Gene expression in isolated plant mitochondria: high fidelity of transcription, splicing and editing of a transgene product in electroporated organelles

Organelle-targeted gene delivery in plants by nanomaterials

Genetic engineering of plants has revolutionized agriculture and has had a significant impact on our everyday life. It has allowed for the production of crops with longer shelf lives, enhanced yields and resistance to pests and disease. The application of nanomaterials in plant genetic engineering has further augmented these programs with higher delivery efficiencies, biocompatibility and the potential for plant regeneration. In particular, subcellular targeting using nanomaterials has recently become possible with the cutting-edge developments within nanomaterials, but remains challenging despite the promise in organellar engineering for the introduction of useful traits and the elucidation of subcellular interactions. This feature article provides an overview of nanomaterial delivery within plants and highlights the application of recent progress in nanomaterials for subcellular organelle-targeted delivery.

Plant biomacromolecule delivery methods in the 21st century

The 21st century witnessed a boom in plant genomics and gene characterization studies through RNA interference and site-directed mutagenesis. Specifically, the last 15 years marked a rapid increase in discovering and implementing different genome editing techniques. Methods to deliver gene editing reagents have also attempted to keep pace with the discovery and implementation of gene editing tools in plants. As a result, various transient/stable, quick/lengthy, expensive (requiring specialized equipment)/inexpensive, and versatile/specific (species, developmental stage, or tissue) methods were developed. A brief account of these methods with emphasis on recent developments is provided in this review article. Additionally, the strengths and limitations of each method are listed to allow the reader to select the most appropriate method for their specific studies. Finally, a perspective for future developments and needs in this research area is presented.

Polymer-coated carbon nanotube hybrids with functional peptides for gene delivery into plant mitochondria

The delivery of genetic material into plants has been historically challenging due to the cell wall barrier, which blocks the passage of many biomolecules. Carbon nanotube-based delivery has emerged as a promising solution to this problem and has been shown to effectively deliver DNA and RNA into intact plants. Mitochondria are important targets due to their influence on agronomic traits, but delivery into this organelle has been limited to low efficiencies, restricting their potential in genetic engineering. This work describes the use of a carbon nanotube-polymer hybrid modified with functional peptides to deliver DNA into intact plant mitochondria with almost 30 times higher efficiency than existing methods. Genetic integration of a folate pathway gene in the mitochondria displays enhanced plant growth rates, suggesting its applications in metabolic engineering and the establishment of stable transformation in mitochondrial genomes. Furthermore, the flexibility of the polymer layer will also allow for the conjugation of other peptides and cargo targeting other organelles for broad applications in plant bioengineering.

The delivery of genetic material into plants is challenging due to the cell wall barrier. Here, the authors hybridize polymer-coated carbon nanotubes with functional peptides to deliver plasmid DNA cargo into intact plant mitochondria for transient expression and homologous recombination at high efficiency.

Applications of CPPs in Genome Editing of Plants

Cell penetrating peptides (CPPs) are short peptides that are able to translocate themselves and their cargo into cells. The progressive and continuous application of CPPs in various fields of basic and applied research shows that they are efficient delivery vectors for an assortment of biomolecules, including nucleic acids and proteins. This feature makes CPPs an excellent tool for modification of plant genomes through transgenesis and genome editing. In this review, we present the progress during the last three decades in application of CPPs for delivery of DNA, RNA, and proteins into plant cells and tissues. Moreover, we highlight the exploiting of CPPs as advantageous and beneficial tool for plant genome editing via delivery of nuclease proteins, and provide a practical example of genome alternation through CPP-delivered nucleases. Finally, the current exploitation of peptides in organelle-specific DNA delivery and modification of organellar genomes is discussed.

Plant organellar RNA editing: what 30 years of research has revealed

The central dogma in biology defines the flow of genetic information from DNA to RNA to protein. Accordingly, RNA molecules generally accurately follow the sequences of the genes from which they are transcribed. This rule is transgressed by RNA editing, which creates RNA products that differ from their DNA templates. Analyses of the RNA landscapes of terrestrial plants have indicated that RNA editing (in the form of C-U base transitions) is highly prevalent within organelles (that is, mitochondria and chloroplasts). Numerous C→U conversions (and in some plants also U→C) alter the coding sequences of many of the organellar transcripts and can also produce translatable mRNAs by creating AUG start sites or eliminating premature stop codons, or affect the RNA structure, influence splicing and alter the stability of RNAs. RNA-binding proteins are at the heart of post-transcriptional RNA expression. The C-to-U RNA editing process in plant mitochondria involves numerous nuclear-encoded factors, many of which have been identified as pentatricopeptide repeat (PPR) proteins that target editing sites in a sequence-specific manner. In this review we report on major discoveries on RNA editing in plant organelles, since it was first documented 30 years ago.

Molecular and Functional Diversity of RNA Editing in Plant Mitochondria

RNA editing is a fundamental biochemical process relating to the modification of nucleotides in messenger RNAs of functional genes in cells. RNA editing leads to re-establishment of conserved amino acid residues for functional proteins in nuclei, chloroplasts, and mitochondria. Identification of RNA editing factors that contributes to target site recognition increases our understanding of RNA editing mechanisms. Significant progress has been made in recent years in RNA editing studies for both animal and plant cells. RNA editing in nuclei and mitochondria of animal cells and in chloroplast of plant cells has been extensively documented and reviewed. RNA editing has been also extensively documented on plant mitochondria. However, functional diversity of RNA editing factors in plant mitochondria is not overviewed. Here, we review the biological significance of RNA editing, recent progress on the molecular mechanisms of RNA editing process, and function diversity of editing factors in plant mitochondrial research. We will focus on: (1) pentatricopeptide repeat proteins in Arabidopsis and in crop plants; (2) the progress of RNA editing process in plant mitochondria; (3) RNA editing-related RNA splicing; (4) RNA editing associated flower development; (5) RNA editing modulated male sterile; (6) RNA editing-regulated cell signaling; and (7) RNA editing involving abiotic stress. Advances described in this review will be valuable in expanding our understanding in RNA editing. The diverse functions of RNA editing in plant mitochondria will shed light on the investigation of molecular mechanisms that underlies plant development and abiotic stress tolerance.

Comparison of mitochondrial gene expression and polysome loading in different tobacco tissues

BACKGROUND

To investigate translational regulation of gene expression in plant mitochondria, a mitochondrial polysome isolation protocol was established for tobacco to investigate polysomal mRNA loading as a proxy for translational activity. Furthermore, we developed an oligonucleotide based microarray platform to determine the level of Nicotiana tabacum and Arabidopsis thaliana mitochondrial mRNA.

RESULTS

Microarray analysis of free and polysomal mRNAs was used to characterize differences in the levels of free transcripts and ribosome-bound mRNAs in various organs of tobacco plants. We have observed higher mitochondrial transcript levels in young leaves, flowers and floral buds as compared to fully expanded leaves and roots. A similar pattern of abundance was observed for ribosome-bound mitochondrial mRNAs in these tissues. However, the accumulation of the mitochondrial protein COX2 was found to be inversely related to that of its ribosome-bound mRNA.

CONCLUSIONS

Our results indicate that the association of mitochondrial mRNAs to ribosomes is largely determined by the total transcript level of a gene. However, at least for Cox2, we demonstrated that the level of ribosome-bound mRNA is not reflected by the amount of COX2 protein.

Electroporation of DNA into Physarum polycephalum Mitochondria: Effects on Transcription and RNA Editing in Isolated Organelles

Mitochondrial RNAs in the acellular slime mold Physarum polycephalum contain nucleotides that are not encoded in the mitochondrial genes from which they are transcribed. These site-specific changes are quite extensive, comprising ~4% of the residues within mRNAs and ~2% of rRNAs and tRNAs. These “extra” nucleotides are added co-transcriptionally, but the means by which this is accomplished have not been elucidated. The cox1 mRNA also contains four sites of C to U changes, which occur post-transcriptionally, most likely via targeted deamination. The currently available in vitro systems for studying P. polycephalum editing are limited in that the template is the entire ~63,000 bp mitochondrial genome. This presents a significant challenge when trying to define the signals that specify editing sites. In an attempt to overcome this issue, a method for introducing DNA into isolated P. polycephalum mitochondria via electroporation has been developed. Exogenous DNA is expressed, but the transcripts synthesized from these templates are not edited under the conditions tested. However, transcripts derived from the mitochondrial genome are accurately edited after electroporation, indicating that the editing machinery is still functional. These findings suggest that this method may ultimately provide a feasible approach to elucidating editing signals.

Gene introduction into the mitochondria of Arabidopsis thaliana via peptide-based carriers

Available methods in plant genetic transformation are nuclear and plastid transformations because similar procedures have not yet been established for the mitochondria. The double membrane and small size of the organelle, in addition to its large population in cells, are major obstacles in mitochondrial transfection. Here we report the intracellular delivery of exogenous DNA localized to the mitochondria of Arabidopsis thaliana using a combination of mitochondria-targeting peptide and cell-penetrating peptide. Low concentrations of peptides were sufficient to deliver DNA into the mitochondria and expression of imported DNA reached detectable levels within a short incubation period (12 h). We found that electrostatic interaction with the cell membrane is not a critical factor for complex internalization, instead, improved intracellular penetration of mitochondria-targeted complexes significantly enhanced gene transfer efficiency. Our results delineate a simple and effective peptide-based method, as a starting point for the development of more sophisticated plant mitochondrial transfection strategies.

RNA metabolism in plant mitochondria

Mitochondria are essential for the eukaryotic cell and are derived from the endosymbiosis of an α-proteobacterial ancestor. Compared to other eukaryotes, RNA metabolism in plant mitochondria is complex and combines bacterial-like traits with novel features that evolved in the host cell. These complex RNA processes are regulated by families of nucleus-encoded RNA-binding proteins. Transcription is particularly relaxed and is initiated from multiple promoters covering the entire genome. The variety of RNA precursors accumulating in mitochondria highlights the importance of post-transcriptional processes to determine the size and abundance of transcripts. Here we review RNA metabolism in plant mitochondria, from RNA transcription to translation, with a special focus on their unique features that are controlled by trans-factors.

Deletions in cox2 mRNA result in loss of splicing and RNA editing and gain of novel RNA editing sites

As previously demonstrated, the maize cox2 RNA is fully edited in cauliflower mitochondria. Use of constructs with a deleted cox2 intron, however, led to a loss of RNA editing at almost all editing sites, with only a few sites still partially edited. Likewise, one deletion in exon 1 and three in exon 2 abolish RNA editing at all cox2 sites analyzed. Furthermore, intron splicing is abolished using these deletions. Mutation of a cytosine residue, which is normally edited and localized directly adjacent to the intron, to thymidine did not result in restoration of splicing, indicating that the loss of splicing was not due to loss of RNA editing. One deletion in exon 2 did not lead to loss of splicing. Instead, most editing sites were found to be edited, only three were not edited. Unexpectedly, we observed additional RNA editing events at new sites. Thus it appears that deletions in the cox2 RNA sequence can have a strong effect on RNA processing, leading to loss of splicing, loss of editing at all sites, or even to a gain of new editing sites. As these effects are not limited to the vicinity of the respective deletions, but appear to be widespread or even affect all editing sites, they may not be explained by the loss of PPR binding sites. Instead, it appears that several parts of the cox2 transcript are required for proper RNA processing. This indicates the roles of the RNA sequence and structural elements in the recognition of the editing sites.

RNA editing in mitochondrial trans-introns is required for splicing

In plant mitochondria, gene expression of translatable mRNAs is a complex process with two critical steps, RNA editing and splicing. We studied the role of RNA editing on non-coding regions of the mat-r-nad1e-nad5c transcript from wheat mitochondria. This RNA contains two trans-introns, 3'-nad1-I4 and 3'-nad5-I2, involved in different trans-splicing events, ensuring the association of nad1d-nad1e and nad5b-nad5c exons from nad1 and nad5 mRNAs respectively. The C-to-U editing changes studied here affect homologous positions on 3'-nad1-I4 and 3'-nad5-I2. It is proposed that these base changes are necessary to place an Adenosine residue in a bulging conformation characteristic of domain VI (D6) from group II introns. In this work, we investigated the role of RNA editing events on 3'-nad1-I4 and 3'-nad5-I2 in the trans-splicing process using in vivo and in organello approaches. When the branched intermediates formed during the splicing process were analyzed, the C residues from D6 intron domains from 3'-nad1-I4 and 3'-nad5-I2 were found changed to U, suggesting that RNA editing of these residues could be mandatory for splicing. This assumption was tested by expressing recombinant mat-r-nad1e transgenes introduced into mitochondria by electroporation. Mutation of the editing target residue dramatically affected trans-splicing. Interestingly, the exon joining efficiency was not recovered by compensatory mutations, suggesting that the role of RNA editing is not confined to the restoration of the secondary structure of domain D6 of the intron. Our results strongly support the hypothesis that RNA editing in trans-introns precedes maturation, and is required for the splicing reaction. In addition, this is the first report using an in organello approach to study the trans-splicing process, opening the way to future studies of this peculiar mechanism.

Targeting nucleic acids into mitochondria: progress and prospects

Given the essential functions of these organelles in cell homeostasis, their involvement in incurable diseases and their potential in biotechnological applications, genetic transformation of mitochondria has been a long pursued goal that has only been reached in a couple of unicellular organisms. The challenge led scientists to explore a wealth of different strategies for mitochondrial delivery of DNA or RNA in living cells. These are the subject of the present review. Targeting DNA into the organelles currently shows promise but remarkably a number of alternative approaches based on RNA trafficking were also established and will bring as well major contributions.

Mitochondrial transfection for studying organellar DNA repair, genome maintenance and aging

Maintenance of the mitochondrial genome is a major challenge for cells, particularly as they begin to age. Although it is established that organelles possess regular DNA repair pathways, many aspects of these complex processes and of their regulation remain to be investigated. Mitochondrial transfection of isolated organelles and in whole cells with customized DNA synthesized to contain defined lesions has wide prospects for deciphering repair mechanisms in a physiological context. We document here the strategies currently developed to transfer DNA of interest into mitochondria. Methodologies with isolated mitochondria claim to exploit the protein import pathway or the natural competence of the organelles, to permeate the membranes or to use conjugal transfer from bacteria. Besides biolistics, which remains restricted to yeast and Chlamydomonas reinhardtii, nanocarriers or fusion proteins have been explored as methods to target custom DNA into mitochondria in intact cells. In further approaches, whole mitochondria have been transferred into recipient cells. Repair failure or error-prone repair leads to mutations which potentially could be rescued by allotopic expression of proteins. The relevance of the different approaches for the analysis of mitochondrial DNA repair mechanisms and of aging is discussed.

A protein shuttle system to target RNA into mitochondria

Mitochondria play a key role in essential cellular functions. A deeper understanding of mitochondrial molecular processes is hampered by the difficulty of incorporating foreign nucleic acids into organelles. Mitochondria of most eukaryotic species import cytosolic tRNAs. Based on this natural process, we describe here a powerful shuttle system to internalize several types of RNAs into isolated mitochondria. We demonstrate that this tool is useful to investigate tRNA processing or mRNA editing in plant mitochondria. Furthermore, we show that the same strategy can be used to address both tRNA and mRNA to isolated mammalian mitochondria. We anticipate our novel approach to be the starting point for various studies on mitochondrial processes. Finally, our study provides new insights into the mechanism of RNA import into mitochondria.

Mitochondrial RNA import: from diversity of natural mechanisms to potential applications

Mitochondria, owing to their bacterial origin, still contain their own DNA. However, the majority of bacterial genes were lost or transferred to the nuclear genome and the biogenesis of the "present-day" mitochondria mainly depends on the expression of the nuclear genome. Thus, most mitochondrial proteins and a small number of mitochondrial RNAs (mostly tRNAs) expressed from nuclear genes need to be imported into the organelle. During evolution, macromolecule import systems were universally established. The processes of protein mitochondrial import are very well described in the literature. By contrast, deciphering the mitochondrial RNA import phenomenon is still a real challenge. The purpose of this review is to present a general survey of our present knowledge in this field in different model organisms, protozoa, plants, yeast, and mammals. Questions still under debate and major challenges are discussed. Mitochondria are involved in numerous human diseases. The targeting of macromolecule to mitochondria represents a promising way to fight mitochondrial disorders and recent developments in this area of research are presented.

Polyadenylation-mediated RNA degradation in plant mitochondria

In plant mitochondria, polyadenylation-mediated RNA degradation is involved in several key aspects of genome expression, including RNA maturation, RNA turnover, and RNA surveillance. We describe here a combination of in vivo, in vitro, and in organello methods that have been developed or optimized to characterize this RNA degradation pathway. These approaches include several PCR-based methods designed to identify polyadenylated RNA substrates, as well as in vitro and in organello systems, to study functional aspects of the RNA degradation processes. Taken together, identification of RNA substrates combined with information from degradation assays are invaluable tools to dissect the mechanisms and roles of RNA degradation in plant mitochondrial genome expression.

Mitochondrial mRNA polymorphisms in different Arabidopsis accessions

In our analysis of 5' and 3' end formation in plant mitochondria, we compared the major transcript ends of all mitochondrial protein-coding genes between the three Arabidopsis (Arabidopsis thaliana) accessions Columbia (Col), C24, and Landsberg erecta (Ler). Differences between transcript patterns were found for seven genes. For atp6-2, no transcripts at all were detected in Ler. This and further analyses suggest that the atp6-2 gene arrangement is absent from the mitochondrial DNA of this accession. All other transcript polymorphisms are attributed to variations at the 5' termini and were consistently observed in all tissues investigated. mRNA phenotyping of reciprocal Col/Ler, Col/C24, and Ler/C24 F(1) hybrids revealed the differing transcript patterns of ccmC to be inherited maternally, suggesting these to arise from differences in the mitochondrial DNA. Biparental inheritance was observed for the polymorphic transcripts of nad4, nad9, ccmB, and rpl5, indicating these differences to be caused by nuclear-encoded trans-factors. Deviant transcript patterns were tested in further accessions and were found in at least three additional accessions. Detailed examination of the nad4 and the nad9 transcripts demonstrates that the respective polymorphisms affect the major mRNAs of these genes. This study shows that natural genetic variation in Arabidopsis can also affect mitochondrial mRNA end processing. These variations can now be used to identify the nuclear genes responsible, as well as the mitochondrial cis-elements required, for 5' end generation of mitochondrial transcripts.

Transcript end mapping and analysis of RNA editing in plant mitochondria

Mitochondria are genetic compartments with their own enzymatic equipment for maintenance and expression of their genetic information. As in all genetic systems, gene expression has to be regulated, and in mitochondria this also has to be coordinated with the expression of nuclear-encoded mitochondrial proteins. Presently, there is virtually no information available about the mechanistic details and the enzymes involved in these processes. There is still much to be learned about how plant mitochondrial gene expression is managed and to what extent the contribution of transcription initiation and posttranscriptional processes, respectively, contribute to this control. As one prerequisite for better understanding of the mechanisms and regulatory controls, more fundamental data on mitochondrial transcription initiation and posttranscriptional RNA processing are necessary. As part of the essential methodology, we present methods for the analysis of the 5' and 3' extremities of mitochondrial transcripts and the identification of transcription initiation sites. An in organello system is described for the functional investigation of ribonucleic acid editing in plant mitochondria.

The process of RNA editing in plant mitochondria

RNA editing changes more than 400 cytidines to uridines in the mRNAs of mitochondria in flowering plants. In other plants such as ferns and mosses, RNA editing reactions changing C to U and U to C are observed at almost equal frequencies. Development of transfection systems with isolated mitochondria and of in vitro systems with extracts from mitochondria has considerably improved our understanding of the recognition of specific editing sites in the last few years. These assays have also yielded information about the biochemical parameters, but the enzymes involved have not yet been identified. Here we summarize our present understanding of the process of RNA editing in flowering plant mitochondria.

In organello gene expression and RNA editing studies by electroporation-mediated transformation of isolated plant mitochondria

Plant mitochondrial gene expression is a complex process involving multiple steps such as transcription, cis- and trans-splicing, RNA trimming, RNA editing, and translation. One of the main hurdles in understanding more about these processes has been the inability to incorporate engineered genes into mitochondria. We recently reported an in organello approach on the basis of the introduction of foreign DNA into isolated plant mitochondria by electroporation. This procedure allows the investigation of transcriptional and posttranscriptional processes, such as splicing and RNA editing, by use of site-directed mutagenesis. Foreign gene expression in organello is strongly dependent on the functional status of mitochondria, thus providing relevant information in conditions closer to the situation found in vivo. The study of mutants that affect RNA splicing and editing provides a novel and powerful method to explain the role of specific sequences involved in these processes. Here we describe a protocol to "transform" isolated plant mitochondria that has allowed us to investigate successfully some aspects of RNA editing.

Approaches to improve heterogeneous gene expression in transgenic plants

With the development of plant genetic engineering, many transformation methods can be used to transfer heterogeneous genes into plants to develop genetic crops. However, a lot of research results have shown that transgene expression remains largely unpredictable and there is great variation of expression level in different transgenic plant lines. Plant genetic engineering research is reviewed in the present paper. We analysed the reasons why low efficiency of heterogeneous gene expression has happened in transgenic plants in terms of DNA modification, localization of proteins and methods of transformation used. Some strategies for improving heterogeneous gene expression in transgenic plants are also discussed.

RNA editing site recognition in heterologous plant mitochondria

RNA editing is a process that modifies the information content of mitochondrial messenger RNAs in flowering plants changing specific cytosine residues into uridine. To gain insight into editing site recognition, we used electroporation to introduce engineered wheat (Triticum aestivum) or potato (Solanum tuberosum) mitochondrial cox2 genes, and an atp9-containing chimeric gene, into non-cognate mitochondria, and observed the efficiency of editing in these contexts. Both wheat and potato mitochondria were able to express "foreign" constructs, and their products were properly spliced. Seventeen and twelve editing sites are present in the coding regions of wheat and potato cox2 transcripts, respectively. Eight are common to both plants, whereas nine are specific to wheat, and four to potato. An analogous situation is found for the atp9 mRNA coding regions from these species. We found that both mitochondria were able to recognize sites that are already present as T at the genomic level, making RNA editing unnecessary for that specific residue in the cognate organelle. Our results demonstrate that non-cognate mitochondria are able to edit residues that are not edited in their own transcripts, and support the hypothesis that the same trans-acting factor may recognize several editing sites.

A pentatricopeptide repeat protein is a site recognition factor in chloroplast RNA editing

In higher plants, RNA editing is a post-transcriptional process that converts C to U in organelle mRNAs. We have previously shown that an Arabidopsis thaliana crr4 mutant is defective with respect to RNA editing for creating the translational initial codon of the plastid ndhD gene (the ndhD-1 site). CRR4 contains 11 pentatricopeptide repeat motifs but does not contain any domains that are likely to be involved in the editing activity. The green fluorescent protein fused to the putative transit peptide of CRR4 targeted the plastid. The recombinant CRR4 expressed in Escherichia coli specifically bound to the 25 nucleotides of the upstream and the 10 nucleotides of the downstream sequences surrounding the editing site of ndhD-1. The target C nucleotide of this editing is not essential for the binding of CRR4. Taken together with the genetic evidence, we conclude that the pentatricopeptide repeat protein CRR4 is a sequence-specific RNA-binding protein that acts as a site recognition factor in plastid RNA editing.

Mono- and dicotyledonous plant-specific RNA editing sites are correctly edited in both in organello systems

We set out to analyse the phylogenetic distribution of cox2 RNA editing sites. Database searches have revealed the presence of mono- and dicotyledonous-specific RNA editing sites. Therefore, to better understand tRNA editing system in plants, we developed a new dicotyledonous in organello RNA editing system using cauliflower mitochondria and analysed the transcription of the cox2 gene for both maize and Arabidopsis. These results were compared with those obtained from a maize mitochondrial in organello system. Surprisingly, both the mono- and dicotyledonous cox2 transcripts were efficiently edited in the mitochondrial cauliflower and maize in organello systems, respectively, even for RNA editing sites not present in the endogenous cox2 sequences. Taken together, our observations support a self-guiding-transcript model for RNA editing in higher plants.

RNA editing sites in plant mitochondria can share cis-elements

RNA editing in flowering plant mitochondria alters numerous C nucleotides in a given mRNA molecule to U residues. To investigate whether neighbouring editing sites can influence each other we analyzed in vitro RNA editing of two sites spaced 30 nt apart. Deletion and competition experiments show that these two sites carry independent essential specificity determinants in the respective upstream 20-30 nucleotides. However, deletion of a an upstream sequence region promoting editing of the upstream site concomitantly decreases RNA editing of the second site 50-70 nucleotides downstream. This result suggests that supporting cis-/trans-interactions can be effective over larger distances and can affect more than one editing event.

Gene expression studies in isolated mitochondria: Solanum tuberosum rps10 is recognized by cognate potato but not by the transcription, splicing and editing machinery of wheat mitochondria

The complex gene expression mechanisms that occur in plant mitochondria, such as RNA editing and splicing, are not yet well understood. RNA editing in higher plant mitochondria is a highly specific process which modifies mRNA sequences by C-to-U conversions. It has been suggested that in some cases this process is required for splicing. Here, we use an experimental model based on the introduction of DNA into isolated mitochondria by electroporation to study organellar gene expression events. Our aim was to compare processing and editing of potato small ribosomal protein 10 gene (rps10) transcripts in heterologous (wheat mitochondria) and homologous (potato mitochondria) contexts. rps10 is a suitable model because it contains a group II intron, is absent in wheat mitochondria but is actively expressed in potato mitochondria, where transcripts are spliced and undergo five C-to-U editing events. For this purpose, conditions for electroporating isolated potato mitochondria were established. rps10 was placed under the control of either potato or wheat cox2 promoters. We found that rps10 was only transcribed under the control of a cognate promoter. In wheat mitochondria, rps10 transcripts were neither spliced nor edited while they are correctly processed in potato mitochondria. Interestingly, a wheat editing site grafted into rps10 was not recognized by wheat mitochondria but was correctly edited in potato mitochondria. Taken together, these results suggest that editing might occur only when the transcripts are engaged in processing and that they would not be available to editing factors outside of a putative RNA maturation machinery complex.

Natural competence of mammalian mitochondria allows the molecular investigation of mitochondrial gene expression

Respiration, a fundamental process in mammalian cells, requires two genomes, those of the nucleus and the mitochondrion (mtDNA). Mutations of mtDNA are being increasingly recognized in disease and may play an important role in the ageing process. Accepting the vital role of mtDNA gene products, our limited knowledge concerning the details of mitochondrial gene expression is surprising. This is, in part, due to our inability to transfect mitochondria and to manipulate their genome. There have been claims of successful DNA import into isolated organelles, but most reports lacked evidence of expression and no method has furthered our understanding of gene expression. Here, we report that mammalian mitochondria possess a natural competence for DNA import. Using five functional assays, we show imported DNA can act as templates for DNA synthesis or promoter-driven transcription, with the resultant polycistronic RNA being processed (5' and 3') and excised mt-tRNA matured. Exploiting this natural competence will allow us to explore mitochondrial gene expression in organello and provides the potential for mitochondrial transfection in vivo.

An in vitro RNA editing system from cauliflower mitochondria: editing site recognition parameters can vary in different plant species

Most of the 400 RNA editing sites in flowering plant mitochondria are found in mRNAs. Consequently, the sequence vicinities of homologous sites are highly conserved between different species and are presumably recognized by likewise conserved trans-factors. To investigate the evolutionary adaptation to sequence variation, we have now analyzed the recognition elements of an editing site with divergent upstream sequences in the two species pea and cauliflower. This variation is tolerated at the site selected, because the upstream cis-elements reach into the 5'-UTR of the mRNA. To compare cis-recognition features in pea and cauliflower mitochondria, we developed a new in vitro RNA editing system for cauliflower. In vitro editing assays with deleted and mutated template RNAs show that the major recognition elements for both species are located within the conserved sequence. In cauliflower, however, the essential upstream nucleotides extend further upstream than they do in pea. In-depth analysis of single-nucleotide mutations reveals critical spacing of the editing site and the specific recognition elements, and shows that the +1 nucleotide identity is important in cauliflower, but not in pea.

Fate of a larch unedited tRNA precursor expressed in potato mitochondria

In higher plant mitochondria, post-transcriptional C to U conversion known as editing mostly affects mRNAs. However, three tRNAs were also shown to be edited. Among them, three editing sites were identified in larch mitochondrial tRNA(His). We have previously shown that only the edited version can undergo maturation in vitro. In this paper, we introduced via direct DNA uptake the edited or unedited version of larch mitochondrial trnH into isolated potato mitochondria and expressed them under the control of potato mitochondrial 18 S rRNA promoter. As expected, the edited form of larch mitochondrial tRNA(His) precursor was processed in the isolated organelles. By contrast, no mature tRNA(His) was detected when using the unedited version of trnH. However, precursor molecules could be characterized by reverse transcription-PCR. These data demonstrate that the potato mitochondrial editing machinery is not able to recognize these "foreign" editing sites and confirm that these unedited tRNA precursor molecules are not correctly processed in organello. As a consequence, the fate of these RNA precursor molecules is likely to be degradation. Indeed, we detected by PCR two 3'-end truncated precursor RNAs. Interestingly, both RNA species exhibit poly(A) tails, a hallmark of degradation in plant mitochondria. Taken together, these data suggest that, in plant mitochondria, a defective unedited RNA precursor that cannot be processed to give a mature stable tRNA, is degraded through a polyadenylation-dependent pathway.

Mitochondrial electroporation and in organello RNA editing of chimeric atp6 transcripts

The Sorghum bicolor atp6-1 gene and chimeric atp6 genes with additional maize sequences were introduced into isolated maize mitochondria via electroporation. Transcripts isolated after in vitro incubation of the transformed organelles were then analysed for RNA editing. Transcripts of the S. bicolor atp6-1 gene, and the RNAs obtained from most of chimeric sorghum-maize atp6 gene constructs tested, were not edited. However, the transcript of one engineered chimeric gene comprising the 5'untranslated sequence and a segment of the N-terminal ORF of the maize atp6 combined with the sorghum atp6 core ORF and 3'untranslated sequence was found to be partially edited. We were able to exclude low RNA stability or insufficient editing capacity as the reason for failure to edit in the other instances. Instead, the data indicate that the maize sequence in the edited fusion transcript provides a structural motif or binding site for a transcript-specific editing factor.

Different patterns in the recognition of editing sites in plant mitochondria

Higher plant mitochondrial mRNAs are extensively modified by highly specific C-to-U conversions. However, the determinants of recognition specificity are, to date, unknown. Here, we analyse the cis-elements involved in the recognition of two editing sites in a cox2 gene in wheat mitochondria. A minimal region of 23 nt was found to be involved in recognition of the editing site C77, similar to our previous report for site C259. These regions were correctly recognized by the mitochondrial editing machinery when placed elsewhere in the transcript. The nearest neighbour residues of the target C play a crucial role in editing, but the nature and position of the residue varies according to the editing site concerned. The target region seems to be formed by two regions 5' and 3', which can be separated by a maximum of two residues. Studies on single residue mutants concerning every position in the 23 nt region indicated that editing sites are affected differently by their neighbouring sequences. These results suggest that, notwithstanding the similar extent and location of cis-elements, the editing site recognition mechanisms may differ in plant mitochondria.

Complex cis-elements determine an RNA editing site in pea mitochondria

The cis-requirements for the first editing site in the atp9 mRNA from pea mitochondria were investigated in an in vitro RNA editing system. Template RNAs deleted 5' of -20 are edited correctly, but with decreased efficiency. Deletions between -20 and the edited nucleotide abolish editing activity. Substitution of the sequences 3' of the editing site has little effect, which suggests that the major determinants reside upstream. Stepwise mutated RNA sequences were used as templates or competitors that divide the cis-elements into several distinct regions. In the template RNAs, mutation of the sequence between -40 and -35 reduces the editing activity, while the region from -15 to -5 is essential for the editing reaction. In competition experiments the upstream region can be titrated, while the essential sequence near the editing site is largely resistant to excess competitor. This observation suggests that either one trans-factor attaches to these separate cis-regions with different affinities or two distinct trans-factors bind to these sequences, and one of which is present in limited amounts, whereas the other one is more abundant in the lysate.

Gamma carbonic anhydrases in plant mitochondria

Three genes from Arabidopsis thaliana with high sequence similarity to gamma carbonic anhydrase (gammaCA), a Zn containing enzyme from Methanosarcina thermophila (CAM), were identified and characterized. Evolutionary and structural analyses predict that these genes code for active forms of gammaCA. Phylogenetic analyses reveal that these Arabidopsis gene products cluster together with CAM and related sequences from alpha and gamma proteobacteria, organisms proposed as the mitochondrial endosymbiont ancestor. Indeed, in vitro and in vivo experiments indicate that these gene products are transported into the mitochondria as occurs with several mitochondrial protein genes transferred, during evolution, from the endosymbiotic bacteria to the host genome. Moreover, putative CAM orthologous genes are detected in other plants and green algae and were predicted to be imported to mitochondria. Structural modeling and sequence analysis performed in more than a hundred homologous sequences show a high conservation of functionally important active site residues. Thus, the three histidine residues involved in Zn coordination (His 81, 117 and 122), Arg 59, Asp 61, Gin 75, and Asp 76 of CAM are conserved and properly arranged in the active site cavity of the models. Two other functionally important residues (Glu 62 and Glu 84 of CAM) are lacking, but alternative amino acids that might serve to their roles are postulated. Accordingly, we propose that photosynthetic eukaryotic organisms (green algae and plants) contain gammaCAs and that these enzymes codified by nuclear genes are imported into mitochondria to accomplish their biological function.

The fertility restorer genes X and T alter the transcripts of a novel mitochondrial gene implicated in CMS1 in chives (Allium schoenoprasum L.)

A chimeric mitochondrial gene configuration, mainly derived from sequences associated with the essential genes atp9 and atp6, was isolated from the sterility-inducing cytoplasm of the CMS1 system in chives (Allium schoenoprasum L.). This sequence is not found in four other cytoplasm types from chives; however, two copies are present in the mitochondrial DNA of CMS1-inducing cytoplasm, whose 5'-sequences are homologous to those of the atp9 gene. We provide evidence to show that one of the two CMS1-specific copies is actively transcribed, and two transcripts which terminate at the same position but differ in their 5'initiation sites were localized using the RACE technique. These transcripts of 942 and 961 nt, respectively, were confirmed to be the major products of this gene in CMS1 plants by Northern hybridization. However, smaller transcripts were found to accumulate in plants in which fertility had been restored. Restoration of fertility was induced either by the gene X, or the gene T at high temperatures. In (S1) X. genotypes a transcript with an estimated size of 440 nt was detected in all tissues examined. An additional hybridization signal with an estimated size of approximately 850 nt is expressed in temperature-sensitive plants [(S1) xxT.], and the intensity of a minor 350-nt transcript is enhanced. These latter alterations, conditioned by the gene T, occur independently of the growth temperature, but are limited to the flowers; they were not observed in leaves. The CMS1 transcripts are edited at seven positions and contain an ORF with a maximum coding capacity of 780 nt (containing the start codon derived from the atp9 gene in-frame). Use of the third in-frame start codon would result in the synthesis of a protein of a size very close to that of a previously described CMS1-specific protein, which has an apparent molecular weight of 18 kDa. The coding sequence that begins at this third in-frame start codon is also present in the sterility-inducing cytoplasms (S) and (T) in the onion, and absent in (N) cytoplasm.

In vitro RNA editing in pea mitochondria requires NTP or dNTP, suggesting involvement of an RNA helicase

To analyze the biochemical parameters of RNA editing in plant mitochondria and to eventually characterize the enzymes involved we developed a novel in vitro system. The high sensitivity of the mismatch-specific thymine glycosylase is exploited to facilitate reliable quantitative evaluation of the in vitro RNA editing products. A pea mitochondrial lysate correctly processes a C to U editing site in the cognate atp9 template. Reaction conditions were determined for a number of parameters, which allow first conclusions on the proteins involved. The apparent tolerance against specific Zn2+ chelators argues against the involvement of a cytidine deaminase enzyme, the theoretically most straightforward catalysator of the deamination reaction. Participation of a transaminase was investigated by testing potential amino group receptors, but none of these increased the RNA editing reaction. Most notable is the requirement of the RNA editing activity for NTPs. Any NTP or dNTP can substitute for ATP to the optimal concentration of 15 mm. This observation suggests the participation of an RNA helicase in the predicted RNA editing protein complex of plant mitochondria.

Electroporation of isolated higher-plant mitochondria: transcripts of an introduced cox2 gene, but not an atp6 gene, are edited in organello

To facilitate the analysis of RNA processing in plant mitochondria, a method was established for introducing foreign DNA into mitochondria isolated from maize and sorghum. This method permits the uptake of DNA of up to 11 kb into the mitochondrial matrix. In vitro incubation of maize mitochondria in a specific buffer system was found to permit splicing and editing of newly synthesized RNAs for a period of at least 7 h. This was shown both for transcripts of endogenous mitochondrial genes (atp6, cox2) and for transcripts derived from an introduced Arabidopsis thaliana cox2 gene. In contrast, when a Sorghum bicolor atp6 gene was introduced into isolated maize mitochondria, the gene was transcribed, but the RNA was not edited, although all the editing sites in maize and sorghum atp6 RNA are identical. This may indicate the presence of transcript-specific cis -acting regions in the up- or downstream untranslated sequences of the mRNA. The system described here should allow further dissection of the mechanism of RNA editing in plant mitochondria.

Plant mitochondria actively import DNA via the permeability transition pore complex

Plant mitochondria are remarkable with respect to their content in foreign, alien and plasmid-like DNA, raising the question of the transfer of this information into the organelles. We demonstrate the existence of an active, transmembrane potential-dependent mechanism of DNA uptake into plant mitochondria. The process is restricted to double-strand DNA, but has no obvious sequence specificity. It is most efficient with linear fragments up to a few kilobase pairs. When containing appropriate information, imported sequences are transcribed within the organelles. The uptake likely involves the voltage-dependent anion channel and the adenine nucleotide translocator, i.e. the core components of the mitochondrial permeability transition pore complex in animal cells, but it does not rely on known mitochondrial membrane permeabilization processes. We conclude that DNA import into plant mitochondria might represent a physiological phenomenon with some functional relevance.

Efficient cloning and engineering of entire mitochondrial genomes in Escherichia coli and transfer into transcriptionally active mitochondria

We have devised an efficient method for replicating and stably maintaining entire mitochondrial genomes in Escherichia coli and have shown that we can engineer these mitochondrial DNA (mtDNA) genome clones using standard molecular biological techniques. In general, we accomplish this by inserting an E.coli replication origin and selectable marker into isolated, circular mtDNA at random locations using an in vitro transposition reaction and then transforming the modified genomes into E.coli. We tested this approach by cloning the 16.3 kb mouse mitochondrial genome and found that the resulting clones could be engineered and faithfully maintained when we used E.coli hosts that replicated them at moderately low copy numbers. When these recombinant mtDNAs were replicated at high copy numbers, however, mtDNA sequences were partially or fully deleted from the original clone. We successfully electroporated recombinant mouse mitochondrial genomes into isolated mouse mitochondria devoid of their own DNA and detected robust in organello RNA synthesis by RT-PCR. This approach for modifying mtDNA and subsequent in organello analysis of the recombinant genomes offers an attractive experimental system for studying many aspects of vertebrate mitochondrial gene expression and is a first step towards true in vivo engineering of mammalian mitochondrial genomes.

Functional importance of nucleotide identities within the pea atp9 mitochondrial promoter sequence

Sequences ranging from nucleotide positions -14 to +4 relative to the transcription start site constitute an in vitro functional pea atp9 promoter. A comparison of respective sequence segments surrounding 11 unambiguously identified transcription initiation sites of various dicotyledoneous plant species revealed the highest level of evolutionary fidelity of nucleotide identities within the conserved nonanucleotide motif (CNM), suggesting their importance for promoter function. Using a mitochondrial in vitro transcription system, a detailed analysis by site-directed mutagenesis now reveals that the alteration of nucleotides -6 to -2 and +1 within the CNM indeed reduces promoter activity by more than 80%. Changes of nucleotide identities at the less conserved positions -12 to -9 within the AT-rich region reduced the initiation efficiency by about 70%. The alteration of the highly conserved position -7 has little influence on promoter function, indicating that evolutionary conservation does not always correlate with the functional importance of certain nucleotides. Mutagenesis of nucleotides at positions +3 or +4 reveals a minimal requirement of at least one purine for wild-type transcription initiation efficiency. The assignment of functionally important nucleotide identities should now facilitate an efficient and reliable prediction of other promoters in mitochondria of dicotyledon plants.

RNA splicing in higher plant mitochondria: determination of functional elements in group II intron from a chimeric cox II gene in electroporated wheat mitochondria

Higher plant mitochondria mainly contain group II introns presenting a secondary structure with six helical domains linked to a central hub. Experimental evidence of functional elements in higher plant mitochondria introns is limited since they are unable to undergo self-splicing and the definition of functional domains is based on data obtained from yeast autocatalytic introns. Here we study the role of putative functional elements required for the splicing reaction. The exon-binding and intron-binding sites (EBS and IBS, respectively), and the domain 6, which is involved in lariat formation, were analysed by site-directed mutagenesis and transient expression in electroporated mitochondria. The data presented here demonstrate the role of EBS1-IBS1 and EBS2-IBS2 interactions and reveal a new secondary-structure interaction. The role of the C to U editing conversion in the IBS1 motif is discussed.

cis Recognition elements in plant mitochondrion RNA editing

RNA editing in higher plant mitochondria modifies mRNA sequences by means of C-to-U conversions at highly specific sites. To determine the cis elements involved in recognition of an editing site in plant mitochondria, deletion and site-directed mutation constructs containing the cognate cox II mitochondrial gene were introduced into purified mitochondria by electroporation. The RNA editing status was analyzed for precursor and spliced transcripts from the test construct. We found that only a restricted number of nucleotides in the vicinity of the target C residue were necessary for recognition by the editing machinery and that the nearest neighbor 3' residues were crucial for the editing process. We provide evidence that two functionally distinguishable sequences can be defined: the 16-nucleotide 5' region, which can be replaced with the same region from another editing site, and a 6-nucleotide 3' region specific to the editing site. The latter region may play a role in positioning the actual editing residue.