Nuclear Pre-mRNA Splicing in Plants

Reddy, A. S. N.

doi:10.1080/20013591099272

Cited by 68 publications

(89 citation statements)

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“…In light of the strong conservation of the spliceosomal machinery between humans and plants (Lorkovic et al 2000;Reddy 2001;Brown et al 2002;Wang and Brendel 2004;Z.J. Lorković, R. Lehner, C. Forstner, and A. Barta, unpubl.…”

Section: Resultsmentioning

confidence: 99%

Evolutionary conservation of minor U12-type spliceosome between plants and humans

Lorković

Lehner²,

Forstner³

et al. 2005

RNA

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Splicing of rare, U12-type or AT-AC introns is mediated by a distinct spliceosome that assembles from U11, U12, U4atac, U6atac, and U5 snRNPs. Although in human cells the protein composition of minor and major snRNPs is similar, differences, particularly in U11 and U12 snRNPs, have been recently described. We have identified an Arabidopsis U11 snRNP-specific 35K protein as an interacting partner of an RS-domain-containing cyclophilin. By using a transient expression system in Arabidopsis protoplasts, we show that the 35K protein incorporates into snRNP. Oligo affinity selection and glycerol gradient centrifugation revealed that the Arabidopsis 35K protein is present in monomeric U11 snRNP and in U11/U12-di snRNP. The interaction of the 35K protein with Arabidopsis SR proteins together with its strong sequence similarity to U1-70K suggests that its function in splicing of minor introns is analogous to that of U1-70K. Analysis of Arabidopsis and Oryza sativa genome sequences revealed that all U11/U12-di-snRNP-specific proteins are conserved in dicot and monocot plants. In addition, we have identified an Arabidopsis gene encoding the homolog of U4atac snRNA and a second Arabidopsis gene encoding U6atac snRNA. Secondary structure predictions indicate that the Arabidopsis U4atac is able to form dimeric complexes with both Arabidopsis U6atac snRNAs. As revealed by RNaseA/T1 protection assay, the U4atac snRNA gene is expressed as an $160-nt RNA, whereas the second U6atac snRNA gene seems to be a pseudogene. Taken together, our data indicate that recognition and splicing of minor, AT-AC introns in plants is highly similar to that in humans.

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Section: Resultsmentioning

confidence: 99%

Evolutionary conservation of minor U12-type spliceosome between plants and humans

Lorković

Lehner²,

Forstner³

et al. 2005

RNA

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“…The distinguishing feature of U2 introns in plants, compared with introns from vertebrates and yeast (Saccharomyces cerevisiae), is their UA richness, which is required for efficient U2 intron splicing and for 59 and 39 splice site selection (Goodall and Filipowicz, 1989;Simpson and Filipowicz, 1996;Brown and Simpson, 1998;Lorković et al, 2000;Reddy, 2001). The role of UA-rich elements in plant splicing is still poorly understood, but they may minimize secondary structure of plant introns or bind specific UA binding proteins to recruit splicing factors early in spliceosome formation (Simpson and Filipowicz, 1996;Brown and Simpson, 1998;Lorković et al, 2000;Reddy, 2001).…”

Section: Introductionmentioning

confidence: 99%

“…The role of UA-rich elements in plant splicing is still poorly understood, but they may minimize secondary structure of plant introns or bind specific UA binding proteins to recruit splicing factors early in spliceosome formation (Simpson and Filipowicz, 1996;Brown and Simpson, 1998;Lorković et al, 2000;Reddy, 2001). Putative UA-rich binding proteins (UBP1, RBP45, and RBP47) with affinity for U-rich sequences have been isolated and characterized (Gniadkowski et al, 1996;Lambermon et al, 2000;Lorković et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

“…As with U2 introns, U12 intron splicing follows a two-step reaction that involves the formation of a characteristic intron lariat intermediate at an adenosine that can be at one of two possible positions within the stringent branchpoint consensus (Tarn and Steitz, 1996a;McConnell et al, 2002). In addition, exon bridging interactions between complexes forming on splice sites of U12 introns and flanking U2 introns can enhance U12-dependent intron splicing (Wu and Krainer, 1996;Dietrich et al, 2001b;Hastings and Krainer, 2001;Kmieciak et al, 2002), and some U12 introns are involved in alternative splicing (Dietrich et al, 2001b;Zhu and Brendel, 2003).The distinguishing feature of U2 introns in plants, compared with introns from vertebrates and yeast (Saccharomyces cerevisiae), is their UA richness, which is required for efficient U2 intron splicing and for 59 and 39 splice site selection (Goodall and Filipowicz, 1989;Simpson and Filipowicz, 1996;Brown and Simpson, 1998;Lorković et al, 2000;Reddy, 2001). The role of UA-rich elements in plant splicing is still poorly understood, but they may minimize secondary structure of plant introns or bind specific UA binding proteins to recruit splicing factors early in spliceosome formation (Simpson and Filipowicz, 1996;Brown and Simpson, 1998;Lorković et al, 2000;Reddy, 2001).…”

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Determinants of Plant U12-Dependent Intron Splicing Efficiency

Lewandowska

Simpson²,

Clark³

et al. 2004

Plant Cell

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Factors affecting splicing of plant U12-dependent introns have been examined by extensive mutational analyses in an in vivo tobacco (Nicotiana tabacum) protoplast system using introns from three different Arabidopsis thaliana genes: CBP20, GSH2, and LD. The results provide evidence that splicing efficiency of plant U12 introns depends on a combination of factors, including UA content, exon bridging interactions between the U12 intron and flanking U2-dependent introns, and exon splicing enhancer sequences (ESEs). Unexpectedly, all three plant U12 introns required an adenosine at the upstream purine position in the branchpoint consensus UCCUURAUY. The exon upstream of the LD U12 intron is a major determinant of its higher level of splicing efficiency and potentially contains two ESE regions. These results suggest that in plants, U12 introns represent a level at which expression of their host genes can be regulated. INTRODUCTIONPre-mRNA splicing in eukaryotes is a fundamental step in gene expression and represents an important level at which the expression of protein-coding genes can be regulated (Reed, 2000;Smith and Valcá rcel, 2000;Graveley, 2001;Hastings and Krainer, 2001;Cartegni et al., 2002;Black, 2003). In higher eukaryotes, there are two classes of nuclear pre-mRNA introns. The most abundant class consists of U2-dependent introns (U2 introns), whereas the second rarer class (<0.4% of introns) consists of U12-dependent introns (U12 introns). U12 introns have been found in the nuclear genomes of vertebrates, plants, and insects (Hall and Padgett, 1994;Sharp and Burge, 1997;Tarn and Steitz, 1997; Krainer, 1998, 1999;Burge et al., 1998;Levine and Durbin, 2001;Patel and Steitz, 2003). Introns belonging to these two distinct classes are spliced by two different spliceosomes: the major U2-type spliceosome and the less abundant U12-type spliceosome (Hall and Padgett, 1996;Tarn and Steitz 1996a. Although the first U12 introns to be described had AT-AC-terminal dinucleotides, the majority of U12-type introns contain GT-AG, and a small number contain other noncanonical terminal dinucleotides, such as AT-AA, AT-AG, AT-AT, GT-AT, or GT-GG (Jackson, 1991;Hall and Padgett, 1994;Dietrich et al., 1997Dietrich et al., , 2001aSharp and Burge, 1997;Burge et al., 1998;Wu and Krainer, 1999;Levine and Durbin, 2001;Zhu and Brendel, 2003). Moreover, functional analyses have shown that AT-AC-terminal dinucleotides are not a defining feature of U12 introns (Dietrich et al., 1997(Dietrich et al., , 2001a. Instead, U12 introns contain highly conserved sequences in the 59 splice site (exon:G/ATATCCTY) and branchpoint region (TCCTTRAY) (Hall and Padgett, 1994;Sharp and Burge, 1997;Burge et al., 1998), which are both required for prespliceosome complex formation (Frilander and Steitz, 1999). The 39 splice site consensus sequence of U12 introns (YAC/G:exon) is less informative than their 59 splice site and branchpoint sequences. U12 introns also lack a polypyrimidine tract and have a short distance between the branchpoint and 39 splice si...

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“…Similar to vertebrate introns, most plant introns have canonical GU and AG dinucleotides at their 5Ј and 3Ј ends, suggesting the presence of a conserved splicing mechanism. However, plant cells have special requirements for intron recognition; for example, the necessity of AU-rich sequences in the intron, a relaxed criteria for branch site selection and the unessential requirement for a polypyrimidine tract (for reviews, see Lorkovic et al, 2000;Reddy, 2001). Given that SR proteins play important roles in both constitutive and alternative pre-mRNA splicing, the larger number of SR proteins in Arabidopsis may be a reflection of specific roles in both constitutive and alternative pre-mRNA splicing among different cell types and developmental stages.…”

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confidence: 99%

Tissue-specific Expression and Dynamic Organization of SR Splicing Factors inArabidopsis

Fang

Hearn

Spector

2004

MBoC

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The organization of the pre-mRNA splicing machinery has been extensively studied in mammalian and yeast cells and far less is known in living plant cells and different cell types of an intact organism. Here, we report on the expression, organization, and dynamics of pre-mRNA splicing factors (SR33, SR1/atSRp34, and atSRp30) under control of their endogenous promoters in Arabidopsis. Distinct tissue-specific expression patterns were observed, and differences in the distribution of these proteins within nuclei of different cell types were identified. These factors localized in a cell type-dependent speckled pattern as well as being diffusely distributed throughout the nucleoplasm. Electron microscopic analysis has revealed that these speckles correspond to interchromatin granule clusters. Time-lapse microscopy revealed that speckles move within a constrained nuclear space, and their organization is altered during the cell cycle. Fluorescence recovery after photobleaching analysis revealed a rapid exchange rate of splicing factors in nuclear speckles. The dynamic organization of plant speckles is closely related to the transcriptional activity of the cells. The organization and dynamic behavior of speckles in Arabidopsis cell nuclei provides significant insight into understanding the functional compartmentalization of the nucleus and its relationship to chromatin organization within various cell types of a single organism. INTRODUCTIONPre-mRNA (pre-mRNA) splicing, a process of excision of introns and ligation of exons, is essential for generating mature transcripts and enhancing mRNA export from the nucleus to the cytoplasm. Splicing occurs within a large macromolecular complex called the spliceosome, which is composed of U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles and a large number of non-small nuclear ribonucleoprotein particle proteins (Zhou et al., 2002). The latter include members of the SR (Ser-Arg) family of pre-mRNA splicing factors characterized by one or two N-terminal RNA recognition motifs that interact with the pre-mRNAs and a C-terminal variable-length Arg/Ser(RS)-rich domain that influences its subcellular localization and splicing activity depending upon its phosphorylation levels (for review, see Graveley, 2000).In mammalian cells, pre-mRNA splicing factors are concentrated in 20 -50 distinct nuclear domains called speckles as well as being diffusely distributed throughout the nucleoplasm, and this distribution corresponds to interchromatin granule clusters (IGCs) and perichromatin fibrils (PFs). PFs often extend from the periphery of IGCs or are present in the nucleoplasm at some distance from an IGCs (for review, see Lamond and Spector, 2003). It has been proposed that IGCs are storage and/or modification/reassembly sites for premRNA splicing factors and that splicing factors are recruited from these compartments to the sites of active transcription (PFs) (Jiménez-García and Spector, 1993). Disassembly of IGCs by overexpression of an SR protein kinase Clk/STY disrupts the coo...

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Nuclear Pre-mRNA Splicing in Plants

Cited by 68 publications

References 0 publications

Evolutionary conservation of minor U12-type spliceosome between plants and humans

Evolutionary conservation of minor U12-type spliceosome between plants and humans

Determinants of Plant U12-Dependent Intron Splicing Efficiency

Tissue-specific Expression and Dynamic Organization of SR Splicing Factors inArabidopsis

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