Insertion sequence-based cassette PCR: Cultivation-independent isolation of γ-hexachlorocyclohexane-degrading genes from soil DNA

Applied Microbiology and Biotechnology

Volumn 79, Issue 4, 2008, Pages 627-632

  Fuchu, Genki ^a   Ohtsubo, Yoshiyuki ^a   Ito, Michihiro ^a   Miyazaki, Ryo ^a   Ono, Akira ^a   Nagata, Yuji ^a   Tsuda, Masataka ^a  

^a TOHOKU UNIVERSITY   (Japan)

Author keywords

Hexachlorocyclohexane; Insertion sequence; Soil DNA

Indexed keywords

BACTERIA; CELL CULTURE; DNA; PESTICIDES; SOILS;

Γ-HEXACHLOROCYCLOHEXANE; INSERTION SEQUENCE; POLYMERASE CHAIN REACTION (PCR); SOIL DNA;

GENES;

DNA; DNA FRAGMENT; LINDANE;

DNA; GENE; HCH; POLYMERASE CHAIN REACTION; SOIL;

ARTICLE; BACTERIAL CELL; BACTERIAL GENE; BIODEGRADATION; CELL CULTURE; DNA EXTRACTION; DNA FLANKING REGION; GENE AMPLIFICATION; GENE FUNCTION; GENE INSERTION SEQUENCE; GENE ISOLATION; HOST CELL; LIN GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; SOIL POLLUTION;

BACTERIAL PROTEINS; BIODEGRADATION, ENVIRONMENTAL; DNA TRANSPOSABLE ELEMENTS; DNA, BACTERIAL; LINDANE; MOLECULAR SEQUENCE DATA; PESTICIDES; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SOIL; SOIL MICROBIOLOGY; SPHINGOMONADACEAE;

BACTERIA (MICROORGANISMS);

EID: 44649177513     PISSN: 01757598     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00253-008-1463-9     Document Type: Article

References (44)

1. Ausubel FM, Brent R, Kingston ER, Moore DD, Seidman GJ, Smith AJ, Struhl K (1991) Current protocols in molecular biology. Wiley, New York
2. Bale MJ, Fry JC, Day MJ (1987) Plasmid transfer between strains of Pseudomonas aeruginosa on membrane filters attached to river stones. J Gen Microbiol 133:3099-3107
3. Boltner D, Moreno-Morillas S, Ramos JL (2005) 16S rDNA phylogeny and distribution of lin genes in novel hexachlorocyclohexane-degrading Sphingomonas strains. Environ Microbiol 7:1329-1338
4. Ceremonie H, Boubakri H, Mavingui P, Simonet P, Vogel TM (2006) Plasmid-encoded γ-hexachlorocyclohexane degradation genes and insertion sequences in Sphingobium francense (ex-Sphingomonas paucimobilis Sp+). FEMS Microbiol Lett 257(2):243-252
5. Clement P, Pieper DH, Gonzalez B (2001) Molecular characterization of a deletion/duplication rearrangement in tfd genes from Ralstonia eutropha JMP134(pJP4) that improves growth on 3-chlorobenzoic acid but abolishes growth on 2,4-dichlorophenoxyacetic acid. Microbiology 147:2141-2148
6. Dogra C, Raina V, Pal R, Suar M, Lal S, Gartemann KH, Holliger C, van der Meer JR, Lal R (2004) Organization of lin genes and IS6100 among different strains of hexachlorocyclohexane-degrading Sphingomonas paucimobilis: evidence for horizontal gene transfer. J Bacteriol 186:2225-2235
7. Ellis RJ, Morgan P, Weightma AJ, Fry JC (2003) Cultivation-dependent and -independent approaches for determining bacterial diversity in heavy-metal-contaminated soil. Appl Environ Microbiol 69:3223-3230
8. Endo R, Kamakura M, Miyauchi K, Fukuda M, Ohtsubo Y, Tsuda M, Nagata Y (2005) Identification and characterization of genes involved in the downstream degradation pathway of γ-hexachlorocyclohexane in Sphingomonas paucimobilis UT26. J Bacteriol 187:847-853
9. Endo R, Ohtsubo Y, Tsuda M, Nagata Y (2007) Identification and characterization of genes encoding a putative ABC-type transporter essential for utilization of γ-hexachlorocyclohexane in Sphingobium japonicum UT26. J Bacteriol 189:3712-3720
10. Fukumori F, Saint CP (1997) Nucleotide sequences and regulational analysis of genes involved in conversion of aniline to catechol in Pseudomonas putida UCC22(pTDN1). J Bacteriol 179:399-408
11. Galas DJ, Chandler M (1989) Bacterial insertion sequence. In: Berg DE, Howe MM (eds) Mobile DNA. Am Soc Microbiol, Washington, D.C., pp 109-162
12. Imai R, Nagata Y, Fukuda M, Takagi M, Yano K (1991) Molecular cloning of a Pseudomonas paucimobilis gene encoding a 17-kilodalton polypeptide that eliminates HCl molecules from γ-hexachlorocyclohexane. J Bacteriol 173:6811-6819
13. Ito M, Prokop Z, Klvana M, Otsubo Y, Tsuda M, Damborsky J, Nagata Y (2007) Degradation of β-hexachlorocyclohexane by haloalkane dehalogenase LinB from γ-hexachlorocyclohexane-utilizing bacterium Sphingobium sp. MI1205. Arch Microbiol 188:313-325
14. Kumari R, Subudhi S, Suar M, Dhingra G, Raina V, Dogra C, Lal S, van der Meer JR, Holliger C, Lal R (2002) Cloning and characterization of lin genes responsible for the degradation of hexachlorocyclohexane isomers by Sphingomonas paucimobilis strain B90. Appl Environ Microbiol 68:6021-6028
15. Lal R, Dogra C, Malhotra S, Sharma P, Pal R (2006) Diversity, distribution and divergence of lin genes in hexachlorocyclohexane-degrading sphingomonads. Trends Biotechnol 24:121-130
16. Liu H, Zhang JJ, Wang SJ, Zhang XE, Zhou NY (2005) Plasmid-borne catabolism of methyl parathion and p-nitrophenol in Pseudomonas sp. strain WBC-3. Biochem Biophys Res Commun 334:1107-1114
17. Maniatis T, Fritsch EF, Sambrook J (1982) A laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor
18. Martin C, Timm J, Rauzier J, Gomez-Lus R, Davies J, Gicquel B (1990) Transposition of an antibiotic resistance element in mycobacteria. Nature 345:739-743
19. Miyauchi K, Suh SK, Nagata Y, Takagi M (1998) Cloning and sequencing of a 2,5-dichlorohydroquinone reductive dehalogenase gene whose product is involved in degradation of γ-hexachlorocyclohexane by Sphingomonas paucimobilis. J Bacteriol 180:1354-1359
20. Miyauchi K, Adachi Y, Nagata Y, Takagi M (1999) Cloning and sequencing of a novel meta-cleavage dioxygenase gene whose product is involved in degradation of γ-hexachlorocyclohexane in Sphingomonas paucimobilis. J Bacteriol 181:6712-6719
21. Miyauchi K, Lee HS, Fukuda M, Takagi M, Nagata Y (2002) Cloning and characterization of linR, involved in regulation of the downstream pathway for γ-hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26. Appl Environ Microbiol 68:1803-1807
22. Miyazaki R, Sato Y, Ito M, Ohtsubo Y, Nagata Y, Tsuda M (2006) Complete nucleotide sequence of an exogenously isolated plasmid, pLB1, involved in γ-hexachlorocyclohexane degradation. Appl Environ Microbiol 72:6923-6933
23. Nagata Y, Nariya T, Ohtomo R, Fukuda M, Yano K, Takagi M (1993) Cloning and sequencing of a dehalogenase gene encoding an enzyme with hydrolase activity involved in the degradation of γ-hexachlorocyclohexane in Pseudomonas paucimobilis. J Bacteriol 175:6403-6410
24. Nagata Y, Ohtomo R, Miyauchi K, Fukuda M, Yano K, Takagi M (1994) Cloning and sequencing of a 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase gene involved in the degradation of γ-hexachlorocyclohexane in Pseudomonas paucimobilis. J Bacteriol 176:3117-3125
25. Nagata Y, Miyauchi K, Takagi M (1999) Complete analysis of genes and enzymes for γ-hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26. J Ind Microbiol Biotechnol 23:380-390
26. Nagata Y, Matsuda M, Komatsu H, Imura Y, Sawada H, Ohtsubo Y, Tsuda M (2005) Organization and localization of the dnaA and dnaK gene regions on the multichromosomal genome of Burkholderia multivorans ATCC 17616. J Biosci Bioeng 99:603-610
27. Nagata Y, Kamakura M, Endo R, Miyazaki R, Ohtsubo Y, Tsuda M (2006) Distribution of γ-hexachlorocyclohexane-degrading genes on three replicons in Sphingobium japonicum UT26. FEMS Microbiol Lett 256:112-118
28. Nagata Y, Endo R, Ito M, Ohtsubo Y, Tsuda M (2007) Aerobic degradation of lindane (γ-hexachlorocyclohexane) in bacteria and its biochemical and molecular basis. Appl Microbiol Biotechnol 76(4):741-752
29. Nakatsu C, Ng J, Singh R, Straus N, Wyndham C (1991) Chlorobenzoate catabolic transposon Tn5271 is a composite class I element with flanking class II insertion sequences. Proc Natl Acad Sci U S A 88:8312-8316
30. Negoro S (2000) Biodegradation of nylon oligomers. Appl Microbiol Biotechnol 54:461-466
31. Ono A, Miyazaki R, Sota M, Ohtsubo Y, Nagata Y, Tsuda M (2007) Isolation and characterization of naphthalene-catabolic genes and plasmids from oil-contaminated soil by using two cultivation-independent approaches. Appl Microbiol Biotechnol 74:501-510
32. Phillips TM, Seech AG, Lee H, Trevors JT (2005) Biodegradation of hexachlorocyclohexane (HCH) by microorganisms. Biodegradation 16(4):363-92
33. Roszak DB, Colwell RR (1987) Survival strategies of bacteria in the natural environment. Microbiol Rev 51:365-379
34. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
35. Sharma P, Raina V, Kumari R, Malhotra S, Dogra C, Kumari H, Kohler HP, Buser HR, Holliger C, Lal R (2006) Haloalkane dehalogenase LinB is responsible for β- and δ-hexachlorocyclohexane transformation in Sphingobium indicum B90A. Appl Environ Microbiol 72:5720-5727
36. Smith B, Dyson P (1995) Inducible transposition in Streptomyces lividans of insertion sequence IS6100 from Mycobacterium fortuitum. Mol Microbiol 18:933-941
37. Sota M, Yano H, Nagata Y, Ohtsubo Y, Genka H, Anbutsu H, Kawasaki H, Tsuda M (2006) Functional analysis of unique class II insertion sequence IS1071. Appl Environ Microbiol 72:291-297
38. Stokes HW, Holmes AJ, Nield BS, Holley MP, Nevalainen KM, Mabbutt BC, Gillings MR (2001) Gene cassette PCR: sequence-independent recovery of entire genes from environmental DNA. Appl Environ Microbiol 67:5240-5246
39. Stuart-Keil KG, Hohnstock AM, Drees KP, Herrick JB, Madsen EL (1998) Plasmids responsible for horizontal transfer of naphthalene catabolism genes between bacteria at a coal tar-contaminated site are homologous to pDTG1 from pseudomonas putida NCIB 9816-4. Appl Environ Microbiol 64:3633-3640
40. Suar M, Hauser A, Poiger T, Buser HR, Muller MD, Dogra C, Raina V, Holliger C, van der Meer JR, Lal R, Kohler HPE (2005) Enantioselective transformation of α-hexachlorocyclohexane by the dehydrochlorinases LinA1 and LinA2 from the soil bacterium Sphingomonas paucimobilis B90A. Appl Environ Microbiol 71:8514-8518
41. Tauch A, Gotker S, Puhler A, Kalinowski J, Thierbach G (2002) The 27.8-kb R-plasmid pTET3 from Corynebacterium glutamicum encodes the aminoglycoside adenyltransferase gene cassette aadA9 and the regulated tetracycline efflux system Tet 33 flanked by active copies of the widespread insertion sequence IS6100. Plasmid 48:117-129
42. Top EM, Holben WE, Forney LJ (1995) Characterization of diverse 2,4-dichlorophenoxyacetic acid-degradative plasmids isolated from soil by complementation. Appl Environ Microbiol 61:1691-1698
43. Torsvik V, Ovreas L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240-245
44. Wu J, Hong Q, Han P, He J, Li S (2007) A gene linB2 responsible for the conversion of β-HCH and 2,3,4,5,6-pentachlorocyclohexanol in Sphingomonas sp. BHC-A. Appl Microbiol Biotechnol 73:1097-105