Quantification of gene expression in methanotrophs by competitive reverse transcription-polymerase chain reaction

Environmental Microbiology

Volumn 6, Issue 4, 2004, Pages 388-399

  Han, Jong In ^a   Semrau, Jeremy D ^a  

^a University of Michigan   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; BACTERIAL RNA;

ARTICLE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; METHYLOCOCCACEAE; MICROBIOLOGY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; STATISTICS;

BACTERIAL PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; METHYLOCOCCACEAE; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, BACTERIAL; SOIL MICROBIOLOGY; STATISTICS;

BACTERIA (MICROORGANISMS); METHYLOCOCCACEAE; PROKARYOTA;

EID: 1842614298     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2004.00572.x     Document Type: Article

References (53)

1. Alfreider, A., Vogt, C., and Babel, W. (2003) Expression of chlorocatechol 1,2-dioxygenase and chlorocatechol 2,3-dioxyegnase genes in chlorobenzene-contaminated subsurface samples. Appl Environ Microbiol 69: 1372-1376.
2. Alm, E.W., and Stahl, D.A. (2000) Critical factors influencing the recovery and integrity of rRNA extracted from environmental samples: use of an optimized protocol to measure depth-related biomass distribution in freshwater sediments. J Microbiol Meth 40: 153-162.
3. Arnal, C., Ferre-Aubinmeau, V., Mignotte, B., Imbert-Marcille, B.-M., and Billaudel, S. (1999) Quantification of hepatitis A virus in shellfish by competitive reverse transcription-PCR with coextraction of standard RNA. Appl Environ Microbiol 65: 322-326.
4. Beck, A., Lehmann, R., Gambaro, G., Häring, H.-U., Schleicher, E.D., Voelter, W., and Ceol, M. (1999) Advances in reverse transcription polymerase chain reaction analysis of cellular mRNA levels of transforming growth factor-β1 by capillary electrophoresis with laser-induced fluorescence detection. Clin Chem Laboratory Med 37: 527-532.
5. Bogan, B.W., Schoenike, B., Lamar, R.T., and Cullen, A. (1996) Mangenase peroxidase mRNA and enzyme activity levels during bioremediation of polycyclic aromatic-hydrocarbon contaminated soil with Phanerochaete chrysporium. Appl Environ Microbiol 62: 2381-2386.
6. Borneman, J., and Triplett, E.W. (1997) Rapid and direct method for extraction of RNA from soil. Soil Biol Biochem 29: 1621-1624.
7. Bürgmann, H., Widmer, F., Sigler, W.V., and Zeyer, J. (2003) mRNA extraction and reverse transcription-PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil. Appl Environ Microbiol 69: 1928-1935.
8. Burrows, K.J., Cornish, A., Scott, D., and Higgins, I.J. (1984) Substrate specificities of the soluble and particulate methane mono-oxygenases of Methylosinus trichosporium OB3b. J Gen Microbiol 130: 3327-3333.
9. Burstcher, C., and Wuertz, S. (2003) Evaluation of the use of PCR and reverse transcriptase PCR for detection of pathogenic bacteria in biosolids from anaerobic digestors and aerobic composters. Appl Environ Microbiol 69: 4618-4627.
10. Cheng, Y.S., Halsey, J.L., Fode, K.A., Remsen, C.C., and Collins, M.L.P. (1999) Detection of methanotrophs in groundwater by PCR. Appl Environ Microbiol 65: 648-651.
11. Chiari, M., Cretich, M., and Horvath, J. (2000) A new adsorbed coating for DNA fragment analysis by capillary electrophoresis. Electrophoresis 21: 1521-1526.
12. Choi, D.W., Kunz, R.C., Boyd, E.S., Semrau, J.D., Antholine, W.E., Han, J.L. et al., (2003) The membrane-associated methane monooxygenase (pMMO) and pMMO-NADH: quinone oxidoreductase complex from Methylococcus capsulatus Bath. J Bacteriol 185: 5755-5764.
13. Chomczynski, P., and Sacchi, N. (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenolchloroform extraction. Anal Biochem 162: 156-159.
14. Ferre, F. (1992) Quantitative or semi-quantitative PCR: reality versus myth. PCR Meth Appl 2: 1-9.
15. Fleming, J.T., Yao, W.-H., and Sayler, G.S. (1998) Optimization of differential display of prokaryotic mRNA: application to pure culture and soil microcosms. Appl Environ Microbiol 64: 3698-3706.
16. Freeman, W.M., Walker, S.J., and Vrana, K.E. (1999) Quantitative RT-PCR: pitfalls and potential. Biotechniques 26: 112-125.
17. Gao, Q., and Yeung, E.S. (1998) A matrix for DNA separation: genotyping and sequencing using poly (vinylpyrrolidone) solution in uncoated capillaries. Anal Chem 70: 1382-1388.
18. Han, F., Xue, J., and Lin, B. (1998) Mannitol influence on the separation of DNA fragments by capillary electrophoresis in entangled polymer solutions. Talanta 46: 735-742.
19. Han, J.-I., Lontoh, S., and Semrau, J.D. (1999) Degradation of chlorinated and brominated hydrocarbons by Methylomicrobium album BG8. Arch Microbiol 172: 393-400.
20. Hanson, R.S., and Hanson, T.E. (1996) Methanotrophic bacteria. Microbiol Rev 60: 439-471.
21. Hill, G.T., Mitkowski, N.A., Aldrich-Wolfe, L., Emele, E.R., Jurkonie, D.D., Ficke, A. et al. (2000) Methods for assessing the composition and diversity of soil microbial communities. Appl Soil Ecol 15: 25-36.
22. Huang, W., Young, T.M., and Schlautman, M.A., Yu, H., and Weber, W.J. (1997) A distributed reactivity model for sorption by soils and sediments. 9. General isotherm nonlinearity and applicability of the dual reactive domain model. Environ Sci Technol 31: 1703-1710.
23. Kreader, C.A. (1996) Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein. Appl Environ Microbiol 62: 1102-1106.
24. Kusher, S.R. (1996) mRNA decay. In Escherichia Coli and Salmonella: Cellular and Molecular Biology, Vol. 1. Neidhardt, F.C., Curtiss, R., Ingraham, J.L., Lin, E.C.C., Low, K.B., Magasanik, B., et al. (eds). Washington, DC: American Society for Microbiology, pp. 849-860.
25. Lehmann, R., Voelter, W., and Liebich, H.M. (1997) Capillary electrophoresis in clinical chemistry. J Chromatogr B 697: 3-35.
26. Lindahl, T. (1993) Instability and decay of the primary structure of DNA. Nature 362: 709-715.
27. Lontoh, S., DiSpirito, A.A., Krema, C.L., Whittaker, M.R., Hooper, A.B., and Semrau, J.D. (2000) Differential inhibition in vivo of ammonia monooxygenase, soluble methane monooxygenase, and membrane-associated methane monooxygenase by phenylacetylene. Environ Microbiol 2: 485-494.
28. Lorenz, M.G., and Wackernagel, W. (1987) Adsorption of DNA to sand and variable degradation rates of adsorbed DNA. Appl Environ Microbiol 53: 2948-2952.
29. McCarty, P.L. (1997) Aerobic cometabolism of chlorinated aliphatic hydrocarbons. In Subsurface Restoration. Ward, C.H., Cherry, J.A., Scalf, M.R., (eds). Ann Arbor, MI: Ann Arbor Press, pp. 373-395.
30. McDonald, I.R., Kenna, E.M., and Murrell, J.C. (1995) Detection of methanotrophic bacteria in environmental samples with the PCR. Appl Environ Microbiol 61: 116-121.
31. McDonald, I.R., and Murrell, J.C. (1997) The particulate methane monooxygenase gene pmoA and its use as a functional gene probe for methanotrophs. FEMS Microbiol Lett 156: 205-210.
32. Meckenstock, R., Steinle, P., van der Meer, J.R., and Snozzi, M. (1998) Quantification of bacterial mRNA involved in degradation of 1,2,4- trichlorobenzene by Pseudomonas sp. strain P51 from liquid culture and from river sediment by reverse transcriptase PCR (RT/PCR). FEMS Microbiol Lett 67: 123-129.
33. Melzak, K.A., Sherwood, C.S., Turner, R.F.B., and Haynes, C.A. (1996) Driving forces for DNA adsorption to silica in perchlorate solutions. J Colloid Interface Sci 181: 635-644.
34. Miskin, I.P., Farrimond, P., and Head, I.M. (1999) Identification of novel bacterial lineages as active members of microbial populations in a freshwater sediment using a rapid RNA extraction procedure and RT-PCR. Microbiology 145: 1977-1987.
35. Moran, M.A., Torsvik, V.L., Torsvik, T., and Hodson, R.E. (1993) Direct extraction and purification of rRNA for ecological studies. Appl Environ Microbiol 59: 915-918.
36. Murrell, J.C. (1992) Genetics and molecular biology of methanotrophs. FEMS Microbiol Rev 88: 233-248.
37. Murrell, J.C., McDonald, I.R., and Bourne, D.G. (1998) Molecular methods for the study of methanotroph ecology. FEMS Microbiol Ecol 27: 103-114.
38. Nogales, B., Timmis, K.N., Nedwell, D.B., and Osborn, A.M. (2002) Detection and diversity of expressed denitrification genes in estuarine sediments after reverse transcription-PCR amplification from mRNA. Appl Environ Microbiol 68: 5017-5025.
39. Ogram, A.V., Mathot, M.L., Harsh, J.B., Boyle, J., and Pettigrew, C.A. (1994) Effects of DNA polymer length on its adsorption to soils. Appl Environ Microbiol 60: 393-396.
40. Oldenhuis, R., Vink, R.L.J.M., Janssen, D.B., and Witholt, B. (1989) Degradation of chlorinated aliphatic hydrocarbon by Methylosinus trichosporium OB3b expressing soluble methane monooxygenase. Appl Environ Microbiol 55: 2819-2826.
41. Rechards, M.P., Ashwell, C.M., and McMurtry, J.P. (2000) Quantitative analysis of leptin mRNA using competitive reverse transcription polymerase chain reaction and capillary electrophoresis with laser-induced fluorescence detection. Electrophoresis 21: 792-798.
42. Semrau, J.D., Chistoserdov, A., Lebron, J., Costello, A., Davignino, J., Kenna, E., et al. (1995) Particulate methane monooxygenase genes in methanotrophs. J Bacteriol 177: 3071-3079.
43. Sheridan, G.E.C., Masters, C.I., Shallcross, J.A., and Mackey, B.M. (1998) Detection of mRNA by reverse transcription-PCR as an indicator of viability in Escherichia coli cells. Appl Environ Microbiol 64: 1313-1318.
44. Shihabi, Z.K. (1999) Capillary electrophoresis of double-stranded DNA in an untreated capillary. J Chromatogr A 853: 349-354.
45. Spring, S., Schulze, R., Overmann, J., and Schleifer, K.-H. (2000) Identification and characterization of ecologically significant prokaryotes in the sediment of freshwater lakes: molecular and cultivation studies. FEMS Microbiol Rev 24: 573-590.
46. Stirling, D.I., Colby, J., and Dalton, H. (1979) A comparison of the substrate and electron-donor specificities of the methane monooxygenase from three strains of methane-oxidizing bacteria. Biochem J 177: 361-364.
47. Stolyar, S., Costello, A.M., Peeples, T.L., and Lidstrom, M.E. (1999) Role of multiple gene copies in particulate methane monooxygenase activity in the methane-oxidizing bacterium Methylococcus capsulatus Bath. Microbiology 145: 1235-1244.
48. Sunada, W.M., and Blanch, H.W. (1997) Polymeric separation media for capillary electrophoresis to the post-polymerase chain reaction analysis of nucleic acids. Electrophoresis 18: 2243-2254.
49. Tsai, S.J., and Wiltbank, M.C. (1998) Standard curve quantitative competitive RT-PCR (SC-QC-RT-PCR): a simple method to quantify absolute concentration of mRNA from limited amounts of sample. In Gene Cloning and Analysis by RT-PCR. Siebert, P.D., and Larrick, J.W., (eds). Westborough, MA: BioTechniques® Books, Eaton Publishing, pp. 91-101.
50. Whittenbury, R.K., Philips, K.D., and Wilkinson, J.F. (1970) Enrichment, isolation and some properties of methane-utilizing bacteria. J Gen Microbiol 61: 205-218.
51. Wilson, S.S., Bakermans, C., and Madsen, E.L. (1999) In situ, real-time catabolic gene expression: extraction and characterization of naphthalene dioxygenase mRNA transcripts from groundwater. Appl Environ Microbiol 65: 80-87.
52. von Wintzingerode, F., Gobel, U.B., and Stackebrandt, E. (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21: 213-229.
53. Zhang, N., and Yeung, E.S. (1998) On-line coupling of polymerase chain reaction and capillary electrophoresis for automatic DNA typing and HIV-1 diagnosis. J Chromatogr B 714: 3-11.