Quantitative variation in components of the maize mitochondrial genome between tissues and between plants with different male-sterile cytoplasms

Linear plasmids in plant mitochondria: peaceful coexistences or malicious invasions?

Plant mitochondria contain small extrachromosomal DNAs in addition to a large and complex main mitochondrial genome. These molecules can be regarded as extrachromosomal replicons or plasmids, of which there are two forms, circular and linear. Linear mitochondrial plasmids are present in many fungi and in some plants, but they seem to be absent from most animal cells. They usually have a common structural feature, called an invertron, that is characterized by the presence of terminal inverted repeats and proteins covalently attached to their 5 termini. Linear mitochondrial plasmids possess one to six ORFs that can encode unknown proteins but often code for the DNA and RNA polymerases. Although the functions of most linear plasmids in plant mitochondria are unknown, some plasmids may be associated with mitochondrial genome rearrangements and may have phenotypic effects due to their integration into mitochondrial genome. The Brassica 11.6-kb plasmid, one of the linear mitochondrial plasmids in plants, shows a non-maternal inheritance, in contrast to mitochondrial genomes. The origin of these plasmids is still a mystery, but indirect evidence indicates the possibility of horizontal transfer from fungal mitochondria. In this review, the main features of these unique DNAs present in plant mitochondria are described.

Restriction fragments homologous to mitochondrial plasmid-like DNAs are located within limited chromosomal regions on the rice nuclear genome

The chromosomal locations of restriction fragments of nuclear DNA that were homologous to four mitochondrial plasmid-like DNAs, namely, B1, B2, B3 and B4, were analyzed by restriction fragment length polymorphism (RFLP) analysis in cultivated rice. Nine kinds of fragments homologous to plasmidlike DNAs were analyzed for their segregation in three different F2 populations derived from intercrosses between rice subspecies; these were found to be localized in three chromosomal regions: three, one and five kinds of nuclear homologues were situated on chromosomes 1,3 and 8, respectively. Nuclear homologues on a given chromosome were tightly linked even though they were homologous to different plasmid-like DNAs. The loci of nuclear homologues found commonly in two or three cultivars were found to be highly conserved, a result that is consistent with their stable transmission. These results and those of the Southern analysis suggest the independent integration of these sequences during the varietal differentiation of rice. The concentration of loci for nuclear homologues on chromosomes 1 and 8 suggests that these sequences were integrated non-randomly into these chromosomal regions.

Sugarbeet minicircular mitochondrial DNAs: high-resolution transcript mapping, transcript abundance and copy number determination

Three minicircular mitochondrial DNAs have been studied to address several aspects of transcription in sugarbeet mitochondria. High-resolution transcript mapping experiments have shown that sequences at the 5' termini of minicircle transcripts are highly homologous and resemble sequences at the 5' termini of sugarbeet mainband mitochondrial genes (atpA, atp6). In addition, they show homology to transcript termini of mitochondrial genes from other dicotyledonous plants, suggesting they may function as promoter sequences. Conserved sequences, which most probably act as RNA processing signals, were also identified at the 3' termini of minicircle transcripts. An oligonucleotide probe to a 14 base conserved sequence was used to determine the relative copy numbers of the three minicircle components in male-fertile mitochondria. Copy numbers were roughly equivalent, suggesting minicircles are replicated and/or transmitted with nearly equal efficiency, at least in sugarbeet taproots. Mc.a and Mc.c transcript levels are equivalent, consistent with their template copy number, however; Mc.d transcript levels were significantly lower than expected, implicating additional factors such as promoter strength and/or transcript stability in determining transcript levels in sugarbeet mitochondria, as recently demonstrated in maize.

Analysis of nuclear sequences homologous to the B4 plasmid-like DNA of rice mitochondria; evidence for sequence transfer from mitochondria to nuclei

Nuclear sequences homologous to the plasmid-like DNA, B4, were analyzed in the Japonica rice variety, Fujiminori. Homologous sequences existed at several positions in the nuclear genome, but each contained only a portion of the B4 sequence. It was impossible to reconstruct the entire sequence of B4 even by collating all the homologous sequences. Overlaps between some of the B4 sequences present in the nuclear genome resulted in parts of the sequence being represented more than once. These features indicate that nuclear sequences homologous to B4 are not the origin of B4 and that they have been transferred from mitochondria and integrated into the nuclear genome. Five other foreign sequences originating in the chloroplast or mitochondrial genome were found within 1 kb of the B4-homologous sequences. Structural analysis is consistent with the hypothesis that the DNA sequences were transferred via RNA.

RFLP analysis of nuclear DNAs homologous with mitochondrial plasmid-like DNAs in cultivated rice

B1 and B2 are small, circular, mitochondrial plasmid-like DNAs found in male-sterile cytoplasm (cms-Bo) of rice. In this study, nuclear sequences homologous to these DNAs were investigated among a number of rice cultivars. Several copies of nuclear B1-and B2-homologous sequences were detected in all examined cultivars, regardless of the presence or absence of the B1 and B2 DNAs in mitochondria, indicating that the existence of the B1- and B2-homologous sequences in the rice nuclear genome was widespread. A restriction fragment length polymorphism (RFLP) was detected for both sequences, and we propose that these DNAs could be useful RFLP markers for the rice nuclear genome. To analyze these nuclear homologues genetically, segregation analysis of the RFLP was carried out in the F2 progenies of an Indica-Japonica rice hybrid. Of the B1 homologues, there were two nonallelic fragments, one specific to the Indica parent and the other to the Japonica. These results indicate that the B1 and B2 homologues were dispersed in the nuclear genome. The integration of B1-homologous DNA into the nuclear DNA may have occurred independently after sexual isolation of the Indica and Japonica rice varietal groups, or a intranuclear transposition of these sequences took place during the process of rice differentiation into the varietal groups.

Transmission of organelles in triploid hybrids produced by gametosomatic fusions of two Nicotiana species

Gametosomatic hybrids produced by the fusion of microspore protoplasts of Nicotiana tabacum Km(+)Sr(+) with somatic cell protoplasts of N. rustica were analysed for their organelle composition. For the analysis of mitochondrial (mt)DNA, species-specific patterns were generated by Southern hybridization of restriction endonuclease digests of total DNA and mtDNA with four DNA probes of mitochondrial origin: cytochrome oxidase subunit I, cytochrome oxidase subunit II, 26s rDNA and 5s-18s rDNA. Of the 22 hybrids analyzed, some had parental-type pattern for some probes and novel-type for the others, indicating interaction between mtDNA of the two parent species. For chloroplast (cp)DNA analysis, species-specific patterns were generated by Southern hybridization of restriction endonuclease digests of total DNA with large subunits of ribulose bisphosphate carboxylase and cpDNA as probes. All the hybrids had N. rustica-specific patterns. Hybrids were not resistant to streptomycin, a trait encoded by the chloroplast genome of N. tabacum. In gametosomatic fusions of the two Nicotiana species, mitochondria but not the chloroplasts are transmitted from the parent contributing microspore protoplasts.

Nucleotide sequence and molecular characterization of plasmid-like DNAs from mitochondria of cytoplasmic male-sterile rice

Two plasmid-like DNAs, B2 and B3, were isolated from mitochondria of the cytoplasmic male-sterile rice, A-58 CMS. Molecular clones having their complete sequences were constructed and used as probes of mitochondrial and nuclear genomes by Southern hybridization. No evidence was found that integrated copies of either one exist in the main mitochondrial genome, but sequences homologous to both were present in the nuclear genome. The complete nucleotide sequences of B2 and B3 were established and compared to those of rice B1 and B4 and to the 1.9- and the 1.4-kbp plasmid-like DNAs of maize. Many of the sequences were common to both plant species.

Properties of the circular plasmid-like DNA, B4, from mitochondria of cytoplasmic male-sterile rice

The plasmid-like DNA, B4, consisting of 969 base pairs (bp), was isolated from mitochondria of the cytoplasmic male-sterile rice, A-58 CMS. Molecular clones containing the complete B4 sequence were constructed and used in Southern hybridization to probe mitochondrial and nuclear genomes. No evidence was found for the existence of integrated copies of B4 in the main mitochondrial genomes of either the male-sterile or fertile rice. Sequences homologous to B4, however, were found in the rice nuclear genome. The complete B4 nucleotide sequence was determined, and a sequence homologous to B4 was found in the 1.9 kbp plasmid-like DNA of maize.

Nucleotide sequence and molecular characterization of a maize mitochondrial plasmid-like DNA

The mitochondrial genome of Black Mexican Sweet maize consists of the principal genome, a 2.3 kb minilinear DNA, a 1,913 bp (1.9 kb) and a 1,445 bp (1.4 kb) minicircular DNA. The three extrachromosomal DNAs exhibit characteristics of autonomous replication in cell suspension culture. The complete sequence of the 1.4 kb minicircle was determined. It has 61 bp of near perfect sequence homology to the 1.9 kb minicircle. Both minicircular DNAs are transcriptionally active; the longest open reading frame of the 1.4 kb minicircle was 231 bp. A putative origin of replication was identified as a high A + T sequence. These minicircles were present in some but not all of 20 maize lines surveyed. None of the lines examined carried the 1.4 kb minicircle without the 1.9 kb minicircle. Nuclear DNA of one line of the seven examined carried homology to both DNAs.

Mitochondrial DNA diversity in the genera of Triticum and Aegilops revealed by southern blot hybridization

Southern blot hybridization of total DNA to defined mitochondrial DNA sequences provides a sensitive assay for mtDNA variation in the genera of Triticum and Aegilops. A clear distinction between cytoplasms of tetraploid species sharing the "AG" haploid genome is reported for the first time. The Sitopsis section of the genus Aegilops showed the most extensive intra- and inter-specific variation, whereas no variation could be detected among the cytoplasms of polyploid Triticum species (wheats) sharing the AB haploid genome. Extensive cytoplasmic intraspecific diversity was revealed in Ae. speltoides.

DNA synthesis in purified maize mitochondria

We have developed an in organelle DNA synthesis system using isolated mitochondria from maize. The organelles used in this assay are shown to be intact by a number of criteria. Both the high molecular weight components and the smaller plasmid-like components of the mitochondrial genome are used as templates; however, the plasmid-like elements are relatively more active as templates. The termini of the linear plasmids--S-1, S-2 and the 2.3 kbp plasmids--are more highly labelled than internal regions, probably as a result of filling in of gaps at the termini mediated by a DNA polymerase or to exonuclease degradation of the 3' OH termini, with subsequent filling in. Although most of the DNA synthesis observed in this system most likely results from this type of synthesis at DNA nicks or termini, a small amount of specific, potentially replication-associated, synthesis is also detected.

The nucleotide sequence of a mitochondrial replicon from maize

The 1913-bp maize mitochondrial (mt) plasmid was isolated from a suspension culture of a Black Mexican Sweet maize strain, cloned into M13mp vectors, and sequenced by a unidirectional progressive deletion method. The 1.9-kb extrachromosomal double-stranded circular DNA plasmid was found to contain regions of sequence which in other systems are known to be part of origins of replication (ori). This plasmid could be used as a carrier for chimeric genes and a molecular probe for replication.