Sequence and expression of potato U2 snRNA genes

Low CD3+CD28-induced interleukin-2 production correlates with decreased reactive oxygen intermediate formation in neonatal T cells

The capacity of neonatal T cells to secrete interleukin-2 (IL-2) has been reported to be variable. We analysed IL-2 production in purified neonatal and adult T cells using polyclonal activator phorbol ester + calcium ionophore (PDBu + iono) or receptor-mediated anti-CD3/anti-CD3+ anti-CD28 stimulation. PDBu + iono induced equally high IL-2 levels in both groups and, when stimulated with plate-bound anti-CD3 monoclonal antibody (mAb), the IL-2 secretion by neonatal cells was undetectable and adult cells produced low amounts of IL-2 (mean 331 +/- 86 pg/ml). The addition of anti-CD28 mAb to anti-CD3-stimulated cells markedly increased IL-2 production in both cell types, but levels of IL-2 in neonatal T cells remained clearly lower than those of adult T cells (respective mean values: 385 +/- 109 pg/ml and 4494 +/- 1199 pg/ml). As NF-kappa B is a critical transcription factor in the control of IL-2 expression, we next analysed its nuclear translocation in neonatal and adult T cells using the electrophoretic mobility shift assay and, because induction of reactive oxygen intermediates (ROI) is required for the activation of NF-kappa B, we also analysed levels of intracellular ROI in these cells using the ROI-reactive fluorochrome DCFH-DA and flow cytometry. In neonatal T cells NF-kappa B activation and ROI formation after anti-CD3 stimulation were low compared with adult T cells and, although addition of anti-CD28 mAb increased induction of NF-kappa B and ROI formation, levels similar to those of adults were not achieved. After PDBu + iono stimulation, the cells showed similar ROI formation and IL-2 secretion. Our results suggest that reduced IL-2 production by neonatal T cells is specific for anti-CD3 and anti-CD3+ anti-CD28-mediated stimulation and that these activators cannot effectively activate the ROI-NF-kappa B signalling pathway in neonatal T cells.

p53 transactivation and protein accumulation are independently regulated by UV light in different phases of the cell cycle

DNA damage-induced activation of the p53 tumor suppressor gene is suggested to be central in the cellular damage response pathway. In this study, we analyzed the responses of p53 to UVC radiation in synchronized mouse fibroblasts in terms of p53 accumulation, transcriptional activation, and sequence-specific DNA-binding activity. UVC was found to induce accumulation of p53 cell cycle dependently in G1/S- and S-phase cells but not in G0 or G1 cells. In contrast, p53 transcriptional activity and its target genes, p21 and GADD45, were stimulated by UVC in G0 and G1 cells in the absence of detectable p53 protein. The accumulation of p53 and increased p21 and GADD45 expression were replication dependent in S-phase cells. Interestingly, sequence-specific p53 DNA-binding activity was stimulated also replication independently in S phase, though the effect was not conveyed to stimulation of p53 target genes, suggesting that additional events are required for p53-stimulated gene expression. The results show that opposed to the cell cycle dependence of p53 accumulation, the UVC-mediated transactivation by p53 is independent of the cell cycle phase and protein stabilization.

The organization of spliceosomal components in the nuclei of higher plants

To analyze the organization of spliceosomal snRNPs in plant nuclei, we have used both immunofluorescence labelling with the antibody 4G3, raised against the human snRNP-specific protein U2B", and in situ hybridization with anti-sense probes to conserved regions of U1, U2 and U6 snRNAs. The organization comprises a fibrous interchromatin network, which may include both interchromatin fibrils and granules, and very prominent nuclear and nucleolar-associated bodies. Double labelling with an anti-p80 coilin antibody shows that these are coiled bodies. Dynamic changes in the labelling pattern were observed through the cell cycle, and in response to and on recovery from heat shock. The similarity of this organization to that observed in mammalian nuclei is strong evidence that it is fundamental to the processing of pre-mRNA in eucaryotes in general.

Molecular characterisation of plant U14 small nucleolar RNA genes: closely linked genes are transcribed as polycistronic U14 transcripts

U14snoRNAs are highly conserved eukaryotic nucleolar small RNAs involved in precursor ribosomal RNA processing. In vertebrates, U14snoRNAs and a number of other snoRNAs are transcribed within introns of protein coding genes and are released by processing. We have isolated potato and maize genomic U14 clones using PCR-amplified plant U14 probes. Plant U14s show extensive homology to those from yeast and animals but contain plant-specific sequences. One of the isolated maize clones contains a cluster of four U14 genes in a region of only 761 bp, confirming the close linkage of U14 genes in maize, potato and barley as established by PCR. The absence of known plant promoter elements, the proximity of the genes and the detection of transcripts containing linked U14s by RT-PCR indicates that some plant U14snoRNAs are transcribed as precursor RNAs which are then processed to release individual U14s. Whether plant U14snoRNAs are intron-encoded or transcribed from novel promoter sequences, remains to be established.

Plant pre-mRNA splicing and splicing components

Pre-mRNA splicing or the removal of introns from precursor messenger RNAs depends on the accurate recognition of intron sequences by the plant splicing machinery. The major components of this machinery are small nuclear ribonucleoprotein protein particles (snRNPs) which consist of snRNAs and snRNP proteins. We have analysed various aspects of intron sequence and structure in relation to splice site selection and splicing efficiency and we have cloned snRNA genes and a gene encoding the snRNP protein, U2B". In the absence of an in vitro splicing system for plants, transient expression in protoplasts and stable plant transformations have been used to analyse splicing of intron constructs. We aim to address the function of the UsnRNP-specific protein, U2B", via the production of transgenic plants expressing antisense U2B" transcripts and epitope-tagged U2B" protein. In addition, we have cloned genes encoding other proteins which potentially interact with RNA, such as RNA helicases, and strategies involving transgenic plants are being developed to analyse their function.

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.

Differential expression of U5snRNA gene variants in maize (Zea mays) protoplasts

The small nuclear ribonucleoprotein particles U1, U2, U4/U6 and U5 participate in the removal of introns from pre-messenger RNAs in the nucleus. Three genes encoding U5snRNAs, the RNA moiety of U5snRNPs, have been isolated from maize. As in other plant UsnRNA gene families the three maize U5snRNA genes exhibit sequence variation. Two of the gene variants (MzU5.1 and MzU5.2) are clearly expressed after transfection into maize leaf protoplasts while the third gene variant (MzU5.3) is expressed at very low levels. These different levels of expression cannot be directly correlated with sequence changes in the highly conserved Upstream Sequence Element (USE) required for expression of Arabidopsis UsnRNA genes nor with differential stability of the U5snRNA transcripts. Further sequence elements may therefore have a role in regulating maize UsnRNA gene expression.

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.

Compilation of small RNA sequences

This is an update containing small RNA sequences published during 1991. Approximately two hundred small RNA sequences are available in this and earlier compilations. The hard copy print out of this set will be available directly from us (inquiries should be addressed to R. Reddy). These files are also available on GenBank computer. Sequences from various sources covered in earlier compilations (see Reddy, R. Nucl. Acids Res. 16:r71; Reddy, R. and Gupta, S. Nucl Acids Res. 1990 Supplement, 18:2231 and 1991 Supplement, 19:2073) are not included in this update but are listed below.

Cloning and characterisation of a U6 small nuclear RNA gene from potato

Using a mixed U6 snRNA gene probe and a low stringency hybridization procedure we have isolated a U6 snRNA containing clone from a potato genomic library in lambda EMBL 3. This clone contains a single U6 snRNA gene which has been subcloned and sequenced. Southern blotting experiments using this gene and the heterologous U6 genes as probes indicate that the potato U6 gene family consists of more than 20 members. The potato U6 gene sequence shows high identity to previously characterised plant U6 snRNA gene sequences and possesses correctly positioned and spaced transcription control elements suggesting that it is an active gene.

Sequence variation and linkage of potato U2snRNA-encoding genes established by PCR

Plant uridylate-rich small nuclear RNA (UsnRNA)-encoding genes (UsnRNA) are present as multigene families exhibiting greater sequence variation than has been described in animal UsnRNA families. The potato U2snRNA multigene family has 25 to 40 potential gene members. Four gene variants have been analysed to date, two of which are linked. In order to investigate U2snRNA expression in potato in terms of the function of such sequence variation in development, the degree of sequence variation in both the coding region and flanking regions in this gene family must be assessed. On the assumption that at least some U2snRNA genes are linked, a polymerase chain reaction (PCR) approach, using primers designed to amplify intergenic nucleotide sequences including coding and 5' flanking regions, has been devised. Six new U2snRNA gene variant sequences and one U2snRNA pseudogene sequence have been generated. In addition, six new flanking region sequences have been produced which, in contrast to other plant UsnRNA gene families, show considerable variation in the important upstream sequence element. This PCR approach may be applicable to the analysis of genomic organisation and sequence variation of other multigene families.

Evolutionary conservation of the spliceosomal protein, U2B''

U1 and U2snRNPs play key roles in pre-mRNA splicing. The interactions between the U1 and U2snRNP-specific proteins, U1A, U2A' and U2B'' and their respective UsnRNAs are of interest both to elucidate their roles in splicing, and as models to study RNA-protein interactions. We have cloned a full-length cDNA, encoding U2B'', from potato. This is the first report of a sequence for a plant UsnRNP protein. The plant U2B'' sequence exhibits extensive similarity with the human U2B'' protein at both the DNA and amino acid levels. The evolutionary conservation at the protein level, particularly in sequences implicated in determining specific binding to U2snRNA, suggests conservation of U2B'' function from plants to man. The significance of amino acid substitutions in the RNP-80 motif with respect to U2snRNA binding in plants is discussed.