Academic literature on the topic 'PPR-Protein'
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Journal articles on the topic "PPR-Protein"
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Manavski, Nikolay, Sébastien Mathieu, Margarita Rojas, Louis-Valentin Méteignier, Andreas Brachmann, Alice Barkan, and Kamel Hammani. "In vivo stabilization of endogenous chloroplast RNAs by customized artificial pentatricopeptide repeat proteins." Nucleic Acids Research 49, no. 10 (May 25, 2021): 5985–97. http://dx.doi.org/10.1093/nar/gkab390.
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Abstract Pentatricopeptide repeat (PPR) proteins are helical repeat-proteins that bind RNA in a modular fashion with a sequence-specificity that can be manipulated by the use of an amino acid code. As such, PPR repeats are promising scaffolds for the design of RNA binding proteins for synthetic biology applications. However, the in vivo functional capabilities of artificial PPR proteins built from consensus PPR motifs are just starting to be explored. Here, we report in vivo functions of an artificial PPR protein, dPPRrbcL, made of consensus PPR motifs that were designed to bind a sequence near the 5′ end of rbcL transcripts in Arabidopsis chloroplasts. We used a functional complementation assay to demonstrate that this protein bound its intended RNA target with specificity in vivo and that it substituted for a natural PPR protein by stabilizing processed rbcL mRNA. We targeted a second protein of analogous design to the petL 5′ UTR, where it substituted for the native stabilizing PPR protein PGR3, albeit inefficiently. These results showed that artificial PPR proteins can be engineered to functionally mimic the class of native PPR proteins that serve as physical barriers against exoribonucleases.
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Gully, Benjamin S., Kunal R. Shah, Mihwa Lee, Kate Shearston, Nicole M. Smith, Agata Sadowska, Amanda J. Blythe, et al. "The design and structural characterization of a synthetic pentatricopeptide repeat protein." Acta Crystallographica Section D Biological Crystallography 71, no. 2 (January 23, 2015): 196–208. http://dx.doi.org/10.1107/s1399004714024869.
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Proteins of the pentatricopeptide repeat (PPR) superfamily are characterized by tandem arrays of a degenerate 35-amino-acid α-hairpin motif. PPR proteins are typically single-stranded RNA-binding proteins with essential roles in organelle biogenesis, RNA editing and mRNA maturation. A modular, predictable code for sequence-specific binding of RNA by PPR proteins has recently been revealed, which opens the door to thede novodesign of bespoke proteins with specific RNA targets, with widespread biotechnological potential. Here, the design and production of a synthetic PPR protein based on a consensus sequence and the determination of its crystal structure to 2.2 Å resolution are described. The crystal structure displays helical disorder, resulting in electron density representing an infinite superhelical PPR protein. A structural comparison with related tetratricopeptide repeat (TPR) proteins, and with native PPR proteins, reveals key roles for conserved residues in directing the structure and function of PPR proteins. The designed proteins have high solubility and thermal stability, and can form long tracts of PPR repeats. Thus, consensus-sequence synthetic PPR proteins could provide a suitable backbone for the design of bespoke RNA-binding proteins with the potential for high specificity.
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Guillaumot, Damien, Mauricio Lopez-Obando, Kevin Baudry, Alexandra Avon, Guillem Rigaill, Andéol Falcon de Longevialle, Benjamin Broche, et al. "Two interacting PPR proteins are major Arabidopsis editing factors in plastid and mitochondria." Proceedings of the National Academy of Sciences 114, no. 33 (July 31, 2017): 8877–82. http://dx.doi.org/10.1073/pnas.1705780114.
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RNA editing is converting hundreds of cytosines into uridines during organelle gene expression of land plants. The pentatricopeptide repeat (PPR) proteins are at the core of this posttranscriptional RNA modification. Even if a PPR protein defines the editing site, a DYW domain of the same or another PPR protein is believed to catalyze the deamination. To give insight into the organelle RNA editosome, we performed tandem affinity purification of the plastidial CHLOROPLAST BIOGENESIS 19 (CLB19) PPR editing factor. Two PPR proteins, dually targeted to mitochondria and chloroplasts, were identified as potential partners of CLB19. These two proteins, a P-type PPR and a member of a small PPR-DYW subfamily, were shown to interact in yeast. Insertional mutations resulted in embryo lethality that could be rescued by embryo-specific complementation. A transcriptome analysis of these complemented plants showed major editing defects in both organelles with a very high PPR type specificity, indicating that the two proteins are core members of E+-type PPR editosomes.
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Tawfeek, Hesham A., and Abdul B. Abou-Samra. "Disruption of parathyroid hormone and parathyroid hormone-related peptide receptor phosphorylation prolongs ERK1/2 MAPK activation and enhances c-fos expression." American Journal of Physiology-Endocrinology and Metabolism 302, no. 11 (June 1, 2012): E1363—E1372. http://dx.doi.org/10.1152/ajpendo.00034.2012.
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Previous studies have demonstrated that parathyroid hormone (PTH) binding to the PTH/PTH-related peptide receptor (PPR) stimulates G protein coupling, receptor phosphorylation, β-arrestin translocation, and internalization of the ligand/receptor complex. The extracellular signal-regulated mitogen-activated protein kinases 1/2 (ERK1/2 MAPK) are downstream effectors of PPR. In the current study, we investigated the role of PPR phosphorylation in the PTH regulation of the ERK1/2 MAPK pathway. Short treatment with PTH (0–40 min) of LLCP-K1 cells stably expressing a wild-type (WT) or a phosphorylation-deficient (PD) PPR (WT-PPR or PD-PPR cells, respectively) results in similar activation of ERK1/2. Interestingly, PTH stimulation of ERK1/2 in the WT-PPR cells then decreases as a result of longer PTH (60 min) treatment, and inhibition of ERK1/2 by PTH is observed at 90 min. Strikingly, the PD-PPR cells exhibit prolonged ERK1/2 activation up to 90 min of PTH treatment. An ERK1/2-dependent increase in c- fos expression is observed in the PD-PPR cells. Subsequently, c- fos expression in the WT-PPR and PD-PPR cells was markedly attenuated by a specific ERK1/2 pathway inhibitor. Further investigations revealed that PTH treatment causes a robust recruitment of a green fluorescent protein-tagged β-arrestin2 (β-arrestin2-GFP) in the WT-PPR cells. In contrast, β-arrestin2 recruitment was reduced in the PD-PPR cells. Importantly, expression of a receptor phosphorylation-independent β-arrestin2 (R169E) in the PD-PPR cells restored the biphasic effect of PTH on ERK1/2 as in the WT-PPR cells. The study reports a novel role for receptor phosphorylation and β-arrestin2 in the subsequent inhibition of the ERK1/2 pathway and in control of gene expression.
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Andrés-Colás, Nuria, Qiang Zhu, Mizuki Takenaka, Bert De Rybel, Dolf Weijers, and Dominique Van Der Straeten. "Multiple PPR protein interactions are involved in the RNA editing system in Arabidopsis mitochondria and plastids." Proceedings of the National Academy of Sciences 114, no. 33 (July 31, 2017): 8883–88. http://dx.doi.org/10.1073/pnas.1705815114.
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Recent identification of several different types of RNA editing factors in plant organelles suggests complex RNA editosomes within which each factor has a different task. However, the precise protein interactions between the different editing factors are still poorly understood. In this paper, we show that the E+-type pentatricopeptide repeat (PPR) protein SLO2, which lacks a C-terminal cytidine deaminase-like DYW domain, interacts in vivo with the DYW-type PPR protein DYW2 and the P-type PPR protein NUWA in mitochondria, and that the latter enhances the interaction of the former ones. These results may reflect a protein scaffold or complex stabilization role of NUWA between E+-type PPR and DYW2 proteins. Interestingly, DYW2 and NUWA also interact in chloroplasts, and DYW2-GFP overexpressing lines show broad editing defects in both organelles, with predominant specificity for sites edited by E+-type PPR proteins. The latter suggests a coordinated regulation of organellar multiple site editing through DYW2, which probably provides the deaminase activity to E+ editosomes.
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Sugita, Mamoru. "An Overview of Pentatricopeptide Repeat (PPR) Proteins in the Moss Physcomitrium patens and Their Role in Organellar Gene Expression." Plants 11, no. 17 (August 31, 2022): 2279. http://dx.doi.org/10.3390/plants11172279.
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Pentatricopeptide repeat (PPR) proteins are one type of helical repeat protein that are widespread in eukaryotes. In particular, there are several hundred PPR members in flowering plants. The majority of PPR proteins are localized in the plastids and mitochondria, where they play a crucial role in various aspects of RNA metabolism at the post-transcriptional and translational steps during gene expression. Among the early land plants, the moss Physcomitrium (formerly Physcomitrella) patens has at least 107 PPR protein-encoding genes, but most of their functions remain unclear. To elucidate the functions of PPR proteins, a reverse-genetics approach has been applied to P. patens. To date, the molecular functions of 22 PPR proteins were identified as essential factors required for either mRNA processing and stabilization, RNA splicing, or RNA editing. This review examines the P. patens PPR gene family and their current functional characterization. Similarities and a diversity of functions of PPR proteins between P. patens and flowering plants and their roles in the post-transcriptional regulation of organellar gene expression are discussed.
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Teramoto, Takamasa, Kipchumba J. Kaitany, Yoshimitsu Kakuta, Makoto Kimura, Carol A. Fierke, and Traci M. Tanaka Hall. "Pentatricopeptide repeats of protein-only RNase P use a distinct mode to recognize conserved bases and structural elements of pre-tRNA." Nucleic Acids Research 48, no. 21 (July 28, 2020): 11815–26. http://dx.doi.org/10.1093/nar/gkaa627.
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Abstract Pentatricopeptide repeat (PPR) motifs are α-helical structures known for their modular recognition of single-stranded RNA sequences with each motif in a tandem array binding to a single nucleotide. Protein-only RNase P 1 (PRORP1) in Arabidopsis thaliana is an endoribonuclease that uses its PPR domain to recognize precursor tRNAs (pre-tRNAs) as it catalyzes removal of the 5′-leader sequence from pre-tRNAs with its NYN metallonuclease domain. To gain insight into the mechanism by which PRORP1 recognizes tRNA, we determined a crystal structure of the PPR domain in complex with yeast tRNAPhe at 2.85 Å resolution. The PPR domain of PRORP1 bound to the structurally conserved elbow of tRNA and recognized conserved structural features of tRNAs using mechanisms that are different from the established single-stranded RNA recognition mode of PPR motifs. The PRORP1 PPR domain-tRNAPhe structure revealed a conformational change of the PPR domain upon tRNA binding and moreover demonstrated the need for pronounced overall flexibility in the PRORP1 enzyme conformation for substrate recognition and catalysis. The PRORP1 PPR motifs have evolved strategies for protein-tRNA interaction analogous to tRNA recognition by the RNA component of ribonucleoprotein RNase P and other catalytic RNAs, indicating convergence on a common solution for tRNA substrate recognition.
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Hao, Yuanyuan, Yunlong Wang, Mingming Wu, Xiaopin Zhu, Xuan Teng, Yinglun Sun, Jianping Zhu, et al. "The nuclear-localized PPR protein OsNPPR1 is important for mitochondrial function and endosperm development in rice." Journal of Experimental Botany 70, no. 18 (May 14, 2019): 4705–20. http://dx.doi.org/10.1093/jxb/erz226.
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Abstract Pentatricopeptide repeat (PPR) proteins constitute one of the largest protein families in land plants. Recent studies revealed the functions of PPR proteins in organellar RNA metabolism and plant development, but the functions of most PPR proteins, especially PPRs localized in the nucleus, remain largely unknown. Here, we report the isolation and characterization of a rice mutant named floury and growth retardation1 (fgr1). fgr1 showed floury endosperm with loosely arranged starch grains, decreased starch and amylose contents, and retarded seedling growth. Map-based cloning showed that the mutant phenotype was caused by a single nucleotide substitution in the coding region of Os08g0290000. This gene encodes a nuclear-localized PPR protein, which we named OsNPPR1, that affected mitochondrial function. In vitro SELEX and RNA-EMSAs showed that OsNPPR1 was an RNA protein that bound to the CUCAC motif. Moreover, a number of retained intron (RI) events were detected in fgr1. Thus, OsNPPR1 was involved in regulation of mitochondrial development and/or functions that are important for endosperm development. Our results provide novel insights into coordinated interaction between nuclear-localized PPR proteins and mitochondrial function.
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Hirai, Takao, Andrei S. Chagin, Tatsuya Kobayashi, Susan Mackem, and Henry M. Kronenberg. "Parathyroid hormone/parathyroid hormone-related protein receptor signaling is required for maintenance of the growth plate in postnatal life." Proceedings of the National Academy of Sciences 108, no. 1 (December 20, 2010): 191–96. http://dx.doi.org/10.1073/pnas.1005011108.
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Parathyroid hormone (PTH)-related protein (PTHrP), regulated by Indian hedgehog and acting through the PTH/PTHrP receptor (PPR), is crucial for normal cartilage development. These observations suggest a possible role of PPR signaling in the postnatal growth plate; however, the role of PPR signaling in postnatal chondrocytes is unknown. In this study, we have generated tamoxifen-inducible and cartilage-specific PPR KO mice to evaluate the physiological role of PPR signaling in postnatal chondrocytes. We found that inactivation of the PPR in chondrocytes postnatally leads to accelerated differentiation of chondrocytes, followed by disappearance of the growth plate. We also observed an increase of TUNEL-positive cells and activities of caspase-3 and caspase-9 in the growth plate, along with a decrease in phosphorylation of Bad at Ser155 in postnatal PPR KO mice. Administration of a low-phosphate diet, which prevents apoptosis of chondrocytes, prevented the disappearance of the growth plate. Taken together, these observations suggest that the major consequences of PPR activation are similar in both the fetal and postnatal growth plates. Moreover, chondrocyte apoptosis through the activation of a mitochondrial pathway may be involved in the process of premature disappearance of the growth plate by postnatal inactivation of the PPR in chondrocytes.
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Pusnik, Mascha, Ian Small, Laurie K. Read, Thomas Fabbro, and André Schneider. "Pentatricopeptide Repeat Proteins in Trypanosoma brucei Function in Mitochondrial Ribosomes." Molecular and Cellular Biology 27, no. 19 (July 23, 2007): 6876–88. http://dx.doi.org/10.1128/mcb.00708-07.
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ABSTRACT The pentatricopeptide repeat (PPR), a degenerate 35-amino-acid motif, defines a novel eukaryotic protein family. Plants have 400 to 500 distinct PPR proteins, whereas other eukaryotes generally have fewer than 5. The few PPR proteins that have been studied have roles in organellar gene expression, probably via direct interaction with RNA. Here we show that the parasitic protozoan Trypanosoma brucei encodes 28 distinct PPR proteins, an extraordinarily high number for a nonplant organism. A comparative analysis shows that seven out of eight selected PPR proteins are mitochondrially localized and essential for oxidative phosphorylation. Six of these are required for the stabilization of mitochondrial rRNAs and, like ribosomes, are associated with the mitochondrial membranes. Furthermore, one of the PPR proteins copurifies with the large subunit rRNA. Finally, ablation of all of the PPR proteins that were tested induces degradation of the other PPR proteins, indicating that they function in concert. Our results show that a significant number of trypanosomal PPR proteins are individually essential for the maintenance and/or biogenesis of mitochondrial rRNAs.
Dissertations / Theses on the topic "PPR-Protein"
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Ishibashi, Kota. "Evolution of Plastid RNA Editing Sites and Molecular Strategy of New Target Acquisition by PPR Protein." Kyoto University, 2020. http://hdl.handle.net/2433/253120.
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Emami, Hossein [Verfasser], Frank [Akademischer Betreuer] Kempken, and Dietrich [Gutachter] Ober. "Characterization of a mitochondrial PPR protein in Arabidopsis thaliana / Hossein Emami ; Gutachter: Dietrich Ober ; Betreuer: Frank Kempken." Kiel : Universitätsbibliothek Kiel, 2020. http://d-nb.info/1217658653/34.
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Zoschke, Reimo. "Charakterisierung essentieller Faktoren des Nukleinsäuremetabolismus von Chloroplasten." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2010. http://dx.doi.org/10.18452/16143.
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Die chloroplastidäre Genexpression ist durch charakteristische posttranskriptionelle Ereignisse, wie RNA-Prozessierung, RNA-Stabilität, RNA-Edierung oder RNA-Spleißen gekennzeichnet. Diese Prozesse werden fast ausnahmslos durch kernkodierte Proteine realisiert. PPR-Proteine (Pentatricopeptid repeat) stellen unter diesen kernkodierten Faktoren die größte Proteinfamilie dar. Das plastidäre Protein P67 gehört zur kleinen Untergruppe der PPR-Proteine mit SMR-Domäne (small MutS-related), deren molekulare Funktion im organellären Nukleinsäuremetabolismus bislang unverstanden ist. P67 zeigt eine nahe Verwandtschaft zu GUN1, einem zentralen Bestandteil retrograder Signalwege. Der hier analysierte P67-Knockout in Mais verursacht hellgrüne Phänotypen, eine drastische Reduktion der plastidären ATPase und Keimlingsletalität, was die essentielle Beteiligung von P67 an den Prozessen der Chloroplastenbiogenese und der Expression der plastidär kodierten ATPase-Untereinheiten vermuten lässt. Mögliche Implikationen eines fehlenden Phänotyps von Mutanten des P67-Orthologs aus Arabidopsis thaliana werden diskutiert. Eine Ausnahmestellung unter den Proteinen des chloroplastidären RNA-Metabolismus nimmt der einzige plastidär kodierte RNA-Reifungsfaktor MatK ein. Die genomische Position des matK-Gens im Intron der trnK-UUU ist in allen grünen Landpflanzen konserviert. MatK ist mit bakteriellen Maturasen verwandt, die spezifisch den Spleißprozess ihres Heimatintrons unterstützen. Dagegen deuten genetische und phylogenetische Studien zusätzliche MatK-Funktionen in trans an. In der vorliegenden Arbeit wird die spezifische Interaktion von MatK mit sieben Gruppe-IIA-Intron enthaltenden Transkripten in vivo gezeigt. Darunter befinden sich vier tRNA-Vorläufer (trnK-UUU mit dem matK-Heimatintron sowie trnV-UAC, trnI-GAU, trnA-UGC) und drei proteinkodierende Vorläufertranskripte (rpl2, rps12, atpF). Die Feinkartierung der MatK-Bindung im trnK-Heimatintron zeigt eine Assoziation mit multiplen Regionen. Organelläre Gruppe-II-Introns gelten als Vorläufer der spleißosomalen Introns. Die Assoziation mit multiplen Gruppe-II-Introns macht MatK somit zu einem interessanten Modell für die Evolution der transaktiven Spleißaktivität im Kern. Analysen der Expression von MatK und seinen Zielen deuten auf ein komplexes Muster möglicher regulativer Interaktionen hin.Chloroplast gene expression is characterized by posttranscriptional events including RNA cleavage, RNA stability, RNA editing, and RNA splicing. The underlying processing machinery is almost exclusively encoded in the nucleus. PPR proteins (pentatricopeptide repeat) form the biggest protein family among these factors and are major players of the aforementioned posttranscriptional processes. The plastidial protein P67 is a member of a small subgroup of PPR proteins with SMR domain (small MutS-related). Molecular functions of this protein family in organellar nucleic acid metabolism are yet unknown. P67 is a close relative of GUN1, an essential component of the chloroplast to nucleus retrograde signalling pathway. It is shown here that a P67 knockout in maize causes pale green phenotypes, a dramatic reduction in ATPase levels, and seedling lethality. This indicates an essential role of P67 for chloroplast biogenesis and expression of the plastid encoded ATPase. The finding that mutants of the P67-orthologe in Arabidopsis lack a phenotype is discussed against the background of physiological differences between maize and Arabidopsis. A special case among proteins involved in plastid RNA metabolism is MatK - the only plastid encoded RNA maturation factor. The genomic position of the matK gene in the trnK-UUU intron is conserved throughout autotrophic land plants. MatK is related to bacterial maturases - highly specific splice factors supporting splice processes of their respective home introns. There is, however, indirect genetic and phylogenetic evidence that MatK acts also in trans as a common plastidial splice factor serving various group II introns. This study shows that MatK interacts specifically with seven group IIA introns in vivo. Among them are four tRNA precursor transcripts (trnK-UUU including the matK home intron as well as trnV-UAC, trnI-GAU, trnA-UGC) and three protein-coding precursors (rpl2, rps12, atpF). Fine mapping of MatK binding sites within the trnK home intron uncovers protein RNA interactions with diverse intron regions. Organellar introns have been suggested as evolutionary ancestors of nuclear spliceosomal introns. Consequently, association of MatK with multiple group II intron ligands makes the plastidial maturase an attractive model for an early trans-acting nuclear splice activity. Analyses of the expression of MatK and its targets revealed a complex pattern of possible regulatory interactions.
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Hernández, Mora José Ramón. "Towards the characterization of the PPR-B protein, responsible for restoration of fertility in the ogura CMS system of radish : functional and evolutionary approaches." Paris 11, 2009. http://www.theses.fr/2009PA112251.
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Nucleo-cytoplasmic male sterility (CMS) systems are natural systems controlled by two genetic factors: a cytoplasmic determinant causing male sterility and a nuclear determinant able to restore fertility. The Ogura CMS system is widely used for the production of hybrid seeds in cultivated Brassicas. The restorer locus of the Ogura system (Rfo) includes three highly related genes encoding PentatricoPeptide Repeat (PPR) proteins. Two of the most important questions regarding restorers of fertility concern the molecular mechanisms by which PPR restorers counter sterility, and the evolutionary relationships between related PPR genes found at restorer loci. The present study launched a functional analysis of the Rfo restorer protein (PPRB) and a study of the evolution of the Rfo locus in radish. A structure-function analysis of PPRB was undertaken in order to identify the protein domains or residues that are essential for impairing ORF138 accumulation. A functional test for the restorer activity was developed, based on the relative quantification of ORF138 in transgenic roots. For the evolutionary study the sequence of an allele of the Rfo locus obtained from a non-restorer genotype was determined. This allele carries two PPR genes closely related to those of the restorer sequence. The comparison of the two allele sequences showed that the Rfo locus evolved rapidly that intergenic and intragenic recombination operated during its evolution. Overall, the results described in this thesis contributes to a better understanding of the structural and biochemical features important for Rfo restoration activity and sheds light on the peculiar evolution of the Rfo locus.
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Schelcher, Cédric. "Détermination du mode d'action et des substrats de RNases P protéiques chez Arabidopsis thaliana." Thesis, Strasbourg, 2017. http://www.theses.fr/2017STRAJ044/document.
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L’activité RNase P est l'activité essentielle qui élimine les séquences 5' supplémentaires des précurseurs d'ARN de transfert. "PRORP" (PROteinaceous RNase P) définit une nouvelle catégorie de RNase P uniquement protéique. Avant la caractérisation de PRORP, on pensait que les enzymes RNase P étaient universellement conservées sous forme de ribonucléoprotéines (RNP). La caractérisation de PRORP a révélé une enzyme avec deux domaines principaux, un domaine N-terminal contenant plusieurs motifs PPR et un domaine NYN C-terminal portant l’activité catalytique. Nous avons utilisé une combinaison d'approches biochimiques et biophysiques pour caractériser le complexe PRORP / ARNt. La structure du complexe en solution a été déterminée par diffusion des rayons X aux petits angles (SAXS) et les Kd des interactions de différents mutants de PRORP avec l’ARNt ont été déterminées par ultracentrifugation analytique. Notre analyse révèle un cas intéressant d'évolution convergente. Il suggère que PRORP a développé un processus de reconnaissance de l'ARN similaire à celui des RNase P RNP. Par ailleurs, nous avons mis en place une approche de co-immunoprécipitation de PRORP avec l’ARN afin de définir le spectre de substrats des RNase P protéiquesRNase P is the essential activity that removes 5'-leader sequences from transfer RNA precursors. “PRORP” (PROteinaceous RNase P) defines a novel category of protein only RNase P. Before the characterization of PRORP, RNase P enzymes were thought to occur universally as ribonucleoproteins (RNP). The characterization of PRORP revealed an enzyme with two main domains, an N-terminal domain containing multiple PPR motifs and a C-terminal NYN domain holding catalytic activity. We used a combination of biochemical and biophysical approaches to characterize the PRORP / tRNA complex. The structure of the complex in solution was determined by small angle X-ray scattering and Kd values of the PRORP / tRNA interaction were determined by analytical ultracentrifugation. We also analyzed direct interaction of a collection of PPR mutants with tRNA in order to determine the relative importance of individual PPR motifs for RNA binding. This reveals to what extent PRORP target recognition process conforms to the mode of action of PPR proteins interacting with linear RNA. Altogether, our analysis reveals an interesting case of convergent evolution. It suggests that PRORP has evolved an RNA recognition process similar to that of RNP RNase P. Moreover, we also implemented a PRORP-RNA co-immunoprecipitation approach to determine the full extent of PRORP substrates
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Ruwe, Hannes. "PPRs and cpRNPs." Doctoral thesis, Humboldt-Universität zu Berlin, Lebenswissenschaftliche Fakultät, 2015. http://dx.doi.org/10.18452/17250.
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Die Genexpressionsmaschinerie in Chloroplasten und Mitochondrien und die ihrer prokaryotischen Vorläufer sind konserviert. Innerhalb eines bakteriellen Grundgerüsts entwickelte sich darüber hinaus ein komplexer RNA-Metabolismus. In der vorliegenden Arbeit wird eine neue Klasse kleiner RNAs (15-50nt) mit plastidärem und mitochondrialen Ursprung beschrieben. Diese kurzen RNAs überlappen mit Bindestellen von RNA-bindenden Proteinen, die mRNAs gegen exonukleolytischen Verdau beschützen. Diese stabilisierende Funktion wird vermutlich hauptsächlich von PPR (Pentatricopeptid repeat) Proteinen und verwandten Proteine bewerkstelligt. Die kleinen RNAs repräsentieren dabei minimale nuklease-resistente Bereiche, sogenannte RNA-Bindeprotein footprints. Solche footprints finden sich in fast jedem intergenischen Bereich, der Prozessierung aufweist. Durch transkriptomweite Untersuchungen von kleinen RNAs in Mutanten von RNA-Bindeproteinen konnte für diese eine Reihe von Bindestellen identifiziert werden. Nuklease-resistente kleine RNAs fehlen in entsprechenden Mutanten. Der Vergleich neu identifizierter Ziele einzelner RNA-Bindeproteine führte dabei zu neuen Erkenntnissen über den Mechanismus der RNA-Erkennung durch PPR Proteine. Im Gegensatz zu Plastiden befinden sich kleine RNAs in Mitochondrien überwiegend an den 3‘ Enden von Transkripten, deren Stabilität vermutlich maßgeblich von diesen RNA-Bindeproteinen beeinflusst wird. Für das chloroplastidäre Ribonukleoprotein CP31A konnte gezeigt werden, dass es an der Stabilisierung der ndhF mRNA beteiligt ist. Die Interaktion mit der ndhF mRNA, die eine zentrale Komponente des NDH-Komplexes kodiert, wird dabei über die 3‘ untranslatierte Region vermittelt. Zusätzlich konnte gezeigt werden, dass CP31A die Stabilität einiger antisense Transkripte beeinflusst. Weiterhin wurden zehn neue Cytidin Desaminierungungen durch die Analyse von RNA-Seq Datensätzen in der Modellpflanze Arabidopsis thaliana identifiziert.Chloroplasts and mitochondria are of endosymbiotic origin. Their basic gene expression machineries are retained from their free-living prokaryotic progenitors. On top of this bacterial scaffold, a number of organelle-specific RNA processing steps evolved. In this thesis, a novel class of organelle-specific short (15-50nt) RNAs is described on a transcriptome-wide scale. The small RNAs are found at binding sites of PPR (Pentatricopeptide repeat) and PPR-like proteins, which protect mRNAs against exonucleolytic decay. The small RNAs represent minimal nuclease resistant RNAs, so called PPR footprints. Small RNAs were identified in almost every intergenic region subjected to intergenic processing. This finding suggests that accumulation of processed transcripts in plastids is mostly due to protection by highly specific RNA-binding proteins. Small RNA sequencing identified a number of nuclease insensitive sites missing in mutants of RNA-binding proteins. Analysis of multiple small RNAs representing target sites of single PPR proteins expands the knowledge of target specificity. In mitochondria, accumulations of small RNAs predicts that at least two thirds of mitochondrial mRNAs are stabilized by RNA-binding proteins binding in their 3’UTR. In sum, small organellar RNAs turned out to be instrumental in elucidating the hitherto enigmatic intercistronic processing of organellar RNAs and allowed novel insights into the function of the dominant family of organellar RNA binding proteins, the PPR proteins. A chloroplast ribonucleoprotein CP31A is shown to be involved in stabilization of an mRNA for a central component of the NDH-complex by interaction with its 3’UTR. In addition, CP31A represents the first factor described that influences the accumulation of chloroplast antisense transcripts. Finally, ten novel plastid C to U RNA-editing sites were identified in the model plant Arabidopsis thaliana, using a novel RNA-Seq based approach.
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FERRARI, ROBERTO. "MOLECULAR BASES OF SVP REGULATORY FUNCTIONS IN ARABIDOPSIS THALIANA." Doctoral thesis, Università degli Studi di Milano, 2017. http://hdl.handle.net/2434/521865.
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Flowering time regulation has a strong impact on plant life cycle, since it allows plants to flower and to reproduce under environmental permissive conditions. Several genes are involved in the regulatory pathways that determine the floral transition step, i.e. the switch from the plant vegetative phase to the reproductive phase and the consequent flower formation and fruit set. Among those genes, SHORT VEGETATIVE PHASE (SVP), a MADS box transcription factor, acts as strong repressor of the so called florigen promoting genes, FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1). Moreover, SVP has been also reported to act as a repressor of flower homeotic gene expression, thus ensuring the correct maintenance of floral meristem identity. Due to the relevance of SVP in both such important plant developmental stages, during my Ph.D. research program I tried to elucidate the molecular mechanisms at the basis of SVP activities. That has been done through different and complementary strategies that had the dual aim to identify SVP protein partners and to move the first steps towards the comprehension of the role of chloroplasts and chloroplast-nucleus signaling pathways in SVP functions.
Co-immunoprecipitation assays followed by Mass Spectrometry analyses have allowed to draw up a list of Arabidopsis putative robust SVP interactors involved, at different levels, in chromatin organization and histone modification. Interestingly, the detailed characterization of the major Arabidopsis trimethyltransferase enzyme, SET DOMAIN GROUP 2 (SDG2), has revealed the existence of an SVP-SDG2 containing protein complex able to regulate the expression of SVP gene at the vegetative and reproductive meristems, by affecting the H3K4 methylation pattern within the first exon of SVP.
Furthermore, our interests on the role of chloroplast-nucleus communication and its possible interactions with the flowering time regulation, have been met through the detailed characterization of two chloroplast-located PENTATRICO-PEPTIDE-REPEAT (PPR) containing proteins, which share three main features: i) they are part of the chloroplast gene expression machinery, ii) they are involved in chloroplast-nucleus communication, iii) they have been reported to be target genes of SVP by ChiP-seq assays.
The detailed characterization of the Arabidopsis PPR proteins, GENOME UNCOUPLED 1 (GUN1) and CHLOROPLAST RNA PROCESSING 1 (AtCRP1), has provided the first preliminary insights into how chloroplast-nucleus signaling mechanisms may enable higher plants to more effectively adapt to the ever-changing internal and external conditions and mitigate detrimental effects to fitness.
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Falcon, de Longevialle Alexis. "Identification des protéines PPR impliquées dans l'épissage des ARN messagers dans les chloroplastes et les mitochondries chez Arabidopsis Thaliana." Thesis, Evry-Val d'Essonne, 2010. http://www.theses.fr/2010EVRY0015.
Full textAbstract:
Le mécanisme d’épissage dans les organites est décrit comme étant l’ancêtre du spliceosome nucléaire. Cependant même si les protéines composant ce dernier sont bien connues, seulement quelques facteurs d’épissage ont été identifiés et caractérisés dans les chloroplastes et les mitochondries. Beaucoup de protéines ayant la faculté de se lier à l’ARN ont acquis des fonctions dans l’épissage, en effet un certain nombre de protéines sans véritable lien ont un rôle essentiel, avec différents degrés de spécificité dans l’épissage de la plupart des introns chloroplastiques chez les plantes. La plus grande famille de protéines se liant à l’ARN est la famille des protéines à domaines « pentatricopetide repeat » (PPR). Ces protéines sont impliquées dans la plupart des processus post-transcriptionnels dans les organites. En 2006, parmi les centaines de protéines PPR décrites chez les plantes, seulement une PPR avait été décrite comme nécessaire à l’épissage d’un intron. Ainsi, PPR4 est absolument et spécifiquement nécessaire pour l’épissage en trans de l’intron 1 de rps12 dans les plastes (Schmitz-Linneweber et al., 2006), suggérant que d’autres protéines PPR pourraient être impliquées dans l’épissage des ARN des organites. Le sujet de cette thèse porte sur la caractérisation d’autres protéines PPR impliquées dans ce processus. En utilisant des approches de génétique inverse et des outils mis en place dans le cadre de la thèse afin de détecter des défauts d’épissage par PCR quantitative, sept nouvelles PPRs impliquées dans l’épissage d’un certain nombre d’introns dans les plastes et les mitochondries ont pu être caractérisées. Dans l’optique de rechercher si des protéines PPR, impliquées dans l’épissage mais aussi dans l’édition des ARN, interagissent avec d’autres protéines, des approches de TAP-TAG ont été réalisées et sont également présentées dans ce manuscrit. L’identification de partenaires protéiques pour 3 PPRs impliquées, nous a ainsi permis de redessiner nos modèles et d’émettre de nouvelles hypothèses. Enfin, une dernière partie est consacrée à la découverte d’isoformes d’épissage pour des gènes PPR sans introns. Phénomène qui permettrait de réguler l’expression des gènes PPR, et/ou d’augmenter la diversité des protéines PPRThe RNA splicing mechanism in organelles is described to be ancestral to that of the nuclear spliceosome. However, whereas this last complex is well known, only very few splicing factors have been identified and characterized in chloroplasts and mitochondria. Many RNA binding proteins have acquired roles in RNA splicing, and indeed a variety of often unrelated RNA binding proteins have essential functions in splicing of many plastid introns in plants, with varying degrees of specificity. The largest family of RNA binding proteins in plant organelles is the pentatricopeptide repeat (PPR) family. PPR proteins are involved in diverse post-transcriptional processes in organelles. In 2006, among hundreds of higher plant proteins of this family, only one was described as being required for a splicing event - PPR4 was shown to be absolutely and specifically required for the trans-splicing of the rps12 intron 1 in plastids (Schmitz-Linneweber et al., 2006). The main purpose of this PhD thesis was to characterize other PPR proteins involved in this process. By using a reverse genetics approach and by developing tools for the detection of splicing defects, seven new PPR proteins involved in RNA splicing of a subset of chloroplast or mitochondria introns have been characterized. In parallel, in order to characterize proteins involved in PPR-containing complexes, a TAP-TAG approach has been carried out on a few PPR proteins involved in splicing or editing of organellar RNA. The identification of partner proteins of 3 PPR proteins allows us to draw new mechanistic models and new hypotheses. Finally, the final part of the manuscript describes the discovery of splicing isoforms of PPR-encoding mRNAs. Alternative splicing may be involved in regulation of PPR gene expression and/or in increasing the diversity of the PPR protein family
Book chapters on the topic "PPR-Protein"
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Cottage, Amanda J., Ellie K. Mott, Jun-Hui Wang, James A. Sullivan, Dan MacLean, Linh Tran, Mun-Kit Choy, et al. "GUN1 (GENOMES UNCOUPLED1) Encodes a Pentatricopeptide Repeat (PPR) Protein Involved in Plastid Protein Synthesis-Responsive Retrograde Signaling to the Nucleus." In Photosynthesis. Energy from the Sun, 1201–5. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6709-9_261.
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Hagenbeek, D., J. Dugardeyn, C. Zhang, and D. Van Der Straeten. "A PPR protein, required for normal plant development, may be involved in control of the ethylene pathway at the posttranscriptional level." In Advances in Plant Ethylene Research, 119–20. Dordrecht: Springer Netherlands, 2007. http://dx.doi.org/10.1007/978-1-4020-6014-4_27.
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