[Show abstract][Hide abstract] ABSTRACT: For 8 years, it was not understood why certain genes of plant mitochondria contain CGG (arginine) codons at positions where tryptophan codons (UGG) are present in the corresponding genes of nonplant species. Identification and sequencing of a tRNA(Trp) gene showed that it is not able to decode the CGG codon. Analysis of different discrepancies in the sequences of plant mitochondrial proteins prompted us to determine directly the corresponding RNA sequences. These experiments showed that plant mitochondrial transcripts are subject to RNA editing that changes C into U, resulting in a better phylogenetic conservation of protein sequences [Gualberto et al. (1989) Nature 341, 660-662].
International Union of Biochemistry and Molecular Biology Life 12/2009; 61(12):1110-3. DOI:10.1002/iub.277 · 3.14 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: In plant mitochondria, RNA editing involves the conversion of specific Cs in the genomic sequence into Us in the mRNA. There are a few reverse conversions. A majority of the editing sites are in coding regions. After RNA editing, plant mitochondria use the universal genetic code if one considers the RNA message. Considering the deduced protein sequence, RNA editing is a correction mechanism. RNA editing is a post‐transcriptional process, active during the maturation of the mRNA. It has no evident polarity. At the translation level, the mRNAs are likely to be fully edited and to code for a unique protein.
[Show abstract][Hide abstract] ABSTRACT: Three reading frames called ccmF(N1), ccmF(N2), and ccmF(c) are found in the mitochondrial genome of Arabidopsis. These sequences are similar to regions of the bacterial gene ccmF involved in cytochrome c maturation. ccmF genes are always absent from animal and fungi genomes but are found in mitochondrial genomes of land plant and several evolutionary distant eukaryotes. In Arabidopsis, ccmF(N2) despite the absence of a classical initiation codon is not a pseudo gene. The 3 ccmF genes of Arabidopsis are expressed at the protein level. Their products are integral proteins of the mitochondrial inner membrane with in total 11 to 13 predicted transmembrane helices. The conserved WWD domain of CcmF(N2) is localized in the inter membrane space. The 3 CcmF proteins are all detected in a high molecular mass complex of 500 kDa by Blue Native PAGE. Direct interaction between CcmF(N2) and both CcmF(N1) and CcmF(C) is shown with the yeast two-hybrid split ubiquitin system, but no interaction is observed between CcmF(N1) and CcmF(C). Similarly, interaction is detected between CcmF(N2) and apocytochrome c but also with apocytochrome c(1). Finally, CcmF(N1) and CcmF(N2) both interact with CCMH previously shown to interact as well with cytochrome c. This strengthens the hypothesis that CcmF and CCMH make a complex that performs the assembly of heme with c-type apocytochromes in plant mitochondria.
[Show abstract][Hide abstract] ABSTRACT: As part of the respiratory chain, c-type cytochromes are essential electron transporters. They are characterized by the covalent attachment of a heme prosthetic group. The biogenesis of these proteins includes all the processes leading to this fixation. Yeast and animals have evolved a comparatively simple mechanism relying on cytochrome c heme lyases. In contrast, plant mitochondria have kept a maturation pathway inherited from their prokaryote ancestor. It involves Ccm proteins encoded in both the nuclear and the mitochondrial genomes of plants. These proteins compose a heme delivery pathway, include an ABC transporter, a redox protein and a putative heme lyase.
[Show abstract][Hide abstract] ABSTRACT: In land plant mitochondria, c-type cytochromes are assembled via a mechanism similar to that found in Gram-negative bacteria and different from that used by mitochondria from other eukaryotes. The wheat mitochondrial genome encodes CCM (for cytochrome c maturation) proteins, among them CcmF(C), a protein similar to the C-terminal part of the bacterial CcmF. The gene is transcribed into a 1.7 kb transcript at steady state. However, the 3' termini of the transcript were found to occur upstream of the deduced gene termination codon. This discrepancy was solved by RNA editing that introduces a novel termination codon, thus shortening the reading frame by 27 codons. The processed transcript is translated into a protein integrated in the mitochondrial inner membrane. We also show that the protein is part of a large (700 kDa) protein complex, that possibly represents a cytochrome c assembly complex.
[Show abstract][Hide abstract] ABSTRACT: A gene (rps2) coding for ribosomal protein S2 (RPS2) is present in the mitochondrial (mt) genome of several monocot plants, but absent from the mtDNA of dicots. Confirming that in dicot plants the corresponding gene has been transferred to the nucleus, a corresponding Arabidopsis thaliana nuclear gene was identified that codes for mitochondrial RPS2. As several yeast and mammalian genes coding for mt ribosomal proteins, the Arabidopsis RPS2 apparently has no N-terminal targeting sequence. In the maize mt genome, two rps2 genes were identified and both are transcribed, although at different levels. As in wheat and rice, the maize genes code for proteins with long C-terminal extensions, as compared to their bacterial counterparts. These extensions are not conserved in sequence. Using specific antibodies against one of the maize proteins we found that a large protein precursor is indeed synthesized, but it is apparently processed to give the mature RPS2 protein which is associated with the mitochondrial ribosome.
[Show abstract][Hide abstract] ABSTRACT: Recently, we and others have reported that mRNAs may be polyadenylated in plant mitochondria, and that polyadenylation accelerates the degradation rate of mRNAs. To further characterize the molecular mechanisms involved in plant mitochondrial mRNA degradation, we have analyzed the polyadenylation and degradation processes of potato atp9 mRNAs. The overall majority of polyadenylation sites of potato atp9 mRNAs is located at or in the vicinity of their mature 3'-extremities. We show that a 3'- to 5'-exoribonuclease activity is responsible for the preferential degradation of polyadenylated mRNAs as compared with non-polyadenylated mRNAs, and that 20-30 adenosine residues constitute the optimal poly(A) tail size for inducing degradation of RNA substrates in vitro. The addition of as few as seven non-adenosine nucleotides 3' to the poly(A) tail is sufficient to almost completely inhibit the in vitro degradation of the RNA substrate. Interestingly, the exoribonuclease activity proceeds unimpeded by stable secondary structures present in RNA substrates. From these results, we propose that in plant mitochondria, poly(A) tails added at the 3' ends of mRNAs promote an efficient 3'- to 5'- degradation process.
[Show abstract][Hide abstract] ABSTRACT: Assembly of cytochromes c is mediated by different proteins depending on the organism and organelle considered. In land plants, mitochondria follow a pathway distinct from that of yeast and animal mitochondria, more similar to that described for alpha- and gamma-proteobacteria. Indeed, in plant mitochondria, four genes were identified based on the similarities of their products with bacterial proteins involved in c-type cytochrome maturation. We report the characterisation of one of these mitochondrial genes in Triticum aestivum, TaccmB, which is proposed to encode a subunit of an ABC transporter. The transcript extremities were mapped and cDNA sequencing revealed 42 C to U editing positions in the 618 nucleotide long coding region. This high editing rate affects the identity of 32 amino acids out of 206. Antibodies directed against wheat CcmB recognise a 28 kDa protein in an enriched inner mitochondrial membrane protein fraction, a location which is in agreement with the high hydrophobicity of the protein and its function as a putative transmembrane domain of an ABC transporter involved in cytochrome c and c1 biogenesis in plant mitochondria.
[Show abstract][Hide abstract] ABSTRACT: Between the different types of Acyl-CoA dehydrogenases (ACADs), those specific for branched chain acyl-CoA derivatives are involved in the catabolism of amino acids. In mammals, isovaleryl-CoA dehydrogenase (IVD), an enzyme of the leucine catabolic pathway, is a mitochondrial protein, as other acyl-CoA dehydrogenases involved in fatty acid beta-oxidation. In plants, fatty acid beta-oxidation takes place mainly in peroxisomes, and the cellular location of the enzymes involved in the catabolism of branched-chain amino acids had not been definitely assigned. Here, we describe that highly purified potato mitochondria have important IVD activity. The enzyme was partially purified and cDNAs from two different genes were obtained. The partially purified enzyme has enzymatic constant values with respect to isovaleryl-CoA comparable to those of the mammalian enzyme. It is not active towards straight-chain acyl-CoA substrates tested, but significant activity was also found with isobutyryl-CoA, implying an additional role of the enzyme in the catabolism of valine. The present study confirms recent reports that in plants IVD activity resides in mitochondria and opens the way to a more detailed study of amino-acid catabolism in plant development.
European Journal of Biochemistry 04/2001; 268(5):1332-9. DOI:10.1046/j.1432-1327.2001.01999.x · 3.58 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The maturation of c-type cytochromes requires the covalent attachment of the heme cofactor to the apoprotein. For this process, plant mitochondria follow a pathway distinct from that of animal or yeast mitochondria, closer to that found in alpha- and gamma-proteobacteria. We report the first characterization of a nuclear-encoded component, namely AtCCME, the Arabidopsis thaliana orthologue of CcmE, a periplasmic heme chaperone in bacteria. AtCCME is targeted to mitochondria, and its N-terminal signal peptide is cleaved upon import. AtCCME is a peripheral protein of the mitochondrial inner membrane, and its major hydrophilic domain is oriented toward the intermembrane space. Although a AtCCME (Met(79)-Ser(256)) is not fully able to complement an Escherichia coli CcmE mutant strain for bacterial holocytochrome c production, it is able to bind heme covalently through a conserved histidine, a feature previously shown for E. coli CcmE. Our results suggest that AtCCME is important for cytochrome c maturation in A. thaliana mitochondria and that its heme-binding function has been conserved evolutionary between land plant mitochondria and alpha-proteobacteria.
[Show abstract][Hide abstract] ABSTRACT: The in organello labeling pattern in wheat (Triticum aestivum) mitochondria isolated from imbibed embryos were compared with those from the commonly used starting material, etiolated
seedlings. Mitochondria from imbibed embryos proved to be metabolically more active than those from etiolated seedlings and
produced a large number of strongly in organello-labeled polypeptides. Immunoprecipitation of the labeled proteins enabled
the identification of mitochondrially encoded subunits of the respiratory chain complex I, some of which could not be detected
by conventional Western blotting due to their high hydrophobicity. A method for mass isolation of wheat embryos is also presented
which allows easy preparation of large amounts of intact and highly active mitochondria suitable for biochemical studies.
[Show abstract][Hide abstract] ABSTRACT: The gene and cDNA of an Arabidopsis thaliana cytidine deaminase (CDA) were cloned and sequenced. The gene, At-cda1, is located on chromosome 2 and is expressed in all plant tissues tested, although with quantitative differences. Expression analysis suggest that At-cda1 probably codes for the housekeeping cytidine deaminase of Arabidopsis. The gene was functionally expressed in Escherichia coli and the protein, At-CDA1, shows similar enzymatic and substrate specificities as conventional cytidine deaminases: it deaminates cytidine and deoxycytidine and is competitively inhibited by cytosine-containing compounds. Because the protein shows no affinity to RNA, it is not likely to be involved in RNA-editing by C-to-U deamination. When compared to cytidine deaminases from other organisms, it becomes clear that At-CDA1 is related, both in sequence and structure, to the CDA of E. coli and other gram-negative bacteria. The eubacterial nature of the Arabidopsis CDA suggests that it is an additional example of a plant gene of endosymbiotic origin.
European Journal of Biochemistry 09/1999; 263(3):896-903. DOI:10.1046/j.1432-1327.1999.00591.x · 3.58 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: In order to isolate the mitochondrial respiratory chain complex I (NADH:ubiquinone oxidoreductase EC 18.104.22.168) from wheat, we developed a one-step immunoaffinity procedure using antibodies raised against the NAD9 subunit. By native electrophoresis we showed that the antibodies are able to recognize the NAD9 subunit on the complex in its native form, therefore allowing the immunoaffinity chromatography. The complex retained on the column proved to be a functional complex I, since the preparation showed NADH:duroquinone and NADH:FeK3(CN)6 reductase activities which were inhibited by rotenone. The pattern of the protein subunits (about 30) eluted from the purified complex showed a high level of similarities with complex I purified from potato and broad bean by conventional techniques. Twelve subunits were identified by cross-reactions with antibodies against heterologous complex I subunits including mitochondrial- and nuclear-encoded proteins. In order to study the genetic origin of the subunits, we purified wheat complex I after in organello labelling of mitochondrial-encoded polypeptides. We found that no other complex I subunit than those corresponding to the nine mitochondrial nad genes sequenced so far, is encoded in the mitochondria of wheat.
[Show abstract][Hide abstract] ABSTRACT: MitBASE is an integrated and comprehensive database of mitochondrial DNA data which collects all available information from different organisms and from intraspecie variants and mutants. Research institutions from different countries are involved, each in charge of developing, collecting and annotating data for the organisms they are specialised in. The design of the actual structure of the database and its implementation in a user-friendly format are the care of the European Bioinformatics Institute. The database can be accessed on the Web at the following address: http://www.ebi.ac. uk/htbin/Mitbase/mitbase.pl. The impact of this project is intended for both basic and applied research. The study of mitochondrial genetic diseases and mitochondrial DNA intraspecie diversity are key topics in several biotechnological fields. The database has been funded within the EU Biotechnology programme.
Nucleic Acids Research 02/1999; 27(1):128-33. DOI:10.1093/nar/27.1.128 · 9.11 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The mitochondrial DNA (mt DNA) of the red alga Chondrus crispus is shown to be transcribed into two large RNA molecules. These primary transcripts are cleaved once, at the level of a tRNA, then the resulting products are processed via multiple maturation events into either mono- or poly-cistronic RNAs. Transcripts were detected for all genes and open reading frames, except for rps11 and orf172. For both transcription units the initiation of transcription was mapped by in vitro RNA capping and primer extension experiments within inverse repeated sequences at the north pole of the molecule. Consistent with primer extension mapping, putative promoter motifs sharing significant similarities with both chicken and Xenopus mitochondrial promoters were found in the C. crispus mitochondrial genome. Altogether C. crispus mitochondrial DNA appears to be transcribed as animal mtDNA is, suggesting that transcription mechanisms in mitochondria are dependent on the overall organization of the mitochondrial genome irrespective of the eukaryotic phylogeny.
[Show abstract][Hide abstract] ABSTRACT: In wheat mitochondria, the gene coding for subunit 2 of the NADH-ubiquinone oxidoreductase (nad2) is divided into five exons located in two distant genomic regions. The first two exons of the gene, a and b, lie 22 kb downstream of exons c, d, and e, on the same DNA strand. All introns of nad2 are group II introns. A trans-splicing event is required to join exons b and c. It involves base pairing of the two precursor RNAs in the stem of domain IV of the intron. A gene coding for tRNA(Tyr) is located upstream of exon c. In addition to splicing processes, mRNA editing is also required for the correct expression of nad2. The mature mRNA is edited at 36 positions, distributed over its five exons, resulting in 28 codon modifications. Editing increases protein hydrophobicity and conservation.
MGG - Molecular and General Genetics 07/1998; 258(5):503-11.
[Show abstract][Hide abstract] ABSTRACT: A gene coding for a protein that shows homologies to prokaryotic ribosomal protein S2 is present in the mitochondrial (mt) genome of wheat (Triticum aestivum). The wheat gene is transcribed as a single mRNA which is edited by C-to-U conversions at seven positions, all resulting in alteration of the encoded amino acid. Homologous gene sequences are also present in the mt genomes of rice and maize, but we failed to identify the corresponding sequences in the mtDNA of all dicotyledonous species tested; in these species the mitochondrial RPS2 is probably encoded in the nucleus. The protein sequence deduced from the wheat rps2 gene sequence has a long C-terminal extension when compared to other prokaryotic RPS2 sequences. This extension presents no similarity with any known sequence and is not conserved in the maize or rice mitochondrial rps2 gene. Most probably, after translation, this peptide extension is processed by a specific peptidase to give rise to the mature wheat mitochondrial RPS2.
MGG - Molecular and General Genetics 07/1998; 258(5):530-7. DOI:10.1007/s004380050764
[Show abstract][Hide abstract] ABSTRACT: We present the nucleotide sequence of the cox 1 gene encoding subunit 1 of cytochrome c oxidase in Euglena gracilis, the first report on a mitochondrial gene from this protist. Its study reveals that the Euglena mitochondrial genome does not appear as a compact and homogeneous structure and that its A+T content is high (about 76%) whereas this value is less than 50% in nuclear DNA. The Euglena cox1 gene does not exhibit any intron, and an amino-acid alignment of Euglena COX1 with homologous proteins shows that the universal genetic code is used. Comparisons of the genomic and cDNA sequences of Euglena cox1 indicate that the transcript does not undergo RNA editing as found in trypanosomes and in higher plants. The phylogeny obtained with COX1 protein sequences is in agreement with that obtained with nuclear rRNA sequences and places Euglena and Trypanosoma far apart from other eukaryotes. This result strengthens the hypothesis that these protists represent the earliest mitochondrion-containing organisms.
Current Genetics 04/1997; 31(3):208-13. · 2.68 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We present the nucleotide sequence of the cox 1 gene encoding subunit 1 of cytochrome c oxidase in Euglena gracilis, the first report on a mitochondrial gene from this protist. Its study reveals that the Euglena mitochondrial genome does not appear as a compact and homogeneous structure and that its A+T content is high (about 76%)
whereas this value is less than 50% in nuclear DNA. The Euglena cox1 gene does not exhibit any intron, and an amino-acid alignment of Euglena COX1 with homologous proteins shows that the universal genetic code is used. Comparisons of the genomic and cDNA sequences
of Euglena cox1 indicate that the transcript does not undergo RNA editing as found in trypanosomes and in higher plants. The phylogeny obtained
with COX1 protein sequences is in agreement with that obtained with nuclear rRNA sequences and places Euglena and Trypanosoma far apart from other eukaryotes. This result strengthens the hypothesis that these protists represent the earliest mitochondrion-containing
Current Genetics 03/1997; 31(3):208-213. DOI:10.1007/s002940050197 · 2.68 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: In the mitochondria and chloroplasts of higher plants there is an RNA editing activity responsible for specific C-to-U conversions and for a few U-to-C conversions leading to RNA sequences different from the corresponding DNA sequences. RNA editing is a post-transcriptional process which essentially affects the transcripts of protein coding genes, but has also been found to modify non-coding transcribed regions, structural RNAs and intron sequences. RNA editing is essential for correct gene expression: proteins translated from edited transcripts are different from the ones deduced from the genes sequences and usually present higher similarity to the corresponding non-plant homologues. Initiation and stop codons can also be created by RNA editing. RNA editing has also been shown to be required for the stabilization of the secondary structure of introns and tRNAs.
The biochemistry of RNA editing in plant organelles is still largely unknown. In mitochondria, recent experiments indicate that RNA editing may be a deamination process. A plastid transformation technique showed to be a powerful tool for the study of RNA editing. The biochemistry as well as the evolutionary features of RNA editing in both organelles are compared in order to identify common as well as organelle-specific components.