Transcripts of mitochondrial tRNA genes in Saccharomyces cerevisiae

Human mitochondrial tRNA processing

tRNA processing is a central event in mammalian mitochondrial gene expression. We have identified key enzymatic activities (ribonuclease P, precursor tRNA 3'-endonuclease, and ATP(CTP)-tRNA-specific nucleotidyltransferase) that are involved in HeLa cell mitochondrial tRNA maturation. Different mitochondrial tRNA precursors are cleaved precisely at the tRNA 5'- and 3'-ends in a homologous mitochondrial in vitro processing system. The cleavage at the 5'-end precedes that at the 3'-end, and the tRNAs are substrates for the specific CCA addition in the same in vitro system. Using a comparative enzymatic approach as well as biochemical and immunological techniques, we furthermore demonstrate that human cells contain two distinct enzymes that remove 5'-extensions from tRNA precursors, the previously characterized nuclear and the newly identified mitochondrial ribonuclease P. These two cellular isoenzymes have different substrate specificities that seem to be well adapted to their structurally disparate mitochondrial and nuclear tRNA substrates. This kind of approach may also help to understand the structural diversities and commonalities of tRNAs.

Suppression of a mitochondrial point mutation in a tRNA gene can cast light on the mechanisms of 3' end-processing

We used a genetic approach to study the nuclear factors involved in the biogenesis of mitochondrial tRNAs. A point mutation in the mitochondrial tRNA(Asp) gene of Saccharomyces cerevisiae had previously been shown to result in a temperature-sensitive respiratory-deficient phenotype as a result of the absence of 3' end-processing of the tRNA(Asp). Analysis of mitochondrial revertants has shown that all revertants sequenced have a G-A compensatory change at position 53, which restores the hydrogen-bond with the mutated nucleotide. We then searched for nuclear suppressors to identify the nuclear gene(s) involved in mitochondrial tRNA 3' end-processing. One such suppressor mutation was further characterized: it restores tRNA(Asp) maturation and growth at 36 degrees C on glycerol medium in heterozygous diploids, but leads to a defective growth phenotype in haploids.

Ordered processing of the polygenic transcripts from a mitochondrial tRNA gene cluster in K. lactis

In Saccharomyces cerevisiae, transcription of the mitochondrial genome starts at multiple initiation sites and is followed by the processing of multigenic transcripts at the 5' and 3' termini of tRNA sequences and in some intergenic regions. We have used a comparative approach to investigate the structure and function of the latter processing sites. We present here an analysis of the transcripts of a cluster of tRNA genes from the mitochondrial genome of Kluyveromyces lactis. The gene order of this cluster is the same as that of the cluster in S. cerevisiae but the sequence of the intergenic regions is different. A detailed analysis of transcripts has been performed using S1 mapping and primer extension techniques. The results can be summarized as follows: (1) transcription of the cluster very probably starts at initiation sites having the nonanucleotide sequence TTATAAGTA (which acts as a promoter in S. cerevisiae) and yields polygenic transcripts; (2) processing of these transcripts seems to occur through an ordered pathway of endonucleolytic events in which some tRNA sequences are preferentially excised and some endonucleolytic cuts occur more readily than others; (3) in two intergenic regions, strong signals indicate the existence of processing events. The sequences around these sites are similar in sequence and localization to S. cerevisiae intergenic processing sites, indicating a possible functional importance in maintaining a conserved order of tRNA genes in different species of yeasts.

Symmetrical transcription in the tRNA region of the mitochondrial genome of Saccharomyces cerevisiae

The occurrence of discrete transcripts originating from the non-coding strand of the yeast mitochondrial genome is described. The region under investigation is localized in the large tRNA gene cluster between the LSU ribosomal RNA and OXI 1 genes. The transcripts originating from the non-coding strand were detected in a wild-type strain and in a rho- mutant. Their size range includes transcripts of about 2000 nucleotides able to accommodate more than one "anti-tRNA". In some cases their extremities can be mapped near highly-conserved nonanucleotides that could function as origins of transcription. The involvement of the tRNA-processing machinery in the cleavage of these transcripts is also hypothesized.

The nuclear SUV3-1 mutation affects a variety of post-transcriptional processes in yeast mitochondria

The SUV3-1 mutation was isolated earlier as a suppressor of a deletion of a conserved RNA processing site (dodecamer) near the 3' end of the var1 gene. Previous studies indicate that the suppressor enhances translation of mutant var1 messages; unexpectedly, it also causes over-accumulation of excised intron RNA of the large rRNA gene intron and blocks cleavage at the dodecamer site within that intron. In this study most mitochondrial genes in SUV3-1 and suv3 nuclear contexts are surveyed for changes in levels of mRNA, for interference with dodecamer cleavage and splicing and for levels of excised intron RNAs. SUV3-1 has little or no effect on the size or abundance of unspliced RNAs tested. It results, however, in a marked increase in the abundance of seven of eight excised group I intron RNAs tested, most of which are not detectable in wild-type (suv3) strains. The suppressor lowers levels of the cob and coxl mRNAs about 2-5 and 20-fold, respectively. The effect on coxl mRNA results from a decrease in the splicing of its intron 5 beta. Despite the reduction in these mRNA levels, the amounts of coxl and cyt b polypeptides were close to wild-type levels in SUV3-1 cells. These data show that the suv3 gene plays a prominent role in post-transcriptional and translation events in yeast mitochondria.

Structure and transcription of the mitochondrial genome in heteroplasmic strains of Saccharomyces cerevisiae

Saccharomyces cerevisiae strain FF1210-6C/170 is respiratory deficient due to a mutation of the penultimate base of the mitochondrial tRNA(Asp) gene. We have identified a number of progeny from this strain which have reverted to respiratory sufficiency by the excision and tandem amplification of a small region of the mitochondrial (mt) DNA carrying the tRNA(Asp) gene, while also maintaining the full-length mtDNA. We have studied the structure of the mtDNA and mitochondrial transcription in a number of these heteroplasmic strains. The exact site of the recombination involved in the excision of the repeating unit of the amplified mtDNA has been determined for five of the revertants. Recombination occurs between identical sequences 4-13 base pairs in length. Each of the different repeating units of the amplified DNA retains an active promoter which has been moved to a site just upstream of the tRNA(Asp) gene by the excision/amplification. Transcripts from the heteroplasmic strains have been characterized to determine the sites of mitochondrial RNA termini. We find that in addition to the 5' and 3' processing of the tRNAs, many of the transcripts terminate at a position about 300 base pairs downstream of the gene for tRNA(Asp). We also find that 3' processing of tRNA(Asp) precursors is absent in petite strains which lack 5' processing indicating that 5' processing of tRNA(Asp) may be a prerequisite for 3' processing in this mutant.

A point mutation in a mitochondrial tRNA gene abolishes its 3' end processing

A temperature sensitive mutation mapping in the tRNA region of the mitochondrial genome of S. cerevisiae has been found to abolish 3' processing of tRNA(asp). Mutant cells grown for a few generations at the non-permissive temperature were found to specifically lack mature tRNA(asp) and to accumulate 3' unprocessed precursors of this tRNA. The accumulation of precursors of other mitochondrial tRNAs was also observed under the same conditions. After longer incubation times, a generalized decrease of mitochondrial transcripts could be observed. The mutation was genetically mapped in a limited region surrounding the tRNA(asp) gene and found, by sequencing, to consist of a C- greater than T transition at position 61 of the tRNA(asp) gene.

Transcription initiation and RNA processing of a yeast mitochondrial tRNA gene cluster

Expression of 5 yeast mitochondrial tRNA genes (Ala, Ile, Tyr, Asn and Metm), localized upstream from the oxil gene has been analyzed by in vitro capping using guanylyltransferase, northern hybridization and S1 nuclease mapping in the wild type and a rho-strain. The 5 tRNA sequences belong to the same transcriptional unit which is initiated 133 bp upstream from the tRNA(Ala) gene at a promoter sequence TTATAAGTA. Furthermore, a truncated tRNA(Tyr) transcript, 2 nucleotides shorter than mature tRNA(Tyr) has been found, only in the rho-strain. This minor transcript may result from secondary transcription initiation at a variant nonanucleotide sequence, ATATAAGGA, which overlaps the tRNA(Tyr) coding sequence by 3 nucleotides. The polycistronic precursor has proven to be useful in investigation of the mechanisms of tRNA processing. Maturation of this primary transcript proceeds exclusively by precise endonucleolytic cleavages at the 5' and 3'-ends of tRNA sequences.

Analysis of transcripts of the major cluster of tRNA genes in the mitochondrial genome of S. cerevisiae

The transcripts of a 6Kbp region of the mitochondrial genome of S. cerevisiae, localized in the 21S rRNA-OXI1 span and including 12 tRNA genes (from tRNA(thr) to tRNA(ala)) and several G+C clusters, have been studied by analysis of in vitro capped primary transcripts and by fine mapping of the 5' ends of transcripts. The study was performed in the w.t. strain D273-10B and in several rho- mutants retaining different, partially overlapping portions of the studied region; the mutants accumulate incompletely-processed precursors of tRNAs due to the absence of the tRNA synthesis locus. Results show the presence in the region of four sites at which initiation occurs at a consensus nonanucleotide ATTATAAGTA (or a minor variant of the same); however different initiation sites are used in different strains, and several differences as compared to initiation in vitro can also be observed. Termini arising by processing are often localized at AATATAA or AATATATTTT sequences localized immediately adjacent to a G+C cluster or a tRNA sequence.

RNase P activity in the mitochondria of Saccharomyces cerevisiae depends on both mitochondrion and nucleus-encoded components

A requisite step in the biosynthesis of tRNA is the removal of 5' leader sequences from tRNA precursors. We have detected an RNase P activity in yeast mitochondrial extracts that can carry out this reaction on a homologous precursor tRNA. This mitochondrial RNase P was sensitive to both micrococcal nuclease and protease, demonstrating that it requires both a nucleic acid and protein for activity. The presence of RNase P activity in vitro directly correlated with the presence of a locus on yeast mitochondrial DNA previously shown by genetic and biochemical studies to be required for tRNA maturation. The product of the locus, the 9S RNA, and this newly described mitochondrial RNase P activity cofractionated, providing further evidence that the 9S RNA is the RNA component of yeast mitochondrial RNase P.

RNase P activity in the mitochondria of Saccharomyces cerevisiae depends on both mitochondrion and nucleus-encoded components

A requisite step in the biosynthesis of tRNA is the removal of 5' leader sequences from tRNA precursors. We have detected an RNase P activity in yeast mitochondrial extracts that can carry out this reaction on a homologous precursor tRNA. This mitochondrial RNase P was sensitive to both micrococcal nuclease and protease, demonstrating that it requires both a nucleic acid and protein for activity. The presence of RNase P activity in vitro directly correlated with the presence of a locus on yeast mitochondrial DNA previously shown by genetic and biochemical studies to be required for tRNA maturation. The product of the locus, the 9S RNA, and this newly described mitochondrial RNase P activity cofractionated, providing further evidence that the 9S RNA is the RNA component of yeast mitochondrial RNase P.

The GC clusters of the mitochondrial genome of yeast and their evolutionary origin

We have studied the primary and secondary structures, the location and the orientation of the 196 GC clusters present in the 90% of the mitochondrial genome of Saccharomyces cerevisiae which have already been sequenced. The vast majority of GC clusters is located in intergenic sequences (including ori sequences, intergenic open reading frames and the gene varl which probably arose from an intergenic spacer) and in intronic closed reading frames (CRF's); most of them can be folded into stem-and-loop systems; both orientations are equally frequent. The primary structures of GC clusters permit to group them into eight families, seven of which are related to the family formed by clusters A, B and C of the ori sequences. On the basis of the present work, we propose that the latter derive from a primitive ori sequence (probably made of only a monomeric cluster C and its flanking sequences r* and r) through (i) a series of duplication inversions generating clusters A and B; and (ii) an expansion process producing the AT stretches of ori sequences. Most GC clusters apparently originated from primary clusters also derived from the primitive ori sequence in the course of its evolution towards the present ori sequences. Finally, we propose that the function of GC clusters is predominantly, or entirely, associated with the structure and organization of the mitochondrial genome of yeast and, indirectly, with the regulation of its expression.

Initiation of transcription of a mitochondrial tRNA gene cluster in S. cerevisiae

In Saccharomyces cerevisiae most mitochondrial tRNA genes are clustered in a 9 kbp region between the cap and oxil genes. Polygenic transcripts of this region have been previously identified. A transcriptional initiation site at a TTATAAGTA box, located upstream from the tRNAcys gene, has now been detected by S1 mapping experiments and by the capping of primary transcripts. Results are consistent with the hypothesis that this box represents the initiation site for transcription of a cluster of tRNA genes, while the adjacent tRNA2thr is cotranscribed with the 21S rRNA. Results obtained with various strains are compared, and the efficiency of this sequence as a transcriptional initiation site in different mitochondrial contexts is discussed.

Organization and processing of the mitochondrial oxi3/oli2 multigenic transcript in yeast

In the present article, we confirm our previous proposal (Faye and Simon 1983a, b) that the oxi3 and oli2 genes belong to the same transcription unit. Furthermore, we have shown that a primary polycistronic transcript covers oxi3, aap1, oli2 and extends beyond URF2. Transcriptional analysis of this region revealed several cleavage points. The examination of the DNA sequence at and surrounding these cleavage points disclosed that some of them take place at or near specific sequences found also in other known multigenic transcripts. Two of the major cleavages involve the stem-loop structure of GC rich clusters. We discuss the possibility that some of these cleavage sites serve as post-transcriptional processing signals and may be necessary for the maturation of the precursor RNA.

Initiation of transcription in yeast mitochondria: analysis of origins of replication and of genes coding for a messenger RNA and a transfer RNA

The initiation of transcription of the yeast mitochondrial genes coding for subunit I of cytochrome c oxidase (COX1) and for tRNA1Thr has been examined. COX1 messenger RNA synthesis is initiated in a conserved nonanucleotide sequence (ATATAAGTA) which we have previously found immediately upstream of ribosomal RNA genes at positions at which RNA synthesis starts. The 5'-end of the precursor of tRNA1Thr is located in a variant nonanucleotide motif (TTATAAGTA), which may be characteristic for tRNA genes. Using a partially purified fraction of mtRNA polymerase, we demonstrate that RNA synthesis is precisely initiated in vitro in nonanucleotide sequences preceding both ribosomal RNA-, tRNA- and messenger RNA-encoding genes and origins of replication.

Characterization of the yeast mitochondrial locus necessary for tRNA biosynthesis: DNA sequence analysis and identification of a new transcript

Most components necessary for the biosynthesis of mitochondrial tRNAs are coded by nuclear genes, but one mitochondrial locus other than the tRNA genes themselves is required to make functional tRNAs in the yeast Saccharomyces cerevisiae. DNA sequence analysis of this yeast mitochondrial tRNA synthesis locus is reported here. This region of mitochondrial DNA is almost exclusively A+T-rich DNA with one G+C-rich element. Despite the unusual structure of the DNA in this region, we have demonstrated that it codes for a heretofore unidentified mitochondrial transcript about 450 bases in length. Since this RNA is the only RNA encoded by the tRNA synthesis locus, it must be the active agent of the locus. This RNA could either act autonomously through RNA-RNA interactions or as part of an RNA-protein complex to effect tRNA biosynthesis.

Identification of a single transcriptional initiation site for the glutamic tRNA and COB genes in yeast mitochondria

We have identified a single transcriptional initiation site for the glutamic tRNA and COB (cytochrome b) genes by using the complementary techniques of in vitro capping of RNA and in vitro transcription. In the capping reaction, mitochondrial RNA is labeled with [alpha-32P]GTP by vaccinia virus guanylyltransferase. This reaction is specific for the 5' ends of RNA retaining the terminal triphosphate of transcriptional initiation. Exploiting the extremely low G+C content (18%) of yeast mitochondrial DNA, we digested in vitro capped transcripts from various petite deletion mutants with the G-specific RNase T1. By petite deletion mapping, a capped transcript giving rise to a 51-base RNase T1-generated oligonucleotide was localized near the glutamic tRNA gene. When the sequence of this oligonucleotide was determined, it perfectly matched the DNA sequence 391 base upstream of the glutamic tRNA. Purified yeast mitochondrial RNA polymerase initiated transcription in vitro at the same site as shown by the sequence of the 33-base oligonucleotide product of the reaction performed in the absence of CTP. Initiation starts at a nonanucleotide sequence previously implicated in yeast mitochondrial transcriptional initiation. Because there is no evidence of an initiation site in the 1,050 bases between the glutamic tRNA and COB genes, the two genes are likely to be transcribed together. Further evidence of a long common transcript was provided by RNA blot hybridization.

Characterization of a yeast mitochondrial locus necessary for tRNA biosynthesis. Deletion mapping and restriction mapping studies

Yeast mitochondrial DNA codes for a complete set of tRNAs. Although most components necessary for the biosynthesis of mitochondrial tRNA are coded by nuclear genes, there is one genetic locus on mitochondrial DNA necessary for the synthesis of mitochondrial tRNAs other than the mitochondrial tRNA genes themselves. Characterization of mutants by deletion mapping and restriction enzyme mapping studies has provided a precise location of this yeast mitochondrial tRNA synthesis locus. Deletion mutants retaining various segments of mitochondrial DNA were examined for their ability to synthesize tRNAs from the genes they retain. A subset of these strains was also tested for the ability to provide the tRNA synthesis function in complementation tests with deletion mutants unable to synthesize mature mitochondrial tRNAs. By correlating the tRNA synthetic ability with the presence or absence of certain wild-type restriction fragments, we have confined the locus to within 780 base pairs of DNA located between the tRNAMetf gene and tRNAPro gene, at 29 units on the wild-type map. Heretofore, no genetic function or gene product had been localized in this area of the yeast mitochondrial genome.