Prokaryotic suppression subtractive hybridization PCR cDNA subtraction, a targeted method to identity differentially expressed genes

Applied and Environmental Microbiology

Volumn 74, Issue 1, 2008, Pages 225-232

  De Long, Susan K ^a   Kinney, Kerry A ^a   Kirisits, Mary Jo ^a  

^a The University of Texas at Austin   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIODEGRADATION; DNA; ENZYMES; MOLECULAR BIOLOGY; TOLUENE;

BIODEGRADATION GENES; BIOLOGICAL TREATMENT SYSTEMS; PROKARYOTIC SUPPRESSION; SUPPRESSION SUBTRACTIVE HYBRIDIZATION (SSH);

GENE EXPRESSION;

ACETIC ACID; BACTERIAL DNA; COMPLEMENTARY DNA; TOLUENE;

BIODEGRADATION; DNA; ENZYME; GENE EXPRESSION; IDENTIFICATION METHOD; MOLECULAR ANALYSIS; POLYMERASE CHAIN REACTION; PROKARYOTE;

ARTICLE; BIODEGRADABILITY; GENE EXPRESSION; GENE IDENTIFICATION; GENE SEQUENCE; MICROBIAL DEGRADATION; MICROBIAL GROWTH; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; POLLUTANT; POLYMERASE CHAIN REACTION; PROKARYOTE; PSEUDOMONAS PUTIDA; SUPPRESSION SUBTRACTIVE HYBRIDIZATION;

ACETIC ACID; GENE EXPRESSION PROFILING; GENETICS, MICROBIAL; NUCLEIC ACID HYBRIDIZATION; POLYMERASE CHAIN REACTION; PSEUDOMONAS PUTIDA; TOLUENE;

EUKARYOTA; PROKARYOTA; PSEUDOMONAS PUTIDA;

EID: 37849046638     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.01647-07     Document Type: Article

References (41)

1. Alleman, B., et al. 2005. SERDP and ESTCP expert panel workshop on research and development needs for the environmental remediation application of molecular biological tools. Final report. http://docs.serdp-estcp.org/viewfile. cfm?Doc=MBT%20Workshop%20Report%2Epdf.
2. Amann, R., B. M. Fuchs, and S. Behrens. 2001. The identification of microorganisms by fluorescence in situ hybridisation. Curr. Opin. Biotechnol. 12:231-236.
3. Bathe, S., and P. R. Norris. 2007. Ferrous iron- and sulfur-induced genes in Sulfolobus metallicus. Appl. Environ. Microbiol. 73:2491-2497.
4. Bauchop, T., and S. R. Elsden. 1960. The growth of micro-organisms in relation to their energy supply. J. Gen. Microbiol. 23:457-469.
5. Becker, P., W. Hufnagle, G. Peters, and M. Herrmann. 2001. Detection of differential gene expression in biofilm-forming versus planktonic populations of Staphylococcus aureus using micro-representational- difference analysis. Appl. Environ. Microbiol. 67:2958-2965.
6. Bowler, L. D., M. Hubank, and B. G. Spratt. 1999. Representational difference analysis of cDNA for the detection of differential gene expression in bacteria: development using a model of iron-regulated gene expression in Neisseria meningitidis. Microbiology 145:3529-3537.
7. Burlage, R. S., S. W. Hooper, and G. S. Sayler. 1989. The TOL (pWW0) catabolic plasmid. Appl. Environ. Microbiol. 55:1323-1328.
8. Cole, A. C., M. J. Semmens, and T. M. LaPara. 2004. Stratification of activity and bacterial community structure in biofilms grown on membranes transferring oxygen. Appl. Environ. Microbiol. 70:1982-1989.
9. Diatchenko, L., Y.-F. C. Lau, A. P. Campbell, A. Chenchik, F. Mogadam, B. Huang, S. Lukyanov, K. Lukyanov, N. Gurskaya, E. D. Sverdlov, and P. D. Siebert. 1996. Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc. Natl. Acad. Sci. USA 93:6025-6030.
10. Domínguez-Cuevas, P., J. E. González-Pastor, S. Marqués, J. L. Ramos, and V. de Lorenzo. 2006. Transcriptional tradeoff between metabolic and stress-response programs in Pseudomonas putida KT2440 cells exposed to toluene. J. Biol. Chem. 281:11981- 11991.
11. Fleming, J. T., W. H. Yao, and G. S. Sayler. 1998. Optimization of differential display of prokaryotic mRNA: application to pure culture and soil microcosms. Appl. Environ. Microbiol. 64:3698-3706.
12. Franklin, F. C. H., M. Bagdasarian, M. M. Bagdasarian, and K. N. Timmis. 1981. Molecular and functional analysis of the TOL plasmid pWW0 from Pseudomonas putida and cloning of genes for the entire regulated aromatic ring meta cleavage pathway. Proc. Natl. Acad. Sci. USA 78:7458-7462.
13. Gerard, G. 1994. Inhibition of SuperScript II reverse transcriptase by common laboratory chemicals. Focus 16:102-103.
14. Greated, A., L. Lambertsen, P. A. Williams, and C. M. Thomas. 2002. Complete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putida. Environ. Microbiol. 4:856-871.
15. Greer, S., and S. Zamenhof. 1962. Studies on depurination of DNA by heat. J. Mol. Biol. 4:123-141.
16. Gurskaya, N. G., L. Diatchenko, A. Chenchik, P. D. Siebert, G. L. Khaspekov, K. A. Lukyanov, L. L. Vagner, O. D. Ermolaeva, S. A. Lukyanov, and E. D. Sverdlov. 1996. Equalizing cDNA subtraction based on selective suppression of polymerase chain reaction: cloning of Jurkat cell transcripts induced by phytohemaglutinin and phorbol 12-myristate 13-acetate. Anal. Biochem. 240:90-97.
17. Hall, S. J., P. Hugenholtz, N. Siyambalapitiya, J. Keller, and L. L. Blackall. 2002. The development and use of real-time PCR for the quantification of nitrifiers in activated sludge. Water Sci. Technol. 46:267-272.
18. Harms, G., A. C. Layton, H. M. Dionisi, I. R. Gregory, V. M. Garrett, S. A. Hawkins, K. G. Robinson, and G. S. Sayler. 2003. Real-time PCR quantification of nitrifying bacteria in a municipal wastewater treatment plant. Environ. Sci. Technol. 37:343-351.
19. Ji, W., M. B. Wright, L. Cai, A. Flament, and K. Lindpaintner. 2002. Efficacy of SSH PCR in isolating differentially expressed genes. BMC Genomics 3:12.
20. Jiménez, J. I., B. Miñambres, J. L. García, and E. Díaz. 2002. Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environ. Microbiol. 4:824-841.
21. Kelly, J. J., S. Siripong, J. McCormack, L. R. Janus, H. Urakawa, S. El Fantroussi, P. A. Noble, L. Sappelsa, B. E. Rittmann, and D. A. Stahl. 2005. DNA microarray detection of nitrifying bacterial 16S rRNA in wastewater treatment plant samples. Water Res. 39:3229-3238.
22. Koizumi, Y., J. J. Kelly, T. Nakagawa, H. Urakawa, S. El-Fantroussi, S. Al-Muzaini, M. Fukui, Y. Urushigawa, and D. A. Stahl. 2002. Parallel characterization of anaerobic toluene- and ethylbenzene-degrading microbial consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization, and DNA microarray technology. Appl. Environ. Microbiol. 68:3215-3225.
23. Layton, A. C., H. Dionisi, H. W. Kuo, K. G. Robinson, V. M. Garrett, A. Meyers, and G. S. Sayler. 2005. Emergence of competitive dominant ammonia-oxidizing bacterial populations in a full-scale industrial wastewater treatment plant. Appl. Environ. Microbiol. 71:1105-1108.
24. Lee, P. K. H., D. R. Johnson, V. F. Holmes, J. Z. He, and L. Alvarez-Cohen. 2006. Reductive dehalogenase gene expression as a biomarker for physiological activity of Dehalococcoides spp. Appl. Environ. Microbiol. 72:6161-6168.
25. Lovley, D. R. 2003. Cleaning up with genomics: applying molecular biology to bioremediation. Nat. Rev. Microbiol. 1:35-44.
26. Loy, A., C. Schulz, S. Lücker, A. Schöpfer-Wendels, K. Stoecker, C. Baranyi, A. Lehner, and M. Wagner. 2005. 16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order "Rhodocyclales". Appl. Environ. Microbiol. 71:1373-1386.
27. Maniatis, T., J. Sambrook, and E. F. Fritsch. 1982. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
28. Marlowe, E. M., J. M. Wang, I. L. Pepper, and R. M. Maier. 2002. Application of a reverse transcription-PCR assay to monitor regulation of the catabolic nahAc gene during phenanthrene degradation. Biodegradation 13: 251-260.
29. Nagel, A. C., J. T. Fleming, G. S. Sayler, and K. L. Beattie. 2001. Screening for ribosomal-based false positives following prokaryotic mRNA differential display. BioTechniques 30:988-996.
30. Nelson, K. E., C. Weinel, I. T. Paulsen, R. J. Dodson, H. Hilbert, V. dos Santos, D. E. Fouts, S. R. Gill, M. Pop, M. Holmes, L. Brinkac, M. Beanan, R. T. DeBoy, S. Daugherty, J. Kolonay, R. Madupu, W. Nelson, O. White, J. Peterson, H. Khouri, I. Hance, P. C. Lee, E. Holtzapple, D. Scanlan, K. Tran, A. Moazzez, T. Utterback, M. Rizzo, K. Lee, D. Kosack, D. Moestl, H. Wedler, J. Lauber, D. Stjepandic, J. Hoheisel, M. Straetz, S. Heim, C. Kiewitz, J. Eisen, K. N. Timmis, A. Düsterhöft, B. Tümmler, and C. M. Fraser. 2002. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ. Microbiol. 4:799-808.
31. Pääbo, S., D. M. Irwin, and A. C. Wilson. 1990. DNA damage promotes jumping between templates during enzymatic amplification. J. Biol. Chem. 265:4718-4721.
32. Paulino, L. C., M. P. de Mello, and L. M. M. Ottoboni. 2002. Differential gene expression in response to copper in Acidithiobacillus ferrooxidans analyzed by RNA arbitrarily primed polymerase chain reaction. Electrophoresis 23:520-527.
33. Pernthaler, A., and R. Amann. 2004. Simultaneous fluorescence in situ hybridization of mRNA and rRNA in environmental bacteria. Appl. Environ. Microbiol. 70:5426-5433.
34. Rittmann, B. E. 2002. The role of molecular methods in evaluating biological treatment processes. Water Environ. Res. 74:421-427.
35. Rivera-Marrero, C. A., M. A. Burroughs, R. A. Masse, F. O. Vannberg, D. L. Leimbach, J. Roman, and J. J. Murtagh. 1998. Identification of genes differentially expressed in Mycobacterium tuberculosis by differential display PCR. Microb. Pathog. 25:307-316.
36. Roger, M., and R. D. Hotchkiss. 1961. Selective heat inactivation of pneumococcal transforming deoxyribonucleate. Proc. Natl. Acad. Sci. USA 47: 653-669.
37. Sharkey, F. H., I. M. Banat, and R. Marchant. 2004. Detection and quantification of gene expression in environmental bacteriology. Appl. Environ. Microbiol. 70:3795-3806.
38. Shepard, B. D., and M. S. Gilmore. 1999. Identification of aerobically and anaerobically induced genes in Enterococcus faecalis by random arbitrarily primed PCR. Appl. Environ. Microbiol. 65:1470-1476.
39. Silyn-Roberts, G., and G. Lewis. 2001. In situ analysis of Nitrosomonas spp. in wastewater treatment wetland biofilms. Water Res. 35:2731-2739.
40. Stoffels, M., R. Amann, W. Ludwig, D. Hekmat, and K. H. Schleifer. 1998. Bacterial community dynamics during start-up of a trickle-bed bioreactor degrading aromatic compounds. Appl. Environ. Microbiol. 64:930-939.
41. Zhang, H., B. E. Logan, J. M. Regan, L. A. Achenbach, and M. A. Bruns. 2005. Molecular assessment of inoculated and indigenous bacteria in biofilms from a pilot-scale perchlorate-rcducing bioreactor. Microb. Ecol. 49: 388-398.