Chloromethane-dependent expression of the cmu gene cluster of Hyphomicrobium chloromethanicum

Applied and Environmental Microbiology

Volumn 70, Issue 7, 2004, Pages 4177-4186

  Borodina, Elena ^a   McDonald, Ian R ^a,b   Murrell, J Colin ^a  

^a UNIVERSITY OF WARWICK   (United Kingdom)

^b UNIVERSITY OF WAIKATO   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; CARBON; GENES; MUTAGENESIS; OPTIMIZATION;

ELECTROPORATION PROTOCOL; GENETIC ANALYSIS; MUTATIONAL INACTIVATION;

MICROBIOLOGY;

5,10 METHYLENETETRAHYDROFOLATE REDUCTASE (FADH2); METHYL CHLORIDE;

MICROBIOLOGY;

ARTICLE; BACTERIAL GROWTH; BACTERIUM TRANSFORMATION; CMU GENE; CMUA GENE; CMUB GENE; CMUC GENE; ELECTROPORATION; ESSENTIAL GENE; FOLD GENE; GENE; GENE EXPRESSION REGULATION; GENE LOCATION; GENE MUTATION; GENE STRUCTURE; GENETIC DISORDER; HUTI GENE; HYPHOMICROBIUM; HYPHOMICROBIUM CHLOROMETHANICUM; METF GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PAAE GENE; RELIABILITY; REPRODUCIBILITY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; TRANSCRIPTION REGULATION; TRANSPOSON;

BASE SEQUENCE; ELECTROPORATION; GENES, BACTERIAL; HYPHOMICROBIUM; METHYL CHLORIDE; METHYLTRANSFERASES; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS); HYPHOMICROBIUM; HYPHOMICROBIUM CHLOROMETHANICUM; METHYLOBACTERIUM; METHYLOBACTERIUM CHLOROMETHANICUM; TRANSPOSONS;

EID: 3242750779     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.70.7.4177-4186.2004     Document Type: Article

References (55)

1. Altschul, S. F., W. Gish, W. Miller, W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Berthier, F., M. Zagorec, M. Champomier-Verges, S. D. Ehrlich, and F. Morel-Deville. 1996. Efficient transformation of Lactobacillus sake by electroporation. Microbiology 142:1273-1279.
3. Blatny, J. M., T. Brautaset, H. C. Winther-Larsen, K. Haugan, and S. Valla. 1997. Construction and use of a versatile set of broad-host-range cloning and expression vectors based on the RK2 replicon. Appl. Environ. Microbiol. 63:370-379.
4. Borodina, E., D. P. Kelly, F. A. Rainey, N. Ward-Rainey, and A. P. Wood. 2000. Dimethylsulfone as a growth substrate for novel methylotrophic species of Hyphomicrobium and Arthrobacter. Arch. Microbiol. 173:425-437.
5. Budavari, S., M. Y. O'Neil, A. Smith, and P. E. Heckelman. 1989. The Merck Index: an encyclopaedia of chemicals, drugs and biologicals. Merck and Co, Inc., Rahway, N.J.
6. Coulter, C., J. T. G. Hamilton, W. C. McRoberts, L. Kulakov, M. J. Larkin, and D. B. Harper. 1999. Halomethane:bisulfide/halide ion methyltransferase, an unusual corrinoid enzyme of environmental significance isolated from an aerobic methylotroph using chloromethane as the sole carbon source. Appl. Environ. Microbiol. 65:4301-4312.
7. Craig, N. L. 1991. Tn7: a target site-specific transposon. Mol. Microbiol. 5:2569-2573.
8. Dennis, J. J., and G. J. Zylstra. 1998. Plasposons: modular self-cloning minitransposon derivatives for rapid genetic analysis of gram-negative bacterial genomes. Appl. Environ. Microbiol. 64:2710-2715.
9. Doronina, N. V., A. P. Sokolov, and Y. A. Trotsenko. 1996. Isolation and initial characterization of aerobic chloromethane-utilizing bacteria. FEMS Microbiol. Lett. 142:179-183.
10. Feinberg, A. P., and B. Vogelstein. 1983. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 132:6-13.
11. Ferrandez, A., B. Minambres, B. Garcia, E. R. Olivera, J. M. Luengo, J. L. Garcia, and E. Diaz. 1998. Catabolism of phenylacetic acid in Escherichia coli-characterization of a new aerobic hybrid pathway. J. Biol. Chem. 273:25974-25986.
12. Gilbert, B., I. R. McDonald, R. Finch, G. P. Stafford, A. K. Nielsen, and J. C. Murrell. 2000. Molecular analysis of the pmo (particulate methane monooxygenase) operons from two type II methanotrophs. Appl. Environ. Microbiol. 66:966-975.
13. Gliesche, C. G. 1997. Transformation of methylotrophic bacteria by electroporation. Can. J. Microbiol. 43:197-201.
14. Goenrich, M., J. Bursy, E. Hubner, D. Linder, A. C. Schwartz, and J. A. Vorholt. 2002. Purification and characterization of the methylene tetrahydromethanopterin dehydrogenase MtdB and the methylene tetrahydrofolate dehydrogenase FolD from Hyphomicrobium zavarzinii ZV580. Arch. Microbiol. 177:299-303.
15. 1 compound-utilizing bacteria and comparison to saturation kinetics. Appl. Environ. Microbiol. 67:5437-5443.
16. Hanahan, D. 1983. Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 166:557-580.
17. Harper, D. B. 2000. The global chloromethane cycle: biosynthesis, biodegradation and metabolic role. Nat. Prod. Rep. 17:337-348.
18. Harper, D. B., and J. T. G. Hamilton. 2003. The global cycles of the naturally-occurring halomethanes, p. 17-41. In G. W. Gribble (ed.), The handbook of environmental chemistry. Springer-Verlag, Berlin, Germany.
19. Harper, D. B., J. T. G. Hamilton, V. Ducroq, J. T. Kennedy, A. Downey, and R. M. Kalin. 2003. The distinctive isotopic signature of plant-derived chloromethane: possible application in constraining the atmospheric chloromethane budget. Chemosphere 52:433-436.
20. Hartmans, S., A. Schmuckle, A. M. Cook, and T. Leisinger. 1986. Methyl chloride: naturally occurring toxicant and C-1 growth substrate. J. Gen. Microbiol. 132:1139-1142.
21. Herrero, M., V. Delorenzo, and K. N. Timmis. 1990. Transposon vectors containing non-antibiotic resistance selection markers for cloning and stable chromosomal insertion of foreign genes in gram-negative bacteria. J. Bacteriol. 172:6557-6567.
22. Hu, W. Y., W. Thompson, C. E. Lawrence, and K. M. Derbyshire. 2001. Anatomy of a preferred target site for the bacterial insertion sequence IS903. J. Mol. Biol. 306:403-416.
23. Keene, W. C., M. A. K. Khalil, D. J. Erickson, A. McCulloch, T. E. Graedel, J. M. Lobert, M. L. Aucott, S. L. Gong, D. B. Harper, G. Kleiman, P. M. Midgley, R. M. Moore, C. Seuzaret, W. T. Sturges, C. M. Benkovitz, V. Koropalov, L. A. Barrie, and Y. F. Li. 1999. Composite global emissions of reactive chlorine from anthropogenic and natural sources: reactive chlorine emissions inventory. J. Geophys. Res. 104:8429-8440.
24. Khalil, M. A. K., R. M. Moore, D. B. Harper, J. M. Lobert, D. J. Erickson, V. Koropalov, W. T. Sturges, and W. C. Keene. 1999. Natural emissions of chlorine-containing gases: reactive chlorine emissions inventory. J. Geophys. Res. 104:8333-8346.
25. Khalil, M. A. K., and R. A. Rasmussen. 1999. Atmospheric methyl chloride. Atmos. Environ. 33:1305-1321.
26. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680-685.
27. Lobert, J. M., W. C. Keene, J. A. Logan, and R. Yevich. 1999. Global chlorine emissions from biomass burning: reactive chlorine emissions inventory. J. Geophys. Res. 104:8373-8389.
28. Luchansky, J. B., P. M. Muriana, and T. R. Klaenhammer. 1988. Application of electroporation for transfer of plasmid DNA to Lactobacillus, Lactococcus, Leuconostoc, Listeria, Pediococcus, Bacillus, Staphylococcus, Enterococcus and Propionibacterium. Mol. Microbiol. 2:637-646.
29. Manoil, C., and J. Beckwith. 1985. TnphoA: a transposon probe for protein export signals. Proc. Natl. Acad. Sci. USA 82:8129-8133.
30. McAnulla, C., I. R. McDonald, and J. C. Murrell. 2001a. Methyl chloride utilising bacteria are ubiquitous in the natural environment. FEMS Microbiol. Lett. 201:151-155.
31. T and development of functional gene probes to detect halomethane-degrading bacteria. Appl. Environ. Microbiol. 67:307-316.
32. McDonald, I. R., K. L. Warner, C. McAnulla, C. A. Woodall, R. S. Oremland, and J. C. Murrell. 2002. A review of bacterial methyl halide degradation: biochemistry, genetics and molecular ecology. Environ. Microbiol. 4:193-203.
33. Messmer, M., G. Wohlfarth, and G. Diekert. 1993. Methyl chloride metabolism of the strictly anaerobic methyl chloride-utilizing homoacetogen strain MC. Arch. Microbiol. 160:383-387.
34. Miller, L. G., R. M. Kalin, S. E. McCauley, J. T. G. Hamilton, D. B. Harper, D. B. Millet, R. S. Oremland, and A. H. Goldstein. 2001. Large carbon isotope fractionation associated with oxidation of methyl halides by methylotrophic bacteria. Proc. Natl. Acad. Sci. USA 98:5833-5837.
35. Miller, L. G., K. L. Warner, S. M. Baesman, R. S. Oremland, I. R. McDonald, S. Radajewski, and J. C. Murrell. Degradation of methyl bromide and methyl chloride in soil microcosms: use of stable C isotope fractionation and stable isotope probing to identify reactions and the responsible microorganisms. Geochim. Cosmochim. Acta, in press.
36. Moore, R. M., W. Groszko, and S. J. Niven. 1996. Ocean-atmosphere exchange of methyl chloride: results from NW Atlantic and Pacific Ocean studies. J. Geophys. Res. 101:28529-28538.
37. Oakley, C. J., and J. C. Murrell. 1988. nifH genes in obligate methane oxidising bacteria. FEMS Microbiol. Lett. 49:53-57.
38. Rhew, R. C., B. R. Miller, and R. F. Weiss. 2000. Natural methyl bromide and methyl chloride emissions from coastal salt marshes. Nature 403:292-295.
39. Sambrook, J., and D. W. Russell. 2001. Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
40. Schaefer, J. K., K. D. Goodwin, I. R. McDonald, J. C. Murrell, and R. S. Oremland. 2002. Leisingera methylohalidivorans gen. nov., sp. nov., a marine methylotroph that grows on methyl bromide. Int. J. Syst. Bacteriol. 52:851-859.
41. Schaefer, J. K., and R. S. Oremland. 1999. Oxidation of methyl halides by the facultative methylotroph strain IMB-1. Appl. Environ. Microbiol. 65:5035-5041.
42. Schäfer, A., A. Tauch, W. Jäger, J. Lalinowski, G. Thierbach, and A. Pühler. 1994. Small mobilisable multi-purpose cloning vector derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum. Gene 145:69-73.
43. Serror, P., T. Sasaki, S. D. Ehrlich, and E. Maguin. 2002. Electrotransformation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis with various plasmids. Appl. Environ. Microbiol. 68:46-52.
44. 1 utilization pathway in Methylobacterium chloromethanicum CM4. J. Bacteriol. 184:3476-3484.
45. Studer, A., E. Stupperich, S. Vuilleumier, and T. Leisinger. 2001. Chloromethane:tetrahydrofolate methyl transfer by two proteins from Methylobacterium chloromethanicum strain CM4. Eur. J. Biochem. 268:2931-2938.
46. 4folate methyltransferase involved in chloromethane utilization by Methylobacterium sp. strain CM4. Eur. J. Biochem. 264:242-249.
47. Suylen, G. M. H. 1988. Microbial metabolism of dimethyl sulphide and related compounds. Ph.D. thesis. University of Technology, Delft, The Netherlands.
48. Tauch A., Z. Zheng, A. Puhler, and J. Kalinowski. 1998. Corynebacterium striatum chloramphenicol resistance transposon Tn5564: genetic organization and transposition in Corynebacterium glutamicum. Plasmid 40:126-139.
49. Thompson, A. E., R. S. Anderson, J. Rudolph, and L. Huang. 2002. Stable carbon isotope signatures of background tropospheric chloromethane and CFC113. Biogeochemistry 60:191-211.
50. Vannelli, T., M., Messmer, A. Studer, S. Vuilleumier, and T. Leisinger. 1999. A corrinoid-dependent catabolic pathway for growth of a Methylobacterium strain with chloromethane. Proc. Natl. Acad. Sci. USA 96:4615-4620.
51. Vannelli, T., A. Studer, M. Kertesz, and T. Leisinger. 1998. Chloromethane metabolism by Methylobacterium sp. strain CM4. Appl. Environ. Microbiol. 64:1933-1936.
52. Watling, R., and D. B. Harper. 1998. Chloromethane production of wood-rotting fungi and an estimate of the global flux to the atmosphere. Mycol. Res. 102:769-787.
53. Woodall, C. A. 2000. Methyl halide degradation by aerobic methylotrophs. Ph.D. thesis. University of Warwick, Coventry, England.
54. Woodall, C. A., K. L. Warner, R. S. Oremland, J. C. Murrell, and I. R. McDonald. 2001. Identification of methyl halide-utilizing genes in the methyl bromide-utilizing bacterial strain IMB-1 suggests a high degree of conservation of methyl halide-specific genes in gram-negative bacteria. Appl. Environ. Microbiol. 67:1959-1963.
55. Yokouchi, Y., M. Ikeda, Y. Inuzuka, and T. Yukawa. 2002. Strong emission of methyl chloride from tropical plants. Nature 416:163-165.