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012 and
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113
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Talavera A, Tamman H, Ainelo A, Konijnenberg A, Hadži S, Sobott F, Garcia-Pino A, Hõrak R, Loris R. A dual role in regulation and toxicity for the disordered N-terminus of the toxin GraT. Nat Commun 2019; 10:972. [PMID: 30814507 PMCID: PMC6393540 DOI: 10.1038/s41467-019-08865-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 01/31/2019] [Indexed: 11/09/2022] Open
Abstract
Bacterial toxin-antitoxin (TA) modules are tightly regulated to maintain growth in favorable conditions or growth arrest during stress. A typical regulatory strategy involves the antitoxin binding and repressing its own promoter while the toxin often acts as a co-repressor. Here we show that Pseudomonas putida graTA-encoded antitoxin GraA and toxin GraT differ from other TA proteins in the sense that not the antitoxin but the toxin possesses a flexible region. GraA auto-represses the graTA promoter: two GraA dimers bind cooperatively at opposite sides of the operator sequence. Contrary to other TA modules, GraT is a de-repressor of the graTA promoter as its N-terminal disordered segment prevents the binding of the GraT2A2 complex to the operator. Removal of this region restores operator binding and abrogates Gr aT toxicity. GraTA represents a TA module where a flexible region in the toxin rather than in the antitoxin controls operon expression and toxin activity. The Pseudomonas putida toxin GraT and antitoxin GraA form a type II toxin-antoxin module. Here the authors present the crystal structures of the GraA dimer, GraTA and GraA-DNA complexes and show that GraT contains a functionally important N-terminal intrinsic disordered region that prevents the binding of the GraTA complex to the operator.
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Affiliation(s)
- Ariel Talavera
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050, Brussel, Belgium. .,Molecular Recognition Unit, Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, B-1050, Brussel, Belgium.
| | - Hedvig Tamman
- Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Andres Ainelo
- Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Albert Konijnenberg
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050, Brussel, Belgium.,Molecular Recognition Unit, Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, B-1050, Brussel, Belgium.,Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020, Antwerpen, Belgium
| | - San Hadži
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050, Brussel, Belgium.,Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020, Antwerpen, Belgium.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Abel Garcia-Pino
- Biologie Structurale et Biophysique, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, B-6041, Gosselies, Belgium
| | - Rita Hõrak
- Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050, Brussel, Belgium. .,Molecular Recognition Unit, Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, B-1050, Brussel, Belgium.
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114
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Genome organisation and comparative genomics of four novel Wolbachia genome assemblies from Indian Drosophila host. Funct Integr Genomics 2019; 19:617-632. [PMID: 30798391 DOI: 10.1007/s10142-019-00664-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 11/12/2018] [Accepted: 02/04/2019] [Indexed: 10/27/2022]
Abstract
Wolbachia has long been known to share an endosymbiotic relationship with its host as an obligate intracellular organism. Wolbachia diversity as different supergroups is found to be host-specific in most cases except a few, where the host species is seen to accommodate multiple strains. Besides, the Wolbachia genome must have undergone several changes in response to the evolving host genome in order to adapt and establish a strong association with its host, thus making a distinctive Wolbachia-host alliance. The present study focusses on four novel genome assembly and genome-wide sequence variations of Indian Wolbachia strains, i.e. wMel and wRi isolated from two different Drosophila hosts. The genome assembly has an average size of ~ 1.1 Mb and contains ~ 1100 genes, which is comparable with the previously sequenced Wolbachia genomes. The comparative genomics analysis of these genomes and sequence-wide comparison of some functionally significant genes, i.e. ankyrin repeats, Wsp and T4SS, highlight their sequence similarities and dissimilarities, further supporting the strain-specific association of Wolbachia to its host. Interestingly, some of the sequence variations are also found to be restricted to only Indian Wolbachia strains. Further analysis of prophage and their flanking regions in the Wolbachia genome reveals the presence of several functional genes which may assist the phage to reside inside the bacterial host, thus providing a trade-off for the endosymbiont-host association. Understanding this endosymbiont genome in different eco-geographical conditions has become imperative for the recent use of Wolbachia in medical entomology as a vector-control agent.
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115
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Characterization and comparative analysis of toxin-antitoxin systems in Acetobacter pasteurianus. J Ind Microbiol Biotechnol 2019; 46:869-882. [PMID: 30805740 DOI: 10.1007/s10295-019-02144-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 01/24/2019] [Indexed: 12/20/2022]
Abstract
Bacterial toxin-antitoxin (TA) systems play important roles in diverse cellular regulatory processes. Here, we characterize three putative type II TA candidates from Acetobacter pasteurianus and investigate the profile of type II TA systems in the genus Acetobacter. Based on the gene structure and activity detection, two-pairs loci were identified as the canonical hicAB and higAB TA systems, respectively, and DB34_01190-DB34_01195 as a putative new one without a canonical TA architecture. Physiologically, the expression of the three pairs conferred E. coli with additional plasmid maintenance and survival when under acetic acid stress. Chromosomal TA systems can be horizontally transferred within an ecological vinegar microbiota by co-option, and there was a tendency for toxin module loss. The antitoxin retention in the genome is suggested to have a broad role in bacterial physiology. Furthermore, A. pasteurianus strains, universally domesticated and used for industrial vinegar fermentation, showed a higher number of type II TA loci compared to the host-associated ones. The amount of TA loci per genome showed little positive relationship to insertion sequences, although its prevalence was species-associated, to the extent of even being strain-associated. The TA system is a candidate of studying the resistant mechanistic network, the TAs-dependent translatome affords a real-time profile to explore stress adaptation of A. pasteurianus, promoting industrial development.
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116
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Vet S, Vandervelde A, Gelens L. Excitable dynamics through toxin-induced mRNA cleavage in bacteria. PLoS One 2019; 14:e0212288. [PMID: 30794601 PMCID: PMC6386449 DOI: 10.1371/journal.pone.0212288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/30/2019] [Indexed: 11/19/2022] Open
Abstract
Toxin-antitoxin (TA) systems in bacteria and archaea are small genetic elements consisting of the genes coding for an intracellular toxin and an antitoxin that can neutralize this toxin. In various cases, the toxins cleave the mRNA. In this theoretical work we use deterministic and stochastic modeling to explain how toxin-induced cleavage of mRNA in TA systems can lead to excitability, allowing large transient spikes in toxin levels to be triggered. By using a simplified network where secondary complex formation and transcriptional regulation are not included, we show that a two-dimensional, deterministic model captures the origin of such toxin excitations. Moreover, it allows to increase our understanding by examining the dynamics in the phase plane. By systematically comparing the deterministic results with Gillespie simulations we demonstrate that even though the real TA system is intrinsically stochastic, toxin excitations can be accurately described deterministically. A bifurcation analysis of the system shows that the excitable behavior is due to a nearby Hopf bifurcation in the parameter space, where the system becomes oscillatory. The influence of stress is modeled by varying the degradation rate of the antitoxin and the translation rate of the toxin. We find that stress increases the frequency of toxin excitations. The inclusion of secondary complex formation and transcriptional regulation does not fundamentally change the mechanism of toxin excitations. Finally, we show that including growth rate suppression and translational inhibition can lead to longer excitations, and even cause excitations in cases when the system would otherwise be non-excitable. To conclude, the deterministic model used in this work provides a simple and intuitive explanation of toxin excitations in TA systems.
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Affiliation(s)
- Stefan Vet
- Applied Physics Research Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels (IB2), VUB-ULB, Brussels, Belgium
- Unité de Chronobiologie théorique, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | | | - Lendert Gelens
- Applied Physics Research Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Laboratory of Dynamics in Biological Systems, KU Leuven, Leuven, Belgium
- * E-mail:
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117
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Pseudomonas putida Responds to the Toxin GraT by Inducing Ribosome Biogenesis Factors and Repressing TCA Cycle Enzymes. Toxins (Basel) 2019; 11:toxins11020103. [PMID: 30744127 PMCID: PMC6410093 DOI: 10.3390/toxins11020103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/29/2019] [Accepted: 02/07/2019] [Indexed: 11/21/2022] Open
Abstract
The potentially self-poisonous toxin-antitoxin modules are widespread in bacterial chromosomes, but despite extensive studies, their biological importance remains poorly understood. Here, we used whole-cell proteomics to study the cellular effects of the Pseudomonas putida toxin GraT that is known to inhibit growth and ribosome maturation in a cold-dependent manner when the graA antitoxin gene is deleted from the genome. Proteomic analysis of P. putida wild-type and ΔgraA strains at 30 °C and 25 °C, where the growth is differently affected by GraT, revealed two major responses to GraT at both temperatures. First, ribosome biogenesis factors, including the RNA helicase DeaD and RNase III, are upregulated in ΔgraA. This likely serves to alleviate the ribosome biogenesis defect of the ΔgraA strain. Secondly, proteome data indicated that GraT induces downregulation of central carbon metabolism, as suggested by the decreased levels of TCA cycle enzymes isocitrate dehydrogenase Idh, α-ketoglutarate dehydrogenase subunit SucA, and succinate-CoA ligase subunit SucD. Metabolomic analysis revealed remarkable GraT-dependent accumulation of oxaloacetate at 25 °C and a reduced amount of malate, another TCA intermediate. The accumulation of oxaloacetate is likely due to decreased flux through the TCA cycle but also indicates inhibition of anabolic pathways in GraT-affected bacteria. Thus, proteomic and metabolomic analysis of the ΔgraA strain revealed that GraT-mediated stress triggers several responses that reprogram the cell physiology to alleviate the GraT-caused damage.
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118
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Mancilla-Rojano J, Castro-Jaimes S, Ochoa SA, Bobadilla Del Valle M, Luna-Pineda VM, Bustos P, Laris-González A, Arellano-Galindo J, Parra-Ortega I, Hernández-Castro R, Cevallos MA, Xicohtencatl-Cortes J, Cruz-Córdova A. Whole-Genome Sequences of Five Acinetobacter baumannii Strains From a Child With Leukemia M2. Front Microbiol 2019; 10:132. [PMID: 30787915 PMCID: PMC6372515 DOI: 10.3389/fmicb.2019.00132] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 01/21/2019] [Indexed: 01/05/2023] Open
Abstract
Acinetobacter baumannii is an opportunistic pathogen and is one of the primary etiological agents of healthcare-associated infections (HAIs). A. baumannii infections are difficult to treat due to the intrinsic and acquired antibiotic resistance of strains of this bacterium, which frequently limits therapeutic options. In this study, five A. baumannii strains (810CP, 433H, 434H, 483H, and A-2), all of which were isolated from a child with leukemia M2, were characterized through antibiotic susceptibility profiling, the detection of genes encoding carbapenem hydrolyzing oxacillinases, pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), adherence and invasion assays toward the A549 cell line, and the whole-genome sequence (WGS). The five strains showed Multidrug resistant (MDR) profiles and amplification of the blaOXA-23 gene, belonging to ST758 and grouped into two PFGE clusters. WGS of 810CP revealed the presence of a circular chromosome and two small plasmids, pAba810CPa and pAba810CPb. Both plasmids carried genes encoding the Sp1TA system, although resistance genes were not identified. A gene-by-gene comparison analysis was performed among the A. baumannii strains isolated in this study and others A. baumannii ST758 strains (HIMFG and INCan), showing that 86% of genes were present in all analyzed strains. Interestingly, the 433H, 434H, and 483H strains varied by 8–10 single-nucleotide variants (SNVs), while the A2 and 810CP strains varied by 46 SNVs. Subsequently, an analysis using BacWGSTdb showed that all of our strains had the same resistance genes and were ST758. However, some variations were observed in relation to virulence genes, mainly in the 810CP strain. The genes involved in the synthesis of hepta-acylated lipooligosaccharides, the pgaABCD locus encoding poly-β-1-6-N-acetylglucosamine, the ompA gene, Csu pili, bap, the two-component system bfms/bfmR, a member of the phospholipase D family, and two iron-uptake systems were identified in our A. baumannii strains genome. The five A. baumannii strains isolated from the child were genetically different and showed important characteristics that promote survival in a hospital environment. The elucidation of their genomic sequences provides important information for understanding their epidemiology, antibiotic resistance, and putative virulence factors.
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Affiliation(s)
- Jetsi Mancilla-Rojano
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez, Mexico City, Mexico.,Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Semiramis Castro-Jaimes
- Centro de Ciencias Genómicas, Programa de Genómica Evolutiva, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Sara A Ochoa
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Miriam Bobadilla Del Valle
- Departamento de Enfermedades Infecciosas Instituto Nacional de Ciencias Médicas y de Nutrición "Salvador Zubirán", Mexico City, Mexico
| | - Victor M Luna-Pineda
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Patricia Bustos
- Centro de Ciencias Genómicas, Programa de Genómica Evolutiva, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Almudena Laris-González
- Departamento de Epidemiología, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - José Arellano-Galindo
- Laboratorio de Infectología, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Israel Parra-Ortega
- Laboratorio Central, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Rigoberto Hernández-Castro
- Departamento de Ecología de Agentes Patógenos Hospital General "Dr. Manuel Gea González", Mexico City, Mexico
| | - Miguel A Cevallos
- Centro de Ciencias Genómicas, Programa de Genómica Evolutiva, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Juan Xicohtencatl-Cortes
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Ariadnna Cruz-Córdova
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
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119
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Tandon H, Sharma A, Sandhya S, Srinivasan N, Singh R. Mycobacterium tuberculosis Rv0366c-Rv0367c encodes a non-canonical PezAT-like toxin-antitoxin pair. Sci Rep 2019; 9:1163. [PMID: 30718534 PMCID: PMC6362051 DOI: 10.1038/s41598-018-37473-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/27/2018] [Indexed: 11/29/2022] Open
Abstract
Toxin-antitoxin (TA) systems are ubiquitously existing addiction modules with essential roles in bacterial persistence and virulence. The genome of Mycobacterium tuberculosis encodes approximately 79 TA systems. Through computational and experimental investigations, we report for the first time that Rv0366c-Rv0367c is a non-canonical PezAT-like toxin-antitoxin system in M. tuberculosis. Homology searches with known PezT homologues revealed that residues implicated in nucleotide, antitoxin-binding and catalysis are conserved in Rv0366c. Unlike canonical PezA antitoxins, the N-terminal of Rv0367c is predicted to adopt the ribbon-helix-helix (RHH) motif for deoxyribonucleic acid (DNA) recognition. Further, the modelled complex predicts that the interactions between PezT and PezA involve conserved residues. We performed a large-scale search in sequences encoded in 101 mycobacterial and 4500 prokaryotic genomes and show that such an atypical PezAT organization is conserved in 20 other mycobacterial organisms and in families of class Actinobacteria. We also demonstrate that overexpression of Rv0366c induces bacteriostasis and this growth defect could be restored upon co-expression of cognate antitoxin, Rv0367c. Further, we also observed that inducible expression of Rv0366c in Mycobacterium smegmatis results in decreased cell-length and enhanced tolerance against a front-line tuberculosis (TB) drug, ethambutol. Taken together, we have identified and functionally characterized a novel non-canonical TA system from M. tuberculosis.
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Affiliation(s)
- Himani Tandon
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Arun Sharma
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, PO Box #4, Faridabad, Haryana, 121001, India
| | - Sankaran Sandhya
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | | | - Ramandeep Singh
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, PO Box #4, Faridabad, Haryana, 121001, India.
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120
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Genotypic differences between strains of the opportunistic pathogen Corynebacterium bovis isolated from humans, cows, and rodents. PLoS One 2018; 13:e0209231. [PMID: 30586440 PMCID: PMC6306256 DOI: 10.1371/journal.pone.0209231] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/30/2018] [Indexed: 01/21/2023] Open
Abstract
Corynebacterium bovis is an opportunistic bacterial pathogen shown to cause eye and prosthetic joint infections as well as abscesses in humans, mastitis in dairy cattle, and skin disease in laboratory mice and rats. Little is known about the genetic characteristics and genomic diversity of C. bovis because only a single draft genome is available for the species. The overall aim of this study was to sequence and compare the genome of C. bovis isolates obtained from different species, locations, and time points. Whole-genome sequencing was conducted on 20 C. bovis isolates (six human, four bovine, nine mouse and one rat) using the Illumina MiSeq platform and submitted to various comparative analysis tools. Sequencing generated high-quality contigs (over 2.53 Mbp) that were comparable to the only reported assembly using C. bovis DSM 20582T (97.8 ± 0.36% completeness). The number of protein-coding DNA sequences (2,174 ± 12.4) was similar among all isolates. A Corynebacterium genus neighbor-joining tree was created, which revealed Corynebacterium falsenii as the nearest neighbor to C. bovis (95.87% similarity), although the reciprocal comparison shows Corynebacterium jeikeium as closest neighbor to C. falsenii. Interestingly, the average nucleotide identity demonstrated that the C. bovis isolates clustered by host, with human and bovine isolates clustering together, and the mouse and rat isolates forming a separate group. The average number of genomic islands and putative virulence factors were significantly higher (p<0.001) in the mouse and rat isolates as compared to human/bovine isolates. Corynebacterium bovis’ pan-genome contained a total of 3,067 genes of which 1,354 represented core genes. The known core genes of all isolates were primarily related to ‘‘metabolism” and ‘‘information storage/processing.” However, most genes were classified as ‘‘function unknown” or “unclassified”. Surprisingly, no intact prophages were found in any isolate; however, almost all isolates had at least one complete CRISPR-Cas system.
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121
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Hosseini N, Pourhajibagher M, Chiniforush N, Hosseinkhan N, Rezaie P, Bahador A. Modulation of Toxin-Antitoxin System Rnl AB Type II in Phage-Resistant Gammaproteobacteria Surviving Photodynamic Treatment. J Lasers Med Sci 2018; 10:21-28. [PMID: 31360364 DOI: 10.15171/jlms.2019.03] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Type II toxin-antitoxin (TA) systems are the particular type of TA modules which take part in different kinds of cellular actions, such as biofilm formation, persistence, stress endurance, defense of the bacterial cell against multiple phage attacks, plasmid maintenance, and programmed cell death in favor of bacterial population. Although several bioinformatics and Pet lab studies have already been conducted to understand the functionality of already discovered TA systems, still, more work in this area is required. Rnl AB type II TA module, which is composed of RnlA toxin and RnlB antitoxin, is a newly discovered type II TA module which takes part in the defense mechanism against T4 bacteriophage attack in Escherichia coli K-12 strain MH1 that has not been widely studied in other bacteria. Because of the significant role of class Gammaproteobacteriacea in a diverse range of health problems, we chose here to focus on this class to survey the presence of the Rnl AB TA module. For better categorization and description of the distribution of this module in this class of bacteria, the corresponding phylogenetic trees are illustrated here. Neighbor-joining and the maximum parsimony methods were used in this study to take a look at the distribution of domains present in RnlA and RnlB proteins, among members of Gammaproteobacteria. Also, the possible roles of photodynamic therapy (PDT) in providing a substrate for better phage therapy are herein discussed.
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Affiliation(s)
- Nava Hosseini
- Department of Microbiology, Faculty of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Maryam Pourhajibagher
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Nasim Chiniforush
- Laser Research Center of Dentistry (LRCD), Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Nazanin Hosseinkhan
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parizad Rezaie
- Department of Microbiology, Faculty of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Abbas Bahador
- Dental Implant Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
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122
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Skjerning RB, Senissar M, Winther KS, Gerdes K, Brodersen DE. The RES domain toxins of RES-Xre toxin-antitoxin modules induce cell stasis by degrading NAD+. Mol Microbiol 2018; 111:221-236. [PMID: 30315706 DOI: 10.1111/mmi.14150] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2018] [Indexed: 12/18/2022]
Abstract
Type II toxin-antitoxin (TA) modules, which are important cellular regulators in prokaryotes, usually encode two proteins, a toxin that inhibits cell growth and a nontoxic and labile inhibitor (antitoxin) that binds to and neutralizes the toxin. Here, we demonstrate that the res-xre locus from Photorhabdus luminescens and other bacterial species function as bona fide TA modules in Escherichia coli. The 2.2 Å crystal structure of the intact Pseudomonas putida RES-Xre TA complex reveals an unusual 2:4 stoichiometry in which a central RES toxin dimer binds two Xre antitoxin dimers. The antitoxin dimers each expose two helix-turn-helix DNA-binding domains of the Cro repressor type, suggesting the TA complex is capable of binding the upstream promoter sequence on DNA. The toxin core domain shows structural similarity to ADP-ribosylating enzymes such as diphtheria toxin but has an atypical NAD+ -binding pocket suggesting an alternative function. We show that activation of the toxin in vivo causes a depletion of intracellular NAD+ levels eventually leading to inhibition of cell growth in E. coli and inhibition of global macromolecular biosynthesis. Both structure and activity are unprecedented among bacterial TA systems, suggesting the functional scope of bacterial TA toxins is much wider than previously appreciated.
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Affiliation(s)
- Ragnhild Bager Skjerning
- Department of Biology, Centre for Bacterial Stress Response and Persistence (BASP), University of Copenhagen, Copenhagen, Denmark
| | - Meriem Senissar
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Kristoffer S Winther
- Department of Biology, Centre for Bacterial Stress Response and Persistence (BASP), University of Copenhagen, Copenhagen, Denmark
| | - Kenn Gerdes
- Department of Biology, Centre for Bacterial Stress Response and Persistence (BASP), University of Copenhagen, Copenhagen, Denmark
| | - Ditlev E Brodersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
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Yadav M, Rathore JS. TAome analysis of type-II toxin-antitoxin system from Xenorhabdus nematophila. Comput Biol Chem 2018; 76:293-301. [DOI: 10.1016/j.compbiolchem.2018.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 05/23/2018] [Accepted: 07/07/2018] [Indexed: 12/23/2022]
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Wang M, Fang K, Hong SMC, Kim I, Jang IS, Hong SH. Medium chain unsaturated fatty acid ethyl esters inhibit persister formation of Escherichia coli via antitoxin HipB. Appl Microbiol Biotechnol 2018; 102:8511-8524. [PMID: 30088019 DOI: 10.1007/s00253-018-9271-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/18/2018] [Accepted: 07/23/2018] [Indexed: 11/28/2022]
Abstract
Persisters represent a small bacterial population that is dormant and that survives under antibiotic treatment without experiencing genetic adaptation. Persisters are also considered one of the major reasons for recalcitrant chronic bacterial infections. Although several mechanisms of persister formation have been proposed, it is not clear how cells enter the dormant state in the presence of antibiotics or how persister cell formation can be effectively controlled. A fatty acid compound, cis-2-decenoic acid, was reported to decrease persister formation as well as revert the dormant cells to a metabolically active state. We reasoned that some fatty acid compounds may be effective in controlling bacterial persistence because they are known to benefit host immune systems. This study investigated persister cell formation by pathogens that were exposed to nine fatty acid compounds during antibiotic treatment. We found that three medium chain unsaturated fatty acid ethyl esters (ethyl trans-2-decenoate, ethyl trans-2-octenoate, and ethyl cis-4-decenoate) decreased the level of Escherichia coli persister formation up to 110-fold when cells were exposed to ciprofloxacin or ampicillin antibiotics. RNA sequencing analysis and gene deletion persister studies elucidated that these fatty acids inhibit bacterial persistence by regulating antitoxin HipB. A similar persister cell reduction was observed for pathogenic E. coli EDL933, Pseudomonas aeruginosa PAO1, and Serratia marcescens ICU2-4 strains. This study demonstrates that fatty acid ethyl esters can be used to disrupt bacterial dormancy to combat persistent infectious diseases.
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Affiliation(s)
- Mengya Wang
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Kuili Fang
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Sung Min Choi Hong
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Inwha Kim
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Ik-Soon Jang
- Division of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon, 305-333, Republic of Korea
| | - Seok Hoon Hong
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA.
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A toxin-antitoxin system is essential for the stability of mosquitocidal plasmid pBsph of Lysinibacillus sphaericus. Microbiol Res 2018; 214:114-122. [PMID: 30031473 DOI: 10.1016/j.micres.2018.06.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 06/13/2018] [Accepted: 06/23/2018] [Indexed: 11/22/2022]
Abstract
Lysinibacillus sphaericus C3-41 carries a large low-copy-number plasmid pBsph, which encodes binary toxin proteins. Our previous study found that the transcriptional activator TubX plays an important role in the newly identified type Ⅲ TubRZC replication/partition system in pBsph, and that a vector consisting of tubRZC and tubX is not as stable as pBsph, indicating the presence of other maintenance module(s). In this study, we identified that orf9 and orf10 are necessary for the stability of pBsph by a series of deletion and complementation experiments. Bioinformatics analysis showed that ORF9 contains a PIN domain of VapBC toxin-antitoxin (TA) system, whereas ORF10 share no significant sequence similarity to any of the characterized antitoxins in the database. Further studies revealed that orf9 and orf10 are transcribed as an operon. The overexpression of ORF9 repressed the growth of both Escherichia coli and L. sphaericus, which can be alleviated by overexpression of ORF10. The deletion of orf10 individually or orf9-10 together resulted a decrease on plasmid stability which was restored by the complementation of corresponding gene(s), suggesting that ORF10 plays an important role in plasmid stability. In addition, it was found the plasmid stability is related with the transcription level of tubRZ, and overexpression of TubRZ could neutralize the negative effect on plasmid stability caused by the deletion of orf9-orf10. Moreover, the recombinant vector containing tubRZC, tubX and orf9-10 was more stable than the ones containing only tubRZC and either tubX or orf9-10. The data indicate that the plasmid maintenance system on pBsph includes orf9-orf10 TA system.
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Timing of DNA damage responses impacts persistence to fluoroquinolones. Proc Natl Acad Sci U S A 2018; 115:E6301-E6309. [PMID: 29915065 DOI: 10.1073/pnas.1804218115] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial persisters are subpopulations of phenotypic variants in isogenic cultures that can survive lethal doses of antibiotics. Their tolerances are often attributed to reduced activities of antibiotic targets, which limit corruption and damage in persisters compared with bacteria that die from treatment. However, that model does not hold for nongrowing populations treated with ofloxacin, a fluoroquinolone, where antibiotic-induced damage is comparable between cells that live and those that die. To understand how those persisters achieve this feat, we employed a genetic system that uses orthogonal control of MazF and MazE, a toxin and its cognate antitoxin, to generate model persisters that are uniformly tolerant to ofloxacin. Despite this complete tolerance, MazF model persisters required the same DNA repair machinery (RecA, RecB, and SOS induction) to survive ofloxacin treatment as their nongrowing, WT counterparts and exhibited similar indicators of DNA damage from treatment. Further investigation revealed that, following treatment, the timing of DNA repair was critical to MazF persister survival because, when repair was delayed until after growth and DNA synthesis resumed, survival was compromised. In addition, we found that, with nongrowing, WT planktonic and biofilm populations, stalling the resumption of growth and DNA synthesis after the conclusion of fluoroquinolone treatment with a prevalent type of stress at infection sites (nutrient limitation) led to near complete survival. These findings illustrate that the timing of events, such as DNA repair, following fluoroquinolone treatment is important to persister survival and provide further evidence that knowledge of the postantibiotic recovery period is critical to understanding persistence phenotypes.
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Ciok A, Budzik K, Zdanowski MK, Gawor J, Grzesiak J, Decewicz P, Gromadka R, Bartosik D, Dziewit L. Plasmids of Psychrotolerant Polaromonas spp. Isolated From Arctic and Antarctic Glaciers - Diversity and Role in Adaptation to Polar Environments. Front Microbiol 2018; 9:1285. [PMID: 29967598 PMCID: PMC6015842 DOI: 10.3389/fmicb.2018.01285] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/25/2018] [Indexed: 12/23/2022] Open
Abstract
Cold-active bacteria of the genus Polaromonas (class Betaproteobacteria) are important components of glacial microbiomes. In this study, extrachromosomal replicons of 26 psychrotolerant Polaromonas strains, isolated from Arctic and Antarctic glaciers, were identified, sequenced, and characterized. The plasmidome of these strains consists of 13 replicons, ranging in size from 3,378 to 101,077 bp. In silico sequence analyses identified the conserved backbones of these plasmids, composed of genes required for plasmid replication, stable maintenance, and conjugal transfer. Host range analysis revealed that all of the identified plasmids are narrow-host-range replicons, only able to replicate in bacteria of closely related genera (Polaromonas and Variovorax) of the Comamonadaceae family. Special attention was paid to the identification of plasmid auxiliary genetic information, which may contribute to the adaptation of bacteria to environmental conditions occurring in glaciers. Detailed analysis revealed the presence of genes encoding proteins potentially involved in (i) protection against reactive oxygen species, ultraviolet radiation, and low temperatures; (ii) transport and metabolism of organic compounds; (iii) transport of metal ions; and (iv) resistance to heavy metals. Some of the plasmids also carry genes required for the molecular assembly of iron-sulfur [Fe-S] clusters. Functional analysis of the predicted heavy metal resistance determinants demonstrated that their activity varies, depending on the host strain. This study provides the first molecular insight into the mobile DNA of Polaromonas spp. inhabiting polar glaciers. It has generated valuable data on the structure and properties of a pool of plasmids and highlighted their role in the biology of psychrotolerant Polaromonas strains and their adaptation to the environmental conditions of Arctic and Antarctic glaciers.
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Affiliation(s)
- Anna Ciok
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Karol Budzik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Marek K. Zdanowski
- Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jan Gawor
- Laboratory of DNA Sequencing and Oligonucleotide Synthesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jakub Grzesiak
- Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Robert Gromadka
- Laboratory of DNA Sequencing and Oligonucleotide Synthesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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128
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Reassessing the Role of Type II Toxin-Antitoxin Systems in Formation of Escherichia coli Type II Persister Cells. mBio 2018; 9:mBio.00640-18. [PMID: 29895634 PMCID: PMC6016239 DOI: 10.1128/mbio.00640-18] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Persistence is a reversible and low-frequency phenomenon allowing a subpopulation of a clonal bacterial population to survive antibiotic treatments. Upon removal of the antibiotic, persister cells resume growth and give rise to viable progeny. Type II toxin-antitoxin (TA) systems were assumed to play a key role in the formation of persister cells in Escherichia coli based on the observation that successive deletions of TA systems decreased persistence frequency. In addition, the model proposed that stochastic fluctuations of (p)ppGpp levels are the basis for triggering activation of TA systems. Cells in which TA systems are activated are thought to enter a dormancy state and therefore survive the antibiotic treatment. Using independently constructed strains and newly designed fluorescent reporters, we reassessed the roles of TA modules in persistence both at the population and single-cell levels. Our data confirm that the deletion of 10 TA systems does not affect persistence to ofloxacin or ampicillin. Moreover, microfluidic experiments performed with a strain reporting the induction of the yefM-yoeB TA system allowed the observation of a small number of type II persister cells that resume growth after removal of ampicillin. However, we were unable to establish a correlation between high fluorescence and persistence, since the fluorescence of persister cells was comparable to that of the bulk of the population and none of the cells showing high fluorescence were able to resume growth upon removal of the antibiotic. Altogether, these data show that there is no direct link between induction of TA systems and persistence to antibiotics.IMPORTANCE Within a growing bacterial population, a small subpopulation of cells is able to survive antibiotic treatment by entering a transient state of dormancy referred to as persistence. Persistence is thought to be the cause of relapsing bacterial infections and is a major public health concern. Type II toxin-antitoxin systems are small modules composed of a toxic protein and an antitoxin protein counteracting the toxin activity. These systems were thought to be pivotal players in persistence until recent developments in the field. Our results demonstrate that previous influential reports had technical flaws and that there is no direct link between induction of TA systems and persistence to antibiotics.
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129
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The ng_ζ1 toxin of the gonococcal epsilon/zeta toxin/antitoxin system drains precursors for cell wall synthesis. Nat Commun 2018; 9:1686. [PMID: 29703974 PMCID: PMC5923241 DOI: 10.1038/s41467-018-03652-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 03/02/2018] [Indexed: 01/14/2023] Open
Abstract
Bacterial toxin–antitoxin complexes are emerging as key players modulating bacterial physiology as activation of toxins induces stasis or programmed cell death by interference with vital cellular processes. Zeta toxins, which are prevalent in many bacterial genomes, were shown to interfere with cell wall formation by perturbing peptidoglycan synthesis in Gram-positive bacteria. Here, we characterize the epsilon/zeta toxin–antitoxin (TA) homologue from the Gram-negative pathogen Neisseria gonorrhoeae termed ng_ɛ1 / ng_ζ1. Contrary to previously studied streptococcal epsilon/zeta TA systems, ng_ɛ1 has an epsilon-unrelated fold and ng_ζ1 displays broader substrate specificity and phosphorylates multiple UDP-activated sugars that are precursors of peptidoglycan and lipopolysaccharide synthesis. Moreover, the phosphorylation site is different from the streptococcal zeta toxins, resulting in a different interference with cell wall synthesis. This difference most likely reflects adaptation to the individual cell wall composition of Gram-negative and Gram-positive organisms but also the distinct involvement of cell wall components in virulence. Toxin–antitoxin (TA) systems are important modulators of bacterial physiology. Here, the authors structurally characterize the epsilon/zeta TA system from the Gram-negative pathogen Neisseria gonorrhoeae and show that the toxin interferes with peptidoglycan and lipopolysaccharide synthesis by phosphorylating the UDP-activated sugar-precursors.
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130
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Armalytė J, Jurėnas D, Krasauskas R, Čepauskas A, Sužiedėlienė E. The higBA Toxin-Antitoxin Module From the Opportunistic Pathogen Acinetobacter baumannii - Regulation, Activity, and Evolution. Front Microbiol 2018; 9:732. [PMID: 29706946 PMCID: PMC5906591 DOI: 10.3389/fmicb.2018.00732] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 03/28/2018] [Indexed: 01/08/2023] Open
Abstract
Acinetobacter baumannii is one of the major causes of hard to treat multidrug-resistant hospital infections. A. baumannii features contributing to its spread and persistence in clinical environment are only beginning to be explored. Bacterial toxin-antitoxin (TA) systems are genetic loci shown to be involved in plasmid maintenance and proposed to function as components of stress response networks. Here we present a thorough characterization of type II system of A. baumannii, which is the most ubiquitous TA module present in A. baumannii plasmids. higBA of A. baumannii is a reverse TA (the toxin gene is the first in the operon) and shows little homology to other TA systems of RelE superfamily. It is represented by two variants, which both are functional albeit exhibit strong difference in sequence conservation. The higBA2 operon is found on ubiquitous 11 Kb pAB120 plasmid, conferring carbapenem resistance to clinical A. baumannii isolates and represents a higBA variant that can be found with multiple sequence variations. We show here that higBA2 is capable to confer maintenance of unstable plasmid in Acinetobacter species. HigB2 toxin functions as a ribonuclease and its activity is neutralized by HigA2 antitoxin through formation of an unusually large heterooligomeric complex. Based on the in vivo expression analysis of gfp reporter gene we propose that HigA2 antitoxin and HigBA2 protein complex bind the higBA2 promoter region to downregulate its transcription. We also demonstrate that higBA2 is a stress responsive locus, whose transcription changes in conditions encountered by A. baumannii in clinical environment and within the host. We show elevated expression of higBA2 during stationary phase, under iron deficiency and downregulated expression after antibiotic (rifampicin) treatment.
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Affiliation(s)
- Julija Armalytė
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Dukas Jurėnas
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Cellular and Molecular Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, Brussels, Belgium
| | - Renatas Krasauskas
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Albinas Čepauskas
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Edita Sužiedėlienė
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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131
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Fei Q, Gao EB, Liu B, Wei Y, Ning D. A Toxin-Antitoxin System VapBC15 from Synechocystis sp. PCC 6803 Shows Distinct Regulatory Features. Genes (Basel) 2018; 9:E173. [PMID: 29561797 PMCID: PMC5924515 DOI: 10.3390/genes9040173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 12/26/2022] Open
Abstract
Type II toxin-antitoxin (TA) systems play important roles in bacterial stress survival by regulating cell growth or death. They are highly abundant in cyanobacteria yet remain poorly characterized. Here, we report the identification and regulation of a putative type II TA system from Synechocystis PCC6803, VapBC15. The VapBC15 system is encoded by the chromosomal operon vapBC15. Exogenous expression of VapC15 dramatically arrested cell growth of Escherichia coli and reduced the numbers of colony-forming units (CFU). The VapC15 toxicity could be which was counteracted neutralized by simultaneous or delayed production of VapB15. Biochemical analysis demonstrated the formation of VapB15-VapC15 complexes by the physical interaction between VapB15 and VapC15. Notably, the VapB15 antitoxin up-regulated the transcription of the vapBC15 operon by directly binding to the promoter region, and the VapC15 toxin abolished the up-regulatory effect by destabilizing the binding. Moreover, VapB15 can be degraded by the proteases Lons and ClpXP2s from Synechocystis PCC6803, thus activating the latent toxicity of VapBC15. These findings suggest that VapBC15 represents a genuine TA system that utilizes a distinct mechanism to regulate toxin activity.
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Affiliation(s)
- Qian Fei
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - E-Bin Gao
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
| | - Biao Liu
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
| | - Yao Wei
- Huai'an Research Center, Institute of Hydrobiology, Chinese Academy of Sciences, Huai'an 223005, China.
| | - Degang Ning
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- Huai'an Research Center, Institute of Hydrobiology, Chinese Academy of Sciences, Huai'an 223005, China.
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132
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Hampton HG, Jackson SA, Fagerlund RD, Vogel AIM, Dy RL, Blower TR, Fineran PC. AbiEi Binds Cooperatively to the Type IV abiE Toxin-Antitoxin Operator Via a Positively-Charged Surface and Causes DNA Bending and Negative Autoregulation. J Mol Biol 2018. [PMID: 29518409 DOI: 10.1016/j.jmb.2018.02.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Bacteria resist phage infection using multiple strategies, including CRISPR-Cas and abortive infection (Abi) systems. Abi systems provide population-level protection from phage predation, via "altruistic" cell suicide. It has recently been shown that some Abi systems function via a toxin-antitoxin mechanism, such as the widespread AbiE family. The Streptococcus agalactiae AbiE system consists of a bicistronic operon encoding the AbiEi antitoxin and AbiEii toxin, which function as a Type IV toxin-antitoxin system. Here we examine the AbiEi antitoxin, which belongs to a large family of transcriptional regulators with a conserved N-terminal winged helix-turn-helix domain. This winged helix-turn-helix is essential for transcriptional repression of the abiE operon. The function of the AbiEi C-terminal domain is poorly characterized, but it contributes to transcriptional repression and is sufficient for toxin neutralization. We demonstrate that a conserved charged surface on one face of the C-terminal domain assists sequence-specific DNA binding and negative autoregulation, without influencing antitoxicity. Furthermore, AbiEi binds cooperatively to two inverted repeats within the abiE promoter and bends the DNA by 72°. These findings demonstrate that the mechanism of DNA binding by the widespread family of AbiEi antitoxins and transcriptional regulators can contribute to negative autoregulation.
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Affiliation(s)
- Hannah G Hampton
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Simon A Jackson
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Robert D Fagerlund
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Anne I M Vogel
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Ron L Dy
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Tim R Blower
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
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Harms A, Brodersen DE, Mitarai N, Gerdes K. Toxins, Targets, and Triggers: An Overview of Toxin-Antitoxin Biology. Mol Cell 2018; 70:768-784. [PMID: 29398446 DOI: 10.1016/j.molcel.2018.01.003] [Citation(s) in RCA: 398] [Impact Index Per Article: 66.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/06/2017] [Accepted: 01/02/2018] [Indexed: 12/01/2022]
Abstract
Bacterial toxin-antitoxin (TA) modules are abundant genetic elements that encode a toxin protein capable of inhibiting cell growth and an antitoxin that counteracts the toxin. The majority of toxins are enzymes that interfere with translation or DNA replication, but a wide variety of molecular activities and cellular targets have been described. Antitoxins are proteins or RNAs that often control their cognate toxins through direct interactions and, in conjunction with other signaling elements, through transcriptional and translational regulation of TA module expression. Three major biological functions of TA modules have been discovered, post-segregational killing ("plasmid addiction"), abortive infection (bacteriophage immunity through altruistic suicide), and persister formation (antibiotic tolerance through dormancy). In this review, we summarize the current state of the field and highlight how multiple levels of regulation shape the conditions of toxin activation to achieve the different biological functions of TA modules.
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Affiliation(s)
- Alexander Harms
- Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Ditlev Egeskov Brodersen
- Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark; Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Namiko Mitarai
- Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark; Niels Bohr Institute, Department of Physics, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Kenn Gerdes
- Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark.
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134
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Van Melderen L, Jurenas D, Garcia-Pino A. Messing up translation from the start: How AtaT inhibits translation initiation in E. coli. RNA Biol 2018; 15:303-307. [PMID: 29099338 DOI: 10.1080/15476286.2017.1391439] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Toxin-antitoxin systems (TA) are widespread in bacteria and archea. They are commonly found in chromosomes and mobile genetic elements. These systems move from different genomic locations and bacterial hosts through horizontal gene transfer, using mobile elements as vehicles. Their potential roles in bacterial physiology are still a matter of debate in the field. The mechanisms of action of different toxin families have been deciphered at the molecular level. Intriguingly, the vast majority of these toxins target protein synthesis. They use a variety of molecular mechanisms and inhibit nearly every step of the translation process. Recently, we have identified a novel toxin, AtaT, presenting acetyltransferase activity. 1 Our work uncovered the molecular activity of AtaT: it specifically acetylates the methionine moiety on the initiator Met-tRNAfMet. This modification drastically impairs recognition by initiation factor 2 (IF2), thereby inhibiting the initiation step of translation.
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Affiliation(s)
- Laurence Van Melderen
- a Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB) , Gosselies , Belgium
| | - Dukas Jurenas
- a Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB) , Gosselies , Belgium.,b Department of Biochemistry and Molecular Biology , Vilnius University Joint Life Sciences Center , Vilnius , Lithuania
| | - Abel Garcia-Pino
- a Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB) , Gosselies , Belgium
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135
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Homologous VapC Toxins Inhibit Translation and Cell Growth by Sequence-Specific Cleavage of tRNA fMet. J Bacteriol 2018; 200:JB.00582-17. [PMID: 29109187 DOI: 10.1128/jb.00582-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 10/30/2017] [Indexed: 01/19/2023] Open
Abstract
Type II toxin-antitoxin (TA) systems play a critical role in the establishment and maintenance of bacterial dormancy. They are composed of a protein toxin and its cognate protein antitoxin. They function to regulate growth under conditions of stress, such as starvation or antibiotic treatment. As cellular proteases degrade the antitoxin, which normally binds and neutralizes the toxin, this frees the toxin to act on its cellular targets and arrest bacterial growth. TA systems are of particular concern in regard to pathogenic organisms, such as nontypeable Haemophilus influenzae (NTHi), as dormancy may lead to chronic infections and failure of antibiotic treatment. Many targets of VapC toxins have not been identified, to date, and this knowledge is crucial to understanding how toxins control the establishment and maintenance of bacterial dormancy. Accordingly, we characterized the target specificity of the VapC toxins from the two paralogous NTHi vapBC TA systems. RNA sequencing and Northern blot analysis revealed that VapC1 and VapC2 cleave tRNAfMet in the anticodon loop. Overexpression of tRNAfMet suppresses VapC toxicity, suggesting that translation inhibition results from the depletion of tRNAfMet These experiments also identified base pairs in the tRNAfMet anticodon stem that play a key role in VapC-specific cleavage of the tRNA. Together these findings suggest the potential for NTHi VapC1 and VapC2 to induce dormancy by sequence-specific cleavage of tRNAfMetIMPORTANCE Bacterial persistence is a significant concern in regard to pathogenic organisms, such as nontypeable Haemophilus influenzae, as it can result in recurrent and chronic infections. Toxin-antitoxin systems can lead to persistence by causing bacteria to enter a slow-growing state that renders them antibiotic tolerant. Type II toxin components affect a wide variety of bacterial targets in order to elicit dormancy, and for many toxin-antitoxin systems, these mechanisms are not well understood. Thus, in order to understand how vapBC toxin-antitoxin systems cause dormancy, it is crucial to investigate the substrate specificity of VapC toxins. This study identifies the target of the VapC1 and VapC2 toxins from NTHi and takes important steps toward understanding the specificity of these toxins for their tRNA target.
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136
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Jaén-Luchoro D, Aliaga-Lozano F, Gomila RM, Gomila M, Salvà-Serra F, Lalucat J, Bennasar-Figueras A. First insights into a type II toxin-antitoxin system from the clinical isolate Mycobacterium sp. MHSD3, similar to epsilon/zeta systems. PLoS One 2017; 12:e0189459. [PMID: 29236773 PMCID: PMC5728571 DOI: 10.1371/journal.pone.0189459] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 11/28/2017] [Indexed: 01/21/2023] Open
Abstract
A putative type II toxin-antitoxin (TA) system was found in the clinical isolate Mycobacterium sp. MHSD3, a strain closely related to Mycobacterium chelonae. Further analyses of the protein sequences of the two genes revealed the presence of domains related to a TA system. BLAST analyses indicated the presence of closely related proteins in the genomes of other recently published M. chelonae strains. The functionality of both elements of the TA system was demonstrated when expressed in Escherichia coli cells, and the predicted structure of the toxin is very similar to those of well-known zeta-toxins, leading to the definition of a type II TA system similar to epsilon/zeta TA systems in strains that are closely related to M. chelonae.
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Affiliation(s)
- Daniel Jaén-Luchoro
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
- * E-mail:
| | - Francisco Aliaga-Lozano
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Laboratorio de Biología Molecular, Clínica Rotger, Palma de Mallorca, Spain
| | - Rosa Maria Gomila
- Serveis Cientifico-Tècnics, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Francisco Salvà-Serra
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
| | - Jorge Lalucat
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Institut Mediterrani d’Estudis Avançats (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Antoni Bennasar-Figueras
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Area de Enfermedades Infecciosas, Instituto Universitario de Investigaciones en Ciencias de la Salud (IUNICS-UIB), Universitat de les Illes Balears, Palma de Mallorca, Spain
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137
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Yassin AF, Langenberg S, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Mukherjee S, Reddy TBK, Daum C, Shapiro N, Ivanova N, Woyke T, Kyrpides NC. Draft genome sequence of Actinotignum schaalii DSM 15541T: Genetic insights into the lifestyle, cell fitness and virulence. PLoS One 2017; 12:e0188914. [PMID: 29216246 PMCID: PMC5720513 DOI: 10.1371/journal.pone.0188914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/15/2017] [Indexed: 11/19/2022] Open
Abstract
The permanent draft genome sequence of Actinotignum schaalii DSM 15541T is presented. The annotated genome includes 2,130,987 bp, with 1777 protein-coding and 58 rRNA-coding genes. Genome sequence analysis revealed absence of genes encoding for: components of the PTS systems, enzymes of the TCA cycle, glyoxylate shunt and gluconeogensis. Genomic data revealed that A. schaalii is able to oxidize carbohydrates via glycolysis, the nonoxidative pentose phosphate and the Entner-Doudoroff pathways. Besides, the genome harbors genes encoding for enzymes involved in the conversion of pyruvate to lactate, acetate and ethanol, which are found to be the end products of carbohydrate fermentation. The genome contained the gene encoding Type I fatty acid synthase required for de novo FAS biosynthesis. The plsY and plsX genes encoding the acyltransferases necessary for phosphatidic acid biosynthesis were absent from the genome. The genome harbors genes encoding enzymes responsible for isoprene biosynthesis via the mevalonate (MVA) pathway. Genes encoding enzymes that confer resistance to reactive oxygen species (ROS) were identified. In addition, A. schaalii harbors genes that protect the genome against viral infections. These include restriction-modification (RM) systems, type II toxin-antitoxin (TA), CRISPR-Cas and abortive infection system. A. schaalii genome also encodes several virulence factors that contribute to adhesion and internalization of this pathogen such as the tad genes encoding proteins required for pili assembly, the nanI gene encoding exo-alpha-sialidase, genes encoding heat shock proteins and genes encoding type VII secretion system. These features are consistent with anaerobic and pathogenic lifestyles. Finally, resistance to ciprofloxacin occurs by mutation in chromosomal genes that encode the subunits of DNA-gyrase (GyrA) and topisomerase IV (ParC) enzymes, while resistant to metronidazole was due to the frxA gene, which encodes NADPH-flavin oxidoreductase.
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Affiliation(s)
- Atteyet F. Yassin
- Institut für medizinische Mikrobiologie und Immunologie der Universität Bonn, Bonn, Germany
- * E-mail:
| | - Stefan Langenberg
- Klinik und Poliklinik für Hals-Nasen-Ohrenheilkunde/Chirurgie, Bonn, Germany
| | - Marcel Huntemann
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Alicia Clum
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Manoj Pillay
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Krishnaveni Palaniappan
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Neha Varghese
- Klinik und Poliklinik für Hals-Nasen-Ohrenheilkunde/Chirurgie, Bonn, Germany
| | - Natalia Mikhailova
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Supratim Mukherjee
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - T. B. K. Reddy
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Chris Daum
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Nicole Shapiro
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
| | - Nikos C. Kyrpides
- Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, United States of America
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138
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Singhal K, Mohanty S. Comparative genomics reveals the presence of putative toxin-antitoxin system in Wolbachia genomes. Mol Genet Genomics 2017; 293:525-540. [PMID: 29214346 DOI: 10.1007/s00438-017-1402-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 12/01/2017] [Indexed: 12/19/2022]
Abstract
Multiple toxin-antitoxin (TA) systems are housed in different locations within the bacterial genome and are known to be associated with various cellular processes and stress-related adaptation. In endosymbionts, although, the TA system has scarce occurrence but studies have highlighted its presence in enhancing host-symbiont interactions. Wolbachia, an obligate endosymbiont, has recently been proposed as a biocontrol agent which may be helpful in controlling vector-borne diseases. There are reports suggesting the role of TA system in inducing cytoplasmic incompatibility in case of Wolbachia, however, the underlying mechanism is still not known. The present study, therefore, aims at exploring the diversity of TA system in four novel (sourced from India) and three reference genomes (NCBI) of Wolbachia strains. Interestingly, we found several putative toxins and antitoxins of RelEB family of Type II TA system in these Wolbachia genomes. The results show wMel genome possessed more number of putative TA loci than wRi genome. In addition, searching through the other sequenced Wolbachia genomes in NCBI, a complete absence of TA system was observed in Wolbachia-infected nematodes. The sequence-wide analysis of all the putative RelEB proteins present amongst the Wolbachia endosymbiont and within the free-living bacterial genomes reveal strain-specific similarities and conserved sequences. However, large amount of sequence diversity was observed between Wolbachia and free-living bacteria. Understanding this sequence variation may help shed light on the differences between these two forms of bacteria and could also explain their niche preferences.
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Affiliation(s)
- Kopal Singhal
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector 62, Noida, Uttar Pradesh, 201 309, India
| | - Sujata Mohanty
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector 62, Noida, Uttar Pradesh, 201 309, India.
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139
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Koonin EV. Viruses and mobile elements as drivers of evolutionary transitions. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0442. [PMID: 27431520 PMCID: PMC4958936 DOI: 10.1098/rstb.2015.0442] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2016] [Indexed: 12/22/2022] Open
Abstract
The history of life is punctuated by evolutionary transitions which engender emergence of new levels of biological organization that involves selection acting at increasingly complex ensembles of biological entities. Major evolutionary transitions include the origin of prokaryotic and then eukaryotic cells, multicellular organisms and eusocial animals. All or nearly all cellular life forms are hosts to diverse selfish genetic elements with various levels of autonomy including plasmids, transposons and viruses. I present evidence that, at least up to and including the origin of multicellularity, evolutionary transitions are driven by the coevolution of hosts with these genetic parasites along with sharing of ‘public goods’. Selfish elements drive evolutionary transitions at two distinct levels. First, mathematical modelling of evolutionary processes, such as evolution of primitive replicator populations or unicellular organisms, indicates that only increasing organizational complexity, e.g. emergence of multicellular aggregates, can prevent the collapse of the host–parasite system under the pressure of parasites. Second, comparative genomic analysis reveals numerous cases of recruitment of genes with essential functions in cellular life forms, including those that enable evolutionary transitions. This article is part of the themed issue ‘The major synthetic evolutionary transitions’.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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140
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Harms A, Liesch M, Körner J, Québatte M, Engel P, Dehio C. A bacterial toxin-antitoxin module is the origin of inter-bacterial and inter-kingdom effectors of Bartonella. PLoS Genet 2017; 13:e1007077. [PMID: 29073136 PMCID: PMC5675462 DOI: 10.1371/journal.pgen.1007077] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 11/07/2017] [Accepted: 10/16/2017] [Indexed: 12/22/2022] Open
Abstract
Host-targeting type IV secretion systems (T4SS) evolved from conjugative T4SS machineries that mediate interbacterial plasmid transfer. However, the origins of effectors secreted by these virulence devices have remained largely elusive. Previous work showed that some effectors exhibit homology to toxins of bacterial toxin-antitoxin modules, but the evolutionary trajectories underlying these ties had not been resolved. We previously reported that FicT toxins of FicTA toxin-antitoxin modules disrupt cellular DNA topology via their enzymatic FIC (filamentation induced by cAMP) domain. Intriguingly, the FIC domain of the FicT toxin VbhT of Bartonella schoenbuchensis is fused to a type IV secretion signal–the BID (Bep intracellular delivery) domain—similar to the Bartonella effector proteins (Beps) that are secreted into eukaryotic host cells via the host-targeting VirB T4SS. In this study, we show that the VbhT toxin is an interbacterial effector protein secreted via the conjugative Vbh T4SS that is closely related to the VirB T4SS and encoded by plasmid pVbh of B. schoenbuchensis. We therefore propose that the Vbh T4SS together with its effector VbhT represent an evolutionary missing link on a path that leads from a regular conjugation system and FicTA toxin-antitoxin modules to the VirB T4SS and the Beps. Intriguingly, phylogenetic analyses revealed that the fusion of FIC and BID domains has probably occurred independently in VbhT and the common ancestor of the Beps, suggesting parallel evolutionary paths. Moreover, several other examples of TA module toxins that are bona fide substrates of conjugative T4SS indicate that their recruitment as interbacterial effectors is prevalent and serves yet unknown biological functions in the context of bacterial conjugation. We propose that the adaptation for interbacterial transfer favors the exaptation of FicT and other TA module toxins as inter-kingdom effectors and may thus constitute an important stepping stone in the evolution of host-targeted effector proteins. Many bacterial pathogens use secretion systems to translocate effector proteins into host cells where they manipulate cell functions in favor of the pathogen. It is well-known that these secretion systems evolved from ancestors with functions in genuine bacterial contexts, but the origins of their secreted effectors have largely remained elusive. In this article we studied the evolutionary history of a host-targeting effector secretion system of the mammalian pathogen Bartonella that belongs to a group of machineries descended from secretion systems originally mediating DNA transfer between bacterial cells. Intriguingly, we found that such a DNA transfer machinery closely related to the host-targeting secretion system of Bartonella has recruited a bacterial protein involved in modulating DNA topology as an interbacterial effector protein that is translocated together with the DNA into recipient cells. The overall setup of this interbacterial effector is remarkably similar to the host-targeted effectors of Bartonella, and we propose that it represents an evolutionary missing link on the path from a genuine bacterial protein to effectors that manipulates host cell functioning. Further analyses showed that interbacterial effectors in DNA transfer may be a more common phenomenon and represent an important reservoir for the evolution of new host-targeted effectors.
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Affiliation(s)
- Alexander Harms
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Marius Liesch
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Jonas Körner
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Maxime Québatte
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Christoph Dehio
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
- * E-mail:
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141
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Identification of novel mazEF/pemIK family toxin-antitoxin loci and their distribution in the Staphylococcus genus. Sci Rep 2017; 7:13462. [PMID: 29044211 PMCID: PMC5647390 DOI: 10.1038/s41598-017-13857-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 10/02/2017] [Indexed: 11/15/2022] Open
Abstract
The versatile roles of toxin-antitoxin (TA) systems in bacterial physiology and pathogenesis have been investigated for more than three decades. Diverse TA loci in Bacteria and Archaea have been identified in genome-wide studies. The advent of massive parallel sequencing has substantially expanded the number of known bacterial genomic sequences over the last 5 years. In staphylococci, this has translated into an impressive increase from a few tens to a several thousands of available genomes, which has allowed us for the re-evalution of prior conclusions. In this study, we analysed the distribution of mazEF/pemIK family TA system operons in available staphylococcal genomes and their prevalence in mobile genetic elements. 10 novel mazEF/pemIK homologues were identified, each with a corresponding toxin that plays a potentially different and undetermined physiological role. A detailed characterisation of these TA systems would be exceptionally useful. Of particular interest are those associated with an SCCmec mobile genetic element (responsible for multidrug resistance transmission) or representing the joint horizontal transfer of TA systems and determinants of vancomycin resistance from enterococci. The involvement of TA systems in maintaining mobile genetic elements and the associations between novel mazEF/pemIK loci and those which carry drug resistance genes highlight their potential medical importance.
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142
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Sprenger H, Kienesberger S, Pertschy B, Pöltl L, Konrad B, Bhutada P, Vorkapic D, Atzmüller D, Feist F, Högenauer C, Gorkiewicz G, Zechner EL. Fic Proteins of Campylobacter fetus subsp. venerealis Form a Network of Functional Toxin-Antitoxin Systems. Front Microbiol 2017; 8:1965. [PMID: 29089929 PMCID: PMC5651007 DOI: 10.3389/fmicb.2017.01965] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 09/25/2017] [Indexed: 01/02/2023] Open
Abstract
Enzymes containing the FIC (filamentation induced by cyclic AMP) domain catalyze post-translational modifications of target proteins. In bacteria the activity of some Fic proteins resembles classical toxin–antitoxin (TA) systems. An excess of toxin over neutralizing antitoxin can enable bacteria to survive some stress conditions by slowing metabolic processes and promoting dormancy. The cell can return to normal growth when sufficient antitoxin is present to block toxin activity. Fic genes of the human and animal pathogen Campylobacter fetus are significantly associated with just one subspecies, which is specifically adapted to the urogenital tract. Here, we demonstrate that the fic genes of virulent isolate C. fetus subsp. venerealis 84-112 form multiple TA systems. Expression of the toxins in Escherichia coli caused filamentation and growth inhibition phenotypes reversible by concomitant antitoxin expression. Key active site residues involved in adenylylation by Fic proteins are conserved in Fic1, Fic3 and Fic4, but degenerated in Fic2. We show that both Fic3 and the non-canonical Fic2 disrupt assembly and function of E. coli ribosomes when expressed independently of a trans-acting antitoxin. Toxicity of the Fic proteins is controlled by different mechanisms. The first involves intramolecular regulation by an inhibitory helix typical for Fic proteins. The second is an unusual neutralization by heterologous Fic–Fic protein interactions. Moreover, a small interacting antitoxin called Fic inhibitory protein 3, which appears unrelated to known Fic antitoxins, has the novel capacity to bind and neutralize Fic toxins encoded in cis and at distant sites. These findings reveal a remarkable system of functional crosstalk occurring between Fic proteins expressed from chromosomal and extrachromosomal modules. Conservation of fic genes in other bacteria that either inhabit or establish pathology in the urogenital tract of humans and animals underscores the significance of these factors for niche-specific adaptation and virulence.
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Affiliation(s)
- Hanna Sprenger
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.,Institute of Pathology, Medical University of Graz, Graz, Austria.,Division of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
| | - Sabine Kienesberger
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.,Institute of Pathology, Medical University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Brigitte Pertschy
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Lisa Pöltl
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Bettina Konrad
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Priya Bhutada
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Dina Vorkapic
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Denise Atzmüller
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Florian Feist
- Vehicle Safety Institute, Graz University of Technology, Graz, Austria
| | - Christoph Högenauer
- Division of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
| | - Gregor Gorkiewicz
- Institute of Pathology, Medical University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Ellen L Zechner
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
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143
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Hernández-Ramírez KC, Chávez-Jacobo VM, Valle-Maldonado MI, Patiño-Medina JA, Díaz-Pérez SP, Jácome-Galarza IE, Ortiz-Alvarado R, Meza-Carmen V, Ramírez-Díaz MI. Plasmid pUM505 encodes a Toxin-Antitoxin system conferring plasmid stability and increased Pseudomonas aeruginosa virulence. Microb Pathog 2017; 112:259-268. [PMID: 28970172 DOI: 10.1016/j.micpath.2017.09.060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/20/2017] [Accepted: 09/28/2017] [Indexed: 12/19/2022]
Abstract
Pseudomonas aeruginosa plasmid pUM505 possesses a pathogenicity island that contains the pumAB genes that encode products with sequence similarity to Toxin-Antitoxin (TA) modules. RT-PCR assays on the overlapping regions of the pumAB genes generated a bicistronic messenger RNA, suggesting that they form an operon. When the pumAB genes were cloned into the pJET vector, recombinant plasmid pJET-pumAB was maintained under nonselective conditions in Escherichia coli cells after six daily subcultures, whereas pJET without pumAB genes was lost. These data indicate that pumAB genes confer post-segregational plasmid stability. In addition, overexpression of the PumA protein in the E. coli BL21 strain resulted in a significant growth inhibition, while BL21 co-expressing the PumA and PumB proteins did not show growth inhibition. These results indicate that pumAB genes encode a TA system where the PumB protein counters the toxic effects of the PumA toxin. Furthermore, P. aeruginosa PAO1 transformants with the pumA gene increased Caenorhabditis elegans and mouse mortality rate and improved mouse organ invasion, effects neutralized by the PumB protein. Moreover, purified recombinant His-PumA protein decreased the viability of C. elegans, indicating that the PumA protein could acts as a toxin. These results indicate that PumA has the potential to promoter the PAO1 virulence against C. elegans and mice when is expressed in absence of PumB. This is the first description, to our knowledge, of a plasmid-encoded TA system that confers plasmid stability and encoded a toxin with the possible ability to increase the P. aeruginosa virulence.
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Affiliation(s)
- K C Hernández-Ramírez
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana, Morelia, Michoacán, Mexico
| | - V M Chávez-Jacobo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana, Morelia, Michoacán, Mexico
| | - M I Valle-Maldonado
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana, Morelia, Michoacán, Mexico
| | - J A Patiño-Medina
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana, Morelia, Michoacán, Mexico
| | - S P Díaz-Pérez
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana, Morelia, Michoacán, Mexico
| | - I E Jácome-Galarza
- Laboratorio Estatal de Salud Pública, Secretaría de Salud Michoacán, Morelia, Mexico
| | - R Ortiz-Alvarado
- Facultad de Químico-Farmacobiología, Universidad Michoacana, Morelia, Mexico
| | - V Meza-Carmen
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana, Morelia, Michoacán, Mexico
| | - M I Ramírez-Díaz
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana, Morelia, Michoacán, Mexico.
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144
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Jurėnas D, Garcia-Pino A, Van Melderen L. Novel toxins from type II toxin-antitoxin systems with acetyltransferase activity. Plasmid 2017; 93:30-35. [PMID: 28941941 DOI: 10.1016/j.plasmid.2017.08.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 08/24/2017] [Accepted: 08/28/2017] [Indexed: 12/21/2022]
Abstract
Type II toxin-antitoxin (TA) systems are widespread in bacterial and archeal genomes. These modules are very dynamic and participate in bacterial genome evolution through horizontal gene transfer. TA systems are commonly composed of a labile antitoxin and a stable toxin. Toxins appear to preferentially inhibit the protein synthesis process. Toxins use a variety of molecular mechanisms and target nearly every step of translation to achieve their inhibitory function. This review focuses on a recently identified TA family that includes acetyltransferase toxins. The AtaT and TacT toxins are the best-characterized to date in this family. AtaT and TacT both inhibit translation by acetylating the amino acid charged on tRNAs. However, the specificities of these 2 toxins are different as AtaT inhibits translation initiation by acetylation of the initiator tRNA whereas TacT acetylates elongator tRNAs. The molecular mechanisms of these toxins are discussed, as well as the functions and possible evolutionary origins of this diverse toxin family.
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Affiliation(s)
- Dukas Jurėnas
- Department of Biochemistry and Molecular Biology, Vilnius University Joint Life Sciences Center, Vilnius, Lithuania; Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Belgium
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Belgium
| | - Laurence Van Melderen
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Belgium.
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145
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Klimina KM, Poluektova EU, Danilenko VN. Bacterial toxin–antitoxin systems: Properties, functional significance, and possibility of use (Review). APPL BIOCHEM MICRO+ 2017. [DOI: 10.1134/s0003683817050076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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146
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Hadži S, Garcia-Pino A, Haesaerts S, Jurenas D, Gerdes K, Lah J, Loris R. Ribosome-dependent Vibrio cholerae mRNAse HigB2 is regulated by a β-strand sliding mechanism. Nucleic Acids Res 2017; 45:4972-4983. [PMID: 28334932 PMCID: PMC5416850 DOI: 10.1093/nar/gkx138] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 02/25/2017] [Indexed: 11/12/2022] Open
Abstract
Toxin–antitoxin (TA) modules are small operons involved in bacterial stress response and persistence. higBA operons form a family of TA modules with an inverted gene organization and a toxin belonging to the RelE/ParE superfamily. Here, we present the crystal structures of chromosomally encoded Vibrio cholerae antitoxin (VcHigA2), toxin (VcHigB2) and their complex, which show significant differences in structure and mechanisms of function compared to the higBA module from plasmid Rts1, the defining member of the family. The VcHigB2 is more closely related to Escherichia coli RelE both in terms of overall structure and the organization of its active site. VcHigB2 is neutralized by VcHigA2, a modular protein with an N-terminal intrinsically disordered toxin-neutralizing segment followed by a C-terminal helix-turn-helix dimerization and DNA binding domain. VcHigA2 binds VcHigB2 with picomolar affinity, which is mainly a consequence of entropically favorable de-solvation of a large hydrophobic binding interface and enthalpically favorable folding of the N-terminal domain into an α-helix followed by a β-strand. This interaction displaces helix α3 of VcHigB2 and at the same time induces a one-residue shift in the register of β-strand β3, thereby flipping the catalytically important Arg64 out of the active site.
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Affiliation(s)
- San Hadži
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050 Brussel, Belgium.,Molecular Recognition Unit, Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050 Brussel, Belgium.,Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Abel Garcia-Pino
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050 Brussel, Belgium.,Biologie Structurale et Biophysique, IBMM-DBM, Université Libre de Bruxelles (ULB), B-6041 Gosselies, Belgium
| | - Sarah Haesaerts
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050 Brussel, Belgium.,Molecular Recognition Unit, Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050 Brussel, Belgium
| | - Dukas Jurenas
- Biologie Structurale et Biophysique, IBMM-DBM, Université Libre de Bruxelles (ULB), B-6041 Gosselies, Belgium
| | - Kenn Gerdes
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Jurij Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050 Brussel, Belgium.,Molecular Recognition Unit, Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050 Brussel, Belgium
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147
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Shidore T, Triplett LR. Toxin-Antitoxin Systems: Implications for Plant Disease. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:161-179. [PMID: 28525308 DOI: 10.1146/annurev-phyto-080516-035559] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Toxin-antitoxin (TA) systems are gene modules that are ubiquitous in free-living prokaryotes. Diverse in structure, cellular function, and fitness roles, TA systems are defined by the presence of a toxin gene that suppresses bacterial growth and a toxin-neutralizing antitoxin gene, usually encoded in a single operon. Originally viewed as DNA maintenance modules, TA systems are now thought to function in many roles, including bacterial stress tolerance, virulence, phage defense, and biofilm formation. However, very few studies have investigated the significance of TA systems in the context of plant-microbe interactions. This review discusses the potential impact and application of TA systems in plant-associated bacteria, guided by insights gained from animal-pathogenic model systems.
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Affiliation(s)
- T Shidore
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, Connecticut 06511:
| | - L R Triplett
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, Connecticut 06511:
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148
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Talavera A, Tamman H, Ainelo A, Hadži S, Garcia-Pino A, Hõrak R, Konijnenberg A, Loris R. Production, biophysical characterization and crystallization of Pseudomonas putida GraA and its complexes with GraT and the graTA operator. Acta Crystallogr F Struct Biol Commun 2017; 73:455-462. [PMID: 28777088 PMCID: PMC5544002 DOI: 10.1107/s2053230x17009438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 06/23/2017] [Indexed: 11/10/2022] Open
Abstract
The graTA operon from Pseudomonas putida encodes a toxin-antitoxin module with an unusually moderate toxin. Here, the production, SAXS analysis and crystallization of the antitoxin GraA, the GraTA complex and the complex of GraA with a 33 bp operator fragment are reported. GraA forms a homodimer in solution and crystallizes in space group P21, with unit-cell parameters a = 66.9, b = 48.9, c = 62.7 Å, β = 92.6°. The crystals are likely to contain two GraA dimers in the asymmetric unit and diffract to 1.9 Å resolution. The GraTA complex forms a heterotetramer in solution. Crystals of the GraTA complex diffracted to 2.2 Å resolution and are most likely to contain a single heterotetrameric GraTA complex in the asymmetric unit. They belong to space group P41 or P43, with unit-cell parameters a = b = 56.0, c = 128.2 Å. The GraA-operator complex consists of a 33 bp operator region that binds two GraA dimers. It crystallizes in space group P31 or P32, with unit-cell parameters a = b = 105.6, c = 149.9 Å. These crystals diffract to 3.8 Å resolution.
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Affiliation(s)
- Ariel Talavera
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Hedvig Tamman
- Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | - Andres Ainelo
- Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | - San Hadži
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna Pot 113, SI-1000 Ljubljana, Slovenia
| | - Abel Garcia-Pino
- Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, 6041 Gosselies, Belgium
| | - Rita Hõrak
- Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | - Albert Konijnenberg
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Remy Loris
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
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149
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Ramisetty BCM, Santhosh RS. Endoribonuclease type II toxin-antitoxin systems: functional or selfish? MICROBIOLOGY-SGM 2017; 163:931-939. [PMID: 28691660 DOI: 10.1099/mic.0.000487] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Most bacterial genomes have multiple type II toxin-antitoxin systems (TAs) that encode two proteins which are referred to as a toxin and an antitoxin. Toxins inhibit a cellular process, while the interaction of the antitoxin with the toxin attenuates the toxin's activity. Endoribonuclease-encoding TAs cleave RNA in a sequence-dependent fashion, resulting in translational inhibition. To account for their prevalence and retention by bacterial genomes, TAs are credited with clinically significant phenomena, such as bacterial programmed cell death, persistence, biofilms and anti-addiction to plasmids. However, the programmed cell death and persistence hypotheses have been challenged because of conceptual, methodological and/or strain issues. In an alternative view, chromosomal TAs seem to be retained by virtue of addiction at two levels: via a poison-antidote combination (TA proteins) and via transcriptional reprogramming of the downstream core gene (due to integration). Any perturbation in the chromosomal TA operons could cause fitness loss due to polar effects on the downstream genes and hence be detrimental under natural conditions. The endoribonucleases encoding chromosomal TAs are most likely selfish DNA as they are retained by bacterial genomes, even though TAs do not confer a direct advantage via the TA proteins. TAs are likely used by various replicons as 'genetic arms' that allow the maintenance of themselves and associated genetic elements. TAs seem to be the 'selfish arms' that make the best use of the 'arms race' between bacterial genomes and plasmids.
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150
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Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements. J Bacteriol 2017; 199:JB.00245-17. [PMID: 28559295 PMCID: PMC5512222 DOI: 10.1128/jb.00245-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 05/17/2017] [Indexed: 12/29/2022] Open
Abstract
Intense biological conflicts between prokaryotic genomes and their genomic parasites have resulted in an arms race in terms of the molecular “weaponry” deployed on both sides. Using a recursive computational approach, we uncovered a remarkable class of multidomain proteins with 2 to 15 domains in the same polypeptide deployed by viruses and plasmids in such conflicts. Domain architectures and genomic contexts indicate that they are part of a widespread conflict strategy involving proteins injected into the host cell along with parasite DNA during the earliest phase of infection. Their unique feature is the combination of domains with highly disparate biochemical activities in the same polypeptide; accordingly, we term them polyvalent proteins. Of the 131 domains in polyvalent proteins, a large fraction are enzymatic domains predicted to modify proteins, target nucleic acids, alter nucleotide signaling/metabolism, and attack peptidoglycan or cytoskeletal components. They further contain nucleic acid-binding domains, virion structural domains, and 40 novel uncharacterized domains. Analysis of their architectural network reveals both pervasive common themes and specialized strategies for conjugative elements and plasmids or (pro)phages. The themes include likely processing of multidomain polypeptides by zincin-like metallopeptidases and mechanisms to counter restriction or CRISPR/Cas systems and jump-start transcription or replication. DNA-binding domains acquired by eukaryotes from such systems have been reused in XPC/RAD4-dependent DNA repair and mitochondrial genome replication in kinetoplastids. Characterization of the novel domains discovered here, such as RNases and peptidases, are likely to aid in the development of new reagents and elucidation of the spread of antibiotic resistance. IMPORTANCE This is the first report of the widespread presence of large proteins, termed polyvalent proteins, predicted to be transmitted by genomic parasites such as conjugative elements, plasmids, and phages during the initial phase of infection along with their DNA. They are typified by the presence of multiple domains with disparate activities combined in the same protein. While some of these domains are predicted to assist the invasive element in replication, transcription, or protection of their DNA, several are likely to target various host defense systems or modify the host to favor the parasite's life cycle. Notably, DNA-binding domains from these systems have been transferred to eukaryotes, where they have been incorporated into DNA repair and mitochondrial genome replication systems.
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