A nucleus-encoded factor, CRR2, is essential for the expression of chloroplast ndhB in Arabidopsis

Chloroplast stromal proteins, CRR6 and CRR7, are required for assembly of the NAD(P)H dehydrogenase subcomplex A in Arabidopsis

In higher plants, the chloroplast NAD(P)H dehydrogenase (NDH) complex mediates chlororespiration and photosystem I (PSI) cyclic electron transport in thylakoid membranes. Because of its low abundance and fragility, our knowledge on the assembly of chloroplast NDH is very limited, and some nuclear-encoded factors may be involved in this process. We show here that two Arabidopsis proteins, CHLORORESPIRATORY REDUCTION 6 (CRR6) and CRR7, which were previously identified in mutants specifically defective in NDH accumulation, are present in the stroma, and their stability is independent of the NDH complex, suggesting that they are unlikely to be NDH subunits. Blue native PAGE analysis showed that the accumulation of NDH subcomplex A, which is a core part of NDH that is conserved in divergent species, was specifically impaired in the crr6 and crr7-1 mutants. However, the expression of plastid-encoded genes encoding the subcomplex A subunits was not affected, suggesting that CRR6 and CRR7 are involved in post-translational steps during the biogenesis of subcomplex A. We also discovered that a substantial quantity of NdhH is present in several protein complexes in the chloroplast stroma, possibly as early assembly intermediates of subcomplex A. Although the accumulation of these stromal complexes was not affected in crr6 or crr7-1, CRR6 was co-purified with NdhH, implying that CRR6 functions in the later step of subcomplex-A biogenesis. Accumulation of CRR7 was independent of that of CRR6; we propose that CRR7 functions in a different step in subcomplex-A biogenesis from CRR6.

Reverse genetic screening identifies five E-class PPR proteins involved in RNA editing in mitochondria of Arabidopsis thaliana

RNA editing in flowering plant mitochondria post-transcriptionally alters several hundred nucleotides from C to U, mostly in mRNAs. Several factors required for specific RNA-editing events in plant mitochondria and plastids have been identified, all of them PPR proteins of the PLS subclass with a C-terminal E-domain and about half also with an additional DYW domain. Based on this information, we here probe the connection between E-PPR proteins and RNA editing in plant mitochondria. We initiated a reverse genetics screen of T-DNA insertion lines in Arabidopsis thaliana and investigated 58 of the 150 E-PPR-coding genes for a function in RNA editing. Six genes were identified to be involved in mitochondrial RNA editing at specific sites. Homozygous mutants of the five genes MEF18-MEF22 display no gross disturbance in their growth or development patterns, suggesting that the editing sites affected are not crucial at least in the greenhouse. These results show that a considerable percentage of the E-PPR proteins are involved in the functional processing of site-specific RNA editing in plant mitochondria.

Two proteins homologous to PsbQ are novel subunits of the chloroplast NAD(P)H dehydrogenase

The PsbQ-like (PQL) proteins 1 and 2, previously shown to be located in the thylakoid lumen of Arabidopsis thaliana, are homologous to PSII oxygen-evolving complex protein PsbQ. Nevertheless, pql mutants showed no defects in PSII but instead the activity of the chloroplast NAD(P)H dehydrogenease (NDH) complex was severely impaired. In line with this observation, the NDH subunits were low in abundance in pql mutants, and, conversely, ndh mutants strongly down-regulated the accumulation of the PQL proteins. In addition, the PQL2 protein was up-regulated in mutant plants deficient in the PSI complex or the thylakoid membrane-bound ferredoxin-NADP(+) oxidoreductase, whereas in pql mutants the PSI complex was slightly up-regulated. Taken together, the two PQL proteins are shown to be novel subunits of the lumenal protuberance of the NDH complex.

Editing of accD and ndhF chloroplast transcripts is partially affected in the Arabidopsis vanilla cream1 mutant

The vanilla cream1 (vac1) albino mutant is defective in a gene encoding a chloroplast-localized pentatricopeptide repeat protein of the DYW subgroup. However, the carboxyl-terminal DYW motif is truncated in VAC1. To identify vac1-specific phenotypes, we compared 34 chloroplast RNA editing sites and approximately 90 chloroplast gene expression patterns among wild type, vac1 and another albino mutant ispH, which is defective in the plastid isoprenoid biosynthesis pathway. We found that the editing of accD and ndhF transcripts is partially affected in vac1. In addition, steady-state levels of chloroplast rRNAs are significantly decreased in vac1. The expression of plastid-encoded RNA polymerase transcribed genes is down-regulated, whereas the expression of nucleus-encoded RNA polymerase transcribed genes is up-regulated in vac1. Although the development and function of mutant chloroplasts are severely impaired, steady-state mRNA levels of nucleus-encoded photosynthetic genes are not affected or are only slightly decreased in vac1. The ZAT10 gene encodes a transcription factor and its expression is down-regulated by norflurazon treatment in wild type. This norflurazon effect was not observed in vac1. These results suggest that the VAC1 protein may be involved in plastid-to-nucleus retrograde signaling in addition to its role in chloroplast RNA editing and gene expression. A defect in a key biosynthetic pathway can have many indirect effects on chloroplast gene expression as is seen in the ispH mutant. Similarly, the vac1 mutant has pleiotropic molecular phenotypes and most of which may be indirect effects.

The moss pentatricopeptide repeat protein with a DYW domain is responsible for RNA editing of mitochondrial ccmFc transcript

In most land plants RNA editing frequently occurs in many organelle transcripts, but little is known about the molecular mechanisms of the organelle RNA editing process. In this study, we have characterized the Physcomitrella patens PpPPR_71 gene that is required for RNA editing of the ccmFc transcript. This transcript harbors two RNA editing sites, ccmF-1 and ccmF-2, that are separated by 18 nucleotides. Complementary DNA sequence analysis of ccmFc suggested that RNA editing at the ccmF-1 site occurred before ccmF-2 editing. RNA editing of the ccmF-2 downstream site was specifically impaired by disruption of the PpPPR_71 gene that encodes a polypeptide with 17 pentatricopeptide repeat motifs and a C-terminal DYW domain. The recombinant PpPPR_71 protein expressed in Escherichia coli specifically bound to the 46-nucleotide sequence containing the ccmF-2 editing site. The binding affinity of the recombinant PpPPR_71 was strongest when using the edited RNA at ccmF-1. In addition, the DYW domain also binds to the surrounding ccmF-2 editing site. We conclude that PpPPR_71 is an RNA-binding protein that acts as a site recognition factor in mitochondrial RNA editing.

Sequence analysis of two alleles reveals that intra-and intergenic recombination played a role in the evolution of the radish fertility restorer (Rfo)

BACKGROUND

Land plant genomes contain multiple members of a eukaryote-specific gene family encoding proteins with pentatricopeptide repeat (PPR) motifs. Some PPR proteins were shown to participate in post-transcriptional events involved in organellar gene expression, and this type of function is now thought to be their main biological role. Among PPR genes, restorers of fertility (Rf) of cytoplasmic male sterility systems constitute a peculiar subgroup that is thought to evolve in response to the presence of mitochondrial sterility-inducing genes. Rf genes encoding PPR proteins are associated with very close relatives on complex loci.

RESULTS

We sequenced a non-restoring allele (L7rfo) of the Rfo radish locus whose restoring allele (D81Rfo) was previously described, and compared the two alleles and their PPR genes. We identified a ca 13 kb long fragment, likely originating from another part of the radish genome, inserted into the L7rfo sequence. The L7rfo allele carries two genes (PPR-1 and PPR-2) closely related to the three previously described PPR genes of the restorer D81Rfo allele (PPR-A, PPR-B, and PPR-C). Our results indicate that alleles of the Rfo locus have experienced complex evolutionary events, including recombination and insertion of extra-locus sequences, since they diverged. Our analyses strongly suggest that present coding sequences of Rfo PPR genes result from intragenic recombination. We found that the 10 C-terminal PPR repeats in Rfo PPR gene encoded proteins result from the tandem duplication of a 5 PPR repeat block.

CONCLUSIONS

The Rfo locus appears to experience more complex evolution than its flanking sequences. The Rfo locus and PPR genes therein are likely to evolve as a result of intergenic and intragenic recombination. It is therefore not possible to determine which genes on the two alleles are direct orthologs. Our observations recall some previously reported data on pathogen resistance complex loci.

Redox state of the photosynthetic electron transport chain in wild-type and mutant leaves of Arabidopsis thaliana: Impact on photosystem II fluorescence

In addition to the photosynthetic linear electron transport, several alternative electron transport routes exist in thylakoids of higher plants. The plastoquinone (PQ) pool acts as a common electron carrier in these pathways. In the cyclic electron flow around photosystem I (PSI), reduced ferredoxin is used by the ferredoxin-quinone reductase (FQR) to reduce the PQ pool. Chlororespiratory pathway consists in the reduction of the PQ pool by the NAD(P)H dehydrogenase (NDH). These alternative pathways and their role in photosynthesis are still not fully understood. In the present study, the accumulation kinetics of quinone acceptors was measured by fluorescence induction in leaves of Arabidopsis thaliana wild-type and mutants altered in alternative electron pathways after various light- and dark-adaptation conditions. Results show that NDH activity can be probed by fluorescence induction during light-to-dark transition of plants. Also, the activity of FQR pathway did not affect directly the FI kinetics. However, the accumulation kinetics of reduced PQ under actinic light was dependant on the redox state of PSI acceptors prior to illumination.

Chloroplast RNA metabolism

The chloroplast genome encodes proteins required for photosynthesis, gene expression, and other essential organellar functions. Derived from a cyanobacterial ancestor, the chloroplast combines prokaryotic and eukaryotic features of gene expression and is regulated by many nucleus-encoded proteins. This review covers four major chloroplast posttranscriptional processes: RNA processing, editing, splicing, and turnover. RNA processing includes the generation of transcript 5' and 3' termini, as well as the cleavage of polycistronic transcripts. Editing converts specific C residues to U and often changes the amino acid that is specified by the edited codon. Chloroplasts feature introns of groups I and II, which undergo protein-facilitated cis- or trans-splicing in vivo. Each of these RNA-based processes involves proteins of the pentatricopeptide motif-containing family, which does not occur in prokaryotes. Plant-specific RNA-binding proteins may underpin the adaptation of the chloroplast to the eukaryotic context.

The pentatricopeptide repeat protein OTP82 is required for RNA editing of plastid ndhB and ndhG transcripts

Several hundred nucleus-encoded factors are required for regulating gene expression in plant organelles. Among them, the most numerous are the members of the pentatricopeptide repeat (PPR) protein family. We found that PPR protein OTP82 is essential for RNA editing of the ndhB-9 and ndhG-1 sites within transcripts encoding subunits of chloroplast NAD(P)H dehydrogenase. Despite the defects in RNA editing, otp82 did not show any phenotypes in NDH activity, stability or interaction with photosystem I, suggesting that the RNA editing events mediated by OTP82 are functionally silent even though they induce amino acid alterations. In agreement with this result, both sites are partially edited even in the wild type, implying the possibility that a single gene produces heterogeneous proteins that are functionally equivalent. Although only five nucleotides separate the ndhB-8 and ndhB-9 sites, the ndhB-8 site is normally edited in otp82 mutants, suggesting that both sites are recognized by different PPR proteins. OTP82 falls into the DYW subclass containing conserved C-terminal E and DYW motifs. As in CRR22 and CRR28, the DYW motif present in OTP82 is not essential for RNA editing in vivo.

Towards characterization of the chloroplast NAD(P)H dehydrogenase complex

The NAD(P)H dehydrogenase (NDH) complex in chloroplast thylakoid membranes functions in cyclic electron transfer, and in chlororespiration. NDH is composed of at least 15 subunits, including both chloroplast- and nuclear-encoded proteins. During the past few years, extensive proteomic and genetic research on the higher plant NDH complex has been carried out, resulting in identification of several novel nuclear-encoded subunits. In addition, a number of auxiliary proteins, which mainly regulate the expression of chloroplast-encoded ndh genes as well as the assembly and stabilization of the NDH complex, have been discovered and characterized. In the absence of detailed crystallographic data, the structure of the NDH complex has remained obscure, and therefore the role of several NDH-associated nuclear-encoded proteins either as auxiliary proteins or structural subunits remains uncertain. In this review, we summarize the current knowledge on the subunit composition and assembly process of the chloroplast NDH complex. In addition, a novel oligomeric structure of NDH, the PSI/NDH supercomplex, is discussed.

A study of new Arabidopsis chloroplast RNA editing mutants reveals general features of editing factors and their target sites

RNA editing in higher plant organelles results in the conversion of specific cytidine residues to uridine residues in RNA. The recognition of a specific target C site by the editing machinery involves trans-acting factors that bind to the RNA upstream of the C to be edited. In the last few years, analysis of mutants affected in chloroplast biogenesis has identified several pentatricopeptide repeat (PPR) proteins from the PLS subfamily that are essential for the editing of particular RNA transcripts. We selected other genes from the same subfamily and used a reverse genetics approach to identify six new chloroplast editing factors in Arabidopsis thaliana (OTP80, OTP81, OTP82, OTP84, OTP85, and OTP86). These six factors account for nine editing sites not previously assigned to an editing factor and, together with the nine PPR editing proteins previously described, explain more than half of the 34 editing events in Arabidopsis chloroplasts. OTP80, OTP81, OTP85, and OTP86 target only one editing site each, OTP82 two sites, and OTP84 three sites in different transcripts. An analysis of the target sites requiring the five editing factors involved in editing of multiple sites (CRR22, CRR28, CLB19, OTP82, and OTP84) suggests that editing factors can generally distinguish pyrimidines from purines and, at some positions, must be able to recognize specific bases.

Efficient operation of NAD(P)H dehydrogenase requires supercomplex formation with photosystem I via minor LHCI in Arabidopsis

In higher plants, the chloroplast NAD(P)H dehydrogenase (NDH) complex mediates photosystem I (PSI) cyclic and chlororespiratory electron transport. We reported previously that NDH interacts with the PSI complex to form a supercomplex (NDH-PSI). In this study, NDH18 and FKBP16-2 (FK506 Binding Protein 16-2), detected in the NDH-PSI supercomplex by mass spectrometry, were shown to be NDH subunits by the analysis of their knockdown lines. On the basis of extensive mutant characterization, we propose a structural model for chloroplast NDH, whereby NDH is divided into four subcomplexes. The subcomplex A and membrane subcomplex are conserved in cyanobacteria, but the subcomplex B and lumen subcomplex are specific to chloroplasts. Two minor light-harvesting complex I proteins, Lhca5 and Lhca6, were required for the full-size NDH-PSI supercomplex formation. Similar to crr pgr5 double mutants that completely lack cyclic electron flow activity around PSI, the lhca6 pgr5 double mutant exhibited a severe defect in growth. Consistent with the impaired NDH activity, photosynthesis was also severely affected in mature leaves of lhca6 pgr5. We conclude that chloroplast NDH became equipped with the novel subcomplexes and became associated with PSI during the evolution of land plants, and this process may have facilitated the efficient operation of NDH.

The making of a chloroplast

Since its endosymbiotic beginning, the chloroplast has become fully integrated into the biology of the host eukaryotic cell. The exchange of genetic information from the chloroplast to the nucleus has resulted in considerable co-ordination in the activities of these two organelles during all stages of plant development. Here, we give an overview of the mechanisms of light perception and the subsequent regulation of nuclear gene expression in the model plant Arabidopsis thaliana, and we cover the main events that take place when proplastids differentiate into chloroplasts. We also consider recent findings regarding signalling networks between the chloroplast and the nucleus during seedling development, and how these signals are modulated by light. In addition, we discuss the mechanisms through which chloroplasts develop in different cell types, namely cotyledons and the dimorphic chloroplasts of the C(4) plant maize. Finally, we discuss recent data that suggest the specific regulation of the light-dependent phases of photosynthesis, providing a means to optimize photosynthesis to varying light regimes.

Rice OGR1 encodes a pentatricopeptide repeat-DYW protein and is essential for RNA editing in mitochondria

RNA editing is the alteration of RNA sequences via insertion, deletion and conversion of nucleotides. In flowering plants, specific cytidine residues of RNA transcribed from organellar genomes are converted into uridines. Approximately 35 editing sites are present in the chloroplasts of higher plants; six pentatricopeptide repeat genes involved in RNA editing have been identified in Arabidopsis. However, although approximately 500 editing sites are found in mitochondrial RNAs of flowering plants, only one gene in Arabidopsis has been reported to be involved in such editing. Here, we identified rice mutants that are defective in seven specific RNA editing sites on five mitochondrial transcripts. Their various phenotypes include delayed seed germination, retarded growth, dwarfism and sterility. Mutant seeds from heterozygous plants are opaque. This mutation, named opaque and growth retardation 1 (ogr1), was generated by T-DNA insertion into a gene that encodes a pentatricopeptide repeat protein containing the DYW motif. The OGR1-sGFP fusion protein is localized to mitochondria. Ectopic expression of OGR1 in the mutant complements the altered phenotypes. We conclude that OGR1 is essential for RNA editing in rice mitochondria and is required for normal growth and development.

AtECB2, a pentatricopeptide repeat protein, is required for chloroplast transcript accD RNA editing and early chloroplast biogenesis in Arabidopsis thaliana

Chloroplast biogenesis is a complex process in higher plants. Screening chloroplast biogenesis mutants, and elucidating their molecular mechanisms, will provide insight into the process of chloroplast biogenesis. In this paper, we obtained an early chloroplast biogenesis mutant atecb2 that displayed albino cotyledons and was seedling lethal. Microscopy observations revealed that the chloroplast of atecb2 mutants lacked an organized thylakoid membrane. The AtECB2 gene, which is highly expressed in cotyledons and seedlings, encodes a pentatricopeptide repeat protein (PPR) with a C-terminal DYW domain. The AtECB2 protein is localized in the chloroplast, and contains a conserved HxEx(n)CxxC motif that is similar to the activated site of cytidine deaminase. The AtECB2 mutation affects the expression pattern of plastid-encoded genes. Immunoblot analyses showed that the levels of photosynthetic proteins decreased substantially in atecb2 mutants. Inspection of all reported plastid RNA editing sites revealed that one editing site, accD, is not edited in atecb2 mutants. Therefore, the AtECB2 protein must regulate the RNA editing of this site, and the dysfunctional AccD protein from the unedited RNA molecules could lead to the mutated phenotype. All of these results indicate that AtECB2 is required for chloroplast transcript accD RNA editing and early chloroplast biogenesis in Arabidopsis thaliana.

Genome-wide analysis of plastid gene expression in potato leaf chloroplasts and tuber amyloplasts: transcriptional and posttranscriptional control

Gene expression in nongreen plastids is largely uncharacterized. To compare gene expression in potato (Solanum tuberosum) tuber amyloplasts and leaf chloroplasts, amounts of transcripts of all plastid genes were determined by hybridization to plastome arrays. Except for a few genes, transcript accumulation was much lower in tubers compared with leaves. Transcripts of photosynthesis-related genes showed a greater reduction in tubers compared with leaves than transcripts of genes for the genetic system. Plastid genome copy number in tubers was 2- to 3-fold lower than in leaves and thus cannot account for the observed reduction of transcript accumulation in amyloplasts. Both the plastid-encoded and the nucleus-encoded RNA polymerases were active in potato amyloplasts. Transcription initiation sites were identical in chloroplasts and amyloplasts, although some differences in promoter utilization between the two organelles were evident. For some intron-containing genes, RNA splicing was less efficient in tubers than in leaves. Furthermore, tissue-specific differences in editing of ndh transcripts were detected. Hybridization of the plastome arrays with RNA extracted from polysomes indicated that, in tubers, ribosome association of transcripts was generally low. Nevertheless, some mRNAs, such as the transcript of the fatty acid biosynthesis gene accD, displayed relatively high ribosome association. Selected nuclear genes involved in plastid gene expression were generally significantly less expressed in tubers than in leaves. Hence, compared with leaf chloroplasts, gene expression in tuber amyloplasts is much lower, with control occurring at the transcriptional, posttranscriptional, and translational levels. Candidate regulatory sequences that potentially can improve plastid (trans)gene expression in amyloplasts have been identified.

LPA66 is required for editing psbF chloroplast transcripts in Arabidopsis

To gain insight into the molecular mechanism of RNA editing, we have characterized the low psii accumulation66 (lpa66) Arabidopsis (Arabidopsis thaliana) mutant, which displays a high chlorophyll fluorescence phenotype. Its perturbed chlorophyll fluorescence is reflected in reduced levels of photosystem II (PSII) proteins. In vivo protein labeling showed that synthesis rates of the PSII reaction center protein D1/D2 were lower, and turnover rates of PSII core proteins higher, than in wild-type counterparts. The assembly of newly synthesized proteins into PSII occurs in the lpa66 mutant but with reduced efficiency compared with the wild type. LPA66 encodes a chloroplast protein of the pentatricopeptide repeat family. In lpa66 mutants, editing of psbF that converts serine to phenylalanine is specifically impaired. Thus, LPA66 is specifically required for editing the psbF transcripts in Arabidopsis, and the amino acid alternation due to lack of editing strongly affects the efficiency of the assembly of PSII complexes.

Quantitative analysis of the relationship between induction kinetics of chlorophyll fluorescence and function of genes in the cyanobacterium Synechocystis sp. PCC 6803

We developed here the quantitative and objective method to analyze chlorophyll fluorescence from the cyanobacterium Synechocystis sp. PCC 6803 in the aim of systematic examination of gene function. The overall similarity of the chlorophyll fluorescence induction kinetics was evaluated for 499 mutants. Mutants of 333 genes showed the difference in the fluorescence kinetics from that of wild type, indicating the wide interaction of photosynthesis with other metabolisms. Hierarchical clustering of the similarity of the mutants enables us to group together the mutants having defect in the regulation of photosystem stoichiometry as well as those having defects in respiration or other functions. Furthermore, wild-type cells treated with inhibitors of respiration and mutants of genes involved in respiration shared similar induction kinetics. Apparently, quantitative comparison of the induction kinetics could be useful to analyze the function of genes as well as to predict the target sites of various chemicals.

AtCYP20-2 is an auxiliary protein of the chloroplast NAD(P)H dehydrogenase complex

AtCYP20-2 is one of 16 immunophilins in thylakoid lumen. The presence of the isomerase domain in AtCYP20-2, an enrichment of AtCYP20-2 in the stroma membranes and it's co-migration with NAD(P)H dehydrogenase (NDH) in native gels provide evidence that AtCYP20-2 is an auxiliary protein of NDH. When different NDH mutants were studied, AtCYP20-2 was found to be strongly reduced especially in mutants deficient in the membrane domain of NDH, thus suggesting a role in the assembly of NDH hydrophobic domain. Lack of AtCYP20-2, however, did not lead to severe malfunction of NDH, indicating redundancy in the function of lumenal immunophilins.

A comparative genomics approach identifies a PPR-DYW protein that is essential for C-to-U editing of the Arabidopsis chloroplast accD transcript

Several nuclear-encoded proteins containing pentatricopeptide repeat (PPR) motifs have previously been identified to be trans-factors essential for particular chloroplast RNA editing events through analysis of mutants affected in chloroplast biogenesis or function. Other PPR genes are known to encode proteins involved in other aspects of organelle RNA metabolism. A function has not been assigned to most members of the large plant PPR gene family. Arabidopsis and rice each contain over 400 PPR genes, of which about a fifth exhibit a C-terminal DYW domain. We describe here a comparative genomics approach that will facilitate identification of the role of RNA-binding proteins in organelle RNA metabolism. We have implemented this strategy to identify an Arabidopsis nuclear-encoded gene RARE1 that is required for editing of the chloroplast accD transcript. RARE1 carries 15 PPR motifs, an E/E+ and a DYW domain, whereas previously reported editing factors CRR4, CRR21, and CLB19 lack a DYW domain. The accD gene encodes the beta carboxyltransferase subunit of acetyl coA carboxylase, which catalyzes the first step in fatty acid biosynthesis in chloroplasts. Despite a lack of accD C794 editing and lack of restoration of an evolutionarily conserved leucine residue in the beta carboxyltransferase protein, rare1 mutants are unexpectedly robust and reproduce under growth room conditions. Previously the serine-to-leucine alteration caused by editing was deemed essential in the light of the finding that a recombinantly expressed "unedited" form of the pea acetyl coA carboxylase was catalytically inactive.

Site-specific binding of a PPR protein defines and stabilizes 5' and 3' mRNA termini in chloroplasts

Chloroplast mRNA populations are characterized by overlapping transcripts derived by processing from polycistronic precursors. The mechanisms and functional significance of these processing events are poorly understood. We describe a pentatricopeptide repeat (PPR) protein, PPR10, whose binding defines mRNA segments derived from two transcription units in maize chloroplasts. PPR10 interacts in vivo and in vitro with two intergenic RNA regions of similar sequence. The processed 5' and 3' RNA termini in these regions overlap by approximately 25 nucleotides. The PPR10-binding sites map precisely to these overlapping sequences, and PPR10 is required specifically for the accumulation of RNAs with these termini. These findings show that PPR10 serves as a barrier to RNA decay from either the 5' or 3' direction and that a bound protein provides an alternative to an RNA hairpin as a barrier to 3' exonucleases. The results imply that protein 'caps' at both 5' and 3' ends can define the termini of chloroplast mRNA segments. These results, together with recent insights into bacterial RNA decay, suggest a unifying model for the biogenesis of chloroplast transcript populations and for the determinants of chloroplast mRNA stability.

Photosynthetic electron transport and proton flux under moderate heat stress

Moderate heat stress has been reported to increase PSI cyclic electron flow (CEF). We subjected leaves of Arabidopsis (Arabidopsis thaliana) mutants disrupted in the regulation of one or the other pathway of CEF flow-crr2 (chlororespiratory reduction, deficient in regulation of chloroplast NAD(P)H dehydrogenase-dependent CEF) and pgr5 (proton gradient regulation, proposed to have reduced efficiency of antimycin-A-sensitive-CEF regulation) to moderate heat stress. Light-adapted leaves were switched from 23 to 40 degrees C in 2 min. Gas exchange, chlorophyll fluorescence, the electrochromic shift (ECS), and P700 were measured. Photosynthesis of crr2 and pgr5 was more sensitive to heat and had less ability to recover than the genetic background gl. The proton conductance in light was increased by heat and it was twice as much in pgr5, which had much smaller light-induced proton motive force. We confirmed that P700 becomes more reduced at high temperature and show that, in contrast, the proportion of PSII open centers (with Q (A) oxidized) increases. The two mutants had much slower P700(+) reduction rate during and after heat than gl. The proportion of light absorbed by PSI versus PSII was increased in gl and crr2 during and after heat treatment, but not in pgr5. We propose that heat alters the redox balance away from PSII and toward PSI and that the regulation of CEF helps photosynthesis tolerate heat stress.

Chloroplast ribonucleoprotein CP31A is required for editing and stability of specific chloroplast mRNAs

Chloroplast ribonucleoproteins (cpRNPs) are nuclear-encoded, highly abundant, and light-regulated RNA binding proteins. They have been shown to be involved in chloroplast RNA processing and stabilization in vitro and are phylogenetically related to the well-described heterogeneous nuclear ribonucleoproteins (hnRNPs). cpRNPs have been found associated with mRNAs present in chloroplasts and have been regarded as nonspecific stabilizers of chloroplast transcripts. Here, we demonstrate that null mutants of the cpRNP family member CP31A exhibit highly specific and diverse defects in chloroplast RNA metabolism. First, analysis of cp31a and cp31a/cp31b double mutants uncovers that these 2 paralogous genes participate nonredundantly in a combinatorial fashion in processing a subset of chloroplast editing sites in vivo. Second, a genome-wide analysis of chloroplast transcript accumulation in cp31a mutants detected a virtually complete loss of the chloroplast ndhF mRNA and lesser reductions for specific other mRNAs. Fluorescence analyses show that the activity of the NADH dehydrogenase complex, which also includes the NdhF subunit, is defective in cp31a mutants. This indicates that cpRNPs are important in vivo for calibrating the expression levels of specific chloroplast mRNAs and impact chloroplast physiology. Taken together, the specificity and combinatorial aspects of cpRNP functions uncovered suggest that these chloroplast proteins are functional equivalents of nucleocytosolic hnRNPs.

Post-transcriptional control of chloroplast gene expression

Chloroplasts contain their own genome, organized as operons, which are generally transcribed as polycistronic transcriptional units. These primary transcripts are processed into smaller RNAs, which are further modified to produce functional RNAs. The RNA processing mechanisms remain largely unknown and represent an important step in the control of chloroplast gene expression. Such mechanisms include RNA cleavage of pre-existing RNAs, RNA stabilization, intron splicing, and RNA editing. Recently, several nuclear-encoded proteins that participate in diverse plastid RNA processing events have been characterised. Many of them seem to belong to the pentatricopeptide repeat (PPR) protein family that is implicated in many crucial functions including organelle biogenesis and plant development. This review will provide an overview of current knowledge of the post-transcriptional processing in chloroplasts.

A DYW domain-containing pentatricopeptide repeat protein is required for RNA editing at multiple sites in mitochondria of Arabidopsis thaliana

RNA editing in flowering plant mitochondria alters 400 to 500 nucleotides from C to U, changing the information content of most mRNAs and some tRNAs. So far, none of the specific or general factors responsible for RNA editing in plant mitochondria have been identified. Here, we characterize a nuclear-encoded gene that is involved in RNA editing of three specific sites in different mitochondrial mRNAs in Arabidopsis thaliana, editing sites rps4-956, nad7-963, and nad2-1160. The encoded protein MITOCHONDRIAL RNA EDITING FACTOR1 (MEF1) belongs to the DYW subfamily of pentatricopeptide repeat proteins. Amino acid identities altered in MEF1 from ecotype C24, in comparison to Columbia, lower the activity at these editing sites; single amino acid changes in mutant plants inactivate RNA editing. These variations most likely modify the affinity of the editing factor to the affected editing sites in C24 and in the mutant plants. Since lowered and even absent RNA editing is tolerated at these sites, the amino acid changes may be silent for the respective protein functions. Possibly more than these three identified editing sites are addressed by this first factor identified for RNA editing in plant mitochondria.

A novel nuclear-encoded protein, NDH-dependent cyclic electron flow 5, is essential for the accumulation of chloroplast NAD(P)H dehydrogenase complexes

The chloroplast NAD(P)H dehydrogenase (NDH) complex, which reduces plastoquinones in thylakoid membranes, is involved in PSI cyclic electron flow and chlororespiration. In addition to land plants, the NDH complex is conserved in cyanobacteria. In this study, we identified a novel NDH-related gene of Arabidopsis, NDH-dependent cyclic electron flow 5 (NDF5, At1g55370). Post-illumination increases in chlorophyll fluorescence were absent in ndf5 mutant plants, which indicated that NDF5 is essential for NDH activity. Sequence analysis did not reveal any known functional motifs in NDF5, but there was some homology in amino acid sequence between NDF5 and NDF2, a known NDH subunit. NDF5 and NDF2 homologs were present in higher plants, but not cyanobacteria. A single homolog, which had similarity to both NDF5 and NDF2, was identified in the moss Physcomitrella patens. Immunoblot analysis showed that NDF5 localizes to membrane fractions of chloroplasts. The stability of NdhH, a subunit of the NDH complex, as well as NDF5 and NDF2, was decreased in ndf5, ndf2 and double ndf2/ndf5 mutants, resulting in a loss of NDH activity in these mutants. These results indicated that both NDF5 and NDF2 have essential functions in the stabilization of the NDH complex. We propose that NDF5 and NDF2 were acquired by land plants during evolution, and that in higher plants both NDF5 and NDF2 are critical to regulate NDH activity and each other's protein stability, as well as the stability of additional NDH subunits.

Reduction of the primary donor P700 of photosystem I during steady-state photosynthesis under low light in Arabidopsis

During steady-state photosynthesis in low-light, 830-nm absorption (A(830)) by leaves was close to that in darkness in Arabidopsis, indicating that the primary donor P700 in the reaction center of photosystem I (PSI) was in reduced form. However, P700 was not fully oxidized by a saturating light pulse, suggesting the presence of a population of PSI centers with reduced P700 that remains thermodynamically stable during the application of the saturating light pulse (i.e., reduced-inactive P700). To substantiate this, the effects of methyl viologen (MV) and far-red light on P700 oxidation by the saturating light pulse were analyzed, and the cumulative effects of repetitive application of the saturating light pulse on photosynthesis were analyzed using a mutant crr2-2 with impaired PSI cyclic electron flow. We concluded that the reduced-inactive P700 in low-light as revealed by saturating light pulse indicates limitations of electron flow at the PSI acceptor side.

Pentatricopeptide repeat proteins with the DYW motif have distinct molecular functions in RNA editing and RNA cleavage in Arabidopsis chloroplasts

The plant-specific DYW subclass of pentatricopeptide repeat proteins has been postulated to be involved in RNA editing of organelle transcripts. We discovered that the DYW proteins CHLORORESPIRATORY REDUCTION22 (CRR22) and CRR28 are required for editing of multiple plastid transcripts but that their DYW motifs are dispensable for editing activity in vivo. Replacement of the DYW motifs of CRR22 and CRR28 by that of CRR2, which has been shown to be capable of endonucleolytic cleavage, blocks the editing activity of both proteins. In return, the DYW motifs of neither CRR22 nor CRR28 can functionally replace that of CRR2. We propose that different DYW family members have acquired distinct functions in the divergent processes of RNA maturation, including RNA cleavage and RNA editing.

Chlororespiration and grana hyperstacking: how an Arabidopsis double mutant can survive despite defects in starch biosynthesis and daily carbon export from chloroplasts

An Arabidopsis (Arabidopsis thaliana) double mutant impaired in starch biosynthesis and the triose phosphate/phosphate translocator (adg1-1/tpt-1) is characterized by a diminished utilization of photoassimilates and the concomitant consumption of reducing power and energy produced in the photosynthetic light reaction. In order to guarantee survival, the double mutant responds to this metabolic challenge with growth retardation, an 80% decline in photosynthetic electron transport, diminished chlorophyll contents, an enhanced reduction state of plastoquinone in the dark (up to 50%), a perturbation of the redox poise in leaves (increased NADPH/NADP ratios and decreased ascorbate/dehydroascorbate ratios), hyperstacking of grana thylakoids, and an increased number of plastoglobules. Enhanced oxygen consumption and applications of inhibitors of alternative mitochondrial and chloroplast oxidases (AOX and PTOX) suggest that chlororespiration as well as mitochondrial respiration are involved in the enhanced plastoquinone reduction state in the dark. Transcript amounts of PTOX and AOX were diminished and nucleus-encoded components related to plastidic NADH reductase (NDH1) were increased in adg1-1/tpt-1 compared with the wild type. Cytochrome b559, proposed to be involved in the reoxidation of photosystem II, was not regulated at the transcriptional level. The hyperstacking of grana thylakoids mimics adaptation to low light, and increased plastoglobule numbers suggest a response to enhanced oxidative stress. Altered chloroplast organization combined with perturbations in the redox poise suggests that adg1-1/tpt-1 could be a tool for the in vivo study of retrograde signaling mechanisms controlling the coordinated expression of nucleus- and plastome-encoded photosynthetic genes.

Three novel subunits of Arabidopsis chloroplastic NAD(P)H dehydrogenase identified by bioinformatic and reverse genetic approaches

Chloroplastic NAD(P)H dehydrogenase (NDH) plays a role in cyclic electron flow around photosystem I to produce ATP, especially in adaptation to environmental changes. Although the NDH complex contains 11 subunits that are homologous to NADH:ubiquinone oxidoreductase (complex I; EC 1.6.5.3), recent genetic and biological studies have indicated that NDH also comprises unique subunits. We describe here an in silico approach based on co-expression analysis and phylogenetic profiling that was used to identify 65 genes as potential candidates for NDH subunits. Characterization of 21 Arabidopsis T-DNA insertion mutants among these ndh gene candidates indicated that three novel ndf (NDH-dependent cyclic electron flow) mutants (ndf1, ndf2 and ndf4) had impaired NDH activity as determined by measurement of chlorophyll fluorescence. The amount of NdhH subunit was greatly decreased in these mutants, suggesting that the loss of NDH activity was caused by a defect in accumulation of the NDH complex. In addition, NDF1, NDF2 and NDF4 proteins co-migrated with the NdhH subunit, as shown by blue native electrophoresis. These results strongly suggest that NDF proteins are novel subunits of the NDH complex. Further analysis revealed that the NDF1 and NDF2 proteins were unstable in the mutants lacking hydrophobic subunits of the NDH complex, but were stable in mutants lacking the hydrophilic subunits, suggesting that NDF1 and NDF2 interact with a hydrophobic sub-complex. NDF4 protein was predicted to possess a redox-active iron-sulfur cluster domain that may be involved in the electron transfer.

The chloroplast NAD(P)H dehydrogenase complex interacts with photosystem I in Arabidopsis

The chloroplast NAD(P)H dehydrogenase (NDH) complex is involved in photosystem I (PSI) cyclic and chlororespiratory electron transport in higher plants. Although biochemical and genetic evidence for its subunit composition has accumulated, it is not enough to explain the complexes putative activity of NAD(P)H-dependent plastoquinone reduction. We analyzed the NDH complex by using blue native PAGE and found that it interacts with PSI to form a novel supercomplex. Mutants lacking NdhL and NdhM accumulated a pigment-protein complex with a slightly lower molecular mass than that of the NDH-PSI supercomplex; this may be an intermediate supercomplex including PSI. This intermediate is unstable in mutants lacking NdhB, NdhD, or NdhF, implying that it includes some NDH subunits. Analysis of thylakoid membrane complexes using sucrose density gradient centrifugation supported the presence of the NDH-PSI supercomplex in vivo. Although the NDH complex exists as a monomer in etioplasts, it interacts with PSI to form a supercomplex within 48 h during chloroplast development.

Characterization of Raphanus sativus pentatricopeptide repeat proteins encoded by the fertility restorer locus for Ogura cytoplasmic male sterility

Cytoplasmic male sterility is a maternally inherited trait in higher plants that prevents the production of functional pollen. Ogura cytoplasmic male sterility in radish (Raphanus sativus) is regulated by the orf138 mitochondrial locus. Male fertility can be restored when orf138 accumulation is suppressed by the nuclear Rfo locus, which consists of three genes putatively encoding highly similar pentatricopeptide repeat proteins (PPR-A, -B, and -C). We produced transgenic rapeseed (Brassica napus) plants separately expressing PPR-A and PPR-B and demonstrated that both encoded proteins accumulated preferentially in the anthers of young flower buds. Immunodetection of ORF138 showed that, unlike PPR-B, PPR-A had no effect on the synthesis of the sterility protein. Moreover, immunolocalization experiments indicated that complete elimination of ORF138 from the tapetum of anthers correlated with the restoration of fertility. Thus, the primary role of PPR-B in restoring fertility is to inhibit ORF138 synthesis in the tapetum of young anthers. In situ hybridization experiments confirmed, at the cellular level, that PPR-B has no effect on the accumulation of orf138 mRNA. Lastly, immunoprecipitation experiments demonstrated that PPR-B, but not PPR-A, is associated with the orf138 RNA in vivo, linking restoration activity with the ability to directly or indirectly interact with the orf138 RNA. Together, our data support a role for PPR-B in the translational regulation of orf138 mRNA.

Two CRM protein subfamilies cooperate in the splicing of group IIB introns in chloroplasts

Chloroplast genomes in angiosperms encode approximately 20 group II introns, approximately half of which are classified as subgroup IIB. The splicing of all but one of the subgroup IIB introns requires a heterodimer containing the peptidyl-tRNA hydrolase homolog CRS2 and one of two closely related proteins, CAF1 or CAF2, that harbor a recently recognized RNA binding domain called the CRM domain. Two CRS2/CAF-dependent introns require, in addition, a CRM domain protein called CFM2 that is only distantly related to CAF1 and CAF2. Here, we show that CFM3, a close relative of CFM2, associates in vivo with those CRS2/CAF-dependent introns that are not CFM2 ligands. Mutant phenotypes in rice and Arabidopsis support a role for CFM3 in the splicing of most of the introns with which it associates. These results show that either CAF1 or CAF2 and either CFM2 or CFM3 simultaneously bind most chloroplast subgroup IIB introns in vivo, and that the CAF and CFM subunits play nonredundant roles in splicing. These results suggest that the expansion of the CRM protein family in plants resulted in two subfamilies that play different roles in group II intron splicing, with further diversification within a subfamily to accommodate multiple intron ligands.

Amino acid sequence variations in Nicotiana CRR4 orthologs determine the species-specific efficiency of RNA editing in plastids

In flowering plants, RNA editing is a posttranscriptional process that converts specific C to U in organelle mRNAs. Nicotiana tabacum is an allotetraploid species derived from the progenitors of Nicotiana sylvestris and Nicotiana tomentosiformis. These Nicotiana species have been used as a model for understanding the mechanism and evolution of RNA editing in plastids. In Nicotiana species, the ndhD-1 site is edited to create the translational initiation codon of ndhD that encodes a subunit of the NAD(P)H dehydrogenease (NDH) complex. An analysis of this RNA editing revealed that editing efficiency in N. tomentosiformis is lower (15%) than that in N. tabacum (42%) and N. sylvestris (37%). However, this level of editing is sufficient for accumulating the NDH complex and its activity. The heterogous complementation of Arabidopsis crr4-3 mutant, in which RNA editing of ndhD-1 is completely impaired, with CRR4 orthologous genes derived from Nicotiana species suggested that the reduction in editing efficiency in N. tomentosiformis is caused by amino acid variations accumulating in CRR4.

Electron transport activities of Arabidopsis thaliana mutants with impaired chloroplastic NAD(P)H dehydrogenase

The activities of electron transport are compared between wild-type Arabidopsis and two Arabidopsis mutants deficient for the chloroplastic NAD(P)H dehydrogenase (NDH) which catalyzes cyclic electron transport around photosystem I. The quantum yield of photosystem II and the degree of non-photochemical quenching of chlorophyll fluorescence were of similar levels in the two NDH-deficient mutants and the wild type under non-stressed standard growth conditions. Stromal over-reduction was induced in Arabidopsis NDH mutants with high light treatment, as is the case in tobacco NDH mutants. However, unlike tobacco mutants, photoinhibition was not observed in the Arabidopsis NDH mutants.

Complex chloroplast RNA metabolism: just debugging the genetic programme?

Background

The gene expression system of chloroplasts is far more complex than that of their cyanobacterial progenitor. This gain in complexity affects in particular RNA metabolism, specifically the transcription and maturation of RNA. Mature chloroplast RNA is generated by a plethora of nuclear-encoded proteins acquired or recruited during plant evolution, comprising additional RNA polymerases and sigma factors, and sequence-specific RNA maturation factors promoting RNA splicing, editing, end formation and translatability. Despite years of intensive research, we still lack a comprehensive explanation for this complexity.

Results

We inspected the available literature and genome databases for information on components of RNA metabolism in land plant chloroplasts. In particular, new inventions of chloroplast-specific mechanisms and the expansion of some gene/protein families detected in land plants lead us to suggest that the primary function of the additional nuclear-encoded components found in chloroplasts is the transgenomic suppression of point mutations, fixation of which occurred due to an enhanced genetic drift exhibited by chloroplast genomes. We further speculate that a fast evolution of transgenomic suppressors occurred after the water-to-land transition of plants.

Conclusion

Our inspections indicate that several chloroplast-specific mechanisms evolved in land plants to remedy point mutations that occurred after the water-to-land transition. Thus, the complexity of chloroplast gene expression evolved to guarantee the functionality of chloroplast genetic information and may not, with some exceptions, be involved in regulatory functions.

NDF6: a thylakoid protein specific to terrestrial plants is essential for activity of chloroplastic NAD(P)H dehydrogenase in Arabidopsis

NAD(P)H dehydrogenase (NDH) is a homolog of respiratory complex I and mediates one of the two pathways of cyclic electron flow around PSI (CEF I). Although 15 ndh subunits have been identified in the chloroplastic and nuclear genomes of higher plants, no electron accepter subunits have been identified to date. To identify the missing chloroplastic NDH subunits, we undertook an in silico approach based on co-expression analysis. In this report, we characterized the novel gene NDF6 (NDH-dependent flow 6; At1g18730) which encodes a protein that is essential for NDH activity. NDF6 has one transmembrane domain and is localized in the thylakoid membrane fraction. Homologous proteins of NDF6 were identified in the genomes of terrestrial plants; however, no homologs have been found in cyanobacteria, which are thought to be the origin of chloroplasts and have a minimal NDH complex unit. NDF6 is unstable in ndhB-impaired or disrupted mutants of higher plants in which the chloroplastic NDH complex is thought to be degraded. These results suggest that NDF6 is a novel subunit of chloroplastic NDH that was added to terrestrial plants during evolution.

The pentatricopeptide repeat protein PPR5 stabilizes a specific tRNA precursor in maize chloroplasts

Genes for pentatricopeptide repeat (PPR) proteins are found in all eukaryotic genomes analyzed but are particularly abundant in land plants. The majority of analyzed PPR proteins play a role in the processing or translation of organellar RNAs. Few PPR proteins have been studied in detail, and the functional repertoire and mechanisms of action of proteins in the PPR family are poorly understood. Here we analyzed a maize ortholog of the embryo-essential Arabidopsis thaliana gene AtPPR5. A genome-wide analysis of chloroplast RNAs that coimmunoprecipitate with Zea mays PPR5 (ZmPPR5) demonstrated that ZmPPR5 is bound in vivo to the unspliced precursor of trnG-UCC. Null and hypomorphic Zmppr5 insertion mutants are embryo viable but are deficient for chloroplast ribosomes and die as seedlings. These mutants show a dramatic decrease in both spliced and unspliced trnG-UCC RNAs, while the transcription of trnG-UCC is unaffected. These results, together with biochemical data documenting the sequence-specific binding of recombinant PPR5 to the trnG-UCC group II intron, suggest that PPR5 stabilizes the trnG-UCC precursor by directly binding and protecting an endonuclease-sensitive site. These findings add to the evidence that chloroplast-localized PPR proteins that are embryo essential in Arabidopsis typically function in the biogenesis of the plastid translation machinery.

The pentratricopeptide repeat protein DELAYED GREENING1 is involved in the regulation of early chloroplast development and chloroplast gene expression in Arabidopsis

An Arabidopsis (Arabidopsis thaliana) mutant that exhibited a delayed greening phenotype (dg1) was isolated from a population of activation-tagged Arabidopsis lines. Young, inner leaves of dg1 mutants were initially very pale, but gradually greened and mature outer leaves, more than 3 weeks old, appeared similar to those of wild-type plants. Sequence and transcription analyses showed that DG1 encodes a chloroplast protein consisting of eight pentratricopeptide repeat domains and that its expression depends on both light and developmental status. In addition, analysis of the transcript profiles of chloroplast genes revealed that plastid-encoded polymerase-dependent transcript levels were markedly reduced, while nucleus-encoded polymerase-dependent transcript levels were increased, in dg1 mutants. Thus, DG1 is probably involved in the regulation of plastid-encoded polymerase-dependent chloroplast gene expression during early stages of chloroplast development.

Organellar RNA editing and plant-specific extensions of pentatricopeptide repeat proteins in jungermanniid but not in marchantiid liverworts

The pyrimidine exchange type of RNA editing in land plant (embryophyte) organelles has largely remained an enigma with respect to its biochemical mechanisms, the underlying specificities, and its raison d'être. Apparently arising with the earliest embryophytes, RNA editing is conspicuously absent in one clade of liverworts, the complex thalloid Marchantiidae. Several lines of evidence suggest that the large gene family of organelle-targeted RNA-binding pentatricopeptide repeat (PPR) proteins plays a fundamental role in the sequence-specific editing of organelle transcripts. We here describe the identification of PPR protein genes with plant-specific carboxyterminal (C-terminal) sequence signatures (E, E+, and DYW domains) in ferns, lycopodiophytes, mosses, hornworts, and jungermanniid liverworts, one subclass of the basal most clade of embryophytes, on DNA and cDNA level. In contrast, we were unable to identify these genes in a wide sampling of marchantiid liverworts (including the phylogenetic basal genus Blasia)--taxa for which no RNA editing is observed in the organelle transcripts. On the other hand, we found significant diversity of this type of PPR proteins also in Haplomitrium, a genus with an extremely high rate of RNA editing and a phylogenetic placement basal to all other liverworts. Although the presence of modularly extended PPR proteins correlates well with organelle RNA editing, the now apparent complete loss of an entire gene family from one clade of embryophytes, the marchantiid liverworts, remains puzzling.

Cross-competition in editing of chloroplast RNA transcripts in vitro implicates sharing of trans-factors between different C targets

C-->U plant organellar RNA editing is required for the translation of evolutionarily conserved and functional proteins. 28 different C targets of RNA editing have been identified in maize chloroplasts, and hundreds of Cs are edited in mitochondria. Mutant analysis in Arabidopsis has indicated that absence of a single site-specific recognition protein can result in loss of editing of a single C target, raising the possibility that each C target requires a recognition protein. Here we show that transcripts encompassing two editing sites, ZMrpoB C467 and ZMrps14 C80, can compete editing activity from each other in vitro despite limited sequence similarity. The signal causing competition overlaps a 5'-cis element required for editing efficiency. A single five-nucleotide mutation spanning the region from -20 to -16 relative to the edited C of rpoB C467 is sufficient to eliminate its substrate editing as well as its ability to compete editing activity from rps14 C80 substrates. A corresponding mutation in an rps14 C80 competitor likewise eliminated its ability to compete editing activity from rpoB C467 substrates. Taken together, our results indicate that the RNA sequences mediating both editing efficiency and cross-competition are highly similar and that a common protein is involved in their editing. Sharing of trans-factors can facilitate editing of the large number of different C targets in plant organelles so that a different protein factor would not be required for every editing site.

Pentatricopeptide repeat (PPR) proteins as sequence-specificity factors in post-transcriptional processes in organelles

PPR (pentatricopeptide repeat) genes form a large family particularly prevalent in higher plants and targeted to organelles. They are involved in many post-transcriptional processes such as splicing, editing, processing and translation. Current data suggest that PPR proteins are involved in targeting effectors to the correct sites on the correct transcripts but the molecular mechanisms for RNA binding and effector recruitment by PPR proteins are not understood yet.

On the expansion of the pentatricopeptide repeat gene family in plants

Pentatricopeptide repeat (PPR) proteins form a huge family in plants (450 members in Arabidopsis and 477 in rice) defined by tandem repetitions of characteristic sequence motifs. Some of these proteins have been shown to play a role in posttranscriptional processes within organelles, and they are thought to be sequence-specific RNA-binding proteins. The origins of this family are obscure as they are lacking from almost all prokaryotes, and the spectacular expansion of the family in land plants is equally enigmatic. In this study, we investigate the growth of the family in plants by undertaking a genome-wide identification and comparison of the PPR genes of 3 organisms: the flowering plants Arabidopsis thaliana and Oryza sativa and the moss Physcomitrella patens. A large majority of the PPR genes in each of the flowering plants are intron less. In contrast, most of the 103 PPR genes in Physcomitrella are intron rich. A phylogenetic comparison of the PPR genes in all 3 species shows similarities between the intron-rich PPR genes in Physcomitrella and the few intron-rich PPR genes in higher plants. Intron-poor PPR genes in all 3 species also display a bias toward a position of their introns at their 5' ends. These results provide compelling evidence that one or more waves of retrotransposition were responsible for the expansion of the PPR gene family in flowering plants. The differing numbers of PPR proteins are highly correlated with differences in organellar RNA editing between the 3 species.

Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa

The diversity of microRNAs and small-interfering RNAs has been extensively explored within angiosperms by focusing on a few key organisms such as Oryza sativa and Arabidopsis thaliana. A deeper division of the plants is defined by the radiation of the angiosperms and gymnosperms, with the latter comprising the commercially important conifers. The conifers are expected to provide important information regarding the evolution of highly conserved small regulatory RNAs. Deep sequencing provides the means to characterize and quantitatively profile small RNAs in understudied organisms such as these. Pyrosequencing of small RNAs from O. sativa revealed, as expected, approximately 21- and approximately 24-nt RNAs. The former contained known microRNAs, and the latter largely comprised intergenic-derived sequences likely representing heterochromatin siRNAs. In contrast, sequences from Pinus contorta were dominated by 21-nt small RNAs. Using a novel sequence-based clustering algorithm, we identified sequences belonging to 18 highly conserved microRNA families in P. contorta as well as numerous clusters of conserved small RNAs of unknown function. Using multiple methods, including expressed sequence folding and machine learning algorithms, we found a further 53 candidate novel microRNA families, 51 appearing specific to the P. contorta library. In addition, alignment of small RNA sequences to the O. sativa genome revealed six perfectly conserved classes of small RNA that included chloroplast transcripts and specific types of genomic repeats. The conservation of microRNAs and other small RNAs between the conifers and the angiosperms indicates that important RNA silencing processes were highly developed in the earliest spermatophytes. Genomic mapping of all sequences to the O. sativa genome can be viewed at http://microrna.bcgsc.ca/cgi-bin/gbrowse/rice_build_3/.

Identification of a plastid intercistronic expression element (IEE) facilitating the expression of stable translatable monocistronic mRNAs from operons

Most plastid genes are part of operons and expressed as polycistronic mRNAs. Many primary polycistronic transcripts undergo post-transcriptional processing in monocistronic or oligocistronic units. At least some polycistronic transcripts are not translatable, and endonucleolytic processing may therefore be a prerequisite for translation to occur. As the requirements for intercistronic mRNA processing into stable monocistronic transcript are not well understood, we have sought to define minimum sequence elements that trigger processing and thus are capable of generating stable translatable monocistronic mRNAs. We describe here the in vivo identification of a small intercistronic expression element that mediates intercistronic cleavage into stable monocistronic transcripts. Separation of foreign genes by this element facilitates transgene stacking in operons, and thus will help to expand the range of applications of transplastomic technology.