1
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Tamman H, Ernits K, Roghanian M, Ainelo A, Julius C, Perrier A, Talavera A, Ainelo H, Dugauquier R, Zedek S, Thureau A, Pérez J, Lima-Mendez G, Hallez R, Atkinson GC, Hauryliuk V, Garcia-Pino A. Structure of SpoT reveals evolutionary tuning of catalysis via conformational constraint. Nat Chem Biol 2023; 19:334-345. [PMID: 36470996 PMCID: PMC9974481 DOI: 10.1038/s41589-022-01198-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 10/05/2022] [Indexed: 12/12/2022]
Abstract
Stringent factors orchestrate bacterial cell reprogramming through increasing the level of the alarmones (p)ppGpp. In Beta- and Gammaproteobacteria, SpoT hydrolyzes (p)ppGpp to counteract the synthetase activity of RelA. However, structural information about how SpoT controls the levels of (p)ppGpp is missing. Here we present the crystal structure of the hydrolase-only SpoT from Acinetobacter baumannii and uncover the mechanism of intramolecular regulation of 'long'-stringent factors. In contrast to ribosome-associated Rel/RelA that adopt an elongated structure, SpoT assumes a compact τ-shaped structure in which the regulatory domains wrap around a Core subdomain that controls the conformational state of the enzyme. The Core is key to the specialization of long RelA-SpoT homologs toward either synthesis or hydrolysis: the short and structured Core of SpoT stabilizes the τ-state priming the hydrolase domain for (p)ppGpp hydrolysis, whereas the longer, more dynamic Core domain of RelA destabilizes the τ-state priming the monofunctional RelA for efficient (p)ppGpp synthesis.
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Affiliation(s)
- Hedvig Tamman
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium.
| | - Karin Ernits
- Department of Experimental Medicine, University of Lund, Lund, Sweden
- Department of Chemistry, Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Mohammad Roghanian
- Department of Experimental Medicine, University of Lund, Lund, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Departement of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Andres Ainelo
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
| | | | - Anthony Perrier
- Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
- Bacterial Cell Cycle and Development, Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
| | - Ariel Talavera
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
| | - Hanna Ainelo
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
| | - Rémy Dugauquier
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
- Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
| | - Safia Zedek
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
| | | | - Javier Pérez
- Synchrotron SOLEIL, Saint-Aubin - BP 48, Gif sur Yvette, France
| | - Gipsi Lima-Mendez
- Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
| | - Régis Hallez
- Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
- Bacterial Cell Cycle and Development, Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
- WELBIO, Brussels, Belgium
| | - Gemma C Atkinson
- Department of Experimental Medicine, University of Lund, Lund, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Vasili Hauryliuk
- Department of Experimental Medicine, University of Lund, Lund, Sweden.
- Department of Molecular Biology, Umeå University, Umeå, Sweden.
- University of Tartu, Institute of Technology, Tartu, Estonia.
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium.
- WELBIO, Brussels, Belgium.
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2
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Ainelo A, Caballero-Montes J, Bulvas O, Ernits K, Coppieters ‘t Wallant K, Takada H, Craig SZ, Mazzucchelli G, Zedek S, Pichová I, Atkinson GC, Talavera A, Martens C, Hauryliuk V, Garcia-Pino A. The structure of DarB in complex with Rel NTD reveals nonribosomal activation of Rel stringent factors. SCIENCE ADVANCES 2023; 9:eade4077. [PMID: 36652515 PMCID: PMC9848473 DOI: 10.1126/sciadv.ade4077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Rel stringent factors are bifunctional ribosome-associated enzymes that catalyze both synthesis and hydrolysis of the alarmones (p)ppGpp. Besides the allosteric control by starved ribosomes and (p)ppGpp, Rel is regulated by various protein factors depending on specific stress conditions, including the c-di-AMP-binding protein DarB. However, how these effector proteins control Rel remains unknown. We have determined the crystal structure of the DarB2:RelNTD2 complex, uncovering that DarB directly engages the SYNTH domain of Rel to stimulate (p)ppGpp synthesis. This association with DarB promotes a SYNTH-primed conformation of the N-terminal domain region, markedly increasing the affinity of Rel for ATP while switching off the hydrolase activity of the enzyme. Binding to c-di-AMP rigidifies DarB, imposing an entropic penalty that precludes DarB-mediated control of Rel during normal growth. Our experiments provide the basis for understanding a previously unknown mechanism of allosteric regulation of Rel stringent factors independent of amino acid starvation.
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Affiliation(s)
- Andres Ainelo
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles 10 (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
| | - Julien Caballero-Montes
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles 10 (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
| | - Ondřej Bulvas
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technicka 5, 166 28 Prague 6, Czech Republic
| | - Karin Ernits
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Kyo Coppieters ‘t Wallant
- Centre for Structural Biology and Bioinformatics, Universite Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC, 1050 Bruxelles, Belgium
| | - Hiraku Takada
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo Motoyama, Kita-ku, Kyoto 603-8555, Japan
| | - Sophie Z. Craig
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles 10 (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, MolSys Research Unit, Liège Université, B-4000 Liège, Belgium
| | - Safia Zedek
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles 10 (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
| | - Iva Pichová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Gemma C. Atkinson
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Ariel Talavera
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles 10 (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
| | - Chloe Martens
- Centre for Structural Biology and Bioinformatics, Universite Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC, 1050 Bruxelles, Belgium
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
- University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles 10 (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium
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3
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Zhang T, Tamman H, Coppieters 't Wallant K, Kurata T, LeRoux M, Srikant S, Brodiazhenko T, Cepauskas A, Talavera A, Martens C, Atkinson GC, Hauryliuk V, Garcia-Pino A, Laub MT. Direct activation of a bacterial innate immune system by a viral capsid protein. Nature 2022; 612:132-140. [PMID: 36385533 PMCID: PMC9712102 DOI: 10.1038/s41586-022-05444-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/13/2022] [Indexed: 11/17/2022]
Abstract
Bacteria have evolved diverse immunity mechanisms to protect themselves against the constant onslaught of bacteriophages1-3. Similar to how eukaryotic innate immune systems sense foreign invaders through pathogen-associated molecular patterns4 (PAMPs), many bacterial immune systems that respond to bacteriophage infection require phage-specific triggers to be activated. However, the identities of such triggers and the sensing mechanisms remain largely unknown. Here we identify and investigate the anti-phage function of CapRelSJ46, a fused toxin-antitoxin system that protects Escherichia coli against diverse phages. Using genetic, biochemical and structural analyses, we demonstrate that the C-terminal domain of CapRelSJ46 regulates the toxic N-terminal region, serving as both antitoxin and phage infection sensor. Following infection by certain phages, newly synthesized major capsid protein binds directly to the C-terminal domain of CapRelSJ46 to relieve autoinhibition, enabling the toxin domain to pyrophosphorylate tRNAs, which blocks translation to restrict viral infection. Collectively, our results reveal the molecular mechanism by which a bacterial immune system directly senses a conserved, essential component of phages, suggesting a PAMP-like sensing model for toxin-antitoxin-mediated innate immunity in bacteria. We provide evidence that CapRels and their phage-encoded triggers are engaged in a 'Red Queen conflict'5, revealing a new front in the intense coevolutionary battle between phages and bacteria. Given that capsid proteins of some eukaryotic viruses are known to stimulate innate immune signalling in mammalian hosts6-10, our results reveal a deeply conserved facet of immunity.
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Affiliation(s)
- Tong Zhang
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hedvig Tamman
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, (ULB), Brussels, Belgium
| | - Kyo Coppieters 't Wallant
- Centre for Structural Biology and Bioinformatics, Université Libre de Bruxelles (ULB), Bruxelles, Belgium
| | - Tatsuaki Kurata
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Michele LeRoux
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sriram Srikant
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Albinas Cepauskas
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, (ULB), Brussels, Belgium
| | - Ariel Talavera
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, (ULB), Brussels, Belgium
| | - Chloe Martens
- Centre for Structural Biology and Bioinformatics, Université Libre de Bruxelles (ULB), Bruxelles, Belgium
| | - Gemma C Atkinson
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, Lund, Sweden.
- Institute of Technology, University of Tartu, Tartu, Estonia.
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, (ULB), Brussels, Belgium.
- WELBIO, Brussels, Belgium.
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
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4
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Mojr V, Roghanian M, Tamman H, Do Pham DD, Petrová M, Pohl R, Takada H, Van Nerom K, Ainelo H, Caballero-Montes J, Jimmy S, Garcia-Pino A, Hauryliuk V, Rejman D. Nonhydrolysable Analogues of (p)ppGpp and (p)ppApp Alarmone Nucleotides as Novel Molecular Tools. ACS Chem Biol 2021; 16:1680-1691. [PMID: 34477366 DOI: 10.1021/acschembio.1c00398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While alarmone nucleotides guanosine-3',5'-bisdiphosphate (ppGpp) and guanosine-5'-triphosphate-3'-diphosphate (pppGpp) are archetypical bacterial second messengers, their adenosine analogues ppApp (adenosine-3',5'-bisdiphosphate) and pppApp (adenosine-5'-triphosphate-3'-diphosphate) are toxic effectors that abrogate bacterial growth. The alarmones are both synthesized and degraded by the members of the RelA-SpoT Homologue (RSH) enzyme family. Because of the chemical and enzymatic liability of (p)ppGpp and (p)ppApp, these alarmones are prone to degradation during structural biology experiments. To overcome this limitation, we have established an efficient and straightforward procedure for synthesizing nonhydrolysable (p)ppNuNpp analogues starting from 3'-azido-3'-deoxyribonucleotides as key intermediates. To demonstrate the utility of (p)ppGNpp as a molecular tool, we show that (i) as an HD substrate mimic, ppGNpp competes with ppGpp to inhibit the enzymatic activity of human MESH1 Small Alarmone Hyrolase, SAH; and (ii) mimicking the allosteric effects of (p)ppGpp, (p)ppGNpp acts as a positive regulator of the synthetase activity of long ribosome-associated RSHs Rel and RelA. Finally, by solving the structure of the N-terminal domain region (NTD) of T. thermophilus Rel complexed with pppGNpp, we show that as an HD substrate mimic, the analogue serves as a bona fide orthosteric regulator that promotes the same intra-NTD structural rearrangements as the native substrate.
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Affiliation(s)
- Viktor Mojr
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Mohammad Roghanian
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umea° Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden
- Department of Clinical Microbiology, Rigshospitalet, 2200 Copenhagen, Denmark
| | - Hedvig Tamman
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles, Campus La Plaine, Building BC, (1C4 203), Boulevard du Triomphe, 1050, Brussels, Belgium
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Duy Dinh Do Pham
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Magdalena Petrová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Hiraku Takada
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umea° Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo, Motoyama, Kita-ku, Kyoto 603-8555, Japan
| | - Katleen Van Nerom
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles, Campus La Plaine, Building BC, (1C4 203), Boulevard du Triomphe, 1050, Brussels, Belgium
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Hanna Ainelo
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles, Campus La Plaine, Building BC, (1C4 203), Boulevard du Triomphe, 1050, Brussels, Belgium
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Julien Caballero-Montes
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles, Campus La Plaine, Building BC, (1C4 203), Boulevard du Triomphe, 1050, Brussels, Belgium
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Steffi Jimmy
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umea° Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden
- Deutsches Elektronen-Synchrotron DESY, Centre for Structural Systems Biology (CSSB), Notkestr. 85, 22607 Hamburg, Germany
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles, Campus La Plaine, Building BC, (1C4 203), Boulevard du Triomphe, 1050, Brussels, Belgium
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Vasili Hauryliuk
- Laboratory for Molecular Infection Medicine Sweden (MIMS) and Umea° Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden
- University of Tartu, Institute of Technology, 50411 Tartu, Estonia
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Dominik Rejman
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
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5
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(p)ppGpp controls stringent factors by exploiting antagonistic allosteric coupling between catalytic domains. Mol Cell 2021; 81:3310-3322.e6. [PMID: 34416138 DOI: 10.1016/j.molcel.2021.07.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 05/26/2021] [Accepted: 07/21/2021] [Indexed: 01/03/2023]
Abstract
Amino acid starvation is sensed by Escherichia coli RelA and Bacillus subtilis Rel through monitoring the aminoacylation status of ribosomal A-site tRNA. These enzymes are positively regulated by their product-the alarmone nucleotide (p)ppGpp-through an unknown mechanism. The (p)ppGpp-synthetic activity of Rel/RelA is controlled via auto-inhibition by the hydrolase/pseudo-hydrolase (HD/pseudo-HD) domain within the enzymatic N-terminal domain region (NTD). We localize the allosteric pppGpp site to the interface between the SYNTH and pseudo-HD/HD domains, with the alarmone stimulating Rel/RelA by exploiting intra-NTD autoinhibition dynamics. We show that without stimulation by pppGpp, starved ribosomes cannot efficiently activate Rel/RelA. Compromised activation by pppGpp ablates Rel/RelA function in vivo, suggesting that regulation by the second messenger (p)ppGpp is necessary for mounting an acute starvation response via coordinated enzymatic activity of individual Rel/RelA molecules. Control by (p)ppGpp is lacking in the E. coli (p)ppGpp synthetase SpoT, thus explaining its weak synthetase activity.
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6
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Steinchen W, Ahmad S, Valentini M, Eilers K, Majkini M, Altegoer F, Lechner M, Filloux A, Whitney JC, Bange G. Dual role of a (p)ppGpp- and (p)ppApp-degrading enzyme in biofilm formation and interbacterial antagonism. Mol Microbiol 2021; 115:1339-1356. [PMID: 33448498 DOI: 10.1111/mmi.14684] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 12/14/2022]
Abstract
The guanosine nucleotide-based second messengers ppGpp and pppGpp (collectively: (p)ppGpp) enable adaptation of microorganisms to environmental changes and stress conditions. In contrast, the closely related adenosine nucleotides (p)ppApp are involved in type VI secretion system (T6SS)-mediated killing during bacterial competition. Long RelA-SpoT Homolog (RSH) enzymes regulate synthesis and degradation of (p)ppGpp (and potentially also (p)ppApp) through their synthetase and hydrolase domains, respectively. Small alarmone hydrolases (SAH) that consist of only a hydrolase domain are found in a variety of bacterial species, including the opportunistic human pathogen Pseudomonas aeruginosa. Here, we present the structure and mechanism of P. aeruginosa SAH showing that the enzyme promiscuously hydrolyses (p)ppGpp and (p)ppApp in a strictly manganese-dependent manner. While being dispensable for P. aeruginosa growth or swimming, swarming, and twitching motilities, its enzymatic activity is required for biofilm formation. Moreover, (p)ppApp-degradation by SAH provides protection against the T6SS (p)ppApp synthetase effector Tas1, suggesting that SAH enzymes can also serve as defense proteins during interbacterial competition.
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Affiliation(s)
- Wieland Steinchen
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Shehryar Ahmad
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Martina Valentini
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - Kira Eilers
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - Mohamad Majkini
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Florian Altegoer
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Marcus Lechner
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - John C Whitney
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.,David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Marburg, Germany
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7
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Takada H, Roghanian M, Caballero-Montes J, Van Nerom K, Jimmy S, Kudrin P, Trebini F, Murayama R, Akanuma G, Garcia-Pino A, Hauryliuk V. Ribosome association primes the stringent factor Rel for tRNA-dependent locking in the A-site and activation of (p)ppGpp synthesis. Nucleic Acids Res 2021; 49:444-457. [PMID: 33330919 PMCID: PMC7797070 DOI: 10.1093/nar/gkaa1187] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/18/2020] [Accepted: 11/20/2020] [Indexed: 11/17/2022] Open
Abstract
In the Gram-positive Firmicute bacterium Bacillus subtilis, amino acid starvation induces synthesis of the alarmone (p)ppGpp by the RelA/SpoT Homolog factor Rel. This bifunctional enzyme is capable of both synthesizing and hydrolysing (p)ppGpp. To detect amino acid deficiency, Rel monitors the aminoacylation status of the ribosomal A-site tRNA by directly inspecting the tRNA’s CCA end. Here we dissect the molecular mechanism of B. subtilis Rel. Off the ribosome, Rel predominantly assumes a ‘closed’ conformation with dominant (p)ppGpp hydrolysis activity. This state does not specifically select deacylated tRNA since the interaction is only moderately affected by tRNA aminoacylation. Once bound to the vacant ribosomal A-site, Rel assumes an ‘open’ conformation, which primes its TGS and Helical domains for specific recognition and stabilization of cognate deacylated tRNA on the ribosome. The tRNA locks Rel on the ribosome in a hyperactivated state that processively synthesises (p)ppGpp while the hydrolysis is suppressed. In stark contrast to non-specific tRNA interactions off the ribosome, tRNA-dependent Rel locking on the ribosome and activation of (p)ppGpp synthesis are highly specific and completely abrogated by tRNA aminoacylation. Binding pppGpp to a dedicated allosteric site located in the N-terminal catalytic domain region of the enzyme further enhances its synthetase activity.
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Affiliation(s)
- Hiraku Takada
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden
| | - Mohammad Roghanian
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden
| | - Julien Caballero-Montes
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Building BC, Room 1C4 203, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Katleen Van Nerom
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Building BC, Room 1C4 203, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Steffi Jimmy
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden
| | - Pavel Kudrin
- University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Fabio Trebini
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
| | - Rikinori Murayama
- Akita Prefectural Research Center for Public Health and Environment, 6-6 Senshu-Kubotamachi, Akita, 010-0874, Japan
| | - Genki Akanuma
- Department of Life Science, Graduate School of Science, Gakushuin University, Tokyo, Japan
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Building BC, Room 1C4 203, Boulevard du Triomphe, 1050 Brussels, Belgium.,WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden.,University of Tartu, Institute of Technology, 50411 Tartu, Estonia
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8
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Tamman H, Van Nerom K, Takada H, Vandenberk N, Scholl D, Polikanov Y, Hofkens J, Talavera A, Hauryliuk V, Hendrix J, Garcia-Pino A. A nucleotide-switch mechanism mediates opposing catalytic activities of Rel enzymes. Nat Chem Biol 2020; 16:834-840. [PMID: 32393900 DOI: 10.1038/s41589-020-0520-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 03/13/2020] [Indexed: 12/22/2022]
Abstract
Bifunctional Rel stringent factors, the most abundant class of RelA/SpoT homologs, are ribosome-associated enzymes that transfer a pyrophosphate from ATP onto the 3' of guanosine tri-/diphosphate (GTP/GDP) to synthesize the bacterial alarmone (p)ppGpp, and also catalyze the 3' pyrophosphate hydrolysis to degrade it. The regulation of the opposing activities of Rel enzymes is a complex allosteric mechanism that remains an active research topic despite decades of research. We show that a guanine-nucleotide-switch mechanism controls catalysis by Thermus thermophilus Rel (RelTt). The binding of GDP/ATP opens the N-terminal catalytic domains (NTD) of RelTt (RelTtNTD) by stretching apart the two catalytic domains. This activates the synthetase domain and allosterically blocks hydrolysis. Conversely, binding of ppGpp to the hydrolase domain closes the NTD, burying the synthetase active site and precluding the binding of synthesis precursors. This allosteric mechanism is an activity switch that safeguards against futile cycles of alarmone synthesis and degradation.
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Affiliation(s)
- Hedvig Tamman
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
| | - Katleen Van Nerom
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
| | - Hiraku Takada
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Niels Vandenberk
- Molecular Imaging and Photonics, Chemistry Department, KU Leuven, Leuven, Belgium
| | - Daniel Scholl
- SFMB, Université Libre de Bruxelles, Brussels, Belgium
| | - Yury Polikanov
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Johan Hofkens
- Molecular Imaging and Photonics, Chemistry Department, KU Leuven, Leuven, Belgium
| | | | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, Umeå, Sweden. .,Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden.
| | - Jelle Hendrix
- Molecular Imaging and Photonics, Chemistry Department, KU Leuven, Leuven, Belgium. .,Dynamic Bioimaging Laboratory, Advanced Optical Microscopy Centre and Biomedical Research Institute, Hasselt University, Agoralaan C (BIOMED), Hasselt, Belgium.
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium. .,WELBIO, Brussels, Belgium.
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Takada H, Roghanian M, Murina V, Dzhygyr I, Murayama R, Akanuma G, Atkinson GC, Garcia-Pino A, Hauryliuk V. The C-Terminal RRM/ACT Domain Is Crucial for Fine-Tuning the Activation of 'Long' RelA-SpoT Homolog Enzymes by Ribosomal Complexes. Front Microbiol 2020; 11:277. [PMID: 32184768 PMCID: PMC7058999 DOI: 10.3389/fmicb.2020.00277] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/06/2020] [Indexed: 11/19/2022] Open
Abstract
The (p)ppGpp-mediated stringent response is a bacterial stress response implicated in virulence and antibiotic tolerance. Both synthesis and degradation of the (p)ppGpp alarmone nucleotide are mediated by RelA-SpoT Homolog (RSH) enzymes which can be broadly divided in two classes: single-domain 'short' and multi-domain 'long' RSH. The regulatory ACT (Aspartokinase, Chorismate mutase and TyrA)/RRM (RNA Recognition Motif) domain is a near-universal C-terminal domain of long RSHs. Deletion of RRM in both monofunctional (synthesis-only) RelA as well as bifunctional (i.e., capable of both degrading and synthesizing the alarmone) Rel renders the long RSH cytotoxic due to overproduction of (p)ppGpp. To probe the molecular mechanism underlying this effect we characterized Escherichia coli RelA and Bacillus subtilis Rel RSHs lacking RRM. We demonstrate that, first, the cytotoxicity caused by the removal of RRM is counteracted by secondary mutations that disrupt the interaction of the RSH with the starved ribosomal complex - the ultimate inducer of (p)ppGpp production by RelA and Rel - and, second, that the hydrolytic activity of Rel is not abrogated in the truncated mutant. Therefore, we conclude that the overproduction of (p)ppGpp by RSHs lacking the RRM domain is not explained by a lack of auto-inhibition in the absence of RRM or/and a defect in (p)ppGpp hydrolysis. Instead, we argue that it is driven by misregulation of the RSH activation by the ribosome.
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Affiliation(s)
- Hiraku Takada
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Mohammad Roghanian
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Victoriia Murina
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Ievgen Dzhygyr
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Rikinori Murayama
- Akita Prefectural Research Center for Public Health and Environment, Akita, Japan
| | - Genki Akanuma
- Department of Life Science, Graduate School of Science, Gakushuin University, Tokyo, Japan
| | | | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
- WELBIO, Brussels, Belgium
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Institute of Technology, University of Tartu, Tartu, Estonia
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10
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Turnbull KJ, Dzhygyr I, Lindemose S, Hauryliuk V, Roghanian M. Intramolecular Interactions Dominate the Autoregulation of Escherichia coli Stringent Factor RelA. Front Microbiol 2019; 10:1966. [PMID: 31507571 PMCID: PMC6719525 DOI: 10.3389/fmicb.2019.01966] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 08/09/2019] [Indexed: 01/08/2023] Open
Abstract
Amino acid starvation in Escherichia coli activates the enzymatic activity of the stringent factor RelA, leading to accumulation of the alarmone nucleotide (p)ppGpp. The alarmone acts as an intercellular messenger to regulate transcription, translation and metabolism to mediate bacterial stress adaptation. The enzymatic activity of RelA is subject to multi-layered allosteric control executed both by ligands - such as "starved" ribosomal complexes, deacylated tRNA and pppGpp - and by individual RelA domains. The auto-regulation of RelA is proposed to act either in cis (inhibition of the enzymatic activity of the N-terminal region, NTD, by regulatory C-terminal region, CTD) or in trans (CTD-mediated dimerization leading to enzyme inhibition). In this report, we probed the regulatory roles of the individual domains of E. coli RelA and our results are not indicative of RelA dimerization being the key regulatory mechanism. First, at growth-permitting levels, ectopic expression of RelA CTD does not interfere with activation of native RelA, indicating lack of regulation via inhibitory complex formation in the cell. Second, in our biochemical assays, increasing RelA concentration does not decrease the enzyme activity, as would be expected in the case of efficient auto-inhibition via dimerization. Third, while high-level CTD expression efficiently inhibits the growth, the effect is independent of native RelA and is mediated by direct inhibition of protein synthesis, likely via direct interaction with the ribosomal A-site. Finally, deletion of the RRM domain of the CTD region leads to growth inhibition mediated by accumulation of (p)ppGpp, suggesting de-regulation of the synthetic activity in this mutant.
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Affiliation(s)
- Kathryn Jane Turnbull
- Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Ievgen Dzhygyr
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Søren Lindemose
- Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Mohammad Roghanian
- Centre for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
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