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Rojas EM, Zhang H, Velu SE, Wu H. Tetracyclic homoisoflavanoid (+)-brazilin: a natural product inhibits c-di-AMP-producing enzyme and Streptococcus mutans biofilms. Microbiol Spectr 2024; 12:e0241823. [PMID: 38591917 PMCID: PMC11064632 DOI: 10.1128/spectrum.02418-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 03/02/2024] [Indexed: 04/10/2024] Open
Abstract
The tenacious biofilms formed by Streptococcus mutans are resistant to conventional antibiotics and current treatments. There is a growing need for novel therapeutics that selectively inhibit S. mutans biofilms while preserving the normal oral microenvironment. Previous studies have shown that increased levels of cyclic di-AMP, an important secondary messenger synthesized by diadenylate cyclase (DAC), favored biofilm formation in S. mutans. Thus, targeting S. mutans DAC is a novel strategy to inhibit S. mutans biofilms. We screened a small NCI library of natural products using a fluorescence detection assay. (+)-Brazilin, a tetracyclic homoisoflavanoid found in the heartwood of Caesalpinia sappan, was identified as one of the 11 "hits," with the greatest reduction (>99%) in fluorescence at 100 µM. The smDAC inhibitory profiles of the 11 "hits" established by a quantitative high-performance liquid chromatography assay revealed that (+)-brazilin had the most enzymatic inhibitory activity (87% at 100 µM) and was further studied to determine its half maximal inhibitory concentration (IC50 = 25.1 ± 0.98 µM). (+)-Brazilin non-competitively inhibits smDAC's enzymatic activity (Ki = 140.0 ± 27.13 µM), as determined by a steady-state Michaelis-Menten kinetics assay. In addition, (+)-brazilin's binding profile with smDAC (Kd = 11.87 µM) was illustrated by a tyrosine intrinsic fluorescence quenching assay. Furthermore, at low micromolar concentrations, (+)-brazilin selectively inhibited the biofilm of S. mutans (IC50 = 21.0 ± 0.60 µM) and other oral bacteria. S. mutans biofilms were inhibited by a factor of 105 in colony-forming units when treated with 50 µM (+)-brazilin. In addition, a significant dose-dependent reduction in extracellular DNA and glucan levels was evident by fluorescence microscopy imaging of S. mutans biofilms exposed to different concentrations of (+)-brazilin. Furthermore, colonization of S. mutans on a representative model of enamel using suspended hydroxyapatite discs showed a >90% reduction with 50 µM (+)-brazilin. In summary, we have identified a drug-like natural product inhibitor of S. mutans biofilm that not only binds to smDAC but can also inhibit the function of smDAC. (+)-Brazilin could be a good candidate for further development as a potent therapeutic for the prevention and treatment of dental caries.IMPORTANCEThis study represents a significant advancement in our understanding of potential therapeutic options for combating cariogenic biofilms produced by Streptococcus mutans. The research delves into the use of (+)-brazilin, a natural product, as a potent inhibitor of Streptococcus mutans' diadenylate cyclase (smDAC), an enzyme crucial in the formation of biofilms. The study establishes (+)-brazilin as a non-competitive inhibitor of smDAC while providing initial insights into its binding mechanism. What makes this finding even more promising is that (+)-brazilin does not limit its inhibitory effects to S. mutans alone. Instead, it demonstrates efficacy in hindering biofilms in other oral bacteria as well. The broader spectrum of anti-biofilm activity suggests that (+)-brazilin could potentially serve as a versatile tool in a natural product-based treatment for combating a range of conditions caused by resilient biofilms.
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Affiliation(s)
- Edwin M. Rojas
- School of Dentistry, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Hua Zhang
- Division of Biomaterial & Biomedical Sciences, School of Dentistry, Oregon Health & Science University, Portland, Oregon, USA
| | - Sadanandan E. Velu
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Hui Wu
- Division of Biomaterial & Biomedical Sciences, School of Dentistry, Oregon Health & Science University, Portland, Oregon, USA
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Jin Z, Song D, Wang W, Feng L, Li Z, Chen H, Xiao X, Liu X. Synthesis and degradation of the cyclic dinucleotide messenger c-di-AMP in the hyperthermophilic archaeon Pyrococcus yayanosii. Protein Sci 2023; 32:e4829. [PMID: 37921047 PMCID: PMC10680344 DOI: 10.1002/pro.4829] [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: 07/09/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/04/2023]
Abstract
Cyclic di-adenosine monophosphate (c-di-AMP) is a newly identified prokaryotic cyclic dinucleotide second messenger well elucidated in bacteria, while less studied in archaea. Here, we describe the enzymes involved in c-di-AMP metabolism in the hyperthermophilic archaeon Pyrococcus yayanosii. Our results demonstrate that c-di-AMP is synthesized from two molecules of ATP by diadenylate cyclase (DAC) and degraded into pApA and then to AMP by a DHH family phosphodiesterase (PDE). DAC can be activated by a wider variety of ions, using two conserved residues, D188 and E244, to coordinate divalent metal ions, which is different from bacterial CdaA and DisA. PDE possesses a broad substrate spectrum like bacterial DHH family PDEs but shows a stricter base selection between A and G in cyclic dinucleotides hydrolysis. PDE shows differences in substrate binding patches from bacterial counterparts. C-di-AMP was confirmed to exist in Thermococcus kodakarensis cells, and the deletion of the dac or pde gene supports that the synthesis and degradation of c-di-AMP are catalyzed by DAC and PDE, respectively. Our results provide a further understanding of the metabolism of c-di-AMP in archaea.
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Affiliation(s)
- Zheng Jin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- Instrumental analysis centerShanghai Jiao Tong UniversityShanghaiChina
| | - Dong Song
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Wei‐Wei Wang
- Shanghai Institute of Applied PhysicsChinese Academy of SciencesShanghaiChina
| | - Lei Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Zheng‐Xin Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Hai‐Feng Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- Joint International Research Laboratory of Metabolic & Developmental Sciences (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiChina
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil EngineeringShanghai Jiao Tong UniversityShanghaiChina
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)ZhuhaiGuangdongChina
| | - Xi‐Peng Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- Joint International Research Laboratory of Metabolic & Developmental Sciences (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiChina
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Zhu X, Baranowski E, Hao Z, Li X, Zhao G, Dong Y, Chen Y, Hu C, Chen H, Citti C, Wang A, Guo A. An atypical GdpP enzyme linking cyclic nucleotide metabolism to osmotic tolerance and gene regulation in Mycoplasma bovis. Front Microbiol 2023; 14:1250368. [PMID: 38098652 PMCID: PMC10720645 DOI: 10.3389/fmicb.2023.1250368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 11/10/2023] [Indexed: 12/17/2023] Open
Abstract
Nucleotide second messengers play an important role in bacterial adaptation to environmental changes. Recent evidence suggests that some of these regulatory molecular pathways were conserved upon the degenerative evolution of the wall-less mycoplasmas. We have recently reported the occurrence of a phosphodiesterase (PDE) in the ruminant pathogen Mycoplasma bovis, which was involved in c-di-AMP metabolism. In the present study, we demonstrate that the genome of this mycoplasma species encodes a PDE of the GdpP family with atypical DHH domains. Characterization of M. bovis GdpP (MbovGdpP) revealed a multifunctional PDE with unusual nanoRNase and single-stranded DNase activities. The alarmone ppGpp was found unable to inhibit c-di-NMP degradation by MbovGdpP but efficiently blocked its nanoRNase activity. Remarkably, MbovGdpP was found critical for the osmotic tolerance of M. bovis under K+ and Na+ conditions. Transcriptomic analyses further revealed the biological importance of MbovGdpP in tRNA biosynthesis, pyruvate metabolism, and several steps in genetic information processing. This study is an important step in understanding the role of PDE and nucleotide second messengers in the biology of a minimal bacterial pathogen.
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Affiliation(s)
- Xifang Zhu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
- Longhu Laboratory of Advanced Immunology, Zhengzhou, China
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | | | - Zhiyu Hao
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xixi Li
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Gang Zhao
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yaqi Dong
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yingyu Chen
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Changmin Hu
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Huanchun Chen
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People’s Republic of China, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, International Research Center for Animal Disease, Ministry of Science and Technology of the People’s Republic of China, Wuhan, China
| | | | - Aiping Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
- Longhu Laboratory of Advanced Immunology, Zhengzhou, China
| | - Aizhen Guo
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People’s Republic of China, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, International Research Center for Animal Disease, Ministry of Science and Technology of the People’s Republic of China, Wuhan, China
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Neumann P, Kloskowski P, Ficner R. Computer-aided design of a cyclic di-AMP synthesizing enzyme CdaA inhibitor. MICROLIFE 2023; 4:uqad021. [PMID: 37223749 PMCID: PMC10167629 DOI: 10.1093/femsml/uqad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/24/2023] [Accepted: 04/13/2023] [Indexed: 05/25/2023]
Abstract
Cyclic di-AMP (c-di-AMP) is an essential secondary messenger regulating cell wall homeostasis and myriads of physiological processes in several Gram-positive and mycobacteria, including human pathogens. Hence, c-di-AMP synthesizing enzymes (DACs) have become a promising antibacterial drug target. To overcome a scarcity of small molecule inhibitors of c-di-AMP synthesizing enzyme CdaA, a computer-aided design of a new compound that should block the enzyme has been performed. This has led to the identification of a molecule comprising two thiazole rings and showing inhibitory potential based on ITC measurements. Thiazole scaffold is a good pharmacophore nucleus known due to its various pharmaceutical applications. It is contained in more than 18 FDA-approved drugs as well as in dozens of experimental drugs. Hence, the designed inhibitor can serve as a potent lead compound for further development of inhibitor against CdaA.
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Affiliation(s)
- Piotr Neumann
- Corresponding author. Department of Molecular Structural Biology, Georg-August-University Goettingen, Institute of Microbiology and Genetics, GZMB, Justus-von-Liebig Weg 11, 37077 Goettingen, Germany. Tel: +495513928624; Fax: +495513928629; E-mail:
| | - Patrick Kloskowski
- Department of Molecular Structural Biology, Georg-August-University Goettingen, Institute of Microbiology and Genetics, GZMB, Justus-von-Liebig Weg 11, 37077 Goettingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Georg-August-University Goettingen, Institute of Microbiology and Genetics, GZMB, Justus-von-Liebig Weg 11, 37077 Goettingen, Germany
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5
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Gautam S, Mahapa A, Yeramala L, Gandhi A, Krishnan S, Kutti R. V, Chatterji D. Regulatory mechanisms of c-di-AMP synthase from Mycobacterium smegmatis revealed by a structure: Function analysis. Protein Sci 2023; 32:e4568. [PMID: 36660887 PMCID: PMC9926474 DOI: 10.1002/pro.4568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/09/2023] [Accepted: 01/13/2023] [Indexed: 01/21/2023]
Abstract
Cyclic-di-nucleotide-based secondary messengers regulate various physiological functions, including stress responses in bacteria. Cyclic diadenosine monophosphate (c-di-AMP) has recently emerged as a crucial second messenger with implications in processes including osmoregulation, antibiotic resistance, biofilm formation, virulence, DNA repair, ion homeostasis, and sporulation, and has potential therapeutic applications. The contrasting activities of the enzymes diadenylate cyclase (DAC) and phosphodiesterase (PDE) determine the equilibrium levels of c-di-AMP. Although c-di-AMP is suspected of playing an essential role in the pathophysiology of bacterial infections and in regulating host-pathogen interactions, the mechanisms of its regulation remain relatively unexplored in mycobacteria. In this report, we biochemically and structurally characterize the c-di-AMP synthase (MsDisA) from Mycobacterium smegmatis. The enzyme activity is regulated by pH and substrate concentration; conditions of significance in the homoeostasis of c-di-AMP levels. Substrate binding stimulates conformational changes in the protein, and pApA and ppApA are synthetic intermediates detectable when enzyme efficiency is low. Unlike the orthologous Bacillus subtilis enzyme, MsDisA does not bind to, and its activity is not influenced in the presence of DNA. Furthermore, we have determined the cryo-EM structure of MsDisA, revealing asymmetry in its structure in contrast to the symmetric crystal structure of Thermotoga maritima DisA. We also demonstrate that the N-terminal minimal region alone is sufficient and essential for oligomerization and catalytic activity. Our data shed light on the regulation of mycobacterial DisA and possible future directions to pursue.
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Affiliation(s)
- Sudhanshu Gautam
- Molecular Biophysics UnitIndian Institute of ScienceBangaloreIndia
| | - Avisek Mahapa
- Molecular Biophysics UnitIndian Institute of ScienceBangaloreIndia
| | - Lahari Yeramala
- National Center for Biological SciencesTata Institute of Fundamental Research, GKVK PostBengaluruIndia
| | - Apoorv Gandhi
- Molecular Biophysics UnitIndian Institute of ScienceBangaloreIndia
| | - Sushma Krishnan
- Electron Microscopy Facility, Division of Biological SciencesIndian Institute of ScienceBangaloreIndia
| | - Vinothkumar Kutti R.
- National Center for Biological SciencesTata Institute of Fundamental Research, GKVK PostBengaluruIndia
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6
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Novotná B, Holá L, Staś M, Gutten O, Smola M, Zavřel M, Vavřina Z, Buděšínský M, Liboska R, Chevrier F, Dobiaš J, Boura E, Rulíšek L, Birkuš G. Enzymatic Synthesis of 3'-5', 3'-5' Cyclic Dinucleotides, Their Binding Properties to the Stimulator of Interferon Genes Adaptor Protein, and Structure/Activity Correlations. Biochemistry 2021; 60:3714-3727. [PMID: 34788017 DOI: 10.1021/acs.biochem.1c00692] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The 3'-5', 3'-5' cyclic dinucleotides (3'3'CDNs) are bacterial second messengers that can also bind to the stimulator of interferon genes (STING) adaptor protein in vertebrates and activate the host innate immunity. Here, we profiled the substrate specificity of four bacterial dinucleotide synthases from Vibrio cholerae (DncV), Bacillus thuringiensis (btDisA), Escherichia coli (dgcZ), and Thermotoga maritima (tDGC) using a library of 33 nucleoside-5'-triphosphate analogues and then employed these enzymes to synthesize 24 3'3'CDNs. The STING affinity of CDNs was evaluated in cell-based and biochemical assays, and their ability to induce cytokines was determined by employing human peripheral blood mononuclear cells. Interestingly, the prepared heterodimeric 3'3'CDNs bound to the STING much better than their homodimeric counterparts and showed similar or better potency than bacterial 3'3'CDNs. We also rationalized the experimental findings by in-depth STING-CDN structure-activity correlations by dissecting computed interaction free energies into a set of well-defined and intuitive terms. To this aim, we employed state-of-the-art methods of computational chemistry, such as quantum mechanics/molecular mechanics (QM/MM) calculations, and complemented the computed results with the {STING:3'3'c-di-ara-AMP} X-ray crystallographic structure. QM/MM identified three outliers (mostly homodimers) for which we have no clear explanation of their impaired binding with respect to their heterodimeric counterparts, whereas the R2 = 0.7 correlation between the computed ΔG'int_rel and experimental ΔTm's for the remaining ligands has been very encouraging.
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Affiliation(s)
- Barbora Novotná
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic.,Faculty of Science, Charles University, Albertov 6, Prague 12800, Czech Republic
| | - Lucie Holá
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Monika Staś
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Ondrej Gutten
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Miroslav Smola
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Martin Zavřel
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Zdeněk Vavřina
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic.,Faculty of Science, Charles University, Albertov 6, Prague 12800, Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Radek Liboska
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Florian Chevrier
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Juraj Dobiaš
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Gabriel Birkuš
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
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Pathania M, Tosi T, Millership C, Hoshiga F, Morgan RML, Freemont PS, Gründling A. Structural basis for the inhibition of the Bacillus subtilis c-di-AMP cyclase CdaA by the phosphoglucomutase GlmM. J Biol Chem 2021; 297:101317. [PMID: 34678313 PMCID: PMC8573169 DOI: 10.1016/j.jbc.2021.101317] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 11/25/2022] Open
Abstract
Cyclic-di-adenosine monophosphate (c-di-AMP) is an important nucleotide signaling molecule that plays a key role in osmotic regulation in bacteria. c-di-AMP is produced from two molecules of ATP by proteins containing a diadenylate cyclase (DAC) domain. In Bacillus subtilis, the main c-di-AMP cyclase, CdaA, is a membrane-linked cyclase with an N-terminal transmembrane domain followed by the cytoplasmic DAC domain. As both high and low levels of c-di-AMP have a negative impact on bacterial growth, the cellular levels of this signaling nucleotide are tightly regulated. Here we investigated how the activity of the B. subtilis CdaA is regulated by the phosphoglucomutase GlmM, which has been shown to interact with the c-di-AMP cyclase. Using the soluble B. subtilis CdaACD catalytic domain and purified full-length GlmM or the GlmMF369 variant lacking the C-terminal flexible domain 4, we show that the cyclase and phosphoglucomutase form a stable complex in vitro and that GlmM is a potent cyclase inhibitor. We determined the crystal structure of the individual B. subtilis CdaACD and GlmM homodimers and of the CdaACD:GlmMF369 complex. In the complex structure, a CdaACD dimer is bound to a GlmMF369 dimer in such a manner that GlmM blocks the oligomerization of CdaACD and formation of active head-to-head cyclase oligomers, thus suggesting a mechanism by which GlmM acts as a cyclase inhibitor. As the amino acids at the CdaACD:GlmM interphase are conserved, we propose that the observed mechanism of inhibition of CdaA by GlmM may also be conserved among Firmicutes.
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Affiliation(s)
- Monisha Pathania
- Section of Molecular Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Tommaso Tosi
- Section of Molecular Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Charlotte Millership
- Section of Molecular Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Fumiya Hoshiga
- Section of Molecular Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Rhodri M L Morgan
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Paul S Freemont
- London Biofoundry, Imperial College Translation and Innovation Hub, White City Campus, London, United Kingdom; Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom; UK Dementia Research Institute Centre for Care Research and Technology, Imperial College London, London, United Kingdom.
| | - Angelika Gründling
- Section of Molecular Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom.
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8
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Heidemann JL, Neumann P, Dickmanns A, Ficner R. Crystal structures of the c-di-AMP-synthesizing enzyme CdaA. J Biol Chem 2019; 294:10463-10470. [PMID: 31118276 DOI: 10.1074/jbc.ra119.009246] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Indexed: 11/06/2022] Open
Abstract
Cyclic di-AMP (c-di-AMP) is the only second messenger known to be essential for bacterial growth. It has been found mainly in Gram-positive bacteria, including pathogenic bacteria like Listeria monocytogenes CdaA is the sole diadenylate cyclase in L. monocytogenes, making this enzyme an attractive target for the development of novel antibiotic compounds. Here we report crystal structures of CdaA from L. monocytogenes in the apo state, in the post-catalytic state with bound c-di-AMP and catalytic Co2+ ions, as well as in a complex with AMP. These structures reveal the flexibility of a tyrosine side chain involved in locking the adenine ring after ATP binding. The essential role of this tyrosine was confirmed by mutation to Ala, leading to drastic loss of enzymatic activity.
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Affiliation(s)
- Jana L Heidemann
- From the Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Piotr Neumann
- From the Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Achim Dickmanns
- From the Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Ralf Ficner
- From the Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, 37077 Göttingen, Germany
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9
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Tosi T, Hoshiga F, Millership C, Singh R, Eldrid C, Patin D, Mengin-Lecreulx D, Thalassinos K, Freemont P, Gründling A. Inhibition of the Staphylococcus aureus c-di-AMP cyclase DacA by direct interaction with the phosphoglucosamine mutase GlmM. PLoS Pathog 2019; 15:e1007537. [PMID: 30668586 PMCID: PMC6368335 DOI: 10.1371/journal.ppat.1007537] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/08/2019] [Accepted: 12/18/2018] [Indexed: 02/05/2023] Open
Abstract
c-di-AMP is an important second messenger molecule that plays a pivotal role in regulating fundamental cellular processes, including osmotic and cell wall homeostasis in many Gram-positive organisms. In the opportunistic human pathogen Staphylococcus aureus, c-di-AMP is produced by the membrane-anchored DacA enzyme. Inactivation of this enzyme leads to a growth arrest under standard laboratory growth conditions and a re-sensitization of methicillin-resistant S. aureus (MRSA) strains to ß-lactam antibiotics. The gene coding for DacA is part of the conserved three-gene dacA/ybbR/glmM operon that also encodes the proposed DacA regulator YbbR and the essential phosphoglucosamine mutase GlmM, which is required for the production of glucosamine-1-phosphate, an early intermediate of peptidoglycan synthesis. These three proteins are thought to form a complex in vivo and, in this manner, help to fine-tune the cellular c-di-AMP levels. To further characterize this important regulatory complex, we conducted a comprehensive structural and functional analysis of the S. aureus DacA and GlmM enzymes by determining the structures of the S. aureus GlmM enzyme and the catalytic domain of DacA. Both proteins were found to be dimers in solution as well as in the crystal structures. Further site-directed mutagenesis, structural and enzymatic studies showed that multiple DacA dimers need to interact for enzymatic activity. We also show that DacA and GlmM form a stable complex in vitro and that S. aureus GlmM, but not Escherichia coli or Pseudomonas aeruginosa GlmM, acts as a strong inhibitor of DacA function without the requirement of any additional cellular factor. Based on Small Angle X-ray Scattering (SAXS) data, a model of the complex revealed that GlmM likely inhibits DacA by masking the active site of the cyclase and preventing higher oligomer formation. Together these results provide an important mechanistic insight into how c-di-AMP production can be regulated in the cell.
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Affiliation(s)
- Tommaso Tosi
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Fumiya Hoshiga
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Charlotte Millership
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Rahul Singh
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Charles Eldrid
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London, United Kingdom
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Delphine Patin
- Institute for Integrative Biology of the Cell, CEA, CNRS, Univ Paris-Sud and Université Paris-Saclay, Gif-sur-Yvette, France
| | - Dominique Mengin-Lecreulx
- Institute for Integrative Biology of the Cell, CEA, CNRS, Univ Paris-Sud and Université Paris-Saclay, Gif-sur-Yvette, France
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London, United Kingdom
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Paul Freemont
- Section of Structural Biology, Department of Medicine, Imperial College London, London, United Kingdom
| | - Angelika Gründling
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
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10
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Making and Breaking of an Essential Poison: the Cyclases and Phosphodiesterases That Produce and Degrade the Essential Second Messenger Cyclic di-AMP in Bacteria. J Bacteriol 2018; 201:JB.00462-18. [PMID: 30224435 DOI: 10.1128/jb.00462-18] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cyclic di-AMP is a second-messenger nucleotide that is produced by many bacteria and some archaea. Recent work has shown that c-di-AMP is unique among the signaling nucleotides, as this molecule is in many bacteria both essential on one hand and toxic upon accumulation on the other. Moreover, in bacteria, like Bacillus subtilis, c-di-AMP controls a biological process, potassium homeostasis, by binding both potassium transporters and riboswitch molecules in the mRNAs that encode the potassium transporters. In addition to the control of potassium homeostasis, c-di-AMP has been implicated in many cellular activities, including DNA repair, cell wall homeostasis, osmotic adaptation, biofilm formation, central metabolism, and virulence. c-di-AMP is synthesized and degraded by diadenylate cyclases and phosphodiesterases, respectively. In the diadenylate cyclases, one type of catalytic domain, the diadenylate cyclase (DAC) domain, is coupled to various other domains that control the localization, the protein-protein interactions, and the regulation of the enzymes. The phosphodiesterases have a catalytic core that consists either of a DHH/DHHA1 or of an HD domain. Recent findings on the occurrence, domain organization, activity control, and structural features of diadenylate cyclases and phosphodiesterases are discussed in this review.
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11
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Drexler DJ, Müller M, Rojas-Cordova CA, Bandera AM, Witte G. Structural and Biophysical Analysis of the Soluble DHH/DHHA1-Type Phosphodiesterase TM1595 from Thermotoga maritima. Structure 2017; 25:1887-1897.e4. [PMID: 29107484 DOI: 10.1016/j.str.2017.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/07/2017] [Accepted: 09/29/2017] [Indexed: 11/26/2022]
Abstract
The concentration of messenger molecules in bacterial cells needs to be tightly regulated. This can be achieved by either controlling the synthesis rate, degradation, or export by specific transporters, respectively. The regulation of the essential second messenger c-di-AMP is achieved by modulation of the diadenylate cyclase activity as well as by specific phosphodiesterases that hydrolyze c-di-AMP in the cell. We provide here structural and biochemical data on the DHH-type phosphodiesterase TmPDE (TM1595) from Thermotoga maritima. Our analysis shows that TmPDE is preferentially degrading linear dinucleotides, such as 5'-pApA, 5'-pGpG, and 5'-pApG, compared with cyclic dinucleotide substrates. The high-resolution structural data provided here describe all steps of the PDE reaction: the ligand-free enzyme, two substrate-bound states, and three post-reaction states. We can furthermore show that Pde2 from Streptococcus pneumoniae shares both structural features and substrate specificity based on small-angle X-ray scattering data and biochemical assays.
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Affiliation(s)
- David Jan Drexler
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Martina Müller
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Carlos Alberto Rojas-Cordova
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Adrian Maurice Bandera
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Gregor Witte
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany.
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12
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Mankan AK, Müller M, Witte G, Hornung V. Cyclic Dinucleotides in the Scope of the Mammalian Immune System. Handb Exp Pharmacol 2017; 238:269-289. [PMID: 28181006 DOI: 10.1007/164_2016_5002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
First discovered in prokaryotes and more recently in eukaryotes, cyclic dinucleotides (CDNs) constitute a unique branch of second messenger signaling systems. Within prokaryotes CDNs regulate a wide array of different biological processes, whereas in the vertebrate system CDN signaling is largely dedicated to activation of the innate immune system. In this book chapter we summarize the occurrence and signaling pathways of these small-molecule second messengers, most importantly in the scope of the mammalian immune system. In this regard, our main focus is the role of the cGAS-STING axis in the context of microbial infection and sterile inflammation and its implications for therapeutic applications.
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Affiliation(s)
- Arun K Mankan
- Institute of Molecular Medicine, University Hospital, University of Bonn, Sigmund-Freud-Str. 25, Bonn, 53127, Germany
| | - Martina Müller
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, Munich, 81377, Germany
| | - Gregor Witte
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, Munich, 81377, Germany
| | - Veit Hornung
- Institute of Molecular Medicine, University Hospital, University of Bonn, Sigmund-Freud-Str. 25, Bonn, 53127, Germany. .,Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, Munich, 81377, Germany. .,Center for Integrated Protein Science (CIPSM), Ludwig-Maximilians-Universitðt Mﺰnchen, Feodor-Lynen-Str. 25, 81377, Munich, Germany.
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13
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Raguse M, Torres R, Seco EM, Gándara C, Ayora S, Moeller R, Alonso JC. Bacillus subtilis DisA helps to circumvent replicative stress during spore revival. DNA Repair (Amst) 2017; 59:57-68. [PMID: 28961460 DOI: 10.1016/j.dnarep.2017.09.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/24/2017] [Accepted: 09/08/2017] [Indexed: 02/06/2023]
Abstract
The mechanisms that allow to circumvent replicative stress, and to resume DNA synthesis are poorly understood in Bacillus subtilis. To study the role of the diadenylate cyclase DisA and branch migration translocase (BMT) RadA/Sms in restarting a stalled replication fork, we nicked and broke the circular chromosome of an inert mature haploid spore, damaged the bases, and measured survival of reviving spores. During undisturbed ripening, nicks and breaks should be repaired by pathways that do not invoke long-range end resection or genetic exchange by homologous recombination, after which DNA replication might be initiated. We found that DNA damage reduced the viability of spores that lacked DisA, BMT (RadA/Sms, RuvAB or RecG), the Holliday junction resolvase RecU, or the translesion synthesis DNA polymerases (PolY1 or PolY2). DisA and RadA/Sms, in concert with RuvAB, RecG, RecU, PolY1 or PolY2, are needed to bypass replication-blocking lesions. DisA, which binds to stalled or reversed forks, did not apparently affect initiation of PriA-dependent DNA replication in vitro. We propose that DisA is necessary to coordinate responses to replicative stress; it could help to circumvent damaged template bases that otherwise impede fork progression.
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Affiliation(s)
- Marina Raguse
- German Aerospace Center (DLReV), Institute of Aerospace Medicine, Radiation Biology Department, Space Microbiology Research Group, Linder Hoehe, D-51147 Cologne (Köln), Germany
| | - Rubén Torres
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Elena M Seco
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Carolina Gándara
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Silvia Ayora
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Ralf Moeller
- German Aerospace Center (DLReV), Institute of Aerospace Medicine, Radiation Biology Department, Space Microbiology Research Group, Linder Hoehe, D-51147 Cologne (Köln), Germany.
| | - Juan C Alonso
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Cantoblanco, 28049 Madrid, Spain.
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14
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Activity and in vivo dynamics of Bacillus subtilis DisA are affected by RadA/Sms and by Holliday junction-processing proteins. DNA Repair (Amst) 2017; 55:17-30. [PMID: 28511132 DOI: 10.1016/j.dnarep.2017.05.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 05/03/2017] [Accepted: 05/04/2017] [Indexed: 12/18/2022]
Abstract
Bacillus subtilis c-di-AMP synthase DisA and RecA-related RadA/Sms are involved in the repair of DNA damage in exponentially growing cells. We provide genetic evidence that DisA or RadA/Sms is epistatic to the branch migration translocase (BMT) RecG and the Holliday junction (HJ) resolvase RecU in response to DNA damage. We provide genetic evidence damage. Functional DisA-YFP formed dynamic foci in exponentially growing cells, which moved through the nucleoids at a speed compatible with a DNA-scanning mode. DisA formed more static structures in the absence of RecU or RecG than in wild type cells, while dynamic foci were still observed in cells lacking the BMT RuvAB. Purified DisA synthesizes c-di-AMP, but interaction with RadA/Sms or with HJ DNA decreases DisA-mediated c-di-AMP synthesis. RadA/Sms-YFP also formed dynamic foci in growing cells, but the foci moved throughout the cells rather than just on the nucleoids, and co-localized rarely with DisA-YFP foci, suggesting that RadA/Sms and DisA interact only transiently in unperturbed conditions. Our data suggest a model in which DisA moving along dsDNA indicates absence of DNA damage/replication stress via normal c-di-AMP levels, while interaction with HJ DNA/halted forks leads to reduced c-di-AMP levels and an ensuing block in cell proliferation. RadA/Sms may be involved in modulating DisA activities.
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15
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Opoku-Temeng C, Dayal N, Miller J, Sintim HO. Hydroxybenzylidene-indolinones, c-di-AMP synthase inhibitors, have antibacterial and anti-biofilm activities and also re-sensitize resistant bacteria to methicillin and vancomycin. RSC Adv 2017. [DOI: 10.1039/c6ra28443d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Hydroxybenzylidene-indolinones, newly identified inhibitors of c-di-AMP synthases, inhibit biofilm formation, Gram-positive bacterial growth and sensitize resistant bacteria to methicillin and vancomycin.
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Affiliation(s)
- Clement Opoku-Temeng
- Purdue Institute for Drug Discovery
- Purdue University
- West Lafayette
- USA
- Biochemistry Graduate Program
| | - Neetu Dayal
- Purdue Institute for Drug Discovery
- Purdue University
- West Lafayette
- USA
- Department of Chemistry
| | - Jacob Miller
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | - Herman O. Sintim
- Purdue Institute for Drug Discovery
- Purdue University
- West Lafayette
- USA
- Department of Chemistry
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16
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Pham TH, Liang ZX, Marcellin E, Turner MS. Replenishing the cyclic-di-AMP pool: regulation of diadenylate cyclase activity in bacteria. Curr Genet 2016; 62:731-738. [PMID: 27074767 DOI: 10.1007/s00294-016-0600-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 03/29/2016] [Accepted: 04/01/2016] [Indexed: 02/08/2023]
Abstract
Bacteria can sense environmental cues and alter their physiology accordingly through the use of signal transduction pathways involving second messenger nucleotides. One broadly conserved second messenger is cyclic-di-AMP (c-di-AMP) which regulates a range of processes including cell wall homeostasis, potassium uptake, DNA repair, fatty acid synthesis, biofilm formation and central metabolism in bacteria. The intracellular pool of c-di-AMP is maintained by the activities of diadenylate cyclase (DAC) and phosphodiesterase (PDE) enzymes, as well as possibly via c-di-AMP export. Whilst extracellular stimuli regulating c-di-AMP levels in bacteria are poorly understood, recent work has identified effector proteins which directly interact and alter the activity of DACs. These include the membrane bound CdaR and the phosphoglucosamine mutase GlmM which both bind directly to the membrane bound CdaA DAC and the recombination protein RadA which binds directly to the DNA binding DisA DAC. The genes encoding these multiprotein complexes are co-localised in many bacteria providing further support for their functional connection. The roles of GlmM in peptidoglycan synthesis and RadA in Holliday junction intermediate processing suggest that c-di-AMP synthesis by DACs will be responsive to these cellular activities. In addition to these modulatory interactions, permanent dysregulation of DAC activity due to suppressor mutations can occur during selection to overcome growth defects, rapid cell lysis and osmosensitivity. DACs have also been investigated as targets for the development of new antibiotics and several small compound inhibitors have recently been identified. This review aims to provide an overview of how c-di-AMP synthesis by DACs can be regulated.
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Affiliation(s)
- Thi Huong Pham
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Mark S Turner
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia.
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, Australia.
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17
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Opoku-Temeng C, Sintim HO. Potent inhibition of cyclic diadenylate monophosphate cyclase by the antiparasitic drug, suramin. Chem Commun (Camb) 2016; 52:3754-7. [PMID: 26824279 DOI: 10.1039/c5cc10446g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
C-di-AMP synthases are essential in several bacteria, including human pathogens; hence these enzymes are potential antibiotic targets. However, there is a dearth of small molecule inhibitors of c-di-AMP metabolism enzymes. Screening of 2000 known drugs against DisA has led to the identification of suramin, an antiparasitic drug as potent inhibitor of c-di-AMP synthase.
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Affiliation(s)
- Clement Opoku-Temeng
- Graduate Program in Biochemistry, University of Maryland, College Park, Maryland 20742, USA and Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Herman O Sintim
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA and Center for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA.
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18
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Opoku-Temeng C, Zhou J, Zheng Y, Su J, Sintim HO. Cyclic dinucleotide (c-di-GMP, c-di-AMP, and cGAMP) signalings have come of age to be inhibited by small molecules. Chem Commun (Camb) 2016; 52:9327-42. [PMID: 27339003 DOI: 10.1039/c6cc03439j] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Bacteria utilize nucleotide-based second messengers to regulate a myriad of physiological processes. Cyclic dinucleotides have emerged as central regulators of bacterial physiology, controlling processes ranging from cell wall homeostasis to virulence production, and so far over thousands of manuscripts have provided biological insights into c-di-NMP signaling. The development of small molecule inhibitors of c-di-NMP signaling has significantly lagged behind. Recent developments in assays that allow for high-throughput screening of inhibitors suggest that the time is right for a concerted effort to identify inhibitors of these fascinating second messengers. Herein, we review c-di-NMP signaling and small molecules that have been developed to inhibit cyclic dinucleotide-related enzymes.
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Affiliation(s)
- Clement Opoku-Temeng
- Department of Chemistry, Center for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA.
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