1
|
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 2024:10.1038/s41589-024-01630-4. [PMID: 38834893 DOI: 10.1038/s41589-024-01630-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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.
Collapse
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.
| |
Collapse
|
2
|
Eun HJ, Lee SY, Lee KY. DNA binding reveals hidden interdomain allostery of a MazE antitoxin from Mycobacterium tuberculosis. Biochem Biophys Res Commun 2024; 710:149898. [PMID: 38598903 DOI: 10.1016/j.bbrc.2024.149898] [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: 03/17/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024]
Abstract
Type II toxin-antitoxin (TA) systems are ubiquitously distributed genetic elements in prokaryotes and are crucial for cell maintenance and survival under environmental stresses. The antitoxin is a modular protein consisting of the disordered C-terminal region that physically contacts and neutralizes the cognate toxin and the well-folded N-terminal DNA binding domain responsible for autorepression of TA transcription. However, how the two functional domains communicate is largely unknown. Herein, we determined the crystal structure of the N-terminal domain of the type II antitoxin MazE-mt10 from Mycobacterium tuberculosis, revealing a homodimer of the ribbon-helix-helix (RHH) fold with distinct DNA binding specificity. NMR studies demonstrated that full-length MazE-mt10 forms the helical and coiled states in equilibrium within the C-terminal region, and that helical propensity is allosterically enhanced by the N-terminal binding to the cognate operator DNA. This coil-to-helix transition may promote toxin binding/neutralization of MazE-mt10 and further stabilize the TA-DNA transcription repressor. This is supported by many crystal structures of type II TA complexes in which antitoxins form an α-helical structure at the TA interface. The hidden helical state of free MazE-mt10 in solution, favored by DNA binding, adds a new dimension to the regulatory mechanism of type II TA systems. Furthermore, complementary approaches using X-ray crystallography and NMR allow us to study the allosteric interdomain interplay of many other full-length antitoxins of type II TA systems.
Collapse
Affiliation(s)
- Hyun-Jong Eun
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Soo-Yeon Lee
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Pocheon-si, 11160, Gyeonggi-Do, Republic of Korea
| | - Ki-Young Lee
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Pocheon-si, 11160, Gyeonggi-Do, Republic of Korea.
| |
Collapse
|
3
|
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: 0] [Impact Index Per Article: 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.
Collapse
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.
| |
Collapse
|
4
|
Nielsen MR, Brodersen DE. Structural Variations and Rearrangements in Bacterial Type II Toxin-Antitoxin Systems. Subcell Biochem 2024; 104:245-267. [PMID: 38963490 DOI: 10.1007/978-3-031-58843-3_11] [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] [Indexed: 07/05/2024]
Abstract
Bacteria encode a wide range of survival and immunity systems, including CRISPR-Cas, restriction-modification systems, and toxin-antitoxin systems involved in defence against bacteriophages, as well as survival during challenging growth conditions or exposure to antibiotics. Toxin-antitoxin (TA) systems are small two- or three-gene cassettes consisting of a metabolic regulator (the "toxin") and its associated antidote (the "antitoxin"), which also often functions as a transcriptional regulator. TA systems are widespread in the genomes of pathogens but are also present in commensal bacterial species and on plasmids. For mobile elements such as plasmids, TA systems play a role in maintenance, and increasing evidence now points to roles of chromosomal toxin-antitoxin systems in anti-phage defence. Moreover, the widespread occurrence of toxin-antitoxin systems in the genomes of pathogens has been suggested to relate to survival during host infection as well as in persistence during antibiotic treatment. Upon repeated exposure to antibiotics, TA systems have been shown to acquire point mutations as well as more dramatic rearrangements such as in-frame deletions with potential relevance for bacterial survival and pathogenesis. In this review, we present an overview of the known functional and structural consequences of mutations and rearrangements arising in bacterial toxin-antitoxin systems and discuss their relevance for survival and persistence of pathogenic species.
Collapse
Affiliation(s)
| | - Ditlev E Brodersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark.
| |
Collapse
|
5
|
Frumkin I, Laub MT. Selection of a de novo gene that can promote survival of Escherichia coli by modulating protein homeostasis pathways. Nat Ecol Evol 2023; 7:2067-2079. [PMID: 37945946 PMCID: PMC10697842 DOI: 10.1038/s41559-023-02224-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 09/12/2023] [Indexed: 11/12/2023]
Abstract
Cellular novelty can emerge when non-functional loci become functional genes in a process termed de novo gene birth. But how proteins with random amino acid sequences beneficially integrate into existing cellular pathways remains poorly understood. We screened ~108 genes, generated from random nucleotide sequences and devoid of homology to natural genes, for their ability to rescue growth arrest of Escherichia coli cells producing the ribonuclease toxin MazF. We identified ~2,000 genes that could promote growth, probably by reducing transcription from the promoter driving toxin expression. Additionally, one random protein, named Random antitoxin of MazF (RamF), modulated protein homeostasis by interacting with chaperones, leading to MazF proteolysis and a consequent loss of its toxicity. Finally, we demonstrate that random proteins can improve during evolution by identifying beneficial mutations that turned RamF into a more efficient inhibitor. Our work provides a mechanistic basis for how de novo gene birth can produce functional proteins that effectively benefit cells evolving under stress.
Collapse
Affiliation(s)
- Idan Frumkin
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Cambridge, MA, USA.
| |
Collapse
|
6
|
Saha R, Bhattacharje G, De S, Das AK. Deciphering the conformational stability of MazE7 antitoxin in Mycobacterium tuberculosis from molecular dynamics simulation study. J Biomol Struct Dyn 2023:1-17. [PMID: 37965715 DOI: 10.1080/07391102.2023.2280675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/01/2023] [Indexed: 11/16/2023]
Abstract
MazEF Toxin-antitoxin (TA) systems are associated with the persistent phenotype of the pathogen, Mycobacterium tuberculosis (Mtb), aiding their survival. Though extensively studied, the mode of action between the antitoxin-toxin and DNA of this family remains largely unclear. Here, the important interactions between MazF7 toxin and MazE7 antitoxin, and how MazE7 binds its promoter/operator region have been studied. To elucidate this, molecular dynamics (MD) simulation has been performed on MazE7, MazF7, MazEF7, MazEF7-DNA, and MazE7-DNA complexes to investigate how MazF7 and DNA affect the conformational change and dynamics of MazE7 antitoxin. This study demonstrated that the MazE7 dimer is disordered and one monomer (Chain C) attains stability after binding to the MazF7 toxin. Both the monomers (Chain C and Chain D) however are stabilized when MazE7 binds to DNA. MazE7 is also observed to sterically inhibit tRNA from binding to MazF7, thus suppressing its toxic activity. Comparative structural analysis performed on all the available antitoxins/antitoxin-toxin-DNA structures revealed MazEF7-DNA mechanism was similar to another TA system, AtaRT_E.coli. Simulation performed on the crystal structures of AtaR, AtaT, AtaRT, AtaRT-DNA, and AtaR-DNA showed that the disordered AtaR antitoxin attains stability by AtaT and DNA binding similar to MazE7. Based on these analyses it can thus be hypothesized that the disordered antitoxins enable tighter toxin and DNA binding thus preventing accidental toxin activation. Overall, this study provides crucial structural and dynamic insights into the MazEF7 toxin-antitoxin system and should provide a basis for targeting this TA system in combating Mycobacterium tuberculosis.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Rituparna Saha
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Gourab Bhattacharje
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Soumya De
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| |
Collapse
|
7
|
Pizzolato-Cezar LR, Spira B, Machini MT. Bacterial toxin-antitoxin systems: Novel insights on toxin activation across populations and experimental shortcomings. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 5:100204. [PMID: 38024808 PMCID: PMC10643148 DOI: 10.1016/j.crmicr.2023.100204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
The alarming rise in hard-to-treat bacterial infections is of great concern to human health. Thus, the identification of molecular mechanisms that enable the survival and growth of pathogens is of utmost urgency for the development of more efficient antimicrobial therapies. In challenging environments, such as presence of antibiotics, or during host infection, metabolic adjustments are essential for microorganism survival and competitiveness. Toxin-antitoxin systems (TASs) consisting of a toxin with metabolic modulating activity and a cognate antitoxin that antagonizes that toxin are important elements in the arsenal of bacterial stress defense. However, the exact physiological function of TA systems is highly debatable and with the exception of stabilization of mobile genetic elements and phage inhibition, other proposed biological functions lack a broad consensus. This review aims at gaining new insights into the physiological effects of TASs in bacteria and exploring the experimental shortcomings that lead to discrepant results in TAS research. Distinct control mechanisms ensure that only subsets of cells within isogenic cultures transiently develop moderate levels of toxin activity. As a result, TASs cause phenotypic growth heterogeneity rather than cell stasis in the entire population. It is this feature that allows bacteria to thrive in diverse environments through the creation of subpopulations with different metabolic rates and stress tolerance programs.
Collapse
Affiliation(s)
- Luis R. Pizzolato-Cezar
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Beny Spira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - M. Teresa Machini
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Roy TB, Sarma SP. Insights into the solution structure and transcriptional regulation of the MazE9 antitoxin in Mycobacterium tuberculosis. Proteins 2023. [PMID: 37737533 DOI: 10.1002/prot.26589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/21/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023]
Abstract
The present study endeavors to decode the details of the transcriptional autoregulation effected by the MazE9 antitoxin of the Mycobacterium tuberculosis MazEF9 toxin-antitoxin system. Regulation of this bicistronic operon at the level of transcription is a critical biochemical process that is key for the organism's stress adaptation and virulence. Here, we have reported the solution structure of the DNA binding domain of MazE9 and scrutinized the thermodynamic and kinetic parameters operational in its interaction with the promoter/operator region, specific to the mazEF9 operon. A HADDOCK model of MazE9 bound to its operator DNA has been calculated based on the information on interacting residues obtained from these studies. The thermodynamics and kinetics of the interaction of MazE9 with the functionally related mazEF6 operon indicate that the potential for intracellular cross-regulation is unlikely. An interesting feature of MazE9 is the cis ⇌ trans conformational isomerization of proline residues in the intrinsically disordered C-terminal domain of this antitoxin.
Collapse
Affiliation(s)
- Tanaya Basu Roy
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Siddhartha P Sarma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| |
Collapse
|
10
|
Chan WT, Garcillán-Barcia MP, Yeo CC, Espinosa M. Type II bacterial toxin-antitoxins: hypotheses, facts, and the newfound plethora of the PezAT system. FEMS Microbiol Rev 2023; 47:fuad052. [PMID: 37715317 PMCID: PMC10532202 DOI: 10.1093/femsre/fuad052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/24/2023] [Accepted: 09/07/2023] [Indexed: 09/17/2023] Open
Abstract
Toxin-antitoxin (TA) systems are entities found in the prokaryotic genomes, with eight reported types. Type II, the best characterized, is comprised of two genes organized as an operon. Whereas toxins impair growth, the cognate antitoxin neutralizes its activity. TAs appeared to be involved in plasmid maintenance, persistence, virulence, and defence against bacteriophages. Most Type II toxins target the bacterial translational machinery. They seem to be antecessors of Higher Eukaryotes and Prokaryotes Nucleotide-binding (HEPN) RNases, minimal nucleotidyltransferase domains, or CRISPR-Cas systems. A total of four TAs encoded by Streptococcus pneumoniae, RelBE, YefMYoeB, Phd-Doc, and HicAB, belong to HEPN-RNases. The fifth is represented by PezAT/Epsilon-Zeta. PezT/Zeta toxins phosphorylate the peptidoglycan precursors, thereby blocking cell wall synthesis. We explore the body of knowledge (facts) and hypotheses procured for Type II TAs and analyse the data accumulated on the PezAT family. Bioinformatics analyses showed that homologues of PezT/Zeta toxin are abundantly distributed among 14 bacterial phyla mostly in Proteobacteria (48%), Firmicutes (27%), and Actinobacteria (18%), showing the widespread distribution of this TA. The pezAT locus was found to be mainly chromosomally encoded whereas its homologue, the tripartite omega-epsilon-zeta locus, was found mostly on plasmids. We found several orphan pezT/zeta toxins, unaccompanied by a cognate antitoxin.
Collapse
Affiliation(s)
- Wai Ting Chan
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Maria Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-Consejo Superior de Investigaciones Científicas, C/Albert Einstein 22, PCTCAN, 39011 Santander, Spain
| | - Chew Chieng Yeo
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine
, Universiti Sultan Zainal Abidin, Jalan Sultan Mahumd, 20400 Kuala Terengganu, Malaysia
| | - Manuel Espinosa
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9, 28040 Madrid, Spain
| |
Collapse
|
11
|
Bruley A, Bitard-Feildel T, Callebaut I, Duprat E. A sequence-based foldability score combined with AlphaFold2 predictions to disentangle the protein order/disorder continuum. Proteins 2023; 91:466-484. [PMID: 36306150 DOI: 10.1002/prot.26441] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/11/2022]
Abstract
Order and disorder govern protein functions, but there is a great diversity in disorder, from regions that are-and stay-fully disordered to conditional order. This diversity is still difficult to decipher even though it is encoded in the amino acid sequences. Here, we developed an analytic Python package, named pyHCA, to estimate the foldability of a protein segment from the only information of its amino acid sequence and based on a measure of its density in regular secondary structures associated with hydrophobic clusters, as defined by the hydrophobic cluster analysis (HCA) approach. The tool was designed by optimizing the separation between foldable segments from databases of disorder (DisProt) and order (SCOPe [soluble domains] and OPM [transmembrane domains]). It allows to specify the ratio between order, embodied by regular secondary structures (either participating in the hydrophobic core of well-folded 3D structures or conditionally formed in intrinsically disordered regions) and disorder. We illustrated the relevance of pyHCA with several examples and applied it to the sequences of the proteomes of 21 species ranging from prokaryotes and archaea to unicellular and multicellular eukaryotes, for which structure models are provided in the AlphaFold protein structure database. Cases of low-confidence scores related to disorder were distinguished from those of sequences that we identified as foldable but are still excluded from accurate modeling by AlphaFold2 due to a lack of sequence homologs or to compositional biases. Overall, our approach is complementary to AlphaFold2, providing guides to map structural innovations through evolutionary processes, at proteome and gene scales.
Collapse
Affiliation(s)
- Apolline Bruley
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Tristan Bitard-Feildel
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Elodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| |
Collapse
|
12
|
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: 0] [Impact Index Per Article: 0] [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.
Collapse
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
| |
Collapse
|
13
|
Wang Y, Zhou Y, Shi C, Liu J, Lv G, Huang H, Li S, Duan L, Zheng X, Liu Y, Zhou H, Wang Y, Li Z, Ding K, Sun P, Huang Y, Lu X, Zhang ZM. A toxin-deformation dependent inhibition mechanism in the T7SS toxin-antitoxin system of Gram-positive bacteria. Nat Commun 2022; 13:6434. [PMID: 36307446 PMCID: PMC9616950 DOI: 10.1038/s41467-022-34034-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 10/11/2022] [Indexed: 12/25/2022] Open
Abstract
Toxin EsaD secreted by some S. aureus strains through the type VII secretion system (T7SS) specifically kills those strains lacking the antitoxin EsaG. Here we report the structures of EsaG, the nuclease domain of EsaD and their complex, which together reveal an inhibition mechanism that relies on significant conformational change of the toxin. To inhibit EsaD, EsaG breaks the nuclease domain of EsaD protein into two independent fragments that, in turn, sandwich EsaG. The originally well-folded ββα-metal finger connecting the two fragments is stretched to become a disordered loop, leading to disruption of the catalytic site of EsaD and loss of nuclease activity. This mechanism is distinct from that of the other Type II toxin-antitoxin systems, which utilize an intrinsically disordered region on the antitoxins to cover the active site of the toxins. This study paves the way for developing therapeutic approaches targeting this antagonism.
Collapse
Affiliation(s)
- Yongjin Wang
- grid.258164.c0000 0004 1790 3548International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, 510632 China
| | - Yang Zhou
- grid.258164.c0000 0004 1790 3548International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, 510632 China
| | - Chaowei Shi
- grid.59053.3a0000000121679639Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026 China
| | - Jiacong Liu
- grid.258164.c0000 0004 1790 3548International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, 510632 China
| | - Guohua Lv
- grid.258164.c0000 0004 1790 3548Division of Histology & Embryology, Medical College, Jinan University, Guangzhou, 510632 China
| | - Huisi Huang
- grid.258164.c0000 0004 1790 3548International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, 510632 China
| | - Shengrong Li
- grid.258164.c0000 0004 1790 3548International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, 510632 China
| | - Liping Duan
- grid.258164.c0000 0004 1790 3548International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, 510632 China
| | - Xinyi Zheng
- grid.258164.c0000 0004 1790 3548International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, 510632 China
| | - Yue Liu
- grid.258164.c0000 0004 1790 3548International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, 510632 China
| | - Haibo Zhou
- grid.258164.c0000 0004 1790 3548International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, 510632 China
| | - Yonghua Wang
- grid.79703.3a0000 0004 1764 3838School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640 China
| | - Zhengqiu Li
- grid.258164.c0000 0004 1790 3548International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, 510632 China
| | - Ke Ding
- grid.258164.c0000 0004 1790 3548International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, 510632 China
| | - Pinghua Sun
- grid.258164.c0000 0004 1790 3548International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, 510632 China
| | - Yun Huang
- grid.5386.8000000041936877XDepartment of Physiology & Biophysics, Weill Cornell Medicine, New York, NY 10065 USA
| | - Xiaoyun Lu
- grid.258164.c0000 0004 1790 3548International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, 510632 China
| | - Zhi-Min Zhang
- grid.258164.c0000 0004 1790 3548International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, 510632 China ,Guangdong Youmei Institute of Intelligent Bio-manufacturing, Foshan, Guangdong 528200 China
| |
Collapse
|
14
|
Koo JS, Kang SM, Jung WM, Kim DH, Lee BJ. The Haemophilus influenzae HipBA toxin-antitoxin system adopts an unusual three-com-ponent regulatory mechanism. IUCRJ 2022; 9:625-631. [PMID: 36071804 PMCID: PMC9438503 DOI: 10.1107/s205225252200687x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Type II toxin-antitoxin (TA) systems encode two proteins: a toxin that inhibits cell growth and an antitoxin that neutralizes the toxin by direct inter-molecular protein-protein inter-actions. The bacterial HipBA TA system is implicated in persister formation. The Haemophilus influenzae HipBA TA system consists of a HipB antitoxin and a HipA toxin, the latter of which is split into two fragments, and here we investigate this novel three-com-ponent regulatory HipBA system. Structural and functional analysis revealed that HipAN corresponds to the N-ter-minal part of HipA from other bacteria and toxic HipAC is inactivated by HipAN, not HipB. This study will be helpful in understanding the detailed regulatory mechanism of the HipBAN+C system, as well as why it is constructed as a three-com-ponent system.
Collapse
Affiliation(s)
- Ji Sung Koo
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung-Min Kang
- College of Pharmacy, Duksung Women’s University, Seoul 01369, Republic of Korea
| | - Won-Min Jung
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Do-Hee Kim
- Jeju Research Institute of Pharmaceutical Sciences, College of Pharmacy, Jeju National University, Jeju 63243, Republic of Korea
- Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, Jeju 63243, Republic of Korea
| | - Bong-Jin Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| |
Collapse
|
15
|
Bajaj P, Manjunath K, Varadarajan R. Structural and functional determinants inferred from deep mutational scans. Protein Sci 2022; 31:e4357. [PMID: 35762712 DOI: 10.1002/pro.4357] [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: 01/31/2022] [Revised: 04/04/2022] [Accepted: 05/11/2022] [Indexed: 11/08/2022]
Abstract
Mutations that affect protein binding to a cognate partner primarily occur either at buried residues or at exposed residues directly involved in partner binding. Distinguishing between these two categories based solely on mutational phenotypes is challenging. The bacterial toxin CcdB kills cells by binding to DNA Gyrase. Cell death is prevented by binding to its cognate antitoxin CcdA, at an extended interface that partially overlaps with the GyrA binding site. Using the CcdAB toxin-antitoxin (TA) system as a model, a comprehensive site-saturation mutagenesis library of CcdB was generated in its native operonic context. The mutational sensitivity of each mutant was estimated by evaluating the relative abundance of each mutant in two strains, one resistant and the other sensitive to the toxic activity of the CcdB toxin, through deep sequencing. The ability to bind CcdA was inferred through a RelE reporter gene assay, since the CcdAB complex binds to its own promoter, repressing transcription. By analyzing mutant phenotypes in the CcdB-sensitive, CcdB-resistant, and RelE reporter strains, it was possible to assign residues to buried, CcdA interacting or GyrA interacting sites. A few mutants were individually constructed, expressed, and biophysically characterized to validate molecular mechanisms responsible for the observed phenotypes. Residues inferred to be important for antitoxin binding, are also likely to be important for rejuvenating CcdB from the CcdB-Gyrase complex. Therefore, even in the absence of structural information, when coupled to appropriate genetic screens, such high-throughput strategies can be deployed for predicting structural and functional determinants of proteins.
Collapse
Affiliation(s)
- Priyanka Bajaj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Kavyashree Manjunath
- Centre for Chemical Biology and Therapeutics, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | | |
Collapse
|
16
|
The Association of the mazEF Toxin-antitoxin System and Vancomycin Resistance in Clinical Isolates of Vancomycin Resistant Enterococcus faecalis. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.2.46] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vancomycin resistant enterococci are challenging bacteria as they are difficult to be eradicated. Toxin-antitoxin (TA) systems are genetic elements located in most prokaryotic genomes. The mazEF TA system is harbored by a plasmid among Enterococcus faecalis (E. faecalis). To explore the relation between the existence of mazEF TA system and vancomycin resistance among clinical isolates of E. faecalis. Samples were collected from patients showing clinical picture of infection. Isolates of E. faecalis were identified by standard microbiological methods and their antimicrobial susceptibility patterns were detected by disk diffusion method. In addition, the E-test was used to confirm vancomycin resistant isolates. All the E. faecalis isolates were screened for the mazEF TA system by PCR. A total of 180 E. faecalis strains were identified with a vancomycin resistance rate of 30.6%. Vancomycin resistance was significantly associated with prolonged hospital stay (P= 0.04) and ICU setting (P= 0.001). The mazEF TA system was detected among 100% of vancomycin resistant isolates, while only 33.6% of the vancomycin sensitive isolates carried the system with a significant difference (P= 0.002). In addition, there was a significant association between the mazEF TA system-positive strains and the ICU setting (P= 0.02). A significant association was found between vancomycin resistance and the presence of the mazEF TA system among E. faecalis isolates. This association supports the current efforts to utilize the mazEF TA system as a possible target for novel antibacterial agents; however, further studies on a wider scale are necessary.
Collapse
|
17
|
Snead KJ, Moore LL, Bourne CR. ParD Antitoxin Hotspot Alters a Disorder-to-Order Transition upon Binding to Its Cognate ParE Toxin, Lessening Its Interaction Affinity and Increasing Its Protease Degradation Kinetics. Biochemistry 2022; 61:34-45. [PMID: 34914378 PMCID: PMC9805813 DOI: 10.1021/acs.biochem.1c00584] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Type-II toxin-antitoxin (TA) systems are comprised of two tightly interacting proteins, and operons encoding these systems have been identified throughout the genomes of bacteria. In contrast to secretion system effector-immunity pairs, TA systems must remain paired to protect the host cell from toxicity. Continual depletion of the antitoxin results in a shorter half-life than that of the toxin, though it is unclear if antitoxins can be effectively degraded when complexed with toxins. The current work probed the protein-protein interface of the PaParDE1 TA system, guided by an X-ray crystal structure, to determine contributions of antitoxin amino acids to interaction kinetics and affinity. These studies identified a "hotspot" position that alters the binding mode and resulting affinity (KD) from 152 pM for a 1:1 model for wild type to 25.5 and 626 nM for a 2:1 model with mutated antitoxin. This correlates with an altered induced secondary structure upon complexation with PaParE1 and increased kinetics of Lon protease digestion of the antitoxin despite the toxin presence. However, the decreased affinity at this hotspot was essentially reversed when the antitoxin dimerization region was deleted, yielding insights into complex interactions involved in the tight association. Removal of the antitoxin C-terminal seven amino acids, corresponding to the site of a disorder-to-order transition, completely prevents association. These studies combine to provide a model for the initiation of the TA interaction and highlight how manipulation of the sequence can impact the antitoxin disorder-to-order transition, weakening the affinity and resulting in increased antitoxin susceptibility to degradation.
Collapse
Affiliation(s)
- Kevin J. Snead
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Landon L. Moore
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States; Present Address: Department of Internal Medicine, Digestive Diseases and Nutrition Section, The University of Oklahoma Health Science Center, 800 Stanton L Young Blvd, Oklahoma City, OK 73104, USA
| | - Christina R. Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| |
Collapse
|
18
|
Bistable Expression of a Toxin-Antitoxin System Located in a Cryptic Prophage of Escherichia coli O157:H7. mBio 2021; 12:e0294721. [PMID: 34844426 PMCID: PMC8630535 DOI: 10.1128/mbio.02947-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Type II toxin-antitoxin (TA) systems are classically composed of two genes that encode a toxic protein and a cognate antitoxin protein. Both genes are organized in an operon whose expression is autoregulated at the level of transcription by the antitoxin-toxin complex, which binds operator DNA through the antitoxin’s DNA-binding domain. Here, we investigated the transcriptional regulation of a particular TA system located in the immunity region of a cryptic lambdoid prophage in the Escherichia coli O157:H7 EDL933 strain. This noncanonical paaA2-parE2 TA operon contains a third gene, paaR2, that encodes a transcriptional regulator that was previously shown to control expression of the TA. We provide direct evidence that the PaaR2 is a transcriptional regulator which shares functional similarities to the lambda CI repressor. Expression of the paaA2-parE2 TA operon is regulated by two other transcriptional regulators, YdaS and YdaT, encoded within the same region. We argue that YdaS and YdaT are analogous to lambda Cro and CII and that they do not constitute a TA system, as previously debated. We show that PaaR2 primarily represses the expression of YdaS and YdaT, which in turn controls the expression of paaR2-paaA2-parE2 operon. Overall, our results show that the paaA2-parE2 TA is embedded in an intricate lambdoid prophage-like regulation network. Using single-cell analysis, we observed that the entire locus exhibits bistability, which generates diversity of expression in the population. Moreover, we confirmed that paaA2-parE2 is addictive and propose that it could limit genomic rearrangements within the immunity region of the CP-933P cryptic prophage.
Collapse
|
19
|
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.
Collapse
|
20
|
Xue L, Khan MH, Yue J, Zhu Z, Niu L. The two paralogous copies of the YoeB-YefM toxin-antitoxin module in Staphylococcus aureus differ in DNA binding and recognition patterns. J Biol Chem 2021; 298:101457. [PMID: 34861238 PMCID: PMC8717551 DOI: 10.1016/j.jbc.2021.101457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 12/13/2022] Open
Abstract
Toxin-antitoxin (TA) systems are ubiquitous regulatory modules for bacterial growth and cell survival following stress. YefM-YoeB, the most prevalent type II TA system, is present in a variety of bacterial species. In Staphylococcus aureus, the YefM-YoeB system exists as two independent paralogous copies. Our previous research resolved crystal structures of the two oligomeric states (heterotetramer and heterohexamer-DNA ternary complex) of the first paralog as well as the molecular mechanism of transcriptional autoregulation of this module. However, structural details reflecting molecular diversity in both paralogs have been relatively unexplored. To understand the molecular mechanism of how Sa2YoeB and Sa2YefM regulate their own transcription and how each paralog functions independently, we solved a series of crystal structures of the Sa2YoeB-Sa2YefM. Our structural and biochemical data demonstrated that both paralogous copies adopt similar mechanisms of transcriptional autoregulation. In addition, structural analysis suggested that molecular diversity between the two paralogs might be reflected in the interaction profile of YefM and YoeB and the recognition pattern of promoter DNA by YefM. Interaction analysis revealed unique conformational and activating force effected by the interface between Sa2YoeB and Sa2YefM. In addition, the recognition pattern analysis demonstrated that residues Thr7 and Tyr14 of Sa2YefM specifically recognizes the flanking sequences (G and C) of the promoter DNA. Together, these results provide the structural insights into the molecular diversity and independent function of the paralogous copies of the YoeB-YefM TA system.
Collapse
Affiliation(s)
- Lu Xue
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui, China; Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Muhammad Hidayatullah Khan
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui, China; Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Jian Yue
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui, China; Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Zhongliang Zhu
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui, China; Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
| | - Liwen Niu
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Molecular and Cellular Biophysics, University of Science and Technology of China, Hefei, Anhui, China; Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
| |
Collapse
|
21
|
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: 1.7] [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.
Collapse
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
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
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: 1.3] [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.
Collapse
|
24
|
Abstract
In life's constant battle for survival, it takes one to kill but two to conquer. Toxin-antitoxin or toxin-antidote (TA) elements are genetic dyads that cheat the laws of inheritance to guarantee their transmission to the next generation. This seemingly simple genetic arrangement—a toxin linked to its antidote—is capable of quickly spreading and persisting in natural populations. TA elements were first discovered in bacterial plasmids in the 1980s and have recently been characterized in fungi, plants, and animals, where they underlie genetic incompatibilities and sterility in crosses between wild isolates. In this review, we provide a unified view of TA elements in both prokaryotic and eukaryotic organisms and highlight their similarities and differences at the evolutionary, genetic, and molecular levels. Finally, we propose several scenarios that could explain the paradox of the evolutionary origin of TA elements and argue that these elements may be key evolutionary players and that the full scope of their roles is only beginning to be uncovered.
Collapse
Affiliation(s)
- Alejandro Burga
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Eyal Ben-David
- Department of Human Genetics, Department of Biological Chemistry, and Howard Hughes Medical Institute, University of California, Los Angeles, California 90095, USA
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University School of Medicine, Jerusalem 91120, Israel
| | - Leonid Kruglyak
- Department of Human Genetics, Department of Biological Chemistry, and Howard Hughes Medical Institute, University of California, Los Angeles, California 90095, USA
| |
Collapse
|
25
|
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: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
|
26
|
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: 0.3] [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.
Collapse
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
| |
Collapse
|
27
|
Song S, Wood TK. Toxin/Antitoxin System Paradigms: Toxins Bound to Antitoxins Are Not Likely Activated by Preferential Antitoxin Degradation. ACTA ACUST UNITED AC 2020; 4:e1900290. [PMID: 32293143 DOI: 10.1002/adbi.201900290] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/27/2020] [Indexed: 12/28/2022]
Abstract
Periodically, a scientific field should examine its early premises. For ubiquitous toxin/antitoxin (TA) systems, several initial paradigms require adjustment based on accumulated data. For example, it is now clear that under physiological conditions, there is little evidence that toxins of TA systems cause cell death and little evidence that TA systems cause persistence. Instead, TA systems are utilized to reduce metabolism during stress, inhibit phages, stabilize genetic elements, and influence biofilm formation (bacterial cells attached via an extracellular matrix). In this essay, it is argued that toxins bound to antitoxins are not likely to become activated by preferential antitoxin degradation but instead, de novo toxin synthesis in the absence of stoichiometric amounts of antitoxin activates toxins.
Collapse
Affiliation(s)
- Sooyeon Song
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, 16802-4400, USA
| | - Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, 16802-4400, USA
| |
Collapse
|
28
|
Huang CY, Gonzalez-Lopez C, Henry C, Mijakovic I, Ryan KR. hipBA toxin-antitoxin systems mediate persistence in Caulobacter crescentus. Sci Rep 2020; 10:2865. [PMID: 32071324 PMCID: PMC7029023 DOI: 10.1038/s41598-020-59283-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/27/2020] [Indexed: 11/09/2022] Open
Abstract
Antibiotic persistence is a transient phenotypic state during which a bacterium can withstand otherwise lethal antibiotic exposure or environmental stresses. In Escherichia coli, persistence is promoted by the HipBA toxin-antitoxin system. The HipA toxin functions as a serine/threonine kinase that inhibits cell growth, while the HipB antitoxin neutralizes the toxin. E. coli HipA inactivates the glutamyl-tRNA synthetase GltX, which inhibits translation and triggers the highly conserved stringent response. Although hipBA operons are widespread in bacterial genomes, it is unknown if this mechanism is conserved in other species. Here we describe the functions of three hipBA modules in the alpha-proteobacterium Caulobacter crescentus. The HipA toxins have different effects on growth and macromolecular syntheses, and they phosphorylate distinct substrates. HipA1 and HipA2 contribute to antibiotic persistence during stationary phase by phosphorylating the aminoacyl-tRNA synthetases GltX and TrpS. The stringent response regulator SpoT is required for HipA-mediated antibiotic persistence, but persister cells can form in the absence of all hipBA operons or spoT, indicating that multiple pathways lead to persister cell formation in C. crescentus.
Collapse
Affiliation(s)
- Charlie Y Huang
- Department of Plant & Microbial Biology, University of California, Berkeley, USA
| | | | - Céline Henry
- Université Paris-Saclay, AgroParisTech, Micalis Institute, PAPPSO, INRAE, 78350, Jouy-en-Josas, France
| | - Ivan Mijakovic
- Division of Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kathleen R Ryan
- Department of Plant & Microbial Biology, University of California, Berkeley, USA.
| |
Collapse
|
29
|
A Gene Cluster That Encodes Histone Deacetylase Inhibitors Contributes to Bacterial Persistence and Antibiotic Tolerance in Burkholderia thailandensis. mSystems 2020; 5:5/1/e00609-19. [PMID: 32047060 PMCID: PMC7018527 DOI: 10.1128/msystems.00609-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The discovery of antibiotics such as penicillin and streptomycin marked a historic milestone in the 1940s and heralded a new era of antimicrobial therapy as the modern standard for medical treatment. Yet, even in those early days of discovery, it was noted that a small subset of cells (∼1 in 105) survived antibiotic treatment and continued to persist, leading to recurrence of chronic infection. These persisters are phenotypic variants that have modified their physiology to survive environmental stress. In this study, we have performed three transcriptomic screens to identify persistence genes that are common between three different stressor conditions. In particular, we identified genes that function in the synthesis of secondary metabolites, small molecules, and complex lipids, which are likely required to maintain the persistence state. Targeting universal persistence genes can lead to the development of clinically relevant antipersistence therapeutics for infectious disease management. Persister cells are genetically identical variants in a bacterial population that have phenotypically modified their physiology to survive environmental stress. In bacterial pathogens, persisters are able to survive antibiotic treatment and reinfect patients in a frustrating cycle of chronic infection. To better define core persistence mechanisms for therapeutics development, we performed transcriptomics analyses of Burkholderia thailandensis populations enriched for persisters via three methods: flow sorting for low proton motive force, meropenem treatment, and culture aging. Although the three persister-enriched populations generally displayed divergent gene expression profiles that reflect the multimechanistic nature of stress adaptations, there were several common gene pathways activated in two or all three populations. These include polyketide and nonribosomal peptide synthesis, Clp proteases, mobile elements, enzymes involved in lipid metabolism, and ATP-binding cassette (ABC) transporter systems. In particular, identification of genes that encode polyketide synthases (PKSs) and fatty acid catabolism factors indicates that generation of secondary metabolites, natural products, and complex lipids could be part of the metabolic program that governs the persistence state. We also found that loss-of-function mutations in the PKS-encoding gene locus BTH_I2366, which plays a role in biosynthesis of histone deacetylase (HDAC) inhibitors, resulted in increased sensitivity to antibiotics targeting DNA replication. Furthermore, treatment of multiple bacterial pathogens with a fatty acid synthesis inhibitor, CP-640186, potentiated the efficacy of meropenem against the persister populations. Altogether, our results suggest that bacterial persisters may exhibit an outwardly dormant physiology but maintain active metabolic processes that are required to maintain persistence. IMPORTANCE The discovery of antibiotics such as penicillin and streptomycin marked a historic milestone in the 1940s and heralded a new era of antimicrobial therapy as the modern standard for medical treatment. Yet, even in those early days of discovery, it was noted that a small subset of cells (∼1 in 105) survived antibiotic treatment and continued to persist, leading to recurrence of chronic infection. These persisters are phenotypic variants that have modified their physiology to survive environmental stress. In this study, we have performed three transcriptomic screens to identify persistence genes that are common between three different stressor conditions. In particular, we identified genes that function in the synthesis of secondary metabolites, small molecules, and complex lipids, which are likely required to maintain the persistence state. Targeting universal persistence genes can lead to the development of clinically relevant antipersistence therapeutics for infectious disease management.
Collapse
|
30
|
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: 3.5] [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.
Collapse
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
| |
Collapse
|
31
|
Garcia-Rodriguez G, Talavera Perez A, Konijnenberg A, Sobott F, Michiels J, Loris R. The Escherichia coli RnlA-RnlB toxin-antitoxin complex: production, characterization and crystallization. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2020; 76:31-39. [PMID: 31929184 DOI: 10.1107/s2053230x19017175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 12/23/2019] [Indexed: 01/17/2023]
Abstract
The Escherichia coli rnlAB operon encodes a toxin-antitoxin module that is involved in protection against infection by bacteriophage T4. The full-length RnlA-RnlB toxin-antitoxin complex as well as the toxin RnlA were purified to homogeneity and crystallized. When the affinity tag is placed on RnlA, RnlB is largely lost during purification and the resulting crystals exclusively comprise RnlA. A homogeneous preparation of RnlA-RnlB containing stoichiometric amounts of both proteins could only be obtained using a His tag placed C-terminal to RnlB. Native mass spectrometry and SAXS indicate a 1:1 stoichiometry for this RnlA-RnlB complex. Crystals of the RnlA-RnlB complex belonged to space group C2, with unit-cell parameters a = 243.32, b = 133.58, c = 55.64 Å, β = 95.11°, and diffracted to 2.6 Å resolution. The presence of both proteins in the crystals was confirmed and the asymmetric unit is likely to contain a heterotetramer with RnlA2:RnlB2 stoichiometry.
Collapse
Affiliation(s)
| | - Ariel Talavera Perez
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Albert Konijnenberg
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Frank Sobott
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | - Jan Michiels
- Center for Microbiology, VIB, B-3000 Leuven, Belgium
| | - Remy Loris
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| |
Collapse
|
32
|
Zamakhaev MV, Goncharenko AV, Shumkov MS. Toxin-Antitoxin Systems and Bacterial Persistence (Review). APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819060140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
33
|
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: 7] [Impact Index Per Article: 1.4] [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]
|
34
|
Kim DH, Kang SM, Park SJ, Jin C, Yoon HJ, Lee BJ. Functional insights into the Streptococcus pneumoniae HicBA toxin-antitoxin system based on a structural study. Nucleic Acids Res 2019; 46:6371-6386. [PMID: 29878152 PMCID: PMC6159526 DOI: 10.1093/nar/gky469] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 05/15/2018] [Indexed: 12/12/2022] Open
Abstract
Streptococcus pneumonia has attracted increasing attention due to its resistance to existing antibiotics. TA systems are essential for bacterial persistence under stressful conditions such as nutrient deprivation, antibiotic treatment, and immune system attacks. In particular, S. pneumoniae expresses the HicBA TA gene, which encodes the stable HicA toxin and the labile HicB antitoxin. These proteins interact to form a non-toxic TA complex under normal conditions, but the toxin is activated by release from the antitoxin in response to unfavorable growth conditions. Here, we present the first crystal structure showing the complete conformation of the HicBA complex from S. pneumonia. The structure reveals that the HicA toxin contains a double-stranded RNA-binding domain that is essential for RNA recognition and that the C-terminus of the HicB antitoxin folds into a ribbon-helix-helix DNA-binding motif. The active site of HicA is sterically blocked by the N-terminal region of HicB. RNase activity assays show that His36 is essential for the ribonuclease activity of HicA, and nuclear magnetic resonance (NMR) spectra show that several residues of HicB participate in binding to the promoter DNA of the HicBA operon. A toxin-mimicking peptide that inhibits TA complex formation and thereby increases toxin activity was designed, providing a novel approach to the development of new antibiotics.
Collapse
Affiliation(s)
- Do-Hee Kim
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Sung-Min Kang
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Sung Jean Park
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, 534-2 Yeonsu-dong, Yeonsu-gu, Incheon 13120, Republic of Korea
| | - Chenglong Jin
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Hye-Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 08826, Republic of Korea
| |
Collapse
|
35
|
A ParDE-family toxin antitoxin system in major resistance plasmids of Enterobacteriaceae confers antibiotic and heat tolerance. Sci Rep 2019; 9:9872. [PMID: 31285520 PMCID: PMC6614396 DOI: 10.1038/s41598-019-46318-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 06/26/2019] [Indexed: 11/16/2022] Open
Abstract
Toxin-antitoxin (TA) systems were initially discovered as plasmid addiction systems on low-copy-number plasmids. Thousands of TA loci have since been identified on chromosomes, plasmids and mobile elements in bacteria and archaea with diverse roles in bacterial physiology and in maintenance of genetic elements. Here, we identified and characterised a plasmid mediated type II TA system in Enterobacteriaceae as a member of the ParDE super family. This system (hereafter, ParDEI) is distributed among IncI and IncF-type antibiotic resistance and virulence plasmids found in avian and human-source Escherichia coli and Salmonella. It is found that ParDEI is a plasmid stability and stress response module that increases tolerance of aminoglycoside, quinolone and β-lactam antibiotics in E. coli by ~100–1,000-fold, and thus to levels beyond those achievable in the course of antibiotic therapy for human infections. ParDEI also confers a clear survival advantage at 42 °C and expression of the ParEI toxin in trans induces the SOS response, inhibits cell division and promotes biofilm formation. This transmissible high-level antibiotic tolerance is likely to be an important factor in the success of the IncI and IncF plasmids which carry it and the important pathogens in which these are resident.
Collapse
|
36
|
Structure and allosteric coupling of type Ⅱ antitoxin CopA SO. Biochem Biophys Res Commun 2019; 514:1122-1127. [PMID: 31101334 DOI: 10.1016/j.bbrc.2019.05.049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 05/06/2019] [Indexed: 11/22/2022]
Abstract
Toxin-antitoxin (TA) systems play critical roles in the environment adaptation of bacteria. Allosteric coupling between the N-terminal DNA-binding domain and the C-terminal toxin-binding domain of antitoxins contributes to conditional cooperativity in the functioning of type II TA. Herein, using circular dichroism (CD), nuclear magnetic resonance (NMR), X-ray crystallography, and size exclusion chromatography (SEC), the structure and DNA binding of CopASO, a newly identified type II antitoxin in Shewanella oneidensis, were investigated. Our data show that CopASO is a typical RHH antitoxin with an ordered N-terminal domain and a disordered C-terminal domain, and furthermore indicate that the C-terminal domain facilitates DNA binding of the N-terminal domain, which in turn induces the C-terminal domain to fold and associate.
Collapse
|
37
|
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: 0.8] [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.
Collapse
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.
| |
Collapse
|
38
|
Schureck MA, Meisner J, Hoffer ED, Wang D, Onuoha N, Ei Cho S, Lollar P, Dunham CM. Structural basis of transcriptional regulation by the HigA antitoxin. Mol Microbiol 2019; 111:1449-1462. [PMID: 30793388 DOI: 10.1111/mmi.14229] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2019] [Indexed: 01/16/2023]
Abstract
Bacterial toxin-antitoxin systems are important factors implicated in growth inhibition and plasmid maintenance. Type II toxin-antitoxin pairs are regulated at the transcriptional level by the antitoxin itself. Here, we examined how the HigA antitoxin regulates the expression of the Proteus vulgaris higBA toxin-antitoxin operon from the Rts1 plasmid. The HigBA complex adopts a unique architecture suggesting differences in its regulation as compared to classical type II toxin-antitoxin systems. We find that the C-terminus of the HigA antitoxin is required for dimerization and transcriptional repression. Further, the HigA structure reveals that the C terminus is ordered and does not transition between disorder-to-order states upon toxin binding. HigA residue Arg40 recognizes a TpG dinucleotide in higO2, an evolutionary conserved mode of recognition among prokaryotic and eukaryotic transcription factors. Comparison of the HigBA and HigA-higO2 structures reveals the distance between helix-turn-helix motifs of each HigA monomer increases by ~4 Å in order to bind to higO2. Consistent with these data, HigBA binding to each operator is twofold less tight than HigA alone. Together, these data show the HigB toxin does not act as a co-repressor suggesting potential novel regulation in this toxin-antitoxin system.
Collapse
Affiliation(s)
- Marc A Schureck
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jeffrey Meisner
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Eric D Hoffer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Dongxue Wang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Nina Onuoha
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Shein Ei Cho
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Pete Lollar
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Christine M Dunham
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| |
Collapse
|
39
|
Talavera A, Tamman H, Ainelo A, Konijnenberg A, Hadži S, Sobott F, Garcia-Pino A, Hõrak R, Loris R. A dual role in regulation and toxicity for the disordered N-terminus of the toxin GraT. Nat Commun 2019; 10:972. [PMID: 30814507 PMCID: PMC6393540 DOI: 10.1038/s41467-019-08865-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 01/31/2019] [Indexed: 11/09/2022] Open
Abstract
Bacterial toxin-antitoxin (TA) modules are tightly regulated to maintain growth in favorable conditions or growth arrest during stress. A typical regulatory strategy involves the antitoxin binding and repressing its own promoter while the toxin often acts as a co-repressor. Here we show that Pseudomonas putida graTA-encoded antitoxin GraA and toxin GraT differ from other TA proteins in the sense that not the antitoxin but the toxin possesses a flexible region. GraA auto-represses the graTA promoter: two GraA dimers bind cooperatively at opposite sides of the operator sequence. Contrary to other TA modules, GraT is a de-repressor of the graTA promoter as its N-terminal disordered segment prevents the binding of the GraT2A2 complex to the operator. Removal of this region restores operator binding and abrogates Gr aT toxicity. GraTA represents a TA module where a flexible region in the toxin rather than in the antitoxin controls operon expression and toxin activity. The Pseudomonas putida toxin GraT and antitoxin GraA form a type II toxin-antoxin module. Here the authors present the crystal structures of the GraA dimer, GraTA and GraA-DNA complexes and show that GraT contains a functionally important N-terminal intrinsic disordered region that prevents the binding of the GraTA complex to the operator.
Collapse
Affiliation(s)
- Ariel Talavera
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050, Brussel, Belgium. .,Molecular Recognition Unit, Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, B-1050, Brussel, Belgium.
| | - Hedvig Tamman
- Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Andres Ainelo
- Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Albert Konijnenberg
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050, Brussel, Belgium.,Molecular Recognition Unit, Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, B-1050, Brussel, Belgium.,Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020, Antwerpen, Belgium
| | - San Hadži
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050, Brussel, Belgium.,Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020, Antwerpen, Belgium.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Abel Garcia-Pino
- Biologie Structurale et Biophysique, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, B-6041, Gosselies, Belgium
| | - Rita Hõrak
- Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050, Brussel, Belgium. .,Molecular Recognition Unit, Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, B-1050, Brussel, Belgium.
| |
Collapse
|
40
|
Yoon WS, Seok SH, Won HS, Cho T, Lee SJ, Seo MD. Structural changes of antitoxin HigA from Shigella flexneri by binding of its cognate toxin HigB. Int J Biol Macromol 2019; 130:99-108. [PMID: 30797012 DOI: 10.1016/j.ijbiomac.2019.02.111] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/19/2019] [Accepted: 02/19/2019] [Indexed: 11/17/2022]
Abstract
In toxin-antitoxin systems, many antitoxin proteins that neutralize their cognate toxin proteins also bind to DNA to repress transcription, and the DNA-binding affinity of the antitoxin is affected by its toxin. We solved crystal structures of the antitoxin HigA (apo-SfHigA) and its complex with the toxin HigB (SfHigBA) from Shigella flexneri. The apo-SfHigA shows a distinctive V-shaped homodimeric conformation with sequestered N-domains having a novel fold. SfHigBA appears as a heterotetramer formed by N-terminal dimerization of SfHigB-bound SfHigA molecules. The conformational change in SfHigA upon SfHigB binding is mediated by rigid-body movements of its C-domains, which accompanied an overall conformational change from wide V-shaped to narrow V-shaped dimer. Consequently, the two putative DNA-binding helices (α7 in each subunit) are repositioned to a conformation more compatible with canonical homodimeric DNA-binding proteins containing HTH motifs. Collectively, this study demonstrates a conformational change in an antitoxin protein, which occurs upon toxin binding and is responsible for regulating antitoxin DNA binding.
Collapse
Affiliation(s)
- Won-Su Yoon
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi 16499, Republic of Korea; College of Pharmacy and Research Institute of Pharmaceutical Science and Technology (RIPST), Ajou University, Suwon, Gyeonggi 16499, Republic of Korea
| | - Seung-Hyeon Seok
- College of Pharmacy and Research Institute of Pharmaceutical Science and Technology (RIPST), Ajou University, Suwon, Gyeonggi 16499, Republic of Korea
| | - Hyung-Sik Won
- Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical & Health Science, Konkuk University, Chungju, Chungbuk 27478, Republic of Korea
| | - Taehwan Cho
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi 16499, Republic of Korea; College of Pharmacy and Research Institute of Pharmaceutical Science and Technology (RIPST), Ajou University, Suwon, Gyeonggi 16499, Republic of Korea
| | - Sang Jae Lee
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Min-Duk Seo
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi 16499, Republic of Korea; College of Pharmacy and Research Institute of Pharmaceutical Science and Technology (RIPST), Ajou University, Suwon, Gyeonggi 16499, Republic of Korea.
| |
Collapse
|
41
|
Mechanism of regulation and neutralization of the AtaR–AtaT toxin–antitoxin system. Nat Chem Biol 2019; 15:285-294. [DOI: 10.1038/s41589-018-0216-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 12/14/2018] [Indexed: 11/08/2022]
|
42
|
Winter AJ, Williams C, Isupov MN, Crocker H, Gromova M, Marsh P, Wilkinson OJ, Dillingham MS, Harmer NJ, Titball RW, Crump MP. The molecular basis of protein toxin HicA-dependent binding of the protein antitoxin HicB to DNA. J Biol Chem 2018; 293:19429-19440. [PMID: 30337369 DOI: 10.1074/jbc.ra118.005173] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/16/2018] [Indexed: 12/15/2022] Open
Abstract
Toxin-antitoxin (TA) systems are present in many bacteria and play important roles in bacterial growth, physiology, and pathogenicity. Those that are best studied are the type II TA systems, in which both toxins and antitoxins are proteins. The HicAB system is one of the prototypic TA systems, found in many bacterial species. Complex interactions between the protein toxin (HicA), the protein antitoxin (HicB), and the DNA upstream of the encoding genes regulate the activity of this system, but few structural details are available about how HicA destabilizes the HicB-DNA complex. Here, we determined the X-ray structures of HicB and the HicAB complex to 1.8 and 2.5 Å resolution, respectively, and characterized their DNA interactions. This revealed that HicB forms a tetramer and HicA and HicB form a heterooctameric complex that involves structural reorganization of the C-terminal (DNA-binding) region of HicB. Our observations indicated that HicA has a profound impact on binding of HicB to DNA sequences upstream of hicAB in a stoichiometric-dependent way. At low ratios of HicA:HicB, there was no effect on DNA binding, but at higher ratios, the affinity for DNA declined cooperatively, driving dissociation of the HicA:HicB:DNA complex. These results reveal the structural mechanisms by which HicA de-represses the HicB-DNA complex.
Collapse
Affiliation(s)
- Ashley J Winter
- From the School of Chemistry, University of Bristol Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Christopher Williams
- From the School of Chemistry, University of Bristol Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Michail N Isupov
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Hannah Crocker
- From the School of Chemistry, University of Bristol Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Mariya Gromova
- From the School of Chemistry, University of Bristol Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Philip Marsh
- From the School of Chemistry, University of Bristol Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Oliver J Wilkinson
- the School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD United Kingdom
| | - Mark S Dillingham
- the School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD United Kingdom
| | - Nicholas J Harmer
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Richard W Titball
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom,
| | - Matthew P Crump
- From the School of Chemistry, University of Bristol Cantock's Close, Bristol BS8 1TS, United Kingdom,
| |
Collapse
|
43
|
Jurėnas D, Van Melderen L, Garcia-Pino A. Crystallization and X-ray analysis of all of the players in the autoregulation of the ataRT toxin-antitoxin system. Acta Crystallogr F Struct Biol Commun 2018; 74:391-401. [PMID: 29969102 PMCID: PMC6038448 DOI: 10.1107/s2053230x18007914] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 05/29/2018] [Indexed: 01/02/2023] Open
Abstract
The ataRT operon from enteropathogenic Escherichia coli encodes a toxin-antitoxin (TA) module with a recently discovered novel toxin activity. This new type II TA module targets translation initiation for cell-growth arrest. Virtually nothing is known regarding the molecular mechanisms of neutralization, toxin catalytic action or translation autoregulation. Here, the production, biochemical analysis and crystallization of the intrinsically disordered antitoxin AtaR, the toxin AtaT, the AtaR-AtaT complex and the complex of AtaR-AtaT with a double-stranded DNA fragment of the operator region of the promoter are reported. Because they contain large regions that are intrinsically disordered, TA antitoxins are notoriously difficult to crystallize. AtaR forms a homodimer in solution and crystallizes in space group P6122, with unit-cell parameters a = b = 56.3, c = 160.8 Å. The crystals are likely to contain an AtaR monomer in the asymmetric unit and diffracted to 3.8 Å resolution. The Y144F catalytic mutant of AtaT (AtaTY144F) bound to the cofactor acetyl coenzyme A (AcCoA) and the C-terminal neutralization domain of AtaR (AtaR44-86) were also crystallized. The crystals of the AtaTY144F-AcCoA complex diffracted to 2.5 Å resolution and the crystals of AtaR44-86 diffracted to 2.2 Å resolution. Analysis of these structures should reveal the full scope of the neutralization of the toxin AtaT by AtaR. The crystals belonged to space groups P6522 and P3121, with unit-cell parameters a = b = 58.1, c = 216.7 Å and a = b = 87.6, c = 125.5 Å, respectively. The AtaR-AtaT-DNA complex contains a 22 bp DNA duplex that was optimized to obtain high-resolution data based on the sequence of two inverted repeats detected in the operator region. It crystallizes in space group C2221, with unit-cell parameters a = 75.6, b = 87.9, c = 190.5 Å. These crystals diffracted to 3.5 Å resolution.
Collapse
Affiliation(s)
- Dukas Jurėnas
- Cellular and Molecular Microbiology, Université Libre de Bruxelles (ULB), Rue des Professeurs Jeener et Brachet 12, B-6041 Gosselies, Belgium
- Department of Biochemistry and Molecular Biology, Vilnius University Joint Life Sciences Center, Sauletekio Ave. 7, LT-10257 Vilnius, Lithuania
| | - Laurence Van Melderen
- Cellular and Molecular Microbiology, Université Libre de Bruxelles (ULB), Rue des Professeurs Jeener et Brachet 12, B-6041 Gosselies, Belgium
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Université Libre de Bruxelles (ULB), Rue des Professeurs Jeener et Brachet 12, B-6041 Gosselies, Belgium
| |
Collapse
|
44
|
Reassessing the Role of Type II Toxin-Antitoxin Systems in Formation of Escherichia coli Type II Persister Cells. mBio 2018; 9:mBio.00640-18. [PMID: 29895634 PMCID: PMC6016239 DOI: 10.1128/mbio.00640-18] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Persistence is a reversible and low-frequency phenomenon allowing a subpopulation of a clonal bacterial population to survive antibiotic treatments. Upon removal of the antibiotic, persister cells resume growth and give rise to viable progeny. Type II toxin-antitoxin (TA) systems were assumed to play a key role in the formation of persister cells in Escherichia coli based on the observation that successive deletions of TA systems decreased persistence frequency. In addition, the model proposed that stochastic fluctuations of (p)ppGpp levels are the basis for triggering activation of TA systems. Cells in which TA systems are activated are thought to enter a dormancy state and therefore survive the antibiotic treatment. Using independently constructed strains and newly designed fluorescent reporters, we reassessed the roles of TA modules in persistence both at the population and single-cell levels. Our data confirm that the deletion of 10 TA systems does not affect persistence to ofloxacin or ampicillin. Moreover, microfluidic experiments performed with a strain reporting the induction of the yefM-yoeB TA system allowed the observation of a small number of type II persister cells that resume growth after removal of ampicillin. However, we were unable to establish a correlation between high fluorescence and persistence, since the fluorescence of persister cells was comparable to that of the bulk of the population and none of the cells showing high fluorescence were able to resume growth upon removal of the antibiotic. Altogether, these data show that there is no direct link between induction of TA systems and persistence to antibiotics.IMPORTANCE Within a growing bacterial population, a small subpopulation of cells is able to survive antibiotic treatment by entering a transient state of dormancy referred to as persistence. Persistence is thought to be the cause of relapsing bacterial infections and is a major public health concern. Type II toxin-antitoxin systems are small modules composed of a toxic protein and an antitoxin protein counteracting the toxin activity. These systems were thought to be pivotal players in persistence until recent developments in the field. Our results demonstrate that previous influential reports had technical flaws and that there is no direct link between induction of TA systems and persistence to antibiotics.
Collapse
|
45
|
Mitić NS, Malkov SN, Kovačević JJ, Pavlović-Lažetić GM, Beljanski MV. Structural disorder of plasmid-encoded proteins in Bacteria and Archaea. BMC Bioinformatics 2018; 19:158. [PMID: 29699482 PMCID: PMC5922023 DOI: 10.1186/s12859-018-2158-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/16/2018] [Indexed: 01/30/2023] Open
Abstract
Background In the last decade and a half it has been firmly established that a large number of proteins do not adopt a well-defined (ordered) structure under physiological conditions. Such intrinsically disordered proteins (IDPs) and intrinsically disordered (protein) regions (IDRs) are involved in essential cell processes through two basic mechanisms: the entropic chain mechanism which is responsible for rapid fluctuations among many alternative conformations, and molecular recognition via short recognition elements that bind to other molecules. IDPs possess a high adaptive potential and there is special interest in investigating their involvement in organism evolution. Results We analyzed 2554 Bacterial and 139 Archaeal proteomes, with a total of 8,455,194 proteins for disorder content and its implications for adaptation of organisms, using three disorder predictors and three measures. Along with other findings, we revealed that for all three predictors and all three measures (1) Bacteria exhibit significantly more disorder than Archaea; (2) plasmid-encoded proteins contain considerably more IDRs than proteins encoded on chromosomes (or whole genomes) in both prokaryote superkingdoms; (3) plasmid proteins are significantly more disordered than chromosomal proteins only in the group of proteins with no COG category assigned; (4) antitoxin proteins in comparison to other proteins, are the most disordered (almost double) in both Bacterial and Archaeal proteomes; (5) plasmidal proteins are more disordered than chromosomal proteins in Bacterial antitoxins and toxin-unclassified proteins, but have almost the same disorder content in toxin proteins. Conclusion Our results suggest that while disorder content depends on genome and proteome characteristics, it is more influenced by functional engagements than by gene location (on chromosome or plasmid). Electronic supplementary material The online version of this article (10.1186/s12859-018-2158-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Nenad S Mitić
- Department of Computer Science, Faculty of Mathematics, University of Belgrade, P.O.B. 550 Studentski trg 16, Belgrade, 11001, Serbia.
| | - Saša N Malkov
- Department of Computer Science, Faculty of Mathematics, University of Belgrade, P.O.B. 550 Studentski trg 16, Belgrade, 11001, Serbia
| | - Jovana J Kovačević
- Department of Computer Science, Faculty of Mathematics, University of Belgrade, P.O.B. 550 Studentski trg 16, Belgrade, 11001, Serbia
| | - Gordana M Pavlović-Lažetić
- Department of Computer Science, Faculty of Mathematics, University of Belgrade, P.O.B. 550 Studentski trg 16, Belgrade, 11001, Serbia
| | - Miloš V Beljanski
- Bio-lab, Institute of General and Physical Chemistry, P.O.B. 45, Studentski trg 12/V, Belgrade, 11001, Serbia
| |
Collapse
|
46
|
Hampton HG, Jackson SA, Fagerlund RD, Vogel AIM, Dy RL, Blower TR, Fineran PC. AbiEi Binds Cooperatively to the Type IV abiE Toxin-Antitoxin Operator Via a Positively-Charged Surface and Causes DNA Bending and Negative Autoregulation. J Mol Biol 2018. [PMID: 29518409 DOI: 10.1016/j.jmb.2018.02.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Bacteria resist phage infection using multiple strategies, including CRISPR-Cas and abortive infection (Abi) systems. Abi systems provide population-level protection from phage predation, via "altruistic" cell suicide. It has recently been shown that some Abi systems function via a toxin-antitoxin mechanism, such as the widespread AbiE family. The Streptococcus agalactiae AbiE system consists of a bicistronic operon encoding the AbiEi antitoxin and AbiEii toxin, which function as a Type IV toxin-antitoxin system. Here we examine the AbiEi antitoxin, which belongs to a large family of transcriptional regulators with a conserved N-terminal winged helix-turn-helix domain. This winged helix-turn-helix is essential for transcriptional repression of the abiE operon. The function of the AbiEi C-terminal domain is poorly characterized, but it contributes to transcriptional repression and is sufficient for toxin neutralization. We demonstrate that a conserved charged surface on one face of the C-terminal domain assists sequence-specific DNA binding and negative autoregulation, without influencing antitoxicity. Furthermore, AbiEi binds cooperatively to two inverted repeats within the abiE promoter and bends the DNA by 72°. These findings demonstrate that the mechanism of DNA binding by the widespread family of AbiEi antitoxins and transcriptional regulators can contribute to negative autoregulation.
Collapse
Affiliation(s)
- Hannah G Hampton
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Simon A Jackson
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Robert D Fagerlund
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Anne I M Vogel
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Ron L Dy
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Tim R Blower
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
| |
Collapse
|
47
|
Harms A, Brodersen DE, Mitarai N, Gerdes K. Toxins, Targets, and Triggers: An Overview of Toxin-Antitoxin Biology. Mol Cell 2018; 70:768-784. [PMID: 29398446 DOI: 10.1016/j.molcel.2018.01.003] [Citation(s) in RCA: 398] [Impact Index Per Article: 66.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/06/2017] [Accepted: 01/02/2018] [Indexed: 12/01/2022]
Abstract
Bacterial toxin-antitoxin (TA) modules are abundant genetic elements that encode a toxin protein capable of inhibiting cell growth and an antitoxin that counteracts the toxin. The majority of toxins are enzymes that interfere with translation or DNA replication, but a wide variety of molecular activities and cellular targets have been described. Antitoxins are proteins or RNAs that often control their cognate toxins through direct interactions and, in conjunction with other signaling elements, through transcriptional and translational regulation of TA module expression. Three major biological functions of TA modules have been discovered, post-segregational killing ("plasmid addiction"), abortive infection (bacteriophage immunity through altruistic suicide), and persister formation (antibiotic tolerance through dormancy). In this review, we summarize the current state of the field and highlight how multiple levels of regulation shape the conditions of toxin activation to achieve the different biological functions of TA modules.
Collapse
Affiliation(s)
- Alexander Harms
- Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Ditlev Egeskov Brodersen
- Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark; Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Namiko Mitarai
- Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark; Niels Bohr Institute, Department of Physics, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Kenn Gerdes
- Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark.
| |
Collapse
|
48
|
New Approaches and Therapeutic Options for Mycobacterium tuberculosis in a Dormant State. Clin Microbiol Rev 2017; 31:31/1/e00060-17. [PMID: 29187395 DOI: 10.1128/cmr.00060-17] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We are far away from the days when tuberculosis (TB) accounted for 1 in 4 deaths during the 19th century. However, Mycobacterium tuberculosis complex (MTBC) strains are still the leading cause of morbidity and mortality by a single infectious disease, with 9.6 million cases and 1.5 million deaths reported. One-third of the world's population is estimated by the WHO to be infected with latent TB. During the last decade, several studies have aimed to define the characteristics of dormant bacteria in these latent infections. General features of the shift to a dormant state encompass several phenotypic changes that reduce metabolic activity. This low metabolic state is thought to increase the resistance of MTBC strains to host/environmental stresses, including antibiotic action. Once the stress ceases (e.g., interruption of treatment), dormant cells can reactivate and cause symptomatic disease again. Therefore, a proper understanding of dormancy could guide the rational development of new treatment regimens that target dormant cells, reducing later relapse. Here, we briefly summarize the latest data on the genetics involved in the regulation of dormancy and discuss new approaches to TB treatment.
Collapse
|
49
|
Jurėnas D, Garcia-Pino A, Van Melderen L. Novel toxins from type II toxin-antitoxin systems with acetyltransferase activity. Plasmid 2017; 93:30-35. [PMID: 28941941 DOI: 10.1016/j.plasmid.2017.08.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 08/24/2017] [Accepted: 08/28/2017] [Indexed: 12/21/2022]
Abstract
Type II toxin-antitoxin (TA) systems are widespread in bacterial and archeal genomes. These modules are very dynamic and participate in bacterial genome evolution through horizontal gene transfer. TA systems are commonly composed of a labile antitoxin and a stable toxin. Toxins appear to preferentially inhibit the protein synthesis process. Toxins use a variety of molecular mechanisms and target nearly every step of translation to achieve their inhibitory function. This review focuses on a recently identified TA family that includes acetyltransferase toxins. The AtaT and TacT toxins are the best-characterized to date in this family. AtaT and TacT both inhibit translation by acetylating the amino acid charged on tRNAs. However, the specificities of these 2 toxins are different as AtaT inhibits translation initiation by acetylation of the initiator tRNA whereas TacT acetylates elongator tRNAs. The molecular mechanisms of these toxins are discussed, as well as the functions and possible evolutionary origins of this diverse toxin family.
Collapse
Affiliation(s)
- Dukas Jurėnas
- Department of Biochemistry and Molecular Biology, Vilnius University Joint Life Sciences Center, Vilnius, Lithuania; Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Belgium
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Belgium
| | - Laurence Van Melderen
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Belgium.
| |
Collapse
|
50
|
Hadži S, Garcia-Pino A, Haesaerts S, Jurenas D, Gerdes K, Lah J, Loris R. Ribosome-dependent Vibrio cholerae mRNAse HigB2 is regulated by a β-strand sliding mechanism. Nucleic Acids Res 2017; 45:4972-4983. [PMID: 28334932 PMCID: PMC5416850 DOI: 10.1093/nar/gkx138] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 02/25/2017] [Indexed: 11/12/2022] Open
Abstract
Toxin–antitoxin (TA) modules are small operons involved in bacterial stress response and persistence. higBA operons form a family of TA modules with an inverted gene organization and a toxin belonging to the RelE/ParE superfamily. Here, we present the crystal structures of chromosomally encoded Vibrio cholerae antitoxin (VcHigA2), toxin (VcHigB2) and their complex, which show significant differences in structure and mechanisms of function compared to the higBA module from plasmid Rts1, the defining member of the family. The VcHigB2 is more closely related to Escherichia coli RelE both in terms of overall structure and the organization of its active site. VcHigB2 is neutralized by VcHigA2, a modular protein with an N-terminal intrinsically disordered toxin-neutralizing segment followed by a C-terminal helix-turn-helix dimerization and DNA binding domain. VcHigA2 binds VcHigB2 with picomolar affinity, which is mainly a consequence of entropically favorable de-solvation of a large hydrophobic binding interface and enthalpically favorable folding of the N-terminal domain into an α-helix followed by a β-strand. This interaction displaces helix α3 of VcHigB2 and at the same time induces a one-residue shift in the register of β-strand β3, thereby flipping the catalytically important Arg64 out of the active site.
Collapse
Affiliation(s)
- San Hadži
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050 Brussel, Belgium.,Molecular Recognition Unit, Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050 Brussel, Belgium.,Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Abel Garcia-Pino
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050 Brussel, Belgium.,Biologie Structurale et Biophysique, IBMM-DBM, Université Libre de Bruxelles (ULB), B-6041 Gosselies, Belgium
| | - Sarah Haesaerts
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050 Brussel, Belgium.,Molecular Recognition Unit, Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050 Brussel, Belgium
| | - Dukas Jurenas
- Biologie Structurale et Biophysique, IBMM-DBM, Université Libre de Bruxelles (ULB), B-6041 Gosselies, Belgium
| | - Kenn Gerdes
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - 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, B-1050 Brussel, Belgium.,Molecular Recognition Unit, Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050 Brussel, Belgium
| |
Collapse
|