The wheat mitochondrial gene for subunit I of the NADH dehydrogenase complex: a trans-splicing model for this gene-in-pieces

Expression of mitochondrial protein-coding genes in Tetrahymena pyriformis

In the ciliate protozoon, Tetrahymena pyriformis, mitochondrial protein-coding genes are highly divergent in sequence, and in a number of cases they lack AUG initiation codons. We asked whether RNA editing might be acting to generate protein sequences that are more conventional than those inferred from the corresponding gene sequences, and/or to create standard AUG initiation codons where these are absent. However, comparison of genomic and cDNA sequences (the latter generated by reverse transcriptase sequencing of T. pyriformis mitochondrial mRNAs) yielded no evidence of mitochondrial RNA editing in this organism. To delineate the 5' ends of mitochondrial protein-coding transcripts, primer extension experiments were conducted. In all cases, 5' termini were found to map within a few nucleotides of potential initiation codons, indicating that T. pyriformis mitochondrial mRNAs have little or no 5' untranslated leader sequence. The pattern of strong primer extension stops suggested that both standard (AUG) and non-standard (AUU, AUA, GUG, UUG) initiation codons are utilized by the Tetrahymena mitochondrial translation system. We also investigated expression of the nad1 gene, which in both T. pyriformis and Paramecium aurelia is split into two portions that are encoded by and transcribed from different DNA strands. Northern hybridization analysis showed that the corresponding transcripts are not trans-spliced, implying that separate N-terminal and C-terminal portions of Nad1 are made in this system. Finally, in a search for primary transcripts, we isolated from a T. pyriformis mitochondrial fraction several small RNAs that were reproducibly labeled by incubation in the presence of [alpha-(32)P]GTP and guanylyltransferase. Partial sequence information revealed that none of these cappable RNAs is encoded in the T. pyriformis mitochondrial genome.

RNA maturation of the rice SPK gene may involve trans-splicing

A gene encoding a calcium-dependent seed-specific protein kinase (SPK) is abundantly expressed in developing rice seeds (Kawasaki, T et al. Gene (1993) 129, 183-189). Rice genomic clones encoding SPK were isolated using the entire cDNA fragment as a probe. Physical mapping of these genomic clones indicated that the genomic region corresponding to the entire cDNA was divided into two different regions, SPK-A and SPK-B, located on different rice chromosomes. The results of RACE-PCR analyses showed that the respective transcripts from SPK-A and SPK-B contained additional sequences which were not found in the SPK cDNA, and that these sequences were removed like introns during maturation of the SPK mRNA. These results suggest that two different RNAs were independently transcribed from SPK-A and SPK-B and joined, possibly by trans-splicing.

In the Nicotiana sylvestris CMSII mutant, a recombination-mediated change 5' to the first exon of the mitochondrial nad1 gene is associated with lack of the NADH:ubiquinone oxidoreductase (complex I) NAD1 subunit

We previously reported that the Nicotiana sylvestris CMSII mutant mitochondrial DNA carried a large deletion. Several expressed sequences, most of which are duplicated, and the unique copy of the nad7 gene encoding the NAD7 subunit of the NADH:ubiquinone oxidoreductase complex (complex I) are found in the deletion. Here, we show that the orf87-nad3-nad1/A cotranscription unit transcribed from a unique promoter element in the wild-type, is disrupted in CMSII. Nad3, orf87 and the promoter element are part of the deleted sequence, whilst the nad1/A sequence is present and transcribed from a new promoter brought by the recombination event, as indicated by Northern and primer extension experiments. However, Western analyses of mitochondrial protein fractions and of complex I purified using anti-NAD9 affinity columns, revealed that NAD1 is lacking in CMSII mitochondria. Our results suggest that translation of nad1 transcripts rather than transcription itself could be altered in the mutant. Consequences of lack of this submit belonging the membrane arm of complex I and thought to contain the ubiquinone-binding site, are discussed.

Organization and expression of the mitochondrial genome in the Nicotiana sylvestris CMSII mutant

Previous analyses suggested that the Nicotiana sylvestris CMSII mutant carried a large deletion in its mitochondrial genome. Here, we show by cosmid mapping that the deletion is 60 kb in length and contains several mitochondrial genes or ORFs, including the complex I nad7 gene. However, due to the presence of large duplications in the progenitor mitochondrial genome, the only unique gene that appears to be deleted is nad7. RNA gel blot data confirm the absence of nad7 expression, strongly suggesting that the molecular basis for the CMSII abnormal phenotype, poor growth and male sterility, is the altered complex I structure. The CMSII mitochondrial genome appears to consist essentially of one of two subgenomes resulting from recombination between direct short repeats. In the progenitor mitochondrial genome both recombination products are detected by PCR and, reciprocally, the parental fragments are detected at the substoichiometric level in the mutant. The CMSII mtDNA organization has been maintained through six sexual generations.

Physiological, biochemical and molecular aspects of mitochondrial complex I in plants

Respiratory complex I of plant mitochondria has to date been investigated with respect to physiological function, biochemical properties and molecular structure. In the respiratory chain complex I is the major entry gate for low potential electrons from matrix NADH, reducing ubiquinone and utilizing the released energy to pump protons across the inner membrane. Plant complex I is active against a background of several other NAD(P)H dehydrogenases, which do not contribute in proton pumping, but permit and establish several different routes of shuttling electrons from NAD(P)H to ubiquinone. Identification of the corresponding molecular structures, that is the proteins and genes of the different NADH dehydrogenases, will allow more detailed studies of this interactive regulatory network in plant mitochondria. Present knowledge of the structure of complex I and the respective mitochondrial and nuclear genes encoding various subunits of this complex in plants is summarized here. Copyright 1998 Elsevier Science B.V.

Plasmon analyses of Triticum (wheat) and Aegilops: PCR-single-strand conformational polymorphism (PCR-SSCP) analyses of organellar DNAs

To investigate phylogenetic relationships among plasmons in Triticum and Aegilops, PCR-single-strand conformational polymorphism (PCR-SSCP) analyses were made of 14.0-kb chloroplast (ct) and 13. 7-kb mitochondrial (mt)DNA regions that were isolated from 46 alloplasmic wheat lines and one euplasmic line. These plasmons represent 31 species of the two genera. The ct and mtDNA regions included 10 and 9 structural genes, respectively. A total of 177 bands were detected, of which 40.6% were variable. The proportion of variable bands in ctDNA (51.1%) was higher than that of mtDNA (28. 9%). The phylogenetic trees of plasmons, derived by two different models, indicate a common picture of plasmon divergence in the two genera and suggest three major groups of plasmons (Einkorn, Triticum, and Aegilops). Because of uniparental plasmon transmission, the maternal parents of all but one polyploid species were identified. Only one Aegilops species, Ae. speltoides, was included in the Triticum group, suggesting that this species is the plasmon and B and G genome donor of all polyploid wheats. ctDNA variations were more intimately correlated with vegetative characters, whereas mtDNA variations were more closely correlated with reproductive characters. Plasmon divergence among the diploids of the two genera largely paralleled genome divergence. The relative times of origin of the polyploid species were inferred from genetic distances from their putative maternal parents.

Evolution of trans-splicing plant mitochondrial introns in pre-Permian times

Trans-splicing in angiosperm plant mitochondria connects exons from independent RNA molecules by means of group II intron fragments. Homologues of trans-splicing introns in the angiosperm mitochondrial nad2 and nad5 genes are now identified as uninterrupted group II introns in the ferns Asplenium nidus and Marsilea drummondii. These fern introns are correctly spliced from the pre-mRNA at the sites predicted from their well-conserved secondary structures. The flanking exon sequences of the nad2 and nad5 genes in the ferns require RNA editing, including the removal of in-frame stop codons by U-to-C changes for correct expression of the genetic information. We conclude that cis-splicing introns like the ones now identified in ferns are the ancestors of trans-splicing introns in angiosperm mitochondria. Intron disruption is apparently due to a size increase of the structurally variable group II intron domain IV followed by DNA recombination in the plant mitochondrial genome.

RNA editing status of nad7 intron domains in wheat mitochondria

The most highly conserved structures of group II introns are the helical domains V and VI near the 3'splice site. Within this region of each of the four introns in the wheat mitochondrial nad7 gene encoding NADH dehydrogenase subunit 7, there are A-C mispairs. To determine whether C-to-U type RNA editing restores conventional A-U pairing, we sequenced RT-PCR products from partially-spliced nad7 template RNA and gel-fractionated, excised intron RNA. We examined transcripts from germinating wheat embryos and seedlings because these two stages of development show pronounced differences in steady state levels of nad7 intronic RNAs. We observed editing at only two of the six predicted sites, and they were located at homologous positions within domain V of the third and fourth introns. A third site was found to be edited within the unmodelled domain VI loop of the fourth intron. Similar patterns of RNA editing were seen in wheat embryos and seedlings. These observations, and the presence of other non-conventional base pairs particularly within domain V of plant mitochondrial introns, indicate weaker helical core structure than in ribozymic group II introns. Moreover, the incompleteness or absence of editing in wheat nad7 excised intron RNA suggests that, although editing may contribute to splicing efficiency, it is not essential for splicing.

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.

A promoter element active in run-off transcription controls the expression of two cistrons of nad and rps genes in Nicotiana sylvestris mitochondria

The expression of two mitochondrial gene clusters (orf87-nad3-nad1/A and orf87-nad3-rps12) was studied in Nicotiana sylvestris. 5' and 3' termini of transcripts were mapped by primer extension and nuclease S1 protection. Processing and transcription initiation sites were differentiated by in vitro phosphorylation and capping experiments. A transcription initiation site, present in both gene clusters, was found 213 nucleotides upstream of orf87. This promoter element matches the consensus motif for dicotyledonous mitochondrial promoters and initiates run-off transcription in a pea mitochondrial purified protein fraction. Processing sites were identified 5' of nad3, nad1/A and rps12 respectively. These results suggest that (i) the expression of the two cistrons is only controlled by one duplicated promoter element, and (ii) multiple processing events are required to produce monocistronic nad3, nad1/A and rps12 transcripts.

Polymerase chain reaction-single strand conformational polymorphism analysis of intra- and interspecific variations in organellar DNA regions of Aegilops mutica and related species

In order to study the phylogeny of Aegilops mutica in the genera of Triticum and Aegilops, variations in chloroplast and mitochondrial DNA regions were investigated by polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) analysis. Nine lines, each of Ae. mutica and Ae. speltoides, were studied together with nine other Triticum and Aegilops species, including T. aestivum. By analyzing 9.7-kb chloroplast and 13.1-kb mitochondrial DNA regions, a total of 268 bands were detected, of which 176 (65.7%) showed variation within and/or between species. The level of intraspecific variation of Ae. mutica was lower than that of Ae. speltoides. The low level of the intraspecific variation of Ae. mutica was contrary to the expectation from previous studies on morphological and cytolo-gical characters. In the phylogenetic trees based on SSCP, Ae. mutica, Ae. speltoides and the other four species of the section Sitopsis (the subsection Emarginata) were separated into three different clusters. In addition, T. aestivum was included in the cluster of Ae. speltoides in the phylogenetic trees. This result suggests that Ae. speltoides is the cytoplasmic donor of common wheat.

Regulation of gene expression in plant mitochondria

Many genes is plant mitochondria have been analyzed in the past 15 years and regulatory processes controlling gene expression can now be investigated. In vitro systems capable of initiating transcription faithfully at promoter sites have been developed for both monocot and dicot plants and will allow the identification of the interacting nucleic acid elements and proteins which specify and guide transcriptional activities. Mitochondrial activity, although required in all plant tissues, is capable of adapting to specific requirements by regulated gene expression. Investigation of the factors governing the quality and quantity of distinct RNAs will define the extent of interorganelle regulatory interference in mitochondrial gene expression.

The rapeseed mitochondrial gene encoding a homologue of the bacterial protein Ccl1 is divided into two independently transcribed reading frames

In the rapeseed mitochondrial genome we identified sequences that have a high similarity to those of a bacterial gene involved in the biogenesis of cytochromes c designated ccl1. The structure of this gene is quite unusual. In rapeseed mitochondria, the ccl1-homologous (orf577) sequence is divided into two parts, which are at least 45 kb apart. These two parts are transcribed separately and their transcripts are edited similarly to the homologous transcripts of wheat and Oenothera. However it was impossible to identify a mature transcript covering the whole coding region, a result that excludes a trans-splicing event. No other copy of this gene was found in either the nuclear genome or the mitochondrial genome. The protein product of orf577 is present in rapeseed mitochondria. These results raise the possibility that this divided gene might be functional and active in rapeseed mitochondria through a novel mechanism of gene expression.

A promiscuous chloroplast DNA fragment is transcribed in plant mitochondria but the encoded RNA is not edited

The RNA editing processes in chloroplasts and mitochondira of higher plants show several similarities which are suggestive of common components and/or biochemical steps between the two plant organelles. The existence of various promiscuous DNA fragments of chloroplast origin in plant mitochondrial genomes allowed us to test the possibility that chloroplast sequences are also edited in mitochondria. An rpoB fragment transferred from chloroplasts to mitochondria in rice was chosen as it contains several editing sites, two of which match sequence motifs surrounding even non-homologous editing sites in both chloroplast and mitochondrial transcripts. Rice chloroplast and mitochondrial rpoB DNA and cDNA sequences were selectively amplified and the editing status of the cDNA sequences was determined. Three of the four potential rpoB editing sites previously detected in maize were found to be edited in the rice chloroplast rpoB transcript, whereas the fourth was found to remain unedited. In mitochondria, however, all four editing sites remain unmodified at the cDNA level. This indicates that the editing processes of higher plant mitochondria and chloroplasts are not identical and that organelle-specific factors are required for eliciting the respective editing events.

Trans-splicing and alternative-tandem-cis-splicing: two ways by which mammalian cells generate a truncated SV40 T-antigen

The early SV40 BstXI-BamHI (Bst/Bam) DNA fragment encodes exclusively for the second exon of the large T-antigen and contains the intact small t-antigen intron. Rat cells transformed by the p14T, a construct that carries the Bst/Bam DNA fragment as a tail-to-head tandem duplication, synthesize a truncated T-antigen (T1-antigen) without having a direct equivalent at the DNA level. Formation of the T1-mRNA occurs by means of two distinct mechanisms: alternative-tandem-cis-splicing and trans-splicing. To generate the T1-mRNA the cells utilize a cryptic 5' splice site, located within the second exon of the large T-antigen and the regular small t-antigen 3' splice site. Since these splice sites are in an inverted order two Bst/Bam transcripts are required to generate one T1-mRNA molecule. For alternative-tandem-cis-splicing the cells utilize a 4.4 kb pre-mRNA that contains the sequence of the entire Bst/Bam tandem repeat. The proximal Bst/Bam segment provides the 5' donor splice site and the distal segment the 3' acceptor site. This requires that the pre-mRNA not be cleaved after the RNA polymerase II has passed the polyadenylation signal of the proximal Bst/Bam DNA segment. Synthesis of the 4.4 kb pre-mRNA was demonstrable by RT-PCR but not by Northern blot analysis. For trans-splicing, the cells utilize two separate pre-mRNA molecules. One transcript provides the cryptic 5' splice donor site and the other the 3' splice acceptor site. To demonstrate this a three base pair deletion was introduced into the proximal Bst/Bam segment of the p14T DNA (p14Tdelta-3) as a marker, destroying the recognition site for Pf/MI restriction enzyme. This deletion allowed the differentiation between the proximal and distal Bst/Bam segment. RT-PCR analysis and DNA sequencing confirmed that the p14Tdelta-3 transformed cells generate the T1-mRNA by intra- and inter-molecular RNA splicing.

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.

Developmental- and tissue-specificity of RNA editing in mitochondria of suspension-cultured maize cells and seedlings

C to U editing of apt9, nad3, and cox2 mRNAs was investigated in maize seedlings at various developmental stages as well as in suspension-cultured cells. Heterogeneity of mRNAs that result from incomplete editing was analyzed for each gene and from five tissues or developmental conditions. The editing status of approximately 30 cDNA clones was determined by digestion with a restriction enzyme that discriminates between unedited and edited DNA sequences. The atp9 and spliced cox2 cDNAs were essentially completely edited in all samples examined. Analysis of three editing sites of nad3 cDNAs indicated that incompletely edited cDNAs were detected in all tissues and treatments with a temporal increase in the overall editing status, from 50% at 3 days to about 75% at 7 days. These results indicate that incompletely edited mRNAs are prevalent for some plant mitochondrial genes, and can change with developmental or growth conditions.

RNA editing of transcripts of the gene for apocytochrome b (cob) in rice mitochondria

RNA editing was examined in rice mitochondrial apocytochrome b (cob) transcripts. Nineteen C-U conversions were found, and most of them changed the polypeptide sequence encoded by genomic DNA sequence. Evidence for partial and excess editing was also found.

The rps4-gene is encoded upstream of the nad2-gene in Arabidopsis mitochondria

In Arabidopsis mitochondria the nad2-gene consists of five exons (a-e) which are separated by three cis-splicing introns and one trans-splicing intron. Sequence analysis of the region upstream of exons a and b reveals an open reading frame encoding ribosomal protein S4 (rps4). In the second nad2 coding region (exons c-e) a pseudo tRNA(Tyr) sequence and a fragment of the plastid psbA gene are located upstream of the trans-spliced exon c. Primer extension analysis identifies RNA 5'-termini within the pseudo-tRNA(Tyr) confirming this sequence to be non-functional. Northern blot analysis suggests the rps4-gene to be cotranscribed with at least the first part of the nad2-gene. The rps4 and nad2 coding sequences as well as the first cis-intron and the trans-intron sequences of the nad2 gene are altered by RNA editing. RNA editing in the open reading frames improves in most instances conservation of the specified amino acids.

Fully edited and partially edited nad9 transcripts differ in size and both are associated with polysomes in potato mitochondria

Two classes of nad9 transcripts are present at different abundances in the steady-state RNA pool of potato mitochondria. The 5'- and 3' termini of the transcripts were determined by primer extension and S1 nuclease protection analyses respectively. Using two primer pairs that will either specifically amplify the larger transcript or amplify both the larger and the smaller transcripts in RT-PCR analyses it was found that the larger nad9 transcripts are partially edited, while the smaller transcripts are fully edited. Both the larger and the smaller transcripts were found to be associated with mitochondrial polysomes. The polysome association was found to be sensitive to EDTA and puromycin treatment. Therefore, both fully and partially edited nad9 transcripts appear to be engaged in translation.

Protein polymorphism generated by differential RNA editing of a plant mitochondrial rps12 gene

The rps12 gene transcripts encoding mitochondrial ribosomal protein S12 are partially edited in petunia mitochondria. Different petunia lines were found vary in the extent of rps12 transcript editing. To test whether multiple forms of RPS12 proteins are produced in petunia mitochondria as a result of partial editing, we probed mitochondrial proteins with specific antibodies against edited and unedited forms of a 13-amino-acid RPS12 peptide spanning two amino acids affected by RNA editing. Both antibodies reacted with mitochondrial proteins at the expected size for RPS12 proteins. The amounts of unedited RPS12 protein in different petunia lines correlate with the abundance of unedited transcripts in these plants. Unedited rps12 translation products are also detected in other plant species, indicating that polymorphism in mitochondrial rps12 expression is widespread. Moreover, we show that RPS12 proteins recognized by both edited-specific and unedited-specific antibodies are present in a petunia mitochondrial ribosome fraction. These results demonstrate that partially edited transcripts can be translated and that the protein product can accumulate to detectable levels. Therefore, genes exhibiting incompletely edited transcripts can encode more than one gene product in plant mitochondria.

Extensive RNA editing of U to C in addition to C to U substitution in the rbcL transcripts of hornwort chloroplasts and the origin of RNA editing in green plants

We cloned and sequenced a portion of chloroplast DNA from the hornwort Anthoceros formosae. A nucleotide sequence of 7556 bp contained structures similar to those of ndhK, ndhC, trnV, trnM, atpE, atpB, rbcL, trnR and accD. The arrangement of these was the same as that of other chloroplast DNA. However, two nonsense codons were located within the putative coding region of rbcL, although they were used as putative termination codons of the genes. RNA was extensively edited in the transcripts of rbcL when cDNA sequences were analyzed. The unusual nonsense codons of TGA and TAA became CGA and CAA respectively. These are examples of U to C type RNA editing, which was never been found before in chloroplast mRNA. In general, 13 Cs of genomic DNA were found as Ts in the cDNA sequence and seven Ts were found as Cs. This is the first finding of RNA editing on the transcripts of rbcL and also in bryophytes. This event had been thought to arise in land plants after the split of bryophytes. The origin of RNA editing is discussed in relation to the landing of green plants.

Creation of an initiation codon by RNA editing in the coxI transcript from tomato mitochondria

Nucleotide-sequence analysis showed that the gene for cytochrome oxidase subunit I (coxI) from tomato mitochondrial DNA has an ACG codon at a conserved position corresponding to an ATG initiation codon in other higher-plant coxI genes. cDNA-sequence analysis of the coxI transcripts showed that 15 positions in the genomic DNA were converted from C to U in the transcripts by RNA editing. One of the editing events is observed at the indicated ACG codon, producing an ATG initiation codon. The nucleotide sequences of 37 cDNA clones showed that the initiation codon was created in 32 out of the 37 clones, while nucleotide positions 254 and 11 were edited in 37 and 34 of the 37 clones examined, respectively, suggesting that creation of the initiation codon is a post-transcriptional event. The BamHI site at nucleotide position 757-762 within the coxI genomic DNA was altered in all 97 cDNA clones examined, demonstrating that RNA editing at this site in the transcripts is very common. RNA editing takes place to a lesser extent at the initiation codon, compared with editing at internal position 254. This indicates that editing is either a random process or that it involves a mechanism favoring less RNA editing in the initiation codon than in internal sites.

Physical and gene organization of mitochondrial DNA from the fertile cytoplasm of sugarbeet (Beta vulgaris L.)

We have constructed a complete physical map of the mitochondrial genome from the male-fertile cytoplasm of sugarbeet. The entire sequence complexity can be represented on a single circular master chromosome of 358 kb. This master chromosome contains three copies of one recombinationally active repeat sequence, with two copies in direct orientation and the other in inverted orientation. The positions of the rRNA genes and of 23 polypeptide genes, determined by filter hybridization, are scattered throughout the genome, with triplicate rrn26 genes located partially or entirely within the recombination-repeat elements. Three ribosomal-protein genes (rps1A, rps14 and rps19) were found to be absent from sugarbeet mtDNA. Our results also reveal that at least six regions homologous with cDNA are dispersed in the mitochondrial genome.

Splicing and editing of rps10 transcripts in potato mitochondria

The structure and expression of the potato mitochondrial gene rps10, encoding ribosomal protein S10, has been characterized. The RPS10 polypeptide of 129 amino acids is encoded by two exons of 307 bp and 80 bp respectively, which are separated by a 774-bp class-II intron. Editing of the complete rps10 coding region was studied by sequence analysis of spliced cDNAs. Four C residues are edited into U, resulting in the creation of a putative translational initiation codon, a new stop codon which eliminated ten carboxy-terminal residues, and two additional amino-acid alterations. All these changes increase the similarity between the potato and liverwort polypeptides. One additional C-to-U RNA editing event, observed in the intron sequence of unspliced cDNAs, improves the stability of the secondary structure in stem I (i) of domain I and may thus be required for the splicing reaction. All spliced cDNAs, and most unspliced cDNAs, were completely edited, suggesting that editing is an early step of rps10 mRNA processing and precedes splicing. Earlier work on potato rps10 (Zanlungo et al. 1994) is now known to comprise only a partial analysis of the gene, since the short downstream exon was not identified.

The trans-spliced intron 1 in the psaA gene of the Chlamydomonas chloroplast: a comparative analysis

In the secondary structure model that has been proposed for the trans-spliced intron 1 in the Chlamydomonas reinhardtii psaA gene, a third RNA species (tscA RNA) interacts with the 5' and 3' intron parts flanking the exons to reconstitute a composite structure with several features of group-II introns. To test the validity of this model, we undertook the sequencing and modelling of equivalent introns in the psaA gene from other unicellular green algae belonging to the highly diversified genus Chlamydomonas. Our comparative analysis supports the model reported for the C. reinhardtii psaA intron 1, and also indicates that the 5' end of the tscA RNA and the region downstream from the psaA exon 1 cannot be folded into a structure typical of domain I as described for most group-II introns. It is possible that a fourth RNA species, yet to be discovered, provides the parts of domain I which are apparently missing.

RNA editing of mat-r transcripts in maize and soybean increases similarity of the encoded protein to fungal and bryophyte group II intron maturases: evidence that mat-r encodes a functional protein

We present evidence that transcripts of the mat-r (maturase-related) genes of maize and soybean contain 15 and 14 uridines (U), respectively, at positions occupied by cytosines (C) in the mat-r gene sequences. Eleven and twelve of these C-->U edits result in an amino acid replacement. Ten C-->U edits are at corresponding nucleotides in the maize and soybean transcripts and, except for a single silent edit, the remainder are at positions in one species that are Us in the other species. This results in an increase in amino acid sequence similarity of the maize and soybean MAT-R proteins. Further, of those amino acids in maize and soybean MAT-R proteins specified by edited codons, ten are conserved in the reverse transcriptase-associated and RNA splicing-associated sequences of the cox1-I2 and/or the cox1-I1 maturases of the fungus Saccharomyces cerevisiae and the bryophyte, Marchantia polymorpha, respectively. The implied strong selection for amino acid sequence conservation indicates that the MAT-R protein is functional. The possibility is discussed that initiation of translation of the mat-r transcripts is at a four nucleotide codon, ATAA or ATGA.

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.

The NADH dehydrogenase subunit 7 gene is interrupted by four group II introns in the wheat mitochondrial genome

We have characterized a wheat mitochondrial gene, designated nad7, capable of encoding a 394-amino acid subunit of the respiratory chain NADH dehydrogenase complex. It contains four introns possessing group II features and their positions differ from those in both the liverwort mitochondrial nad7 pseudogene and the nuclear gene encoding the homologous 49 kDa subunit of complex I in Neurospora. The derived amino acid sequence of the wheat nad7 gene is strongly conserved relative to its nuclear or organellar counterparts in other organisms. C-to-U type RNA editing, which is observed at 32 positions within the coding region of wheat nad7 transcripts, strengthens protein sequence similarity. RNA editing is also predicted to improve base-pairing within the domain V/VI regions of all four introns.

Evidence for a group II intron in Escherichia coli inserted into a highly conserved reading frame associated with mobile DNA sequences

The distribution of group II introns in the living world is an important aspect of the hypothesis which postulates their evolutionary relation to the nuclear spliceosome. As an alternative to the restricted experimental approaches towards their identification we devised a strategy to recognize group II introns in sequence data. By this approach we identified a locus on a plasmid in the bacterium Escherichia coli. Modelling of the derived RNA secondary structure reveals the presence of perfectly conserved domains V and VI as typical features of group II introns. An intron internal reading frame upstream of domain V is homologous to group II intron encoded maturases. A reading frame downstream of the predicted 3'-splice site is highly similar to a small polypeptide encoded in the central part of the Agrobacterium tumefaciens T-DNA. With the TBLASTN algorithm a set of plasmid-borne insertion sequences in Agrobacteria and Rhizobia and surprisingly also in a Yersinia pseudotuberculosis strain was identified which contain this highly conserved reading frame.

Intron loss from the NADH dehydrogenase subunit 4 gene of lettuce mitochondrial DNA: evidence for homologous recombination of a cDNA intermediate

The mitochondrial gene coding for subunit 4 of the NADH dehydrogenase complex I (nad4) has been isolated and characterized from lettuce, Lactuca sativa. Analysis of nad4 genes in a number of plants by Southern hybridization had previously suggested that the intron content varied between species. Characterization of the lettuce gene confirms this observation. Lettuce nad4 contains two exons and one group IIA intron, whereas previously sequenced nad4 genes from turnip and wheat contain three group IIA introns. Northern analysis identified a transcript of 1600 nucleotides, which represents the mature nad4 mRNA and a primary transcript of 3200 nucleotides. Sequence analysis of lettuce and turnip nad4 cDNAs was used to confirm the intron/exon border sequences and to examine RNA editing patterns. Editing is observed at the 5' and 3' ends of the lettuce transcript, but is absent from sequences that correspond to exons two, three and the 5' end of exon four in turnip and wheat. In contrast, turnip transcripts are highly edited in this region, suggesting that homologous recombination of an edited and spliced cDNA intermediate was involved in the loss of introns two and three from an ancestral lettuce nad4 gene.

Differential RNA editing in closely related introns in Oenothera mitochondria

Introns a/b of the nad2 gene and b/c of the nad1 gene in Oenothera mitochondria were found to be closely related. Within a scaffold of conserved sequence regions, a 48 bp sequence element covering intron domain V and flanking nucleotides is identical in both group II introns. The third nucleotide of this element is edited in the nad2, but not in the nad1 intervening sequence. The C to U editing event compensates an nad2-specific nucleotide mismatch in the stem domain IV and thus improves secondary structure stability. This differential editing event indicates that the identical upstream 2 and downstream 45 nucleotides are not sufficient to specify this editing site. Comparison of adjacent exon editing patterns in spliced and unspliced transcripts shows a higher degree of editing in processed sequences, confirming that RNA editing is a posttranscriptional process in plant mitochondria.

Differential screening of mitochondrial cDNA libraries from male-fertile and cytoplasmic male-sterile sugar-beet reveals genome rearrangements at atp6 and atpA loci

As part of a strategy to define differences in genome organization and expression between cytoplasmic male-sterile (CMS) and male-fertile (MF) sugar-beet mitochondria, cDNA libraries from both mitochondrial genotypes were constructed. Preliminary screening with ribosomal RNA gene probes identified candidate cDNA clones corresponding to structural genes. In addition, reciprocal hybridization experiments were performed using labelled first-strand cDNA to identify uniquely transcribed sequences. One cDNA clone (pYC700) is unique to CMS mitochondria and is located upstream of the F0F1-ATPase subunit 6 gene (atp6). Another cDNA clone (pYC130), when used as a probe in northern hybridization analysis, revealed novel transcript profiles in CMS sugar-beet mitochondria. Sequence analysis of this cDNA showed strong homology with the F0F1-ATPase subunit alpha (atpA) coding sequences from several higher plants. The atp6 and atpA loci from each genotype were cloned and the genomic organization, DNA sequence and transcription of each locus was studied. Differences in the transcript profiles of each gene are a consequence of genomic rearrangements 5' to the coding sequence.

Expression of CMS-unique and flanking mitochondrial DNA sequences in Phaseolus vulgaris L

The expression of mitochondrial DNA sequences unique to a cytoplasmically male-sterile (CMS) line of Phaseolus vulgaris was investigated. RNA-blot hybridizations with strand-specific probes demonstrated CMS-unique transcripts (7.0, 6.8, 4.7, 3.3 and 2.8 kb) to be in the sense orientation with respect to the longest open reading frames within the CMS-unique region. Hybridizations revealed co-transcription of CMS-unique and upstream, atpA-coding sequences to generate the 6.8-kb RNA. However, hybridizations with CMS-unique and flanking DNA probes accounted for only 4.9 kb of the longest and most abundant (7.0 kb) CMS-unique transcript, providing indirect evidence for the involvement of a splicing process in the generation of this transcript. Sedimentation experiments demonstrated the association of 7.0- and 6.8-kb CMS-unique transcripts with polyribosomes in seedlings and floral buds of a CMS line and a line restored to fertility by the nuclear gene Fr2. However, steady-state levels of the 7.0- and 6.8-kb transcripts were decreased in the restored line relative to the CMS line.

Subunit 6 of the Fo-ATP synthase complex from cytoplasmic male-sterile radish: RNA editing and NH2-terminal protein sequencing

RNA editing and NH2-terminal processing of subunit 6 (atp6) of the mitochondrial Fo-ATPase complex has been investigated for the normal (fertile) and Ogura (male-sterile) radish cytoplasms to determine if previously identified differences between the Ogura atp6 locus and its normal radish counterpart are associated with cytoplasmic male sterility. Analysis of cDNA clones from five different sterile and fertile radish lines identified one C-to-U transition, which results in the replacement of a proline with a serine, in several of the lines. No editing of atp6 transcripts was observed in two lines, Scarlet Knight (normal radish) and sterile CrGC15 (Ogura radish). This is the first example of a naturally occurring plant mitochondrial gene that is not edited. The Ogura atp6 polypeptide is synthesized with a predicted NH2-terminal extension of 174 amino acids in contrast to the nine amino acid extension found in normal radish. In spite of the lack of similarity between the two extensions, NH2-terminal sequence analysis indicates that both polypeptides are processed to yield identical core proteins with a serine as the NH2-terminal residue. These results indicate that ATPase subunit 6 is synthesized normally in Ogura radish, and that it is unlikely that the atp6 locus is associated with Ogura cytoplasmic male sterility.

The nad6 gene and the exon d of nad1 are co-transcribed in wheat mitochondria

The exon d of nad1 is located 993 bp upstream of the nad6 gene in the wheat mitochondrial genome. Transcription analyses of both sequences (nad1 exon d and the nad6 gene) were done by Northern hybridization using RNA from wheat seedlings and tissue cultures derived from immature embryos. A complicated pattern was generated with a probe including exon d of nad1 and the whole nad6 gene. An 0.71-kb transcript is specific to nad1 exon d whereas a 1.2-kb transcript is specific to the nad6 gene. Three larger transcripts hybridize to both probes suggesting that nad1 exon d and nad6 are co-transcribed. This co-transcription has been directly demonstrated by cDNA synthesis on mtRNAs and sequencing of the PCR amplification product.

Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function

Many group II introns encode reverse transcriptase-like proteins that potentially function in intron mobility and RNA splicing. We compared 34 intron-encoded open reading frames and four related open reading frames that are not encoded in introns. Many of these open reading frames have a reverse transcriptase-like domain, followed by an additional conserved domain X, and a Zn(2+)-finger-like region. Some open reading frames have lost conserved sequence blocks or key amino acids characteristic of functional reverse transcriptases, and some lack the Zn(2+)-finger-like region. The open reading frames encoded by the chloroplast tRNA(Lys) genes and the related Epifagus virginiana matK open reading frame lack a Zn(2+)-finger-like region and have only remnants of a reverse transcriptase-like domain, but retain a readily identifiable domain X. Several findings lead us to speculate that domain X may function in binding of the intron RNA during reverse transcription and RNA splicing. Overall, our findings are consistent with the hypothesis that all of the known group II intron open reading frames evolved from an ancestral open reading frame, which contained reverse transcriptase, X, and Zn(2+)-finger-like domains, and that the reverse transcriptase and Zn(2+)-finger-like domains were lost in some cases. The retention of domain X in most proteins may reflect an essential function in RNA splicing, which is independent of the reverse transcriptase activity of these proteins.

Higher plant mitochondria encode an homologue of the nuclear-encoded 30-kDa subunit of bovine mitochondrial complex I

We describe the structure and expression of a wheat mitochondrial gene, which codes for a subunit of mitochondrial NADH dehydrogenase. The deduced protein sequence has 70% similarity to the 30-kDa subunit of bovine mitochondrial complex I and 65% similarity to the 31-kDa subunit of Neurospora crassa complex I, components of the iron-sulfur-protein fraction, both nuclear-encoded proteins. We named this wheat mitochondrial gene as nad9. The wheat nad9 gene is transcribed in a single mRNA of 0.9 kb that is edited (C-to-U conversions) in 14 positions. Transcript mapping revealed that the first ATG codon is just 20 nucleotides downstream of the mRNA 5' end and that the 3' end is just 23 nucleotides downstream of the nad9 stop codon. The expression of the nad9 gene in plant mitochondria was studied. Polyclonal antibodies prepared against a wheat NAD9 fusion protein specifically recognise the 30-kDa subunit of bovine mitochondrial complex I and a 27.5-kDa protein in the membrane fractions of wheat, maize and common bean mitochondria, whereas the same serum recognizes a 30-kDa protein in the mitochondria of pea, chickpea and lentil.

The sugar beet mitochondrial genome contains an ORF sharing sequence homology with the gene for the 30 kDa subunit of bovine mitochondrial complex I

From a sugar beet mitochondrial DNA library, we have isolated an open reading frame (ORF192) showing extensive homology to the gene for the 30 kDa subunit of the bovine mitochondrial complex I (NADH: ubiquinone reductase). The ORF192 was found to be actively transcribed to give an RNA of approximately 1.0 kb. We have designated this gene nad9. Transcripts from the nad9 locus are edited by five C to U transitions, increasing similarity with the amino acid sequence of the corresponding bovine and Neurospora crassa polypeptides. Southern blot hybridization also indicates that nad9 is present in the mitochondrial genomes of a variety of higher plant species.

Inverse splicing of a group II intron

I describe the self-splicing of an RNA that consists of exon sequences flanked by group II intron sequences. I find that this RNA undergoes accurate splicing in vitro, yielding an excised exon circle. This splicing reaction involves the joining of the 5' splice site at the end of an exon to the 3' splice site at the beginning of the same exon; thus, I term it inverse splicing. Inverse splicing provides a potential mechanism for exon scrambling, for exon deletion in alternative splicing pathways, and for exon shuffling in gene evolution.

A gene involved in the biogenesis of c-type cytochromes is co-transcribed with a ribosomal protein gene in wheat mitochondria [corrected]

Sequence analysis of a transcribed region of the wheat mitochondrial (mt) genome revealed two open reading frames (orfs) coding for proteins of 589 and 174 amino acids. Both genes are co-transcribed in a 2.6-kb RNA. The largest orf codes for a hydrophobic protein which bears similarity to a bacterial protein involved in the biogenesis of c-type cytochromes. Its corresponding RNA sequence is fully edited at 34 positions. The second orf encodes a protein homologous to the amino-terminal third of E. coli ribosomal protein S1, corresponding to the ribosome-binding domain of this protein. Its RNA sequence is edited at four positions, one of the edits creating a stop codon. The presence of both proteins in wheat mitochondria was demonstrated using specific antibodies raised against fusion proteins obtained in E. coli from the corresponding cDNAs.

Occurrence and transcription of genes for nad1, nad3, nad4L, and nad6, coding for NADH dehydrogenase subunits 1, 3, 4L, and 6, in liverwort mitochondria

The genes encoding subunits 1, 3, 4L, and 6 of NADH dehydrogenase (nad1, nad3, nad4L, nad6) in the mitochondrial genome of a liverwort, Marchantia polymorpha, were characterized by comparing homologies of the amino-acid sequences of the subunits with those of other organisms. The nad3 and nad4L genes are split by single and double group II introns, respectively. The 5'-half portion of the nad6 gene was repeated at an identity of 89% to form a reading frame consisting of 100 amino-acid residues. The Northern hybridization analysis showed that all four genes are transcribed in the liverwort mitochondria.

Editing of rps3/rpl16 transcripts creates a premature truncation of the rpl16 open reading frame

Overlapping open reading frames corresponding to maize mitochondrial genes rps3 and rpl16 have been found in Petunia mitochondrial DNA. The DNA region associated with these two genes is part of the Petunia mitochondrial recombination repeat and is iterated three times. Analysis of transcripts from these genes shows that there is RNA editing of the coding regions and that one of the editing sites detected in the open reading frame overlap creates a premature stop codon in the rpl16 sequence. No transcripts were detected that were unedited at this site. Thus, in Petunia editing of rpl16 appears to render this gene nonfunctional.

Group I introns in the liverwort mitochondrial genome: the gene coding for subunit 1 of cytochrome oxidase shares five intron positions with its fungal counterparts

The complete nucleotide sequence of the mitochondrial DNA (mtDNA) from a liverwort, Marchantia polymorpha, contains thirty-two introns. Twenty-five of these introns possess the characteristic secondary structures and consensus sequences of group II introns. The remaining seven are group I introns, six of which happen to interrupt the gene coding for subunit 1 of cytochrome oxidase (cox1). Interestingly, the insertion sites of one group II and four group I introns in the cox1 gene coincide with those of the respective fungal mitochondrial interns. Moreover, comparison of the four group I introns with their fungal counterparts shows that group I introns inserted at identical genomic sites in different organisms are indeed related to one another, in terms of the peptide sequences generated from the complete or fragmental ORFs encoded by these introns. At the same time, the liverwort introns turned out to be more divergent from their fungal cognates than the latter are from one another. We therefore conclude that vertical transmission from a common ancestor organism is the simplest explanation for the presence of cognate introns in liverwort and fungal mitochondrial genomes.

RNA editing gives a new meaning to the genetic information in mitochondria and chloroplasts

RNA editing in plant mitochondria and chloroplasts alters mRNA sequences to code for different proteins than the DNA. Most of these C-to-U transitions occur in open reading frames, but a few are observed in intron sequences. Influences of the nuclear genome on editing patterns suggest that cytoplasmic factors participate in this process.