An alternatively spliced domain of the NDC1 NAD(P)H dehydrogenase gene strongly influences the expression of the ACTIN2 reference gene in Arabidopsis thaliana

Plant Science

Volumn 183, Issue , 2012, Pages 190-196

  Wallström, Sabá V ^a   Aidemark, Mari ^a   Escobar, Matthew A ^b   Rasmusson, Allan G ^a  

^a LUND UNIVERSITY   (Sweden)

^b CALIFORNIA STATE UNIVERSITY   (United States)

Author keywords

ACTIN2; Alternative splicing; NAD(P)H dehydrogenase; Quantitative PCR reference gene; T DNA mutant

Indexed keywords

ACT2 PROTEIN, ARABIDOPSIS; ACTIN; ARABIDOPSIS PROTEIN; BACTERIAL DNA; NDC1 PROTEIN, ARABIDOPSIS; OXIDOREDUCTASE; PLANT RNA; T DNA; T-DNA;

ARABIDOPSIS; ARTICLE; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SPLICING; STANDARD; TRANSGENIC PLANT;

ACTINS; ARABIDOPSIS; ARABIDOPSIS PROTEINS; DNA, BACTERIAL; GENE EXPRESSION REGULATION, PLANT; MUTAGENESIS, INSERTIONAL; NADH, NADPH OXIDOREDUCTASES; PLANTS, GENETICALLY MODIFIED; REFERENCE STANDARDS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA SPLICE SITES; RNA, PLANT;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 84155181018     PISSN: 01689452     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plantsci.2011.08.011     Document Type: Article

References (34)

1. Black D.L. Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem. 2003, 72:291-336.
2. Filichkin S.A., Priest H.D., Givan S.A., Shen R., Bryant D.W., Fox S.E., Wong W.K., Mockler T.C. Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res. 2010, 20:45-58.
3. Simpson C.G., Lewandowska D., Fuller J., Maronova M., Kalyna M., Davidson D., McNicol J., Raczynska D., Jarmolowski A., Barta A., Brown J.W. Alternative splicing in plants. Biochem. Soc. Trans. 2008, 36:508-510.
4. Shen J.B., Orozco E.M., Ogren W.L. Expression of the two isoforms of spinach ribulose 1,5-bisphosphate carboxylase activase and essentiality of the conserved lysine in the consensus nucleotide-binding domain. J. Biol. Chem. 1991, 266:8963-8968.
5. Hasse D., Mikkat S., Hagemann M., Bauwe H. Alternative splicing produces an H-protein with better substrate properties for the P-protein of glycine decarboxylase. FEBS J. 2009, 276:6985-6991.
6. Zhang X.N., Mount S.M. Two alternatively spliced isoforms of the Arabidopsis SR45 protein have distinct roles during normal plant development. Plant Physiol. 2009, 150:1450-1458.
7. Rasmusson A.G., Soole K.L., Elthon T.E. Alternative NAD(P)H dehydrogenases of plant mitochondria. Annu. Rev. Plant Biol. 2004, 55:23-39.
8. Møller I.M. Plant mitochondria and oxidative stress: electron transport NADPH turnover, and metabolism of reactive oxygen species. Annu. Rev. Plant Physiol. Plant Mol. Biol. 2001, 52:561-591.
9. Clifton R., Lister R., Parker K.L., Sappl P.G., Elhafez D., Millar A.H., Day D.A., Whelan J. Stress-induced co-expression of alternative respiratory chain components in Arabidopsis thaliana. Plant Mol. Biol. 2005, 58:193-212.
10. Escobar M.A., Geisler D.A., Rasmusson A.G. Reorganization of the alternative pathways of the Arabidopsis respiratory chain by nitrogen supply: opposing effects of ammonium and nitrate. Plant J. 2006, 45:775-788.
11. Kerscher S.J. Diversity and origin of alternative NADH: ubiquinone oxidoreductases. Biochim. Biophys. Acta 2000, 1459:274-283.
12. Michalecka A.M., Svensson å.S., Johansson F.I., Agius S.C., Johanson U., Brennicke A., Binder S., Rasmusson A.G. Arabidopsis genes encoding mitochondrial type II NAD(P)H dehydrogenases have different evolutionary origin and show distinct responses to light. Plant Physiol. 2003, 133:642-652.
13. Carrie C., Murcha M.W., Kuehn K., Duncan O., Barthet M., Smith P.M., Eubel H., Meyer E., Day D.A., Millar A.H., Whelan J. Type II NAD(P)H dehydrogenases are targeted to mitochondria and chloroplasts or peroxisomes in Arabidopsis thaliana. FEBS Lett. 2008, 582:3073-3079.
14. Elhafez D., Murcha M.W., Clifton R., Soole K.L., Day D.A., Whelan J. Characterization of mitochondrial alternative NAD(P)H dehydrogenases in Arabidopsis: intraorganelle location and expression. Plant Cell Physiol. 2006, 47:43-54.
15. Vidi P.A., Kanwischer M., Baginsky S., Austin J.R., Csucs G., Dörmann P., Kessler F., Brehelin C. Tocopherol cyclase (VTE1) localization and vitamin E accumulation in chloroplast plastoglobule lipoprotein particles. J. Biol. Chem. 2006, 281:11225-11234.
16. Ytterberg A.J., Peltier J.B., van Wijk K.J. Protein profiling of plastoglobules in chloroplasts and chromoplasts. A surprising site for differential accumulation of metabolic enzymes. Plant Physiol. 2006, 140:984-997.
17. Escobar M.A., Franklin K.A., Svensson A.S., Salter M.G., Whitelam G.C., Rasmusson A.G. Light regulation of the Arabidopsis respiratory chain. Multiple discrete photoreceptor responses contribute to induction of type II NAD(P)H dehydrogenase genes. Plant Physiol. 2004, 136:2710-2721.
18. Escobar M.A., Rasmusson A.G. Photocontrol of respiratory type II NAD(P)H dehydrogenase genes: cryptochrome, but not hy5, is a critical component of light signaling. Photosynthesis: Fundamental Aspects to Global Perspectives 2005, 909-911. Allen Press Inc., Lawrence, KS. A. van der Est, D. Bruce (Eds.).
19. Rosso M.G., Li Y., Strizhov N., Reiss B., Dekker K., Weisshaar B. An Arabidopsis thaliana T-DNA mutagenized population (GABI-Kat) for flanking sequence tag-based reverse genetics. Plant Mol. Biol. 2003, 53:247-259.
20. Aljanabi S.M., Martinez I. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res. 1997, 25:4692-4693.
21. Liu Y.J., Nunes-Nesi A., Wallström S.V., Lager I., Michalecka A.M., Norberg F.E., Widell S., Fredlund K.M., Fernie A.R., Rasmusson A.G. A redox-mediated modulation of stem bolting in transgenic Nicotiana sylvestris differentially expressing the external mitochondrial NADPH dehydrogenase. Plant Physiol. 2009, 150:1248-1259.
22. Lager I., Andreasson O., Dunbar T., Andreasson E., Escobar M.A., Rasmusson A.G. Changes in external pH rapidly alter plant gene expression and modulate auxin and elicitor responses. Plant Cell Environ. 2010, 33:1513-1528.
23. Taylor S., Wakem M., Dijkman G., Alsarraj M., Nguyen M. A practical approach to RT-qPCR-publishing data that conform to the MIQE guidelines. Methods 2010, 50:S1-S5.
24. McCurdy R.D., McGrath J.J., Mackay-Sim A. Validation of the comparative quantification method of real-time PCR analysis and a cautionary tale of housekeeping gene selection. Gene Ther. Mol. Biol. 2008, 12:15-24.
25. Boyes D.C., Zayed A.M., Ascenzi R., McCaskill A.J., Hoffman N.E., Davis K.R., Gorlach J. Growth stage-based phenotypic analysis of Arabidopsis: a model for high throughput functional genomics in plants. Plant Cell 2001, 13:1499-1510.
26. Czechowski T., Stitt M., Altmann T., Udvardi M.K., Scheible W.R. Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiol. 2005, 139:5-17.
27. Campbell M.A., Haas B.J., Hamilton J.P., Mount S.M., Buell C.R. Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics 2006, 7:327.
28. Shyu A.B., Wilkinson M.F., van Hoof A. Messenger RNA regulation: to translate or to degrade. EMBO J. 2008, 27:471-481.
29. Barth C., De Tullio M., Conklin P.L. The role of ascorbic acid in the control of flowering time and the onset of senescence. J. Exp. Bot. 2006, 57:1657-1665.
30. An Y.Q., McDowell J.M., Huang S., McKinney E.C., Chambliss S., Meagher R.B. Strong, constitutive expression of the Arabidopsis ACT2/ACT8 actin subclass in vegetative tissues. Plant J. 1996, 10:107-121.
31. Zhang J., Addepalli B., Yun K.Y., Hunt A.G., Xu R., Rao S., Li Q.Q., Falcone D.L. A polyadenylation factor subunit implicated in regulating oxidative signaling in Arabidopsis thaliana. PLoS One 2008, 3:e2410.
32. Kandasamy M.K., McKinney E.C., Meagher R.B. A single vegetative actin isovariant overexpressed under the control of multiple regulatory sequences is sufficient for normal Arabidopsis development. Plant Cell 2009, 21:701-718.
33. Guenin S., Mauriat M., Pelloux J., Van Wuytswinkel O., Bellini C., Gutierrez L. Normalization of qRT-PCR data: the necessity of adopting a systematic experimental conditions-specific, validation of references. J. Exp. Bot. 2009, 60:487-493.
34. Gutierrez L., Mauriat M., Guenin S., Pelloux J., Lefebvre J.F., Louvet R., Rusterucci C., Moritz T., Guerineau F., Bellini C., Van Wuytswinkel O. The lack of a systematic validation of reference genes: a serious pitfall undervalued in reverse transcription-polymerase chain reaction (RT-PCR) analysis in plants. Plant Biotechnol. J. 2008, 6:609-618.