Evaluation of reference genes for real-time quantitative PCR in the marine flavobacterium Zobellia galactanivorans

Journal of Microbiological Methods

Volumn 84, Issue 1, 2011, Pages 61-66

  Thomas, François ^a   Barbeyron, Tristan ^a   Michel, Gurvan ^a,b  

^a SORBONNE UNIVERSITÉ   (France)

^b STATION BIOLOGIQUE DE ROSCOFF   (France)

Author keywords

Algae; Marine Bacteroidetes; Marine polysaccharide; Reference genes; RT qPCR; Zobellia

Indexed keywords

AMINO ACID; AROMATIC COMPOUND; CITRIC ACID; DIHYDROFOLIC ACID; GLYCINE HYDROXYMETHYLTRANSFERASE; GUANYLATE KINASE; ISOCITRATE DEHYDROGENASE (NADP); NUCLEOTIDE; PEPTIDOGLYCAN;

ARTICLE; BACTERIAL GENE; CARBON SOURCE; CONTROLLED STUDY; FLAVOBACTERIUM; GENE EXPRESSION; GENETIC STABILITY; MARINE SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RNA EXTRACTION; SEQUENCE ANALYSIS; TEMPERATURE STRESS; TRANSCRIPTION INITIATION; TRANSCRIPTOMICS; TRANSLATION INITIATION; ZOBELLIA GALACTANIVORANS;

FLAVOBACTERIACEAE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; POLYMERASE CHAIN REACTION; REFERENCE STANDARDS;

ALGAE; BACTEROIDETES; FLAVOBACTERIA; FLAVOBACTERIUM; ZOBELLIA; ZOBELLIA GALACTANIVORANS;

EID: 78650200972     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2010.10.016     Document Type: Article

References (37)

1. Ahn K., Huh J.W., Park S.J., Kim D.S., Ha H.S., Kim Y.J., et al. Selection of internal reference genes for SYBR green qRT-PCR studies of rhesus monkey (Macaca mulatta) tissues. BMC Mol. Biol. 2008, 9:78.
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.
3. Barbeyron T., L'Haridon S., Corre E., Kloareg B., Potin P. Zobellia galactanovorans gen. nov., sp. nov., a marine species of Flavobacteriaceae isolated from a red alga, and classification of. Int. J. Syst. Evol. Microbiol. 2001, 51:985-997.
4. Barbeyron T., L'Haridon S., Michel G., Czjzek M. Mariniflexile fucanivorans sp. nov., a marine member of the Flavobacteriaceae that degrades sulphated fucans from brown algae. Int. J. Syst. Evol. Microbiol. 2008, 58:2107-2113.
5. Barsalobres-Cavallari C.F., Severino F.E., Maluf M.P., Maia I.G. Identification of suitable internal control genes for expression studies in Coffea arabica under different experimental conditions. BMC Mol. Biol. 2009, 10:1.
6. Bauer M., Kube M., Teeling H., Richter M., Lombardot T., Allers E., et al. Whole genome analysis of the marine Bacteroidetes 'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter. Environ. Microbiol. 2006, 8:2201-2213.
7. Bustin S.A., Benes V., Garson J.A., Hellemans J., Huggett J., Kubista M., et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin. Chem. 2009, 55:611-622.
8. Colin S., Deniaud E., Jam M., Descamps V., Chevolot Y., Kervarec N., et al. Cloning and biochemical characterization of the fucanase FcnA: definition of a novel glycoside hydrolase family specific for sulfated fucans. Glycobiology 2006, 16:1021-1032.
9. Cosse A., Leblanc C., Potin P. Dynamic defense of marine macroalgae against pathogens: from early activated to gene-regulated responses. Adv. Bot. Res. 2007, 46:221-266.
10. de Boer M.E., de Boer T.E., Marien J., Timmermans M.J., Nota B., van Straalen N.M., et al. Reference genes for QRT-PCR tested under various stress conditions in Folsomia candida and Orchesella cincta (Insecta, Collembola). BMC Mol. Biol. 2009, 10:54.
11. Dheda K., Huggett J.F., Bustin S.A., Johnson M.A., Rook G., Zumla A. Validation of housekeeping genes for normalizing RNA expression in real-time PCR. Biotechniques 2004, 37:112-119.
12. Duchaud E., Boussaha M., Loux V., Bernardet J.F., Michel C., Kerouault B., et al. Complete genome sequence of the fish pathogen Flavobacterium psychrophilum. Nat. Biotechnol. 2007, 25:763-769.
13. Eilers H., Pernthaler J., Peplies J., Glockner F.O., Gerdts G., Amann R. Isolation of novel pelagic bacteria from the German bight and their seasonal contributions to surface picoplankton. Appl. Environ. Microbiol. 2001, 67:5134-5142.
14. Flament D., Barbeyron T., Jam M., Potin P., Czjzek M., Kloareg B., et al. Alpha-agarases define a new family of glycoside hydrolases, distinct from beta-agarase families. Appl. Environ. Microbiol. 2007, 73:4691-4694.
15. Gomez-Pereira P.R., Fuchs B.M., Alonso C., Oliver M.J., van Beusekom J.E., Amann R. Distinct flavobacterial communities in contrasting water masses of the north Atlantic Ocean. ISME J. 2010, 4:472-487.
16. Guibet M., Colin S., Barbeyron T., Genicot S., Kloareg B., Michel G., et al. Degradation of lambda-carrageenan by Pseudoalteromonas carrageenovora lambda-carrageenase: a new family of glycoside hydrolases unrelated to kappa- and iota-carrageenases. Biochem. J. 2007, 404:105-114.
17. Hehemann J.H., Correc G., Barbeyron T., Helbert W., Czjzek M., Michel G. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 2010, 464:908-912.
18. Higuchi R., Dollinger G., Walsh P.S., Griffith R. Simultaneous amplification and detection of specific DNA sequences. Biotechnology 1992, 10:413-417.
19. Huggett J., Dheda K., Bustin S., Zumla A. Real-time RT-PCR normalisation; strategies and considerations. Genes Immun. 2005, 6:279-284.
20. Jooste P.J., Hugo C.J. The taxonomy, ecology and cultivation of bacterial genera belonging to the family Flavobacteriaceae. Int. J. Food Microbiol. 1999, 53:81-94.
21. Kirchman D.L. The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol. Ecol. 2002, 39:91-100.
22. Le Bail A., Dittami S.M., de Franco P.O., Rousvoal S., Cock M.J., Tonon T., et al. Normalisation genes for expression analyses in the brown alga model Ectocarpus siliculosus. BMC Mol. Biol. 2008, 9:75.
23. Lee K.S., Alvarenga T.A., Guindalini C., Andersen M.L., Castro R.M., Tufik S. Validation of commonly used reference genes for sleep-related gene expression studies. BMC Mol. Biol. 2009, 10:45.
24. Marshall O.J. PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR. Bioinformatics 2004, 20:2471-2472.
25. Michel G., Nyval-Collen P., Barbeyron T., Czjzek M., Helbert W. Bioconversion of red seaweed galactans: a focus on bacterial agarases and carrageenases. Appl. Microbiol. Biotechnol. 2006, 71:23-33.
26. Michel G., Tonon T., Scornet D., Cock J.M., Kloareg B. Central and storage carbon metabolism of the brown alga Ectocarpus siliculosus: insights into the origin and evolution of storage carbohydrates in Eukaryotes. New Phytol. 2010, 188:67-81.
27. Michel G., Tonon T., Scornet D., Cock J.M., Kloareg B. The cell wall polysaccharide metabolism of the brown alga Ectocarpus siliculosus. Insights into the evolution of extracellular matrix polysaccharides in Eukaryotes. New Phytol. 2010, 188:82-97.
28. Nieto P.A., Covarrubias P.C., Jedlicki E., Holmes D.S., Quatrini R. Selection and evaluation of reference genes for improved interrogation of microbial transcriptomes: case study with the extremophile Acidithiobacillus ferrooxidans. BMC Mol. Biol. 2009, 10:63.
29. Nolan T., Hands R.E., Bustin S.A. Quantification of mRNA using real-time RT-PCR. Nat. Protoc. 2006, 1:1559-1582.
30. Paolacci A.R., Tanzarella O.A., Porceddu E., Ciaffi M. Identification and validation of reference genes for quantitative RT-PCR normalization in wheat. BMC Mol. Biol. 2009, 10:11.
31. Rebuffet E., Barbeyron T., Jeudy A., Jam M., Czjzek M., Michel G. Identification of catalytic residues and mechanistic analysis of family GH82 iota-carrageenases. Biochemistry 2010, 49:7590-7599.
32. Ritz M., Garenaux A., Berge M., Federighi M. Determination of rpoA as the most suitable internal control to study stress response in C. jejuni by RT-qPCR and application to oxidative stress. J. Microbiol. Meth. 2009, 76:196-200.
33. Staufenberger T., Thiel V., Wiese J., Imhoff J.F. Phylogenetic analysis of bacteria associated with Laminaria saccharina. FEMS Microbiol. Ecol. 2008, 64:65-77.
34. Theis T., Skurray R.A., Brown M.H. Identification of suitable internal controls to study expression of a Staphylococcus aureus multidrug resistance system by quantitative real-time PCR. J. Microbiol. Meth. 2007, 70:355-362.
35. Vandesompele J., De Preter K., Pattyn F., Poppe B., Van Roy N., De Paepe A., et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002, 3. RESEARCH0034.
36. Wong M.L., Medrano J.F. Real-time PCR for mRNA quantitation. Biotechniques 2005, 39:75-85.
37. ZoBell C. Studies on marine bacteria I The cultural requirements of heterotrophic aerobes. J. Mar. Res. 1941, 4:42-75.