DNA sequence and secondary structures of the large subunit rRNA coding regions and its two class I introns of mitochondrial DNA from Podospora anserina

The Cryphonectria parasitica mitochondrial rns gene: plasmid-like elements, introns and homing endonucleases

The mt-rns gene of Cryphonectria parasitica is 9872bp long and includes two group I and two group II introns. An analysis of intronic protein-encoding sequences revealed that LAGLIDADG ORFs, which usually are associated with group I introns, were transferred at least twice into group II introns. A plasmid-like mitochondrial element (plME) that appears in high amounts in previously mutagen-induced mit1 and mit2 hypovirulent mutants of the Ep155 standard virulent strain of C. parasitica was found to be derived from a short region of the mt-rns gene, including the exon 1 and most of the first intron. The plME is a 4.2-kb circular, multimeric DNA and an autonomously-replicating mtDNA fragment. Although sexual transmission experiments indicate that the plME does not directly cause hypovirulence, its emergence is one manifestation of the many complex molecular and genetic events that appear to underlie this phenotype.

The sporadic occurrence of a group I intron-like element in the mtDNA rnl gene of Ophiostoma novo-ulmi subsp. americana

The presence of group I intron-like elements within the U7 region of the mtDNA large ribosomal subunit RNA gene (rnl) was investigated in strains of Ophiostoma novo-ulmi subsp. americana from Canada, Europe and Eurasia, and in selected strains of O. ips, O. minus, O. piceae, O. ulmi, and O. himal-ulmi. This insertion is of interest as it has been linked previously to the generation of plasmid-like mtDNA elements in diseased strains of O. novo-ulmi. Among 197 O. novo-ulmi subsp. americana strains tested, 61 contained a 1.6kb insertion within the rnl-U7 region and DNA sequence analysis suggests the presence of a group I intron (IA1 type) that encodes a potential double motif LAGLIDADG homing endonuclease-like gene (HEG). Phylogenetic analysis of rnl-U7 intron encoded HEG-like elements supports the view that double motif HEGs originated from a duplication event of a single-motif HEG followed by a fusion event that combined the two copies into one open reading frame (ORF). The data also show that rnl-U7 intron encoded ORFs belong to a clade that includes ORFs inserted into different types of group I introns, e.g. IB, ID, IC3, IA1, present within a variety of different mtDNA genes, such as the small ribosomal subunit RNA gene (rns), apo-cytochrome b gene (cob), NADH dehydrogenase subunit 5 (nad5), cytochrome oxidase subunit 1 gene (coxI), and ATPase subunit 9 gene (atp9). We also compared the occurrence of the rnl-U7 intron in our collection of 227 strains with the presence of the rnl-U11 group I intron and concluded that the U7 intron appears to be an optional element and the U11 intron is probably essential among the strains tested.

Mitochondrial biology and disease in Dictyostelium

The cellular slime mold Dictyostelium discoideum has become an increasingly useful model for the study of mitochondrial biology and disease. Dictyostelium is an amoebazoan, a sister clade to the animal and fungal lineages. The mitochondrial biology of Dictyostelium exhibits some features which are unique, others which are common to all eukaryotes, and still others that are otherwise found only in the plant or the animal lineages. The AT-rich mitochondrial genome of Dictyostelium is larger than its mammalian counterpart and contains 56kb (compared to 17kb in mammals) encoding tRNAs, rRNAs, and 33 polypeptides (compared to 13 in mammals). It produces a single primary transcript that is cotranscriptionally processed into multiple monocistronic, dicistronic, and tricistronic mRNAs, tRNAs, and rRNAs. The mitochondrial fission mechanism employed by Dictyostelium involves both the extramitochondrial dynamin-based system used by plant, animal, and fungal mitochondria and the ancient FtsZ-based intramitochondrial fission process inherited from the bacterial ancestor. The mitochondrial protein-import apparatus is homologous to that of other eukaryote, and mitochondria in Dictyostelium play an important role in the programmed cell death pathways. Mitochondrial disease in Dictyostelium has been created both by targeted gene disruptions and by antisense RNA and RNAi inhibition of expression of essential nucleus-encoded mitochondrial proteins. This has revealed a regular pattern of aberrant mitochondrial disease phenotypes caused not by ATP insufficiency per se, but by chronic activation of the universal eukaryotic energy-sensing protein kinase AMPK. This novel insight into the cytopathological mechanisms of mitochondrial dysfunction suggests new possibilities for therapeutic intervention in mitochondrial and neurodegenerative diseases.

Optional mitochondrial introns and evidence for a homing-endonuclease gene in the mtDNA rnl gene in Ophiostoma ulmi s. lat

Strains of Ophiostoma ulmi, O. novo-ulmi subsp. americana, O. novo-ulmi subsp. novo-ulmi and O. himal-ulmi were examined for optional introns/insertions within the following mitochondrial genes: small subunit RNA gene (rns), large ribosomal subunit gene (rnl) and the cytochrome oxidase subunit I gene (coxI). Insertions were noted in the rns and coxI genes in strains of O. ulmi, the less aggressive species, but absent in strains of the more aggressive O. novo-ulmi subsp. americana. Strains of all species examined had a group I intron present in the U11 region of the mitochondrial-rnl gene. In all but two strains of O. novo-ulmi subsp. americana, this rnl-U11 intron was about 1.5 kb in length whereas a 2.6 kb version of this element was present in all strains representing O. ulmi, O. novo-ulmi subsp. novo-ulmi, and Ophiostoma himal-ulmi. Irrespective of size, this intron based on RNA folds is a class IA1 group I intron and it encodes a putative ORF for the rps3 ribosomal protein. The size variation of the rnl-U11 intron was examined in detail for two strains of O. novo-ulmi subsp. americana and sequence data suggests the presence of a complex ORF within the 2.6 kb version of this intron; here a homing endonuclease-like gene has been inserted in frame and fused to the carboxyl-terminus of the putative rps3 coding region. The mitochondrial optional introns/insertions in combination with nuclear markers might be useful in distinguishing among the various species and subspecies of the O. ulmi s. lat. complex.

Fungi vectored by the introduced bark beetle Tomicus piniperda in Ontario, Canada, and comments on the taxonomy of Leptographium lundbergii, Leptographium terebrantis, Leptographium truncatum, and Leptographium wingfieldii

Fungi isolated from Tomicus piniperda (L.) galleries in infected trap logs, standing trees, and directly from insects were identified using morphological features and molecular data obtained from the mitochondrial and nuclear DNA region. Identified strains represented Leptographium wingfieldii Morelet, Leptographium procerum (Kendr.) Wingf., Leptographium lundbergii Lag. & Melin sensu Jacobs & Wingfield, Ophiostoma ips (Rumb.) Nannf., Ophiostoma minus (Hedg.) H. & P. Syd., and Sphaeropsis sapinea sensu lato. Leptographium wingfieldii is believed to be a potentially pathogenic introduced fungus, but sequence data suggest a possible connection between it and the teleomorph of Ophiostoma aureum (Robinson-Jeffrey & Davids.) T.C. Harrington (reported from British Columbia and the western United States). Our data also show that the ex-type culture of Leptographium terebrantis Barras & Perry, a species very similar morphologically to L. wingfieldii, also grouped with L. wingfieldii. We also identified strains of Leptographium truncatum (Wingf. & Marasas) Wingf.; this species has been synonymized with L. lundbergii, but our data indicate that these are distinct species, and therefore, the name L. truncatum should be reinstated. We also report the extended presence of L. procerum in Ontario. Previously viewed as a “southern” species frequently associated with pine-root decline diseases, it has been infrequently reported from New York state and but once each from Ontario and Quebec.

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 secondary structure and phylogenetic relationship deduced from complete nucleotide sequence of mitochondrial small subunit rRNA in yeast Hansenula wingei

We have accomplished the nucleotide sequence of the 1537 bp mitochondrial gene coding for small subunit (SSU) rRNA of yeast Hansenula wingei, and also determined the 5'- and 3'-termini by S1 nuclease mapping. Eight universally conserved (U) elements of the SSU rRNA were identified. Comparison of U regions among five fungal mitochondrial SSU rRNA shows the striking similarity between H. wingei and Saccharomyces cerevisiae. The construction of the secondary structure revealed a core structure similar to the counterpart of Escherichia coli 16S rRNA. The secondary structure also enabled us the specify seven variable (V) regions differing from those of other mitochondrial SSU rRNAs in size, sequence and possible secondary structure. Molecular phylogenetic evaluation based on U regions of five fungi indicates that mitochondria of H. wingei and S. cerevisiae diverged from the same lineage. This suggests that the evolution of mitochondria-encoded genes does not directly correlate with the alteration of mitochondrial genetic system: genome size, gene organization and codon usage.

Nucleotide-sequence analysis indicates that a DNA plasmid in a diseased isolate of Ophiostoma novo-ulmi is derived by recombination between two long repeat sequences in the mitochondrial large subunit ribosomal RNA gene

The nucleotide sequence of a mitochondrial plasmid (2234 bp) in a diseased isolate of Ophiostoma novo-ulmi, and sequences of the mitochondrial DNA that overlap and flank the plasmid end-points, have been determined. The plasmid was shown to be derived from the O. novo-ulmi mitochondrial large subunit ribosomal RNA gene and contained most of intron 1, the whole of exon 2, and probably the first part of intron 2. Within intron 1 there is an open reading frame with the potential to encode a 323 amino-acid polypeptide which contained dodecapeptide sequences typical of RNA maturases and DNA endonucleases. The endpoints of the plasmid in the mtDNA were located within two 90-bp direct imperfect repeat sequences, one of which comprised the last 7 bp of exon 1 and the first 83 bp of intron 1 whilst the other comprised the last 7 bp of exon 2 and the first 83 bp of intron 2. It is proposed that the Ld plasmid was generated by intramolecular recombination between these two repeats with the crossover point probably within the last 15 bp.

Identification of group-I introns in the 28s rDNA of the entomopathogenic fungus Beauveria brongniartii

The length of the 28s ribosomal DNA differs significantly between two strains (Bt102 and Bt114) of the entomopathogenic fungus Beauveria brongniartii. RFLP analysis on PCR products revealed the presence of three insertional elements of 350-450 bp in strain Bt114. One of the insertions has been cloned and sequenced and shown to possess all the characteristic sequences and secondary structures of a group-IC intron. Its length is 428 bp and it is devoid of any long open reading frame. The distribution of this intron elsewhere in the genome of Bt114, as well as in the chromosomal ribosomal DNA, was studied. It seems to be present as seven copies in different genes not corresponding to the mitochondrial DNA. The presence of the intron in other strains of B. brongniartii was examined by the hybridization method. Some of them seemed to possess introns with a similar core although others presented no homology with the cloned fragment.

Group I introns interrupt the chloroplast psaB and psbC and the mitochondrial rrnL gene in Chlamydomonas

The polymerase chain reaction was used to identify novel IAI subgroup introns in cpDNA-enriched preparations from the interfertile green algae Chlamydomonas eugametos and Chlamydomonas moewusii. These experiments along with sequence analysis disclosed the presence, in both green algae, of a single IA1 intron in the psaB gene and of two group I introns (IA2 and IA1) in the psbC gene. In addition, two group I introns (IA1 and IB4) were found in the peptidyltransferase region of the mitochondrial large subunit rRNA gene at the same positions as previously reported Chlamydomonas chloroplast introns. The 188 bp segment preceding the first mitochondrial intron revealed extensive sequence similarity to the distantly spaced rRNA-coding modules L7 and L8 in the Chlamydomonas reinhardtii mitochondrial DNA, indicating that these two modules have undergone rearrangements in Chlamydomonas. The IA1 introns in psaB and psbC were found to be related in sequence to the first intron in the C. moewusii chloroplast psbA gene. The similarity between the former introns extends to the immediate 5' flanking exon sequence, suggesting that group I intron transposition occurred from one of the two genes to the other through reverse splicing.

Interaction between mitochondrial DNA and mitochondrial plasmids in Claviceps purpurea: analysis of plasmid-homologous sequences upstream of the lrRNA-gene

Homology of two linear, mitochondrial (mt) Claviceps purpurea plasmids, pClK1 and pClT5, to the upstream region of the large ribosomal RNA gene in the mtDNA of three strains (W3, T5 and K) has been investigated in detail to explore the widespread phenomenon of homology between mt plasmids and mtDNA in C. purpurea. Sequence comparison indicates that recombination between free plasmids and mtDNA is the cause of the observed homology. The process is similar to the integration of the structurally related adenoviruses into the mammalian genome. As in other fungi, palindromic sequences seem to be involved in this mitochondrial recombination process.

Mitochondrial genes in the colourless alga Prototheca wickerhamii resemble plant genes in their exons but fungal genes in their introns

The mitochondrial DNA from the colourless alga Prototheca wickerhamii contains two mosaic genes as was revealed from complete sequencing of the circular extranuclear genome. The genes for the large subunit of the ribosomal RNA (LSUrRNA) as well as for subunit I of the cytochrome oxidase (coxI) carry two and three intronic sequences respectively. On the basis of their canonical nucleotide sequences they can be classified as group I introns. Phylogenetic comparisons of the coxI protein sequences allow us to conclude that the P.wickerhamii mtDNA is much closer related to higher plant mtDNAs than to those of the chlorophyte alga C.reinhardtii. The comparison of the intron sequences revealed several unusual features: (1) The P.wickerhamii introns are structurally related to mitochondrial introns from various ascomycetous fungi. (2) Phylogenetic analyses indicate a close relationship between fungal and algal intronic sequences. (3) The P. wickerhamii introns are located at positions within the structural genes which can be considered as preferred intron insertion sites in homologous mitochondrial genes from fungi or liverwort. In all cases, the sequences adjacent to the insertion sites are very well conserved over large evolutionary distances. Our finding of highly similar introns in fungi and algae is consistent with the idea that introns have already been present in the bacterial ancestors of present day mitochondria and evolved concomitantly with the organelles.

A site-specific deletion in mitochondrial DNA of Podospora is under the control of nuclear genes

In the filamentous fungus Podospora anserina, the association of two nuclear genes inevitably leads to a "premature death" phenotype consisting of an early end of vegetative growth a few days after ascospore germination. Mycelia showing this phenotype contain a mitochondrial chromosome that always bears the same deletion. One of the break points is exactly at the 5' splice site of a particular mitochondrial intron, suggesting that the deletion event could result from molecular mechanisms also involved in intron mobility. One of the nuclear genes involved in triggering this site-specific event belongs to the mating-type minus haplotype; the other is a mutant allele of a gene encoding a cytosolic ribosomal protein.

Six group I introns and three internal transcribed spacers in the chloroplast large subunit ribosomal RNA gene of the green alga Chlamydomonas eugametos

The chloroplast large subunit rRNA gene of Chlamydomonas eugametos and its 5' flanking region encoding tRNA(Ile) (GAU) and tRNA(Ala) (UGC) have been sequenced. The DNA sequence data along with the results of a detailed RNA analysis disclosed two unusual features of this green algal large subunit rRNA gene: (1) the presence of six group I introns (CeLSU.1-CeLSU.6) whose insertion positions have not been described previously, and (2) the presence of three short internal transcribed spacers that are post-transcriptionally excised to yield four rRNA species of 280, 52, 810 and 1720 nucleotides, positioned in this order (5' to 3') in the primary transcript. Together, these RNA species can assume a secondary structure that is almost identical to that proposed for the 23 S rRNA of Escherichia coli. All three internal transcribed spacers map to variable regions of primary sequence and/or potential secondary structure, whereas all six introns lie within highly conserved regions. The first three introns are inserted within the sequence encoding the 810 nucleotide rRNA species and map within domain II of the large subunit rRNA structure; the remaining introns, found in the sequence encoding the 1720 nucleotide rRNA species, lie within either domain IV or V, as is the case for all other large subunit rDNA introns that have been documented to date. CeLSU.5 and CeLSU.6 each contain a long open reading frame (ORF) of more than 200 codons. While the CeLSU.6 ORF is not related to any known ORFs, the CeLSU.5 ORF belongs to a family of ORFs that have been identified in Podospora and Neurospora mitochondrial group I introns. The finding that a polymorphic marker showing unidirectional gene conversion during crosses between C. eugametos and Chlamydomonas moewusii is located within the CeLSU.5 ORF makes it likely that this intron is a mobile element and that its ORF encodes a site-specific endonuclease promoting the transfer of the intron DNA sequence.

Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis

Alignment of the 87 available sequences of group I self-splicing introns reveals numerous instances of covariation between distant sites. Some of these covariations cannot be ascribed to historical coincidences or the known secondary structure of group I introns, and are, therefore, best explained as reflecting tertiary contacts. With the help of stereochemical modelling, we have taken advantage of these novel interactions to derive a three-dimensional model of the conserved core of group I introns. Two noteworthy features of that model are its extreme compactness and the fact that all of the most evolutionarily conserved residues happen to converge around the two helices that constitute the substrate of the core ribozyme and the site that binds the guanosine cofactor necessary for self-splicing. Specific functional implications are discussed, both with regard to the way the substrate helices are recognized by the core and possible rearrangements of the introns during the self-splicing process. Concerning potential long-range interactions, emphasis is put on the possible recognition of two consecutive purines in the minor groove of a helix by a GAAA or related terminal loop.

A mitochondrial DNA rearrangement and three new mitochondrial plasmids from long-lived strains of Podospora anserina

The excision-junction sites of a mtDNA rearrangement of a long-lived strain of Podospora anserina, Mn19, were cloned and sequenced. Analysis of sequence and hybridization data lead to the conclusion that the Mn19 mtDNA consists of two nonoverlapping circular molecules. Three plasmids, LMt-2, LMt-3, and LMt-4, cloned from long-lived progeny of crosses between the Mn19 strain and wild type were cloned and sequenced. These plasmids share features and excision-junction sites with previously described longevity and senescence plasmids. The Mn19 mtDNA rearrangement and plasmids LMt-2, LMt-3, and LMt-4 are described. The possible significance of similarities to previously described plasmids is discussed.

The complete DNA sequence of the mitochondrial genome of Podospora anserina

The complete 94,192 bp sequence of the mitochondrial genome from race s of Podospora anserina is presented (1 kb = 10(3) base pairs). Three regions unique to race A are also presented bringing the size of this genome to 100,314 bp. Race s contains 31 group I introns (33 in race A) and 2 group II introns (3 in race A). Analysis shows that the group I introns can be categorized according to families both with regard to secondary structure and their open reading frames. All identified genes are transcribed from the same strand. Except for the lack of ATPase 9, the Podospora genome contains the same genes as its fungal counterparts, N. crassa and A. nidulans. About 20% of the genome has not yet been identified. DNA sequence studies of several excision-amplification plasmids demonstrate a common feature to be the presence of short repeated sequences at both termini with a prevalence of GGCGCAAGCTC.

Mitochondrial DNA sequence analysis of the cytochrome oxidase subunit II gene from Podospora anserina. A group IA intron with a putative alternative splice site

A 5 kb region of the 95 kb mitochondrial genome of Podospora anserina race s has been mapped and sequenced (1 kb = 10(3) base-pairs). This DNA region is continuous with the sequence for the ND4L and ND5 gene complex in the accompanying paper. We show that this sequence contains the gene for cytochrome oxidase subunit II (COII). This gene is 4 kb in length and is interrupted by a subgroup IB intron (1267 base-pairs (bp) in length) and a subgroup IA intron (1992 bp in length). This group IA intron has a long open reading frame (ORF; 472 amino acid residues) discontinuous with the upstream exon sequence. A putative alternative splice site is present, which brings the ORF into phase with the 5' exon sequence. The 5'- and 3'-flanking regions of the COII gene contain G + C-rich palindromic sequences that resemble similar sequences flanking many Neurospora crassa mitochondrial genes.

DNA sequence analysis of the mitochondrial ND4L-ND5 gene complex from Podospora anserina. Duplication of the ND4L gene within its intron

A 15 kb region of the 100 kb mitochondrial genome of Podospora anserina has been mapped and sequenced (1 kb = 10(3) base-pairs). The genes for ND4L and ND5 are identified as contiguous genes with overlapping termination and initiation codons. In race A (101 kb) the gene for ND4L (4.3 kb) has a gene duplication within an intron including a second subgroup IC intron. Race s (95 kb) lacks this second gene complex. Each intron has the identical 5' exon boundary. Secondary structure analysis showed that the closest relative of the second intron is the first intron itself. The open reading frames of the two introns are also closely related to each other as well as to their counterpart in the ND4L gene of Neurospora crassa. The 9.9 kb ND5 gene starts immediately at the termination codon of ND4L and is split by two group IB introns, one group IC intron and one group II intron. The group II intron is closely related to other group II introns although its open reading frame sequence similarity with retroviral reverse transcriptase appears to be more divergent. The similarities in secondary structure and open reading frames for these six introns are discussed.

Insertion of an LrDNA gene fragment and of filler DNA at a mitochondrial exon-intron junction in Podospora

A rearrangement of the mitochondrial genome of a long lived mutant of Podospora anserina is presented. It consists in the insertion of 191 bp of the LrDNA gene (coding for the large ribosomal RNA) at the junction between exon1 and intron alpha of gene co1 (coding for subunit 1 of cytochrome oxidase). This insertion is accompanied by a 53 bp deletion of the junction and the presence of extra A and T nucleotides at both sides of the inserted sequence. We discuss possible mechanisms of production of this rearrangement. The presence of extra nucleotides at the recombination junctions suggests that it may pass through a stage of free DNA ends originating from a DNA break at the junction between exon1 and intron alpha of gene co1. The possibility that such a DNA break plays a major role in the instability of the mitochondrial genome is envisaged.

DNA sequence analysis of the 24.5 kilobase pair cytochrome oxidase subunit I mitochondrial gene from Podospora anserina: a gene with sixteen introns

The DNA sequence of a 26.7 Kilobase pair (10(3) base pairs = 1 Kb) region of the mitochondrial genomes of races s and A from Podospora anserina was determined. Within this region, the 24.5 Kb cytochrome oxidase subunit I gene was located and its exon sequences determined by computer analysis comparisons with other fungal genes. The Podospora COI gene was interrupted by two group II introns (one in race s) and fourteen group I introns ranging in size from about 2.2 Kb to 404 bp. Earlier studies on secondary structure analysis, as well as comparison of their open reading frames (ORFs), showed that the two group II introns were closely related. The fourteen group I introns were representatives of three subgroupings (IB, C and a new category, subgroup ID). Two of these group I introns were separated by just a single exon codon. The analysis of all these introns is discussed in comparison with other fungal introns as well as with the known Podospora anserina introns.

DNA sequence analysis of the apocytochrome b gene of Podospora anserina: a new family of intronic open reading frame

The 5,969 bp (base pair) DNA sequence of the apocytochrome b mitochondrial (mt) gene of race A Podospora anserina was located in a 8.5 Kbp region. This gene contained a 2,499 bp subgroup IB and a 1,306 bp subgroup ID intron as well as a 990 bp subgroup IB intron which is present in race A but not race s. The large subgroup IB intron and the race A specific IB intron both contained potential alternate splice sites which brought their open reading frames into phase with their upstream exon sequences. All three introns were compared with regard to their secondary structures and open reading frames to the other 30 group I introns in Podospora anserina, as well as to other fungal introns. We detected a new family of intronic ORFs comprising seven P. anserina introns, several N. crassa introns, as well as the T4td bacteriophage intron. Sequence similarities to intron-encoded endonucleases were noteworthy. The DNA sequences reported here and in the accompanying paper complete the analysis of race s and race A mitochondrial DNA.

An unusual region of Paramecium mitochondrial DNA containing chloroplast-like genes

Based on DNA and amino acid comparisons with known genes and their products, a region of the Paramecium aurelia mitochondrial (mt) genome has been found to encode the following gene products: (1) photosystem II protein G (psbG); (2) a large open reading frame (ORF400) which is also found encoded in the chloroplast (cp) DNA of tobacco (as ORF393) and liverwort (as ORF392), and in the kinetoplast maxicircle DNA of Leishmania tarentolae (as ORFs 3 and 4); (3) ribosomal protein L2 (rpl2); (4) ribosomal protein S12 (rps12); (5) ribosomal protein S14 (rps14); and (6) NADH dehydrogenase subunit 2 (ndh2). All of these genes have been found in cp DNA, but the psbG gene has never been identified in a mt genome, and ribosomal protein genes have never been located in an animal or protozoan mitochondrion. The ndh2 gene has been found in both mitochondria and plastids. The Paramecium genes are among the most divergent of those sequenced to date. Two of the genes are encoded on the strand of DNA complementary to that encoding all other known Paramecium mt genes. No gene contains an identifiable intron. The rps12 and psbG genes are probably overlapping. It is not yet known whether these genes are transcribed or have functional gene products. The presence of these genes in the mt genome raises interesting questions concerning their evolutionary origin.