Normalization strategies for real-time expression data in Chlamydia trachomatis

Journal of Microbiological Methods

Volumn 82, Issue 3, 2010, Pages 256-264

  Borges, V ^a   Ferreira, R ^a   Nunes, A ^a   Nogueira, P ^a   Borrego, M J ^a   Gomes, J P ^a  

^a NATIONAL INSTITUTE OF HEALTH DR RICARDO JORGE   (Portugal)

Author keywords

Chlamydia trachomatis; Endogenous control; Expression; Genomic DNA; Housekeeping; Normalization

Indexed keywords

BACTERIAL PROTEIN; CYCLOSERINE; GENOMIC DNA; PROTEIN HEMN 2; PROTEIN KINASE FER; PROTEIN MAP; PROTEIN OPPA 2; PROTEIN TYRP 2; PROTEIN YAEL; PROTEIN YRAL; RADA PROTEIN; RNA 16S; UNCLASSIFIED DRUG;

ACCURACY; ARTICLE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; CHLAMYDIA TRACHOMATIS; COMPUTER PROGRAM; CONTROLLED STUDY; DEVELOPMENTAL STAGE; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE NUMBER; GENETIC ALGORITHM; GENETIC STABILITY; GENETIC VARIABILITY; HOUSEKEEPING GENE; INTERMETHOD COMPARISON; INTRACELLULAR BACTERIUM; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RELIABILITY; STABLE EXPRESSION; STRAIN DIFFERENCE; VALIDATION PROCESS;

BACTERIA (MICROORGANISMS); CHLAMYDIA TRACHOMATIS;

EID: 77955664179     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2010.06.013     Document Type: Article

References (41)

1. Albrecht M., Sharma C.M., Reinhardt R., Vogel J., Rudel T. Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome. Nucleic Acids Res. 2010, 38:868-877.
2. Andersen C.L., Jensen J.L., Orntoft T.F. Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res. 2004, 64:5245-5250. [http://www.mdl.dk/publicationsnormfinder.htm].
3. Applied Biosystems Guide to Performing Relative Quantitation of Gene Expression Using Real-Time Quantitative PCR 2008.
4. Belland R.J., Zhong G., Crane D.D., Hogan D., Sturdevant D., Sharma J., Beatty W.L., Caldwell H.D. Genomic transcriptional profiling of the developmental cycle of Chlamydia trachomatis. Proc. Natl. Acad. Sci. U. S. A. 2003, 100:8478-8483.
5. Bustin S.A. Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. J. Mol. Endocrinol. 2002, 29:23-39.
6. Bustin S.A., Benes V., Nolan T., Pfaffl M.W. Quantitative real-time RT-PCR - a perspective. J. Mol. Endocrinol. 2005, 34:597-601.
7. Coulson D.T., Brockbank S., Quinn J.G., Murphy S., Ravid R., Irvine G.B., Johnston J.A. Identification of valid reference genes for the normalization of RT qPCR gene expression data in human brain tissue. BMC Mol. Biol. 2008, 9:46.
8. Eleaume H., Jabbouri S. Comparison of two standardisation methods in real-time quantitative RT-PCR to follow Staphylococcus aureus genes expression during in vitro growth. J. Microbiol. Meth. 2004, 59:363-370.
9. Engström P., Bailey L., Onskog T., Bergström S., Johansson J. A comparative study of RNA and DNA as internal gene expression controls early in the developmental cycle of Chlamydia pneumoniae. FEMS Immunol. Med. Microbiol. 2010, 58:244-253.
10. Gomes J.P., Hsia R.C., Mead S., Borrego M.J., Dean D. Immunoreactivity and differential developmental expression of known and putative Chlamydia trachomatis membrane proteins for biologically variant serovars representing distinct disease groups. Microbes Infect. 2005, 7:410-420.
11. Gomes J.P., Borrego M.J., Atik B., Santo I., Azevedo J., Brito de Sá A., Nogueira P., Dean D. Correlating Chlamydia trachomatis infectious load with urogenital ecological success and disease pathogenesis. Microbes Infect. 2006, 8:16-26.
12. Gordon B.F., Quan A.L. Susceptibility of Chlamydia to antibacterial drugs: tests in cell culture. Antimicrob. Agents Chemother. 1972, 2:242-244.
13. Hendriks-Balk M.C., Michel M.C., Alewijnse A.E. Pitfalls in the normalization of real-time polymerase chain reaction data. Basic Res. Cardiol. 2007, 102:195-197.
14. Hoogewijs D., Houthoofd K., Matthijssens F., Vandesompele J., Vanfleteren J.R. Selection and validation of a set of reliable reference genes for quantitative sod gene expression analysis in C. elegans. BMC Mol. Biol. 2008, 9:9.
15. How S.J., Hobson D., Hart C.A. Studies in vitro of the nature and synthesis of the cell wall of Chlamydia trachomatis. Curr. Microbiol. 1984, 10:269-274.
16. Hu R., Fan C., Li H., Zhang Q., Fu Y.F. Evaluation of putative reference genes for gene expression normalization in soybean by quantitative real-time RT-PCR. BMC Mol. Biol. 2009, 10:93.
17. Huggett J., Dheda K., Bustin S., Zumla A. Real-time normalization; strategies and considerations. Genes Immun. 2005, 6:279-284.
18. Johnson D.R., Lee P.K., Holmes V.F., Alvarez-Cohen L. An internal reference technique for accurately quantifying specific mRNAs by real-time PCR with application to the tceA reductive dehalogenase gene. Appl. Environ. Microbiol. 2005, 71:3866-3871.
19. Karrer E.E., Lincoln J.E., Hogenhout S., Bennett A.B., Bostock R.M., Martineau B., Lucas W.J., Gilchrist D.G., Alexander D. In situ isolation of mRNA from individual plant cells: creation of cell-specific cDNA libraries. Proc. Natl. Acad. Sci. U. S. A. 1995, 92:3814-3818.
20. Klos A., Thalmann J., Peters J., Gérard H.C., Hudson A.P. The transcript profile of persistent Chlamydophila (Chlamydia) pneumoniae in vitro depends on the means by which persistence is induced. FEMS Microbiol. Lett. 2009, 291:120-126.
21. Lamond A.I., Travers A.A. Stringent control of bacterial transcription. Cell 1985, 41:6-8.
22. Mathews S.A., Volp K.M., Timms P. Development of a quantitative gene expression assay for Chlamydia trachomatis identified temporal expression of sigma factors. FEBS Lett. 1999, 458:354-358.
23. Mäurer A.P., Mehlitz A., Mollenkopf H.J., Meyer T.F. Gene expression profiles of Chlamydophila pneumoniae during the developmental cycle and iron depletion-mediated persistence. PLoS Pathog. 2007, 3:e83.
24. McCoy A.J., Maurelli A.T. Characterization of Chlamydia MurC-Ddl, a fusion protein exhibiting d-alanyl-d-alanine ligase activity involved in peptidoglycan synthesis and d-cycloserine sensitivity. Mol. Microbiol. 2005, 57:41-52.
25. Miyairi I., Mahdi O.S., Ouellette S.P., Belland R.J., Byrne G.I. Different growth rates of Chlamydia trachomatis biovars reflect pathotype. J. Infect. Dis. 2006, 194:350-357.
26. Moulder J.W., Norosel D.L., Officer J.E. Inhibition of the growth of agents of the psitticosis group by d-cycloserine and its specific reversal by d-alanine. J. Bacteriol. 1962, 85:707-711.
27. Nicholson T.L., Olinger L., Chong K., Schoolnik G., Stephens R.S. Global stage-specific gene regulation during the developmental cycle of Chlamydia trachomatis. J. Bacteriol. 2003, 185:3179-3189.
28. Nicholson T.L., Chiu K., Stephens R.S. Chlamydia trachomatis lacks an adaptive response to changes in carbon source availability. Infect. Immun. 2004, 72:4286-4289.
29. Nielsen K.K., Boye M. Real-time quantitative reverse transcription-PCR analysis of expression stability of Actinobacillus pleuropneumoniae housekeeping genes during in vitro growth under iron-depleted conditions. Appl. Environ. Microbiol. 2005, 71:2949-2954.
30. Nunes A., Gomes J.P., Mead S., Florindo C., Correia H., Borrego M.J., Dean D. Comparative expression profiling of the Chlamydia trachomatis pmp gene family for clinical and reference strains. PLoS ONE 2007, 12:e878.
31. Nunes A., Nogueira P.J., Borrego M.J., Gomes J.P. Chlamydia trachomatis diversity viewed as a tissue-specific coevolutionary arms race. Genome Biol. 2008, 9:R153.
32. Ouellette S.P., Hatch T.P., AbdelRahman Y.M., Rose L.A., Belland R.J., Byrne G.I. Global transcriptional upregulation in the absence of increased translation in Chlamydia during IFNgamma-mediated host cell tryptophan starvation. Mol. Microbiol. 2006, 62:1387-1401.
33. Pfaffl M.W., Tichopad A., Prgomet C., Neuvians T.P. Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper - Excel-based tool using pair-wise correlations. Biotechnol. Lett. 2004, 26:509-515.
34. Savli H., Karadenizli A., Kolayli F., Gundes S., Ozbek U., Vahaboglu H. Expression stability of six housekeeping genes: a proposal for resistance gene quantification studies of Pseudomonas aeruginosa by real-time quantitative RT-PCR. J. Med. Microbiol. 2003, 52:403-408.
35. Shaw E.I., Dooley C.A., Fischer E.R., Scidmore M.A., Fields K.A., Hackstadt T. Three temporal classes of gene expression during the Chlamydia trachomatis developmental cycle. Mol. Microbiol. 2000, 37:913-925.
36. Thellin O., Zorzi W., Lakaye B., De Borman B., Coumans B., Hennen G., Grisar T., Igout A., Heinen E. Housekeeping genes as internal standards: use and limits. J. Biotechnol. 1999, 75:291-295.
37. Vandecasteele S.J., Peetermans W.E., Merckx R., Van Eldere J. Quantification of expression of Staphylococcus epidermidis housekeeping genes with Taqman quantitative PCR during in vitro growth and under different conditions. J. Bacteriol. 2001, 183:7094-7101.
38. Vandecasteele S.J., Peetermans W.E., Merckx R., Van Ranst M., Van Eldere J. Use of gDNA as internal standard for gene expression in Staphylococci in vitro and in vivo. Biochem. Biophys. Res. Commun. 2002, 291:528-534.
39. Vandesompele J., De Preter K., Pattyn F., Poppe B., Van Roy N., De Paepe A., Speleman F. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002, 3. research0034.1-0034.11. [http://genomebiology.com/2002/3/7/research/0034].
40. Wooters M.A., Kaufhold R.M., Field J.A., Indrawati L., Heinrichs J.H., Smith J.G. A real-time quantitative polymerase chain reaction assay for the detection of Chlamydia in the mouse genital tract model. Diagn. Microbiol. Infect. Dis. 2009, 63:140-147.
41. Zhong H., Simons J.W. Direct comparison of GAPDH, beta-actin, cyclophilin, and 28S rRNA as internal standards for quantifying RNA levels under hypoxia. Biochem. Biophys. Res. Commun. 1999, 16:523-526.