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Cai T, Zhao QH, Xiang WL, Zhu L, Rao Y, Tang J. HigBA toxin-antitoxin system of Weissella cibaria is involved in response to the bile salt stress. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:6749-6756. [PMID: 35633128 DOI: 10.1002/jsfa.12042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 05/25/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Toxin-antitoxin (TA) systems are prevalent adaptive genetic elements in bacterial genomes, which can respond to environmental stress. While, few studies have addressed TA systems in probiotics and their roles in the adaptation to gastrointestinal transit (GIT) environments. RESULTS The Weissella cibaria 018 could survive in pH 3.0-5.0 and 0.5-3.0 g L-1 bile salt, and its HigBA system responded to the bile salt stress, but not to acid stress. The toxin protein HigB and its cognate antitoxin protein HigA had 85.1% and 100% similarity with those of Lactobacillus plantarum, respectively, and they formed the stable tetramer HigB-(HigA)2 -HigB structure in W. cibaria 018. When exposed to 1.5-3.0 g L-1 bile salt, the transcriptions of higB and higA were up-regulated with 4.39-19.29 and 5.94-30.91 folds, respectively. Meanwhile, W. cibaria 018 gathered into a mass with 48.07% survival rate and its persister cells were found to increase 8.21% under 3.0 g L-1 bile salt. CONCLUSION The HigBA TA system of W. cibaria 018 responded to the bile salt stress, but not to acid stress, which might offer novel perspectives to understand the tolerant mechanism of probiotics to GIT environment. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Ting Cai
- School of Food and Bioengineering, Xihua University, Chengdu, China
| | - Qiu-Huan Zhao
- School of Food and Bioengineering, Xihua University, Chengdu, China
| | - Wen-Liang Xiang
- School of Food and Bioengineering, Xihua University, Chengdu, China
- Key Laboratory of Food Biotechnology of Sichuan, Xihua University, Chengdu, China
| | - Lin Zhu
- School of Food and Bioengineering, Xihua University, Chengdu, China
| | - Yu Rao
- School of Food and Bioengineering, Xihua University, Chengdu, China
| | - Jie Tang
- School of Food and Bioengineering, Xihua University, Chengdu, China
- Key Laboratory of Food Biotechnology of Sichuan, Xihua University, Chengdu, China
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Deciphering the Regulatory Circuits of RA3 Replication Module - Mechanisms of the Copy Number Control. Int J Mol Sci 2022; 23:ijms23179964. [PMID: 36077372 PMCID: PMC9455977 DOI: 10.3390/ijms23179964] [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: 08/06/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 12/03/2022] Open
Abstract
The RA3 plasmid, the archetype of IncU incompatibility group, represents a mosaic-modular genome of 45.9 kb. The replication module encompasses repA and repB (initiator) surrounded by two long repetitive sequences DR1 and DR2 of unknown function. Here, we mapped the origin of replication oriV to the 3′ end of repB and showed that oriV was activated by the transcription coming from orf02revp in the adjacent stability module. Using various in vivo and in vitro methods we demonstrated that the repB expression proceeded either from repBp located in the intergenic repA-repB region or from the upstream strong repAp that was autoregulated by RepA. Additionally, the repBp activity was modulated by the transcription from the overlapping, divergently oriented repXp. Both repXmRNA (antisense for repAmRNA) and its small polypeptide product, RepX, were strong incompatibility determinants. Hence, we showed that the sophisticated RA3 copy number control combined the multivalent regulation of repB expression, RepB titration by DR1, and transcriptional activation of oriV, dependent on the RA3 global regulatory network. Similarly organized replicons have been found in diverse bacterial species confirming the significance of these mechanisms in establishing the IncU plasmids in a broad spectrum of hosts.
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De Bruyn P, Girardin Y, Loris R. Prokaryote toxin-antitoxin modules: Complex regulation of an unclear function. Protein Sci 2021; 30:1103-1113. [PMID: 33786944 PMCID: PMC8138530 DOI: 10.1002/pro.4071] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 12/29/2022]
Abstract
Toxin–antitoxin (TA) modules are small operons in bacteria and archaea that encode a metabolic inhibitor (toxin) and a matching regulatory protein (antitoxin). While their biochemical activities are often well defined, their biological functions remain unclear. In Type II TA modules, the most common class, both toxin and antitoxin are proteins, and the antitoxin inhibits the biochemical activity of the toxin via complex formation with the toxin. The different TA modules vary significantly regarding structure and biochemical activity. Both regulation of protein activity by the antitoxin and regulation of transcription can be highly complex and sometimes show striking parallels between otherwise unrelated TA modules. Interplay between the multiple levels of regulation in the broader context of the cell as a whole is most likely required for optimum fine‐tuning of these systems. Thus, TA modules can go through great lengths to prevent activation and to reverse accidental activation, in agreement with recent in vivo data. These complex mechanisms seem at odds with the lack of a clear biological function.
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Affiliation(s)
- Pieter De Bruyn
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel and Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - Yana Girardin
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel and Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - Remy Loris
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel and Vlaams Instituut voor Biotechnologie, Brussels, Belgium
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Song Y, Luo G, Zhu Y, Li T, Li C, He L, Zhao N, Zhao C, Yang J, Huang Q, Mu X, Tang X, Kang M, Wu S, He Y, Bao R. Pseudomonas aeruginosa antitoxin HigA functions as a diverse regulatory factor by recognizing specific pseudopalindromic DNA motifs. Environ Microbiol 2020; 23:1541-1558. [PMID: 33346387 DOI: 10.1111/1462-2920.15365] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 02/05/2023]
Abstract
Type II toxin-antitoxin (TA) systems modulate many essential cellular processes in prokaryotic organisms. Recent studies indicate certain type II antitoxins also transcriptionally regulate other genes, besides neutralizing toxin activity. Herein, we investigated the diverse transcriptional repression properties of type II TA antitoxin PaHigA from Pseudomonas aeruginosa. Biochemical and functional analyses showed that PaHigA recognized variable pseudopalindromic DNA sequences and repressed expression of multiple genes. Furthermore, we presented high resolution structures of apo-PaHigA, PaHigA-PhigBA and PaHigA-Ppa2440 complex, describing how the rearrangements of the HTH domain accounted for the different DNA-binding patterns among HigA homologues. Moreover, we demonstrated that the N-terminal loop motion of PaHigA was associated with its apo and DNA-bound states, reflecting a switch mechanism regulating HigA antitoxin function. Collectively, this work extends our understanding of how the PaHigB/HigA system regulates multiple metabolic pathways to balance the growth and stress response in P. aeruginosa and could guide further development of anti-TA oriented strategies for pathogen treatment.
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Affiliation(s)
- Yingjie Song
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Guihua Luo
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Yibo Zhu
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Tao Li
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Changcheng Li
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Lihui He
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Ninglin Zhao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Chang Zhao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Jing Yang
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Qin Huang
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Xingyu Mu
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Xinyue Tang
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Mei Kang
- Department of Laboratory medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Siying Wu
- Department of Laboratory medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yongxing He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Rui Bao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
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2.09 Å Resolution structure of E. coli HigBA toxin-antitoxin complex reveals an ordered DNA-binding domain and intrinsic dynamics in antitoxin. Biochem J 2020; 477:4001-4019. [PMID: 33000860 DOI: 10.1042/bcj20200363] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/15/2020] [Accepted: 09/30/2020] [Indexed: 12/24/2022]
Abstract
The toxin-antitoxin (TA) systems are small operon systems that are involved in important physiological processes in bacteria such as stress response and persister cell formation. Escherichia coli HigBA complex belongs to the type II TA systems and consists of a protein toxin called HigB and a protein antitoxin called HigA. The toxin HigB is a ribosome-dependent endoribonuclease that cleaves the translating mRNAs at the ribosome A site. The antitoxin HigA directly binds the toxin HigB, rendering the HigBA complex catalytically inactive. The existing biochemical and structural studies had revealed that the HigBA complex forms a heterotetrameric assembly via dimerization of HigA antitoxin. Here, we report a high-resolution crystal structure of E. coli HigBA complex that revealed a well-ordered DNA binding domain in HigA antitoxin. Using SEC-MALS and ITC methods, we have determined the stoichiometry of complex formation between HigBA and a 33 bp DNA and report that HigBA complex as well as HigA homodimer bind to the palindromic DNA sequence with nano molar affinity. Using E. coli growth assays, we have probed the roles of key, putative active site residues in HigB. Spectroscopic methods (CD and NMR) and molecular dynamics simulations study revealed intrinsic dynamic in antitoxin in HigBA complex, which may explain the large conformational changes in HigA homodimer in free and HigBA complexes observed previously. We also report a truncated, heterodimeric form of HigBA complex that revealed possible cleavage sites in HigBA complex, which can have implications for its cellular functions.
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Chimal-Cázares F, Hernández-Martínez G, Pacheco S, Ares MA, Soria-Bustos J, Sánchez-Gutiérrez M, Izquierdo-Vega JA, Ibarra JA, González-Y-Merchand JA, Gorvel JP, Méresse S, De la Cruz MA. Molecular Characterization of SehB, a Type II Antitoxin of Salmonella enterica Serotype Typhimurium: Amino Acid Residues Involved in DNA-Binding, Homodimerization, Toxin Interaction, and Virulence. Front Microbiol 2020; 11:614. [PMID: 32328049 PMCID: PMC7160566 DOI: 10.3389/fmicb.2020.00614] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/19/2020] [Indexed: 11/22/2022] Open
Abstract
Salmonella enterica serotype Typhimurium is a bacterium that causes gastroenteritis and diarrhea in humans. The genome of S. Typhimurium codes for diverse virulence factors, among which are the toxin-antitoxin (TA) systems. SehAB is a type II TA, where SehA is the toxin and SehB is the antitoxin. It was previously reported that the absence of the SehB antitoxin affects the growth of S. Typhimurium. In addition, the SehB antitoxin can interact directly with the SehA toxin neutralizing its toxic effect as well as repressing its own expression. We identified conserved residues on SehB homologous proteins. Point mutations were introduced at both N- and C-terminal of SehB antitoxin to analyze the effect of these changes on its transcription repressor function, on its ability to form homodimers and on the virulence of S. Typhimurium. All changes in amino acid residues at both the N- and C-terminal affected the repressor function of SehB antitoxin and they were required for DNA-binding activity. Mutations in the amino acid residues at the N-terminal showed a lower capacity for homodimer formation of the SehB protein. However, none of the SehB point mutants were affected in the interaction with the SehA toxin. In terms of virulence, the eight single-amino acid mutations were attenuated for virulence in the mouse model. In agreement with our results, the eight amino acid residues of SehB antitoxin were required for its repressor activity, affecting both homodimerization and DNA-binding activity, supporting the notion that both activities of SehB antitoxin are required to confer virulence to Salmonella enterica.
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Affiliation(s)
- Fernando Chimal-Cázares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico.,Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Gabriela Hernández-Martínez
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico.,Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Sabino Pacheco
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Miguel A Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Jorge Soria-Bustos
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico.,Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | | | | | - Jose Antonio Ibarra
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Jorge A González-Y-Merchand
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | | | | | - Miguel A De la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
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