Characterization of precursors to tRNA in yeast

Repression of ribosome and tRNA synthesis in secretion-defective cells is signaled by a novel branch of the cell integrity pathway

The transcription of ribosomal DNA, ribosomal protein (RP) genes, and 5S and tRNA genes by RNA polymerases (Pols) I, II, and III, respectively, is rapidly and coordinately repressed upon interruption of the secretory pathway in Saccharomyces cerevisiae. We find that repression of ribosome and tRNA synthesis in secretion-defective cells involves activation of the cell integrity pathway. Transcriptional repression requires the upstream components of this pathway, including the Wsc family of putative plasma membrane sensors and protein kinase C (PKC), but not the downstream Bck1-Mkk1/2-Slt2 mitogen-activated protein kinase cascade. These findings reveal a novel PKC effector pathway that controls more than 85% of nuclear transcription. It is proposed that the coordination of ribosome and tRNA synthesis with cell growth may be achieved, in part, by monitoring the turgor pressure of the cell.

The use of a synthetic tRNA gene as a novel approach to study in vivo transcription and chromatin structure in yeast

To monitor in vivo transcription and chromatin structure of yeast tRNA genes, we constructed a synthetic tRNA gene that can be used as a reporter. Constructs in which this synthetic tRNA gene is combined with different flanking regions can be integrated into the genome as single copies. The artificial tRNA gene is tagged by the insertion of an intron-like sequence that cannot be spliced out from the precursor and transcripts can thus be identified and quantitated. By several criteria, the artificial tRNA gene behaves like a resident tRNA gene. By measuring the accessibility towards DNaseI in chromatin, we found that the artificial tRNA gene exhibits the same characteristic pattern as resident tRNA genes. Three DNaseI-sensitive sites across the transcribed part of the gene and the immediate flanking regions reflect the formation of the stable transcription complex; positioned nucleosomes are observed in the upstream flanking region. We are confident that the system we have established will prove useful for studying regulatory aspects of tRNA gene expression as well as aspects of pre-tRNA processing and splicing.

In vivo pre-tRNA processing in Saccharomyces cerevisiae

We have surveyed intron-containing RNAs of the yeast Saccharomyces cerevisiae by filter hybridization with pre-tRNA intron-specific oligonucleotide probes. We have classified various RNAs as pre-tRNAs, splicing intermediates, or excised intron products according to apparent size and structure. Linear, excised intron products were detected, and one example was isolated and sequenced directly. Additional probes designed to detect other precursor sequences were used to verify the identification of several intermediates. Pre-tRNA species with both 5' leader and 3' extension, with 3' extension only, and with mature ends were distinguished. From these results, we conclude that the processing reactions used to remove the 5' leader and 3' extension from the transcript are ordered 5' end trimming before 3' end trimming. Splicing intermediates containing the 5' exon plus the intron were detected. The splice site cleavage reactions are probably ordered 3' splice site cleavage before 5' splice site cleavage. Surprisingly, we also detected a splicing intermediate with the 5' leader and a spliced product with both 5' leader and 3' extension. Evidently, splicing and end trimming are not ordered relative to each other, splicing occurring either before or after end trimming.

In vivo pre-tRNA processing in Saccharomyces cerevisiae

We have surveyed intron-containing RNAs of the yeast Saccharomyces cerevisiae by filter hybridization with pre-tRNA intron-specific oligonucleotide probes. We have classified various RNAs as pre-tRNAs, splicing intermediates, or excised intron products according to apparent size and structure. Linear, excised intron products were detected, and one example was isolated and sequenced directly. Additional probes designed to detect other precursor sequences were used to verify the identification of several intermediates. Pre-tRNA species with both 5' leader and 3' extension, with 3' extension only, and with mature ends were distinguished. From these results, we conclude that the processing reactions used to remove the 5' leader and 3' extension from the transcript are ordered 5' end trimming before 3' end trimming. Splicing intermediates containing the 5' exon plus the intron were detected. The splice site cleavage reactions are probably ordered 3' splice site cleavage before 5' splice site cleavage. Surprisingly, we also detected a splicing intermediate with the 5' leader and a spliced product with both 5' leader and 3' extension. Evidently, splicing and end trimming are not ordered relative to each other, splicing occurring either before or after end trimming.

Axoplasmic transport of transfer RNA in the chick optic system

It has previously been shown that 4S RNA is transported in the optic nerve of the chick, but that no movement of rRNA can be detected. The 4S component behaved as though it were composed mainly of transfer RNA (tRNA), but the possibility remained that it could contain significant amounts of material resulting from RNA degradation. The transport of this 4S component has been examined in more detail to determine its nature. In addition, the transported material was examined to establish whether the transport of tRNA is a general phenomenon or that there are only a limited number of species involved. This was done using the same principles applied in the previous study; i.e., the specific activities of separated 4S RNA species appearing in the optic tectum 4 days after intraocular injection of [3H]uridine were compared with that of 5S RNA, a nontransported species. The separation was accomplished using 2.8-5-10-17% slab polyacrylamide gels, and 18 separate regions of 4S species could be identified. The results show that at least most, if not all 4S RNA species are transported. In a separate series of experiments the 4S RNA was aminoacylated and again separated on slab gels. In this instance, the RNA was labelled with [3H]uridine and the aminoacyl component with [14C]amino acids. Gel profiles of these dual-labelled components showed excellent correspondence between the two labels, demonstrating that 4S RNA species could be aminoacylated and were therefore tRNA species.(ABSTRACT TRUNCATED AT 250 WORDS)

The genes coding for tRNA Tyr of Drosophila melanogaster: localization of determination of the gene numbers

Transfer RNA(Tyr) (anticodon G psi A) was isolated from Drosophila melanogaster by means of Sepharose 4B, RPC-5, and polyacrylamide gel electrophoresis. The rRNA was iodinated in vitro with Na125 I and hybridized in situ to salivary gland chromosomes from Drosophila. The genes of rRNA(Tyr) were localized in eight regions of the genome by autoradiography. Restriction enzyme analysis of genomic DNA indicated that the haploid Drosophila genome codes for about 23 tRNA(Tyr) genes. The regions 22F and 85A each contain four to five tRNA(Tyr) genes, whereas the regions 28C, 41AB, 42A, 42E, and 56D each contain two to three tRNA(Tyr) genes.

The localization of tRNA5Asn, tRNAHis, and tRNAAla genes from drosophila melanogaster by in situ hybridization to polytene salivary gland chromosomes

Transfer RNA5 gammaAsn, tRNA gamma His, and tRNAAla were isolated from Drosophila melanogaster by means of Sepharose 4B chromatography and 2-dimensional polyacrylamide gel electrophoresis. The tRNAs were iodinated in vitro with Na125I and hybridized in situ salivary gland chromosomes from Drosophila. Subsequent autoradiography allowed the localization of the genes for tRNA 5 gammaAsn in the regions 42A, 59F, 60C, and 84F; for tRNAHis in the regions 48F and 56E; and for tRNAAla in the regions 63A and 90C. From these and our previous results it can be concluded that the genes for the Q-base containing tRNAs (tRNAAsn, tRNAAsp, and tRNAHis, are not clustered in the Drosophila melanogaster genome.

The localization of tRNAAsp2 genes from Drosophila melanogaster by "in situ" hybridization

Transfer RNAAsp2delta was isolated from Drosophila melanogaster by affinity chromatography on concanavalin A-Sepharose. The tRNA was iodinated "in vitro" with Na [125I] and hybridized "in situ" to salivary gland chromosomes from Drosophila. Subsequent autoradiography allowed the localization of the genes for tRNAAsp2 to the left arm of the second chromosome in the regions 29 D and E.

Transcription and processing of intervening sequences in yeast tRNA genes

Genes for yeast tRNATyr and tRNAPhe have been sequenced (Goodman, Olson and Hall, 1977; Valenzuela et al., 1978) which contain additional nucleotides (intervening sequences) within the middle of the gene that are not present in the mature tRNA. We have isolated precursors to rRNATyr and tRNAPhe from a yeast temperature-sensitive mutant (at the rna1 locus) which accumulates only certain precursor tRNAs at the nonpermissive temperature. The tRNATyr and tRNAPhe precursors were analyzed by oligonucleotide mapping; they each contain the intervening sequence and fully matured 5' and 3' termini. Furthermore, these precursors were used as substrates to search for an enzymatic activity which can remove the intervening sequences and religate the ends. We have shown that wild-type yeast contains such an activity, and that this activity specifically removes the intervening sequences to produce mature-sized RNAs.

A yeast mutant which accumulates precursor tRNAs

It has been proposed that the conditional yeast mutant ts136 is defective in the transport of mRNA from the nucleus to the cytoplasm (Hutchinson, Hartwell and McLaughlin, 1969). We have examined ts136 to determine whether it is defective in tRNA biosynthesis. At the restrictive temperature, the mutant accumulates twelve new species of RNA. These species co-migrate on polyacrylamide gels with some of the pulse-labeled precursor tRNAs. Three of the new RNAs (species 1a, 1b and 1c are large enough to contain two tandom tRNAs. Although RNAs 1a, 1b, and 1c do not contain detectable levels of modified and methylated bases, at least one of them hybridizes to DNA from an E. coli plasmid containing a yeast tRNA gene. All the remaining RNAs (2--8) contain modified and methylated bases typical of tRNA. Three of these species were tested and were found to hybridize to tRNA genes. Ribosomal RNA synthesis is also defective in ts136. It is suggested that ts136 may be defective in a nucleolytic activity, which is a prerequisite to RNA transport.

Arangement of transfer-RNA -genes in yeast

The redundancy and the arrangement of the genes for specific transfer ribonucleic acids in yeast were studied by the hybridization techniques developed by Birnstiel et al., e.g.[1]. The redundancy was found to be in the order of 10 genes for tRNA1Met, tRNA3Met, tRNA2Ser, and tRNA-Pro. High molecular weight yeast DNA was fractionated by density gradient centrifugation in cesium chloride and the [32p]tRNAs were hybridized to the single fractions. The results together with earlier findings [2] suggest that the cistrons for these tRNAs are arranged in tandem interspersed by 6 to 10 times longer segments of spacer DNA which varies in (G+C) content for the different tRNA species.

The primary structure of a non-initiating methionine-specific tRNA from brewer's yeast

tRNA3Met, one of the non-initiating methionine-specific tRNAs in brewer's yeast was purified from bulk tRNA labelled with [32P]phosphate by two column chromatographic steps. The primary structure of this tRNA was determined by the usual fingerprinting technique. Analyses of the isolated nucleotides and oligonucleotides from digests with pancreatic and T1 ribonucleases were in good agreement and stated that tRNA3Met consists of 76 nucleotide residues including 13 minor nucleotides. Overlaps from which the complete sequence could be deduced were derived from the analyses of 15 fragments obtained by partial digestion with T1 ribonuclease.

Detailed analysis of the ribosomal RNA synthesis in yeast

In order to study the biosynthesis of ribosomal RNA in Saccharomyces carlsbergensis the labelling kinetics of the various precursor and mature rRNA species were determined using pulse-labelling of protoplasts with [5-3H] uridine at 15 degrees C. Label appears almost immediately in 37 S RNA, the precursor common to both 26 S and 17 S rRNA. Labelled 29 S and 18 S RNA, the immediate precursors of 26 S and 17 S rRNA respectively, were found to appear about 4 min and about 8 min after addition of the isotope respectively. These data indicate that the topography of the 37 S precursor RNA is: 5'-17 S -26 S-3'. The pool size of 29 S RNA is about twice as large as that of either 37 S or 18 S RNA, indicating that under the conditions used processing of 18 S to 17 S rRNA proceeds more rapidly than processing of 29 S to 26 S rRNA. The labelling kinetics of 5.8 S rRNA are in agreement with the existence of a 7 S precursor rRNA, the identity of which was previously established (Trapman, J., de Jonge, P. and Planta, R.J. (1975) FEBS Lett. 57, 26--30) and which, in turn, probably is derived from 29 S precursor rRNA. The labelling kinetics of 5 S rRNA suggest that 5 S RNA sequences, rather than also being part of the common 37 S precursor, are located on a separate primary transcription product. Whether this transcript still contains excess sequences remains to be determined. However, because of the rapid appearance of labelled 5 S RNA, such a precursor would have to be very short lived.

Number of genes and base composition of mitochondrial tRNA from Saccharomyces cerevisiae

Increasing amounts of mitochondrial [32P] tRNA (4S fraction), were hybridized with mitochondrial DNA OF Saccharomyces cerevisiae. At saturation, the calculated number of genes for 4S mitochondrial RNA was 20. Mitochondrial [32P] tRNA eluted from the hydrids obtained either with an excess of tRNA or an excess of DNA showed, after alkaline hydrolysis and chromatography, a G+C content of 28 and 35 p. cent respectively. This last value is similar to that found with the total 4S fraction. The odd nucleotides T (about 1T per sequence), U, hU are present in mitochondrial tRNA. Some sequence may begin with pG.

tRNAs undermethylation in a met-regulatory mutant of Saccharomyces cerevisiae

A study of in vivo and in vitro methylation of tRNAs in regulatory mutants affected in methionine-mediated repression (eth2, eth3, eth10) has led to the following results: 1) The eth2-2 carrying strain presents a great undermethylation of its tRNAs of the same order of magnitude as observed during methionine starvation of methionine auxotrophs. 2) This undermethylation leads to a shift of the tRNAIII met peak on a BD cellulose column, while tRNAIII met peak is unchanged. 3) The study of a double mutant strain carrying eth2 and met2 mutations has shown that this undermethylation is a consequence of the high internal pool of methionine. 4) Undermethylation unequally affects the different bases and the different tRNA species.