Evolution of bacterial and archaeal multicomponent monooxygenases

Journal of Molecular Evolution

Volumn 56, Issue 4, 2003, Pages 435-445

  Notomista, Eugenio ^a   Lahm, Armin ^b   Di Donato, Alberto ^a   Tramontano, Anna ^c  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^b IRBM   (Italy)

^c SAPIENZA UNIVERSITY OF ROME   (Italy)

Author keywords

Monooxygenase; Operon; Recombination

Indexed keywords

CATECHOL 2,3 DIOXYGENASE; METHANE MONOOXYGENASE; UNSPECIFIC MONOOXYGENASE;

ARTICLE; BACTERIAL GENE; ENZYME POLYMORPHISM; GENE TRANSFER; GENETIC RECOMBINATION; METHYLOCOCCUS CAPSULATUS; NONHUMAN; OPERON; PHYLOGENETIC TREE; PSEUDOMONAS; SULFOLOBUS SOLFATARICUS;

ARCHAEA; BACTERIA; EVOLUTION, MOLECULAR; MIXED FUNCTION OXYGENASES; OPERON; PHYLOGENY; RECOMBINATION, GENETIC;

ARCHAEA; BACTERIA (MICROORGANISMS); METHYLOCOCCUS; METHYLOCOCCUS CAPSULATUS; PROKARYOTA; PSEUDOMONAS; SULFOLOBUS; SULFOLOBUS SOLFATARICUS;

EID: 0037381328     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-002-2414-1     Document Type: Article

References (43)

1. Coufal DE, Blazyk JL, Whittington DA, Wu WW, Rosenzweig AC, Lippard SJ (2000) Sequencing and analysis of the Methylococcus capsulatus (Bath) solublemethane monooxygenase genes. Eur J Biochem 267:2174-2185
2. Sullivan J, Dickinson D, Chase H (1998) Methanotrophs, Methylosinus trichosporium OB3b, sMMO, and their application to bioremediation. Crit Rev Microbiol 24:335-373
3. Chauhan S, Barbieri P, Wood T (1998) Oxidation of trichloroethylene, 1,1-dichloroethylene, and chloroform by toluene/o-xylene monooxygenase from Pseudomonas stutzeri OX1. Appl Environ Microbiol 64:3023-4302
4. Aziz CE, Georgiou G, Speitel GE (1999) Cometabolism of chlorinated solvents and binary chlorinated solvent mixtures using M. trichosporium OB3b PP358. Biotechnol Bioeng 65:100-107
5. Gallagher SC, Cammack R, Dalton H (1997) Alkene monooxygenase from Nocardia corallina B-276 is a member of the class of dinuclear iron proteins capable of stereospecific epoxygenation reactions. Eur J Biochem 247:635-641
6. Pikus JD, Studts JM, Achim C, Kauffmann KE, Munck E, Steffan RJ, McClay K, Fox BG (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
7. Elango N, Radhakrishnan R, Froland WA, Wallar BJ, Earhart CA, Lipscomb JD, Ohlendorf DH (1997) Crystal structure of the hydroxylase component of methane moonooxygenase from Methylosinus trichosporium OB3b. Protein Sci 6:556-568
8. Powlowski, J, Shingler V (1994) Genetics and biochemistry of phenol degradation by Pseudomonas sp. CF600. Biodegradation 5:219-236
9. Rosenzweig AC, Frederick CA, Lippard SJ, Nordlund P (1993) Crystal structure of a bacterial non-haem iron hydroxylase that catalyses the biological oxidation of methane. Nature 366:537-543
10. Rosenzweig AC, Nordlund P, Takahara PM, Frederick CA, Lippard SJ (1995) Geometry of the soluble methane monooxygenase catalytic diiron center in two oxidation states. Chem Biol 2:409-418
11. Rosenzweig AC, Brandstetter H, Whittington DA, Nordlund P, Lippard SJ, Fredrick CA (1997) Crystal structures of the methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath): Implications for substrate gating and component interactions. Proteins 29:141-152
12. Whittington DA, Lippard SJ (2001) Crystal structures of the Soluble methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath) Demonstrating geometrical variability at the pinuclear iron active site. J Am Chem Soc 123:827-838
13. Chang SL, Wallar B J, Lipscomb JD, Mayo KH (1999) Solution structure of component B from methane monooxygenase derived through heteronuclear NMR and molecular modeling. Biochemistry 38:5799-5812
14. Walters KJ, Gassner GT, Lippard SJ, Wagner G (1999) Structure of the soluble methane monooxygenase regulatory protein B. Proc Natl Acad Sci USA 96:7877-7882
15. Qian H, Edlund U, Powlowski J, Shingler V, Sethson I (1997) Solution structure of phenol hydroxylase protein component P2 determined by NMR spectroscopy. Biochemistry 36:495-504
16. Hemmi H, Studts JM, Chae YK, Song JL, Markley JL, Fox BG (2001) Solution structure of the toluene 4-monooxygenase effector protein (T4moD). Biochemistry 40:3512-3524
17. Wallar BJ, Lipscomb JD (2001) Methane monooxygenase component b mutants alter the kinetics of steps throughout the catalytic cycle. Biochemistry 40:2220-2233
18. Gassner GT, Lippard SJ (1999) Component interactions in the soluble methane monooxygenase system from Methylococcus capsulatus (Bath). Biochemistry 38:12768-12785
19. Gallagher SC, Callaghan AJ, Zhao J, Dalton H, Trewhella J (1999) Global conformational changes control the reactivity of methane monooxygenase. Biochemistry 38:6752-6760
20. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
21. She Q, et al. (2001) The complete genome of the Crenarchaeote Sulfolobus solfataricus P2. Proc Natl Acad Sci USA 98:7835-7840
22. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
23. Galtier N, Gouy M, Gautier C (1996) SEAVIEW and PHYLO_WIN: Two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12:543-548
24. Page RD (1996) TreeView: An application to display phylogenetic trees on personal computers. Comput Appl Biosci 12: 357-358
25. Bartilson M, Nordlund I, Shingler V (1990) Location and organization of the dimethylphenol catabolic genes of Pseudomonas CF600. Mol Gen Genet 220:294-300
26. Saeki H, Akira M, Furuhashi K, Averhoff B, Gottschalk G (1999) Degradation of trichloroethene by a linear-plasmid-encoded alkene monooxygenase in Rhodococcus corallinus (Nocardia corallina) B-276. Microbiology 145:721-1730
27. 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
28. Bertoni G, Bolognese F, Galli E, Barbieri P (1996) Cloning of the genes for and characterization of the early stages of toluene and o-xylene catabolism in Pseudomonas stutzeri OX1. Appl Environ Microbiol 62:3704-3711
29. Lipscomb JD (1994) Biochemistry of the soluble methane monooxygenase. Annu Rev Microbiol 48:371-399
30. Paller G, Hommel RK, Kleber HP (1995) Phenol degradation by Acinetobacter calcoaceticus NCIB 8250. J Basic Microbiol 35:325-335
31. Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304
32. de la Cruz I, Davies I (2000) Horizontal gene transfer and the origin of species: Lessons from bacteria. Trends Microbiol 8:128-133
33. Wright A, Olsen RH (1994) Self-mobilization and organization of the genes encoding the toluene metabolic pathway of Pseudomonas mendocina KR1. Appl Environ Microbiol 60:235-242
34. Arenghi FL, Berlanda D, Gall E, Sello S, Barbieri P (2001) Organization and regulation of meta cleavage pathway genes for toluene and o-xylene derivative degradation in Pseudomonas stutzeri OX1. Appl Environ Microbiol 67:3304-3308
35. Senda T, Yamada T, Sakurai N, Kubota M, Nishizaki T, Masai E, Fukuda M, Mitsuidagger Y (2000) Crystal structure of NADH-dependent ferredoxin reductase component in biphenyl dioxygenase. J Mol Biol 304:397-410
36. Tan HM, Tang HY, Joannou CL, Abdel-Wahab NH, Mason JR (1993) Pseudomonas putida ML2 plasmid-encoded genes for benzene dioxygenase are unusual in codon usage and low in G+C content. Gene 130:33-39
37. Subramanian V, Liu TN, Yeh WK, Serdar CM, Wackett LP, Gibson DT (1985) Purification and properties of ferredoxin-TOL. A component of toluene dioxygenase from Pseudomonas putida F1. J Biol Chem 260:2355-2363
38. Zylstra GJ, Gibson DT (1989) Toluene degradation by Pseudomonas pulida F1. Nucleotide sequence of the todC1C2-BADE genes and their expression in Escherichia coli. J Biol Chem 264:14940-14946
39. Mason JR, Cammack R (1992) The electron-transport proteins of hydroxylating acterial dioxygenase. Annu Rev Microbiol 46:277-305
40. Williams PA, Sayers JR (1994) The evolution of pathways for aromatic hydrocarbon oxidation in Pseudomonas. Biodegradation 5:195-217
41. Kukor JJ, Olsen RH (1992) Complete nucleotide sequence of tbuD, the gene encoding phenol/cresol hydroxylase from Pseudomonas pickettii PKO1, and functional analysis of the encoded enzyme. J Bacteriol 174:6518-6526
42. Olsen RH, Kukor JJ, Byrne AM, Johnson GR (1997) Evidence for the evolution of a single component phenol/cresol hydroxylase from a multicomponent toluene monooxygenas. J Ind Microbiol Biotechnol 19:360-368
43. Eppink MH, Schreuder HA, Van Berkel WJ (1997) Identification of a novel conserved sequence motif in flavoprotein hydroxylases with a putative dual function in FAD/NAD(P)H binding. Protein Sci 6:2454-2458