A subgroup of MYB transcription factor genes undergoes highly conserved alternative splicing in Arabidopsis and rice

Journal of Experimental Botany

Volumn 57, Issue 6, 2006, Pages 1263-1273

  Li, Jigang ^a   Li, Xiaojuan ^a   Guo, Lei ^a   Lu, Feng ^a   Feng, Xiaojie ^a   He, Kun ^a   Wei, Liping ^a   Chen, Zhangliang ^a,b   Qu, Li Jia ^a,b   Gu, Hongya ^a  

^a PEKING UNIVERSITY   (China)

^b National Plant Gene Research Center (Beijing)   (China)

Author keywords

Alternative splicing; MYB transcription factors; Non canonical introns; Nuclear localization signals; Nucleotide repeats

Indexed keywords

CROPS; DATA ACQUISITION; DATABASE SYSTEMS; HORMONES; PLANTS (BOTANY); PROTEINS;

ALTERNATIVE SPLICING; MYB TRANSCRIPTION FACTORS; NON-CANONICAL INTRONS; NUCLEAR LOCALIZATION SIGNALS;

GENES;

ARABIDOPSIS PROTEIN; ATR1 PROTEIN, ARABIDOPSIS; CPC PROTEIN, ARABIDOPSIS; MYB PROTEIN, PLANT; PROTEIN C MYB; VEGETABLE PROTEIN;

ALTERNATIVE RNA SPLICING; AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; GENE EXPRESSION; GENETICS; INTRON; MOLECULAR GENETICS; NUCLEAR LOCALIZATION SIGNAL; ONCOGENE MYB; ONION; RICE; RNA SPLICING; SEQUENCE HOMOLOGY; UNTRANSLATED REGION;

ALTERNATIVE SPLICING; AMINO ACID SEQUENCE; ARABIDOPSIS; ARABIDOPSIS PROTEINS; GENE EXPRESSION; GENES, MYB; INTRONS; MOLECULAR SEQUENCE DATA; NUCLEAR LOCALIZATION SIGNALS; ONIONS; ORYZA SATIVA; PLANT PROTEINS; PROTO-ONCOGENE PROTEINS C-MYB; RNA SPLICE SITES; SEQUENCE HOMOLOGY; UNTRANSLATED REGIONS;

FARM CROPS; GENES; HORMONES; PLANTS; PROTEINS;

ARABIDOPSIS;

EID: 32344440773     PISSN: 00220957     EISSN: 14602431     Source Type: Journal    
DOI: 10.1093/jxb/erj094     Document Type: Article

References (40)

1. Bailey-Serres J. 1999. Selective translation of cytoplasmic mRNAs in plants. Trends in Plant Science 4, 142-148.
2. Brett D, Hanke J, Lehmann G, Haase S, Delbruck S, Krueger S, Reich J, Bork P. 2000. EST comparison indicates 38% of human mRNAs contain possible alternative splice forms. FEBS Letters 474, 83-86.
3. Brown JW, Simpson CG. 1998. Splice site selection in plant pre-mRNA splicing. Annual Review of Plant Physiology and Plant Molecular Biology 49, 77-95.
4. Burge CB, Padgett RA, Sharp PA. 1998. Evolutionary fates and origins of U12-type introns. Molecular Cell 2, 773-785.
5. Carrasco JL, Ancillo G, Mayda E, Vera P. 2003. A novel transcription factor involved in plant defence endowed with protein phosphatase activity. The EMBO Journal 22, 3376-3384.
6. Chen Y, Yang X, He K, et al. 2006. The MYB transcription factor superfamily of Arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family. Plant Molecular Biology 60, 107-124.
7. Dietrich RC, Incorvaia R, Padgett RA. 1997. Terminal intron dinucleotide sequences do not distinguish between U2- and U12-dependent introns. Molecular Cell 1, 151-160.
8. Felsenstein J. 1989. PHYLIP: Phylogeny Inference Package (Version 3.2). Cladistics 5, 164-166.
9. Grotewold E, Athma P, Peterson T. 1991. Alternatively spliced products of the maize P gene encode proteins with homology to the DNA-binding domain of myb-like transcription factors. Proceedings of the National Academy of Sciences, USA 88, 4587-4591.
10. Hall SL, Padgett RA. 1994. Conserved sequences in a class of rare eukaryotic nuclear introns with non-consensus splice sites. Journal of Molecular Biology 239, 357-365.
11. Hanke J, Brett D, Zastrow I, Aydin A, Delbruck S, Lehmann G, Luft F, Reich J, Bork P. 1999. Alternative splicing of human genes: more the rule than the exception? Trends in Genetics 15, 389-390.
12. Hardtke CS, Berleth T. 1998. The Arabidopsis gene MONOPTEROS encodes a transcription factor mediating embryo axis formation and vascular development. The EMBO Journal 17, 1405-1411.
13. Horstmann S, Ferrari S, Klempnauer KH. 2000. An alternatively spliced isoform of B-Myb is a transcriptional inhibitor. Oncogene 19, 5428-5434.
14. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409, 860-921.
15. Jefferson RA, Kavanagh TA, Bevan MW. 1987. GUS fusions: beta-glucuronidase as a sensitive and versatile gene fusion marker in higher plants. EMBO Journal 6, 3901-3907.
16. Jiang C, Gu X, Peterson T. 2004. Identification of conserved gene structures and carboxy-terminal motifs in the Myb gene family of Arabidopsis and Oryza sativa L. ssp. indica. Genome Biology 5, R46.
17. Kazan K. 2003. Alternative splicing and proteome diversity in plants: the tip of the iceberg has just emerged. Trends in Plant Science 8, 468-471.
18. Kochetov AV, Syrnik OA, Rogozin IB, Glazko GV, Komarova ML, Shumnyi VK. 2002. Context organization of mRNA 5′-untranslated regions of higher plants. Molecular Biology 36, 649-656.
19. Kozak M. 1999. Initiation of translation in prokaryotes and eukaryotes. Gene 234, 187-208.
20. Kozak M. 2002. Pushing the limits of the scanning mechanism for initiation of translation. Gene 299, 1-34.
21. Larsen LK, Amri EZ, Mandrup S, Pacot C, Kristiansen K. 2002. Genomic organization of the mouse peroxisome proliferator-activated receptor beta/delta gene: alternative promoter usage and splicing yield transcripts exhibiting differential translational efficiency. Biochemical Journal 366, 767-775.
22. Lee TH, Kim SJ, Kang SW, Lee KK, Rhee SG, Yu DY. 2000. Molecular cloning and characterization of the mouse peroxiredoxin V gene. Biochemical and Biophysical Research Communications 270, 356-362.
23. Levine A, Durbin R. 2001. A computational scan for U12-dependent introns in the human genome sequence. Nucleic Acids Research 29, 4006-4013.
24. Lewandowska D, Simpson CG, Clark GP, Jennings NS, Barciszewska-Pacak M, Lin CF, Makalowski W, Brown JW, Jarmolowski A. 2004. Determinants of plant U12-dependent intron splicing efficiency. The Plant Cell 16, 1340-1352.
25. Locatelli F, Magnani E, Vighi C, Lanzanova C, Coraggio I. 2002. Inhibitory effect of myb7 uORF on downstream gene expression in homologous (rice) and heterologous (tobacco) systems. Plant Molecular Biology 48, 309-318.
26. Lorkovic ZJ, Wieczorek Kirk DA, Lambermon MH, Filipowicz W. 2000. Pre-mRNA splicing in higher plants. Trends in Plant Science 5, 160-167.
27. Macknight R, Bancroft I, Page T, et al. 1997. FCA, a gene controlling flowering time in Arabidopsis, encodes a protein containing RNA-binding domains. Cell 89, 737-745.
28. Magaraggia F, Solinas G, Valle G, Giovinazzo G, Coraggio I. 1997. Maturation and translation mechanisms involved in the expression of a myb gene of rice. Plant Molecular Biology 35, 1003-1008.
29. Reddy ASN. 2001. Nuclear pre-mRNA splicing in plants. Critical Reviews in Plant Sciences 20, 523-571.
30. Rosinski JA, Atchley WR. 1998. Molecular evolution of the Myb family of transcription factors: evidence for polyphyletic origin. Journal of Molecular Evolution 46, 74-83.
31. Sharp PA, Burge CB. 1997. Classification of introns: U2-type or U12-type. Cell 91, 875-879.
32. Shen-Ong GL. 1987. Alternative internal splicing in c-myb RNAs occurs commonly in normal and tumor cells. EMBO Journal 6, 4035-4039.
33. Stracke R, Werber M, Weisshaar B. 2001. The R2R3-MYB gene family in Arabidopsis thaliana. Current Opinion in Plant Biology 4, 447-456.
34. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4673-4680.
35. Wang L, Wessler SR. 1998. Inefficient reinitiation is responsible for upstream open reading frame-mediated translational repression of the maize R gene. The Plant Cell 10, 1733-1746.
36. Wiese A, Elzinga N, Wobbes B, Smeekens S. 2004. A conserved upstream open reading frame mediates sucrose-induced repression of translation. The Plant Cell 16, 1717-1729.
37. Wu Q, Krainer AR. 1996. U1-mediated exon definition interactions between AT-AC and GT-AG introns. Science 274, 1005-1008.
38. Yi L, Qu LJ, Chang S, Su Y, Gu H, Chen Z. 2002. Two nuclear localization signals required for the nuclear localization of rice ribosomal protein S4. Plant Science 162, 251-256.
39. Zhou Y, Zhou C, Ye L, Dong J, Xu H, Cai L, Zhang L, Wei L. 2003. Database and analyses of known alternatively spliced genes in plants. Genomics 82, 584-595.
40. Zhu W, Brendel V. 2003. Identification, characterization and molecular phylogeny of U12-dependent introns in the Arabidopsis thaliana genome. Nucleic Acids Research 31, 4561-4572.