Plant small nuclear RNAs. V. U4 RNA is present in broad bean plants in the form of sequence variants and is base-paired with U6 RNA

Identification of a plant serine-arginine-rich protein similar to the mammalian splicing factor SF2/ASF

We show that the higher plant Arabidopsis thaliana has a serine-arginine-rich (SR) protein family whose members contain a phosphoepitope shared by the animal SR family of splicing factors. In addition, we report the cloning and characterization of a cDNA encoding a higher-plant SR protein from Arabidopsis, SR1, which has striking sequence and structural homology to the human splicing factor SF2/ASF. Similar to SF2/ASF, the plant SR1 protein promotes splice site switching in mammalian nuclear extracts. A novel feature of the Arabidopsis SR protein is a C-terminal domain containing a high concentration of proline, serine, and lysine residues (PSK domain), a composition reminiscent of histones. This domain includes a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2.

The U6 small nuclear RNA gene family of potato

Using the inverse polymerase chain reaction (IPCR), 19 U6snRNA gene promoters were isolated from the potato genome. Analysis of their nucleotide sequences revealed the existence of two subfamilies. Promoters from class 1 harbour the typical sequence elements required for plant snRNA gene transcription whereas those from class 2 do not have a TATA box. Three promoters were fused to a modified U6snRNA-coding sequence to allow their activity to be monitored in tobacco protoplasts. Two of the promoters, one from either class, were found to be active. Comparison of potato U6snRNA gene promoter sequences with those found in other plant species showed various degrees of homology. In addition, the entire nucleotide sequences of seven potato U6snRNA genes and one pseudogene were determined. The overall frequency of nucleotide changes after PCR was found to be 1.15 x 10(-3). The mutations appeared to be clustered in a distinct area and were all A-to-G/T-to-C substitutions.

Characterization of the genes encoding U4 small nuclear RNAs in Arabidopsis thaliana

Three genes encoding U4 small nuclear RNA (U4 snRNA) in the higher plant Arabidopsis thaliana have been isolated and characterized. Two of the genes, AtU4.1 and AtU4.2, contain all the transcriptional signals known to be essential for U-snRNA gene activity in dicot plants: the Upstream Sequence Element (USE), the -30 TATA box and the downstream 3' end formation sequence. The USE and TATA elements are centered approximately four helical DNA turns apart, a feature characteristic of RNA polymerase II-transcribed U-snRNA genes of plants. The genes AtU4.1 and AtU4.2 are actively transcribed in transfected plant protoplasts and in Arabidopsis plants. Expression of the third gene, AtU4.3, could not be demonstrated. Since this gene is missing the downstream signal important for RNA 3' end formation, it probably represents a pseudogene. The genes AtU4.1 and AtU4.2 encode 152-153 nt long RNAs which show 85-89% sequence similarity with broad bean and pea U4 RNAs and 60-65% similarity with mammalian U4 RNAs. Arabidopsis U4 and U6 snRNAs can be folded into the base-paired Y-shaped model supporting the importance of the U4/U6 interaction during pre-mRNA splicing in plants as well as animals.

Developmental expression of plant snRNAs

Although the number of plant U1, U2, U4 and U5 small nuclear RNA (snRNA) variants sequenced has steadily increased over the past few years, the function of these variants in plant splicing is still not understood. In an effort to elucidate the function of plant snRNA variants, we have examined the expression of U1-U6 snRNA variants during pea seedling development. In contrast to mammalian nuclei which express a single, abundant form of each snRNA, pea nuclei express several equally abundant variants of the same snRNA. Comparison of the snRNAs in pea seeds and seedlings has revealed that four (U1, U2, U4, U5) of the five snRNAs required for pre-mRNA splicing have differentially- and developmentally-regulated forms detectable on Northerns. Only U6 snRNA, which fractionates as a single species on Northerns, appears to be constitutively expressed. Switches in the expression of the pea U1, U2 and U4 snRNAs occur at three distinct stages in development: seed maturation, seed germination and seedling maturation. Surprisingly, the snRNA profiles of mature desiccated seeds and mature leaf tissues are nearly identical and different from developing seeds and seedlings suggesting that switches in the snRNA population occur at transitions between active and inactive transcription. Sequence analysis and differential hybridization of the U1 snRNA variants has demonstrated that some of the developmentally-regulated forms represent sequence variants. We conclude that select subsets of pea snRNAs accumulate at particular stages during plant development.

cDNA cloning of U1, U2, U4 and U5 snRNA families expressed in pea nuclei

Differences observed between plant and animal pre-mRNA splicing may be the result of primary or secondary structure differences in small nuclear RNAs (snRNAs). A cDNA library of pea snRNAs was constructed from anti-trimethylguanosine (m3(2,2,7)G immunoprecipitated pea nuclear RNA. The cDNA library was screened using oligo-deoxyribonucleotide probes specific for the U1, U2, U4 and U5 snRNAs. cDNA clones representing U1, U2, U4 and U5 snRNAs expressed in seedling tissue have been isolated and sequenced. Comparison of the pea snRNA variants with other organisms suggest that functionally important primary sequences are conserved phylogenetically even though the overall sequences have diverged substantially. Structural variations in U1 snRNA occur in regions required for U1-specific protein binding. In light of this sequence analysis, it is clear that the dicot snRNA variants do not differ in sequences implicated in RNA:RNA interactions with pre-mRNA. Instead, sequence differences occur in regions implicated in the binding of small ribonucleoproteins (snRNPs) to snRNAs and may result in the formation of unique snRNP particles.

A phylogenetic study of U4 snRNA reveals the existence of an evolutionarily conserved secondary structure corresponding to 'free' U4 snRNA

The nucleotide sequence of Physarum polycephalum U4 snRNA*** was determined and compared to published U4 snRNA sequences. The primary structure of P polycephalum U4 snRNA is closer to that of plants and animals than to that of fungi. But, both fungi and P polycephalum U4 snRNAs are missing the 3' terminal hairpin and this may be a common feature of lower eucaryote U4 snRNAs. We found that the secondary structure model we previously proposed for 'free' U4 snRNA is compatible with the various U4 snRNA sequences published. The possibility to form this tetrahelix structure is preserved by several compensatory base substitutions and by compensatory nucleotide insertions and deletions. According to this finding, association between U4 and U6 snRNAs implies the disruption of 2 internal helical structures of U4 snRNA. One has a very low free energy, but the other, which represents one-half of the helical region of the 5' hairpin, requires 4 to 5 kcal to be open. The remaining part of the 5' hairpin is maintained in the U4/U6 complex and we observed the conservation, in all U4 snRNAs studied, of a U bulge residue at the limit between the helical region which has to be melted and that which is maintained. The 3' domain of U4 snRNA is less conserved in both size and primary structure than the 5' domain; its structure is also more compact in the RNA in solution. In this domain, only the Sm binding site and the presence of a bulge nucleotide in the hairpin on the 5' side of the Sm site are conserved throughout evolution.

Molecular analysis of a U3 RNA gene locus in tomato: transcription signals, the coding region, expression in transgenic tobacco plants and tandemly repeated pseudogenes

By screening a tomato genomic library with a tomato U3 RNA probe, we detected a U3 genomic locus whose coding region was determined by primer extension (5' end) and direct RNA sequencing of purified U3 RNA from tomato (3' end). Tomato U3 RNA is 216 nucleotides long, contains all the four evolutionarily highly conserved sequence blocks (Boxes A to D), has at its 5' end a cap not precipitable with anti-m3G antibodies and can be folded into a peculiar secondary structure with two stem-loops at its 5' end. A tagged derivative of the U3 gene was faithfully expressed in transgenic tobacco plants. In the 5' flanking region both plant-specific UsnRNA transcription signals [the TATA-like sequence and the upstream sequence element (USE)] were present, but were positioned closer to each other and also to the cap site in the U3 gene than in the genes for the plant spliceosomal UsnRNAs studied so far. The 3' flanking region of the tomato U3 gene lacked the consensus sequence of the putative termination signal established for the plant spliceosomal UsnRNA genes and contained a pyrimidine-rich tract (R1) followed by four tandemly repeated U3 pseudogenes (U3.1 ps to U3.4 ps) flanked by slightly altered forms (R2 to R5) of R1 and most probably generated by DNA-mediated events. Our results are in line with the conjecture that the enzyme transcribing the tomato U3 gene has different structural requirements for transcriptional activity than the enzyme transcribing plant U1, U2 and U5 genes.

Maize U2 snRNAs: gene sequence and expression

The complexity of plant U-type small nuclear ribonucleoprotein particles (UsnRNPs) may represent one level at which differences in splicing between animals and plants and between monocotyledonous and dicotyledonous plants could be effected. The maize (monocot.) U2snRNA multigene family consists of some 25 to 40 genes which from RNA blot and RNase protection analyses produce U2snRNAs varying in both size and sequence. The first 77 nucleotides of the maize U2-27 snRNA gene are identical to U2snRNA genes of Arabidopsis (dicot). Despite much lower sequence homology in the remaining 120 nucleotides the secondary structure of the RNA is conserved. The difference in splicing between monocot. and dicot. plants cannot be explained on the basis of sequence differences between monocot, and dicot. U2snRNAs in the region which may interact with intron branch point sequences.

Small nuclear RNAs from budding yeasts: phylogenetic comparisons reveal extensive size variation

Homologues of each of the five metazoan snRNAs required for pre-mRNA splicing have recently been identified in the budding yeast Saccharomyces cerevisiae on the basis of shared structural elements and evidence of similar roles during splicing. However, the spliceosomal snRNAs in this yeast are up to six times larger than their mammalian counterparts, suggesting that they may perform additional, perhaps species-specific, functions in the pre-mRNA processing pathway. We have undertaken a survey of 23 other budding yeasts to determine whether increased snRNA size is unique to Sacch. cerevisiae and, if not, to look for common structural motifs among homologous snRNAs. Our studies reveal that the spliceosomal snRNAs exhibit a surprising degree of size variation among these species. Furthermore, partial sequence analysis has identified a specific domain in the U6 snRNA which accounts for the observed size polymorphisms.

Molecular analysis of eight U1 RNA gene candidates from tomato that could potentially be transcribed into U1 RNA sequence variants differing from each other in similar regions of secondary structure

From a tomato genomic library we isolated and characterized eight U1 RNA gene candidates (U1.1 to U1.8) all of which possessed the canonical plant U-snRNA transcription signals in their 5' and 3' flanking regions and exhibited nucleotide sequence conservation in the 5' splice site recognition sequence, in the Sm antigen binding site and in Loops B, C, D as well as in Stems III and IV of their coding region. Deviations from the U1 RNA consensus sequence were mainly localized to Loop A and Stems I and II, suggesting that the putative transcripts of the tomato U1.1-U1.8 genes would differ from each other in their capacity of binding to the U1 RNA-specific snRNP proteins.

Molecular analysis of dicot and monocot small nuclear RNA populations

Oligonucleotides directed against conserved small nuclear RNA (snRNA) sequences have been used to identify the individual U1, U2, U4, U5, and U6 snRNAs in dicot and monocot nuclei. The plant snRNA populations are significantly more heterogeneous than the mammalian or Saccharomyces cerevisiae snRNA populations. U6 snRNA exists as a single species of similar size in monocot and dicot nuclei. The abundance and molecular weights of the U1, U2, U4, and U5 snRNAs expressed in monocot and dicot nuclei are significantly different. Whereas most dicot nuclei contain one or two predominant forms of U2 snRNA and a small number of U4 snRNAs, monocot nuclei contain multiple forms of U2 snRNA ranging from 208 to 260 nucleotides and multiple forms of U4 snRNA from 159 to 176 nucleotides. Multiple forms of U1 and U5 snRNA exist in both plant groups. All prominent size variants of U1, U2, U4, and U5 snRNA identified in monocot nuclei can be immunoprecipitated with anti-trimethylguanosine antibody. We conclude that the sizes and number of snRNA molecules involved in intron excision differ considerably in dicot and monocot nuclei. In wheat nuclei, we have identified an additional U1-like RNA that is differentially expressed during development.

Purification of the major UsnRNPs from broad bean nuclear extracts and characterization of their protein constituents

Small nuclear ribonucleoprotein particles containing the five major nucleoplasmic snRNAs U1, U2, U4, U5 and U6 as well as two smaller sized snRNAs were purified from broad bean nuclear extracts by anti-m3G, monoclonal antibody, immunoaffinity chromatography. We have so far defined 13 polypeptides of approximate mol. wts. of 11 kd, 11.5 kd, 12.5 kd, 16 kd, 17 kd, 17.5 kd, 18.5 kd, 25 kd (double band), 30 kd, 31 kd, 35 kd, 36 kd and 54 kd. Upon fractionation of the UsnRNPs by anion exchange chromatography, essentially pure U5 snRNPs were obtained, containing the 11 kd, 11.5 kd, 12.5 kd, 16 kd, 17 kd, 17.5 kd, 35 kd and 36 kd polypeptides. These may therefore represent the common snRNP polypeptides and which may also be present in the other snRNPs. By immunoblotting studies, using anti-Sm sera and mouse monoclonal antibodies we show that the 35 kd and 36 kd proteins are immunologically related to the mammalian common B/B' proteins. The broad bean 16 kd and 17 kd proteins appear to share structural elements with the mammalian D protein. The three proteins of mol. wts. 11 kd, 11.5 kd and 12.5 kd probably represent the broad bean polypeptides E, F, and G. Cross-reactivity of proteins of mol. wts of 30 kd and 31 kd with Anti-(U1/U2)RNP antibodies suggests that they may represent the broad bean A and B" polypeptides. The 54 kd protein and the 18.5 kd protein could be candidates for the U1 specific 70 k and C polypeptides. Our results demonstrate a strong similarity between the overall structure of broad bean and mammalian snRNPs.

Structure and expression of the U5 snRNA gene of Arabidopsis thaliana. Conserved upstream sequence elements in plant U-RNA genes

We have previously characterized the U2 small nuclear (sn) RNA gene family of Arabidopsis thaliana. To find out the structural features of upstream and downstream non-coding regions that are shared by different U-RNA genes in higher plants we have isolated the gene encoding a 125 nt-long U5 snRNA of Arabidopsis. Activity of the cloned gene was demonstrated in stably transformed tobacco calli and by transient expression in transfected protoplasts of Nicotiana plumbaginifolia. Southern analysis indicated that the Arabidopsis genome contains 8-9 copies of the U5 gene. Alignment of upstream non-coding regions revealed two elements conserved between all plant U-RNA genes characterized so far: the sequence RTCCCACATCG (-70/-80 region, 100% conservation) and the TATA homology around position -30. The coding regions in all genes are followed by the sequence CAN4-9AGTN (A/T)AA which may correspond to a termination and/or processing signal.