Sequence homologies of (guanosine + cytidine)-rich regions of mitochondrial DNA of Saccharomyces cerevisiae

Lessons from a small, dispensable genome: the mitochondrial genome of yeast

This article reviews the investigations on the mitochondrial genomes of yeast carried out in the author's laboratory during a quarter of a century (to be precise between 1966 and 1992). Our studies dealt with the structural basis for the cytoplasmic petite mutation, the replication, the transcription and the recombination of the mitochondrial genome, a genome which is dispensable and which comprises abundant non-coding sequences. This work led to some general conclusions on the nuclear genome of eukaryotes. Some recent results in apparent contradiction with our conclusions on ori sequences will also be briefly discussed.

The AT spacers and the var1 genes from the mitochondrial genomes of Saccharomyces cerevisiae and Torulopsis glabrata: evolutionary origin and mechanism of formation

Intergenic sequences represent 63% of the mitochondrial 'long' (85 kb) genome of Saccharomyces cerevisiae. They comprise 170-200 AT spacers that correspond to 47% of the genome and are separated from each other by GC clusters, ORFs, ori sequences, as well as by protein-coding genes. Intergenic AT spacers have an average size of 190 bp, and a GC level of 5%; they are formed by short (20-30 nt on the average) A/T stretches separated by C/G mono- to trinucleotides. An analysis of the primary structures of all intergenic AT spacers already sequenced (32 kb; 80% of the total) has shown that they are characterized by an extremely high level of short sequence repetitiveness and by a characteristic sequence pattern; the frequencies of A/T isostichs conspicuously deviate from statistical expectations, and exponentially decrease when their (AT + TA)/(AA + TT) ratio, R, decreases. A situation basically identical was found in the AT spacers of the mitochondrial genome (19 kb) of Torulopsis glabrata. The sequence features of the AT spacers indicate that they were built in evolution by an expansion process mainly involving rounds of duplication, inversion and translocation events which affected an initial oligodeoxynucleotide (endowed with a particular R ratio) and the sequences derived from it. In turn, the initial oligodeoxynucleotide appears to have arisen from an ancestral promoter-replicator sequence which was at the origin of the nonanucleotide promoters present in the mitochondrial genomes of several yeasts. Common sequence patterns indicate that the AT spacers so formed gave rise to the var1 gene (by linking and phasing of short ORFs), to the DNA stretches corresponding to the untranslated mRNA sequences and to the central stretches of ori sequences from S. cerevisiae.

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.

Sequence organization of the mitochondrial genome of yeast--a review

We have compiled the available primary structural data for the mitochondrial genome of Saccharomyces cerevisiae and have estimated the size of the remaining gaps, which represent 12-13% of the genome. The lengths of sequenced regions and of gaps lead to a new assessment of genome sizes; these range (in round figures) from 85 000 bp for the long genomes, to 78 000 bp for the short genomes, to 74 000 bp for the supershort genome of Saccharomyces carlsbergensis. These values are 8-11% higher than those previously estimated from restriction fragments. Interstrain differences concern not only facultative intervening sequences (introns) and mini-inserts, but also insertions/deletions in intergenic sequences. The primary structure appears to be extremely conserved in genes and ori sequences, and highly conserved in intergenic sequences. Since coding sequences represent at most 33-35% of the genome, at least two thirds of the genome are formed by noncoding and yet highly conserved sequences. The G + C level of genes or exon is 25%, and that of intronic open reading frames (ORFs) 22%; increasingly lower values are shown by intronic closed reading frames (CRFs), 20%, ori sequences, 19%, intergenic ORFs, 17.5% and intergenic sequences, 15%.

Two modules from the hypersuppressive rho- mitochondrial DNA are required for plasmid replication in yeast

In the yeast hypersuppressive (HS) rho- mutants most of the mitochondrial genome is deleted, but the remainder containing one of the three rep sequences is amplified. One of these sequences, rep2, and its flanking regions have been previously cloned and reported to promote autonomous plasmid replication in yeast. The present study suggests that the Ars activity associated with this HS rho- mitochondrial DNA (mtDNA) fragment is due to the presence in cis of at least two modules: (i) the 11-bp consensus sequence 5'-ATAAACTATAAAAT-3', common to several ars sequences, and (ii) a palindromic sequence of the mitochondrial replicator. Proper spacing between the two modules, which varies from about 100 to 200 bp, is required for the Ars+ activity.

Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure

The complete sequences of nine Saccharomyces cerevisiae mitochondrial introns, six of which carry long open reading frames, have already been published. We have recently determined the sequence of an intron in the large ribosomal mitochondrial RNA of Kluyveromyces thermotolerans (Jacquier et al., in preparation), which we found to be closely related to its S. cerevisiae counterpart. This latter result prompted us to undertake a systematic search for possible homologous elements in the other, available sequences with the help of an original computer program. A previously unsuspected wealth of evolutionarily conserved sequences and secondary structures was thus uncovered. Seven at least of the available sequences may be folded up into elaborate secondary structure models, the cores of which are nearly identical. These models result in bringing together the exon-intron junctions into relatively close spatial proximity and looping out either all or most of the sequences in open reading frame, when present. These results and their possible implications with respect to the mechanism of splicing are discussed in the light of available genetic and biochemical data.

Highly conserved GC-rich palindromic DNA sequences flank tRNA genes in Neurospora crassa mitochondria

In sequencing a 2200 bp region of the Neurospora crassa mitochondrial DNA encoding the 3' end of the large rRNA gene and a cluster of six tRNA genes, we have found that the tRNA genes are flanked by highly conserved GC-rich palindromic DNA sequences. An 18 bp long core sequence, 5'-CC CTGCAG TA CTGCAG GG-3', containing two closely spaced Pst I sites, is common to all these palindromic sequences. Each of the eight Pst I sites mapped in the 2200 bp region consists of two closely spaced Pst I sites; thus this 2200 bp long segment actually contains 16 Pst I sites. Between 5-10% of the N. crassa DNA may consist of these GC-rich palindromic sequences that include the 18 base long core sequence. The same core sequence is present within both the 5' and 3' side of the intervening sequence of the large rRNA gene, close to, but not at, the intron-exon boundaries. We discuss probable roles for these sequences in N. crassa mitochondrial function, including their role as signals either in the synthesis or processing (or both) of RNA in the mitochondria.

Sequence of the intron and flanking exons of the mitochondrial 21S rRNA gene of yeast strains having different alleles at the omega and rib-1 loci

The complete nucleotide sequence has been determined for the intron, its junctions and the flanking exon regions of the 21S rRNA gene in three genetically characterized strains differing by their omega alleles (omega+, omega- and omega n) and by their chloramphenicol-resistant mutations at the rib-1 locus. Comparison of these DNA sequences shows that: --omega+ differs from omega- and omega n by the presence of the intron (1143 bp), as well as by a second and unexpected mini-insert (66 bp) located 156 bp upstream within the exon, whose nature and functions are still unknown but whose striking palindromic structure may suggest a mitochondrial transposable element. --The two mutations C321R and C323R correspond to two different monosubstitutions, 56 bp apart in the omega- and omega n strains but separated by the intron in the omega+ strains. In relation to previous genetic results, a model is discussed assuming that the interactions of two different regions or genetic loci determine the chloramphenicol resistance, one of which contains the omega n mutations. --A long uninterrupted coding sequence able to specify a 235 amino acid polypeptide exists within the intron. This remarkable observation gives new insight into the origin of the mitochondrial introns and raises the question of the possible functions of intron-encoded polypeptides. Finally, sequence comparisons with evolutionarily distant organisms, showing that different rRNA introns are inserted at different positions of an otherwise highly conserved region of the gene, suggest a recent insertion of these introns and a mechanism for splicing after the assembly of the large ribosomal subunit.

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.

Some yeast mitochondrial RNAs are circular

11S and 18S fractions of yeast mitochondrial RNAs, isolated by electrophoresis through agarose gels, have been found by electron microscopy to contain approximately 50% circular molecules. Circles in the 11S fraction have a contour length of 0.36 +/- 0.02 micron, which is approximately equal to the length of the majority of linear molecules also present. Circles in the 18S fraction have an average length of 0.78 +/- 0.11 micron. The size distribution is broader than for the 11S fraction, and we cannot exclude the possibility that more than one size class may be present. The 11S circular RNA forms circular R loops and RNA-DNA hybrids with DNA fragments of the oxi 3 region of mtDNA, which contains the structural gene for subunit 1 of cytochrome oxidase. As judged from the electron micrographs, the complete RNA participates in hybrid formation and the sequences coding for it appear to be continuous. Both 11S and 18S circles withstand treatment with DNAase and pronase. They are not eliminated by treatment with 1 M glyoxal in 50% formamide for 1 hr at 50 degrees C. We conclude that they are covalently closed. The function of the circular RNAs is unknown. They may be active as mRNAs, storage forms, or arise in a cut-and-splice process which generates mRNAs from longer transcripts.

Excision sequences in the mitochondrial genome of yeast

It is well established that spontaneous cytoplasmic 'petite' mutants of Saccharomyces cerevisiae have mitochondrial genome units in which an excised segment of the parental wild-type genome has been tandemly amplified (Fig. 1), so that the excised segment becomes the repeat unit of the petite genome; the latter may in turn undergo further deletions leading to secondary petite genomes having shorter repeat units (see ref. 1 for a brief review). Recent investigations on the mitochondrial genomes of several spontaneous petite mutants have shown that frequently the ends of the excised segment correspond to short sequences of the wild-type genome which are extremely rich in GC, the GC clusters; alternatively, they seem to be located in the long AT-rich stretches, the AT spacers, which form at least half of the genome. As sequence repetitions have been demonstrated in both GC clusters and AT spacers, it is very likely that excision takes place by a mechanism involving illegitimate site-specific recombination events between homologous sequences, as previously postulated. We show here that the sequences involved in the excision of a particular spontaneous petite genome are direct nucleotide repeats located in the AT spacers.

The nucleotide sequence of the mitochondrial genome of a spontaneous "petite" mutant of yeast

The nucleotide sequence of the repeat unit of the mitochondrial genome of a spontaneous petite mutant of S. cerevisiae is reported. The sequence provides direct information on the AT-spacers and GC-clusters of the mitochondrial genome of yeast.