The mapping of mutations in tRNA and cytochrome oxidase genes located in the cap-par segment of the mitochondrial genome of S. cerevisiae

A missense mutation in the nuclear gene coding for the mitochondrial aspartyl-tRNA synthetase suppresses a mitochondrial tRNA(Asp) mutation

The nuclear suppressor allele NSM3 in strain FF1210-6C/170-E22 (E22), which suppresses a mutation of the yeast mitochondrial tRNA(Asp)gene in Saccharomyces cerevisiae, was cloned and identified. To isolate the NSM3 allele, a genomic DNA library using the vector YEp13 was constructed from strain E22. Nine YEp13 recombinant plasmids were isolated and shown to suppress the mutation in the mitochondrial tRNA(Asp)gene. These nine plasmids carry a common 4. 5-kb chromosomal DNA fragment which contains an open reading frame coding for yeast mitochondrial aspartyl-tRNA synthetase (AspRS) on the basis of its sequence identity to the MSD1 gene. The comparison of NSM3 DNA sequences between the suppressor and the wild-type version, cloned from the parental strain FF1210-6C/170, revealed a G to A transition that causes the replacement of amino acid serine (AGU) by an asparagine (AAU) at position 388. In experiments switching restriction fragments between the wild type and suppressor versions of the NSM3 gene, the rescue of respiratory deficiency was demonstrated only when the substitution was present in the construct. We conclude that the base substitution causes the respiratory rescue and discuss the possible mechanism as one which enhances interaction between the mutated tRNA(Asp)and the suppressor version of AspRS.

Mutational studies of the major tRNA region of the S. cerevisiae mitochondrial genome

The major tRNA genes in S. cerevisiae mitochondria are contained within a 20 kb segment of the mitochondrial DNA. In order to analyze the functional role of this region we have isolated several mitochondrial mutations, which are temperature-sensitive for growth on non-fermentable carbon sources. These mutations, localized in the major tRNA cluster region, can be classified in different groups according to their (a) genetic and physical localization, (b) spectrum of suppression and (c) biochemical characteristics. Some of these are mutations in tRNA genes which affect tRNA function; others alter the synthesis of the gene product. Finally, we found two mutations localized in, or in the vicinity of, the open reading frame RF2. RF2 has been postulated to be a maturase-like protein (Michel 1984) but no function for it has yet been demonstrated. The existence of defective mutants may confirm that RF2 is indeed necessary for mitochondrial biogenesis and so allow for a study of the expression of this gene.

A mitochondrial frameshift suppressor maps in the tRNASer-var1 region of the mitochondrial genome of the yeast S. cerevisiae

A polypeptide chain-terminating mutation (M5631) previously has been shown to be a +1T insertion in the yeast mitochondrial gene oxi1, coding for subunit II of the cytochrome c oxidase. A spontaneously arisen frameshift suppressor (mfs-1) that is mitochondrially inherited suppresses this mutation to a considerable extent. The suppressor mutation was mapped by genetic and molecular analyses in the mitochondrial tRNASer-var1 region of the mitochondrial genome of the yeast S. cerevisiae. Genetic analyses show that the suppressor mfs-1 does not suppress other known mitochondrial frameshift mutations, or missense and nonsense mutations.

Nuclear and mitochondrial revertants of a yeast mitochondrial tRNA mutant

We isolated revertants capable of respiration from the respiratory deficient yeast mutant, FF1210-6C/170, which displays greatly decreased mitochondrial protein synthesis due to a single base substitution at the penultimate base of the tRNAAsp gene on mitochondrial (mt) DNA. Three classical types of revertant were identified: (1) same-site revertants; (2) intragenic revertants which restore the base pairing in the acceptor stem of the mitochondrial tRNAAsp; and (3) extragenic suppressors located in nuclear DNA. In addition a fourth type of revertant was identified in which the mutant tRNAAsp is amplified due to the maintenance of both the original mutant mtDNA and a modified form of the mutant mtDNA in which only a small region around the tRNAAsp gene is retained and amplified. The latter form resembles the mtDNA in vegetative petite (rho-) strains which normally segregates rapidly from the wild-type mtDNA. Each revertant type was characterized genetically and by both DNA sequence analysis of the mitochondrial tRNAAsp gene and analysis of the quantity and size of RNA containing the tRNAAsp sequence. These results indicate that the mitochondrial tRNAAsp of the mutant retains a low level of activity and that the presence of the terminal base pair in tRNAAsp is a determinant of both tRNAAsp function and the maintenance of wild-type levels of tRNAAsp.

A single base change in the extra-arm of yeast mitochondrial tyrosine tRNA affects its conformational stability and impairs aminoacylation

The mitochondrial temperature-sensitive mutation tsm-8 maps on a 1.8 kb HpaII fragment of mitochondrial DNA (mt DNA) which contains genes for tRNA(Ala), tRNA(Ile) and tRNA(Tyr). The phenotype of this mutation is, among multiple pleiotropic defects, a temperature-induced reduction of mitochondrial translation. DNA sequencing of the HpaII fragment from the wild type and mutant tsm-8 revealed a single transversion from T to A in position 56 of the mutant tRNA(Tyr) gene. This nucleotide change disrupts a base pairing in the long extra arm of the tRNA cloverleaf. Revertants of the tsm-8 mutant restore correct base pairing in the extra arm by a second-site mutation in the tRNA(Tyr) gene. Analysis of the tRNA(Tyr) transcripts revealed that neither transcription nor processing of the tRNA is affected in the mutant. However, the base alteration destabilizes the conformation of the tRNA and affects its charging parameters. At the non-permissive temperature, the Michaelis-Menten constant of the mitochondrial tyrosyl-tRNA synthetase for the mutant tRNA is increased over 20-fold when compared to the wild-type tRNA. As a consequence, mitochondrial protein synthesis is drastically reduced at the restrictive temperature. Moreover, synthesis of apocytochrome b and of cytochrome oxidase subunit 3 is decreased relative to the other mitochondrially synthesized polypeptides.

Sequence and expression of four mutant aspartic acid tRNA genes from the mitochondria of Saccharomyces cerevisiae

Expression of the mitochondrial tRNAAsp gene of Saccharomyces cerevisiae has been examined in five syn- mutants known to affect tRNAAsp function, and in a rho- mutant which accumulates precursor tRNAs. By comparison of wild-type versus mutant DNA sequence, the lesion in each syn- mutant has been identified as a single base change within the mitochondrial tRNAAsp structural gene. The mutant tRNAAsp genes are transcribed, and the transcripts can be processed to mature 4S-size tRNAAsp. The steady-state level of each mutant tRNAAsp is lower than that of wild-type tRNAAsp. The RNA from two of the syn- mutants contained a second, slow-migrating form of mitochondrial tRNAAsp which is correctly processed at the 5' end. We conclude that the lesions in the syn- mitochondrial tRNAAsp genes block neither transcription of these genes, nor 5'-end processing of the transcripts. The effect of each point mutation must be manifested at the level of 3'-end processing, or at a functional level.

Nucleotide substitutions in a yeast mitochondria cis-acting mutant located in the last intron of the apocytochrome b gene

The region of mitochondrial DNA corresponding to the intron mutant M6-200 in Saccharomyces cerevisiae D273-10B has been isolated, and the nucleotide sequence of a 519 bp RsaI fragment has been determined. Three nucleotide substitutions were found at nucleotides +2650 (G----T), +2668 (G----A) and +2798 (A----G), all within the genetically defined location in the gene. Particular significance can be attributed to the first two changes (+2650 and +2668), that can be genetically isolated from the third substitution and, in addition, alter conserved sequence features detected in a study [(1982) Biochimie 64, 867-881] of fungal mitochondrial introns.

Identification and consequences of a guanosine-15 to adenosine-15 change in the yeast mitochondrial tRNASerUCX gene

We have characterized a mutation affecting the yeast mitochondrial tRNASerUCX. The mutation is a single nucleotide substitution located within the structural portion of the tRNASerUCX gene which causes the strain to be respiratory deficient. The substitution is a G leads to A transition located in the dihydrouridine arm. The tRNASerUCX transcripts from the mutant gene are present in the same amount and are the same size as transcripts from the wild-type gene. The mutant tRNASerUCX can be charged in vitro with mitochondrial aminoacyl-tRNA synthetase. Mitochondrial protein synthesis does occur in the mutant, but the amount of cytochrome oxidase subunit I is significantly decreased relative to other mitochondrial translation products.

Transfer RNA genes in the cap-oxil region of yeast mitochondrial DNA

A cytoplasmic "petite" (rho-) clone of Saccharomyces cerevisiae has been isolated and found through DNA sequencing to contain the genes for cysteine, histidine, leucine, glutamine, lysine, arginine, and glycine tRNAs. This clone, designated DS502, has a tandemly repeated 3.5 kb segment of the wild type genome from 0.7 to 5.6 units. All the tRNA genes are transcribed from the same strand of DNA in the direction cap to oxil. The mitochondrial DNA segment of DS502 fills a sequence gap that existed between the histidine and lysine tRNAs. The new sequence data has made it possible to assign accurate map positions to all the tRNA genes in the cap-oxil span of the yeast mitochondrial genome. A detailed restriction map of the region from 0 to 17 map units along with the locations of 16 tRNA genes have been determined. The secondary structures of the leucine and glutamine tRNAs have been deduced from their gene sequences. The leucine tRNA exhibits 64% sequence homology to an E. coli leucine tRNA.

Assembly of the mitochondrial membrane system: isolation of mitochondrial transfer ribonucleic acid mutants and characterization of transfer ribonucleic acid genes of Saccharomyces cerevisiae

A method is described for isolating cytoplasmic mutants of Saccharomyces cerevisiae with lesions in mitochondrial transfer ribonucleic acids (tRNA's). The mutants were selected for slow growth on glycerol and for restoration of wild-type growth by cytoplasmic "petite" testers that contain regions of mitochondrial deoxyribonucleic acid (DNA) with tRNA genes. The aminoacylated mitochondrial tRNA's of several presumptive tRNA mutants were analyzed by reverse-phase chromatography on RPC-5. Two mutant strains, G76-26 and G76-35, were determined to carry mutations in the cysteine and histidine tRNA genes, respectively. The cysteine tRNA mutant was used to isolate cytoplasmic petite mutants whose retained segments of mitochondrial DNA contain the cysteine tRNA gene. The segment of one such mutant (DS504) was sequenced and shown to have the cysteine, histidine, and threonine tRNA genes. The structures of the three mitochondrial tRNA's were deduced from the DNA sequence.

Assembly of the mitochondrial membrane system: sequences of yeast mitochondrial valine and an unusual threonine tRNA gene

The mitochondrial DNA segments of two independently isolated rho- clones of S. cerevisiae carrying a genetic marker for a threonine tRNA have been characterized by restriction endonuclease analysis and DNA sequencing. The DNA sequences of the two segments have been used to deduce the primary and secondary structures of the tRNA. The threonine tRNA is unusual in having a leucine anticodon (3'-GAU-5'). Despite the anomalous anticodon, the tRNA is proposed to function in mitochondrial protein synthesis. One of the rho- clones contains an additional coding sequence that has been identified as a valine tRNA genes have been located on the wild-type physical map and determined to be transcribed from two different strands.

The genetic map of transfer RNA genes of yeast mitochondria: correction and extension

Ninety five rho- mitochondrial DNA's of Saccharomyces cerevisiae were compared for their deletion structure by means of 15 genetic markers and 22 tRNA genes. The patterns of co-deletion and co-retention of different tRNA genes allowed us to determine their positions with respect to each other. The deduced order of tRNA genes was consistent with the order of the genetic markers established by independent genetic approaches. Our previously proposed mitochondrial tRNA gene map has been revised and extended. Transfer RNA genes, corresponding to all 20 aminoacids, and two isoacceptor tRNA genes were localized. The possible position of each tRNA gene has been indicated on the physical map of mitochondrial DNA. Seventeen tRNA genes are carried by a narrow region representing less than 20% of the wild type genome.

Assembly of the mitochondrial membrane system: two separate genes coding for threonyl-tRNA in the mitochondrial DNA of Saccharomyces cerevisiae

1. Mitochondria of Saccharomyces cerevisiae contain two tRNA's that are acylated with threonine. The two isoaccepting species (tRNA1Thr and tRNA2Thr) can be separated by reversed-phase chromatography on RPC-5. 2. A cytoplasmic mutant has been isolated which lacks tRNA1Thr but has normal levels of tRNA2Thr. This mutation was previously shown to map between the oxi 1 and oxi 2 loci on mitochondrial DNA. 3. tRNA1Thr and tRNA2Thr hybridize to wild type mitochondrial but not nuclear DNA and are capable of partially competing with each other. Hybridization of each species to different segments of mitochondrial DNA isolated from p- clones indicate that there are two threonyl tRNA genes. One gene is located between oxi 1 and oxi 2 and codes for tRNA1Thr. The second gene codes for tRNA2Thr and is near the cap locus. 4. Binding assays to E. coli ribosomes indicate that tRNA2Thr recognizes the threonine triplet ACA and may also recognize the other three triplets but with a much lower efficiency. None of the four codons for threonine stimulate the binding of tRNA1Thr to the ribosomes.