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

A rapid PCR procedure for the specific identification of Lactobacillus sanfranciscensis, based on the 16S-23S intergenic spacer regions

AIMS

The organization of ribosomal RNA (rrn) operons in Lactobacillus sanfranciscensis was studied in order to establish an easy-to-perform method for identification of L. sanfranciscensis strains, based on the length and sequence polymorphism of the 16S-23S rDNA intergenic spacer region (ISR).

METHODS AND RESULTS

PCR amplification of the 16S-23S rDNA ISRs of L. sanfranciscensis gave three products distinguishing this micro-organism from the remaining Lactobacillus species. Sequence analysis revealed that two of the rrn operons were organized as in previously reported lactobacilli: large spacer (L-ISR), containing tRNA(Ile) and tRNA(Ala) genes; small spacer (S-ISR) without tRNA genes. The third described spacer (medium, M-ISR), original for L. sanfranciscensis, harboured a tRNA-like structure. An oligonucleotide sequence targeting the variable region between tDNA(Ile) and tDNA(Ala) of L. sanfranciscensis L-ISR was approved to be suitable in species-specific identification procedure. Analysis by pulse-field gel electrophoresis of the chromosomal digest with the enzyme I-CeuI showed the presence of seven rrn clusters. Lactobacillus sanfranciscensis genome size was estimated at c. 1.3 Mb.

CONCLUSIONS

Direct amplification of 16S-23S ISRs or PCR with specific primer derived from L-ISR showed to be useful for specific typing of L. sanfranciscensis. This was due to the specific rrn operon organization of L. sanfranciscensis strains.

SIGNIFICANCE AND IMPACT OF THE STUDY

In this paper, we have reported a rapid procedure for L. sanfranciscensis identification based on specific structures found in its rrn operon.

Genomic reduction and evolution of novel genetic membranes and protein-targeting machinery in eukaryote-eukaryote chimaeras (meta-algae)

Chloroplasts originated just once, from cyanobacteria enslaved by a biciliate protozoan to form the plant kingdom (green plants, red and glaucophyte algae), but subsequently, were laterally transferred to other lineages to form eukaryote-eukaryote chimaeras or meta-algae. This process of secondary symbiogenesis (permanent merger of two phylogenetically distinct eukaryote cells) has left remarkable traces of its evolutionary role in the more complex topology of the membranes surrounding all non-plant (meta-algal) chloroplasts. It took place twice, soon after green and red algae diverged over 550 Myr ago to form two independent major branches of the eukaryotic tree (chromalveolates and cabozoa), comprising both meta-algae and numerous secondarily non-photosynthetic lineages. In both cases, enslavement probably began by evolving a novel targeting of endomembrane vesicles to the perialgal vacuole to implant host porter proteins for extracting photosynthate. Chromalveolates arose by such enslavement of a unicellular red alga and evolution of chlorophyll c to form the kingdom Chromista and protozoan infrakingdom Alveolata, which diverged from the ancestral chromalveolate chimaera. Cabozoa arose when the common ancestor of euglenoids and cercozoan chlorarachnean algae enslaved a tetraphyte green alga with chlorophyll a and b. I suggest that in cabozoa the endomembrane vesicles originally budded from the Golgi, whereas in chromalveolates they budded from the endoplasmic reticulum (ER) independently of Golgi-targeted vesicles, presenting a potentially novel target for drugs against alveolate Sporozoa such as malaria parasites and Toxoplasma. These hypothetical ER-derived vesicles mediated fusion of the perialgal vacuole and rough ER (RER) in the ancestral chromist, placing the former red alga within the RER lumen. Subsequently, this chimaera diverged to form cryptomonads, which retained the red algal nucleus as a nucleomorph (NM) with approximately 464 protein-coding genes (30 encoding plastid proteins) and a red or blue phycobiliprotein antenna pigment, and the chromobiotes (heterokonts and haptophytes), which lost phycobilins and evolved the brown carotenoid fucoxanthin that colours brown seaweeds, diatoms and haptophytes. Chromobiotes transferred the 30 genes to the nucleus and lost the NM genome and nuclear-pore complexes, but retained its membrane as the periplastid reticulum (PPR), putatively the phospholipid factory of the periplastid space (former algal cytoplasm), as did the ancestral alveolate independently. The chlorarachnean NM has three minute chromosomes bearing approximately 300 genes riddled with pygmy introns. I propose that the periplastid membrane (PPM, the former algal plasma membrane) of chromalveolates, and possibly chlorarachneans, grows by fusion of vesicles emanating from the NM envelope or PPR. Dinoflagellates and euglenoids independently lost the PPM and PPR (after diverging from Sporozoa and chlorarachneans, respectively) and evolved triple chloroplast envelopes comprising the original plant double envelope and an extra outermost membrane, the EM, derived from the perialgal vacuole. In all metaalgae most chloroplast proteins are coded by nuclear genes and enter the chloroplast by using bipartite targeting sequences--an upstream signal sequence for entering the ER and a downstream chloroplast transit sequence. I present a new theory for the four-fold diversification of the chloroplast OM protein translocon following its insertion into the PPM to facilitate protein translocation across it (of both periplastid and plastid proteins). I discuss evidence from genome sequencing and other sources on the contrasting modes of protein targeting, cellular integration, and evolution of these two major lineages of eukaryote "cells within cells". They also provide powerful evidence for natural selection's effectiveness in eliminating most functionless DNA and therefore of a universally useful non-genic function for nuclear non-coding DNA, i.e. most DNA in the biosphere, and dramatic examples of genomic reduction. I briefly argue that chloroplast replacement in dinoflagellates, which happened at least twice, may have been evolutionarily easier than secondary symbiogenesis because parts of the chromalveolate protein-targeting machinery could have helped enslave the foreign plastids.

Identification and characterization of the trnS/pseudo-tRNA/nad3/rps12 gene cluster from Coix lacryma-jobi L: organization, transcription and RNA editing

During a study of mitochondrial sequence conservation between the liverwort Marchantia polymorpha and several Angiosperm species, as revealed by heterologous hybridization experiments, the trnS/pseudo-tRNA/nad3/rps12 gene cluster in Coix lacryma-jobi L., an Asian grass species from the Andropogoneae, was identified using the mitochondrial probe orf167 from M. polymorpha. The Coix gene cluster was cloned and sequenced, and its expression analyzed. The gene sequence and gene locus organization were found to be similar to the corresponding cluster in wheat and maize. Northern hybridization and reverse transcription-polymerase chain reaction analyses indicated that nad3 and rps12 genes were co-transcribed as a 1.25 kb RNA molecule. The transcript displayed 20 and six RNA edition sites, in the nad3 and rps12 genes, respectively, that changed the codon identities to amino acids, which are better conserved in different organisms. Twenty-three cDNA clones were analysed for the edition process and revealed different partial editing patterns without apparent sequential processing.

Molecular analysis of a 21.1-kb fragment of wheat chloroplast DNA bearing RNA polymerase subunit (rpo) genes

The entire nucleotide sequence of a 21.1-kb fragment of wheat chloroplast (ct) DNA was determined. This fragment carries 18 intact genes and parts of two additional genes, including the three RNA polymerase genes rpoB, rpoC1, and rpoC2. The gene arrangement of this region is conserved in wheat, rice, and maize, but not in non-grass species. Comparison of these 20 genes in wheat, rice, and maize showed that tRNA genes evolved more slowly than protein-coding genes in the chloroplast genome. Intergenic regions evolved much faster than both types of genes. Although the 19 genes of wheat, except for orf42, showed high identity to those of other plants, there were three novel structural features in the wheat rpoC2 gene; a deletion of 81 bp in the middle region, a variable insertion (408 bp), and a nonsense mutation in the 3' terminal region, resulting in truncation of a sequence of ca. 10 amino acids. An intermolecular recombination between the stretches of CTTAT and CTTTT was suggested as the mechanism of the 81-bp deletion in the wheat rpoC2 gene. Evolutionary distance between the chloroplast genomes of wheat and maize was larger than those between wheat and rice and between rice and maize.

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.

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.

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.

Three mitochondrial unassigned open reading frames of Podospora anserina represent remnants of a viral-type RNA polymerase gene

The mitochondrial DNA of Podospora anserina is complex, consisting of a characteristic set of genes with a large number of introns and a substantial amount of sequence of unknown function and origin. In addition, as indicated by various types of reorganization, this genome is highly flexible. Here we report the identification of three unassigned mitochondrial open reading frames (ORF P', ORF Q', ORF 11) as remnants of a rearranged viral-type RNA polymerase gene. These ORFs are not transcribed and may be derived from the integration of a linear plasmid of the type recently identified in a mutant of P. anserina.

A tRNA(Val) (GAC) gene of chloroplast origin in sunflower mitochondria is not transcribed

A tRNA(Val) (GAC) gene is located in opposite orientation 552 nucleotides (nt) down-stream of the cytochrome oxidase subunit III (coxIII) gene in sunflower mitochondria. The comparison with the homologous chloroplast DNA revealed that the tRNA(Val) gene is part of a 417 nucleotides DNA insertion of chloroplast origin in the mitochondrial genome. No tRNA(Val) is encoded in monocot mitochondrial DNA (mtDNA), whereas two tRNA(Val) species are coded for by potato mtDNA. The mitochondrial genomes of different plant species thus seem to encode unique sets of tRNAs and must thus be competent in importing the missing differing sets of tRNAs.

Editing corrects mispairing in the acceptor stem of bean and potato mitochondrial phenylalanine transfer RNAs

Editing is a general event in plant mitochondrial messenger RNAs, but has never been detected in a plant mitochondrial transfer RNA (tRNA). We demonstrate here the occurrence of a tRNA editing event in higher plant mitochondria: in both bean and potato, the C encoded at position 4 in the mitochondrial tRNA(Phe)(GAA) gene is converted into a U in the mature tRNA. This nucleotide change corrects the mismatched C4-A69 base-pair which appears when folding the gene sequence into the cloverleaf structure and it is consistent with the fact that C to U transitions constitute the common editing events affecting plant mitochondrial messenger RNAs. The tRNA(Phe)(GAA) gene is located upstream of the single copy tRNA(Pro)(UGG) gene in both the potato and the bean mitochondrial DNAs. The sequences of potato and bean tRNA(Pro)(UGG) genes are colinear with the sequence of the mature bean mitochondrial tRNA(Pro)(UGG), demonstrating that this tRNA is not edited. A single copy tRNA(Ser)(GCU) gene was found upstream of the tRNA(Phe) gene in the potato mitochondrial DNA. A U6-U67 mismatched base-pair appears in the cloverleaf folding of this gene and is maintained in the mature potato mitochondrial tRNA(Ser)(GCU), which argues in favour of the hypothesis that the editing system of plant mitochondria can only perform C to U or occasionally U to C changes.

The rice mitochondrial nad3 gene has an extended reading frame at its 5' end: nucleotide sequence analysis of rice trnS, nad3, and rps12 genes

The nucleotide sequences of the tRNASer (trnS), pseudo-tRNA, NADH dehydrogenase subunit 3 (nad3), and ribosomal protein S12 (rps12) genes from rice mitochondrial DNA (mtDNA) were determined. Both trnS and nad3 were confirmed to be single copy genes by Southern blot analysis. The nad3 and rps12 genes were arranged in tandem, and the two were co-transcribed. The order of the above four genes in rice mtDNA differed from the linear order observed for the wheat and maize genes. In rice mitochondria, the trnS and pseudo-tRNA genes were found upstream of the cytochrome c oxidase subunit I gene, instead of the nad3 and rps12 genes as observed in maize and wheat. Additionally, while the rice nad3 and rps12 genes remain paired, they too are in a different sequence environment from the wheat and maize genes. The apparent split of the two pairs of genes indicates the occurrence of a mitochondrial intramolecular recombinational event. Another peculiarity is that the sequence upstream of the translational initiation codon of the rice nad3 gene is different from that of the wheat and maize versions. The ATG initiation codon of wheat and maize nad3 is replaced by TTG in the rice nad3. A subsequent deduction of the amino acid sequence, accompanied by a primer extension analysis, indicates that the predicted rice NAD3 protein has an additional 37 amino acid residues at its N-terminus compared to the wheat and maize NAD3 proteins. cDNA sequence analysis showed no introns or the occurrence of RNA editing at the newly replaced TTG codon.

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.

Localization and organization of tRNA genes on the mitochondrial genomes of fertile and male sterile lines of maize

Maize mitochondrial (mt) tRNA genes were localized on the mt master circles of two fertile lines (WF9-N and B37-N) and of one cytoplasmic male sterile line (B37-cmsT) of maize. The three genomes contain 16 tRNA genes with 14 different anticodons which correspond to 13 amino acids. Out of these 16 tRNA genes, 6 show a high degree of homology with the corresponding chloroplast (cp) tRNA genes and were shown to originate from cp DNA insertions and to be expressed in the mitochondria. The organization of the mt tRNA genes in both fertile lines is similar. The same genes are found, in the same environment, as judged from the restriction maps, in fertile and male sterile lines that have the same nuclear background, but the relative organization of the mt tRNA genes on the master circle is completely different.

Transfer RNAs of potato (Solanum tuberosum) mitochondria have different genetic origins

Total transfer RNAs were extracted from highly purified potato mitochondria. From quantitative measurements, the in vivo tRNA concentration in mitochondria was estimated to be in the range of 60 microM. Total potato mitochondrial tRNAs were fractionated by two-dimensional polyacrylamide gel electrophoresis. Thirty one individual tRNAs, which could read all sense codons, were identified by aminoacylation, sequencing or hybridization to specific oligonucleotides. The tRNA population that we have characterized comprises 15 typically mitochondrial, 5 'chloroplast-like' and 11 nuclear-encoded species. One tRNA(Ala), 2 tRNAs(Arg), 1 tRNA(Ile), 5 tRNAs(Leu) and 2 tRNAs(Thr) were shown to be coded for by nuclear DNA. A second, mitochondrial-encoded, tRNA(Ile) was also found. Five 'chloroplast-like' tRNAs, tRNA(Trp), tRNA(Asn), tRNA(His), tRNA(Ser)(GGA) and tRNA(Met)m, presumably transcribed from promiscuous chloroplast DNA sequences inserted in the mitochondrial genome, were identified, but, in contrast to wheat (1), potato mitochondria do not seem to contain 'chloroplast-like' tRNA(Cys) and tRNA(Phe). The two identified tRNAs(Val), as well as the tRNA(Gly), were found to be coded for by the mitochondrial genome, which again contrasts with the situation in wheat, where the mitochondrial genome apparently contains no tRNA(Val) or tRNA(Gly) gene (2).

In vitro processing of mitochondrial and plastid derived tRNA precursors in a plant mitochondrial extract

A lysate of purified mitochondria of the higher plant Oenothera processes in vitro synthesized tRNA precursors to the mature tRNA size. In vitro synthesized transcripts containing genuine plant mitochondrial tRNAs and analogous RNAs from mitochondrial loci with plastid derived tRNA sequences are accurately processed by an RNAase P-like activity to yield the mature 5'-terminus. A four nucleotide deletion in the anticodon stem-loop structure, however, prevents processing. The results show that in vitro transcripts containing tRNAs from sequence fragments of plastid origin integrated in plant mitochondrial genomes can be processed correctly in plant mitochondria, if tRNA sequences and structures are intact.

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.

Chloroplast-like transfer RNA genes expressed in wheat mitochondria

In the course of a systematic survey of wheat mitochondrial tRNA genes, we have sequenced chloroplast-like serine (trnS-GGA), phenylalanine (trnF-GAA) and cysteine (trnC-GCA) tRNA genes and their flanking regions. These genes are remnants of 'promiscuous' chloroplast DNA that has been incorporated into wheat mtDNA in the course of its evolution. Each gene differs by one or a few nucleotides from the authentic chloroplast homolog previously characterized in wheat or other plants, and each could potentially encode a functional tRNA whose secondary structure shows no deviations from the generalized model. To determine whether these chloroplast-like tRNA genes are actually expressed, wheat mitochondrial tRNAs were resolved by a series of polyacrylamide gel electrophoreses, after being specifically end-labeled in vitro by 3'-CCA addition mediated by wheat tRNA nucleotidyltransferase. Subsequent direct RNA sequence analysis identified prominent tRNA species corresponding to the mitochondrial and not the chloroplast trnS, trnF and trnC genes. This analysis also revealed chloroplast-like elongator methionine, asparagine and tryptophan tRNAs. Our results suggest that at least some chloroplast-like tRNA genes in wheat mtDNA are transcribed, with transcripts undergoing processing, post-transcriptional modification and 3'-CCA addition, to produce mature tRNAs that may participate in mitochondrial protein synthesis.

Three mitochondrial tRNA genes from Arabidopsis thaliana: evidence for the conversion of a tRNAPhe gene into a tRNATyr gene

Three tRNA genes have been isolated from a genomic library of Arabidopsis thaliana: a tRNASer (GCU), a tRNATyr (GUA) and a tRNAGlu (UUC) genes. These genes are located closely on the same DNA fragment. The tRNASer and the tRNAGlu genes have both 99% sequence similarity with their mitochondrial counterparts from higher plants indicating that these three tRNA genes are mitochondrial. The tRNATyr gene shows a particular high sequence similarity with the mitochondrial tRNAPhe pseudogene from maize, and both genes are flanked by a tRNASer gene in the upstream region. Extensive sequence comparisons of the Arabidopsis thaliana mitochondrial sequence containing the three tRNA genes and the corresponding region from maize and soybean mitochondria have shown evidence that the tRNA Tyr gene has been generated from a mitochondrial tRNAPhe gene. The conversion was accomplished by three genetic events: a 4 base-pair deletion, a mutation and a recombination, which led to the transformation of the acceptor stem and the anticodon.

Codon reassignment (codon capture) in evolution

The genetic code, once thought to be "frozen," shows variations from the universal code. Variations are found in mitochondria, Mycoplasma, and ciliated protozoa. The variations result from reassignment of codons, especially stop codons. The reassignments take place by disappearance of a codon from coding sequences, followed by its reappearance in a new role. Simultaneously, a changed anticodon must appear. We discuss the role of directional mutation pressure in the events, and we also describe the possibility that such events have taken place during early evolution of the genetic code and can occur during its present evolution.

The genes coding for subunit 3 of NADH dehydrogenase and for ribosomal protein S12 are present in the wheat and maize mitochondrial genomes and are co-transcribed

A region of about 2 kb which is almost identical in the wheat and maize mitochondrial genomes has been sequenced. It contains a tRNA(Ser) gene, a pseudo-tRNA gene and two open reading frames coding for subunit 3 of the NADH dehydrogenase (118 amino acids) and for ribosomal protein S12 (125 amino acids). The two protein genes are separated by 47 bp and are co-transcribed in wheat and maize. Two transcripts of about 0.9 kb and 3.0 kb, each coding for both proteins, have been characterized, but no monocistronic transcript was detected. Each gene is preceded by a putative ribosome binding site. The pseudo-tRNA gene is interrupted by two insertion sequences in wheat and by one in maize. The origin of the additional interrupting sequence found in the wheat pseudo-tRNA gene, which is also present elsewhere in the mitochondrial genomes, is discussed.

Transfer RNA genes and the genetic code in Chlamydomonas reinhardtii mitochondria

Only three tRNA genes are present within a sequenced 12.35 kbp region of the 15.8 kbp mtDNA of Chlamydomonas reinhardtii, a unicellular green alga. The corresponding tRNAs, whose anticodons are specific for TGG (Trp), CAA/G (Gln) and ATG (Met) codons, all display conventional secondary structures. The tRNA(Met) gene encodes an elongator rather than initiator species. The standard genetic code is used in C. reinhardtii mitochondria, but codon distribution is highly biased: in a collection of six identified protein coding genes, nine codons (including TGA) are not used at all, while four other sense codons occur very infrequently. In spite of the absence of certain codons, a minimum of 23 tRNAs (assuming separate initiator and elongator tRNAs(Met) are used) is needed to translate the C. reinhardtii mitochondrial genetic code. It appears unlikely that this minimal tRNA set is encoded by C. reinhardtii mtDNA.

Location, identity, amount and serial entry of chloroplast DNA sequences in crucifer mitochondrial DNAs

Southern blot hybridization techniques were used to examine the chloroplast DNA (cpDNA) sequences present in the mitochondrial DNAs (mtDNAs) of two Brassica species (B. campestris and B. hirta), two closely related species belonging to the same tribe as Brassica (Raphanus sativa, Crambe abyssinica), and two more distantly related species of crucifers (Arabidopsis thaliana, Capsella bursa-pastoris). The two Brassica species and R. sativa contain roughly equal amounts (12-14 kb) of cpDNA sequences integrated within their 208-242 kb mtDNAs. Furthermore, the 11 identified regions of transferred DNA, which include the 5' end of the chloroplast psaA gene and the central segment of rpoB, have the same mtDNA locations in these three species. Crambe abyssinica mtDNA has the same complement of cpDNA sequences, plus an additional major region of cpDNA sequence similarity which includes the 16S rRNA gene. Therefore, except for the more recently arrived 16S rRNA gene, all of these cpDNA sequences appear to have entered the mitochondrial genome in the common ancestor of these three genera. The mitochondrial genomes of A. thaliana and Capsella bursa-pastoris contain significantly less cpDNA (5-7 kb) than the four other mtDNAs. However, certain cpDNA sequences, including the central portion of the rbcL gene and the 3' end of the psaA gene, are shared by all six crucifer mtDNAs and appear to have been transferred in a common ancestor of the crucifer family over 30 million years ago. In conclusion, DNA has been transferred sequentially from the chloroplast to the mitochondrion during crucifer evolution and there cpDNA sequences can persist in the mitochondrial genome over long periods of evolutionary time.