Extensive mitochondrial specific transcription of the Brassica campestris mitochondrial genome

Genomics Armed With Diversity Leads the Way in Brassica Improvement in a Changing Global Environment

Meeting the needs of a growing world population in the face of imminent climate change is a challenge; breeding of vegetable and oilseed Brassica crops is part of the race in meeting these demands. Available genetic diversity constituting the foundation of breeding is essential in plant improvement. Elite varieties, land races, and crop wild species are important resources of useful variation and are available from existing genepools or genebanks. Conservation of diversity in genepools, genebanks, and even the wild is crucial in preventing the loss of variation for future breeding efforts. In addition, the identification of suitable parental lines and alleles is critical in ensuring the development of resilient Brassica crops. During the past two decades, an increasing number of high-quality nuclear and organellar Brassica genomes have been assembled. Whole-genome re-sequencing and the development of pan-genomes are overcoming the limitations of the single reference genome and provide the basis for further exploration. Genomic and complementary omic tools such as microarrays, transcriptomics, epigenetics, and reverse genetics facilitate the study of crop evolution, breeding histories, and the discovery of loci associated with highly sought-after agronomic traits. Furthermore, in genomic selection, predicted breeding values based on phenotype and genome-wide marker scores allow the preselection of promising genotypes, enhancing genetic gains and substantially quickening the breeding cycle. It is clear that genomics, armed with diversity, is set to lead the way in Brassica improvement; however, a multidisciplinary plant breeding approach that includes phenotype = genotype × environment × management interaction will ultimately ensure the selection of resilient Brassica varieties ready for climate change.

Plant Mitochondria are a Riddle Wrapped in a Mystery Inside an Enigma

A fundamental paradox motivates the study of plant mitochondrial genomics: the mutation rate is very low (lower than in the nucleus) but the rearrangement rate is high. A landmark paper published in Journal of Molecular Evolution in 1988 established these facts and revealed the paradox. Jeffrey Palmer and Laura Herbon did a prodigious amount of work in the pre-genome sequencing era to identify both the high frequency of rearrangements between closely related species, and the low frequency of mutations, observations that have now been confirmed many times by sequencing. This paper was also the first to use molecular data on rearrangements as a phylogenetic trait to build a parsimonious tree. The work was a technical tour-de-force, its findings are still at the heart of plant mitochondrial genomics, and the underlying molecular mechanisms that produce this paradox are still not completely understood.

DEX1, a novel plant protein, is required for exine pattern formation during pollen development in Arabidopsis

To identify factors that are required for proper pollen wall formation, we have characterized the T-DNA-tagged, dex1 mutation of Arabidopsis, which results in defective pollen wall pattern formation. This study reports the isolation and molecular characterization of DEX1 and morphological and ultrastructural analyses of dex1 plants. DEX1 encodes a novel plant protein that is predicted to be membrane associated and contains several potential calcium-binding domains. Pollen wall development in dex1 plants parallels that of wild-type plants until the early tetrad stage. In dex1 plants, primexine deposition is delayed and significantly reduced. The normal rippling of the plasma membrane and production of spacers observed in wild-type plants is also absent in the mutant. Sporopollenin is produced and randomly deposited on the plasma membrane in dex1 plants. However, it does not appear to be anchored to the microspore and forms large aggregates on the developing microspore and the locule walls. Based on the structure of DEX1 and the phenotype of dex1 plants, several potential roles for the protein are proposed.

Molecular characterization of glyoxalase II from Arabidopsis thaliana

Glyoxalase II is part of the glutathione-dependent glyoxalase detoxification system. In addition to its role in the detoxification of cytotoxic 2-oxo-aldehydes, specifically methylglyoxal, it has been suggested that the glyoxalase system may also play a role in controlling cell differentiation and proliferation. During the analysis of a T-DNA-tagged mutant of Arabidopsis we identified the gene for a glyoxalase II isozyme (GLY1) that appears to be mitochondrially localized. The cDNA encoding a glyoxalase II cytoplasmic isozyme (GLY2) was also isolated and characterized. Southern blot and sequence analyses indicate that glyoxalase II proteins are encoded by at least two multigene families in Arabidopsis. Escherichia coli cells expressing either GLY1 or GLY2 exhibit increased glyoxalase II activity, confirming that they do, in fact, encode glyoxalase II proteins. Northern analysis shows that the two genes are differentially expressed. Transcripts for the mitochondrial isozyme are most abundant in roots, while those for the cytoplasmic isozyme are highest in flower buds. The identification of glyoxalase II isozymes that are differentially expressed suggests that they may play different roles in the cell.

Mitochondrial genome diversity and cytoplasmic male sterility in higher plants

Characteristic differences exist between the mitochondrial genome organization of fertile and cytoplasmic male-sterile (CMS) lines in a range of plant species. Current evidence suggests that these characteristic mitochondrial genotypes arose by aberrant recombination events, generating chimeric mitochondrial DNA sequences which have subsequently become stabilized, possibly by selective amplification. An investigation of the variation in stoichiometry of the fouratpA gene types in maize have suggested evolutionary mechanisms for the generation of mitochondrial genome diversity which are based on amplification of pre-existing, rare recombinant DNA molecules. As with a number of other well-documented examples of genome rearrangement, those involving theatpA gene appear to have no obvious phenotypic significance. However, in a number of cases, recombination events have resulted in either modification of existing mitochondrial genes, leading to the synthesis of a modified polypeptide, e.g. thecoxI gene in the 9E sorghum cytoplasm, or the generation of novel open reading frames. In the latter case the unique open reading frame found in the mitochondrial DNA of CMS-T maize plants encodes a 13 kDa polypeptide, previously identified as a CMS-T-specific mitochondrial translation product. Current studies are directed towards establishing a causal link between the 13 kDa polypeptide, mitochondrial enzyme complexes, and the CMS phenotype.

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.

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.

Nuclear genes associated with a single Brassica CMS restorer locus influence transcripts of three different mitochondrial gene regions

Previous studies have shown that the mitochondrial orf224/atp6 gene region is correlated with the Polima (pol) cytoplasmic male sterility (CMS) of Brassica napus. We now extend this correlation by showing that the effects of nuclear fertility restoration on orf224/atp6 transcripts cosegregate with the pol restorer gene Rfp1 in genetic crosses. We also show, however, that the recessive rfp1 allele, or a very tightly linked gene, acts as a dominant gene, designated Mmt (modifier of mitochondrial transcripts), in controlling the presence of additional smaller transcripts of the nad4 gene and a gene possibly involved in cytochrome c biogenesis. A common sequence, TTGTGG, maps immediately downstream of the 5' termini of both of the transcripts specific to plants with the Mmt gene and may serve as a recognition motif in generation of these transcripts. A similar sequence, TTGTTG, that may be recognized by the product of the alternate allele (or haplotype), Rfp1, is found within orf224 just downstream of the major 5' transcript terminus specific to fertility restored plants. Our results suggest that Rfp1/ Mmt is a novel nuclear genetic locus that affects the expression of multiple mitochondrial gene regions, with different alleles or haplotypes exerting specific effects on different mitochondrial genes.

Multiple initiation sites for transcription of a gene for subunit 1 of F1-ATPase (atp1) in rice mitochondria

We identified the sites for the initiation of transcription of a gene for subunit 1 of F1-ATPase (atp1) in rice mitochondrial DNA. Capping and ribonuclease protection experiments in vitro, together with primer extension analysis, demonstrated that there were at least eight transcription initiation sites upstream of atp1. One initiation site, expressed most actively, was flanked by a sequence identical to the consensus promotor motif of rice mitochondrial genes. However, the sequences surrounding the other seven initiation sites exhibited no similarity to the consensus sequence.

Transcript mapping and processing of mitochondrial RNA in the chlorophyte alga Prototheca wickerhamii

The detailed transcript map of the circular 55328 bp mitochondrial (mt) genome from the colourless chlorophycean alga Prototheca wickerhamii has been determined. On each half of this genome the genes are encoded only on one DNA strand, forming transcriptional units comprising variable numbers of genes. With the exception of four genes coding for ribosomal proteins, transcripts of the three rRNA genes and all protein-coding genes have been detected by both northern analysis and primer extension experiments. Polycistronic transcripts of protein coding and tRNA genes were verified by northern analyses, primer extension and RNAse mapping experiments. The 5' and 3' ends of different RNA species are often located in close proximity to putative stem-loop structures and some 5' termini of mRNAs coincide with the 3' end of tRNAs located immediately upstream. Transcript mapping in a putative promoter region revealed two different possible transcription initiation sites; no significant sequence homology to putative mt promoters from higher plants could be found. In addition, two out of three group I introns residing in the cox1 gene were found to be self-splicing in vitro under reaction conditions developed for related mt introns from a filamentous fungus. Mitochondrial gene expression of P. wickerhamii and of filamentous fungi has several features in common, such as intron splicing and the processing of longer polycistronic transcripts. The similarities in RNA maturation between higher-plant and P. wickerhamii mitochondria are less pronounced, since plants rarely use tRNAs as processing signals for their relatively short mitochondrial co-transcripts.

The rps3-rpl16-nad3-rps12 gene cluster in rice mitochondrial DNA is transcribed from alternative promoters

The two gene clusters rps3-rpl16 and nad3-rps12 are separated from each other in the mitochondrial genome and are expressed as the individual transcription units in many plants. In rice mitochondrial DNA (mtDNA), the four genes rps3, rpl16, nad3 and rps12 are located within a region of 6 kbp. Northern-blot analysis revealed that a large transcript (6.6 kb) hybridized to both the rps3-rpl16 and the nad3-rps12 gene clusters. Using RT-PCR, we amplified a fragment of anticipated size (790 bp) from two primers that corresponded to sequences in the coding regions of rpl16 and nad3, demonstrating that at least two of the four genes, namely rpl16 and nad3, were co-transcribed. These results together indicated that all four genes, namely, rps3, rpl16, nad3 and rps12, were co-transcribed in rice mitochondria. Transcription initiation sites were determined by an in vitro capping/ribonuclease protection assay and primer extension analysis. Two initiation sites were identified in the rps3-rpl16-nad3-rps12 gene cluster: one was located upstream of rps3 and the other was located between rpl16 and nad3. This evidence indicates that the rps3-rpl16-nad3-rps12 gene cluster is transcribed from two alternative promoters.

Organ-specific reduction in the abundance of a mitochondrial protein accompanies fertility restoration in cytoplasmic male-sterile radish

The mitochondrial DNA of plants containing the male sterility-causing Ogura cytoplasm of radish contain a novel gene, orf138, that is transcribed as part of a bicistronic mRNA. Genetic studies have previously linked male sterility with the orf138 locus. To determine if orf138 is expressed at the protein level, and investigate the effect of fertility restoration on ORF138 levels, we have raised antibodies to an ORF138-glutathione S-transferase fusion protein. Anti-ORF138 antibodies detect a 20 kDa protein that is associated with the mitochondrial membrane of sterile Ogura radish plants. Nuclear restoration is accompanied by a dramatic reduction in the amount of this protein in mitochondria of flowers and leaves, but not roots of fertile Ogura radish plants. The presence or absence of fertility restoration genes has no detectable effect on the size, abundance, or RNA editing patterns of orf138 transcripts. These results support genetic studies that have implicated orf138 in Ogura cytoplasmic male sterility and suggest that the restorer genes may be affecting either the translation or stability of ORF138.

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.

A DNA-polymerase-related reading frame (pol-r) in the mtDNA of Secale cereale

Mitochondrial (mt)DNA of Secale cereale contains an open reading frame (pol-r), the potential translation product of which shows significant homology to the type-B DNA polymerase encoded by the S1 plasmid of Zea mays; it contains the highly-conserved domains IIa to V of family B polymerases. The pol-r ORF is transcribed, as proven by RT-PCR, but the transcript is not edited. Upstream of the putative start codon a potential promoter motif was detected, fitting well into the postulated consensus sequence of the transcription initiation regions of Z. mays and Triticum aestivum. The pol-r ORF occurs in mtDNA of the fertile rye variety "Halo" and the cytoplasmic male-sterile (CMS) line "Pampa". Both ORFs are almost identical, apart from the 3' terminus; pol-r from Halo can code for 289 amino acids, pol-r from Pampa for 312 amino acids. Based on codon usage and the lack of editing, pol-r is considered to be a "young" gene, probably introduced in the mtDNA of rye by recombination with an mt plasmid.

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.

Chloroplast and mitochondrial DNA diversity in Theobroma cacao

The variability of cocoa (Theobroma cacao) cytoplasmic genomes has been investigated. A total of 177 cocoa clones was surveyed for restriction fragment length polymorphism (RFLP) in chloroplast DNA and in mitochondrial DNA using two restriction endonucleases and various heterologous cytoplasmic probes. A high level of polymorphism was found for the mitochondrial genome. This study points up a structuring of the species that fits with the distinction between the Criollo and Forastero populations. In contrast to all previous analyses, a higher level of polymorphism is found among the Criollo clones while the Forastero clones form quite a homogeneous group.

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

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

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.

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.

Organizational differences between cytoplasmic male sterile and male fertile Brassica mitochondrial genomes are confined to a single transposed locus

Comparison of the physical maps of male fertile (cam) and male sterile (pol) mitochondrial genomes of Brassica napus indicates that structural differences between the two mtDNAs are confined to a region immediately upstream of the atp6 gene. Relative to cam mtDNA, pol mtDNA possesses a 4.5 kb segment at this locus that includes a chimeric gene that is cotranscribed with atp6 and lacks an approximately 1kb region located upstream of the cam atp6 gene. The 4.5 kb pol segment is present and similarly organized in the mitochondrial genome of the common nap B.napus cytoplasm; however, the nap and pol DNA regions flanking this segment are different and the nap sequences are not expressed. The 4.5 kb CMS-associated pol segment has thus apparently undergone transposition during the evolution of the nap and pol cytoplasms and has been lost in the cam genome subsequent to the pol-cam divergence. This 4.5 kb segment comprises the single DNA region that is expressed differently in fertile, pol CMS and fertility restored pol cytoplasm plants. The finding that this locus is part of the single mtDNA region organized differently in the fertile and male sterile mitochondrial genomes provides strong support for the view that it specifies the pol CMS trait.

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.

Variation in mitochondrial translation products in fertile and cytoplasmic male-sterile sugar beets

Intact and functional mitochondria were isolated from sugar beet plants (Beta vulgaris L.) containing normal fertile (F) or cytoplasmic male-sterile (S1-S4) cytoplasms. Incorporation of (35)S-methionine by mitochondria isolated from both roots and leaves showed approximately 20 major and ten minor translation products. Comparison of the polypeptide synthesis patterns produced by leaf mitochondria from fertile plants of three different species within the genus Beta revealed several taxonomically related differences. Contrary to this, the patterns of polypeptides synthesized by mitochondria from roots and leaves of sugar beet plants containing the F and S1-S4 cytoplasms were very similar; in the S1 and S2 cytoplasms no qualitative, and only a few quantitative, differences from the F cytoplasm were observed. Thus, in these cases, cytoplasmic male sterility in sugar beet is not correlated with the constitutive expression of variant polypeptides. In the S3 cytoplasm, however, an additional 6 kDa polypeptide was synthesized and in the S4 cytoplasm an additional 10 kDa polypeptide was observed when compared with the F cytoplasm. The expression of cytoplasmic male sterility in sugar beet may be associated with these variant polypeptides. The mitochondrial polypeptides synthesized were identical in plants with different nuclear backgrounds but with identical S1 cytoplasms. Mitochondria from plants with variants of the S4 cytoplasm in the same nuclear genotype also showed identical patterns of polypeptide synthesis, including the synthesis of the 10 kDa S4-specific polypeptide. Pulse-chase experiments did not affect the synthesis of this polypeptide.

Sequence and transcript analysis of the Nco2.5 Ogura-specific fragment correlated with cytoplasmic male sterility in Brassica cybrids

Sequence analysis of the Ogura-specific mitochondrial DNA (mtDNA) fragment isolated previously from Brassica cybrids carrying Ogura cytoplasmic male sterility (cms) revealed a tRNA(fMet) sequence, a putative 138 amino acid open reading frame (orf138), and a 158 amino acid ORF (orf158) previously observed in mitochondrial genomes from several other plant species. Transcription mapping showed that both ORFs are present on a 1.4 kb cms-specific transcript. The orf158 sequence is also transcribed in fertile plants on a different mRNA, and thus is unlikely to be related to cms. On the other hand, fertile revertant plants lack transcripts of the orf138 sequence, whose possible role in the mechanism of Ogura cms is discussed.

Novel mitochondrial genomes in Brassica napus somatic hybrids

The mitochondrial genomes of nine male-fertile and two Ogura cytoplasmic male-sterile (cms) Brassica napus somatic hybrids were probed with 46 mitochondrial DNA fragments. The distribution of information obtained from each fusion partner was not random. Several regions, including the coxI gene and a major recombination repeat sequence, were always derived from the Brassica campestris fusion partner, and some regions were always derived from the Ogura mitochondrial genome. Novel fragments occurred in seven distinct regions. Some of the rearrangement breakpoints were located near the evolutionary breakpoints relating the mitochondrial genomes of the Brassica species. The sizes of the mitochondrial genomes in the somatic hybrids ranged from 224.8 to 285.3 kb. A direct correlation between a specific gene and the cms phenotype was not observed; however, a possible cms-associated region was identified. It corresponds to a region that was identified through analysis of fertile revertants from a cms B. napus cybrid.

Transcription in maize mitochondria: effects of tissue and mitochondrial genotype

Mitochondrial run-on assays were used to determine transcriptional rates for nine B37(N) maize mitochondrial genes. Quantitation by radiographic imaging detected a 15-fold range in transcriptional rates; the order of apparent promoter strength was rps12 greater than rrn26 greater than atp6 greater than rrn18 greater than cox2 greater than atp alpha greater than atp9 greater than cox3 greater than cob. By probing single-stranded DNAs of both polarities with the run-on-products we showed that gene-specific antisense transcription did not occur. We also tested whether relative transcriptional rates were dependent on either the mitochondrial genotype or the tissue from which the mitochondria were isolated. Although tissue-specific differences in transcriptional rates were not detected, significant variation in apparent promoter strength for at least one gene, rps12, was dependent on the cytoplasmic genotype; rps12 had a five-fold reduced transcriptional rate in B37(T), the Texas male cytoplasmic strain of maize. Pulse-chase experiments suggested that differential transcript stability was not a major determinant of steady state mitochondrial RNA levels. These results indicate not only that promoter strength is an important component of the regulation of transcript levels in maize mitochondria, but also that the strength of a specific gene promoter can be dependent on the cytoplasmic genotype. Finally, the high transcriptional rate of both ribosomal RNA genes and the one mitochondrially encoded ribosomal protein gene studied suggests coordinate transcriptional regulation of both RNA and protein components of the mitochondrial ribosome.

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.

Suppression of cytoplasmic male sterility by nuclear genes alters expression of a novel mitochondrial gene region

To identify regions of the mitochondrial genome that potentially could specify the "Polima" (pol) cytoplasmic male sterility (CMS) of Brassica napus, transcripts of 14 mitochondrial genes from nap (male fertile), pol (male sterile), and nuclear fertility-restored pol cytoplasm plants were analyzed. Transcriptional differences among these plants were detected only with the ATPase subunit 6 (atp6) gene. Structural analysis of the atp6 gene regions of pol and nap mitochondrial DNAs showed that rearrangements in the pol mitochondrial genome occurring upstream of atp6 have generated a chimeric 224-codon open reading frame, designated orf224, that is cotranscribed with atp6. In CMS plants, most transcripts of this region are dicistronic, comprising both orf224 and atp6 sequences. Nuclear restorer genes at either of two distinct loci appear to specifically alter this transcript pattern such that monocistronic atp6 transcripts predominate. The differences in expression of this region appear to result, in part, from differential processing of a tRNA-like element comprising a tRNA pseudogene present immediately upstream of atp6 in both the sterile and fertile mitochondrial DNAs. Possible mechanisms by which expression of the orf224/atp6 locus and the Polima CMS trait may be specifically related are considered.

Extensive nuclear influence on mitochondrial transcription and genome structure in male-fertile and male-sterile alloplasmic Nicotiana materials

Nuclear influences on mitochondrial transcription and genome organization were analysed in six different male-fertile and male-sterile alloplasmic Nicotiana cultivars. The alloplasmic materials were compared with the corresponding nuclear species (N. tabacum) and cytoplasmic donor species (N. debneyi, N. rapanda or N. suaveolens) in Northern and Southern analyses using twelve different mitochondrial genes as probes. The investigation revealed that the nucleus exerts extensive influence on the expression and structure of the mitochondrial genome. For the majority of the probes, changes in both mitochondrial transcription and DNA patterns in alloplasmic cultivars were detected. Even though changes in transcription patterns, which correlated with male sterility, were detected for three of the probes (atpA, orf25 and coxII), the changes were not consistent for all the male-sterile materials. Likewise, no consistent association between mtDNA restriction patterns and cytoplasmic male sterility (CMS) was detected.

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

The nad1 gene encoding subunit I of the respiratory chain NADH dehydrogenase is fragmented into five unique-copy coding segments that are scattered over at least 40 kb and interspersed with other genes in the wheat mitochondrial genome. The nad1 segments are flanked by sequences with group II intron features, and transcript analysis demonstrates the presence of correctly spliced mRNAs. RNA editing occurs at sites asymmetrically distributed along the wheat nad1 coding region, and the initiation codon is created by RNA editing. The unusual organization of the wheat nad1 gene is attributed to mitochondrial DNA rearrangements within introns, and a trans-splicing model involving secondary structural interactions between group II-like intron pieces is proposed for its expression.

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.

Structural organization and transcription of plant mitochondrial and chloroplast genomes

Experimental evidence is presented showing that the plant mitochondrial and chloroplast genomes are multipartite and, that besides a large circular genomic DNA, they contain subgenomic minicircular and plasmid-like molecules. It is demonstrated that plant mitochondrial and chloroplast DNAs are packaged into deoxynucleoprotein fibrils comprising nucleosome-like and nucleomere-like globules; the fibrils form loops and rosette-like structures with central proteinaceous components. A similar structure is characteristic of the subgenomic DNAs. The basic proteins involved in the formation of nucleosome-like globules are quite different from the nuclear histones, indeed the basic proteins from plant mitochondria and chloroplasts are also distinct. Some of the basic proteins share common antigens with the E. coli HU protein. The genetic code for the mitochondrial and chloroplast genes is universal. The only codon now thought to be different from the universal in the mitochondrial genome is corrected during post-transcriptional mRNA editing. There are two hexanucleotides in the promoters of the chloroplast genes homologous to the sequences in -10 and -35 regions of the prokaryotic genes promoters requisite for transcription. Promoter sequences of the plant mitochondria genes responsible for transcription regulation were not identified. Immunoelectronmicroscopic evidence suggest that mitochondrial and chloroplast RNA polymerases have antigens in common with the beta-subunit of E. coli RNA polymerase. It is shown that the mitochondrial genes are intensely transcribed in the dark and repressed by illumination. Electron microscopy demonstrated that about 70% of plant mitochondria contain numerous RNA polymerase molecules in the dark, but this percentage falls to 10-15% after light exposure.

Homologies to plastid DNA in the nuclear and mitochondrial genomes of potato

Potato plastid DNA clones, representing onefourth of the potato plastome complexity and containing sequences of the 16SrRNA, rps16, atpA, atpE, psaA, psaB, trnK, trnV, and trnG genes, were used as hybridization probes on nuclear- and mitochondrial-enriched DNAs. Each probe hybridized to multiple nuclear restriction fragments distinct from the plastid cleavage products generated by the same endonucleases. The nuclear hybridizable fragments are highly methylated at their Hpall target sequences (C/CGG). In some instances, the transfer seemed to involve plastid regions of several kilobase pairs, as reflected by the co-integration in the nucleus of restriction sites that are distant in the plastome. Three clones hybridized additionally to distinct mitochondrial fragments. These results indicate that extensive DNA transfers did occur between plastids and other organelles in potato.

Sugarbeet mitochondria contain an open reading frame showing extensive sequence homology to the subunit 2 gene of the NADH: ubiquinone reductase complex

Sequence analysis of a transcribed region of mitochondrial DNA (mtDNA) from male fertile sugarbeet (Beta vulgaris L.) revealed an open reading frame showing extensive sequence homology to the subunit 2 gene of the NADH: ubiquinone reductase complex (nad2). Sugarbeet nad2 in common with its proposed counterpart in animal mitochondria has no intron and thereby differs from the corresponding chloroplast gene. Northern RNA analysis of sugarbeet nad2 suggested that transcription of this locus gives rise to at least three transcripts. No differences in transcript profile were detected between male fertile and cytoplasmic male sterile sugarbeet. This constitutes the first report of a mitochondrial nad2 gene in higher plants.

Transcriptional and Post-Transcriptional Regulation of RNA Levels in Maize Mitochondria

Relatively little is known about the mechanisms that govern the expression of plant mitochondrial genomes. We have addressed this problem by analyzing the transcriptional activity of different regions of the maize mitochondrial genome using both in vivo and isolated mitochondrial pulse-labeling systems. The regions examined included the protein genes atpA, atp6, and coxII, the 26S, 18S, and 5S rRNA genes, and sequences surrounding the rRNA genes. The rRNAs were found to be transcribed at rates fivefold to 10-fold higher than the protein genes. These rate differences are comparable with the differences in abundance of these species in the total or steady-state RNA population. Pulse-labeled RNA unexpectedly detected transcription of all regions examined, including approximately 21 kilobases of presumed noncoding sequences flanking the rRNA genes for which stable transcripts were not detected. The results obtained with RNA labeled for short pulses in vivo and in isolated mitochondria were similar, suggesting that isolated mitochondria provide a faithful run-on transcription assay. Our results indicate that the absence in total RNA of transcripts homologous to a given region of maize mitochondrial DNA does not necessarily exclude transcriptional activity of that region and that both transcriptional and post-transcriptional processes play important roles in maize mitochondrial genome expression.

Synthesis of male sterile, triazine-resistant Brassica napus by somatic hybridization between cytoplasmic male sterile B. oleracea and atrazine-resistant B. campestris

Fusion of leaf protoplasts from an inbred line of Brassica oleracea ssp. botrytis (cauliflower, n=9) carrying the Ogura (R1) male sterile cytoplasm with hypocotyl protoplasts of B. campestris ssp. oleifera (cv "Candle", n=10) carrying an atrazine-resistant (ATR) cytoplasm resulted in the production of synthetic B. napus (n=19). Thirty-four somatic hybrids were produced; they were characterized for morphology, phosphoglucose isomerase isoenzymes, ribosomal DNA hybridization patterns, chromosome numbers, and organelle composition. All somatic hybrids carried atrazine-resistant chloroplasts derived from B. campestris. The mitochondrial genomes in 19 hybrids were examined by restriction endonuclease and Southern blot analyses. Twelve of the 19 hybrids contained mitochondria showing novel DNA restriction patterns; of these 12 hybrids, 5 were male sterile and 7 were male fertile. The remaining hybrids contained mitochondrial DNA that was identical to that of the ATR parent and all were male fertile.

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.

Organization and nucleotide sequence of the broad bean chloroplast genes trnL-UAG, ndhF and two unidentified open reading frames

We have determined the nucleotide sequence of a 6.9 kbp BamHI-XbaI fragment of broad bean chloroplasts. Part of this fragment (subfragment BglII-ClaI) is known to contain three tRNA genes (trnL-CAA, trnL-UAA and trnF). We have now further identified a gene coding for the third tRNA(Leu) isoacceptor (trnL-UAG) which is located close to trnF. The BamHI-XbaI fragment also contains the gene for subunit 5 of NADH dehydrogenase (ndhF) and two unidentified open reading frames (ORFx and ORF48). ORFx shares a high sequence homology with the long reading frames of tobacco (ORF1708), spinach (ORF2131), and liverwort (ORF2136), while ORF48 shares sequence homology with ORF69 of liverwort and ORF55 of tobacco.

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.

Multiple sequence rearrangements accompanying the duplication of a tRNA(Pro) gene in wheat mitochondrial DNA

In the course of isolating tRNA genes from wheat mtDNA, we have found the same tRNA(Pro) gene in two different Hind III restriction fragments, H-P1 (0.7 kbp) and H-P2 (1.7 kbp). Sequences immediately flanking these duplicate genes are closely related, although not identical; sequence comparisons suggest that multiple rearrangements have occurred in the vicinity of the H-P2 tRNA(Pro) gene, relative to the H-P1 version. The chimeric nature of H-P2 is emphasized by the presence of sequences that are also found upstream of the wheat mitochondrial 26S rRNA gene, as well as sequences derived from chloroplast DNA. Comparison of H-P2 with H-P1 plus upstream sequences provides some insight into possible molecular events that might have generated H-P2. In particular, such comparisons suggest a model in which the homologous sequences in H-P2 are seen to be derived from H-P1 plus upstream sequences as a result of an intragenomic, site-specific rearrangement event, followed by amplification of the product, its fixation in the mitochondrial genome, and subsequent sequence divergence (single base changes as well as insertions/deletions of up to 50 nucleotides). The results reported here implicate particular primary sequence motifs in certain of the rearrangements that characterize H-P2.

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.