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Dominguez-Molina L, Kurata T, Cepauskas A, Echemendia-Blanco D, Zedek S, Talavera-Perez A, Atkinson GC, Hauryliuk V, Garcia-Pino A. Mechanisms of neutralization of toxSAS from toxin-antitoxin modules. Nat Chem Biol 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.
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Affiliation(s)
- Lucia Dominguez-Molina
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Tatsuaki Kurata
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Albinas Cepauskas
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Dannele Echemendia-Blanco
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Safia Zedek
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Ariel Talavera-Perez
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Gemma C Atkinson
- Department of Experimental Medical Science, Lund University, Lund, Sweden.
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, Lund, Sweden.
- Faculty of Science and Technology, University of Tartu Institute of Technology, Tartu, Estonia.
- Science for Life Laboratory, Lund, Sweden.
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Brussels, Belgium.
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2
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Chrenková A, Bisiak F, Brodersen DE. Breaking bad nucleotides: understanding the regulatory mechanisms of bacterial small alarmone hydrolases. Trends Microbiol 2024:S0966-842X(23)00363-3. [PMID: 38262803 DOI: 10.1016/j.tim.2023.12.011] [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: 11/11/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/25/2024]
Abstract
Guanosine tetra- and pentaphosphate nucleotides, (p)ppGpp, function as central secondary messengers and alarmones in bacterial cell biology, signalling a range of stress conditions, including nutrient starvation and exposure to cell-wall-targeting antibiotics, and are critical for survival. While activation of the stringent response and alarmone synthesis on starved ribosomes by members of the RSH (Rel) class of proteins is well understood, much less is known about how single-domain small alarmone synthetases (SASs) and their corresponding alarmone hydrolases, the small alarmone hydrolases (SAHs), are regulated and contribute to (p)ppGpp homeostasis. The substrate spectrum of these enzymes has recently been expanded to include hyperphosphorylated adenosine nucleotides, suggesting that they take part in a highly complex and interconnected signalling network. In this review, we provide an overview of our understanding of the SAHs and discuss their structure, function, regulation, and phylogeny.
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Affiliation(s)
- Adriana Chrenková
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000 Aarhus C, Denmark
| | - Francesco Bisiak
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000 Aarhus C, Denmark
| | - Ditlev E Brodersen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000 Aarhus C, Denmark.
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Zhou RW, Gordon IJ, Hei Y, Wang B. Synthetase and Hydrolase Specificity Collectively Excludes 2'-Deoxyguanosine from Bacterial Alarmone. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.06.574488. [PMID: 38260349 PMCID: PMC10802352 DOI: 10.1101/2024.01.06.574488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
In response to starvation, virtually all bacteria pyrophosphorylate the 3'-hydroxy group of GTP or GDP to produce two messenger nucleotides collectively denoted as (p)ppGpp. Also known as alarmones, (p)ppGpp reprograms bacterial physiology to arrest growth and promote survival. Intriguingly, although cellular concentration of dGTP is two orders of magnitude lower than that of GTP, alarmone synthetases are highly selective against using 2'-deoxyguanosine (2dG) nucleotides as substrates. We thus hypothesize that production of 2dG alarmone, (p)pp(dG)pp, is highly deleterious, which drives a strong negative selection to exclude 2dG nucleotides from alarmone signaling. In this work, we show that the B. subtilis SasB synthetase prefers GDP over dGDP with 65,000-fold higher kcat/Km, a specificity stricter than RNA polymerase selecting against 2'-deoxynucleotides. Using comparative chemical proteomics, we found that although most known alarmone-binding proteins in Escherichia coli cannot distinguish ppGpp from pp(dG)pp, hydrolysis of pp(dG)pp by the essential hydrolase, SpoT, is 1,000-fold slower. This inability to degrade 2'-deoxy-3'-pyrophosphorylated substrate is a common feature of the alarmone hydrolase family. We further show that SpoT is a binuclear metallopyrophoshohydrolase and that hydrolysis of ppGpp and pp(dG)pp shares the same metal dependence. Our results support a model in which 2'-OH directly coordinates the Mn2+ at SpoT active center to stabilize the hydrolysis-productive conformation of ppGpp. Taken together, our study reveals a vital role of 2'-OH in alarmone degradation, provides new insight on the catalytic mechanism of alarmone hydrolases, and leads to the conclusion that 2dG nucleotides must be strictly excluded from alarmone synthesis because bacteria lack the key machinery to down-regulate such products.
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Affiliation(s)
- Rich W Zhou
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Isis J Gordon
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yuanyuan Hei
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Boyuan Wang
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
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Dominguez-Molina L, Talavera A, Cepauskas A, Kurata T, Echemendia-Blanco D, Hauryliuk V, Garcia-Pino A. Biochemical and X-ray analyses of the players involved in the faRel2/aTfaRel2 toxin-antitoxin operon. Acta Crystallogr F Struct Biol Commun 2023; 79:247-256. [PMID: 37728608 PMCID: PMC10565793 DOI: 10.1107/s2053230x23007288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/19/2023] [Indexed: 09/21/2023] Open
Abstract
The aTfaRel2/faRel2 operon from Coprobacillus sp. D7 encodes a bicistronic type II toxin-antitoxin (TA) module. The FaRel2 toxin is a toxic small alarmone synthetase (toxSAS) that inhibits translation through the pyrophosphorylation of uncharged tRNAs at the 3'-CCA end. The toxin is neutralized by the antitoxin ATfaRel2 through the formation of an inactive TA complex. Here, the production, biophysical analysis and crystallization of ATfaRel2 and FaRel2 as well as of the ATfaRel2-FaRel2 complex are reported. ATfaRel2 is monomeric in solution. The antitoxin crystallized in space group P21212 with unit-cell parameters a = 53.3, b = 34.2, c = 37.6 Å, and the best crystal diffracted to a resolution of 1.24 Å. Crystals of FaRel2 in complex with APCPP, a nonhydrolysable ATP analogue, belonged to space group P21, with unit-cell parameters a = 31.5, b = 60.6, c = 177.2 Å, β = 90.6°, and diffracted to 2.6 Å resolution. The ATfaRel2-FaRel2Y128F complex forms a heterotetramer in solution composed of two toxins and two antitoxins. This complex crystallized in two space groups: F4132, with unit-cell parameters a = b = c = 227.1 Å, and P212121, with unit-cell parameters a = 51.7, b = 106.2, c = 135.1 Å. The crystals diffracted to 1.98 and 2.1 Å resolution, respectively.
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Affiliation(s)
- Lucia Dominguez-Molina
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
| | - Ariel Talavera
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
| | - Albinas Cepauskas
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
| | - Tatsuaki Kurata
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Dannele Echemendia-Blanco
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- University of Tartu Institute of Technology, Tartu, Estonia
- Science for Life Laboratory, Lund, Sweden
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC (1C4 203), 1050 Brussels, Belgium
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Njenga R, Boele J, Öztürk Y, Koch HG. Coping with stress: How bacteria fine-tune protein synthesis and protein transport. J Biol Chem 2023; 299:105163. [PMID: 37586589 PMCID: PMC10502375 DOI: 10.1016/j.jbc.2023.105163] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023] Open
Abstract
Maintaining a functional proteome under different environmental conditions is challenging for every organism, in particular for unicellular organisms, such as bacteria. In order to cope with changing environments and stress conditions, bacteria depend on strictly coordinated proteostasis networks that control protein production, folding, trafficking, and degradation. Regulation of ribosome biogenesis and protein synthesis are cornerstones of this cellular adaptation in all domains of life, which is rationalized by the high energy demand of both processes and the increased resistance of translationally silent cells against internal or external poisons. Reduced protein synthesis ultimately also reduces the substrate load for protein transport systems, which are required for maintaining the periplasmic, inner, and outer membrane subproteomes. Consequences of impaired protein transport have been analyzed in several studies and generally induce a multifaceted response that includes the upregulation of chaperones and proteases and the simultaneous downregulation of protein synthesis. In contrast, generally less is known on how bacteria adjust the protein targeting and transport machineries to reduced protein synthesis, e.g., when cells encounter stress conditions or face nutrient deprivation. In the current review, which is mainly focused on studies using Escherichia coli as a model organism, we summarize basic concepts on how ribosome biogenesis and activity are regulated under stress conditions. In addition, we highlight some recent developments on how stress conditions directly impair protein targeting to the bacterial membrane. Finally, we describe mechanisms that allow bacteria to maintain the transport of stress-responsive proteins under conditions when the canonical protein targeting pathways are impaired.
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Affiliation(s)
- Robert Njenga
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany; Faculty of Biology, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Julian Boele
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Yavuz Öztürk
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany.
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6
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Fung DK, Wang JD. The τ of alarmone hydrolysis. Nat Chem Biol 2023; 19:257-258. [PMID: 36470997 DOI: 10.1038/s41589-022-01200-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Danny K Fung
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Jue D Wang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
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7
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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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