Autonomously replicating RNA in mitochondria of maize plants with S-type cytoplasm

Trans-splicing and RNA editing of LSU rRNA in Diplonema mitochondria

Mitochondrial ribosomal RNAs (rRNAs) often display reduced size and deviant secondary structure, and sometimes are fragmented, as are their corresponding genes. Here we report a mitochondrial large subunit rRNA (mt-LSU rRNA) with unprecedented features. In the protist Diplonema, the rnl gene is split into two pieces (modules 1 and 2, 534- and 352-nt long) that are encoded by distinct mitochondrial chromosomes, yet the rRNA is continuous. To reconstruct the post-transcriptional maturation pathway of this rRNA, we have catalogued transcript intermediates by deep RNA sequencing and RT-PCR. Gene modules are transcribed separately. Subsequently, transcripts are end-processed, the module-1 transcript is polyuridylated and the module-2 transcript is polyadenylated. The two modules are joined via trans-splicing that retains at the junction ∼26 uridines, resulting in an extent of insertion RNA editing not observed before in any system. The A-tail of trans-spliced molecules is shorter than that of mono-module 2, and completely absent from mitoribosome-associated mt-LSU rRNA. We also characterize putative antisense transcripts. Antisense-mono-modules corroborate bi-directional transcription of chromosomes. Antisense-mt-LSU rRNA, if functional, has the potential of guiding concomitantly trans-splicing and editing of this rRNA. Together, these findings open a window on the investigation of complex regulatory networks that orchestrate multiple and biochemically diverse post-transcriptional events.

Antisense transcript and RNA processing alterations suppress instability of polyadenylated mRNA in chlamydomonas chloroplasts

In chloroplasts, the control of mRNA stability is of critical importance for proper regulation of gene expression. The Chlamydomonas reinhardtii strain Delta26pAtE is engineered such that the atpB mRNA terminates with an mRNA destabilizing polyadenylate tract, resulting in this strain being unable to conduct photosynthesis. A collection of photosynthetic revertants was obtained from Delta26pAtE, and gel blot hybridizations revealed RNA processing alterations in the majority of these suppressor of polyadenylation (spa) strains, resulting in a failure to expose the atpB mRNA 3' poly(A) tail. Two exceptions were spa19 and spa23, which maintained unusual heteroplasmic chloroplast genomes. One genome type, termed PS+, conferred photosynthetic competence by contributing to the stability of atpB mRNA; the other, termed PS-, was required for viability but could not produce stable atpB transcripts. Based on strand-specific RT-PCR, S1 nuclease protection, and RNA gel blots, evidence was obtained that the PS+ genome stabilizes atpB mRNA by generating an atpB antisense transcript, which attenuates the degradation of the polyadenylated form. The accumulation of double-stranded RNA was confirmed by insensitivity of atpB mRNA from PS+ genome-containing cells to S1 nuclease digestion. To obtain additional evidence for antisense RNA function in chloroplasts, we used strain Delta26, in which atpB mRNA is unstable because of the lack of a 3' stem-loop structure. In this context, when a 121-nucleotide segment of atpB antisense RNA was expressed from an ectopic site, an elevated accumulation of atpB mRNA resulted. Finally, when spa19 was placed in a genetic background in which expression of the chloroplast exoribonuclease polynucleotide phosphorylase was diminished, the PS+ genome and the antisense transcript were no longer required for photosynthesis. Taken together, our results suggest that antisense RNA in chloroplasts can protect otherwise unstable transcripts from 3'-->5' exonuclease activity, a phenomenon that may occur naturally in the symmetrically transcribed and densely packed chloroplast genome.

Double-stranded RNA replicons associated with chloroplasts of a green alga, Bryopsis cinicola

Double-stranded RNAs (dsRNAs) associated with chloroplasts and mitochondria have been found in the coenocytic green alga Bryopsis cinicola. In this study we report molecular properties of the four chloroplast-associated dsRNAs (BDRC1 to BDRC4). The longest dsRNA molecule (BDRC1) was sequenced entirely (1959 bp) and a single large ORF of 1722 bp was found within it. Database searches revealed similarities between the deduced amino acid sequence of this ORF and RNA-dependent RNA polymerase (RdRp) sequences from several RNA viruses. The most similar sequence in the database was the RdRp of beet cryptic virus 3. Phylogenetic analysis revealed that the RdRp-like sequence of BDRC1 can be placed in the Partitiviridae clade. To detect autonomous replication of these dsRNAs, RdRp assays were carried out with actinomycin D, which is an inhibitor of DNA-dependent RNA synthesis. Incorporation of [alpha-32P]UTP was detected specifically in the chloroplast and mitochondrial dsRNAs, indicating that both the chloroplast dsRNAs (BDRCs) and the mitochondrial dsRNA (BDRM) of B. cinicola are RNA replicons. The green alga B. cinicola harbors different dsRNA replicons in its chloroplasts and mitochondria.

Post-transcriptional and developmental regulation of a CMS-associated mitochondrial gene region by a nuclear restorer gene

Transcripts of the mitochondrial gene region orf224/atp6, which is associated with the Polima or pol cytoplasmic male sterility (CMS) of Brassica napus, differ among fertile, sterile and nuclear-restored plants. We show here that the effects of the restorer gene Rfp on orf224/atp6 transcripts varies among different floral organs. Relative to monocistronic atp6 transcripts, levels of the dicistronic transcripts spanning orf224 and atp6 are dramatically reduced in petals, stamens and carpels, but not sepals, of restored flowers. In pol CMS plants, the relative levels of different orf224/atp6 transcripts are similar among the floral organs. Analysis of guanylyltransferase-labeled mtRNA indicates that only the dicistronic 2.2 and 1.9 kb orf224/atp6 transcripts carry an initiator 5' terminus; hence the 1.4 and 1.3 kb transcripts of restored plants, as well as the 1.1 kb atp6 transcript common to all genotypes, are generated by RNA processing and not de novo initiation. Although steady-state levels of dicistronic transcripts in flower buds are lower in restored than in sterile plants, run-on transcription experiments show that these transcripts are synthesized at the same rate in both types of flowers. These findings imply that the restorer gene acts by conditioning the removal of sequences from the 5' end of dicistronic transcripts in a developmentally regulated manner. Run-on transcription experiments indicate that the single 1.1 kb atp6 transcript of nap cytoplasm is also generated by removal of sequences from the 5' end of a precursor. We suggest that specific endonucleolytic cleavage of a precursor RNA, followed by non-specific 3' to 5' exonuclease action, may represent a common mechanism for tailoring transcripts in plant mitochondria.

Evolutionary relationships among putative RNA-dependent RNA polymerases encoded by a mitochondrial virus-like RNA in the Dutch elm disease fungus, Ophiostoma novo-ulmi, by other viruses and virus-like RNAs and by the Arabidopsis mitochondrial genome

The nucleotide sequence (2617 nucleotides) of virus-like double-stranded (ds) RNA 3a in a diseased isolate, Log1/3-8d2 (Ld), of the ascomycete fungus Ophiostoma novo-ulmi has been determined. One strand of the dsRNA contains an open reading frame (ORF) with the potential to encode a protein of 718 amino acids, and the complementary strand contains two smaller ORFs with the potential to encode proteins of 178 and 182 amino acids, respectively. The large ORF contains 12 UGA codons which code for tryptophan in ascomycete mitochondria and has a codon bias typical of mitochondrial genes, consistent with the localization of Ld dsRNAs within the mitochondria. The amino acid sequence contains motifs characteristic of RNA-dependent RNA polymerases (RdRps). This putative RdRp was shown to be related to putative RdRps of mitochondrial dsRNAs of another ascomycete and a basidiomycete fungus and also to a putative RdRp encoded by the mitochondrial genome of Arabidopsis thaliana. In multiple sequence alignments, the fungal mitochondrial dsRNA-encoded RdRp-like proteins formed a cluster, ancestrally related to the RdRps of the yeast 20S and 23S RNA replicons and of the positive-stranded RNA bacteriophages of the Leviviridae family, but distinct from RdRps of other families and genera of fungal RNA viruses and related plant and animal RNA viruses. Northern blot analysis with RNA 3a strand-specific probes indicated that nucleic acid extracts of Ld contain more single-stranded (positive-stranded) RNA than dsRNA, consistent with an evolutionary relationship between RNA 3a and positive-stranded RNA phages.

The maize mitochondrial plasmid RNA b is associated with protein during synthesis but is not encapsidated

RNA b is the most abundant member of a family of autonomously replicating single- and double-stranded RNA plasmids found in maize mitochondria. The extent to which this molecule is associated with proteins was investigated by rate zonal and CsCl equilibrium density gradient centrifugation of clarified lysates of S cytoplasm maize mitochondria. A soluble complex of RNA b, responsible for synthesis of the more abundant (+) RNA b strand in mitochondrial lysates, was identified. The complex had a buoyant density of 1.49 g/cm3, indicating a substantial non-nucleic acids content. The sedimentation coefficient of the complex, however, was only slightly larger than that of deproteinized RNA b. Synthesis of RNA b as well as the larger RNA plasmid, RNA a, was resistant to heparin, suggesting that, for both RNAs, preformed complexes between an RNA template and an RNA-dependent RNA polymerase capable of elongating in vivo preinitiated RNA plasmid strands, were present in the lysate. Only a small fraction of RNA b molecules were bound in the complex; the bulk of RNA b sedimented at the same rate as the deproteinized RNA. Thus, after replication, maize mitochondrial plasmids are not associated with nucleoprotein capsids although their synthesis takes place through ribonucleoprotein replication complexes.

Cell-Specific Expression of Mitochondrial Transcripts in Maize Seedlings

Although mitochondria are thought to assume crucial and possibly novel physiological functions during male gametogenesis, it is not known to what extent mitochondrial function is necessary for other aspects of plant development or to what degree the expression of plant mitochondrial genes is subject to cell-specific regulation, particularly during vegetative growth. We have used in situ hybridization to show that extensive differences exist in the levels of mitochondrial RNAs (mtRNAs) among different tissues and among different individual cell types within the same organ of maize seedlings. The expression of all examined mtRNAs is enhanced in vascular bundles, particularly in procambium- and xylem-forming cells. Mitochondrial transcript levels correlated highly with cell division activity. For example, in roots, the transcripts are abundant in the dividing cells of the meristem but drop to very low levels in the nondividing cells of the root cap and the meristem quiescent center. By comparison, levels of functional mitochondria, as assessed by rhodamine-123 fluorescence, did not vary greatly among the same group of cells. In shoots, in situ hybridization and blot hybridization revealed differences in the patterns of localization among different mtRNAs. The results indicate that during vegetative growth, mitochondrial gene expression at the transcript level is subject to an unexpected degree of cell-specific regulation and that different controls may operate on different trancripts.

Nuclear genes associated with a single Brassica CMS restorer locus influence transcripts of three different mitochondrial gene regions

Previous studies have shown that the mitochondrial orf224/atp6 gene region is correlated with the Polima (pol) cytoplasmic male sterility (CMS) of Brassica napus. We now extend this correlation by showing that the effects of nuclear fertility restoration on orf224/atp6 transcripts cosegregate with the pol restorer gene Rfp1 in genetic crosses. We also show, however, that the recessive rfp1 allele, or a very tightly linked gene, acts as a dominant gene, designated Mmt (modifier of mitochondrial transcripts), in controlling the presence of additional smaller transcripts of the nad4 gene and a gene possibly involved in cytochrome c biogenesis. A common sequence, TTGTGG, maps immediately downstream of the 5' termini of both of the transcripts specific to plants with the Mmt gene and may serve as a recognition motif in generation of these transcripts. A similar sequence, TTGTTG, that may be recognized by the product of the alternate allele (or haplotype), Rfp1, is found within orf224 just downstream of the major 5' transcript terminus specific to fertility restored plants. Our results suggest that Rfp1/ Mmt is a novel nuclear genetic locus that affects the expression of multiple mitochondrial gene regions, with different alleles or haplotypes exerting specific effects on different mitochondrial genes.

Variation in protein and RNA synthesis activity in isolated mitochondria of the developing rice (Oryza sativa L.) panicle

We have studied variation in mitochondrial protein and RNA synthesis during the development of a specialized rice (Oryza sativa L.) reproductive organ in a bacteria-free environment. Mitochondria were prepared from the maturing panicle during microsporogenesis when meiosis occurred and from etiolated seedlings at two growth stages. We found (1) that there was no discernible qualitative difference among the polypeptides synthesized by these three mitochondrial samples; (2) that the quantity of proteins synthesized by panicle mitochondria was approximately 3 times that of the seedling mitochondria, while the two seedling samples exhibited only a minor quantitative difference; (3) that panicle and seedling mitochondria samples synthesized qualitatively the same RNA but at distinctly different rates and that more RNA products were synthesized by panicle than by seedling mitochondria. These results, taken together, suggest that either the regulation of mitochondrial transcription and translation or the copy number of mitochondrial DNA per mitochondrion change discretely in the developing panicle and consequently that the level of mitochondrial gene expression increases considerably during the development of the reproductive structure in rice.

A small mitochondrial double-stranded (ds) RNA element associated with a hypovirulent strain of the chestnut blight fungus and ancestrally related to yeast cytoplasmic T and W dsRNAs

A small double-stranded (ds) RNA element was isolated from a moderately hypovirulent strain of the chestnut blight fungus Cryphonectria parasitica (Murr.) Barr. from eastern New Jersey. Virulence was somewhat lower in the dsRNA-containing strain than in a virulent dsRNA-free control strain, but colony morphology and sporulation levels were comparable. A library of cDNA clones was constructed, and overlapping clones representing the entire genome were sequenced. The 2728-bp dsRNA was considerably smaller than previously characterized C. parasitica dsRNAs, which are 12-13 kb and ancestrally related to the Potyviridae family of plant viruses. Sequence analysis revealed one large open reading frame, but only if mitochondrial codon usage (UGA = Trp) was invoked. Nuclease assays of purified mitochondria confirmed that the dsRNA was localized within mitochondria. Assuming mitochondrial translation, the deduced amino acid sequence had landmarks typical of RNA-dependent RNA polymerases. Alignments of the conserved regions indicate that this dsRNA is more closely related to yeast T and W dsRNAs and single-stranded RNA bacteriophages such as Q beta than to other hypovirulence-associated dsRNAs.

RNA editing of transcripts of a chimeric mitochondrial gene associated with cytoplasmic male-sterility in Brassica

The orf224 gene is a chimeric open reading frame associated with the Polima or pol cytoplasmic male sterility of Brassica napus. The first 58 codons and 5' upstream region of orf224 are derived from a conventional mitochondrial gene, orfB, while the origin of the remaining portion of the gene is unknown. Transcripts of the orf224 gene were found to be edited at a single site in the region of the gene that does not correspond to a known sequence. Oligonucleotides corresponding to the edited and unedited forms were shown to hybridize specifically to respective in vitro orf224 transcripts. Analysis of floral mtRNA by this method indicated that virtually all orf224 transcripts of both sterile and fertile, nuclear-restored pol cytoplasm plants are edited. Our results indicate that transcripts of novel, CMS-associated genes may be edited, but that, at least in this case, the degree of editing does not appear to be directly related to the male-sterile phenotype.

Vesicle-associated double-stranded ribonucleic acid genetic elements in Agaricus bisporus

Double-stranded ribonucleic acids (dsRNAs) were isolated from fruit bodies of commercial strains of the cultivated mushroom (Agaricus bisporus) by polyethylene glycol-NaCl precipitation, differential centrifugation, rate-zonal centrifugation in sucrose, and equilibrium centrifugation in cesium sulphate. In all seven of the mushroom isolates examined, three dsRNAs were identified: two major dsRNA segments of > 13.1-kb (L-RNA) and 2.4-kb (S-RNA) and a minor segment of 5.2-kb (M-RNA). L-, M-, and S-RNAs co-purified with spherical fungal vesicles measuring approximately 75 nm in diameter. The three dsRNAs were intimately associated with the vesicles as suggested by their lower buoyant density in cesium sulphate (1.27 g/cc) compared to that of phenol-extracted dsRNAs (1.42 g/cc) and by their resistance to hydrolysis by ribonuclease at low ionic strength. Using a variety of conditions during purification, no virus-like particles were found to be associated with the dsRNAs. In Northern analysis, L-, M-, and S-RNAs failed to cross-hybridize with the genomic dsRNAs of La France isometric virus. We report here the first description of non-encapsidated, vesicle-associated, dsRNA genetic elements in the common cultivated mushroom.

Characterization of expression of a mitochondrial gene region associated with the Brassica "Polima" CMS: developmental influences

The mitochondrial genome of the Polima (pol) male-sterile cytoplasm of Brassica napus contains a chimeric 224-codon open reading frame (orf224) that is located upstream of, and co-transcribed with, the atp6 gene. The N-terminal coding region of orf224 is derived from a conventional mitochondrial gene, orfB, while the origin of the remainder of the sequence is unknown. We show that an apparently functional copy of orfB is present in the pol mitochondrial genome, indicating that the pol CMS is not caused by the absence of an intact, expressed orfB gene. The 5' termini of orf224/atp6 transcripts present in both sterile and fertility-restored (Rf) pol cytoplasm plants are shown to map to sequences resembling mitochondrial transcription-initiation sites, whereas the 5' termini of two transcripts specific to restored lines map to sequences which resemble neither one another nor mitochondrial promoter motifs. It is suggested that the complex orf224/atp6 transcript pattern of Rf plants is generated by a combination of multiple transcription initiation and processing events and that the nuclear restorer gene acts to specifically alter orf224/atp6 transcripts by affecting RNA processing. Northern analyses demonstrate that the effect of the restorer gene on orf224/atp6 transcripts is not tissue or developmental-stage specific. However, the expression of the atp6 region is developmentally regulated in pol plants, resulting in decreased levels of monocistronic atp6 transcripts in floral tissue relative to seedlings. It is suggested that this developmental regulation may be related to the absence of overt phenotypic effects of the CMS mutation in vegetative tissues.

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.

Association of particles that contain double-stranded RNAs with algal chloroplasts and mitochondria

Linear dsRNAs (double-stranded RNAs) belonging to several distinct size classes were found to be localized in chloroplasts and mitochondria of Bryopsis spp., raising the possibility that these dsRNAs are prokaryotic in nature. The algal cytosol and nuclei did not contain dsRNAs. The amount of the dsRNAs in the organelles appeared constant, and there were about 500 copies per chloroplast. The four major dsRNAs from Bryopsis chloroplasts were about 2 kbp (kilobase pairs) in length and originated from discrete isometric particles of about 25 nm diameter. These virus-like particles were purified by CsCl density gradient centrifugation after extraction from isolated chloroplasts with chloroformbutanol and subsequent precipitation with polyethylene glycol. They had a buoyant density of about 1.40 g · cm(-3) and contained four major and three minor proteins. Mitochondrial dsRNAs were about 4.5 kbp in length and formed less-stable particles of about 40 nm in diameter with a buoyant density of 1.47 g · cm(-3). Some observations support the hypothesis that vertical transmission of the protein-coated, non-infectious dsRNAs occurs within cell organelles. Double-stranded RNAs of various sizes were found in most green, red, and brown algae. The characteristics of the algal dsRNAs are compared with those of dsRNAs from higher plants and the biological significance of the dsRNAs in cell organelles is discussed.

Suppression of cytoplasmic male sterility by nuclear genes alters expression of a novel mitochondrial gene region

To identify regions of the mitochondrial genome that potentially could specify the "Polima" (pol) cytoplasmic male sterility (CMS) of Brassica napus, transcripts of 14 mitochondrial genes from nap (male fertile), pol (male sterile), and nuclear fertility-restored pol cytoplasm plants were analyzed. Transcriptional differences among these plants were detected only with the ATPase subunit 6 (atp6) gene. Structural analysis of the atp6 gene regions of pol and nap mitochondrial DNAs showed that rearrangements in the pol mitochondrial genome occurring upstream of atp6 have generated a chimeric 224-codon open reading frame, designated orf224, that is cotranscribed with atp6. In CMS plants, most transcripts of this region are dicistronic, comprising both orf224 and atp6 sequences. Nuclear restorer genes at either of two distinct loci appear to specifically alter this transcript pattern such that monocistronic atp6 transcripts predominate. The differences in expression of this region appear to result, in part, from differential processing of a tRNA-like element comprising a tRNA pseudogene present immediately upstream of atp6 in both the sterile and fertile mitochondrial DNAs. Possible mechanisms by which expression of the orf224/atp6 locus and the Polima CMS trait may be specifically related are considered.

Characterization of transcription initiation sites on the soybean mitochondrial genome allows identification of a transcription-associated sequence motif

Transcription initiation sites on the soybean mitochondrial genome have been characterized by sequence analysis of in vitro-capped soybean mtRNAs and corresponding mtDNA regions. The most abundant, discrete soybean mtRNA species labeled by guanylyltransferase and [alpha-32P]GTP are shown to correspond to the major transcript of the atp9 gene and to a group of small RNAs consisting of a discrete 80 nucleotide (nt) species plus heterogeneous species ranging in size from 133 to 148 nt. The 133-148 nt RNAs represent a set of transcripts with a common 5' terminus and ragged 3' ends, while the 80 nt RNA corresponds to positions 53-133 of the 133 nt species. The major, discrete in vitro-capped RNA species thus correspond to primary transcripts originating at three sites located in two regions of the soybean mitochondrial genome. The sequences extending from 13 nucleotides upstream to 8 nucleotides downstream of the initiation sites for the atp9 and 133-148 nt transcripts are identical at 18 of 21 positions. Sequences closely resembling this motif are located at some other 5' transcript termini of dicot plant mitochondria. Less closely related sequences are found at transcription initiation sites of wheat and maize mitochondria.

The double-stranded RNA associated with the '447' cytoplasmic male sterility in Vicia faba is packaged together with its replicase in cytoplasmic membranous vesicles

The 447 male sterility trait in Vicia faba is strictly correlated with the presence of well-defined membranous vesicles or 'cytoplasmic spherical bodies' not found in fertile isogenic maintainer plants, and by the occurrence of a discrete high molecular weight double-stranded RNA. We have purified these cytoplasmic membranous vesicles and find that they contain the dsRNA together with an RNA-dependent RNA polymerase whose activity depends upon the presence of Mg2+, requires the four-nucleoside triphosphates and is unaffected by inhibitors of cellular transcriptases, e.g. alpha-amanitin and Actinomycin D. The dsRNA can be labelled in vitro by incubating the cytoplasmic vesicles with radioactive NTPs, and the RNA synthesized in vitro is also in a double-stranded form as judged by its resistance to RNase digestion at high salt and its behaviour upon CF-11 chromatography. Treatment of the vesicles with a non-ionic detergent releases the dsRNA in the form of a complex with the RNA-dependent RNA polymerase. The enzyme can still carry out the specific synthesis of dsRNA in these solubilized complexes. The cytoplasmic vesicles therefore isolate this vertically transmitted, self-replicating dsRNA from the cellular milieu: the possible mode of action and relevance of this novel genetic element to the 447 cytoplasmic male sterility trait are discussed.

Double-stranded RNA and male sterility in rice

Double-stranded RNA (dsRNA) was isolated from rice Oryza sativa ssp. japonica, but not from other subspecies. The dsRNA has been found in all of the examined cytoplasmic male-sterile (CMS) lines of BT (Chinsurah Boro II)-type rice, but was not detected in their companionate maintainer lines. It is uniquely and positivley correlated with the CMS trait in BT-type rice. Recently, the dsRNA was also found in a nuclear malesterile (NMS) rice, Nongken 58s, but was not found in its normal Nongken 58. The molecular weight of this dsRNA was estimated to be about 18 kb. Electron microscopic analysis reveals that it is linear snapped. The double strandedness of the RNA molecules was characterized by CF-11 cellulose column chromatography and nuclease treatments. It bound to CF-11 cellulose in the presence of 15% ethanol. It was sensitive to RNase A at low salt concentrations, but insensitive to DNase I, SI nuclease, and RNase A at high salt concentrations. The dsRNA was detected in both mitochondrial and cytoplasmic fractions. Dot-blot hybridization reveals that there is no sequence homology between this dsRNA and mtDNA, but there is homology between this dsRNA and nuclear genomic DNA. We have not been able to transmit this dsRNA to fertile rice.

Transcriptional and Post-Transcriptional Regulation of RNA Levels in Maize Mitochondria

Relatively little is known about the mechanisms that govern the expression of plant mitochondrial genomes. We have addressed this problem by analyzing the transcriptional activity of different regions of the maize mitochondrial genome using both in vivo and isolated mitochondrial pulse-labeling systems. The regions examined included the protein genes atpA, atp6, and coxII, the 26S, 18S, and 5S rRNA genes, and sequences surrounding the rRNA genes. The rRNAs were found to be transcribed at rates fivefold to 10-fold higher than the protein genes. These rate differences are comparable with the differences in abundance of these species in the total or steady-state RNA population. Pulse-labeled RNA unexpectedly detected transcription of all regions examined, including approximately 21 kilobases of presumed noncoding sequences flanking the rRNA genes for which stable transcripts were not detected. The results obtained with RNA labeled for short pulses in vivo and in isolated mitochondria were similar, suggesting that isolated mitochondria provide a faithful run-on transcription assay. Our results indicate that the absence in total RNA of transcripts homologous to a given region of maize mitochondrial DNA does not necessarily exclude transcriptional activity of that region and that both transcriptional and post-transcriptional processes play important roles in maize mitochondrial genome expression.

On the mechanism of cytoplasmic male sterility in the 447 line of Vicia faba

The trait of cytoplasmic male sterility, expressed in plants bearing the 447 cytoplasm of Vicia faba, is uniquely and positively correlated with the presence of a linear double-stranded RNA molecule (dsRNA) 16.7 kb in size. Restriction enzyme digestion profiles of mitochondrial DNA isolated from fertile and cytoplasmic malesterile (CMS) lines do show a limited number of specific differences in fragment intensities and mobilities. However, mitochondria isolated from the progeny of the cross CMS × Restorer line contain DNA with an identical restriction profile as the male-sterile parent: moreover, subsequent generations are completely and permanently fertile, even upon segregation of the nuclear restoration gene. Southern hybridizations, using cDNA clones as probes, reveal homology between the CMS-associated dsRNA and the nuclear genome of both sterile and fertile lines. The regions cloned, representing approximately 22% of the total dsRNA sequence, show no homology to organelle DNA. We have not been able to stably transmit the dsRNA to fertile lines of V. faba or any other plant species, using a variety of standard virological techniques.

Inheritance of large mitochondrial RNA's in alfalfa

Several large RNA molecules that migrated to electrophoretic positions ranging from 1.7-10 kb were observed in preparation of alfalfa (Medicago sativa) mitochondria. F1 progenies inherited the RNA's from both maternal and paternal parents (Fig. 1). Treatment of intact mitochondria with RNase A failed to remove the RNA's, indicating that they were contained within an RNase impermeable compartment. Further purification of mitochondria in linear sucrose gradients failed to separate the RNA's from mitochondria. Transmission electron microscopic examination of sucrose gradient purified mitochondria revealed that mitochondria were free of contamination by virus-like particles, indicating that the RNA's were contained within the mitochondrion. Biparental inheritance of large mitochondrial RNA's in alfalfa provides evidence that mitochondria are inherited biparentally in this species.

Attempts to detect extra genomial factors in cytoplasmic male-sterile petunia lines

In the present study we examined the possibility that viruses, viroids or dsRNA are associated with cytoplasmic male sterile (cms) petunia. The assumption was made that if viruses or viroids were present, the treatments for elimination of viruses and viroids would produce "healthy" fertile plants. Male sterile plants were subjected to heat and cold treatments for 10 weeks and/ or for 5 months, after which apical meristems were isolated and cultured with the addition of antiviral factors. The mother plants, the regenerated plants and their progeny were sterile. These treatments did not affect sterility in sterile plants or the fertility of fertile plants. No dsRNA was found in cms petunia by gel electrophoresis. Thus, our data suggest that there are no viruses, viroids or dsRNA associated with cms petunia. Our data are in agreement with recent data, which suggests that the mitochondrial DNA is the site of the cytoplasmic male sterile gene in petunia.

In organello transcription in maize mitochondria and its sensitivity to inhibitors of RNA synthesis

Purified mitochondrial preparations from etiolated maize shoots support the incorporation of radioactivity from labeled UTP into RNA. The incorporation is linear with time for up to 2 hours, shows Michaelis-Menton kinetics with respect to the concentration of the labeled substrate, UTP, and has salt and pH optima which are different than those previously reported for RNA synthesis by isolated chloroplasts. When a crude mitochondrial preparation is subjected to isopycnic sucrose gradient centrifugation, the bulk of the RNA synthetic activity co-sediments with mitochondrial marker enzymes and with the mitochondrial 26S and 18S rRNAs. Maize mitochondrial RNA synthesis is prevented by actinomycin D and ethidium bromide but unaffected by alpha-amanitin. It is strongly inhibited by rifampicin at concentrations which have no effect on nuclear and chloroplast RNA synthesis, but only moderately inhibited by rifampicin at concentrations which completely inhibit bacterial RNA synthesis. The optimization, cell fractionation, and inhibitor data all suggest that contaminating organelles and bacteria do not contribute appreciably to the RNA synthesis in purified mitochondrial preparations.

Terminal protein association and sequence homology in linear mitochondrial plasmid-like DNAs of sorghum and maize

The linear extrachromosomal mitochondrial plasmid-like DNAs from the Ru cytoplasm of maize, and M35-1 and IS1112C cytoplasms of sorghum, possess 5' terminally-attached proteins. These molecules required proteinase K treatment for mobility in agarose gels and were susceptible to exonuclease III but not lambda exonuclease cleavage. Hybridizations, under stringent conditions, indicated that the sorghum plasmid-like DNAs, N1 and N2, did not possess DNA sequence homology to cloned central regions of S1 and S2, the linear mitochondrial plasmid-like DNAs present in S cytoplasm of maize. In addition, a novel 4.2kb, DNAase sensitive, RNAase insensitive band, exhibiting homology to internal sequences from maize S2, was observed in the sorghum IS1112C cytoplasm only.