1887

Abstract

The methionine salvage pathway (MSP) is critical for regeneration of -adenosyl--methionine (SAM), a widely used cofactor involved in many essential metabolic reactions. The MSP has been completely elucidated in aerobic organisms, and found to rely on molecular oxygen. Since anaerobic organisms do not use O, an alternative pathway(s) must be operating. We sought to evaluate whether the functions of two annotated MSP enzymes from , a methylthioinosine phosphorylase (MTIP) and a methylthioribose 1-phosphate isomerase (MTRI), are consistent with functioning in a modified anaerobic MSP (AnMSP). We show here that recombinant MTIP is active with six different purine nucleosides, consistent with its function as a general purine nucleoside phosphorylase for both AnMSP and purine salvage. Recombinant MTRI is active with both 5-methylthioribose 1-phosphate and 5-deoxyribose 1-phosphate as substrates, which are generated from phosphororolysis of 5′-methylthioinosine and 5′-deoxyinosine by MTIP, respectively. Together, these data suggest that MTIP and MTRI may function in a novel pathway for recycling the 5′-deoxyadenosine moiety of SAM in . These enzymes may also enable biosynthesis of 6-deoxy-5-ketofructose 1-phosphate (DKFP), an essential intermediate in aromatic amino acid biosynthesis. Finally, we utilized a homocysteine auxotrophic strain of (HcyAux) to identify potential AnMSP intermediates . Growth recovery experiments of the HcyAux were performed with known and proposed intermediates for the AnMSP. Only one metabolite, 2-keto-(4-methylthio)butyric acid, rescued growth of HcyAux in the absence of homocysteine. This observation may indicate that AnMSP pathways substantially differ among methanogens from phylogenetically divergent genera.

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2018-07-01
2024-04-19
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References

  1. Fontecave M, Atta M, Mulliez E. S-adenosylmethionine: nothing goes to waste. Trends Biochem Sci 2004; 29:243–249 [View Article][PubMed]
    [Google Scholar]
  2. Cantoni GL. Biological methylation: selected aspects. Annu Rev Biochem 1975; 44:435–451 [View Article][PubMed]
    [Google Scholar]
  3. Booker SJ, Grove TL. Mechanistic and functional versatility of radical SAM enzymes. F1000 Biol Rep 2010; 2:52 [View Article][PubMed]
    [Google Scholar]
  4. Bauerle MR, Schwalm EL, Booker SJ. Mechanistic diversity of radical S-adenosylmethionine (SAM)-dependent methylation. J Biol Chem 2015; 290:3995–4002 [View Article][PubMed]
    [Google Scholar]
  5. Hiscox MJ, Driesener RC, Roach PL. Enzyme catalyzed formation of radicals from S-adenosylmethionine and inhibition of enzyme activity by the cleavage products. Biochim Biophys Acta 2012; 1824:1165–1177 [View Article][PubMed]
    [Google Scholar]
  6. Kozbial PZ, Mushegian AR. Natural history of S-adenosylmethionine-binding proteins. BMC Struct Biol 2005; 5:19–44 [View Article][PubMed]
    [Google Scholar]
  7. Avila MA, García-Trevijano ER, Lu SC, Corrales FJ, Mato JM. Methylthioadenosine. Int J Biochem Cell Biol 2004; 36:2125–2130 [View Article][PubMed]
    [Google Scholar]
  8. Albers E. Metabolic characteristics and importance of the universal methionine salvage pathway recycling methionine from 5'-methylthioadenosine. IUBMB Life 2009; 61:1132–1142 [View Article][PubMed]
    [Google Scholar]
  9. Backlund PS, Smith RA. Methionine synthesis from 5'-methylthioadenosine in rat liver. J Biol Chem 1981; 256:1533–1535[PubMed]
    [Google Scholar]
  10. Shapiro SK, Schlenk F. Conversion of 5'-methylthioadenosine into S-adenosylmethionine by yeast cells. Biochim Biophys Acta 1980; 633:176–180 [View Article][PubMed]
    [Google Scholar]
  11. Nakano T, Saito Y, Yokota A, Ashida H. Plausible novel ribose metabolism catalyzed by enzymes of the methionine salvage pathway in Bacillus subtilis. Biosci Biotechnol Biochem 2013; 77:1104–1107 [View Article]
    [Google Scholar]
  12. Buckoreelall K, Sun Y, Hobrath JV, Wilson L, Parker WB. Identification of Rv0535 as methylthioadenosine phosphorylase from Mycobacterium tuberculosis. Tuberculosis 2012; 92:139–147 [View Article][PubMed]
    [Google Scholar]
  13. Saito Y, Ashida H, Kojima C, Tamura H, Matsumura H et al. Enzymatic characterization of 5-methylthioribose 1-phosphate isomerase from Bacillus subtilis. Biosci Biotechnol Biochem 2007; 71:2021–2028 [View Article][PubMed]
    [Google Scholar]
  14. Ashida H, Saito Y, Kojima C, Yokota A. Enzymatic characterization of 5-methylthioribulose-1-phosphate dehydratase of the methionine salvage pathway in Bacillus subtilis. Biosci Biotechnol Biochem 2008; 72:959–967 [View Article]
    [Google Scholar]
  15. Saito Y, Ashida H, Sakiyama T, de Marsac NT, Danchin A et al. Structural and functional similarities between a ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO)-like protein from Bacillus subtilis and photosynthetic RuBisCO. J Biol Chem 2009; 284:13256–13264 [View Article][PubMed]
    [Google Scholar]
  16. Myers RW, Wray JW, Fish S, Abeles RH. Purification and characterization of an enzyme involved in oxidative carbon-carbon bond cleavage reactions in the methionine salvage pathway of Klebsiella pneumoniae. J Biol Chem 1993; 268:24785–24791[PubMed]
    [Google Scholar]
  17. Dai Y, Wensink PC, Abeles RH. One protein, two enzymes. J Biol Chem 1999; 274:1193–1195 [View Article][PubMed]
    [Google Scholar]
  18. Backlund PS, Chang CP, Smith RA. Identification of 2-keto-4-methylthiobutyrate as an intermediate compound in methionine synthesis from 5'-methylthioadenosine. J Biol Chem 1982; 257:4196–4202[PubMed]
    [Google Scholar]
  19. Sekowska A, Dénervaud V, Ashida H, Michoud K, Haas D et al. Bacterial variations on the methionine salvage pathway. BMC Microbiol 2004; 4:9 [View Article][PubMed]
    [Google Scholar]
  20. Dey S, North JA, Sriram J, Evans BS, Tabita FR. In vivo studies in Rhodospirillum rubrum indicate that ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) catalyzes two obligatorily required and physiologically significant reactions for distinct carbon and sulfur metabolic pathways. J Biol Chem 2015; 290:30658–30668 [View Article][PubMed]
    [Google Scholar]
  21. North JA, Sriram J, Chourey K, Ecker CD, Sharma R et al. Metabolic regulation as a consequence of anaerobic 5-methylthioadenosine recycling in Rhodospirillum rubrum. mBio 2016; 7:e00855-16 [View Article][PubMed]
    [Google Scholar]
  22. Ashida H, Saito Y, Kojima C, Kobayashi K, Ogasawara N et al. A functional link between RuBisCO-like protein of Bacillus and photosynthetic RuBisCO. Science 2003; 302:286–290 [View Article][PubMed]
    [Google Scholar]
  23. Sato T, Atomi H, Imanaka T. Archaeal type III RuBisCOs function in a pathway for AMP metabolism. Science 2007; 315:1003–1006 [View Article][PubMed]
    [Google Scholar]
  24. Grochowski LL, Xu H, White RH. Methanocaldococcus jannaschii uses a modified mevalonate pathway for biosynthesis of isopentenyl diphosphate. J Bacteriol 2006; 188:3192–3198 [View Article][PubMed]
    [Google Scholar]
  25. North JA, Miller AR, Wildenthal JA, Young SJ, Tabita FR. Microbial pathway for anaerobic 5'-methylthioadenosine metabolism coupled to ethylene formation. Proc Natl Acad Sci USA 2017; 114:E10455E10464 [View Article][PubMed]
    [Google Scholar]
  26. Miller D, O'Brien K, Xu H, White RH. Identification of a 5'-deoxyadenosine deaminase in Methanocaldococcus jannaschii and its possible role in recycling the radical S-adenosylmethionine enzyme reaction product 5'-deoxyadenosine. J Bacteriol 2014; 196:1064–1072 [View Article][PubMed]
    [Google Scholar]
  27. Rauch BJ, Gustafson A, Perona JJ. Novel proteins for homocysteine biosynthesis in anaerobic microorganisms. Mol Microbiol 2014; 94:1330–1342 [View Article][PubMed]
    [Google Scholar]
  28. Davidson JG, Fiore PJ. A direct and efficient synthesis of 5′-deoxy-2′, 3′-. Nucleos Nucleot 1991; 10:1477–1483 [View Article]
    [Google Scholar]
  29. Graham DE, Xu H, White RH. Identification of coenzyme M biosynthetic phosphosulfolactate synthase: a new family of sulfonate-biosynthesizing enzymes. J Biol Chem 2002; 277:13421–13429 [View Article][PubMed]
    [Google Scholar]
  30. Kezmarsky ND, Xu H, Graham DE, White RH. Identification and characterization of a L-tyrosine decarboxylase in Methanocaldococcus jannaschii. Biochim Biophys Acta 2005; 1722:175–182 [View Article][PubMed]
    [Google Scholar]
  31. Bradford MM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 1976; 72:248–254 [View Article][PubMed]
    [Google Scholar]
  32. Miller D, Xu H, White RH. A new subfamily of agmatinases present in methanogenic Archaea is Fe(II) dependent. Biochemistry 2012; 51:3067–3078 [View Article][PubMed]
    [Google Scholar]
  33. Sober HA. Handbook of BiochemistrySelected Data for Molecular Biology Cleveland, OH: The Chemical Rubber Co; 1970
    [Google Scholar]
  34. Sowers KR, Boone JE, Gunsalus RP. Disaggregation of Methanosarcina spp. and growth as single cells at elevated osmolarity. Appl Environ Microbiol 1993; 59:3832–3839[PubMed]
    [Google Scholar]
  35. Metcalf WW, Zhang JK, Shi X, Wolfe RS. Molecular, genetic, and biochemical characterization of the serC gene of Methanosarcina barkeri Fusaro. J Bacteriol 1996; 178:5797–5802 [View Article][PubMed]
    [Google Scholar]
  36. Guss AM, Rother M, Zhang JK, Kulkarni G, Metcalf WW. New methods for tightly regulated gene expression and highly efficient chromosomal integration of cloned genes for Methanosarcina species. Archaea 2008; 2:193–203 [View Article][PubMed]
    [Google Scholar]
  37. Guan R, Ho MC, Almo SC, Schramm VL. Methylthioinosine phosphorylase from Pseudomonas aeruginosa. Structure and annotation of a novel enzyme in quorum sensing. Biochemistry 2011; 50:1247–1254 [View Article][PubMed]
    [Google Scholar]
  38. Friedmin M. Desoxyribose-1-phosphate. II. The isolation of crystalline desoxyribose-1-phosphate. J Biol Chem 1950; 184:449–460[PubMed]
    [Google Scholar]
  39. Erion MD, Takabayashi K, Smith HB, Kessi J, Wagner S et al. Purine nucleoside phosphorylase. 1. Structure-function studies. Biochemistry 1997; 36:11725–11734 [View Article][PubMed]
    [Google Scholar]
  40. Pugmire MJ, Ealick SE. Structural analyses reveal two distinct families of nucleoside phosphorylases. Biochem J 2002; 361:1–25 [View Article][PubMed]
    [Google Scholar]
  41. UniProt Consortium UniProt: a hub for protein information. Nucleic Acids Res 2015; 43: [View Article][PubMed]
    [Google Scholar]
  42. Shi W, Ting LM, Kicska GA, Lewandowicz A, Tyler PC et al. Plasmodium falciparum purine nucleoside phosphorylase: crystal structures, immucillin inhibitors, and dual catalytic function. J Biol Chem 2004; 279:18103–18106 [View Article][PubMed]
    [Google Scholar]
  43. Miller DV, Brown AM, Xu H, Bevan DR, White RH. Purine salvage in Methanocaldococcus jannaschii: elucidating the role of a conserved cysteine in adenine deaminase. Proteins 2016; 84:828–840 [View Article][PubMed]
    [Google Scholar]
  44. Tamura H, Saito Y, Ashida H, Inoue T, Kai Y et al. Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis: implications for catalytic mechanism. Protein Sci 2008; 17:126–135 [View Article][PubMed]
    [Google Scholar]
  45. Bumann M, Djafarzadeh S, Oberholzer AE, Bigler P, Altmann M et al. Crystal structure of yeast Ypr118w, a methylthioribose-1-phosphate isomerase related to regulatory eIF2B subunits. J Biol Chem 2004; 279:37087–37094 [View Article][PubMed]
    [Google Scholar]
  46. Fenn TD, Ringe D, Petsko GA. Xylose isomerase in substrate and inhibitor michaelis states: atomic resolution studies of a metal-mediated hydride shift. Biochemistry 2004; 43:6464–6474 [View Article][PubMed]
    [Google Scholar]
  47. Rose IA. Mechanism of the aldose-ketose isomerase reactions. Adv Enzymol Relat Areas Mol Biol 1975; 43:491–517[PubMed]
    [Google Scholar]
  48. White RH. L-aspartate semialdehyde and a 6-deoxy-5-ketohexose 1-phosphate are the precursors to the aromatic amino acids in Methanocaldococcus jannaschii. Biochemistry 2004; 43:7618–7627 [View Article][PubMed]
    [Google Scholar]
  49. Gulko MK, Dyall-Smith M, Gonzalez O, Oesterhelt D. How do haloarchaea synthesize aromatic amino acids?. PLoS One 2014; 9:e107475 [View Article][PubMed]
    [Google Scholar]
  50. Pittard J, Yang J. Biosynthesis of the aromatic amino acids. EcoSal Plus 2008; 3:1–75 [View Article]
    [Google Scholar]
  51. White RH, Xu H. Methylglyoxal is an intermediate in the biosynthesis of 6-deoxy-5-ketofructose-1-phosphate: a precursor for aromatic amino acid biosynthesis in Methanocaldococcus jannaschii. Biochemistry 2006; 45:12366–12379 [View Article][PubMed]
    [Google Scholar]
  52. Thornalley PJ. Pharmacology of methylglyoxal: formation, modification of proteins and nucleic acids, and enzymatic detoxification-a role in pathogenesis and antiproliferative chemotherapy. Gen Pharmacol 1996; 27:565–573 [View Article][PubMed]
    [Google Scholar]
  53. Misra K, Banerjee AB, Ray S, Ray M. Glyoxalase III from Escherichia coli: a single novel enzyme for the conversion of methylglyoxal into D-lactate without reduced glutathione. Biochem J 1995; 305:999–1003 [View Article][PubMed]
    [Google Scholar]
  54. Booth IR, Ferguson GP, Miller S, Li C, Gunasekera B et al. Bacterial production of methylglyoxal: a survival strategy or death by misadventure?. Biochem Soc Trans 2003; 31:1406–1408 [View Article][PubMed]
    [Google Scholar]
  55. Greig N, Wyllie S, Patterson S, Fairlamb AH. A comparative study of methylglyoxal metabolism in trypanosomatids. FEBS J 2009; 276:376–386 [View Article][PubMed]
    [Google Scholar]
  56. Richard JP. Acid-base catalysis of the elimination and isomerization reactions of triose phosphates. J Am Chem Soc 1984; 106:4926–4936 [View Article]
    [Google Scholar]
  57. Richard JP. Kinetic parameters for the elimination reaction catalyzed by triosephosphate isomerase and an estimation of the reaction's physiological significance. Biochemistry 1991; 30:4581–4585 [View Article][PubMed]
    [Google Scholar]
  58. Challand MR, Ziegert T, Douglas P, Wood RJ, Kriek M et al. Product inhibition in the radical S-adenosylmethionine family. FEBS Lett 2009; 583:1358–1362 [View Article][PubMed]
    [Google Scholar]
  59. Miller DV, Ruhlin M, Ray WK, Xu H, White RH. N5,N10 -methylenetetrahydromethanopterin reductase from Methanocaldococcus jannaschii also serves as a methylglyoxal reductase. FEBS Lett 2017; 591:2269–2278 [View Article][PubMed]
    [Google Scholar]
  60. Allen KD, Miller DV, Rauch BJ, Perona JJ, White RH. Homocysteine is biosynthesized from aspartate semialdehyde and hydrogen sulfide in methanogenic archaea. Biochemistry 2015; 54:3129–3132 [View Article][PubMed]
    [Google Scholar]
  61. Pajula RL, Raina A. Methylthioadenosine, a potent inhibitor of spermine synthase from bovine brain. FEBS Lett 1979; 99:343–345 [View Article][PubMed]
    [Google Scholar]
  62. Raina A, Tuomi K, Pajula RL. Inhibition of the synthesis of polyamines and macromolecules by 5'-methylthioadenosine and 5'-alkylthiotubercidins in BHK21 cells. Biochem J 1982; 204:697–703 [View Article][PubMed]
    [Google Scholar]
  63. Pirkov I, Norbeck J, Gustafsson L, Albers E. A complete inventory of all enzymes in the eukaryotic methionine salvage pathway. FEBS J 2008; 275:4111–4120 [View Article][PubMed]
    [Google Scholar]
  64. Allen KD, White RH. Occurrence and biosynthesis of 3-mercaptopropionic acid in Methanocaldococcus jannaschii. FEMS Microbiol Lett 2016; 363:fnw217 [View Article][PubMed]
    [Google Scholar]
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