The unusual varl gene of yeast mitochondrial DNA

The translational activator Sov1 coordinates mitochondrial gene expression with mitoribosome biogenesis

Mitoribosome biogenesis is an expensive metabolic process that is essential to maintain cellular respiratory capacity and requires the stoichiometric accumulation of rRNAs and proteins encoded in two distinct genomes. In yeast, the ribosomal protein Var1, alias uS3m, is mitochondrion-encoded. uS3m is a protein universally present in all ribosomes, where it forms part of the small subunit (SSU) mRNA entry channel and plays a pivotal role in ribosome loading onto the mRNA. However, despite its critical functional role, very little is known concerning VAR1 gene expression. Here, we demonstrate that the protein Sov1 is an in bona fide VAR1 mRNA translational activator and additionally interacts with newly synthesized Var1 polypeptide. Moreover, we show that Sov1 assists the late steps of mtSSU biogenesis involving the incorporation of Var1, an event necessary for uS14 and mS46 assembly. Notably, we have uncovered a translational regulatory mechanism by which Sov1 fine-tunes Var1 synthesis with its assembly into the mitoribosome.

Effects of Psoralen on Histone-DNA Interactions Studied by Using Atomic Force Microscopy

The investigation of the DNA-histone interactions and factors that affect such interactions in the nucleosome is essential for understanding the role of chromatin organization in all cellular processes involved in the repair, transcription, and replication of the eukaryotic genome. As a kind of photosensitive molecule, psoralen (PSO) is used in the treatment of skin disease with ultraviolet light (PSO and ultra violet light, type A). The effect of treatment is remarkable, but the side effect is also obvious. PSO can be embedded in a 5' TA sequence in double-stranded DNA (dsDNA), and dsDNA is mainly wrapped around a histone octamer to form a nucleosome structure in human cells. Therefore, it is very necessary to explore the influence of PSO on DNA-histone interactions. To this end, the binding specificity and mode of DNA and histone in the presence or absence of PSO are investigated systematically. The results show that the presence of PSO (no matter if there is ultra violet light treatment) can increase the overall probability of histone binding to dsDNA while lowering the selectivity of histone binding to the specific DNA sequence in vitro. In addition, the increase of solution ionic strength can lower the ratio of histone binding to nonspecific DNA.

Population structure of mitochondrial genomes in Saccharomyces cerevisiae

Background

Rigorous study of mitochondrial functions and cell biology in the budding yeast, Saccharomyces cerevisiae has advanced our understanding of mitochondrial genetics. This yeast is now a powerful model for population genetics, owing to large genetic diversity and highly structured populations among wild isolates. Comparative mitochondrial genomic analyses between yeast species have revealed broad evolutionary changes in genome organization and architecture. A fine-scale view of recent evolutionary changes within S. cerevisiae has not been possible due to low numbers of complete mitochondrial sequences.

Results

To address challenges of sequencing AT-rich and repetitive mitochondrial DNAs (mtDNAs), we sequenced two divergent S. cerevisiae mtDNAs using a single-molecule sequencing platform (PacBio RS). Using de novo assemblies, we generated highly accurate complete mtDNA sequences. These mtDNA sequences were compared with 98 additional mtDNA sequences gathered from various published collections. Phylogenies based on mitochondrial coding sequences and intron profiles revealed that intraspecific diversity in mitochondrial genomes generally recapitulated the population structure of nuclear genomes. Analysis of intergenic sequence indicated a recent expansion of mobile elements in certain populations. Additionally, our analyses revealed that certain populations lacked introns previously believed conserved throughout the species, as well as the presence of introns never before reported in S. cerevisiae.

Conclusions

Our results revealed that the extensive variation in S. cerevisiae mtDNAs is often population specific, thus offering a window into the recent evolutionary processes shaping these genomes. In addition, we offer an effective strategy for sequencing these challenging AT-rich mitochondrial genomes for small scale projects.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1664-4) contains supplementary material, which is available to authorized users.

Programmed translational bypassing elements in mitochondria: structure, mobility, and evolutionary origin

Programmed translational bypassing enables ribosomes to 'ignore' a precise mRNA interval of several dozen nucleotides. Well-characterized bypassed sequences include hop and byp elements, present in bacteriophage T4 and mitochondria of the yeast Magnusiomyces capitatus, respectively. The bypassing mechanism of byps is probably similar to that of hop, yet the former appears more effective and less constrained as to sequence context. Furthermore, both elements are mobile but hop moves as part of a cassette including a homing endonuclease, whereas byps seem to spread like miniature DNA transposable elements known as GC clusters. Here, we argue that hop and byps arose independently by convergent evolution, and that byps evolved in magnusiomycete mitochondria due to (as yet unknown) alterations of the mitochondrial translation machinery.

Maintenance and expression of the S. cerevisiae mitochondrial genome--from genetics to evolution and systems biology

As a legacy of their endosymbiotic eubacterial origin, mitochondria possess a residual genome, encoding only a few proteins and dependent on a variety of factors encoded by the nuclear genome for its maintenance and expression. As a facultative anaerobe with well understood genetics and molecular biology, Saccharomyces cerevisiae is the model system of choice for studying nucleo-mitochondrial genetic interactions. Maintenance of the mitochondrial genome is controlled by a set of nuclear-coded factors forming intricately interconnected circuits responsible for replication, recombination, repair and transmission to buds. Expression of the yeast mitochondrial genome is regulated mostly at the post-transcriptional level, and involves many general and gene-specific factors regulating splicing, RNA processing and stability and translation. A very interesting aspect of the yeast mitochondrial system is the relationship between genome maintenance and gene expression. Deletions of genes involved in many different aspects of mitochondrial gene expression, notably translation, result in an irreversible loss of functional mtDNA. The mitochondrial genetic system viewed from the systems biology perspective is therefore very fragile and lacks robustness compared to the remaining systems of the cell. This lack of robustness could be a legacy of the reductive evolution of the mitochondrial genome, but explanations involving selective advantages of increased evolvability have also been postulated.

The mitochondrial genomes of sponges provide evidence for multiple invasions by Repetitive Hairpin-forming Elements (RHE)

Background

The mitochondrial (mt) genomes of sponges possess a variety of features, which appear to be intermediate between those of Eumetazoa and non-metazoan opisthokonts. Among these features is the presence of long intergenic regions, which are common in other eukaryotes, but generally absent in Eumetazoa. Here we analyse poriferan mitochondrial intergenic regions, paying particular attention to repetitive sequences within them. In this context we introduce the mitochondrial genome of Ircinia strobilina (Lamarck, 1816; Demospongiae: Dictyoceratida) and compare it with mtDNA of other sponges.

Results

Mt genomes of dictyoceratid sponges are identical in gene order and content but display major differences in size and organization of intergenic regions. An even higher degree of diversity in the structure of intergenic regions was found among different orders of demosponges. One interesting observation made from such comparisons was of what appears to be recurrent invasions of sponge mitochondrial genomes by repetitive hairpin-forming elements, which cause large genome size differences even among closely related taxa. These repetitive hairpin-forming elements are structurally and compositionally divergent and display a scattered distribution throughout various groups of demosponges.

Conclusion

Large intergenic regions of poriferan mt genomes are targets for insertions of repetitive hairpin- forming elements, similar to the ones found in non-metazoan opisthokonts. Such elements were likely present in some lineages early in animal mitochondrial genome evolution but were subsequently lost during the reduction of intergenic regions, which occurred in the Eumetazoa lineage after the split of Porifera. Porifera acquired their elements in several independent events. Patterns of their intra-genomic dispersal can be seen in the mt genome of Vaceletia sp.

Biogenesis and replication of small plasmid-like derivatives of the mitochondrial DNA in Neurospora crassa

For reasons that are not obvious, sets of related, small, plasmid-like elements appear spontaneously and become amplified in the mitochondria of some cytochrome-deficient and/or UV-sensitive mutants of Neurospora crassa. These plasmid-like DNAs are multimeric series of circular molecules, each consisting of a finite number of identical tandem repeats of a relatively short mtDNA-derived nucleotide sequence (monomer). The plasmid-like elements that have been characterized in this study consist of monomers that vary in length from 125 to 296 base pairs, depending on the strain of origin. Each monomer includes a GC-rich palindrome that is followed by the promoter and a short section of the 5' terminal region of the mitochondrial large-subunit rRNA gene (rnl). Analyses of the nucleotide sequences of variants of this group of elements indicates that they are not generated by intra-molecular recombination, but are the result of single- or double-strand DNA breaks that are produced by a mismatch or base excision repair process. These elements do not appear to contain a defined origin of replication, but replicate by a recombination-dependent rolling-circle mechanism. One- and two-dimensional gel electrophoresis of the plasmid-like element derived Hind III and Pst I fragments combined with S1 nuclease treatments suggest that the intergenic GC-rich palindromes, which are ubiquitous in the mtDNA Neurospora, could be replication fork pausing points.

Intramolecular recombination and deletions in mitochondrial DNA of senescent, a nuclear-gene mutant of Neurospora crassa exhibiting “death” phenotype

In Neurospora crassa, a nuclear-gene mutant, senescent, derived from a phenotypically normal wild isolate of Neurospora intermedia exhibits a 'death' phenotype. Regardless of the composition of the culture medium, the mycelium ceases to grow in 2-6 subcultures at 26 degrees C and 1 or 2 subcultures at 34 degrees C. Senescence of vegetative mycelium is associated with deficiencies in cytochromes aa3 and b and reduced oxygen uptake. The restriction fragment analysis of mitochondrial DNA from senescing mycelia showed deletions and gross sequence rearrangements. Analysis of mitochondrial DNA of (sen + sen+) heterokaryons constructed with "excess" sen cytoplasm suggested correlation between mtDNA deletions and senescence. Three novel sen-specific EcoRI fragments of sizes 3.6, 3.9, and 4.4 kb were cloned, sequenced, and analyzed. Nucleotide sequences of the sen-specific EcoRI fragments suggested that deletions were a consequence of intramolecular recombination between EcoRI-5 and -10 and/or between EcoRI-8 and -10. The recombination junctions were close to stretches of GC-rich-PstI palindromic sequences that potentially form stable hairpin structures and might facilitate recombination between homologous repeats as short as 6-10 bp. These observations suggest that the wild-type (sen+) allele encodes a factor that protects the mitochondrial genome from undergoing intramolecular recombination and deletions. In this respect sen+ (linkage group V) has a function similar to nd+ (linkage group I) and the two gene products probably have mutually exclusive roles in suppressing cruciform-associated and homologous recombination, respectively, thus safeguarding mitochondrial genome integrity. The sen+ allele most likely codes for a factor involved in recombination, repair or replication of the mitochondrial genome, or a transcription factor that regulates the expression of genes affiliated with mitochondrial DNA metabolism.

GC clusters and the stability of mitochondrial genomes of Saccharomyces cerevisiae and related yeats

The occurrence of GC clusters in Saccharomyces spp. and related yeasts was examined to clarify their association with the stability of intact mitochondrial genome. Abundance of nonspecific or specific GC clusters in these species decreases with phylogenetic distance from S. cerevisiae. Their number but not the number of replication origins correlates with the ability to form respiration-deficient mutants induced by ethidium bromide. This effect is not associated with the nuclear background since the cybrids having identical nuclei and mitochondria from different species gave similar results. In contrast to grand genomes, the presence of GC clusters in rho- mutants does not play any role in ethidium bromide induced mtDNA loss. The most plausible explanation for mitotically lost petite mtDNA seems to be dilution during the distribution.

Double-hairpin elements in the mitochondrial DNA of allomyces: evidence for mobility

The mitochondrial DNA (mtDNA) of the chytridiomycete fungus Allomyces macrogynus contains 81 G+C-rich sequence elements that are 26-79 bases long and can be folded into a unique secondary structure consisting of two stem-loops. At the primary sequence level, the conservation of these double-hairpin elements (DHEs) is variable, ranging from marginal to complete identity. Forty of these DHEs are inserted in intergenic regions, 35 in introns, and 6 in variable regions of rRNA genes. Ten DHEs are inserted into other DHE elements (twins); two even form triplets. A comparison of DHE sequences shows that loop regions contain more sequence variation than helical regions and that the latter often contain compensatory base changes. This suggests a functional importance of the DHE secondary structure. We further identified nine DHEs in a 4-kb region of Allomyces arbusculus, a close relative of A. macrogynus. Eight of these DHEs are highly similar in sequence (90%-100%) to those in A. macrogynus, but only five are inserted at the same positions as in A. macrogynus. Interestingly, DHEs are also found in the mtDNAs of other chytridiomycetes, as well as certain zygomycete and ascomycete fungi. The overall distribution pattern of DHEs in fungal mtDNAs suggests that they are mobile elements.

The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae

The currently available yeast mitochondrial DNA (mtDNA) sequence is incomplete, contains many errors and is derived from several polymorphic strains. Here, we report that the mtDNA sequence of the strain used for nuclear genome sequencing assembles into a circular map of 85,779 bp which includes 10 kb of new sequence. We give a list of seven small hypothetical open reading frames (ORFs). Hot spots of point mutations are found in exons near the insertion sites of optional mobile group I intron-related sequences. Our data suggest that shuffling of mobile elements plays an important role in the remodelling of the yeast mitochondrial genome.

The ATP-dependent PIM1 protease is required for the expression of intron-containing genes in mitochondria

The ATP-dependent PIM1 protease, a Lon-like protease localized in the mitochondrial matrix, is required for mitochondrial genome integrity in yeast. Cells lacking PIM1 accumulate lesions in the mitochondrial DNA (mtDNA) and therefore lose respiratory competence. The identification of a multicopy suppressor, which stabilizes mtDNA in the absence of PIM1, enabled us to characterize novel functions of PIM1 protease during mitochondrial biogenesis. The synthesis of mitochondrially encoded cytochrome c oxidase subunit I (CoxI) and cytochrome b (Cob) is impaired in pim1 mutants containing mtDNA. PIM1-mediated proteolysis is required for the translation of mature COXI mRNA. Moreover, deficiencies in the splicing of COXI and COB transcripts, which appear to be restricted to introns encoding mRNA maturases, were observed in cells lacking the PIM1 gene. Transcripts of COXI and COB genes harboring multiple introns are degraded in the absence of PIM1. These results establish multiple, essential functions of the ATP-dependent PIM1 protease during mitochondrial gene expression.

Mitochondrial ribosomal proteins (MRPs) of yeast

Mitochondrial ribosomal proteins (MRPs) are the counterparts in that organelle of the cytoplasmic ribosomal proteins in the host. Although the MRPs fulfil similar functions in protein biosynthesis, they are distinct in number, features and primary structures from the latter. Most progress in the eludication of the properties of individual MRPs, and in the characterization of the corresponding genes, has been made in baker's yeast (Saccharomyces cerevisiae). To date, 50 different MRPs have been determined, although biochemical data and mutational analysis propose a total number which is substantially higher. Surprisingly, only a minority of the MRPs that have been characterized show significant sequence similarities to known ribosomal proteins from other sources, thus limiting the deduction of their functions by simple comparison of amino acid sequences. Further, individual MRPs have been characterized functionally by mutational studies, and the regulation of expression of MRP genes has been described. The interaction of the mitochondrial ribosomes with transcription factors specific for individual mitochondrial mRNAs, and the communication between mitochondria and the nucleus for the co-ordinated expression of ribosomal constituents, are other aspects of current MRP research. Although the mitochondrial translational system is still far from being described completely, the yeast MRP system serves as a model for other organisms, including that of humans.

Molecular genetics of the peptidyl transferase center and the unusual Var1 protein in yeast mitochondrial ribosomes

Mitochondria possess their own ribosomes responsible for the synthesis of a small number of proteins encoded by the mitochondrial genome. In yeast, Saccharomyces cerevisiae, the two ribosomal RNAs and a single ribosomal protein, Var1, are products of mitochondrial genes, and the remaining approximately 80 ribosomal proteins are encoded in the nucleus. The mitochondrial translation system is dispensable in yeast, providing an excellent experimental model for the molecular genetic analysis of the fundamental properties of ribosomes in general as well as adaptations required for the specialized role of ribosomes in mitochondria. Recent studies of the peptidyl transferase center, one of the most highly conserved functional centers of the ribosome, and the Var1 protein, an unusual yet essential protein in the small ribosomal subunit, have provided new insight into conserved and divergent features of the mitochondrial ribosome.

Contribution of ultra-short invasive elements to the evolution of the mitochondrial genome in the genus Podospora

In the filamentous fungus Podospora anserina, senescence is associated with major rearrangements of the mitochondrial DNA. The undecamer GGCGCAAGCTC has been described as a preferential site for these recombination events. We show that: (i) copies of this short sequence GGCGCAAGCTC are present in unexpectedly high numbers in the mitochondrial genome of this fungus; (ii) a short cluster of this sequence, localised in a group II intronic ORF, encodes amino acids that disrupt a protein domain that is otherwise highly conserved between various species; (iii) most of the polymorphisms observed between three related species, P.anserina, P.curvicolla and P.comata, are associated with the presence/absence of this sequence; (iv) this element lies at the boundaries of major rearrangements of the mitochondrial genomes; (v) at least two other short elements in the Podospora mitochondrial genomes display similar features. We suggest that these short elements, called MUSEs (mitochondrial ultra-short elements), could be mobile and that they contribute to evolution of the mitochondrial genome in the genus Podospora. A model for mobility involving a target DNA-primed reverse transcription step is discussed.

The gene for a subunit of an ABC-type heme transporter is transcribed together with the gene for subunit 6 of NADH dehydrogenase in rice mitochondria

We previously identified a chloroplast-derived (ct-derived) sequence of 32 base pairs (bp) in rice mitochondrial DNA that includes a part (30 bp; psitrnI) of a gene for isoleucine tRNA (CAU) of the chloroplast. Analyzing the ct-derived psitrnI, we found that an open reading frame (orf240), which was homologous to the gene for a subunit of an ATP-binding cassette-type (ABC-type) heme transporter, namely helC, of Rhodobacter capsulatus, and a gene for subunit 6 of NADH dehydrogenase (nad6) were located upstream of and downstream from the ct-derived psitrnI, respectively. Northern-blot hybridization and analysis by reverse transcription-polymerase chain reaction (RT-PCR) revealed that both orf240 and nad6 were co-transcribed in rice mitochondria. An analysis of PCR-amplified fragments of the region of orf240/nad6 from the DNA of some Gramineae suggests that the arrangement of orf240/nad6 was generated in the mitochondrial genome of the genus Oryza during evolution after its divergence from the other Gramineae. Most of the transcripts of orf240 are edited, with a change from cytidine to uridine, at 35 positions. Editing of the RNA changes 33 amino-acid residues among the 240 encoded amino-acid residues, suggesting that the orf240 gene is functional in rice mitochondria.

Incorporation of the yeast mitochondrial ribosomal protein Mrp2 into ribosomal subunits requires the mitochondrially encoded Var1 protein

Mrp2 is a protein component of the small subunit of mitochondrial ribosomes in the yeast Saccharomyces cerevisiae. We have examined the expression of Mrp2 in yeast mutants lacking mitochondrial DNA and found that the steady-state level of Mrp2 is dramatically decreased relative to wild type. These data suggest that the accumulation of Mrp2 depends on the expression of one or more mitochondrial gene products. The mitochondrial genome of S. cerevisiae encodes two components of the small ribosomal subunit, 15S rRNA and the Var1 protein, both of which are necessary for the formation of mature 37S subunits. Several studies have shown that in the absence of Var1 incomplete subunits accumulate, which lack a limited number of ribosomal proteins. Here, we show that Mrp2 is one of the proteins absent from subunits lacking Var1, indicating that Var1 plays an important role in the incorporation of Mrp2 into mitochondrial ribosomal subunits.

Suppression of a yeast mitochondrial RNA processing defect by nuclear mutations

The S. cerevisiae strain h56 is a temperature-sensitive mit- mutant containing a single nucleotide substitution in the region 5' to the reading frame of the mitochondrial var1 gene. The mutation decreases the efficiency of processing of a precursor RNA such that little var1 mRNA is produced at the restrictive temperature, 36 degrees C. This communication reports the isolation and characterization of several strains carrying nuclear mutations which suppress the temperature-sensitivity of h56. Both dominant and recessive suppressor mutations were isolated. One dominant suppressor strain (h56-S4) was characterized biochemically, and the mechanism of suppression shown to involve a restoration of precursor RNA processing at the restrictive temperature, with a concomitant increase in the synthesis of the var1 protein. It appears likely that the suppressing allele encodes a component of an RNA processing endoribonuclease active on var1 transcripts. A genomic library was constructed from the h56-S4 strain, and several plasmids showing suppressed activity were isolated. A preliminary analysis of these plasmids is presented.

Analysis of the role of the NUC1 endo/exonuclease in yeast mitochondrial DNA recombination

Mitochondrial DNA recombination was reduced in an yeast mutant lacking the NUC1 endo/exonuclease. Between linked markers in either the omega or cob region the frequency of recombination decreased nearly 50% compared to wild-type. Gene conversion frequencies in the var1 gene and in the omega region were also lower in the mutant strain. In particular, the gradient of gene conversion at omega was most affected by the absence of the NUC1 nuclease. In crosses between nuclease-deficient and wild-type strains, gene conversion frequencies at omega were reduced only when the omega+ allele was contributed to the zygote by the nuclease-deficient parent. We propose that the 5' exonuclease activity of the NUC1 nuclease functions during recombination to enlarge heteroduplex tracts following a double-strand break in DNA. In crosses between nuclease-deficient and wild-type strains, the anisotropy in gene conversion frequencies at omega is hypothesized to be due to the slow mixing of parental mitochondrial membranes as they fuse in the zygote.

Genes for ribosomal proteins S3, L16, L5 and S14 are clustered in the mitochondrial genome of Brassica napus L

We have cloned and sequenced an 8.9-kb mitochondrial-DNA fragment from rapeseed (Brassica napus L.). The nucleotide sequence indicates a gene cluster that encodes four ribosomal proteins (S3, L16, L5, S14), two tRNA genes (trnD, trnK), and the 5' region of the cob gene. The arrangement of these seven genes is trnD-trnK-rps3-rpl16-rpl5-rps14-cob. The rps3 and rpl16 frames overlap by 131 bp. The rpl5 and rps14 genes are separated by a 4-bp spacer. A 1474-basepair intron is located in the rps3 gene. The tRNA(Asp) gene (trnD) is very similar to the corresponding gene from chloroplasts (cp-like-tRNA(Asp)). Gene-specific probes for each ribosomal protein gene, and for the cp-like-trnD, trnK and cob genes, hybridized to a common pre-mRNA of an estimated size of 10 kilobases, indicating that these seven genes may be expressed as a single transcription unit. The rps3-rpl16-rpl5-rps14 region of B. napus mtDNA may function as a ribosomal operon, similar to the S10 and SPC operons of Escherichia coli and to the ribosomal protein operon of the chloroplast genome from Euglena gracilis.

Ribosomal protein gene rpl5 is cotranscribed with the nad3 gene in Oenothera mitochondria

The rpl5 ribosomal protein gene was identified in the mitochondrial genome of the higher plant Oenothera berteriana. The gene is present in a unique genomic location upstream of the gene encoding subunit 3 of the NADH dehydrogenase (nad3). Both genes are cotranscribed, and the mRNA is modified at several cytidine residues by RNA editing. Analysis of the editing profiles of both genes by direct cDNA analysis and polymerase chain reaction (PCR) revealed that not all transcripts are fully edited at all sites. Eight of the nine C to U conversions in the rpl5 reading frame are non-silent and change the deduced amino acid sequence. The genes of the prokaryotic-like cistron that includes the rpsl9, rps3, rpl16, rpl5, and rpsl4 genes, which is at least partially conserved in the mitochondrial genomes of other higher and lower plants, are dispersed in the Oenothera mitochondrial genome.

RNA editing in trypanosomes. The us(e) of guide RNAs

Guide RNAs are encoded in maxicircle and minicircle DNA of trypanosome mitochondria. They play a pivotal role in RNA editing, a process during which the nucleotide sequence of mitochondrial RNAs is altered by U-insertion and deletion. Guide RNAs vary in length from 35 to 78 nucleotides, which correlates with the variation in length of the three functionally important regions of which they are composed: (i) a 4-14 nucleotide 'anchor' sequence embedded in the 5' region, which is complementary to a target sequence on the pre-edited RNA downstream of an editing domain, (ii) a middle part containing the editing information, which ranges from guiding the insertion of just one U into one site to that of the insertion of 32 Us into 10 sites, and (iii) a 5-24 nucleotide 3' terminal oligo [U] extension. Moreover, a variable uridylation site creates gRNAs containing a varying segment of editing information for the same domain. Comparison of different guide RNAs demonstrates that, besides the U-tail, they have no obvious common primary and secondary sequence motifs, each particular sequence being unique. The occurrence in vivo and the synthesis in vitro of chimeric molecules, in which a guide RNA is covalently linked through its 3' U-tail to an editing site of a pre-edited RNA, suggests that RNA editing occurs by consecutive transesterification reactions and is evidence that the guide RNAs not only provide the genetic information, but also the Us themselves.

Gene clusters for ribosomal proteins in the mitochondrial genome of a liverwort, Marchantia polymorpha

We detected 16 genes for ribosomal proteins in the complete sequence of the mitochondrial DNA from a liverwort, Marchantia polymorpha. The genes formed two major clusters, rps12-rps7 and rps10-rpl2-rps19-rps3-rpl16-rpl5- rps14-rps8- rpl6-rps13-rps11-rps1, very similar in organization to Escherichia coli ribosomal protein operons (str and S10-spc-alpha operons, respectively). In contrast, rps2 and rps4 genes were located separately in the liverwort mitochondrial genome (the latter was part of the alpha operon in E. coli). Furthermore, several ribosomal proteins encoded by the liverwort mitochondrial genome differed substantially in size from their counterparts in E. coli and liverwort chloroplast.

Ribosomal protein S19 is encoded by the mitochondrial genome in Petunia hybrida

The rps19 ribosomal protein gene, which has not been previously reported in any mitochondrial genome, was identified by sequence analysis in the mitochondrial DNA of the higher plant Petunia hybrida. According to the sequence of eight rps19 cDNAs, seven C to U conversions with respect to the genomic sequence are present in rps19 transcripts. Not all transcripts are fully edited at these seven sites. Six of the seven C to U conversions change the encoded amino acid sequence by altering four codons. The rps19 gene is located entirely within a repeat sequence which is present in three copies on the 443 kb genome. Due to intragenomic recombination across these repeats, Petunia rps19 is present in nine different genomic environments.

Polymorphisms in tandemly repeated sequences of Saccharomyces cerevisiae mitochondrial DNA

A spontaneously arising mitochondrial DNA (mtDNA) variant of Saccharomyces cerevisiae has been formed by two extra copies of a 14-bp sequence (TTAATTAAATTATC) being added to a tandem repeat of this unit. Similar polymorphisms in tandemly repeated sequences have been found in a comparison between mtDNAs from our strain and others. In 5850 bp of intergenic mtDNA sequence, polymorphisms in tandemly repeated sequences of three or more base pairs occur approximately every 400-500 bp whereas differences in 1-2 bp occur approximately every 60 bp. Some polymorphisms are associated with optional G + C-rich sequences (GC clusters). Two such optional GC clusters and one A + T repeat polymorphism have been discovered in the tRNA synthesis locus. In addition, the variable presence of large open reading frames are documented and mechanisms for generating intergenic sequence diversity in S. cerevisiae mtDNA are discussed.

Short dispersed repeats localized in spacer regions of Chlamydomonas reinhardtii mitochondrial DNA

In the mtDNA of Chlamydomonas reinhardtii, a unicellular green alga, we have identified a set of short repeated sequences up to 65 nucleotides long, each of which contains the palindromic consensus motif CTCGG(N4-14)CCGAG. Most of these repeated elements are localized in spacer regions that flank the transcribed coding regions of C. reinhardtii mtDNA. These algal mitochondrial repeats have features reminiscent of short repeats in some fungal mtDNAs, such as GC clusters in Saccharomyces cerevisiae and PstI palindromes in Neurospora crassa. The location of these elements suggests that they could play a role in gene expression, e.g., post-transcriptional processing, in C. reinhardtii mitochondria.

A GC cluster repeat is a hotspot for mit- macro-deletions in yeast mitochondrial DNA

In a random collection of mit- mutations of the yeast strain 777-3A we find that deletions are exceptionally frequent in the OXI3 gene, a large mosaic gene coding for subunit I of cytochrome oxidase. About 10% of all oxi3-mutants carry the same macro-deletion, del-A, extending from the 5' non-translated leader of OXI3 to intron 5b of this gene. Determination of the respective wild-type sequences and of the del-A junction sequence revealed that the end-points of the deletion are in two GC clusters with 31 bp sequence identity which are located at a distance of 11.3 kb. We speculate that not only the sequence identity of the two GC clusters but also the palindromic structure of these putatively mobile elements of yeast mitochondrial DNA (mtDNA) plays a role in deletion formation.

Mitochondrial genome of Saccharomyces douglasii: genes coding for components of the protein synthetic apparatus

Mitochondrial genes coding for some components of the protein synthetic apparatus in S. douglasii have been studies in detail. A region containing stretches of high homology to the S. cerevisiae tRNA synthesis locus (TSL) and the tRNA(fmet) gene has been identified and sequenced. The organization of this region was very similar to that present in S. cerevisiae, including the presence of a possible transcription starting signal. The S. douglasii TSL gene is shorter due to several deletions which, however, do not involve the regions coding for RNA domains know to be required for the catalytic activity of mitochondrial RNAse P. The S. douglasii LSU rRNA gene has been shown to contain a typical group I intron highly homologous to its S. cerevisiae counterpart, except for the absence of the open reading frame which in S. cerevisiae codes for I-SceI endonuclease.

Mobility of two optional G + C-rich clusters of the var1 gene of yeast mitochondrial DNA

Yeast mtDNA contains two different kinds of mobile optional sequences, two group I introns and a short G + C-rich insertion to some var1 genes. Movement of each element in crosses has been called gene conversion though little is known about the mechanism of G + C cluster conversion. A new allele of the var1 gene found in mtDNA of Saccharomyces capensis is described that permitted a more detailed comparison between intron mobility and G + C cluster conversion. The S. capensis var1 gene lacks the cc+ element present in all S. cerevisiae var 1 genes and the previously described optional a+ element. In crosses with cc+ a- and cc+ a+ S. cerevisiae strains, both clusters were found to be mobile and, in the latter cross, appear to convert independently and only to homologous insertion sites. No evidence for flanking marker coconversion (a hallmark feature of intron conversion) was obtained despite the availability of nearby physical markers on both sides of cluster conversion sites. These data indicate that G + C cluster conversion has only a superficial resemblance to intron mobility; analogies to procaryotic transposition mechanisms are considered.

Behavior of the [mi-3] mutation and conversion of polymorphic mtDNA markers in heterokaryons of Neurospora crassa

We have examined the behavior of the [mi-3] mitochondrial mutation and two physical mtDNA markers in heterokaryotic cultures of Neurospora crassa. Previous workers showed that a 1.2-kilobase insertion in the larger polymorphic form of EcoRI-5 restriction fragment is a site of high frequency and rapid unidirectional gene conversion. We have confirmed this observation and determined by DNA sequence analysis that the insertion in the EcoRI-5 fragment corresponds precisely to an optional intron that contains a long open reading frame in the ND1 gene. Thus, the conversion of the short, intron-lacking, form of EcoRI-5 to the longer, intron-containing, form may be analogous to the unidirectional gene conversion events catalyzed by intron-encoded proteins in other organisms. The resolution of two polymorphic forms of the mtDNA EcoRI-9 restriction fragment in our heterokaryons differs from that observed previously and suggests that this locus is not a site of gene conversion in our heterokaryon pair. The size polymorphism of the EcoRI-9 fragments is due to a tandemly reiterated 78-base-pair sequence which occurs two times in the short form and three times in the long form. One copy of the repeat unit and 66 base pairs following it have been duplicated from the ND2 gene which is located about 30 kilobases distant on the mtDNA. In contrast to the [poky] mitochondrial mutant, which was completely dominant over wild-type mitochondria in heterokaryons, the [mi-3] mutant was recovered in only seven of twenty heterokaryons after ten cycles of conidiation and subculturing. The resolution of the [mi-3] or wild-type phenotype in heterokaryons may depend solely on random factors such as allele input frequency, drift, and segregation rather than specific dominant or suppressive effects.

Putative target sites for mobile G + C rich clusters in yeast mitochondrial DNA: single elements and tandem arrays

GC clusters constitute the major repetitive elements in the mitochondrial (mt) genome of the yeast Saccharomyces cerevisiae. Many of these clusters are optional and thus contribute much to the polymorphism of yeast mtDNAs. We have made a systematic search for polymorphic sites by comparing mtDNA sequences of various yeast strains. Most of the 26 di- or polymorphic sites found differ by the presence or absence of a GC cluster of the majority class, here referred to as the M class, which terminate with an AGGAG motif. Comparison of sequences with and without the GC clusters reveal that elements of the subclasses M1 and M2 are inserted 3' to a TAG, flanked by A + T rich sequences. M3 elements, in contrast, only occur in tandem arrays of two to four GC clusters; they are consistently inserted 3' to the AGGAG terminal sequence of a preexisting cluster. The TAG or the terminal AGGAG, therefore, are regarded as being part of the target sites for M1 and M2 or M3 elements, respectively. The dinucleotide AG is in common to both target sites; it also occurs at the 3' terminus (AGGAG). This suggests its duplication during GC cluster insertion. This notion is supported by the observation that GC clusters of the minor classes G and V similarily repeat at their 3' terminus a GT or an AA dinucleotide, respectively, from their putative target sites.

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.

A latent intron-encoded maturase is also an endonuclease needed for intron mobility

Some yeast mitochondrial introns encode proteins that promote either splicing (maturases) or intron propagation via gene conversion (the fit1 endonuclease). We surveyed introns in the coxl gene for their ability to engage in gene conversion and found that the group I intron, al4 alpha, was efficiently transmitted to genes lacking it. An endonucleolytic cleavage is detectable in recipient DNA molecules near the site of intron insertion in vivo and in vitro. Conversion is dependent on an intact al4 alpha open reading frame. This intron product is a latent maturase, but these data show that it is also a potent endonuclease involved in recombination. Dual function proteins that cleave DNA and facilitate RNA splicing may have played a pivotal role in the propagation and tolerance of introns.

The genes coding for subunit 3 of NADH dehydrogenase and for ribosomal protein S12 are present in the wheat and maize mitochondrial genomes and are co-transcribed

A region of about 2 kb which is almost identical in the wheat and maize mitochondrial genomes has been sequenced. It contains a tRNA(Ser) gene, a pseudo-tRNA gene and two open reading frames coding for subunit 3 of the NADH dehydrogenase (118 amino acids) and for ribosomal protein S12 (125 amino acids). The two protein genes are separated by 47 bp and are co-transcribed in wheat and maize. Two transcripts of about 0.9 kb and 3.0 kb, each coding for both proteins, have been characterized, but no monocistronic transcript was detected. Each gene is preceded by a putative ribosome binding site. The pseudo-tRNA gene is interrupted by two insertion sequences in wheat and by one in maize. The origin of the additional interrupting sequence found in the wheat pseudo-tRNA gene, which is also present elsewhere in the mitochondrial genomes, is discussed.

Studies of sequence heterogeneity of mitochondrial DNA from rat and mouse tissues: evidence for an increased frequency of deletions/additions with aging

To obtain information on the extent of random nucleotide changes in mitochondrial DNA (mtDNA) from different organs of young adult and senescent Fischer 344 rats, the temperature of thermal denaturation (tm) was measured in (1) the native mtDNA cut at a single SstI site and (2) the reannealed duplexes formed after the initial melting of the mtDNA sample. No change was found between the two tm values in either young or senescent mtDNA, suggesting that the overall mismatch in nucleotide sequence in these samples was below the resolution of the method estimated at about 0.2%. In another experiment, mtDNA samples from young adult or senescent BALB/c mouse liver were digested with EcoRI, denatured and allowed to reanneal. The duplexes formed by the 14-kb EcoRI fragment were analyzed in randomly taken electron micrographs for the occurrence of mismatched segments. About 1.8% of reconstituted duplexes in adult mtDNA and 11% of those in senescent mtDNA contained small loops or knobs suggestive of deletions/additions of about 400 +/- 150 nucleotides. These data correspond to about 1% of the native mtDNA population in adult liver and about 5% in senescent liver having deleted/inserted segments. Although deletions/insertions may occur at variable sites, their distribution appears to be non-random. These findings suggest that small sequence rearrangements, which have been observed previously in unicircular dimers of mouse and human mtDNA, occur also in monomeric mtDNA from normal tissues and accumulate with aging.

In vivo double-strand breaks occur at recombinogenic G + C-rich sequences in the yeast mitochondrial genome

An optional 46-base-pair G + C-rich element (GC cluster) in the coding region of the yeast mitochondrial var1 gene inserts preferentially in crosses into recipient alleles that lack the sequence. Unlike a similar gene conversion event involving the insertion of an optional 1143-base-pair intron, the mitochondrial 21S rRNA gene, which requires the action of a protein encoded by a gene within that intron, conversion of the var1 GC cluster does not require any protein product of the mitochondrial genome. We have detected double-strand breaks in the var1 gene in mitochondrial DNA isolated from unmated haploid rho+ and rho- strains at or near the boundaries of the optional GC cluster, as well as at a conserved copy of that sequence 160 base pairs upstream. No double-strand breaks were detected in the recipient var1 DNA molecules in the vicinity of the optional GC cluster target sequence. This contrasts with 21S rRNA-encoding DNA (rDNA) intron conversion where the recipient, but not the donor DNA, is cleaved at the element insertion site. These results suggest that although the 21S rDNA intron and the var1 GC cluster are preferentially inserted into their respective short alleles, these conversions probably occur by different mechanisms.

The mitochondrial S13 ribosomal protein gene is silent in wheat embryos and seedlings

The sequence of a wheat mitochondrial reading frame encoding a protein homologous to the E. coli S13 small subunit ribosomal protein has been determined. The gene is located immediately downstream of a 1.4 kb recombinationally-active repeat element that contains the ATPase subunit 6 gene. The coding regions of the two genes are separated by only 153 bp, the shortest distance yet observed between protein-coding genes in plant mitochondria. However, their transcript profiles differ markedly. The ATPase 6 gene displays a single, prominent mRNA of approximately 1.4 kb, whereas the S13 gene shows no stable transcript as judged by Northern blot analysis of wheat mitochondrial RNA isolated from different developmental stages. A short segment of the 26S rRNA gene is located downstream of the S13 gene and its presence illustrates the frequent DNA duplication/rearrangements found in wheat mitochondria.

Excision-amplification of mitochondrial DNA during senescence in Podospora anserina. A potential role for an 11 base-pair consensus sequence in the excision process

Three novel mitochondrial excision-amplification plasmids of Podospora anserina were identified and the excision-junction sites on the mitochondrial genome determined. All three plasmids were at least partially derived from a common region of the mitochondrial genome termed EcoRI-7 (E7). The entire 5651 base-pair sequence of E7 is presented. Included within this sequence are the E7-specific excision-junction sites of these novel plasmids, the localizations of nine tRNA genes, and the localization of a class I intron of the large rRNA mitochondrial gene. The E7 region contains the 3' portion of this large rRNA gene. Formation of these three novel plasmids as well as other previously described mitochondrial plasmids was found to be associated with the presence of an 11 base-pair consensus sequence, GGCGCAAGCTC, or its complementary sequence. A possible role for this consensus sequence and its complement in plasmid formation and the senescence process of Podospora is discussed. A possible role for the tRNA genes in plasmid formation is considered.

Kinetic and segregational analysis of mitochondrial DNA recombination in yeast

A pair of yeast strains of opposite mating type was constructed to contain polymorphisms at three loci on the mitochondrial genome--the 21 S rRNA gene, var1, and cob--such that parental and recombinant forms of these genes could be easily detected by Southern blot analysis. These polymorphisms were used to measure in a single cross gene conversions at the 21 S rRNA and var1 loci and a reciprocal recombination at cob. For all three loci, recombination initiates at about the same time, 4 to 6 h after mixing cells, and increases with similar kinetics over a 24-h period. The segregation of parental and recombinant forms of these genes was then followed by pedigree analysis. The results, which show a high variance in the distribution of parental and recombinant forms of all three genes in cells derived from both the first bud and the mother zygote, are consistent with the segregation of a small number of mitochondrial DNA molecules from the zygote to diploid buds. Based on these results and previous experiments of this type, a limited "zone of mixing" of parental mitochondrial DNA molecules probably exists in the zygote. The extent of sampling from this zone, together with the intrinsic properties of the recombination events themselves, is likely to determine the observed pattern of recombination of mitochondrial DNA sequences at the population level.

Transmission of mitochondrial and chloroplast genomes in crosses of Chlamydomonas

Physical differences between organelle genomes of the interfertile species Chlamydomonas reinhardtii and Chlamydomonas smithii have been used to demonstrate that sexual zygotes transmit chloroplast and mitochondrial DNA from opposite mating types. Processes responsible can be separated functionally and genetically, although both are controlled by mating type. In vegetative diploids, chloroplast and mitochondrial genomes are transmitted biparentally, but a 1-kilobase insert present in the C. smithii mitochondrial genome spreads unidirectionally to all C. reinhardtii genomes in a manner reminiscent of the intron found in the mitochondrial 21S rRNA gene of omega + strains of yeast.