1
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Dominguez-Molina L, Kurata T, Cepauskas A, Echemendia-Blanco D, Zedek S, Talavera-Perez A, Atkinson GC, Hauryliuk V, Garcia-Pino A. Mechanisms of neutralization of toxSAS from toxin-antitoxin modules. Nat Chem Biol 2025; 21:182-192. [PMID: 38834893 PMCID: PMC11782079 DOI: 10.1038/s41589-024-01630-4] [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: 07/17/2023] [Accepted: 04/22/2024] [Indexed: 06/06/2024]
Abstract
Toxic small alarmone synthetase (toxSAS) enzymes constitute a family of bacterial effectors present in toxin-antitoxin and secretion systems. toxSASs act through either translation inhibition mediated by pyrophosphorylation of transfer RNA (tRNA) CCA ends or synthesis of the toxic alarmone adenosine pentaphosphate ((pp)pApp) and adenosine triphosphate (ATP) depletion, exemplified by FaRel2 and FaRel, respectively. However, structural bases of toxSAS neutralization are missing. Here we show that the pseudo-Zn2+ finger domain (pZFD) of the ATfaRel2 antitoxin precludes access of ATP to the pyrophosphate donor site of the FaRel2 toxin, without affecting recruitment of the tRNA pyrophosphate acceptor. By contrast, (pp)pApp-producing toxSASs are inhibited by Tis1 antitoxin domains though occlusion of the pyrophosphate acceptor-binding site. Consequently, the auxiliary pZFD of AT2faRel is dispensable for FaRel neutralization. Collectively, our study establishes the general principles of toxSAS inhibition by structured antitoxin domains, with the control strategy directly coupled to toxSAS substrate specificity.
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Affiliation(s)
- Lucia Dominguez-Molina
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Tatsuaki Kurata
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Albinas Cepauskas
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Dannele Echemendia-Blanco
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Safia Zedek
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Ariel Talavera-Perez
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Gemma C Atkinson
- Department of Experimental Medical Science, Lund University, Lund, Sweden.
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, Lund, Sweden.
- Faculty of Science and Technology, University of Tartu Institute of Technology, Tartu, Estonia.
- Science for Life Laboratory, Lund, Sweden.
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Brussels, Belgium.
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2
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Hadži S, Živič Z, Kovačič M, Zavrtanik U, Haesaerts S, Charlier D, Plavec J, Volkov AN, Lah J, Loris R. Fuzzy recognition by the prokaryotic transcription factor HigA2 from Vibrio cholerae. Nat Commun 2024; 15:3105. [PMID: 38600130 PMCID: PMC11006873 DOI: 10.1038/s41467-024-47296-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
Disordered protein sequences can exhibit different binding modes, ranging from well-ordered folding-upon-binding to highly dynamic fuzzy binding. The primary function of the intrinsically disordered region of the antitoxin HigA2 from Vibrio cholerae is to neutralize HigB2 toxin through ultra-high-affinity folding-upon-binding interaction. Here, we show that the same intrinsically disordered region can also mediate fuzzy interactions with its operator DNA and, through interplay with the folded helix-turn-helix domain, regulates transcription from the higBA2 operon. NMR, SAXS, ITC and in vivo experiments converge towards a consistent picture where a specific set of residues in the intrinsically disordered region mediate electrostatic and hydrophobic interactions while "hovering" over the DNA operator. Sensitivity of the intrinsically disordered region to scrambling the sequence, position-specific contacts and absence of redundant, multivalent interactions, point towards a more specific type of fuzzy binding. Our work demonstrates how a bacterial regulator achieves dual functionality by utilizing two distinct interaction modes within the same disordered sequence.
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Affiliation(s)
- San Hadži
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Zala Živič
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Matic Kovačič
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova, 19, 1000, Ljubljana, Slovenia
| | - Uroš Zavrtanik
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Sarah Haesaerts
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Daniel Charlier
- Research group of Microbiology, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova, 19, 1000, Ljubljana, Slovenia
| | - Alexander N Volkov
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Jean Jeener NMR Centre, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Jurij Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia.
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
- Centre for Structural Biology, VIB, Pleinlaan 2, 1050, Brussels, Belgium.
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3
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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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4
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Dominguez-Molina L, Talavera A, Cepauskas A, Kurata T, Echemendia-Blanco D, Hauryliuk V, Garcia-Pino A. Biochemical and X-ray analyses of the players involved in the faRel2/aTfaRel2 toxin-antitoxin operon. Acta Crystallogr F Struct Biol Commun 2023; 79:247-256. [PMID: 37728608 PMCID: PMC10565793 DOI: 10.1107/s2053230x23007288] [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: 07/11/2023] [Accepted: 08/19/2023] [Indexed: 09/21/2023] Open
Abstract
The aTfaRel2/faRel2 operon from Coprobacillus sp. D7 encodes a bicistronic type II toxin-antitoxin (TA) module. The FaRel2 toxin is a toxic small alarmone synthetase (toxSAS) that inhibits translation through the pyrophosphorylation of uncharged tRNAs at the 3'-CCA end. The toxin is neutralized by the antitoxin ATfaRel2 through the formation of an inactive TA complex. Here, the production, biophysical analysis and crystallization of ATfaRel2 and FaRel2 as well as of the ATfaRel2-FaRel2 complex are reported. ATfaRel2 is monomeric in solution. The antitoxin crystallized in space group P21212 with unit-cell parameters a = 53.3, b = 34.2, c = 37.6 Å, and the best crystal diffracted to a resolution of 1.24 Å. Crystals of FaRel2 in complex with APCPP, a nonhydrolysable ATP analogue, belonged to space group P21, with unit-cell parameters a = 31.5, b = 60.6, c = 177.2 Å, β = 90.6°, and diffracted to 2.6 Å resolution. The ATfaRel2-FaRel2Y128F complex forms a heterotetramer in solution composed of two toxins and two antitoxins. This complex crystallized in two space groups: F4132, with unit-cell parameters a = b = c = 227.1 Å, and P212121, with unit-cell parameters a = 51.7, b = 106.2, c = 135.1 Å. The crystals diffracted to 1.98 and 2.1 Å resolution, respectively.
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Affiliation(s)
- Lucia Dominguez-Molina
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
| | - Ariel Talavera
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
| | - Albinas Cepauskas
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
| | - Tatsuaki Kurata
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Dannele Echemendia-Blanco
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- University of Tartu Institute of Technology, Tartu, Estonia
- Science for Life Laboratory, Lund, Sweden
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
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5
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Ernits K, Saha CK, Brodiazhenko T, Chouhan B, Shenoy A, Buttress JA, Duque-Pedraza JJ, Bojar V, Nakamoto JA, Kurata T, Egorov AA, Shyrokova L, Johansson MJO, Mets T, Rustamova A, Džigurski J, Tenson T, Garcia-Pino A, Strahl H, Elofsson A, Hauryliuk V, Atkinson GC. The structural basis of hyperpromiscuity in a core combinatorial network of type II toxin-antitoxin and related phage defense systems. Proc Natl Acad Sci U S A 2023; 120:e2305393120. [PMID: 37556498 PMCID: PMC10440598 DOI: 10.1073/pnas.2305393120] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/11/2023] [Indexed: 08/11/2023] Open
Abstract
Toxin-antitoxin (TA) systems are a large group of small genetic modules found in prokaryotes and their mobile genetic elements. Type II TAs are encoded as bicistronic (two-gene) operons that encode two proteins: a toxin and a neutralizing antitoxin. Using our tool NetFlax (standing for Network-FlaGs for toxins and antitoxins), we have performed a large-scale bioinformatic analysis of proteinaceous TAs, revealing interconnected clusters constituting a core network of TA-like gene pairs. To understand the structural basis of toxin neutralization by antitoxins, we have predicted the structures of 3,419 complexes with AlphaFold2. Together with mutagenesis and functional assays, our structural predictions provide insights into the neutralizing mechanism of the hyperpromiscuous Panacea antitoxin domain. In antitoxins composed of standalone Panacea, the domain mediates direct toxin neutralization, while in multidomain antitoxins the neutralization is mediated by other domains, such as PAD1, Phd-C, and ZFD. We hypothesize that Panacea acts as a sensor that regulates TA activation. We have experimentally validated 16 NetFlax TA systems and used domain annotations and metabolic labeling assays to predict their potential mechanisms of toxicity (such as membrane disruption, and inhibition of cell division or protein synthesis) as well as biological functions (such as antiphage defense). We have validated the antiphage activity of a RosmerTA system encoded by Gordonia phage Kita, and used fluorescence microscopy to confirm its predicted membrane-depolarizing activity. The interactive version of the NetFlax TA network that includes structural predictions can be accessed at http://netflax.webflags.se/.
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Affiliation(s)
- Karin Ernits
- Department of Experimental Medicine, Lund University, Lund221 84, Sweden
| | - Chayan Kumar Saha
- Department of Experimental Medicine, Lund University, Lund221 84, Sweden
| | | | - Bhanu Chouhan
- Department of Experimental Medicine, Lund University, Lund221 84, Sweden
- Department of Molecular Biology, Umeå University, Umeå901 87, Sweden
| | - Aditi Shenoy
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Solna171 21, Sweden
| | - Jessica A. Buttress
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon TyneNE2 4AX, United Kingdom
| | | | - Veda Bojar
- Department of Experimental Medicine, Lund University, Lund221 84, Sweden
| | - Jose A. Nakamoto
- Department of Experimental Medicine, Lund University, Lund221 84, Sweden
| | - Tatsuaki Kurata
- Department of Experimental Medicine, Lund University, Lund221 84, Sweden
| | - Artyom A. Egorov
- Department of Experimental Medicine, Lund University, Lund221 84, Sweden
| | - Lena Shyrokova
- Department of Experimental Medicine, Lund University, Lund221 84, Sweden
| | | | - Toomas Mets
- Department of Experimental Medicine, Lund University, Lund221 84, Sweden
- Institute of Technology, University of Tartu, Tartu50411, Estonia
| | - Aytan Rustamova
- Institute of Technology, University of Tartu, Tartu50411, Estonia
| | | | - Tanel Tenson
- Institute of Technology, University of Tartu, Tartu50411, Estonia
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles, Brussels1050, Belgium
| | - Henrik Strahl
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon TyneNE2 4AX, United Kingdom
| | - Arne Elofsson
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Solna171 21, Sweden
| | - Vasili Hauryliuk
- Department of Experimental Medicine, Lund University, Lund221 84, Sweden
- Institute of Technology, University of Tartu, Tartu50411, Estonia
- Science for Life Laboratory, Lund221 84, Sweden
- Lund University Virus Centre, Lund221 84, Sweden
| | - Gemma C. Atkinson
- Department of Experimental Medicine, Lund University, Lund221 84, Sweden
- Lund University Virus Centre, Lund221 84, Sweden
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6
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Lee KY, Lee BJ. Dynamics-Based Regulatory Switches of Type II Antitoxins: Insights into New Antimicrobial Discovery. Antibiotics (Basel) 2023; 12:antibiotics12040637. [PMID: 37106997 PMCID: PMC10135005 DOI: 10.3390/antibiotics12040637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
Type II toxin-antitoxin (TA) modules are prevalent in prokaryotes and are involved in cell maintenance and survival under harsh environmental conditions, including nutrient deficiency, antibiotic treatment, and human immune responses. Typically, the type II TA system consists of two protein components: a toxin that inhibits an essential cellular process and an antitoxin that neutralizes its toxicity. Antitoxins of type II TA modules typically contain the structured DNA-binding domain responsible for TA transcription repression and an intrinsically disordered region (IDR) at the C-terminus that directly binds to and neutralizes the toxin. Recently accumulated data have suggested that the antitoxin's IDRs exhibit variable degrees of preexisting helical conformations that stabilize upon binding to the corresponding toxin or operator DNA and function as a central hub in regulatory protein interaction networks of the type II TA system. However, the biological and pathogenic functions of the antitoxin's IDRs have not been well discussed compared with those of IDRs from the eukaryotic proteome. Here, we focus on the current state of knowledge about the versatile roles of IDRs of type II antitoxins in TA regulation and provide insights into the discovery of new antibiotic candidates that induce toxin activation/reactivation and cell death by modulating the regulatory dynamics or allostery of the antitoxin.
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Affiliation(s)
- Ki-Young Lee
- College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Pocheon-si 11160, Republic of Korea
| | - Bong-Jin Lee
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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7
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Li M, Chen Q, Wu C, Li Y, Wang S, Chen X, Qiu B, Li Y, Mao D, Lin H, Yu D, Cao Y, Huang Z, Cui C, Zhong Z. A Novel Module Promotes Horizontal Gene Transfer in Azorhizobium caulinodans ORS571. Genes (Basel) 2022; 13:genes13101895. [PMID: 36292780 PMCID: PMC9601964 DOI: 10.3390/genes13101895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/02/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Azorhizobium caulinodans ORS571 contains an 87.6 kb integrative and conjugative element (ICEAc) that conjugatively transfers symbiosis genes to other rhizobia. Many hypothetical redundant gene fragments (rgfs) are abundant in ICEAc, but their potential function in horizontal gene transfer (HGT) is unknown. Molecular biological methods were employed to delete hypothetical rgfs, expecting to acquire a minimal ICEAc and consider non-functional rgfs as editable regions for inserting genes related to new symbiotic functions. We determined the significance of rgf4 in HGT and identified the physiological function of genes designated rihF1a (AZC_3879), rihF1b (AZC_RS26200), and rihR (AZC_3881). In-frame deletion and complementation assays revealed that rihF1a and rihF1b work as a unit (rihF1) that positively affects HGT frequency. The EMSA assay and lacZ-based reporter system showed that the XRE-family protein RihR is not a regulator of rihF1 but promotes the expression of the integrase (intC) that has been reported to be upregulated by the LysR-family protein, AhaR, through sensing host’s flavonoid. Overall, a conservative module containing rihF1 and rihR was characterized, eliminating the size of ICEAc by 18.5%. We propose the feasibility of constructing a minimal ICEAc element to facilitate the exchange of new genetic components essential for symbiosis or other metabolic functions between soil bacteria.
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Affiliation(s)
- Mingxu Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qianqian Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chuanhui Wu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiyang Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Sanle Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuelian Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Bowen Qiu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuxin Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Dongmei Mao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hong Lin
- Animal, Plant and Food Inspection Center, Nanjing Customs, No. 39, Chuangzhi Road, Nanjing 210019, China
| | - Daogeng Yu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Science, Danzhou 571737, China
| | - Yajun Cao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhi Huang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (Z.H.); (C.C.); Tel.: +86-25-84396645 (Z.H.)
| | - Chunhong Cui
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (Z.H.); (C.C.); Tel.: +86-25-84396645 (Z.H.)
| | - Zengtao Zhong
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
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8
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Shehreen S, Birkholz N, Fineran P, Brown C. Widespread repression of anti-CRISPR production by anti-CRISPR-associated proteins. Nucleic Acids Res 2022; 50:8615-8625. [PMID: 35947749 PMCID: PMC9410906 DOI: 10.1093/nar/gkac674] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/06/2022] [Accepted: 07/25/2022] [Indexed: 12/24/2022] Open
Abstract
Many bacteria use CRISPR-Cas systems to defend against invasive mobile genetic elements (MGEs). In response, MGEs have developed strategies to resist CRISPR-Cas, including the use of anti-CRISPR (Acr) proteins. Known acr genes may be followed in an operon by a putative regulatory Acr-associated gene (aca), suggesting the importance of regulation. Although ten families of helix-turn-helix (HTH) motif containing Aca proteins have been identified (Aca1-10), only three have been tested and shown to be transcriptional repressors of acr-aca expression. The AcrIIA1 protein (a Cas9 inhibitor) also contains a functionally similar HTH containing repressor domain. Here, we identified and analysed Aca and AcrIIA1 homologs across all bacterial genomes. Using HMM models we found aca-like genes are widely distributed in bacteria, both with and without known acr genes. The putative promoter regions of acr-aca operons were analysed and members of each family of bacterial Aca tested for regulatory function. For each Aca family, we predicted a conserved inverted repeat binding site within a core promoter. Promoters containing these sites directed reporter expression in E. coli and were repressed by the cognate Aca protein. These data demonstrate that acr repression by Aca proteins is widely conserved in nature.
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Affiliation(s)
- Saadlee Shehreen
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand,Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Nils Birkholz
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand,Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand,Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, New Zealand,Genetics Otago, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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9
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Leben K, Strmšek Ž, Lebar T, Verbič A, Dragovan M, Omersa N, Anderluh G, Jerala R. Binding of the transcription activator-like effector augments transcriptional regulation by another transcription factor. Nucleic Acids Res 2022; 50:6562-6574. [PMID: 35670660 PMCID: PMC9226504 DOI: 10.1093/nar/gkac454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/02/2022] [Indexed: 01/27/2023] Open
Abstract
DNA transcription is regulated by a range of diverse mechanisms and primarily by transcription factors that recruit the RNA polymerase complex to the promoter region on the DNA. Protein binding to DNA at nearby or distant sites can synergistically affect this process in a variety of ways, but mainly through direct interactions between DNA-binding proteins. Here we show that a Transcription Activator-Like Effector (TALE), which lacks an activation domain, can enhance transcription in mammalian cells when it binds in the vicinity of and without direct interaction with several different dimeric or monomeric transcription factors. This effect was observed for several TALEs regardless of the recognition sequences and their DNA-bound orientation. TALEs can exert an effect over the distance of tens of nucleotides and it also potentiated KRAB-mediated repression. The augmentation of transcriptional regulation of another transcription factor is characteristic of TALEs, as it was not observed for dCas9/gRNA, zinc finger, or Gal4 DNA-binding domains. We propose that this mechanism involves an allosteric effect exerted on DNA structure or dynamics. This mechanism could be used to modulate transcription but may also play a role in the natural context of TALEs.
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Affiliation(s)
- Katja Leben
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,Interdisciplinary Doctoral Programme in Biomedicine, University of Ljubljana, Kongresni trg 12, SI-1000 Ljubljana, Slovenia
| | - Žiga Strmšek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Tina Lebar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Anže Verbič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,Interdisciplinary Doctoral Programme in Biomedicine, University of Ljubljana, Kongresni trg 12, SI-1000 Ljubljana, Slovenia
| | - Matej Dragovan
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Neža Omersa
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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10
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Abstract
Toxin-antitoxin systems are widespread in bacterial genomes. They are usually composed of two elements: a toxin that inhibits an essential cellular process and an antitoxin that counteracts its cognate toxin. In the past decade, a number of new toxin-antitoxin systems have been described, bringing new growth inhibition mechanisms to light as well as novel modes of antitoxicity. However, recent advances in the field profoundly questioned the role of these systems in bacterial physiology, stress response and antimicrobial persistence. This shifted the paradigm of the functions of toxin-antitoxin systems to roles related to interactions between hosts and their mobile genetic elements, such as viral defence or plasmid stability. In this Review, we summarize the recent progress in understanding the biology and evolution of these small genetic elements, and discuss how genomic conflicts could shape the diversification of toxin-antitoxin systems.
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11
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Garcia-Rodriguez G, Girardin Y, Volkov AN, Singh RK, Muruganandam G, Van Dyck J, Sobott F, Versées W, Charlier D, Loris R. Entropic pressure controls the oligomerization of the Vibrio cholerae ParD2 antitoxin. Acta Crystallogr D Struct Biol 2021; 77:904-920. [PMID: 34196617 PMCID: PMC8251345 DOI: 10.1107/s2059798321004873] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/07/2021] [Indexed: 11/22/2022] Open
Abstract
ParD2 is the antitoxin component of the parDE2 toxin-antitoxin module from Vibrio cholerae and consists of an ordered DNA-binding domain followed by an intrinsically disordered ParE-neutralizing domain. In the absence of the C-terminal intrinsically disordered protein (IDP) domain, V. cholerae ParD2 (VcParD2) crystallizes as a doughnut-shaped hexadecamer formed by the association of eight dimers. This assembly is stabilized via hydrogen bonds and salt bridges rather than by hydrophobic contacts. In solution, oligomerization of the full-length protein is restricted to a stable, open decamer or dodecamer, which is likely to be a consequence of entropic pressure from the IDP tails. The relative positioning of successive VcParD2 dimers mimics the arrangement of Streptococcus agalactiae CopG dimers on their operator and allows an extended operator to wrap around the VcParD2 oligomer.
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Affiliation(s)
- Gabriela Garcia-Rodriguez
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- VIB–VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
| | - Yana Girardin
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- VIB–VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
| | - Alexander N. Volkov
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- VIB–VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
- Jean Jeener NMR Center, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Ranjan Kumar Singh
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- VIB–VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
| | - Gopinath Muruganandam
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- VIB–VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jeroen Van Dyck
- Department of Chemistry, Universiteit Antwerpen, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Frank Sobott
- Department of Chemistry, Universiteit Antwerpen, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Wim Versées
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- VIB–VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
| | - Daniel Charlier
- Research Group of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Remy Loris
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- VIB–VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
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12
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Proteolysis and multimerization regulate signaling along the two-component regulatory system AdeRS. iScience 2021; 24:102476. [PMID: 34113820 PMCID: PMC8169943 DOI: 10.1016/j.isci.2021.102476] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 03/15/2021] [Accepted: 04/23/2021] [Indexed: 11/23/2022] Open
Abstract
Bacterial two-component regulatory systems are ubiquitous environment-sensing signal transducers involved in pathogenesis and antibiotic resistance. The Acinetobacter baumannii two-component regulatory system AdeRS is made up of a sensor histidine kinase AdeS and a cognate response regulator AdeR, which together reduce repression of the multidrug-resistant efflux pump AdeABC. Herein we demonstrate that an N-terminal intrinsically disordered tail in AdeR is important for the upregulation of adeABC expression, although it greatly increases the susceptibility of AdeR to proteasome-mediated degradation. We also show that AdeS assembles into a hexameric state that is necessary for its full histidine kinase activity, which appears to occur via cis autophosphorylation. Taken together, this study demonstrates new structural mechanisms through which two-component systems can transduce environmental signals to impact gene expression and enlightens new potential antimicrobial approach by targeting two-component regulatory systems. Crystal structure of AdeR dimer with traceable N-terminal intrinsically disordered region. N-terminal intrinsically disordered region AdeR is involved in proteasome proteolysis. Crystal structure of AdeS catalytic domain demonstrates cis autophosphorylation. AdeS can assemble into hexamer and is crucial for its full kinase activity.
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13
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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: 26] [Impact Index Per Article: 6.5] [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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14
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The Disordered C-Terminus of the Chaperone DnaK Increases the Competitive Fitness of Pseudomonas putida and Facilitates the Toxicity of GraT. Microorganisms 2021; 9:microorganisms9020375. [PMID: 33668424 PMCID: PMC7918210 DOI: 10.3390/microorganisms9020375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 11/23/2022] Open
Abstract
Chaperone proteins are crucial for proper protein folding and quality control, especially when cells encounter stress caused by non-optimal temperatures. DnaK is one of such essential chaperones in bacteria. Although DnaK has been well characterized, the function of its intrinsically disordered C-terminus has remained enigmatic as the deletion of this region has been shown to either enhance or reduce its protein folding ability. We have shown previously that DnaK interacts with toxin GraT of the GraTA toxin-antitoxin system in Pseudomonas putida. Interestingly, the C-terminal truncation of DnaK was shown to alleviate GraT-caused growth defects. Here, we aim to clarify the importance of DnaK in GraT activity. We show that DnaK increases GraT toxicity, and particularly important is the negatively charged motif in the DnaK C-terminus. Given that GraT has an intrinsically disordered N-terminus, the assistance of DnaK is probably needed for re-modelling the toxin structure. We also demonstrate that the DnaK C-terminal negatively charged motif contributes to the competitive fitness of P. putida at both high and optimal growth temperatures. Thus, our data suggest that the disordered C-terminal end of DnaK enhances the chaperone functionality.
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15
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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: 14] [Impact Index Per Article: 2.8] [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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16
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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: 0.8] [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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17
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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: 1.4] [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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18
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Zhang SP, Wang Q, Quan SW, Yu XQ, Wang Y, Guo DD, Peng L, Feng HY, He YX. Type II toxin–antitoxin system in bacteria: activation, function, and mode of action. BIOPHYSICS REPORTS 2020. [DOI: 10.1007/s41048-020-00109-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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19
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Rosendahl S, Tamman H, Brauer A, Remm M, Hõrak R. Chromosomal toxin-antitoxin systems in Pseudomonas putida are rather selfish than beneficial. Sci Rep 2020; 10:9230. [PMID: 32513960 PMCID: PMC7280312 DOI: 10.1038/s41598-020-65504-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/06/2020] [Indexed: 11/09/2022] Open
Abstract
Chromosomal toxin-antitoxin (TA) systems are widespread genetic elements among bacteria, yet, despite extensive studies in the last decade, their biological importance remains ambivalent. The ability of TA-encoded toxins to affect stress tolerance when overexpressed supports the hypothesis of TA systems being associated with stress adaptation. However, the deletion of TA genes has usually no effects on stress tolerance, supporting the selfish elements hypothesis. Here, we aimed to evaluate the cost and benefits of chromosomal TA systems to Pseudomonas putida. We show that multiple TA systems do not confer fitness benefits to this bacterium as deletion of 13 TA loci does not influence stress tolerance, persistence or biofilm formation. Our results instead show that TA loci are costly and decrease the competitive fitness of P. putida. Still, the cost of multiple TA systems is low and detectable in certain conditions only. Construction of antitoxin deletion strains showed that only five TA systems code for toxic proteins, while other TA loci have evolved towards reduced toxicity and encode non-toxic or moderately potent proteins. Analysis of P. putida TA systems' homologs among fully sequenced Pseudomonads suggests that the TA loci have been subjected to purifying selection and that TA systems spread among bacteria by horizontal gene transfer.
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Affiliation(s)
- Sirli Rosendahl
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Hedvig Tamman
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Age Brauer
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Maido Remm
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Rita Hõrak
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
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20
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Prolič-Kalinšek M, De Bruyn P, Jurėnas D, Van Melderen L, Loris R, Volkov AN. 1H, 13C, and 15N backbone and side chain chemical shift assignment of YdaS, a monomeric member of the HigA family. BIOMOLECULAR NMR ASSIGNMENTS 2020; 14:25-30. [PMID: 31625047 DOI: 10.1007/s12104-019-09915-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/03/2019] [Indexed: 06/10/2023]
Abstract
The cryptic prophage CP-933P in Escherichia coli O157:H7 contains a parDE-like toxin-antitoxin module, the operator region of which is recognized by two flanking transcription regulators: PaaR2 (ParE associated Regulator), which forms part of the paaR2-paaA2-parE2 toxin-antitoxin operon and YdaS (COG4197), which is encoded in the opposite direction but shares the operator. Here we report the 1H, 15N and 13C backbone and side chain chemical shift assignments of YdaS from Escherichia coli O157:H7 in its free state. YdaS is a distinct relative to HigA antitoxins but behaves as a monomer in solution. The BMRB Accession Number is 27917.
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Affiliation(s)
- Maruša Prolič-Kalinšek
- Structural Biology Brussels, Department of Biotechnology (DBIT), Vrije Universiteit Brussel, Brussels, Belgium
- VIB-VUB Center for Structural Biology, Brussels, Belgium
| | - Pieter De Bruyn
- Structural Biology Brussels, Department of Biotechnology (DBIT), Vrije Universiteit Brussel, Brussels, Belgium
- VIB-VUB Center for Structural Biology, Brussels, Belgium
| | - Dukas Jurėnas
- Cellular and Molecular Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, Gosselies, Belgium
| | - Laurence Van Melderen
- Cellular and Molecular Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, Gosselies, Belgium
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology (DBIT), Vrije Universiteit Brussel, Brussels, Belgium.
- VIB-VUB Center for Structural Biology, Brussels, Belgium.
| | - Alexander N Volkov
- Structural Biology Brussels, Department of Biotechnology (DBIT), Vrije Universiteit Brussel, Brussels, Belgium
- VIB-VUB Center for Structural Biology, Brussels, Belgium
- Jean Jeener NMR Centre, Vrije Universiteit Brussel, Brussels, Belgium
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21
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Abstract
Type II toxin-antitoxin (TA) systems are small genetic elements composed of a toxic protein and its cognate antitoxin protein, the latter counteracting the toxicity of the former. While TA systems were initially discovered on plasmids, functioning as addiction modules through a phenomenon called postsegregational killing, they were later shown to be massively present in bacterial chromosomes, often in association with mobile genetic elements. Extensive research has been conducted in recent decades to better understand the physiological roles of these chromosomally encoded modules and to characterize the conditions leading to their activation. Type II toxin-antitoxin (TA) systems are small genetic elements composed of a toxic protein and its cognate antitoxin protein, the latter counteracting the toxicity of the former. While TA systems were initially discovered on plasmids, functioning as addiction modules through a phenomenon called postsegregational killing, they were later shown to be massively present in bacterial chromosomes, often in association with mobile genetic elements. Extensive research has been conducted in recent decades to better understand the physiological roles of these chromosomally encoded modules and to characterize the conditions leading to their activation. The diversity of their proposed roles, ranging from genomic stabilization and abortive phage infection to stress modulation and antibiotic persistence, in conjunction with the poor understanding of TA system regulation, resulted in the generation of simplistic models, often refuted by contradictory results. This review provides an epistemological and critical retrospective on TA modules and highlights fundamental questions concerning their roles and regulations that still remain unanswered.
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22
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Liu Y, Gao Z, Liu G, Geng Z, Dong Y, Zhang H. Structural Insights Into the Transcriptional Regulation of HigBA Toxin-Antitoxin System by Antitoxin HigA in Pseudomonas aeruginosa. Front Microbiol 2020; 10:3158. [PMID: 32038588 PMCID: PMC6987408 DOI: 10.3389/fmicb.2019.03158] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/30/2019] [Indexed: 12/21/2022] Open
Abstract
HigB-HigA is a bacterial toxin-antitoxin (TA) system in which the antitoxin HigA can mask the endoribonuclease activity of toxin HigB and repress the transcription of the TA operon by binding to its own promoter region. The opportunistic pathogen Pseudomonas aeruginosa HigBA (PaHigBA) is closely associated with the pathogenicity by reducing the production of multiple virulence factors and biofilm formation. However, the molecular mechanism underlying HigBA TA operon transcription by PaHigA remains elusive. Here, we report the crystal structure of PaHigA binding to the promoter region of higBA operon containing two identical palindromic sequences at 3.14 Å resolution. The promoter DNA is bound by two cooperative dimers to essentially encircle the intact palindrome region. The helix-turn-helix (HTH) motifs from the two dimers insert into the major grooves of the DNA at the opposite sides. The DNA adopts a canonical B-DNA conformation and all the hydrogen bonds between protein and DNA are mediated by the DNA phosphate backbone. A higher resolution structure of PaHigA-DNA complex at 2.50 Å further revealed three water molecules bridged the DNA-binding interface and mediated the interactions between the bases of palindromic sequences and PaHigA (Thr40, Asp43, and Arg49). Structure-based mutagenesis confirmed these residues are essential for the specific DNA-binding ability of PaHigA. Our structure-function studies therefore elucidated the cooperative dimer-dimer transcription repression mechanism, and may help to understand the regulation of multiple virulence factors by PaHigA in P. aeruginosa.
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Affiliation(s)
- Ying Liu
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Zengqiang Gao
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Guangfeng Liu
- National Center for Protein Science Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Zhi Geng
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Yuhui Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Heng Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
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23
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Lu H, Wang L, Li S, Pan C, Cheng K, Luo Y, Xu H, Tian B, Zhao Y, Hua Y. Structure and DNA damage-dependent derepression mechanism for the XRE family member DG-DdrO. Nucleic Acids Res 2019; 47:9925-9933. [PMID: 31410466 PMCID: PMC6765133 DOI: 10.1093/nar/gkz720] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/04/2019] [Accepted: 08/07/2019] [Indexed: 12/25/2022] Open
Abstract
DdrO is an XRE family transcription repressor that, in coordination with the metalloprotease PprI, is critical in the DNA damage response of Deinococcus species. Here, we report the crystal structure of Deinococcus geothermalis DdrO. Biochemical and structural studies revealed the conserved recognizing α-helix and extended dimeric interaction of the DdrO protein, which are essential for promoter DNA binding. Two conserved oppositely charged residues in the HTH motif of XRE family proteins form salt bridge interactions that are essential for promoter DNA binding. Notably, the C-terminal domain is stabilized by hydrophobic interactions of leucine/isoleucine-rich helices, which is critical for DdrO dimerization. Our findings suggest that DdrO is a novel XRE family transcriptional regulator that forms a distinctive dimer. The structure also provides insight into the mechanism of DdrO-PprI-mediated DNA damage response in Deinococcus.
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Affiliation(s)
- Huizhi Lu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Liangyan Wang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Shengjie Li
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Chaoming Pan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Kaiying Cheng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Yuxia Luo
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Hong Xu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Bing Tian
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Ye Zhao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Yuejin Hua
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
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24
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Manav MC, Turnbull KJ, Jurėnas D, Garcia-Pino A, Gerdes K, Brodersen DE. The E. coli HicB Antitoxin Contains a Structurally Stable Helix-Turn-Helix DNA Binding Domain. Structure 2019; 27:1675-1685.e3. [DOI: 10.1016/j.str.2019.08.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/28/2019] [Accepted: 08/16/2019] [Indexed: 11/30/2022]
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25
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De Bruyn P, Hadži S, Vandervelde A, Konijnenberg A, Prolič-Kalinšek M, Sterckx YGJ, Sobott F, Lah J, Van Melderen L, Loris R. Thermodynamic Stability of the Transcription Regulator PaaR2 from Escherichia coli O157:H7. Biophys J 2019; 116:1420-1431. [PMID: 30979547 DOI: 10.1016/j.bpj.2019.03.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 02/26/2019] [Accepted: 03/19/2019] [Indexed: 11/25/2022] Open
Abstract
PaaR2 is a putative transcription regulator encoded by a three-component parDE-like toxin-antitoxin module from Escherichia coli O157:H7. Although this module's toxin, antitoxin, and toxin-antitoxin complex have been more thoroughly investigated, little remains known about its transcription regulator PaaR2. Using a wide range of biophysical techniques (circular dichroism spectroscopy, size-exclusion chromatography-multiangle laser light scattering, dynamic light scattering, small-angle x-ray scattering, and native mass spectrometry), we demonstrate that PaaR2 mainly consists of α-helices and displays a concentration-dependent octameric build-up in solution and that this octamer contains a global shape that is significantly nonspherical. Thermal unfolding of PaaR2 is reversible and displays several transitions, suggesting a complex unfolding mechanism. The unfolding data obtained from spectroscopic and calorimetric methods were combined into a unifying thermodynamic model, which suggests a five-state unfolding trajectory. Furthermore, the model allows the calculation of a stability phase diagram, which shows that, under physiological conditions, PaaR2 mainly exists as a dimer that can swiftly oligomerize into an octamer depending on local protein concentrations. These findings, based on a thorough biophysical and thermodynamic analysis of PaaR2, may provide important insights into biological function such as DNA binding and transcriptional regulation.
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Affiliation(s)
- Pieter De Bruyn
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium; Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - San Hadži
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium; Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium; Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Alexandra Vandervelde
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium; Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - Albert Konijnenberg
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium; Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium; Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerpen, Belgium
| | - Maruša Prolič-Kalinšek
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium; Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
| | - Yann G-J Sterckx
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium; Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium; Laboratory of Medical Biochemistry, University of Antwerp, Campus Drie Eiken, Wilrijk, Belgium
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerpen, Belgium; Astbury Centre for Structural Molecular Biology, Leeds, United Kingdom; School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Jurij Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Laurence Van Melderen
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, Gosselies, Belgium
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Brussels, Belgium; Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.
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26
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Pseudomonas putida Responds to the Toxin GraT by Inducing Ribosome Biogenesis Factors and Repressing TCA Cycle Enzymes. Toxins (Basel) 2019; 11:toxins11020103. [PMID: 30744127 PMCID: PMC6410093 DOI: 10.3390/toxins11020103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/29/2019] [Accepted: 02/07/2019] [Indexed: 11/21/2022] Open
Abstract
The potentially self-poisonous toxin-antitoxin modules are widespread in bacterial chromosomes, but despite extensive studies, their biological importance remains poorly understood. Here, we used whole-cell proteomics to study the cellular effects of the Pseudomonas putida toxin GraT that is known to inhibit growth and ribosome maturation in a cold-dependent manner when the graA antitoxin gene is deleted from the genome. Proteomic analysis of P. putida wild-type and ΔgraA strains at 30 °C and 25 °C, where the growth is differently affected by GraT, revealed two major responses to GraT at both temperatures. First, ribosome biogenesis factors, including the RNA helicase DeaD and RNase III, are upregulated in ΔgraA. This likely serves to alleviate the ribosome biogenesis defect of the ΔgraA strain. Secondly, proteome data indicated that GraT induces downregulation of central carbon metabolism, as suggested by the decreased levels of TCA cycle enzymes isocitrate dehydrogenase Idh, α-ketoglutarate dehydrogenase subunit SucA, and succinate-CoA ligase subunit SucD. Metabolomic analysis revealed remarkable GraT-dependent accumulation of oxaloacetate at 25 °C and a reduced amount of malate, another TCA intermediate. The accumulation of oxaloacetate is likely due to decreased flux through the TCA cycle but also indicates inhibition of anabolic pathways in GraT-affected bacteria. Thus, proteomic and metabolomic analysis of the ΔgraA strain revealed that GraT-mediated stress triggers several responses that reprogram the cell physiology to alleviate the GraT-caused damage.
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