Pre-mRNA splicing in plants: characterization of Ser/Arg splicing factors.

Lopato, Serguei; Mayeda, Akila; Krainer, Adrian R.; Barta, Andrea

doi:10.1073/pnas.93.7.3074

Cited by 83 publications

(70 citation statements)

References 49 publications

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“…Candidate intron recognition factors include two proteins from Nicotiana plumbaginifolia with poly(U) af®nity (Gniadkowski et al, 1996). Members of the serinearginine-rich protein family of splicing factors have also been identi®ed in plants (Lazar et al, 1995;Lopato et al, 1996), although their exact roles in pre-mRNA splicing are unclear presently. Our analysis of experimental studies of splicing of animal genes in plants suggests that the plant-speci®c compositional contrast between exons and introns is suf®cient to explain success and failure of splicing.…”

Section: Discussionmentioning

confidence: 99%

Prediction of splice sites in plant pre-mRNA from sequence properties

Brendel

Kleffe

Carle-Urioste

et al. 1998

Journal of Molecular Biology

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Heterologous introns are often inaccurately or inef®ciently processed in higher plants. The precise features that distinguish the process of premRNA splicing in plants from splicing in yeast and mammals are unclear. One contributing factor is the prominent base compositional contrast between U-rich plant introns and¯anking G C-rich exons. Inclusion of this contrast factor in recently developed statistical methods for splice site prediction from sequence inspection signi®cantly improved prediction accuracy. We applied the prediction tools to re-analyze experimental data on splice site selection and splicing ef®ciency for native and more than 170 mutated plant introns. In almost all cases, the experimentally determined preferred sites correspond to the highest scoring sites predicted by the model. In native genes, about 90% of splice sites are the locally highest scoring sites within the bounds of the¯anking exon and intron. We propose that, in most cases, local context (about 50 bases upstream and downstream from a potential intron end) is suf®cient to account for intrinsic splice site strength, and that competition for transacting factors determines splice site selection in vivo. We suggest that computer-aided splice site prediction can be a powerful tool for experimental design and interpretation.

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Section: Discussionmentioning

confidence: 99%

Prediction of splice sites in plant pre-mRNA from sequence properties

Brendel

Kleffe

Carle-Urioste

et al. 1998

Journal of Molecular Biology

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“…Immunoblot analysis with mAb104 suggested previously that the complexity of the SR protein family is higher in animals than in plants (Lopato et al 1996a), as several higher molecular mass proteins have been identified in SR preparations from mammals but not from those in plants. The existence of two SF2/ASF-like factors in Arabidopsis may compensate for the absence of orthologs of other members of the SR protein family.…”

Section: Two Sf2/asf-like Splicing Factors In Arabidopsismentioning

confidence: 99%

“…The proteins were detected with the monoclonal antibody mAb104, specific for a shared phosphoepitope in all SR proteins, and with a monoclonal antibody specific for the human SF2/ASF splicing factor (Lopato et al 1996a). A protein of ∼50 kD from the carrot SR preparation, which was recognized by both antibodies, was isolated and partially sequenced.…”

Section: Isolation and Sequencing Of Genomic And Cdna Clones Of Atsrp30mentioning

confidence: 99%

“…As SR proteins play a critical role in correct splice-site selection in mammals, it is of interest to characterize the corresponding protein family in plants. We screened for similar proteins in plants previously by using the mAb104 antibody or a specific monoclonal antibody raised against human SF2/ASF, and demonstrated that plants do possess SR proteins, including SF2/ASF-like proteins (Lopato et al 1996a). However, the plant SR proteins are of different size and are smaller than 55 kD.…”

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confidence: 99%

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atSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes

Lopato¹,

Kalyna²,

Dorner³

et al. 1999

Genes & Development

150

199

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SR proteins are nuclear phosphoproteins with a characteristic Ser/Arg-rich domain and one or two RNA recognition motifs. They are highly conserved in animals and plants and play important roles in spliceosome assembly and alternative splicing regulation. We have now isolated and partially sequenced a plant protein, which crossreacts with antibodies to human SR proteins. The sequence of the corresponding cDNA and genomic clones from Arabidopsis revealed a protein, atSRp30, with strong similarity to the human SR protein SF2/ASF and to atSRp34/SR1, a previously identified SR protein, indicating that plants possess two SF2/ASF-like proteins. atSRp30 expresses alternatively spliced mRNA isoforms that are expressed differentially in various organs and during development. Overexpression of atSRp30 via a strong constitutive promoter resulted in changes in alternative splicing of several endogenous plant genes, including atSRp30 itself. Interestingly, atSRp30 overexpression resulted in a pronounced down-regulation of endogenous mRNA encoding full-length atSRp34/SR1 protein. Transgenic plants overexpressing atSRp30 showed morphological and developmental changes affecting mostly developmental phase transitions. atSRp30-and atSRp34/ SR1-promoter-GUS constructs exhibited complementary expression patterns during early seedling development and root formation, with overlapping expression in floral tissues. The results of the structural and expression analyses of both genes suggest that atSRp34/SR1 acts as a general splicing factor, whereas atSRp30 functions as a specific splicing modulator.

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“…43 Ser/Arg-rich (SR) proteins comprise a conserved family of premRNA splicing factors which function in splice site recognition and the spliceosome assembly, and that are required for constitutive and some aspects of alternative splicing. 46,47 At least 2 SR proteins, namely SRZ-21 and SRZ-22, interact with the plant U1 snRNP 70K protein. 48 Analyses of the biogenesis of miRNAs derived from intron-containing MIR genes in Arabidopsis null mutants of selected SR genes showed that the levels of mature miR161, miR163, and miR171 were decreased in 3 out of 4 mutants tested (rs31-1, rs2z33-1, and sr34-1).…”

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confidence: 99%