title: Soluble di-iron monooxygenase gene diversity in soils, sediments and ethene enrichments.
abstract: Soluble di-iron monooxygenases (SDIMOs) are key enzymes in the bacterial oxidation of hydrocarbons, and have applications in environmental and industrial biotechnology. SDIMOs from pure cultures are unlikely to represent the total diversity of this enzyme family, so we used polymerase chain reaction to survey the diversity of SDIMO alpha subunit genes in environmental samples, ethene enrichments and ethene-degrading bacterial isolates. From 178 cloned amplicons, 98 restriction fragment length polymorphism types were seen, from which 75 representative SDIMO sequences were obtained; 45 from environmental samples, 25 from enrichments and seven from isolates. The sequences were diverse, including genes similar to ethene (etnC), propene (amoC, pmoC), propane (prmA) and butane (bmoX) monooxygenases, in addition to many novel sequences comprising a new SDIMO group (group 6). Environmental samples showed the highest diversity, with strong representation of group 6 SDIMOs and prmA-like genes. Ethene stimulation of samples resulted in increased frequencies of group 4 SDIMOs (etnC-like). Four ethene-utilizing Mycobacterium isolates (NBB1-NBB4) from enrichments all contained etnC; one isolate (NBB4) also contained three additional SDIMO genes (bmoX-like, amoC-like and group 6). The primers, database, clone libraries and strains reported here provide a resource for future bioremediation and biocatalysis studies, with particular relevance for chlorinated alkene and alkane compounds.
authors.affiliation: School of Molecular and Microbial Biosciences, Building G08, University of Sydney, NSW 2006, Australia.
authors.forename: Nicholas V
authors.initials: NV
authors.lastname: Coleman
authors.forename: Nga B
authors.initials: NB
authors.lastname: Bui
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Holmes
mesh_terms: D001431:Bacteriological Techniques / Q000379:methods; D001673:Biodegradation, Environmental; D005030:Ethylenes / Q000378:metabolism*; D006899:Mixed Function Oxygenases / Q000235:genetics* / Q000378:metabolism; D009161:Mycobacterium / Q000235:genetics / Q000378:metabolism; D010105:Oxygenases / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology; D013379:Substrate Specificity
chemical_list: D005030:Ethylenes; C036216:ethylene; D006899:Mixed Function Oxygenases; D010105:Oxygenases; C072883:alkene monooxygenase