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Bustamante P, Ramos-Corominas MN, Martinez-Medina M. Contribution of Toxin-Antitoxin Systems to Adherent-Invasive E. coli Pathogenesis. Microorganisms 2024; 12:1158. [PMID: 38930540 PMCID: PMC11205521 DOI: 10.3390/microorganisms12061158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 05/24/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Pathobionts have been implicated in various chronic diseases, including Crohn's disease (CD), a multifactorial chronic inflammatory condition that primarily affects the gastrointestinal tract, causing inflammation and damage to the digestive system. While the exact cause of CD remains unclear, adherent-invasive Escherichia coli (AIEC) strains have emerged as key contributors to its pathogenesis. AIEC are characterized by their ability to adhere to and invade intestinal epithelial cells and survive and replicate inside macrophages. However, the mechanisms underlying the virulence and persistence of AIEC within their host remain the subject of intensive research. Toxin-antitoxin systems (TAs) play a potential role in AIEC pathogenesis and may be therapeutic targets. These systems generally consist of two components: a toxin harmful to the cell and an antitoxin that neutralizes the toxin's effects. They contribute to bacterial survival in adverse conditions and regulate bacterial growth and behavior, affecting various cellular processes in bacterial pathogens. This review focuses on the current information available to determine the roles of TAs in the pathogenicity of AIEC. Their contribution to the AIEC stress response, biofilm formation, phage inhibition, the maintenance of mobile genetic elements, and host lifestyles is discussed.
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Affiliation(s)
- Paula Bustamante
- Molecular and Cellular Microbiology Laboratory, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago 8910060, Chile
| | - María Núria Ramos-Corominas
- Microbiology of Intestinal Diseases, Biology Department, Universitat de Girona, 17003 Girona, Spain; (M.N.R.-C.); (M.M.-M.)
| | - Margarita Martinez-Medina
- Microbiology of Intestinal Diseases, Biology Department, Universitat de Girona, 17003 Girona, Spain; (M.N.R.-C.); (M.M.-M.)
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Singh A, Lankapalli AK, Mendem SK, Semmler T, Ahmed N. Unraveling the evolutionary dynamics of toxin-antitoxin systems in diverse genetic lineages of Escherichia coli including the high-risk clonal complexes. mBio 2024; 15:e0302323. [PMID: 38117088 PMCID: PMC10790755 DOI: 10.1128/mbio.03023-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE Large-scale genomic studies of E. coli provide an invaluable opportunity to understand how genomic fine-tuning contributes to the transition of bacterial lifestyle from being commensals to mutualists or pathogens. Within this context, through machine learning-based studies, it appears that TA systems play an important role in the classification of high-risk clonal lineages and could be attributed to their epidemiological success. Due to these profound indications and assumptions, we attempted to provide unique insights into the ordered world of TA systems at the population level by investigating the diversity and evolutionary patterns of TA genes across 19 different STs of E. coli. Further in-depth analysis of ST-specific TA structures and associated genetic coordinates holds the potential to elucidate the functional implications of TA systems in bacterial cell survival and persistence, by and large.
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Affiliation(s)
- Anuradha Singh
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, Telangana State, India
| | - Aditya Kumar Lankapalli
- Department of Biology and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom
| | - Suresh Kumar Mendem
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, Telangana State, India
| | | | - Niyaz Ahmed
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, Telangana State, India
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Gosain TP, Singh M, Singh C, Thakur KG, Singh R. Disruption of MenT2 toxin impairs the growth of Mycobacterium tuberculosis in guinea pigs. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36342835 DOI: 10.1099/mic.0.001246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Toxin-antitoxin (TA) systems are abundantly present in the genomes of various bacterial pathogens. TA systems have been implicated in either plasmid maintenance or protection against phage infection, stress adaptation or disease pathogenesis. The genome of Mycobacterium tuberculosis encodes for more than 90 TA systems and 4 of these belong to the type IV subfamily (MenAT family). The toxins and antitoxins belonging to type IV TA systems share sequence homology with the AbiEii family of nucleotidyl transferases and the AbiEi family of putative transcriptional regulators, respectively. Here, we have performed experiments to understand the role of MenT2, a toxin from the type IV TA system, in mycobacterial physiology and disease pathogenesis. The ectopic expression of MenT2 using inducible vectors does not inhibit bacterial growth in liquid cultures. Bioinformatic and molecular modelling analysis suggested that the M. tuberculosis genome has an alternative start site upstream of the annotated menT2 gene. The overexpression of the reannotated MenT2 resulted in moderate growth inhibition of Mycobacterium smegmatis. We show that both menT2 and menA2 transcript levels are increased when M. tuberculosis is exposed to nitrosative stress, in vitro. When compared to the survival of the wild-type and the complemented strain, the ΔmenT2 mutant strain of M. tuberculosis was more resistant to being killed by nitrosative stress. However, the survival of both the ΔmenT2 mutant and the wild-type strain was similar in macrophages and when exposed to other stress conditions. Here, we show that MenT2 is required for the establishment of disease in guinea pigs. Gross pathology and histopathology analysis of lung tissues from guinea pigs infected with the ∆menT2 strain revealed significantly reduced tissue damage and inflammation. In summary, these results provide new insights into the role of MenT2 in mycobacterial pathogenesis.
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Affiliation(s)
- Tannu Priya Gosain
- Infection and Immunology Group, Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad Gurugram Expressway, Faridabad-121001, India
| | - Manisha Singh
- Infection and Immunology Group, Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad Gurugram Expressway, Faridabad-121001, India
| | - Charandeep Singh
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh-160036, India
| | - Krishan Gopal Thakur
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh-160036, India
| | - Ramandeep Singh
- Infection and Immunology Group, Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad Gurugram Expressway, Faridabad-121001, India
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Cellular Memory of HipA-Induced Growth Arrest: The Length of Cell Growth Arrest Becomes Shorter for Each Successive Induction. Microorganisms 2021; 9:microorganisms9122594. [PMID: 34946194 PMCID: PMC8705531 DOI: 10.3390/microorganisms9122594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/04/2021] [Accepted: 12/11/2021] [Indexed: 11/17/2022] Open
Abstract
Toxin-antitoxin (TA) systems are genetic modules found commonly in bacterial genomes. HipA is a toxin protein encoded from the hipBA TA system in the genome of Escherichia coli. Ectopic expression of hipA induces cell growth arrest. Unlike the cell growth arrest caused by other TA toxins, cells resume growth from the HipA-induced cell growth arrest phase after a defined period of time. In this article, we describe the change in the length of growth arrest while cells undergo repeated cycles of hipA induction, growth arrest and regrowth phases. In the multiple conditions tested, we observed that the length of growth arrest became successively shorter for each round of induction. We verified that this was not due to the appearance of HipA-resistant mutants. Additionally, we identified conditions, such as the growth phase of the starting culture and growth vessels, that alter the length of growth arrest. Our results showed that the length of HipA-induced growth arrest was dependent on environmental factors-in particular, the past growth environment of cells, such as a previous hipA induction. These effects lasted even after multiple rounds of cell divisions, indicating the presence of cellular "memory" that impacts cells' response to HipA-induced toxicity.
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YgfY Contributes to Stress Tolerance in Shewanella oneidensis Neither as an Antitoxin Nor as a Flavinylation Factor of Succinate Dehydrogenase. Microorganisms 2021; 9:microorganisms9112316. [PMID: 34835442 PMCID: PMC8621075 DOI: 10.3390/microorganisms9112316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/02/2021] [Accepted: 11/02/2021] [Indexed: 11/16/2022] Open
Abstract
YgfY(SdhE/CptB) is highly conserved while has controversial functions in bacteria. It works as an antitoxin and composes a type IV toxin-antitoxin system with YgfX(CptA) typically in Escherichia coli, while functions as an flavinylation factor of succinate dehydrogenase and fumarate reductase typically in Serratia sp. In this study, we report the contribution of YgfY in Shewanella oneidensis MR-1 to tolerance of low temperature and nitrite. YgfY deficiency causes several growth defects of S. oneidensis MR-1 at low temperature, while YgfX do not cause a growth defect or morphological change of S. oneidensis MR1-1 and E. coli. YgfY do not interact with FtsZ and MreB nor with YgfX examined by bacterial two-hybrid assay. YgfY effect on growth under low temperature is not attributed to succinate dehydrogenase (SDH) because a mutant without SDH grows comparably with the wild-type strain in the presence of succinate. The ygfY mutant shows impaired tolerance to nitrite. Transcription of nitrite reductase and most ribosome proteins is significantly decreased in the ygfY mutant, which is consistent with the phenotypes detected above. Effects of YgfY on growth and nitrite tolerance are closely related to the RGXXE motif in YgfY. In summary, this study demonstrates pleiotropic impacts of YgfY in S. oneidensis MR-1, and sheds a light on the physiological versatility of YgfY in bacteria.
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Srivastava A, Pati S, Kaushik H, Singh S, Garg LC. Toxin-antitoxin systems and their medical applications: current status and future perspective. Appl Microbiol Biotechnol 2021; 105:1803-1821. [PMID: 33582835 DOI: 10.1007/s00253-021-11134-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 01/13/2021] [Accepted: 01/20/2021] [Indexed: 12/11/2022]
Abstract
Almost all bacteria synthesize two types of toxins-one for its survival by regulating different cellular processes and another as a strategy to interact with host cells for pathogenesis. Usually, "bacterial toxins" are contemplated as virulence factors that harm the host organism. However, toxins produced by bacteria, as a survival strategy against the host, also hamper its cellular processes. To overcome this, the bacteria have evolved with the production of a molecule, referred to as antitoxin, to negate the deleterious effect of the toxin against itself. The toxin and antitoxins are encoded by a two-component toxin-antitoxin (TA) system. The antitoxin, a protein or RNA, sequesters the toxins of the TA system for neutralization within the bacterial cell. In this review, we have described different TA systems of bacteria and their potential medical and biotechnological applications. It is of interest to note that while bacterial toxin-antitoxin systems have been well studied, the TA system in unicellular eukaryotes, though predicted by the investigators, have never been paid the desired attention. In the present review, we have also touched upon the TA system of eukaryotes identified to date. KEY POINTS: Bacterial toxins harm the host and also affect the bacterial cellular processes. The antitoxin produced by bacteria protect it from the toxin's harmful effects. The toxin-antitoxin systems can be targeted for various medical applications.
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Affiliation(s)
- Akriti Srivastava
- Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, Greater Noida, Uttar Pradesh, 201314, India
| | - Soumya Pati
- Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, Greater Noida, Uttar Pradesh, 201314, India
| | - Himani Kaushik
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, 110067, India
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Lalit C Garg
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, 110067, India.
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Antitoxin autoregulation of M. tuberculosis toxin-antitoxin expression through negative cooperativity arising from multiple inverted repeat sequences. Biochem J 2020; 477:2401-2419. [PMID: 32519742 PMCID: PMC7319586 DOI: 10.1042/bcj20200368] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/06/2020] [Accepted: 06/10/2020] [Indexed: 12/20/2022]
Abstract
Toxin-antitoxin systems play key roles in bacterial adaptation, including protection from antibiotic assault and infection by bacteriophages. The type IV toxin-antitoxin system AbiE encodes a DUF1814 nucleotidyltransferase-like toxin, and a two-domain antitoxin. In Streptococcus agalactiae, the antitoxin AbiEi negatively autoregulates abiE expression through positively co-operative binding to inverted repeats within the promoter. The human pathogen Mycobacterium tuberculosis encodes four DUF1814 putative toxins, two of which have antitoxins homologous to AbiEi. One such M. tuberculosis antitoxin, named Rv2827c, is required for growth and whilst the structure has previously been solved, the mode of regulation is unknown. To complete the gaps in our understanding, we first solved the structure of S. agalactiae AbiEi to 1.83 Å resolution for comparison with M. tuberculosis Rv2827c. AbiEi contains an N-terminal DNA binding domain and C-terminal antitoxicity domain, with bilateral faces of opposing charge. The overall AbiEi fold is similar to Rv2827c, though smaller, and with a 65° difference in C-terminal domain orientation. We further demonstrate that, like AbiEi, Rv2827c can autoregulate toxin-antitoxin operon expression. In contrast with AbiEi, the Prv2827c promoter contains two sets of inverted repeats, which bind Rv2827c with differing affinities depending on the sequence consensus. Surprisingly, Rv2827c bound with negative co-operativity to the full Prv2827c promoter, demonstrating an unexpectedly complex form of transcriptional regulation.
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ElBanna SA, Moneib NA, Aziz RK, Samir R. Genomics-guided identification of a conserved CptBA-like toxin-antitoxin system in Acinetobacter baumannii. J Adv Res 2020; 30:159-170. [PMID: 34026293 PMCID: PMC8132199 DOI: 10.1016/j.jare.2020.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 01/07/2023] Open
Abstract
Introduction Toxin-antitoxin (TA) systems are widespread among bacteria, archaea and fungi. They are classified into six types (I-VI) and have recently been proposed as novel drug targets. Objectives This study aimed to screen the pathogen Acinetobacter baumannii, known for its alarming antimicrobial resistance, for TA systems and identified a CptBA-like type IV TA, one of the least characterized systems. Methods In silico methods included secondary structure prediction, comparative genomics, multiple sequence alignment, and phylogenetic analysis, while in vitro strategies included plasmid engineering and expression of the TA system in Escherichia coli BL21, growth measurement, and transcription analysis with quantitative reverse-transcription polymerase chain reaction. Results Comparative genomics demonstrated the distribution of CptBA-like systems among Gram-negative bacteria, while phylogenetic analysis delineated two major groups, in each of which Acinetobacter spp. proteins clustered together. Sequence alignment indicated the conservation of cptA and cptB in 4,732 strains of A. baumannii in the same syntenic order. Using A. baumannii recombinant cptA and cptB, cloned under different promoters, confirmed their TA nature, as cptB expression was able to reverse growth inhibition by CptA in a dose-time dependent manner. Furthermore, transcriptional analysis of cptBA in clinical and standard A. baumannii strains demonstrated the downregulation of this system under oxidative and antibiotic stress. Conclusion Combining in silico and in vitro studies confirmed the predicted TA nature of a cptBA-like system in A. baumannii . Transcriptional analysis suggests a possible role of cptBA in response to antibiotics and stress factors in A. baumannii, making it a promising drug target.
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Affiliation(s)
- Shahira A ElBanna
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, 11562 Cairo, Egypt
| | - Nayera A Moneib
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, 11562 Cairo, Egypt
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, 11562 Cairo, Egypt.,The Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt
| | - Reham Samir
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, 11562 Cairo, Egypt.,The Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt
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AimB Is a Small Protein Regulator of Cell Size and MreB Assembly. Biophys J 2020; 119:593-604. [PMID: 32416080 DOI: 10.1016/j.bpj.2020.04.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/17/2020] [Accepted: 04/27/2020] [Indexed: 12/27/2022] Open
Abstract
The MreB actin-like cytoskeleton assembles into dynamic polymers that coordinate cell shape in many bacteria. In contrast to most other cytoskeleton systems, few MreB-interacting proteins have been well characterized. Here, we identify a small protein from Caulobacter crescentus, an assembly inhibitor of MreB (AimB). AimB overexpression mimics inhibition of MreB polymerization, leading to increased cell width and MreB delocalization. Furthermore, aimB appears to be essential, and its depletion results in decreased cell width and increased resistance to A22, a small-molecule inhibitor of MreB assembly. Molecular dynamics simulations suggest that AimB binds MreB at its monomer-monomer protofilament interaction cleft and that this interaction is favored for C. crescentus MreB over Escherichia coli MreB because of a closer match in the degree of opening with AimB size, suggesting coevolution of AimB with MreB conformational dynamics in C. crescentus. We support this model through functional analysis of point mutants in both AimB and MreB, photo-cross-linking studies with site-specific unnatural amino acids, and species-specific activity of AimB. Together, our findings are consistent with AimB promoting MreB dynamics by inhibiting monomer-monomer assembly interactions, representing a new mechanism for regulating actin-like polymers and the first identification of a non-toxin MreB assembly inhibitor. Because AimB has only 104 amino acids and small proteins are often poorly characterized, our work suggests the possibility of more bacterial cytoskeletal regulators to be found in this class. Thus, like FtsZ and eukaryotic actin, MreB may have a rich repertoire of regulators to tune its precise assembly and dynamics.
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Evaluating the Potential for Cross-Interactions of Antitoxins in Type II TA Systems. Toxins (Basel) 2020; 12:toxins12060422. [PMID: 32604745 PMCID: PMC7354431 DOI: 10.3390/toxins12060422] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 01/21/2023] Open
Abstract
The diversity of Type-II toxin–antitoxin (TA) systems in bacterial genomes requires tightly controlled interaction specificity to ensure protection of the cell, and potentially to limit cross-talk between toxin–antitoxin pairs of the same family of TA systems. Further, there is a redundant use of toxin folds for different cellular targets and complexation with different classes of antitoxins, increasing the apparent requirement for the insulation of interactions. The presence of Type II TA systems has remained enigmatic with respect to potential benefits imparted to the host cells. In some cases, they play clear roles in survival associated with unfavorable growth conditions. More generally, they can also serve as a “cure” against acquisition of highly similar TA systems such as those found on plasmids or invading genetic elements that frequently carry virulence and resistance genes. The latter model is predicated on the ability of these highly specific cognate antitoxin–toxin interactions to form cross-reactions between chromosomal antitoxins and invading toxins. This review summarizes advances in the Type II TA system models with an emphasis on antitoxin cross-reactivity, including with invading genetic elements and cases where toxin proteins share a common fold yet interact with different families of antitoxins.
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MazF Endoribonucleolytic Toxin Conserved in Nitrospira Specifically Cleaves the AACU, AACG, and AAUU Motifs. Toxins (Basel) 2020; 12:toxins12050287. [PMID: 32365819 PMCID: PMC7291052 DOI: 10.3390/toxins12050287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/28/2020] [Accepted: 04/28/2020] [Indexed: 11/27/2022] Open
Abstract
MazF is an endoribonucleolytic toxin that cleaves intracellular RNAs in sequence-specific manners. It is liberated in bacterial cells in response to environmental changes and is suggested to contribute to bacterial survival by inducing translational regulation. Thus, determining the cleavage specificity provides insights into the physiological functions of MazF orthologues. Nitrospira, detected in a wide range of environments, is thought to have evolved the ability to cope with their surroundings. To investigate the molecular mechanism of its environmental adaption, a MazF module from Nitrospira strain ND1, which was isolated from the activated sludge of a wastewater treatment plant, is examined in this study. By combining a massive parallel sequencing method and fluorometric assay, we detected that this functional RNA-cleaving toxin specifically recognizes the AACU, AACG, and AAUU motifs. Additionally, statistical analysis suggested that this enzyme regulates various specific functions in order to resist environmental stresses.
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Eida AA, Bougouffa S, L’Haridon F, Alam I, Weisskopf L, Bajic VB, Saad MM, Hirt H. Genome Insights of the Plant-Growth Promoting Bacterium Cronobacter muytjensii JZ38 With Volatile-Mediated Antagonistic Activity Against Phytophthora infestans. Front Microbiol 2020; 11:369. [PMID: 32218777 PMCID: PMC7078163 DOI: 10.3389/fmicb.2020.00369] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 02/19/2020] [Indexed: 12/12/2022] Open
Abstract
Salinity stress is a major challenge to agricultural productivity and global food security in light of a dramatic increase of human population and climate change. Plant growth promoting bacteria can be used as an additional solution to traditional crop breeding and genetic engineering. In the present work, the induction of plant salt tolerance by the desert plant endophyte Cronobacter sp. JZ38 was examined on the model plant Arabidopsis thaliana using different inoculation methods. JZ38 promoted plant growth under salinity stress via contact and emission of volatile compounds. Based on the 16S rRNA and whole genome phylogenetic analysis, fatty acid analysis and phenotypic identification, JZ38 was identified as Cronobacter muytjensii and clearly separated and differentiated from the pathogenic C. sakazakii. Full genome sequencing showed that JZ38 is composed of one chromosome and two plasmids. Bioinformatic analysis and bioassays revealed that JZ38 can grow under a range of abiotic stresses. JZ38 interaction with plants is correlated with an extensive set of genes involved in chemotaxis and motility. The presence of genes for plant nutrient acquisition and phytohormone production could explain the ability of JZ38 to colonize plants and sustain plant growth under stress conditions. Gas chromatography-mass spectrometry analysis of volatiles produced by JZ38 revealed the emission of indole and different sulfur volatile compounds that may play a role in contactless plant growth promotion and antagonistic activity against pathogenic microbes. Indeed, JZ38 was able to inhibit the growth of two strains of the phytopathogenic oomycete Phytophthora infestans via volatile emission. Genetic, transcriptomic and metabolomics analyses, combined with more in vitro assays will provide a better understanding the highlighted genes' involvement in JZ38's functional potential and its interaction with plants. Nevertheless, these results provide insight into the bioactivity of C. muytjensii JZ38 as a multi-stress tolerance promoting bacterium with a potential use in agriculture.
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Affiliation(s)
- Abdul Aziz Eida
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Salim Bougouffa
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- BioScience Core Lab, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - Intikhab Alam
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Laure Weisskopf
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Vladimir B. Bajic
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Maged M. Saad
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Heribert Hirt
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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Jena P, Bhattacharya M, Bhattacharjee G, Satpati B, Mukherjee P, Senapati D, Srinivasan R. Bimetallic gold-silver nanoparticles mediate bacterial killing by disrupting the actin cytoskeleton MreB. NANOSCALE 2020; 12:3731-3749. [PMID: 31993609 DOI: 10.1039/c9nr10700b] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The actin cytoskeleton is required for the maintenance of the cell shape and viability of bacteria. It remains unknown to which extent nanoparticles (NPs) can orchestrate the mechanical instability by disrupting the cytoskeletal network in bacterial cells. Our work demonstrates that Au-Ag NPs disrupt the bacterial actin cytoskeleton specifically, fluidize the inner membrane and lead to killing of bacterial cells. In this study, we have tried to emphasize on the key parameters important for NP-cell interactions and found that the shape, specific elemental surface localization and enhanced electrostatic interaction developed due to the acquired partial positive charge by silver atoms in the aggregated NPs are some of the major factors contributing towards better NP interactions and subsequent cell death. In vivo studies in bacterial cells showed that the NPs exerted a mild perturbation of the membrane potential. However, its most striking effect was on the actin cytoskeleton MreB resulting in morphological changes in the bacterial cell shape from rods to predominantly spheres. Exposure to NPs resulted in the delocalization of MreB patches from the membrane but not the tubulin homologue FtsZ. Concomitant with the redistribution of MreB localization, a dramatic increase of membrane fluid regions was observed. Our studies reveal for the first time that Au-Ag NPs can mediate bacterial killing and disrupt the actin cytoskeletal functions in bacteria.
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Affiliation(s)
- Prajna Jena
- Centre for Research in Nanoscience and Nanotechnology, University of Calcutta, JD-2, sector -3, Salt Lake City, Kolkata, India.
| | - Maireyee Bhattacharya
- Chemical Sciences Division, Saha Institute of Nuclear Physics, HBNI, 1/AF, Bidhannagar, Kolkata-700064, India.
| | - Gourab Bhattacharjee
- Surface Physics and Materials Science Division, Saha Institute of Nuclear Physics, HBNI, 1/AF, Bidhannagar, Kolkata-700064, India
| | - Biswarup Satpati
- Surface Physics and Materials Science Division, Saha Institute of Nuclear Physics, HBNI, 1/AF, Bidhannagar, Kolkata-700064, India
| | - Prasun Mukherjee
- Centre for Research in Nanoscience and Nanotechnology, University of Calcutta, JD-2, sector -3, Salt Lake City, Kolkata, India.
| | - Dulal Senapati
- Chemical Sciences Division, Saha Institute of Nuclear Physics, HBNI, 1/AF, Bidhannagar, Kolkata-700064, India.
| | - Ramanujam Srinivasan
- School of Biological Sciences, National Institute of Science Education and Research (NISER), HBNI, Bhubaneswar, Odisha 752050, India.
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14
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Awuni E. Status of Targeting MreB for the Development of Antibiotics. Front Chem 2020; 7:884. [PMID: 31998684 PMCID: PMC6965359 DOI: 10.3389/fchem.2019.00884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/06/2019] [Indexed: 12/15/2022] Open
Abstract
Although many prospective antibiotic targets are known, bacterial infections and resistance to antibiotics remain a threat to public health partly because the druggable potentials of most of these targets have yet to be fully tapped for the development of a new generation of therapeutics. The prokaryotic actin homolog MreB is one of the important antibiotic targets that are yet to be significantly exploited. MreB is a bacterial cytoskeleton protein that has been widely studied and is associated with the determination of rod shape as well as important subcellular processes including cell division, chromosome segregation, cell wall morphogenesis, and cell polarity. Notwithstanding that MreB is vital and conserved in most rod-shaped bacteria, no approved antibiotics targeting it are presently available. Here, the status of targeting MreB for the development of antibiotics is concisely summarized. Expressly, the known therapeutic targets and inhibitors of MreB are presented, and the way forward in the search for a new generation of potent inhibitors of MreB briefly discussed.
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Affiliation(s)
- Elvis Awuni
- Department of Biochemistry, School of Biological Sciences, CANS, University of Cape Coast, Cape Coast, Ghana
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15
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Genome-Wide Screening for Identification of Novel Toxin-Antitoxin Systems in Staphylococcus aureus. Appl Environ Microbiol 2019; 85:AEM.00915-19. [PMID: 31375497 DOI: 10.1128/aem.00915-19] [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: 04/19/2019] [Accepted: 07/11/2019] [Indexed: 01/24/2023] Open
Abstract
Toxin-antitoxin (TA) systems consist of toxin-inhibiting diverse cellular functions (e.g., DNA replication, transcription, and translation) and a noncoding RNA or protein antitoxin. TA systems are associated with various cellular events, such as stress responses, programmed cell death, and bacterial pathogenicity. Recent advances in genome sequencing and bioinformatics research have demonstrated that most bacteria harbor various kinds of TA modules on their chromosomes; however, there is little understanding of chromosomally encoded TA systems in the Gram-positive pathogen Staphylococcus aureus Here, we report on newly discovered S. aureus TA systems, each of which is composed of two proteins. Manual search and gene operon prediction analysis identified eight 2-gene operons as potential candidates for TA systems. Subsequently, using an Escherichia coli host killing and rescue assay, we demonstrated that four of the eight candidates worked as TA systems, designated tsaAT, tsbAT, tscAT, and tsdAT Moreover, the TsaT, TsbT, TscT, and TsdT toxins inhibited S. aureus growth, and the toxicity of TsbT was neutralized by coexpressing the tsbA gene in the native host, S. aureus Further, the bioinformatics analysis of the gene clusters revealed that TsaAT, TsbAT, TscAT, and TsdAT did not exhibit sequence similarity to known bacterial TA systems, and their homologues were present only within Staphylococcus species and not among any other bacteria. Our results further advance not only the understanding of S. aureus TA systems but also the study of unannotated TA systems in various bacterial species.IMPORTANCE Recent advances in genome sequencing and bioinformatics research have demonstrated that most pathogenic bacteria harbor a large number of chromosomally encoded toxin-antitoxin (TA) modules. However, little is known about the TA systems in S. aureus Here, we newly identified four S. aureus TA systems using a combination of manual base-by-base screening and functional analysis in E. coli Moreover, all toxins of the identified TA systems caused growth inhibition in the native host S. aureus Although the newly identified TA systems did not exhibit sequence similarity with known bacterial TA systems, their orthologues were conserved only among other Staphylococcus species, indicating their uniqueness to staphylococci. Our approach opens the possibility for studying unannotated TA systems in various bacterial species.
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16
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Paul P, Sahu BR, Suar M. Plausible role of bacterial toxin-antitoxin system in persister cell formation and elimination. Mol Oral Microbiol 2019; 34:97-107. [PMID: 30891951 DOI: 10.1111/omi.12258] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/22/2019] [Accepted: 03/16/2019] [Indexed: 12/11/2022]
Abstract
Although, a large proportion of pathogenic bacteria gets eliminated from hosts after antibiotic treatment, a fraction of population confronts against such effects and undergoes growth arrest to form persisters. Persistence in bacteria is a dormant physiological state where cells escape the effects of antimicrobials as well as other host immune defences without any genetic mutations. The state of dormancy is achieved through various complex phenomena and it is known that a gene pair named as toxin-antitoxin (TA) acts as a key player of persister cell formation where the toxin is activated either stochastically or after an environmental insult, thereby silencing the physiological processes. However, the controversial role of TA modules in persister cell formation has also been documented with reasonable clarity. Persisters may revert back from state of quiescence and regrow when conditions become favourable for their propagation. Therefore, the elimination of dormant bacteria is crucial, and currently, research interest is highly focussed on developing several antipersister strategies that may kill persister bacteria by targeting different molecules. It is worth examining these targets to develop appropriate therapeutic interventions against bacterial infections and it is believed that earmarking TA system can be a novel approach for resuscitation of persisters. In this review, we discussed the role of TA modules in mediating persistence with highlighting on the debatable issues regarding contribution of these modules in dormant bacteria formation. Furthermore, we discussed if these modules in bacteria can be targeted for successful elimination of dormant persister cells.
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Affiliation(s)
- Prajita Paul
- School of Biotechnology, KIIT (Deemed to be University), Bhubaneswar, India
| | - Bikash R Sahu
- School of Biotechnology, KIIT (Deemed to be University), Bhubaneswar, India
| | - Mrutyunjay Suar
- School of Biotechnology, KIIT (Deemed to be University), Bhubaneswar, India
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17
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Chatterjee R, Shreenivas MM, Sunil R, Chakravortty D. Enteropathogens: Tuning Their Gene Expression for Hassle-Free Survival. Front Microbiol 2019; 9:3303. [PMID: 30687282 PMCID: PMC6338047 DOI: 10.3389/fmicb.2018.03303] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 12/19/2018] [Indexed: 12/27/2022] Open
Abstract
Enteropathogenic bacteria have been the cause of the majority of foodborne illnesses. Much of the research has been focused on elucidating the mechanisms by which these pathogens evade the host immune system. One of the ways in which they achieve the successful establishment of a niche in the gut microenvironment and survive is by a chain of elegantly regulated gene expression patterns. Studies have shown that this process is very elaborate and is also regulated by several factors. Pathogens like, enteropathogenic Escherichia coli (EPEC), Salmonella Typhimurium, Shigellaflexneri, Yersinia sp. have been seen to employ various regulated gene expression strategies. These include toxin-antitoxin systems, quorum sensing systems, expression controlled by nucleoid-associated proteins (NAPs), several regulons and operons specific to these pathogens. In the following review, we have tried to discuss the common gene regulatory systems of enteropathogenic bacteria as well as pathogen-specific regulatory mechanisms.
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Affiliation(s)
- Ritika Chatterjee
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India.,Division of Biological Sciences, Indian Institute of Science, Bengaluru, India
| | - Meghanashree M Shreenivas
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India.,Division of Biological Sciences, Indian Institute of Science, Bengaluru, India.,Undergraduate Studies, Indian Institute of Science, Bengaluru, India
| | - Rohith Sunil
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India.,Division of Biological Sciences, Indian Institute of Science, Bengaluru, India.,Undergraduate Studies, Indian Institute of Science, Bengaluru, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India.,Division of Biological Sciences, Indian Institute of Science, Bengaluru, India.,Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India
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18
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Miyamoto T, Yokota A, Ota Y, Tsuruga M, Aoi R, Tsuneda S, Noda N. Nitrosomonas europaea MazF Specifically Recognises the UGG Motif and Promotes Selective RNA Degradation. Front Microbiol 2018; 9:2386. [PMID: 30349517 PMCID: PMC6186784 DOI: 10.3389/fmicb.2018.02386] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/18/2018] [Indexed: 01/08/2023] Open
Abstract
Toxin-antitoxin (TA) systems are implicated in prokaryotic stress adaptation. Previously, bioinformatics analysis predicted that such systems are abundant in some slowly growing chemolithotrophs; e.g., Nitrosomonas europaea. Nevertheless, the molecular functions of these stress-response modules remain largely unclear, limiting insight regarding their physiological roles. Herein, we show that one of the putative MazF family members, encoded at the ALW85_RS04820 locus, constitutes a functional toxin that engenders a TA pair with its cognate MazE antitoxin. The coordinate application of a specialised RNA-Seq and a fluorescence quenching technique clarified that a unique triplet, UGG, serves as the determinant for MazF cleavage. Notably, statistical analysis predicted that two transcripts, which are unique in the autotroph, comprise the prime targets of the MazF endoribonuclease: hydroxylamine dehydrogenase (hao), which is essential for ammonia oxidation, and a large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase (rbcL), which plays an important role in carbon assimilation. Given that N. europaea obtains energy and reductants via ammonia oxidation and the carbon for its growth from carbon dioxide, the chemolithotroph might use the MazF endoribonuclease to modulate its translation profile and subsequent biochemical reactions.
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Affiliation(s)
- Tatsuki Miyamoto
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Akiko Yokota
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Yuri Ota
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Masako Tsuruga
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Rie Aoi
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Naohiro Noda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
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19
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Bratton BP, Shaevitz JW, Gitai Z, Morgenstein RM. MreB polymers and curvature localization are enhanced by RodZ and predict E. coli's cylindrical uniformity. Nat Commun 2018; 9:2797. [PMID: 30022070 PMCID: PMC6052060 DOI: 10.1038/s41467-018-05186-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 06/20/2018] [Indexed: 12/31/2022] Open
Abstract
The actin-like protein MreB has been proposed to coordinate the synthesis of the cell wall to determine cell shape in bacteria. MreB is preferentially localized to areas of the cell with specific curved geometries, avoiding the cell poles. It remains unclear whether MreB’s curvature preference is regulated by additional factors, and which specific features of MreB promote specific features of rod shape growth. Here, we show that the transmembrane protein RodZ modulates MreB curvature preference and polymer number in E. coli, properties which are regulated independently. An unbiased machine learning analysis shows that MreB polymer number, the total length of MreB polymers, and MreB curvature preference are key correlates of cylindrical uniformity, the variability in radius within a single cell. Changes in the values of these parameters are highly predictive of the resulting changes in cell shape (r2 = 0.93). Our data thus suggest RodZ promotes the assembly of geometrically-localized MreB polymers that lead to the growth of uniform cylinders. The actin-like protein MreB coordinates the synthesis of the cell wall, which determines cell shape in bacteria. Here, Bratton et al. show that the transmembrane protein RodZ modulates MreB polymer number and curvature preference, contributing to the cylindrical uniform shape of E. coli cells.
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Affiliation(s)
- Benjamin P Bratton
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.,Department of Physics and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Joshua W Shaevitz
- Department of Physics and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
| | - Randy M Morgenstein
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA. .,Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA.
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20
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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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21
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GhoT of the GhoT/GhoS toxin/antitoxin system damages lipid membranes by forming transient pores. Biochem Biophys Res Commun 2018; 497:467-472. [PMID: 29470981 DOI: 10.1016/j.bbrc.2018.01.067] [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: 01/04/2018] [Accepted: 01/10/2018] [Indexed: 11/20/2022]
Abstract
GhoT is a bacterial toxin of the type V toxin/antitoxin system that allows Escherichia coli to reduce its metabolism in response to oxidative and bile stress. GhoT functions by increasing membrane permeability and reducing both ATP levels and the proton motive force. However, how GhoT damages the inner membrane has not been elucidated. Here we investigated how GhoT damages membranes by studying its interaction with lipid bilayers and determined that GhoT does not cause macroscopic disruption of the lipid bilayer to increase membrane permeability to the dye carboxyfluorescein. Using circular dichroism, we found that GhoT forms an alpha helical structure in lipid bilayers that agrees with the structure predicted by the I-TASSER protein structure prediction program. The structure generated using I-TASSER was used to conduct coarse-grained molecular dynamics simulations, which indicate that GhoT damages the cell membrane, as a multimer, by forming transient transmembrane pores.
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22
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Li Z, Song Q, Wang Y, Xiao X, Xu J. Identification of a functional toxin-antitoxin system located in the genomic island PYG1 of piezophilic hyperthermophilic archaeon Pyrococcus yayanosii. Extremophiles 2018; 22:347-357. [PMID: 29335804 DOI: 10.1007/s00792-018-1002-2] [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] [Received: 09/21/2017] [Accepted: 12/23/2017] [Indexed: 12/01/2022]
Abstract
Toxin-antitoxin (TA) system is bacterial or archaeal genetic module consisting of toxin and antitoxin gene that be organized as a bicistronic operon. TA system could elicit programmed cell death, which is supposed to play important roles for the survival of prokaryotic population under various physiological stress conditions. The phage abortive infection system (AbiE family) belongs to bacterial type IV TA system. However, no archaeal AbiE family TA system has been reported so far. In this study, a putative AbiE TA system (PygAT), which is located in a genomic island PYG1 in the chromosome of Pyrococcus yayanosii CH1, was identified and characterized. In Escherichia coli, overexpression of the toxin gene pygT inhibited its growth while the toxic effect can be suppressed by introducing the antitoxin gene pygA in the same cell. PygAT also enhances the stability of shuttle plasmids with archaeal plasmid replication protein Rep75 in E. coli. In P. yayanosii, disruption of antitoxin gene pygA cause a significantly growth delayed under high hydrostatic pressure (HHP). The antitoxin protein PygA can specifically bind to the PygAT promoter region and regulate the transcription of pygT gene in vivo. These results show that PygAT is a functional TA system in P. yayanosii, and also may play a role in the adaptation to HHP environment.
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Affiliation(s)
- Zhen Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Institute of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Qinghao Song
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Institute of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Institute of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Institute of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China. .,Institute of Oceanography, Shanghai Jiao Tong University, Shanghai, China.
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23
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CbtA toxin of Escherichia coli inhibits cell division and cell elongation via direct and independent interactions with FtsZ and MreB. PLoS Genet 2017; 13:e1007007. [PMID: 28931012 PMCID: PMC5624674 DOI: 10.1371/journal.pgen.1007007] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 10/02/2017] [Accepted: 09/06/2017] [Indexed: 12/12/2022] Open
Abstract
The toxin components of toxin-antitoxin modules, found in bacterial plasmids, phages, and chromosomes, typically target a single macromolecule to interfere with an essential cellular process. An apparent exception is the chromosomally encoded toxin component of the E. coli CbtA/CbeA toxin-antitoxin module, which can inhibit both cell division and cell elongation. A small protein of only 124 amino acids, CbtA, was previously proposed to interact with both FtsZ, a tubulin homolog that is essential for cell division, and MreB, an actin homolog that is essential for cell elongation. However, whether or not the toxic effects of CbtA are due to direct interactions with these predicted targets is not known. Here, we genetically separate the effects of CbtA on cell elongation and cell division, showing that CbtA interacts directly and independently with FtsZ and MreB. Using complementary genetic approaches, we identify the functionally relevant target surfaces on FtsZ and MreB, revealing that in both cases, CbtA binds to surfaces involved in essential cytoskeletal filament architecture. We show further that each interaction contributes independently to CbtA-mediated toxicity and that disruption of both interactions is required to alleviate the observed toxicity. Although several other protein modulators are known to target FtsZ, the CbtA-interacting surface we identify represents a novel inhibitory target. Our findings establish CbtA as a dual function toxin that inhibits both cell division and cell elongation via direct and independent interactions with FtsZ and MreB. Bacterially encoded toxin-antitoxin systems, which consist of a small toxin protein that is co-produced with a neutralizing antitoxin, are a potential avenue for the identification of novel antibiotic targets. These toxins typically target essential cellular processes, causing growth arrest or cell death when unchecked by the antitoxin. Our study is focused on the CbtA toxin of E. coli, which was known to inhibit both bacterial cell division and also bacterial cell elongation (the process by which rod-shaped bacteria grow prior to cell division). We report that the effects of CbtA on cell division and cell elongation are genetically separable, and that they are due to direct and independent interactions with its targets FtsZ and MreB, essential cytoskeletal proteins that direct cell division and cell elongation, respectively. Our genetic analysis defines the functionally relevant target surfaces on FtsZ and MreB; in the case of FtsZ this surface represents a novel inhibitory target. As a dual-function toxin that independently targets two essential cytoskeletal elements, CbtA could guide the design of dual-function antibiotics whose ability to independently target more than one essential cellular process might impede the development of drug resistance, which is a growing public health threat.
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24
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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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25
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Abstract
Toxin-antitoxin systems are widespread in the bacterial kingdom, including in pathogenic species, where they allow rapid adaptation to changing environmental conditions through selective inhibition of key cellular processes, such as DNA replication or protein translation. Under normal growth conditions, type II toxins are inhibited through tight protein-protein interaction with a cognate antitoxin protein. This toxin-antitoxin complex associates into a higher-order macromolecular structure, typically heterotetrameric or heterooctameric, exposing two DNA binding domains on the antitoxin that allow auto-regulation of transcription by direct binding to promoter DNA. In this chapter, we review our current understanding of the structural characteristics of type II toxin-antitoxin complexes in bacterial cells, with a special emphasis on the staggering variety of higher-order architecture observed among members of the VapBC family. This structural variety is a result of poor conservation at the primary sequence level and likely to have significant and functional implications on the way toxin-antitoxin expression is regulated.
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Affiliation(s)
- Kirstine L Bendtsen
- Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100, Copenhagen, Denmark
| | - Ditlev E Brodersen
- Centre for Bacterial Stress Response and Persistence, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, 8000, Aarhus C, Denmark.
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26
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Kim Y, Choi E, Hwang J. Functional Studies of Five Toxin-Antitoxin Modules in Mycobacterium tuberculosis H37Rv. Front Microbiol 2016; 7:2071. [PMID: 28066388 PMCID: PMC5175181 DOI: 10.3389/fmicb.2016.02071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 12/07/2016] [Indexed: 11/25/2022] Open
Abstract
Toxin–antitoxin (TA) systems, which consist of an intracellular toxin and its antidote (antitoxin), are encoded by ubiquitous genetic modules in prokaryotes. Commonly, the activity of a toxin is inhibited by its antitoxin under normal growth conditions. However, antitoxins are degraded in response to environmental stress, and toxins liberated from antitoxins consequently induce cell death or growth arrest. In free-living prokaryotes, TA systems are often present in large numbers and are considered to be associated with the adaptation of pathogenic bacteria or extremophiles to various unfavorable environments by shifting cells to a slow growth rate. Genomic analysis of the human pathogen Mycobacterium tuberculosis H37Rv (Mtb) revealed the presence of a large number of TA systems. Accordingly, we investigated five uncharacterized TA systems (Rv2019-Rv2018, Rv3697c-Rv3697A, Rv3180c-Rv3181c, Rv0299-Rv0298, and Rv3749c-Rv3750c) of Mtb. Among these, the expression of the Rv2019 toxin inhibited the growth of Escherichia coli, and M. smegmatis and this growth defect was recovered by the expression of the Rv2018 antitoxin. Interestingly, Rv3180c was toxic only in M. smegmatis, whose toxicity was neutralized by Rv3181c antitoxin. In vivo and in vitro assays revealed the ribosomal RNA (rRNA) cleavage activity of the Rv2019 toxin. Moreover, mRNAs appeared to be substrates of Rv2019. Therefore, we concluded that the ribonuclease activity of the Rv2019 toxin triggers the growth defect in E. coli and that the Rv2018 antitoxin inhibits the ribonuclease activity of the Rv2019 toxin.
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Affiliation(s)
- Yoonji Kim
- Department of Microbiology, Pusan National University Busan, Republic of Korea
| | - Eunsil Choi
- Department of Microbiology, Pusan National University Busan, Republic of Korea
| | - Jihwan Hwang
- Department of Microbiology, Pusan National University Busan, Republic of Korea
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27
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Structure, Biology, and Therapeutic Application of Toxin-Antitoxin Systems in Pathogenic Bacteria. Toxins (Basel) 2016; 8:toxins8100305. [PMID: 27782085 PMCID: PMC5086665 DOI: 10.3390/toxins8100305] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/17/2016] [Accepted: 10/18/2016] [Indexed: 01/09/2023] Open
Abstract
Bacterial toxin–antitoxin (TA) systems have received increasing attention for their diverse identities, structures, and functional implications in cell cycle arrest and survival against environmental stresses such as nutrient deficiency, antibiotic treatments, and immune system attacks. In this review, we describe the biological functions and the auto-regulatory mechanisms of six different types of TA systems, among which the type II TA system has been most extensively studied. The functions of type II toxins include mRNA/tRNA cleavage, gyrase/ribosome poison, and protein phosphorylation, which can be neutralized by their cognate antitoxins. We mainly explore the similar but divergent structures of type II TA proteins from 12 important pathogenic bacteria, including various aspects of protein–protein interactions. Accumulating knowledge about the structure–function correlation of TA systems from pathogenic bacteria has facilitated a novel strategy to develop antibiotic drugs that target specific pathogens. These molecules could increase the intrinsic activity of the toxin by artificially interfering with the intermolecular network of the TA systems.
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28
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Goeders N, Chai R, Chen B, Day A, Salmond GPC. Structure, Evolution, and Functions of Bacterial Type III Toxin-Antitoxin Systems. Toxins (Basel) 2016; 8:toxins8100282. [PMID: 27690100 PMCID: PMC5086642 DOI: 10.3390/toxins8100282] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/14/2016] [Accepted: 09/19/2016] [Indexed: 01/21/2023] Open
Abstract
Toxin-antitoxin (TA) systems are small genetic modules that encode a toxin (that targets an essential cellular process) and an antitoxin that neutralises or suppresses the deleterious effect of the toxin. Based on the molecular nature of the toxin and antitoxin components, TA systems are categorised into different types. Type III TA systems, the focus of this review, are composed of a toxic endoribonuclease neutralised by a non-coding RNA antitoxin in a pseudoknotted configuration. Bioinformatic analysis shows that the Type III systems can be classified into subtypes. These TA systems were originally discovered through a phage resistance phenotype arising due to a process akin to an altruistic suicide; the phenomenon of abortive infection. Some Type III TA systems are bifunctional and can stabilise plasmids during vegetative growth and sporulation. Features particular to Type III systems are explored here, emphasising some of the characteristics of the RNA antitoxin and how these may affect the co-evolutionary relationship between toxins and cognate antitoxins in their quaternary structures. Finally, an updated analysis of the distribution and diversity of these systems are presented and discussed.
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Affiliation(s)
- Nathalie Goeders
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK.
| | - Ray Chai
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK.
| | - Bihe Chen
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK.
| | - Andrew Day
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK.
| | - George P C Salmond
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK.
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Lobato-Márquez D, Díaz-Orejas R, García-Del Portillo F. Toxin-antitoxins and bacterial virulence. FEMS Microbiol Rev 2016; 40:592-609. [PMID: 27476076 DOI: 10.1093/femsre/fuw022] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2016] [Indexed: 12/25/2022] Open
Abstract
Bacterial virulence relies on a delicate balance of signals interchanged between the invading microbe and the host. This communication has been extensively perceived as a battle involving harmful molecules produced by the pathogen and host defenses. In this review, we focus on a largely unexplored element of this dialogue, as are toxin-antitoxin (TA) systems of the pathogen. TA systems are reported to respond to stresses that are also found in the host and, as a consequence, could modulate the physiology of the intruder microbe. This view is consistent with recent studies that demonstrate a contribution of distinct TA systems to virulence since their absence alters the course of the infection. TA loci are stress response modules that, therefore, could readjust pathogen metabolism to favor the generation of slow-growing or quiescent cells 'before' host defenses irreversibly block essential pathogen activities. Some toxins of these TA modules have been proposed as potential weapons used by the pathogen to act on host targets. We discuss all these aspects based on studies that support some TA modules as important regulators in the pathogen-host interface.
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Affiliation(s)
- Damián Lobato-Márquez
- Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, 28049 Madrid, Spain Centro de Investigaciones Biológicas-CSIC (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Ramón Díaz-Orejas
- Centro de Investigaciones Biológicas-CSIC (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Francisco García-Del Portillo
- Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, 28049 Madrid, Spain
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YodL and YisK Possess Shape-Modifying Activities That Are Suppressed by Mutations in Bacillus subtilis mreB and mbl. J Bacteriol 2016; 198:2074-88. [PMID: 27215790 DOI: 10.1128/jb.00183-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/18/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Many bacteria utilize actin-like proteins to direct peptidoglycan (PG) synthesis. MreB and MreB-like proteins are thought to act as scaffolds, guiding the localization and activity of key PG-synthesizing proteins during cell elongation. Despite their critical role in viability and cell shape maintenance, very little is known about how the activity of MreB family proteins is regulated. Using a Bacillus subtilis misexpression screen, we identified two genes, yodL and yisK, that when misexpressed lead to loss of cell width control and cell lysis. Expression analysis suggested that yodL and yisK are previously uncharacterized Spo0A-regulated genes, and consistent with these observations, a ΔyodL ΔyisK mutant exhibited reduced sporulation efficiency. Suppressors resistant to YodL's killing activity occurred primarily in mreB mutants and resulted in amino acid substitutions at the interface between MreB and the highly conserved morphogenic protein RodZ, whereas suppressors resistant to YisK occurred primarily in mbl mutants and mapped to Mbl's predicted ATP-binding pocket. YodL's shape-altering activity appears to require MreB, as a ΔmreB mutant was resistant to the effects of YodL but not YisK. Similarly, YisK appears to require Mbl, as a Δmbl mutant was resistant to the cell-widening effects of YisK but not of YodL. Collectively, our results suggest that YodL and YisK likely modulate MreB and Mbl activity, possibly during the early stages of sporulation. IMPORTANCE The peptidoglycan (PG) component of the cell envelope confers structural rigidity to bacteria and protects them from osmotic pressure. MreB and MreB-like proteins are thought to act as scaffolds for PG synthesis and are essential in bacteria exhibiting nonpolar growth. Despite the critical role of MreB-like proteins, we lack mechanistic insight into how their activities are regulated. Here, we describe the discovery of two B. subtilis proteins, YodL and YisK, which modulate MreB and Mbl activities. Our data suggest that YodL specifically targets MreB, whereas YisK targets Mbl. The apparent specificities with which YodL and YisK are able to differentially target MreB and Mbl make them potentially powerful tools for probing the mechanics of cytoskeletal function in bacteria.
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31
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Abu Bakar F, Yeo CC, Harikrishna JA. Neutralization of Bacterial YoeBSpn Toxicity and Enhanced Plant Growth in Arabidopsis thaliana via Co-Expression of the Toxin-Antitoxin Genes. Int J Mol Sci 2016; 17:ijms17040321. [PMID: 27104531 PMCID: PMC4848878 DOI: 10.3390/ijms17040321] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Revised: 02/24/2016] [Accepted: 02/25/2016] [Indexed: 12/02/2022] Open
Abstract
Bacterial toxin-antitoxin (TA) systems have various cellular functions, including as part of the general stress response. The genome of the Gram-positive human pathogen Streptococcus pneumoniae harbors several putative TA systems, including yefM-yoeBSpn, which is one of four systems that had been demonstrated to be biologically functional. Overexpression of the yoeBSpn toxin gene resulted in cell stasis and eventually cell death in its native host, as well as in Escherichia coli. Our previous work showed that induced expression of a yoeBSpn toxin-Green Fluorescent Protein (GFP) fusion gene apparently triggered apoptosis and was lethal in the model plant, Arabidopsis thaliana. In this study, we investigated the effects of co-expression of the yefMSpn antitoxin and yoeBSpn toxin-GFP fusion in transgenic A. thaliana. When co-expressed in Arabidopsis, the YefMSpn antitoxin was found to neutralize the toxicity of YoeBSpn-GFP. Interestingly, the inducible expression of both yefMSpn antitoxin and yoeBSpn toxin-GFP fusion in transgenic hybrid Arabidopsis resulted in larger rosette leaves and taller plants with a higher number of inflorescence stems and increased silique production. To our knowledge, this is the first demonstration of a prokaryotic antitoxin neutralizing its cognate toxin in plant cells.
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Affiliation(s)
- Fauziah Abu Bakar
- Centre for Research in Biotechnology for Agriculture (CEBAR) and Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Chew Chieng Yeo
- Biomedical Research Centre, Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 21300 Kuala Terengganu, Malaysia.
| | - Jennifer Ann Harikrishna
- Centre for Research in Biotechnology for Agriculture (CEBAR) and Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.
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Xu K, Dedic E, Brodersen DE. Structural analysis of the active site architecture of the VapC toxin from Shigella flexneri. Proteins 2016; 84:892-9. [PMID: 26833558 DOI: 10.1002/prot.25002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 01/07/2016] [Accepted: 01/18/2016] [Indexed: 12/12/2022]
Abstract
The VapC toxin from the Shigella flexneri 2a virulence plasmid pMYSH6000 belongs to the PIN domain protein family, which is characterized by a conserved fold with low amino acid sequence conservation. The toxin is a bona fide Mg(2+) -dependent ribonuclease and has been shown to target initiator tRNA(fMet) in vivo. Here, we present crystal structures of active site catalytic triad mutants D7A, D7N, and D98N of the VapC toxin in absence of antitoxin. In all structures, as well as in solution, VapC forms a dimer. In the D98N structure, a Hepes molecule occupies both active sites of the dimer and comparison with the structure of RNase H bound to a DNA/RNA hybrid suggests that the Hepes molecule mimics the position of an RNA nucleotide in the VapC active site. Proteins 2016; 84:892-899. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Kehan Xu
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, Aarhus C, DK-8000, Denmark
| | - Emil Dedic
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, Aarhus C, DK-8000, Denmark
| | - Ditlev E Brodersen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, Aarhus C, DK-8000, Denmark
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Masuda H, Awano N, Inouye M. ydfD encodes a novel lytic protein in Escherichia coli. FEMS Microbiol Lett 2016; 363:fnw039. [PMID: 26887840 DOI: 10.1093/femsle/fnw039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2016] [Indexed: 11/13/2022] Open
Abstract
Bacteria carry a number of genes that cause cell growth arrest or cell lysis upon expression. Notably, defective prophages retain many lysis proteins. Here, we identified a novel lytic gene, ydfD, on the Qin prophage segment of the Escherichia coli genome. YdfD lyses 99.9% of cells within 2 h of its induction. The co-expression of the upstream gene, dicB, encoding a cell division inhibitor, as well as sulA, encoding another cell division inhibitor, abolished YdfD-induced cell lysis. These results imply that YdfD-induced lysis is a cell division-dependent event. We further found that by deleting the hydrophobic 22-residue N-terminal domain, the resulting 42-residue C-terminal domain was still toxic to cause cell lysis. We propose that YdfD, associated with the cytoplasmic membrane, inhibits an essential cellular process(s).
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Affiliation(s)
- Hisako Masuda
- School of Sciences, Department of Chemistry Indiana University Kokomo, 2300 S Washington St, Kokomo, IN 46902, USA
| | - Naoki Awano
- Department of Biochemistry & Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Rutgers University, and Center for Advanced Biotechnology and Medicine, 675 Hoes Lane, Piscataway, NJ 08854, USA
| | - Masayori Inouye
- Department of Biochemistry & Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Rutgers University, and Center for Advanced Biotechnology and Medicine, 675 Hoes Lane, Piscataway, NJ 08854, USA
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Maklashina E, Rajagukguk S, Starbird CA, McDonald WH, Koganitsky A, Eisenbach M, Iverson TM, Cecchini G. Binding of the Covalent Flavin Assembly Factor to the Flavoprotein Subunit of Complex II. J Biol Chem 2015; 291:2904-16. [PMID: 26644464 DOI: 10.1074/jbc.m115.690396] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Indexed: 01/23/2023] Open
Abstract
Escherichia coli harbors two highly conserved homologs of the essential mitochondrial respiratory complex II (succinate:ubiquinone oxidoreductase). Aerobically the bacterium synthesizes succinate:quinone reductase as part of its respiratory chain, whereas under microaerophilic conditions, the quinol:fumarate reductase can be utilized. All complex II enzymes harbor a covalently bound FAD co-factor that is essential for their ability to oxidize succinate. In eukaryotes and many bacteria, assembly of the covalent flavin linkage is facilitated by a small protein assembly factor, termed SdhE in E. coli. How SdhE assists with formation of the covalent flavin bond and how it binds the flavoprotein subunit of complex II remain unknown. Using photo-cross-linking, we report the interaction site between the flavoprotein of complex II and the SdhE assembly factor. These data indicate that SdhE binds to the flavoprotein between two independently folded domains and that this binding mode likely influences the interdomain orientation. In so doing, SdhE likely orients amino acid residues near the dicarboxylate and FAD binding site, which facilitates formation of the covalent flavin linkage. These studies identify how the conserved SdhE assembly factor and its homologs participate in complex II maturation.
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Affiliation(s)
- Elena Maklashina
- From the Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121, the Department of Biochemistry & Biophysics, University of California, San Francisco, California 94158
| | - Sany Rajagukguk
- From the Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121
| | | | - W Hayes McDonald
- the Department of Biochemistry and Mass Spectrometry Research Center
| | - Anna Koganitsky
- the Department of Biological Chemistry, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Michael Eisenbach
- the Department of Biological Chemistry, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Tina M Iverson
- the Department of Biochemistry and Mass Spectrometry Research Center, the Department of Pharmacology, the Center for Structural Biology, and the Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, and
| | - Gary Cecchini
- From the Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121, the Department of Biochemistry & Biophysics, University of California, San Francisco, California 94158,
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Hernández-Rocamora VM, Alfonso C, Margolin W, Zorrilla S, Rivas G. Evidence That Bacteriophage λ Kil Peptide Inhibits Bacterial Cell Division by Disrupting FtsZ Protofilaments and Sequestering Protein Subunits. J Biol Chem 2015; 290:20325-35. [PMID: 26124275 DOI: 10.1074/jbc.m115.653329] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Indexed: 11/06/2022] Open
Abstract
The effects of Kil peptide from bacteriophage λ on the assembly of Escherichia coli FtsZ into one subunit thick protofilaments were studied using combined biophysical and biochemical methods. Kil peptide has recently been identified as the factor from bacteriophage λ responsible for the inhibition of bacterial cell division during lytic cycle, targeting FtsZ polymerization. Here, we show that this antagonist blocks FtsZ assembly into GTP-dependent protofilaments, producing a wide distribution of smaller oligomers compared with the average size of the intact protofilaments. The shortening of FtsZ protofilaments by Kil is detectable at concentrations of the peptide in the low micromolar range, the mid-point of the inhibition being close to its apparent affinity for GDP-bound FtsZ. This antagonist not only interferes with FtsZ assembly but also reverses the polymerization reaction. The negative regulation by Kil significantly reduces the GTPase activity of FtsZ protofilaments, and FtsZ polymers assembled in guanosine-5'-[(α,β)-methyleno]triphosphate are considerably less sensitive to Kil. Our results suggest that, at high concentrations, Kil may use an inhibition mechanism involving the sequestration of FtsZ subunits, similar to that described for other inhibitors like the SOS response protein SulA or the moonlighting enzyme OpgH. This mechanism is different from those employed by the division site selection antagonists MinC and SlmA. This work provides new insight into the inhibition of FtsZ assembly by phages, considered potential tools against bacterial infection.
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Affiliation(s)
- Víctor M Hernández-Rocamora
- From the Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain and
| | - Carlos Alfonso
- From the Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain and
| | - William Margolin
- the Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, Texas 77030
| | - Silvia Zorrilla
- From the Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain and
| | - Germán Rivas
- From the Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain and
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Bakar FA, Yeo CC, Harikrishna JA. Expression of the Streptococcus pneumoniae yoeB chromosomal toxin gene causes cell death in the model plant Arabidopsis thaliana. BMC Biotechnol 2015; 15:26. [PMID: 25887501 PMCID: PMC4430920 DOI: 10.1186/s12896-015-0138-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 03/03/2015] [Indexed: 01/18/2023] Open
Abstract
Background Bacterial toxin-antitoxin systems usually comprise of a pair of genes encoding a stable toxin and its cognate labile antitoxin and are located in the chromosome or in plasmids of several bacterial species. Chromosomally-encoded toxin-antitoxin systems are involved in bacterial stress responses and activation of the toxins usually leads to cell death or dormancy. Overexpression of the chromosomally-encoded YoeB toxin from the yefM-yoeB toxin-antitoxin locus of the Gram-positive bacterium Streptococcus pneumoniae has been shown to cause cell death in S. pneumoniae as well as E. coli. Results Induction of a YoeB-GFP fusion protein using a 17-β-estradiol-inducible plant expression system in Arabidopsis thaliana Col 0, was lethal in all T2 progeny. Examination of plants by fluorescent confocal microscopy showed GFP fluorescence in all parts of the leaves at 24 hours after 17-β-estradiol induction, continuing up to plant death. Quantitative RT-PCR analysis revealed that the expression of the yoeB toxin gene peaked at 3 days after induction with 17-β-estradiol, coinciding with the onset of visible effects on the plants. Moreover, we detected DNA laddering in the transgenic plants at 24 hours after yoeB induction, indicative of apoptosis. Conclusions Expression of the YoeB toxin from Streptococcus pneumoniae is lethal in Arabidopsis. We believe this is the first report of a toxin from a bacterial toxin-antitoxin system functioning in plants. The results presented here mark an important milestone towards the development of a cell ablation based bio-containment strategy, which may be useful for functional studies and for the control of spread of transgenic plants.
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Affiliation(s)
- Fauziah Abu Bakar
- Centre for Research in Biotechnology for Agriculture (CEBAR) and Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Chew Chieng Yeo
- Biomedical Research Centre, Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Malaysia.
| | - Jennifer Ann Harikrishna
- Centre for Research in Biotechnology for Agriculture (CEBAR) and Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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Mutational Analysis of the Antitoxin in the Lactococcal Type III Toxin-Antitoxin System AbiQ. Appl Environ Microbiol 2015; 81:3848-55. [PMID: 25819963 DOI: 10.1128/aem.00572-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 03/23/2015] [Indexed: 01/21/2023] Open
Abstract
The lactococcal abortive phage infection mechanism AbiQ recently was classified as a type III toxin-antitoxin system in which the toxic protein (ABIQ) is regulated following cleavage of its repeated noncoding RNA antitoxin (antiQ). In this study, we investigated the role of the antitoxin in antiphage activity. The cleavage of antiQ by ABIQ was characterized using 5' rapid amplification of cDNA ends PCR and was located in an adenine-rich region of antiQ. We next generated a series of derivatives with point mutations within antiQ or with various numbers of antiQ repetitions. These modifications were analyzed for their effect on the antiphage activity (efficiency of plaquing) and on the endoribonuclease activity (Northern hybridization). We observed that increasing or reducing the number of antiQ repeats significantly decreased the antiphage activity of the system. Several point mutations had a similar effect on the antiphage activity and were associated with changes in the digestion profile of antiQ. Interestingly, a point mutation in the putative pseudoknot structure of antiQ mutants led to an increased AbiQ antiphage activity, thereby offering a novel way to increase the activity of an abortive infection mechanism.
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Translation elongation factor EF-Tu modulates filament formation of actin-like MreB protein in vitro. J Mol Biol 2015; 427:1715-27. [PMID: 25676310 DOI: 10.1016/j.jmb.2015.01.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 01/02/2015] [Accepted: 01/27/2015] [Indexed: 11/20/2022]
Abstract
EF-Tu has been shown to interact with actin-like protein MreB and to affect its localization in Escherichia coli and in Bacillus subtilis cells. We have purified YFP-MreB in an active form, which forms filaments on glass slides in vitro and was active in dynamic light-scattering assays, polymerizing in milliseconds after addition of magnesium. Purified EF-Tu enhanced the amount of MreB filaments, as seen by sedimentation assays, the speed of filament formation and the length of MreB filaments in vitro. EF-Tu had the strongest impact on MreB filaments in a 1:1 ratio, and EF-Tu co-sedimented with MreB filaments, revealing a stoichiometric interaction between both proteins. This was supported by cross-linking assays where 1:1 species were well detectable. When expressed in E. coli cells, B. subtilis MreB formed filaments and induced the formation of co-localizing B. subtilis EF-Tu structures, indicating that MreB can direct the positioning of EF-Tu structures in a heterologous cell system. Fluorescence recovery after photobleaching analysis showed that MreB filaments have a higher turnover in B. subtilis cells than in E. coli cells, indicating different filament kinetics in homologous or heterologous cell systems. The data show that MreB can direct the localization of EF-Tu in vivo, which in turn positively affects the formation and dynamics of MreB filaments. Thus, EF-Tu is a modulator of the activity of a bacterial actin-like protein.
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Cut to the chase--Regulating translation through RNA cleavage. Biochimie 2015; 114:10-7. [PMID: 25633441 DOI: 10.1016/j.biochi.2015.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 01/19/2015] [Indexed: 11/23/2022]
Abstract
Activation of toxin-antitoxin (TA) systems provides an important mechanism for bacteria to adapt to challenging and ever changing environmental conditions. Known TA systems are classified into five families based on the mechanisms of antitoxin inhibition and toxin activity. For type II TA systems, the toxin is inactivated in exponentially growing cells by tightly binding its antitoxin partner protein, which also serves to regulate cellular levels of the complex through transcriptional auto-repression. During cellular stress, however, the antitoxin is degraded thus freeing the toxin, which is then able to regulate central cellular processes, primarily protein translation to adjust cell growth to the new conditions. In this review, we focus on the type II TA pairs that regulate protein translation through cleavage of ribosomal, transfer, or messenger RNA.
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Dy RL, Przybilski R, Semeijn K, Salmond GP, Fineran PC. A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. Nucleic Acids Res 2014; 42:4590-605. [PMID: 24465005 PMCID: PMC3985639 DOI: 10.1093/nar/gkt1419] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 12/23/2013] [Accepted: 12/26/2013] [Indexed: 01/17/2023] Open
Abstract
Bacterial abortive infection (Abi) systems are 'altruistic' cell death systems that are activated by phage infection and limit viral replication, thereby providing protection to the bacterial population. Here, we have used a novel approach of screening Abi systems as a tool to identify and characterize toxin-antitoxin (TA)-acting Abi systems. We show that AbiE systems are encoded by bicistronic operons and function via a non-interacting (Type IV) bacteriostatic TA mechanism. The abiE operon was negatively autoregulated by the antitoxin, AbiEi, a member of a widespread family of putative transcriptional regulators. AbiEi has an N-terminal winged-helix-turn-helix domain that is required for repression of abiE transcription, and an uncharacterized bi-functional C-terminal domain, which is necessary for transcriptional repression and sufficient for toxin neutralization. The cognate toxin, AbiEii, is a predicted nucleotidyltransferase (NTase) and member of the DNA polymerase β family. AbiEii specifically bound GTP, and mutations in conserved NTase motifs (I-III) and a newly identified motif (IV), abolished GTP binding and subsequent toxicity. The AbiE systems can provide phage resistance and enable stabilization of mobile genetic elements, such as plasmids. Our study reveals molecular insights into the regulation and function of the widespread bi-functional AbiE Abi-TA systems and the biochemical properties of both toxin and antitoxin proteins.
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Affiliation(s)
- Ron L. Dy
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, PO Box 56, Dunedin 9054, New Zealand and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Rita Przybilski
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, PO Box 56, Dunedin 9054, New Zealand and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Koen Semeijn
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, PO Box 56, Dunedin 9054, New Zealand and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - George P.C. Salmond
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, PO Box 56, Dunedin 9054, New Zealand and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Peter C. Fineran
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, PO Box 56, Dunedin 9054, New Zealand and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
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Demidenok OI, Kaprelyants AS, Goncharenko AV. Toxin-antitoxinvapBClocus participates in formation of the dormant state inMycobacterium smegmatis. FEMS Microbiol Lett 2014; 352:69-77. [DOI: 10.1111/1574-6968.12380] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 12/31/2013] [Accepted: 12/31/2013] [Indexed: 01/01/2023] Open
Affiliation(s)
- Oksana I. Demidenok
- Laboratory of Biochemistry of Stresses in Microorganisms; A.N. Bach Institute of Biochemistry Russian Academy of Sciences; Moscow Russia
| | - Arseny S. Kaprelyants
- Laboratory of Biochemistry of Stresses in Microorganisms; A.N. Bach Institute of Biochemistry Russian Academy of Sciences; Moscow Russia
| | - Anna V. Goncharenko
- Laboratory of Biochemistry of Stresses in Microorganisms; A.N. Bach Institute of Biochemistry Russian Academy of Sciences; Moscow Russia
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Unterholzner SJ, Poppenberger B, Rozhon W. Toxin-antitoxin systems: Biology, identification, and application. Mob Genet Elements 2013; 3:e26219. [PMID: 24251069 PMCID: PMC3827094 DOI: 10.4161/mge.26219] [Citation(s) in RCA: 230] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/16/2013] [Accepted: 08/19/2013] [Indexed: 02/07/2023] Open
Abstract
Toxin–antitoxin (TA) systems are small genetic elements composed of a toxin gene and its cognate antitoxin. The toxins of all known TA systems are proteins while the antitoxins are either proteins or non-coding RNAs. Based on the molecular nature of the antitoxin and its mode of interaction with the toxin the TA modules are currently grouped into five classes. In general, the toxin is more stable than the antitoxin but the latter is expressed to a higher level. If supply of the antitoxin stops, for instance under special growth conditions or by plasmid loss in case of plasmid encoded TA systems, the antitoxin is rapidly degraded and can no longer counteract the toxin. Consequently, the toxin becomes activated and can act on its cellular targets. Typically, TA toxins act on crucial cellular processes including translation, replication, cytoskeleton formation, membrane integrity, and cell wall biosynthesis. TA systems and their components are also versatile tools for a multitude of purposes in basic research and biotechnology. Currently, TA systems are frequently used for selection in cloning and for single protein expression in living bacterial cells. Since several TA toxins exhibit activity in yeast and mammalian cells they may be useful for applications in eukaryotic systems. TA modules are also considered as promising targets for the development of antibacterial drugs and their potential to combat viral infection may aid in controlling infectious diseases.
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Affiliation(s)
- Simon J Unterholzner
- 1 Biotechnology of Horticultural Crops; Technische Universität München; Freising, Germany
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McNeil MB, Iglesias-Cans MC, Clulow JS, Fineran PC. YgfX (CptA) is a multimeric membrane protein that interacts with the succinate dehydrogenase assembly factor SdhE (YgfY). MICROBIOLOGY-SGM 2013; 159:1352-1365. [PMID: 23657679 DOI: 10.1099/mic.0.068510-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Serratia sp. strain ATCC 39006 produces the red-pigmented antibiotic prodigiosin. Prodigiosin biosynthesis is regulated by a complex hierarchy that includes the uncharacterized protein YgfX (DUF1434). The ygfX gene is co-transcribed with sdhE, an FAD assembly factor essential for the flavinylation and activation of the SdhA subunit of succinate dehydrogenase (SDH), a central enzyme in the tricarboxylic acid cycle and electron transport chain. The sdhEygfX operon is highly conserved within the Enterobacteriaceae, suggesting that SdhE and YgfX function together. We performed an extensive mutagenesis to gain molecular insights into the uncharacterized protein YgfX, and have investigated the relationship between YgfX and SdhE. YgfX localized to the membrane, interacted with itself, forming dimers or larger multimers, and interacted with SdhE. The transmembrane helices of YgfX were critical for protein function and the formation of YgfX multimers. Site-directed mutagenesis of residues conserved in DUF1434 proteins revealed a periplasmic tryptophan and a cytoplasmic aspartate that were crucial for YgfX activity. Both of these amino acids were required for the formation of YgfX multimers and interactions with SdhE but not membrane localization. Multiple cell division proteins were identified as putative interaction partners of YgfX and overexpression of YgfX had effects on cell morphology. These findings represent an important step in understanding the function of DUF1434 proteins. In contrast to a recent report, we found no evidence that YgfX and SdhE form a toxin-antitoxin system. In summary, YgfX functions as a multimeric membrane-bound protein that interacts with SdhE, an important FAD assembly factor that controls SDH activity.
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Affiliation(s)
- Matthew B McNeil
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Marina C Iglesias-Cans
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - James S Clulow
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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Sberro H, Leavitt A, Kiro R, Koh E, Peleg Y, Qimron U, Sorek R. Discovery of functional toxin/antitoxin systems in bacteria by shotgun cloning. Mol Cell 2013; 50:136-48. [PMID: 23478446 DOI: 10.1016/j.molcel.2013.02.002] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 11/21/2012] [Accepted: 01/31/2013] [Indexed: 01/21/2023]
Abstract
Toxin-antitoxin (TA) modules, composed of a toxic protein and a counteracting antitoxin, play important roles in bacterial physiology. We examined the experimental insertion of 1.5 million genes from 388 microbial genomes into an Escherichia coli host using more than 8.5 million random clones. This revealed hundreds of genes (toxins) that could only be cloned when the neighboring gene (antitoxin) was present on the same clone. Clustering of these genes revealed TA families widespread in bacterial genomes, some of which deviate from the classical characteristics previously described for such modules. Introduction of these genes into E. coli validated that the toxin toxicity is mitigated by the antitoxin. Infection experiments with T7 phage showed that two of the new modules can provide resistance against phage. Moreover, our experiments revealed an "antidefense" protein in phage T7 that neutralizes phage resistance. Our results expose active fronts in the arms race between bacteria and phage.
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Affiliation(s)
- Hila Sberro
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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Ribonucleases in bacterial toxin-antitoxin systems. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:523-31. [PMID: 23454553 DOI: 10.1016/j.bbagrm.2013.02.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 02/05/2013] [Accepted: 02/14/2013] [Indexed: 11/21/2022]
Abstract
Toxin-antitoxin (TA) systems are widespread in bacteria and archaea and play important roles in a diverse range of cellular activities. TA systems have been broadly classified into 5 types and the targets of the toxins are diverse, but the most frequently used cellular target is mRNA. Toxins that target mRNA to inhibit translation can be classified as ribosome-dependent or ribosome-independent RNA interferases. These RNA interferases are sequence-specific endoribonucleases that cleave RNA at specific sequences. Despite limited sequence similarity, ribosome-independent RNA interferases belong to a limited number of structural classes. The MazF structural family includes MazF, Kid, ParE and CcdB toxins. MazF members cleave mRNA at 3-, 5- or 7-base recognition sequences in different bacteria and have been implicated in controlling cell death (programmed) and cell growth, and cellular responses to nutrient starvation, antibiotics, heat and oxidative stress. VapC endoribonucleases belong to the PIN-domain family and inhibit translation by either cleaving tRNA(fMet) in the anticodon stem loop, cleaving mRNA at -AUA(U/A)-hairpin-G- sequences or by sequence-specific RNA binding. VapC has been implicated in controlling bacterial growth in the intracellular environment and in microbial adaptation to nutrient limitation (nitrogen, carbon) and heat shock. ToxN shows structural homology to MazF and is also a sequence-specific endoribonuclease. ToxN confers phage resistance by causing cell death upon phage infection by cleaving cellular and phage RNAs, thereby interfering with bacterial and phage growth. Notwithstanding our recent progress in understanding ribonuclease action and function in TA systems, the environmental triggers that cause release of the toxin from its cognate antitoxin and the precise cellular function of these systems in many bacteria remain to be discovered. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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Schuster CF, Bertram R. Toxin-antitoxin systems are ubiquitous and versatile modulators of prokaryotic cell fate. FEMS Microbiol Lett 2013; 340:73-85. [DOI: 10.1111/1574-6968.12074] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 12/24/2012] [Accepted: 01/03/2013] [Indexed: 10/27/2022] Open
Affiliation(s)
- Christopher F. Schuster
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin; Lehrbereich Mikrobielle Genetik; Eberhard Karls Universität Tübingen; Waldhäuser Str. 70/8; Tübingen; Germany
| | - Ralph Bertram
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin; Lehrbereich Mikrobielle Genetik; Eberhard Karls Universität Tübingen; Waldhäuser Str. 70/8; Tübingen; Germany
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Prokaryotic assembly factors for the attachment of flavin to complex II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:637-47. [PMID: 22985599 DOI: 10.1016/j.bbabio.2012.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/05/2012] [Accepted: 09/07/2012] [Indexed: 01/01/2023]
Abstract
Complex II (also known as Succinate dehydrogenase or Succinate-ubiquinone oxidoreductase) is an important respiratory enzyme that participates in both the tricarboxylic acid cycle and electron transport chain. Complex II consists of four subunits including a catalytic flavoprotein (SdhA), an iron-sulphur subunit (SdhB) and two hydrophobic membrane anchors (SdhC and SdhD). Complex II also contains a number of redox cofactors including haem, Fe-S clusters and FAD, which mediate electron transfer from succinate oxidation to the reduction of the mobile electron carrier ubiquinone. The flavin cofactor FAD is an important redox cofactor found in many proteins that participate in oxidation/reduction reactions. FAD is predominantly bound non-covalently to flavoproteins, with only a small percentage of flavoproteins, such as complex II, binding FAD covalently. Aside from a few examples, the mechanisms of flavin attachment have been a relatively unexplored area. This review will discuss the FAD cofactor and the mechanisms used by flavoproteins to covalently bind FAD. Particular focus is placed on the attachment of FAD to complex II with an emphasis on SdhE (a DUF339/SDH5 protein previously termed YgfY), the first protein identified as an assembly factor for FAD attachment to flavoproteins in prokaryotes. The molecular details of SdhE-dependent flavinylation of complex II are discussed and comparisons are made to known cofactor chaperones. Furthermore, an evolutionary hypothesis is proposed to explain the distribution of SdhE homologues in bacterial and eukaryotic species. Mechanisms for regulating SdhE function and how this may be linked to complex II function in different bacterial species are also discussed. This article is part of a Special Issue entitled: Respiratory complex II: Role in cellular physiology and disease.
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Yakhnina AA, Gitai Z. The small protein MbiA interacts with MreB and modulates cell shape in Caulobacter crescentus. Mol Microbiol 2012; 85:1090-104. [PMID: 22804814 DOI: 10.1111/j.1365-2958.2012.08159.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In Caulobacter crescentus, the actin homologue MreB is critical for cell shape maintenance. Despite the central importance of MreB for cell morphology and viability, very little is known about MreB-interacting factors. Here, we use an overexpression approach to identify a novel MreB interactor, MbiA. MbiA interacts with MreB in both biochemical and genetic assays, colocalizes with MreB throughout the cell cycle, and relies on MreB for its localization. MbiA overexpression mimics the loss of MreB function, severely perturbing cell morphology, inhibiting growth and inducing cell lysis. Additionally, mbiA deletion shows a synthetic growth phenotype with a hypomorphic allele of the MreB interactor RodZ, suggesting that these two MreB-interacting proteins either have partially redundant functions or participate in the same functional complex. Our work thus establishes MbiA as a novel cell shape regulator that appears to function through regulating MreB, and opens avenues for discovery of more MreB-regulating factors by showing that overexpression screens are a valuable tool for uncovering potentially redundant cell shape effectors.
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Affiliation(s)
- Anastasiya A Yakhnina
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Princeton, NJ 08544, USA
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Masuda H, Tan Q, Awano N, Wu KP, Inouye M. YeeU enhances the bundling of cytoskeletal polymers of MreB and FtsZ, antagonizing the CbtA (YeeV) toxicity in Escherichia coli. Mol Microbiol 2012; 84:979-89. [DOI: 10.1111/j.1365-2958.2012.08068.x] [Citation(s) in RCA: 175] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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