The mycobacterial guaB1 gene encodes a guanosine 5'-monophosphate reductase with a cystathionine-β-synthase domain

. 2022 Sep ; 289 (18) : 5571-5598. [epub] 20220406

Jazyk angličtina Země Velká Británie, Anglie Médium print-electronic

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid35338694

Mycobacteria express enzymes from both the de novo and purine-salvage pathways. However, the regulation of these processes and the roles of individual metabolic enzymes have not been sufficiently detailed. Both Mycobacterium tuberculosis (Mtb) and Mycobacterium smegmatis (Msm) possess three guaB genes, but information is only available on guaB2, which encodes an essential inosine 5'-monophosphate dehydrogenase (IMPDH) involved in de novo purine biosynthesis. This study shows that guaB1, annotated in databases as a putative IMPDH, encodes a guanosine 5'-monophosphate reductase (GMPR), which recycles guanosine monophosphate to inosine monophosphate within the purine-salvage pathway and contains a cystathionine-β-synthase domain (CBS), which is essential for enzyme activity. GMPR activity is allosterically regulated by the ATP/GTP ratio in a pH-dependent manner. Bioinformatic analysis has indicated the presence of GMPRs containing CBS domains across the entire Actinobacteria phylum.

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el Kouni MH. Potential chemotherapeutic targets in the purine metabolism of parasites. Pharmacol Ther. 2003;99:283–309. PubMed

Malathi VG, Ramakrishnan T. Biosynthesis of nucleic acid purines in Mycobacterium tuberculosis H37rv. Biochem J. 1966;98:594–5970. PubMed PMC

Bandekar AC, Subedi S, Ioerger TR, Sassetti CM. Cell cycle‐associated expression patterns predict gene function in mycobacteria. Curr Biol. 2020;30:3961–71.e6. PubMed PMC

Keer J, Smeulders MJ, Williams HD. A purF mutant of Mycobacterium smegmatis has impaired survival during oxygen‐starved stationary phase. Microbiology (Reading). 2001;147:473–81. PubMed

Wheeler PR. Biosynthesis and scavenging of purines by pathogenic mycobacteria including Mycobacterium leprae . J Gen Microbiol. 1987;133:2999–3011. PubMed

Ducati RG, Breda A, Basso LA, Santos DS. Purine salvage pathway in Mycobacterium tuberculosis . Curr Med Chem. 2011;18:1258–75. PubMed

Cox JA, Mugumbate G, Del Peral LV, Jankute M, Abrahams KA, Jervis P, et al. Novel inhibitors of Mycobacterium tuberculosis GuaB2 identified by a target based high‐throughput phenotypic screen. Sci Rep. 2016;6:38986. PubMed PMC

Gollapalli DR, MacPherson IS, Liechti G, Gorla SK, Goldberg JB, Hedstrom L. Structural determinants of inhibitor selectivity in prokaryotic IMP dehydrogenases. Chem Biol. 2010;17:1084–91. PubMed PMC

Hedstrom L, Liechti G, Goldberg JB, Gollapalli DR. The antibiotic potential of prokaryotic IMP dehydrogenase inhibitors. Curr Med Chem. 2011;18:1909–18. PubMed PMC

Chacko S, Boshoff HIM, Singh V, Ferraris DM, Gollapalli DR, Zhang M, et al. Expanding benzoxazole‐based inosine 5'‐monophosphate dehydrogenase (IMPDH) inhibitor structure‐activity as potential antituberculosis agents. J Med Chem. 2018;61:4739–56. PubMed PMC

Chen L, Wilson DJ, Xu Y, Aldrich CC, Felczak K, Sham YY, et al. Triazole‐linked inhibitors of inosine monophosphate dehydrogenase from human and Mycobacterium tuberculosis . J Med Chem. 2010;53:4768–78. PubMed PMC

Juvale K, Shaik A, Kirubakaran S. Inhibitors of inosine 5'‐monophosphate dehydrogenase as emerging new generation antimicrobial agents. MedChemComm. 2019;10:1290–301. PubMed PMC

Makowska‐Grzyska M, Kim Y, Gorla SK, Wei Y, Mandapati K, Zhang M, et al. Mycobacterium tuberculosis IMPDH in complexes with substrates, products and antitubercular compounds. PLoS One. 2015;10:e0138976. PubMed PMC

Sahu NU, Singh V, Ferraris DM, Rizzi M, Kharkar PS. Hit discovery of Mycobacterium tuberculosis inosine 5'‐monophosphate dehydrogenase, GuaB2, inhibitors. Bioorg Med Chem Lett. 2018;28:1714–8. PubMed

Singh V, Donini S, Pacitto A, Sala C, Hartkoorn RC, Dhar N, et al. The inosine monophosphate dehydrogenase, GuaB2, is a vulnerable new bactericidal drug target for tuberculosis. ACS Infect Dis. 2017;3:5–17. PubMed PMC

Usha V, Gurcha SS, Lovering AL, Lloyd AJ, Papaemmanouil A, Reynolds RC, et al. Identification of novel diphenyl urea inhibitors of Mt‐GuaB2 active against Mycobacterium tuberculosis . Microbiology. 2011;157:290–9. PubMed

Sassetti CM, Boyd DH, Rubin EJ. Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol. 2003;48:77–84. PubMed

Sassetti CM, Boyd DH, Rubin EJ. Comprehensive identification of conditionally essential genes in mycobacteria. Proc Natl Acad Sci USA. 2001;98:12712–7. PubMed PMC

Hedstrom L. The dynamic determinants of reaction specificity in the IMPDH/GMPR family of (beta/alpha)(8) barrel enzymes. Crit Rev Biochem Mol Biol. 2012;47:250–63. PubMed PMC

Hedstrom L. IMP dehydrogenase: structure, mechanism and inhibition. Chem Rev. 2009;109:2903–28. PubMed PMC

Hedstrom L, Gan L. IMP dehydrogenase: structural schizophrenia and an unusual base. Curr Opin Chem Biol. 2006;10:520–5. PubMed

Ereno‐Orbea J, Oyenarte I, Alfonso Martinez‐Cruz L. CBS domains: ligand binding sites and conformational variability. Arch Biochem Biophys. 2013;540:70–81. PubMed

Nimmesgern E, Black J, Futer O, Fulghum JR, Chambers SP, Brummel CL, et al. Biochemical analysis of the modular enzyme inosine 5'‐monophosphate dehydrogenase. Protein Expr Purif. 1999;17:282–9. PubMed

Gan L, Petsko GA, Hedstrom L. Crystal structure of a ternary complex of Tritrichomonas foetus inosine 5'‐monophosphate dehydrogenase: NAD(+) orients the active site loop for catalysis. Biochemistry. 2002;41:13309–17. PubMed

Makowska‐Grzyska M, Kim Y, Maltseva N, Osipiuk J, Gu M, Zhang M, et al. A novel cofactor‐binding mode in bacterial IMP dehydrogenases explains inhibitor selectivity. J Biol Chem. 2015;290:5893–911. PubMed PMC

Pimkin M, Markham GD. The CBS subdomain of inosine 5'‐monophosphate dehydrogenase regulates purine nucleotide turnover. Mol Microbiol. 2008;68:342–59. PubMed PMC

Pimkin M, Pimkina J, Markham GD. A regulatory role of the bateman domain of IMP dehydrogenase in adenylate nucleotide biosynthesis. J Biol Chem. 2009;284:7960–9. PubMed PMC

Bessho T, Okada T, Kimura C, Shinohara T, Tomiyama A, Imamura A, et al. Novel characteristics of Trypanosoma brucei guanosine 5'‐monophosphate reductase distinct from host animals. PLoS Negl Trop Dis. 2016;10:e0004339. PubMed PMC

Sarwono AEY, Suganuma K, Mitsuhashi S, Okada T, Musinguzi SP, Shigetomi K, et al. Identification and characterization of guanosine 5'‐monophosphate reductase of Trypanosoma congolense as a drug target. Parasitol Int. 2017;66:537–44. PubMed

Smith S, Boitz J, Chidambaram ES, Chatterjee A, Ait‐Tihyaty M, Ullman B, et al. The cystathionine‐beta‐synthase domains on the guanosine 5'‐monophosphate reductase and inosine 5'‐monophosphate dehydrogenase enzymes from Leishmania regulate enzymatic activity in response to guanylate and adenylate nucleotide levels. Mol Microbiol. 2016;100:824–40. PubMed PMC

Imamura A, Okada T, Mase H, Otani T, Kobayashi T, Tamura M, et al. Allosteric regulation accompanied by oligomeric state changes of Trypanosoma brucei GMP reductase through cystathionine‐beta‐synthase domain. Nat Commun. 2020;11:1837. PubMed PMC

Magasanik B, Karibian D. Purine nucleotide cycles and their metabolic role. J Biol Chem. 1960;235:2672–81. PubMed

Patton GC, Stenmark P, Gollapalli DR, Sevastik R, Kursula P, Flodin S, et al. Cofactor mobility determines reaction outcome in the IMPDH and GMPR (beta‐alpha)8 barrel enzymes. Nat Chem Biol. 2011;7:950–8. PubMed PMC

Endo T, Uratani B, Freese E. Purine salvage pathways of Bacillus subtilis and effect of guanine on growth of GMP reductase mutants. J Bacteriol. 1983;155:169–79. PubMed PMC

Benson CE, Gots JS. Regulation of GMP reductase in Salmonella typhimurium . Biochim Biophys Acta. 1975;403:47–57. PubMed

Kessler AI, Gots JS. Regulation of guaC expression in Escherichia coli . J Bacteriol. 1985;164:1288–93. PubMed PMC

Griffin JE, Gawronski JD, Dejesus MA, Ioerger TR, Akerley BJ, Sassetti CM. High‐resolution phenotypic profiling defines genes essential for mycobacterial growth and cholesterol catabolism. PLoS Pathog. 2011;7:e1002251. PubMed PMC

DeJesus MA, Gerrick ER, Xu W, Park SW, Long JE, Boutte CC, et al. Comprehensive essentiality analysis of the Mycobacterium tuberculosis genome via saturating transposon mutagenesis. MBio. 2017;8:e02133‐16. PubMed PMC

Minato Y, Gohl DM, Thiede JM, Chacon JM, Harcombe WR, Maruyama F, et al. Genomewide assessment of Mycobacterium tuberculosis conditionally essential metabolic pathways. mSystems. 2019;4:e00070‐19. PubMed PMC

Rao M, Streur TL, Aldwell FE, Cook GM. Intracellular pH regulation by Mycobacterium smegmatis and Mycobacterium bovis BCG. Microbiology (Reading). 2001;147:1017–24. PubMed

Vandal OH, Roberts JA, Odaira T, Schnappinger D, Nathan CF, Ehrt S. Acid‐susceptible mutants of Mycobacterium tuberculosis share hypersusceptibility to cell wall and oxidative stress and to the host environment. J Bacteriol. 2009;191:625–31. PubMed PMC

Zhang Y, Scorpio A, Nikaido H, Sun Z. Role of acid pH and deficient efflux of pyrazinoic acid in unique susceptibility of Mycobacterium tuberculosis to pyrazinamide. J Bacteriol. 1999;181:2044–9. PubMed PMC

Knejzlik Z, Herkommerova K, Pichova I. Catabolism of 8‐oxo‐purines is mainly routed via the guanine to xanthine interconversion pathway in Mycobacterium smegmatis . Tuberculosis. 2019;119:101879. PubMed

Knejzlik Z, Herkommerova K, Hockova D, Pichova I. Hypoxanthine‐guanine phosphoribosyltransferase is dispensable for Mycobacterium smegmatis viability. J Bacteriol. 2020;202:e00710‐19. PubMed PMC

Zbornikova E, Knejzlik Z, Hauryliuk V, Krasny L, Rejman D. Analysis of nucleotide pools in bacteria using HPLC‐MS in HILIC mode. Talanta. 2019;205:120161. PubMed

Buey RM, Ledesma‐Amaro R, Velazquez‐Campoy A, Balsera M, Chagoyen M, de Pereda JM, et al. Guanine nucleotide binding to the bateman domain mediates the allosteric inhibition of eukaryotic IMP dehydrogenases. Nat Commun. 2015;6:8923. PubMed PMC

Johnson MC, Kollman JM. Cryo‐EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation. Elife. 2020;9:e53243. PubMed PMC

Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, et al. Experimental and computational assessment of conditionally essential genes in Escherichia coli . J Bacteriol. 2006;188:8259–71. PubMed PMC

Kobayashi K, Ehrlich SD, Albertini A, Amati G, Andersen KK, Arnaud M, et al. Essential Bacillus subtilis genes. Proc Natl Acad Sci USA. 2003;100:4678–83. PubMed PMC

Salama NR, Shepherd B, Falkow S. Global transposon mutagenesis and essential gene analysis of Helicobacter pylori . J Bacteriol. 2004;186:7926–35. PubMed PMC

Le Breton Y, Belew AT, Valdes KM, Islam E, Curry P, Tettelin H, et al. Essential genes in the core genome of the human pathogen Streptococcus pyogenes . Sci Rep. 2015;5:9838. PubMed PMC

Deng Y, Wang Z, Ying K, Gu S, Ji C, Huang Y, et al. NADPH‐dependent GMP reductase isoenzyme of human (GMPR2). Expression, purification, and kinetic properties. Int J Biochem Cell Biol. 2002;34:1035–50. PubMed

Martinelli LK, Ducati RG, Rosado LA, Breda A, Selbach BP, Santos DS, et al. Recombinant Escherichia coli GMP reductase: kinetic, catalytic and chemical mechanisms, and thermodynamics of enzyme‐ligand binary complex formation. Mol Biosyst. 2011;7:1289–305. PubMed

Mitchell A, Sin IL, Finch LR. Enzymes of purine metabolism in Mycoplasma mycoides subsp. mycoides . J Bacteriol. 1978;134:706–12. PubMed PMC

Spector T, Jones TE, Miller RL. Reaction mechanism and specificity of human GMP reductase. Substrates, inhibitors, activators, and inactivators. J Biol Chem. 1979;254:2308–15. PubMed

Heyde E, Nagabhushanam A, Vonarx M, Morrison JF. Studies on inosine monophosphate dehydrogenase – steady‐state kinetics. Biochim Biophys Acta. 1976;429:645–60. PubMed

Kerr KM, Cahoon M, Bosco DA, Hedstrom L. Monovalent cation activation in Escherichia coli inosine 5'‐monophosphate dehydrogenase. Arch Biochem Biophys. 2000;375:131–7. PubMed

Riera TV, Zheng L, Josephine HR, Min D, Yang W, Hedstrom L. Allosteric activation via kinetic control: potassium accelerates a conformational change in IMP dehydrogenase. Biochemistry. 2011;50:8508–18. PubMed PMC

Rostirolla DC, Milech de Assunção T, Bizarro CV, Basso LA, Santos DS. Biochemical characterization of Mycobacterium tuberculosis IMP dehydrogenase: kinetic mechanism, metal activation and evidence of a cooperative system. RSC Adv. 2014;4:26271–87.

Xiang BS, Taylor JC, Markham GD. Monovalent cation activation and kinetic mechanism of inosine 5'‐monophosphate dehydrogenase. J Biol Chem. 1996;271:1435–40. PubMed

Stephens RW, Whittaker VK. Calf thymus GMP reductase: control by XMP. Biochem Biophys Res Commun. 1973;53:975–81. PubMed

Goldbeck O, Eck AW, Seibold GM. Real time monitoring of NADPH concentrations in Corynebacterium glutamicum and Escherichia coli via the genetically encoded sensor mBFP. Front Microbiol. 2018;9:2564. PubMed PMC

Vandal OH, Pierini LM, Schnappinger D, Nathan CF, Ehrt S. A membrane protein preserves intrabacterial pH in intraphagosomal Mycobacterium tuberculosis . Nat Med. 2008;14:849–54. PubMed PMC

Darby CM, Ingolfsson HI, Jiang X, Shen C, Sun M, Zhao N, et al. Whole cell screen for inhibitors of pH homeostasis in Mycobacterium tuberculosis . PLoS One. 2013;8:e68942. PubMed PMC

Peterson ND, Rosen BC, Dillon NA, Baughn AD. Uncoupling environmental pH and intrabacterial acidification from pyrazinamide susceptibility in Mycobacterium tuberculosis . Antimicrob Agents Chemother. 2015;59:7320–6. PubMed PMC

Morimoto YV, Kami‐Ike N, Miyata T, Kawamoto A, Kato T, Namba K, et al. High‐resolution pH imaging of living bacterial cells to detect local pH differences. MBio. 2016;7:e01911‐16. PubMed PMC

Lu P, Haagsma AC, Pham H, Maaskant JJ, Mol S, Lill H, et al. Pyrazinoic acid decreases the proton motive force, respiratory ATP synthesis activity, and cellular ATP levels. Antimicrob Agents Chemother. 2011;55:5354–7. PubMed PMC

Gengenbacher M, Rao SPS, Pethe K, Dick T. Nutrient‐starved, non‐replicating Mycobacterium tuberculosis requires respiration, ATP synthase and isocitrate lyase for maintenance of ATP homeostasis and viability. Microbiology (Reading). 2010;156:81–7. PubMed

Rao SP, Alonso S, Rand L, Dick T, Pethe K. The protonmotive force is required for maintaining ATP homeostasis and viability of hypoxic, nonreplicating Mycobacterium tuberculosis . Proc Natl Acad Sci USA. 2008;105:11945–50. PubMed PMC

Patil V, Jain V. Insights into the physiology and metabolism of a mycobacterial cell in an energy‐compromised state. J Bacteriol. 2019;201:e00210‐19. PubMed PMC

Lamprecht DA, Finin PM, Rahman MA, Cumming BM, Russell SL, Jonnala SR, et al. Turning the respiratory flexibility of Mycobacterium tuberculosis against itself. Nat Commun. 2016;7:12393. PubMed PMC

Dutta NK, Klinkenberg LG, Vazquez MJ, Segura‐Carro D, Colmenarejo G, Ramon F, et al. Inhibiting the stringent response blocks Mycobacterium tuberculosis entry into quiescence and reduces persistence. Sci Adv. 2019;5:eaav2104. PubMed PMC

Shenkerman Y, Elharar Y, Vishkautzan M, Gur E. Efficient and simple generation of unmarked gene deletions in Mycobacterium smegmatis . Gene. 2014;533:374–8. PubMed

Arnold FM, Hohl M, Remm S, Koliwer‐Brandl H, Adenau S, Chusri S, et al. A uniform cloning platform for mycobacterial genetics and protein production. Sci Rep. 2018;8:9539. PubMed PMC

Ehrt S, Guo XV, Hickey CM, Ryou M, Monteleone M, Riley LW, et al. Controlling gene expression in mycobacteria with anhydrotetracycline and Tet repressor. Nucleic Acids Res. 2005;33:e21. PubMed PMC

Studier FW. Stable expression clones and auto‐induction for protein production in E. coli . Methods Mol Biol. 2014;1091:17–32. PubMed

Wojdyr Marcin. Fityk: a general‐purpose peak fitting program. J Appl Crystallogr. 2010;43:1126–8.

Mueller U, Forster R, Hellmig M, Huschmann FU, Kastner A, Malecki P, et al. The macromolecular crystallography beamlines at BESSY II of the Helmholtz‐Zentrum Berlin: current status and perspectives. Eur Phys J Plus. 2015;130:141.

Kabsch W. XDS. Acta Crystallogr D Biol Crystallogr. 2010;66:125–32. PubMed PMC

Krug M, Weiss MS, Heinemann U, Mueller U. XDSAPP: a graphical user interface for the convenient processing of diffraction data using XDS. J Appl Crystallogr. 2012;45:568–72.

Zhang RG, Evans G, Rotella FJ, Westbrook EM, Beno D, Huberman E, et al. Characteristics and crystal structure of bacterial inosine‐5'‐monophosphate dehydrogenase. Biochemistry. 1999;38:4691–700. PubMed

Emsley P, Lohkamp B, Scott WG, Cowtan K. Features and development of Coot. Acta Crystallogr D Biol Crystallogr. 2010;66:486–501. PubMed PMC

Afonine PV, Grosse‐Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr. 2012;68:352–67. PubMed PMC

Liebschner D, Afonine PV, Baker ML, Bunkoczi G, Chen VB, Croll TI, et al. Macromolecular structure determination using X‐rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr D Struct Biol. 2019;75:861–77. PubMed PMC

Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis LN, et al. MolProbity: more and better reference data for improved all‐atom structure validation. Protein Sci. 2018;27:293–315. PubMed PMC

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10. PubMed

Yang M, Derbyshire MK, Yamashita RA, Marchler‐Bauer A. NCBI's conserved domain database and tools for protein domain analysis. Curr Protoc Bioinformatics. 2020;69:e90. PubMed PMC

Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, et al. Phylogeny.fr: robust phylogenetic analysis for the non‐specialist. Nucleic Acids Res. 2008;36:W465–9. PubMed PMC

Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7. PubMed PMC

Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000;17:540–52. PubMed

Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003;52:696–704. PubMed

Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021;49:W293–6. PubMed PMC

Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, et al. InterProScan 5: genome‐scale protein function classification. Bioinformatics. 2014;30:1236–40. PubMed PMC

Anisimova M, Gascuel O. Approximate likelihood‐ratio test for branches: a fast, accurate, and powerful alternative. Syst Biol. 2006;55:539–52. PubMed

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RefSeq
ABK74721, ABK69632, ABK75325

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