Novel Formaldehyde-activating Enzyme in Methylobacterium Extorquens AM1 Required for Growth on Methanol

Overview

Journal J Bacteriol

Publisher American Society for Microbiology

Specialty Microbiology

Date 2000 Nov 14

PMID 11073907

Citations 82

Authors

J A Vorholt

C J Marx

M E Lidstrom

R K Thauer

Affiliations

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Abstract

Formaldehyde is toxic for all organisms from bacteria to humans due to its reactivity with biological macromolecules. Organisms that grow aerobically on single-carbon compounds such as methanol and methane face a special challenge in this regard because formaldehyde is a central metabolic intermediate during methylotrophic growth. In the alpha-proteobacterium Methylobacterium extorquens AM1, we found a previously unknown enzyme that efficiently catalyzes the removal of formaldehyde: it catalyzes the condensation of formaldehyde and tetrahydromethanopterin to methylene tetrahydromethanopterin, a reaction which also proceeds spontaneously, but at a lower rate than that of the enzyme-catalyzed reaction. Formaldehyde-activating enzyme (Fae) was purified from M. extorquens AM1 and found to be one of the major proteins in the cytoplasm. The encoding gene is located within a cluster of genes for enzymes involved in the further oxidation of methylene tetrahydromethanopterin to CO(2). Mutants of M. extorquens AM1 defective in Fae were able to grow on succinate but not on methanol and were much more sensitive toward methanol and formaldehyde. Uncharacterized orthologs to this enzyme are predicted to be encoded by uncharacterized genes from archaea, indicating that this type of enzyme occurs outside the methylotrophic bacteria.

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References

Hagemeier C, Chistoserdova L, Lidstrom M, Thauer R, Vorholt J . Characterization of a second methylene tetrahydromethanopterin dehydrogenase from Methylobacterium extorquens AM1. Eur J Biochem. 2000; 267(12):3762-9. DOI: 10.1046/j.1432-1327.2000.01413.x. View

Kawarabayasi Y, Sawada M, Horikawa H, Haikawa Y, Hino Y, Yamamoto S . Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3 (supplement). DNA Res. 1998; 5(2):147-55. DOI: 10.1093/dnares/5.2.147. View

Breitung J, Borner G, Scholz S, Linder D, Stetter K, Thauer R . Salt dependence, kinetic properties and catalytic mechanism of N-formylmethanofuran:tetrahydromethanopterin formyltransferase from the extreme thermophile Methanopyrus kandleri. Eur J Biochem. 1992; 210(3):971-81. DOI: 10.1111/j.1432-1033.1992.tb17502.x. View

Grafstrom R, Fornace Jr A, Autrup H, Lechner J, Harris C . Formaldehyde damage to DNA and inhibition of DNA repair in human bronchial cells. Science. 1983; 220(4593):216-8. DOI: 10.1126/science.6828890. View

Yasueda H, Kawahara Y, Sugimoto S . Bacillus subtilis yckG and yckF encode two key enzymes of the ribulose monophosphate pathway used by methylotrophs, and yckH is required for their expression. J Bacteriol. 1999; 181(23):7154-60. PMC: 103674. DOI: 10.1128/JB.181.23.7154-7160.1999. View

Escalante-Semerena J, Rinehart Jr K, WOLFE R . Tetrahydromethanopterin, a carbon carrier in methanogenesis. J Biol Chem. 1984; 259(15):9447-55. View

Pomper B, Vorholt J, Chistoserdova L, Lidstrom M, Thauer R . A methenyl tetrahydromethanopterin cyclohydrolase and a methenyl tetrahydrofolate cyclohydrolase in Methylobacterium extorquens AM1. Eur J Biochem. 1999; 261(2):475-80. DOI: 10.1046/j.1432-1327.1999.00291.x. View

Mitsui R, Sakai Y, Yasueda H, Kato N . A novel operon encoding formaldehyde fixation: the ribulose monophosphate pathway in the gram-positive facultative methylotrophic bacterium Mycobacterium gastri MB19. J Bacteriol. 2000; 182(4):944-8. PMC: 94368. DOI: 10.1128/JB.182.4.944-948.2000. View

Case G, Benevenga N . Significance of formate as an intermediate in the oxidation of the methionine, S-methyl-L-cysteine and sarcosine methyl carbons to CO2 in the rat. J Nutr. 1977; 107(9):1665-76. DOI: 10.1093/jn/107.9.1665. View

10.

Bult C, White O, Olsen G, Zhou L, Fleischmann R, Sutton G . Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science. 1996; 273(5278):1058-73. DOI: 10.1126/science.273.5278.1058. View

11.

Vorholt J, Chistoserdova L, Stolyar S, Thauer R, Lidstrom M . Distribution of tetrahydromethanopterin-dependent enzymes in methylotrophic bacteria and phylogeny of methenyl tetrahydromethanopterin cyclohydrolases. J Bacteriol. 1999; 181(18):5750-7. PMC: 94096. DOI: 10.1128/JB.181.18.5750-5757.1999. View

12.

Kaesler B, Schonheit P . The role of sodium ions in methanogenesis. Formaldehyde oxidation to CO2 and 2H2 in methanogenic bacteria is coupled with primary electrogenic Na+ translocation at a stoichiometry of 2-3 Na+/CO2. Eur J Biochem. 1989; 184(1):223-32. DOI: 10.1111/j.1432-1033.1989.tb15010.x. View

13.

Karrasch M, Borner G, Enssle M, Thauer R . Formylmethanofuran dehydrogenase from methanogenic bacteria, a molybdoenzyme. FEBS Lett. 1989; 253(1-2):226-30. DOI: 10.1016/0014-5793(89)80964-0. View

14.

Kallen R, Jencks W . The dissociation constants of tetrahydrofolic acid. J Biol Chem. 1966; 241(24):5845-50. View

15.

Fulton G, Nunn D, Lidstrom M . Molecular cloning of a malyl coenzyme A lyase gene from Pseudomonas sp. strain AM1, a facultative methylotroph. J Bacteriol. 1984; 160(2):718-23. PMC: 214796. DOI: 10.1128/jb.160.2.718-723.1984. View

16.

Bradford M . A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976; 72:248-54. DOI: 10.1016/0003-2697(76)90527-3. View

17.

Schonheit P, Moll J, Thauer R . Nickel, cobalt, and molybdenum requirement for growth of Methanobacterium thermoautotrophicum. Arch Microbiol. 1979; 123(1):105-7. DOI: 10.1007/BF00403508. View

18.

Vieira J, Messing J . Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985; 33(1):103-19. DOI: 10.1016/0378-1119(85)90120-9. View

19.

Kallen R, Jencks W . Equilibria for the reaction of amines with formaldehyde and protons in aqueous solution. A re-examination of the formol titration. J Biol Chem. 1966; 241(24):5864-78. View

20.

Reizer J, Reizer A, Saier M . Is the ribulose monophosphate pathway widely distributed in bacteria?. Microbiology (Reading). 1997; 143 ( Pt 8):2519-2520. DOI: 10.1099/00221287-143-8-2519. View