Molecular analysis of mitochondria from a fertility restorer line of maize

Summary Inbred line Ky21 carries nuclear genes which restore fertility to all three cytoplasmic male sterile (cms) types of maize: T, C and S. By substituting the Ky21 cytoplasm into a nuclear background lacking all of the nuclear restorer genes, we have demonstrated that Ky21 contains a fertile (normal) cytoplasm. Gel electrophoresis of mitochondrial DNA from Ky21 demonstrated an approximately 2.1 kb plasmid and no evidence for a 2.35 kb plasmid found in many normal cytoplasms of North American lines of maize. A 2.1 kb plasmid had been reported to be diagnostic for the T-type cms. However, the restriction endonuclease digestion pattern of Ky21 mtDNA more closely resembled that of normal lines than T-cms. Furthermore, mitochondria of Ky21 plants did not synthesize a 13 kilodalton polypeptide, which has only been found to be synthesized by T-type mitochondria. From these molecular criteria, as well as from the genetic analysis, we conclude that the mitochondria of the Ky21 universal restorer line are normal. In having a shorter form of a linear mtDNA plasmid, Ky21 resembles cytoplasms found in Mexican races of maize.     

Variable presence of the 1.94kb mitochondrial plasmid in maize S cytoplasm and its relationship to cytoplasmic male sterility

Mitochondrial DNA (mtDNA) was isolated from over 100 different maize nucleo-cytoplasmic combinations. DNA preparations were assayed for the presence of the 1.94kb mitochondrial plasmid by agarose gel electrophoresis and hybridization to a recombinant clone of the plasmid. The plasmid was present in all tested inbreds which carried N, male fertile, cytoplasm or the cytoplasmically male sterile (cms) groups,cms-T andcms-C. However, members of thecms-S group differed with respect to the presence of the plasmid. Cytoplasms I, J and S possessed the plasmid, whereas cytoplasms B, CA, D, G, H, IA, ME, ML, PS, RD and VG did not.Cms-S group lines which had spontaneously reverted to fertility (nuclear and cytoplasmic revertants) did not exhibit a concomitant change in 1.94kb plasmid levels, although all such lines showed the previously reported alteration in levels of the linear mtDNAs, S1 and S2. The presence or absence of the plasmid was not correlated with (i) frequency of reversion to fertility, (ii) the degree of male sterility expressed, (iii) the presence or absence of standard nuclear restorer to fertility genes and (iv) nuclear genotype. Latin American races carrying RU cytoplasm possessed the plasmid, as did sweet corn varieties. The relevance of the data tocms and evolution of thecms-S group is discussed.     

An S1 episomal gene of maize mitochondria is expressed in male sterile and fertile plants of the S-type cytoplasm

Summary Maize mitochondria of cytoplasmic male sterile (cms-S) plants contain two linear episomes, S1 (6397 bp) and S2 (5453 bp). S1 contains three long open reading frames URF2 (1017 bp), URF3 (2782 bp) and URF4 (768 bp). We have demonstrated that the URF3 sequence of S1 encodes a protein with an apparent molecular weight of 103 kDa which is found in cms-S but undetectable in cms-T, cms-C or normal (fertile) mitochondria. A translational fusion containing the 5 terminus of the lacZ gene and 800 bp of the 3 end of URF3 was isolated from a cms-S mitochondrial genomic library in the expression vector gt11. Polyclonal antibodies raised against the resulting fusion protein immunoprecipitated a 103 kDa polypeptide from among [³⁵S]-methionine-labeled cms-S mitochondrial proteins but not from normal mitochondrial proteins. The mitochondria of fertile F1 plants resulting from a cross between B37 cms-S and Ky21 (universal restorer) contain as much of this 103 kDa protein as is observed in sterile cms-S mitochondria. The mitochondria of fertile cytoplasmic revertants from cms-RD and cms-LM in a WF9 nuclear background also synthesized the 103 kDa protein. We conclude that the URF3 sequence of the S1 episome is expressed in vivo and that the presence of its gene product in maize mitochondria is not sufficient to confer the male sterile phenotype.     

Structural features and expression analysis of a linear mitochondrial plasmid in rapeseed (Brassica napus L.)

A linear plasmid molecule about 11 kb in length is present in the mitochondria of some varieties of rapeseed (Brassica napus L.). This plasmid can be inherited from the male parent, through the pollen, as well as by the usual maternal route, although the main mitochondrial genome is maternally inherited in rapeseed. We determined the complete nucleotide sequence of this plasmid DNA and clarified its genetic organization. The length of the linear plasmid is 11,640 bp. At the termini of the plasmid molecule are inverted repeats of 327 bp. The GC content of the plasmid DNA is 30.9%; thus, the plasmid is quite AT-rich compared to the main mitochondrial genome in higher plants. The plasmid has six ORFs, two of which encode a phage-type DNA polymerase and a phage-type RNA polymerase, respectively. RT-PCR analyses revealed that all six ORFs are transcribed, and all four ORFs on the minus strand are probably cotranscribed from a single promoter located in the terminal inverted repeat. We also show here that at least three of the six ORFs are translated into proteins in rapeseed mitochondria, and expressed at relatively high levels in flowers, as shown by Western analysis. These results suggest that this linear DNA molecule is able to replicate as an autonomous replicon and to express the genes it carries in rapeseed mitochondria.     

Molecular cloning and physical characterization of a Brassica linear mitochondrial plasmid

Summary A linear mitochondrial plasmid reported to be associated with cytoplasmic male sterility in the genus Brassica was analyzed. A protein was found to be associated with the 5 ends of the plasmid. The entire plasmid was cloned by the homopolymer tailing technique via free hydroxyl groups present at its 3 ends. DNA sequence analysis of the cloned plasmid revealed a perfect terminal inverted repeat of 325 base pairs. Southern hybridization and restriction enzyme mapping analysis confirmed colinearity of the native plasmid and the clone, which showed significant homology with organelle DNA but not with nuclear DNA. Under high-stringency hybridization conditions, an internal 4.6 kb fragment of the 11.5 kb plasmid hybridized to the main mitochondrial genome in several species. Although the hybridization signal was weaker, the chloroplast genome also showed homology to the mitochondrial plasmid. The plasmid was undetectable at a molar ratio of less than 1/10 000 of the main mitochondrial genome in some lines of Brassica and Raphanus that contain the Ogura male sterile cytoplasm (cms). The absence of the plasmid in these sterile lines demonstrates that the plasmid is not required for the expression and maternal inheritance of male sterility.     

The linear mitochondrial plasmid pClK1 of the phytopathogenic fungus Claviceps purpurea may code for a DNA polymerase and an RNA polymerase

Summary Plasmid pClK1, a linear mitochondrial plasmid of Claviceps purpurea, was completely sequenced. The sequence contains two long open reading frames (ORF1, 3291 bp; ORF2, 2910 bp), and at least four smaller ORFs. The potential polypeptide derived from ORF1 shows homology to the family B type DNA polymerases. The product of ORF2 has significant homology to the mitochondrial RNA polymerase of yeast and RNA polymerases from bacteriophages. ORF1 and ORF2 show homology to URF3 and URF1 of the maize plasmids S1 and S2, respectively. No homology to any published protein sequence was found for the smaller ORFs. The origin of the terminal protein attached to the 5 ends of pClK1 remains open; several alternatives for its origin are discussed. The sequence data as a whole confirm the virus-like character of pClK1 already postulated from structural properties. Thus pClK1 together with S plasmids of maize and several other linear plasmids make up a distinct class of DNA species of plants and fungi probably derived from a common virus-like ancestor.     

Homology between the ribosomal DNA of Escherichia coli and mitochondrial DNA preparations of maize is principally to sequences other than mitochondrial rRNA genes

E. coli ribosomal DNA has been used to probe maize mitochondrial DNA. It hybridizes primarily with chloroplast ribosomal DNA sequences and with fungal and bacterial sequences which may contaminate the mtDNA preparations. It also hybridizes to the chloroplast 16S ribosomal RNA gene sequence present in the mitochondrial genome (1) as well as to the mitochondrial 18S ribosomal RNA gene sequence. Weak sequence homology was detected between E. coli rDNA and the mitochondrial 26S ribosomal RNA gene.     

Plastid DNA diversity in natural populations of Beta maritima showing additional variation in sexual phenotype and mitochondrial DNA

Summary Plants of two natural populations of Beta maritima, characterized by high percentages of male-sterile plants, have been investigated for organelle DNA polymorphism. We confirm the two classes of mitochondrial DNA variation previously described: (i) mitochondrial DNA (mtDNA) type N is associated with male fertility, whereas mtDNA type S can cause cytoplasmic male sterility (CMS); (ii) the 10.4-kb linear plasmid is observed in both types of mitochondria and is not correlated with the cytoplasmic male sterility occurring in this plant material. A third polymorphism is now described for chloroplast DNA (ctDNA). This polymorphism occurs within single populations of Beta maritima. Three different ctDNA types have been identified by HindIII restriction analysis. Among the plants studied, ctDNA type 1 is associated with N mitochondria and type 2 with S mitochondria. Chloroplast DNA type 3 has been found both in a fertile N plant and in a sterile S plant. This finding suggests that the chloroplast DNA polymorphism reported is not involved in the expression of male sterility. A comparison with Beta vulgaris indicates that ctDNA type 3 of Beta maritima corresponds to the ctDNA of fertile sugar beet maintainer lines. The three types of Beta maritima ctDNA described in this study differ from the ctDNA of male-sterile sugar beet.     

Linear mitochondrial DNAs from yeasts: telomeres with large tandem repetitions

The terminal structure of the linear mitochondrial DNA (mtDNA) from the yeast Candida parapsilosis was investigated. This mtDNA, 30 kb long, has symmetrical ends forming inverted terminal repeats. These repeats are made up of a variable number of tandemly repeating units of 738 by each; the terminal nucleotide corresponds to a precise position within the last repeat unit sequence. The ends had an open structure accessible to enzymes, with a 5 single-stranded extension of about 110 nucleotides. No circular forms were detected in the DNA preparations. Two other unrelated species, Pichia philodendra and Candida salmanticensis also appear to have a linear mtDNA of similar organization. These linear DNAs (which we name Type 2 linear mtDNAs) are distinct from the previously described linear mtDNAs of yeasts whose termini are formed by a closed hairpin loop (Type 1 linear mtDNA). The terminal structure of C. parapsilosis mtDNA is reminiscent of the linear mitochondrial genomes of the ciliate Tetrahymena although, in the latter, the telomeric tandem repeat unit is considerably shorter.     

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

Summary The amounts of a 1.9 kb mitochondrial plasmid relative to sequences in another mitochondrial DNA replicon and also to nuclear ribosomal DNA sequences have been compared in maize leaves and anthers. Similar comparisons have been made between plants with the same nuclear genotype but containing normal, S, or T cytoplasms. The ratio of 1.9 kb plasmid to nuclear rDNA is lower in plants with normal cytoplasm than in plants with S or T cytoplasm. It also differs between leaves and anthers. Furthermore, the relative concentration of the mitochondrial DNA sequences belonging to different replicons differs between leaves and anthers. It is concluded that components of different mitochondrial replicons are not maintained in fixed ratios during development and that the concentration of the 1.9 kb plasmid is regulated, in part, by cytoplasmically-inherited determinants. The 1.9 kb plasmid is absent from lines with the Vg cytoplasm, but related sequences are found in the maize nuclear genome.     

Nucleotide sequence of the soybean mitochondrial 18S rRNA gene: evidence for a slow rate of divergence in the plant mitochondrial genome

Summary The nucleotide sequence of the 18S rRNA gene from soybean mitochondria was determined and is presented here in comparison to the 18S rRNA genes from wheat and maize mitochondria. All three genes exhibit remarkable sequence similarity supporting the proposal that there is a slower rate of nucleotide divergence in plant mitochondrial DNA (mtDNA) as compared to the mtDNA of animals. A lower degree of sequence similarity is observed between the dicotyledenous plant soybean and either wheat (84%) or maize (85%) than between the two monocots (96%). A possible secondary structure for the soybean 18S rRNA is presented that is analogous to the proposed structure for the E. coli 16S rRNA.     

The conjugative plasmid SLP2 of Streptomyces lividans is a 50 kb linear molecule

The SLP2 plasmid had previously been demonstrated genetically to exist In Streptomyces lividans by its ability to promote conjugation and to elicit‘pocks’on recipient (SLP2^?) cultures, but it had not been physically detected. Using pulsed-field gel electrophoresis, a 50kb linear DNA was isolated from SLP2⁺ but not SLP2^? strains of S. lividans, and from Streptomyces coelicolor and Streptomyces parvulus strains to which SLP2 had been transferred by conjugation or transformation. We conclude that this linear DNA is SLP2. The terminal fragments of SLP2 were cloned. The determined sequences revealed a 44 bp imperfect terminal inverted repeat. The terminal 12 bp sequence of SLP2 was identical to those of two other Streptomyces linear plasmids, pSLA2 and pSCL, and similar to the terminal sequences of another Streptomyces linear plasmid, SCP1. The termini of SLP2 DNA were resistant to digestion by λ exonuclease and ExoIII. A truncated (probably crippled) copy of Tn4811 is present on the plasmid. While the SLP2 plasmid exists as a tree form in the host, a 15.7 kb sequence corresponding to the segment of SLP2 from Tn4811 to the right terminus is also present (at a copy number similar to the free form) elsewhere in the genome of S. lividans. Furthermore, SLP2 is partially homologous to a newly discovered 650 kb linear plasmid in S. parvulus.     

Analysis of a 120-Kilobase Mitochondrial Chromosome in Maize

The organization of the mitochondrial genome in plants is not well understood. In maize mitochondrial DNA (mtDNA) several subgenomic circular molecules as well as an abundant fraction of linear molecules have been seen by electron microscopy. It has been hypothesized that the circular molecules are the genetic entities of the mitochondrial genome while the linear molecules correspond to randomly sheared mtDNA. A model has been proposed that explains the mechanism of generation of subgenomic circles (of a predictable size) by homologous recombination between pairs of large direct repeats found on a large (approximately 570 kb for the fertile (N) cytoplasm) master circle. So far the physical entities of the mitochondrial genome, as they exist in vivo, and the genes they carry, have not been identified. For this purpose, we used two gel systems (pulsed field gel electrophoresis and Eckhardt gels) designed to resolve large DNA. Large DNA was prepared from the Black Mexican Sweet (BMS) cultivar. We resolved several size classes of mtDNA circles and designate these as chromosomes. A 120 kb chromosome was mapped in detail. It is shown to contain the three ribosomal genes (rrn26, rrn18 and rrn5) plus two genes encoding subunits of cytochrome oxidase (Cox1 and Cox3); it appears to be colinear with the 570-kb master circle map of another fertile cytoplasm (B37N) except at the "breakpoints" required to form the 120-kb circle. The presence of the 120-kb chromosome could not have been predicted by homologous recombination through any of the known repetitive sequences nor is it a universal feature of normal maize mitochondria. It is present in mitochondria of BMS suspension cultures and seedlings, but is not detectable in seedlings of B37N. No master genome was detected in BMS.     

Cloning of mtDNA fragments homologous to mitochondrial S2 plasmid-like DNA in maize

Summary Mitochondria from S-type cytoplasmic male-sterile maize contain two small DNA species, S1 and S2, which are absent from other fertile and male-sterile cytoplasms. These species have been cloned in plasmid pBR322 by the homopolymer extension method. Probes made with these recombinant plasmids have been used to establish the homology between high molecular weight mitochondrial DNAs of fertile and male-sterile cytoplasms, and small mitochondrial plasmid-like molecules. Hybridization and mapping data show that S2 DNA copies are homologuous with sequences of the normal mitochondrial genome. A comparison of physical maps of different isolated mtDNA fragments indicates a heterogeneous arrangement of S2 sequences in the mtDNA population of normal fertile maize cytoplasm. The origin of this heterogeneity is discussed.     

Characterization of a new mitochondrial plasmid from Fusarium proliferatum

A 10.3kb linear mitochondrial DNA plasmid designated pFP1 was isolated from Fusarium proliferatum. The DNA sequence of the plasmid consists of 10,336bp with perfect terminal inverted repeats of 400bp. Two major, non-overlapping ORFs were identified on opposite strands, encoding a phage-type RNA polymerase and a family B type DNA polymerase, respectively. One additional minor ORF encoding a putative highly basic protein was also identified. The copy number of pFP1, as determined by RT-PCR, ranged between 1.8 and 3.1 per mtDNA copies depending on the host strain. Real-time PCR analysis of a total of 400 cultures surviving ethidium bromide curing indicated that no plasmid-free strains could be obtained by this treatment. Further single spore selections of the survivors with reduced plasmid content were needed to obtain plasmid-free clones. No phenotypic differences were found between the wild-type strains and their plasmid-free progenies.     

Detection and distribution of six linear mitochondrial plasmids in the shiitake mushroom,Lentinula edodes

The presence of plasmids was surveyed in 90 wild isolates ofLentinula edodes collected from geographically different world regions. DNA plasmids of different sizes were found in about 80% of the isolates. The plasmids detected were of six kinds, designated as pLE1 (9.0 kb), pLE2 (11.1 kb,=pLLE1 described by other authors), pLE3A (9.8 kb), pLE3B (10.8 kb), pLE3C (12.1 kb), and pLE3D (12.3 kb). Hybridization analysis suggested that pLE1 and pLE2 were distinct plasmid types of different homology groups to each other, and the four other plasmids were variant types belonging to a third homology group. These plasmids had no homology with their host's and non-host's nuclear and mitochondrial genome DNAs. Restriction analysis and electron microscopy indicated that the plasmids are linear in form. Since all six plasmids were transmitted uniparentally in sexual crosses and were consistently associated with the DNA preparations from mitochondria fractionated from mycelia of representative isolates, they were suggested to be located in mitochondria, similar to many other known fungal DNA plasmids. Geographically, pLE1 and pLE2 were widely distributed in natural populations ofL. edodes, while the remaining four plasmids were uniquely present in delimited natural populations. Contribution No. 322 from the Tottori Mycological Institute.