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

Utility of in vitro culture to the study of plant mitochondrial genome configuration and its dynamic features

Recombination activity plays an important role in the heteroplasmic and stoichiometric variation of plant mitochondrial genomes. Recent studies show that the nuclear gene MSH1 functions to suppress asymmetric recombination at 47 repeat pairs within the Arabidopsis mitochondrial genome. Two additional nuclear genes, RECA3 and OSB1, have also been shown to participate in the control of mitochondrial DNA exchange in Arabidopsis. Here, we demonstrate that repeat-mediated de novo recombination is enhanced in Arabidopsis and tobacco mitochondrial genomes following passage through tissue culture, which conditions the MSH1 and RECA3 suppressions. The mitochondrial DNA changes arising through in vitro culture in tobacco were reversible by plant regeneration, with correspondingly restored MSH1 transcript levels. For a growing number of plant species, mitochondrial genome sequence assembly has been complicated by insufficient information about recombinationally active repeat content. Our data suggest that passage through cell culture provides a rapid and effective means to decipher the dynamic features of a mitochondrial genome by comparative analysis of passaged and non-passaged mitochondrial DNA samples following next-generation sequencing and assembly.

Double-strand break repair processes drive evolution of the mitochondrial genome in Arabidopsis

Background

The mitochondrial genome of higher plants is unusually dynamic, with recombination and nonhomologous end-joining (NHEJ) activities producing variability in size and organization. Plant mitochondrial DNA also generally displays much lower nucleotide substitution rates than mammalian or yeast systems. Arabidopsis displays these features and expedites characterization of the mitochondrial recombination surveillance gene MSH1 (MutS 1 homolog), lending itself to detailed study of de novo mitochondrial genome activity. In the present study, we investigated the underlying basis for unusual plant features as they contribute to rapid mitochondrial genome evolution.

Results

We obtained evidence of double-strand break (DSB) repair, including NHEJ, sequence deletions and mitochondrial asymmetric recombination activity in Arabidopsis wild-type and msh1 mutants on the basis of data generated by Illumina deep sequencing and confirmed by DNA gel blot analysis. On a larger scale, with mitochondrial comparisons across 72 Arabidopsis ecotypes, similar evidence of DSB repair activity differentiated ecotypes. Forty-seven repeat pairs were active in DNA exchange in the msh1 mutant. Recombination sites showed asymmetrical DNA exchange within lengths of 50- to 556-bp sharing sequence identity as low as 85%. De novo asymmetrical recombination involved heteroduplex formation, gene conversion and mismatch repair activities. Substoichiometric shifting by asymmetrical exchange created the appearance of rapid sequence gain and loss in association with particular repeat classes.

Conclusions

Extensive mitochondrial genomic variation within a single plant species derives largely from DSB activity and its repair. Observed gene conversion and mismatch repair activity contribute to the low nucleotide substitution rates seen in these genomes. On a phenotypic level, these patterns of rearrangement likely contribute to the reproductive versatility of higher plants.

The selection of mosaic (MSC) phenotype after passage of cucumber (Cucumis sativus L.) through cell culture — a method to obtain plant mitochondrial mutants

Mosaic (MSC) mutants of cucumber (Cucumis sativus L.) appear after passage through cell cultures. The MSC phenotype shows paternal transmission and is associated with mitochondrial DNA rearrangements. This review describes the origins and phenotypes of independently produced MSC mutants of cucumber, including current knowledge on their mitochondrial DNA rearrangements, and similarities of MSC with other plant mitochondrial mutants. Finally we propose that passage of cucumber through cell culture can be used as a unique and efficient method to generate mitochondrial mutants of a higher plant in a highly homozygous nuclear background.

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.

Rearrangements in sugar beet mitochondrial DNA induced by cell suspension, callus cultures and regeneration

Structural alterations in mitochondrial DNAs (mtDNAs) from a plant of a sterile sugar beet line, callus derived from it, suspension-cultured cells and plants regenerated from the callus were studied. BamHI restriction analysis revealed that structural alterations between the mtDNAs of the callus and the control plant had occurred. Multiple rearrangements were also demonstrated in the mtDNA from the suspension culture, of which some were similar to those appearing in the callus, and others had arisen de novo. Rearrangements were also identified by means of blot hybridization of BamHI-digested mtDNA from suspension-cultured cells with the genes encoding subunit II of cytochrome oxidase (cox II) and subunit 1 of NADH-dehydrogenase (Nd1). No alterations were observed in the mitochondrial genome of the callus and regenerants. The location of the genes for the α-subunit of F1-ATPase (atpA) and apocytochrome b (cob) in the mtDNA remained unchanged.Our salient finding was of a plant with an altered mitochondrial genome as judged by EcoRI and BamHI restriction analysis. This exceptional plant had retained the sterile phenotype like all of the other regenerants and the parent. The set of plasmid-like molecules of mtDNA remained the same as that in the control plant and in all of the regenerants, callus and suspension-cultured cells. The only type of plasmid-like molecule found in all of the DNAs was the 1.6-kbp minicircle, which is a feature of sterile cytoplasms. These structural changes in mtDNA were obviously a consequence of somaclonal variation during the in vitro cultivation of the sugar beet cells.

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.

Alteration of mitochondrial genomes containing atpA genes in the sexual progeny of cybrids between Raphanus sativus cms line and Brassica napus cv. Westar

We have investigated the fate of the mitochondrial genomes of cybrids derived from "donor-recipient" protoplast fusion between X-irradiated Raphanus sativus (cms line) and iodoacetamide-treated Brassica napus cv. Westar. Two out of ten fusion products were male-sterile with the diploid chromosome number of B. napus. The mitochondrial (mt) genomes of the cybrids and their progeny were further analyzed by DNA-DNA hybridizaion using the pea mitochondrial ATPase subunit gene (atpA) as a probe. One cybrid, 18-3, had a 3.0 kb fragment characteristic of B. napus and a 2.0 kb non-parental fragment when the BamHI-digested DNA was hybridized with the probe. In the first-backcrossed progeny of this cybrid, the hybridization pattern was not stably inherited. A 4.0 kb radish fragment, not detectable in the cybrid, appeared in one of the BC1 generation siblings, and the 2.0 kb non-parental fragment was lost in another. The hybridization patterns in BC1 progeny siblings of cybrid 12-9 were also varied. The alteration of mtDNA in the cybrid progeny continued to the BC2 generation. There was no clear evidence of a heteroplasmic state or of sub-stoichiometric molecules in the mt genome of cybrid 18-3. A possible cause of the observed alteration in the mt genome is discussed.

Non-random inheritance of organellar genomes in symmetric and asymmetric somatic hybrids between Lycopersicon esculentum and L. pennellii

The organization of the mitochondrial genome and the genotype of the chloroplast genome was characterized using restriction fragment length polymorphisms in a population (82 individuals) of symmetric and asymmetric somatic hybrids of tomato. The protoplast fusion products were regenerated following the fusion of leaf mesophyll protoplasts of Lycopersicon esculentum (tomato cv 'UC82') with suspension cell protoplasts of L. pennellii that had been irradiated with 5, 10, 15, 25, 50, or 100 kRads from a gamma source. The chloroplast genome in the somatic hybrids showed a random pattern of inheritance, i.e., either parental genome was present in equal numbers of regenerants, while in asymmetric somatic hybrids, the chloroplast genotype reflected the predominant nuclear genotype, i.e., tomato. The mitochondrial genome in the symmetric somatic hybrids showed a non-random pattern of inheritance, i.e., predominantly from the L. pennellii parent; asymmetric somatic hybrids had more tomato-specific mitochondrial sequences than symmetric somatic hybrids. The non-random inheritance of the chloroplast and mitochondrial DNA in these tomato protoplast fusion products appears to be influenced by the nuclear background of the regenerant.

Amplification of substoichiometric recombinant mitochondrial DNA sequences in a nuclear, male sterile mutant regenerated from protoplast culture in Nicotiana sylvestris

A Nicotiana sylvestris plant regenerated from protoplast culture was found to be mutated in both the mitochondrial (mt) and nuclear genomes. The novel mt DNA organization, called U, is due to the amplification of recombinant substoichiometric DNA sequences that preexist in the parent line. The recombination event involves two 404 bp repeats, which hybridize to a 2.1 kb transcript. Although the sequence of both repeats was not altered by the recombination, an additional transcript of 2.5 kb was detected in U mitochondria. In addition to this mitochondrial reorganization, the protoclone carried a recessive nuclear mutation conferring male sterility (ms4). A possible role of ms4 in the appearance of the U mt DNA organization was investigated by introducing this gene into normal N. sylvestris cytoplasm. No mt DNA change could be found in homozygous ms4/ms4 plants of the F2 generation.

Biochemical and molecular analysis of plants derived from embryogenic tissue cultures of napier grass (Pennisetum purpureum K. Schum)

We have investigated the extent of biochemical and molecular variation in 63 plants of napier grass (Pennisetum purpureum K. Schum.) regenerated from 3- to 24-week-old embryogenic callus cultures. The calli were derived from cultured basal segments of young leaves and immature inflorescences obtained from a single fieldgrown donor plant. The entire population was analyzed for the activity of 14 isozyme systems, but no qualitative variation was found at any of the loci examined. Similarly, no restriction fragment length polymorphisms (RFLPs) were detected in the mitochondrial, plastid and nuclear genomes in a representative sample of regenerated plants. Our results confirm earlier reports of the genetic uniformity of plants derived from somatic embryos and highlight their value both for clonal propagation and for genetic transformation.

Mitochondrial genome variability in Sorghum cell culture protoclones

Sorghum bicolor cv NK300 seedlings, a cell suspension culture, and five protoclone suspension cultures were compared for the occurrence of somaclonal variation by analysis of their mitochondrial DNA (mtDNA). Restriction digests of the mtDNA showed qualitative and quantitative variation of restriction fragments. Southern analyses were performed using a 14.7-kb EcoRI mitochondrial genome fragment and regions carrying mitochondrial protein coding genes, atpA, atp6, cob, and coxI as probes. These analyses revealed part of the 14.7-kb EcoRI region to be present as a repeat in planta, and to be hypervariable when cells were subjected to protoplast culture. All protoclones differed from each other, from the parental cell suspension culture, and from the seedlings in their mitochondrial genome arrangement. Seedlings of five independent sorghum accessions, unrelated to cv NK300, of diverse geographic origin showed conservation of this mitochondrial fragment. Southern analyses of the mtDNA showed no variation for genomic organization of the region carrying coxI, and atpA was identical in all the tissue culture lines. The atp6 gene was present as two copies in the seedlings, and one copy was rearranged upon tissue culture. The region carrying the cob gene was also found to be variant between tissue culture and seedling mtDNA. A substoichiometric 3.3-kb EcoRI cob fragment present in seedlings was amplified in the tissue culture lines. Protoclone S63 differed from the original suspension culture and remaining protoclones in that it had lost the 3.0-kb EcoRI band, the most abundant fragment in seedlings. A new set of fragments was detected in this protoclone. Northern analysis for the cob gene demonstrated altered transcript size in protoclone S63.

Mitochondrial genome structure of rice suspension culture from cytoplasmic male-sterile line (A-58CMS): reappraisal of the master circle

The mitochondrial DNA (mtDNA) from the cultured cells of a cytoplasmic male-sterile line (A-58CMS) of rice (Oryza sativa) was cloned and its physical map was constructed. There was structural alteration on the mitochondrial genome during the cell culture. Detailed restriction analysis of cosmid clones having mtDNA fragments suggested either that the master genome has a 100-kb duplication (the genome size becomes 450 kb) or that a master circle is not present in the genome (the net structural complexity becomes 350 kb). The physical map of plant mitochondrial genomes thus far reported is illustrated in a single circle, namely a master circle. However, no circular DNA molecule corresponding to a master circle has yet been proved. In the present report, representation of plant mitochondrial genomes and a possibility for mitochondrial genome without a master circle are discussed.

Comprehensive molecular characterization of tissue-culture-derived Hordeum marinum plants

Scuttelar calli of Hordeum marinum readily and efficiently regenerate functional plants. In order to assess genetic variability among the regenerants we employed multiple analytic tools, which included molecular and biochemical assays. Total DNA extract from regenerated plants was digested with at least two restriction enzymes and hybridized to four nuclear and six mitochondrial coding sequences, in addition to one nuclear and three mitochondrial noncoding probes. SDS-PAGE analyses of hordein extracted from seeds of regenerated plants and activity assays of α-amylase were also performed. The nuclear and mitochondrial genomes of 50 regenerated plants demonstrated relative stability when assessed with coding sequences and by biochemical analyses. However, the mitochondrial noncoding probes revealed one qualitative somaclonal variant characterized by a loss of a hybridizing fragment. Moreover, changes in the methylation patterns of the rRNA genes and the nontranscribed spacer were revealed in another regenerated plant. The albino plant regenerated was characterized by a loss of three chloroplast DNA BamHI fragments.

Comparison of the organization of the mitochondrial genome in tomato somatic hybrids and cybrids

The organization of the mitochondrial genome in somatic hybrids and cybrids regenerated following fusion of protoplasts from cultivated tomato, Lycopersicon esculentum, and the wild species, L. Pennellii, was compared to assess the role of the nuclear genotype on the inheritance of organellar genomes. No organellar-encoded traits were required for the recorvery of either somatic hybrids or cybrids. The organization of the mitochondrial genome was characterized using Southern hybridization of restriction digestions of total DNA isolated from ten cybrids and ten somatic hybrids. A bank of cosmid clones carrying tomato mitochondrial DNA was used as probes, as well as a putative repeated sequence from L. pennellii mitchondrial DNA. The seven cosmids used to characterize the mitochondrial genomes are predicted to encompass at least 60% of the genome. The frequency of nonparental organizations of the mitochondrial genome was highest with a probe derived from a putative repeat element from the L. pennellii mitochondrial DNA. There was no difference in the average frequency of rearranged mitochondrial sequences in somatic hybrids (12%) versus cybrids (10%), although there were individual cybrids with a very high frequency of novel fragments (30%). The frequency of tomato-specific mtDNA sequences was higher in cybrids (25%) versus somatic hybrids (12%), suggesting a nuclear-cytoplasmic interaction on the inheritance of tomato mitochondrial sequences.

Tomato cybrids with mitochondrial DNA from Lycopersicon pennelli

Cybrids have been regenerated following protoplast fusion of iodoacetamide-treated leaf mesophyll cells of Lycopersion esculentum cv UC82 and gamma-irradiated cell suspensions of L. pennellii, LA716. The cybrids were recovered in the regenerant population at a frequency of 19%, no selection pressure was applied for the persistence of the donor cytoplasm. The nuclear genotype of ten cybrids was characterized extensively using isozyme markers, cDNA-based restriction fragment length polymorphisms (RFLPs), and the morphology of the plants. No nuclear genetic information from L. pennellii was detected in the cybrids. The organellar genotype of the cybrids was determined using cloned probes and species-specific RFLPs. All the cybrids had inherited the tomato chloroplast genome and had varying amounts of L. pennellii mitochondrial DNA. The cybrids all had a diploid chromosome number of 24, produced pollen, and set seed.

Nucleo-cytoplasmic incompatibility in cybrid plants possessing an Atropa genome and a Nicotiana plastome

Twenty-nine cybrids possessing an Atropa belladonna nuclear genome and a Nicotiana tabacum plastome were selected from two independent protoplast fusion experiments. In contrast to the previously described reciprocal, green and fertile cybrids with a Nicotiana nuclear genome and an Atropa plastome (Kushnir et al. 1987), the plants obtained were totally chlorophyll-deficient. An Atropa nuclear genome and a Nicotiana plastome from these chlorophyll-deficient cybrids were combined with an Atropa or a Scopolia plastome and a Nicotiana nuclear genome, respectively, in control fusion experiments. All of these nuclear genome/plastome combinations gave rise to normal, green plants. Therefore, we conclude that an N. tabacum plastome is incompatible with an A. belladonna nuclear genome.

Intergeneric transfer of cytoplasmic male sterility between Raphanus sativus (cms line) and Brassica napus through cytoplast-protoplast fusion

Cytoplasts isolated from hypocotyl protoplasts of Raphanus sativus cv Kosena (cms line) by ultracentrifugation through Percoll/mannitol discontinuous gradient were fused with iodoacetamide(IOA)-treated protoplasts of Brassica napus cv Westar. Seventeen randomly selected regenerated plants were characterized for morphology and chromosome numbers. All of the regenerated plants had morphology identical to B. napus and 10 of them possessed the diploid chromosome number of B. napus. The remaining plants had chimeric or aneuploid chromosome numbers. The mitochondrial genomes in the 10 fusion products possessing the diploid chromosome numbers of B. napus were examined by Southern hybridization analysis. Four of the 10 plants contained mitochondrial DNA showing novel hybridization patterns. Of these 4 plants, 1 was male sterile, and 3 were male fertile. The remaining plants showed mitochondrial DNA patterns identical to B. napus and were male fertile.

Molecular analysis of the extent of asymmetry in two asymmetric somatic hybrids of tomato

Two somatic hybrid plants generated from a single fusion event between Lycopersicon esculentum and irradiated L. pennellii protoplasts have been analyzed at the molecular level. Over 30 loci have been analyzed using isozymes and RFLPs. All loci tested on chromosomes 2-10 were heterozygous, while those loci on chromosome 12 were homozygous L. pennellii in both somatic hybrids. In one of the somatic hybrids, 2850, loci on chromosome 1 were also homozygous L. pennellii. The other somatic hybrid, 28F5, was heterozygous at all chromosome 1 loci tested, but exhibited altered stoichiometry of parental bands as compared to the sexual hybrid. Loci on chromosome 2 from both somatic hybrids have altered stoichiometry, with L. pennellii alleles being four times more abundant than expected. Both somatic hybrids contain the L. esculentum chloroplast genome, while only L. pennellii polymorphisms have been detected in the mitochondrial genome.

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.