Sphingobium sp. HV3 degrades both herbicides and polyaromatic hydrocarbons using ortho- and meta-pathways with differential expression shown by RT-PCR

Biodegradation

Volumn 21, Issue 5, 2010, Pages 771-784

  Sipilä, Timo P ^a   Väisänen, Pave ^a   Paulin, Lars ^b   Yrjälä, Kim ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

^b UNIVERSITY OF HELSINKI   (Finland)

Author keywords

Biodegradation; Extradiol dioxygenase; Gene expression; Intradiol dioxygenase; Phenanthrene; Real time PCR; Sphingomonas; Tn5 transposon; Toluene; Xylene

Indexed keywords

DIOXYGENASE GENES; DIOXYGENASES; EXTRADIOL; REAL-TIME PCR; SPHINGOMONAS; TN5 TRANSPOSON;

ANTHRACENE; AROMATIC HYDROCARBONS; AROMATIZATION; CLONING; DEGRADATION; GENES; HERBICIDES; MICROBIOLOGY; MUTAGENESIS; TERNARY SYSTEMS; TOLUENE; TRANSCRIPTION; WEED CONTROL; XYLENE;

BIODEGRADATION;

AROMATIC HYDROCARBON; CATECHOL DERIVATIVE; DIOXYGENASE; HERBICIDE;

AROMATIC HYDROCARBON; BACTERIUM; BIODEGRADATION; ENZYME ACTIVITY; GENE EXPRESSION; HERBICIDE; META-ANALYSIS; PLASMID;

AGAR GEL ELECTROPHORESIS; ARTICLE; BACTERIAL GENE; BIOREMEDIATION; ENZYMOLOGY; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR CLONING; MUTAGENESIS; MUTATION; PHENOTYPE; PHYLOGENY; PLASMID; RESTRICTION MAPPING; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SPHINGOMONADACEAE; TIME; TRANSPOSON;

BIODEGRADATION, ENVIRONMENTAL; CATECHOLS; CLONING, MOLECULAR; DIOXYGENASES; DNA TRANSPOSABLE ELEMENTS; ELECTROPHORESIS, AGAR GEL; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; HERBICIDES; HYDROCARBONS, AROMATIC; METABOLIC NETWORKS AND PATHWAYS; MUTAGENESIS; MUTATION; PHENOTYPE; PHYLOGENY; PLASMIDS; RESTRICTION MAPPING; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SPHINGOMONADACEAE; TIME FACTORS;

BACTERIA (MICROORGANISMS); SPHINGOBIUM; SPHINGOMONAS;

EID: 77955269398     PISSN: 09239820     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10532-010-9342-3     Document Type: Article

References (52)

1. Ausubel FM, Brent R, Kingston R, Moore D, Seidman J, Smith JA, Struhl K (1987) Current protocols in molecular biology. Wiley, New York, USA.
2. Basta T, Keck A, Klein J, Stolz A (2004) Detection and characterization of conjugative degradative plasmids in xenobiotic-degrading Sphingomonas strains. J Bacteriol 186: 3862-3872.
3. Cho O, Choi KY, Zylstra GJ, Kim YS, Kim SK, Lee JH, Sohn HY, Kwon GS, Kim YM, Kim E (2005) Catabolic role of a three-component salicylate oxygenase from Sphingomonasyanoikuyae B1 in polycyclic aromatic hydrocarbon degradation. Biochem Biophys Res Commun 327: 656-662.
4. Corbella M, Puyet A (2003) Real-time reverse transcription-PCR analysis of expression of halobenzoate and salicylate catabolism-associated operons in two strains of Pseudomonasaeruginosa. Appl Environ Microbiol 69: 2269-2275.
5. Demaneche S, Meyer C, Micoud J, Louwagie M, Willison JC, Jouanneau Y (2004) Identification and functional analysis of two aromatic-ring-hydroxylating dioxygenases from a Sphingomonas strain that degrades various polycyclic aromatic hydrocarbons. Appl Environ Microbiol 70: 6714-6725.
6. Denef V, Klappenbach J, Patrauchan M, Florizone C, Rodrigues J, Tsoi T, Verstraete W, Eltis L, Tiedje J (2006) Genetic and Genomic Insights into the Role of Benzoate-Catabolic Pathway Redundancy in Burkholderiaxenovorans LB400. Appl Environ Microbiol 72: 585-595.
7. Dominguez-Cuevas P, Gonzalez-Pastor JE, Marques S, Ramos JL, de Lorenzo V (2006) Transcriptional tradeoff between metabolic and stress-response programs in Pseudomonasputida KT2440 cells exposed to toluene. J Biol Chem 281: 11981-11982.
8. Fredrickson JK, Balkwill DL, Drake GR, Romine MF, Ringelberg DB, White DC (1995) Aromatic-degrading Sphingomonas isolates from the deep subsurface. Appl Environ Microbiol 61: 1917-1922.
9. Horvath RS, Alexander M (1970) Cometabolism of m-chlorobenzoate by an Arthrobacter. Appl Environ Microbiol 20: 254-258.
10. Jouanneau Y, Meyer C (2006) Purification and characterization of an arene cis-dihydrodiol dehydrogenase endowed with broad substrate specificity toward polycyclic aromatic hydrocarbon dihydrodiols. Appl Environ Microbiol 72: 4726-4734.
11. Keck A, Conradt D, Mahler A, Stolz A, Mattes R, Klein J (2006) Identification and functional analysis of the genes for naphthalenesulfonate catabolism by Sphingomonasxenophaga BN6. Microbiology 152: 1929-1940.
12. Khan AA, Wang RF, Cao WW, Franklin W, Cerniglia CE (1996) Reclassification of a polycyclic aromatic hydrocarbon-metabolizing bacterium, Beijerinckia sp. strain B1, as Sphingomonasyanoikuyae by fatty acid analysis, protein pattern analysis, DNA-DNA hybridization, and 16S ribosomal DNA sequencing. Int J Syst Bacteriol 46: 466-469.
13. Kilpi S (1980) Degradation of some phenoxy acid herbicides by mixed cultures of bacteria isolated from soil treated with 2-(2-methyl-4-chloro) phenoxypropionic acid. Microb Ecol 6: 261-270.
14. Kilpi S, Backstrom V, Korhola M (1980) Degradation of 2-methyl-4-chlorophenoxyacetic acid (MCPA), 2, 4-dichlorophenoxyacetic acid (2, 4-D), benzoic acid and salicylic acid by Pseudomonas sp. HV3. FEMS Microbiol Lett 8: 177-182.
15. Kilpi S, Backstrom V, Korhola M (1983) Degradation of catechol, methylcatechols and chlorocatechols by Pseudomonas sp. HV3. FEMS Microbiol Lett 18: 1-5.
16. Kilpi S, Himberg K, Yrjälä K, Backstrom V (1988) The degradation of biphenyl and chlorobiphenyls by mixed bacterial cultures. FEMS Microbiol Lett 53: 19-26.
17. Kim E, Zylstra G (1999) Functional analysis of genes involved in biphenyl, naphthalene, phenanthrene, and m-xylene degradation by Sphingomonasyanoikuyae B1. J Ind Microbiol Biotechnol 23: 294-302.
18. Kiyohara H, Torigoe S, Kaida N, Asaki T, Iida T, Hayashi H, Takizawa N (1994) Cloning and characterization of a chromosomal gene cluster, pah, that encodes the upper pathway for phenanthrene and naphthalene utilization by Pseudomonasputida OUS82. J Bacteriol 176: 2439-2443.
19. Kleinsteuber S, Riis V, Fetzer I, Harms H, Muller S (2006) Population dynamics within a microbial consortium during growth on diesel fuel in saline environments. Appl Environ Microbiol 72: 3531-3542.
20. Kohler HP (1999) Sphingomonasherbicidovorans MH: a versatile phenoxyalkanoic acid herbicide degrader. J Ind Microbiol Biotechnol 23: 336-340.
21. Kouzuma A, Pinyakong O, Nojiri H, Omori T, Yamane H, Habe H (2006) Functional and transcriptional analyses of the initial oxygenase genes for acenaphthene degradation from Sphingomonas sp. strain A4. Microbiology 152: 2455-2467.
22. Lang GH, Ogawa N, Tanaka Y, Fujii T, Fulthorpe RR, Fukuda M, Miyashita K (2005) Two kinds of chlorocatechol 1, 2-dioxygenase from 2, 4-dichlorophenoxyacetate-degrading Sphingomonas sp. strain TFD44. Biochem Biophys Res Commun 332: 941-948.
23. Leander M, Vallaeys T, Fulthorpe R (1998) Amplification of putative chlorocatechol dioxygenase gene fragments from-and-proteobacteria. Can J Microbiol 44: 482-486.
24. Leys NM, Ryngaert A, Bastiaens L, Verstraete W, Top EM, Springael D (2004) Occurrence and phylogenetic diversity of Sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons. Appl Environ Microbiol 70: 1944-1955.
25. Lim JS, Jung MK, Kim MS, Ahn JH, Ka JO (2004) Genetic and phenotypic diversity of (R/S)-mecoprop [2-(2-methyl-4-chlorophenoxy)propionic acid]-degrading bacteria isolated from soils. J Microbiol 42: 87-93.
26. Parnell JJ, Denef VJ, Park J, Tsoi T, Tiedje JM (2010) Environmentally relevant parameters affecting PCB degradation: carbon source-and growth phase-mitigated effects of the expression of the biphenyl pathway and associated genes in Burkholderiaxenovorans LB400. Biodegradation 21: 147-156.
27. Peng RH, Xiong AS, Xue Y, Fu XY, Gao F, Zhao W, Tian YS, Yao QH (2008) Microbial biodegradation of polyaromatic hydrocarbons. FEMS Microbiol Rev 32: 927-955.
28. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29: 2002-2007.
29. Pinyakong O, Habe H, Omori T (2003a) The unique aromatic catabolic genes in sphingomonads degrading polycyclic aromatic hydrocarbons (PAHs). J Gen Appl Microbiol 49: 11-19.
30. Pinyakong O, Habe H, Yoshida T, Nojiri H, Omori T (2003b) Identification of three novel salicylate 1-hydroxylases involved in the phenanthrene degradation of Sphingobium sp. strain P2. Biochem Biophys Res Commun 301: 350-357.
31. Reineke W (1998) Development of hybrid strains for the mineralization of chloroaromatics by patchwork assembly. Annu Rev Microbiol 52: 287-331.
32. Romine MF, Stillwell LC, Wong K, Thurston SJ, Sisk EC, Sensen C, Gaasterland T, Fredrickson JK, Saffer JD (1999) Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonasaromaticivorans F199. J Bacteriol 181: 1585-1602.
33. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
34. Simon R, Quandt J, Klipp W (1989) New derivatives of transposon Tn5 suitable for mobilization of replicons, generation of operon fusions and induction of genes in gram-negative bacteria. Gene 80: 161-169.
35. Sipilä TP, Riisio H, Yrjälä K (2006) Novel upper meta-pathway extradiol dioxygenase gene diversity in polluted soil. FEMS Microbiol Ecol 58: 134-144.
36. Sipilä TP, Keskinen AK, Akerman ML, Fortelius C, Haahtela K, Yrjälä K (2008) High aromatic ring-cleavage diversity in birch rhizosphere: PAH treatment-specific changes of I. E. 3 group extradiol dioxygenases and 16S rRNA bacterial communities in soil. ISME J 2: 968-981.
37. Stolz A (2009) Molecular characteristics of xenobiotic-degrading sphingomonads. Appl Microbiol Biotechnol 81: 793-811.
38. Tajima F, Nei M (1984) Note on genetic drift and estimation of effective population size. Genetics 106: 569-574.
39. Takeuchi M, Hamana K, Hiraishi A (2001) Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 51: 1405-1417.
40. Thiel M, Kaschabek SR, Gröning J, Mau M, Schlömann M (2005) Two unusual chlorocatechol catabolic gene clusters in Sphingomonas sp. TFD44. Arch Microbiol 183: 80-94.
41. Tyystjarvi T, Herranen M, Aro EM (2001) Regulation of translation elongation in cyanobacteria: membrane targeting of the ribosome nascent-chain complexes controls the synthesis of D1 protein. Mol Microbiol 40: 476-484.
42. Wheatcroft R, Williams PA (1981) Rapid methods for the study of both stable and unstable plasmids in Pseudomonas. J Gen Microbiol 124: 433-437.
43. White DC, Sutton SD, Ringelberg DB (1996) The genus Sphingomonas: physiology and ecology. Curr Opin Biotechnol 7: 301-306.
44. Williams PA, Murray K (1974) Metabolism of benzoate and the methylbenzoates by Pseudomonasputida (arvilla) mt-2: evidence for the existence of a TOL plasmid. J Bacteriol 120: 416-423.
45. Willison JC (2004) Isolation and characterization of a novel sphingomonad capable of growth with chrysene as sole carbon and energy source. FEMS Microbiol Lett 241: 143-150.
46. Yabuuchi E, Kosako Y, Fujiwara N, Naka T, Matsunaga I, Ogura H, Kobayashi K (2002) Emendation of the genus Sphingomonas Yabuuchi et al. 1990 and junior objective synonymy of the species of three genera, Sphingobium, Novosphingobium and Sphingopyxis, in conjunction with Blastomonasursincola. Int J Syst Evol Microbiol 52: 1485-1496.
47. Yanisch-Perron C, Vieira J, Messing J (1985) Improved M 13 phage cloning vectors and host strains: nucleotide sequences of the M 13 mp 18 and pUC 19 vectors. Gene 33: 103-119.
48. Yen KM, Serdar CM (1988) Genetics of naphthalene catabolism in pseudomonads. Crit Rev Microbiol 15: 247-268.
49. Yrjälä K, Paulin L, Kilpi S, Romantschuk M (1994) Cloning of cmpE, a plasmid-borne catechol 2, 3-dioxygenase-encoding gene from the aromatic- and chloroaromatic-degrading Pseudomonas sp. HV3. Gene 138: 119-121.
50. Yrjälä K, Paulin L, Romantschuk M (1997) Novel organization of catechol meta-pathway genes in Sphingomonas sp. HV3 pSKY4 plasmid. FEMS Microbiol Lett 154: 403-408.
51. Yrjälä K, Suomalainen S, Suhonen EL, Kilpi S, Paulin L, Romantschuk M (1998) Characterization and reclassification of an aromatic- and chloroaromatic-degrading Pseudomonas sp., strain HV3, as Sphingomonas sp. HV3. Int J Syst Bacteriol 48: 1057-1062.
52. Zipper C, Nickel K, Angst W, Kohler HP (1996) Complete microbial degradation of both enantiomers of the chiral herbicide mecoprop [(RS)-2-(4-chloro-2-methylphenoxy)propionic acid] in an enantioselective manner by Sphingomonasherbicidovorans sp. nov. Appl Environ Microbiol 62: 4318-4322.