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Volume 148, Issue 11

Molecular analysis of the soluble butane monooxygenase from ‘’

aThe GenBank accession number for the sequence is AY093933.

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Abstract

‘’ is capable of growth with butane via the oxidation of butane to 1-butanol, which is catalysed by a soluble butane monooxygenase (sBMO). oxidation of ethylene (an alternative substrate for sBMO) was reconstituted in the soluble portion of cell extracts and was NADH-dependent. Butane monooxygenase was separated into three components which were obligately required for substrate oxidation. The N-terminal sequences of the peptides associated with butane monooxygenase led to the cloning and sequencing of the 5797 nucleotide gene cluster. Comparisons of the deduced amino acid sequences with other multicomponent monooxygenases suggest that sBMO is a multimeric hydroxylase with 61, 45 and 19 kDa subunits encoded by , a 40 kDa oxidoreductase encoded by , and a 15 kDa regulatory protein encoded by . A sixth structural gene () encodes a 96 kDa protein with similarity exclusively to (), a putative metal centre assembly protein of the soluble methane monooxygenases. Insertional inactivation of resulted in a mutant ‘’ strain incapable of growth with butane. A putative promoter element characteristic of promoters associated with σ-dependent transcription initiation was located upstream of the genes. Expression of all six genes was detected in butane-induced cells. Butane monooxygenase from ‘’ aligns most closely with non-haem carboxylate-bridged diiron monooxygenases and, moreover, contains the characteristic iron-binding motif. The structural and mechanistic implications of the high sequence identity (up to 64%) between the peptides of butane monooxygenase and methane monooxygenases are discussed.

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Keyword(s): alkane oxidation , BMOB, butane monooxygenase regulatory protein , BMOD, bmoD gene product , BMOH, butane monooxygenase hydroxylase , BMOR, butane monooxygenase reductase , butane metabolism , diiron monooxygenase , MMOB, methane monooxygenase regulatory protein , MMOD, mmoD (orfY) gene product , MMOH, methane monooxygenase hydroxylase , MMOR, methane monooxygenase reductase , pMMO, particulate methane monooxygenase , sBMO, soluble butane monooxygenase and sMMO, soluble methane monooxygenase
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References

  1. Altschul S. F, Madden T. L, Schaffer A. A, Zhang J, Zhang Z, Miller W., Lipman D. J. 1997; Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
     [Google Scholar]
  2. Anzai Y, Kim H, Park J. Y, Wakabayashi H., Oyaizu H. 2000; Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int J Syst Evol Microbiol 50:1563–1589
     [Google Scholar]
  3. Arp D. J. 1999; Butane metabolism by butane-grown Pseudomonas butanovora . Microbiology 145:1173–1180
     [Google Scholar]
  4. Arp D. J, Yeager C. M., Hyman M. R. 2001; Molecular and cellular fundamentals of aerobic cometabolism of trichloroethylene. Biodegradation 12:81–103
     [Google Scholar]
  5. Ashraf W, Mihdhir A., Murrell J. C. 1994; Bacterial oxidation of propane. FEMS Microbiol Lett 122:1–6
     [Google Scholar]
  6. Barrios H, Valderrama B., Morett E. 1999; Compilation and analysis of sigma(54)-dependent promoter sequences. Nucleic Acids Res 27:4305–4313
     [Google Scholar]
  7. Cardy D. L. N, Laidler V, Salmond G. P. C., Murrell J. C. 1991; Molecular analysis of the methane monooxygenase (MMO) gene cluster of Methylosinus trichosporium OB3b. Mol Microbiol 5:335–342
     [Google Scholar]
  8. Chang S. L, Wallar B. J, Lipscomb J. D., Mayo K. H. 2001; Residues in Methylosinus trichosporium OB3b methane monooxygenase component B involved in molecular interactions with reduced- and oxidized-hydroxylase component: a role for the N-terminus. Biochemistry 40:9539–9551
     [Google Scholar]
  9. Colby J., Dalton H. 1978; Resolution of the methane monooxygenase of Methylococcus capsulatus (Bath) into three components. Purification and properties of component C, a flavoprotein. Biochem J 171:461–468
     [Google Scholar]
  10. Coufal D. E, Blazyk J. L, Whittington D. A, Wu W. W, Rosenzweig A. C., Lippard S. J. 2000; Sequencing and analysis of the Methylococcus capsulatus (Bath) soluble methane monooxygenase genes. Eur J Biochem 267:2174–2185
     [Google Scholar]
  11. Dewitt J. G, Bentsen J. G, Rosenzweig A. C. 7 other authors 1991; X-ray absorption, Mossbauer, and EPR studies of the dinuclear iron center in the hydroxylase component of methane monooxygenase. J Am Chem Soc 113:9219–9235
     [Google Scholar]
  12. Elango N, Radhakrishnan R, Froland W. A, Wallar B. J, Earhart C. A, Lipscomb J. D., Ohlendorf D. H. 1997; Crystal structure of the hydroxylase component of methane monooxygenase from Methylosinus trichosporium OB3b. Protein Sci 6:556–568
     [Google Scholar]
  13. Fox B, Froland W, Dege J., Lipscomb J. 1989; Methane monooxygenase from Methylosinus trichosporium OB3b. Purification and properties of a three-component system with high specific activity from a type II methanotroph. J Biol Chem 264:10023–10033
     [Google Scholar]
  14. Gassner G. T., Lippard S. J. 1999; Component interactions in the soluble methane monooxygenase system from Methylococcus capsulatus (Bath). Biochemistry 38:12768–12785
     [Google Scholar]
  15. Gornall A. G, Bardawill C. J., David M. M. 1949; Determination of serum proteins by means of the Biuret reaction. J Biol Chem 177:751–766
     [Google Scholar]
  16. Green J., Dalton H. 1985; Protein B of soluble methane monooxygenase from Methylococcus capsulatus (Bath). J Biol Chem 260:15795–15801
     [Google Scholar]
  17. Green J., Dalton H. 1989; Substrate specificity of soluble methane monooxygenase. Mechanistic implications. J Biol Chem 264:17698–17703
     [Google Scholar]
  18. Grosse S, Laramee L, Wendlandt K. D, McDonald I. R, Miguez C. B., Kleber H. P. 1999; Purification and characterization of the soluble methane monooxygenase of the type II methanotrophic bacterium Methylocysti s sp. strain WI 14. Appl Environ Microbiol 65:3929–3935
     [Google Scholar]
  19. Hamamura N, Page C, Long T, Semprini L., Arp D. J. 1997; Chloroform cometabolism by butane-grown CF8, Pseudomonas butanovora , and Mycobacterium vaccae JOB5 and methane-grown Methylosinus trichosporium OB3b. Appl Environ Microbiol 63:3607–3613
     [Google Scholar]
  20. Hamamura N, Storfa R. T, Semprini L., Arp D. J. 1999; Diversity in butane monooxygenases among butane-grown bacteria. Appl Environ Microbiol 65:4586–4593
     [Google Scholar]
  21. Hamamura N, Yeager C. M., Arp D. J. 2001; Two distinct monooxygenases for alkane oxidation in Nocardioides sp. strain CF8. Appl Environ Microbiol 67:4992–4998
     [Google Scholar]
  22. Hemmi H, Studts J. M, Chae Y. K, Song J, Markley J. L., Fox B. G. 2001; Solution structure of the toluene 4-monooxygenase effector protein (T4moD. Biochemistry 40:3512–3524
     [Google Scholar]
  23. Hyman M. R., Wood P. M. 1985; Suicidal inactivation and labeling of ammonia monooxygenase by acetylene. Biochem J 227:719–725
     [Google Scholar]
  24. Johnson G. R., Olsen R. H. 1995; Nucleotide sequence analysis of genes encoding toluene/benzene-2-monooxygenase from Pseudomonas sp. strain JS150. Appl Environ Microbiol 61:3336–3346
     [Google Scholar]
  25. Kok M, Oldenhuis R, van der Linden M. P. G, Raatjes P, Kingma J, van Lelyveld P. H., Witholt B. 1989; The Pseudomonas oleovorans alkane hydroxylase gene. Sequence and expression. J Biol Chem 264:5435–5441
     [Google Scholar]
  26. Kokotek W., Lotz W. 1989; Construction of a lacZ -kanamycin-resistance cassette, useful for site-directed mutagenesis and as a promoter probe. Gene 84:467–471
     [Google Scholar]
  27. Laemmli U. K. 1970; Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680–685
     [Google Scholar]
  28. Lelong C, Setif P, Bottin H, Andre F., Neumann J. M. 1995; 1H and 15N NMR sequential assignment, secondary structure, and tertiary fold of [2Fe-2S] ferredoxin from Synechocystis sp.PCC 6803. Biochemistry 34:14462–14473
     [Google Scholar]
  29. Lipscomb J. D. 1994; Biochemistry of the soluble methane monooxygenase. Annu Rev Microbiol 48:371–399
     [Google Scholar]
  30. Liu Y, Nesheim J. C, Lee S.-K., Lipscomb J. D. 1995; Gating effects of component B on oxygen activation by the methane monooxygenase hydroxylase component. J Biol Chem 270:24662–24665
     [Google Scholar]
  31. Lloyd J. S, Bhambra A, Murrell J. C., Dalton H. 1997; Inactivation of the regulatory protein B of soluble methane monooxygenase from Methylococcus capsulatus (Bath) by proteolysis can be overcome by a Gly to Gln modification. Eur J Biochem 248:72–79
     [Google Scholar]
  32. McDonald I. R, Uchiyama H, Kambe S, Yagi O., Murrell J. C. 1997; The soluble methane monooxygenase gene cluster of the trichloroethylene-degrading methanotroph Methylocystis sp. strain M. Appl Environ Microbiol 63:1898–1904
     [Google Scholar]
  33. McKenna E. V., Coon M. J. 1970; Enzymatic ω-oxidation. IV. Purification and properties of the ω-hydroxylase of Pseudomonas oleovorans . J Biol Chem 245:3882–3889
     [Google Scholar]
  34. Merkx M., Lippard S. J. 2002; Why OrfY?. Characterization of MMOD, a long overlooked component of the soluble methane monooxygenase from Methylococcus capsulatus (Bath). J Biol Chem 277:5858–5865
     [Google Scholar]
  35. Merkx M, Kopp D. A, Sazinsky M. H, Blazyk J. L, Muller J., Lippard S. J. 2001; Dioxygen activation and methane hydroxylation by soluble methane monooxygenase: a tale of two irons and three proteins. Angew Chem Int Ed Engl 40:2782–2807
     [Google Scholar]
  36. Miura A., Dalton H. 1995; Purification and characterization of the alkene monooxygenase from Nocardia corallina B-276. Biosci Biotechnol Biochem 59:853–859
     [Google Scholar]
  37. Muller J, Lugovskoy A. A, Wagner G., Lippard S. J. 2002; NMR structure of the [2Fe-2S] ferredoxin domain from soluble methane monooxygenase reductase and interaction with its hydroxylase. Biochemistry 41:42–51
     [Google Scholar]
  38. Murray N. E, Brammar W. J., Murray K. 1977; Lambdoid phages that simplify the recovery of in vitro recombinants. Mol Gen Genet 150:53–61
     [Google Scholar]
  39. Murrell J. C, McDonald I. R., Gilbert B. 2000; Regulation of expression of methane monooxygenases by copper ions. Trends Microbiol 8:221–225
     [Google Scholar]
  40. Newman L. M., Wackett L. P. 1995; Purification and characterization of toluene 2-monooxygenase from Burkholderia cepacia G4. Biochemistry 34:14066–14076
     [Google Scholar]
  41. Nielsen A. K, Gerdes K, Degn H., Murrell J. C. 1996; Regulation of bacterial methane oxidation: transcription of the soluble methane mono-oxygenase operon of Methylococcus capsulatus (Bath) is repressed by copper ions. Microbiology 142:1289–1296
     [Google Scholar]
  42. Nielsen A. K, Gerdes K., Murrell J. C. 1997; Copper-dependent reciprocal transcriptional regulation of methane monooxygenase genes in Methylococcus capsulatus and Methylosinus trichosporium . Mol Microbiol 25:399–409
     [Google Scholar]
  43. Nordlund I, Powlowski J., Shingler V. 1990; Complete nucleotide sequence and polypeptide analysis of multicomponent phenol hydroxylase from Pseudomonas sp. strain CF600. J Bacteriol 172:6826–6833
     [Google Scholar]
  44. Nordlund P, Dalton H., Eklund H. 1992; The active site structure of methane monooxygenase is closely related to the binuclear iron center of ribonucleotide reductase. FEBS Lett 307:257–262
     [Google Scholar]
  45. Padda R. S, Pandey K. K, Kaul S, Nair V. D, Jain R. K, Basu S. K., Chakrabarti T. 2001; A novel gene encoding a 54 kDa polypeptide is essential for butane utilization by Pseudomonas sp. IMT37. Microbiology 147:2479–2491
     [Google Scholar]
  46. Pikus J. D, Studts J. M, Achim C, Kauffmann K. E, Munck E, Steffan R. J, McClay K., Fox B. G. 1996; Recombinant toluene-4-monooxygenase: catalytic and Mossbauer studies of the purified diiron and Rieske components of a four-protein complex. Biochemistry 35:9106–9119
     [Google Scholar]
  47. Powlowski J., Shingler V. 1990; In vitro analysis of polypeptide requirements of multicomponent phenol hydroxylase from Pseudomonas sp. strain CF600. J Bacteriol 172:6834–6840
     [Google Scholar]
  48. Powlowski J, Sealy J, Shingler V., Cadieux E. 1997; On the role of DmpK, an auxiliary protein associated with multicomponent phenol hydroxylase from Pseudomonas sp. strain CF600. J Biol Chem 272:945–951
     [Google Scholar]
  49. Prior S. D., Dalton H. 1985; Acetylene as a suicide substrate and active site probe for methane monooxygenase from Methylococcus capsulatus (Bath). FEMS Microbiol Lett 29:105–109
     [Google Scholar]
  50. Ratajczak A, Geissdorfer W., Hillen W. 1998; Alkane hydroxylase from Acinetobacter sp. strain ADP1 is encoded by alkM and belongs to a new family of bacterial integral-membrane hydrocarbon hydroxylases. Appl Environ Microbiol 64:1175–1179
     [Google Scholar]
  51. Rose T. M, Schultz E. R, Henikoff J. G, Pietrokovski S, McCallum C. M., Henikoff S. 1998; Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences. Nucleic Acids Res 26:1628–1635
     [Google Scholar]
  52. Rosenzweig A. C, Frederick C. A, Lippard S. J., Nordlund P. 1993; Crystal structure of a bacterial non-haem iron hydroxylase that catalyses the biological oxidation of methane. Nature 366:537–543
     [Google Scholar]
  53. Saeki H., Keizo F. 1994; Cloning and characterization of a Nocardia corallina B-276 gene cluster encoding alkene monooxygenase. J Ferment Bioeng 78:399–406
     [Google Scholar]
  54. Sambrook J, Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
     [Google Scholar]
  55. Sayavedra-Soto L. A, Byrd C. M., Arp D. J. 2001; Induction of butane consumption in Pseudomonas butanovora . Arch Microbiol 176:114–120
     [Google Scholar]
  56. Shanklin J, Whittle E., Fox B. G. 1994; Eight histidine residues are catalytically essential in a membrane-associated iron enzyme, stearoyl-CoA desaturase, and are conserved in alkane hydroxylase and xylene monooxygenase. Biochemistry 33:12787–12794
     [Google Scholar]
  57. Shigematsu T, Hanada S, Eguchi M, Kamagata Y, Kanagawa T., Kurane R. 1999; Soluble methane monooxygenase gene clusters from trichloroethylene-degrading Methylomonas sp. strains and detection of methanotrophs during in situ bioremediation. Appl Environ Microbiol 65:5198–5206
     [Google Scholar]
  58. Small F. J., Ensign S. A. 1997; Alkene monooxygenase from Xanthobacter strain Py2. J Biol Chem 272:24913–24920
     [Google Scholar]
  59. Stainthorpe A. C, Lees V, Salmond G. P, Dalton H., Murrell J. C. 1990; The methane monooxygenase gene cluster of Methylococcus capsulatus (Bath. Gene 91:27–34
     [Google Scholar]
  60. Stanley S. H, Prior D. J, Leak D. J., Dalton H. 1983; Copper stress underlines the fundamental change in intracellular location of methane mono-oxygenase in methane utilizing organisms: studies in batch and continuous cultures. Biotechnol Lett 5:487–492
     [Google Scholar]
  61. Stephens G. M., Dalton H. 1986; The role of the terminal and subterminal oxidation pathways in propane metabolism by bacteria. J Gen Microbiol 132:2453–2462
     [Google Scholar]
  62. Stirling D. I., Dalton H. 1979; Properties of the methane mono-oxygenase from extracts of Methylosinus trichosporium OB3b and evidence for its similarity to the enzyme from Methylococcus capsulatus (Bath). Eur J Biochem 96:205–212
     [Google Scholar]
  63. Subramanian V, Liu T.-N, Yeh W.-K, Narro M., Gibson D. T. 1979; Toluene dioxygenase: purification of an iron-sulfur protein by affinity chromatography. Biochem Biophys Res Commun 91:1131–1139
     [Google Scholar]
  64. Subramanian V, Liu T.-N, Yeh W.-K, Narro M., Gibson D. T. 1981; Purification and properties of NADH-ferredoxinTOL reductase: a component of toluene dioxygenase from Pseudomonas putida . J Biol Chem 256:2723–2730
     [Google Scholar]
  65. Subramanian V, Liu T.-N, Yeh W. K, Serdar C. M, Wackett L. P., Gibson D. T. 1985; Purification and properties of ferredoxinTOL: a component of toluene dioxygenase from Pseudomonas putida F1. J Biol Chem 260:2355–2363
     [Google Scholar]
  66. Suzuki M, Hayakawa T, Shaw J. P, Rekik M., Harayama S. 1991; Primary structure of xylene monooxygenase: similarities to and differences from the alkane hydroxylation system. J Bacteriol 173:1690–1695
     [Google Scholar]
  67. Takahashi J, Ichikawa Y, Sagae H, Komura I, Kanou H., Yamada K. 1980; Isolation and identification of n -butane-assimilating bacterium. Agric Biol Chem 44:1835–1840
     [Google Scholar]
  68. Vangnai A. S., Arp D. J. 2001; An inducible 1-butanol dehydrogenase, a quinohemoprotein, is involved in the oxidation of butane by Pseudomonas butanovora . Microbiology 147:745–756
     [Google Scholar]
  69. Vangnai A. S, Arp D. J., Sayavedra-Soto L. A. 2002; Two distinct alcohol dehydrogenases participate in butane metabolism by Pseudomonas butanovora . J Bacteriol 184:1916–1924
     [Google Scholar]
  70. Wallar B. J., Lipscomb J. D. 1996; Dioxygen activation by enzymes containing binuclear non-heme iron clusters. Chem Rev 96:2625–2658
     [Google Scholar]
  71. Wallar B. J., Lipscomb J. D. 2001; Methane monooxygenase component B mutants alter the kinetics of steps throughout the catalytic cycle. Biochemistry 40:2220–2233
     [Google Scholar]
  72. Walters K. J, Gassner G. T, Lippard S. J., Wagner G. 1999; Structure of the soluble methane monooxygenase regulatory protein B. Proc Natl Acad Sci USA 96:7877–7882
     [Google Scholar]
  73. Whittington D. A., Lippard S. J. 2001; Crystal structures of the soluble methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath) demonstrating geometrical variability at the dinuclear iron active site. J Am Chem Soc 123:827–838
     [Google Scholar]
  74. Yanisch-Perron C, Vieira J., Messing J. 1985; Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33:103–119
     [Google Scholar]
  75. Yen K. M., Karl M. R. 1992; Identification of a new gene, tmoF , in the Pseudomonas mendocina KR1 gene cluster encoding toluene-4-monooxygenase. J Bacteriol 174:7253–7261
     [Google Scholar]
  76. Yen K. M, Karl M. R, Blatt L. M, Simon M. J, Winter R. B, Fausset P. R, Lu H. S, Harcourt A. A., Chen K. K. 1991; Cloning and characterization of a Pseudomonas mendocina KR1 gene cluster encoding toluene-4-monooxygenase. J Bacteriol 173:5315–5327
     [Google Scholar]
  77. Zahn J. A., DiSpirito A. 1996; Membrane-associated methane monooxygenase from Methylococcus capsulatus (Bath. J Bacteriol 178:1018–1029
     [Google Scholar]
  78. Zhou N. Y, Jenkins A, Chan Kwo Chion C. K., Leak D. J. 1999; The alkene monooxygenase from Xanthobacter strain Py2 is closely related to aromatic monooxygenases and catalyzes aromatic monohydroxylation of benzene, toluene, and phenol. Appl Environ Microbiol 65:1589–1595
     [Google Scholar]
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Molecular analysis of the soluble butane monooxygenase from ‘Pseudomonas butanovora’aaThe GenBank accession number for the bmoXYBZDC sequence is AY093933.
Microbiology 148, 3617 (2002); https://doi.org/10.1099/00221287-148-11-3617
/content/journal/micro/10.1099/00221287-148-11-3617
/content/journal/micro/10.1099/00221287-148-11-3617
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