The maize mitochondrial genome of the normal type and the cytoplasmic male sterile type T have very different organization

High and Variable Rates of Repeat-Mediated Mitochondrial Genome Rearrangement in a Genus of Plants

For 30 years, it has been clear that angiosperm mitochondrial genomes evolve rapidly in sequence arrangement (i.e., synteny), yet absolute rates of rearrangement have not been measured in any plant group, nor is it known how much these rates vary. To investigate these issues, we sequenced and reconstructed the rearrangement history of seven mitochondrial genomes in Monsonia (Geraniaceae). We show that rearrangements (occurring mostly as inversions) not only take place at generally high rates in these genomes but also uncover significant variation in rearrangement rates. For example, the hyperactive mitochondrial genome of Monsonia ciliata has accumulated at least 30 rearrangements over the last million years, whereas the branch leading to M. ciliata and its sister species has sustained rearrangement at a rate that is at least ten times lower. Furthermore, our analysis of published data shows that rates of mitochondrial genome rearrangement in seed plants vary by at least 600-fold. We find that sites of rearrangement are highly preferentially located in very close proximity to repeated sequences in Monsonia. This provides strong support for the hypothesis that rearrangement in angiosperm mitochondrial genomes occurs largely through repeat-mediated recombination. Because there is little variation in the amount of repeat sequence among Monsonia genomes, the variable rates of rearrangement in Monsonia probably reflect variable rates of mitochondrial recombination itself. Finally, we show that mitochondrial synonymous substitutions occur in a clock-like manner in Monsonia; rates of mitochondrial substitutions and rearrangements are therefore highly uncoupled in this group.

Comparisons among two fertile and three male-sterile mitochondrial genomes of maize

We have sequenced five distinct mitochondrial genomes in maize: two fertile cytotypes (NA and the previously reported NB) and three cytoplasmic-male-sterile cytotypes (CMS-C, CMS-S, and CMS-T). Their genome sizes range from 535,825 bp in CMS-T to 739,719 bp in CMS-C. Large duplications (0.5-120 kb) account for most of the size increases. Plastid DNA accounts for 2.3-4.6% of each mitochondrial genome. The genomes share a minimum set of 51 genes for 33 conserved proteins, three ribosomal RNAs, and 15 transfer RNAs. Numbers of duplicate genes and plastid-derived tRNAs vary among cytotypes. A high level of sequence conservation exists both within and outside of genes (1.65-7.04 substitutions/10 kb in pairwise comparisons). However, sequence losses and gains are common: integrated plastid and plasmid sequences, as well as noncoding "native" mitochondrial sequences, can be lost with no phenotypic consequence. The organization of the different maize mitochondrial genomes varies dramatically; even between the two fertile cytotypes, there are 16 rearrangements. Comparing the finished shotgun sequences of multiple mitochondrial genomes from the same species suggests which genes and open reading frames are potentially functional, including which chimeric ORFs are candidate genes for cytoplasmic male sterility. This method identified the known CMS-associated ORFs in CMS-S and CMS-T, but not in CMS-C.

Selective DNA amplification regulates transcript levels in plant mitochondria

Most plant mitochondrial genomes exist as subgenomic-size fragments apparently due to recombination between repetitive sequences. This leads to the possibility that independently replicating subgenomic domains could result in mitochondrial gene copy number variation. We show, through Southern-blot analysis of both restricted and intact mtDNA, that there are gene-specific copy number differences in the monocot Zea mays. Comparison of two different maize genotypes, B37(N) and B37(T), a cytoplasmic male-sterile strain, reveal fewer gene copy number differences for B37(T) than for B37(N). In contrast to maize, significant gene copy number differences are not detected in the dicot Brassica hirta. We also demonstrate that mitochondrial transcriptional rates in both species are apparently dependent on gene copy number since relative rates determined by run-on analysis are proportional to relative gene copy numbers. Thus a direct relationship exists between plant mitochondrial gene copy number and transcriptional rate.

Translation in a wheat germ cell-free system of RNA from mitochondria of the normal and Texas male-sterile cytoplasms of maize (Zea mays L.)

RNA isolated from etiolated seedling shoot mitochondria of maize (Zea mays L.) with normal (N) or Texas male-sterile (T) cytoplasm stimulated the incorporation of [35S]-methionine into protein when added to a cell-free protein-synthesizing system from wheat germ. Discrete polypeptides with molecular masses of up to approximately 67 kDa were synthesized, and the pattern of bands was distinct from that obtained with total RNA. Products of translation of T-urf13 RNA were identified by immunoprecipitation, and of atpA, coxI, and coxII RNA by hybrid arrest of translation by the cloned gene. Several polypeptides were differentially synthesized from N and T mitochondrial RNA; these differences were more extensive than those found when isolated, intact, N and T mitochondria are allowed to synthesize proteins.

Intraspecific heterogeneity of the Vicia faba mitochondrial genome: evidence for multiregional rearrangements in the mitochondrial chromosome associated with coxII-orf192 chimeric gene formation

Previous RFLP-analysis of mtDNA isolated from different lines and cultivars of Vicia faba with respect to variability of the coxII gene revealed two types of mitochondrial genome: one with a normal coxII gene and the other with both normal coxII and chimeric coxII-orf192 genes. In this study we analyzed other regions of these two types of mitochondrial genome and found significant differences in the arrangement of regions around the coxII, coxIII, cob, rrn26 and atpA genes. More detailed analysis of the rrn26 and atpA gene regions showed that these genes are associated with recombinationally active repeats. Restriction maps of the rrn26 and atpA gene regions in different recombinative variants are presented.

Variation in mitochondrial translation products in fertile and cytoplasmic male-sterile sugar beets

Intact and functional mitochondria were isolated from sugar beet plants (Beta vulgaris L.) containing normal fertile (F) or cytoplasmic male-sterile (S1-S4) cytoplasms. Incorporation of (35)S-methionine by mitochondria isolated from both roots and leaves showed approximately 20 major and ten minor translation products. Comparison of the polypeptide synthesis patterns produced by leaf mitochondria from fertile plants of three different species within the genus Beta revealed several taxonomically related differences. Contrary to this, the patterns of polypeptides synthesized by mitochondria from roots and leaves of sugar beet plants containing the F and S1-S4 cytoplasms were very similar; in the S1 and S2 cytoplasms no qualitative, and only a few quantitative, differences from the F cytoplasm were observed. Thus, in these cases, cytoplasmic male sterility in sugar beet is not correlated with the constitutive expression of variant polypeptides. In the S3 cytoplasm, however, an additional 6 kDa polypeptide was synthesized and in the S4 cytoplasm an additional 10 kDa polypeptide was observed when compared with the F cytoplasm. The expression of cytoplasmic male sterility in sugar beet may be associated with these variant polypeptides. The mitochondrial polypeptides synthesized were identical in plants with different nuclear backgrounds but with identical S1 cytoplasms. Mitochondria from plants with variants of the S4 cytoplasm in the same nuclear genotype also showed identical patterns of polypeptide synthesis, including the synthesis of the 10 kDa S4-specific polypeptide. Pulse-chase experiments did not affect the synthesis of this polypeptide.

Transcription in maize mitochondria: effects of tissue and mitochondrial genotype

Mitochondrial run-on assays were used to determine transcriptional rates for nine B37(N) maize mitochondrial genes. Quantitation by radiographic imaging detected a 15-fold range in transcriptional rates; the order of apparent promoter strength was rps12 greater than rrn26 greater than atp6 greater than rrn18 greater than cox2 greater than atp alpha greater than atp9 greater than cox3 greater than cob. By probing single-stranded DNAs of both polarities with the run-on-products we showed that gene-specific antisense transcription did not occur. We also tested whether relative transcriptional rates were dependent on either the mitochondrial genotype or the tissue from which the mitochondria were isolated. Although tissue-specific differences in transcriptional rates were not detected, significant variation in apparent promoter strength for at least one gene, rps12, was dependent on the cytoplasmic genotype; rps12 had a five-fold reduced transcriptional rate in B37(T), the Texas male cytoplasmic strain of maize. Pulse-chase experiments suggested that differential transcript stability was not a major determinant of steady state mitochondrial RNA levels. These results indicate not only that promoter strength is an important component of the regulation of transcript levels in maize mitochondria, but also that the strength of a specific gene promoter can be dependent on the cytoplasmic genotype. Finally, the high transcriptional rate of both ribosomal RNA genes and the one mitochondrially encoded ribosomal protein gene studied suggests coordinate transcriptional regulation of both RNA and protein components of the mitochondrial ribosome.

Large size and complex structure of mitochondrial DNA in two nonflowering land plants

We report the first estimates of genome size and complexity for mitochondrial DNAs (mtDNAs) from nonflowering land plants. The mtDNA of Onoclea sensibilis (sensitive fern) is approximately 300 kb in size, while that of Equisetum arvense (common horsetail) is at least 200 kb. Sufficient mtDNA of Onoclea was available to permit an estimation of the copy number and a linkage analysis of nine mitochondrial genes. Six of these genes appear to be present in only one or two copies in the Onoclea genome, whereas three other genes are present in multiple copies. Five of the approximately ten genes encoding 26S rRNA are located on a large, greater than 10 kb, dispersed repeat that also contains closely linked genes for 18S rRNA and the alpha subunit of ATPase (atpA). The other 26S genes belong to a second dispersed repeat family of greater than 8 kb whose elements do not contain any other identified genes. Because flowering plant mtDNAs are also large and contain dispersed, gene-containing, repeats, it appears that these features arose early in the evolution of land plants, or perhaps even in their green algal ancestors.

Rapid hybridization-based assays for identification by DNA probes of male-sterile and male-fertile cytoplasms of the sugar beet Beta vulgaris L

Methods are described whereby hybridization of mitochondrial (mt) DNA with different DNA probes can definitely distinguish male-fertile and and male-sterile (cms) cytoplasms of sugar beet Beta vulgaris L. We have developed two types of miniassays. (1) Comparative methods requiring the isolation and restriction of total cellular DNA, hybridization with cloned mtDNA fragments from either fertile or male-sterile cytoplasms, and comparison of the hybridization patterns to the fertile-and sterile-specific patterns of mtDNA of sugar beet for the given mtDNA probe. For these analyses, we routinely used 1 g of plant material to determine the type of cytoplasm. (2) Noncomparative ("plus-minus") methods requiring neither the isolation of pure DNA nor restriction, electrophoresis, or Southern blotting. Instead, alkaline-SDS plant extracts from as little as 50 mg of plant material were dot-blotted and hybridized with fertile-specific (mitochondrial minicircular DNA) and/or cms-specific probes (consisting of a 2.3-kb mtDNA sequence exclusively occurring in the cms cytoplasm). The assays are simple to perform, give definitive results, are nonde-structive to the plants, and may be used in mass screening of sugar beet populations for hybrid production or in in vitro culture processes.

The Texas Cytoplasm of Maize: Cytoplasmic Male Sterility and Disease Susceptibility

The Texas cytoplasm of maize carries two cytoplasmically inherited traits, male sterility and disease susceptibility, which have been of great interest both for basic research and plant breeding. The two traits are inseparable and are associated with an unusual mitochondrial gene, T-urf13, which encodes a 13-kilodalton polypeptide (URF13). An interaction between fungal toxins and URF13, which results in permeabilization of the inner mitochondrial membrane, accounts for the specific susceptibility to the fungal pathogens.

Cytoplasmic male sterility in beta is associated with structural rearrangements of the mitochondrial DNA and is not due to interspecific organelle transfer

Chloroplast (ct) and mitochondrial (mt) DNAs from four cytoplasmic male sterile (cms) and 22 normal fertile sugar beet lines and accessions of wild beets from the genus Beta have been compared with restriction analyses and Southern hybridizations. We have used restriction analyses of ctDNA as a phylogenetic marker to confirm the taxonomic relationships between the different cytoplasms. According to the ctDNA data, all four cms cytoplasms belong to the same taxonomic section, Beta. Restriction patterns of ct and mtDNA from fertile accessions produced analogous trees of similarity and showed a close correlation between the organellar DNA diversity and the accepted taxonomic classification of the species studied. However, the mt-DNA restriction profiles of the four cms types differed dramatically from each other and from those of all fertile accessions from the genus. No indication of cytoplasmic introgression was found in any of the four investigated cms types. Southern hybridization to mtDNA revealed variant genomic arrangements in the different fertile and cms cytoplasms, indicating that rearrangement of the mitochondrial genome is a common denominator to the different cms systems in Beta. It may, indeed, be a common property to spontaneously occurring cms in all or most species.

Localization and organization of tRNA genes on the mitochondrial genomes of fertile and male sterile lines of maize

Maize mitochondrial (mt) tRNA genes were localized on the mt master circles of two fertile lines (WF9-N and B37-N) and of one cytoplasmic male sterile line (B37-cmsT) of maize. The three genomes contain 16 tRNA genes with 14 different anticodons which correspond to 13 amino acids. Out of these 16 tRNA genes, 6 show a high degree of homology with the corresponding chloroplast (cp) tRNA genes and were shown to originate from cp DNA insertions and to be expressed in the mitochondria. The organization of the mt tRNA genes in both fertile lines is similar. The same genes are found, in the same environment, as judged from the restriction maps, in fertile and male sterile lines that have the same nuclear background, but the relative organization of the mt tRNA genes on the master circle is completely different.

Contrasting modes and tempos of genome evolution in land plant organelles

Despite inhabiting the same cell lineage for roughly a billion years and being dependent on the same nucleus for most of their gene products and genetic control, the two organelle genomes of land plants exhibit remarkably different tempos and patterns of evolutionary change. With a few notable exceptions, chloroplast genomes are highly conserved in size and gene arrangement, whereas mitochondrial genomes vary enormously in size and organization. Conversely, nucleotide substitution rates are on average several times higher in chloroplast DNA than in mitochondrial DNA. Mechanistic and selective forces underlying these differences are only poorly understood.

Physical organization of the 18S and 5S ribosomal RNA genes in the mitochondrial genome of rye (Secale cereale L.)

The mitochondrial 18S and 5S ribosomal RNA (rRNA) genes of rye, plus a total of about 90 kilobase pairs of flanking DNA, have been cloned and maps of restriction enzyme cleavage sites have been constructed. Like their homologs from hexaploid wheat, the rye genes are closely linked and are part of a three-copy family of recombining repeats (the "18S/5S repeat"). The rye repeat probably also contains a mitochondrial tRNA(fMet) gene, which the wheat repeat is known to carry. However, despite the overall organizational similarity between the wheat and rye 18S/5S repeats in the immediate vicinity of their coding regions, extensive rearrangement of flanking sequences has taken place during evolutionary divergence of the two species. Our data provide additional support for an emerging picture of plant mitochondrial genomes as evolving much more rapidly in structure than in sequence.