A rapid inexpensive method for the isolation of restrictable mitochondrial DNA from various plant sources

Nucleo-cytoplasmic interactions affect the 5' terminal transcription of mitochondrial genes between the isonuclear CMS line UG93A and its maintainer line UG93B of kenaf (Hibiscus cannabinus)

Gene expression and translation in plant mitochondria remain poorly understood due to the complicated transcription of its mRNA. In this study, we report the 5' and 3' RNA extremities and promoters of five mitochondrial genes, atp1, atp4, atp6, atp9, and cox3. The results reveal that four genes (atp1, atp4, atp6, and cox3) are transcribed from multiple initiation sites but with a uniform transcript at the 3' end, indicating that heterogeneity of the 5' end is a common feature in the transcription of kenaf mitochondrial genes. Furthermore, we found that the transcription initiation sites of these four genes are significantly different in UG93A, UG93B, and the F₁ hybrid. These data indicate that nuclear loci and unknown transcription factors within the mitochondria of different cytoplasmic types may be involved in mitochondrial transcription. Promoter architecture analysis showed that the promoter core sequences are conserved in the kenaf mitochondrial genome but are highly divergent, suggesting that these elements are essential for the promoter activity of mitochondrial genes in kenaf. Our results reveal that the heterogeneity of the 5' end and uniformity at the 3' end are common transcriptional features of mitochondrial genes. These data provide essential information for understanding the transcription of mitochondrial genes in kenaf and can be used as a reference for other plants.

Complete sequence of kenaf (Hibiscus cannabinus) mitochondrial genome and comparative analysis with the mitochondrial genomes of other plants

Plant mitochondrial (mt) genomes are species specific due to the vast of foreign DNA migration and frequent recombination of repeated sequences. Sequencing of the mt genome of kenaf (Hibiscus cannabinus) is essential for elucidating its evolutionary characteristics. In the present study, single-molecule real-time sequencing technology (SMRT) was used to sequence the complete mt genome of kenaf. Results showed that the complete kenaf mt genome was 569,915 bp long and consisted of 62 genes, including 36 protein-coding, 3 rRNA and 23 tRNA genes. Twenty-five introns were found among nine of the 36 protein-coding genes, and five introns were trans-spliced. A comparative analysis with other plant mt genomes showed that four syntenic gene clusters were conserved in all plant mtDNAs. Fifteen chloroplast-derived fragments were strongly associated with mt genes, including the intact sequences of the chloroplast genes psaA, ndhB and rps7. According to the plant mt genome evolution analysis, some ribosomal protein genes and succinate dehydrogenase genes were frequently lost during the evolution of angiosperms. Our data suggest that the kenaf mt genome retained evolutionarily conserved characteristics. Overall, the complete sequencing of the kenaf mt genome provides additional information and enhances our better understanding of mt genomic evolution across angiosperms.

AFLP studies on downy-mildew-resistant and downy-mildew-susceptible genotypes of opium poppy

Downy mildew (DM) caused by Peronospora arborescens, is a serious disease in opium poppy (Papaver somniferum), which has a world-wide spread. The establishment of DM-resistant cultivars appears to be a sustainable way to control the In this paper, we present the results of a study aimed at the identification of amplified fragment length polymorphism (AFLP) markers for DM-resistance in opium poppy. Three opium poppy genotypes (inbred over about 10 years): Pps-1 (DM-resistant), Jawahar-16 (DM-susceptible) and H-9 (DM-susceptible) were crossed in a diallel manner and the F(1) progeny along with the parents were subjected to AFLP analysis of chloroplast (cp) and nuclear DNA with seven and nine EcoRI / MseI primer combinations, respectively. cpDNA AFLP analysis identified 24 Pps-1 (DM-resistant)-specific unique fragments that were found to be maternally inherited in both the crosses, Pps-1 x Jawahar-16 and Pps-1 x H-9. In the case of nuclear DNA AFLP analysis, it was found that 17 fragments inherited from Pps-1 were common to the reciprocal crosses of both (i) Pps-1 and Jawahar-16 as well as (ii) Pps-1 and H-9. This is the first molecular investigation on the identification of polymorphism between DM-resistant and DM-susceptible opium poppy genotypes and development of DM-resistant opium poppy genotypespecific AFLP markers. These AFLP markers could be used in future genetic studies for analysis of linkage to the downy mildew resistance trait.

Purification of mitochondrial and plastid DNA

The size, structure and conformation of mitochondrial and plastid genomes differ dramatically among eukaryotes. Similarly, the yield and purity of extracted organelle DNA also vary, and are crucial factors for the success of restriction mapping and sequencing experiments. We describe here procedures for the purification of organelle DNA from a broad range of eukaryotes. By emphasizing the underlying principles, these procedures will facilitate the development of new species-specific protocols. The presented purification schemes involve either isolation of organelles and subsequent extraction of DNA from this subcellular fraction, or processing of whole-cell lysates followed by CsCl gradient centrifugation to separate nuclear and organelle DNAs according to their A + T content. We have successfully used the described procedures for organelle genome sequencing from diverse eukaryotes, including non-axenic protists. Procedures can be completed in 3-5 days, typically yielding a few micrograms of DNA-ample for sequencing complete genomes.

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

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

Investigation of plant organellar DNAs by pulsed-field gel electrophoresis

Mitochondrial (mt) DNAs from several higher-plant species (Arabidopsis thaliana, Beta vulgaris, Brassica hirta, Chenopodium album, Oenothera berteriana, Zea mays) were separated by pulsed-field gel electrophoresis (PFGE). Hybridization of the separated DNA with mtDNA-specific probes revealed an identical distribution of mtDNA sequences in all cases: part of the DNA formed a smear of linear molecules migrating into the gel, the rest remained in the well. Hybridization signals in the compression zone of the gels disappeared after RNase or alkaline treatment. It was shown that the linear molecules are not products of unspecific degradation by nucleases. All plastid (pt) DNA from leaves of Nicotiana tabacum remained in the well after PFGE. Separation of linear monomers and oligomers of the chloroplast chromosomes of N. tabacum was achieved by mild DNase treatment of the well-bound DNA. DNase treatment of well-bound mtDNA, however, generated a smear of linear molecules. PtDNA from cultured cells of C. album was found after PFGE to be partly well-bound, and partly separated into linear molecules with sizes of monomeric and oligomeric chromosomes. The ease with which it was possible to detect large linear molecules of plastid DNA indicates that shearing forces alone can not explain the smear of linear molecules obtained after PFGE of mtDNA. The results are discussed in relation to the structural organization of the mt genome of higher plants.

Characterization of the S7 ribosomal protein gene in wheat mitochondria

By screening a wheat mitoplast cDNA bank, we have identified an open reading frame of 444 bp that has a derived amino acid sequence homologous to bacterial-type S7 ribosomal proteins. This gene, designated rps7, is located upstream of one of two 26S rRNA gene copies in the wheat mitochondrial genome and is expressed as an abundant mRNA of approximately 0.7 kb. Its 5' terminus maps to the end of an 80 bp element that is closely related to sequences preceding the wheat coxII, orf25 and atp6 genes. Southern hybridization analysis indicates that rps7-homologous sequences are present in the mitochondria of rice and pea, but not soybean.

Fertile asymmetric somatic hybrids between Lycopersicon esculentum Mill. and Lycopersicon peruvianum var. dentatum Dun

Thirteen nuclear asymmetric hybrids were regenerated under selective conditions following fusion of chlorophyll-deficient protoplasts from cultivated tomato (Lycopersicon esculentum Mill.) and gamma-irradiated protoplasts from the wild species Lycopersicon peruvianum var. dentatum Dun. All hybrid plants were classified as being asymmetric based on morphological traits, chromosome numbers and isozyme patterns. The majority of the hybrids inherited Lycopersicon peruvianum var. dentatum chloroplasts. Mitochondrial DNA analysis revealed mixed mitochondrial populations deriving from both parents in some of the hybrids and rearranged mitochondrial DNA in others. The asymmetric hybrids express some morphological traits that are not found in either of the parental species. Fertile F1 plants were obtained after self-pollination of the asymmetric hybrids in four cases. The results obtained confirm the potential of asymmetric hybridization as a new source of genetic variation, and as a method for transferring of a part of genetic material from donor to recipient, and demonstrate that it is possible to produce fertile somatic hybrids by this technique.

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.

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.

Intraspecific diversity of sugar beet (Beta vulgaris) mitochondrial DNA

Mitochondrial (mt) DNA, isolated from different sugar beet populations, was analyzed using BamHI and EcoRI restriction enzymes. It was shown that plants possessing the new mtDNA types are revealed among O-type fertilizers quite frequently. Among cytoplasmic male sterile (cms) plants, which evolved during cultivation of O-type fertilizers, plants with altered mt genome were found.

Molecular analysis of the mitochondrial genome of Helianthus annuus in relation to cytoplasmic male sterility and phylogeny

A circular supercoiled mitochondrial DNA plasmid P1 (1.45 kb) is shown in both normal fertile plants of Helianthus annuus, and some cytoplasmic male sterile lines (CMS A and CMS P). In contrast, no plasmid is found in some other types of CMS C, I, B and K. A circular supercoiled DNA (P2) of higher molecular weight (1.8 kb) is observed in CMS F. The mitochondrial plasmid P1 was cloned, nick-translated and hybridized with native mitochondrial DNA from different lines of male fertile, CMS or wild Helianthus. No sequence homology has been detected between plasmid DNA P1 and high molecular weight mitochondrial DNA in any line examined. A slight hybridization occurs between plasmids P1 and P2. Thus, there is no apparent relationship between mitochondrial plasmid DNA and CMS or Helianthus species. On the contrary, each Helianthus CMS and male fertile strain can be characterized by digestion fragment patterns (Sal I and Bgl I). Analysis of mitochondrial DNA from wild Helianthus strains indicated a relation between some CMS and the strain from which they were maternally derived, as for example CMS I and H. annuus ssp lenticularis and CMS F and H. petiolaris fallax. On the basis of restriction endonuclease patterns, a CMS phylogenic tree is proposed which illustrates a molecular polymorphism in the mitochondrial genome of Helianthus.

Mitochondrial DNA rearrangements in Pennisetum associated with reversion from cytoplasmic male sterility to fertility

Endonuclease restriction fragment patterns of Pennisetum americanum L. mitochondrial DNAs (mtDNAs) from a cytoplasmic male-sterile (CMS-A1), fertile revertants and a normal fertile cytoplasm were variable, while chloroplast DNA from those lines lacked variation. Comparisons between mtDNAs of CMS-A1 (parental) and fertile revertant lines revealed the presence of a unique 4.7 kbp PstI fragment in the sterile line that was not detected in any of the revertant lines. A 9.7 kbp PstI fragment was found in all of the revertants, but not in the CMS-A1. Neither of those fragments was found in the normal cytoplasm mtDNA. Hybridization studies revealed two sets of multiple homologies: 1) the 4.7 kbp fragment had homology with a 10.9 kbp and a 13.6 kbp fragment; and 2) the 9.7 kbp fragment was homologous with the 13.6 kbp fragment. The presence of those two repeated mitochondrial sequences on the altered fragments suggests that they may be involved in the recombinational associated events with reversion from CMS to fertility in P. americanum.

Properties of the linear N1 and N2 plasmid-like DNAs from mitochondria of cytoplasmic male-sterile Sorghum bicolor

The linear N1 and N2 plasmid-like DNAs were recovered from mitochondria of the IS1112C line of cytoplasmic male-sterile (CMS) Sorghum bicolor (S. bicolor). Molecular clones containing internal sequences of these plasmids were constructed. These clones were used to probe Southern blots of mitochondrial genomes from six CMS and five male-fertile (MF) lines of S. bicolor, as well as Southern blots of IS1112C chloroplast, IS1112C nuclear and kafir nuclear genomes. We found no evidence for integrated copies of N1 or N2 in any of the mitochondrial, chloroplast or nuclear genomes probed in this study. Our clones did detect an N1-homologous transcript of 3.1 kb and N2-homologous transcripts of 3.9 and 1.4 kb in IS1112C mitochondrial RNA prepared from lines with and without nuclear, fertility-restoring genes.N1 and N2 DNAs were degraded by exonuclease III but were resistant to lambda exonuclease, presumably due to the presence of 5' terminal proteins. We detected multimeric forms of N1 and N2 in Southern blots of unrestricted, IS1112C mitochondrial DNA (mtDNA). These forms apparently also had associated protein molecules.