Direct protein sequencing of wheat mitochondrial ATP synthase subunit 9 confirms RNA editing in plants

Specificities of the plant mitochondrial translation apparatus

Mitochondria are endosymbiotic organelles responsible for energy production in most eukaryotic cells. They host a genome and a fully functional gene expression machinery. In plants this machinery involves hundreds of pentatricopeptide repeat (PPR) proteins. Translation, the final step of mitochondrial gene expression is performed by mitochondrial ribosomes (mitoribosomes). The nature of these molecular machines remained elusive for a very long time. Because of their bacterial origin, it was expected that mitoribosomes would closely resemble bacterial ribosomes. However, recent advances in cryo-electron microscopy have revealed the extraordinary diversity of mitoribosome structure and composition. The plant mitoribosome was characterized for Arabidopsis. In plants, in contrast to other species such as mammals and kinetoplastids where rRNA has been largely reduced, the mitoribosome could be described as a protein/RNA-augmented bacterial ribosome. It has an oversized small subunit formed by expanded ribosomal RNAs and additional protein components when compared to bacterial ribosomes. The same holds true for the large subunit. The small subunit is characterized by a new elongated domain on the head. Among its additional proteins, several PPR proteins are core mitoribosome proteins. They mainly act at the structural level to stabilize and maintain the plant-specific ribosomal RNA expansions but could also be involved in translation initiation. Recent advances in plant mitoribosome composition and structure, its specialization for membrane protein synthesis, translation initiation, the regulation and dynamics of mitochondrial translation are reviewed here and put in perspective with the diversity of mitochondrial translation processes in the green lineage and in the wider context of eukaryote evolution.

Comparative RNA editing profile of mitochondrial transcripts in cytoplasmic male sterile and fertile pigeonpea reveal significant changes at the protein level

RNA editing is a process which leads to post-transcriptional alteration of the nucleotide sequence of the corresponding mRNA molecule which may or may not lead to changes at the protein level. Apart from its role in providing variability at the transcript and protein levels, sometimes, such changes may lead to abnormal expression of the mitochondrial gene leading to a cytoplasmic male sterile phenotype. Here we report the editing status of 20 major mitochondrial transcripts in both male sterile (AKCMS11) and male fertile (AKPR303) pigeonpea genotypes. The validation of the predicted editing sites was done by mapping RNA-seq reads onto the amplified mitochondrial genes, and 165 and 159 editing sites were observed in bud tissues of the male sterile and fertile plant respectively. Among the resulting amino acid alterations, the most frequent one was the conversion of hydrophilic amino acids to hydrophobic. The alterations thus detected in our study indicates differential editing, but no major change in terms of the abnormal protein structure was detected. However, the above investigation provides an insight into the behaviour of pigeonpea mitochondrial genome in native and alloplasmic state and could hold clues in identification of editing factors and their role in adaptive evolution in pigeonpea.

BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology

BindingDB, www.bindingdb.org, is a publicly accessible database of experimental protein-small molecule interaction data. Its collection of over a million data entries derives primarily from scientific articles and, increasingly, US patents. BindingDB provides many ways to browse and search for data of interest, including an advanced search tool, which can cross searches of multiple query types, including text, chemical structure, protein sequence and numerical affinities. The PDB and PubMed provide links to data in BindingDB, and vice versa; and BindingDB provides links to pathway information, the ZINC catalog of available compounds, and other resources. The BindingDB website offers specialized tools that take advantage of its large data collection, including ones to generate hypotheses for the protein targets bound by a bioactive compound, and for the compounds bound by a new protein of known sequence; and virtual compound screening by maximal chemical similarity, binary kernel discrimination, and support vector machine methods. Specialized data sets are also available, such as binding data for hundreds of congeneric series of ligands, drawn from BindingDB and organized for use in validating drug design methods. BindingDB offers several forms of programmatic access, and comes with extensive background material and documentation. Here, we provide the first update of BindingDB since 2007, focusing on new and unique features and highlighting directions of importance to the field as a whole.

Subunit 9 of the mitochondrial ATP synthase of Trypanosoma brucei is nuclearly encoded and developmentally regulated

We have previously shown that the mitochondrial ATP synthase is developmentally regulated through the life cycle of Trypanosoma brucei. The mechanism of this regulation is as yet unknown. We are currently examining regulation of expression of several key subunits of the ATP synthase to investigate this mechanism. In the work presented here, we have cloned, sequenced, and confirmed the identity of the ATPase subunit 9 homologue from T. brucei. The ATPase subunit 9 gene that we have identified from T. brucei has between 40 and 600% identity with subunit 9 from a variety of organisms. This gene possesses a putative mitochondrial import sequence at the N terminus of the encoded protein sequence. The protein expressed from this gene by in vitro transcription/translation comigrates with native protein isolated from inner mitochondrial membrane vesicles from T. brucei. We have shown that the cDNA identifies a copy of this gene in the nuclear genome, but does not identify a similar gene in kinetoplast DNA (kDNA) prepared from T. brucei. This gene does not show homology to any published sequence data from maxicircle DNA or edited maxicircle derived sequences. Steady state transcripts of a single size have been identified by Northern analysis and demonstrate significant developmental regulation through the T. brucei life cycle. Northern analysis and quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) results show that the transcript is 10-14-fold higher in procyclic form than in early and late bloodstream forms.

Fully edited and partially edited nad9 transcripts differ in size and both are associated with polysomes in potato mitochondria

Two classes of nad9 transcripts are present at different abundances in the steady-state RNA pool of potato mitochondria. The 5'- and 3' termini of the transcripts were determined by primer extension and S1 nuclease protection analyses respectively. Using two primer pairs that will either specifically amplify the larger transcript or amplify both the larger and the smaller transcripts in RT-PCR analyses it was found that the larger nad9 transcripts are partially edited, while the smaller transcripts are fully edited. Both the larger and the smaller transcripts were found to be associated with mitochondrial polysomes. The polysome association was found to be sensitive to EDTA and puromycin treatment. Therefore, both fully and partially edited nad9 transcripts appear to be engaged in translation.

Protein polymorphism generated by differential RNA editing of a plant mitochondrial rps12 gene

The rps12 gene transcripts encoding mitochondrial ribosomal protein S12 are partially edited in petunia mitochondria. Different petunia lines were found vary in the extent of rps12 transcript editing. To test whether multiple forms of RPS12 proteins are produced in petunia mitochondria as a result of partial editing, we probed mitochondrial proteins with specific antibodies against edited and unedited forms of a 13-amino-acid RPS12 peptide spanning two amino acids affected by RNA editing. Both antibodies reacted with mitochondrial proteins at the expected size for RPS12 proteins. The amounts of unedited RPS12 protein in different petunia lines correlate with the abundance of unedited transcripts in these plants. Unedited rps12 translation products are also detected in other plant species, indicating that polymorphism in mitochondrial rps12 expression is widespread. Moreover, we show that RPS12 proteins recognized by both edited-specific and unedited-specific antibodies are present in a petunia mitochondrial ribosome fraction. These results demonstrate that partially edited transcripts can be translated and that the protein product can accumulate to detectable levels. Therefore, genes exhibiting incompletely edited transcripts can encode more than one gene product in plant mitochondria.

Control of gene expression by base deamination: the case of RNA editing in wheat mitochondria

The term 'RNA editing' was used for the first time in 1986 to describe the process of uridylate insertion into trypanosomal mitochondrial transcripts. Since then, the term has been used more generally to describe a large variety of processes involving base insertions, deletions and conversions that generate RNAs with a primary sequence different to those encoded by the gene. RNA editing has been observed in the mitochondrial fraction of trypanosomes, plants and other organisms, in the animal nuclear fraction in the case of the apolipoprotein B and glutamate brain receptors mRNAs as well as in viruses like paramyxovirus, hepatitis delta and probably HIV. The role of cytidine and adenine deamination leading to C to U and A to I transitions has became pivotal to explain this process by base conversion. In this review we will focus mainly on the work performed in our group on plant mitochondria and more specifically on the mechanism and the functional significance of RNA editing in wheat organelles. The original contributions of our laboratory in this field are: i) showing that RNA editing is reflected at the protein level; ii) settling three in vitro systems to assay C to U conversion using a wheat mitochondrial lysate as source of enzymes and factors, and unedited mRNA from the same source, as substrate; iii) determination by double labelling of the unedited substrate that RNA editing in wheat mitochondria occurs via a deamination step; and iv) that introducing unedited proteins in the mitochondria of transgenic plants leads to the emergence of cytoplasmic male sterility supporting the idea that the role of this process is to produce functional proteins. Using the antisense approach in transgenic plants we were able to obtain a significant male fertility restoration.

RNA editing in higher plant mitochondria: analysis of biochemistry and specificity

RNA editing alters genomically encoded cytidines to uridines posttranscriptionally in higher plant mitochondria. Most of these editing events occur in translated regions and consequently alter the amino acid sequence. In Oenothera berteriana more than 500 editing sites have been detected and the total number of editing sites exceeds 1000 sites in this mitochondrial genome. To identify the components involved in this process we investigated the factors determining the specificity of RNA editing and the apparent conversion of cytidine to uridine residues. The possible biochemical reactions responsible for RNA editing in plant mitochondria are de- or transamination, base substitution and nucleotide replacement. In order to discriminate between these different biochemical mechanisms we followed the fate of the sugar-phosphate backbone by analysing radiolabeled nucleotides after incorporation into high molecular mass RNA. Plant mitochondria were supplied with [alpha-32P]CTP to radiolabel CMP residues in newly synthesized transcripts. Radiolabeled mtRNA was extracted and digested with nuclease P1 to hydrolyse the RNA to monophosphates. The resulting monophosphates were analysed on one- and two-dimensional TLC systems to separate pC from pU. Radiolabeled pU was detected in increasing quantities during the course of incubation. These results suggest that RNA editing in plant mitochondria involves either a deamination or a transglycosylation reaction. The editing product was identified as uridine and not as a hypermodified nucleotide which is recognized as uridine. Similar results have been obtained by incubating in vitro transcribed mRNAs with mitochondrial lysates indicating that RNA editing and transcription is not directly linked in plant mitochondria.(ABSTRACT TRUNCATED AT 250 WORDS)

RNA editing in wheat mitochondria

C to U transitions in plant mitochondrial mRNA (RNA editing) lead to amino acid changes as well as to the creation of new initiation or termination codons. We established an in vitro system to assay and to dissect the process of wheat mitochondrial mRNA editing. A deamination mechanism explains most easily the observed C to U transitions. Several fractions of organellar protein participate in the editing machinery. Some of these proteins presumably carry the catalytic activity while others are typical RNA binding proteins and may confer specificity to the 'editosome' complex. To investigate the functional properties of protein products synthesized from unedited mRNAs, we constructed transgenic tobacco plants carrying an unedited gene coding for subunit 9 (ATP9) of the ATP synthase complex. The nuclear encoded 'unedited' protein product is targeted to the mitochondria with a heterologous presequence. A significant number of male sterile tobacco plants were obtained suggesting that at least the functional ATP9 protein requires RNA editing. This result suggests a novel approach to obtain artificial male sterile plants by using a physiological effect resulting in CMS which mimics the situation found in many natural populations.

The 42.5 kDa subunit of the NADH: ubiquinone oxidoreductase (complex I) in higher plants is encoded by the mitochondrial nad7 gene

The N-terminal amino acid sequence of a 42.5 kDa subunit of the NADH: ubiquinone oxidoreductase (complex I) from potato has been determined by direct protein sequencing. The sequence was found to be homologous to that of the nuclear-encoded 49 kDa complex I subunit of bovine and Neurospora mitochondria and to the sequence deduced from the mitochondrial nad7 gene identified in the mitochondrial (mt) DNA of tryp anosomes and the moss Marchantia. An oligonucleotide probe derived from the potato N-terminal protein sequence hybridized only to the plant mtDNA. Immunoprecipitation of in-organello 35S-labelled potato and wheat mitochondrial translation products with an antibody directed against the Neurospora 49 kDa complex I subunit indicates that at least in these plants the NAD7 protein is synthesized within the organelle. Comparisons of genomic, cDNA and protein sequences of the 5' coding region reveal three codons that are changed by RNA-editing and confirm translation of the edited transcripts in plant mitochondria. The NAD7 protein appears to undergo post-translational processing since the N-terminal methionine residue is absent from the mature mitochondrial protein.

Large scale bacterial gene discovery by similarity search

DNA sequencing efforts frequently uncover genes other than the targeted ones. We have used rapid database scanning methods to search for undescribed eubacterial and archean protein coding frames in regions flanking known genes. By searching all prokaryotic DNA sequences not marked as coding for proteins or stable RNAs against the protein databases, we have identified more than 450 new examples of bacterial proteins, as well as a smaller number of possible revisions to known proteins, at a surprisingly high rate of one new protein or revision for every 24 initial DNA sequences or 8,300 nucleotides examined. Seven proteins are members of families which have not been described in prokaryotic sequences. We also describe 49 re-interpretations of existing sequence data of particular biological significance.

RNA editing of a conserved reading frame in plant mitochondria increases its similarity to two overlapping reading frames in Escherichia coli

An open reading frame (orfx) in mitochondria of the higher plants Oenothera berteriana and Arabidopsis thaliana is homologous to orf244 in the mitochondrial genome of Marchantia polymorpha. Homologous sequences are also present in carrot, potato and sugar beet. Profile analysis revealed similarity to two overlapping reading frames in the Escherichia coli genome. Potential translation initiation at conserved ATA (isoleucine) and TTG (leucine) codons is discussed. Transcripts of the open reading frame are altered by RNA editing in Arabidopsis and Oenothera downstream of these codons, suggesting this to be the functionally important region.

RNA editing of apocytochrome b (cob) transcripts in mitochondria from two genera of plants

Editing of the complete coding region of cob transcripts from two genera of plants has been studied by cDNA sequence analysis. Eighteen and nine C residues are edited into U in the mitochondrial transcripts from wheat and potato respectively. Both systems share eight common editing sites; ten codons edited in wheat are "pre-edited" at the genomic level in potato, and one codon edited in potato is "pre-edited" in wheat. Most amino-acid modifications lead to hydrophobic residues and increase the homology between the COB polypeptides and the corresponding protein of other species. In two out of the nine potato cDNA clones, an additional C-to-T modification, which also leads to a change in the encoded amino acid, was identified. Heterogeneity observed at the carboxy-terminus of the COB open reading frame in Triticum aestivum and Triticum timopheevi is not corrected by editing.

Male-sterility induction in transgenic tobacco plants with an unedited atp9 mitochondrial gene from wheat

Cytoplasmic male sterility in plants is associated with mitochondrial dysfunction. We have proposed that a nuclear-encoded chimeric peptide formed by mitochondrial sequences when imported into the mitochondria may impair organelle function and induce male sterility in plants. A model developed to test this hypothesis is reported here. Assuming that the editing process in higher plant mitochondria reflects a requirement for producing active proteins, we have used edited and unedited coding sequences of wheat ATP synthase subunit 9 (atp9) fused to the coding sequence of a yeast coxIV transit peptide. Transgenic plants containing unedited atp9 exhibited either fertile, semifertile, or male-sterile phenotypes; controls containing edited atp9 or only the selectable marker gave fertile plants. Pollen fertility ranged from 31% to 75% in fertile plants, 10% to 20% in semifertile plants, and < 2% in male-sterile plants. Genetic and molecular data showed that the chimeric plasmid containing the transgene is inherited as a Mendelian trait. The transgenic protein is imported into the mitochondria. The production and frequency of semifertile or male-sterile transgenic plants conform to the proposed hypothesis.

RNA editing gives a new meaning to the genetic information in mitochondria and chloroplasts

RNA editing in plant mitochondria and chloroplasts alters mRNA sequences to code for different proteins than the DNA. Most of these C-to-U transitions occur in open reading frames, but a few are observed in intron sequences. Influences of the nuclear genome on editing patterns suggest that cytoplasmic factors participate in this process.

RNA editing of rapeseed mitochondrial atp9 transcripts: RNA editing changes four amino acids, but termination codon is already encoded by genomic sequence

The gene encoding subunit 9 of Fo-ATPase of rapeseed mitochondria has been isolated. The complete genomic DNA sequence and cDNA sequence corresponding to the atp9 gene transcript have been determined by a method involving cDNA synthesis, using specific oligonucleotides as primers, followed by PCR amplification, cloning and sequencing of the amplification products. In comparison of cDNA sequences to genomic one, four modifications, C-to-U conversions, have been found. When compared with RNA editing patterns of atp9 transcripts among plant mitochondria, that of rapeseed atp9 transcript is more simple; there are only four editing sites on the coding region, and its termination codon is already encoded by genomic sequence.

RNA editing in plant mitochondria and chloroplasts

In the mitochondria and chloroplasts of flowering plants (angiosperms), transcripts of protein-coding genes are altered after synthesis so that their final primary nucleotide sequence differs from that of the corresponding DNA sequence. This posttranscriptional mRNA editing consists almost exclusively of C-to-U substitutions. Editing occurs predominantly within coding regions, mostly at isolated C residues, and usually at first or second positions of codons, thereby almost always changing the amino acid from that specified by the unedited codon. Editing may also create initiation and termination codons. The net effect of C-to-U RNA editing in plants is to make proteins encoded by plant organelles more similar in sequence to their nonplant homologs. In a few cases, a strong argument can be made that specific C-to-U editing events are essential for the production of functional plant mitochondrial proteins. Although the phenomenon of RNA editing in plants is now well documented, fundamental questions remain to be answered: What determines the specificity of editing? What is the biochemical mechanism (deamination, base exchange, or nucleotide replacement)? How did the system evolve? RNA editing in plants, as in other organisms, challenges our traditional notions of genetic information transfer.

Familial clustering of IGHC deletions and duplications: functional and molecular analysis

The human immunoglobulin heavy chain constant region locus (IGHC) comprises nine genes and two pseudogenes clustered in a 350 kilobase (kb) region on chromosome 14q32. Several IGHC haplotypes with single or multiple gene deletions and duplications have been characterized. The most likely mechanism accounting for these unusual haplotypes is the unequal crossing-over between homologous regions within the locus. Here we report the analysis of an unusual case of familial clustering of deletions/duplications. In the two branches of the BON family, three duplicated and two deleted haplotypes, all probably independent in origin, have been characterized. The structure of the haplotypes, one of which is described here for the first time, supports the hypothesis of homologous unequal crossing-over as the origin of recombinant haplotypes. The analysis of serological markers in a subject carrying one deleted and one duplicated haplotype allowed us the first direct inferences concerning the functions of the duplicated IGHC haplotypes.

Regenerating good sense: RNA editing and trans splicing in plant mitochondria

The protein products of plant mitochondrial genes cannot be predicted accurately from genomic sequences, since RNA editing modifies almost all mRNA sequences post-transcriptionally. Furthermore, RNA editing alters leader, trailer and intron sequences, and may be required for processing of these sequences. For several plant mitochondrial transcripts, processing includes trans splicing, which connects exons scattered throughout the genome. The mature transcripts are assembled via split group II intron sequences.

Poisson, compound Poisson and process approximations for testing statistical significance in sequence comparisons

DNA and protein sequence comparisons are performed by a number of computational algorithms. Most of these algorithms search for the alignment of two sequences that optimizes some alignment score. It is an important problem to assess the statistical significance of a given score. In this paper we use newly developed methods for Poisson approximation to derive estimates of the statistical significance of k-word matches on a diagonal of a sequence comparison. We require at least q of the k letters of the words to match where 0 less than q less than or equal to k. The distribution of the number of matches on a diagonal is approximated as well as the distribution of the order statistics of the sizes of clumps of matches on the diagonal. These methods provide an easily computed approximation of the distribution of the longest exact matching word between sequences. The methods are validated using comparisons of vertebrate and E. coli protein sequences. In addition, we compare two HLA class II transplantation antigens by this method and contrast the results with a dynamic programming approach. Several open problems are outlined in the last section.

Parametric sequence comparisons

Current algorithms can find optimal alignments of two nucleic acid or protein sequences, often by using dynamic programming. While the choice of algorithm penalty parameters greatly influences the quality of the resulting alignments, this choice has been done in an ad hoc manner. In this work, we present an algorithm to efficiently find the optimal alignments for all choices of the penalty parameters. It is then possible to systematically explore these alignments for those with the most biological or statistical interest. Several examples illustrate the method.

An in vitro system for the editing of ATP synthase subunit 9 mRNA using wheat mitochondrial extracts

A posttranscriptional modification (C-to-U) at specific positions of plant mitochondrial mRNA leads to changes in the amino acid sequence as well as to the emergence of novel initiation or termination sites. This phenomenon, named RNA editing, has been described for several mitochondrial genes from different plant sources. We have found recently that RNA editing of the ATP synthase subunit 9 (atp9) mRNA involves eight changes including the creation of a new stop codon. In this article, we describe an in vitro system devised to follow the editing of wheat mitochondrial atp9 mRNA. Nonedited mRNA was obtained to serve as substrate for this reaction by in vitro transcription of the corresponding gene with T7 RNA polymerase. The source of conversion factor(s) was a soluble fraction obtained from purified wheat mitochondria lysed with salt and detergent. Edited RNA molecules were detected by hybridization with an end-labeled synthetic oligodeoxynucleotide probe complementary to a short region containing four editing events. Optimal conditions for the in vitro RNA editing reaction were determined. The reaction is sensitive to high temperature and protease digestion. Pretreatment with micrococcal nuclease decreased RNA editing activity in the mitochondrial extract, suggesting that a nucleic acid is necessary for the enzymatic reactions. Analysis of the edited mRNA showed that the in vitro reaction led to the same products as those observed in vivo.

Editing of mitochondrial atp9 transcripts from two sorghum lines

Genomic and cDNA sequences of the ATP synthase complex subunit 9 (atp9) genes from two sorghum lines were determined. Sequences of cDNAs revealed eight C to U transcript editing events resulting in six amino acid changes and a new stop codon which eliminated 12 carboxy-terminal residues, compared to the genomic sequence. Sorghum atp9 has a unique five-residue amino-extension relative to other higher plants. The resulting predicted 79-residue gene product has a molecular weight of 8.179 kDa. The predicted phe-val-phe carboxy-terminus is identical to that from cDNA sequences of wheat, Oenothera, and petunia. Partial editing of transcripts was detected in each sorghum line.

RNA editing of sorghum mitochondrial atp6 transcripts changes 15 amino acids and generates a carboxy-terminus identical to yeast

Sequencing of sorghum mitochondrial atp6 cDNA clones revealed 19 C-to-U transcript editing events within a 756 bp-conserved core gene; three were silent and 16 resulted in 15 amino acid changes. Only one edit, which was silent, was found in the 381 bp amino-extension to the core gene. Eleven of the 15 changed amino acids were identical with or else represented conservative changes compared to yeast atp6. Editing of a CAA codon to TAA truncates the carboxy-terminus to a position identical to that of yeast. The frequency of editing at sites which change amino acids was very high in contrast to partial editing at silent, third base, sites.

A termination codon is created by RNA editing in the petunia atp9 transcript

Analysis of the cDNA of the atp9-1 gene transcript from petunia mitochondria has revealed that ten C residues of the gene sequence are edited into U in the mRNA. Seven of these edits result in amino acid changes and one introduces a stop codon before the end of the open reading frame predicted from the gene sequence. The resulting protein is better conserved when compared to the same protein in other organisms. Comparison of the edited petunia sequence with other plant mitochondrial atp9 gene sequences idicates variation in the number and positions of edits required to obtain the same amino acids in ATP9 polypeptides of higher plants.

Cytochrome oxidase subunit II mRNAs in Oenothera mitochondria are edited at 24 sites

Analysis of cDNA clones covering the entire coding region of cytochrome oxidase subunit II in Oenothera mitochondria reveals 24 potential editing sites: 23 C to U transitions and one U to C conversion. One editing event is observed outside the open reading frame in the 3' non-coding region. Thirteen editing sites are found altered in all cDNA clones, whereas the other eleven sites are only edited in some of the cDNA clones. These differentially edited sites occur most frequently at silent codon positions or in triplets at non-conserved amino acids.