Sequence of histidyl tRNA, present as a chloroplast insert in mtDNA ofZea mays

Rapid shifts in mitochondrial tRNA import in a plant lineage with extensive mitochondrial tRNA gene loss

In most eukaryotes, transfer RNAs (tRNAs) are one of the very few classes of genes remaining in the mitochondrial genome, but some mitochondria have lost these vestiges of their prokaryotic ancestry. Sequencing of mitogenomes from the flowering plant genus Silene previously revealed a large range in tRNA gene content, suggesting rapid and ongoing gene loss/replacement. Here, we use this system to test longstanding hypotheses about how mitochondrial tRNA genes are replaced by importing nuclear-encoded tRNAs. We traced the evolutionary history of these gene loss events by sequencing mitochondrial genomes from key outgroups (Agrostemma githago and Silene [=Lychnis] chalcedonica). We then performed the first global sequencing of purified plant mitochondrial tRNA populations to characterize the expression of mitochondrial-encoded tRNAs and the identity of imported nuclear-encoded tRNAs. We also confirmed the utility of high-throughput sequencing methods for the detection of tRNA import by sequencing mitochondrial tRNA populations in a species (Solanum tuberosum) with known tRNA trafficking patterns. Mitochondrial tRNA sequencing in Silene revealed substantial shifts in the abundance of some nuclear-encoded tRNAs in conjunction with their recent history of mt-tRNA gene loss and surprising cases where tRNAs with anticodons still encoded in the mitochondrial genome also appeared to be imported. These data suggest that nuclear-encoded counterparts are likely replacing mitochondrial tRNAs even in systems with recent mitochondrial tRNA gene loss, and the redundant import of a nuclear-encoded tRNA may provide a mechanism for functional replacement between translation systems separated by billions of years of evolutionary divergence.

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.

Identification and structural characterization of nucleus-encoded transfer RNAs imported into wheat mitochondria

Despite its large size (200-2400 kilobase pairs), the mitochondrial genome of angiosperms does not encode the minimal set of tRNAs required to support mitochondrial protein synthesis. Here we report the identification of cytosolic-like tRNAs in wheat mitochondria using a method involving quantitative hybridization to distinguish among three tRNA classes: (i) those encoded by mitochondrial DNA (mtDNA) and localized in mitochondria, (ii) those encoded by nuclear DNA and located in the cytosol, and (iii) those encoded by nuclear DNA and found in both the cytosol and mitochondria. The latter class comprises tRNA species that are considered to be imported into mitochondria to compensate for the deficiency of mtDNA-encoded tRNAs. In a comprehensive survey of the wheat mitochondrial tRNA population, we identified 14 such imported tRNAs, the structural characterization of which is presented here. These imported tRNAs complement 16 mtDNA-encoded tRNAs, for a total of at least 30 distinct tRNA species in wheat mitochondria. Considering differences in the set of mtDNA-encoded and imported tRNAs in the mitochondria of various land plants, the import system must be able to adapt relatively rapidly over evolutionary time with regard to the particular cytosolic-like tRNAs that are brought into mitochondria.

Striking differences in mitochondrial tRNA import between different plant species

A systematic comparison of the tRNAs imported into the mitochondria of larch, maize and potato reveals considerable differences among the three species. Larch mitochondria import at least eleven different tRNAs (more than half of those tested) corresponding to ten different amino acids. For five of these tRNAs [tRNA(Phe(GAA)), tRNA(Lys(CUU)), tRNA(Pro(UGG)), tRNA(Ser(GCU)) and tRNA(Ser(UGA))] this is the first report of import into mitochondria in any plant species. There are also differences in import between relatively closely related plants; wheat mitochondria, unlike maize mitochondria import tRNA(His), and sunflower mitochondria, unlike mitochondria from other angiosperms tested, import tRNA(Ser(GCU)) and tRNA(Ser(UGA)). These results suggest that the ability to import each tRNA has been acquired independently at different times during the evolution of higher plants, and that there are few apparent restrictions on which tRNAs can or cannot be imported. The implications for the mechanisms of mitochondrial tRNA import in plants are discussed.

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.

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.

Evolutionary variations in DNA sequences transferred from chloroplast genomes to mitochondrial genomes in the Gramineae

The transfer of fragments of DNA from chloroplast genomes to mitochondrial genomes is considered to be a general phenomenon in higher plants. In the present study, Southern hybridization, together with amplification by PCR and DNA sequencing techniques, was used to examine the regions homologous to chloroplast rps19 in the mitochondrial genomes of several gramineous plants. In all the mitochondrial DNAs from the gramineous plants examined, except for that from wheat, the transferred fragments of chloroplast DNA were found to be maintained and the same junctions of mitochondrion-specific and chloroplast-like sequences were found at one terminus. This finding indicates that the transfer of the chloroplast sequence occurred in the distant past during the evolution of gramineous plants. Subsequent analysis revealed that the fragments had been variously rearranged among species with respect to the other terminus. Considering the current diversity of this one particular transferred fragment of chloroplast DNA, we propose that chloroplast-derived DNA sequences that have lost their original functions tend to be rearranged during evolution in mitochondrial genomes.

Identification of the entire set of transferred chloroplast DNA sequences in the mitochondrial genome of rice

The entire set of transferred chloroplast DNA sequences in the mitochondrial genome of rice (Oryza sativa cv. Nipponbare) was identified using clone banks that cover the chloroplast and mitochondrial genomes. The mitochondrial fragments that were homologous to chloroplast DNA were mapped and sequenced. The nucleotide sequences around the termini of integrated chloroplast sequences in the rice mtDNA revealed no common sequences or structures that might enhance the transfer of DNA. Sixteen chloroplast sequences, ranging from 32 bases to 6.8 kb in length, were found to be dispersed throughout the rice mitochondrial genome. The total length of these sequences is equal to approximately 6% (22 kb) of the rice mitochondrial genome and to 19% of the chloroplast genome. The transfer of segments of chloroplast DNA seems to have occurred at different times, both before and after the divergence of rice and maize. The mitochondrial genome appears to have been rearranged after the transfer of chloroplast sequences as a result of recombination at these sequences. The rice mitochondrial DNA contains nine intact tRNA genes and three tRNA pseudogenes derived from the chloroplast genome.

Structure and expression of tomato mitochondrial genes coding for tRNA(Cys) (GCA), tRNA(Asn) (GUU) and tRNA(Tyr) (GUA): a native tRNA(Cys) gene is present in dicot plants but absent in monocot plants

The nucleotide sequences of tRNA(Asn) (GUU) and tRNA(Tyr) (GUA) genes from tomato mitochondria and their flanking regions have been determined. The tomato mitochondrial tRNA(Asn) gene is located 2.1 kb downstream from the tRNA(Cys) gene reported previously (Izuchi and Sugita 1989) and shows a nearly complete identity with the corresponding chloroplast gene. The tRNA(Tyr) gene, which shows only 73% homology with the corresponding chloroplast gene, has to be considered a "native" mitochondrial tRNA gene and is 535 bp from the "chloroplast-like" tRNA(Asn) gene on the same strand. Northern hybridization analysis revealed that the three tRNA genes are transcribed in tomato mitochondria. Southern hybridization analysis of tomato, sugar beet. rice and wheat mitochondrial DNAs, with oligonucleotide probes for mitochondrial or chloroplast tRNA genes, demonstrated that the mitochondrial tRNA(Cys) gene found in tomato is present in dicot plants but not in monocots. On the other hand, a chloroplast-like tRNA(Cys) gene exists in monocot plants.

Genes for tRNA(Gly), tRNA(His), tRNA(Lys), tRNA(Phe), tRNA(Ser) and tRNA(Tyr) are encoded in Oenothera mitochondrial DNA

The genes coding for tRNA(Gly), tRNA(His), tRNA(Lys), tRNA(Phe), tRNA(Ser) and tRNA(Tyr) have been identified in Oenothera mitochondrial DNA. Sequence analysis of these genes and their surrounding sequences are presented and compared with other known tRNA genes from plant mitochondria. All six deduced tRNA sequences can be folded into the classical cloverleaf structure model. Only the tRNA(His) gene shows high homology with the corresponding chloroplast gene and thus appears to be derived from a transfer event of chloroplast sequences into the mitochondrial genome. The sequences surrounding this gene, however, show little similarity with the chloroplast genome. The other five deduced tRNAs display a much lower similarity with their chloroplast counterparts and thus appear to be genuine mitochondrial tRNAs. These tRNAs are highly conserved between monocots and dicots with maximally three nucleotides differing between the Oenothera sequences and their wheat homologues. A purine-rich sequence is found upstream of each tRNA gene in Oenothera, similar to wheat mitochondrial tRNA genes, that could be involved in transcription signalling.

Sequence analysis of the tRNA(Tyr) and tRNA(Lys) genes and evidence for the transcription of a chloroplast-like tRNA(Met) in maize mitochondria

The nucleotide sequences of three tRNA genes and their flanking regions from the maize mitochondrial genome is reported. These genes, which are located in the same region of the genome between the 14-kb inverted repeats, are transcribed in the mitochondria and code for tRNA(Lys) (anticodon UUU) tRNA(Met) (CAU) and tRNA(Tyr) (GUA). The very high homology shown by the tRNA(Met) gene with its chloroplast counterpart indicates that it probably originates from a chloroplast DNA insertion. The analysis of the upstream regions of these genes showed that the tRNA(Tyr) and the tRNA(Lys) genes possess the consensus sequence AAGAANRR, which could act as a promoter sequence in higher plant mitochondria.

Sequence and transcriptional analysis of a chloroplast insert in the mitochondrial genome of Zea mays

The complete sequence of a mitochondrial DNA insertional event containing the 3' portion of the chloroplast 23S-4.5S rRNA gene, the entire 5S rRNA gene and intervening sequence and all but the 3' 6 nucleotides of the arginine tRNA gene is reported. Also reported are both chloroplast/mitochondrial DNA junction sequences, 551 nucleotides of flanking mitochondrial sequences and the genomic location of this insert in Zea mays mitochondria. Utilizing the distinctive transcriptional pattern seen for mitochondrial RNA derived from root tissue relative to shoot tissue, we also reported a general experimental test for whether chloroplast sequences transposed to the mitochondrion are transcribed. Although results for the insert reported suggest it is transcriptionally inactive, the technique should be generally applicable to any transposed sequence.

Genes for tRNA(Asp), tRNA (Pro), tRNA (Tyr) and two tRNAs (Ser) in wheat mitochondrial DNA

We have begun a systematic search for potential tRNA genes in wheat mtDNA, and present here the sequences of regions of the wheat mitochondrial genome that encode genes for tRNA(Asp) (anticodon GUC), tRNA(Pro) (UGG), tRNA(Tyr) (GUA), and two tRNAs(Ser) (UGA and GCU). These genes are all solitary, not immediately adjacent to other tRNA or known protein coding genes. Each of the encoded tRNAs can assume a secondary structure that conforms to the standard cloverleaf model, and that displays none of the structural aberrations peculiar to some of the corresponding mitochondrial tRNAs from other eukaryotes. The wheat mitochondrial tRNA sequences are, on average, substantially more similar to their eubacterial and chloroplast counterparts than to their homologues in fungal and animal mitochondria. However, an analysis of regions ∼ 150 nucleotides upstream and ∼ 100 nucleotides downstream of the tRNA coding regions has revealed no obvious conserved sequences that resemble the promoter and terminator motifs that regulate the expression of eubacterial and some chloroplast tRNA genes. When restriction digests of wheat mtDNA are probed with (32)P-labelled wheat mitochondrial tRNAs, <20 hybridizing bands are detected, whether enzymes with 4 bp or 6 bp recognition sites are used. This suggests that the wheat mitochondrial genome, despite its large size, may carry a relatively small number of tRNA genes.

Presence of a chloroplast-like elongator tRNAMet gene in the mitochondrial genomes of soybean and Arabidopsis thaliana

The nucleotide sequence of elongator tRNA(Met) genes from soybean chloroplast and mitochondria and Arabidopsis thaliana mitochondria have been determined. The mitochondrial tRNA(Met) genes from soybean and A. thaliana are identical, and they differ from the soybean chloroplast tRNA(Met) gene by only four nucleotides. Analysis of the flanking regions indicates that the mitochondrial tRNA(Met) gene is not present on a large chloroplast DNA insertion in the mitochondrial genome, but it suggests that they have a common origin. Comparison of the three genes and the evolutionary implications are discussed.

Location and nucleotide sequence of two tRNA genes and a tRNA pseudo-gene in the maize mitochondrial genome: evidence for the transcription of a chloroplast gene in mitochondria

We report the nucleotide sequence of three tRNA genes from maize mitochondria. The genes are located in two BamHI fragments, 3.55 and 5.7 kb long, adjacent to the S2 sequence in the maize mitochondrial genome. On the 3.55 kb BamHI fragment, we have characterized a tRNA(Cys)(GCA) gene. A strong sequence homology of this tRNA(Cys)(GCA) gene with its chloroplast counterpart in wheat suggests that it may be part of a chloroplast DNA insertion into the mitochondrial genome. This gene has been found to be transcribed in the mitochondrion. Two tRNA genes are located on the 5.7 kb BamHI fragment, separated from each other by 250 bp. One is a mitochondrial tRNA(Ser)(GCU) gene. The other, a non-transcribed tRNA(Phe)-like gene, is interrupted by a 49 base-pair inserted DNA sequence in the variable loop and has a Leu (UAA) anticodon.

Homology in the region containing a tRNA(Trp) gene and a (complete or partial) tRNA(Pro) gene in wheat mitochondrial and chloroplast genomes

We have used bean mitochondrial (mt) and chloroplast (cp) tRNA(Trp) as probes to locate the corresponding genes on the mt and cp genomes of wheat and we have determined the nucleotide sequences of the wheat mt and cp tRNA(Trp) genes and of the flanking regions. Sequence comparisons show that the wheat mt and cp tRNA(Trp) genes are 97% homologous. On the wheat cp DNA, a tRNA(UGGPro) gene was found 139 bp upstream of the cp tRNA(Trp) gene. On the wheat mt DNA, a sequence of 23 nucleotides completely homologous with the 3' end of this cp tRNA(Pro) gene was found 136 bp upstream of the mt tRNA(Trp) gene, but there is only 38% homology between cp and mt wheat genomes in the intergenic regions. The overall organization of this region in the chloroplast genome (a tRNA(Trp) gene separated by about 140 bp from a tRNA(Pro) gene) is also found in the mitochondrial genome, suggesting that this mitochondrial fragment might have originated from a chloroplast DNA insertion. A comparison of the genes and of the intergenic regions located between the tRNA(Trp) gene and the tRNA(Pro) (or partial tRNA(Pro)) gene shows that there is an almost complete conservation of these sequences in the mitochondrial DNA of wheat and maize, whereas wheat mt and cp intergenic regions show more sequence divergence. Wheat mt tRNA(Trp) gene is encoded by the main mt genome (accounted for by the master chromosome) but, in the case of maize mitochondria, this gene was found to be encoded by the 2.3 kb linear plasmid, indicating that this plasmid is not dispensable in maize mitochondria.

Sequences of initiator and elongator methionine tRNAs in bean mitochondria : Localization of the corresponding genes on maize and wheat mitochondrial genomes

Two bean mitochondria methionine transfer RNAs, purified by RPC-5 chromatography and two-dimensional gel electrophoresis, have been sequenced usingin vitro post-labeling techniques.One of these tRNAs(Met) has been identified by formylation using anE. coli enzyme as the mitochondrial tRNAF (Met). It displays strong structural homologies with prokaryotic and chloroplast tRNAF (Met) sequences (70.1-83.1%) and with putative initiator tRNAm (Met) genes described for wheat, maize andOenothera mitochondrial genomes (88.3-89.6%).The other tRNA(Met), which is the mitochondrial elongator tRNAF (Met), shows a high degree of sequence homology (93.3-96%& with chloroplast tRNAm (Met), but a weak homology (40.7%) with a sequenced maize mitochondrial putative elongator tRNAm (Met) gene.Bean mitochondrial tRNAF (Met) and tRNAm (Met) were hybridized to Southern blots of the mitochondrial genomes of wheat and maize, whose maps have been recently published (15, 22), in order to locate the position of their genes.

Sequences of two bean mitochondria tRNAs(Tyr) which differ in the level of post-transcriptional modification and have a prokaryotic-like large extra-loop

Two bean mitochondrial tRNAs(Tyr) purified by RPC-5 chromatography and two-dimensional gel electrophoresis have been sequenced using post-labeling techniques. These two tRNAs only differ by three post-transcriptional modifications in the D-loop. They have a large variable loop and therefore resemble prokaryotic tRNAs(Tyr) rather than eukaryotic cytoplasmic tRNAs(Tyr).