Factors affecting authentic 5' splice site selection in plant nuclei

A Silent Exonic Mutation in a Rice Integrin-α FG-GAP Repeat-Containing Gene Causes Male-Sterility by Affecting mRNA Splicing

Pollen development plays crucial roles in the life cycle of higher plants. Here we characterized a rice mutant with complete male-sterile phenotype, pollen-less 1 (pl1). pl1 exhibited smaller anthers with arrested pollen development, absent Ubisch bodies, necrosis-like tapetal hypertrophy, and smooth anther cuticular surface. Molecular mapping revealed a synonymous mutation in the fourth exon of PL1 co-segregated with the mutant phenotype. This mutation disrupts the exon-intron splice junction in PL1, generating aberrant mRNA species and truncated proteins. PL1 is highly expressed in the tapetal cells of developing anther, and its protein is co-localized with plasma membrane (PM) and endoplasmic reticulum (ER) signal. PL1 encodes an integrin-α FG-GAP repeat-containing protein, which has seven β-sheets and putative Ca²⁺-binding motifs and is broadly conserved in terrestrial plants. Our findings therefore provide insights into both the role of integrin-α FG-GAP repeat-containing protein in rice male fertility and the influence of exonic mutation on intronic splice donor site selection.

Endogenous mechanisms for the origins of spliceosomal introns

Over 30 years since their discovery, the origin of spliceosomal introns remains uncertain. One nearly universally accepted hypothesis maintains that spliceosomal introns originated from self-splicing group-II introns that invaded the uninterrupted genes of the last eukaryotic common ancestor (LECA) and proliferated by "insertion" events. Although this is a possible explanation for the original presence of introns and splicing machinery, the emphasis on a high number of insertion events in the genome of the LECA neglects a considerable body of empirical evidence showing that spliceosomal introns can simply arise from coding or, more generally, nonintronic sequences within genes. After presenting a concise overview of some of the most common hypotheses and mechanisms for intron origin, we propose two further hypotheses that are broadly based on central cellular processes: 1) internal gene duplication and 2) the response to aberrant and fortuitously spliced transcripts. These two nonmutually exclusive hypotheses provide a powerful way to explain the establishment of spliceosomal introns in eukaryotes without invoking an exogenous source.

Inactivation of the UGPase1 gene causes genic male sterility and endosperm chalkiness in rice (Oryza sativa L.)

A rice genic male-sterility gene ms-h is recessive and has a pleiotropic effect on the chalky endosperm. After fine mapping, nucleotide sequencing analysis of the ms-h gene revealed a single nucleotide substitution at the 3'-splice junction of the 14th intron of the UDP-glucose pyrophosphorylase 1 (UGPase1; EC2.7.7.9) gene, which causes the expression of two mature transcripts with abnormal sizes caused by the aberrant splicing. An in vitro functional assay showed that both proteins encoded by the two abnormal transcripts have no UGPase activity. The suppression of UGPase by the introduction of a UGPase1-RNAi construct in wild-type plants nearly eliminated seed set because of the male defect, with developmental retardation similar to the ms-h mutant phenotype, whereas overexpression of UGPase1 in ms-h mutant plants restored male fertility and the transformants produced T(1) seeds that segregated into normal and chalky endosperms. In addition, both phenotypes were co-segregated with the UGPase1 transgene in segregating T(1) plants, which demonstrates that UGPase1 has functional roles in both male sterility and the development of a chalky endosperm. Our results suggest that UGPase1 plays a key role in pollen development as well as seed carbohydrate metabolism.

Identification of the photorespiratory 2-phosphoglycolate phosphatase, PGLP1, in Arabidopsis

The chloroplastidal enzyme 2-phosphoglycolate phosphatase (PGLP), PGLP1, catalyzes the first reaction of the photorespiratory C(2) cycle, a major pathway of plant primary metabolism. Thirteen potential PGLP genes are annotated in the Arabidopsis (Arabidopsis thaliana) genome; however, none of these genes has been functionally characterized, and the gene encoding the photorespiratory PGLP is not known. Here, we report on the identification of the PGLP1 gene in a higher plant and provide functional evidence for a second, nonphotorespiratory PGLP, PGLP2. Two candidate genes, At5g36700 (AtPGLP1) and At5g47760 (AtPGLP2), were selected by sequence similarity to known PGLPs from microorganisms. The two encoded proteins were overexpressed in Escherichia coli and both show PGLP activity. T-DNA knockout of one of these genes, At5g36700, results in very low leaf PGLP activity. The mutant is unviable in normal air but grows well in air enriched with 0.9% CO(2). In contrast, deletion of At5g47760 does not result in a visible phenotype, and leaf PGLP activity is unaltered. Sequencing of genomic DNA from another PGLP-deficient mutant revealed a combined missense and missplicing point mutation in At5g36700. These combined data establish At5g36700 as the gene encoding the photorespiratory PGLP, PGLP1.

Mapping of the loci controlling oleic and linolenic acid contents and development of fad2 and fad3 allele-specific markers in canola (Brassica napus L.)

The quality of canola oil is determined by its constituent fatty acids such as oleic acid (C18:1), linoleic acid (C18:2) and linolenic acid (C18:3). Most canola cultivars normally produce oil with about 55-65% oleic acid and 8-12% linolenic acid. High concentrations of linolenic acid lead to oil instability and off-type flavor, while high levels of oleic acid increase oxidative stability and nutritional value of oil. Therefore, development of canola cultivars with increased oleic acid and reduced linolenic acid is highly desirable for canola oil quality. In this study, we have mapped one locus that has a major effect and one locus that has a minor effect for high oleic acid and two loci that have major effects for low linolenic acid in a doubled haploid population. The major locus for high C18:1 was proven to be the fatty acid desaturase-2 (fad2) gene and it is located on the linkage group N5; the minor locus is located on N1. One major QTL for C18:3 is the fatty acid desaturase-3 gene of the genome C (fad3c) and it is located on N14. The second major QTL resides on N4 and is the fad3a gene of the A genome. We have sequenced genomic clones of the fad2 and fad3c genes amplified from an EMS-induced mutant and a wild-type canola cultivar. A comparison of the mutant and wild-type allele sequences of the fad2 and fad3c genes revealed single nucleotide mutations in each of the genes. Detailed sequence analyses suggested mechanisms by which both the mutations can cause altered fatty acid content. Based on the sequence differences between the mutant and wild-type alleles, two single nucleotide polymorphism (SNP) markers, corresponding to the fad2 and fad3c gene mutations, were developed. These markers will be highly useful for direct selection of desirable fad2 and fad3c alleles during marker-assisted trait introgression and breeding of canola with high oleic and low linolenic acid.

Computational comparative analyses of alternative splicing regulation using full-length cDNA of various eukaryotes

We previously reported a computational approach to infer alternative splicing patterns from Mus musculus full-length cDNA clones and microarray data. Although we predicted a large number of unreported splice variants, the general mechanisms regulating alternative splicing were yet unknown. In the present study, we compared alternative exons and constitutive exons in terms of splice-site strength and frequency of potential regulatory sequences. These regulatory features were further compared among five different species: Homo sapiens, M. musculus, Arabidopsis thaliana, Oryza sativa, and Drosophila melanogaster. Solid statistical validations of our comparative analyses indicated that alternative exons have (1) weaker splice sites and (2) more potential regulatory sequences than constitutive exons. Based on our observations, we propose a combinatorial model of alternative splicing mechanisms, which suggests that alternative exons contain weak splice sites regulated alternatively by potential regulatory sequences on the exons.

Dual functionality of a plant U-rich intronic sequence element

In potato invertase genes, the constitutively included, 9-nucleotide (nt)-long mini-exon requires a strong branchpoint and U-rich polypyrimidine tract for inclusion. The strength of these splicing signals was demonstrated by greatly enhanced splicing of a poorly spliced intron and by their ability to support splicing of an artificial mini-exon, following their introduction. Plant introns also require a second splicing signal, UA-rich intronic elements, for efficient intron splicing. Mutation of the branchpoint caused loss of mini-exon inclusion without loss of splicing enhancement, showing that the same U-rich sequence can function as either a polypyrimidine tract or a UA-rich intronic element. The distinction between the splicing signals depended on intron context (the presence or absence of an upstream, adjacent and functional branchpoint), and on the sequence context of the U-rich elements. Polypyrimidine tracts tolerated C residues while UA-rich intronic elements tolerated As. Thus, in plant introns, U-rich splicing elements can have dual roles as either a general plant U-rich splicing signal or a polypyrimidine tract. Finally, overexpression of two different U-rich binding proteins enhanced intron recognition significantly. These results highlight the importance of co-operation between splicing signals, the importance of other nucleotides within U-rich elements for optimal binding of competing splicing factors and effects on splicing efficiency of U-rich binding proteins.

Intron-mediated enhancement of gene expression in transgenic plants using chimeric constructs composed of the Peanut chlorotic streak virus (PClSV) promoter-leader and the antisense orientation of PClSV ORF VII (p7R)

The antisense orientation of the Peanut chlorotic streak virus (PClSV) open reading frame (ORF) VII (denoted as p7R), in conjunction with the sense orientation of the PClSV leader sequence, acts as an intron and enhances the expression of a reporter gene, analyzed in protoplasts and transgenic plants of tobacco ( Nicotiana tabacum L.). Correct 5' and 3' splicing sites were determined for intron removal from the chimeric constructs using either beta-glucuronidase (GUS) or chloramphenicol acetyltransferase (CAT) as a reporter gene. In this splicing process, the active consensus 5' splicing donor site (AG/GTATA) is located at position +283 to +289 from the transcription start site (TSS) of the PClSV full-length transcript (FLt). The 3' splice site (TAG/GATT) is located on the p7R sequence at position +785 to +791 from the TSS. The combination of PClSV FLt leader and p7R enhanced the expression of reporter genes (CAT and GUS) by as much as 2-fold compared to the strong constitutive PClSV FLt promoter without an interfering leader sequence and about 30- to 800-fold compared to constructs containing the sense orientation of PClSV ORF VII (p7) in both protoplast transient-expression experiments and stably transformed transgenic plants. An increased level of mature transcripts accompanied this. This suggests that this combination of elements can mediate the intron-mediated enhancement (IME) phenomenon. We also demonstrated comparative IME with other heterologous promoters from caulimoviruses.

Splicing of the maize Sh1 first intron is essential for enhancement of gene expression, and a T-rich motif increases expression without affecting splicing

Certain plant and animal introns increase expression of protein-coding sequences when placed in the 5' region of the transcription unit. The mechanisms of intron-mediated enhancement have not been defined, but are generally accepted to be post- or cotranscriptional in character. One of the most effective plant introns in stimulating gene expression is the 1,028-bp first intron of the Sh1 gene that encodes maize (Zea mays) sucrose synthase. To address the mechanisms of intron-mediated enhancement, we used reporter gene fusions to identify features of the Sh1 first intron required for enhancement in cultured maize cells. A 145-bp derivative conferred approximately the same 20- to 50-fold stimulation typical for the full-length intron in this transient expression system. A 35-bp motif contained within the intron is required for maximum levels of enhancement but not for efficient transcript splicing. The important feature of this redundant 35-bp motif is T-richness rather than the specific sequence. When transcript splicing was abolished by mutations at the intron borders, enhancement was reduced to about 2-fold. The requirement of splicing for enhancement was not because of upstream translation initiation codons contained in unspliced transcripts. On the basis of our current findings, we conclude that splicing of the Sh1 intron is integral to enhancement, and we hypothesize that transcript modifications triggered by the T-rich motif and splicing may link the mRNA with the trafficking system of the cell.

Mutational analysis of a plant branchpoint and polypyrimidine tract required for constitutive splicing of a mini-exon

The branchpoint sequence and associated polypyrimidine tract are firmly established splicing signals in vertebrates. In plants, however, these signals have not been characterized in detail. The potato invertase mini-exon 2 (9 nt) requires a branchpoint sequence positioned around 50 nt upstream of the 5' splice site of the neighboring intron and a U11 element found adjacent to the branchpoint in the upstream intron (Simpson et al., RNA, 2000, 6:422-433). Utilizing the sensitivity of this plant splicing system, these elements have been characterized by systematic mutation and analysis of the effect on inclusion of the mini-exon. Mutation of the branchpoint sequence in all possible positions demonstrated that branchpoints matching the consensus, CURAY, were most efficient at supporting splicing. Branchpoint sequences that differed from this consensus were still able to permit mini-exon inclusion but at greatly reduced levels. Mutation of the downstream U11 element suggested that it functioned as a polypyrimidine tract rather than a UA-rich element, common to plant introns. The minimum sequence requirement of the polypyrimidine tract for efficient splicing was two closely positioned groups of uridines 3-4 nt long (<6 nt apart) that, within the context of the mini-exon system, required being close (<14 nt) to the branchpoint sequence. The functional characterization of the branchpoint sequence and polypyrimidine tract defines these sequences in plants for the first time, and firmly establishes polypyrimidine tracts as important signals in splicing of at least some plant introns.

Molecular structure of three mutations at the maize sugary1 locus and their allele-specific phenotypic effects

Starch production in all plants examined is altered by mutations of isoamylase-type starch-debranching enzymes (DBE), although how these proteins affect glucan polymer assembly is not understood. Various allelic mutations in the maize (Zea mays) gene sugary1 (su1), which codes for an isoamylase-type DBE, condition distinct kernel phenotypes. This study characterized the recessive mutations su1-Ref, su1-R4582::Mu1, and su1-st, regarding their molecular basis, chemical phenotypes, and effects on starch metabolizing enzymes. The su1-Ref allele results in two specific amino acid substitutions without affecting the Su1 mRNA level. The su1-R4582::Mu1 mutation is a null allele that abolishes transcript accumulation. The su1-st mutation results from insertion of a novel transposon-like sequence, designated Toad, which causes alternative pre-mRNA splicing. Three su1-st mutant transcripts are produced, one that is nonfunctional and two that code for modified SU1 polypeptides. The su1-st mutation is dominant to the null allele su1-R4582::Mu1, but recessive to su1-Ref, suggestive of complex effects involving quaternary structure of the SU1 enzyme. All three su1- alleles severely reduce or eliminate isoamylase-type DBE activity, although su1-st kernels accumulate less phytoglycogen and Suc than su1-Ref or su1-R4582::Mu1 mutants. The chain length distribution of residual amylopectin is significantly altered by su1-Ref and su1-R4582::Mu1, whereas su1-st has modest effects. These results, together with su1 allele-specific effects on other starch- metabolizing enzymes detected in zymograms, suggest that total DBE catalytic activity is the not the sole determinant of Su1 function and that specific interactions between SU1 and other components of the starch biosynthetic system are required.

RBP45 and RBP47, two oligouridylate-specific hnRNP-like proteins interacting with poly(A)+ RNA in nuclei of plant cells

Introns in plant nuclear pre-mRNAs are highly enriched in U or U + A residues and this property is essential for efficient splicing. Moreover, 3'-untranslated regions (3'-UTRs) in plant pre-mRNAs are generally UA-rich and contain sequences that are important for the polyadenylation reaction. Here, we characterize two structurally related RNA-binding proteins (RBPs) from Nicotiana plumbaginifolia, referred to as RBP45 and RBP47, having specificity for oligouridylates. Both proteins contain three RBD-type RNA-binding domains and a glutamine-rich N-terminus, and share similarity with Nam8p, a protein associated with U1 snRNP in the yeast Saccharomyces cerevisiae. Deletion analysis of RBP45 and RBP47 indicated that the presence of at least two RBD are required for interaction with RNA and that domains other than RBD do not significantly contribute to binding. mRNAs for RBP45 and RBP47 and mRNAs encoding six related proteins in Arabidopsis thaliana are constitutively expressed in different plant organs. Indirect immunofluorescence and fractionation of cell extracts showed that RBP45 and RBP47 are localized in the nucleus. In vivo UV crosslinking experiments demonstrated their association with the nuclear poly(A)+ RNA. In contrast to UBP1, another oligouridylate-binding nuclear three-RBD protein of N. plumbaginifolia (Lambermon et al., EMBO J, 2000, 19:1638-1649), RBP45 and RBP47 do not stimulate mRNA splicing and accumulation when transiently overexpressed in protoplasts. Properties of RBP45 and RBP47 suggest they represent hnRNP-proteins participating in still undefined steps of pre-mRNA maturation in plant cell nuclei.

dull: rice mutants with tissue-specific effects on the splicing of the waxy pre-mRNA

In the endosperm of japonica rice, du-1 and du-2 mutations cause the reduction of amylose contents. It was previously shown that the Wx(b) allele of rice, which is predominantly distributed in japonica rice, has a mutation in the 5' splice site of intron 1 resulting in the creation of two weak 5' splice sites within exon 1. In du-1 and du-2 mutants, spliced Wx(b) transcripts were highly reduced, whereas the processing of transcripts derived from three other genes highly expressed in endosperm was not apparently influenced. Results of competitive RT-PCR analysis indicate that transcripts spliced at the two newly created 5' splice sites were equally affected in these two mutants. Genetic and molecular analyses of the effects of du-1 and du-2 on Wx(a) pre-mRNA with normal splice sites indicate that these two mutations do not affect the processing of Wx(a) pre-mRNA after splicing, suggesting that du-1 and du-2 are mutations of genes required for the efficient splicing of mutated Wx(b) pre-mRNA. Furthermore, du-1 and du-2 showed differential effects in endosperm and pollen. Although both mutations caused similar effects on the splicing of Wx(a) transcripts in endosperm, du-1 caused higher reduction of Wx(b) mRNA in pollen than in endosperm, while du-2 had a lesser effect in pollen than in endosperm. Based on these results, we propose that the du-1 and du-2 loci of rice encode tissue-specifically regulated splicing factors that are involved in alternative splicing of pre-mRNA in rice.

Pre-mRNA splicing in higher plants

Most plant mRNAs are synthesized as precursors containing one or more intervening sequences (introns) that are removed during the process of splicing. The basic mechanism of spliceosome assembly and intron excision is similar in all eukaryotes. However, the recognition of introns in plants has some unique features, which distinguishes it from the reactions in vertebrates and yeast. Recent progress has occurred in characterizing the splicing signals in plant pre-mRNAs, in identifying the mutants affected in splicing and in discovering new examples of alternatively spliced mRNAs. In combination with information provided by the Arabidopsis genome-sequencing project, these studies are contributing to a better understanding of the splicing process and its role in the regulation of gene expression in plants.

Test of the combinatorial model of intron recognition in a native maize gene

Previous studies have established that splice site selection and splicing efficiency in plants depend strongly on local compositional contrast consisting of high exon G+C content relative to high intron U content. The combinatorial model of plant intron recognition posits that splice site sequences as well as local intron and exon sequences contribute to splice site selection and splicing efficiency. Most of the previous studies used synthetic or chimeric constructs, often tested in heterologous hosts. To perform a more critical test of the combinatorial model in a native context, the single intron of the maize Bronze2 gene and its flanking exons were modified by site-directed mutagenesis. Splicing efficiency was tested in maize protoplasts. Results show that a higher U content in the flanking 5' exon, whether close to or distant from the 5' splice site, did not modify splicing efficiency. Decreasing exon G+C content dramatically impaired splicing. Increasing intron G+C content or decreasing intron U content adversely impacted splicing. In all constructs splicing occurred exclusively at the original 5' and 3' splice sites. These results are consistent with the hypothesis that exon G+C content and intron U content contribute separate but complementary aspects of intron definition in the native Bz2 transcript.

A splice site mutant of maize activates cryptic splice sites, elicits intron inclusion and exon exclusion, and permits branch point elucidation

DNA sequence analysis of the bt2-7503 mutant allele of the maize brittle-2 gene revealed a point mutation in the 5' terminal sequence of intron 3 changing GT to AT. This lesion completely abolishes use of this splice site, activates two cryptic splice sites, and alters the splicing pattern from extant splice sites. One activated donor site, located nine nt 5' to the normal splice donor site, begins with the dinucleotide GC. While non-consensus, this sequence still permits both trans-esterification reactions of pre-mRNA splicing. A second cryptic site located 23 nt 5' to the normal splice site and beginning with GA, undergoes the first trans-esterification reaction leading to lariat formation, but lacks the ability to participate in the second reaction. Accumulation of this splicing intermediate and use of an innovative reverse transcriptase-polymerase chain reaction technique (J. Vogel, R.H. Wolfgang, T. Borner [1997] Nucleic Acids Res 25: 2030-2031) led to the identification of 3' intron sequences needed for lariat formation. In most splicing reactions, neither cryptic site is recognized. Most mature transcripts include intron 3, while the second most frequent class lacks exon 3. Traditionally, the former class of transcripts is taken as evidence for the intron definition of splicing, while the latter class has given credence to the exon definition of splicing.

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

Granule-bound starch synthase (GBSS), a product of the waxy gene in rice (Oryza sativa L.), is necessary for the synthesis of amylose in the endosperm. In an extended pedigree of 89 rice cultivars, we have previously shown that all cultivars with more than 18% amylose had the sequence AGGTATA at the leader intron 5' splice site, while all cultivars with a lower proportion of amylose had the sequence AGTTATA. This single-nucleotide polymorphism reduces the efficiency of GBSS pre-mRNA processing. It also results in alternate splicing at multiple sites, some of which have non-consensus sequences. Here we demonstrate that this same G-to-T polymorphism is also associated with differential sensitivity to temperature during the period of grain development. Cultivars with the sequence AGTTATA have a substantial increase in accumulation of mature GBSS transcripts at 18 degrees C compared to 25 or 32 degrees C. The selection of leader intron 5' splice sites is also affected by temperature in these cultivars. A 5' splice site -93 upstream from that used in high-amylose varieties predominates at 18 degrees C. At higher temperatures there is increased utilization of a 5' splice site at -I and a non-consensus site at +1. Potential implications of differential 5' splice site selection and associated differences in 3' splice site selection on transcript stability and translational efficiency are discussed.

The AG dinucleotide terminating introns is important but not always required for pre-mRNA splicing in the maize endosperm

Previous RNA analysis of lesions within the 15 intron-containing Sh2 (shrunken2) gene of maize (Zea mays) revealed that the majority of these mutants affect RNA splicing. Here we decipher further two of these mutants, sh2-i (shrunken2 intermediate phenotype) and sh2-7460. Each harbors a G-to-A transition in the terminal nucleotide of an intron, hence destroying the invariant AG found at the terminus of virtually all nuclear introns. Consequences of the mutations, however, differ dramatically. In sh2-i the mutant site is recognized as an authentic splice site in approximately 10% of the primary transcripts processed in the maize endosperm. The other transcripts exhibited exon skipping and lacked exon 3. A G-to-A transition in the terminus of an intron was also found in the mutant sh2-7460, in this case intron 12. The lesion activates a cryptic acceptor site downstream 22 bp within exon 13. In addition, approximately 50% of sh2-7460 transcripts contain intron 2 and 3 sequences.

Multiple forms of the U2 small nuclear ribonucleoprotein auxiliary factor U2AF subunits expressed in higher plants

Requirements for intron recognition during pre-mRNA splicing in plants differ from those in vertebrates and yeast. Plant introns contain neither conserved branch points nor distinct 3' splice site-proximal polypyrimidine tracts characteristic of the yeast and vertebrate introns, respectively. However, they are strongly enriched in U residues throughout the intron, property essential for splicing. To understand the roles of different sequence elements in splicing, we are characterizing proteins involved in intron recognition in plants. In this work we show that Nicotiana plumbaginifolia, a dicotyledonous plant, contains two genes encoding different homologs of the large 50-65-kDa subunit of the polypyrimidine tract binding factor U2AF, characterized previously in animals and Schizosaccharomyces pombe. Both plant U2AF65 isoforms, referred to as NpU2AF65a and NpU2AF65b, support splicing of an adenovirus pre-mRNA in HeLa cell nuclear extracts depleted of the endogenous U2AF factor. Both proteins interact with RNA fragments containing plant introns and show affinity for poly(U) and, to a lesser extend, poly(C) and poly(G). The branch point or the 3' splice site regions do not contribute significantly to intron recognition by NpU2AF65. The existence of multiple isoforms of U2AF may be quite general in plants because two genes expressing U2AF65 have been identified in Arabidopsis, and different isoforms of the U2AF small subunit are expressed in rice.

Prediction of locally optimal splice sites in plant pre-mRNA with applications to gene identification in Arabidopsis thaliana genomic DNA

Prediction of splice site selection and efficiency from sequence inspection is of fundamental interest (testing the current knowledge of requisite sequence features) and practical importance (genome annotation, design of mutant or transgenic organisms). In plants, the dominant variables affecting splice site selection and efficiency include the degree of matching to the extended splice site consensus and the local gradient of U- and G+C-composition (introns being U-rich and exons G+C-rich). We present a novel method for splice site prediction, which was particularly trained for maize and Arabidopsis thaliana. The method extends our previous algorithm based on logitlinear models by considering three variables simultaneously: intrinsic splice site strength, local optimality and fit with respect to the overall splice pattern prediction. We show that the method considerably improves prediction specificity without compromising the high degree of sensitivity required in gene prediction algorithms. Applications to gene identification are illustrated for Arabidopsis and suggest that successful methods must combine scoring for splice sites, coding potential and similarity with potential homologs in non-trivial ways. A WWW version of the SplicePredictor program is available at http:/gnomic.stanford.edu/volker/SplicePredi ctor.html/

Use of alternate splice sites in granule-bound starch synthase mRNA from low-amylose rice varieties

The rice Waxy gene encodes a granule-bound starch synthase (GBSS) necessary for the synthesis of amylose in endosperm tissue. We have previously shown that a CT microsatellite near the transcriptional start site of the GBSS gene can distinguish 7 alleles that accounted for more than 80% of the variation in apparent amylose content in an extended pedigree of 89 US rice cultivars (Oryza sativa L.). Furthermore, all the cultivars with 18% or less amylose were shown to have the sequence AGTTATA at the putative leader intron 5' splice site, while all cultivars with a higher proportion of amylose had AGGTATA. Here we demonstrate that this single-base mutation reduces the efficiency of GBSS pre-mRNA processing and results in alternate splicing at three cryptic sites. The predominant 5' splice site in CT18 low-amylose varieties is 93 bp upstream of the splice site used in intermediate and high amylose varieties and is immediately 5' to the CT microsatellite that we previously demonstrated to be tightly correlated with amylose content. Use of the leader intron 5' splice site at either -93 or -1 in conjunction with the predominant 3' splice site results in formation of a small open reading frame 38 bp upstream of the normal ATG and out of frame with it. This open reading frame is not produced when any of the 5' leader intron splice sites are used in conjunction with an alternate 3' splice site five bases further downstream which was observed in all rice varieties tested.

An intragenic suppressor of the Arabidopsis floral organ identity mutant apetala3-1 functions by suppressing defects in splicing

The Arabidopsis floral organ identity gene APETALA3 (AP3) specifies the identity of petals and stamens in the flower. In flowers mutant for the temperature-sensitive ap3-1 allele, the petals and stamens are partially converted to sepals and carpels, respectively. ap3-1 contains a single nucleotide change in the AP3 gene that alters both an amino acid in the AP3 protein and the 5' splice consensus site for intron 5. Surprisingly, the Ap3-1 mutant phenotype is not due to the missense mutation but instead is due to defects in splicing; specifically, exon 5 is frequently skipped by the splicing machinery at the restrictive temperature. In a screen for suppressors of ap3-1, we isolated an intragenic suppressor, ap3-11, that functions to suppress the splicing defects of ap3-1. Using a reverse transcriptase-polymerase chain reaction assay, we demonstrate that the percentage of full-length exon 5-containing AP3 RNAs correlates with the phenotype of the flowers in both ap3-1 and ap3-11. Rather surprisingly, the ap3-11 suppressor mutation is located in intron 4. One model explaining the function of ap3-11 is that the ap3-11 suppressor creates a novel branch point sequence that causes exon 5 to be more frequently recognized by the splicing machinery. The identification of such a suppressor strongly suggests that exon-scanning models of intron-exon recognition are operative in plants.

Characterization of exon skipping mutants of the COP1 gene from Arabidopsis

The removal of introns from pre-mRNA requires accurate recognition and selection of the intron splice sites. Mutations which alter splice site selection and which lead to skipping of specific exons are indicative of intron/exon recognition mechanisms involving an exon definition process. In this paper, three independent mutants to the COP1 gene in Arabidopsis which show exon skipping were identified and the mutations which alter the normal splicing pattern were characterized. The mutation in cop1-1 was a G-->A change 4 nt upstream from the 3' splice site of intron 5, while the mutation in cop1-2 was a G-->A at the first nucleotide of intron 6, abolishing the conserved G within the 5' splice site consensus. The effect of these mutations was skipping of exon 6. The mutation in cop1-8 was G-->A in the final nucleotide of intron 10 abolishing the conserved G within the 3' splice site consensus and leading to skipping of exon 11. The splicing patterns surrounding exons 6 and 11 of COP1 in these three mutant lines of Arabidopsis provide evidence for exon definition mechanisms operating in plant splicing.

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

In cultivated rice two wild-type alleles, Wxa and Wxb, predominate at the waxy locus, which encodes granule-bound starch synthase. The activity of Wxa is 10-fold higher than that of Wxb at the level of both protein and mRNA. Wxb has a +1G to T mutation at the 5' splice site of the first intron. Sequence analysis of Wxb transcripts revealed that splicing occurs at the mutant AG/UU site and at two cryptic sites: the first is A/GUU, one base upstream of the original site and the second is AG/GU found approximately 100 bases upstream of the mutant splice site. We introduced single base mutations to the 5' splice sites of both Wxa and Wxb, fused with the gus reporter gene and introduced them into rice protoplasts. Analysis of GUS activities and transcripts indicated that a G to T mutation in Wxa reduced GUS activity and the level of spliced RNA. Conversely, a T to G mutation of Wxb restored GUS activity and the level of spliced RNA to that of wild-type Wxa. These results demonstrated that the low level expression of Wxb results from a single base mutation at the 5' splice site of the first intron. It is of interest that the Wxb allele of rice carrying the G to T mutation of intron 1 has been conserved in the history of rice cultivation because there is a low amylose content of the seed caused by this mutation.

SPLICE SITE SELECTION IN PLANT PRE-mRNA SPLICING

The purpose of this review is to highlight the unique and common features of splice site selection in plants compared with the better understood yeast and vertebrate systems. A key question in plant splicing is the role of AU sequences and how and at what stage they are involved in spliceosome assembly. Clearly, intronic U- or AU-rich and exonic GC- and AG-rich elements can influence splice site selection and splicing efficiency and are likely to bind proteins. It is becoming clear that splicing of a particular intron depends on a fine balance in the "strength" of the multiple intron signals involved in splice site selection. Individual introns contain varying strengths of signals and what is critical to splicing of one intron may be of less importance to the splicing of another. Thus, small changes to signals may severely disrupt splicing or have little or no effect depending on the overall sequence context of a specific intron/exon organization.

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

Heterologous introns are often inaccurately or inefficiently processed in higher plants. The precise features that distinguish the process of pre-mRNA 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 flanking G + C-rich exons. Inclusion of this contrast factor in recently developed statistical methods for splice site prediction from sequence inspection significantly improved prediction accuracy. We applied the prediction tools to re-analyze experimental data on splice site selection and splicing efficiency 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 flanking exon and intron. We propose that, in most cases, local context (about 50 bases upstream and downstream from a potential intron end) is sufficient 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.

The Arabidopsis AUX1 gene: a model system to study mRNA processing in plants

It is advantageous for an organism to be able to remove aberrant mRNAs that have either been incorrectly transcribed or processed in order to prevent the accumulation of potentially harmful proteins. The selective degradation of nonsense containing transcripts has been described in yeast. Caenorhabditis elegans and plants. The ease of identification of new mutant alleles in the AUX1 gene of Arabidopsis thaliana has provided a useful system to study novel mutations affecting mRNA stability and pre-mRNA splicing. To date 50 alleles of AUX1 have been identified of which 14 have been characterised at the sequence level. Eight of the characterised alleles encode missense mutations while the others cause nonsense mutations or splicing defects. The 2 splicing mutants identified affect the 5' or 3' splice sites and lead to cryptic splicing events resulting in premature stop codons. The AUX1 mRNA levels of the nonsense containing mutants are reduced compared to the wild-type or missense mutants whereas those of a control transcript (SecY) are unaltered. This provides further evidence for a nonsense-mediated mRNA degradation mechanism in plants and provides a system to study the phenomenon further in Arabidopsis.

Intronic and exonic sequences modulate 5' splice site selection in plant nuclei

Pre-mRNA transcripts in a variety of organisms, including plants, Drosophila and Caenorhabditis elegans, contain introns which are significantly richer in adenosine and uridine residues than their flanking exons. Previous analyses using exonic and intronic replacements between two nonequivalent 5'splice sites in the 469 nt long rbcS3A intron 1 provided the first evidence indicating that, in both tobacco and Drosophila nuclei, 5'splice site selection is strongly influenced by the position of that site relative to the AU transition point between exon and intron. To differentiate between two potential models for 5'splice site recognition, we have expressed a completely different set of intronic and exonic replacement constructs containing identical 5'splice sites upstream of beta-conglycinin intron 4 (115 nt). Mutagenesis and deletion of the upstream 5'splice site demonstrate that intronic AU-rich sequences function by promoting recognition of the most upstream 5'splice site rather than by masking the downstream 5'splice site. Sequence insertions define a role for AG-rich exonic sequences in plant pre-mRNA splicing by demonstrating that an AG-rich element is capable of promoting downstream 5'splice site recognition. We conclude that AU-rich intronic sequences, AG-rich exonic sequences and the 5'splice site itself collectively define 5'intron boundaries in dicot nuclei.

Splicing of precursors to mRNA in higher plants: mechanism, regulation and sub-nuclear organisation of the spliceosomal machinery

The removal of introns from pre-mRNA transcripts and the concomitant ligation of exons is known as pre-mRNA splicing. It is a fundamental aspect of constitutive eukaryotic gene expression and an important level at which gene expression is regulated. The process is governed by multiple cis-acting elements of limited sequence content and particular spatial constraints, and is executed by a dynamic ribonucleoprotein complex termed the spliceosome. The mechanism and regulation of pre-mRNA splicing, and the sub-nuclear organisation of the spliceosomal machinery in higher plants is reviewed here. Heterologous introns are often not processed in higher plants indicating that, although highly conserved, the process of pre-mRNA splicing in plants exhibits significant differences that distinguish it from splicing in yeast and mammals. A fundamental distinguishing feature is the presence of and requirement for AU or U-rich intron sequence in higher-plant pre-mRNA splicing. In this review we document the properties of higher-plant introns and trans-acting spliceosomal components and discuss the means by which these elements combine to determine the accuracy and efficiency of pre-mRNA processing. We also detail examples of how introns can effect regulated gene expression by affecting the nature and abundance of mRNA in plants and list the effects of environmental stresses on splicing. Spliceosomal components exhibit a distinct pattern of organisation in higher-plant nuclei. Effective probes that reveal this pattern have only recently become available, but the domains in which spliceosomal components concentrate were identified in plant nuclei as enigmatic structures some sixty years ago. The organisation of spliceosomal components in plant nuclei is reviewed and these recent observations are unified with previous cytochemical and ultrastructural studies of plant ribonuleoprotein domains.

Expression of the Volvox gene encoding nitrate reductase: mutation-dependent activation of cryptic splice sites and intron-enhanced gene expression from a cDNA

Use of the nitrate reductase encoding gene (nitA) as selection marker has facilitated the successful nuclear transformation of Volvox carteri. The Volvox nitA gene contains 10 introns. A stable nitA mutation in the Volvox recipient strain 153-81 resides in a G-to-A transition of the first nucleotide in the 5' splice site of nitA intron 2. This mutation resulted in at least three non-functional splice variants, namely: (1) intron 2 was not spliced at all; (2) a cryptic 5' splice site 60 nt upstream or (3) a cryptic 5' splice site 16 nt downstream of the mutation were activated and used for splicing. When we used nitA cDNA (pVcNR13) for transformation of V. carteri 153-81, a low efficiency of about 5 x 10(-5) transformants per reproductive cell was observed. Re-integration of either intron 1 (pVcNR15) or introns 9 and 10 (pVcNR16) in the transforming cDNA increased transformation rates to 5 x 10(-4). In parallel, pVcNR15-transformed Volvox exhibited growth rates that were 100-fold increased over the pVcNR13-transformed alga. This intron-enhancement of nitA gene expression appears to be associated with post-transcriptional processing and 'channelling' of the message. These data suggest an important role of splicing for gene expression in V. carteri.

Characterization of intronic uridine-rich sequence elements acting as possible targets for nuclear proteins during pre-mRNA splicing in Nicotiana plumbaginifolia

Introns of nuclear pre-mRNAs in dicotyledonous plants, unlike introns in vertebrates or yeast, are distinctly rich in A+U nucleotides and this feature is essential for their processing. In order to define more precisely sequence elements important for intron recognition in plants, we investigated the effects of short insertions, either U-rich or A-rich, on splicing of synthetic introns in transfected protoplast of Nicotiana plumbaginifolia. It was found that insertions of U-rich (sequence UUUUUAU) but not A-rich (AUAAAAA) segments can activate splicing of a GC-rich synthetic infron, and that U-rich segments, or multimers thereof, can function irrespective of the site of insertion within the intron. Insertions of multiple U-rich segments, either at the same or different locations, generally had an additive, stimulatory effect on splicing. Mutational analysis showed that replacement of one or two U residues in the UUUUUAU sequence with A or C residues had only a small effect on splicing, but replacement with G residues was strongly inhibitory. Proteins that interact with fragments of natural and synthetic pre-mRNAs in vitro were identified in nuclear extracts of N.plumbaginifolia by UV cross- linking. The profile of cross-linked plant proteins was considerably less complex than that obtained with a HeLa cell nuclear extract. Two major cross-linkable plant proteins had apparent molecular mass of 50 and 54 kDa and showed affinity for oligouridilates present in synGC introns or for poly(U).

The unusual 5' splicing border GC is used in myrosinase genes of the Brassicaceae

Myrosinase (thioglucosidase glucohydrolase; EC 3.2.3.1) is a group of isoenzymes in the Brassicaceae, which hydrolyze glucosinolates. Genes encoding myrosinase contain 12 exons and 11 introns. Sequence comparison of two myrosinase genes from Arabidopsis thaliana, TGG1 and TGG2, with the corresponding cDNA from leaves, showed preferential use of a GC dinucleotide as the 5' splicing border in intron 1 instead of an adjacent GT dinucleotide four bp further 3'. This 5' GC splice site is conserved in all seven myrosinase genes characterized from three different species. Likewise, in the 3' region of intron 1 two AG dinucleotides are located seven bp apart. Only the most 5' of these dinucleotides was found to be used in splicing. Sequence analyses of TGG1 cDNA isolated from seeds, siliques and vegetative tissue using reverse transcription PCR showed that the splicing pattern of this intron is identical in these tissues for TGG1. The GT and the most 3' AG dinucleotides mentioned above have been assumed to be the intron borders of intron 1 in several myrosinase genes. The present investigation shows that this assumption is not correct.

Cloning and characterization of two cDNA clones encoding seed-specific antimicrobial peptides from Mirabilis jalapa L

We have isolated and characterized two cDNA clones (designated MJ1 and MJ2) encoding the two Mirabilis jalapa antimicrobial peptides (Mj-AMP1 and Mj-AMP2, respectively), which were previously purified from seeds of this plant species (Cammue et al. (1992), J Biol Chem 267: 2228-2233). In both cases, the deduced amino acid sequences reveal the presence of a putative signal sequence preceding the mature peptide, indicating that the Mj-AMPs are expressed as preproteins. The Mj-AMP1- and Mj-AMP2-encoding genes are interrupted in their coding sequences by a single intron (380 bp and 900 bp for Mj-AMP1 and Mj-AMP2 genes, respectively). Southern blot analysis indicates that the Mj-AMP-encoding genes belong to a gene family of low complexity. Northern blot analysis suggests seed-specific expression of Mj-AMPs since transcripts of the expected size could only be detected in near-mature and in mature seeds of M. jalapa.

Impaired splicing of phytochrome B pre-mRNA in a novel phyB mutant of Arabidopsis

Phytochrome is the red/far-red absorbing photoreceptor active in photomorphogenesis, the apoprotein of which is encoded by a small gene family (PHYA, PHYB, PHYC, PHYD and PHYE). A novel phytochrome B-deficient mutant, phyB-103, was isolated from a screen of EMS-mutagenised Arabidopsis M2 seed. phyB-103 carries a G-to-A base substitution at the 5' splice site +1 G nucleotide of intron 1 of PHYB. The phyB-103 PHYB transcript is larger than the wild-type PHYB transcript and DNA sequence analysis showed that the entire intron is retained in the mature PHYB transcript of phyB-103. Thus the phyB-103 G-to-A substitution prevents intron splicing. The retained intron contains within it an in-frame stop codon, and the predicted PHYB-003 apoprotein thus terminates prematurely. phyB-103 is therefore likely to be a null allele of PHYB, consistent with the observation that the phenotype conferred by phyB-103 is as severe as that conferred by previously described phyB null alleles.

Effects of secondary structure on pre-mRNA splicing: hairpins sequestering the 5' but not the 3' splice site inhibit intron processing in Nicotiana plumbaginifolia

We have performed a systematic study of the effect of artificial hairpins on pre-mRNA splicing in protoplasts of a dicot plant, Nicotiana plumbaginifolia. Hairpins with a potential to form 18 or 24 bp stems strongly inhibit splicing when they sequester the 5' splice site or are placed in the middle of short introns. However, similar 24 bp hairpins sequestering the 3' splice site do not prevent this site from being used as an acceptor. Utilization of the stem-located 3' site requires that the base of the stem is separated from the upstream 5' splice site by a minimum of approximately 45 nucleotides and that another 'helper' 3' splice site is present downstream of the stem. The results indicate that the spliceosome or factors associated with it may have a potential to unfold secondary structure present in the downstream portion of the intron, prior to or at the step of the 3' splice site selection. The finding that the helper 3' site is required for utilization of the stem-located acceptor confirms and extends previous observations, obtained with HeLa cell in vitro splicing systems, indicating that the 3' splice site may be recognized at least twice during spliceosome assembly.

In vivo analysis of intron processing using splicing-dependent reporter gene assays

The mechanisms of intron recognition and processing have been well-studied in mammals and yeast, but in plants the biochemistry of splicing is not known and the rules for intron recognition are not clearly defined. To increase understanding of intron processing in plants, we have constructed new pairs of vectors, pSuccess and pFail, to assess the efficiency of splicing in maize cells. In the pFail series we use translation of pre-mRNA to monitor the amount of unspliced RNA. We inserted an ATG codon in the Bz2 (Bronze-2) intron in frame with luciferase: this construct will express luciferase activity only when splicing fails. In the pSuccess series the spliced message is monitored by inserting an ATG upstream of the Bz2 intron in frame with luciferase: this construct will express luciferase activity only when splicing succeeds. We show here, using both the wild-type Bz2 intron and the same intron with splice site mutations, that the efficiency of splicing can be estimated by the ratio between the luciferase activities of the vector pairs. We also show that mutations in the unique U-rich motif inside the intron can modulate splicing. In addition, a GC-rich insertion in the first exon increases the efficiency of splicing, suggesting that exons also play an important role in intron recognition and/or processing.

Expression of maize Adh1 intron mutants in tobacco nuclei

In vivo and in vitro gene transfer experiments have suggested that the elements mediating intron recognition differ in mammalian, yeast and plant nuclei. Differences in the sequence dependencies, which also exist between dicotyledonous and monocotyledonous nuclei, have prevented some monocot introns from being spliced in dicot nuclei. To locate elements which modulate efficient recognition of introns in dicot nuclei, the maize Adh1 gene has been expressed in full-length and single intron constructs in Nicotiana benthamiana nuclei using an autonomously replicating plant expression vector. Quantitative PCR-Southern analyses indicate that the inefficient splicing of the maize Adh1 intron 1 (57% AU) in these dicot nuclei can be dramatically enhanced by increasing the degree of U1 snRNA complementarity at the 5' splice site. This indicates that the 5' splice site plays a significant role in defining the splicing efficiency of an intron in dicot nuclei and that, most importantly, the remainder of this monocot intron contains no elements which inhibit its accurate recognition in dicot nuclei. Deletions in intron 3 (66% AU) which effectively move the 3' boundary between AU-rich intron and GC-rich exon sequences strongly activate a cryptic upstream splice site; those which do not reposition this boundary activate a downstream cryptic splice site. This suggests that 3' splice site selection in dicot nuclei is extremely flexible and not dependent on strict sequence requirements but rather on the transition points between introns and exons. Our results are consistent with a model in which potential splice sites are selected if they are located upstream (5' splice site) or downstream (3' splice site) of AU transition points and not if they are embedded within AU-rich sequences.