Evaluation of Clostridium ljungdahlii DSM 13528 reference genes in gene expression studies by qRT-PCR

Journal of Bioscience and Bioengineering

Volumn 116, Issue 4, 2013, Pages 460-464

  Liu, Juanjuan ^a,b   Tan, Yang ^b   Yang, Xiaohong ^a   Chen, Xiaohua ^b   Li, Fuli ^b  

^a SOUTHWEST UNIVERSITY   (China)

^b QINGDAO INSTITUTE OF BIOENERGY AND BIOPROCESS TECHNOLOGY   (China)

Author keywords

Carbon source; Clostridium ljungdahlii; Quantitative real time PCR; Reference genes; Stress

Indexed keywords

BIOLOGICAL CHARACTERISTIC; CARBON SOURCE; CLOSTRIDIUM LJUNGDAHLII; DIFFERENT CARBON SOURCES; GENE EXPRESSION ANALYSIS; QUANTITATIVE REAL TIME PCR; QUANTITATIVE REAL-TIME POLYMERASE CHAIN REACTION; REFERENCE GENES;

CARBON; CLOSTRIDIUM; POLYMERASE CHAIN REACTION; RNA; STRESSES;

GENE EXPRESSION;

BACTERIAL PROTEIN; DNA DIRECTED RNA POLYMERASE; DNA TOPOISOMERASE (ATP HYDROLYSING) A; FORMATE TETRAHYDROFOLATE LIGASE; GUANYLATE KINASE; RECA PROTEIN; RHO FACTOR; RNA 16S;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; CARBON SOURCE; CLOSTRIDIUM; CLOSTRIDIUM LJUNGDAHLII; GENE EXPRESSION; GENETIC STABILITY; NONHUMAN; PROTEIN EXPRESSION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; STABLE EXPRESSION;

CLOSTRIDIUM LJUNGDAHLII;

CARBON SOURCE; CLOSTRIDIUM LJUNGDAHLII; QUANTITATIVE REAL-TIME PCR; REFERENCE GENES; STRESS;

BIOFUELS; CLOSTRIDIUM; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENES, BACTERIAL; REAL-TIME POLYMERASE CHAIN REACTION; REFERENCE STANDARDS; REPRODUCIBILITY OF RESULTS;

EID: 84883264901     PISSN: 13891723     EISSN: 13474421     Source Type: Journal    
DOI: 10.1016/j.jbiosc.2013.04.011     Document Type: Article

References (36)

1. Vandesompele, J., De Preter, K., Pattyn, F., Poppe, B., Van Roy, N., De Paepe, A., and Speleman, F.: Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes, Genome Biol.,3, RESEARCH0034 (2002).
2. Garson J.A., Grant P.R., Ayliffe U., Ferns R.B., Tedder R.S. Real-time PCR quantitation of hepatitis B virus DNA using automated sample preparation and murine cytomegalovirus internal control. J.Virol. Methods 2005, 126:207-213.
3. Ginzinger D.G. Gene quantification using real-time quantitative PCR: an emerging technology hits the mainstream. Exp. Hematol. 2002, 30:503-512.
4. Held C.A., Stevens J., Livak K.J., Williams P.M. Real time quantitative PCR. Genome Res. 1996, 6:986-994.
5. Bustin S.A., Benes V., Nolan T., Pfaffl M.W. Quantitative real-time RT-PCR-a perspective. J.Mol. Endocrinol. 2005, 34:597-601.
6. Giulietti A., Overbergh L., Valckx D., Decallonne B., Bouillon R., Mathieu C. An overview of real-time quantitative PCR: applications to quantify cytokine gene expression. Methods 2001, 25:386-401.
7. Weis J.H., Tan S.S., Martin B.K., Wittwer C.T. Detection of rare mRNAs via quantitative RT-PCR. Trends Genet. 1992, 8:263-264.
8. Gachon C., Mingam A., Charrier B. Real-time PCR: what relevance to plant studies?. J.Exp. Bot. 2004, 55:1445-1454.
9. 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.
10. Metcalf D., Sharif S., Weese J.S. Evaluation of candidate reference genes in Clostridium difficile for gene expression normalization. Anaerobe 2010, 16:439-443.
11. Reiter L., Kolsto A.B., 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.
12. Galisa P.S., da Silva H.A., Macedo A.V., Reis V.M., Vidal M.S., Baldani J.I., Simoes-Araujo J.L. Identification and validation of reference genes to study the gene expression in Gluconacetobacter diazotrophicus grown in different carbon sources using RT-qPCR. J.Microbiol. Methods 2012, 91:1-7.
13. 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.
14. Jin C., Yao M.F., Liu H.F., Lee C.F.F., Ji J. Progress in the production and application of n-butanol as a biofuel. Renew. Sust. Energy Rev. 2011, 15:4080-4106.
15. Bredwell M.D., Srivastava P., Worden R.M. Reactor design issues for synthesis-gas fermentations. Biotechnol. Prog. 1999, 15:834-844.
16. Heiskanen H., Virkajarvi I., Viikari L. The effect of syngas composition on the growth and product formation of Butyribacterium methylotrophicum. Enzyme Microb. Technol. 2007, 41:362-367.
17. Cotter J.L., Chinn M.S., Grunden A.M. Ethanol and acetate production by Clostridium ljungdahlii and Clostridium autoethanogenum using resting cells. Bioprocess Biosyst. Eng. 2009, 32:369-380.
18. Younesi H., Najafpour G., Mohamed A.R. Ethanol and acetate production from synthesis gas via fermentation processes using anaerobic bacterium, Clostridium ljungdahlii. Biochem. Eng. J. 2005, 27:110-119.
19. Köpke M., Held C., Hujer S., Liesegang H., Wiezer A., Wollherr A., Ehrenreich A., Liebl W., Gottschalk G., Durre P. Clostridium ljungdahlii represents a microbial production platform based on syngas. Proc. Natl. Acad. Sci. USA 2010, 107:13087-13092.
20. Köpke M., Mihalcea C., Liew F., Tizard J.H., Ali M.S., Conolly J.J., Al-Sinawi B., Simpson S.D. 2,3-butanediol production by acetogenic bacteria, an alternative route to chemical synthesis, using industrial waste gas. Appl. Environ. Microbiol. 2011, 77:5467-5475.
21. 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.
22. 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.
23. 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, 43:429-435.
24. Piston F., Dorado G., Martin A., Barro F. Cloning and characterization of a gamma-3 hordein mRNA (cDNA) from Hordeum chilense (Roem. et Schult.). Theor. Appl. Genet. 2004, 108:1359-1365.
25. Doshi K.M., Eudes F., Laroche A., Gaudet D. Anthocyanin expression in marker free transgenic wheat and triticale embryos. In Vitro Cell. Dev. Biol. Plant 2007, 43:429-435.
26. Katayama S., Dupuy B., Garnier T., Cole S.T. Rapid expansion of the physical and genetic map of the chromosome of Clostridium perfringens CPN50. J.Bacteriol. 1995, 177:5680-5685.
27. Kilian M., Scholz C.F., Lomholt H.B. Multilocus sequence typing and phylogenetic analysis of Propionibacterium acnes. J.Clin. Microbiol. 2012, 50:1158-1165.
28. 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.
29. 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.
30. 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.
31. Dhalluin A., Bourgeois I., Pestel-Caron M., Camiade E., Raux G., Courtin P., Chapot-Chartier M.P., Pons J.L. Acd, a peptidoglycan hydrolase of Clostridium difficile with N-acetylglucosaminidase activity. Microbiology 2005, 151:2343-2351.
32. Deneve C., Delomenie C., Barc M.C., Collignon A., Janoir C. Antibiotics involved in Clostridium difficile-associated disease increase colonization factor gene expression. J.Med. Microbiol. 2008, 57:732-738.
33. Condon C., Squires C., Squires C.L. Control of rRNA transcription in Escherichia coli. Microbiol. Mol. Biol. Rev. 1995, 59:623-645.
34. Ruiz-Garbajosa P., Bonten M.J., Robinson D.A., Top J., Nallapareddy S.R., Torres C., Coque T.M., Canton R., Baquero F., Murray B.E., del Campo R., Willems R.J. Multilocus sequence typing scheme for Enterococcus faecalis reveals hospital-adapted genetic complexes in a background of high rates of recombination. J.Clin. Microbiol. 2006, 44:2220-2228.
35. Wan H., Zhao Z., Qian C., Sui Y., Malik A.A., Chen J. Selection of appropriate reference genes for gene expression studies by quantitative real-time polymerase chain reaction in cucumber. Anal. Biochem. 2010, 399:257-261.
36. Bin W.S., Wei L.K., Ping D.W., Li Z., Wei G., Bing L.J., Gui P.B., Jian W.H., Feng C.J. Evaluation of appropriate reference genes for gene expression studies in pepper by quantitative real-time PCR. Mol. Breed. 2012, 30:1393-1400.