Unusual mitochondrial genome organization in cytoplasmic male sterile common bean and the nature of cytoplasmic reversion to fertility

Molecular advances in research and applications of male sterility systems in tomato

Tomato, belonging to the nightshade family, is globally considered as a model system for classical and molecular genetics, genomics, and reproductive developmental studies. In the current scenario of climate change, hybrid development is among the crucial elements in the genetic improvement of crop plants. The phenomenon of male sterility is a viable approach for ensuring hybrid seed purity and reducing the cost of hybrid seed production. This review aims to shed light on the use of neoteric genomics and genome editing tools in understanding the genetics and molecular regulation of male sterility in tomato. Plant male gametophyte development is highly susceptible to environmental stress. Abnormalities at any stage of male reproductive development, such as premature or delayed tapetal cell degradation triggered by oxidative stress and programmed cell death (PCD) leads to male sterility in tomato. In tomato, more than 55 sporogenous, structural, and functional male sterile mutants, which are mainly under the control of recessive nuclear genes, have been reported. Recently, the role of open reading frames (ORFs) in governing cytoplasmic male sterility in tomato has also been documented. This review highlights the genetic and genomic progress in the investigation of underlying molecular pathways and practical application of potential male sterile mutants in tomato breeding. The applications and future prospects of genome engineering with CRISPR/Cas9 and mitoTALEN in the generation of novel male sterile systems to expedite tomato breeding is discussed.

Exploiting sterility and fertility variation in cytoplasmic male sterile vegetable crops

Cytoplasmic male sterility (CMS) has long been used to economically produce hybrids that harness growth vigor through heterosis. Yet, how CMS systems operate within commercially viable seed production strategies in various economically important vegetable crops, and their underlying molecular mechanisms, are often overlooked details that could expand the utility of CMS as a cost-effective and stable system. We provide here an update on the nature of cytoplasmic-nuclear interplay for pollen sterility and fertility transitions in vegetable crops, based on the discovery of components of nuclear fertility restoration and reversion determinants. Within plant CMS systems, pollen fertility can be rescued by the introduction of nuclear fertility restorer genes (Rfs), which operate by varied mechanisms to countermand the sterility phenotype. By understanding these systems, it is now becoming feasible to achieve fertility restoration with Rfs designed for programmable CMS-associated open reading frames (ORFs). Likewise, new opportunities exist for targeted disruption of CMS-associated ORFs by mito-TALENs in crops where natural Rfs have not been readily identified, providing an alternative approach to recovering fertility of cytoplasmic male sterile lines in crops. Recent findings show that facultative gynodioecy, as a reproductive strategy, can coordinate the sterility and fertility transition in response to environmental cues and/or metabolic signals that reflect ecological conditions of reproductive isolation. This information is important to devising future systems that are more inherently stable.

Organellar protein multi-functionality and phenotypic plasticity in plants

With the increasing impact of climate instability on agricultural and ecological systems has come a heightened sense of urgency to understand plant adaptation mechanisms in more detail. Plant species have a remarkable ability to disperse their progeny to a wide range of environments, demonstrating extraordinary resiliency mechanisms that incorporate epigenetics and transgenerational stability. Surprisingly, some of the underlying versatility of plants to adapt to abiotic and biotic stress emerges from the neofunctionalization of organelles and organellar proteins. We describe evidence of possible plastid specialization and multi-functional organellar protein features that serve to enhance plant phenotypic plasticity. These features appear to rely on, for example, spatio-temporal regulation of plastid composition, and unusual interorganellar protein targeting and retrograde signalling features that facilitate multi-functionalization. Although we report in detail on three such specializations, involving MSH1, WHIRLY1 and CUE1 proteins in Arabidopsis, there is ample reason to believe that these represent only a fraction of what is yet to be discovered as we begin to elaborate cross-species diversity. Recent observations suggest that plant proteins previously defined in one context may soon be rediscovered in new roles and that much more detailed investigation of proteins that show subcellular multi-targeting may be warranted.

This article is part of the theme issue ‘Linking the mitochondrial genotype to phenotype: a complex endeavour’.

Physical mapping and candidate gene prediction of fertility restorer gene of cytoplasmic male sterility in cotton

Background

Cytoplasmic male sterility (CMS) is a maternally inherited trait failing to produce functional pollen. It plays a pivotal role in the exploitation of crop heterosis. The specific locus amplified fragment sequencing (SLAF-seq) as a high-resolution strategy for the identification of new SNPs on a large-scale is gradually applied for functional gene mining. The current study combined the bulked segregant analysis (BSA) with SLAF-seq to identify the candidate genes associated with fertility restorer gene (Rf) in CMS cotton.

Methods

Illumina sequencing systematically investigated the parents. A segregating population comprising of 30 + 30 F₂ individuals was developed using 3096A (female parent) as sterile and 866R (male parent) as a restorer. The original data obtained by dual-index sequencing were analyzed to obtain the reads of each sample that were compared to the reference genome in order to identify the SLAF tag with a polymorphism in parent lines and the SNP with read-associated coverage. Based on SLAF tags, SNP-index analysis, Euclidean distance (ED) correlation analysis, and whole genome resequencing, the hot regions were annotated.

Results

A total of 165,007 high-quality SLAF tags, with an average depth of 47.90× in the parents and 50.78× in F₂ individuals, were sequenced. In addition, a total of 137,741 SNPs were detected: 113,311 and 98,861 SNPs in the male and female parent, respectively. A correlation analysis by SNP-index and ED initially located the candidate gene on 1.35 Mb of chrD05, and 20 candidate genes were identified. These genes were involved in genetic variations, single base mutations, insertions, and deletions. Moreover, 42 InDel markers of the whole genome resequencing were also detected.

Conclusions

In this study, associated markers identified by super-BSA could accelerate the study of CMS in cotton, and as well as in other crops. Some of the 20 genes’ preliminary characteristics provided useful information for further studies on CMS crops.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4406-y) contains supplementary material, which is available to authorized users.

ORFH79 impairs mitochondrial function via interaction with a subunit of electron transport chain complex III in Honglian cytoplasmic male sterile rice

Cytoplasmic male sterility (CMS) has attracted great interest because of its application in crop breeding. Despite increasing knowledge of CMS, not much is understood about its molecular mechanisms. Previously, orfH79 was cloned and identified as the CMS gene in Honglian rice, but how the ORFH79 protein causes pollen abortion is still unknown. Through bacterial two-hybrid library screening, P61, a subunit of the mitochondrial electron transport chain (ETC) complex III, was selected as a candidate that interacts with ORFH79. Bimolecular fluorescence complementation (BiFC) and coimmunoprecipitation (coIP) assays verified their interaction inside mitochondria. Blue native polyacrylamide gel electrophoresis (BN-PAGE) and western blotting showed ORF79 and P61 colocalized in mitochondrial ETC complex III of CMS lines. Compared with the maintainer line, Yuetai B (YB), a significant decrease of enzyme activity was detected in mitochondrial complex III of the CMS line, Yuetai A (YA), which resulted in decreased ATP concentrations and an increase in the reactive oxygen species (ROS) content. We propose that the CMS protein, ORFH79, can bind to complex III and decrease its enzyme activity through interaction with P61. This defect results in energy production dysfunction and oxidative stress in mitochondria, which may work as retrograde signals that lead to abnormal pollen development.

Cytoplasmic male sterility in plants: molecular evidence and the nucleocytoplasmic conflict

A much-debated issue in plant evolutionary biology concerns the maintenance of a high frequency of male sterility in natural populations. For the past decade, a theoretical framework has been provided by the concept of nucleocytoplasmic conflict. Recent molecular studies on cytoplasmic male sterility indicate that novel chimeric genes, resulting from duplications and rearrangements of mitochondrial DNA sequences, are involved In its control. Thus, male sterility, which is phenotypically the loss of the male function, is encoded by a new mitochondrial function at the molecular level. Molecular data are in agreement with theoretical models that consider cytoplasmic male sterility as a stage in the coevolution between nucleus and mitochondria, and not simply as a deleterious mitochondrial mutation.

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.

Heteroplasmy and stoichiometric complexity of plant mitochondrial genomes--though this be madness, yet there's method in't

Mitochondrial heteroplasmy is defined as the coexistence of divergent mitochondrial genotypes in a cell. The ratio of the alternative genomes may be variable, but in plants, the usually prevalent main genome is accompanied by sublimons--substoichiometric mitochondrial DNA (mtDNA) molecules. Plant mitochondrial heteroplasmy was originally viewed as being associated with pathological mutations or was found in non-natural plant populations. Currently, it is considered to be a common situation in plants. Recent years have changed the previous view on the role of homologous recombination, small-scale mutations, and paternal leakage of mtDNA in the generation of heteroplasmy. Newly developed sensitive techniques have allowed the precise estimation of mtDNA stoichiometry. Mechanisms of maintenance and transmission of heteroplasmic genomes, including DNA recombination and replication, as well as mitochondrial fusion and fission, have been studied. This review describes the high level of plant mitochondrial genome complication--the 'madness' resulting from the heteroplasmic state and explains the method hidden in this madness. Heteroplasmy is described as the evolutionary strategy of uniparentally inherited plant mitochondrial genomes which do not undergo sexual recombination. In order to compensate for this deficiency, alternative types of mtDNA are substoichiometrically accumulated as a reservoir of genetic variability and may undergo accelerated evolution. Occasionally, sublimons are selected and amplified in the process called substoichiometric shifting, to take over the role of the main genome. Alternative mitochondrial genomes may recombine, yielding new mtDNA variants, or segregate during plant growth resulting in plants with mosaic phenotypes. Two opposite roles of mitochondrial heteroplasmy with respect to acceleration or counteracting of mutation accumulation are also discussed. Finally, nuclear control of heteroplasmy and substoichiometric shifting is described.

Diversity of the Arabidopsis mitochondrial genome occurs via nuclear-controlled recombination activity

The plant mitochondrial genome is recombinogenic, with DNA exchange activity controlled to a large extent by nuclear gene products. One nuclear gene, MSH1, appears to participate in suppressing recombination in Arabidopsis at every repeated sequence ranging in size from 108 to 556 bp. Present in a wide range of plant species, these mitochondrial repeats display evidence of successful asymmetric DNA exchange in Arabidopsis when MSH1 is disrupted. Recombination frequency appears to be influenced by repeat sequence homology and size, with larger size repeats corresponding to increased DNA exchange activity. The extensive mitochondrial genomic reorganization of the msh1 mutant produced altered mitochondrial transcription patterns. Comparison of mitochondrial genomes from the Arabidopsis ecotypes C24, Col-0, and Ler suggests that MSH1 activity accounts for most or all of the polymorphisms distinguishing these genomes, producing ecotype-specific stoichiometric changes in each line. Our observations suggest that MSH1 participates in mitochondrial genome evolution by influencing the lineage-specific pattern of mitochondrial genetic variation in higher plants.

Counting mtDNA molecules in Phaseolus vulgaris: sublimons are constantly produced by recombination via short repeats and undergo rigorous selection during substoichiometric shifting

Sublimons are substoichiometric DNA molecules which are generated by recombinations across short repeats, located in main mitochondrial genome of plants. Since short repeats are believed to recombine irreversibly and to be usually inactive, it is unknown how substoichiometric sequences are maintained. Occasionally, sublimons are amplified during substoichiometric shifting (SSS) and take the role of the main genome. Using the Phaseolus vulgaris system, we have addressed the questions concerning accumulation of sublimons, the role of recombination in their maintenance and selective amplification during SSS. We found that sublimons accompanied by parental recombination sequences were maintained by constant recombination across a short 314-bp repeat. The abundance of these sublimons was three orders of magnitude higher than accumulation of those which could not be maintained by recombination because their parental forms were absent from the main genome. As expected for active recombination, two recombination-derived sublimons were equimolar and so were their parental forms. One parental and one substoichiometric form shared the A/C polymorphism indicating their frequent inter-conversion. Only the C variant of the sublimon was amplified during substoichiometric shift implying strong selection of DNA molecules operating during SSS.

Plant mitochondrial recombination surveillance requires unusual RecA and MutS homologs

For >20 years, the enigmatic behavior of plant mitochondrial genomes has been well described but not well understood. Chimeric genes appear, and occasionally are differentially replicated or expressed, with significant effects on plant phenotype, most notably on male fertility, yet the mechanisms of DNA replication, chimera formation, and recombination have remained elusive. Using mutations in two important genes of mitochondrial DNA metabolism, we have observed reproducible asymmetric recombination events occurring at specific locations in the mitochondrial genome. Based on these experiments and existing models of double-strand break repair, we propose a model for plant mitochondrial DNA replication, chimeric gene formation, and the illegitimate recombination events that lead to stoichiometric changes. We also address the physiological and developmental effects of aberrant events in mitochondrial genome maintenance, showing that mitochondrial genome rearrangements, when controlled, influence plant reproduction, but when uncontrolled, lead to aberrant growth phenotypes and dramatic reduction of the cell cycle.

Heteroplasmy as a common state of mitochondrial genetic information in plants and animals

Plant and animal mitochondrial genomes, although quite distinct in size, structure, expression and evolutionary dynamics both may exhibit the state of heteroplasmy--the presence of more than one type of mitochondrial genome in an organism. This review is focused on heteroplasmy in plants, but we also highlight the most striking similarities and differences between plant and animal heteroplasmy. First we summarize the information on heteroplasmy generation and methods of its detection. Then we describe examples of quantitative changes in heteroplasmic populations of mitochondrial DNA (mtDNA) and consequences of such events. We also summarize the current knowledge about transmission and somatic segregation of heteroplasmy in plants and animals. Finally, factors which influence the stoichiometry of heteroplasmic mtDNA variants are discussed. Despite the apparent differences between the plant and animal heteroplasmy, the observed similarities allow one to conclude that this condition must play an important role in the mitochondrial biology of living organisms.

Copy number of bean mitochondrial genes estimated by real-time PCR does not correlate with the number of gene loci and transcript levels

Structural rearrangements characteristic for plant mitochondrial DNA often result in the appearance of genes in new genomic environments. The determination of the real number of gene copies is difficult since the in vivo structure of plant mitochondrial genomes is questionable. It is still uncertain whether the gene copy number regulates transcription in plant mitochondria. Using the real-time PCR technique we have quantified the copies of mitochondrial genes and their transcripts in four related Phaseolus vulgaris lines. We found low intergenomic variation both in the copy number of particular genes and the abundance of their transcripts, while the intragenomic differences between copy numbers and transcripts levels of various genes were much higher. Furthermore, we found that the appearance of a gene in a new location is not correlated with a proportional increase in its copy number estimated by real-time PCR. This observation seems to result from gene dosage compensation which is probably associated with the multimolecular plant mitochondrial genome structure and particularly with the recombinogenic activity of large repeats. Based on the relative gene copy numbers we propose the existence of two types of Phaseolus mitochondrial genomes: one associated with fertility and the other inducing cytoplasmic male sterility. We also show that there is no correlation between the observed number of copies of the analyzed genes and the steady-state level of their transcripts.

Plant mitochondrial dynamics

Higher plant mitochondria are dynamic, pleomorphic organelles. The higher plant chondriome (all mitochondria in a cell collectively) is typically composed of numerous, physically discrete, mitochondria. However, frequent inter-mitochondrial fusion, enabling the mixing and recombination of mtDNA, ensures that the higher plant chondriome functions, at least genetically, as a discontinuous whole. Nothing is known about the genes controlling mitochondrial fusion in plants; there are no plant homologues of most of the genes known to be involved in fusion in other organisms. In contrast, the mitochondrial fission apparatus is generally conserved. Higher plant mitochondria use dynamin-like and Fis-type proteins for division; like yeast and animals, higher plants have lost the mitochondrial-specific form of the prokaryote-derived protein, FtsZ. In addition to being providers of energy for life, mitochondria provide a trigger for death. The role of mitochondrial dynamics in the initiation and promulgation of cell death is conserved in higher plants although there are specific differences in the genes and mechanisms involved relative to other higher eukaryotes.

Genetic analysis of the species cytoplasm specific gene (scs d) derived from durum wheat

The action of species cytoplasm specific (scs) gene(s) can be observed when a durum (Triticum turgidum L.) nucleus is placed in the Aegilops longissimum S. & M. cytoplasm. This alloplasmic combination, (lo) durum, results in nonviable progeny. A scs gene derived from T. timopheevii Zhuk. (scs(ti)) produced compatibility with the (lo) cytoplasm. The resulting hemizygous (lo) scs(ti)- durum line was male sterile and when crossed to normal durum produced a 1:1 ratio of plump, viable (PV) seeds with scs(ti) and shriveled inviable (SIV) seeds without scs(ti). In a systematic characterization of durum lines an unusual line was identified that when crossed to (lo) scs(ti)- produced all PV seeds. When planted these PV seeds segregated at a 1:1 ratio of normal vigor plants (NVPs) and low vigor plants (LVPs). The LVP senescence before full maturity. The NVPs were male sterile and when crossed to common durum lines resulted in all plump seeds that again segregated at a 1:1 ratio of NVPs to LVPs. The crosses of these NVPs to common durum lines resulted in a 1:1 ratio of PV to SIV seeds. This study was extended to 317 individuals segregating for scs(ti) and the new locus, derived from durum wheat (scs(d)), establishing the allelic relationship of these two genes.

A mitochondrial mutator system in maize

The P2 line of maize (Zea mays) is characterized by mitochondrial genome destabilization, initiated by recessive nuclear mutations. These alleles alter copy number control of mitochondrial subgenomes and disrupt normal transfer of mitochondrial genomic components to progeny, resulting in differences in mitochondrial DNA profiles among sibling plants and between parents and progeny. The mitochondrial DNA changes are often associated with variably defective phenotypes, reflecting depletion of essential mitochondrial genes. The P2 nuclear genotype can be considered a natural mutagenesis system for maize mitochondria. It dramatically accelerates mitochondrial genomic divergence by increasing low copy-number subgenomes, by rapidly amplifying aberrant recombination products, and by causing the random loss of normal components of the mitochondrial genomes.

The pea mitochondrial atp6: RNA editing and similarity of presequences in the Vicieae tribe

The atp6 gene has been identified as a single-copy sequence in the mitochondrial genome of the pea. An unexpected finding concerns the atp6 5' extension which is known to be poorly conserved at the sequence level, even between closely related plant species. We have shown that the presequences of ATP6 from the pea and other species belonging to the Vicieae tribe of Fabaceae (broad bean, hairy vetch) share a sequence similarity which extends to long 5' untranslated transcript termini. The reason for the observed conservation is not clear but may simply reflect the close phylogenetic relationship of species from the Vicieae tribe. The result of editing analysis indicates the occurrence of fully and partially edited transcripts of atp6 in the pea mitochondria. The majority of the editing sites are targeted to the last transmembrane domain of the pea ATP6, important in proton translocation and interactions with other subunits of ATP synthase.

Detailed mapping of the species cytoplasm-specific (scs) gene in durum wheat

The compatibility-inducing action of the scs(ti) (species cytoplasm-specific gene derived from Triticum timopheevii) and Vi (vitality) genes can be observed when a durum (T. turgidum) nucleus is placed in T. longissimum cytoplasm. These two genes restore compatibility between an otherwise incompatible nucleus and cytoplasm. The objective of this study was to localize the scs(ti) gene on a linkage map of chromosome 1A, which could eventually be used to clone the gene. The mapping population consisted of 110 F2 individuals derived from crossing a Langdon-T. dicoccoides chromosome 1A substitution line with a euplasmic (normal cytoplasm) line homozygous for the scs(ti) gene. Through a series of testcrosses the genotypes of the 110 individuals were determined: 22 had two copies, 59 had one copy, and 29 had no copy of the scs(ti) gene. Data from RFLP, AFLP, and microsatellite analysis were used to create a linkage map. The flanking marker loci found for the scs(ti) gene were Xbcd12 and Xbcd1449-1A.2 with distances of 2.3 and 0.6 cM, respectively. Nearly 10% of individuals in this population were double recombinant for a genetic interval of <3 cM. A blistering phenotype reminiscent of the phenotype observed in maize brittle-1 mutable was also evident in these individuals. The higher frequency of double recombination within this region and seed-blistering phenotype could be an indication of a transposable element(s) in this locus.

Mosaic (MSC) cucumbers regenerated from independent cell cultures possess different mitochondrial rearrangements

Passage of the highly inbred cucumber ( Cucumis sativus L.) line B through cell culture produces progenies with paternally transmitted, mosaic (MSC) phenotypes. Because the mitochondrial genome of cucumber shows paternal transmission, we evaluated for structural polymorphisms by hybridizing cosmids spanning the entire mitochondrial genome of Arabidopsis thaliana L. to DNA-gel blots of four independently generated MSC and four wild-type cucumbers. Polymorphisms were identified by cosmids carrying rrn18, nad5-exon2, rpl5, and the previously described JLV5 deletion. Polymorphisms revealed by rrn18 and nad5-exon2 were due to one rearrangement bringing together these two coding regions. The polymorphism revealed by rpl5 was unique to MSC16 and was due to rearrangement(s) placing the rpl5 region next to the forward junction of the JLV5 deletion. The rearrangement near rpl5 existed as a sublimon in wild-type inbred B, but was not detected in the cultivar Calypso. Although RNA-gel blots revealed reduced transcription of rpl5 in MSC16 relative to wild-type cucumber, Western analyses revealed no differences for the RPL5 protein and the genetic basis of the MSC16 phenotype remains enigmatic. We evaluated 17 MSC and wild-type lines regenerated from independent cell-culture experiments for these structural polymorphisms and identified eight different patterns, indicating that the passage of cucumber through cell culture may be a unique mechanism to induce or select for novel rearrangements affecting mitochondrial gene expression.

Substoichiometric shifting in the plant mitochondrial genome is influenced by a gene homologous to MutS

The plant mitochondrial genome is retained in a multipartite structure that arises by a process of repeat-mediated homologous recombination. Low-frequency ectopic recombination also occurs, often producing sequence chimeras, aberrant ORFs, and novel subgenomic DNA molecules. This genomic plasticity may distinguish the plant mitochondrion from mammalian and fungal types. In plants, relative copy number of recombination-derived subgenomic DNA molecules within mitochondria is controlled by nuclear genes, and a genomic shifting process can result in their differential copy number suppression to nearly undetectable levels. We have cloned a nuclear gene that regulates mitochondrial substoichiometric shifting in Arabidopsis. The CHM gene was shown to encode a protein related to the MutS protein of Escherichia coli that is involved in mismatch repair and DNA recombination. We postulate that the process of substoichiometric shifting in plants may be a consequence of ectopic recombination suppression or replication stalling at ectopic recombination sites to effect molecule-specific copy number modulation.

Microscopy of a cytoplasmic male-sterile soybean from an interspecific cross between Glycine max and G. soja (Leguminosae)

Cytoplasmic male sterility has been found independently in soybean three times since 1995, but no microscopic investigation has been published. The purpose of this microscopic study was to establish the developmental sequence leading to sterility in a cytoplasmic male-sterile soybean line that has been found to be stable under all environmental conditions tested and to demarcate the temporal and spatial parameters that result in degeneration of the microspores and pollen grains. Light microscopy showed an abnormal development and/or premature degeneration of the tapetum after meiosis II, but some pollen grains persisted until after microspore mitosis. The pollen grains never completely filled with reserves. Premature formation of the endothecium also was evident. Histochemical staining for water-insoluble carbohydrates revealed an abnormal pattern of starch deposition in anther walls that coincided with lack of pollen filling. Electron microscopy showed degeneration of the inner mitochondrial membrane in the tapetal cells as the first detectable change leading to cell degeneration. Subsequently, the tapetal endoplasmic reticulum exhibited atypical concentric rings. Pollen grains displayed mitochondria with unusually enlarged inner mitochondrial spaces, degraded plastids, a rudimentary intine, and no starch or lipid reserves. Results link mitochondrial degeneration, premature formation of the endothecium, and energy deprivation to male sterility.

Tracing evolutionary and developmental implications of mitochondrial stoichiometric shifting in the common bean

The recombination and copy number shifting activities of the plant mitochondrial genome are widely documented across plant genera, but these genome processes have not been as well examined with regard to their roles in plant evolution. Because of the extensive plant collections of Phaseolus spp and the degree to which cytoplasmic male sterility (cms) has been characterized in the common bean, this system would be valuable for investigating mitochondrial genome dynamics in natural populations. We have used the cms-associated sequence pvs-orf239 as a mitochondrial genetic marker for these studies and have demonstrated its universal presence throughout a diversity of undomesticated Phaseolus lines. Within these populations, the pvs-orf239 sequence is present in high copy number in approximately 10% of the lines, but substoichiometric in all others. This mitochondrial sequence, derived apparently by at least two recombination events, is well conserved with two point mutations identified that are both apparently silent with regard to the sterility phenotype. A putative progenitor sequence was identified in Phaseolus glabelus in substoichiometric levels, suggesting that the present-day pvs-orf239 sequence was likely introduced substoichiometrically. Copy number shifting within the mitochondrial genome results in a 1000- to 2000-fold change, so that substoichiometric forms are estimated at less than one copy per every 100 cells. On the basis of PCR analysis of root tips, we postulate that a mitochondrial "transmitted form" resides within the meristem to assure transmission of a complete genetic complement to progeny.

Male sterility in plants: occurrence, determinism, significance and use

Most of higher plant species are hermaphroditic and male-sterility is often considered as an accident of development. In fact among the multiple possible causes of male-sterility, the most frequently met in nature is cytoplasmic male-sterility (cms) which is a maternally inherited trait playing an active role in the evolution of gynodioecious species. Recent molecular studies have shown that this trait is determined by additional genes created in plant mitochondrial genomes due to their high recombinogenic activity. The physiological mechanisms by which the products of these genes interfere with the formation of male gametophytes are still the subject of intense research.

A novel orfB-related gene of carrot mitochondrial genomes that is associated with homeotic cytoplasmic male sterility (CMS)

Three types of orfB-related genes, orfB-F1, orfB-F2 and orfB-CMS, were found in carrot mitochondrial genomes. OrfB-F1 has a structure similar to the reported orfB gene in sunflower, and orfB-F2 is a novel chimeric gene with about 200 bp of unknown sequence at the 3' end of the orfB-related sequence. All fertile plants examined contained either orfB-F1 or orfB-F2. OrfB-CMS is also a novel chimeric orfB-related gene with an additional 170 bp of unknown sequence at the 3' end. Fifteen carrot lines including petaloid CMS were examined by PCR analysis and all petaloid CMS plants were found to contain the orfB-CMS gene. The orfB-F2 and orfB-CMS genes coexist in three lines, and these lines exhibit a CMS phenotype, suggesting that the CMS phenotype is associated with orfB-CMS and is independent of the presence of orfB-F2. Interestingly, differences in predicted amino acid sequence between orfB-CMS and orfB-F2 were very limited and restricted to the carboxy-terminal region of the protein. The orfB-related genes were transcribed as expected from their DNA structures, but orfB-CMS protein accumulated only in floral organs of the CMS lines. Four RNA editing sites were common to orfB-CMS and orfB-F2, and C-to-U editing occurred in both floral and leaf organs for orfB-CMS. These results strongly suggest that the orfB-CMS gene is closely associated with the petaloid phenotype and its expression is not regulated by RNA editing, but by post-transcriptional events.

Genomic context influences the activity of maize mitochondrial cox2 promoters

Plant mitochondrial genomes are highly recombinogenic, with a variety of species-specific direct and inverted repeats leading to in vivo accumulation of multiple DNA forms. In maize, the cox2 gene, which encodes subunit II of cytochrome c oxidase, lies immediately downstream of a 0.7-kilobase direct repeat, which is present in two copies in the 570-kilobase master chromosome. Promoters for cox2 exist upstream of both of these copies, in regions we have termed A and B. Three region B promoters are active for cox2 transcription in the master chromosome, whereas two region A promoters are active for cox2 transcription after recombination across the direct repeats. We have measured the proportion of genomes carrying region A or B upstream of cox2 in maize seedlings and found a ratio of approximately 1:6. Promoter strength, based on run-on transcription assays, shows a ratio of 1:4 for region A to region B promoters. These data allowed us to predict the relative contributions of region A and B to mitochondrial transcript accumulation, based on a simple product of genome-form abundance and promoter strength. When promoter use was determined by using quantitative reverse transcriptase-PCR, however, we found that region A promoters were used at an unexpectedly high rate when upstream of cox2 and used less than expected when not upstream of cox2. Thus, the use of this set of promoters seems to respond to genomic context. These results suggest a role for intragenomic and intergenomic recombination in regulating plant mitochondrial gene expression.

Construction and characterization of a common bean bacterial artificial chromosome library

We have constructed a common bean (Phaseolus vulgaris L.) bacterial artificial chromosome (BAC) library consisting of 33,792 clones and an estimated 3- to 5-fold coverage of the common bean genome. Leaf nuclei were used as the source for high-molecular-weight DNA, and an endonuclease/methylase competition assay was employed to partially cleave the DNA. The library was screened with a number of nuclear and mitochondrial probes. Each nuclear probe identified at least two BACs with an average insert size of ca. 100 kb. Only 26 clones were identified after hybridizing with mitochondrial probes, indicating contamination with organellar sequences is low. Numerous clones could be identified after screening the library with two repetitive probes flanking the nuclear fertility restorer Fr. Intriguingly, 12 clones appeared to hybridize to both markers, and restriction analysis of these clones revealed that they can be assembled into maximally four contigs, suggesting that these repetitive probes may be useful for the physical mapping of the Fr locus.

Organization and expression of the mitochondrial genome in the Nicotiana sylvestris CMSII mutant

Previous analyses suggested that the Nicotiana sylvestris CMSII mutant carried a large deletion in its mitochondrial genome. Here, we show by cosmid mapping that the deletion is 60 kb in length and contains several mitochondrial genes or ORFs, including the complex I nad7 gene. However, due to the presence of large duplications in the progenitor mitochondrial genome, the only unique gene that appears to be deleted is nad7. RNA gel blot data confirm the absence of nad7 expression, strongly suggesting that the molecular basis for the CMSII abnormal phenotype, poor growth and male sterility, is the altered complex I structure. The CMSII mitochondrial genome appears to consist essentially of one of two subgenomes resulting from recombination between direct short repeats. In the progenitor mitochondrial genome both recombination products are detected by PCR and, reciprocally, the parental fragments are detected at the substoichiometric level in the mutant. The CMSII mtDNA organization has been maintained through six sexual generations.

Stoichiometric shifts in the common bean mitochondrial genome leading to male sterility and spontaneous reversion to fertility

The plant mitochondrial genome is characterized by a complex, multipartite structure. In cytoplasmic male-sterile (CMS) common bean, the sterility-inducing mitochondrial configuration maps as three autonomous DNA molecules, one containing the sterility-associated sequence pvs-or f 239. We constructed a physical map of the mitochondrial genome from the direct progenitors to the CMS cytoplasm and have shown that it maps as a single, circular master configuration. With long-exposure autoradiography of DNA gel blots and polymerase chain reaction analysis, we demonstrate that the three-molecule CMS-associated configuration was present at unusually low copy number within the progenitor genome and that the progenitor form was present substoichiometrically within the genome of the CMS line. Furthermore, upon spontaneous reversion to fertility, the progenitor genomic configuration as well as the molecule containing the pvs-or f 239 sterility-associated sequence were both maintained at substoichiometric levels within the revertant genome. In vitro mitochondrial incubation results demonstrated that the genomic shift of the pvs-or f 239-containing molecule to substoichiometric levels upon spontaneous reversion was a reversible phenomenon. Moreover, we demonstrate that substoichiometric forms, apparently silent with regard to gene expression, are transcriptionally and translationally active once amplified. Thus, copy number suppression may serve as an effective means of regulating gene expression in plant mitochondria.

NUCLEAR CONTROL OF PLASTID AND MITOCHONDRIAL DEVELOPMENT IN HIGHER PLANTS

The nucleus must coordinate organelle biogenesis and function on a cell and tissue-specific basis throughout plant development. The vast majority of plastid and mitochondrial proteins and components involved in organelle biogenesis are encoded by nuclear genes. Molecular characterization of nuclear mutants has illuminated chloroplast development and function. Fewer mutants exist that affect mitochondria, but molecular and biochemical approaches have contributed to a greater understanding of this organelle. Similarities between organelles and prokaryotic regulatory molecules have been found, supporting the prokaryotic origin of chloroplasts and mitochondria. A striking characteristic for both mitochondria and chloroplast is that most regulation is posttranscriptional.

Altered mitochondrial gene expression in a maternal distorted leaf mutant of Arabidopsis induced by chloroplast mutator

Chloroplast mutator (chm) of Arabidopsis is a recessive nuclear mutation that causes green and white variegation in leaves and is inherited in a non-Mendelian fashion. In this study, we have identified and characterized a mutant observed in F1 and backcrossed BC1 populations from a cross between chm1-3 and ecotype Columbia. This mutant, maternal distorted leaf (MDL), grows very poorly and is distinguished by distorted rough leaves and aborted flowering organs. Electron microscopic observation showed that in MDL plants, a significant portion of mitochondria are abnormal and appear to be nonfunctional. DNA gel blot and sequence analysis of the MDL mitochondrial DNA (mtDNA) revealed rearrangements in two mtDNA fragments associated with rps3-rpl16 genes (encoding ribosomal proteins S3 and L16, respectively). One rearrangement resulted in the insertion of the rps3-rpl16 operon downstream of atp9. An independent deletion in this region had eliminated the majority of rps3. In contrast, another rearrangement deleted part of rpl16, whereas rps3 remained intact. RNA gel blot analysis indicated that expression of these genes is also altered as a consequence of the mtDNA rearrangements. Thus, a mutation at the CHM locus affects mitochondrial gene expression, and impaired mitochondrial function may result in the distorted phenotype.

Mitochondrial genome diversity in soybean: repeats and rearrangements

Mitochondrial (mt) genome organization in soybean was examined at the molecular level. This study builds upon previous reports that four soybean cytoplasmic groups, Bedford, Arksoy, Lincoln, and soja-forage, are differentiated by polymorphisms detected with a 2.3 kb Hind III mtDNA probe [12]. The variation detected results from DNA alterations in a region within and around a 4.8 kb repeat. The Bedford-type cytoplasm is the only cytoplasm that contains copies of a 4.8 kb repeat in four different genomic environments, evidence that it is recombinationally active. The Lincoln- and Arksoy-type cytoplasms each contain two copies of the repeat, as well as unique fragments that appear to result from rare recombination events outside, but near, the repeat. The soja-forage-type cytoplasm contains no complete copies of the repeat, but does contain a unique truncated version of the repeat. Sequence analysis indicates that the truncation is a result of recombination across a 9 bp repeated sequence, CCCCTCCCC. The structural rearrangements that have occurred in the region surrounding the 4.8 kb repeat may provide a means to dissect species relationships and evolution within the subgenus soja.

A chimeric and truncated mitochondrial atpA gene is transcribed in alloplasmic cytoplasmic male-sterile tobacco with Nicotiana bigelovii mitochondria

Protoplast fusions were performed between two sexually produced alloplasmic male-sterile tobacco cultivars, with cytoplasms from Nicotiana bigelovii [Nta (big)S] and N. undulata[Nta(und)S], both of which exhibit homeotic-like phenotypes affecting the petal and stamen whorls. Among the fusion products obtained, both novel male-sterile and pollen-producing cybrid plants were identified. Of the pollen-producing cybrid plants, all of which were indehiscent, some had flowers with stamens that appeared normal when compared to male-fertile tobacco plants. Other hybrid plants were incompletely restored as they exhibited petaloid structures on the anther-bearing pollen-producing stamens. In this study, gel-blot analyses with mitochondrial geneprobes were conducted comparing the mitochondrial DNA of cybrids and male-sterile parents. It was found that the flower morphology typical of the Nta(big)S parental plants, as well as of the novel male-sterile cybrids, coincided with the presence of a chimeric atpA gene copy where an open reading frame of unknown origin was found to be linked in-frame to the 3'-end of a truncated atpA gene. RNA gel-blot hybridizations revealed the presence of atpA transcripts in the malesterile parent Nta(big)S and novel male-sterile cybrids, but which were absent in cybrids capable of pollen production.

Pollen fertility restoration by nuclear gene Fr in CMS common bean: an Fr linkage map and the mode of Fr action

The Fr gene in common bean, Phaseolus vulgaris L., is a unique gene for the study of plant nuclear-mitochondrial interactions because it appears to directly influence plant mitochondrial genome structure, resulting in the restoration of pollen fertility in cytoplasmic male sterile plants. This gene action is distinct from other pollen fertility restoration systems characterized to date. As a first step towards the map-based cloning of this unusual nuclear gene, we identified RAPD markers linked to Fr using bulked segregant analysis of near-isogenic lines. Using DNA gel blot hybridization, we localized the identified RAPD markers to a linkage group on the common bean RFLP map and constructed a linkage map of the Fr region using both RAPD markers and RFLP markers. Analysis of the mode of Fr action with the aid of identified Fr-linked DNA markers indicated that Fr functions in a semidominant fashion, showing dosage effect in controlling the dynamics of a heteroplasmic mitochondrial population. We also present our observations on the developmental distinctions, crucial in the accurate mapping of the Fr gene, between spontaneous cytoplasmic reversion and Fr-driven fertility restoration, two phenomena that are phenotypically indistinguishable.

Specific expression in reproductive tissues and fate of a mitochondrial sterility-associated protein in cytoplasmic male-sterile bean

In common bean, cytoplasmic male sterility has been associated with a unique sequence found in the mitochondrial genome, designated pvs (for Phaseolus vulgaris sterility sequence). Within the pvs sequence, two open reading frames are encoded, ORF98 and ORF239. We have raised rabbit polyclonal antibodies against Pvs-ORF239 to evaluate the role of this putative male sterility-associated protein. Histological investigation of pollen development revealed that in the male-sterile bean line, callose deposition was abnormal and microspores remained as tetrads as previously reported. Pvs-ORF239 was found to be localized within the reproductive tissues of the male-sterile bean line, in contrast to all other cytoplasmic male sterility systems studied to date. This protein was associated with mitochondria, the callose layer, and developing primary cell walls during microsporogenesis. Expression of pvs-orf239 was not detected in fertile plants containing restorer gene Fr2. These observations, together with previous reports, suggest that nuclear restorer gene Fr2 interferes with expression of the pvs region post-transcriptionally.