A new method for analyzing gene expression based on frequency analysis of RT-PCR products obtained with degenerate primers

Acta Physiologiae Plantarum

Volumn 32, Issue 3, 2010, Pages 495-502

  Kiselev, Konstantin V ^a   Dubrovina, Alexandra S ^a  

^a INSTITUTE OF BIOLOGY AND SOIL SCIENCE   (Russian Federation)

Author keywords

Degenerate primers; Expression profiles; Gene expression analysis

Indexed keywords

VITACEAE; VITIS AMURENSIS;

EID: 78049253538     PISSN: 01375881     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11738-009-0426-9     Document Type: Article

References (33)

1. Aggarwal BB, Bhardwaj A, Aggarwal RS, Seeram NP, Shishodia S, Takada Y (2004) Role of resveratrol in prevention and therapy of cancer: preclinical and clinical studies. Anticancer Res 24:2783-2840
2. Asano T, Tanaka N, Yang G, Hayashi N, Komatsu S (2005) Genome-wide identification of the rice calcium-dependent protein kinase and its closely related kinase gene families: comprehensive analysis of the CDPKs gene family in rice. Plant Cell Physiol 46:356-366
3. Boudeau J, Miranda-Saavedra D, Barton GJ, Alessi DR (2006) Emerging roles of pseudokinases. Trends Cell Biol 16:443-452
4. Bulgakov VP, Veselova MV, Tchernoded GK, Kiselev KV, Fedoreyev SA, Zhuravlev YN (2005) Inhibitory effect of the Agrobacterium rhizogenes rolC gene on rabdosiin and rosmarinic acid production in Eritrichium sericeum and Lithospermum erythrorhizon transformed cell cultures. Planta 221:471-478
5. Cheng SH, Willmann MR, Chen HC, Sheen J (2002) Calcium signaling through protein kinases. The Arabidopsis calcium-dependent protein kinase gene family. Plant Physiol 129:469-485
6. Dubrovina AS, Kiselev KV, Veselova MV, Isaeva GA, Fedoreyev SA, Zhuravlev YN (2009) Enhanced resveratrol accumulation in rolB-transgenic cultures of Vitis amurensis correlates with unusual changes in CDPK gene expression. J Plant Physiol 166:1194-1206
7. Fuchs T, Malecova B, Linhart C, Sharan R, Khen M, Herwig R, Shmulevich D, Elkon R, Steinfath M, O'Brien JK, Radelof U, Lehrach H, Lancet D, Shamir R (2002) DEFOG: a practical scheme for deciphering families of genes. Genomics 80:295-302
8. Giulietti A, Overbergh L, Valckx D, Decallonne B, Bouillon R, Mathieu C (2001) An overview of real-time quantitative PCR: applications to quantify cytokine gene expression. Methods 25:386-401
9. Gomase VS, Tagore S (2008) Transcriptomics. Curr Drug Metab 9:245-249
10. Harbers M, Carninci P (2005) Tag-based approaches for transcriptome research and genome annotation. Nat Methods 2:495-502
11. Inyushkina YV, Kiselev KV, Bulgakov VP, Zhuravlev YN (2009) Specific genes of Cytochrome P450 enzymes are involved in biosynthesis of caffeic acid metabolites in the rolC-transgenic culture of Eritrichium sericeum. Biochemistry (Moscow) 74:917-924
12. Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Adam-Blondon AF, Weissenbach J, Quetier F, Wincker P (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463
13. Jarman SN (2007) Amplicon: software for designing PCR primers on aligned DNA sequences. Bioinformatics 20:1644-1645
14. Jarman SN, Deagle BE, Gales NJ (2003) Group-specific PCR for DNA based analysis of species diversity and identity in dietary samples. Mol Ecol 13:1313-1322
15. Jeandet P, Douillt-Breuil AC, Bessis R, Debord S, Sbaghi M, Adrian M (2002) Phytoalexins from the vitaceae: biosynthesis, phytoalexin gene expression in transgenic plants, antifungal activity, and metabolism. J Agric Food Chem 50:2731-2741
16. Kiselev KV, Tchernoded GK (2009) Increased expression of WUS and SERK genes in the oncogene rolC expressed embryogenic cell cultures of Panax ginseng. Russ J Genet 45:445-452
17. Kiselev KV, Kusaykin MI, Dubrovina AS, Bezverbny DA, Zvyagintseva TN, Bulgakov VP (2006) The rolC gene induces expression of a pathogenesis-related beta-1,3-glucanase in transformed ginseng cells. Phytochemistry 67:2225-2231
18. Kiselev KV, Dubrovina AS, Veselova MV, Bulgakov VP, Fedoreyev SA, Zhuravlev YN (2007) The rolB gene-induced overproduction of resveratrol in Vitis amurensis transformed cells. J Biotechnol 128:681-692
19. Kiselev KV, Gorpenchenko TY, Tchernoded GK, Dubrovina AS, Grishchenko OV, Bulgakov VP, Zhuravlev YN (2008) Calciumdependent mechanism of somatic embryogenesis in Panax ginseng cell cultures expressing the rolC oncogene. Mol Biol 42:243-252
20. Kiselev KV, Dubrovina AS, Bulgakov VP (2009a) Phenylalanine ammonia-lyase and stilbene synthase gene expression in rolB-transgenic cell cultures of Vitis amurensis. Appl Microbiol Biot 82:647-655
21. Kiselev KV, Turlenko AV, Zhuravlev YN (2009b) CDPK gene expression in somatic embryos of Panax ginseng expressing rolC. Plant Cell Tissue Organ Cult 99:141-149
22. Kiselev KV, Turlenko AV, Zhuravlev YN (2009b) PgWUS expression during somatic embryo development in a Panax ginseng 2c3 cell culture expressing the rolC oncogene. Plant Growth Regul 59:237-243
23. Kiselev KV, Grishchenko OV, Zhuravlev YN (2009d) CDPK gene expression in salt tolerant rolB and rolC transformed cell cultures of Panax ginseng. Biol Plant (in press)
24. Kwok S, Chang S, Sninsky J, Wang A (1994) A guide to the design and use of mismatched and degenerate primers. PCR Methods Appl 3:S39-S47
25. Langcake P, Pryce RJ (1977) A new class of phytoalexins from grapevines. Experientia 33:151-152
26. Lecourieux D, Ranjeva R, Pugin A (2006) Calcium in plant defencesignalling pathways. New Phytol 171:249-269
27. Najafabadi HS, Torabi N, Chamankhah M (2008) Designing multiple degenerate primers via consecutive pairwise alignments. BMC Bioinform 9:55
28. Nakamura Y, Gojobori T, Ikemura T (2000) Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res 28:292
29. Persiyanova EV, Kiselev KV, Bulgakov VP, Timchenko NF, Chernoded GK, Zhuravlev YN (2008) Defense response mechanisms of ginseng callus cultures induced by Yersinia pseudotuberculosis, a human pathogen. Russ J Plant Physiol 55:748-755
30. Rupprich N, Hildebrand H, Kindl H (1980) Substrate specificity in vivo and in vitro in the formation of stilbenes-biosynthesis of rhaponticin. Arch Biochem Biophys 200:72-78
31. Spena A, Schmulling T, Koncz C, Schell JS (1987) Independent and synergetic activity of rol A, B and C loci in stimulating abnormal growth in plants. EMBO J 6:3891-3899
32. Staden R, Beal KF, Bonfield JK (1999) The Staden Package 1998. Comput Meth Mol Biol 132:115-130
33. Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, Pruss D, Pindo M, Fitzgerald LM, Vezzulli S, Reid J et al (2007) A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE 2:e1326