Nonsense suppression in Schizosaccharomyces pombe: the S. pombe Sup3-e tRNASerUGA gene is active in S. cerevisiae

The gene encoding the efficient UGA suppressor sup3-e of Schizosaccharomyces pombe was isolated by in vivo transformation of Saccharomyces cerevisiae UGA mutants with S. pombe sup3-e DNA. DNA from a clone bank of EcoRI fragments from a S. pombe sup3-e strain in the hybrid yeast vector YRp17 was used to transform the S. cerevisiae multiple auxotroph his4-260 leu2-2 trp1-1 to prototrophy. Transformants were isolated at a low frequency; they lost the ability to grow in minimal medium after passaging in non-selective media. This suggested the presence of the suppressor gene on the non-integrative plasmid. Plasmid DNA, isolated from the transformed S. cerevisiae cells and subsequently amplified in E. coli, transformed S. cerevisiae his4-260 leu2-2 trp1-1 to prototrophy. In this way a 2.4 kb S. pombe DNA fragment carrying the sup3-e gene was isolated. Sequence analysis revealed the presence of two tRNA coding regions separated by a spacer of only seven nucleotides. The sup3-e tRNASerUGA tRNA gene is followed by a sequence coding for the initiator tRNAMet. The transformation results demonstrate that the cloned S. pombe UGA suppressor is active in S. cerevisiae UGA mutant strains.

Post-transcriptional nucleotide addition is responsible for the formation of the 5' terminus of histidine tRNA

All sequenced histidine tRNAs have one additional nucleotide at the 5' end when compared to other tRNA species. Sequence analysis of histidine tRNA genes from Drosophila melanogaster and Schizosaccharomyces pombe showed that the terminal guanylate residue of the mature tRNAs is not encoded by the genes. Analysis of the products from in vitro transcription of these genes in extracts from Drosophila Kc cells demonstrated that the 5'-terminal nucleotide present in the mature tRNA is added post-transcriptionally. The addition reaction requires ATP. A portion of the mature tRNAs are then modified at the 5'-terminal pG. Analysis of the RNA species formed during the in vitro maturation of the Drosophila histidine tRNA primary transcript uncovered the following maturation scheme: (i) the primary transcript is processed by RNase P at the 5' end to form an intermediate precursor; (ii) the 3'-flanking sequence is endonucleolytically removed, and a guanylate moiety is added to the 5' end to form mature-sized histidine tRNA; and (iii) a fraction of the 5'-terminal guanylate residues then undergoes modification. In contrast to the capping of eukaryotic mRNA, the guanylate addition to histidine tRNA results in the formation of a (3'-5')-phosphodiester bond. There are no precedents for the post-transcriptional addition of nucleotides (in phosphodiester linkage) to the 5' end of RNA precursors.

E. coli initiator tRNA analogs with different nucleotides in the discriminator base position

The effect of base changes at the fourth position from the 3'-terminus of Escherichia coli initiator tRNAMet has been studied to test the 'discriminator hypothesis' which proposed that the nucleotide in this position might have a role in the specificity of the aminoacylation reaction. E. coli initiator tRNA lacking the 3'-terminal tetranucleotide was prepared by partial digestion with S1 nuclease. To construct tRNA analogs with different bases in the fourth position this truncated tRNA was joined by RNA ligase to each of four chemically synthesized 2',3'-ethoxy-methylidene tetranucleotides pACCA(em), pCCCA(em), pGCCA(em), and pUCCA(em). In vitro aminoacylation studies showed that all four molecules accepted methionine, albeit with different Vmax values.

Genes for tRNALys5 from Drosophila melanogaster

The sequences of two cloned genes from Drosophila which hybridize with tRNALys5 are reported. One gene, in plasmid pDt39, has a sequence which corresponds to the sequence of tRNA. The other gene, in pDt59R, differs in three nucleotides pairs. Both plasmids are transcribed in vitro with extracts of Drosophila Kc cells to give full-sized tRNA precursors with four additional nucleotides at the 5'-end as well as truncated molecules containing 35 nucleotides. This premature termination occurs in a block of four T residues within the mature coding region. Sequences flanking the tRNA genes show little in common except for the blocks of five or more T-residues beyond the 3'-end of the gene. pDt39 hybridizes to 84AB on the polytene chromosomes of Drosophila and pDt59R hybridizes to 29A.

Escherichia coli glutaminyl-tRNA synthetase. II. Characterization of the glnS gene product

Glutaminyl-tRNA synthetase has been purified by a simple, two-column procedure from an Escherichia coli K12 strain carrying the glnS structural gene on plasmid pBR322. The primary sequence of this enzyme as derived from the DNA sequence (see accompanying paper) has been confirmed. Manual Edman degradation was used to identify the NH2-terminal sequence of the protein. Oligopeptides scattered throughout the primary sequence of glutaminyl-tRNA synthetase were sequenced by the gas chromatographic-mass spectrometric method and matched to the theoretical peptides derived from the translated DNA sequence. The expected carboxyl terminus at position 550 was verified by carboxypeptidase B digestion. The primary sequence of glutaminyl-tRNA synthetase contains no extensive sequence repeats. A search was made for sequence homologies between this enzyme and the few other aminoacyl-tRNA synthetases for which primary sequences are available. A single homologous region is shared by at least three of the synthetases examined here.

Escherichia coli glutaminyl-tRNA synthetase. I. Isolation and DNA sequence of the glnS gene

We have isolated a lambda-transducing phage carrying the gene (glnS) for Escherichia coli glutaminyl-tRNA synthetase. The location of the glnS gene within the 13.5-kilobase E. coli DNA transducing fragment was determined by genetic means. The glnS gene was recloned into plasmid pBR322 and its nucleotide sequence was established. The DNA sequence translates to a protein of 550 amino acids.

The minimum intragenic sequences required for promotion of eukaryotic tRNA gene transcription

Transcription of eukaryotic tRNA genes is controlled by two intragenic regions, the D-control region (which in the tRNA codes for the D-stem and -loop) and the T-control region (which in the tRNA codes for the T psi C loop). To determine whether these sequences alone are sufficient to promote tRNA gene transcription in vitro, the two control regions of a Drosophila tRNAArg gene were cloned separately from the context of the parental DNA (these constructions are called tRNA minigenes). The tRNA minigene that contains both intragenic control regions supports in vitro RNA synthesis in Xenopus laevis oocyte and HeLa cell transcription systems. The mutant which has deletions to nucleotide 7 within the mature tRNA coding region, pArg5.7, and minigenes derived from it do not support RNA synthesis in a Drosophila Kc cell transcription system. Xenopus and Hela extracts transcribe pArg5.7 albeit at reduced levels compared to the wild-type gene. The tRNA minigene that contained only the D-control region was not able to support RNA synthesis in any of these three transcription systems. A mutant tRNA gene comprising the 3' half of the tRNAArg gene similarly was not able to support RNA synthesis. These experiments show that the DNA sequence from nucleotides 7-58, which contains both intragenic control regions of the tRNA gene, possesses sufficient information to initiate specific transcription by RNA polymerase III in Xenopus and HeLa systems. The transcription efficiency of this tRNA minigene however is reduced to about 20% the transcription level of the wild type tRNA gene. This lowered level of transcriptional efficiency results from deleting the ends of the native tRNA gene and its adjacent flanking sequences. The affects of deleting 5' sequences are most pronounced in the Drosophila transcription system.

The 5.8S RNA gene sequence and the ribosomal repeat of Schizosaccharomyces pombe

We have characterized the rRNA gene repeat in Schizosaccharomyces pombe. This repeat, which does not contain the 5S RNA gene, is found in a 10.4 kb HindIII DNA fragment. We have determined the nucleotide sequences of the S. pombe 5.8S RNA gene and intergenic spacers from two different 10.4 kb DNA fragments. Analysis of isolated total cellular 5.8S RNA revealed the presence of eight species of 5.8S RNA, differing in the number of nucleotides at the 5'-end. The eight 4.8S RNA species vary in length from 158 to 165 nucleotides. Apart from the heterogeneity observed at the 5'-end, the sequence of the eight 5.8S RNA species appears to be identical and is the same sequence as coded for by the 5.8S genes. The gene sequence shows great homology to the 5.8S RNA genes or S. cerevisiae and N. crassa. Most of the base differences are confined to the highly variable stem though to be involved in co-axial helix stacking with the 25S RNA, where base pairing is nearly identical despite the sequence differences. Secondary structure models are examined in light of 5.8S RNA oligonucleotide conservation across species from yeasts to higher eukaryotes.

The 5S RNA genes of Schizosaccharomyces pombe

The genomic arrangement and sequences of S. pombe 5S RNA genes are reported here. The 5S gene sequences appear to be dispersed within the genome, and are found independently of other rRNA genes. The sequences of two 5S genes examined show identical coding regions of 119 base pairs but have widely varying flanking sequences. A tRNAAsp gene is found in the 3' flanking region of one of the 5S genes. The tRNAAsp gene is faithfully transcribed in an X. laevis in vitro system, while the 5S genes are not transcribed in this system. The phylogenetic position of S. pombe is examined through comparison of 5S RNA sequences.

Identification of regulatory sequences contained in the 5'-flanking region of Drosophila lysine tRNA2 genes

Transcription of Drosophila tRNA genes is controlled by signals within and outside the region coding for the mature tRNA. Deletion analysis has revealed an oligonucleotide sequence in the 5'-flanking region of a Drosophila tRNA2Lys gene to be responsible for the poor transcriptional activity of this and of other tRNA genes. The low template activity of this gene was maintained even after deletion of the 5'-flanking region up to nucleotide -23. Removal of nine additional nucleotides resulted in complete loss of transcriptional repression. The oligonucleotide responsible for transcriptional repression is GGCAGTTTTTG and is located 13 nucleotides upstream from the mature tRNA coding sequence. Since the sequence of the undecanucleotide is well conserved within the 5'-flanking region of all known Drosophila tRNA2Lys genes, we have investigated why the transcription of all these genes is not similarly repressed. Deletion or insertion of nucleotides between the mature tRNA coding region and this oligonucleotide resulted in tRNA genes with increased template activity. This observation suggests that the position of this oligonucleotide relative to some element downstream influences the extent of transcriptional repression.

The initiator tRNA genes of Drosophila melanogaster: evidence for a tRNA pseudogene

We have isolated four segments of Drosophila melanogaster DNA that hybridize to homologous initiator tRNAMet. Three of the cloned fragments contain initiator tRNA genes, each of which can be transcribed in vitro. The fourth clone, pPW568, contains an initiator tRNA pseudogene which is not transcribed in vitro by RNA polymerase III. The pseudogene is contained in a 1.15 kb DNA fragment. This fragment has the characteristics of dispersed repetitive DNA and hybridizes in situ to at least 30 sites in the Drosophila genome. The arrangement of the initiator tRNA genes we have isolated, is different to that of other Drosophila tRNA gene families. The initiator tRNA genes are not clustered nor intermingled with other tRNA genes. They occur as single copies within an approximately 415-bp repeat segment, which is separated from other initiator tRNA genes by a mean distance of 17 kb. In situ hybridization to polytene chromosomes localizes these genes to the 61D region of the Drosophila genome. Hybridization analysis of genomic DNA indicates the presence of 8-9 non-allelic initiator tRNA genes in Drosophila melanogaster.

Internal control regions for transcription of eukaryotic tRNA genes

We have identified the region within a eukaryotic tRNA gene required for initiation of transcription. These results were obtained by systematically constructing deletions extending from the 5' or the 3' flanking regions into a cloned Drosophila tRNAArg gene by using nuclease BAL 31. The ability of the newly generated deletion clones to direct the in vitro synthesis of tRNA precursors was measured in transcription systems from Xenopus laevis oocytes, Drosophila Kc cells, and HeLa cells. Two control regions within the coding sequence were identified. The first was essential for transcription and was contained between nucleotides 8 and 25 of the mature tRNA sequence. Genes devoid of the second control region, which was contained between nucleotides 50 and 58 of the mature tRNA sequence, could be transcribed but with reduced efficiency. Thus, the promoter regions within a tRNA gene encode the tRNA sequences of the D stem and D loop, the invariant uridine at position 8, and the semi-invariant G-T-psi-C sequence.

Transcription of cloned tRNA and 5S RNA genes in a Drosophila cell free extract

We describe the preparation of a cell-free extract from Drosophila Kc cells which allows transcription of a variety of cloned eukaryotic RNA polymerase III genes. The extract has low RNA-processing nuclease activity and thus the major products obtained are primary transcripts.

Partial purification of RNase P from Schizosaccharomyces pombe

Ribonuclease P from the fission yeast Schizosaccharomyces pombe was partially purified using DEAE-cellulose and phosphocellulose column chromatography. The yeast RNase P enzyme cleaves Escherichia coli tRNATyr precursor to give tRNATyr containing its mature 5' end. The enzyme activity is inhibited after treatment with nucleases; this indicates the requirement of a nucleic acid component for activity. The enzyme purification was greatly facilitated by using a synthetically prepared radioactive ApApApCOH ligated to the 5'-terminal phosphate of E. coli tRNAfMet (ApApApCp-tRNA) substrate. (p denotes a [32P]phosphate group.) This substrate was cleaved by yeast RNase P to the mature tRNA and a tetranucleoside triphosphate ApApApCOH. The synthetic substrate allowed the utilization of a simple assay procedure measuring the trichloroacetic acid solubility of the ApApApC product, thus avoiding the more cumbersome gel electrophoric separation of reaction products.

A conversational system for the computer analysis of nucleic acid sequences

We present a conversational system for the computer analysis of nucleic acid and protein sequences based on the well-known Queen and Korn program (1). The system can be used by persons with only minimal knowledge of computers.

Dimeric tRNA precursors in yeast

Two DNA fragments, each containing tRNA(Arg)3 and a tRNA(Asp) gene in close conjunction, have been isolated from different genomic regions of Saccharomyces cerevisiae. Nucleotide Nucleotide sequence analysis of the gene regions revealed that in both fragments the tRNA(Arg)3 coding region is located 5'-proximal to the tRNA(Asp) coding region. They are separated by an identical spacer of 10 nucleotides. Although the 5'-flanking sequences are different in the two plasmids, some similarities are observed. To test the mode of expression of this gene configuration, we transcribed the DNA fragments in a Xenopus oocyte nuclear extract. Specific transcription of the yeast tRNA genes took place in an RNA precursor which comprised both tRNA species. We report here that the precursor RNA was processed to the mature-sized tRNA molecules, indicating the presence of an enzyme activity in the Xenopus nucleus capable of cutting a dimeric tRNA precursor. This is the first observation of a eukaryotic dimeric tRNA precursor.

Dimeric transfer RNA precursors in S. pombe

Sequence analysis of a Schizosaccharomyces pombe DNA fragment revealed two tRNA coding regions separated by a seven nucleotide spacer. the 5'-proximal tRNA gene encodes a tRNAUCGSer sequence, which is interrupted by a 16 nucleotide intron at the 3' side of the base adjacent to the anticodon. The second tRNA gene encodes an initiator tRNAMet sequence. This DNA fragment, cloned into pBR322, was used as template for in vitro transcription in a nuclear extract of Xenopus oocytes. The tRNA genes were transcribed into one RNA precursor which contained both tRNA sequences. The primary transcription product initiates with pppG, contains a 9 nucleotide leader sequence, a 16 nucleotide intron, a 7 nucleotide spacer between the two tRNA molecules and an 8--9 nucleotide trailer sequence. RNA initiation was only observed upstream of the 5'-proximal tRNASer. We used RNA analysis to establish a sequence of the enzymatic steps of tRNA maturation in the nuclear extract. The first step in processing the dimeric precursor is an endonuclease cleavage which generates the mature 5' end of the tRNAMet. Further steps include the removal of the flanking sequences and addition of the CCAOH 3' terminus. The last step is the splicing of the tRNASer precursor to remove the intervening sequence.