Intron sequences in nuclear pre-mRNAs are excised with either the major U2 snRNA-dependent spliceosomal pathway or the minor U12 snRNA-dependent spliceosomal pathway that exist in most eukaryotic organisms. While the predominant dinucleotides bordering each of these types of introns and the catalytic mechanism used in their excision are conserved in plants and animals, several features aiding in the recognition of plant introns are distinct from those in animals and yeast. Along with their short length, high AU content and high variation in their 5′ and 3′ splice sites and branchpoint consensus sequences are the most prominent characteristics of plant introns. Detailed surveys of site-directed mutant introns tested in vivo and chemically induced and naturally mutant introns analyzed in planta emphasize the effects of changing individual nucleotides in these splice site consensus sequences and highlight a number of noncanonical dinucleotides that are functional in plant systems.
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Ahlfors R, Lang S, Overmyer K, Jaspers P, Brosche A, Tauriainen A, Kollist H, Tuominen H, Belles-Boix E, Piippo M, Inze D, Palva ET, Kangasjarvi J (2004) Arabidopsis RADICAL-INDUCED CELL DEATH1 belongs to the WWE protein-protein interaction domain protein family and modulates abscisic acid, ethylene, and methyl jasmonate responses. Plant Cell 16:1925–1937
Alexandrov NN, Troukhan ME, Brover VV, Tatarinova T, Flavell RB, Feldmann KA (2006) Features of Arabidopsis genes and genome discovered using full-length cDNAs. Plant Mol Biol 60:69–85
Ayres NM, McClung AM, Larkin PD, Bligh HFJ, Jones CA, Park WD (1997) Microsatellites and a single-nucleotide polymorphism differentiate apparent amylose classes in an extended pedigree of US rice germ plasm. TAG Theor Appl Genet 94:773–781
Baynton CE, Potthoff SJ, McCullough AJ, Schuler MA (1996) U-rich tracts enhance 3′’ splice site recognition in plant nuclei. Plant J 10:703–711
Bligh HF, Larkin PD, Roach PS, Jones CA, Fu H, Park WD (1998) Use of alternate splice sites in granule-bound starch synthase mRNA from low-amylose rice varieties. Plant Mol Biol 38:407–415
Brown JWS (1996) Arabidopsis intron mutations and pre-mRNA splicing. Plant J 10:771–780
Burbulis IE, Iacobucci M, Shirley BW (1996) A null mutation in the first enzyme of flavonoid biosynthesis does not affect male fertility in Arabidopsis. Plant Cell 8:1013–1025
Burge CB, Padgett RA, Sharp PA (1998) Evolutionary fates and origins of U12-type introns. Mol Cell 2:773–785
Cai XL, Wang ZY, Xing YY, Zhang JL, Hong MM (1998) Aberrant splicing of intron 1 leads to the heterogeneous 5′ UTR and decreased expression of waxy gene in rice cultivars of intermediate amylose content. Plant J 14:459–465
Chanfreau G, Legrain P, Dujon B, Jacquier A (1994) Interaction between the first and last nucleotides of pre-mRNA introns is a determinant of 3′ splice site selection in S. cerevisiae. Nucleic Acids Res 22:1981–1987
Choe S, Tanaka A, Noguchi T, Fujioka S, Takatsuto S, Ross AS, Tax FE, Yoshida S, Feldmann KA (2000) Lesions in the sterol delta reductase gene of Arabidopsis cause dwarfism due to a block in brassinosteroid biosynthesis. Plant J 21:431–443
Dehesh K, Franci C, Parks BM, Seeley KA, Short TW, Tepperman JM, Quail PH (1993) Arabidopsis HY8 locus encodes phytochrome A. Plant Cell 5:1081–1088
Egoavil C, Marton HA, Baynton CE, McCullough AJ, Schuler MA (1997) Structural analysis of elements contributing to 5E splice site selection in plant pre-mRNA transcripts. Plant J 12:971–980
Gniadkowski G, Hemmings-Mieszczak , Klahre U, Liu H-X, Filipowicz W (1996) Characterization of intronic uridine-rich sequence elements acting as possible targets for nuclear proteins during pre-mRNA splicing in Nicotiana plumbaginifolia. Nucleic Acids Res 24:619–627
Goodall GJ, Filipowicz W (1989) The AU-rich sequences present in the introns of plant nuclear pre-mRNAs are required for splicing. Cell 58:473–483
Goodall GJ, Filipowicz W (1991) Different effects of intron nucleotide composition and secondary structure on pre-mRNA splicing in monocot and dicot plants. EMBO J 10:2635–2644
Hall SL, Padgett RA (1994) Conserved sequences in a class of rare eukaryotic nuclear introns with non-consensus splice sites. J Mol Biol 239:357–365
Hall SL, Padgett RA (1996) Requirement of U12 snRNA for in vivo splicing of a minor class of eukaryotic nuclear pre-mRNA introns. Science 271:1716–1718
Haseloff J, Siemering KR, Prasher DC, Hodge S (1997) Removal of a cryptic intron and subcellular localization of green fluorescent protein are required to mark transgenic Arabidopsis plants brightly. Proc Natl Acad Sci USA 94:2122–2127
Hong X, Scofield DG, Lynch H (2006) Intron size, abundance, and distribution within untranslated regions of genes. Mol Biol Evol 23:2392–2404
Hornig H, Aebi H, Weissmann, C (1986) Effect of mutations at the lariat branch acceptor site on beta-globin pre-mRNA splicing in vitro. Nature 324:589–591
Ibrahim AF, Watters JA, Clark GP, Thomas CJ, Brown JW, Simpson CG (2001) Expression of intron-containing GUS constructs is reduced due to activation of a cryptic 5′ splice site. Mol Genet Genomics 265:455–460
Isshiki I, Morino K, Nakajima M, Okagaki RJ, Wessler SR, Izawa T, Shimamoto K (1998) A naturally occurring functional allele of the rice waxy locus has a GT to TT mutation at the 5′ splice site of the first intron. Plant J:15:133–138
Jack T, Brockman, LL, Meyerowitz, EM (1992) The homeotic gene APETALA3 of Arabidopsis thaliana encodes a MADS box and is expressed in petals and stamens. Cell 68:683–697
Jackson IJ (1991) A reappraisal of non-consensus mRNA splice sites. Nucleic Acids Res 19:3795–3798
Jacobsen SE, Binkowski KA, Olszewski NE (1996) SPINDLY, a tetratricopeptide repeat protein involved in gibberellin signal transduction in Arabidopsis. Proc Natl Acad Sci USA 93:9292–9296
Jones L, Ennos AR, Turner SR (2001) Cloning and characterization of irregular xylem4 (irx4): a severely lignin-deficient mutant of Arabidopsis. Plant J 26:205–216
Kitamura-Abe S, Itoh H, Washio T, Tsutsumi A, Tomita M (2004) Characterization of the splice sites in GT-AG and GC-AG introns in higher eukaryotes using full-length cDNAs. J Bioinform Comput Biol 2:309–331
Kmieciak K, Simpson CG, Lewandowska D, Brown JW, Jarmolowski A (2002) Cloning and characterization of two subunits of Arabidopsis thaliana nuclear cap-binding complex. Gene 283:171–183
Ko CH, Brendel V, Taylor RD, Walbot V (1998) U-richness is a defining feature of plant introns and may function as an intron recognition signal in maize. Plant Mol Biol 36:573–583
Kramer A (1996) The structure and function of proteins involved in mammalian pre-mRNA splicing. Annu Rev Biochem 65:367–409
Lal S, Choi J-H, Hannah LC. (1999a) The AG dinucleotide terminating introns is important but not always required for pre-mRNA splicing in the maize endosperm. Plant Physiol. 120:65–72
Lal S, Choi JH, Shaw JR, Hannah LC (1999b) A splice site mutant of maize activates cryptic splice sites, elicits intron inclusion and exon exclusion, and permits branch point elucidation. Plant Physiol 121:411–418
Larkin PD, Park WD (1999) Transcript accumulation and utilization of alternate and non-consensus splice sites in rice granule-bound starch synthase are temperature-sensitive and controlled by a single-nucleotide polymorphism. Plant Mol Biol 40:719–727
Lazarova GI, Kerckhoffs LH, Brandstadter J, Matsui L, Kendrick RE, Cordonnier-Pratt MM, Pratt LH (1998) Molecular analysis of PHYA in wild-type and phytochrome A-deficient mutants of tomato. Plant J 14:653–662
Levine A, Durbin R (2001) A computational scan for U12-dependent introns in the human genome sequence. Nucleic Acids Res 29:4006–4013
Lewandowska D, Simpson CG, Clark GP, Jennings NS, Barciszewska-Pacak L, Lin CF, Makalowski W, Brown JW, Jarmolowski A (2004) Determinants of plant U12-dependent intron splicing efficiency. Plant Cell 16:1340–1352
Liu H-X, Filipowicz W (1996) Mapping of branchpoint nucleotides in mutant pre-mRNAs expressed in plant cells. Plant J 9:381–389
Lou H, McCullough AJ, Schuler MA (1993a) 3′ splice site selection in dicot plant nuclei is position-dependent. Mol Cell Biol 13:4485–4493
Lou H, McCullough AJ, Schuler MA (1993b) Expression of maize Adh1 intron mutants in tobacco nuclei. Plant J 3:393–403
Luehrsen KR, Walbot V (1994) Addition of A- and U-rich sequence increases the splicing efficiency of a deleted form of a maize intron. Plant Mol Biol 24:449–463
Luukkonen BGM, Seraphin B (1997) The role of branchpoint-3′ splice site spacing and interaction between intron terminal nucleotides in 3′ splice site selection in Saccharomyces cerevisiae. EMBO J 16:779–792
McCullough AJ, Lou H, Schuler MA (1991) In vivo analysis of plant pre-mRNA splicing using an autonomously replicating vector. Nucleic Acids Res 19:3001–3009
McCullough AJ, Schuler MA (1993) AU-rich intronic elements affect pre-mRNA 5′ splice site selection in Drosophila melanogaster. Mol Cell Biol 13:7689–7697
McCullough AJ, Baynton CE, Schuler MA (1996) Interactions across exons can influence splice site recognition in plant nuclei. Plant Cell 8:2295–2307
McCullough AJ, Schuler MA (1997) Intronic and exonic sequences modulate 5′ splice site selection in plant nuclei. Nucleic Acids Res 25:1071–1077
McNellis TW, von Arnim AG, Araki T, Komeda Y, Misera S, Deng XW (1994) Genetic and molecular analysis of an allelic series of cop1 mutants suggests functional roles for the multiple protein domains. Plant Cell 6:487–500
Merritt H, McCullough AJ, Schuler MA (1997) Internal AU-rich elements modulate activity of two competing 3′ splice sites in plant nuclei. Plant J 12:937–943
Moore MJ, Query CC, Sharp PA (1993) Splicing of precursors to messenger RNAs by the spliceosome. In: Gesteland R, Atkins J (eds) The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp 303–357
Newman AJ (1997) The role of U5 snRNP in pre-mRNA splicing. EMBO J 16:5797–5800
Newman AJ, Norman C (1992) U5 snRNA interacts with exon sequences at 5′ and 3′ splice sites. Cell 68:743–754
Orozco BM, McClung CR, Werneke JM, Ogren WL (1993) Molecular basis of the ribulose-1, 5-bisphosphate carboxylase/oxygenase activase mutation in Arabidopsis thaliana is a guanine-to-adenine transition at the 5′-splice junction of intron 3. Plant Physiol 102:227–232
Park S, Rodermel SR (2004) Mutations in ClpC2/Hsp100 suppress the requirement for FtsH in thylakoid membrane biogenesis. Proc Natl Acad Sci USA 101:12765–12770
Parker R, Siliciano PG (1993) Evidence for an essential non-Watson-Crick interaction between the first and last nucleotides of a nuclear pre-mRNA intron. Nature 361:660–662
Patel AA, Steitz JA (2003) Splicing double: insights from the second spliceosome. Nat Rev Mol Cell Biol 4:960–970
Pepper A, Delaney T, Washburn T, Poole D, Chory J (1994) DET1, a negative regulator of light-mediated development and gene expression in Arabidopsis, encodes a novel nuclear-localized protein. Cell 78:109–116
Query CC, Moore MJ, Sharp PA (1994) Branch nucleophile selection in pre-mRNA splicing: evidence for the bulged duplex model. Genes Dev 8:587–597
Ruis BL, Kivens WJ, Siliciano PG (1994) The interaction between the first and last intron nucleotides in the second step of pre-mRNA splicing is independent of other conserved intron nucleotides. Nucleic Acids Res 22:5190–5195
Ruskin B, Greene JM, Green MR (1985) Cryptic branch point activation allows accurate in vitro splicing of human R-globin intron mutants. Cell 41:833–844
Rymond BC, Rosbash R (1992) Yeast pre-mRNA splicing. In: Jones EW, Pringle JR, Broach JR (eds) The Molecular and Cellular Biology of the Yeast Saccharomyces: Gene Expression. Cold Spring Harbor Laboratory Press, pp 143–193
Sablowski RW, Meyerowitz EM (1998) Temperature-sensitive splicing in the floral homeotic mutant apetala3–1. Plant Cell 10:1453–1463
Scadden ADJ, Smith CWJ (1995) Interactions between the terminal bases of mammalian introns are retained in inosine-containing pre-mRNAs. EMBO J 14:3236–3246
Schuler MA (1998) Plant pre-mRNA splicing. In: Bailey-Serres J, Gallie Daniel RA (eds) Look Beyond Transcription: Mechanisms Determining mRNA Stability and Translation in Plants. American Society Plant Physiologists pp 1–19
Schumacher K, Vafeados D, McCarthy S, Sze H, Wilkins T, Chory J (1999) The Arabidopsis det3 mutant reveals a central role for the vacuolar H+-ATPase in plant growth and development. Genes Dev 13:3259–3270
Segault V, Will CL, Polycarpou-Schwarz S, Mattaj IW, Branlant C, Luhrmann R (1999) Conserved loop I of U5 small nuclear RNA is dispensable for both catalytic steps of pre-mRNA splicing in HeLa nuclear extracts. Mol Cell Biol 19:2782–2790
Sheth N, Roca X, Hastings ML, Roeder T, Krainer AR, Sachidanandam R (2006) Comprehensive splice-site analysis using comparative genomics. Nucleic Acids Res 34:3955–3967
Sieburth LE, Running MP, Meyerowitz EM (1995) Genetic separation of third and fourth whorl functions of AGAMOUS. Plant Cell 7:1249–1258
Siliciano PG, Guthrie C (1988) 5S splice site selection in yeast: genetic alterations in base pairing with U1 reveal additional requirements. Genes Dev 2:1258–1267
Simpson GG, Filipowicz W (1996) Splicing of precursors to messenger RNA in higher plants: mechanism, regulation and sub-nuclear organization of the spliceosomal machinery. Plant Mol Biol 32:1–41
Simpson CG, Clark G, Davidson D, Smith P, Brown JWS (1996) Mutation of putative branchpoint consensus sequences in plant introns reduces splicing efficiency. Plant J 9:369–380
Simpson CG, McQuade C, Lyon J, Brown JW (1998) Characterization of exon skipping mutants of the COP1 gene from Arabidopsis. Plant J 15:125–131
Simpson CG, Hedley PE, Watters JA, Clark GP, McQuade C, Machray GC, Brown JW (2000) Requirements for mini-exon inclusion in potato invertase mRNAs provides evidence for exon-scanning interactions in plants. RNA 6:422–433
Simpson CG, Thow G, Clark GP, Jennings SN, Watters JA, Brown JW (2002) Mutational analysis of a plant branchpoint and polypyrimidine tract required for constitutive splicing of a mini-exon. RNA 8:47–56
Simpson CG. Jennings SN, Clark GP, Thow G, Brown JW (2004) Dual functionality of a plant U-rich intronic sequence element. Plant J 37:82–91
Smith CW, Chu TT, Nadal-Ginard B (1993) Scanning and competition between AGs are involved in 3′ splice site selection in mammalian introns. Mol Cell Biol 13:4939–4952
Smith CW, Porro EB, Patton JG, Nadal-Ginard B (1989) Scanning from an independently specified branch point defines the 3′ splice site of mammalian introns. Nature 342:243–247
Tarn W-Y, Steitz JA (1996a) A novel spliceosome containing U11, U12, and U5 snRNPs excises a minor class (AT-AC) intron in vitro. Cell 84:801–811
Tarn W-Y, Steitz JA (1996b) Highly diverged U4 and U6 small nuclear RNAs required for splicing rare AT-AC introns. Science 273:1824–1832
Wakem MP, Kohalmi SE (2003) Mutation in the ap2–6 allele causes recognition of a cryptic splice site. J Exp Bot 54:2655–2660
Wang BB, Brendel V (2006) Genomewide comparative analysis of alternative splicing in plants. Proc Natl Acad Sci USA 103:7175–7180
Wang ZY, Zheng FQ, Shen GZ, Gao JP, Snustad DP, Li MG, Zhang JL, Hong MM (1995) The amylose content in rice endosperm is related to the post-transcriptional regulation of the waxy gene. Plant J 7:613–622
Wiebauer K, Herrero J-J, Filipowicz W (1988) Nuclear pre-mRNA processing in plants: Distinct modes of 3′-splice site selection in plants and animals. Mol Cell Biol 8:2042–2051
Wong GK, Wang J, Tao L, Tan J, Zhang J, Passey DA, Yu J (2002) Compositional gradients in Gramineae genes. Genome Res 12:851–856
Wyatt JR, Sontheimer EJ, Steitz JA (1992) Site-specific crosslinking of mammalian U5 snRNP to the 5′ splice site prior to the first step of premessenger RNA splicing. Genes Dev 6:2542–2553
Yi J, Jack T (1998) An intragenic suppressor of the Arabidopsis floral organ identity mutant apetala3–1 functions by suppressing defects in splicing. Plant Cell 10:1465–1477
Yu J, Hu S, Wang J et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92
Zhu W, Brendel V (2003) Identification, characterization and molecular phylogeny of U12-dependent introns in the Arabidopsis thaliana genome. Nucleic Acids Res 31:4561–4572
Zhuang Y, Weiner AM (1986) A compensatory base change in U1 snRNA suppresses a 5′ splice site mutation. Cell 46:827–835
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Schuler, M.A. (2008). Splice Site Requirements and Switches in Plants. In: Reddy, A.S.N., Golovkin, M. (eds) Nuclear pre-mRNA Processing in Plants. Current Topics in Microbiology and Immunology, vol 326. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-76776-3_3
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