Real-time reverse transcription PCR analysis of expression of atrazine catabolism genes in two bacterial strains isolated from soil

Journal of Microbiological Methods

Volumn 56, Issue 1, 2004, Pages 3-15

  Devers, Marion ^a   Soulas, Guy ^a   Martin Laurent, Fabrice ^a  

^a UNIVERSITÉ DE BOURGOGNE   (France)

Author keywords

Atrazine; atz gene; Biodegradation; Gene expression; RT qPCR

Indexed keywords

ATRAZINE; TELLURIUM DERIVATIVE;

ANALYTIC METHOD; ARTICLE; BACTERIAL STRAIN; BACTERIUM ISOLATION; CATABOLISM; CHELATOBACTER HEINTZII; CULTURE MEDIUM; DEGRADATION KINETICS; ENZYME DEGRADATION; MICROORGANISM; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; PRIORITY JOURNAL; PROTEIN EXPRESSION; PSEUDOMONAS; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; UPREGULATION;

AMINOBACTER AMINOVORANS; BACTERIA (MICROORGANISMS); CHELATOBACTER HEINTZII; PSEUDOMONAS; PSEUDOMONAS SP.; PSEUDOMONAS SP. ADP;

EID: 0347990402     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2003.08.015     Document Type: Article

References (52)

1. Alberts B., Bray D., Lewis J., Raff M., Roberts K., Watson J. Molecular biology of the cell. The Cell. 2nd ed. 1989;1219 Garland Publishing, New York.
2. Barriuso E., Houot S. Rapid mineralization of the s-triazine ring atrazine in soils in relation to soil management. Soil Biol. Biochem. 28:1996;1341-1348.
3. Barriuso E., Calvet R., Schiavon M., Soulas G. Les pesticides et les polluants organiques des sols: transformations et dissipation. Etude et Gestion des Sols. 1996;279-296 AFES, Paris, France.
4. Boundy-Mills K., Souza M.D., Mandelbaum R., Wackett L., Sadowsky M. The atzB gene of Pseudomonas sp. strain ADP encodes the second enzyme of a novel atrazine degradation pathway. Appl. Environ. Microbiol. 63:1997;916-923.
5. Bouquard C., Ouazzani J., Promé J., Michel-Briand Y., Plésiat P. Dechlorination of atrazine by a Rhizobium sp. isolate. Appl. Environ. Microbiol. 63:1997;862-866.
6. Combourieu B., Besse P., Sancelme M., Veschambre H., Delort A., Poupin P., Truffaut N. Morpholine degradation pathway of Mycobacterium aurum MO1: direct evidence of intermediates by in situ 1H Nuclear Magnetic Resonance. Appl. Environ. Microbiol. 64:1998;153-158.
7. Condon C., Squires C., Squires C.L. Control of rRNA transcription in Escherichia coli. Microbiol. Rev. 59:1995;623-645.
8. Corbella M., Puyet A. Real-time reverse transcription-PCR analysis of expression of halobenzoate and salicylate catabolism-associated operons in two strains of Pseudomonas aeruginosa. Appl. Environ. Microbiol. 69:2003;2269-2275.
9. De Souza M., Wackett L., Sadowsky M. Atrazine chlorohydrolase from Pseudomonas sp. strain ADP: gene sequence, enzyme purification, and protein characterisation. J. Bacteriol. 178:1996;4894-4900.
10. De Souza M., Wackett L., Sadowsky M. The atrazine catabolism genes atzABC are widespread and highly conserved. J. Bacteriol. 180:1998;1951-1954.
11. De Souza M., Wackett L., Sadowsky M. The atzABC genes encoding atrazine metabolism are located on a self-transmissible plasmid in Pseudomonas sp. strain ADP. Appl. Environ. Microbiol. 64:1998;2323-2326.
12. Franken P., Gnädinger F. Analysis of parsley arbuscular endomycorrhiza: infection development and mRNA levels of defense-related genes. Mol. Plant-Microb. Interact. 7:1994;612-620.
13. Gebendinger N., Radosevich M. Inhibition of atrazine degradation by cyanazine and exogenous nitrogen in bacterial isolate M91-3. Appl. Environ. Biotechnol. 51:1999;375-381.
14. Goerke C., Bayer M., Wolz C. Quantification of bacterial transcripts during infection using competitive reverse transcription-PCR (RT-PCR) and LightCycler RT-PCR. Clin. Diagn. Lab. Immunol. 8:2001;279-282.
15. Heid C., Stevens J., Livak K., Williams P. Real Time Quantitative PCR. Genome Res. 6:1996;986-994.
16. Hein J., Schellenberg U., Bein G., Hackstein H. Quantification of murine IFN-gamma mRNA and protein expression: impact of real-time kinetic RT-PCR using SYBR green I dye. Scand. J. Immunol. 54:2001;285-291.
17. Houot S., Topp E., Yassir A., Soulas G. Dependence of accelerated degradation of atrazine on soil pH in French and Canadian soils. Soil Biol. Biochem. 32:2000;615-625.
18. Kahnert A., Mirleau P., Wait R., Kertesz M. The LysR-type regulator SftR is involved in soil survival and sulphate ester metabolism in Pseudomonas putida. Environ. Microbiol. 4:2002;225-237.
19. Karns J. Gene sequence and properties of an s-triazine ring-cleavage enzyme from Pseudomonas sp. strain NRRLB-12227. Appl. Environ. Microbiol. 65:1999;3512-3517.
20. Katz I., Green M., Ruskol Y., Dosoretz C. Characterization of atrazine degradation and nitrate reduction by Pseudomonas sp. strain ADP. Water Res. 4:2000;219-224.
21. Kennell D. Processing endoribonucleases and mRNA degradation in bacteria. J. Bacteriol. 184:2002;4645-4657.
22. Kreuzer K., Lass U., Landt O., Nitsche A., Laser J., Ellerbrok H., Pauli G., Huhn D., Schmidt C. Highly sensitive and specific fluorescence reverse transcription-PCR assay for the pseudogene-free detection of β-actin transcripts as quantitative reference. Clin. Chem. 45:1999;297-300.
23. Ma L., Selim H. Atrazine retention and transport in soils. Rev. Environ. Contam. Toxicol. 145:1996;129-173.
24. Mandelbaum R., Wackett L., Allan D. Mineralization of the s-triazine ring of atrazine by stable bacterial mixed cultures. Appl. Environ. Microbiol. 59:1993;1695-1701.
25. Mandelbaum R., Allan D., Wackett L. Isolation and characterization of a Pseudomonas sp. that mineralizes the s-triazine herbicide atrazine. Appl. Environ. Microbiol. 61:1995;1451-1457.
26. Martinez B., Tomkins J., Wackett L., Wing R., Sadowsky M. Complete nucleotide sequence and organization of the atrazine catabolic plasmid pADP-1 from Pseudomonas sp. ADP. J. Bacteriol. 183:2001;5684-5697.
27. Martin-Laurent F., Van Tuinen D., Dumas-Gaudot E., Gianinazzi-Pearson V., Gianinazzi S., Franken P. Differential display analysis of RNA accumulation in arbuscular mycorrhiza of pea and isolation of a novel symbiosis-regulated plant gene. Mol. Gen. Genet. 256:1997;37-44.
28. Martin-Laurent F., Hallet S., Philippot L., Catroux G., Soulas G. Study of the expression level of Pseudomonas sp. pADP atzA, B and C degrading gene in response to atrazine and pH. 9th International Symposium on Microbial Ecology. 2001;355 ISME, Amsterdam, Netherland.
29. Mulbry W., Zhu H., Nour S., Topp E. The triazine hydrolase gene trzN from Nocardioides sp. strain C190: cloning and construction of gene-specific primers. FEMS Microbiol. Lett. 206:2002;75-79.
30. Nomura M., Gourse R., Baughman G. Regulation of the synthesis of ribosomes and ribosomal components. Annu. Rev. Biochem. 53:1984;75-117.
31. Piutti S., Hallet S., Rousseaux S., Philippot L., Soulas G., Martin-Laurent F. Accelerated mineralisation of atrazine in maize rhizosphere soil. Biol. Fertil. Soils. 36:2002;434-441.
32. Piutti S., Semon E., Landry D., Hartmann A., Dousset S., Lichtfouse E., Topp E., Soulas G., Martin-Laurent F. Isolation and characterisation of Nocardioides sp. SP12, an atrazine-degrading bacterial strain possessing the gene trzN from bulk- and maize rhizosphere soil. FEMS Microbiol. Lett. 221:2003;111-117.
33. Pussemier L., Goux S., Vanderheyden V., Debongnie P., Trésinie I., Foucart G. Rapid dissipation of atrazine in soils taken from various maize fields. Weed Res. 37:1997;171-179.
34. Radosevich M., Traina S., Hao Y., Tuovinen O. Degradation and mineralization of atrazine by a soil bacterial isolate. Appl. Environ. Microbiol. 61:1995;297-302.
35. Reid S., Green N., Buss J., Lei B., Musser J. Multilocus analysis of extracellular putative virulence proteins made by group A Streptococcus: population genetics, human serologic response, and gene transcription. Proc. Natl. Acad. Sci. U. S. A. 98:2001;7552-7557.
36. Rokbi B., Seguin D., Guy B., Mazarin V., Vidor E., Mion F., Cadoz M., Quentin-Millet M. Assessment of Helicobacter pylori gene expression within mouse and human gastric mucosae by real-time reverse transcriptase PCR. Infect. Immun. 69:2001;4759-4766.
37. Rousseaux S., Hartmann A., Soulas G. Isolation and characterisation of new Gram-negative and Gram-positive atrazine degrading bacteria from different French soils. FEMS Microbiol. Ecol. 36:2001;211-222.
38. Rousseaux S., Soulas G., Hartmann A. Plasmid localisation of atrazine-degrading genes in newly described Chelatobacter and Arthrobacter strains. FEMS Microbiol. Ecol. 41:2002;69-75.
39. Sadowsky M., Tong Z., Souza M.D., Wackett L. AtzC is a new member of the amidohydrolase protein superfamily and is homologous to other atrazine-metabolizing enzymes. J. Bacteriol. 180:1998;152-158.
40. Semighini C., Marins M., Goldman M.S., Goldman G. Quantitative analysis of the relative transcript levels of ABC transporter Atr genes in Aspergillus nidulans by real-time reverse transcription-PCR assay. Appl. Environ. Microbiol. 68:2002;1351-1357.
41. Smoot L., Smoot J., Graham M., Somerville G., Sturdevant D., Migliaccio C., Sylva G., Musser J. Global differential gene expression in response to growth temperature alteration in group A Streptococcus. Proc. Natl. Acad. Sci. U. S. A. 98:2001;10416-10421.
42. Solomon K., Baker D., Richards R., Dixon K., Klaine S., Point T., Kendall R., Weisskopf C., Giddings J., Giesy J., Hall L.J., Williams W. Ecological risk assessment of atrazine in North American surface waters. Environ. Toxicol. Chem. 15:1996;31-76.
43. Spliid N., Koppen B. Occurrence of pesticides in Danish shallow ground water. Chemosphere. 37:1998;1307-1316.
44. Struthers J., Jayachandran K., Moorman T. Biodegradation of atrazine by Agrobacterium J14a and use of this strain in bioremediation of contaminated soil. Appl. Environ. Microbiol. 64:1998;3368-3375.
45. Topp E., Mulbry W., Zhu H., Nour S., Cuppels D. Characterization of s-triazine herbicide metabolism by a Nocardioides sp. isolated from agricultural soils. Appl. Environ. Microbiol. 66:2000;3134-3141.
46. Topp E., Zhu H., Nour S., Houot S., Lewis M., Cuppels D. Characterization of an atrazine-degrading Pseudoaminobacter sp. isolated from Canadian and French agricultural soils. Appl. Environ. Microbiol. 66:2000;2773-2782.
47. Van der Meer J., Frijters A., Leveau J., Eggen R., Zehnder A., De Vos W. Characterization of the Pseudomonas sp. strain P51 gene tcbR, a LysR-type transcriptional activator of the tbcCDEF chlorocatechol oxidative operon, and analysis of the regulatory region. J. Bacteriol. 173:1991;3700-3708.
48. Vandecasteele S., Peetermans W., Merckx R., Eldere J.V. Quantification of expression of Staphylococcus epidermidis housekeeping genes with taqman quantitative PCR during in vitro growth and under different conditions. J. Bacteriol. 183:2001;7094-7101.
49. Wilson M., Bakermans C., Madsen E. In situ, real-time catabolic gene expression: extraction and characterization of naphtalene dioxygenase mRNA transcripts from groundwater. Appl. Environ. Microbiol. 65:1999;80-87.
50. Yajima T., Yagihashi A., Kameshima H., Kobayashi D., Furuya D., Hirata K., Watanabe N. Quantitative reverse transcription-PCR assay of the RNA component of human telomerase using the TaqMan fluorogenic detection system. Clin. Chem. 44:1998;2441-2445.
51. Yanze-Kontchou C., Gschwind N. Mineralization of the herbicide atrazine as a carbon source by a Pseudomonas strain. Appl. Environ. Microbiol. 60:1994;4297-4302.
52. Yuan A., Yu C., Luh K., Chen W., Lin F., Kuo S., Yang P. Quantification of VEGF mRNA expression in non-small cell lung cancer using a real-time quantitative reverse transcription-PCR assay and a comparison with quantitative competitive reverse transcription-PCR. Lab. Invest. 80:2000;1671-1680.