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

Mitochondrial cytochrome c oxidase and F1Fo-ATPase dysfunction in peppers (Capsicum annuum L.) with cytoplasmic male sterility and its association with orf507 and Ψatp6-2 genes

Cytoplasmic male sterility (CMS) in pepper (Capsicum annuum L.) has been associated with novel genes in the mitochondria, such as orf507 and Ψatp6-2. Plant sterility has been proved to result from the rearrangement of the mitochondrial genome. Previous studies have demonstrated that orf507 is co-transcribed with the cox II gene, and Ψatp6-2 is truncated at the 3' region of the atp6-2 that is found in the maintainer line. Until this time, little has been known about the relationship between the novel gene and the function of its corresponding enzyme in mitochondria from the CMS pepper line. Moreover, the aberrant function of the mitochondrial enzymes is seldom reported in pepper. In this study, we observed that anther abortion occurred after the tetrad stage in the CMS line (HW203A), which was accompanied by premature programmed cell death (PCD) in the tapetum. The spatiotemporal expression patterns of orf507 and Ψatp6-2 were analyzed together with the corresponding enzyme activities to investigate the interactions of the genes and mitochondrial enzymes. The two genes were both highly expressed in the anther. The orf507 was down-regulated in HW203A (CMS line), with nearly no expression in HW203B (the maintainer line). In contrast, the cytochrome c oxidase activity in HW203A showed the opposite trend, reaching its highest peak at the tetrad stage when compared with HW203B at the same stage. The Ψatp6-2 in the CMS line was also down-regulated, but it was up-regulated in the maintainer line. The corresponding F(1)F(o)-ATPase activity in the CMS line was gradually decreased along with the development of the anther, which showed the same trend for Ψatp6-2 gene expression. On the contrary, with up-regulated gene expression of atp6-2 in the maintainer line, the F(1)F(o)-ATPase activity sharply decreased after the initial development stage, but gradually increased following the tetrad stage, which was contrary to what happened in the CMS line. Taken together, all these results may provide evidence for the involvement of aberrant mitochondrial cytochrome c oxidase and F(1)F(o)-ATPase in CMS pepper anther abortion. Moreover, the novel orf507 and Ψatp6-2 genes in the mitochondria may be involved in the dysfunction of the cytochrome c oxidase and F(1)F(o)-ATPase, respectively, which are responsible for the abortion of anthers in the CMS line.

Altered expression of wheat AINTEGUMENTA homolog, WANT-1, in pistil and pistil-like transformed stamen of an alloplasmic line with Aegilops crassa cytoplasm

Homeotic transformation of stamens into pistil-like structures, called pistillody, has been reported in some alloplasmic common wheat lines with Aegilops crassa cytoplasm. An alloplasmic line of Chinese Spring ditelosomic 7BS (CSdt7BS) with Ae. crassa cytoplasm lacking the long arm of the chromosome 7B shows pistillody, and the pistils and transformed stamens are sterile due to abnormal ovule development. To elucidate the molecular mechanism of the ovule abnormality, we compared the expression profiles of floral organs between euplasmic and alloplasmic CSdt7BS lines. Two differential display methods of mRNA profiling demonstrated that Ae. crassa cytoplasm largely affects nuclear gene expression profiles of common wheat. Of the differentially expressed genes, a wheat AINTEGUMENTA (ANT) homolog, WANT-1, was preferentially expressed in pistils but not in stamens, and accumulation of the transcript was limited to ovule primordia at the floral organ development stage. In alloplasmic wheat, WANT-1 expression was patchy and weak at the ovule-development stages. On the other hand, no significant difference in gene expression patterns of wheat AGAMOUS (AG) homologs (WAG-1 and WAG-2) was observed between fertile and sterile pistils. These results indicated that alteration of gene expression after initiation of ovule primordia results in abnormal ovule development, and that the aberrant ovule formation is at least partly associated with the weak expression of WANT-1 around ovule primordia in alloplasmic wheat with Ae. crassa cytoplasm.

Mitochondrial genotypes with variable parts of Arabidopsis thaliana DNA affect development in Brassica napus lines

Phenotypic, genetic and molecular studies were made of Brassica napus lines with mitochondrial genomes consisting of DNA from both B. napus and Arabidopsis thaliana. The lines were isogenic regarding the nuclear and plastid genomes. Out of 21 lines, 10 were male-sterile, 3 semi-sterile and 8 male-fertile. Screening of the mitochondrial genomes with a dense set of A. thaliana specific markers showed that most lines contained large but variable portions of A. thaliana mitochondrial DNA. Several of the A. thaliana sequences in the mitochondrial genomes lead to the accumulation of novel transcripts. In addition, the restorer line showed different ability to restore male-fertility in the male-sterile lines. These results indicate that CMS is caused by several mitochondrial loci or combinations of loci. Beside petal and stamen morphology, growth rate and adenylate content varied among the lines. Furthermore, we found that the mitochondrial background had a distinct influence on nuclear gene expression. A clear example is the reduced expression of the two B-genes APETALA3 and PISTILATA in the male-sterile lines. From the studies made comparing the mitochondrial loci and the observed phenotypic alterations, our interpretation is that different loci in the mitochondrial genome influence nuclear gene expression via several retrograde signalling pathways.

Transgenic induction of mitochondrial rearrangements for cytoplasmic male sterility in crop plants

Stability of the mitochondrial genome is controlled by nuclear loci. In plants, nuclear genes suppress mitochondrial DNA rearrangements during development. One nuclear gene involved in this process is Msh1. Msh1 appears to be involved in the suppression of illegitimate recombination in plant mitochondria. To test the hypothesis that Msh1 disruption leads to the type of mitochondrial DNA rearrangements associated with naturally occurring cytoplasmic male sterility in plants, a transgenic approach for RNAi was used to modulate expression of Msh1 in tobacco and tomato. In both species, these experiments resulted in reproducible mitochondrial DNA rearrangements and a condition of male (pollen) sterility. The male sterility was, in each case, heritable, associated with normal female fertility, and apparently maternal in its inheritance. Segregation of the transgene did not reverse the male sterile phenotype, producing stable, nontransgenic male sterility. The reproducible transgenic induction of mitochondrial rearrangements in plants is unprecedented, providing a means to develop novel cytoplasmic male sterile lines for release as non-GMO or transgenic materials.

Microarray analysis reveals altered expression of a large number of nuclear genes in developing cytoplasmic male sterile Brassica napus flowers

To gain new insights into the mechanism underlying cytoplasmic male sterility (CMS), we compared the nuclear gene expression profiles of flowers of a Brassica napus CMS line with that of the fertile B. napus maintainer line using Arabidopsis thaliana flower-specific cDNA microarrays. The CMS line used has a B. napus nuclear genome, but has a rearranged mitochondrial (mt) genome consisting of both B. napus and A. thaliana DNA. Gene expression profiling revealed that a large number of genes differed in expression between the two lines. For example, nuclear genes coding for proteins that are involved in protein import into organelles, genes expressed in stamens and pollen, as well as genes implicated in either cell-wall remodeling or architecture, were repressed in the CMS line compared with B. napus. These results show that the mt genome of the CMS line strongly influences nuclear gene expression, and thus reveal the importance of retrograde signalling between the mitochondria and the nucleus. Furthermore, flowers of the CMS line are characterized by a replacement of stamens with carpelloid organs, and thus partially resemble the APETALA3 (AP3) and PISTILLATA (PI) mutants. In accordance with this phenotype, AP3 expression was downregulated in the stamens, shortly before these organs developed carpelloid characteristics, even though it was initiated correctly. Repression of PI succeeded that of AP3 and might be a consequence of a loss of AP3 activity. These results suggest that AP3 expression in stamens depends on proper mt function and a correct nuclear-mt interaction, and that mt alterations cause the male sterility phenotype of the CMS line.

RFLP analysis for mitochondrial genome of CMS-rice

Restriction fragment length polymorphism (RFLP) was used to analyze mitochondrial (mt) genome of cytoplasmic male sterility (CMS) rice. Differences were observed among mitochondrial genomes of the sterile line (A) and maintain line (B) of nine types of CMS rice; Mitochondrial genomic differences were also detected between A and B in many functional gene regions. Even the materials with the same nucleic background have differences in their mtDNA. This provides molecular evidence for the cytoplasmic heterogeneity and the CMS mechanism research.

Alloplasmic effects on mitochondrial transcriptional activity and RNA turnover result in accumulated transcripts of Arabidopsis orfs in cytoplasmic male-sterile Brassica napus

Mitochondrial transcription was investigated in a cytoplasmic male-sterile (CMS) Brassica napus line with rearranged mitochondrial (mt) DNA mostly inherited from Arabidopsis thaliana. The transcript patterns were compared with the corresponding male-fertile progenitors, B. napus and A. thaliana, and a fertility-restored line. Transcriptional activities, gene stoichiometry and transcript steady-state levels were analysed for all protein and rRNA coding genes and for several orfs present in the A. thaliana mitochondrial genome. The transcriptional activities were highly variable when comparing the parental species, while the CMS and restored lines displayed similar activities. For several ribosomal protein genes transcriptional activity was reduced while it was increased for orf139 in comparison with the parental species. The differences in transcriptional activity observed could be related to differences in relative promoter strength, as gene stoichiometry between lines was very limited. Transcript steady-state levels were more homogenous than the transcriptional activities demonstrating RNA turnover as a compensating mechanism. In the CMS line higher transcript abundance and novel transcript patterns in comparison with the parental lines were found for several genes. Of those, the transcripts for orf139, orf240a and orf294 were less abundant in the fertility-restored line. These putative CMS-associated transcripts were mapped by cRT-PCR. In conclusion we show that (mt) DNA from A. thaliana was non-correctly transcribed and processed/degraded in the B. napus nuclear background. Furthermore, the introgressed nuclear A. thaliana DNA in the fertility-restored line contributes to a more rapid degradation of transcripts accumulated from A. thaliana derived orfs in the CMS line.

Alloplasmic male sterility in Brassica napus (CMS 'Tournefortii-Stiewe') is associated with a special gene arrangement around a novel atp9 gene

To identify regions of the mitochondrial genome potentially involved in the expression of alloplasmic 'Tournefortii-Stiewe' cytoplasmic male sterility (CMS) in Brassica napus, transcripts of 25 mitochondrial genes were analysed in fertile and near isogenic male-sterile plants (BC(8) generation). Differences were detected in the transcription of genes for subunit 9 of ATP synthase (atp9), cytochrome b (cob) and subunit 2 of NADH dehydrogenase (nad2). Structural analysis of these gene regions revealed differences in genome organisation around atp9 between male-sterile and fertile plants. Three atp9 genes, two of which were hitherto unknown, are present in the mitochondria of CMS plants, and rearrangements upstream of one of these genes have generated a chimeric 193-codon ORF, designated orf193. This region is transcribed as a CMS specific bi-cistronic mRNA of 1.58 kb comprising orf193 and atp9. The level of the aberrant 1.58-kb transcript is reduced in plants restored to fertility by as yet uncharacterized nuclear genes. orf193 encodes a polypeptide of 22.7 kDa which exhibits partial sequence identity to the subunit 6 of the ATP synthase complex. However, as it forms an uninterrupted ORF with one of the newly discovered atp9 genes it may also be translated as a chimeric 30.2-kDa protein. It is likely that either or both gene products interfere with the function or assembly of the mitochondrial F(0)F(1)-ATP synthase, thus impairing the highly ATP-dependent process of pollen development. The novel molecular features of alloplasmic 'Tournefortii-Stiewe' CMS are discussed with respect to the other known mechanisms of CMS in B. napus.

NUCLEAR CONTROL OF PLASTID AND MITOCHONDRIAL DEVELOPMENT IN HIGHER PLANTS

The nucleus must coordinate organelle biogenesis and function on a cell and tissue-specific basis throughout plant development. The vast majority of plastid and mitochondrial proteins and components involved in organelle biogenesis are encoded by nuclear genes. Molecular characterization of nuclear mutants has illuminated chloroplast development and function. Fewer mutants exist that affect mitochondria, but molecular and biochemical approaches have contributed to a greater understanding of this organelle. Similarities between organelles and prokaryotic regulatory molecules have been found, supporting the prokaryotic origin of chloroplasts and mitochondria. A striking characteristic for both mitochondria and chloroplast is that most regulation is posttranscriptional.

Alloplasmic male-sterile Brassica lines containing B. tournefortii mitochondria express an ORF 3' of the atp6 gene and a 32 kDa protein. off

Analyses of mitochondrial transcription and in organello translation were performed with the Brassica tournefortii cytoplasm. This cytoplasm causes alloplasmic male sterility when combined with the nuclear genomes of B. napus and B. juncea. Mitochondrial RNA and protein banding patterns were compared between the fertile wild species B. tournefortii, an alloplasmic male-sterile B. juncea line, an alloplasmic male-sterile B. napus line and an alloplasmic B. napus line with restored fertility. The analyses were carried out to identify differences in gene expression and to investigate whether alterations in gene expression accompanied male sterility. A difference in transcription patterns between the fertile B. tournefortii and the alloplasmic lines was found for the atp6 gene. The atp6 region was investigated further, since a similar alteration in atp6 transcription has been observed in two other Brassica cytoplasms which are associated with cytoplasmic male sterility (CMS). The additional longer atp6 transcript detected in the alloplasmic lines in the present study was found to contain an open reading frame (ORF) located downstream of the atp6 gene. DNA sequencing revealed that the ORF, orf263, could encode a protein with a predicted molecular weight of about 29 kDa. In organello analysis detected two proteins of 29 and 32 kDa respectively, which were found only in the alloplasmic lines. Furthermore, the 32 kDa protein accompanied male sterility since it was absent in alloplasmic plants restored to fertility. The protein analysis might indicate that orf263 is translated and causes CMS.

A chimeric and truncated mitochondrial atpA gene is transcribed in alloplasmic cytoplasmic male-sterile tobacco with Nicotiana bigelovii mitochondria

Protoplast fusions were performed between two sexually produced alloplasmic male-sterile tobacco cultivars, with cytoplasms from Nicotiana bigelovii [Nta (big)S] and N. undulata[Nta(und)S], both of which exhibit homeotic-like phenotypes affecting the petal and stamen whorls. Among the fusion products obtained, both novel male-sterile and pollen-producing cybrid plants were identified. Of the pollen-producing cybrid plants, all of which were indehiscent, some had flowers with stamens that appeared normal when compared to male-fertile tobacco plants. Other hybrid plants were incompletely restored as they exhibited petaloid structures on the anther-bearing pollen-producing stamens. In this study, gel-blot analyses with mitochondrial geneprobes were conducted comparing the mitochondrial DNA of cybrids and male-sterile parents. It was found that the flower morphology typical of the Nta(big)S parental plants, as well as of the novel male-sterile cybrids, coincided with the presence of a chimeric atpA gene copy where an open reading frame of unknown origin was found to be linked in-frame to the 3'-end of a truncated atpA gene. RNA gel-blot hybridizations revealed the presence of atpA transcripts in the malesterile parent Nta(big)S and novel male-sterile cybrids, but which were absent in cybrids capable of pollen production.

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.

Intertribal somatic hybrids between Brassica napus and Thlaspi perfoliatum with high content of the T. perfoliatum-specific nervonic acid

Protoplast fusions were performed between hypocotyl protoplasts of Brassica napus and mesophyll protoplasts of Thlaspi perfoliatum. The two species are members of the Lepidieae and Brassiceae tribes, respectively, in the family of Brassicaceae. Seeds of T. perfoliatum are rich in the fatty acid C24∶1 (nervonic acid), an oil valuable for technical purposes. In the search for renewable oils to replace the mineral oils, plant breeders have been trying to develop oil crops with a high content of long-chain fatty acids. After fusion of B. napus protoplasts with non-irradiated as well as irradiated protoplasts of T. perfoliatum selection was carried out by flow cytometry and cell sorting. Of the shoots regenerated from different calli 27 were verified as hybrids or partial hybrids using the isoenzyme phosphoglucose isomerase (PGI) as a marker. Another 6 plants were identified as partial hybrids using a T. perfoliatum-specific repetitive DNA sequence. Slot blot experiments were performed to estimate the copy number of the repetitive DNA sequence in the parental species and in the hybrids. In T. perfoliatum there were approximately 10(5) copies per haploid genome, and the range in the hybrids was 1-37% of the value in T. perfoliatum. When the nuclear DNA content of the regenerated shoots was analysed we found partial as well as symmetric hybrids. Even though the rooting and establishment of hybrid shoots in the greenhouse were difficult, resulting in the death of many plants, 19 plants were cultured to full maturity. Seeds obtained from 15 plants were analysed to determine whether they contained nervonic acid, and 5 of the hybrids were found to contain significantly greater amounts of nervonic acid than B. napus.

A high frequency of intergenomic mitochondrial recombination and an overall biased segregation of B. campestris or recombined B. campestris mitochondria were found in somatic hybrids made within Brassicaceae

Mitochondrial segregation and rearrangements were studied in regenerated somatic hybrids from seven different species combinations produced using reproducible and uniform methods. The interspecific hybridizations were made between closely or more distantly related species within the Brassicaceae and were exemplified by three intrageneric, two intergeneric and two intertribal species combinations. The intrageneric combinations were represented by Brassica campestris (+) B. oleracea, B. napus (+) B. nigra and B. napus (+) B. juncea (tournefortii) hybrids, the intergeneric combinations by B. napus (+) Raphanus sativus and B. napus (+) Eruca sativa hybrids, and the intertribal combinations by B. napus (+) Thlaspi perfoliatum and B. napus (+) Arabidopsis thaliana hybrids. In each species combination, one of the two mitochondrial genotypes was B. campestris since the B. napus cultivar used in the fusions contained this cytoplasm. Mitochondrial DNA (mtDNA) analyses were performed using DNA hybridization with nine different mitochondrial genes as probes. Among the various species combinations, 43-95% of the hybrids demonstrated mtDNA rearrangements. All examined B. campestris mtDNA regions could undergo intergenomic recombination since hybrid-specific fragments were found for all of the mtDNA probes analysed. Furthermore, hybrids with identical hybrid-specific fragments were found for all probes except cox II and rrn18/rrn5, supporting the suggestion that intergenomic recombination can involve specific sequences. A strong bias of hybrids having new atp A-or atp9-associated fragments observed in the intra- and intergeneric combinations could imply that these regions contain sequences that have a high reiteration number, which gives them a higher probability of recombining. A biased segregation of B. campestris-or B. campestris-like mitochondria was found in all combinations. A different degree of phylogenetic relatedness between the fusion partners did not have a significant influence on mitochondrial segregation in the hybrids in this study.

Non-random chloroplast segregation inNicotiana tabacum (+)N. rustica somatic hybrids selected by dual nuclear-encoded resistance

Nicotiana tabacum (+)N. rustica interspecific somatic hybrids were produced by fusion of leaf mesophyll protoplasts of transgenic methotrexate-resistantNicotiana tabacum L. with leaf mesophyll protoplasts of transgenic kanamycin-resistantN. rustica L. Somatic hybrids were selected on the basis of resistance to both methotrexate and kanamycin. Evidence for nuclear hybridization was obtained for 21 hybrids by restriction-fragment-length-polymorphism (RFLP) analysis using a heterologous wheat nuclear ribosomal-DNA (rDNA) probe and by analysis of glutamate-oxaloacetate transaminase (GOT) isoenzymes. Chloroplasts segregated non-randomly as 20 of the somatic hybrids possessedN. rustica chloroplasts and only one hadN. tabacum chloroplasts. Patterns of mitochondrial inheritance were examined by hybridization of a heterologous wheat cytochrome oxidase subunit II (coxII) gene with genomic DNA of the somatic hybrids. Four somatic hybrids with hybridization patterns similar toN. rustica and 17 with hybridization patterns consistent with mitochondrial DNA (mtDNA) rearrangement or recombination were obtained. None of the somatic hybrids had patterns ofcoxll hybridization identical withN. tabacum. Male-fertility levels in the hybrids ranged from undetectable to 87% and only nine hybrids produced a limited amount of viable seed. There was no apparent correlation between the patterns of organelle inheritance in the somatic hybrids and the relative degree of fertility.

Mitochondrial DNA of cytoplasmic male-sterile Triticum timopheevi: rearrangement of upstream sequences of the atp6 and orf25 genes

The organization of mitochondrial DNA (mtDNA) and transcript patterns of the atp6 and orf25 genes were examined in cytoplasmic male-sterile (CMS) and fertile Triticum lines. Major differences are observed between CMS T. timopheevi and fertile T. aestivum for both mitochondrial genes. The T. aestivum mt genome carries two atp6 gene copies, whereas only a single copy of the atp6 gene is present in T. timopheevi mtDNA. Sequence data suggest that identical sequences upstream of the atp6 gene and the orf25 gene are involved in homologous recombination in both cytoplasms. The differences in the upstream sequences of the atp6 or the orf25 genes affect transcript sizes in both cytoplasms. Transcription initiation may occur at conserved promoter elements located at variable distances upstream of the aminoacid coding sequences. The correlation between the gene rearrangements and the CMS phenomenon in T. timopheevi is discussed.