HCF152, an Arabidopsis RNA binding pentatricopeptide repeat protein involved in the processing of chloroplast psbB-psbT-psbH-petB-petD RNAs

RNA immunoprecipitation and microarray analysis show a chloroplast Pentatricopeptide repeat protein to be associated with the 5' region of mRNAs whose translation it activates

Plant nuclear genomes encode hundreds of predicted organellar RNA binding proteins, few of which have been connected with their physiological RNA substrates and functions. In fact, among the largest family of putative RNA binding proteins in plants, the pentatricopeptide repeat (PPR) family, no physiologically relevant RNA ligands have been firmly established. We used the chloroplast-splicing factor CAF1 to demonstrate the fidelity of a microarray-based method for identifying RNAs associated with specific proteins in chloroplast extract. We then used the same method to identify RNAs associated with the maize (Zea mays) PPR protein CRP1. Two mRNAs whose translation is CRP1-dependent were strongly and specifically enriched in CRP1 coimmunoprecipitations. These interactions establish CRP1 as a translational regulator by showing that the translation defects in crp1 mutants are a direct consequence of the absence of CRP1. Additional experiments localized these interactions to the 5' untranslated regions and suggested a possible CRP1 interaction motif. These results enhance understanding of the PPR protein family by showing that a PPR protein influences gene expression through association with specific mRNAs in vivo, suggesting an unusual mode of RNA binding for PPR proteins, and highlighting the possibility that translational regulation may be a particularly common function of PPR proteins. Analogous methods should have broad application for the study of native RNA-protein interactions in both mitochondria and chloroplasts.

Polyadenylation and degradation of human mitochondrial RNA: the prokaryotic past leaves its mark

RNA polyadenylation serves a purpose in bacteria and organelles opposite from the role it plays in nuclear systems. The majority of nucleus-encoded transcripts are characterized by stable poly(A) tails at their mature 3' ends, which are essential for stabilization and translation initiation. In contrast, in bacteria, chloroplasts, and plant mitochondria, polyadenylation is a transient feature which promotes RNA degradation. Surprisingly, in spite of their prokaryotic origin, human mitochondrial transcripts possess stable 3'-end poly(A) tails, akin to nucleus-encoded mRNAs. Here we asked whether human mitochondria retain truncated and transiently polyadenylated transcripts in addition to stable 3'-end poly(A) tails, which would be consistent with the preservation of the largely ubiquitous polyadenylation-dependent RNA degradation mechanisms of bacteria and organelles. To this end, using both molecular and bioinformatic methods, we sought and revealed numerous examples of such molecules, dispersed throughout the mitochondrial genome. The broad distribution but low abundance of these polyadenylated truncated transcripts strongly suggests that polyadenylation-dependent RNA degradation occurs in human mitochondria. The coexistence of this system with stable 3'-end polyadenylation, despite their seemingly opposite effects, is so far unprecedented in bacteria and other organelles.

Cloning and characterization of a pentatricopeptide protein encoding gene (LOJ) that is specifically expressed in lateral organ junctions in Arabidopsis thaliana

A line exhibiting expression of beta-glucuronidase (GUS) in the lateral organ junctions and shoot apical meristem (SAM) was identified from a population of T-DNA tagged lines carrying a promoter-less GUS gene. Southern hybridization confirmed the presence of a single T-DNA insertion in this line. The plant sequences flanking the T-DNA were cloned by TAIL PCR and sequenced. The insertion of T-DNA was found to be in the upstream region of a hypothetical gene (At2g39230). This gene, which we term as LOJ to indicate its specific expression in all lateral organ junctions encodes a predicted protein containing pentatricopeptide (PPR) motifs. This gene appears to belong to a group of TATA-less promoters and codes for a long ORF without any intron. The gene apparently codes for a protein of 97.65 kD with a mitochondrial target sequence at the N-terminal. Transcript analysis revealed that the expression of the gene is specifically restricted to the lateral organ junctions throughout the life of the plants. 5' RACE analysis revealed a 95 nucleotide long UTR region for this hypothetical gene. In silico analysis of the upstream region failed to identify a TATA box within -146 nucleotides. GUS expression analysis of the line 149 and the transgenic plants generated with constructs carrying the upstream sequences of this gene fused to uidA identified that the specificity of the expression of this gene resides within -569 to -152 bp region. The specific expression of LOJ at the base of lateral organ and shoot apical meristem (SAM) suggests an important role of LOJ in lateral organ development and boundary demarcation.

Characterization of heterologous multigene operons in transgenic chloroplasts: transcription, processing, and translation

The first characterization of transcriptional, posttranscriptional, and translational processes of heterologous operons expressed via the tobacco (Nicotiana tabacum) chloroplast genome is reported here. Northern-blot analyses performed on chloroplast transgenic lines harboring seven different heterologous operons revealed that polycistronic mRNA was the predominant transcript produced. Despite the lack of processing of such polycistrons, large amounts of foreign protein accumulation was observed in these transgenic lines, indicating abundant translation of polycistrons. This is supported by polysome fractionation assays, which allowed detection of polycistronic RNA in lower fractions of the sucrose gradients. These results show that the chloroplast posttranscriptional machinery can indeed detect and translate multigenic sequences that are not of chloroplast origin. In contrast to native transcripts, processed and unprocessed heterologous polycistrons were stable, even in the absence of 3' untranslated regions (UTRs). Unlike native 5'UTRs, heterologous secondary structures or 5'UTRs showed efficient translational enhancement independent of cellular control. Abundant read-through transcripts were observed in the presence of chloroplast 3'UTRs but they were efficiently processed at introns present within the native operon. Heterologous genes regulated by the psbA (the photosystem II polypeptide D1) promoter, 5' and 3'UTRs have greater abundance of transcripts than the endogenous psbA gene because transgenes were integrated into the inverted repeat region. Addressing questions about polycistrons, and the sequences required for their processing and transcript stability, are essential in chloroplast metabolic engineering. Knowledge of such factors would enable engineering of foreign pathways independent of the chloroplast complex posttranscriptional regulatory machinery.

OsPPR1, a pentatricopeptide repeat protein of rice is essential for the chloroplast biogenesis

In this paper, we report a novel pentatricopeptide repeat (PPR) protein gene in rice. PPR, a characteristic repeat motif consisted of tandem 35 amino acids, has been found in various biological systems including plant. Sequence analysis revealed that the gene designated OsPPR1 consisted of an open reading frame of 2433 nucleotides encoding 810 amino acids that include 11 PPR motifs. Blast search result indicated that the gene did not align with any of the characterized PPR genes in plant. The OsPPR1 gene was found to contain a putative chloroplast transit peptide in the N-terminal region, suggesting that the gene product targets to the chloroplast. Southern blot hybridization indicated that the OsPPR1 is the member of a gene family within the rice genome. Expression analysis and immunoblot analysis suggested that the OsPPR1 was accumulated mainly in rice leaf. Antisense transgenic strategy was used to suppress the expression of OsPPR1 and the resulted transgenic rice showed the typical phenotypes of chlorophyll-deficient mutants; albinism and lethality. Cytological observation using microscopy revealed that the antisense transgenic plant contained a significant defect in the chloroplast development. Taken together, the results suggest that the OsPPR1 is a nuclear gene of rice, encoding the PPR protein that might play a role in the chloroplast biogenesis. This is the first report on the PPR protein required for the chloroplast biogenesis in rice.

Arabidopsis emb175 and other ppr knockout mutants reveal essential roles for pentatricopeptide repeat (PPR) proteins in plant embryogenesis

Pentatricopeptide repeat proteins (PPRPs) constitute one of the largest superfamilies in plants, with more than 440 identified in the Arabidopsis thaliana (L.) Heynh genome. While some PPRPs are known to take part in organelle gene expression, little is known about the broader biological contexts of PPRP gene function. Here, using developmental- and reverse-genetic approaches, we demonstrate that a number of PPRPs are essential early in plant development. We have characterized the Arabidopsis embryo-defective175 mutant and identified the EMB175 gene. Emb175 consistently displays aberrant cell organization and undergoes morphological arrest before the globular-heart transition. The emb175 mutation disrupts an intronless open reading frame encoding a predicted chloroplast-localized PPR protein- the first to be rigorously associated with an early embryo-lethal phenotype. To determine if other PPRP genes act in embryogenesis, we searched Arabidopsis insertion mutant collections for pprp knockout alleles, and identified 29 mutants representing 11 loci potentially associated with embryo-defective phenotypes. We assessed gene structures, T-DNA insertion position, and allelism for these loci and were able to firmly establish essential functions for six PPRP genes in addition to EMB175. Interestingly, Nomarski DIC microscopy revealed diverse embryonic defects in these lines, ranging from early lethality to dramatic late-stage morphological defects such as enlarged shoot apices and stunted cotyledons. Together, emb175 and these pprp knockout mutants establish essential roles for PPRPs in embryogenesis, thus broadening the known organismal context for PPRP gene function. The diversity of emb-pprp knockout phenotypes indicates that mutation of different PPRPs can, directly or indirectly, have distinct impacts on embryo morphogenesis.

The nuclear gene HCF107 encodes a membrane-associated R-TPR (RNA tetratricopeptide repeat)-containing protein involved in expression of the plastidial psbH gene in Arabidopsis

Expression of the genes of plastidial psbB operon (psbB-psbT-psbH-petB-petD) involves multiple processing events and formation of several mono-, di- and multi-cistronic transcripts which are further regulated by differential stability and expression. Here we describe the identification of the HCF107 gene that is involved in the 5'-end processing/stability and/or translation of the psbH gene and in the translation of the psbB gene. HCF107 is an RNA-TPR-containing protein with 11 RTPRs that are tandemly arranged. A single mutation in the third RTPR that changes a conserved alanine residue to a threonine affects both 5'-end-processed psbH transcript accumulation as well as psbB translation, resulting in disruption of PSII and seedling lethal plants. The protein is localized to the plastid membranes and is present as part of a multi-subunit complex in the range of 60-190 and 600-800 kDa. HCF107 thus represents a new member of the growing helical repeat family of proteins that seem to play a gene-specific role in regulating plastidial gene expression and biogenesis.

Chloroplast RNA-binding and pentatricopeptide repeat proteins

Chloroplast gene expression is mainly regulated at the post-transcriptional level by numerous nuclear-encoded RNA-binding protein factors. In the present study, we focus on two RNA-binding proteins: cpRNP (chloroplast ribonucleoprotein) and PPR (pentatricopeptide repeat) protein. These are suggested to be major contributors to chloroplast RNA metabolism. Tobacco cpRNPs are composed of five different proteins containing two RNA-recognition motifs and an acidic N-terminal domain. The cpRNPs are abundant proteins and form heterogeneous complexes with most ribosome-free mRNAs and the precursors of tRNAs in the stroma. The complexes could function as platforms for various RNA-processing events in chloroplasts. It has been demonstrated that cpRNPs contribute to RNA stabilization, 3'-end formation and editing. The PPR proteins occur as a superfamily only in the higher plant species. They are predicted to be involved in RNA/DNA metabolism in chloroplasts or mitochondria. Nuclear-encoded HCF152 is a chloroplast-localized protein that usually has 12 PPR motifs. The null mutant of Arabidopsis, hcf152, is impaired in the 5'-end processing and splicing of petB transcripts. HCF152 binds the petB exon-intron junctions with high affinity. The number of PPR motifs controls its affinity and specificity for RNA. It has been suggested that each of the highly variable PPR proteins is a gene-specific regulator of plant organellar RNA metabolism.

A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts

RNA editing is a process of RNA maturation involved in the insertion, deletion or modification of nucleotides. In organellar transcripts of higher plants, specific cytidine residues are converted into uridine residues. In many cases, editing results in the restoration of conserved amino acid residues, a process that is essential for protein function in plastids. Despite the technical breakthrough in establishing systems in vivo and in vitro for analysing RNA editing, its machinery still remains to be identified in higher plants. Here we introduce a genetic approach and report the discovery of a gene responsible for the specific RNA editing event in the chloroplast.

Cell-specific regulation of a Brassica napus CMS-associated gene by a nuclear restorer with related effects on a floral homeotic gene promoter

Cytoplasmic male sterility (CMS) is a maternally inherited defect in pollen production specified by novel mitochondrial genes. It can be suppressed by nuclear restorer (Rf) genes which normally downregulate expression of a CMS-associated novel mitochondrial gene. Two forms of Brassica napus CMS, nap and pol, are associated with related chimeric genes, orf222 and orf224, respectively. We show that in pol and nap CMS, anther locule development is asynchronous and asymmetric, that one or more locules within each anther may fail to develop entirely and that CMS anthers display polarity in locule development. We show, by in situ hybridization, that orf222 transcripts accumulate in sterile anthers prior to development of morphological differences between CMS and restored stamens, and remain preferentially localized to microsporangia. In fertility-restored anthers, however, orf222 transcript levels remain low throughout development. Some sporogenous and meiotic cells differentiate within CMS anthers and form functional pollen despite retaining high orf222 transcript levels, suggesting that the effect of orf222 expression in blocking pollen development is limited to an early and specific stage. Transcripts of other mitochondrial genes, exemplified by atp6 and cob, and of the nuclear-encoded ATP synthase gamma subunit, accumulate preferentially in the microsporangia of both sterile and fertile anthers. Thus nuclear fertility restoration reduces orf222 transcript levels in a gene and tissue-specific manner. We observe differences between CMS and fertile plants in the timing and patterning of APETALA3 promoter activity that suggest a possible basis for the developmental abnormalities of CMS flowers.

New Functions of the Thylakoid Membrane Proteome of Arabidopsis thaliana Revealed by a Simple, Fast, and Versatile Fractionation Strategy

Identification of membrane proteomes remains challenging. Here, we present a simple, fast, and scalable off-line procedure based on three-phase partitioning with butanol to fractionate membrane proteomes in combination with both in-gel and in-solution digestions and mass spectrometry. This should help to further accelerate the field of membrane proteomics. Using this new strategy, we analyzed the salt-stripped thylakoid membrane of chloroplasts of Arabidopsis thaliana. 242 proteins were identified, at least 40% of which are integral membrane proteins. The functions of 86 proteins are unknown; these include proteins with TPR, PPR, rhodanese, and DnaJ domains. These proteins were combined with all known thylakoid proteins and chloroplast (associated) envelope proteins, collected from primary literature, resulting in 714 non-redundant proteins. They were assigned to functional categories using a classification developed for MapMan (Thimm, O., Blasing, O., Gibon, Y., Nagel, A., Meyer, S., Kruger, P., Selbig, J., Muller, L. A., Rhee, S. Y., and Stitt, M. (2004) Plant J. 37, 914-939), updated with information from primary literature. The analysis elucidated the likely location of many membrane proteins, including 190 proteins of unknown function, holding the key to better understanding the two membrane systems. The three-phase partitioning procedure added a new level of dynamic resolution to the known thylakoid proteome. An automated strategy was developed to track possible ambiguous identifications to more than one gene model or family member. Mass spectrometry search results, ambiguities, and functional classifications can be searched via the Plastid Proteome Database.

Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis

The complete sequence of the Arabidopsis thaliana genome revealed thousands of previously unsuspected genes, many of which cannot be ascribed even putative functions. One of the largest and most enigmatic gene families discovered in this way is characterized by tandem arrays of pentatricopeptide repeats (PPRs). We describe a detailed bioinformatic analysis of 441 members of the Arabidopsis PPR family plus genomic and genetic data on the expression (microarray data), localization (green fluorescent protein and red fluorescent protein fusions), and general function (insertion mutants and RNA binding assays) of many family members. The basic picture that arises from these studies is that PPR proteins play constitutive, often essential roles in mitochondria and chloroplasts, probably via binding to organellar transcripts. These results confirm, but massively extend, the very sparse observations previously obtained from detailed characterization of individual mutants in other organisms.

Identification of genes required for embryo development in Arabidopsis

A long-term goal of Arabidopsis research is to define the minimal gene set needed to produce a viable plant with a normal phenotype under diverse conditions. This will require both forward and reverse genetics along with novel strategies to characterize multigene families and redundant biochemical pathways. Here we describe an initial dataset of 250 EMB genes required for normal embryo development in Arabidopsis. This represents the first large-scale dataset of essential genes in a flowering plant. When compared with 550 genes with other knockout phenotypes, EMB genes are enriched for basal cellular functions, deficient in transcription factors and signaling components, have fewer paralogs, and are more likely to have counterparts among essential genes of yeast (Saccharomyces cerevisiae) and worm (Caenorhabditis elegans). EMB genes also represent a valuable source of plant-specific proteins with unknown functions required for growth and development. Analyzing such unknowns is a central objective of genomics efforts worldwide. We focus here on 34 confirmed EMB genes with unknown functions, demonstrate that expression of these genes is not embryo-specific, validate a strategy for identifying interacting proteins through complementation with epitope-tagged proteins, and discuss the value of EMB genes in identifying novel proteins associated with important plant processes. Based on sequence comparison with essential genes in other model eukaryotes, we identify 244 candidate EMB genes without paralogs that represent promising targets for reverse genetics. These candidates should facilitate the recovery of additional genes required for seed development.

Expression analysis suggests novel roles for the plastidic phosphate transporter Pht2;1 in auto- and heterotrophic tissues in potato and Arabidopsis

A cDNA encoding Pht2;1 from potato, a new member of the plant Pht2 gene family of low-affinity orthophosphate (Pi) transporters, was isolated. The expression pattern of the corresponding gene as well as its ortholog from Arabidopsis was analyzed and the encoded proteins were localized in the two plants. Pht2;1 expression is strongly upregulated by light in potato and Arabidopsis leaf tissue. RNA gel blot analysis, reverse transcription-polymerase chain reaction (RT-PCR), promoter/GUS, and protein/green fluorescent protein (GFP) fusion studies, respectively, indicate that the gene is expressed in both auto- and heterotrophic tissues and its encoded protein is localized to the plastids. The similar patterns of Pht2;1 gene regulation in potato and Arabidopsis prompted us to screen publicly available gene expression data from 228 Arabidopsis oligonucleotide microarrays covering 83 different experimental conditions. Modulation of Pht2;1 transcript levels was overall moderate, except for a limited number of experimental conditions where Pht2;1 mRNA concentrations varied between 2- and 3.7-fold. Overall, these analyses suggest involvement of the Pht2;1 protein in cell wall metabolism in young, rapidly growing tissues, independent of other Pi transporters such as the high-affinity Solanum tuberosum Pi transporter 1 (StPT1). Cluster analysis allowed identification of colinear or antiparallel expression profiles of a small set of genes involved in post-translational regulation, and photosynthetic carbon metabolism. These data give clues about the possible biological function of Pht2;1 and shed light on the complex web of interactions in which Pht2;1 could play a role.

PPR motifs of the nucleus-encoded factor, PGR3, function in the selective and distinct steps of chloroplast gene expression in Arabidopsis

Plastid gene expression is regulated by a variety of nuclear genes. We have isolated Arabidopsis thaliana proton gradient regulation 3 (pgr3) mutants, which display aberrant chlorophyll fluorescence because of defects in chloroplast gene expression. High chlorophyll fluorescence (HCF) because of a reduced level of the cytochrome b6/f complex was observed in two alleles, pgr3-1 and pgr3-2 but not in pgr3-3. In contrast, a transient increase in fluorescence after turning off the actinic light, which was ascribed to chloroplast NADPH dehydrogenase (NDH) activity, was impaired in pgr3-1 and pgr3-3 but not in pgr3-2. Both phenotypes were complemented by the introduction of a single gene, PGR3, encoding a protein containing 27 pentatrico-peptide repeat (PPR) motifs. PPR motifs are present in proteins functioning in the post-transcriptional regulation of organellar gene expression. The conserved threonine in the motif was substituted by isoleucine in the 15th and 12th PPR motifs in pgr3-1 and pgr3-2, respectively, and the conserved leucine by phenylalanine in the final incomplete motif of pgr3-3. We consider that the different domains of the PPR repeats in PGR3 might have different functions in conferring RNA stability and probably allowing translation as well as recognizing at least two distinct target RNAs.

Cooperation of Endo- and Exoribonucleases in Chloroplast mRNA Turnover

Chloroplasts were acquired by eukaryotic cells through endosymbiosis and have retained their own gene expression machinery. One hallmark of chloroplast gene regulation is the predominance of posttranscriptional control, which is exerted both at the gene-specific and global levels. This review focuses on how chloroplast mRNA stability is regulated, through an examination of poly(A)-dependent and independent pathways. The poly(A)-dependent pathway is catalyzed by polynucleotide phosphorylase (PNPase), which both adds and degrades destabilizing poly(A) tails, whereas RNase II and PNPase may both participate in the poly(A)-independent pathway. Each system is initiated through endonucleolytic cleavages that remove 3' stem-loop structures, which are catalyzed by the related proteins CSP41a and CSP41b and possibly an RNase E-like enzyme. Overall, chloroplasts have retained the prokaryotic endonuclease-exonuclease RNA degradation system despite evolution in the number and character of the enzymes involved. This reflects the presence of the chloroplast within a eukaryotic host and the complex responses that occur to environmental and developmental cues.

Chloroplast RNA processing and stability

Primary chloroplast transcripts are processed in a number of ways, including intron splicing, internal cleavage of polycistronic RNAs, and endonucleolytic or exonucleolytic cleavages at the transcript termini. All chloroplast RNAs are also subject to degradation, although a curious feature of many chloroplast mRNAs is their relative longevity. Some of these processes, e.g., psbA splicing and stability of a number of chloroplast mRNAs, are regulated in response to light-dark cycles or nutrient availability. This review highlights recent advances in our understanding of these processes in the model organism Chlamydomonas reinhardtii, focusing on results since the extensive reviews published in 1998 [Herrin DL et al. 1998 (pp. 183-195), Nickelsen Y 1998 (pp. 151-163), Stern DB and Drager RG 1998 (pp. 164-182), in Rochaix JD et al. (eds) The Molecular Biology of Chloroplasts and Mitochondria in Chlamydomonas. Kluwer Academic Publishers, Dordrecht, The Netherlands]. We also allude to studies with other organisms, and to the potential impact of the Chlamydomonas genome project where appropriate.

A chloroplast-localized PPR protein required for plastid ribosome accumulation

The pentatricopeptide repeat (PPR) is a degenerate 35-amino acid repeating motif that is found in animal, fungal, and plant proteins. The PPR protein family is particularly large in plants, where the majority of family members are predicted to be targeted to mitochondria or chloroplasts. PPR proteins are believed to fall into the larger family of helical repeat proteins, which typically bind macromolecules through a surface formed by the stacking of consecutive helical repeating units. Prior findings implicate several PPR proteins in organellar RNA metabolism, but the biological functions of few PPR proteins have been explored and in no case has a direct substrate been definitively identified. We present a characterization of the maize nuclear gene ppr2, which encodes a chloroplast PPR protein. PPR2 is found in large, heterogeneous protein complexes in the chloroplast stroma, some of which may be associated with RNA. Null ppr2 mutants have albino leaves and lack plastid rRNA and translation products. Plastid rRNAs are absent in both dark- and light-grown leaf tissues, indicating that their absence does not result from photo-oxidative damage. The population of plastid transcripts in ppr2 mutants is similar to that in other maize mutants lacking plastid ribosomes, and no ppr2-specific defects in plastid RNA metabolism have been detected. Taken together, the results suggest that ppr2 functions in the synthesis or assembly of one or more component of the plastid translation machinery.

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

The chloroplast NDH complex, NAD(P)H dehydrogenase, reduces the plastoquinone pool non-photochemically and is involved in cyclic electron flow around photosystem I (PSI). A transient increase in chlorophyll fluorescence after turning off actinic light is a result of NDH activity. We focused on this subtle change in chlorophyll fluorescence to isolate nuclear mutants affected in chloroplast NDH activity in Arabidopsis by using chlorophyll fluorescence imaging. crr2-1 and crr2-2 (chlororespiratory reduction) are recessive mutant alleles in which accumulation of the NDH complex is impaired. Except for the defect in NDH activity, photosynthetic electron transport was unaffected. CRR2 encodes a member of the plant combinatorial and modular protein (PCMP) family consisting of more than 200 genes in Arabidopsis. CRR2 functions in the intergenic processing of chloroplast RNA between rps7 and ndhB, which is possibly essential for ndhB translation. We have determined the function of a PCMP family member, indicating that the family is closely related to pentatrico-peptide PPR proteins involved in the maturation steps of organellar RNA.

RNA-binding properties of HCF152, an Arabidopsis PPR protein involved in the processing of chloroplast RNA

The nonphotosynthetic mutant of Arabidopsis hcf152 is impaired in the processing of the chloroplast polycistronic transcript, psbB-psbT-psbH-petB-petD, resulting in nonproduction of the essential photosynthetic cytochrome b6f complex. The nucleus-encoded HCF152gene was identified to encode a pentatricopeptide repeat (PPR) protein composed primarily of 12 PPR motifs, similar to other proteins of this family that were identified in mutants defected in chloroplast gene expression. To understand the molecular mechanism of how HCF152 modulates chloroplast gene expression, the molecular and biochemical properties should be revealed. To this end, HCF152 and several truncated versions were produced in bacteria and analyzed for RNA-binding and protein-protein interaction. It was found that two HCF152 polypeptides bind to form a homodimer, and that this binding is impaired by a single amino acid substitute near the carboxyl terminus, replacing leucine with proline. Recombinant HCF152 bound with higher affinity RNA molecules, resembling the petB exon-intron junctions, as well as several other molecules. The highest affinity was found to RNA composed of the poly(A) sequence. When truncated proteins composed of different numbers of PPR motifs were analyzed for RNA-binding, it was found that two PPR motifs were required for RNA-binding, but had very low affinity. The affinity to RNA increased significantly when proteins composed of more PPR motifs were analyzed, displaying the highest affinity with the full-length protein composed of 12 PPR motifs. Together, our data characterized the nuclear-encoded HCF152 to be a chloroplast RNA-binding protein that may be involved in the processing or stabilization of the petB transcript by binding to the exon-intron junctions.

Chloroplast RNA-binding proteins

Chloroplast gene expression is regulated by nucleus-encoded factors, which mainly act at the post-transcriptional level. Plastid RNA-binding proteins (RBPs) represent good candidates for mediating these functions. The picture emerging from recent analyses is that of a great number of differentially regulated RBPs, which are organized in distinct, spatially separated supramolecular complexes. This reflects the complexity of the regulatory network that underlies the intracellular communication system between the nucleus and the chloroplast.