1
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Yancheva Y, Kaya SG, Belyy A, Fraaije MW, Tych KM. Impact of Ligand-Induced Oligomer Dissociation on Enzyme Diffusion, Directly Observed at the Single-Molecule Level. NANO LETTERS 2025; 25:2373-2380. [PMID: 39879145 PMCID: PMC11831976 DOI: 10.1021/acs.nanolett.4c05792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Revised: 01/20/2025] [Accepted: 01/24/2025] [Indexed: 01/31/2025]
Abstract
The existence of the phenomenon of enhanced enzyme diffusion (EED) has been a topic of debate in recent literature. One proposed mechanism to explain the origin of EED is oligomeric enzyme dissociation. We used mass photometry (MP), a label-free single-molecule technique, to investigate the dependence of the oligomeric states of several enzymes on their ligands. The studied enzymes of interest are catalase, aldolase, alkaline phosphatase, and vanillyl-alcohol oxidase (VAO). We compared the ratios of oligomeric states in the presence and absence of the substrate as well as different substrate and inhibitor concentrations. Catalase and aldolase were found to dissociate into smaller oligomers in the presence of their substrates, independently of inhibition, while for alkaline phosphatase and VAO, different behaviors were observed. Thus, we have identified a possible mechanism which explains the previously observed diffusion enhancement in vitro. This enhancement may occur due to the dissociation of oligomers through ligand binding.
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Affiliation(s)
- Yulia
D. Yancheva
- Chemical
Biology 1, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Saniye G. Kaya
- Molecular
Enzymology, University of Groningen, Nijenborgh 3, 9747 AG Groningen, The Netherlands
| | - Alexander Belyy
- Membrane
Enzymology, University of Groningen, Nijenborgh 3, 9747 AG Groningen, The Netherlands
| | - Marco W. Fraaije
- Molecular
Enzymology, University of Groningen, Nijenborgh 3, 9747 AG Groningen, The Netherlands
| | - Katarzyna M. Tych
- Chemical
Biology 1, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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2
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Frick DN, Shittu M, Bock CR, Wardle ZP, Rauf AA, Ramos JN, Thomson JG, Sheibley DJ, O'Handley SF. Optimization of a high throughput screening platform to identify inhibitors of asymmetric diadenosine polyphosphatases. Anal Biochem 2025; 697:115713. [PMID: 39521360 PMCID: PMC11624979 DOI: 10.1016/j.ab.2024.115713] [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: 07/02/2024] [Revised: 10/23/2024] [Accepted: 11/06/2024] [Indexed: 11/16/2024]
Abstract
When stressed, cells synthesize di-adenosine polyphosphates (ApnA), and cellular organisms also express proteins that degrade these compounds to release ATP. Most of these proteins are members of the nudix hydrolase superfamily, and several are involved in bacterial pathogenesis, neurodevelopment, and cancer. The goal of this project is to assist in the discovery of inhibitors of these enzymes that could be used to study ApnA function and the cellular role of these nudix enzymes. Because these enzymes cleave Ap4A and Ap5A to produce ATP, two standard ATP detection techniques were optimized and compared here for their suitability for high throughput screening. In the first assay, cleavage is monitored by coupling to a reaction catalyzed by firefly luciferase. In the second assay, cleavage is detected by coupling to hexokinase, glucose 6-phosphate dehydrogenase, and diaphorase. Although the former assay was more sensitive, the latter was more reproducible, linear, and suitable for screening and kinetic analyses. The assays were used to characterize the kinetics of reactions catalyzed by various nudix enzymes isolated from E. coli, humans, and Mycobacterium tuberculosis, the bacterium that causes tuberculosis. Results reveal subtle differences between the proteins that might be exploited to identify specific small molecule inhibitors.
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Affiliation(s)
- David N Frick
- Department of Chemistry & Biochemistry, University of Wisconsin, Milwaukee, United States.
| | - Mujidat Shittu
- Department of Chemistry & Biochemistry, University of Wisconsin, Milwaukee, United States
| | - Chase R Bock
- Department of Chemistry & Biochemistry, University of Wisconsin, Milwaukee, United States
| | - Zoe P Wardle
- Department of Chemistry & Biochemistry, University of Wisconsin, Milwaukee, United States
| | - Abdullah A Rauf
- Department of Chemistry & Biochemistry, University of Wisconsin, Milwaukee, United States
| | - Julian N Ramos
- School of Chemistry and Materials Science, Rochester Institute of Technology, United States
| | - Joshua G Thomson
- School of Chemistry and Materials Science, Rochester Institute of Technology, United States
| | - Daniel J Sheibley
- School of Chemistry and Materials Science, Rochester Institute of Technology, United States
| | - Suzanne F O'Handley
- School of Chemistry and Materials Science, Rochester Institute of Technology, United States.
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3
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Yang K, Hu S, Yao Y, Li K, Wang Z, Wang X, Ma D, Bi M, Mo X. Investigation of the Structure and Functional Activity of the YqeK Protein in Streptococcus pyogenes with High Efficiency in Hydrolyzing Ap4A. Microorganisms 2025; 13:230. [PMID: 40005597 PMCID: PMC11857287 DOI: 10.3390/microorganisms13020230] [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: 12/26/2024] [Revised: 01/19/2025] [Accepted: 01/20/2025] [Indexed: 02/27/2025] Open
Abstract
Streptococcus pyogenes is an important zoonotic Gram-positive bacterium that appears in chains, without spores or flagella, and belongs to the beta-hemolytic streptococci. It can be transmitted through droplets or contact, with the preferred antibiotics being penicillin, erythromycin, or cephalosporins. However, the misuse of these drugs has led to antibiotic resistance, posing a significant threat to both human and animal health. Studying resistance genes encoding proteins is crucial for mitigating the emergence of resistant strains and improving treatment outcomes. Interestingly, a dinucleotide known as diadenosine tetraphosphate (Ap4A) exists in Streptococcus pyogenes; its accumulation in response to various stress signals can inhibit bacterial pathogenicity and enhance antibiotic susceptibility. Our research focuses on the Sp-yqeK protein, which we have identified as a hydrolase that symmetrically cleaves Ap4A. The Sp-yqeK protein effectively cleaves Ap4A, producing adenosine diphosphate (ADP) molecules. Results indicate that this enzyme exhibits optimal activity at pH 7.0 and a temperature of 45 °C. Furthermore, we determined the crystal structure of the Sp-yqeK, Mg2+, and ADP complex at a resolution of 2.0 Å, providing insights into the interactions crucial for catalytic efficiency between Sp-yqeK and ADP. This complex reveals unique folding characteristics of the HD domain superfamily proteins, accommodating both ADP and Mg2+. These components are securely embedded into the polar cavity of the yqeK protein through conserved residues (His29, Lys62, His91, His117, Asp135, Leu172, Phe180, and Thr183), highlighting the residues responsible for Ap4A hydrolysis and Mg2+ binding. Our research offers a deeper understanding of the hydrolysis mechanism of Ap4A and the specificity of Sp-yqeK, providing structural insights that may support future studies on antibiotic resistance in Streptococcus pyogenes and other Gram-positive bacteria.
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Affiliation(s)
| | | | | | | | | | | | | | - Mingfang Bi
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (K.Y.); (S.H.); (Y.Y.); (K.L.); (Z.W.); (X.W.); (D.M.)
| | - Xiaobing Mo
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (K.Y.); (S.H.); (Y.Y.); (K.L.); (Z.W.); (X.W.); (D.M.)
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4
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Young MK, Wang JD. From dusty shelves toward the spotlight: growing evidence for Ap4A as an alarmone in maintaining RNA stability and proteostasis. Curr Opin Microbiol 2024; 81:102536. [PMID: 39216180 PMCID: PMC11390322 DOI: 10.1016/j.mib.2024.102536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 08/08/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024]
Abstract
Bacteria thrive in diverse environments and must withstand various stresses. A key stress response mechanism is the reprogramming of macromolecular biosynthesis and metabolic processes through alarmones - signaling nucleotides that accumulate intracellularly in response to metabolic stress. Diadenosine tetraphosphate (Ap4A), a putative alarmone, is produced in a noncanonical reaction by universally conserved aminoacyl-tRNA synthetases. Ap4A is ubiquitous across all domains of life and accumulates during heat and oxidative stress. Despite its early discovery in 1966, Ap4A's alarmone status remained inconclusive. Recent discoveries identified Ap4A as a precursor to RNA 5' caps in Escherichia coli. Additionally, Ap4A was found to directly bind to and allosterically inhibit the purine biosynthesis enzyme inosine 5'-monophosphate dehydrogenase, regulating guanosine triphosphate levels and enabling heat resistance in Bacillus subtilis. These findings, along with previous research, strongly suggest that Ap4A plays a crucial role as an alarmone, warranting further investigation to fully elucidate its functions.
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Affiliation(s)
- Megan Km Young
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jue D Wang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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5
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Bulvas O, Knejzlík Z, Sýs J, Filimoněnko A, Čížková M, Clarová K, Rejman D, Kouba T, Pichová I. Deciphering the allosteric regulation of mycobacterial inosine-5'-monophosphate dehydrogenase. Nat Commun 2024; 15:6673. [PMID: 39107302 PMCID: PMC11303537 DOI: 10.1038/s41467-024-50933-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 07/24/2024] [Indexed: 08/10/2024] Open
Abstract
Allosteric regulation of inosine 5'-monophosphate dehydrogenase (IMPDH), an essential enzyme of purine metabolism, contributes to the homeostasis of adenine and guanine nucleotides. However, the precise molecular mechanism of IMPDH regulation in bacteria remains unclear. Using biochemical and cryo-EM approaches, we reveal the intricate molecular mechanism of the IMPDH allosteric regulation in mycobacteria. The enzyme is inhibited by both GTP and (p)ppGpp, which bind to the regulatory CBS domains and, via interactions with basic residues in hinge regions, lock the catalytic core domains in a compressed conformation. This results in occlusion of inosine monophosphate (IMP) substrate binding to the active site and, ultimately, inhibition of the enzyme. The GTP and (p)ppGpp allosteric effectors bind to their dedicated sites but stabilize the compressed octamer by a common mechanism. Inhibition is relieved by the competitive displacement of GTP or (p)ppGpp by ATP allowing IMP-induced enzyme expansion. The structural knowledge and mechanistic understanding presented here open up new possibilities for the development of allosteric inhibitors with antibacterial potential.
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Affiliation(s)
- Ondřej Bulvas
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Zdeněk Knejzlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jakub Sýs
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Anatolij Filimoněnko
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Monika Čížková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Kamila Clarová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Dominik Rejman
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tomáš Kouba
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Iva Pichová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
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6
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Schicketanz M, Petrová M, Rejman D, Sosio M, Donadio S, Zhang YE. Direct detection of stringent alarmones (pp)pGpp using malachite green. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:312-320. [PMID: 39119257 PMCID: PMC11307201 DOI: 10.15698/mic2024.08.834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/05/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024]
Abstract
The alarmone (p)ppGpp serves as the signalling molecule for the bacterial universal stringent response and plays a crucial role in bacterial virulence, persistence, and stress adaptation. Consequently, there is a significant focus on developing new drugs that target and modulate the levels of (p)ppGpp as a potential strategy for controlling bacterial infections. However, despite the availability of various methods for detecting (p)ppGpp, a simple and straightforward detection method is needed. In this study, we demonstrated that malachite green, a well-established compound used for phosphate detection, can directly detect (p)ppGpp and its analogues esp., pGpp. By utilizing malachite green, we identified three new inhibitors of the hydrolase activity of SpoT, one of the two RelA-SpoT homolog (RSH) proteins responsible for making and hydrolyzing (p)ppGpp in Escherichia coli. These findings highlight the convenience and practicality of malachite green, which can be widely employed in high-throughput studies to investigate (pp)pGpp in vitro and discover novel regulators of RSH proteins.
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Affiliation(s)
- Muriel Schicketanz
- Department of Biology, University of CopenhagenCopenhagen, DK-2200Denmark
| | - Magdalena Petrová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences v.v.iPragueCzech Republic
| | - Dominik Rejman
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences v.v.iPragueCzech Republic
| | | | | | - Yong Everett Zhang
- Department of Biology, University of CopenhagenCopenhagen, DK-2200Denmark
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7
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Cervoni M, Sposato D, Ferri G, Bähre H, Leoni L, Rampioni G, Visca P, Recchiuti A, Imperi F. The diadenosine tetraphosphate hydrolase ApaH contributes to Pseudomonas aeruginosa pathogenicity. PLoS Pathog 2024; 20:e1012486. [PMID: 39159286 PMCID: PMC11361744 DOI: 10.1371/journal.ppat.1012486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 08/29/2024] [Accepted: 08/07/2024] [Indexed: 08/21/2024] Open
Abstract
The opportunistic bacterial pathogen Pseudomonas aeruginosa causes a wide range of infections that are difficult to treat, largely because of the spread of antibiotic-resistant isolates. Antivirulence therapy, í.e. the use of drugs that inhibit the expression or activity of virulence factors, is currently considered an attractive strategy to reduce P. aeruginosa pathogenicity and complement antibiotic treatments. Because of the multifactorial nature of P. aeruginosa virulence and the broad arsenal of virulence factors this bacterium can produce, the regulatory networks that control the expression of multiple virulence traits have been extensively explored as potential targets for antivirulence drug development. The intracellular signaling molecule diadenosine tetraphosphate (Ap4A) has been reported to control stress resistance and virulence-related traits in some bacteria, but its role has not been investigated in P. aeruginosa so far. To fill this gap, we generated a mutant of the reference strain P. aeruginosa PAO1 that lacks the Ap4A-hydrolysing enzyme ApaH and, consequently, accumulates high intracellular levels of Ap4A. Phenotypic and transcriptomic analyses revealed that the lack of ApaH causes a drastic reduction in the expression of several virulence factors, including extracellular proteases, elastases, siderophores, and quorum sensing signal molecules. Accordingly, infection assays in plant and animal models demonstrated that ApaH-deficient cells are significantly impaired in infectivity and persistence in different hosts, including mice. Finally, deletion of apaH in P. aeruginosa clinical isolates demonstrated that the positive effect of ApaH on the production of virulence-related traits and on infectivity is conserved in P. aeruginosa. This study provides the first evidence that the Ap4A-hydrolysing enzyme ApaH is important for P. aeruginosa virulence, highlighting this protein as a novel potential target for antivirulence therapies against P. aeruginosa.
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Affiliation(s)
| | | | - Giulia Ferri
- Department of Medical, Oral and Biotechnology Sciences, University of Chieti-Pescara, Chieti, Italy
| | - Heike Bähre
- Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Livia Leoni
- Department of Science, University Roma Tre, Rome, Italy
| | - Giordano Rampioni
- Department of Science, University Roma Tre, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Paolo Visca
- Department of Science, University Roma Tre, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Antonio Recchiuti
- Department of Medical, Oral and Biotechnology Sciences, University of Chieti-Pescara, Chieti, Italy
| | - Francesco Imperi
- Department of Science, University Roma Tre, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
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8
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Kennelly C, Tran P, Prindle A. Environmental purines decrease Pseudomonas aeruginosa biofilm formation by disrupting c-di-GMP metabolism. Cell Rep 2024; 43:114154. [PMID: 38669142 PMCID: PMC11197132 DOI: 10.1016/j.celrep.2024.114154] [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: 11/06/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Cyclic di-guanosine monophosphate (c-di-GMP) is a bacterial second messenger that governs the lifestyle switch between planktonic and biofilm states. While substantial investigation has focused on the proteins that produce and degrade c-di-GMP, less attention has been paid to the potential for metabolic control of c-di-GMP signaling. Here, we show that micromolar levels of specific environmental purines unexpectedly decrease c-di-GMP and biofilm formation in Pseudomonas aeruginosa. Using a fluorescent genetic reporter, we show that adenosine and inosine decrease c-di-GMP even when competing purines are present. We confirm genetically that purine salvage is required for c-di-GMP decrease. Furthermore, we find that (p)ppGpp prevents xanthosine and guanosine from producing an opposing c-di-GMP increase, reinforcing a salvage hierarchy that favors c-di-GMP decrease even at the expense of growth. We propose that purines can act as a cue for bacteria to shift their lifestyle away from the recalcitrant biofilm state via upstream metabolic control of c-di-GMP signaling.
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Affiliation(s)
- Corey Kennelly
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Peter Tran
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Arthur Prindle
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.
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9
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Ayoub N, Gedeon A, Munier-Lehmann H. A journey into the regulatory secrets of the de novo purine nucleotide biosynthesis. Front Pharmacol 2024; 15:1329011. [PMID: 38444943 PMCID: PMC10912719 DOI: 10.3389/fphar.2024.1329011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/01/2024] [Indexed: 03/07/2024] Open
Abstract
De novo purine nucleotide biosynthesis (DNPNB) consists of sequential reactions that are majorly conserved in living organisms. Several regulation events take place to maintain physiological concentrations of adenylate and guanylate nucleotides in cells and to fine-tune the production of purine nucleotides in response to changing cellular demands. Recent years have seen a renewed interest in the DNPNB enzymes, with some being highlighted as promising targets for therapeutic molecules. Herein, a review of two newly revealed modes of regulation of the DNPNB pathway has been carried out: i) the unprecedent allosteric regulation of one of the limiting enzymes of the pathway named inosine 5'-monophosphate dehydrogenase (IMPDH), and ii) the supramolecular assembly of DNPNB enzymes. Moreover, recent advances that revealed the therapeutic potential of DNPNB enzymes in bacteria could open the road for the pharmacological development of novel antibiotics.
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Affiliation(s)
- Nour Ayoub
- Institut Pasteur, Université Paris Cité, INSERM UMRS-1124, Paris, France
| | - Antoine Gedeon
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS UMR7203, Laboratoire des Biomolécules, LBM, Paris, France
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10
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Potužník JF, Cahova H. If the 5' cap fits (wear it) - Non-canonical RNA capping. RNA Biol 2024; 21:1-13. [PMID: 39007883 PMCID: PMC11253889 DOI: 10.1080/15476286.2024.2372138] [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: 04/10/2024] [Revised: 06/10/2024] [Accepted: 06/18/2024] [Indexed: 07/16/2024] Open
Abstract
RNA capping is a prominent RNA modification that influences RNA stability, metabolism, and function. While it was long limited to the study of the most abundant eukaryotic canonical m7G cap, the field recently went through a large paradigm shift with the discovery of non-canonical RNA capping in bacteria and ultimately all domains of life. The repertoire of non-canonical caps has expanded to encompass metabolite caps, including NAD, FAD, CoA, UDP-Glucose, and ADP-ribose, alongside alarmone dinucleoside polyphosphate caps, and methylated phosphate cap-like structures. This review offers an introduction into the field, presenting a summary of the current knowledge about non-canonical RNA caps. We highlight the often still enigmatic biological roles of the caps together with their processing enzymes, focusing on the most recent discoveries. Furthermore, we present the methods used for the detection and analysis of these non-canonical RNA caps and thus provide an introduction into this dynamic new field.
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Affiliation(s)
- Jiří František Potužník
- Institute of Organic Chemistry and Biochemistry of the CAS, Prague 6, Czechia
- Department of Cell Biology, Charles University, Faculty of Science, Prague 2, Czechia
| | - Hana Cahova
- Institute of Organic Chemistry and Biochemistry of the CAS, Prague 6, Czechia
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11
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Zamakhov IM, Anashkin VA, Moiseenko AV, Orlov VN, Vorobyeva NN, Sokolova OS, Baykov AA. The Structure and Nucleotide-Binding Characteristics of Regulated Cystathionine β-Synthase Domain-Containing Pyrophosphatase without One Catalytic Domain. Int J Mol Sci 2023; 24:17160. [PMID: 38138989 PMCID: PMC10742508 DOI: 10.3390/ijms242417160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Regulatory adenine nucleotide-binding cystathionine β-synthase (CBS) domains are widespread in proteins; however, information on the mechanism of their modulating effects on protein function is scarce. The difficulty in obtaining structural data for such proteins is ascribed to their unusual flexibility and propensity to form higher-order oligomeric structures. In this study, we deleted the most movable domain from the catalytic part of a CBS domain-containing bacterial inorganic pyrophosphatase (CBS-PPase) and characterized the deletion variant both structurally and functionally. The truncated CBS-PPase was inactive but retained the homotetrameric structure of the full-size enzyme and its ability to bind a fluorescent AMP analog (inhibitor) and diadenosine tetraphosphate (activator) with the same or greater affinity. The deletion stabilized the protein structure against thermal unfolding, suggesting that the deleted domain destabilizes the structure in the full-size protein. A "linear" 3D structure with an unusual type of domain swapping predicted for the truncated CBS-PPase by Alphafold2 was confirmed by single-particle electron microscopy. The results suggest a dual role for the CBS domains in CBS-PPase regulation: they allow for enzyme tetramerization, which impedes the motion of one catalytic domain, and bind adenine nucleotides to mitigate or aggravate this effect.
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Affiliation(s)
- Ilya M. Zamakhov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia (V.A.A.)
- Department of Chemistry, Lomonosov Moscow State University, 119899 Moscow, Russia
| | - Viktor A. Anashkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia (V.A.A.)
| | - Andrey V. Moiseenko
- Department of Biology, Lomonosov Moscow State University, 119899 Moscow, Russia (O.S.S.)
| | - Victor N. Orlov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia (V.A.A.)
| | - Natalia N. Vorobyeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia (V.A.A.)
| | - Olga S. Sokolova
- Department of Biology, Lomonosov Moscow State University, 119899 Moscow, Russia (O.S.S.)
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
| | - Alexander A. Baykov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia (V.A.A.)
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12
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Fung DK, Trinquier AE, Wang JD. Crosstalk between (p)ppGpp and other nucleotide second messengers. Curr Opin Microbiol 2023; 76:102398. [PMID: 37866203 PMCID: PMC10842992 DOI: 10.1016/j.mib.2023.102398] [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: 08/07/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/24/2023]
Abstract
In response to environmental cues, bacteria produce intracellular nucleotide messengers to regulate a wide variety of cellular processes and physiology. Studies on individual nucleotide messengers, such as (p)ppGpp or cyclic (di)nucleotides, have established their respective regulatory themes. As research on nucleotide signaling networks expands, recent studies have begun to uncover various crosstalk mechanisms between (p)ppGpp and other nucleotide messengers, including signal conversion, allosteric regulation, and target competition. The multiple layers of crosstalk implicate that (p)ppGpp is intricately linked to different nucleotide signaling pathways. From a physiological perspective, (p)ppGpp crosstalk enables fine-tuning and feedback regulation with other nucleotide messengers to achieve optimal adaptation.
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Affiliation(s)
- Danny K Fung
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Aude E Trinquier
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jue D Wang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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13
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Herzberg C, Meißner J, Warneke R, Stülke J. The many roles of cyclic di-AMP to control the physiology of Bacillus subtilis. MICROLIFE 2023; 4:uqad043. [PMID: 37954098 PMCID: PMC10636490 DOI: 10.1093/femsml/uqad043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/21/2023] [Accepted: 10/19/2023] [Indexed: 11/14/2023]
Abstract
The dinucleotide cyclic di-AMP (c-di-AMP) is synthesized as a second messenger in the Gram-positive model bacterium Bacillus subtilis as well as in many bacteria and archaea. Bacillus subtilis possesses three diadenylate cyclases and two phosphodiesterases that synthesize and degrade the molecule, respectively. Among the second messengers, c-di-AMP is unique since it is essential for B. subtilis on the one hand but toxic upon accumulation on the other. This role as an "essential poison" is related to the function of c-di-AMP in the control of potassium homeostasis. C-di-AMP inhibits the expression and activity of potassium uptake systems by binding to riboswitches and transporters and activates the activity of potassium exporters. In this way, c-di-AMP allows the adjustment of uptake and export systems to achieve a balanced intracellular potassium concentration. C-di-AMP also binds to two dedicated signal transduction proteins, DarA and DarB. Both proteins seem to interact with other proteins in their apo state, i.e. in the absence of c-di-AMP. For DarB, the (p)ppGpp synthetase/hydrolase Rel and the pyruvate carboxylase PycA have been identified as targets. The interactions trigger the synthesis of the alarmone (p)ppGpp and of the acceptor molecule for the citric acid cycle, oxaloacetate, respectively. In the absence of c-di-AMP, many amino acids inhibit the growth of B. subtilis. This feature can be used to identify novel players in amino acid homeostasis. In this review, we discuss the different functions of c-di-AMP and their physiological relevance.
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Affiliation(s)
- Christina Herzberg
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Janek Meißner
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Robert Warneke
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
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14
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van der Does C, Braun F, Ren H, Albers SV. Putative nucleotide-based second messengers in archaea. MICROLIFE 2023; 4:uqad027. [PMID: 37305433 PMCID: PMC10249747 DOI: 10.1093/femsml/uqad027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/07/2023] [Accepted: 06/02/2023] [Indexed: 06/13/2023]
Abstract
Second messengers transfer signals from changing intra- and extracellular conditions to a cellular response. Over the last few decades, several nucleotide-based second messengers have been identified and characterized in especially bacteria and eukaryotes. Also in archaea, several nucleotide-based second messengers have been identified. This review will summarize our understanding of nucleotide-based second messengers in archaea. For some of the nucleotide-based second messengers, like cyclic di-AMP and cyclic oligoadenylates, their roles in archaea have become clear. Cyclic di-AMP plays a similar role in osmoregulation in euryarchaea as in bacteria, and cyclic oligoadenylates are important in the Type III CRISPR-Cas response to activate CRISPR ancillary proteins involved in antiviral defense. Other putative nucleotide-based second messengers, like 3',5'- and 2',3'-cyclic mononucleotides and adenine dinucleotides, have been identified in archaea, but their synthesis and degradation pathways, as well as their functions as secondary messengers, still remain to be demonstrated. In contrast, 3'-3'-cGAMP has not yet been identified in archaea, but the enzymes required to synthesize 3'-3'-cGAMP have been found in several euryarchaeotes. Finally, the widely distributed bacterial second messengers, cyclic diguanosine monophosphate and guanosine (penta-)/tetraphosphate, do not appear to be present in archaea.
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Affiliation(s)
- Chris van der Does
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Frank Braun
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Hongcheng Ren
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, 79104 Freiburg, Germany
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15
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Zegarra V, Mais CN, Freitag J, Bange G. The mysterious diadenosine tetraphosphate (AP4A). MICROLIFE 2023; 4:uqad016. [PMID: 37223742 PMCID: PMC10148737 DOI: 10.1093/femsml/uqad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/15/2023] [Accepted: 04/21/2023] [Indexed: 05/25/2023]
Abstract
Dinucleoside polyphosphates, a class of nucleotides found amongst all the Trees of Life, have been gathering a lot of attention in the past decades due to their putative role as cellular alarmones. In particular, diadenosine tetraphosphate (AP4A) has been widely studied in bacteria facing various environmental challenges and has been proposed to be important for ensuring cellular survivability through harsh conditions. Here, we discuss the current understanding of AP4A synthesis and degradation, protein targets, their molecular structure where possible, and insights into the molecular mechanisms of AP4A action and its physiological consequences. Lastly, we will briefly touch on what is known with regards to AP4A beyond the bacterial kingdom, given its increasing appearance in the eukaryotic world. Altogether, the notion that AP4A is a conserved second messenger in organisms ranging from bacteria to humans and is able to signal and modulate cellular stress regulation seems promising.
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Affiliation(s)
- Victor Zegarra
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg 35043, Germany
| | - Christopher-Nils Mais
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg 35043, Germany
| | - Johannes Freitag
- Department of Biology, Philipps University Marburg, Marburg 35043, Germany
| | - Gert Bange
- Corresponding author. Karl-von-Frisch Strasse 14, 35043 Marburg, Germany. E-mail:
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16
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Hengge R, Pruteanu M, Stülke J, Tschowri N, Turgay K. Recent advances and perspectives in nucleotide second messenger signaling in bacteria. MICROLIFE 2023; 4:uqad015. [PMID: 37223732 PMCID: PMC10118264 DOI: 10.1093/femsml/uqad015] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/28/2023] [Accepted: 04/13/2023] [Indexed: 05/25/2023]
Abstract
Nucleotide second messengers act as intracellular 'secondary' signals that represent environmental or cellular cues, i.e. the 'primary' signals. As such, they are linking sensory input with regulatory output in all living cells. The amazing physiological versatility, the mechanistic diversity of second messenger synthesis, degradation, and action as well as the high level of integration of second messenger pathways and networks in prokaryotes has only recently become apparent. In these networks, specific second messengers play conserved general roles. Thus, (p)ppGpp coordinates growth and survival in response to nutrient availability and various stresses, while c-di-GMP is the nucleotide signaling molecule to orchestrate bacterial adhesion and multicellularity. c-di-AMP links osmotic balance and metabolism and that it does so even in Archaea may suggest a very early evolutionary origin of second messenger signaling. Many of the enzymes that make or break second messengers show complex sensory domain architectures, which allow multisignal integration. The multiplicity of c-di-GMP-related enzymes in many species has led to the discovery that bacterial cells are even able to use the same freely diffusible second messenger in local signaling pathways that can act in parallel without cross-talking. On the other hand, signaling pathways operating with different nucleotides can intersect in elaborate signaling networks. Apart from the small number of common signaling nucleotides that bacteria use for controlling their cellular "business," diverse nucleotides were recently found to play very specific roles in phage defense. Furthermore, these systems represent the phylogenetic ancestors of cyclic nucleotide-activated immune signaling in eukaryotes.
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Affiliation(s)
- Regine Hengge
- Corresponding author. Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Philippstr. 13 – Haus 22, 10115 Berlin, Germany. Tel: +49-30-2093-49686; Fax: +49-30-2093-49682; E-mail:
| | | | - Jörg Stülke
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Natalia Tschowri
- Institute of Microbiology, Leibniz-Universität Hannover, 30419 Hannover, Germany
| | - Kürşad Turgay
- Institute of Microbiology, Leibniz-Universität Hannover, 30419 Hannover, Germany
- Max Planck Unit for the Science of Pathogens, 10115 Berlin, Germany
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Singh S, Anand R. Diverse strategies adopted by nature for regulating purine biosynthesis via fine-tuning of purine metabolic enzymes. Curr Opin Chem Biol 2023; 73:102261. [PMID: 36682088 DOI: 10.1016/j.cbpa.2022.102261] [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: 08/30/2022] [Revised: 11/18/2022] [Accepted: 12/21/2022] [Indexed: 01/24/2023]
Abstract
Purine nucleotides, generated by de novo synthesis and salvage pathways, are essential for metabolism and act as building blocks of genetic material. To avoid an imbalance in the nucleotide pool, nature has devised several strategies to regulate/tune the catalytic performance of key purine metabolic enzymes. Here, we discuss some recent examples, such as stress-regulating alarmones that bind to select pathway enzymes, huge ensembles like dynamic metabolons and self-assembled filaments that highlight the layered fine-control prevalent in the purine metabolic pathway to fulfill requisite purine demands. Examples of enzymes that turn-on only under allosteric control, are regulated via long-distance communication that facilitates transient conduits have additionally been explored.
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Affiliation(s)
- Sukhwinder Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India; DBT-Wellcome Trust India Alliance Senior Fellow, Mumbai 400076, India.
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18
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Leiva LE, Zegarra V, Bange G, Ibba M. At the Crossroad of Nucleotide Dynamics and Protein Synthesis in Bacteria. Microbiol Mol Biol Rev 2023; 87:e0004422. [PMID: 36853029 PMCID: PMC10029340 DOI: 10.1128/mmbr.00044-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Nucleotides are at the heart of the most essential biological processes in the cell, be it as key protagonists in the dogma of molecular biology or by regulating multiple metabolic pathways. The dynamic nature of nucleotides, the cross talk between them, and their constant feedback to and from the cell's metabolic state position them as a hallmark of adaption toward environmental and growth challenges. It has become increasingly clear how the activity of RNA polymerase, the synthesis and maintenance of tRNAs, mRNA translation at all stages, and the biogenesis and assembly of ribosomes are fine-tuned by the pools of intracellular nucleotides. With all aspects composing protein synthesis involved, the ribosome emerges as the molecular hub in which many of these nucleotides encounter each other and regulate the state of the cell. In this review, we aim to highlight intracellular nucleotides in bacteria as dynamic characters permanently cross talking with each other and ultimately regulating protein synthesis at various stages in which the ribosome is mainly the principal character.
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Affiliation(s)
- Lorenzo Eugenio Leiva
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
| | - Victor Zegarra
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Michael Ibba
- Schmid College of Science and Technology, Chapman University, Orange, California, USA
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Metabolic Promiscuity of an Orphan Small Alarmone Hydrolase Facilitates Bacterial Environmental Adaptation. mBio 2022; 13:e0242222. [PMID: 36472432 PMCID: PMC9765508 DOI: 10.1128/mbio.02422-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Small alarmone hydrolases (SAHs) are alarmone metabolizing enzymes found in both metazoans and bacteria. In metazoans, the SAH homolog Mesh1 is reported to function in cofactor metabolism by hydrolyzing NADPH to NADH. In bacteria, SAHs are often identified in genomes with toxic alarmone synthetases for self-resistance. Here, we characterized a bacterial orphan SAH, i.e., without a toxic alarmone synthetase, in the phytopathogen Xanthomonas campestris pv. campestris (XccSAH) and found that it metabolizes both cellular alarmones and cofactors. In vitro, XccSAH displays abilities to hydrolyze multiple nucleotides, including pppGpp, ppGpp, pGpp, pppApp, and NADPH. In vivo, X. campestris pv. campestris cells lacking sah accumulated higher levels of cellular (pp)pGpp and NADPH compared to wild-type cells upon amino acid starvation. In addition, X. campestris pv. campestris mutants lacking sah were more sensitive to killing by Pseudomonas during interbacterial competition. Interestingly, loss of sah also resulted in reduced growth in amino acid-replete medium, a condition that did not induce (pp)pGpp or pppApp accumulation. Further metabolomic characterization revealed strong depletion of NADH levels in the X. campestris pv. campestris mutant lacking sah, suggesting that NADPH/NADH regulation is an evolutionarily conserved function of both bacterial and metazoan SAHs and Mesh1. Overall, our work demonstrates a regulatory role of bacterial SAHs as tuners of stress responses and metabolism, beyond functioning as antitoxins. IMPORTANCE Small alarmone hydrolases (SAHs) comprise a widespread family of alarmone metabolizing enzymes. In metazoans, SAHs have been reported to control multiple aspects of physiology and stress resistance through alarmone and NADPH metabolisms, but their physiological functions in bacteria is mostly uncharacterized except for a few reports as antitoxins. Here, we identified an SAH functioning independently of toxins in the phytopathogen Xanthomonas campestris pv. campestris. We found that XccSAH hydrolyzed multiple alarmones and NADPH in vitro, and X. campestris pv. campestris mutants lacking sah displayed increased alarmone levels during starvation, loss of interspecies competitive fitness, growth defects, and strong reduction in NADH. Our findings reveal the importance of NADPH hydrolysis by a bacterial SAH. Our work is also the first report of significant physiological roles of bacterial SAHs beyond functioning as antitoxins and suggests that SAHs have far broader physiological roles and share similar functions across domains of life.
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