Identification and validation of reference genes to study the gene expression in Gluconacetobacter diazotrophicus grown in different carbon sources using RT-qPCR

Journal of Microbiological Methods

Volumn 91, Issue 1, 2012, Pages 1-7

  Galisa, Péricles S ^a,c   da Silva, Helder A P ^b,c   Macedo, Aline V M ^c   Reis, Verônica M ^c   Vidal, Márcia S ^c   Baldani, José I ^c   Simes Araújo, Jean L ^c  

^a FEDERAL RURAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^b FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^c EMBRAPA AGROBIOLOGIA   (Brazil)

Author keywords

Endophytic diazotrophic; Gluconacetobacter diazotrophicus; Reference gene

Indexed keywords

GLUCOSE; GLYCEROL; MANNITOL; MESSENGER RNA; SUCROSE;

23SRRNA GENE; ARTICLE; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIAL STRAIN; CARBON SOURCE; DNAG GENE; FABD GENE; GENE EXPRESSION; GENE IDENTIFICATION; GLUCONACETOBACTER; GLUCONACETOBACTER DIAZOTROPHICUS; GMK GENE; GYRB GENE; GYRBC GENE; LDHD GENE; LPXC GENE; MATE GENE; NONHUMAN; OMP16 GENE; PRIORITY JOURNAL; QUANTITATIVE REAL TIME POLYMERASE CHAIN REACTION; REAL TIME POLYMERASE CHAIN REACTION; RECA GENE; RECF GENE; RHO GENE; RPOA GENE; RPOC GENE; RPOD GENE; SUCA GENE;

CARBON; GENE EXPRESSION PROFILING; GENES, BACTERIAL; GLUCONACETOBACTER; REAL-TIME POLYMERASE CHAIN REACTION; REFERENCE STANDARDS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

ANANAS COMOSUS; BACTERIA (MICROORGANISMS); GLUCONACETOBACTER DIAZOTROPHICUS; IPOMOEA BATATAS; PENNISETUM PURPUREUM;

EID: 84864183959     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2012.07.005     Document Type: Article

References (52)

1. Alqueres S.M.C., Oliveira J.H.M., Nogueira E.M., Guedes H.V., Oliveira P.L., Camara F., Baldani J.I., Martins O.B. Antioxidant pathways are up-regulated during biological nitrogen fixation to prevent ROS-induced nitrogenase inhibition in Gluconacetobacter diazotrophicus. Arch. Microbiol. 2010, 192:835-841.
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. Baldani J.I., Caruso L., Baldani V.L.D., Goi S.R., Döbereiner J. Recent advances in BNF with non-legume plants. Soil Biol. Biochem. 1997, 29:911-922.
4. Baldo L., Desjardins C.A., Russell J.A., Stahlhut J.K., Werren J.H. Accelerated microevolution in an outer membrane protein (OMP) of the intracellular bacteria Wolbachia. BMC Evol. Biol. 2010, 10:48.
5. Bertalan M., Albano R., Pádua V., Rouws L., Rojas C., Hemerly A., et al. Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus Pal5. BMC Genomics 2009, 10:450.
6. Bustin S.A., Benes V., Garson J.A., Hellemans J., Huggett J., Kubista M., Mueller R., Nolan T., Pfaffl M.W., Shipley G.L., Vandesompele J., Wittwer C.T. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin. Chem. 2009, 55:611-622.
7. Cavalcante V.A., Dobereiner J. New acid-tolerant nitrogen-fixing bacterium associated with sugarcane. Plant Soil 1988, 1008:23-31.
8. Cinar M.U., Islam M.A., Uddin M.J., Tholen E., Tesfaye D., Looft C., Schellander K. Evaluation of suitable reference genes for gene expression studies in porcine alveolar macrophages in response to LPS and LTA. BMC Res. Notes 2012, 5:107.
9. Desroche N., Beltramo C., Guzzo J. Determination of an internal control to apply reverse transcription quantitative PCR to study stress response in the lactic acid bacterium Oenococcus oeni. J. Microbiol. Methods 2005, 60:325-333.
10. 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, 371:112-114.
11. Dheda K., Huggett J.F., Chang J.S., Kim L.U., Bustin S.A., Johnson M.A., Rook G.A., Zumla A. The implications of using an inappropriate reference gene for realtime reverse transcription PCR data normalization. Anal. Biochem. 2005, 344:141-143.
12. Dong Z., Canny M.J., Mccully M.E., Roboredo M.R., Abadilla C.F., Ortega E.E., Rodes R. A nitrogen-fixing endophyte of sugarcane stems (a new role for the apoplast). Plant Physiol. 1994, 105:1139-1147.
13. Fiocco D., Crisetti E., Capozzi V., Spano G. Validation of a internal control gene to apply reverse transcription quantitative PCR to study heat, cold and ethanol stresses in Lactobacillus plantarum. World J. Microbiol. Biotechnol. 2008, 24:899-902.
14. Freeman W.M., Walker S.J., Vrana K.E. Quantitative RT-PCR: pitfalls and potential. Biotechniques 1999, 26:112-122.
15. Ginzinger D.G. Gene quantification using real-time quantitative PCR: an emerging technology hits the mainstream. Exp. Hematol. 2002, 30:503-512.
16. Glare E.M., Divjak M., Bailey M.J., Walters E.H. Beta-actin and GAPDH housekeeping gene expression in asthmatic airways is variable and not suitable for normalizing mRNA levels. Thorax 2002, 57:765-770.
17. Hanna A.L., Youssef H.Y., Amer W.M., Monib M., Fayez M., Hegazi N.A. Diversity of bacteria nesting the plant cover of north Sinai deserts. J. Adv. Res. 2012, 10.1016/j.jare.2011.11.003.
18. Hellemans J., Mortier G., De Paepe A., Speleman F., Vandesompele J. qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol. 2007, 8:R19. 10.1186/gb-2007-8-2-r19.
19. Hommais F., Zghidi-Abouzid O., Oger-Desfeux C., Pineau-Chapelle E., Van Gijsegem F., Nasser W., Reverchon S. lpxC and yafS are the most suitable internal controls to normalize real time RT-qPCR expression in the phytopathogenic bacteria Dickeya dadantii. PLoS One 2011, 10.1371/journal.pone.0020269.
20. Huggett J., Dheda K., Bustin S., Zumla A. Real-time RT-PCR normalization; strategies and considerations. Genes Immun. 2005, 6:279-284.
21. Jimenez-Salgado T., Fuentes-Ramirez L.E., Tapia-Hernandez A., Mascarua-Esparza M.A., Martinez-Romero E.E., Caballero-Mellado E. Coffea arabica L., a new host plant for Acetobacter diazotrophicus, and isolation of other nitrogen-fixing acetobacteria. Appl. Environ. Microbiol. 1997, 63:3676-3683.
22. Kaatz G.W., McAleese F., Seo S.M. Transport protein multidrug and toxin extrusion (MATE) due to overexpression of a novel multidrug resistance in Staphylococcus aureus. Antimicrob. Agents Chemother. 2005, 49:1857-1864.
23. Kesters K., Lisdiyanti P., Komagata K., Swings J. The family Acetobacteriaceae: the genera Acetobacter, Acidomonas, Asaia, Gluconoacetobacter, Gluconobacter, and Kozakia. The Prokaryotes 2006, 163-200. Springer-Verlag, New York, NY. M. Dworkin, S. Falkow, E. Rosenberg, K.H. Schleifer, E. Stackebrandt (Eds.).
24. Kim J., Rees D. Nitrogenase and biological nitrogen fixation. Biochemistry 1994, 33:389-397.
25. Kriegova E., Arakelyan A., Fillerova R., Zatloukal J., Mrazek F., Navratilova Z., Kolek V., du Bois R.M., Petrek M. PSMB2 and RPL32 are suitable denominators to normalize gene expression profiles in bronchoalveolar cells. BMC Mol. Biol. 2008, 9:69.
26. Liedert C., Peltola M., Bernhardt J., Neubauer P., Salkinoja-Salonen M. Physiology of resistant Deinococcus geothermalis bacterium aerobically cultivated in low-manganese medium. J. Bacteriol. 2012, 194:1552-1561.
27. Loganathan P., Nair S. Crop specific endophytic colonization by a novel, salttolerant, nitrogen fixing and phosphate-solubilizing Gluconacetobacter spp. from wild rice. Biotechnol. Lett. 2003, 25:497-501.
28. Logeshwaran P., Thangaraju M., Rajasundari K. Hydroxamate siderophores of endophytic bacteria Gluconacetobacter diazotrophicus isolated from sugarcane roots. Aust. J. Basic Appl. Sci. 2009, 3:3564-3567.
29. Long X., Liu Y., Rocheleau H., Ouellet T., Chen G. Identification and validation of internal control genes for genes expression in wheat leaves infected by strip rust. Intern. J. Plant Breed. Genet. 2011, 5:255-267.
30. Madhaiyan M., Saravanan V.S., Jovi D.B.S.S., Lee H., Thenmozhi R., Hari K., Sa T. Occurrence of Gluconacetobacter diazotrophicus in tropical and subtropical plants of Western Ghats, India. Microbiol. Res. 2004, 159:233-243.
31. Magalhães F.M., Baldani J.I., Souto S.M., Kuyrendall J.R., Dobereiner J. A new acid-tolerant Azospirillum species. An. Acad. Bras. Cienc. 1983, 55:417-430.
32. Metcalf D., Sharif S., Weese J.S. Evaluation of candidate reference genes in Clostridium difficile for gene expression normalization. Anaerobe 2010, 16:439-443.
33. Nakano S., Fukaya M. Analysis of proteins responsive to acetic acid in Acetobacter: molecular mechanisms conferring acetic acid resistance in acetic acid bacteria. Int. J. Food Microbiol. 2008, 125:54-59.
34. 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.
35. 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, 63:1-11.
36. Oliveira L.R., Marcelino F.C., Barcellos F.G., Rodrigues E.P., Megías M., Hungria M. The nodC, nodG, and glgX genes of Rhizobium tropici strain PRF 81. Funct. Integr. Genomics 2010, 10:425-431.
37. Pasquevich K.A., Samartino G.C., Coria L.M., Estein S.M., Zwerdling A., Ibañez A.E., Barrionuevo P., Oliveira F.S., Carvalho N.B., Borkowski J., Oliveira S.C., Warzecha H., Giambartolomei G.H., Cassataro J. Oral acquired brucellosis self-adjuvanting vaccine against systemic and immune response, and is a promising activates dendritic cells in vivo, induces a Th1 pathogen-associated molecular pattern that membrane protein 16 is a new bacterial. J. Immunol. 2012, 184:5200-5212.
38. Paula M.A., Reis V.M., Dobereiner J. Interactions of Glomus clarum with Acetobacter diazotrophicus in infection of sweet potato, sugar cane and sweet sorghum. Biol. Fertil. Soils 1991, 11:111-115.
39. 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.
40. Piehler A.P., Grimholt R.M., Ovstebo R., Berg J.P. Gene expression results in lipopolysaccharide-stimulated monocytes depend significantly on the choice of reference genes. BMC Immunol. 2010, 11:21.
41. Reis V.M., Olivares F.L., Döbereiner J. Improved methodology for isolation of Acetobacter diazotrophicus and confirmation of its endophytic habitat. World J. Microbiol. Biotechnol. 1994, 10:401-405.
42. Reiter L., Kolstø A., Piehler A.P. Reference genes for quantitative, reverse-transcription PCR in Bacillus cereus group strains throughout the bacterial life cycle. J. Microbiol. Methods 2011, 86:210-217.
43. 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. Methods 2009, 76:196-200.
44. Rozen S., Skaletsky J.H. Primer3 on the WWW for general users and for biologist programmers. Bioinformatics Methods and Protocols: Methods in Molecular Biology 2000, 365-386. S. Krawetz, S. Misener (Eds.).
45. Stevenson D.M., Weimer P.J. Expression of 17 genes in Clostridium thermocellum ATCC 27405 during fermentation of cellulose or cellobiose in continuous culture. Appl. Environ. Microbiol. 2005, 71:4672-4678.
46. Tapia-Hernández A., Bustillos-Cristales M.R., Jiménez-Salgado T., Caballero-Mellado J., Fuentes-Ramírez L.E. Natural endophytic occurrence of Acetobacter diazotrophicus in pineapple plants. Microb. Ecol. 2000, 39:49-55.
47. 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. Methods 2007, 70:355-362.
48. Thomas F., Barbeyron T., Michel G. Evaluation of reference genes for real-time quantitative PCR in the marine flavobacterium Zobellia galactanivorans. J. Microbiol. Methods 2011, 84:61-66.
49. Urquiaga S., Cruz K.H.S., Boddey R.M. Contribution of nitrogen fixation to sugar cane: nitrogen-15 and nitrogen balance estimates. Soil Sci. Soc. Am. J. 1992, 56:105-114.
50. 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, 3:1-12.
51. Zhao S., Russel F. Comprehensive algorithm for quantitative real-time polymerase chain reaction. J. Comput. Biol. 2005, 12:1047-1064.
52. Zhou K., Zhou L., Lim K.E., Zou R., Stephanopoulos G., Too H. Novel reference genes for quantifying transcriptional responses of Escherichia coli to protein overexpression by quantitative PCR. BMC Mol. Biol. 2011, 12:18.