Arangement of transfer-RNA -genes in yeast

Putative frameshift suppressors in Schizosaccharomyces pombe

Nine genetically distinct suppressors of ICR-170-induced ade6 and ade7 mutations have been identified in Schizosaccharomyces pombe. The nine suppressors of ICR-170-induced and spontaneous origin have been assigned to the three chromosomes by haploidization and meiotic analysis. They do not suppress missense or nonsense mutations and are therefore likely to be frameshift suppressors. Based on the spectrum of suppression, the nine suppressors fall into two mutually exclusive groups. Group I comprises the two dominant suppressors sufl and suf11. Group II consists of the seven dominant suppressors suf2 through suf8. The suppressors of both groups are inefficient and all lead to a marked reduction of growth rate. Within suppressor groups, combinations of suppressors lead to drastic reductions of growth rates and to an increased efficiency of suppression. Freely segregating modifiers of suppression increasing and decreasing the efficiency of supression have been found for all the suppressors. The two omnipotent suppressors sup1 and sup2 increase the efficiency of suppression of some frameshift suppressors. The suf5 locus is unstable and reverts at very high frequency both meiotically and mitotically.

Sequencing the yeast genome: an international achievement

The yeast genome is currently being sequenced by a Consortium of European laboratories, in collaboration with a wider international network of researchers. It is expected that within the next two years Saccharomyces cerevisiae will become the first eukaryotic organism to have been completely genetically mapped and sequenced. This article traces the sequencing enterprise from its beginnings, outlining the intentions, the organisation, and the achievements so far. The tasks which remain are discussed, emphasising the follow-on research into the evolution of primitive karyotypes, and, more particularly, into the nature of novel genes revealed during sequencing. The functional analysis of novel genes is attracting an ever wider community of yeast scientists, so that research which began with a decision to sequence a simple genome promises to remain a focus for international cooperation.

The complete DNA sequence of yeast chromosome III

The entire DNA sequence of chromosome III of the yeast Saccharomyces cerevisiae has been determined. This is the first complete sequence analysis of an entire chromosome from any organism. The 315-kilobase sequence reveals 182 open reading frames for proteins longer than 100 amino acids, of which 37 correspond to known genes and 29 more show some similarity to sequences in databases. Of 55 new open reading frames analysed by gene disruption, three are essential genes; of 42 non-essential genes that were tested, 14 show some discernible effect on phenotype and the remaining 28 have no overt function.

tRNAGlu(GAA) genes from the cellular slime mold Dictyostelium discoideum

The haploid genome of the cellular slime mold Dictyostelium discoideum contains at least 18 gene copies coding for a tRNAGlu(GAA). Using a combination of parasexual genetic analysis and molecular biology techniques, 14 of the 18 individual members of this gene family could be assigned to particular linkage groups. According ot this analysis four tRNAGlu genes are located on group I (C, H, I, K), two genes on group II (D,J), seven genes on either group III or VI (A, B, E, F, L, M, N), and one gene on group VII (G). Eight of the tRNAGlu(GAA) genes have been cloned and characterized. All genes are identical in that part of the gene which corresponds to the mature tRNA, thus representing true nonallelic members of this gene family. Different members of this gene family can be distinguished from each other because they reside on restriction fragments of different lengths and because each gene contains unique 5'- and 3'-flanking regions. Nevertheless, a certain degree of sequence conservation within these flanking regions is apparent for members of this gene family. According to in vivo expression analyses of individual genes in Saccharomyces cerevisiae, all isolated tRNAGlu(GAA) copies represent functional transcription units.

The methionine initiator tRNA genes of yeast

We have isolated three distinct tRNAimet genes from a yeast DNA clone bank. The complete sequence of two shows that these genes are colinear with the mature tRNAimet and supports the RNA sequence of tRNAimet. Southern analysis of yeast genomic DNA indicates the presence of four copies of tRNAimet gene per haploid genome.

Genes and pseudogenes in a reiterated rat tRNA gene cluster

A 13.4 kb rat genomic DNA fragment containing two related tRNA gene clusters was isolated from a rat lambda recombinant and analyzed for gene arrangement and nucleotide sequence. One cluster was found to contain a tRNALeuCUG gene while the second contained a tRNALeuCUA pseudogene with multiple base substitutions. The tRNALeu gene was found to possess an intact coding region and a functional transcription termination signal at the 3' end as demonstrated by in vitro transcription and processing of precursors to mature size tRNA. The first tRNA gene cluster was found to contain in addition to tRNALeu, three other transcribable genes coding for tRNAAspGAC(U), tRNAGlyGGA(G) and tRNAGluGAG; the second cluster contained in addition to tRNALeu pseudogene, the tRNAAsp tRNAGly and tRNAGlu genes. Examination of flanking sequences of the corresponding tRNA genes in the two clusters shows no homology at the 5' ends and partial conservation of sequences at the 3'-end region. Genomic rat DNA blot hybridizations show that the tRNALeu gene is distributed together with the tRNAAsp, tRNAGly and tRNAGlu on a 10 fold repeat of 3.2 kb EcoRI fragment.

Nucleotide sequences of two regions of the human genome containing tRNAAsn genes

The primary structures of two human tRNAAsn genes and 600-700 nucleotides of their flanking regions have been determined from two separate isolates of a fetal DNA library in phage lambda vector. The tRNA gene from one clone differs from the major mammalian tRNAAsn by a single base substitution at position 47, with an A replacing a G, while the tRNAAsn gene from the second clone has base substitutions at positions 17 and 65, with a G replacing a C and a T replacing a C, respectively. The sequences of the noncoding 5'- and 3'-flanking regions of both clones are over 90% homologous. As with other mammalian tRNA genes, these two human tRNAAsn genes contain CTTTTPu, which might act as a transcription termination signal, 11 bp 3' to the structural gene. In vitro transcription experiments in a HeLa cell extract demonstrate that both cloned tRNAAsn genes can be transcribed and processed to mature-sized tRNAs.

Molecular cloning, sequence analysis and in vitro expression of a rat tRNA gene cluster

A rat genomic DNA fragment containing a tRNA gene cluster was isolated from a lambda phage library. Hybridization and nucleotide sequence analysis revealed the presence of a 83 bp tRNALeuCUG gene and a 72 bp tRNAAspGUG gene. Both genes possessed intact coding regions and putative transcription termination signals at their respective 3' ends. In vitro transcription analysis of the two subcloned genes in a HeLa cell S-100 system demonstrated the specific synthesis of a number of RNAs by RNA polymerase III. Studies carried out in the presence of alpha-amanitin showed that the larger RNAs are precursors for the final processed transcripts of the tRNALeu and tRNAAsp genes, respectively. Further nucleotide sequence analysis of the cluster revealed the presence of tRNAGly and a tRNAGlu pseudogenes with missing areas within their coding regions which are essential for transcription by RNA polymerase III. Within the region of DNA between the tRNALeu and tRNAAsp genes is a sequence which is 65% homologous to a region of the rat B1 element. The significance of this latter structure within the gene cluster is unknown.

A rat tRNA gene cluster containing the genes for tRNAPro and tRNALys. Analysis of nucleotide sequences of the genes and the surrounding regions

A lambda clone carrying a rat DNA fragment of 11.9 kb was isolated from a rat gene library with total rat tRNA as a probe. Nucleotide sequence analysis revealed that the DNA fragment contained six tRNA genes, three for tRNAPro and three for tRNALys. Of the six genes all but one tRNAPro gene have the same polarity. Each tRNA gene is separated by a DNA region of 0.1 to 3.6 kb. The 5'-flanking regions of the six rat genes in the cluster do not have any significant sequence homology, but in the 3'-flanking region, each gene has a short T cluster, which is supposed to be a transcription termination signal.

Characterization of a rat tRNA gene cluster containing the genes for tRNAAsp, tRNAGly and tRNAGlu, and pseudogenes

The putative genes for tRNAGAUAsp(C), tRNAGGAGly(G) and tRNAGAGGlu are in a cluster on the rat chromosome and are present exclusively in a 3.3 kb region cleaved with a restriction endonuclease EcoRI. The cluster reiterates about 10 times on the haploid DNA. Four lambda clones each containing an independent repeating unit were isolated from a rat gene library. The studies on the cloned DNA revealed that the length of the repeating unit including the 3.3 kb EcoRI fragment was at least 13.5 kb. Nucleotide sequence analysis of the 3.3 kb DNA in the isolated clones showed sequence variations among the repeating units and incomplete genes for tRNAGly and tRNAGlu within the clusters.

Nucleotide sequence of the SUF2 frameshift suppressor gene of Saccharomyces cerevisiae

To elucidate the molecular mechanism of frameshift suppression by the SUF2 gene of yeast, the sequences of DNA fragments carrying the SUF2-1 and suf2+ alleles of the gene and surrounding regions have been determined. Comparison of the suppressor and wild-type sequences indicates that the SUF2 gene product is a proline tRNA. Disregarding possible base modifications, we find that the wild-type suf2+ anticodon of the tRNA inferred from the DNA sequence is 3'-GGA-5'. The SUF2-1 mutation represents the insertion of a G-C base pair at a position in the gene that corresponds to the anticodon loop of the tRNA. Replacement of the wild-type suf2+ anticodon by a 3'-GGGA-5' fourbase anticodon enables the SUF2-1 tRNA to suppress the 5'-CCCU-3' four-base codons generated as the result of the his4-712 and his4-713 frameshift mutations. This nontriplet codon-anticodon interaction restores the correct reading frame and allows synthesis of a functional his4 protein.

Isolation and characterization of cloned rat DNA fragment carrying tRNA genes

A rat genomic library was screened for tRNA genes with an unfractionated rat liver tRNA probe. About 70 clones containing tRNA genes were detected per rat genome. The organization of tRNA genes in five clones was analyzed by restriction endonuclease digestion, RNA-DNA hybridization and in vitro transcription with nuclear extracts from Xenopus oocytes. Evidence is presented suggesting that tRNA genes are distributed in the rat genome in small clusters spanning 1 to 2 kb and interspersed with large regions (minimum 8 to 20 kb) of non tRNA-coding DNA. The tRNA gene clusters were found to contain the sequences for a variety of tRNA species. Genes for a single isoacceptor, were found in more than one clone. The detailed study of one clone shows the repetition of a cluster of four tRNA sequences at a distance of about 8 kb. The arrangement of tRNA genes in rat appears to follow the irregular pattern of tRNA gene organization previously reported in Drosophila and Xenopus.

Sequence of a yeast DNA fragment containing a chromosomal replicator and a tRNA Glu 3 gene

The sequence of a 1.9 kb Bam x Hind III fragment from yeast has been determined. This fragment is part of a yeast 6.7 kb Hind III segment cloned into pBR322 (pY20). The fragment carries a single gene for a glutamate tRNA which has no intron. According to genetic analyses [1] this fragment also contains a yeast chromosomal replicator. We have analyzed the sequence for potential open reading frames and for several structural features which are thought to be involved in the initiation of DNA replication. Hybridization studies have revealed that portions of this sequence are repeated within the yeast genome.

Structural comparison of two yeast tRNA Glu 3 genes

DNA sequences in a 1.7 kb Pst fragment from yeast have been determined. This fragment is part of a yeast 7.4 kb Hind III segment cloned ino pBR322 (pY 5). The fragment carries a single gene for a glutamate tRNA. The coding portion of this gene is identical in sequence to that of the tRNA Glu 3 gene from pY 20 [1]. The flanking regions differ in their sequences, but possible secondary structures within the 5'-flanking regions bear similar features. Sequence homologies between pY 5 and pY 20 were detected far outside the tRNA genes. More surprisingly, extended sequence homologies were seen between the flanking regions of the pY 20 tRNA Glu 3 gene and a tRNA Ser gene [2,3]. We have also checked the known tRNA genes for structural similarities. Hybridization studies indicate that portions of the Pst fragment are repeated within the yeast genome.

Mammalian tRNA genes: nucleotide sequence of rat genes for tRNAAsp, tRNAGly and tRNAGlu

A cloned 2.1 kb fragment of rat DNA hybridized to purified tRNAAsp has been sequenced. The result revealed that in addition to the putative gene for tRNAAspGAU(C), the fragment contained the tRNAGlyGGA(G) and tRNAGluGAG genes. The genes for tRNAAsp, tRNAGly and tRNAGlu have the same polarity, are arranged in this order and are regularly separated by DNA regions of about 450 bp. These rat genes contain neither intervening sequences nor the CCA sequence expected in the 3'-end of the mature tRNA. As observed in lower eukaryotic tRNA genes, the 5'-flanking regions of the three rat genes do not have any significant sequence homology as a regulatory element. In the 3'-flanking region, the sequences CTTTTTG and CTTTTG are present 11 bp downstream from the 3'-end of the genes for tRNAAsp and tRNAGly, respectively. The same CTTTTG sequence is repeated twice in regions 47 and 60 bp away from the tRNAGlu gene. The short T cluster common to the three genes might be the transcription termination site as in lower eukaryotic tRNA genes.

Evolution of a D. melanogaster glutamate tRNA gene cluster

We have determined the DNA sequence of a cloned cluster of essentially identical glutamate tRNA genes of D. melanogaster. The cluster consists of five genes: a gene triplet spanning approximately 0.55 kb followed by a 0.45 kb gene doublet 3.0 kb downstream. The genes are all arranged with the same polarity, do not encode the tRNA CCA end and contain no intervening sequences. Examination of the 5' and 3' sequences immediately flanking each gene reveals a striking pattern of sequence homologies between certain of the genes, which suggests a possible evolutionary history of this gene cluster. We propose that two ancestral genes each gave rise to gene doublets by duplication, while one of these gene pairs then gave rise, in turn, to a trio of genes as a result of unequal crossover.

Structure of a yeast non-initiating methionine-tRNA gene

4 to 8 kb Hind III fragments of yeast DNA were cloned into pBR322. One of these clones (pY6m3) containing a single tRNA3Met gene has been characterized in detail. The DNA sequence of the structural gene is colinear with the tRNA sequence, which means that in this case no intervening sequence is present. The 5'-leader and 3'-trailer sequences have also been determined. The 5'-flanking region can be folded up into possible secondary structures.

Studies on tRNA adaptation, tRNA turnover, precursor tRNA and tRNA gene distribution in Bombyx mori by using two-dimensional polyacrylamide gel electrophoresis

Eighteen out of twenty amino acids have been used for identifying tRNAs from the silkworm Bombyx mori L. fractionated on two-dimensional polyacrylamide gel electrophoresis. 43 spots out of 53 have been identified. This mapping confirms previous results and brings new answers to some questions on the regulation of tRNA biosynthesis. 1. In addition to quantitative adaptation of tRNAs to the composition of silk proteins (fibroin from the posterior silk gland, sericin from the middle part) and of iso-tRNAs from posterior silk gland to the major codons of fibroin mRNA, we also observe adaptation of tRNA from various tissues to the average amino acid content of proteins from fat body, gut, gonads and carcass of the silkworm. 2. In the silk gland, turnover rates of several tRNA species are similar. The selective accumulation of tRNAs needed for decoding fibroin and sericin mRNAs which takes place during the Vth larval instar, cannot be explained by the occurrence of a preferential degradation of some tRNA species. 3. Under given conditions for incubating silk glands, it is possible to obtain an accumulation of precursor tRNA species, which are enriched in pre-tRNAAla and pre-tRNAGly in the posterior silk gland and pre-tRNASer in the middle part. 4. The distribution of tRNA genes is not random. tRNA genes for glycine, alanine and serine are prominent. Selective transcription of batteries of iso-tRNA genes could explain our data.

Ribosomal genes in Physarum polycephalum: transcribed and non-transcribed sequences have similar base compositions

The transcribed and non-transcribed sequences in Physarum polycephalum ribosomal DNA (rDNA) were separated by restriction nuclease digestion of pure rDNA and the products fractionated by zone sedimentation in sucrose gradients. The base compositions of the fragments were determined by analytical centrifugation in CsCl or in CsCl with netropsin. All the fragments had dA + dT contents in the range 44-48%. From the known sequence arrangement and transcription pattern of Physarum rDNA it was concluded that coding sequences, transcribed but non-coding sequences, and non-transcribed sequences all possess similar base compositions, contrary to the situation in many other systems. The thermal denaturation profile of Physarum rDNA is reported. It suggests the rDNA sequence is complex and supports the above conclusion of limited heterogeneity of base composition.

Sequence organization of a cloned tDNA met fragment from Xenopus laevis

3.18 kb fragments of X. laevis DNA coding for tRNA 1 met have been inserted into a lambda vector via Hind III termini and cloned in E. coli. The organization of one cloned fragment has been analyzed by restriction endonuclease digestion and RNA-DNA hybridization. From the distribution of sites for three enzymes, this fragment appears to be typical of the majority of X. laevis tandem tDNA 1 met repeat units. Evidence is presented to suggest that it contains two genes coding for tRNA 1 met and at least one gene coding for a second as yet unidentified 4S RNA species. The two tRNA 1 met genes are located on the same DNA strand 0.96 and 1.38 kb from one end of the repeat unit. A detailed restriction map for 19 enzymes reveals that the spacers between these genes are not identical, and it provides no indication of short repetitive sequence elements within the spacers.

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.

Structure of yeast phenylalanine-tRNA genes: an intervening DNA segment within the region coding for the tRNA

Sixteen bacterial clones containing sequences complementary to yeast PhetRNA were isolated from a collection of hybrid plasmids containing BamHI restriction endonuclease-generated yeast DNA fragments inserted in the plasmid vector pBR315. Ten of these clones contained hybrid plasmids with distinct BamHI fragments. The sequence of the Phe-tRNA structural genes and adjacent regions of three of these clones is reported here. In the region flanking the tRNA gene, the sequence of two of the cloned DNAs is similar; the sequence of the third varies considerably. All three of the tRNA genes are bordered by A,T-rich regions. In particular, near the region coding for the 3' end of the tRNA there is a long sequence of As in the coding strand. This is reminiscent of the region of termination of transcription of the yeast 5S rRNA gene. The sequences coding for the Phe-tRNA contain an additional segment of 18 or 19 base pairs (depending upon the clone) not predicted by the yeast Phe-tRNA sequence. These intervening segments are nearly identical in the three clones and are located within the structural gene, two base pairs from the nucleotides coding for the tRNA anticodon.

A comparison of transcriptional linkage of tRNA cistrons in yeast and E. coli by the ultraviolet light technique

The ultraviolet light mapping technique was employed to determine the lengths of tRNA cistrons in yeast. The applicability of the method was first tested in the E. coli system, in which the mapping positions for some tRNA cistrons and the ribosomal 5S RNA genes as well as the existence of multimeric transcription units for tRNAs are known. Rates of the synthesis of the tRNAs and small rRNAs after irradiation with various doses of UV light were determined by pulse labeling and quantitation of the RNA species after twodimensional gel electrophoreses. The small ribosomal RNAs served for internal calibration in the estimtion of the target sizes. Our results suggest that--in contrast to the prokaryotic system--in yeast the majority of the tRNA genes are not linked into transcriptional units.

Cloning of yeast transfer RNA genes in Escherichia coli

Four thousand Escherichia coli clones containing yeast DNA inserted into the plasmid pBR313 have been isolated. Of these, 175 clones were identified as carrying yeast transfer RNA genes. The initial analysis of the inserted transfer RNA genes via the colony hybridization technique with individual radioactive transfer RNA species is reported. The data indicate that yeast transfer RNA genes are not highly clustered, although some clustering exists. In addition, it was observed that the reiteration number of different transfer RNA genes may vary extensively.