A tRNA gene transcription initiation site is similar to mRNA and rRNA promoters in plant mitochondria

Determining mitochondrial transcript termini for the study of transcription start sites and transcript 5' end maturation

Mitochondrial gene expression in plants is considerably more complex than in animals or fungi. In plants, mitochondrial transcripts are generated from transcription initiation at numerous, poorly conserved promoters located throughout the mitochondrial genome. Most genes have more than one transcription start site. Posttranscriptional RNA 5' end maturation contributes to the diversity of transcripts produced from each mitochondrial gene. Understanding transcriptional mechanisms and transcript maturation requires knowledge on transcription start sites and processing sites. This chapter describes two different, complementary experimental approaches for determining these sites in mitochondrial genomes through mapping of transcript 5' ends. In order to distinguish 5' ends deriving from transcription initiation, both strategies exploit the presence of triphosphates at these specific 5' termini.

PLMItRNA, a database on the heterogeneous genetic origin of mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes

The updated version of PLMItRNA reports information and multialignments on 609 genes and 34 tRNA molecules active in the mitochondria of Viridiplantae (27 Embryophyta and 10 Chlorophyta), and photosynthetic algae (one Cryptophyta, four Rhodophyta and two Stramenopiles). Colour-code based tables reporting the different genetic origin of identified genes allow hyper-textual link to single entries. Promoter sequences identified for tRNA genes in the mitochondrial genomes of Angiospermae are also reported. The PLMItRNA database is accessible at http://bighost.area.ba.cnr.it/PLMItRNA/.

Transcription of two sunflower (Helianthus annuus L.) mitochondrial tRNA genes having different genetic origins

The divergent transcription of two tRNA genes encoded in sunflower mitochondrial DNA, proposed as genes of different genetic origin, has been studied in detail. The transcription initiation site (TIS) for both transcript precursors has been identified by hybridization with in vitro (32)P-capped total RNAs and primer extension. The location of two TISs and the analysis of distribution of sequence elements (motifs) usually present in higher plant mitochondrial promoters led to the identification of two short regions (about 30-40 bp) which can be proposed as the promoters for the transcription of two genes. This conclusion is supported by the observation that within the short intergenic region included between the 5' termini of two genes (1924 bp) the distribution of those specific motifs is unique around the TISs, although not identical for the two promoters. Based on specific experimental results the trnE promoter shows a higher efficiency in comparison with that of the trnH promoter. This result is in good agreement with its structure which strictly conforms to those described for mitochondrial genes of dicot plants. Instead the other promoter shows some divergences which could be responsible for its lower efficiency. The context in which trnH lies in the sunflower mitochondrial genome and other features described in the paper may suggest that, despite the high similarity with the chloroplast counterpart, the trnH gene could have a native origin.

Sensitivity to Alternaria alternata toxin in citrus because of altered mitochondrial RNA processing

Specificity in the interaction between rough lemon (Citrus jambhiri Lush.) and the fungal pathogen Alternaria alternata rough lemon pathotype is determined by a host-selective toxin, ACR-toxin. Mitochondria from rough lemon are sensitive to ACR-toxin whereas mitochondria from resistant plants, including other citrus species, are resistant. We have identified a C. jambhiri mitochondrial DNA sequence, designated ACRS (ACR-toxin sensitivity gene), that confers toxin sensitivity to Escherichia coli. ACRS is located in the group II intron of the mitochondrial tRNA-Ala and is translated into a SDS-resistant oligomeric protein in C. jambhiri mitochondria but is not translated in the toxin-insensitive mitochondria. ACRS is present in the mitochondrial genome of both toxin-sensitive and -insensitive citrus. However, in mitochondria of toxin-insensitive plants, the transcripts from ACRS are shorter than those in mitochondria of sensitive plants. These results demonstrate that sensitivity to ACR-toxin and hence specificity of the interaction between A. alternata rough lemon pathotype and C. jambhiri is due to differential posttranscriptional processing of a mitochondrial gene.

The RNA world of plant mitochondria

Mitochondria are well known as the cellular power factory. Much less is known about these organelles as a genetic system. This is particularly true for mitochondria of plants, which subsist with respect to attention by the scientific community in the shadow of the chloroplasts. Nevertheless the mitochondrial genetic system is essential for the function of mitochondria and thus for the survival of the plant. In plant mitochondria the pathway from the genetic information encoded in the DNA to the functional protein leads through a very diverse RNA world. How the RNA is generated and what kinds of regulation and control mechanisms are operative in transcription are current topics in research. Furthermore, the modes of posttranscriptional alterations and their consequences for RNA stability and thus for gene expression in plant mitochondria are currently objects of intensive investigations. In this article current results obtained in the examination of plant mitochondrial transcription, RNA processing, and RNA stability are illustrated. Recent developments in the characterization of promoter structure and the respective transcription apparatus as well as new aspects of RNA processing steps including mRNA 3' processing and stability, mRNA polyadenylation, RNA editing, and tRNA maturation are presented. We also consider new suggestions concerning the endosymbiont hypothesis and evolution of mitochondria. These novel considerations may yield important clues for the further analysis of the plant mitochondrial genetic system. Conversely, an increasing knowledge about the mechanisms and components of the organellar genetic system might reveal new aspects of the evolutionary history of mitochondria.

Organellar RNA polymerases of higher plants

The nuclear genome of the model plant Arabidopsis thaliana contains a small gene family consisting of three genes encoding RNA polymerases of the single-subunit bacteriophage type. There is evidence that similar gene families also exist in other plants. Two of these RNA polymerases are putative mitochondrial enzymes, whereas the third one may represent the nuclear-encoded RNA polymerase (NEP) active in plastids. In addition, plastid genes are transcribed from another, entirely different multisubunit eubacterial-type RNA polymerase, the core subunits of which are encoded by plastid genes [plastid-encoded RNA polymerase (PEP)]. This core enzyme is complemented by one of several nuclear-encoded sigma-like factors. The development of photosynthetically active chloroplasts requires both PEP and NEP. Most NEP promoters show certain similarities to mitochondrial promoters in that they include the sequence motif 5'-YRTA-3' near the transcription initiation site. PEP promoters are similar to bacterial promoters of the -10/-35 sigma 70 type.

Continuous primary sequence requirements in the 18-nucleotide promoter of dicot plant mitochondria

The nucleotide requirements of mitochondrial promoters of dicot plants were studied in detail in a pea in vitro transcription system. Deletions in the 5' regions of three different transcription initiation sites from pea, soybean, and Oenothera identified a crucial AT-rich sequence element (AT-Box) comprising nucleotide positions -14 to -9 relative to the first transcribed nucleotide. Transversion of the AT-Box sequence to comple- mentary nucleotide identities results in an almost complete loss of promoter activity, suggesting that primary structure rather than a simple accumulation of adenines and thymidines in this region is essential for promoter activity. This promoter segment thus appears to be involved in sequence specific binding of a respective protein factor(s) rather than merely loosening and melting the DNA helix during or for an initiation event. Manipulation of nucleotide identities in the 3' portion of the pea atp9 promoter and the respective 3'-flanking region revealed that essential sequences extend to positions +3/+4 beyond this transcription start site. Efficient transcription initiation at an 18-base pair promoter sequence ranging from nucleotide positions -14 to +4 integrated into different sequence contexts shows this element to be sufficient for autonomous promoter function independent of surrounding sequences.

Compilation and analysis of plant mitochondrial promoter sequences: An illustration of a divergent evolution between monocot and dicot mitochondria

We have analyzed 67 sequences surrounding transcription initiation sites identified in higher plant mitochondria. The sequences were classified, independently for monocots and dicots, according to the presence of the CRTA core element found upstream of the first transcribed nucleotide and previously reported as an essential element of plant mitochondrial consensus promoters. This compilation provides new elements concerning the structure of consensus promoters and the relative importance of non-conserved promoters in plant mitochondria. It can be emphasized that promoter regions exhibit several differences between monocot and dicot mitochondria, presumably reflecting a divergent evolution: The sequences classified among consensus promoters as well as the distance between the first transcribed nucleotide and the core element are highly conserved in dicots while more plasticity is observed in monocots. It also appears that the proportion of promoters with neither the conserved promoter sequence nor any conserved motif is far greater in dicots than in monocots.

Evolution of a mitochondrial tRNA PHE gene in A. thaliana: import of cytosolic tRNA PHE into mitochondria

Previously we have described a putative tRNATyr in Arabidopsis thaliana mitochondria, the sequence of which is different from that of other plant mitochondrial tRNATyr genes. We show here that this tRNATyr gene sequence is present in several copies in the mitochondrial genome of A. thaliana. One copy of these tRNATyr gene sequences, termed here tRNATyr-1, could encode a functional tRNA. Expression analysis has shown that the tRNATyr-1 gene is cotranscribed with the downstream tRNAGlu gene, and that the corresponding mature-sized tRNA is present in mitochondria. We also show that the native tRNATyr gene, similar to the mitochondrial tRNATyr genes found in plants, is present in the A. thaliana mitochondrial genome and expressed. The tRNATyr-1 gene has been previously suggested to be derived from a tRNAPhe gene sequence. We show here that, as a consequence, there is no tRNAPhe gene in the mitochondrial genome of A. thaliana and that a cytosolic tRNAPhe is imported in A. thaliana mitochondria.

Transcription initiation sites for sorghum mitochondrial atp9 are positioned immediately 3' to trnfM

Sorghum mitochondrial atp9 is polymorphic among male-sterile cytoplasms, but each cytoplasm is characterized by a major 650 nt transcript, regardless of fertility status. The gene is positioned 323 bp 3' to trnfM. Primer extension revealed multiple atp9 5' transcript termini, distributed from +1 to +28 3' to trnfM; the termini could be labeled with polynucleotide kinase, suggesting that they result from the maturation of trnfM. Guanylyltransferase experiments, however, showed that four of the termini were capable. The juxtaposition of a putative promoter 3' to trnfM results in a unique atp9 transcript population consisting of primary and processed transcripts.

A promoter element active in run-off transcription controls the expression of two cistrons of nad and rps genes in Nicotiana sylvestris mitochondria

The expression of two mitochondrial gene clusters (orf87-nad3-nad1/A and orf87-nad3-rps12) was studied in Nicotiana sylvestris. 5' and 3' termini of transcripts were mapped by primer extension and nuclease S1 protection. Processing and transcription initiation sites were differentiated by in vitro phosphorylation and capping experiments. A transcription initiation site, present in both gene clusters, was found 213 nucleotides upstream of orf87. This promoter element matches the consensus motif for dicotyledonous mitochondrial promoters and initiates run-off transcription in a pea mitochondrial purified protein fraction. Processing sites were identified 5' of nad3, nad1/A and rps12 respectively. These results suggest that (i) the expression of the two cistrons is only controlled by one duplicated promoter element, and (ii) multiple processing events are required to produce monocistronic nad3, nad1/A and rps12 transcripts.

Regulation of gene expression in plant mitochondria

Many genes is plant mitochondria have been analyzed in the past 15 years and regulatory processes controlling gene expression can now be investigated. In vitro systems capable of initiating transcription faithfully at promoter sites have been developed for both monocot and dicot plants and will allow the identification of the interacting nucleic acid elements and proteins which specify and guide transcriptional activities. Mitochondrial activity, although required in all plant tissues, is capable of adapting to specific requirements by regulated gene expression. Investigation of the factors governing the quality and quantity of distinct RNAs will define the extent of interorganelle regulatory interference in mitochondrial gene expression.

A single editing event is a prerequisite for efficient processing of potato mitochondrial phenylalanine tRNA

In bean, potato, and Oenothera plants, the C encoded at position 4 (C4) in the mitochondrial tRNA Phe GAA gene is converted into a U in the mature tRNA. This nucleotide change corrects a mismatched C4-A69 base pair which appears when the gene sequence is folded into the cloverleaf structure. C-to-U conversions constitute the most common editing events occurring in plant mitochondrial mRNAs. While most of these conversions introduce changes in the amino acids specified by the mRNA and appear to be essential for the synthesis of functional proteins in plant mitochondria, the putative role of mitochondrial tRNA editing has not yet been defined. Since the edited form of the tRNA has the correct secondary and tertiary structures compared with the nonedited form, the two main processes which might be affected by a nucleotide conversion are aminoacylation and maturation. To test these possibilities, we determined the aminoacylation properties of unedited and edited potato mitochondrial tRNAPhe in vitro transcripts, as well as the processing efficiency of in vitro-synthesized potato mitochondrial tRNAPhe precursors. Reverse transcription-PCR amplification of natural precursors followed by cDNA sequencing was also used to investigate the influence of editing on processing. Our results show that C-to-U conversion at position 4 in the potato mitochondrial tRNA Phe GAA is not required for aminoacylation with phenylalanine but is likely to he essential for efficient processing of this tRNA.

Transcript mapping and processing of mitochondrial RNA in the chlorophyte alga Prototheca wickerhamii

The detailed transcript map of the circular 55328 bp mitochondrial (mt) genome from the colourless chlorophycean alga Prototheca wickerhamii has been determined. On each half of this genome the genes are encoded only on one DNA strand, forming transcriptional units comprising variable numbers of genes. With the exception of four genes coding for ribosomal proteins, transcripts of the three rRNA genes and all protein-coding genes have been detected by both northern analysis and primer extension experiments. Polycistronic transcripts of protein coding and tRNA genes were verified by northern analyses, primer extension and RNAse mapping experiments. The 5' and 3' ends of different RNA species are often located in close proximity to putative stem-loop structures and some 5' termini of mRNAs coincide with the 3' end of tRNAs located immediately upstream. Transcript mapping in a putative promoter region revealed two different possible transcription initiation sites; no significant sequence homology to putative mt promoters from higher plants could be found. In addition, two out of three group I introns residing in the cox1 gene were found to be self-splicing in vitro under reaction conditions developed for related mt introns from a filamentous fungus. Mitochondrial gene expression of P. wickerhamii and of filamentous fungi has several features in common, such as intron splicing and the processing of longer polycistronic transcripts. The similarities in RNA maturation between higher-plant and P. wickerhamii mitochondria are less pronounced, since plants rarely use tRNAs as processing signals for their relatively short mitochondrial co-transcripts.

Characterization of the potato mitochondrial transcription unit containing 'native' trnS (GCU), trnF (GAA) and trnP (UGG)

In order to identify the sequences promoting the expression of plant mitochondrial tRNA genes, we have characterized the trnS (GCU), trnF (GAA) and trnP (UGG) transcription unit of the potato mitochondrial genome. These three tRNA genes were shown to be co-transcribed as a 1800 nt long primary transcript. The transcription initiation site located 305 to 312 nt upstream of trnS is surrounded by a purine-rich region but does not contain the consensus motif proposed as a promoter element in dicotyledonous plants. Differential labelling of potato mitochondrial RNA with either guanylyltransferase or T4 polynucleotide kinase suggests that this site corresponds to the unique functional region responsible for the transcription of the three tRNA genes. The initiation site recently found upstream of Oenothera mitochondrial trnF does not seem to be used in potato mitochondria, although a very similar sequence is present 317 nt upstream of the corresponding potato gene. Major processing sites were identified at the 3' end of each tRNA gene. Another processing site, surrounded by a double hairpin structure, is located 498 nt downstream of trnP in stretch of 10 A residues. As judged from northern experiments, this region is close to the determination site of this transcription unit.

RNA editing is required for efficient excision of tRNA(Phe) from precursors in plant mitochondria

RNA editing corrects a 4C-A69 mismatch to a conventional 4T-A69 Watson-Crick base pair in the acceptor stem of the mitochondrially encoded tRNAPhe in plants. In vitro processing of edited and unedited Oenothera tRNA Phe precursor RNAs with pea mitochondrial protein extracts shows a significant effect of this RNA-editing event on the efficiency of 5' and 3' processing. While mature tRNA molecules are rapidly generated by in vitro processing from edited precursors, the formation of mature tRNAs from unedited pre-tRNAs is considerably reduced. Primer extension analyses of in vitro processing products show that processing at both 5' and 3' termini is governed by the RNA-editing event. Investigation of edited and unedited precursor RNAs by lead cleavage experiments reveals differences in the higher order structures of the pre-tRNAs. The differing conformations are most likely responsible for the altered processing efficiencies of edited and unedited precursor molecules. RNA editing of the tRNAPhe precursors is thus a prerequisite for efficient excision of the mature tRNAPhe in vitro. Hence RNA editing might be involved in regulating the amount of mature tRNAPhe in the steady state RNA pool of mitochondria in higher plants.

Identification and mapping of tRNA genes on the Helianthus annuus mitochondrial genome

The physical map for seventeen tRNA genes on the mitochondrial genome of the dicotyledonous plant Helianthus annuus has been established. Eleven are genuine mitochondrial genes, while the other six show a high degree of similarity with the chloroplast counterparts. The genes, with the exception of the genuine trnS(GCT) and of the chloroplast-like trnV and trnP, are expressed. The comparison of the organization of some tRNA genes in the H. annuus mitochondrial genome with that of similar genes detectable in other plants reveals that their association is common to several dicotyledons.

Editing and import: strategies for providing plant mitochondria with a complete set of functional transfer RNAs

The recombinations and mutations that plant mitochondrial DNA has undergone during evolution have led to the inactivation or complete loss of a number of the 'native' transfer RNA genes deriving from the genome of the ancestral endosymbiont. Following sequence divergence in their genes, some native mitochondrial tRNAs are 'rescued' by editing, a post-transcriptional process which changes the RNA primary sequence. According to in vitro studies with the native mitochondrial tRNA(Phe) from potato and tRNA(His) from larch, editing is required for efficient processing. Some of the native tRNA genes which have been inactivated or lost have been replaced by tRNA genes present in plastid DNA sequences acquired by the mitochondrial genome during evolution, which raises the problem of the transcriptional regulation of tRNA genes in plant mitochondria. Finally, tRNAs for which no gene is present in the mitochondrial genome are imported from the cytosol. This process is highly specific for certain tRNAs, and it has been suggested that the cognate aminoacyl-tRNA synthetases may be responsible for this specificity. Indeed, a mutation which blocks recognition of the cytosolic Arabidopsis thaliana tRNA(Ala) by the corresponding alanyl-tRNA synthetase also prevents mitochondrial import of this tRNA in transgenic plants. Conversely, no significant mitochondrial co-import of the normally cytosol-specific tRNA(Asp) was detected in transgenic plants expressing the yeast cytosolic aspartyl-tRNA synthetase fused to a mitochondrial targeting sequence, suggesting that, although necessary, recognition by a cognate aminoacyl-tRNA synthetase might not be sufficient to allow tRNA import into plant mitochondria.

A novel pea mitochondrial in vitro transcription system recognizes homologous and heterologous mRNA and tRNA promoters

To elucidate the mechanism involved in the transcription initiation process in mitochondria of dicotyledonous plants, an in vitro transcription system was established for pea (Pisum sativum L.). The partially purified mitochondrial protein extract initiates transcription on homologous pea templates as well as on heterologous mitochondrial DNA from other dicot plant species. In vitro transcription begins within the nonanucleotide 5'-(-7)CRTAAGAGA(+2)-3' (transcription start site is underlined) conserved at most of the identified transcription initiation sites in dicot plant mitochondria. The in vitro initiation at promoters of protein as well as of tRNA coding genes indicates a common mode of transcription initiation for different types of RNA. The competent recognition of different heterologous templates supports a general functional role of the conserved nonanucleotide within mitochondrial promoters of dicotyledonous plants. Initial studies of the promoter structure by deletion analysis in the 5' region of the pea atp9 promoter show that in addition to the conserved nonanucleotide, which is essential for transcription initiation in vitro, sequences up to 25 nucleotides upstream of the transcription start site are necessary for an efficient initiation event.

Mitochondrial transcription initiation: promoter structures and RNA polymerases

A diversity of promoter structures. It is evident that tremendous diversity exists between the modes of mitochondrial transcription initiation in the different eukaryotic kingdoms, at least in terms of promoter structures. Within vertebrates, a single promoter for each strand exists, which may be unidirectional or bidirectional. In fungi and plants, multiple promoters are found, and in each case, both the extent and the primary sequences of promoters are distinct. Promoter multiplicity in fungi, plants and trypanosomes reflects the larger genome size and scattering of genes relative to animals. However, the dual roles of certain promoters in transcription and replication, at least in yeast, raises the interesting question of how the relative amounts of RNA versus DNA synthesis are regulated, possibly via cis-elements downstream from the promoters. Mitochondrial RNA polymerases. With respect to mitochondrial RNA polymerases, characterization of human, mouse, Xenopus and yeast enzymes suggests a marked degree of conservation in their behavior and protein composition. In general, these systems consist of a relatively non-selective core enzyme, which itself is unable to recognize promoters, and at least one dissociable specificity factor, which confers selectivity to the core subunit. In most of these systems, components of the RNA polymerase have been shown to induce a conformational change in their respective promoters and have also been assigned the role of a primase in the replication of mtDNA. While studies of the yeast RNA polymerase have suggested it has both eubacterial (mtTFB) and bacteriophage (RPO41) origins, it is not yet clear whether these characteristics will be conserved in the mitochondrial RNA polymerases of all eukaryotes. mtTFA-mtTFB; conserved but dissimilar functions. With respect to transcription factors, mtTFA has been found in both vertebrates and yeast, and may be a ubiquitous protein in mitochondria. However, the divergence in non-HMG portions of the proteins, combined with differences in promoter structure, has apparently relegated mtTFA to alternative, or at least non-identical, physiological roles in vertebrates and fungi. The relative ease with which mtTFA can be purified (Fisher et al. 1991) suggests that, where present, it should be facile to detect. mtTFB may represent a eubacterial sigma factor adapted for interaction with the mitochondrial RNA polymerase.(ABSTRACT TRUNCATED AT 400 WORDS)

A small repeated sequence contains the transcription initiation sites for both trnfM and rrn26 in rice mitochondria

The 76 bp sequence found in the upstream region of a gene for 26S rRNA (rrn26) is duplicated in the upstream region of a gene for initiator methionine tRNA (trnfM) in the mitochondrial genome of rice. An in vitro capping/ribonuclease protection assay and primer extension analysis demonstrated that the transcription of trnfM and of rrn26, which are at least 190 kb from one another in the rice mitochondrial genome, starts from these same sequences in the upstream regions of the respective genes. This result indicates that the short sequence that is duplicated in the upstream regions of trnfM and rrn26 in rice mtDNA is recognized as the promoter of each respective gene.

Identification and mapping of trnI, trnE and trnfM genes in the sunflower mitochondrial genome

Three sunflower mitochondrial HindIII restriction fragments containing the tRNA genes trnI, trnE and trnfM have been sequenced. The genes are present in single copy on the whole genome and are transcribed. Hybridization experiments and sequence analysis of the HindIII fragments allowed the precise mapping and orientation of each gene on the sunflower mitochondrial genome.

Transcription of potato mitochondrial 26S rRNA is initiated at its mature 5' end

Transcription initiation sites in plant mitochondria can be located by in vitro capping of primary 5' transcript termini. Direct sequencing of a cap-labelled mitochondrial RNA from potato shows its sequence to be identical to the 5' terminal part of the 26S rRNA. Primer extension analysis indicates the mature 5' end to be the sole detectable 5' transcript terminus. In potato mitochondria the mature 5' end of the 26S rRNA is thus created by transcription initiation without any further 5' processing. The nucleotide sequence surrounding this transcription initiation site shows only limited similarity to other putative promoter sequences from dicot plant mitochondria suggesting the possibility that divergent RNA polymerases, and/or transcription initiation factors, are present in plant mitochondria.

RNA editing of tRNA(Phe) and tRNA(Cys) in mitochondria of Oenothera berteriana is initiated in precursor molecules

We have analyzed the role of RNA editing in the correction of mismatched base pairs in tRNA secondary structures in mitochondria of the flowering plant Oenothera berteriana. Comparison of genomic and cDNA sequences from unprocessed primary transcripts of the newly characterized genes for tRNA(Cys), tRNA(Asn) and tRNA(Ile) and the previously described gene for tRNA(Phe) revealed single nucleotide discrepancies in the tRNA(Cys) and tRNA(Phe) sequences. While the change in the anticodon stem of tRNA(Cys) alters a C-T to a T-T mismatch, the nucleotide transition in the tRNA(Phe) restores a conventional T-A Watson-Crick base pair, replacing a C-A mismatch in the acceptor stem. Since both nucleotide alterations are conversions from genomic cytidines to thymidines in the cDNA (uridines in the tRNAs), they are attributed to RNA editing, which is observed in nearly all mRNAs from plant mitochondria.