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Peng A, Yin G, Zuo W, Zhang L, Du G, Chen J, Wang Y, Kang Z. Regulatory RNAs in Bacillus subtilis: A review on regulatory mechanism and applications in synthetic biology. Synth Syst Biotechnol 2024; 9:223-233. [PMID: 38385150 PMCID: PMC10877136 DOI: 10.1016/j.synbio.2024.01.013] [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: 12/10/2023] [Revised: 01/15/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
Bacteria exhibit a rich repertoire of RNA molecules that intricately regulate gene expression at multiple hierarchical levels, including small RNAs (sRNAs), riboswitches, and antisense RNAs. Notably, the majority of these regulatory RNAs lack or have limited protein-coding capacity but play pivotal roles in orchestrating gene expression by modulating transcription, post-transcription or translation processes. Leveraging and redesigning these regulatory RNA elements have emerged as pivotal strategies in the domains of metabolic engineering and synthetic biology. While previous investigations predominantly focused on delineating the roles of regulatory RNA in Gram-negative bacterial models such as Escherichia coli and Salmonella enterica, this review aims to summarize the mechanisms and functionalities of endogenous regulatory RNAs inherent to typical Gram-positive bacteria, notably Bacillus subtilis. Furthermore, we explore the engineering and practical applications of these regulatory RNA elements in the arena of synthetic biology, employing B. subtilis as a foundational chassis.
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Affiliation(s)
- Anqi Peng
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Guobin Yin
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Wenjie Zuo
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Luyao Zhang
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yang Wang
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Zhen Kang
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
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Jin C, Kang SM, Kim DH, Lee Y, Lee BJ. Discovery of Antimicrobial Agents Based on Structural and Functional Study of the Klebsiella pneumoniae MazEF Toxin-Antitoxin System. Antibiotics (Basel) 2024; 13:398. [PMID: 38786127 PMCID: PMC11117207 DOI: 10.3390/antibiotics13050398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/15/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Klebsiella pneumoniae causes severe human diseases, but its resistance to current antibiotics is increasing. Therefore, new antibiotics to eradicate K. pneumoniae are urgently needed. Bacterial toxin-antitoxin (TA) systems are strongly correlated with physiological processes in pathogenic bacteria, such as growth arrest, survival, and apoptosis. By using structural information, we could design the peptides and small-molecule compounds that can disrupt the binding between K. pneumoniae MazE and MazF, which release free MazF toxin. Because the MazEF system is closely implicated in programmed cell death, artificial activation of MazF can promote cell death of K. pneumoniae. The effectiveness of a discovered small-molecule compound in bacterial cell killing was confirmed through flow cytometry analysis. Our findings can contribute to understanding the bacterial MazEF TA system and developing antimicrobial agents for treating drug-resistant K. pneumoniae.
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Affiliation(s)
- Chenglong Jin
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea;
- Mastermeditech Ltd., Gangseo-gu, Seoul 16499, Republic of Korea
| | - Sung-Min Kang
- College of Pharmacy, Duksung Women’s University, Seoul 01369, Republic of Korea;
| | - Do-Hee Kim
- College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Republic of Korea;
| | - Yuno Lee
- Korea Research Institute of Chemical Technology, Korea Chemical Bank Daejeon, Daejeon 34114, Republic of Korea;
| | - Bong-Jin Lee
- Mastermeditech Ltd., Gangseo-gu, Seoul 16499, Republic of Korea
- College of Pharmacy, Ajou University, Yeongtong-gu, Suwon 16499, Republic of Korea
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Shafipour M, Mohammadzadeh A, Ghaemi EA, Mahmoodi P. PCR Development for Analysis of Some Type II Toxin-Antitoxin Systems, relJK, mazEF3, and vapBC3 Genes, in Mycobacterium tuberculosis and Mycobacterium bovis. Curr Microbiol 2024; 81:90. [PMID: 38311651 DOI: 10.1007/s00284-023-03599-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 12/22/2023] [Indexed: 02/06/2024]
Abstract
Toxin-Antitoxin (TA) systems are some small genetic modules in bacteria that play significant roles in resistance and tolerance development to antibiotics. Whole genome sequencing (WGS) is an effective method to analyze TA systems in pathogenic Mycobacteria. However, this study aimed to use a simple and inexpensive PCR-Sequencing approach to investigate the type II TA system. Using data from the WGS of Mycobacterium tuberculosis (M. tuberculosis) strain H37Rv and Mycobacterium bovis (M. bovis) strain BCG, primers specific to the relJK, mazEF3, and vapBC3 gene families were designed by Primer3 software. Following that, a total of 90 isolates were examined using the newly developed PCR assay, consisting of 64 M. tuberculosis and 26 M. bovis isolates, encompassing both 45 rifampin-sensitive and 45 rifampin-resistant strains. Finally, 28 isolates (including 14 rifampin-resistant isolates) were sent for sequencing, and their sequences were aligned and compared to the mentioned reference sequences. The amplicons size of mazEF3, relJK, and vapBC3 genes were 825, 875, and 934 bp, respectively. Furthermore, all tested isolates showed the specific amplicons for these TA families. To evaluate the specificity of the primers, PCR was performed on S. aureus and E.coli isolates. None of the examined samples had the desired amplicons. Therefore, the primers had acceptable specificity. The results indicated that the developed PCR-Sequencing approach can be used to effectively investigate certain types of TA systems. Considering high costs of WGS and difficulty in interpreting its results, such a simple and inexpensive method is beneficial in the evaluation of TA systems in Mycobacteria.
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Affiliation(s)
- Maryam Shafipour
- Department of Pathobiology, Faculty of Veterinary Medicine, Bu-Ali Sina University, Hamedan, Iran
| | - Abdolmajid Mohammadzadeh
- Department of Pathobiology, Faculty of Veterinary Medicine, Bu-Ali Sina University, Hamedan, Iran.
| | - Ezzat Allah Ghaemi
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Pezhman Mahmoodi
- Department of Pathobiology, Faculty of Veterinary Medicine, Bu-Ali Sina University, Hamedan, Iran
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4
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Khan S, Ahmad F, Ansari MI, Ashfaque M, Islam MH, Khubaib M. Toxin-Antitoxin system of Mycobacterium tuberculosis: Roles beyond stress sensor and growth regulator. Tuberculosis (Edinb) 2023; 143:102395. [PMID: 37722233 DOI: 10.1016/j.tube.2023.102395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/15/2023] [Accepted: 08/10/2023] [Indexed: 09/20/2023]
Abstract
The advent of effective drug regimen and BCG vaccine has significantly decreased the rate of morbidity and mortality of TB. However, lengthy treatment and slower recovery rate, as well as reactivation of the disease with the emergence of multi-drug, extensively-drug, and totally-drug resistance strains, pose a serious concern. The complexities associated are due to the highly evolved and complex nature of the bacterium itself. One of the unique features of Mycobacterium tuberculosis [M.tb] is that it has undergone reductive evolution while maintaining and amplified a few gene families. One of the critical gene family involved in the virulence and pathogenesis is the Toxin-Antitoxin system. These families are believed to harbor virulence signature and are strongly associated with various stress adaptations and pathogenesis. The M.tb TA systems are linked with growth regulation machinery during various environmental stresses. The genes of TA systems are differentially expressed in the host during an active infection, oxidative stress, low pH stress, and starvation, which essentially indicate their role beyond growth regulators. Here in this review, we have discussed different roles of TA gene families in various stresses and their prospective role at the host-pathogen interface, which could be exploited to understand the M.tb associated pathomechanisms better and further designing the new strategies against the pathogen.
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Affiliation(s)
- Saima Khan
- Department of Biosciences, Integral University, Lucknow, India
| | - Firoz Ahmad
- Department of Biosciences, Integral University, Lucknow, India
| | | | | | | | - Mohd Khubaib
- Department of Biosciences, Integral University, Lucknow, India.
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5
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Pizzolato-Cezar LR, Spira B, Machini MT. Bacterial toxin-antitoxin systems: Novel insights on toxin activation across populations and experimental shortcomings. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 5:100204. [PMID: 38024808 PMCID: PMC10643148 DOI: 10.1016/j.crmicr.2023.100204] [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] [Indexed: 12/01/2023] Open
Abstract
The alarming rise in hard-to-treat bacterial infections is of great concern to human health. Thus, the identification of molecular mechanisms that enable the survival and growth of pathogens is of utmost urgency for the development of more efficient antimicrobial therapies. In challenging environments, such as presence of antibiotics, or during host infection, metabolic adjustments are essential for microorganism survival and competitiveness. Toxin-antitoxin systems (TASs) consisting of a toxin with metabolic modulating activity and a cognate antitoxin that antagonizes that toxin are important elements in the arsenal of bacterial stress defense. However, the exact physiological function of TA systems is highly debatable and with the exception of stabilization of mobile genetic elements and phage inhibition, other proposed biological functions lack a broad consensus. This review aims at gaining new insights into the physiological effects of TASs in bacteria and exploring the experimental shortcomings that lead to discrepant results in TAS research. Distinct control mechanisms ensure that only subsets of cells within isogenic cultures transiently develop moderate levels of toxin activity. As a result, TASs cause phenotypic growth heterogeneity rather than cell stasis in the entire population. It is this feature that allows bacteria to thrive in diverse environments through the creation of subpopulations with different metabolic rates and stress tolerance programs.
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Affiliation(s)
- Luis R. Pizzolato-Cezar
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Beny Spira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - M. Teresa Machini
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
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6
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Kang SM. Focused Overview of Mycobacterium tuberculosis VapBC Toxin-Antitoxin Systems Regarding Their Structural and Functional Aspects: Including Insights on Biomimetic Peptides. Biomimetics (Basel) 2023; 8:412. [PMID: 37754163 PMCID: PMC10526153 DOI: 10.3390/biomimetics8050412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023] Open
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis, is a lethal infectious disease of significant public health concern. The rise of multidrug-resistant and drug-tolerant strains has necessitated novel approaches to combat the disease. Toxin-antitoxin (TA) systems, key players in bacterial adaptive responses, are prevalent in prokaryotic genomes and have been linked to tuberculosis. The genome of M. tuberculosis strains harbors an unusually high number of TA systems, prompting questions about their biological roles. The VapBC family, a representative type II TA system, is characterized by the VapC toxin, featuring a PilT N-terminal domain with nuclease activity. Its counterpart, VapB, functions as an antitoxin, inhibiting VapC's activity. Additionally, we explore peptide mimics designed to replicate protein helical structures in this review. Investigating these synthetic peptides offers fresh insights into molecular interactions, potentially leading to therapeutic applications. These synthetic peptides show promise as versatile tools for modulating cellular processes and protein-protein interactions. We examine the rational design strategies employed to mimic helical motifs, their biophysical properties, and potential applications in drug development and bioengineering. This review aims to provide an in-depth understanding of TA systems by introducing known complex structures, with a focus on both structural aspects and functional and molecular details associated with each system.
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Affiliation(s)
- Sung-Min Kang
- College of Pharmacy, Duksung Women's University, Seoul 01369, Republic of Korea
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Chan WT, Garcillán-Barcia MP, Yeo CC, Espinosa M. Type II bacterial toxin-antitoxins: hypotheses, facts, and the newfound plethora of the PezAT system. FEMS Microbiol Rev 2023; 47:fuad052. [PMID: 37715317 PMCID: PMC10532202 DOI: 10.1093/femsre/fuad052] [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: 06/26/2023] [Revised: 08/24/2023] [Accepted: 09/07/2023] [Indexed: 09/17/2023] Open
Abstract
Toxin-antitoxin (TA) systems are entities found in the prokaryotic genomes, with eight reported types. Type II, the best characterized, is comprised of two genes organized as an operon. Whereas toxins impair growth, the cognate antitoxin neutralizes its activity. TAs appeared to be involved in plasmid maintenance, persistence, virulence, and defence against bacteriophages. Most Type II toxins target the bacterial translational machinery. They seem to be antecessors of Higher Eukaryotes and Prokaryotes Nucleotide-binding (HEPN) RNases, minimal nucleotidyltransferase domains, or CRISPR-Cas systems. A total of four TAs encoded by Streptococcus pneumoniae, RelBE, YefMYoeB, Phd-Doc, and HicAB, belong to HEPN-RNases. The fifth is represented by PezAT/Epsilon-Zeta. PezT/Zeta toxins phosphorylate the peptidoglycan precursors, thereby blocking cell wall synthesis. We explore the body of knowledge (facts) and hypotheses procured for Type II TAs and analyse the data accumulated on the PezAT family. Bioinformatics analyses showed that homologues of PezT/Zeta toxin are abundantly distributed among 14 bacterial phyla mostly in Proteobacteria (48%), Firmicutes (27%), and Actinobacteria (18%), showing the widespread distribution of this TA. The pezAT locus was found to be mainly chromosomally encoded whereas its homologue, the tripartite omega-epsilon-zeta locus, was found mostly on plasmids. We found several orphan pezT/zeta toxins, unaccompanied by a cognate antitoxin.
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Affiliation(s)
- Wai Ting Chan
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Maria Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-Consejo Superior de Investigaciones Científicas, C/Albert Einstein 22, PCTCAN, 39011 Santander, Spain
| | - Chew Chieng Yeo
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine
, Universiti Sultan Zainal Abidin, Jalan Sultan Mahumd, 20400 Kuala Terengganu, Malaysia
| | - Manuel Espinosa
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9, 28040 Madrid, Spain
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8
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Shahbazi S, Shivaee A, Nasiri M, Mirshekar M, Sabzi S, Sariani OK. Zinc oxide nanoparticles impact the expression of the genes involved in toxin-antitoxin systems in multidrug-resistant Acinetobacter baumannii. J Basic Microbiol 2023; 63:1007-1015. [PMID: 36086811 DOI: 10.1002/jobm.202200382] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/20/2022] [Accepted: 08/25/2022] [Indexed: 11/09/2022]
Abstract
The aim of this study was to investigate the effect of zinc oxide nanoparticles (ZnO-NPs) on the expression of genes involved in toxin-antitoxin (TA) systems in multidrug-resistant (MDR) Acinetobacter baumannii. Seventy clinical isolates of A. baumannii were collected from variuos clinical samples. Antimicrobial susceptibility test was determined by disk diffusion. Type II TA system-related genes including GNAT, XRE-like, hipA, hipB, hicA, hicB were screened using polymerase chain reaction (PCR). ZnO-NPs prepared and characterized by field emission scanning electron microscopy and X-ray diffraction. MIC of ZnO-NPs of A. baumannii isolates was performed using the microdilution method. The expression of type II TA systems-related genes were assessed with and without exposure to ZnO-NPs using real-time PCR. The highest rate of resistance and sensitivity was observed against cefepime (77.14%), and ampicillin/sulbactam (42.85%), respectively. All A. baumannii isolates were considered as MDR. In this study, three TA loci were identified for A. baumannii including GNAT/XRE-like, HicA/HicB, and HipA/HipB and their prevalence was 100%, 42%, and 27.1%, respectively. There was no significant relationship between the prevalence of these systems and the origin of A. baumannii. Our data showed significant correlations between the presence of HicA/HicB system and resistance to ceftazidime, meropenem, imipenem, and cefepime (p < 0.05), and the presence of HipA/HipB system and resistance to ceftazidime, meropenem, imipenem, and cefepime (p < 0.05). In presence of ZnO-NPs, the expression of all studied genes decreased. GNAT and hicB showed the highest and lowest expression changes by 2.4 folds (p < 0.001) and 1.3 folds (p < 0.05), respectively. This study demonstrates the promising potential of nanoparticles to impact the expression of the genes involved in TA Systems. So, the application of ZnO-NPs may be helpful to design target-based strategies towards MDRs pathogens for empowered clinical applications by microbiologists and nanotechnologists.
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Affiliation(s)
- Shahla Shahbazi
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran
| | - Ali Shivaee
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Marzieh Nasiri
- Department of Genetics, College of Sciences, Kazerun Branch, Islamic Azad University, Kazerun, Iran
| | - Maryam Mirshekar
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Samira Sabzi
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Omid K Sariani
- Department of Genetics, College of Sciences, Kazerun Branch, Islamic Azad University, Kazerun, Iran
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Xu X, Usher B, Gutierrez C, Barriot R, Arrowsmith TJ, Han X, Redder P, Neyrolles O, Blower TR, Genevaux P. MenT nucleotidyltransferase toxins extend tRNA acceptor stems and can be inhibited by asymmetrical antitoxin binding. Nat Commun 2023; 14:4644. [PMID: 37591829 PMCID: PMC10435456 DOI: 10.1038/s41467-023-40264-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/20/2023] [Indexed: 08/19/2023] Open
Abstract
Mycobacterium tuberculosis, the bacterium responsible for human tuberculosis, has a genome encoding a remarkably high number of toxin-antitoxin systems of largely unknown function. We have recently shown that the M. tuberculosis genome encodes four of a widespread, MenAT family of nucleotidyltransferase toxin-antitoxin systems. In this study we characterize MenAT1, using tRNA sequencing to demonstrate MenT1 tRNA modification activity. MenT1 activity is blocked by MenA1, a short protein antitoxin unrelated to the MenA3 kinase. X-ray crystallographic analysis shows blockage of the conserved MenT fold by asymmetric binding of MenA1 across two MenT1 protomers, forming a heterotrimeric toxin-antitoxin complex. Finally, we also demonstrate tRNA modification by toxin MenT4, indicating conserved activity across the MenT family. Our study highlights variation in tRNA target preferences by MenT toxins, selective use of nucleotide substrates, and diverse modes of MenA antitoxin activity.
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Affiliation(s)
- Xibing Xu
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Ben Usher
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Claude Gutierrez
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Roland Barriot
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Tom J Arrowsmith
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Xue Han
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Peter Redder
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Olivier Neyrolles
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Tim R Blower
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK.
| | - Pierre Genevaux
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France.
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10
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Gruzdev N, Pitcovski J, Katz C, Ruimi N, Eliahu D, Noach C, Rosenzweig E, Finger A, Shahar E. Development of toxin-antitoxin self-destructive bacteria, aimed for salmonella vaccination. Vaccine 2023:S0264-410X(23)00777-6. [PMID: 37400285 DOI: 10.1016/j.vaccine.2023.06.074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/19/2023] [Accepted: 06/24/2023] [Indexed: 07/05/2023]
Abstract
The most common source of foodborne Salmonella infection in humans is poultry eggs and meat, such that prevention of human infection is mostly achieved by vaccination of farm animals. While inactivated and attenuated vaccines are available, both present drawbacks. This study aimed to develop a novel vaccination strategy, which combines the effectiveness of live-attenuated and safety of inactivated vaccines by construction of inducible self-destructing bacteria utilizing toxin-antitoxin (TA) systems. Hok-Sok and CeaB-CeiB toxin-antitoxin systems were coupled with three induction systems aimed for activating cell killing upon lack of arabinose, anaerobic conditions or low concentration of metallic di-cations. The constructs were transformed into a pathogenic Salmonella enterica serovar Enteritidis strain and bacteria elimination was evaluated in vitro under specific activating conditions and in vivo following administration to chickens. Four constructs induced bacterial killing under the specified conditions, both in growth media and within macrophages. Cloacal swabs of all chicks orally administered transformed bacteria had no detectable levels of bacteria within 9 days of inoculation. By day ten, no bacteria were identified in the spleen and liver of most birds. Antibody immune response was raised toward TA carrying Salmonella which resembled response toward the wildtype bacteria. The constructs described in this study led to self-destruction of virulent Salmonella enteritidis both in vitro and in inoculated animals within a period which is sufficient for the induction of a protective immune response. This system may serve as a safe and effective live vaccine platform against Salmonella as well as other pathogenic bacteria.
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Affiliation(s)
- Nady Gruzdev
- MIGAL Research Institute in the Galilee, Kiryat Shmona, Israel
| | - Jacob Pitcovski
- MIGAL Research Institute in the Galilee, Kiryat Shmona, Israel; Tel-Hai Academic College, Upper Galilee, Israel
| | - Chen Katz
- MIGAL Research Institute in the Galilee, Kiryat Shmona, Israel
| | - Nili Ruimi
- MIGAL Research Institute in the Galilee, Kiryat Shmona, Israel
| | - Dalia Eliahu
- MIGAL Research Institute in the Galilee, Kiryat Shmona, Israel
| | | | | | | | - Ehud Shahar
- MIGAL Research Institute in the Galilee, Kiryat Shmona, Israel; Tel-Hai Academic College, Upper Galilee, Israel.
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Kang SM. Mycobacterium tuberculosis Rv0229c Shows Ribonuclease Activity and Reveals Its Corresponding Role as Toxin VapC51. Antibiotics (Basel) 2023; 12:antibiotics12050840. [PMID: 37237743 DOI: 10.3390/antibiotics12050840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
The VapBC system, which belongs to the type II toxin-antitoxin (TA) system, is the most abundant and widely studied system in Mycobacterium tuberculosis. The VapB antitoxin suppresses the activity of the VapC toxin through a stable protein-protein complex. However, under environmental stress, the balance between toxin and antitoxin is disrupted, leading to the release of free toxin and bacteriostatic state. This study introduces the Rv0229c, a putative VapC51 toxin, and aims to provide a better understanding of its discovered function. The structure of the Rv0229c shows a typical PIN-domain protein, exhibiting an β1-α1-α2-β2-α3-α4-β3-α5-α6-β4-α7-β5 topology. The structure-based sequence alignment showed four electronegative residues in the active site of Rv0229c, which is composed of Asp8, Glu42, Asp95, and Asp113. By comparing the active site with existing VapC proteins, we have demonstrated the justification for naming it VapC51 at the molecular level. In an in vitro ribonuclease activity assay, Rv0229c showed ribonuclease activity dependent on the concentration of metal ions such as Mg2+ and Mn2+. In addition, magnesium was found to have a greater effect on VapC51 activity than manganese. Through these structural and experimental studies, we provide evidence for the functional role of Rv0229c as a VapC51 toxin. Overall, this study aims to enhance our understanding of the VapBC system in M. tuberculosis.
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Affiliation(s)
- Sung-Min Kang
- College of Pharmacy, Duksung Women's University, Seoul 01369, Republic of Korea
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12
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Ahmed S, Chattopadhyay G, Manjunath K, Bhasin M, Singh N, Rasool M, Das S, Rana V, Khan N, Mitra D, Asok A, Singh R, Varadarajan R. Combining cysteine scanning with chemical labeling to map protein-protein interactions and infer bound structure in an intrinsically disordered region. Front Mol Biosci 2022; 9:997653. [PMID: 36275627 PMCID: PMC9585320 DOI: 10.3389/fmolb.2022.997653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
The Mycobacterium tuberculosis genome harbours nine toxin-antitoxin (TA) systems of the mazEF family. These consist of two proteins, a toxin and an antitoxin, encoded in an operon. While the toxin has a conserved fold, the antitoxins are structurally diverse and the toxin binding region is typically intrinsically disordered before binding. We describe high throughput methodology for accurate mapping of interfacial residues and apply it to three MazEF complexes. The method involves screening one partner protein against a panel of chemically masked single cysteine mutants of its interacting partner, displayed on the surface of yeast cells. Such libraries have much lower diversity than those generated by saturation mutagenesis, simplifying library generation and data analysis. Further, because of the steric bulk of the masking reagent, labeling of virtually all exposed epitope residues should result in loss of binding, and buried residues are inaccessible to the labeling reagent. The binding residues are deciphered by probing the loss of binding to the labeled cognate partner by flow cytometry. Using this methodology, we have identified the interfacial residues for MazEF3, MazEF6 and MazEF9 TA systems of M. tuberculosis. In the case of MazEF9, where a crystal structure was available, there was excellent agreement between our predictions and the crystal structure, superior to those with AlphaFold2. We also report detailed biophysical characterization of the MazEF3 and MazEF9 TA systems and measured the relative affinities between cognate and non-cognate toxin–antitoxin partners in order to probe possible cross-talk between these systems.
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Affiliation(s)
- Shahbaz Ahmed
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | | | - Munmun Bhasin
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Neelam Singh
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Mubashir Rasool
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Sayan Das
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Varsha Rana
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Neha Khan
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Debarghya Mitra
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Aparna Asok
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Ramandeep Singh
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- *Correspondence: Raghavan Varadarajan,
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13
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王 欣, 罗 涛, 陈 宗, 廖 伟, 王 怡, 鲍 朗. [Effect of Mycobacterium tuberculosis higBA on Bacterial Stress Response and Intracellular Infection and Immunity]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2022; 53:828-833. [PMID: 36224685 PMCID: PMC10408798 DOI: 10.12182/20220960209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Indexed: 06/16/2023]
Abstract
Objective To investigate the effect of Mycobacterium tuberculosis ( Mtb) higBA on bacterial stress response and intracellular infection and immunity. Methods The target gene amplified from Mtb H37Rv genome was cloned to the vector and then transferred to Mycobacterium smegmatis ( Ms) to construct a recombinant strain. Stress response experiment and Raw264.7 mouse macrophage infection was carried out with Ms_higBA, the recombinant strain, and Ms_ vec, the vector strain. Tests were conducted to measure bacterial colony forming unit (CFU) and transcriptional levels of cytokines, including interleukin ( IL)-1β, IL-6, IL-10, IL-12 p40, interferon ( IFN)- γ, tumor necrosis factor ( TNF)- α, and inducible nitric oxide synthase ( iNOS). Results The recombinant strain, Ms_higBA, was constructed successfully. According to the findings of the stress response experiment, higBA could indeed enhance bacterial survival under certain conditions of in vitro culture. Intracellular infection experiment demonstrated that higBA enhanced bacterial survival in macrophages and influenced the transcriptional level of cytokines. Conclusion The higBA genes from Mtb play a role in bacterial stress response and intracellular infection and immunity.
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Affiliation(s)
- 欣妍 王
- 四川大学华西基础医学与法医学院 病原生物系感染免疫研究室 (成都 610041)Laboratory of Infection and Immunology, Department of Pathogenic Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - 涛 罗
- 四川大学华西基础医学与法医学院 病原生物系感染免疫研究室 (成都 610041)Laboratory of Infection and Immunology, Department of Pathogenic Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - 宗海 陈
- 四川大学华西基础医学与法医学院 病原生物系感染免疫研究室 (成都 610041)Laboratory of Infection and Immunology, Department of Pathogenic Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - 伟 廖
- 四川大学华西基础医学与法医学院 病原生物系感染免疫研究室 (成都 610041)Laboratory of Infection and Immunology, Department of Pathogenic Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - 怡 王
- 四川大学华西基础医学与法医学院 病原生物系感染免疫研究室 (成都 610041)Laboratory of Infection and Immunology, Department of Pathogenic Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - 朗 鲍
- 四川大学华西基础医学与法医学院 病原生物系感染免疫研究室 (成都 610041)Laboratory of Infection and Immunology, Department of Pathogenic Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
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14
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Dai Z, Wu T, Xu S, Zhou L, Tang W, Hu E, Zhan L, Chen M, Yu G. Characterization of toxin-antitoxin systems from public sequencing data: A case study in Pseudomonas aeruginosa. Front Microbiol 2022; 13:951774. [PMID: 36051757 PMCID: PMC9424990 DOI: 10.3389/fmicb.2022.951774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
The toxin-antitoxin (TA) system is a widely distributed group of genetic modules that play important roles in the life of prokaryotes, with mobile genetic elements (MGEs) contributing to the dissemination of antibiotic resistance gene (ARG). The diversity and richness of TA systems in Pseudomonas aeruginosa, as one of the bacterial species with ARGs, have not yet been completely demonstrated. In this study, we explored the TA systems from the public genomic sequencing data and genome sequences. A small scale of genomic sequencing data in 281 isolates was selected from the NCBI SRA database, reassembling the genomes of these isolates led to the findings of abundant TA homologs. Furthermore, remapping these identified TA modules on 5,437 genome/draft genomes uncovers a great diversity of TA modules in P. aeruginosa. Moreover, manual inspection revealed several TA systems that were not yet reported in P. aeruginosa including the hok-sok, cptA-cptB, cbeA-cbtA, tomB-hha, and ryeA-sdsR. Additional annotation revealed that a large number of MGEs were closely distributed with TA. Also, 16% of ARGs are located relatively close to TA. Our work confirmed a wealth of TA genes in the unexplored P. aeruginosa pan-genomes, expanded the knowledge on P. aeruginosa, and provided methodological tips on large-scale data mining for future studies. The co-occurrence of MGE, ARG, and TA may indicate a potential interaction in their dissemination.
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15
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Feucherolles M, Nennig M, Becker SL, Martiny D, Losch S, Penny C, Cauchie HM, Ragimbeau C. Combination of MALDI-TOF Mass Spectrometry and Machine Learning for Rapid Antimicrobial Resistance Screening: The Case of Campylobacter spp. Front Microbiol 2022; 12:804484. [PMID: 35250909 PMCID: PMC8894766 DOI: 10.3389/fmicb.2021.804484] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/28/2021] [Indexed: 01/15/2023] Open
Abstract
While MALDI-TOF mass spectrometry (MS) is widely considered as the reference method for the rapid and inexpensive identification of microorganisms in routine laboratories, less attention has been addressed to its ability for detection of antimicrobial resistance (AMR). Recently, some studies assessed its potential application together with machine learning for the detection of AMR in clinical pathogens. The scope of this study was to investigate MALDI-TOF MS protein mass spectra combined with a prediction approach as an AMR screening tool for relevant foodborne pathogens, such as Campylobacter coli and Campylobacter jejuni. A One-Health panel of 224 C. jejuni and 116 C. coli strains was phenotypically tested for seven antimicrobial resistances, i.e., ciprofloxacin, erythromycin, tetracycline, gentamycin, kanamycin, streptomycin, and ampicillin, independently, and were submitted, after an on- and off-plate protein extraction, to MALDI Biotyper analysis, which yielded one average spectra per isolate and type of extraction. Overall, high performance was observed for classifiers detecting susceptible as well as ciprofloxacin- and tetracycline-resistant isolates. A maximum sensitivity and a precision of 92.3 and 81.2%, respectively, were reached. No significant prediction performance differences were observed between on- and off-plate types of protein extractions. Finally, three putative AMR biomarkers for fluoroquinolones, tetracyclines, and aminoglycosides were identified during the current study. Combination of MALDI-TOF MS and machine learning could be an efficient and inexpensive tool to swiftly screen certain AMR in foodborne pathogens, which may enable a rapid initiation of a precise, targeted antibiotic treatment.
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Affiliation(s)
- Maureen Feucherolles
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology, Belval, Luxembourg
- *Correspondence: Maureen Feucherolles,
| | - Morgane Nennig
- Laboratoire National de Santé, Epidemiology and Microbial Genomics, Dudelange, Luxembourg
| | - Sören L. Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Delphine Martiny
- National Reference Centre for Campylobacter, Laboratoire des Hôpitaux Universitaires de Bruxelles-Universitaire Laboratorium Brussel (LHUB-ULB), Brussels, Belgium
- Université de Mons (UMONS), Mons, Belgium
| | - Serge Losch
- Laboratoire de Médecine Vétérinaire de l’Etat, Dudelange, Luxembourg
| | - Christian Penny
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology, Belval, Luxembourg
- Chambre des Députés du Grand-Duché de Luxembourg, Parliamentary Research Service, Luxembourg, Luxembourg
| | - Henry-Michel Cauchie
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology, Belval, Luxembourg
- Henry-Michel Cauchie,
| | - Catherine Ragimbeau
- Laboratoire National de Santé, Epidemiology and Microbial Genomics, Dudelange, Luxembourg
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16
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Choi E, Huh A, Oh C, Oh JI, Kang HY, Hwang J. Functional characterization of HigBA toxin-antitoxin system in an Arctic bacterium, Bosea sp. PAMC 26642. J Microbiol 2022; 60:192-206. [PMID: 35102526 DOI: 10.1007/s12275-022-1619-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/15/2021] [Accepted: 12/20/2021] [Indexed: 01/02/2023]
Abstract
Toxin-antitoxin (TA) systems are growth-controlling genetic elements consisting of an intracellular toxin protein and its cognate antitoxin. TA systems have been spread among microbial genomes through horizontal gene transfer and are now prevalent in most bacterial and archaeal genomes. Under normal growth conditions, antitoxins tightly counteract the activity of the toxins. Upon stresses, antitoxins are inactivated, releasing activated toxins, which induce growth arrest or cell death. In this study, among nine functional TA modules in Bosea sp. PAMC 26642 living in Arctic lichen, we investigated the functionality of BoHigBA2. BohigBA2 is located close to a genomic island and adjacent to flagellar gene clusters. The expression of BohigB2 induced the inhibition of E. coli growth at 37°C, which was more manifest at 18°C, and this growth defect was reversed when BohigA2 was co-expressed, suggesting that this BoHigBA2 module might be an active TA module in Bosea sp. PAMC 26642. Live/dead staining and viable count analyses revealed that the BoHigB2 toxin had a bactericidal effect, causing cell death. Furthermore, we demonstrated that BoHigB2 possessed mRNA-specific ribonuclease activity on various mRNAs and cleaved only mRNAs being translated, which might impede overall translation and consequently lead to cell death. Our study provides the insight to understand the cold adaptation of Bosea sp. PAMC 26642 living in the Arctic.
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Affiliation(s)
- Eunsil Choi
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea.,Microbiological Resource Research Institute, Pusan National University, Busan, 46241, Republic of Korea
| | - Ahhyun Huh
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea
| | - Changmin Oh
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea
| | - Jeong-Il Oh
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea.,Microbiological Resource Research Institute, Pusan National University, Busan, 46241, Republic of Korea
| | - Ho Young Kang
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea.,Microbiological Resource Research Institute, Pusan National University, Busan, 46241, Republic of Korea
| | - Jihwan Hwang
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea. .,Microbiological Resource Research Institute, Pusan National University, Busan, 46241, Republic of Korea.
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17
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Kim DH, Kang SM, Baek SM, Yoon HJ, Jang DM, Kim H, Lee S, Lee BJ. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2319-2333. [PMID: 35141752 PMCID: PMC8887465 DOI: 10.1093/nar/gkab1288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 11/24/2022] Open
Abstract
Staphylococcus aureus is a notorious and globally distributed pathogenic bacterium. New strategies to develop novel antibiotics based on intrinsic bacterial toxin–antitoxin (TA) systems have been recently reported. Because TA systems are present only in bacteria and not in humans, these distinctive systems are attractive targets for developing antibiotics with new modes of action. S. aureus PemIK is a type II TA system, comprising the toxin protein PemK and the labile antitoxin protein PemI. Here, we determined the crystal structures of both PemK and the PemIK complex, in which PemK is neutralized by PemI. Our biochemical approaches, including fluorescence quenching and polarization assays, identified Glu20, Arg25, Thr48, Thr49, and Arg84 of PemK as being important for RNase function. Our study indicates that the active site and RNA-binding residues of PemK are covered by PemI, leading to unique conformational changes in PemK accompanied by repositioning of the loop between β1 and β2. These changes can interfere with RNA binding by PemK. Overall, PemK adopts particular open and closed forms for precise neutralization by PemI. This structural and functional information on PemIK will contribute to the discovery and development of novel antibiotics in the form of peptides or small molecules inhibiting direct binding between PemI and PemK.
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Affiliation(s)
| | | | - Sung-Min Baek
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hye-Jin Yoon
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong Man Jang
- Research Institute, National Cancer Center, Goyang, Gyeonggi 10408, Republic of Korea
| | - Hyoun Sook Kim
- Research Institute, National Cancer Center, Goyang, Gyeonggi 10408, Republic of Korea
| | - Sang Jae Lee
- Correspondence may also be addressed to Sang Jae Lee. Tel: +82 54 279 1490;
| | - Bong-Jin Lee
- To whom correspondence should be addressed. Tel: +82 2 880 7869;
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18
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Singh G, Yadav M, Ghosh C, Rathore JS. Bacterial toxin-antitoxin modules: classification, functions, and association with persistence. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100047. [PMID: 34841338 PMCID: PMC8610362 DOI: 10.1016/j.crmicr.2021.100047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/04/2021] [Accepted: 07/05/2021] [Indexed: 11/24/2022] Open
Abstract
Ubiquitously present bacterial Toxin-Antitoxin (TA) modules consist of stable toxin associated with labile antitoxin. Classification of TAs modules based on inhibition of toxin through antitoxin in 8 different classes. Variety of specific toxin targets and the abundance of TA modules in various deadly pathogens. Specific role of TAs modules in conservation of the resistant genes, emergence of persistence & biofilm formation. Proposed antibacterial strategies involving TA modules for elimination of multi-drug resistance.
Toxin-antitoxin (TA) modules are ubiquitous gene loci among bacteria and are comprised of a toxin part and its cognate antitoxin part. Under normal physiological conditions, antitoxin counteracts the toxicity of the toxin whereas, during stress conditions, TA modules play a crucial role in bacterial physiology through involvement in the post-segregational killing, abortive infection, biofilms, and persister cell formation. Most of the toxins are proteinaceous that affect translation or DNA replication, although some other intracellular molecular targets have also been described. While antitoxins may be a protein or RNA, that generally neutralizes its cognate toxin by direct interaction or with the help of other signaling elements and thus helps in the TA module regulation. In this review, we have discussed the current state of the multifaceted TA (type I–VIII) modules by highlighting their classification and specific targets. We have also discussed the presence of TA modules in the various pathogens and their role in antibiotic persistence development as well as biofilm formation, by influencing the different cellular processes. In the end, assembling knowledge about ubiquitous TA systems from pathogenic bacteria facilitated us to propose multiple novel antibacterial strategies involving artificial activation of TA modules.
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Affiliation(s)
- Garima Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, Yamuna Expressway, Uttar Pradesh, India
| | - Mohit Yadav
- School of Biotechnology, Gautam Buddha University, Greater Noida, Yamuna Expressway, Uttar Pradesh, India
| | - Chaitali Ghosh
- Department of Zoology Gargi College, University of Delhi, New Delhi, India
| | - Jitendra Singh Rathore
- School of Biotechnology, Gautam Buddha University, Greater Noida, Yamuna Expressway, Uttar Pradesh, India
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Xue L, Khan MH, Yue J, Zhu Z, Niu L. The two paralogous copies of the YoeB-YefM toxin-antitoxin module in Staphylococcus aureus differ in DNA binding and recognition patterns. J Biol Chem 2021; 298:101457. [PMID: 34861238 PMCID: PMC8717551 DOI: 10.1016/j.jbc.2021.101457] [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: 09/11/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 12/13/2022] Open
Abstract
Toxin-antitoxin (TA) systems are ubiquitous regulatory modules for bacterial growth and cell survival following stress. YefM-YoeB, the most prevalent type II TA system, is present in a variety of bacterial species. In Staphylococcus aureus, the YefM-YoeB system exists as two independent paralogous copies. Our previous research resolved crystal structures of the two oligomeric states (heterotetramer and heterohexamer-DNA ternary complex) of the first paralog as well as the molecular mechanism of transcriptional autoregulation of this module. However, structural details reflecting molecular diversity in both paralogs have been relatively unexplored. To understand the molecular mechanism of how Sa2YoeB and Sa2YefM regulate their own transcription and how each paralog functions independently, we solved a series of crystal structures of the Sa2YoeB-Sa2YefM. Our structural and biochemical data demonstrated that both paralogous copies adopt similar mechanisms of transcriptional autoregulation. In addition, structural analysis suggested that molecular diversity between the two paralogs might be reflected in the interaction profile of YefM and YoeB and the recognition pattern of promoter DNA by YefM. Interaction analysis revealed unique conformational and activating force effected by the interface between Sa2YoeB and Sa2YefM. In addition, the recognition pattern analysis demonstrated that residues Thr7 and Tyr14 of Sa2YefM specifically recognizes the flanking sequences (G and C) of the promoter DNA. Together, these results provide the structural insights into the molecular diversity and independent function of the paralogous copies of the YoeB-YefM TA system.
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Affiliation(s)
- Lu Xue
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui, China; Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Muhammad Hidayatullah Khan
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui, China; Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Jian Yue
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui, China; Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Zhongliang Zhu
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui, China; Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
| | - Liwen Niu
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui, China; Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
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20
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Heikema AP, Strepis N, Horst-Kreft D, Huynh S, Zomer A, Kelly DJ, Cooper KK, Parker CT. Biomolecule sulphation and novel methylations related to Guillain-Barré syndrome-associated Campylobacter jejuni serotype HS:19. Microb Genom 2021; 7. [PMID: 34723785 PMCID: PMC8743553 DOI: 10.1099/mgen.0.000660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Campylobacter jejuni strains that produce sialylated lipooligosaccharides (LOS) can cause the immune-mediated disease Guillain-Barré syndrome (GBS). The risk of GBS after infection with C. jejuni Penner serotype HS:19 is estimated to be at least six times higher than the average risk. Aside from LOS biosynthesis genes, genomic characteristics that promote an increased risk for GBS following C. jejuni HS:19 infection, remain uncharacterized. We hypothesized that strains with the HS:19 serotype have unique genomic features that explain the increased risk for GBS. We performed genome sequencing, alignments, single nucleotide polymorphisms' analysis and methylome characterization on a subset, and pan-genome analysis on a large number of genomes to compare HS:19 with non-HS:19 C. jejuni genome sequences. Comparison of 36 C. jejuni HS:19 with 874 C. jejuni non-HS:19 genome sequences led to the identification of three single genes and ten clusters containing contiguous genes that were significantly associated with C. jejuni HS:19. One gene cluster of seven genes, localized downstream of the capsular biosynthesis locus, was related to sulphation of biomolecules. This cluster also encoded the campylobacter sialyl transferase Cst-I. Interestingly, sulphated bacterial biomolecules such as polysaccharides can promote immune responses and, therefore, (in the presence of sialic acid) may play a role in the development of GBS. Additional gene clusters included those involved in persistence-mediated pathogenicity and gene clusters involved in restriction-modification systems. Furthermore, characterization of methylomes of two HS:19 strains exhibited novel methylation patterns (5′-CATG-3 and 5′-m6AGTNNNNNNRTTG-3) that could differentially effect gene-expression patterns of C. jejuni HS:19 strains. Our study provides novel insight into specific genetic features and possible virulence factors of C. jejuni associated with the HS:19 serotype that may explain the increased risk of GBS.
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Affiliation(s)
- Astrid P. Heikema
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre (Erasmus MC), Rotterdam, The Netherlands
- *Correspondence: Astrid P. Heikema,
| | - Nikolaos Strepis
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre (Erasmus MC), Rotterdam, The Netherlands
| | - Deborah Horst-Kreft
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre (Erasmus MC), Rotterdam, The Netherlands
| | - Steven Huynh
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, United States Department of Agriculture, Albany, California, USA
| | - Aldert Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - David J. Kelly
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Kerry K. Cooper
- School of Animal and Comparative Biomedical Sciences, College of Agriculture and Life Sciences, University of Arizona, Tucson, Arizona, USA
| | - Craig T. Parker
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, United States Department of Agriculture, Albany, California, USA
- *Correspondence: Craig T. Parker,
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21
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Jeon H, Choi E, Hwang J. Identification and characterization of VapBC toxin-antitoxin system in Bosea sp. PAMC 26642 isolated from Arctic lichens. RNA (NEW YORK, N.Y.) 2021; 27:1374-1389. [PMID: 34429367 PMCID: PMC8522696 DOI: 10.1261/rna.078786.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Toxin-antitoxin (TA) systems are genetic modules composed of a toxin interfering with cellular processes and its cognate antitoxin, which counteracts the activity of the toxin. TA modules are widespread in bacterial and archaeal genomes. It has been suggested that TA modules participate in the adaptation of prokaryotes to unfavorable conditions. The Bosea sp. PAMC 26642 used in this study was isolated from the Arctic lichen Stereocaulon sp. There are 12 putative type II TA loci in the genome of Bosea sp. PAMC 26642. Of these, nine functional TA systems have been shown to be toxic in Escherichia coli The toxin inhibits growth, but this inhibition is reversed when the cognate antitoxin genes are coexpressed, indicating that these putative TA loci were bona fide TA modules. Only the BoVapC1 (AXW83_01405) toxin, a homolog of VapC, showed growth inhibition specific to low temperatures, which was recovered by the coexpression of BoVapB1 (AXW83_01400). Microscopic observation and growth monitoring revealed that the BoVapC1 toxin had bacteriostatic effects on the growth of E. coli and induced morphological changes. Quantitative real time polymerase chain reaction and northern blotting analyses showed that the BoVapC1 toxin had a ribonuclease activity on the initiator tRNAfMet, implying that degradation of tRNAfMet might trigger growth arrest in E. coli Furthermore, the BoVapBC1 system was found to contribute to survival against prolonged exposure at 4°C. This is the first study to identify the function of TA systems in cold adaptation.
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Affiliation(s)
- Hyerin Jeon
- Department of Microbiology, Pusan National University, Busan 46241, Republic of Korea
| | - Eunsil Choi
- Department of Microbiology, Pusan National University, Busan 46241, Republic of Korea
- Microbiological Resource Research Institute, Pusan National University, Busan 46241, Republic of Korea
| | - Jihwan Hwang
- Department of Microbiology, Pusan National University, Busan 46241, Republic of Korea
- Microbiological Resource Research Institute, Pusan National University, Busan 46241, Republic of Korea
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22
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Yadav SK, Magotra A, Ghosh S, Krishnan A, Pradhan A, Kumar R, Das J, Sharma M, Jha G. Immunity proteins of dual nuclease T6SS effectors function as transcriptional repressors. EMBO Rep 2021; 22:e51857. [PMID: 33786997 PMCID: PMC8183406 DOI: 10.15252/embr.202051857] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 02/26/2021] [Accepted: 03/08/2021] [Indexed: 12/31/2022] Open
Abstract
Bacteria utilize type VI secretion system (T6SS) to deliver antibacterial toxins to target co-habiting bacteria. Here, we report that Burkholderia gladioli strain NGJ1 deploys certain T6SS effectors (TseTBg), having both DNase and RNase activities to kill target bacteria. RNase activity is prominent on NGJ1 as well as other bacterial RNA while DNase activity is pertinent to only other bacteria. The associated immunity (TsiTBg) proteins harbor non-canonical helix-turn-helix motifs and demonstrate transcriptional repression activity, similar to the antitoxins of type II toxin-antitoxin (TA) systems. Genome analysis reveals that homologs of TseTBg are either encoded as TA or T6SS effectors in diverse bacteria. Our results indicate that a new ORF (encoding a hypothetical protein) has evolved as a result of operonic fusion of TA type TseTBg homolog with certain T6SS-related genes by the action of IS3 transposable elements. This has potentially led to the conversion of a TA into T6SS effector in Burkholderia. Our study exemplifies that bacteria can recruit toxins of TA systems as T6SS weapons to diversify its arsenal to dominate during inter-bacterial competitions.
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Affiliation(s)
- Sunil Kumar Yadav
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Ankita Magotra
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Srayan Ghosh
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Aiswarya Krishnan
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Amrita Pradhan
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Rahul Kumar
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Joyati Das
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Mamta Sharma
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Gopaljee Jha
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
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23
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Hossain T, Deter HS, Peters EJ, Butzin NC. Antibiotic tolerance, persistence, and resistance of the evolved minimal cell, Mycoplasma mycoides JCVI-Syn3B. iScience 2021; 24:102391. [PMID: 33997676 PMCID: PMC8091054 DOI: 10.1016/j.isci.2021.102391] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 02/01/2021] [Accepted: 03/31/2021] [Indexed: 12/22/2022] Open
Abstract
Antibiotic resistance is a growing problem, but bacteria can evade antibiotic treatment via tolerance and persistence. Antibiotic persisters are a small subpopulation of bacteria that tolerate antibiotics due to a physiologically dormant state. Hence, persistence is considered a major contributor to the evolution of antibiotic-resistant and relapsing infections. Here, we used the synthetically developed minimal cell Mycoplasma mycoides JCVI-Syn3B to examine essential mechanisms of antibiotic survival. The minimal cell contains only 473 genes, and most genes are essential. Its reduced complexity helps to reveal hidden phenomenon and fundamental biological principles can be explored because of less redundancy and feedback between systems compared to natural cells. We found that Syn3B evolves antibiotic resistance to different types of antibiotics expeditiously. The minimal cell also tolerates and persists against multiple antibiotics. It contains a few already identified persister-related genes, although lacking many systems previously linked to persistence (e.g. toxin-antitoxin systems, ribosome hibernation genes).
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Affiliation(s)
- Tahmina Hossain
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA
| | - Heather S. Deter
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Eliza J. Peters
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA
| | - Nicholas C. Butzin
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA
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24
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Jin C, Kang SM, Kim DH, Lee BJ. Structural and functional analysis of the Klebsiella pneumoniae MazEF toxin-antitoxin system. IUCRJ 2021; 8:362-371. [PMID: 33953923 PMCID: PMC8086154 DOI: 10.1107/s2052252521000452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
Bacterial toxin-antitoxin (TA) systems correlate strongly with physiological processes in bacteria, such as growth arrest, survival and apoptosis. Here, the first crystal structure of a type II TA complex structure of Klebsiella pneumoniae at 2.3 Å resolution is presented. The K. pneumoniae MazEF complex consists of two MazEs and four MazFs in a heterohexameric assembly. It was estimated that MazEF forms a dodecamer with two heterohexameric MazEF complexes in solution, and a truncated complex exists in heterohexameric form. The MazE antitoxin interacts with the MazF toxin via two binding modes, namely, hydro-phobic and hydro-philic interactions. Compared with structural homologs, K. pneumoniae MazF shows distinct features in loops β1-β2, β3-β4 and β4-β5. It can be inferred that these three loops have the potential to represent the unique characteristics of MazF, especially various substrate recognition sites. In addition, K. pneumoniae MazF shows ribonuclease activity and the catalytic core of MazF lies in an RNA-binding pocket. Mutation experiments and cell-growth assays confirm Arg28 and Thr51 as critical residues for MazF ribonuclease activity. The findings shown here may contribute to the understanding of the bacterial MazEF TA system and the exploration of antimicrobial candidates to treat drug-resistant K. pneumoniae.
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Affiliation(s)
- Chenglong Jin
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Sung-Min Kang
- College of Pharmacy, Duksung Women’s University, Seoul, 01369, Republic of Korea
| | - Do-Hee Kim
- College of Pharmacy, Jeju National University, Jeju, 63243, Republic of Korea
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju, 63243, Republic of Korea
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul, 08826, Republic of Korea
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25
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Kahan R, Worm DJ, de Castro GV, Ng S, Barnard A. Modulators of protein-protein interactions as antimicrobial agents. RSC Chem Biol 2021; 2:387-409. [PMID: 34458791 PMCID: PMC8341153 DOI: 10.1039/d0cb00205d] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/27/2021] [Indexed: 12/12/2022] Open
Abstract
Protein-Protein interactions (PPIs) are involved in a myriad of cellular processes in all living organisms and the modulation of PPIs is already under investigation for the development of new drugs targeting cancers, autoimmune diseases and viruses. PPIs are also involved in the regulation of vital functions in bacteria and, therefore, targeting bacterial PPIs offers an attractive strategy for the development of antibiotics with novel modes of action. The latter are urgently needed to tackle multidrug-resistant and multidrug-tolerant bacteria. In this review, we describe recent developments in the modulation of PPIs in pathogenic bacteria for antibiotic development, including advanced small molecule and peptide inhibitors acting on bacterial PPIs involved in division, replication and transcription, outer membrane protein biogenesis, with an additional focus on toxin-antitoxin systems as upcoming drug targets.
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Affiliation(s)
- Rashi Kahan
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Dennis J Worm
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Guilherme V de Castro
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Simon Ng
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
| | - Anna Barnard
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane London W12 0BZ UK
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26
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Kang SM, Moon H, Han SW, Kim BW, Kim DH, Kim BM, Lee BJ. Toxin-Activating Stapled Peptides Discovered by Structural Analysis Were Identified as New Therapeutic Candidates That Trigger Antibacterial Activity against Mycobacterium tuberculosis in the Mycobacterium smegmatis Model. Microorganisms 2021; 9:microorganisms9030568. [PMID: 33801872 PMCID: PMC8000039 DOI: 10.3390/microorganisms9030568] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 11/17/2022] Open
Abstract
The structure-function relationships of toxin-antitoxin (TA) systems from Mycobacterium tuberculosis have prompted the development of novel and effective antimicrobial agents that selectively target this organism. The artificial activation of toxins by peptide inhibitors can lead to the growth arrest and eventual death of bacterial cells. Optimizing candidate peptides by hydrocarbon α-helix stapling based on structural information from the VapBC TA system and in vitro systematic validation led to V26-SP-8, a VapC26 activator of M. tuberculosis. This compound exhibited highly enhanced activity and cell permeability owing to the stabilizing helical propensity of the peptide. These characteristics will increase its efficacy against multidrug-resistant tuberculosis and extensively drug-resistant tuberculosis. Similar approaches utilizing structural and biochemical information for new antibiotic targets opens a new era for developing TB therapies.
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Affiliation(s)
- Sung-Min Kang
- College of Pharmacy, Duksung Women’s University, Seoul 01369, Korea;
| | - Heejo Moon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Korea; (H.M.); (B.W.K.)
| | - Sang-Woo Han
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea;
| | - Byeong Wook Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Korea; (H.M.); (B.W.K.)
| | - Do-Hee Kim
- College of Pharmacy, Jeju National University, Jeju 63243, Korea;
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju 63243, Korea
| | - Byeong Moon Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Korea; (H.M.); (B.W.K.)
- Correspondence: (B.M.K.); (B.-J.L.); Tel.: +82-2-880-6634 (B.M.K.); +82-2-880-7868 (B.-J.L.)
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea;
- Correspondence: (B.M.K.); (B.-J.L.); Tel.: +82-2-880-6634 (B.M.K.); +82-2-880-7868 (B.-J.L.)
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27
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Kang S, Jin C, Kim D, Park SJ, Han S, Lee B. Structure-based design of peptides that trigger Streptococcus pneumoniae cell death. FEBS J 2021; 288:1546-1564. [PMID: 32770723 PMCID: PMC7984235 DOI: 10.1111/febs.15514] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 06/30/2020] [Accepted: 08/06/2020] [Indexed: 01/08/2023]
Abstract
Toxin-antitoxin (TA) systems regulate key cellular functions in bacteria. Here, we report a unique structure of the Streptococcus pneumoniae HigBA system and a novel antimicrobial agent that activates HigB toxin, which results in mRNA degradation as an antibacterial strategy. In this study, protein structure-based peptides were designed and successfully penetrated the S. pneumoniae cell membrane and exerted bactericidal activity. This result represents the time during which inhibitors triggered S. pneumoniae cell death via the TA system. This discovery is a remarkable milestone in the treatment of antibiotic-resistant S. pneumoniae, and the mechanism of bactericidal activity is completely different from those of current antibiotics. Furthermore, we found that the HigBA complex shows a crossed-scissor interface with two intermolecular β-sheets at both the N and C termini of the HigA antitoxin. Our biochemical and structural studies provided valuable information regarding the transcriptional regulation mechanisms associated with the structural variability of HigAs. Our in vivo study also revealed the potential catalytic residues of HigB and their functional relationships. An inhibition study with peptides additionally proved that peptide binding may allosterically inhibit HigB activity. Overall, our results provide insights into the molecular basis of HigBA TA systems in S. pneumoniae, which can be applied for the development of new antibacterial strategies. DATABASES: Structural data are available in the PDB database under the accession number 6AF4.
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Affiliation(s)
- Sung‐Min Kang
- Research Institute of Pharmaceutical Sciences, College of PharmacySeoul National UniversityGwanak‐guSeoulKorea
| | - Chenglong Jin
- Research Institute of Pharmaceutical Sciences, College of PharmacySeoul National UniversityGwanak‐guSeoulKorea
| | - Do‐Hee Kim
- College of PharmacyJeju National UniversityJejuKorea
- Interdisciplinary Graduate Program in Advanced Convergence Technology & ScienceJeju National UniversityJejuKorea
| | - Sung Jean Park
- Gachon Institute of Pharmaceutical Sciences, College of PharmacyGachon UniversityIncheonKorea
| | - Sang‐Woo Han
- Research Institute of Pharmaceutical Sciences, College of PharmacySeoul National UniversityGwanak‐guSeoulKorea
| | - Bong‐Jin Lee
- Research Institute of Pharmaceutical Sciences, College of PharmacySeoul National UniversityGwanak‐guSeoulKorea
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28
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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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29
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Xue L, Yue J, Ke J, Khan MH, Wen W, Sun B, Zhu Z, Niu L. Distinct oligomeric structures of the YoeB-YefM complex provide insights into the conditional cooperativity of type II toxin-antitoxin system. Nucleic Acids Res 2020; 48:10527-10541. [PMID: 32845304 PMCID: PMC7544224 DOI: 10.1093/nar/gkaa706] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 08/07/2020] [Accepted: 08/14/2020] [Indexed: 12/21/2022] Open
Abstract
YoeB-YefM, the widespread type II toxin-antitoxin (TA) module, binds to its own promoter to autoregulate its transcription: repress or induce transcription under normal or stress conditions, respectively. It remains unclear how YoeB-YefM regulates its transcription depending on the YoeB to YefM TA ratio. We find that YoeB-YefM complex from S.aureus exists as two distinct oligomeric assemblies: heterotetramer (YoeB-YefM2-YoeB) and heterohexamer (YoeB-YefM2-YefM2-YoeB) with low and high DNA-binding affinities, respectively. Structures of the heterotetramer alone and heterohexamer bound to promoter DNA reveals that YefM C-terminal domain undergoes disorder to order transition upon YoeB binding, which allosterically affects the conformation of N-terminal DNA-binding domain. At TA ratio of 1:2, unsaturated binding of YoeB to the C-terminal regions of YefM dimer forms an optimal heterohexamer for DNA binding, and two YefM dimers with N-terminal domains dock into the adjacent major grooves of DNA to specifically recognize the 5'-TTGTACAN6AGTACAA-3' palindromic sequence, resulting in transcriptional repression. In contrast, at TA ratio of 1:1, binding of two additional YoeB molecules onto the heterohexamer induces the completely ordered conformation of YefM and disassembles the heterohexamer into two heterotetramers, which are unable to bind the promoter DNA optimally due to steric clashes, hence derepresses TA operon transcription.
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Affiliation(s)
- Lu Xue
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui 230026, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jian Yue
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui 230026, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jiyuan Ke
- Lead Discovery Department, H3 Biomedicine Inc, 300 Technology Square FL 5, Cambridge, MA 02139, USA
| | - Muhammad Hidayatullah Khan
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui 230026, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Wen Wen
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Baolin Sun
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zhongliang Zhu
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui 230026, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Liwen Niu
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui 230026, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
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30
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Kang SM, Jin C, Kim DH, Lee Y, Lee BJ. Structural and Functional Study of the Klebsiella pneumoniae VapBC Toxin-Antitoxin System, Including the Development of an Inhibitor That Activates VapC. J Med Chem 2020; 63:13669-13679. [PMID: 33146528 DOI: 10.1021/acs.jmedchem.0c01118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Klebsiella pneumoniae is one of the most critical opportunistic pathogens. TA systems are promising drug targets because they are related to the survival of bacterial pathogens. However, structural information on TA systems in K. pneumoniae remains lacking; therefore, it is necessary to explore this information for the development of antibacterial agents. Here, we present the first crystal structure of the VapBC complex from K. pneumoniae at a resolution of 2.00 Å. We determined the toxin inhibitory mechanism of the VapB antitoxin through an Mg2+ switch, in which Mg2+ is displaced by R79 of VapB. This inhibitory mechanism of the active site is a novel finding and the first to be identified in a bacterial TA system. Furthermore, inhibitors, including peptides and small molecules, that activate the VapC toxin were discovered and investigated. These inhibitors can act as antimicrobial agents by disrupting the VapBC complex and activating VapC. Our comprehensive investigation of the K. pneumoniae VapBC system will help elucidate an unsolved conundrum in VapBC systems and develop potential antimicrobial agents.
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Affiliation(s)
- Sung-Min Kang
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Chenglong Jin
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Do-Hee Kim
- College of Pharmacy, Jeju National University, Jeju 63243, Korea.,Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju 63243, Korea
| | - Yuno Lee
- Korea Chemical Bank, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
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31
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Similarities and differences between 6S RNAs from Bradyrhizobium japonicum and Sinorhizobium meliloti. J Microbiol 2020; 58:945-956. [PMID: 33125669 DOI: 10.1007/s12275-020-0283-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/03/2020] [Accepted: 08/03/2020] [Indexed: 10/23/2022]
Abstract
6S RNA, a conserved and abundant small non-coding RNA found in most bacteria, regulates gene expression by inhibiting RNA polymerase (RNAP) holoenzyme. 6S RNAs from α-proteobacteria have been studied poorly so far. Here, we present a first in-depth analysis of 6S RNAs from two α-proteobacteria species, Bradyrhizobium japonicum and Sinorhizobium meliloti. Although both belong to the order Rhizobiales and are typical nitrogen-fixing symbionts of legumes, their 6S RNA expression profiles were found to differ: B. japonicum 6S RNA accumulated in the stationary phase, thus being reminiscent of Escherichia coli 6S RNA, whereas S. meliloti 6S RNA level peaked at the transition to the stationary phase, similarly to Rhodobacter sphaeroides 6S RNA. We demonstrated in vitro that both RNAs have hallmarks of 6S RNAs: they bind to the σ70-type RNAP holoenzyme and serve as templates for de novo transcription of so-called product RNAs (pRNAs) ranging in length from ∼13 to 24 nucleotides, with further evidence of the synthesis of even longer pRNAs. Likewise, stably bound pRNAs were found to rearrange the 6S RNA structure to induce its dissociation from RNAP. Compared with B. japonicum 6S RNA, considerable conformational heterogeneity was observed for S. meliloti 6S RNA and its complexes with pRNAs, even though the two 6S RNAs share ∼75% sequence identity. Overall, our findings suggest that the two rhizobial 6S RNAs have diverged with respect to their regulatory impact on gene expression throughout the bacterial life cycle.
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32
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Kang SM, Moon H, Han SW, Kim DH, Kim BM, Lee BJ. Structure-Based De Novo Design of Mycobacterium Tuberculosis VapC-Activating Stapled Peptides. ACS Chem Biol 2020; 15:2493-2498. [PMID: 32840352 DOI: 10.1021/acschembio.0c00492] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Toxin-antitoxin (TA) systems have been considered essential factors for bacterial survival. During our drug development program aimed against tuberculosis (TB), we discovered certain peptides that mimic the binding of the VapBC30 complex, leading to the arrest of bacterial cell growth and eventually cell death. Herein, we optimized these candidate peptides based on a hydrocarbon stapling strategy and performed biological in vitro evaluations. The V30-SP-8 peptide successfully penetrated Mycobacterium smegmatis cell membranes and exerted bactericidal activity at a minimum inhibitory concentration that inhibited 50% of the isolates (MIC50) < 6.25 μM. With the aid of structural and biochemical information for the VapBC30 TA system from M. tuberculosis, we suggest potential antimicrobial agents that could provide a platform to establish a novel antibacterial strategy. Reflecting the limited number of therapeutic agents targeting TA systems, we believe that this study not only provides chemical tools for exploring the biological events relevant to TA systems but also opens a new gateway toward TB drug discovery.
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Affiliation(s)
- Sung-Min Kang
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Heejo Moon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang-Woo Han
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Do-Hee Kim
- College of Pharmacy, Jeju National University, Jeju 63243, Republic of Korea
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju, 63243 Republic of Korea
| | - Byeong Moon Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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33
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Sharma A, Chattopadhyay G, Chopra P, Bhasin M, Thakur C, Agarwal S, Ahmed S, Chandra N, Varadarajan R, Singh R. VapC21 Toxin Contributes to Drug-Tolerance and Interacts With Non-cognate VapB32 Antitoxin in Mycobacterium tuberculosis. Front Microbiol 2020; 11:2037. [PMID: 33042034 PMCID: PMC7517352 DOI: 10.3389/fmicb.2020.02037] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/31/2020] [Indexed: 12/13/2022] Open
Abstract
The prokaryotic ubiquitous Toxin-antitoxin (TA) modules encodes for a stable toxin and an unstable antitoxin. VapBC subfamily is the most abundant Type II TA system in M. tuberculosis genome. However, the exact physiological role for most of these Type II TA systems are still unknown. Here, we have comprehensively characterized the VapBC21 TA locus from M. tuberculosis. The overexpression of VapC21 inhibited mycobacterial growth in a bacteriostatic manner and as expected, growth inhibition was abrogated upon co-expression of the cognate antitoxin, VapB21. We observed that the deletion of vapC21 had no noticeable influence on the in vitro and in vivo growth of M. tuberculosis. Using co-expression and biophysical studies, we observed that in addition to VapB21, VapC21 is also able to interact with non-cognate antitoxin, VapB32. The strength of interaction varied between the cognate and non-cognate TA pairs. The overexpression of VapC21 resulted in differential expression of approximately 435 transcripts in M. tuberculosis. The transcriptional profiles obtained upon ectopic expression of VapC21 was similar to those reported in M. tuberculosis upon exposure to stress conditions such as nutrient starvation and enduring hypoxic response. Further, VapC21 overexpression also led to increased expression of WhiB7 regulon and bacterial tolerance to aminoglycosides and ethambutol. Taken together, these results indicate that a complex network of interactions exists between non-cognate TA pairs and VapC21 contributes to drug tolerance in vitro.
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Affiliation(s)
- Arun Sharma
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | | | - Pankaj Chopra
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Munmun Bhasin
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India
| | - Chandrani Thakur
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Sakshi Agarwal
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
| | - Shahbaz Ahmed
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Ramandeep Singh
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, India
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Targeting Type II Toxin-Antitoxin Systems as Antibacterial Strategies. Toxins (Basel) 2020; 12:toxins12090568. [PMID: 32899634 PMCID: PMC7551001 DOI: 10.3390/toxins12090568] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 08/31/2020] [Accepted: 08/31/2020] [Indexed: 12/13/2022] Open
Abstract
The identification of novel targets for antimicrobial agents is crucial for combating infectious diseases caused by evolving bacterial pathogens. Components of bacterial toxin–antitoxin (TA) systems have been recognized as promising therapeutic targets. These widespread genetic modules are usually composed of two genes that encode a toxic protein targeting an essential cellular process and an antitoxin that counteracts the activity of the toxin. Uncontrolled toxin expression may elicit a bactericidal effect, so they may be considered “intracellular molecular bombs” that can lead to elimination of their host cells. Based on the molecular nature of antitoxins and their mode of interaction with toxins, TA systems have been classified into six groups. The most prevalent are type II TA systems. Due to their ubiquity among clinical isolates of pathogenic bacteria and the essential processes targeted, they are promising candidates for the development of novel antimicrobial strategies. In this review, we describe the distribution of type II TA systems in clinically relevant human pathogens, examine how these systems could be developed as the targets for novel antibacterials, and discuss possible undesirable effects of such therapeutic intervention, such as the induction of persister cells, biofilm formation and toxicity to eukaryotic cells.
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35
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Janczak M, Hyz K, Bukowski M, Lyzen R, Hydzik M, Wegrzyn G, Szalewska-Palasz A, Grudnik P, Dubin G, Wladyka B. Chromosomal localization of PemIK toxin-antitoxin system results in the loss of toxicity - Characterization of pemIK Sa1-Sp from Staphylococcus pseudintermedius. Microbiol Res 2020; 240:126529. [PMID: 32622987 DOI: 10.1016/j.micres.2020.126529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 11/20/2022]
Abstract
Toxin-antitoxin (TA) systems are ubiquitous in bacteria and on numerous occasions have been postulated to play a role in virulence of pathogens. Some Staphylococcus aureus strains carry a plasmid, which encodes the highly toxic PemIKSa TA system involved in maintenance of the plasmid but also implicated in modulation of gene expression. Here we showed that pemIKSa1-Sp TA system, homologous to the plasmid-encoded PemIKSa, is present in virtually each chromosome of S. pseudintermedius strain, however exhibits sequence heterogeneity. This results in two length variants of the PemKSa1-Sp toxin. The shorter (96 aa), C-terminally truncated toxin is enzymatically inactive, whereas the full length (112 aa) variant is an RNase, though nontoxic to the host cells. The lack of toxicity of the active PemKSa-Sp2 toxin is explained by increased substrate specificity. The pemISa1-Sp antitoxin gene seems pseudogenized, however, the whole pemIKSa1-Sp system is transcriptionally active. When production of N-terminally truncated antitoxins using alternative start codons is assumed, there are five possible length variants. Here we showed that even substantially truncated antitoxins are able to interact with PemKSa-Sp2 toxin and inhibit its RNase activity. Moreover, the antitoxins can rescue bacterial cells from toxic effects of overexpression of plasmid-encoded PemKSa toxin. Collectively, our data indicates that, contrary to the toxic plasmid-encoded PemIKSa TA system, location of pemIKSa1-Sp in the chromosome of S. pseudintermedius results in the loss of its toxicity. Interestingly, the retained RNase activity of PemKSa1-Sp2 toxin and functionality of the putative, N-terminally truncated antitoxins suggest the existence of evolutionary pressure for alleviation/mitigation of the toxin's toxicity and retention of the inhibitory activity of the antitoxin, respectively.
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Affiliation(s)
- Monika Janczak
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Karolina Hyz
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Michal Bukowski
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Robert Lyzen
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdansk, Gdansk, Poland
| | - Marcin Hydzik
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Grzegorz Wegrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | | | - Przemyslaw Grudnik
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Benedykt Wladyka
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
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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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37
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Kang SM, Koo JS, Kim CM, Kim DH, Lee BJ. mRNA Interferase Bacillus cereus BC0266 Shows MazF-Like Characteristics Through Structural and Functional Study. Toxins (Basel) 2020; 12:toxins12060380. [PMID: 32521689 PMCID: PMC7354611 DOI: 10.3390/toxins12060380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/05/2020] [Accepted: 06/06/2020] [Indexed: 11/16/2022] Open
Abstract
Toxin–antitoxin (TA) systems are prevalent in bacteria and are known to regulate cellular growth in response to stress. As various functions related to TA systems have been revealed, the importance of TA systems are rapidly emerging. Here, we present the crystal structure of putative mRNA interferase BC0266 and report it as a type II toxin MazF. The MazF toxin is a ribonuclease activated upon and during stressful conditions, in which it cleaves mRNA in a sequence-specific, ribosome-independent manner. Its prolonged activity causes toxic consequences to the bacteria which, in turn, may lead to bacterial death. In this study, we conducted structural and functional investigations of Bacillus cereus MazF and present the first toxin structure in the TA system of B. cereus. Specifically, B. cereus MazF adopts a PemK-like fold and also has an RNA substrate-recognizing loop, which is clearly observed in the high-resolution structure. Key residues of B. cereus MazF involved in the catalytic activity are also proposed, and in vitro assay together with mutational studies affirm the ribonucleic activity and the active sites essential for its cellular toxicity.
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Affiliation(s)
- Sung-Min Kang
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanakgu, Seoul 08826, Korea; (S.-M.K.); (J.S.K.); (C.-M.K.)
| | - Ji Sung Koo
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanakgu, Seoul 08826, Korea; (S.-M.K.); (J.S.K.); (C.-M.K.)
| | - Chang-Min Kim
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanakgu, Seoul 08826, Korea; (S.-M.K.); (J.S.K.); (C.-M.K.)
| | - Do-Hee Kim
- College of Pharmacy, Jeju National University, Jeju 63243, Korea;
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanakgu, Seoul 08826, Korea; (S.-M.K.); (J.S.K.); (C.-M.K.)
- Correspondence: ; Tel.: +82-2-880-7869
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Characterization of a toxin-antitoxin system in Mycobacterium tuberculosis suggests neutralization by phosphorylation as the antitoxicity mechanism. Commun Biol 2020; 3:216. [PMID: 32382148 PMCID: PMC7205606 DOI: 10.1038/s42003-020-0941-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/10/2020] [Indexed: 01/06/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) encodes an exceptionally large number of toxin-antitoxin (TA) systems, supporting the hypothesis that TA systems are involved in pathogenesis. We characterized the putative Mtb Rv1044-Rv1045 TA locus structurally and functionally, demonstrating that it constitutes a bona fide TA system but adopts a previously unobserved antitoxicity mechanism involving phosphorylation of the toxin. While Rv1045 encodes the guanylyltransferase TglT functioning as a toxin, Rv1044 encodes the novel atypical serine protein kinase TakA, which specifically phosphorylates the cognate toxin at residue S78, thereby neutralizing its toxicity. In contrast to previous predictions, we found that Rv1044-Rv1045 does not belong to the type IV TA family because TglT and TakA interact with each other as substrate and kinase, suggesting an unusual type of TA system. Protein homology analysis suggests that other COG5340-DUF1814 protein pairs, two highly associated but uncharacterized protein families widespread in prokaryotes, might share this unusual antitoxicity mechanism. Xia Yu et al. report the characterization of a toxin-antitoxin system with an unusual mechanism in Mycobacterium tuberculosis. They find that the antitoxin locus Rv1044 encodes an atypical serine protein kinase that phosphorylates the toxin to neutralize toxicity.
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Sterling AJ, Snelling WJ, Naughton PJ, Ternan NG, Dooley JSG. Competent but complex communication: The phenomena of pheromone-responsive plasmids. PLoS Pathog 2020; 16:e1008310. [PMID: 32240270 PMCID: PMC7117660 DOI: 10.1371/journal.ppat.1008310] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Enterococci are robust gram-positive bacteria that are found in a variety of surroundings and that cause a significant number of healthcare-associated infections. The genus possesses a high-efficiency pheromone-responsive plasmid (PRP) transfer system for genetic exchange that allows antimicrobial-resistance determinants to spread within bacterial populations. The pCF10 plasmid system is the best characterised, and although other PRP systems are structurally similar, they lack exact functional homologues of pCF10-encoded genes. In this review, we provide an overview of the enterococcal PRP systems, incorporating functional details for the less-well-defined systems. We catalogue the virulence-associated elements of the PRPs that have been identified to date, and we argue that this reinforces the requirement for elucidation of the less studied systems.
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Affiliation(s)
- Amy J. Sterling
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Londonderry, Northern Ireland
- * E-mail:
| | - William J. Snelling
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Londonderry, Northern Ireland
| | - Patrick J. Naughton
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Londonderry, Northern Ireland
| | - Nigel G. Ternan
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Londonderry, Northern Ireland
| | - James S. G. Dooley
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Londonderry, Northern Ireland
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40
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Opazo-Capurro A, Higgins PG, Wille J, Seifert H, Cigarroa C, González-Muñoz P, Quezada-Aguiluz M, Domínguez-Yévenes M, Bello-Toledo H, Vergara L, González-Rocha G. Genetic Features of Antarctic Acinetobacter radioresistens Strain A154 Harboring Multiple Antibiotic-Resistance Genes. Front Cell Infect Microbiol 2019; 9:328. [PMID: 31608244 PMCID: PMC6755334 DOI: 10.3389/fcimb.2019.00328] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/02/2019] [Indexed: 12/03/2022] Open
Abstract
While antibiotic-resistant bacteria have been detected in extreme environments, including Antarctica, to date there are no reports of Acinetobacter species isolated from this region. Here, we characterized by whole-genome sequencing (WGS) the genetic content of a single antibiotic-resistant Acinetobacter spp. isolate (A154) collected in Antarctica. The isolate was recovered in 2013 from soil samples at Fildes Peninsula, Antarctica, and was identified by detection of the intrinsic OXA-23 gene, and confirmed by Tetra Correlation Search (TCS) and WGS. The antibiotic susceptibility profile was determined by disc diffusion, E-test, and broth microdilution methods. From WGS data, the acquired resistome and insertion sequence (IS) content were identified by in silico analyses. Plasmids were studied by the alkaline lysis method followed by pulsed-field gel electrophoresis and conventional PCR. The A154 isolate was identified as A. radioresistens by WGS analysis and displayed >99.9 of similarity by TCS in relation with the databases. Moreover, it was resistant to ampicillin, ceftriaxone, ceftazidime, cefepime, cefotaxime, streptomycin, and kanamycin. Likewise, in addition to the intrinsic blaOXA−23−like gene, A154 harbored the plasmid-encoded antibiotic-resistance genes blaPER−2, tet(B), aph(3′)-Vla, strA, and strB, as well as a large diversity of ISs. This is the first report of antibiotic-resistant A. radioresistens in Antarctica. Our findings show the presence of several resistance genes which could be either intrinsic or acquired in the region.
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Affiliation(s)
- Andrés Opazo-Capurro
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.,Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Julia Wille
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Camila Cigarroa
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Paulina González-Muñoz
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.,Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile.,Departamento de Ciencias Biológicas y Químicas, Facultad de Medicina y Ciencia, Universidad San Sebastián, Concepción, Chile
| | - Mario Quezada-Aguiluz
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.,Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Mariana Domínguez-Yévenes
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.,Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Helia Bello-Toledo
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.,Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Luis Vergara
- Departamento de Ciencias Biológicas y Químicas, Facultad de Medicina y Ciencia, Universidad San Sebastián, Concepción, Chile
| | - Gerardo González-Rocha
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.,Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
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41
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Soutourina O. Type I Toxin-Antitoxin Systems in Clostridia. Toxins (Basel) 2019; 11:toxins11050253. [PMID: 31064056 PMCID: PMC6563280 DOI: 10.3390/toxins11050253] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 04/30/2019] [Accepted: 05/02/2019] [Indexed: 12/20/2022] Open
Abstract
Type I toxin-antitoxin (TA) modules are abundant in both bacterial plasmids and chromosomes and usually encode a small hydrophobic toxic protein and an antisense RNA acting as an antitoxin. The RNA antitoxin neutralizes toxin mRNA by inhibiting its translation and/or promoting its degradation. This review summarizes our current knowledge of the type I TA modules identified in Clostridia species focusing on the recent findings in the human pathogen Clostridium difficile. More than ten functional type I TA modules have been identified in the genome of this emerging enteropathogen that could potentially contribute to its fitness and success inside the host. Despite the absence of sequence homology, the comparison of these newly identified type I TA modules with previously studied systems in other Gram-positive bacteria, i.e., Bacillus subtilis and Staphylococcus aureus, revealed some important common traits. These include the conservation of characteristic sequence features for small hydrophobic toxic proteins, the localization of several type I TA within prophage or prophage-like regions and strong connections with stress response. Potential functions in the stabilization of genome regions, adaptations to stress conditions and interactions with CRISPR-Cas defence system, as well as promising applications of TA for genome-editing and antimicrobial developments are discussed.
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Affiliation(s)
- Olga Soutourina
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette CEDEX, France.
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42
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In Silico Analysis of Genetic VapC Profiles from the Toxin-Antitoxin Type II VapBC Modules among Pathogenic, Intermediate, and Non-Pathogenic Leptospira. Microorganisms 2019; 7:microorganisms7020056. [PMID: 30791633 PMCID: PMC6406750 DOI: 10.3390/microorganisms7020056] [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: 01/29/2019] [Revised: 02/09/2019] [Accepted: 02/15/2019] [Indexed: 11/16/2022] Open
Abstract
Pathogenic Leptospira spp. is the etiological agent of leptospirosis. The high diversity among Leptospira species provides an array to look for important mediators involved in pathogenesis. Toxin-antitoxin (TA) systems represent an important survival mechanism on stress conditions. vapBC modules have been found in nearly one thousand genomes corresponding to about 40% of known TAs. In the present study, we investigated TA profiles of some strains of Leptospira using a TA database and compared them through protein alignment of VapC toxin sequences among Leptospira spp. genomes. Our analysis identified significant differences in the number of putative vapBC modules distributed in pathogenic, saprophytic, and intermediate strains: four in L. interrogans, three in L. borgpetersenii, eight in L. biflexa, and 15 in L. licerasiae. The VapC toxins show low identity among amino acid sequences within the species. Some VapC toxins appear to be exclusively conserved in unique species, others appear to be conserved among pathogenic or saprophytic strains, and some appear to be distributed randomly. The data shown here indicate that these modules evolved in a very complex manner, which highlights the strong need to identify and characterize new TAs as well as to understand their regulation networks and the possible roles of TA systems in pathogenic bacteria.
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