Aberrant splicing of Drosophila alcohol dehydrogenase transcripts in Saccharomyces cerevisiae

Plant pre-mRNA splicing in fission yeast, Schizosaccharomyces pombe

Pre-mRNA splicing or the removal of introns from precursor messenger RNAs depends on the accurate recognition of intron sequences by the splicing machinery. We have analyzed various aspects of intron sequence and structure in relation to splice site selection and splicing efficiency of a plant gene AmA1 in Schizosaccharomyces pombe. Earlier, we reported the cloning of AmA1, a seed albumin gene from Amaranthus hypochondriacus [A. Raina, A. Datta, Proc. Natl. Acad. Sci. USA 89 (1992) 11774]. In the absence of an in vitro splicing system for plants, the expression of AmA1 genomic clone in S. pombe has been used to analyze splicing of intron constructs. We aim to focus on S. pombe as a possible alternative and examined its effectiveness as a host for plant gene splicing. The results show here that pre-mRNA transcripts of AmA1 gene underwent splicing in S. pombe.

Analysis of Pneumocystis carinii introns

Pneumocystis carinii is an ascomycete phylogenetically related to Schizosaccharomyces pombe. Little is known about gene regulation in P. carinii. The removal of introns from pre-mRNA requires spliceosomal recognition of the intron-exon boundary. In S. pombe and higher eukaryotes, this boundary and a branch site within the intron are conserved. We recently demonstrated that P. carinii cdc2 cDNA can complement S. pombe containing conditional mutations of cdc2, an essential gene involved in cell cycle regulation. We next tested whether P. carinii genomic cdc2 (with six introns) could also complement S. pombe cdc2 mutants and found genomic sequences incapable of this activity. Reverse transcriptase PCR confirmed the inability of the S. pombe cdc2 mutants to splice the P. carinii genomic cdc2. Analysis of 83 introns from 19 P. carinii protein-encoding genes demonstrated that the sequence GTWWDW functions as a donor consensus in P. carinii, whereas YAG serves as an acceptor consensus. These sequences are similar in S. pombe; however, a branch site sequence was not found in the P. carinii genes studied.

Synthesis of Drosophila melanogaster alcohol dehydrogenase in yeast

Expression systems for the heterologous expression of Drosophila melanogaster alcohol dehydrogenase (ADH) in Saccharomyces cerevisiae have been designed, analyzed and compared. Four different yeast/Escherichia coli shuttle vectors were constructed and used to transform four different yeast strains. Expression was detectable in ADH- yeast strains, from either a constitutive promoter, yeast ADH1 promoter (ADCp), or a regulated promoter, yeast GALp. The highest amount of D. melanogaster ADH was obtained from a multicopy plasmid with the D. melanogaster Adh gene expressed constitutively under the control of yeast ADCp promoter. The D. melanogaster enzyme was produced in cell extracts, as assessed by Coomassie blue staining and Western blotting after polyacrylamide-gel electrophoresis and it was fully active and able to complement the yeast ADH deficiency. Results show that D. melanogaster ADH subunits synthesized in yeast are able to assemble into functional dimeric forms. The synthesized D. melanogaster ADH represents up to 3.5% of the total extracted yeast protein.

An intron in the genes for U3 small nucleolar RNAs of the yeast Saccharomyces cerevisiae

The origin of the intervening sequences (introns), which are removed during RNA maturation, is currently unknown. They are found in most genes encoding messenger RNAs, but are lacking in almost all small nuclear (sn)RNAs. One exceptional snRNA (U6) is part of the spliceosomal machinery that is involved in messenger RNA maturation. It has been suggested that its intron arose as a result of incorrect splicing of a messenger RNA precursor. This study revealed the presence of an intron, with the characteristic features of nuclear introns from precursors to messenger RNA, in the two genes coding for Saccharomyces cerevisiae U3 snRNA. The branch point was GACTAAC instead of the TACTAAC sequence found in all yeast introns examined so far. As U3 is a nucleolar snRNA required for maturation of ribosomal RNA, its intron could not have been acquired from aberrant messenger RNA processing in a spliceosome.

The evolutionary conservation of eukaryotic gene transcription

The basic components required for eukaryotic gene transcription have been highly conserved in evolution. Structural and functional homology has now been documented among promoters, promoter factors, regulatory proteins, and RNA polymerases from eukaryotes as diverse as yeast and mammals. The ability of these proteins and DNA sequences to function across phylogenetic boundaries demonstrates that common molecular mechanisms underlie gene control in all eukaryotic cells, and provides the basis for powerful new approaches to the study of eukaryotic gene transcription.

The 5' splice site: phylogenetic evolution and variable geometry of association with U1RNA

The 5' splice site sequences of 3294 introns from various organisms (1-672) were analyzed in order to determine the rules governing evolution of this sequence, which may shed light on the mechanism of cleavage at the exon-intron junction. The data indicate that, currently, in all organisms, a common sequence 1GUAAG6U and its derivatives are used as well as an additional sequence and its derivatives, which differ in metazoa (G/1GUgAG6U), lower eucaryotes (1GUAxG6U) and higher plants (AG/1GU3A). They all partly resemble the prototype sequence AG/1GUAAG6U whose 8 contigous nucleotides are complementary to the nucleotides 4-11 of U1RNA, which are perfectly conserved in the course of phylogenetic evolution. Detailed examination of the data shows that U1RNA can recognize different parts of 5' splice sites. As a rule, either prototype nucleotides at position -2 and -1 or at positions 4, 5 or 6 or at positions 3-4 are dispensable provided that the stability of the U1RNA-5' splice site hybrid is conserved. On the basis of frequency of sequences, the optimal size of the hybridizable region is 5-7 nucleotides. Thus, the cleavage at the exon-intron junction seems to imply, first, that the 5' splice site is recognized by U1RNA according to a "variable geometry" program; second, that the precise cleavage site is determined by the conserved sequence of U1RNA since it occurs exactly opposite to the junction between nucleotides C9 and C10 of U1RNA. The variable geometry of the U1RNA-5' splice site association provides flexibility to the system and allows diversification in the course of phylogenetic evolution.

Synthesis of Saccharomyces cerevisiae invertase by Schizosaccharomyces pombe

In order to gain information on the ability of the glycosylation system of Schizosaccharomyces pombe to process heterologous glycoproteins, the expression of Saccharomyces cerevisiae invertase in the former yeast was studied. Sc. pombe cells are able to produce enzymatically active invertase from the S. cerevisiae SUC2 gene introduced by transformation and the enzyme is glycosylated and secreted into the cell wall. However, Sc. pombe transformants do not glycosylate the heterologous enzyme as their own invertase since it is not bound by the lectin from Bandeiraea simplicifolia seeds, which indicates the absence of terminal galactose residues. Moreover, the electrophoretic mobility of the heterologous invertase is similar to that of the large enzyme from S. cerevisiae, both in its native form and after being deglycosylated with Endo H. These results suggest that the polypeptide chain of S. cerevisiae invertase is the primary factor for the glycosylation in Sc. pombe cells.

Conserved putative signals in 3' intron junctions in rodents

Several 3' splice signals are known todate. At the 3' splice site an AG doublet is frequently found. Just upstream of the splice site there is a string of 6-11 pyrimidines. More recently it has been found that one of the stages in the splicing process involves formation of a lariat, in which the 5' end of the intron forms a 2'-5' branch with an A residue located 18-37 nucleotides upstream of the 3' splice site. The branching-point consensus is weakly defined and consists of the sequence YNYTRAY, where Y is a pyrimidine, R a purine and N any base. The A in the sixth position is the one with which branching occurs. Here we present the results of extensive searches for additional putative signals around the branching-point consensus and the 3' splice site in rodent nuclear precursor mRNAs. The signals obtained for the over 370 rodent introns are compared with those found in a larger eukaryotic sample containing over 900 nuclear pre-mRNA introns. Of particular interest are GGGA and CCCA. In both analyses GGGA occurs about 60 nucleotides upstream and CCCA is found 3-40 nucleotides downstream from the 3' splice site. A model explaining some of the putative signals discussed here is also proposed. This model involves formation of alternate stem-loop structures around the branching point and 3' splice site. Such signals and structures can possibly aid in protein or nucleoprotein branching point and splice site recognition.

The role of small nuclear ribonucleoprotein particles in pre-mRNA splicing

A small set of distinctive short RNA molecules are found in the nuclei of all higher eukaryotic cells and yeast, in protein complexes known as 'small nuclear ribonucleoprotein particles', or snRNPs. Recent work has confirmed early suggestions that these particles form part of the machinery by which primary RNA transcripts are processed to their mature, functional form. In particular, snRNPs have been shown to be an integral part of the 'spliceosome', a multi-component complex involved in the removal of intron sequences from the coding regions of messenger RNA precursors.

Molecular characterisation of the DNA ligase gene, CDC17, from the fission yeast Schizosaccharomyces pombe

We have sequenced a 4200-base-pair fragment of Schizosaccharomyces pombe DNA which encompasses the entire DNA ligase gene, CDC17. S1 mapping has enabled us to identify two small introns (40 and 62 nucleotides) at the 5' end of the coding region of the gene and their 3' internal conserved sequences match the CTRAY consensus found in other S. pombe introns. The major transcription initiation and 3' polyadenylation sites have been mapped and are preceded by higher eukaryotic-like TATA and AATAAA sequences respectively. Furthermore, the CDC17 mRNA carries a poly(A) tail whose length (approximately 250 nucleotides) is typical of that found in higher eukaryotic mRNAs, and is in contrast to the much shorter polyadenylated sequences found for the mRNAs of the budding yeast, Saccharomyces cerevisiae. The deduced amino acid sequence of the S. pombe DNA ligase predicts a protein of 86182 daltons, and an overall 53% homology with the same enzyme from S. cerevisiae. In particular, a stretch of 24 amino acids with 100% sequence homology spans the putative ATP-binding region which is also conserved in T4 and T7 bacteriophage DNA ligases.

Splicing of plant pre-mRNAs in animal systems and vice versa

To investigate similarities and differences of pre-mRNA splicing between higher plants and animals, we tested whether pre-mRNAs of higher plants can be accurately spliced in animal systems, and whether an animal pre-mRNA can be spliced in plant cells. Pre-mRNAs of the maize bronze locus and oat phytochrome type 3 are accurately spliced with moderate efficiency in a human (HeLa cell) nuclear extract. The first intervening sequence (IVS1) of bean phaseolin pre-mRNA is not excised in the human nuclear extract, but is removed (although at low efficiency) in intact monkey cells. However, the IVS1 of human alpha-globin pre-mRNA is not removed in tobacco cells. Our data suggest that the mechanisms of pre-mRNA splicing are similar, but not identical, in plants and animals.

Expression of polyoma virus middle-T antigen in Saccharomyces cerevisiae

The polyoma middle-T gene, lacking its intron, was inserted into a yeast expression plasmid containing the phosphoglycerate kinase promoter. Such plasmids transformed yeast at low frequency and these transformants expressed middle-T antigen at a level of approximately 0.1% cell protein. Furthermore, expression of this protein was frequently lost during growth in liquid culture and this loss of middle-T was accompanied by a twofold increase in the rate of growth. The spontaneous production of a truncated middle-T antigen, lacking the C terminus, was also observed; the expression of this protein did not inhibit the growth rate of the cells. Recovery and analysis of the expression plasmids encoding the truncated molecule showed that a single C X G base pair had been deleted from a run of nine consecutive C X G base pairs (Pyr nucleotide 1239--1247) within the middle-T coding region. This frame-shift mutation results in premature termination of the protein and loss of the strongly hydrophobic region of the molecule believed to be responsible for the membrane association of middle-T antigen.

Fission yeast Schizosaccharomyces pombe correctly excises a mammalian RNA transcript intervening sequence

Study of heterologous gene expression in the budding yeast Saccharomyces cerevisiae has shown that this organism is incapable of correctly removing intervening sequences from transcripts of higher eukaryotic genes. This is probably due to the stringent requirement for the presence of a TACTAAC box close to the 3' end of the intervening sequence if splicing in S. cerevisiae is to occur. Comparison of the introns found in the fission yeast Schizosaccharomyces pombe has identified conserved sequences similar to those found in higher eukaryotes. Therefore, we have investigated whether Schiz. pombe is capable of accurately excising intervening sequences from the transcripts of higher eukarotic genes. We show here that both the 5' and 3' splice sites of the simian virus 40 (SV40) small-T antigen transcript are accurately utilized when cloned viral DNA is expressed in Schiz. pombe cells. These data suggest that Schiz. pombe may be a better model system than S. cerevisiae for the genetic study of RNA splicing and for expressing higher eukaryotic genes.

Point mutations identify the conserved, intron-contained TACTAAC box as an essential splicing signal sequence in yeast

Our previous deletion experiments have shown that a short region of yeast nuclear gene introns containing the conserved sequence 5'-TACTAACA-3' is essential for splicing. In this report we show that the chemically synthesized decanucleotide 5'-TGTACTAACA-3', when introduced into a hybrid gene forming unspliceable RNA molecules, results in the generation of spliceable transcripts. Single A----C transversions in the fourth or eighth position of this sequence eliminated its intron-generating capacity. The C----T transition in the fifth position, generated by sodium bisulphite mutagenesis, did not affect the efficiency and accuracy of splicing. These results clearly demonstrate the biological significance of this conserved intron sequence and shed further light on its possible functioning.