Physicochemical characterization of mitochondrial DNA from pea leaves

The Mitochondrial Endonuclease M20 Participates in the Down-Regulation of Mitochondrial DNA in Pollen Cells

Maintaining the appropriate number of mitochondrial DNA (mtDNA) molecules is crucial for supporting mitochondrial metabolism and function in both plant and animal cells. For example, a substantial decrease in mtDNA levels occurs as a key part of pollen development. The molecular mechanisms regulating mtDNA copy number are largely unclear, particularly with regard to those that reduce mtDNA levels. Here, we identified and purified a 20-kD endonuclease, M20, from maize (Zea mays) pollen mitochondria. We found M20 to be an His-Asn-His/Asn (H-N-H/N) nuclease that degrades linear and circular DNA in the presence of Mg²⁺ or Mn²⁺ Arabidopsis (Arabidopsis thaliana) AtM20, which shared high sequence similarity with maize M20, localized to the mitochondria, had a similar H-N-H/N structure, and degraded both linear and circular DNA. AtM20 transcript levels increased during pollen development, in parallel with a rapid reduction in mtDNA. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 genome-editing techniques were used to generate knockout lines of AtM20 (atm20), which exhibited a significant delay in the reduction in mtDNA levels in pollen vegetative cells but normal mtDNA levels in somatic cells. The delayed reduction in pollen mtDNA levels was rescued by the transgenic expression of AtM20 in atm20 plants. This study thus uncovers an endonucleolytic DNase in plant mitochondria and its crucial role in reducing mtDNA levels, pointing to the complex mechanism regulating mtDNA levels in plants.

The Gastrodia elata genome provides insights into plant adaptation to heterotrophy

We present the 1.06 Gb sequenced genome of Gastrodia elata, an obligate mycoheterotrophic plant, which contains 18,969 protein-coding genes. Many genes conserved in other plant species have been deleted from the G. elata genome, including most of those for photosynthesis. Additional evidence of the influence of genome plasticity in the adaptation of this mycoheterotrophic lifestyle is evident in the large number of gene families that are expanded in G. elata, including glycoside hydrolases and urease that likely facilitate the digestion of hyphae are expanded, as are genes associated with strigolactone signaling, and ATPases that may contribute to the atypical energy metabolism. We also find that the plastid genome of G. elata is markedly smaller than that of green plant species while its mitochondrial genome is one of the largest observed to date. Our report establishes a foundation for studying adaptation to a mycoheterotrophic lifestyle.

The Gastrodia elata genome provides insights into plant adaptation to heterotrophy

We present the 1.06 Gb sequenced genome of Gastrodia elata, an obligate mycoheterotrophic plant, which contains 18,969 protein-coding genes. Many genes conserved in other plant species have been deleted from the G. elata genome, including most of those for photosynthesis. Additional evidence of the influence of genome plasticity in the adaptation of this mycoheterotrophic lifestyle is evident in the large number of gene families that are expanded in G. elata, including glycoside hydrolases and urease that likely facilitate the digestion of hyphae are expanded, as are genes associated with strigolactone signaling, and ATPases that may contribute to the atypical energy metabolism. We also find that the plastid genome of G. elata is markedly smaller than that of green plant species while its mitochondrial genome is one of the largest observed to date. Our report establishes a foundation for studying adaptation to a mycoheterotrophic lifestyle.

DNA maintenance in plastids and mitochondria of plants

The DNA molecules in plastids and mitochondria of plants have been studied for over 40 years. Here, we review the data on the circular or linear form, replication, repair, and persistence of the organellar DNA (orgDNA) in plants. The bacterial origin of orgDNA appears to have profoundly influenced ideas about the properties of chromosomal DNA molecules in these organelles to the point of dismissing data inconsistent with ideas from the 1970s. When found at all, circular genome-sized molecules comprise a few percent of orgDNA. In cells active in orgDNA replication, most orgDNA is found as linear and branched-linear forms larger than the size of the genome, likely a consequence of a virus-like DNA replication mechanism. In contrast to the stable chromosomal DNA molecules in bacteria and the plant nucleus, the molecular integrity of orgDNA declines during leaf development at a rate that varies among plant species. This decline is attributed to degradation of damaged-but-not-repaired molecules, with a proposed repair cost-saving benefit most evident in grasses. All orgDNA maintenance activities are proposed to occur on the nucleoid tethered to organellar membranes by developmentally-regulated proteins.

Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella

We report the complete mitochondrial genome sequence of the flowering plant Amborella trichopoda. This enormous, 3.9-megabase genome contains six genome equivalents of foreign mitochondrial DNA, acquired from green algae, mosses, and other angiosperms. Many of these horizontal transfers were large, including acquisition of entire mitochondrial genomes from three green algae and one moss. We propose a fusion-compatibility model to explain these findings, with Amborella capturing whole mitochondria from diverse eukaryotes, followed by mitochondrial fusion (limited mechanistically to green plant mitochondria) and then genome recombination. Amborella's epiphyte load, propensity to produce suckers from wounds, and low rate of mitochondrial DNA loss probably all contribute to the high level of foreign DNA in its mitochondrial genome.

Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates

A pair of species within the genus Silene have evolved the largest known mitochondrial genomes, coinciding with extreme changes in mutation rate, recombination activity, and genome structure.

Genome size and complexity vary tremendously among eukaryotic species and their organelles. Comparisons across deeply divergent eukaryotic lineages have suggested that variation in mutation rates may explain this diversity, with increased mutational burdens favoring reduced genome size and complexity. The discovery that mitochondrial mutation rates can differ by orders of magnitude among closely related angiosperm species presents a unique opportunity to test this hypothesis. We sequenced the mitochondrial genomes from two species in the angiosperm genus Silene with recent and dramatic accelerations in their mitochondrial mutation rates. Contrary to theoretical predictions, these genomes have experienced a massive proliferation of noncoding content. At 6.7 and 11.3 Mb, they are by far the largest known mitochondrial genomes, larger than most bacterial genomes and even some nuclear genomes. In contrast, two slowly evolving Silene mitochondrial genomes are smaller than average for angiosperms. Consequently, this genus captures approximately 98% of known variation in organelle genome size. The expanded genomes reveal several architectural changes, including the evolution of complex multichromosomal structures (with 59 and 128 circular-mapping chromosomes, ranging in size from 44 to 192 kb). They also exhibit a substantial reduction in recombination and gene conversion activity as measured by the relative frequency of alternative genome conformations and the level of sequence divergence between repeat copies. The evolution of mutation rate, genome size, and chromosome structure can therefore be extremely rapid and interrelated in ways not predicted by current evolutionary theories. Our results raise the hypothesis that changes in recombinational processes, including gene conversion, may be a central force driving the evolution of both mutation rate and genome structure.

A fundamental challenge in evolutionary biology is to explain why organisms exhibit dramatic variation in genome size and complexity. One hypothesis predicts that high rates of mutation in DNA sequence create selection against large and complex genomes, which are more susceptible to mutational disruption. Species of flowering plants in the genus Silene vary by approximately 100-fold in the rates of mutation in their mitochondrial DNA, providing an excellent opportunity to test the predicted effects of high mutation rates on genome evolution. Contrary to expectation, Silene species with elevated mutation rates have experienced dramatic expansions in mitochondrial genome size compared to their slowly evolving relatives, resulting in the largest known mitochondrial genomes. In addition to the increases in size and mutation rate, these genomes also reveal a history of rapid change in genome structure. They have been fragmented into dozens of chromosomes and appear to have experienced major reductions in recombination activity. All of these changes have occurred in just the past few million years. This mitochondrial genome diversity within the genus Silene provides a striking example of rapid genomic change and raises new hypotheses regarding the relationship between mutation rate and genome evolution.

Origins and recombination of the bacterial-sized multichromosomal mitochondrial genome of cucumber

Members of the flowering plant family Cucurbitaceae harbor the largest known mitochondrial genomes. Here, we report the 1685-kb mitochondrial genome of cucumber (Cucumis sativus). We help solve a 30-year mystery about the origins of its large size by showing that it mainly reflects the proliferation of dispersed repeats, expansions of existing introns, and the acquisition of sequences from diverse sources, including the cucumber nuclear and chloroplast genomes, viruses, and bacteria. The cucumber genome has a novel structure for plant mitochondria, mapping as three entirely or largely autonomous circular chromosomes (lengths 1556, 84, and 45 kb) that vary in relative abundance over a twofold range. These properties suggest that the three chromosomes replicate independently of one another. The two smaller chromosomes are devoid of known functional genes but nonetheless contain diagnostic mitochondrial features. Paired-end sequencing conflicts reveal differences in recombination dynamics among chromosomes, for which an explanatory model is developed, as well as a large pool of low-frequency genome conformations, many of which may result from asymmetric recombination across intermediate-sized and sometimes highly divergent repeats. These findings highlight the promise of genome sequencing for elucidating the recombinational dynamics of plant mitochondrial genomes.

The mitochondrial genome of the legume Vigna radiata and the analysis of recombination across short mitochondrial repeats

The mitochondrial genomes of seed plants are exceptionally fluid in size, structure, and sequence content, with the accumulation and activity of repetitive sequences underlying much of this variation. We report the first fully sequenced mitochondrial genome of a legume, Vigna radiata (mung bean), and show that despite its unexceptional size (401,262 nt), the genome is unusually depauperate in repetitive DNA and "promiscuous" sequences from the chloroplast and nuclear genomes. Although Vigna lacks the large, recombinationally active repeats typical of most other seed plants, a PCR survey of its modest repertoire of short (38–297 nt) repeats nevertheless revealed evidence for recombination across all of them. A set of novel control assays showed, however, that these results could instead reflect, in part or entirely, artifacts of PCR-mediated recombination. Consequently, we recommend that other methods, especially high-depth genome sequencing, be used instead of PCR to infer patterns of plant mitochondrial recombination. The average-sized but repeat- and feature-poor mitochondrial genome of Vigna makes it ever more difficult to generalize about the factors shaping the size and sequence content of plant mitochondrial genomes.

Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm Silene latifolia

Background

Mitochondrial gene loss and functional transfer to the nucleus is an ongoing process in many lineages of plants, resulting in substantial variation across species in mitochondrial gene content. The Caryophyllaceae represents one lineage that has experienced a particularly high rate of mitochondrial gene loss relative to other angiosperms.

Results

In this study, we report the first complete mitochondrial genome sequence from a member of this family, Silene latifolia. The genome can be mapped as a 253,413 bp circle, but its structure is complicated by a large repeated region that is present in 6 copies. Active recombination among these copies produces a suite of alternative genome configurations that appear to be at or near "recombinational equilibrium". The genome contains the fewest genes of any angiosperm mitochondrial genome sequenced to date, with intact copies of only 25 of the 41 protein genes inferred to be present in the common ancestor of angiosperms. As observed more broadly in angiosperms, ribosomal proteins have been especially prone to gene loss in the S. latifolia lineage. The genome has also experienced a major reduction in tRNA gene content, including loss of functional tRNAs of both native and chloroplast origin. Even assuming expanded wobble-pairing rules, the mitochondrial genome can support translation of only 17 of the 61 sense codons, which code for only 9 of the 20 amino acids. In addition, genes encoding 18S and, especially, 5S rRNA exhibit exceptional sequence divergence relative to other plants. Divergence in one region of 18S rRNA appears to be the result of a gene conversion event, in which recombination with a homologous gene of chloroplast origin led to the complete replacement of a helix in this ribosomal RNA.

Conclusions

These findings suggest a markedly expanded role for nuclear gene products in the translation of mitochondrial genes in S. latifolia and raise the possibility of altered selective constraints operating on the mitochondrial translational apparatus in this lineage.

Restriction endonuclease analysis of mitochondrial DNA from normal and Texas cytoplasmic male-sterile maize

Mitochondrial DNA from normal and cytoplasmic male-sterile maize was digested with restriction endonucleases RI from Escherichia coli or dIII from Hemophilus influenzae. Electrophoresis of resulting fragments revealed distinctions between the two cytoplasmic types. These distinctions suggest that factors responsible or cytoplasmic male sterility are located in the mitochondrial DNA, and that the mitochondrial genome is not inherited paternally.

Extensive and widespread homologies between mitochondrial DNA and chloroplast DNA in plants

We used hybridization techniques to demonstrate that numerous sequence homologies exist between cloned mung bean and spinach chloroplast DNA (ctDNA) restriction fragments and mtDNAs from corn, mung bean, spinach, and pea. The strongest cross-homologies are between clones derived from the ctDNA inverted repeat and mtDNA from corn and pea, although all the ctDNA clones tested hybridized to at least one mtDNA restriction fragment. Known chloroplast genes showing strong mtDNA homologies include those for the large subunit of ribulosebisphosphate carboxylase, which hybridizes to corn mtDNA, and the beta subunit of the chloroplast ATPase, which hybridizes to mung bean mtDNA. Certain of these homologies were confirmed by using cloned spinach mtDNA restriction fragments as probes in reciprocal hybridizations to ctDNA. Several of these ctDNA-homologous mtDNA sequences were shown to be much more closely related to ctDNA from the same species than to that of a distantly related species. We interpret these differential homologies as evidence for relatively recent DNA sequence transfer events, suggesting that transpostion between the two genomes is an ongoing evolutionary process.

Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae)

The mitochondrial genomes of seed plants are unusually large and vary in size by at least an order of magnitude. Much of this variation occurs within a single family, the Cucurbitaceae, whose genomes range from an estimated 390 to 2,900 kb in size. We sequenced the mitochondrial genomes of Citrullus lanatus (watermelon: 379,236 nt) and Cucurbita pepo (zucchini: 982,833 nt)--the two smallest characterized cucurbit mitochondrial genomes--and determined their RNA editing content. The relatively compact Citrullus mitochondrial genome actually contains more and longer genes and introns, longer segmental duplications, and more discernibly nuclear-derived DNA. The large size of the Cucurbita mitochondrial genome reflects the accumulation of unprecedented amounts of both chloroplast sequences (>113 kb) and short repeated sequences (>370 kb). A low mutation rate has been hypothesized to underlie increases in both genome size and RNA editing frequency in plant mitochondria. However, despite its much larger genome, Cucurbita has a significantly higher synonymous substitution rate (and presumably mutation rate) than Citrullus but comparable levels of RNA editing. The evolution of mutation rate, genome size, and RNA editing are apparently decoupled in Cucurbitaceae, reflecting either simple stochastic variation or governance by different factors.

Comparison of promoters controlling on the sunflower mitochondrial genome the transcription of two copies of the same native trnK gene reveals some differences in their structure

Two copies of native trnK (UUU) gene are encoded on the sunflower mitochondrial DNA. They lie within two 12-kb direct repeats, presumably generated by a duplication event. During an investigation aimed at detecting DNA regions activating the trnK1 and trnK2 genes, three distinct promoters have been identified. Their locations were deduced using standard procedures (RT-PCR, RNA capping and 5'RACE) usually employed for the detection of transcription initiation sites (TISs). Promoters P3 and P2 control two independent partially overlapping transcription units containing the trnK2 and ccb206 genes, respectively. Promoter P1 has been mapped about 5200 bp upstream of the trnK1 gene which is part of a transcription unit also containing exons c, d and e of the nad2 gene, 5' to the tRNA gene. Most probably this promoter is not alone in controlling this transcription unit because this DNA region could be cotranscribed, at least partially, starting from other two promoters located upstream of the trnC and trnN genes, respectively. These genes have been previously mapped in a 5' region adjacent to the cluster containing nad2 exons c, d and e and the trnK1 gene. The comparative analysis of promoters P3 and P1 suggests that the difference between them could be related to the duplication event generating the second copy of trnK gene. The availability of a high number of new promoters belonging to dicot mitochondrial genomes makes possible to note some of their specific features.

Variable structures of promoters regulating transcription of cp-like tRNA genes and of some native genes on the sunflower mitochondrial genome

Promoter regions regulating the transcription of all cp-like tRNA genes encoded by the sunflower chondriome have been identified. Some of these genes are part of clusters where the first gene is a typical mitochondrial isoform. Promoters regulating the transcription of single cp-like tRNA genes have a variable structure whereas those regulating the transcription of native genes or clusters with typical mitochondrial genes in the first position conform to a similar common structure. The variability of promoter regions described in this paper could be the result of modifications of regions having, at the moment of the cpDNA insertion event, only minimal structural features as promoters.

Phylogenetic analysis reveals five independent transfers of the chloroplast gene rbcL to the mitochondrial genome in angiosperms

We used the chloroplast gene rbcL as a model to study the frequency and relative timing of transfer of chloroplast sequences to the mitochondrial genome. Southern blot survey of 20 mitochondrial DNAs confirmed three previously reported groups of plants containing rbcL in their mitochondrion, while PCR studies identified a new mitochondrial rbcL. Published and newly determined mitochondrial and chloroplast rbcL sequences were used to reconstruct rbcL phylogeny. The results imply five or six separate interorganellar transfers of rbcL among the angiosperms examined, and hundreds of successful transfers across all flowering plants. By taxonomic criteria, the crucifer transfer is the most ancient, two separate transfers within the grass family are of intermediate ancestry, and the morning-glory transfer is most recent. All five mitochondrial copies of rbcL examined exhibit insertion and/or deletion events that disrupt the reading frame (three are grossly truncated); and all are elevated in the proportion of nonsynonymous substitutions, providing clear evidence that these sequences are pseudogenes.

Characterization of the radish mitochondrial nad3/rps12 locus: analysis of recombination repeats and RNA editing

In order to further investigate sequences that are responsible for low-frequency recombination in plant mitochondrial DNAs and RNA editing in radish mitochondria, the nad3/rps12 locus has been isolated and characterized from a normal cultivar of radish and the male-sterile Ogura cytoplasm. A repeated sequence that has been implicated in other radish mitochondrial DNA rearrangements was identified at the breakpoint between the two loci indicating that it was also involved in the nad3/rps12 rearrangement. Similar to some other radish mitochondrial genes, nad3/rps12 genomic sequences already contain several, but not all, of the bases that are typically edited in plant mitochondrial nad3 and rps12 genes. Analysis of nad3/rps12 cDNAs indicated that the mRNAs are not edited. One partially edited transcript was identified out of the twenty two that were examined. This finding, along with the observation that nad3/rps12 RNAs are present at very low levels, raises the possibility that radish mitochondria may not encode functional copies of these genes. Consistent with this hypothesis, DNA-blot analysis detects nad3/rps12 sequences in the nucleus.

Electron microscopic investigation of mitochondrial DNA from Chenopodium album (L.)

DNA molecules from mitochondria of whole plants and a suspension culture of Chenopodium album were prepared, by a gentle method, for analysis by electron microscopy. Mitochondrial (mt) DNA preparations from both sources contained mostly linear molecules of variable sizes (with the majority of molecules ranging from 40 to 160 kb). Open circular molecules with contour lengths corresponding to 0. 3-183 kb represented 23-26% of all mtDNA molecules in the preparations from the suspension culture and 13-15% in the preparations from whole plants. More than 90% of the circular DNA was smaller than 30 kb. Virtually no size classes of the mtDNA molecules could be identified, and circular or linear molecules of the genome size (about 270 kb) were not observed. In contrast, plastid (pt) DNA preparations from the suspension culture contained linear and circular molecules falling into size classes corresponding to monomers, dimers and trimers of the chromosome. About 23% of the ptDNA molecules were circular. DNA preparations from mitochondria contained a higher percentage of more complex molecules (rosette-like structures, catenate-like molecules) than preparations of ptDNA. Sigma-like molecules (putative intermediates of rolling-circle replication) were observed in mtDNA preparations from the suspension culture (18% of the circles), and in much lower amount (1%) in preparations from whole plants. The results are compared with data obtained previously by pulsed-field gel electrophoresis and discussed in relation to the structural organization and replication of the mt genome of higher plants.

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.

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.

Unusual mitochondrial genome organization in cytoplasmic male sterile common bean and the nature of cytoplasmic reversion to fertility

Spontaneous reversion to pollen fertility and fertility restoration by the nuclear gene Fr in cytoplasmic male sterile common bean (Phaseolus vulgaris L.) are associated with the loss of a large portion of the mitochondrial genome. To understand better the molecular events responsible for this DNA loss, we have constructed a physical map of the mitochondrial genome of a stable fertile revertant line, WPR-3, and the cytoplasmic male sterile line (CMS-Sprite) from which it was derived. This involved a cosmid clone walking strategy with comparative DNA gel blot hybridizations. Mapping data suggested that the simplest model for the structure of the CMS-Sprite genome consists of three autonomous chromosomes differing only in short, unique regions. The unique region contained on one of these chromosomes is the male sterility-associated 3-kb sequence designated pvs. Based on genomic environments surrounding repeated sequences, we predict that chromosomes can undergo intra- and intermolecular recombination. The mitochondrial genome of the revertant line appeared to contain only two of the three chromosomes; the region containing the pvs sequence was absent. Therefore, the process of spontaneous cytoplasmic reversion to fertility likely involves the disappearance of an entire mitochondrial chromosome. This model is supported by the fact that we detected no evidence of recombination, excision or deletion events within the revertant genome that could account for the loss of a large segment of mitochondrial DNA.

Characterization of the radish mitochondrial orfB locus: possible relationship with male sterility in Ogura radish

The orfB locus of the normal (fertile) and Ogura (male-sterile) radish mitochondrial genomes has been characterized in order to determine if this region, which has previously been correlated with cytoplasmic male sterility (CMS) in Brassica napus cybrids (Bonhomme et al. 1991; Temple et al. 1992), could also be involved in radish CMS. In normal radish, orfB is expressed as a 600-nucleotide (nt) transcript. In Ogura radish, orfB is present as the second gene of a 1200-nt transcript that also contains a 138-codon open reading frame (orf138). Sequences showing similarity to orf138 are present in normal radish, but are not expressed.

Characterization of the Brassica campestris mitochondrial gene for subunit six of NADH dehydrogenase: nad6 is present in the mitochondrion of a wide range of flowering plants

We have isolated the Brassica campestris mitochondrial gene nad6, coding for subunit six of NADH dehydrogenase. The deduced amino-acid sequence of this gene shows considerable similarity to mitochondrially encoded NAD6 proteins of other organisms as well as to NAD6 proteins coded for by plant chloroplast DNAs. The B. campestris nad6 gene appears to lack introns and produces an abundant transcript which is comparable in size to a previously described, unidentified transcript (#18) mapped to the B. campestris mitochondrial genome. An alignment of NAD6 proteins (deduced from DNA sequences) suggests that B. campestris nad6 transcripts are edited. Southern-blot hybridization indicates that nad6 is present in the mitochondrial genome of all of a wide range of flowering plant species examined.

Variable intron content of the NADH dehydrogenase subunit 4 gene of plant mitochondria

The gene nad4, encoding subunit four of the mitochondrial NADH dehydrogenase complex I, has been isolated and characterized from turnip, Brassica campestris. The 8 kb turnip nad4 gene contains four exons, which potentially encode a NAD4 polypeptide of 495 amino acids, and three large group II introns. Northern analysis identifies an abundant 2 kb transcript that most likely serves as the nad4 mRNA, while several larger transcripts (putative splicing intermediates) are also detected. Analysis of the nad4 locus in three distantly related dicotyledons indicates that introns 2 and 3 are optional. Mung bean has the same nad4 organization as turnip, whereas spinach nad4 contains introns 1 and 3, and lettuce nad4 has intron 1 only. We infer that all three group II introns were present in the nad4 gene of an angiosperm common ancestor and have persisted in certain lineages for over 200 million years, with two of the introns having been lost in other lineages.

Large size and complex structure of mitochondrial DNA in two nonflowering land plants

We report the first estimates of genome size and complexity for mitochondrial DNAs (mtDNAs) from nonflowering land plants. The mtDNA of Onoclea sensibilis (sensitive fern) is approximately 300 kb in size, while that of Equisetum arvense (common horsetail) is at least 200 kb. Sufficient mtDNA of Onoclea was available to permit an estimation of the copy number and a linkage analysis of nine mitochondrial genes. Six of these genes appear to be present in only one or two copies in the Onoclea genome, whereas three other genes are present in multiple copies. Five of the approximately ten genes encoding 26S rRNA are located on a large, greater than 10 kb, dispersed repeat that also contains closely linked genes for 18S rRNA and the alpha subunit of ATPase (atpA). The other 26S genes belong to a second dispersed repeat family of greater than 8 kb whose elements do not contain any other identified genes. Because flowering plant mtDNAs are also large and contain dispersed, gene-containing, repeats, it appears that these features arose early in the evolution of land plants, or perhaps even in their green algal ancestors.

Atrazine-resistant cytoplasmic male-sterile-nigra broccoli obtained by protoplast fusion between cytoplasmic male-sterile Brassica oleracea and atrazine-resistant Brassica campestris

Protoplast fusion was used to combine the cytoplasmic traits of atrazine resistance and male sterility in Brassica oleracea var. italica (broccoli). Leaf protoplasts from broccoli with the petaloid B. nigra type of cytoplasmic male sterility were fused with hypocotyl protoplasts from an atrazine-resistant biotype of B. campestris var. oleifera cv Candle (oilseed rape). A total of 19 colonies regenerated shoots, all of which were broccolilike in phenotype, i.e., lacked trichomes. Four shoots, all from one colony, were atrazine resistant, surviving and growing in the presence of 25 μM atrazine. A leaf piece assay also confirmed that they were atrazine resistant. Molecular analysis showed that they contain chloroplasts from the atrazine-resistant B. campestris parent and mitochondria from the B. nigra parent. No recombination or rearrangement of the mitochondrial genomes in the fusion products was detected. These four plants and their progeny all showed the petaloid B. nigra type of male sterility.

The role of coxI-associated repeated sequences in plant mitochondrial DNA rearrangements and radish cytoplasmic male sterility

The gene coxI, encoding subunit I of mitochondrial cytochrome c oxidase, has been characterized from the normal (fertile) and Ogura (male-sterile) cytoplasms of radish to determine if a previously identified mitochondrial DNA rearrangement, and its associated transcriptional differences, could play a role in Ogura cytoplasmic male sterility (CMS). The normal and Ogura loci are virtually identical for 2.8 kb, including a 527-codon open reading frame whose product is approximately 95% identical to other plant COXI polypeptides. A rearrangement 120 bp 5' to the coding region results in different 5' transcript termini for the two genes. A comparison of several crucifer mitochondrial DNAs indicates that this rearrangement also occurs in the normal radish cytoplasm and is, therefore, not involved in Ogura CMS. Sequences present at the coxI locus belong to at least two different dispersed repeat families, members of which are also associated with other rearranged genes in radish.

Different fates of the chloroplast tufA gene following its transfer to the nucleus in green algae

Previous work suggested that the tufA gene, encoding protein synthesis elongation factor Tu, was transferred from the chloroplast to the nucleus within the green algal lineage giving rise to land plants. In this report we investigate the timing and mode of transfer by examining chloroplast and nuclear DNA from the three major classes of green algae, with emphasis on the class Charophyceae, the proposed sister group to land plants. Filter hybridizations reveal a chloroplast tufA gene in all Ulvophyceae and Chlorophyceae and in some but not all Charophyceae. One charophycean alga, Coleochaete orbicularis, is shown to contain an intact but highly divergent chloroplast tufA gene, whose product is predicted to be non-functional in protein synthesis. We propose that a copy of the tufA gene was functionally transferred from the chloroplast to the nucleus early in the evolution of the Charophyceae, with chloroplast copies of varying function being retained in some but not all of the subsequently diverging lineages. This proposal is supported by the demonstration of multiple tufA-like sequences in Coleochaete nuclear DNA and in nuclear DNA from all other Charophyceae examined.

A nuclear sequence associated with self-incompatibility in Nicotiana alata has homology with mitochondrial DNA

A 1.0-kb nuclear fragment located 5' to a coding sequence associated with self-incompatibility in N. alata shows homology with mitochondrial chromosomal DNA on Southern blots. This sequence is also present in the mitochondrial DNA of two species of tomato, L. esculentum and L. pennellii, but shows no homology to mtDNA of Zea mays. The homologous mitochondrial fragment from N. alata was cloned and sequenced. A short region of 56 bp matches the nuclear sequence in 53/56 bp. Other matched but misaligned segments flank the 3' end. The nuclear sequence is marked at the 5' end by two 8 bp direct repeats. The function of the nuclear sequence is not known although, it is located 397 bp upstream from the site of transcription of the self-incompatibility gene. The mitochondrial sequence contains only limited open reading frames and the nuclear sequence has none. There is evidence that additional segments of the mitochondrial clone hybridize to other nuclear sequences. The exchange of sequences between the mitochondrial and nuclear genomes of plants is discussed.

Rearrangement, amplification, and assortment of mitochondrial DNA molecules in cultured cells of Brassica campestris

We compared Brassica campestris mitochondrial and chloroplast DNAs from whole plants and from a 2-year-old cell culture. No differences were observed in the chloroplast DNAs (cpDNAs), whereas the culture mitochondrial DNA (mtDNA) was extensively altered. Hybridization analysis revealed that the alterations are due entirely to rearrangement. At least two inversions and one large duplication are found in the culture mtDNA. The duplication element is shown to have the usual properties of a plant mtDNA high frequency "recombination repeat". The culture mtDNA exists as a complex heterogeneous population of rearranged and unrearranged molecules. Some of the culture-associated rearranged molecules are present in low levels in native plant tissue and appear to have sorted out and amplified in the culture. Other mtDNA rearrangements may have occurred de novo. In addition to alterations of the main mitochondrial genome, an 11.3 kb linear mtDNA plasmid present in whole plants is absent from the culture. Contrary to findings in cultured cells of other plants, small circular mtDNA molecules were not detected in the B. campestris cell culture.

Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence

We examined the tempo and mode of mitochondrial DNA (mtDNA) evolution in six species of crucifers from two genera, Brassica and Raphanus. The six mtDNAs have undergone numerous internal rearrangements and therefore differ dramatically with respect to the sizes of their subgenomic circular chromosomes. Between 3 and 14 inversions must be postulated to account for the structural differences found between any two species. In contrast, these mtDNAs are extremely similar in primary sequence, differing at only 1-8 out of every 1000 bp. The point mutation rate in these plant mtDNAs is roughly 4 times slower than in land plant chloroplast DNA (cpDNA) and 100 times slower than in animal mtDNA. Conversely, the rate of rearrangements is extraordinarily faster in plant mtDNA than in cpDNA and animal mtDNA.

Location, identity, amount and serial entry of chloroplast DNA sequences in crucifer mitochondrial DNAs

Southern blot hybridization techniques were used to examine the chloroplast DNA (cpDNA) sequences present in the mitochondrial DNAs (mtDNAs) of two Brassica species (B. campestris and B. hirta), two closely related species belonging to the same tribe as Brassica (Raphanus sativa, Crambe abyssinica), and two more distantly related species of crucifers (Arabidopsis thaliana, Capsella bursa-pastoris). The two Brassica species and R. sativa contain roughly equal amounts (12-14 kb) of cpDNA sequences integrated within their 208-242 kb mtDNAs. Furthermore, the 11 identified regions of transferred DNA, which include the 5' end of the chloroplast psaA gene and the central segment of rpoB, have the same mtDNA locations in these three species. Crambe abyssinica mtDNA has the same complement of cpDNA sequences, plus an additional major region of cpDNA sequence similarity which includes the 16S rRNA gene. Therefore, except for the more recently arrived 16S rRNA gene, all of these cpDNA sequences appear to have entered the mitochondrial genome in the common ancestor of these three genera. The mitochondrial genomes of A. thaliana and Capsella bursa-pastoris contain significantly less cpDNA (5-7 kb) than the four other mtDNAs. However, certain cpDNA sequences, including the central portion of the rbcL gene and the 3' end of the psaA gene, are shared by all six crucifer mtDNAs and appear to have been transferred in a common ancestor of the crucifer family over 30 million years ago. In conclusion, DNA has been transferred sequentially from the chloroplast to the mitochondrion during crucifer evolution and there cpDNA sequences can persist in the mitochondrial genome over long periods of evolutionary time.

Mitochondrial DNA rearrangements and transcriptional alterations in the male-sterile cytoplasm of Ogura radish

Maternally inherited mutations, such as cytoplasmic male sterility, provide useful systems in which to study the function of plant mitochondrial genomes and also their interaction with nuclear genes. We have studied the organization and expression of the organelle genomes of the male-sterile cytoplasm of Ogura radish and compared them with those of normal radish to identify alterations that might be involved in cytoplasmic male sterility. The chloroplast DNAs of Ogura and normal radish are virtually indistinguishable, whereas their mitochondrial DNAs are highly rearranged. Alignment of a restriction map constructed for the 257-kilobase Ogura mitochondrial genome with that published for the 242-kilobase genome of normal radish reveals that the two mitochondrial DNAs differ in arrangement by at least 10 inversions. The transcriptional patterns of several known mitochondrial genes and of rearranged mitochondrial sequences were examined in three nuclear backgrounds. Altered transcripts were observed for three mitochondrial genes, atpA, atp6, and coxI. Rearrangements map near each of these genes and therefore may be responsible for their transcriptional alterations. Radish nuclear genes that restore fertility to the Ogura cytoplasm have no effect on the atp6 and coxI transcripts, but do influence the atpA transcriptional pattern.

Physical and gene organization of mitochondrial DNA in fertile and male sterile sunflower. CMS-associated alterations in structure and transcription of the atpA gene

To study the molecular basis of cytoplasmic male sterility (CMS) in sunflower (Helianthus annuus), we compared the physical organization and transcriptional properties of mitochondrial DNAs (mtDNAs) from isonuclear fertile and CMS lines. Mapping studies revealed much greater similarity between the two mtDNAs than in previous comparisons of fertile and CMS lines from other plant species. The two sunflower mtDNAs 1) are nearly identical in size (300 kb and 305 kb); 2) contain the same 12 kb recombination repeat and associated tripartite structure; 3) have the same dispersed distribution of mitochondrial genes and chloroplast DNA-homologous sequences; 4) are greater than 99.9% identical in primary sequence; and 5) are colinear over a contiguous region encompassing 94% of the genome. Detectable alterations are limited to a 17 kb region of the genome and reflect as few as two mutations--a 12 kb inversion and a 5 kb insertion/deletion. One endpoint of both rearrangements is located within or near atpA, which is also the only mitochondrial gene whose transcripts differ between the fertile and CMS lines. Furthermore, a nuclear gene that restores fertility to CMS plants specifically influences the pattern of atpA transcripts. Rearrangements at the atpA locus may, therefore, be responsible for CMS in sunflower.

Mitochondrial DNA rearrangements and transcriptional alterations in the male-sterile cytoplasm of Ogura radish

Maternally inherited mutations, such as cytoplasmic male sterility, provide useful systems in which to study the function of plant mitochondrial genomes and also their interaction with nuclear genes. We have studied the organization and expression of the organelle genomes of the male-sterile cytoplasm of Ogura radish and compared them with those of normal radish to identify alterations that might be involved in cytoplasmic male sterility. The chloroplast DNAs of Ogura and normal radish are virtually indistinguishable, whereas their mitochondrial DNAs are highly rearranged. Alignment of a restriction map constructed for the 257-kilobase Ogura mitochondrial genome with that published for the 242-kilobase genome of normal radish reveals that the two mitochondrial DNAs differ in arrangement by at least 10 inversions. The transcriptional patterns of several known mitochondrial genes and of rearranged mitochondrial sequences were examined in three nuclear backgrounds. Altered transcripts were observed for three mitochondrial genes, atpA, atp6, and coxI. Rearrangements map near each of these genes and therefore may be responsible for their transcriptional alterations. Radish nuclear genes that restore fertility to the Ogura cytoplasm have no effect on the atp6 and coxI transcripts, but do influence the atpA transcriptional pattern.

Presence of a chloroplast-like elongator tRNAMet gene in the mitochondrial genomes of soybean and Arabidopsis thaliana

The nucleotide sequence of elongator tRNA(Met) genes from soybean chloroplast and mitochondria and Arabidopsis thaliana mitochondria have been determined. The mitochondrial tRNA(Met) genes from soybean and A. thaliana are identical, and they differ from the soybean chloroplast tRNA(Met) gene by only four nucleotides. Analysis of the flanking regions indicates that the mitochondrial tRNA(Met) gene is not present on a large chloroplast DNA insertion in the mitochondrial genome, but it suggests that they have a common origin. Comparison of the three genes and the evolutionary implications are discussed.

Intraspecific variation and multicircularity in Brassica mitochondrial DNAs

Intraspecific variation was examined among 25 mitochondrial DNAs (mtDNAs), representing between two and five lines of eight agriculturally important Brassica species. Each of the approximately 140 restriction sites surveyed was invariant within each species. Only two length polymorphisms, deletions of 700 bp and 100 bp in a Brassica nigra line, were detected. A single inversion polymorphism was found; this distinguished two different mtDNA populations within a single line of Brassica hirta. Approximately 60% of the mtDNA molecules in this line and in two other B. hirta lines were identical, whereas the other 40% of the molecules in the first line differed by a 62-kb inversion. Levels of within-species variability in mtDNA appear to be lower in Brassica than in other groups of plants. These mtDNA comparisons are in agreement with cpDNA studies regarding the maternal ancestry of three amphidiploid Brassica species. This agreement and others imply that the two cytoplasmic genomes must have shared a common, maternal mode of transmission throughout the history of the genus. Finally, analysis of a supercoiled fraction of mtDNA from cauliflower (Brassica oleracea) provides the strongest evidence yet in support of the multicircular model for plant mtDNAs.

A theoretical model for quantitatively inherited traits influenced by nuclear-cytoplasmic interactions

Cytoplasmic genes of crop species exhibit non-Mendelian inheritance and affect quantitative traits such as biomass and grain yield. Photosynthesis and respiration are physiological processes responsible, in part, for the expression of such quantitative traits and are regulated by enzymes encoded in both the cytoplasm and nucleus. Cytoplasmic genes are located in the chloroplast and mitochondrial genomes. Unlike the nuclear genome, the cytoplasmic genomes consist of single, circular, double-stranded molecules of DNA, and in many crop species, the cytoplasmic genomes are inherited solely through the maternal parent. Maternal inheritance of cytoplasmic genomes and Mendelian inheritance of the nuclear genome were used to model the genotypic value of an individual. The model then was utilized to derive genetic variances and covariances for a random-mating population. Finally, the use of reciprocal mating designs to estimate variance components was investigated.

Extensive mitochondrial specific transcription of the Brassica campestris mitochondrial genome

We constructed a complete transcriptional map of the 218 kb Brassica campestris (turnip) mitochondrial genome. Twenty-four abundant and positionally distinct transcripts larger than 500 nucleotides were identified by Northern analyses. Approximately 30% (61 kb) of the genome is highly transcribed. In addition, a number of less abundant transcripts, many of which overlap with each other and with the major transcripts, were also detected. If each abundant transcript represents a distinct rRNA or protein species, then plant mitochondria would appear to encode a significantly larger number of proteins than do animal mitochondria. Although B. campestris mitochondrial DNA contains a number of chloroplast DNA-derived sequences, none of these chloroplast sequences appear to be transcribed within the mitochondrion. We determined the positions of 12 genes in the B. campestris mitochondrial genome. The order of these genes in B. campestris is completely different than in maize (1) and spinach (2).

Unicircular structure of the Brassica hirta mitochondrial genome

Restriction mapping studies reveal that the mitochondrial genome of white mustard (Brassica hirta) exists in the form of a single circular 208 kb chromosome. The B. hirta genome has only one copy of the two sequences which, in several related Brassica species, are duplicated and undergo intramolecular recombination. This first report of a plant mitochondrial DNA that does not exist in a multipartite structure indicates that high frequency intramolecular recombination is not an obligatory feature of plant mitochondrial genomes. Heterologous filter hybridizations reveal that the mitochondrial genomes of B. hirta and B. campestris have diverged radically in sequence arrangement, as the result of approximately 10 large inversions. At the same time, however, the two genomes are similar in size, sequence content, and primary sequence.

Tricircular mitochondrial genomes of Brassica and Raphanus: reversal of repeat configurations by inversion

We constructed complete physical maps of the tripartite mitochondrial genomes of two Crucifers, Brassica nigra (black mustard) and Raphanus sativa (radish). Both genomes contain two copies of a direct repeat engaged in intragenomic recombination. The outcome of this recombination in black mustard is to interconvert a 231 kb master chromosome with two subgenomic circles of 135 kb and 96 kb. In radish, a 242 kb master chromosome interconverts with subgenomic circles of 139 kb and 103 kb. The recombination repeats are 7 kb in size in black mustard and 10 kb in radish, and are nearly identical except for two insertions in the radish repeat relative to the black mustard one. The two repeat configurations present on the master chromosome of black mustard are located on the subgenomes of radish and vice-versa. To explain this, we postulate the existence of an evolutionarily intermediate mitochondrial genome in which the recombination repeats were (are) present in an inverted orientation. The recombination repeats described for these two species are completely different from those previously found in the closely related species B. campestris, implying that such repeats are created and lost frequently in plant mitochondrial DNAs and making it less than likely that recombination occurs in a site-specific manner.

Molecular analysis of mitochondrial DNA from rye (Secale cereale L.)

Molecular characterization of mitochondrial (mt) DNA of rye (Secale cereale L.), free of significant amounts of contaminating chloroplast (cp) DNA, was initiated using the open-pollinated cultivar 'Halo' as a source of mtDNA. Based on the compilation of data from restriction patterns, the molecular size of the mtDNA was estimated to be 410 Kb and its buoyant density was determined as 1.705 g/ml. Southern hybridization, using labelled cp genes (P700 and ribulosebiphosphate-carboxylase large subunit), indicated the presence of cpDNA-homologous regions on putative mtDNA fragments. Mt DNAs of inbred lines with fertile and cytoplasmic male sterile (CMS) 'Pampa' cytoplasm were also analysed. Whereas the restriction patterns of mtDNAs of 'Halors and the fertile line turned out to be identical, 'Pampa' mtDNA showed a unique restriction pattern, indicating (as in most other CMS systems) the involvement of mtDNA rearrangements in the expression of male sterility in rye. All 3 mtDNAs investigated contain regions homologous to the plasmid S1 of the CMS-S cytoplasm of Maize (Zea mays), as indicated by hybridization experiments. In 'Pampa' cytoplasm the S-homologous sequence is located within a rearranged region of mtDNA.

Tripartite mitochondrial genome of spinach: physical structure, mitochondrial gene mapping, and locations of transposed chloroplast DNA sequences

A complete physical map of the spinach mitochondrial genome has been established. The entire sequence content of 327 kilobase pairs (kb) is postulated to occur as a single circular molecule. Two directly repeated elements of approximately 6 kb, located on this "master chromosome", are proposed to participate in an intragenomic recombination event that reversibly generates two "subgenomic" circles of 93 kb and 234 kb. The positions of protein and ribosomal RNA-encoding genes, determined by heterologous filter hybridizations, are scattered throughout the genome, with duplicate 26S rRNA genes located partially or entirely within the 6 kb repeat elements. Filter hybridizations between spinach mitochondrial DNA and cloned segments of spinach chloroplast DNA reveal at least twelve dispersed regions of inter-organellar sequence homology.

The watermelon mitochondrial URF-1 gene: evidence for a complex structure

We have cloned and sequenced a fragment of watermelon mitochondrial DNA (mtDNA) which contains a gene homologous to mitochondrial URF-1 (Unidentified Reading Frame-1) of vertebrates, Drosophila yakuba and Aspergillus nidulans. URF-1 is thought to encode a component of the respiratory chain NADH dehydrogenase. Two coding regions in the watermelon gene are separated by approximately 1,450 bp of untranslatable DNA. These two exons encode the central portions of URF-1, and are highly conserved. We postulate that three additional exons, selected by their map location and amino acid homology to other URF-1 sequences, encode the remainder of the polypeptide. This is the first description of a plant mitochondrial gene with multiple introns.

Extrachromosomal DNA of pea-root (Pisum sativum) has repeated sequences and ribosomal genes

Restriction endonuclease digestion and Southern blotting procedure were used to determine differences between extrachromosomal, nuclear, plastid, and mitochondrial DNAs from meristematic cells of cultured pea roots.Extrachromosomal and nuclear DNA are highly methylated and neither DNA is homologous to plastid or mitochondrial DNA. Hybridization of extrachromosomal DNA to nuclear DNA indicated that extrachromosomal DNA differed quantitatively from total nuclear DNA in repetitive sequences. Cloned rDNA showed that extrachromosomal DNA contains rRNA genes but the hybridization signal indicated that the copy number was less than that expected if the molecules were amplified. These and cytological findings suggest that extrachromosomal DNA is involved in or a product of genomic changes associated with the onset of differentiation by precursor cells of vascular parenchyma and the root cap.