The lba1 mutation of UPF1 RNA helicase involved in nonsense-mediated mRNA decay causes pleiotropic phenotypic changes and altered sugar signalling in Arabidopsis

Plant Journal

Volumn 47, Issue 1, 2006, Pages 49-62

  Yoine, Masato ^a   Ohto, Masa Aki ^b,d   Onai, Kiyoshi ^a,b   Mita, Satoru ^c   Nakamura, Kenzo ^a  

^a NAGOYA UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE FOR BASIC BIOLOGY   (Japan)

^c SHIZUOKA UNIVERSITY   (Japan)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Alternative splicing; lba1 atupf1 1; Nonsense mediated mRNA decay; Sugar signalling; UPF1

Indexed keywords

CARBOXYLIC ACIDS; MUTAGENESIS; PLANTS (BOTANY); RNA; SEED; SUGAR (SUCROSE);

ALTERNATIVE SPLICING; LBA1/ATUPF1-1; NONSENSE-MEDIATED MRNA DECAY; SUGAR SIGNALLING; UPF1;

ENZYMES;

ARABIDOPSIS PROTEIN; BETA AMYLASE; CARBOHYDRATE; COMPLEMENTARY DNA; MESSENGER RNA; RNA HELICASE; TRANSCRIPTION FACTOR IIIA; UPF1 PROTEIN, ARABIDOPSIS;

ALTERNATIVE RNA SPLICING; AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC COMPLEMENTATION; GENETICS; METABOLISM; MISSENSE MUTATION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYSIOLOGY; SIGNAL TRANSDUCTION; STOP CODON;

ALTERNATIVE SPLICING; AMINO ACID SEQUENCE; ARABIDOPSIS; ARABIDOPSIS PROTEINS; BETA-AMYLASE; CARBOHYDRATES; CODON, NONSENSE; DNA MUTATIONAL ANALYSIS; DNA, COMPLEMENTARY; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENETIC COMPLEMENTATION TEST; MOLECULAR SEQUENCE DATA; MUTATION, MISSENSE; PHENOTYPE; RNA HELICASES; RNA, MESSENGER; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTOR TFIIIA;

AMYLASE; GERMINATION; NUCLEIC ACIDS; SEEDS;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 33745112583     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2006.02771.x     Document Type: Article

References (54)

1. Ahn, S.J., Shin, R. Schachtman, D.P. ( 2004) Expression of KT/KUP genes in Arabidopsis and the role of root hairs in K+ uptake. Plant Physiol. 134, 1135 1145.
2. Baker, K.E. Parker, R. ( 2004) Nonsense-mediated mRNA decay: terminating erroneous gene expression. Curr. Opin. Cell Biol. 16, 293 299.
3. Chapman, B. Brown, C. ( 2004) Translation termination in Arabidopsis thaliana: characterisation of three versions of release factor 1. Gene, 341, 219 225.
4. Conti, E. Izaurralde, E. ( 2005) Nonsense-mediated mRNA decay: molecular insights and mechanistic variations across species. Curr. Opin. Cell Biol. 17, 316 325.
5. Culbertson, M.R. Leeds, P.F. ( 2003) Looking at mRNA decay pathways through the window of molecular evolution. Curr. Opin. Genet. Dev. 13, 207 214.
6. Czaplinski, K., Weng, Y., Hagan, K.W. Peltz, S.W. ( 1995) Purification and characterization of the Upf1p: a factor involved in mRNA turnover. RNA, 1, 610 623.
7. Czechowski, T., Stitt, M., Altmann, T., Udvardi, M.K. Scheible, W.R. ( 2005) Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiol. 139, 5 17.
8. Davis, J.M., Egelkrout, E.E., Coleman, G.D., Chen, T.H., Haissig, B.E., Riemenschneider, D.E. Gordon, M.P. ( 1993) A family of wound-induced genes in Populus shares common features with genes encoding vegetative storage proteins. Plant Mol. Biol. 23, 135 143.
9. Finkelstein, R. ( 1994) Mutations at two new Arabidopsis ABA response loci are similar to the abi3 mutations. Plant J. 5, 765 771
10. Fujiki, Y., Yoshikawa, Y., Sato, T., Inada, N., Ito, M., Nishida, I. Watanabe, A. ( 2001) Dark-inducible genes from Arabidopsis thaliana are associated with leaf senescence and repressed by sugars. Physiol. Plant. 111, 345 352.
11. Gadjieva, R., Axelsson, E., Olsson, U., Vallon-Christersson, J. Hansson, M. ( 2004) Nonsense-mediated mRNA decay in barley mutants allows the cloning of mutated genes by a microarray approach. Plant Physiol. Biochem. 42, 681 685.
12. Gan, Y., Filleur, S., Rahman, A., Gotensparre, S. Forde, B.G. ( 2005) Nutritional regulation of ANR1 and other root-expressed MADS-box genes in Arabidopsis thaliana. Planta, 222, 730 742.
13. Gibson, S.I. ( 2005) Control of plant development and gene expression by sugar signaling. Curr. Opin. Plant Biol. 8, 93 102.
14. González, C.I., Bhattacharya, A., Wang, W. Peltz, S.W. ( 2001) Nonsense-mediated mRNA decay in Saccharomyces cerevisiae. Gene, 274, 15 25.
15. Gutierrez, R.A., MacIntosh, G.C. Green, P.J. ( 1999) Current perspectives on mRNA stability in plants: multiple levels and mechanisms of control. Trends Plant Sci. 4, 429 438.
16. He, F., Li, X., Spatrick, P., Casillo, R., Dong, S. Jacobson, A. ( 2003) Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5′ to 3′ mRNA decay pathways in yeast. Mol. Cell 12, 1439 1452.
17. Helliwell, C.A., Sheldon, C.C., Olive, M.R., Walker, A.R.W., Zeevaart, J.A.D., Peacock, W.J. Dennis, E.S. ( 1998) Cloning of the Arabidopsis ent-kaurene oxidase gene GA3. Proc. Natl Acad. Sci. USA 95, 9019 9024.
18. Hodgman, T.C. ( 1988) A new superfamily of replicative proteins. Nature, 333, 22 23.
19. Hori, K. Watanabe, Y. ( 2005) UPF3 suppresses aberrant spliced mRNA in Arabidopsis. Plant J. 43, 530 540.
20. Husselstein-Muller, T., Schaller, H. Benveniste, P. ( 2001) Molecular cloning and expression in yeast of 2,3-oxidosqualene-triterpenoid cyclases from Arabidopsis thaliana. Plant Mol. Biol. 45, 75 92.
21. Iida, K., Seki, M., Sakurai, T., Satou, M., Akiyama, K., Toyoda, T., Konagaya, A. Shinozaki, K. ( 2004) Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences. Nucleic Acids Res. 32, 5096 5103.
22. Isshiki, M., Yamamoto, Y., Satoh, H. Shimamoto, K. ( 2001) Nonsense-mediated decay of mutant waxy mRNA in rice. Plant Physiol. 125, 1388 1395.
23. Jang, J.C., Leon, P., Zhou, L. Sheen, J. ( 1997) Hexokinase as a sugar sensor in higher plants. Plant Cell, 9, 5 19.
24. Kang, H.-G., Foley, R.C., Oñate-Sánchez, L., Lin, C. Singh, K.B. ( 2003) Target genes for OBP3, a Dof transcription factor, include novel basic helix-loop-helix domain proteins inducible by salicylic acid. Plant J. 35, 362 372.
25. Kumar, S., Tamura, K. Nei, M. ( 2004) mega3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform. 5, 150 163.
26. Leeds, P., Wood, J.M., Lee, B.S. Culbertson, M.R. ( 1992) Gene products that promote mRNA turnover in Saccharomyces cerevisiae. Mol. Cell Biol. 12, 2165 2177.
27. Lejeune, F. Maquat, L.E. ( 2005) Mechanistic links between nonsense-mediated mRNA decay and pre-mRNA splicing in mammalian cells. Curr. Opin. Cell Biol. 17, 309 315.
28. Lew, J.E., Enomoto, S. Berman, J. ( 1998) Telomere length regulation and telomeric chromatin require the nonsense-mediated mRNA decay pathway. Mol. Cell Biol. 18, 6121 6130.
29. Lohman, K., Gan, S., John, M. Amasino, R.M. ( 1994) Molecular analysis of natural leaf senescence in Arabidopsis thaliana. Physiol. Plant. 92, 322 328.
30. Malboobi, M.A. Lefebvre, D.D. ( 1997) A phosphate-starvation inducible beta-glucosidase gene (psr3.2) isolated from Arabidopsis thaliana is a member of a distinct subfamily of the BGA family. Plant Mol. Biol. 34, 57 68.
31. Masaki, T., Mitsui, N., Tsukagoshi, H., Nishii, T., Morikami, A. Nakamura, K. ( 2005a) ACTIVATOR OF Spomin::LUC1/WRINKLED1 of Arabidopsis thaliana transactivates sugar-inducible promoters. Plant Cell Physiol. 46, 547 556.
32. Masaki, T., Tsukagoshi, H., Mitsui, N., Nishii, T., Hattori, T., Morikami, A. Nakamura, K. ( 2005b) Activation tagging of a gene for a protein with novel class of CCT-domain activates expression of a subset of sugar-inducible genes in Arabidpsis thaliana. Plant J. 43, 142 152.
33. Mathieu, O., Yukawa, Y., Prieto, J.L., Vaillant, I., Sugiura, M. Tourmente, S. ( 2003) Identification and characterization of transcription factor IIIA and ribosomal protein L5 from Arabidopsis thaliana. Nucleic Acids Res. 31, 2424 2433.
34. Mendell, J.T., Sharifi, N.A., Meyers, J.L., Martinez-Murillo, F. Dietz, H.C. ( 2004) Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat. Genet. 36, 1073 1078.
35. Mita, S., Murano, N., Akaike, M. Nakamura, K. ( 1997) Mutants of Arabidopsis thaliana with pleiotropic effects on the expression of the gene for β-amylase and on the accumulation of anthocyanin that are inducible by sugars. Plant J. 11, 841 851.
36. Mou, Z., Wang, X., Fu, Z., Dai, Y., Han, C., Ouyang, J., Bao, F., Hu, Y. Li, J. ( 2002) Silencing of phosphoethanolamine N-methyltransferase results in temperature-sensitive male sterility and salt hypersensitivity in Arabidopsis. Plant Cell, 14, 2031 2043.
37. Neff, M.M., Turk, F. Kalishman, M. ( 2002) Web-based primer design for single nucleotide polymorphism analysis. Trends Genet. 18, 613 615.
38. Pego, J.V., Weisbeek, P.J. Smeekens, S.C. ( 1999) Mannose inhibits Arabidopsis germination via a hexokinase-mediated step. Plant Physiol. 119, 1017 1023.
39. Ratcliffe, O.J., Kumimoto, R.W., Wong, B.J. Riechmann, J.L. ( 2003) Analysis of the Arabidopsis mads affecting flowering gene family: MAF2 prevents vernalization by short periods of cold. Plant Cell, 15, 1159 1169.
40. Rehwinkel, J., Letunic, I., Raes, J., Bork, P. Izaurralde, E. ( 2005) Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets. RNA, 11, 1530 1544.
41. Rolland, F., Moore, B. Sheen, J. ( 2002) Sugar sensing and signaling in plants. Plant Cell, 14 Suppl., S185 205.
42. Rook, F. Bevan, M.W. ( 2003) Genetic approaches to understanding sugar-response pathways. J. Exp. Bot. 54, 495 501.
43. Samach, A., Onouchi, H., Gold, S.E., Ditta, G.S., Schwarz-Sommer, Z., Yanofsky, M.F. Coupland, G. ( 2000) Distinct roles of CONSTANS target genes in reproductive development of Arabidopsis. Science, 288, 1613 1616.
44. Satoh, R., Fujita, Y., Nakashima, K., Shinozaki, K. Yamaguchi-Shinozaki, K. ( 2004) A novel subgroup of bZIP proteins functions as transcriptional activators in hypoosmolarity-responsive expression of the ProDH gene in Arabidopsis. Plant Cell Physiol. 45, 309 317.
45. Shibuya, T., Tange, T.O., Sonenberg, N. Moore, M.J. ( 2004) eIF4AIII binds spliced mRNA in the exon junction complex and is essential for nonsense-mediated decay. Nat. Struct. Mol. Biol. 11, 346 351.
46. Smeekens, S. ( 2000) Sugar-induced signal transduction in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 51, 49 81.
47. Tarantino, D., Petit, J.M., Lobreaux, S., Briat, J.F., Soave, C. Murgia, I. ( 2003) Differential involvement of the IDRS cis-element in the developmental and environmental regulation of the AtFer1 ferritin gene from Arabidopsis. Planta, 217, 709 716.
48. Thomma, B.P.H.J., Eggermont, K., Penninckx, I.A.M.A., Mauch-Mani, B., Vogelsang, R., Cammue, B.P.A. Broekaert, W.F. ( 1998) Separate jasmonate-dependent and salicylate-dependent defense-response pathways in Arabidopsis are essential for resistance to distinct microbial pathogens. Proc. Natl Acad. Sci. USA 95, 15107 15111.
49. Tian, Q., Uhlir, N.J. Reed, J.W. ( 2002) Arabidopsis SHY2/IAA3 inhibits auxin-regulated gene expression. Plant Cell, 14, 301 319.
50. Toledo-Ortiz, G., Huq, E. Quail, P.H. ( 2003) The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell, 15, 1749 1770.
51. Tsukagoshi, H., Saijo, T., Shibata, D., Morikami, A. Nakamura, K. ( 2005) Analysis of a sugar response mutant of Arabidopsis thaliana identified a novel B3 domain protein that functions as an active transcriptional repressor. Plant Physiol. 138, 675 685.
52. Weaver, L.M., Gan, S., Quirino, B. Amasino, R.M. ( 1998) A comparison of the expression patterns of several senescence-associated genes in response to stress and hormone treatment. Plant Mol. Biol. 37, 455 469.
53. Weng, Y., Czaplinski, K. Peltz, S.W. ( 1996) Genetic and biochemical characterization of mutations in the ATPase and helicase regions of the Upf1 protein. Mol. Cell Biol. 16, 5477 5490.
54. Yoine, M., Nishii, T. Nakamura, K. ( 2006) Arabidopsis UPF1 RNA helicase for nonsense-mediated mRNA decay is involved in seed size control and is essential for growth. Plant Cell Physiol., 48, doi: 10.1093/pcp/pcj035.