The mitochondrial genome on its way to the nucleus: different stages of gene transfer in higher plants

Multiple losses and transfers to the nucleus of two mitochondrial succinate dehydrogenase genes during angiosperm evolution

Unlike in animals, the functional transfer of mitochondrial genes to the nucleus is an ongoing process in plants. All but one of the previously reported transfers in angiosperms involve ribosomal protein genes. Here we report frequent transfer of two respiratory genes, sdh3 and sdh4 (encoding subunits 3 and 4 of succinate dehydrogenase), and we also show that these genes are present and expressed in the mitochondria of diverse angiosperms. Southern hybridization surveys reveal that sdh3 and sdh4 have been lost from the mitochondrion about 40 and 19 times, respectively, among the 280 angiosperm genera examined. Transferred, functional copies of sdh3 and sdh4 were characterized from the nucleus in four and three angiosperm families, respectively. The mitochondrial targeting presequences of two sdh3 genes are derived from preexisting genes for anciently transferred mitochondrial proteins. On the basis of the unique presequences of the nuclear genes and the recent mitochondrial gene losses, we infer that each of the seven nuclear sdh3 and sdh4 genes was derived from a separate transfer to the nucleus. These results strengthen the hypothesis that angiosperms are experiencing a recent evolutionary surge of mitochondrial gene transfer to the nucleus and reveal that this surge includes certain respiratory genes in addition to ribosomal protein genes.

Mitochondrial sequence migrated downstream to a nuclear V-ATPase B gene is transcribed but non-functional

A promiscuous nuclear sequence containing a mitochondrial DNA fragment was isolated from rice. Nucleotide sequence analysis reveals that the cDNA clone #21 carries a mitochondrial sequence homologous to the 3' portion of the rps19 gene followed by the 5' portion of the rps3 gene. The mitochondrial sequence is present in an antisense orientation. Sequence comparison of the #21 cDNA with the original mitochondrial sequence shows 99% similarity, suggesting a recent transfer event. Moreover, evidence for a lack of an RNA editing event and retaining of the group II intron sequence strongly suggests that the sequence was transferred from mitochondrion to the nucleus via DNA rather than RNA as an intermediate. The upstream region to the mitochondria-derived sequence shows homology to part of the vacuolar H(+)-ATPase B subunit (V-ATPase B) gene. Isolation of a functional V-ATPase B cDNA and its comparison with the #21 cDNA reveal a number of nucleotide substitutions resulting in many translational stop codons in the #21 cDNA. This indicates that the #21 cDNA sequence is not functional. Analysis of genomic sequences shows the presence of five intron sequences in the #21 cDNA, whereas the functional V-ATPase B gene has 14 introns. Of these, three exons and their internal two introns are homologous to each other, suggesting a duplication event of V-ATPase B genomic DNA. The results of this investigation strongly suggest that the mitochondrial sequence was integrated in an antisense orientation into the pre-existing V-ATPase B pseudogene that can be transcribed and spliced. This represents a case of unsuccessful gene transfer from mitochondrion to the nucleus.

Subunit II of cytochrome c oxidase in Chlamydomonad algae is a heterodimer encoded by two independent nuclear genes

The mitochondrial genomes of Chlamydomonad algae lack the cox2 gene that encodes the essential subunit COX II of cytochrome c oxidase. COX II is normally a single polypeptide encoded by a single mitochondrial gene. In this work we cloned two nuclear genes encoding COX II from both Chlamydomonas reinhardtii and Polytomella sp. The cox2a gene encodes a protein, COX IIA, corresponding to the N-terminal portion of subunit II of cytochrome c oxidase, and the cox2b gene encodes COX IIB, corresponding to the C-terminal region. The cox2a and cox2b genes are located in the nucleus and are independently transcribed into mRNAs that are translated into separate polypeptides. These two proteins assemble with other cytochrome c oxidase subunits in the inner mitochondrial membrane to form the mature multi-subunit complex. We propose that during the evolution of the Chlorophyte algae, the cox2 gene was divided into two mitochondrial genes that were subsequently transferred to the nucleus. This event was evolutionarily distinct from the transfer of an intact cox2 gene to the nucleus in some members the Leguminosae plant family.

Reducing the genome size of organelles favours gene transfer to the nucleus

Endosymbiotic organelles exhibit strong genetic erosion during their evolution as a result of the loss of unnecessary genes and of gene transfer to the nucleus. The reasons for this erosion are much debated. Unidirectionality of DNA exchange between cell compartments could favour biased gene transfer, but selection might also act to favour nuclear localization of genes, for example, because organelles accumulate more mutations than do nuclei. Selection for rapid replication might be a general cause of organelle genome reduction. This selection also accounts for the compactness of organelle genomes.

Expression and translocation of Drosophila nuclear encoded cytochrome b(5) proteins to mitochondria

DNA sequence studies of cytochrome b(5) (Cyt-b) genes from Drosophila melanogaster and Drosophila virilis predict that the Drosophila Cyt-b proteins are extremely hydrophobic and have at least eight potential transmembrane spanning domains. Primary protein sequence analysis also predicts that the Cyt-b proteins have mitochondrial targeting sequences and they contain sites for potential post-translational modification similar to other cytochrome proteins. We report the characterization of the cytochrome b(5) proteins from Drosophila melanogaster and Drosophila virilis. We have used a Drosophila cytochrome b(5) specific antibody to demonstrate that cytochrome b(5) proteins are expressed in muscle-containing tissues in the fly. We also provide evidence that the nuclear encoded cytochrome b(5) protein that contains a mitochondrial targeting sequence is translocated to mitochondria.

Unusual location of a mitochondrial gene. Subunit III of cytochrome C oxidase is encoded in the nucleus of Chlamydomonad algae

The algae of the family Chlamydomonadaceae lack the gene cox3 that encodes subunit III of cytochrome c oxidase in their mitochondrial genomes. This observation has raised the question of whether this subunit is present in cytochrome c oxidase or whether the corresponding gene is located in the nucleus. Cytochrome c oxidase was isolated from the colorless chlamydomonad Polytomella spp., and the existence of subunit III was established by immunoblotting analysis with an antibody directed against Saccharomyces cerevisiae subunit III. Based partly upon the N-terminal sequence of this subunit, oligodeoxynucleotides were designed and used for polymerase chain reaction amplification, and the resulting product was used to screen a cDNA library of Chlamydomonas reinhardtii. The complete sequences of the cox3 cDNAs from Polytomella spp. and C. reinhardtii are reported. Evidence is provided that the genes for cox3 are encoded by nuclear DNA, and the predicted polypeptides exhibit diminished physical constraints for import as compared with mitochondrial-DNA encoded homologs. This indicates that transfer of this gene to the nucleus occurred before Polytomella diverged from the photosynthetic Chlamydomonas lineage and that this transfer may have occurred in all chlamydomonad algae.

Organellar genes: why do they end up in the nucleus?

Many mitochondrial and plastid proteins are derived from their bacterial endosymbiotic ancestors, but their genes now reside on nuclear chromosomes instead of remaining within the organelle. To become an active nuclear gene and return to the organelle as a functional protein, an organellar gene must first be assimilated into the nuclear genome. The gene must then be transcribed and acquire a transit sequence for targeting the protein back to the organelle. On reaching the organelle, the protein must be properly folded and modified, and in many cases assembled in an orderly manner into a larger protein complex. Finally, the nuclear copy must be properly regulated to achieve a fitness level comparable with the organellar gene. Given the complexity in establishing a nuclear copy, why do organellar genes end up in the nucleus? Recent data suggest that these genes are worse off than their nuclear and free-living counterparts because of a reduction in the efficiency of natural selection, but do these population-genetic processes drive the movement of genes to the nucleus? We are now at a stage where we can begin to discriminate between competing hypotheses using a combination of experimental, natural population, bioinformatic and theoretical approaches.

Frequent assimilation of mitochondrial DNA by grasshopper nuclear genomes

Multiple copies of mitochondrial-like DNA were found in the brown mountain grasshopper, Podisma pedestris (Orthoptera: Acrididae), paralogous to COI and ND5 regions. The same was discovered using the ND5 regions of nine other grasshopper species from four separate subfamilies (Podisminae, Calliptaminae, Cyrtacanthacridinae, and Gomphocerinae). The extra ND5-like sequences were shown to be nuclear in the desert locust, Schistocerca gregaria (Cyrtacanthacridinae), and probably so in P. pedestris and an Italopodisma sp. (Podisminae). Eighty-seven different ND5-like nuclear mitochondrial pseudogenes (Numts) were sequenced from 12 grasshopper individuals. Different nuclear mitochondrial pseudogenes, if descended from the same mitochondrial immigrant, will have diverged from each other under no selective constraints because of their loss of functionality. Evidence of selective constraints in the differences between any two Numt sequences (e.g., if most differences are at third positions of codons) implies that they have separate mitochondrial origins. Through pairwise comparisons of pseudogene sequences, it was established that there have been at least 12 separate mtDNA integrations into P. pedestris nuclear genomes. This is the highest reported rate of horizontal transfer between organellar and nuclear genomes within a single animal species. The occurrence of numerous mitochondrial pseudogenes in nuclear genomes derived from separate integration events appears to be a common phenomenon among grasshoppers. More than one type of mechanism appears to have been involved in generating the observed grasshopper Numts.

Nuclear integrations of mitochondrial DNA in primates: inference of associated mutational events

To infer the possible mutational events taking place along the interorganellar transfer of genetic material from mitochondria to the nucleus, four integrations of mitochondrial DNA (mtDNA) in the human genome were characterized together with their flanking nuclear sequences. By determining their presence/absence status in different primate species, these integrations were inferred to have occurred on the lineages leading to catarrhines (Old World monkeys and hominoids), to hominoids and to humans, respectively. In case of a polymorphic state, with respect to its presence in a certain species, each preintegration sequence was either cloned in the same species or in a primate taxon that branched off before the transfer of the mtDNA to the nucleus took place. For the four mtDNA integrations presented here, random mobilization of the mtDNA and differing mechanisms for generating free ends in the nuclear target sequences can be inferred. Additionally, no common sequence features at the preintegration sites could be observed for these integrations. Moreover, the comparisons of the sites before and after integration suggest different ways of integration. Thus, mtDNA integrations represent unique molecular recombinations in the evolutionary history and can, according to their presence/absence status in different species, help to determine the branching order in phylogenetic trees.

The mitochondrial genome of Arabidopsis is composed of both native and immigrant information

Plants contain large mitochondrial genomes, which are several times as complex as those in animals, fungi or algae. However, genome size is not correlated with information content. The mitochondrial genome (mtDNA) of Arabidopsis specifies only 58 genes in 367 kb, whereas the 184 kb mtDNA in the liverwort Marchantia polymorpha codes for 66 genes, and the 58 kb genome in the green alga Prototheca wickerhamii encodes 63 genes. In Arabidopsis' mtDNA, genes for subunits of complex II, for several ribosomal proteins and for 16 tRNAs are missing, some of which have been transferred recently to the nuclear genome. Numerous integrated fragments originate from alien genomes, including 16 sequence stretches of plastid origin, 41 fragments of nuclear (retro)transposons and two fragments of fungal viruses. These immigrant sequences suggest that the large size of plant mitochondrial genomes is caused by secondary expansion as a result of integration and propagation, and is thus a derived trait established during the evolution of land plants.

A single nuclear transcript encoding mitochondrial RPS14 and SDHB of rice is processed by alternative splicing: common use of the same mitochondrial targeting signal for different proteins

The rice mitochondrial genome has a sequence homologous to the gene for ribosomal protein S14 (rps14), but the coding sequence is interrupted by internal stop codons. A functional rps14 gene was isolated from the rice nuclear genome, suggesting a gene-transfer event from the mitochondrion to the nucleus. The nuclear rps14 gene encodes a long N-terminal extension showing significant similarity to a part of mitochondrial succinate dehydrogenase subunit B (SDHB) protein from human and a malarial parasite (Plasmodium falciparum). Isolation of a functional rice sdhB cDNA and subsequent sequence comparison to the nuclear rps14 indicate that the 5' portions of the two cDNAs are identical. The sdhB genomic sequence shows that the SDHB-coding region is divided into two exons. Surprisingly, the RPS14-coding region is located between the two exons. DNA gel blot analysis indicates that both sdhB and rps14 are present at a single locus in the rice nucleus. These findings strongly suggest that the two gene transcripts result from a single mRNA precursor by alternative splicing. Protein blot analysis shows that the size of the mature RPS14 is 16.5 kDa, suggesting removal of the N-terminal 22.6-kDa peptide region. Considering that the rice mitochondrial genome lacks the sdhB gene but contains the rps14-related sequence, transfer of the sdhB gene seems to have occurred before the transfer of the rps14 gene. The migration of the mitochondrial rps14 sequence into the already existing sdhB gene could bestow the capacity for nuclear expression and mitochondrial targeting.

Plastids and protein targeting

Plastids with two bounding membranes--as exemplified by red algae, green algae, plants, and glaucophytes--derive from primary endosymbiosis; a process involving engulfment and retention of a cyanobacterium by a phagotrophic eukaryote. Plastids with more than two bounding membranes (such as those of euglenoids, dinoflagellates, heterokonts, haptopytes, apicomplexa, cryptomonads, and chlorarachniophytes) probably arose by secondary endosymbiosis, in which a eukaryotic alga (itself the product of primary endosymbiosis) was engulfed and retained by a phagotroph. Secondary endosymbiosis transfers photosynthetic capacity into heterotrophic lineages, has apparently occurred numerous times, and has created several major eukaryotic lineages comprising upwards of 42,600 species. Plastids acquired by secondary endosymbiosis are sometimes referred to as "second-hand." Establishment of secondary endosymbioses has involved transfer of genes from the endosymbiont nucleus to the secondary host nucleus. Limited gene transfer could initially have served to stabilise the endosymbioses, but it is clear that the transfer process has been extensive, leading in many cases to the complete disappearance of the endosymbiont nucleus. One consequence of these gene transfers is that gene products required in the plastid must be targeted into the organelle across multiple membranes: at least three for stromal proteins in euglenoids and dinoflagellates, and across five membranes in the case of thylakoid lumen proteins in plastids with four bounding membranes. Evolution of such targeting mechanisms was obviously a key step in the successful establishment of each different secondary endosymbiosis. Analysis of targeted proteins in the various organisms now suggests that a similar system is used by each group. However, rather than interpreting this similarity as evidence of an homologous origin, I believe that targeting has evolved convergently by combining and recycling existing protein trafficking mechanisms already existing in the endosymbiont and host. Indeed, by analyzing the multiple motifs in targeting sequences of some genes it is possible to infer that they originated in the plastid genome, transferred from there into the primary host nucleus, and subsequently moved into the secondary host nucleus. Thus, each step of the targeting process in "second-hand" plastids recapitulates the gene's previous intracellular transfers.

Transfer of rps14 from the mitochondrion to the nucleus in maize implied integration within a gene encoding the iron-sulphur subunit of succinate dehydrogenase and expression by alternative splicing

The maize mitochondrial genome does not contain a gene coding for ribosomal protein S14. In this paper we show that the functional rps14 gene was translocated to the nucleus and acquired the signals conferring expression and product targeting to the mitochondrion in a way not previously described. Transferred rps14 was found integrated between both exons of a gene encoding the iron-sulphur subunit of the respiratory complex II (sdh2). Sdh2 exon 1 and rps14 were separated by a typical plant nuclear intron that was spliced to give a mature poly(A)+ mRNA of 1.4 kb. This processed mRNA encoded a chimeric SDH2 (truncated)-RPS14 polypeptide, and we show that this chimeric polypeptide is targeted into isolated plant mitochondria, where it is proteolytically processed in a complex way. An alternative splicing event utilizing the same 5' splice site and a different downstream 3' splice site generated a second mature poly(A)+ mRNA of 1.3 kb that contained both sdh2 exons. This sdh2 transcript encoded an SDH2 polypeptide highly conserved compared with its homologues in other organisms, and it contained the three cysteine-rich clusters that made up the three non-heme iron-sulphur centres responsible for electron transport. To our knowledge, these results constitute the first evidence of alternative splicing playing a role in the expression and targeting of two mitochondrial proteins with different functions from the same gene.

Targeted disruption of the plastid RNA polymerase genes rpoA, B and C1: molecular biology, biochemistry and ultrastructure

The plastid encoded RNA polymerase subunit genes rpoA, B and C1 of tobacco were disrupted individually by PEG-mediated plastid transformation. The resulting off-white mutant phenotype is identical for inactivation of the different genes. The mutants pass through a normal ontogenetic cycle including flower formation and production of fertile seeds. Their plastids reveal a poorly developed internal membrane system consisting of large vesicles and, occasionally, flattened membranes, reminiscent of stacked thylakoids. The rpo- material is capable of synthesising pigments and lipids, similar in composition but at lower amounts than the wild-type. Western analysis demonstrates that plastids contain nuclear-coded stroma and thylakoid polypeptides including terminally processed lumenal components of the Sec but not of the DeltapH thylakoid translocation machineries. Components using the latter route accumulate as intermediates. In striking contrast, polypeptides involved in photosynthesis encoded by plastid genes could not be detected by Western analysis, although transcription of plastid genes, including the rrn operon, by the plastid RNA polymerase of nuclear origin is found as expected. Remarkably, ultrastructural, sedimentation and Northern analyses as well as pulse experiments suggest that rpo- plastids contain functional ribosomes. The detection of the plastid-encoded ribosomal protein Rpl2 is consistent with these results. The findings demonstrate that the consequences of rpo gene disruption, and implicitly the integration of the two plastid polymerase types into the entire cellular context, are considerably more complex than presently assumed.

A novel plant nuclear gene encoding chloroplast ribosomal protein S9 has a transit peptide related to that of rice chloroplast ribosomal protein L12

We have cloned a novel nuclear gene for a ribosomal protein of rice and Arabidopsis that is like the bacterial ribosomal protein S9. To determine the subcellular localization of the gene product, we fused the N-terminal region and green fluorescent protein and expressed it transiently in rice seedlings. Localized fluorescence was detectable only in chloroplasts, indicating that this nuclear gene encodes chloroplast ribosomal protein S9. The N-terminal region of rice ribosomal protein S9 was found to have a high sequence similarity to the transit peptide region of the rice chloroplast ribosomal protein L12, suggesting that these transit peptides have a common lineage.

Reductive evolution of resident genomes

Small, asexual populations are expected to accumulate deleterious substitutions and deletions in an irreversible manner, which in the long-term will lead to mutational meltdown and genome decay. Here, we discuss the influence of such reductive processes on the evolution of genomes that replicate within the domain of a host genome.

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.

The genome and genes of Neurospora crassa

Neurospora crassa is an organism with a 7-decade contribution to genetic research. in a genome of 42.9 Mb and just over 1000 map units, to date over 800 different genes have been identified by phenotype and/or map location, and 222 genes have been characterized by sequencing. Methods by which analysis of the genome has been carried out are discussed, including linkage, RFLP, and chromosome walking. Characterized centomeres, telomeres, the nucleolar organizer and the dispersed 5S rRNA genes are discussed. Analysis of the protein-encoding genes is undertaken, using new software for the querying of standard sequence databases. Gene analysis includes consensus sequences for transcription and RNA splicing and new insights into codon usage.

The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides

We have determined the complete sequence of the mitochondrial DNA in the model plant species Arabidopsis thaliana, affording access to the first of its three genomes. The 366,924 nucleotides code for 57 identified genes, which cover only 10% of the genome. Introns in these genes add about 8%, open reading frames larger than 100 amino acids represent 10% of the genome, duplications account for 7%, remnants of retrotransposons of nuclear origin contribute 4% and integrated plastid sequences amount to 1%-leaving 60% of the genome unaccounted for. With the significant contribution of duplications, imported foreign DNA and the extensive background of apparently functionless sequences, the mosaic structure of the Arabidopsis thaliana mitochondrial genome features many aspects of size-relaxed nuclear genomes.

Genetic mapping of genes for twelve nuclear-encoded polypeptides associated with the thylakoid membranes in Beta vulgaris L

Thylakoid membranes of chloroplasts are composed of approx. 75 polypeptide species. Nearly 60% originate in nuclear genes, the remainder in plastid genes. In order to localize representatives of the nuclear-encoded gene complement in a eukaryotic plant genome (sugar beet, Beta vulgaris L.), we have investigated the RFLP patterns of 21 cDNAs from spinach that code for thylakoid proteins or proteins peripherally associated with thylakoid membranes. Differences in gene dosage were noted between both related species. Polymorphism was found for 12 cDNA loci in a segregating sugar beet F2 population. These loci were mapped along with genomic RFLP, isozyme, and morphological markers, and shown to be distributed in six of the nine sugar beet linkage groups. The lack of positional clustering even of genes that encode components of the same supramolecular membrane assembly is commensurate with phylogenetically independent gene translocations from the plastid (endosymbiont), and raises the question of the functional integration of various translocated genes into common signal transduction chains.

The plant mitochondrial 22 kDa (PSST) subunit of respiratory chain complex I is encoded by a nuclear gene with enhanced transcript levels in flowers

Genes for subunits of respiratory chain complex I are found in mitochondrial, plastid and/or nuclear genomes with varying distributions in the diverse eukaryotic species. The intrinsic PSST subunit of complex I is a mitochondrially encoded protein in Paramecium but is specified by a nuclear gene in animals. In plants to date only the homologous plastid encoded NDH-K gene product has been described. The analogous plant mitochondrial protein is now identified as the 22 kDa complex I subunit and found to be encoded in the nuclear genome of Arabidopsis and potato. The cDNA sequences of clones isolated from both plants are 79% identical in the conserved coding region, while the 5' parts of the reading frames specifying the N-terminal presequences for mitochondrial import differ significantly. The expression of the genes examined in different organs of both plants by Northern blot analysis shows elevated steady-state mRNA levels in flowers. Hence, expression of the gene appears to be organ-specifically regulated by its transcription rate and/or mRNA stability. A 1.6 kb long genomic DNA sequence of Arabidopsis upstream of the transcribed gene region encoding the PSST subunit in Arabidopsis contains several putative promoter sequence motifs. The results are discussed with regard to the appearance of a nuclearly integrated, former mitochondrial gene.

A ribosomal protein L2 gene is transcribed, spliced, and edited at one site in rice mitochondria

The mitochondrial ribosomal protein L2 gene (rpl2) is coded by two exons of 840 and 669 bp separated by an intron sequence of 1481 bp in the rice mitochondrial genome. The rpl2 gene is located three nucleotides upstream of the ribosomal protein S19 gene (rps19) and both genes are co-transcribed. cDNA sequence analysis identified splicing of the intron sequence from the rpl2 mRNA as well as RNA editing events. The deduced secondary structure of the rpl2 intron sequence shows the characteristic features of a group-II intron. A single RNA editing site is identified in rpl2 and six editing sites in rps19 transcripts. In addition, one editing site is observed in the 3 nucleotide intergenic region. Analysis of individual cDNA clones showed a different extent of RNA editing. The rice rpl2 intron is located at a different site and shows no significant nucleotide sequence similarity with the rpl2 intron of liverwort. However, 60% nucleotide sequence identity is observed between the rice rpl2 intron and the Oenothera nad5 intron in a 234 nucleotide region. The mitochondrial rpl2 sequence is absent from the pea mitochondrial genome and we consequently propose that the mitochondrial RPL2 protein is encoded by a nuclear gene in pea.

Conservation of the organization of the mitochondrial nad3 and rps12 genes in evolutionarily distant angiosperms

The organization of the genes nad3 and rps12 has been investigated in the mitochondrial genome of two dicotyledonous plants - Helianthus and Magnolia - and one monocotyledonous plant (Allium). These plants all contain a complete rps12 gene downstream of the nad3 gene. This arrangement is thus highly conserved within angiosperms. The two genes are co-transcribed and the transcript is modified at several positions by RNA editing of the C to U-type, thus confirming that both genes encode functional proteins. Some 26, 35 and 27 editing events have been identified in the PCR-derived nad3-rps12 cDNA population from sunflower, Magnolia and onion, respectively. Editing of the nad3-rps12 transcript is thus more extensive in Magnolia than in the other angiosperms so far investigated and radically changes the genomically encoded polypeptide sequence. A novel species-specific codon modification was observed in Magnolia. Several homologous sites show differences in editing pattern among plant species. A C-to-U alteration is also found in the non-coding region separating the nad3 and rps12 genes in sunflower. The PCR-derived cDNA populations from the nad3-rps12 loci analysed were found to be differently edited. In addition the plant species show marked variations in the completeness of RNA editing, with only the Magnolia nad3 mRNA being edited fully.

A reverse transcriptase activity in potato mitochondria

A reverse transcriptase activity has been detected in potato mitochondria using special RNAs as templates: a bacterial RNA coding for neomycin phosphotransferase (neo pa RNA) and a Neurospora crassa mitochondrial RNA (184 nt RNA). Surprisingly, no exogenous primer addition was required. These RNA templates share a primary and secondary structure similar to the T psi CG loop of tRNAs that could constitute the recognition site for the enzyme. Reverse transcriptase activity was inhibited by ddTTP, ethidium bromide and aphidicolin, while potato mitochondrial DNA polymerase was not inhibited by aphidicolin indicating that these activities correspond to distinct enzymes. A conserved sequence of reverse transcriptases was detected in potato mitochondrial DNA suggesting that this enzyme could be mitochondrially encoded.

Plasmid RNA polymerase-like mitochondrial sequences in Agaricus bitorquis

A linear mitochondrial plasmid, pEM, found in certain isolates of the basidiomycete Agaricus bitorquis, potentially encodes virus-like DNA and RNA polymerases. Mitochondrial DNA from Agaricus bisporus that hybridizes to an internal region of pEM contains a fragmented and potentially non-functional version of the carboxy terminal end of the plasmid RNA polymerase. In this study, we present the sequence of the corresponding region of mitochondrial DNA from A. bitorquis. This sequence contained the same region of the plasmid RNA polymerase gene as was reported for the mitochondrial DNA of A. bisporus, and the level of similarity between the A. bisporus and A. bitorquis mitochondrial sequences was much higher than the level of similarity between either mitochondrial sequence and the plasmid. We propose that this plasmid RNA polymerase-like sequence was present in the Agaricus mitochondrial genome before the divergence of A. bisporus and A. bitorquis, and thus is unlikely to be a recent derivative of the plasmid pEM.

Escape and migration of nucleic acids between chloroplasts, mitochondria, and the nucleus

The escape and migration of genetic information between mitochondria, chloroplasts, and nuclei have been an integral part of evolution and has a continuing impact on the biology of cells. The evolutionary transfer of functional genes and fragments of genes from chloroplasts to mitochondria, from chloroplasts to nuclei, and from mitochondria to nuclei has been documented for numerous organisms. Most documented instances of genetic material transfer have involved the transfer of information from mitochondria and chloroplasts to the nucleus. The pathways for the escape of DNA from organelles may include transient breaches in organellar membranes during fusion and/or budding processes, terminal degradation of organelles by autophagy coupled with the subsequent release of nucleic acids to the cytoplasm, illicit use of nucleic acid or protein import machinery, or fusion between heterotypic membranes. Some or all of these pathways may lead to the escape of DNA or RNA from organellar compartments with subsequent uptake of nucleic acids from the cytoplasm into the nucleus. Investigations into the escape of DNA from mitochondria in yeast have shown the rate of escape for gene-sized fragments of DNA from mitochondria and its subsequent migration to the nucleus to be roughly equivalent to the rate of spontaneous mutation of nuclear genes. Smaller fragments of mitochondrial DNA may appear in the nucleus even more frequently. Mutations of nuclear genes that define gene products important in controlling the rate of DNA escape from mitochondria in yeast also have been described. The escape of genetic material from mitochondria and chloroplasts has clearly had an impact on nuclear genetic organization throughout evolution and may also affect cellular metabolic processes.

Editing and import: strategies for providing plant mitochondria with a complete set of functional transfer RNAs

The recombinations and mutations that plant mitochondrial DNA has undergone during evolution have led to the inactivation or complete loss of a number of the 'native' transfer RNA genes deriving from the genome of the ancestral endosymbiont. Following sequence divergence in their genes, some native mitochondrial tRNAs are 'rescued' by editing, a post-transcriptional process which changes the RNA primary sequence. According to in vitro studies with the native mitochondrial tRNA(Phe) from potato and tRNA(His) from larch, editing is required for efficient processing. Some of the native tRNA genes which have been inactivated or lost have been replaced by tRNA genes present in plastid DNA sequences acquired by the mitochondrial genome during evolution, which raises the problem of the transcriptional regulation of tRNA genes in plant mitochondria. Finally, tRNAs for which no gene is present in the mitochondrial genome are imported from the cytosol. This process is highly specific for certain tRNAs, and it has been suggested that the cognate aminoacyl-tRNA synthetases may be responsible for this specificity. Indeed, a mutation which blocks recognition of the cytosolic Arabidopsis thaliana tRNA(Ala) by the corresponding alanyl-tRNA synthetase also prevents mitochondrial import of this tRNA in transgenic plants. Conversely, no significant mitochondrial co-import of the normally cytosol-specific tRNA(Asp) was detected in transgenic plants expressing the yeast cytosolic aspartyl-tRNA synthetase fused to a mitochondrial targeting sequence, suggesting that, although necessary, recognition by a cognate aminoacyl-tRNA synthetase might not be sufficient to allow tRNA import into plant mitochondria.

Genomic evolution drives the evolution of the translation system

Our thesis is that the characteristics of the translational machinery and its organization are selected in part by evolutionary pressure on genomic traits have nothing to do with translation per se. These genomic traits include size, composition, and architecture. To illustrate this point, we draw parallels between the structure of different genomes that have adapted to intracellular niches independently of each other. Our starting point is the general observation that the evolutionary history of organellar and parasitic bacteria have favored bantam genomes. Furthermore, we suggest that the constraints of the reductive mode of genomic evolution account for the divergence of the genetic code in mitochondria and the genetic organization of the translational system observed in parasitic bacteria. In particular, we associate codon reassignments in animal mitochondria with greatly simplified tRNA populations. Likewise, we relate the organization of translational genes in the obligate intracellular parasite Rickettsia prowazekii to the processes supporting the reductive mode of genomic evolution. Such findings provide strong support for the hypothesis that genomes of organelles and of parasitic bacteria have arisen from the much larger genomes of ancestral bacteria that have been reduced by intrachromosomal recombination and deletion events. A consequence of the reductive mode of genomic evolution is that the resulting translation systems may deviate markedly from conventional systems.

Evolutionary divergence of the cytochrome b5 gene of Drosophila

Cytochrome proteins perform a broad spectrum of biological functions ranging from oxidative metabolism to electron transport and are thus essential to all organisms. The b-type cytochrome proteins bind heme noncovalently, are expressed in many different forms and are localized to various cellular compartments. We report the characterization of the cytochrome b5 (Cyt-b) gene of Drosophila virilis and compare its structure to the Cyt-b gene of Drosophila melanogaster. As in D. melanogaster, the D. virilis gene is nuclear encoded and single copy. Although the intron/exon structures of these homologues differ, the Cyt-b proteins of D. melanogaster and D. virilis are approximately 75% identical and share the same size coding regions (1,242 nucleotides) and protein products (414 amino acids). The Drosophila Cyt-b proteins show sequence similarity to other b-type cytochromes, especially in the N-terminal heme-binding domain, and may be targeted to the mitochondrial membrane. The greatest levels of similarity are observed in areas of potential importance for protein structure and function. The exon sequences of the D. virilis Cyt-b gene differ by a total of 292 base changes. However, 62% of these changes are silent. The high degree of conservation between species separated by 60 million years of evolution in both the DNA and amino acid sequences suggests this nuclear cytochrome b5 locus encodes an essential product of the Drosophila system.

Characterization of the nuclear gene encoding chloroplast ribosomal protein S13 from Arabidopsis thaliana

We have characterised a cDNA clone and a nuclear gene encoding the chloroplast 30 s ribosomal protein S13 from Arabidopsis thaliana. The identification is based on the high similarity of the predicted amino-acid sequence with eubacterial S13 protein sequences, and immunodetection of a 14.5-kDa chloroplast ribosomal polypeptide using antibodies raised against the polypeptide produced from part of the cDNA expressed in bacteria. The predicted amino-acid sequence contains an N-terminal extension which has several features characteristic of chloroplast transit peptides. Experiments suggest there is a single copy of this gene in A. thaliana and multiple copies in Brassica species. The origin of the mitochondrial S13 polypeptide in crucifers is also discussed.

The gene for ribosomal protein S10 is present in mitochondria of pea and potato but absent from those of Arabidopsis and Oenothera

A novel group II intron has been identified in the pea (Pisum sativum) mitochondrial genome. The gene harbouring this intron is identified as rps10 (encoding protein S10 of the small ribosomal subunit) by similarity to its known homologues in bacteria and in the mitochondrion of the liverwort Marchantia polymorpha. The rps10 gene is transcribed in pea, the intron is removed, and RNA editing in the rps10 reading frame increases similarity to its homologue in the M. polymorpha mitochondrion. Contrary to the situation in bacteria and Marchantia, rps10 is not part of a ribosomal-protein gene cluster in pea. It is flanked upstream by the genes trnF and trnP, encoding phenylalanine- and proline-accepting tRNAs, and downstream by cox1, encoding subunit 1 of the cytochrome-c-oxidase. Southern hybridization shows that sequences homologous to rps10 exist in potato mitochondria but not in mitochondria of Oenothera berteriana and Arabidopsis thaliana. The pea rps10 intron is homologous to introns in rrn26 and cox3 in the Marchantia mitochondrial genome, while the Marchantia rps10 gene lacks an intron.

The evolution of mitochondrial DNA

Although the massive sequencing of mitochondrial DNA from various organisms, together with studies of a different nature, has contributed enormously to the knowledge of the organization and function of this cytoplasmic genome, many issues, mainly the relationships with the nuclear genome, remain unsolved. This review critically evaluates the most recent advances in research on the evolution of the mitochondrial DNA from a qualitative and quantitative point of view, underlining the multiplicity of structures and genetic organization of this genome, which contrasts with its reduced, but rather constant, information content in various organisms. It also highlights the role that mitochondrial DNA is now playing, particularly in metazoans, in different disciplines and application fields. Among these, particular attention is focused on the discovery of the mitochondrial origin of several diseases affecting primarily the neuromuscular system.

Promiscuous mitochondrial group II intron sequences in plant nuclear genomes

Gene translocations from the organelles to the nucleus are postulated by the endosymbiont hypothesis. We here report evidence for sequence insertions in the nuclear genomes of plants that are derived from noncoding regions of the mitochondrial genome. Fragments of mitochondrial group II introns are identified in the nuclear genomes of tobacco and a bean species. The duplicated intron sequences of 75-140 bp are derived from cis- and trans-splicing introns of genes encoding subunits 1 and 5 of the NADH dehydrogenase. The mitochondrial sequences are inserted in the vicinities of a lectin gene, different glucanase genes and a gene encoding a subunit of photosystem II. Sequence similarities between the nuclear and mitochondrial copies are in the range of 80 to 97%, suggesting recent transfer events that occurred in the basic glucanase genes before and in the lectin gene after the gene duplications in the evolution of the nuclear gene families. Overlapping regions of the same introns are in two instances also involved in intramitochondrial sequence duplications.

Origin and evolution of organelle genomes

Molecular data (particularly sequence analyses) have established that two eukaryotic organelles, the mitochondrion and the plastid, are the descendants of endosymbiotic (eu)bacteria whose closest living relatives are the alpha-Proteobacteria (mitochondrion) and Cyanobacteria (plastid). This review describes recent data that favor the view that each organelle arose via this primary endosymbiotic pathway only once (monophyletic origin), such as the discovery of group I introns that appear to be structurally homologous and have identical insertion sites in metaphyte, chlorophyte and fungal mitochondrial genomes. However, it is also evident that the plastids in certain algal groups were acquired secondarily through a eukaryotic rather than a prokaryotic endosymbiont.