Hostname: page-component-78c5997874-dh8gc Total loading time: 0 Render date: 2024-10-31T23:03:50.489Z Has data issue: false hasContentIssue false
  • English
  • Français

Alternative splicing of pre-mRNA in plants

Published online by Cambridge University Press:  15 June 2007

Guo Xiao-Qin ,
Zhang Hong-Zhi  and
Li De-Bao
Guo Xiao-Qin
Affiliation:
College of Foresty and Biotechnology, Zhejiang Forestry University, Lin'an 311300, China College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, China
Zhang Hong-Zhi
Affiliation:
Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
Li De-Bao*
Affiliation:
College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, China
*
*Corresponding author. E-mail: lidb@mail.hz.zj.cn
Get access Rights & Permissions [Opens in a new window]

Abstract

Alternative splicing is an important cellular mechanism that increases the diversity of gene products. The study of alternatively spliced genes reported so far in plants is far less documented than that in mammals, but considerable results have been reported, showing the role of these genes in regulating mechanisms, influencing factors, and specificities and function of alternative splicing in plants. This review summarizes briefly the major progress made on alternative splicing in plants.

Keywords

plantpre-mRNAalternative splicing
Type
Research Article
Information
Chinese Journal of Agricultural Biotechnology , Volume 4 , Issue 1 , April 2007 , pp. 1 - 8
Copyright
Copyright © China Agricultural University and Cambridge University Press 2007

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Footnotes

First published in Journal of Agricultural Biotechnology 2006, 14(5): 809–815

References

Ayliffe, MA, Frost, DV, Finnegan, EJ, Lawrence, GJ, Anderson, PA and Ellis, JG (1999) Analysis of alternative transcripts of the flax L6 rust resistance gene. Plant Journal 17: 287–292.CrossRefGoogle ScholarPubMed
Bournay, AS, Hedley, PE, Maddison, A, Waugh, R and Machray, GC (1996) Exon skipping induced by cold stress in a potato invertase gene transcript. Nucleic Acids Research 24: 2347–2351.CrossRefGoogle Scholar
Brack, C, Hirama, M, Lenhard-Schuller, R and Tonegawa, S (1978) A complete immunoglobulin gene is created by somatic recombination. Cell 15: 1–14.CrossRefGoogle ScholarPubMed
Brown, JW and Simpson, CG (1998) Splice site selection in plant pre-mRNA splicing. Annual Review Plant Physiology Plant Molecular Biology 49: 77–95.CrossRefGoogle ScholarPubMed
Carle-Urioste, JC, Brendel, V and Walbot, V (1997) A combinatorial role for exon, intron and splice site sequences in splicing in maize. Plant Journal 11: 1253–1263.CrossRefGoogle ScholarPubMed
Choi, E, Kuehl, M and Wall, R (1980) RNA splicing generates a variant light chain from an aberrantly rearranged kappa gene. Nature 286: 776–779.CrossRefGoogle ScholarPubMed
de la Fuente, van Bentem, Vossen, JH, Vermeer, JE, et al. (2003) The subcellular localization of plant protein phosphatase 5 isoforms is determined by alternative splicing. Plant Physiology 133: 702–712.CrossRefGoogle Scholar
Dinesh-Kumar, SP and Baker, BJ (2000) Alternatively spliced N resistance gene transcripts: their possible role in tobacco mosaic virus resistance. Proceedings of the National Academy of Sciences of the USA 97: 1908–1913.CrossRefGoogle ScholarPubMed
Ferrier-Cana, E, Macadre, C, Sevignac, M, David, P, Langin, T and Geffroy, V (2005) Distinct post-transcriptional modifications result in seven alternative transcripts of the CC-NBS-LRR gene JA1tr of Phaseolus vulgaris. Theoretical and Applied Genetics 110: 895–905.CrossRefGoogle ScholarPubMed
Garcia-Ortiz, MV, Ariza, RR, Hoffman, PD, Hays, JB and Roldan-Arjona, T (2004) Arabidopsis thaliana AtPOLK encodes a DinB-like DNA polymerase that extends mispaired primer termini and is highly expressed in a variety of tissues. Plant Journal 39: 84–97.CrossRefGoogle Scholar
Golovkin, M and Reddy, AS (1998) The plant U1 small nuclear ribonucleoprotein particle 70K protein interacts with two novel serine/arginine-rich proteins. Plant Cell 10: 1637–1648.Google ScholarPubMed
Golovkin, M and Reddy, AS (1999) An SC35-like protein and a novel serine/arginine-rich protein interact with Arabidopsis U1–70 protein. Journal of Biological Chemistry 274: 36428–36438.CrossRefGoogle Scholar
Gupta, S, Wang, BB, Stryker, GA, Zanetti, ME and Lal, SK (2005) Two novel arginine/serine (SR) proteins in maize are differentially spliced and utilize non-canonical splice sites. Biochimica et Biophysica Acta 1728: 105–114.CrossRefGoogle ScholarPubMed
Halterman, DA, Wei, F and Wise, RP (2003) Powdery mildew-induced Mla mRNAs are alternatively spliced and contain multiple upstream open reading frames. Plant Physiology 131: 558–567.CrossRefGoogle ScholarPubMed
Hamada, S, Ito, H, Hiraga, S, et al. (2002) Differential characteristics and subcellular localization of two starch-branching enzyme isoforms encoded by a single gene in Phaseolus vulgaris L. Journal of Biological Chemistry 277: 16538–16546.CrossRefGoogle ScholarPubMed
Hanano, S, Sugita, M and Sugiura, M (1996) Isolation of a novel RNA-binding protein and its association with a large ribonucleoprotein particle present in the nucleoplasm of tobacco cells. Plant Molecular Biology 31: 57–68.CrossRefGoogle ScholarPubMed
Iida, K, Seki, M, Sakurai, T, et al. (2004) Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences. Nucleic Acids Research 32: 5096–5103.CrossRefGoogle ScholarPubMed
Isshiki, M, Yamamoto, Y, Satoh, H and Shimamoto, K (2001) Nonsense-mediated decay of mutant waxy mRNA in rice. Plant Physiology 125: 1388–1395.CrossRefGoogle ScholarPubMed
Itoh, H, Washio, T and Tomita, M (2004) Computational comparative analyses of alternative splicing regulation using full-length cDNA of various eukaryotes. RNA 10: 1005–1018.CrossRefGoogle ScholarPubMed
Jia, Y, del Rio, HS, Robbins, AL and Louzada, ES (2004) Cloning and sequence analysis of a low temperature-induced gene from trifoliate orange with unusual pre-mRNA processing. Plant Cell Reports 23: 159–166.CrossRefGoogle ScholarPubMed
Johnson, JM, Castle, J, Garrett-Engele, P, et al. (2003) Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302, 2141–2144.CrossRefGoogle ScholarPubMed
Kikuchi, S, Satoh, K, Nagata, T, et al. (2003) Collection, mapping and annotation of over 28,000 cDNA clones from japonica rice. Science 301, 376–379.CrossRefGoogle Scholar
Kitagawa, N, Washio, T, Kosugi, S, et al. (2005) Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa). Bioinformatics 21: 1758–1763.CrossRefGoogle ScholarPubMed
Kong, J, Gong, JM, Zhang, ZG, Zhang, JS and Chen, SY (2003) A new AOX homologous gene OsIM1 from rice (Oryza sativa L.) with an alternative splicing mechanism under salt stress. Theoretical and Applied Genetics 107: 326–331.CrossRefGoogle ScholarPubMed
Krecic, AM and Swanson, MS (1999) hnRNP complexes: composition, structure, and function. Current Opinion in Cell Biology 11: 363–371.CrossRefGoogle ScholarPubMed
Lal, S, Choi, JH, Shaw, JR and Hannah, LC (1999) A splice site mutant of maize activates cryptic splice sites, elicits intron inclusion and exon exclusion, and permits branch point elucidation. Plant Physiology 121: 411–418.CrossRefGoogle ScholarPubMed
Lambermon, MH, Simpson, GG, Wieczorek Kirk, DA, Hemmings-Mieszczak, M, Klahre, U and Filipowicz, W (2000) UBP1, a novel hnRNP-like protein that functions at multiple steps of higher plant nuclear pre-mRNA maturation. EMBO Journal 19: 1638–1649.CrossRefGoogle ScholarPubMed
Lambermon, MH, Fu, Y, Wieczorek Kirk, DA, Dupasquier, M, Filipowicz, W and Lorkovic, ZJ (2002) UBA1 and UBA2, two proteins that interact with UBP1, a multifunctional effector of pre-mRNA maturation in plants. Molecular and Cellular Biology 22: 4346–4357.CrossRefGoogle ScholarPubMed
Lazar, G and Goodman, HM (2000) The Arabidopsis splicing factor SR1 is regulated by alternative splicing. Plant Molecular Biology 42: 571–581.CrossRefGoogle ScholarPubMed
Liu, HX, Goodall, GJ, Kole, R and Filipowicz, W (1995) Effects of secondary structure on pre-mRNA splicing: hairpins sequestering the 5′ but not the 3′ splice site inhibit intron processing in Nicotiana plumbaginifolia. EMBO Journal 14: 377–388.CrossRefGoogle Scholar
Liu, K, Jiang, H, Moore, SL, Watkins, CB and Jahn, MM (2006) Isolation and characterization of a lipid transfer protein expressed in ripening fruit of Capsicum chinense. Planta 223: 672–683.CrossRefGoogle ScholarPubMed
Lopato, S, Kalyna, M, Dorner, S, Kobayashi, R, Krainer, AR and Barta, A (1999) atSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes. Genes and Development 13: 987–1001.CrossRefGoogle ScholarPubMed
Lorkovic, ZJ, Lopato, S, Pexa, M, Lehner, R and Barta, A (2004) Interactions of Arabidopsis RS domain containing cyclophilins with SR proteins and U1 and U11 small nuclear ribonucleoprotein-specific proteins suggest their involvement in pre-mRNA splicing. Journal of Biological Chemistry 279: 33890–33898.CrossRefGoogle ScholarPubMed
Lorkovic, ZJ, Wieczorek Kirk, DA, Lambermon, MH and Filipowicz, W (2000) Pre-mRNA splicing in higher plants. Trends in Plant Science 5: 160–167.CrossRefGoogle ScholarPubMed
Ner-Gaon, H, Halachmi, R, Savaldi-Goldstein, S, Rubin, E, Ophir, R and Fluhr, R (2004) Intron retention is a major phenomenon in alternative splicing in Arabidopsis. Plant Journal 39: 877–885.CrossRefGoogle Scholar
Savaldi-Goldstein, S, Aviv, D, Davydov, O and Fluhr, R (2003) Alternative splicing modulation by a LAMMER kinase impinges on developmental and transcriptome expression. Plant Cell 15: 926–938.CrossRefGoogle ScholarPubMed
Schmucker, D, Clemens, JC, Shu, H, et al. (2000) Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity. Cell 101: 671–684.CrossRefGoogle ScholarPubMed
Shomron, N, Alberstein, M, Reznik, M and Ast, G (2005) Stress alters the subcellular distribution of hSlu7 and thus modulates alternative splicing. Journal of Cell Science 118: 1151–1159.CrossRefGoogle ScholarPubMed
Simpson, GG and Filipowicz, W (1996) Splicing of precursors to mRNA in higher plants: mechanism, regulation and sub-nuclear organisation of the spliceosomal machinery. Plant Molecular Biology 32: 1–41.CrossRefGoogle ScholarPubMed
Tantikanjana, T, Nasrallah, ME, Stein, JC, Chen, CH and Nasrallah, JB (1993) An alternative transcript of the S locus glycoprotein gene in a class II pollen-recessive self-incompatibility haplotype of Brassica oleracea encodes a membrane-anchored protein. Plant Cell 5: 657–666.Google Scholar
Tao, NG, Xu, J, Cheng, YJ and Deng, XX (2005) Lycopene-epsilon-cyclase pre-mRNA is alternatively spliced in Cara Cara navel orange (Citrus sinensis Osbeck). Biotechnology Letters 27: 779–782.CrossRefGoogle ScholarPubMed
Wang, F, Wang, HB, Liu, B and Wang, JF (2006). Cloning and characterization of a novel splicing isoform of the iron-superoxide dismutase gene in rice (Oryza sativa L.). Plant Cell Reports 24: 734–742.Google Scholar
Werneke, JM, Chatfield, JM and Ogren, WL (1989) Alternative mRNA splicing generates the two ribulose bisphosphate carboxylase/oxygenase activase polypeptides in spinach and Arabidopsis. Plant Cell 1: 815–825.Google ScholarPubMed
Yoshimura, K, Yabuta, Y, Ishikawa, T and Shigeoka, S (2002) Identification of a cis element for tissue-specific alternative splicing of chloroplast ascorbate peroxidase pre-mRNA in higher plants. Journal of Biological Chemistry 277: 40623–40632.CrossRefGoogle ScholarPubMed
Zhang, H, Sreenivasulu, N, Weschke, W, et al. (2004) Large-scale analysis of the barley transcriptome based on expressed sequence tags. Plant Journal 40: 276–290.CrossRefGoogle ScholarPubMed
Zhang, N and Portis, AR Jr (1999) Mechanism of light regulation of Rubisco: a specific role for the larger Rubisco activase isoform involving reductive activation by thioredoxin-f. Proceedings of the National Academy of Sciences of the USA 96: 9438–9443.CrossRefGoogle ScholarPubMed
Zhang, XC and Gassmann, W (2003) RPS4-mediated disease resistance requires the combined presence of RPS4 transcripts with full-length and truncated open reading frames. Plant Cell 15: 2333–2342.CrossRefGoogle ScholarPubMed
Zhang, Z, Honda, C, Kita, M, et al. (2003) Structure and expression of spermidine synthase genes in apple: two cDNAs are spatially and developmentally regulated through alternative splicing. Molecular Genetics and Genomics 268: 799–807.CrossRefGoogle ScholarPubMed
Zhou, Y, Zhou, CL, Ye, L, et al. (2003) Database and analyses of known alternatively spliced genes in plants. Genomics 82: 584–595.CrossRefGoogle ScholarPubMed