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Girardin Y, Galle M, Vanden Abeele Y, De Greve H, Loris R. Evaluation of different strategies to produce Vibrio cholerae ParE2 toxin. Protein Expr Purif 2024; 215:106403. [PMID: 37977515 DOI: 10.1016/j.pep.2023.106403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/08/2023] [Accepted: 11/12/2023] [Indexed: 11/19/2023]
Abstract
Toxin-antitoxin (TA) systems are small operons that are omnipresent in bacteria and archaea with suggested roles in stabilization of mobile genetic elements, bacteriophage protection, stress response and possibly persister formation. A major bottleneck in the study of TA toxins is the production of sufficient amounts of well-folded, functional protein. Here we examine alternative approaches for obtaining the VcParE2 toxin from Vibrio cholerae. VcParE2 can be successfully produced via bacterial expression in presence of its cognate antitoxin VcParD2, followed by on-column unfolding and refolding. Alternatively, the toxin can be expressed in Spodoptera frugiperda (Sf9) insect cells. The latter requires disruption of the VcparE2 gene via introduction of an insect cell intron. Both methods provide protein with similar structural and functional characteristics.
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Affiliation(s)
- Yana Girardin
- Molecular Recognition Unit, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium; Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050, Brussels, Belgium
| | - Margot Galle
- Molecular Recognition Unit, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium; Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050, Brussels, Belgium
| | - Yaël Vanden Abeele
- Molecular Recognition Unit, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Henri De Greve
- Molecular Recognition Unit, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Remy Loris
- Molecular Recognition Unit, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium; Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050, Brussels, Belgium.
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Garcia-Rodriguez G, Girardin Y, Kumar Singh R, Volkov AN, Van Dyck J, Muruganandam G, Sobott F, Charlier D, Loris R. Toxin:antitoxin ratio sensing autoregulation of the Vibrio cholerae parDE2 module. SCIENCE ADVANCES 2024; 10:eadj2403. [PMID: 38181072 PMCID: PMC10776004 DOI: 10.1126/sciadv.adj2403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 12/04/2023] [Indexed: 01/07/2024]
Abstract
The parDE family of toxin-antitoxin (TA) operons is ubiquitous in bacterial genomes and, in Vibrio cholerae, is an essential component to maintain the presence of chromosome II. Here, we show that transcription of the V. cholerae parDE2 (VcparDE) operon is regulated in a toxin:antitoxin ratio-dependent manner using a molecular mechanism distinct from other type II TA systems. The repressor of the operon is identified as an assembly with a 6:2 stoichiometry with three interacting ParD2 dimers bridged by two ParE2 monomers. This assembly docks to a three-site operator containing 5'- GGTA-3' motifs. Saturation of this TA complex with ParE2 toxin results in disruption of the interface between ParD2 dimers and the formation of a TA complex of 2:2 stoichiometry. The latter is operator binding-incompetent as it is incompatible with the required spacing of the ParD2 dimers on the operator.
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Affiliation(s)
- Gabriela Garcia-Rodriguez
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
- Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Yana Girardin
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
- Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Ranjan Kumar Singh
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
- Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Alexander N. Volkov
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
- Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, B-1050 Brussel, Belgium
- Jean Jeener NMR Centre, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Jeroen Van Dyck
- Department of Chemistry, Universiteit Antwerpen, Groenenborgerlaan 171, Antwerpen 2020, Belgium
| | - Gopinath Muruganandam
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
- Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Frank Sobott
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Daniel Charlier
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
- Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, B-1050 Brussel, Belgium
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Wang C, Niu C, Hidayatullah KM, Xue L, Zhu Z, Niu L. Structural insights into the PrpTA toxin-antitoxin system in Pseudoalteromonas rubra. Front Microbiol 2022; 13:1053255. [PMID: 36504814 PMCID: PMC9731233 DOI: 10.3389/fmicb.2022.1053255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 10/31/2022] [Indexed: 11/27/2022] Open
Abstract
Bacteria could survive stresses by a poorly understood mechanism that contributes to the emergence of bacterial persisters exhibiting multidrug tolerance (MDT). Recently, Pseudoalteromonas rubra prpAT module was found to encode a toxin PrpT and corresponding cognate antidote PrpA. In this study, we first reported multiple individual and complex structures of PrpA and PrpT, which uncovered the high-resolution three-dimensional structure of the PrpT:PrpA2:PrpT heterotetramer with the aid of size exclusion chromatography-multi-angle light scattering experiments (SEC-MALS). PrpT:PrpA2:PrpT is composed of a PrpA homodimer and two PrpT monomers which are relatively isolated from each other and from ParE family. The superposition of antitoxin monomer structures from these structures highlighted the flexible C-terminal domain (CTD). A striking conformational change in the CTDs of PrpA homodimer depolymerized from homotetramer was provoked upon PrpT binding, which accounts for the unique PrpT-PrpARHH mutual interactions and further neutralizes the toxin PrpT. PrpA2-54-form I and II crystal structures both contain a doughnut-shaped hexadecamer formed by eight homodimers organized in a cogwheel-like form via inter-dimer interface dominated by salt bridges and hydrogen bonds. Moreover, PrpA tends to exist in solution as a homodimer other than a homotetramer (SEC-MALS) in the absence of flexible CTD. Multiple multi-dimers, tetramer and hexamer included, of PrpA2-54 mediated by the symmetric homodimer interface and the complicated inter-dimer interface could be observed in the solution. SEC-MALS assays highlighted that phosphate buffer (PB) and the increase in the concentration appear to be favorable for the PrpA2-54 oligomerization in the solution. Taken together with previous research, a model of PrpA2-54 homotetramer in complex with prpAT promoter and the improved mechanism underlying how PrpTA controls the plasmid replication were proposed here.
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Affiliation(s)
- Chenchen Wang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Chuanying Niu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Khan Muhammad Hidayatullah
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Lu Xue
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zhongliang Zhu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Liwen Niu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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Song X, Lin Z, Yuan W. Toxin-antitoxin systems in pathogenic Vibrio species: a mini review from a structure perspective. 3 Biotech 2022; 12:125. [PMID: 35542053 DOI: 10.1007/s13205-022-03178-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/31/2022] [Indexed: 11/01/2022] Open
Abstract
Toxin-antitoxin (TA) genetic modules have been found to widely exist in bacterial chromosomes and mobile genetic elements. They are composed of stable toxins and less stable antitoxins that can counteract the toxicity of toxins. The interactions between toxins and antitoxins could play critical roles in the virulence and persistence of pathogenic bacteria. There are at least eight types of TA systems which have been identified in a variety of bacteria. Vibrio, a genus of Gram-negative bacteria, is widespread in aquatic environments and can cause various human diseases, such as epidemic cholera. In this review, we mainly explore the structures and functions of TA modules found in common Vibrio pathogens, mainly V. cholerae, for better understanding of TA action mechanisms in pathogenic bacteria.
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Insights into the Neutralization and DNA Binding of Toxin-Antitoxin System ParE SO-CopA SO by Structure-Function Studies. Microorganisms 2021; 9:microorganisms9122506. [PMID: 34946107 PMCID: PMC8706911 DOI: 10.3390/microorganisms9122506] [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: 08/31/2021] [Revised: 11/25/2021] [Accepted: 11/27/2021] [Indexed: 12/03/2022] Open
Abstract
ParESO-CopASO is a new type II toxin–antitoxin (TA) system in prophage CP4So that plays an essential role in circular CP4So maintenance after the excision in Shewanella oneidensis. The toxin ParESO severely inhibits cell growth, while CopASO functions as an antitoxin to neutralize ParESO toxicity through direct interactions. However, the molecular mechanism of the neutralization and autoregulation of the TA operon transcription remains elusive. In this study, we determined the crystal structure of a ParESO-CopASO complex that adopted an open V-shaped heterotetramer with the organization of ParESO-(CopASO)2-ParESO. The structure showed that upon ParESO binding, the intrinsically disordered C-terminal domain of CopASO was induced to fold into a partially ordered conformation that bound into a positively charged and hydrophobic groove of ParESO. Thermodynamics analysis showed the DNA-binding affinity of CopASO was remarkably higher than that of the purified TA complex, accompanied by the enthalpy change reversion from an exothermic reaction to an endothermic reaction. These results suggested ParESO acts as a de-repressor of the TA operon transcription at the toxin:antitoxin level of 1:1. Site-directed mutagenesis of ParESO identified His91 as the essential residue for its toxicity by cell toxicity assays. Our structure-function studies therefore elucidated the transcriptional regulation mechanism of the ParESO-CopASO pair, and may help to understand the regulation of CP4So maintenance in S. oneidensis.
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