Journal articles: 'PPR-Protein'

1

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.

Full text

Abstract:

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.

APA, Harvard, Vancouver, ISO, and other styles

2

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.

Full text

Abstract:

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.

APA, Harvard, Vancouver, ISO, and other styles

3

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.

Full text

Abstract:

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.

APA, Harvard, Vancouver, ISO, and other styles

4

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.

Full text

Abstract:

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.

APA, Harvard, Vancouver, ISO, and other styles

5

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.

Full text

Abstract:

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.

APA, Harvard, Vancouver, ISO, and other styles

6

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.

Full text

Abstract:

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.

APA, Harvard, Vancouver, ISO, and other styles

7

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.

Full text

Abstract:

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.

APA, Harvard, Vancouver, ISO, and other styles

8

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.

Full text

Abstract:

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.

APA, Harvard, Vancouver, ISO, and other styles

9

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.

Full text

Abstract:

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.

APA, Harvard, Vancouver, ISO, and other styles

10

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.

Full text

Abstract:

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.

APA, Harvard, Vancouver, ISO, and other styles

11

Liu, Rui, Shi-Kai Cao, Aqib Sayyed, Chunhui Xu, Feng Sun, Xiaomin Wang, and Bao-Cai Tan. "The Mitochondrial Pentatricopeptide Repeat Protein PPR18 Is Required for the cis-Splicing of nad4 Intron 1 and Essential to Seed Development in Maize." International Journal of Molecular Sciences 21, no. 11 (June 5, 2020): 4047. http://dx.doi.org/10.3390/ijms21114047.

Full text

Abstract:

Pentatricopeptide repeat (PPR) protein comprises a large family, participating in various aspects of organellar RNA metabolism in land plants. There are approximately 600 PPR proteins in maize, but the functions of many PPR proteins remain unknown. In this study, we defined the function of PPR18 in the cis-splicing of nad4 intron 1 in mitochondria and seed development in maize. Loss function of PPR18 seriously impairs embryo and endosperm development, resulting in the empty pericarp (emp) phenotype in maize. PPR18 encodes a mitochondrion-targeted P-type PPR protein with 18 PPR motifs. Transcripts analysis indicated that the splicing of nad4 intron 1 is impaired in the ppr18 mutant, resulting in the absence of nad4 transcript, leading to severely reduced assembly and activity of mitochondrial complex I and dramatically reduced respiration rate. These results demonstrate that PPR18 is required for the cis-splicing of nad4 intron 1 in mitochondria, and critical to complex I assembly and seed development in maize.

APA, Harvard, Vancouver, ISO, and other styles

12

Zhou, Wen, Qingtao Lu, Qingwei Li, Lei Wang, Shunhua Ding, Aihong Zhang, Xiaogang Wen, Lixin Zhang, and Congming Lu. "PPR-SMR protein SOT1 has RNA endonuclease activity." Proceedings of the National Academy of Sciences 114, no. 8 (February 6, 2017): E1554—E1563. http://dx.doi.org/10.1073/pnas.1612460114.

Full text

Abstract:

Numerous attempts have been made to identify and engineer sequence-specific RNA endonucleases, as these would allow for efficient RNA manipulation. However, no natural RNA endonuclease that recognizes RNA in a sequence-specific manner has been described to date. Here, we report that SUPPRESSOR OF THYLAKOID FORMATION 1 (SOT1), anArabidopsispentatricopeptide repeat (PPR) protein with a small MutS-related (SMR) domain, has RNA endonuclease activity. We show that the SMR moiety of SOT1 performs the endonucleolytic maturation of 23S and 4.5S rRNA through the PPR domain, specifically recognizing a 13-nucleotide RNA sequence in the 5′ end of the chloroplast 23S–4.5S rRNA precursor. In addition, we successfully engineered the SOT1 protein with altered PPR motifs to recognize and cleave a predicted RNA substrate. Our findings point to SOT1 as an exciting tool for RNA manipulation.

APA, Harvard, Vancouver, ISO, and other styles

13

Legen, Julia, Sara Dühnen, Anton Gauert, Michael Götz, and Christian Schmitz-Linneweber. "A CRR2-Dependent sRNA Sequence Supports Papillomavirus Vaccine Expression in Tobacco Chloroplasts." Metabolites 13, no. 3 (February 21, 2023): 315. http://dx.doi.org/10.3390/metabo13030315.

Full text

Abstract:

Introduction: Human papillomavirus (HPV) infection is the leading cause of cervical cancer, and vaccination with HPV L1 capsid proteins has been successful in controlling it. However, vaccination coverage is not universal, particularly in developing countries, where 80% of all cervical cancer cases occur. Cost-effective vaccination could be achieved by expressing the L1 protein in plants. Various efforts have been made to produce the L1 protein in plants, including attempts to express it in chloroplasts for high-yield performance. However, manipulating chloroplast gene expression requires complex and difficult-to-control expression elements. In recent years, a family of nuclear-encoded, chloroplast-targeted RNA-binding proteins, the pentatricopeptide repeat (PPR) proteins, were described as key regulators of chloroplast gene expression. For example, PPR proteins are used by plants to stabilize and translate chloroplast mRNAs. Objectives: To demonstrate that a PPR target site can be used to drive HPV L1 expression in chloroplasts. Methods: To test our hypothesis, we used biolistic chloroplast transformation to establish tobacco lines that express two variants of the HPV L1 protein under the control of the target site of the PPR protein CHLORORESPIRATORY REDUCTION2 (CRR2). The transgenes were inserted into a dicistronic operon driven by the plastid rRNA promoter. To determine the effectiveness of the PPR target site for the expression of the HPV L1 protein in the chloroplasts, we analyzed the accumulation of the transgenic mRNA and its processing, as well as the accumulation of the L1 protein in the transgenic lines. Results: We established homoplastomic lines carrying either the HPV18 L1 protein or an HPV16B Enterotoxin::L1 fusion protein. The latter line showed severe growth retardation and pigment loss, suggesting that the fusion protein is toxic to the chloroplasts. Despite the presence of dicistronic mRNAs, we observed very little accumulation of monocistronic transgenic mRNA and no significant increase in CRR2-associated small RNAs. Although both lines expressed the L1 protein, quantification using an external standard suggested that the amounts were low. Conclusions: Our results suggest that PPR binding sites can be used to drive vaccine expression in plant chloroplasts; however, the factors that modulate the effectiveness of target gene expression remain unclear. The identification of dozens of PPR binding sites through small RNA sequencing expands the set of expression elements available for high-value protein production in chloroplasts.

APA, Harvard, Vancouver, ISO, and other styles

14

Houdijk, J. G. M., I. Kyriazakis, R. L. Coop, and F. Jackson. "Effects of metabolizable protein on performance and faecal egg count of the parasitized ewe." Proceedings of the British Society of Animal Science 1999 (1999): 17. http://dx.doi.org/10.1017/s1752756200001721.

Full text

Abstract:

The periparturient relaxation (PPR) in acquired immunity in ewes has been ascribed to various factors, including poor nutrition (Barger, 1993). Clinically, the faecal egg count (FEC) may increase during PPR when the ewe is continuously infected with gastrointestinal parasites. As such, the periparturient ewe plays an important role in the epidemiology of parasitic infections. The nutritional basis of PPR probably includes metabolizable protein (MP), since host's responses, in terms of immunity and resilience, are highly proteinaceous by nature. We propose that the PPR directly results from less MP being available to maintain acquired immunity and resilience, since an increasing amount of MP is directed to bodily functions with higher priority (reproduction). It is hypothesized that the increased FEC in the parasitized periparturient ewe reduces if her MP-intake exceeds her assumed MP-requirement (AFRC, 1993).

APA, Harvard, Vancouver, ISO, and other styles

15

Li, Xiulan, Mengdi Sun, Shijuan Liu, Qian Teng, Shihui Li, and Yueshui Jiang. "Functions of PPR Proteins in Plant Growth and Development." International Journal of Molecular Sciences 22, no. 20 (October 19, 2021): 11274. http://dx.doi.org/10.3390/ijms222011274.

Full text

Abstract:

Pentatricopeptide repeat (PPR) proteins form a large protein family in land plants, with hundreds of different members in angiosperms. In the last decade, a number of studies have shown that PPR proteins are sequence-specific RNA-binding proteins involved in multiple aspects of plant organellar RNA processing, and perform numerous functions in plants throughout their life cycle. Recently, computational and structural studies have provided new insights into the working mechanisms of PPR proteins in RNA recognition and cytidine deamination. In this review, we summarized the research progress on the functions of PPR proteins in plant growth and development, with a particular focus on their effects on cytoplasmic male sterility, stress responses, and seed development. We also documented the molecular mechanisms of PPR proteins in mediating RNA processing in plant mitochondria and chloroplasts.

APA, Harvard, Vancouver, ISO, and other styles

16

Nakamura, T., G. Schuster, M. Sugiura, and M. Sugita. "Chloroplast RNA-binding and pentatricopeptide repeat proteins." Biochemical Society Transactions 32, no. 4 (August 1, 2004): 571–74. http://dx.doi.org/10.1042/bst0320571.

Full text

Abstract:

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.

APA, Harvard, Vancouver, ISO, and other styles

17

Tavares-Carreón, Faviola, Yolanda Camacho-Villasana, Angélica Zamudio-Ochoa, Miguel Shingú-Vázquez, Alfredo Torres-Larios, and Xochitl Pérez-Martínez. "The Pentatricopeptide Repeats Present in Pet309 Are Necessary for Translation but Not for Stability of the Mitochondrial COX1 mRNA in Yeast." Journal of Biological Chemistry 283, no. 3 (November 26, 2007): 1472–79. http://dx.doi.org/10.1074/jbc.m708437200.

Full text

Abstract:

Pet309 is a protein essential for respiratory growth. It is involved in translation of the yeast mitochondrial COX1 gene, which encodes subunit I of the cytochrome c oxidase. Pet309 is also involved in stabilization of the COX1 mRNA. Mutations in a similar human protein, Lrp130, are associated with Leigh syndrome, where cytochrome c oxidase activity is affected. The sequence of Pet309 reveals the presence of at least seven pentatricopeptide repeats (PPRs) located in tandem in the central portion of the protein. Proteins containing PPR motifs are present in mitochondria and chloroplasts and are in general involved in RNA metabolism. Despite the increasing number of proteins from this family found to play essential roles in mitochondria and chloroplasts, little is understood about the mechanism of action of the PPR domains present in these proteins. In a series of in vivo analyses we constructed a pet309 mutant lacking the PPR motifs. Although the stability of the COX1 mRNA was not affected, synthesis of Cox1 was abolished. The deletion of one PPR motif at a time showed that all the PPR motifs are required for COX1 mRNA translation and respiratory growth. Mutations of basic residues in PPR3 caused reduced respiratory growth. According to a molecular model, these residues are facing a central cavity that could be involved in mRNA-binding activity, forming a possible path for this molecule on Pet309. Our results show that the RNA metabolism function of Pet309 is found in at least two separate domains of the protein.

APA, Harvard, Vancouver, ISO, and other styles

18

Su, Hong-Gang, Bo Li, Xin-Yuan Song, Jian Ma, Jun Chen, Yong-Bin Zhou, Ming Chen, Dong-Hong Min, Zhao-Shi Xu, and You-Zhi Ma. "Genome-Wide Analysis of the DYW Subgroup PPR Gene Family and Identification of GmPPR4 Responses to Drought Stress." International Journal of Molecular Sciences 20, no. 22 (November 12, 2019): 5667. http://dx.doi.org/10.3390/ijms20225667.

Full text

Abstract:

Pentatricopeptide-repeat (PPR) proteins were identified as a type of nucleus coding protein that is composed of multiple tandem repeats. It has been reported that PPR genes play an important role in RNA editing, plant growth and development, and abiotic stresses in plants. However, the functions of PPR proteins remain largely unknown in soybean. In this study, 179 DYW subgroup PPR genes were identified in soybean genome (Glycine max Wm82.a2.v1). Chromosomal location analysis indicated that DYW subgroup PPR genes were mapped to all 20 chromosomes. Phylogenetic relationship analysis revealed that DYW subgroup PPR genes were categorized into three distinct Clusters (I to III). Gene structure analysis showed that most PPR genes were featured by a lack of intron. Gene duplication analysis demonstrated 30 PPR genes (15 pairs; ~35.7%) were segmentally duplicated among Cluster I PPR genes. Furthermore, we validated the mRNA expression of three genes that were highly up-regulated in soybean drought- and salt-induced transcriptome database and found that the expression levels of GmPPR4 were induced under salt and drought stresses. Under drought stress condition, GmPPR4-overexpressing (GmPPR4-OE) plants showed delayed leaf rolling; higher content of proline (Pro); and lower contents of H2O2, O2− and malondialdehyde (MDA) compared with the empty vector (EV)-control plants. GmPPR4-OE plants exhibited increased transcripts of several drought-inducible genes compared with EV-control plants. Our results provided a comprehensive analysis of the DYW subgroup PPR genes and an insight for improving the drought tolerance in soybean.

APA, Harvard, Vancouver, ISO, and other styles

19

Dong, Shanshan, Chaoxian Zhao, Shouzhou Zhang, Hong Wu, Weixue Mu, Tong Wei, Na Li, et al. "The Amount of RNA Editing Sites in Liverwort Organellar Genes Is Correlated with GC Content and Nuclear PPR Protein Diversity." Genome Biology and Evolution 11, no. 11 (October 25, 2019): 3233–39. http://dx.doi.org/10.1093/gbe/evz232.

Full text

Abstract:

Abstract RNA editing occurs in the organellar mRNAs of all land plants but the marchantioid liverworts, making liverworts a perfect group for studying the evolution of RNA editing. Here, we profiled the RNA editing of 42 exemplars spanning the ordinal phylogenetic diversity of liverworts, and screened for the nuclear-encoded pentatricopeptide repeat (PPR) proteins in the transcriptome assemblies of these taxa. We identified 7,428 RNA editing sites in 128 organellar genes from 31 non-marchantioid liverwort species, and characterized 25,059 PPR protein sequences. The abundance of organellar RNA editing sites varies greatly among liverwort lineages, genes, and codon positions, and shows strong positive correlations with the GC content of protein-coding genes, and the diversity of the PLS class of nuclear PPR proteins.

APA, Harvard, Vancouver, ISO, and other styles

20

Yagi, Yusuke, Takamasa Teramoto, Shuji Kaieda, Takayoshi Imai, Tadamasa Sasaki, Maiko Yagi, Nana Maekawa, and Takahiro Nakamura. "Construction of A Versatile, Programmable RNA-binding Protein using Designer PPR Proteins and Its Application for Splicing Control in Mammalian Cells." Cells 11, no. 22 (November 8, 2022): 3529. http://dx.doi.org/10.3390/cells11223529.

Full text

Abstract:

RNAs play many essential roles in gene expression and are involved in various human diseases. Although genome editing technologies have been established, the engineering of sequence-specific RNA-binding proteins that manipulate particular cellular RNA molecules is immature, in contrast to nucleotide-based RNA manipulation technology, such as siRNA- and RNA-targeting CRISPR/Cas. Here, we demonstrate a versatile RNA manipulation technology using pentatricopeptide-repeat (PPR)-motif-containing proteins. First, we developed a rapid construction and evaluation method for PPR-based designer sequence-specific RNA-binding proteins. This system has enabled the steady construction of dozens of functional designer PPR proteins targeting long 18 nt RNA, which targets a single specific RNA in the mammalian transcriptome. Furthermore, the cellular functionality of the designer PPR proteins was first demonstrated by the control of alternative splicing of either a reporter gene or an endogenous CHK1 mRNA. Our results present a versatile protein-based RNA manipulation technology using PPR proteins that facilitates the understanding of unknown RNA functions and the creation of gene circuits and has potential for use in future therapeutics.

APA, Harvard, Vancouver, ISO, and other styles

21

Kubo, Tomohiko, Takumi Arakawa, Yujiro Honma, and Kazuyoshi Kitazaki. "What Does the Molecular Genetics of Different Types of Restorer-of-Fertility Genes Imply?" Plants 9, no. 3 (March 13, 2020): 361. http://dx.doi.org/10.3390/plants9030361.

Full text

Abstract:

Cytoplasmic male sterility (CMS) is a widely used trait for hybrid seed production. Although male sterility is caused by S cytoplasm (male-sterility inducing mitochondria), the action of S cytoplasm is suppressed by restorer-of-fertility (Rf), a nuclear gene. Hence, the genetics of Rf has attained particular interest among plant breeders. The genetic model posits Rf diversity in which an Rf specifically suppresses the cognate S cytoplasm. Molecular analysis of Rf loci in plants has identified various genes; however, pentatricopeptide repeat (PPR) protein (a specific type of RNA-binding protein) is so prominent as the Rf-gene product that Rfs have been categorized into two classes, PPR and non-PPR. In contrast, several shared features between PPR- and some non-PPR Rfs are apparent, suggesting the possibility of another grouping. Our present focus is to group Rfs by molecular genetic classes other than the presence of PPRs. We propose three categories that define partially overlapping groups of Rfs: association with post-transcriptional regulation of mitochondrial gene expression, resistance gene-like copy number variation at the locus, and lack of a direct link to S-orf (a mitochondrial ORF associated with CMS). These groups appear to reflect their own evolutionary background and their mechanism of conferring S cytoplasm specificity.

APA, Harvard, Vancouver, ISO, and other styles

22

Yang, Jing, Yang Cui, Xiangbo Zhang, Zhijia Yang, Jinsheng Lai, Weibin Song, Jingang Liang, and Xinhai Li. "Maize PPR278 Functions in Mitochondrial RNA Splicing and Editing." International Journal of Molecular Sciences 23, no. 6 (March 11, 2022): 3035. http://dx.doi.org/10.3390/ijms23063035.

Full text

Abstract:

Pentatricopeptide repeat (PPR) proteins are a large protein family in higher plants and play important roles during seed development. Most reported PPR proteins function in mitochondria. However, some PPR proteins localize to more than one organelle; functional characterization of these proteins remains limited in maize (Zea mays L.). Here, we cloned and analyzed the function of a P-subfamily PPR protein, PPR278. Loss-function of PPR278 led to a lower germination rate and other defects at the seedling stage, as well as smaller kernels compared to the wild type. PPR278 was expressed in all investigated tissues. Furthermore, we determined that PPR278 is involved in the splicing of two mitochondrial transcripts (nad2 intron 4 and nad5 introns 1 and 4), as well as RNA editing of C-to-U sites in 10 mitochondrial transcripts. PPR278 localized to the nucleus, implying that it may function as a transcriptional regulator during seed development. Our data indicate that PPR278 is involved in maize seed development via intron splicing and RNA editing in mitochondria and has potential regulatory roles in the nucleus.

APA, Harvard, Vancouver, ISO, and other styles

23

Barik, Sailen. "The Nature and Arrangement of Pentatricopeptide Domains and the Linker Sequences Between Them." Bioinformatics and Biology Insights 14 (January 2020): 117793222090643. http://dx.doi.org/10.1177/1177932220906434.

Full text

Abstract:

The tricopeptide (amino acid number in the 30s) repeats constitute some of the most common amino acid repeats in proteins of diverse organisms. The most important representatives of this class are the 34-residue and 35-residue repeats, eponymously known as tetratricopeptide repeat (TPR) and pentatricopeptide repeat (PPR), respectively. The unit motif of both consists of a pair of alpha helices. As members of the large, all-helical repeat classes, TPR and PPR share structural similarities, but also play specific roles in protein function. In this study, a comprehensive bioinformatic analysis of the PPR units and the linkers that connect them was conducted. The results suggested the existence of PPR repeats of various formats, as well as smaller, PPR-unrelated repeats. Besides their length, these repeats differed in amino acid arrangements and location of key amino acids. These findings provide a broader and unified perspective of the pentatricopeptide family while raising provocative questions about the assembly and evolution of these domains.

APA, Harvard, Vancouver, ISO, and other styles

24

Junk, Stefanie V., Melchior Lauten, Gunnar Cario, Nicole Wittner, Martin Schrappe, Brigitte Schlegelberger, and Nils von Neuhoff. "Can Bortezomib Treatment Overcome Glucocorticoid Resistance of Childhood Acute Lymphoblastic Leukemia Cells?." Blood 110, no. 11 (November 16, 2007): 2801. http://dx.doi.org/10.1182/blood.v110.11.2801.2801.

Full text

Abstract:

Abstract The response to initial glucocorticoid (gc) therapy in childhood acute lymphoblastic leukemia (ALL) reliably predicts the response to multiagent chemotherapy. In a recent study, we identified the valosin-containing protein (VCP) as a part of the ubiquitin proteasome degradation pathway (UPDP) as one of the proteins overexpressed in prednisone poor responder (PPR) patients. Therefore, we investigated whether treatment of ALL cell lines with the proteasome inhibitor bortezomib acted synergistically with glucocorticoid treatment. Human B-cell precursor leukemic cell lines MHH cALL 2 (PPR) and MHH cALL 3 (PGR) were treated with prednisone(6.3μM) as baseline and also with different concentrations of the proteasome inhibitor bortezomib for 96hours (h). To study drug effects, cells were sampled every 24h for immunofluorescence (IF) staining, protein and RNA extraction, viability (Trypan blue, WST-1) and apoptosis assays. Western blot analyses using an anti-p97 antibody were performed on whole cell lysates (wcl) and fractions and separated by differential detergent fractionation. VCP RNA expression was analyzed by real-time PCR. Single bortezomib treatment with 3nM or higher concentrations led to a significant decline in vitality of both cell lines. Within 24h, the PPR cell line lost about half and the PGR about one-fourth of their vitality. In combination with prednisone, 1.5nM bortezomib reduced the vitality by about 50% within 96h for both cell lines. Combining both drugs decreased the vitality rate by about 10% in the PPR cell line, whereas the PGR cells showed no decrease compared to single gc treatment. In FACS analyses, stages of different quantities of apoptosis were detected in PPR and PGR cells. PPR cells treated with both drugs showed a strong increase of necrotic cells at 24h. PGR cells started with an accession of apoptotic cells and initially had no necrotic cells, but started to rise from 48h on. We hence propose that the PPR cells react more quickly to the combined therapy. Under single gc treatment, VCP RNA expression increased in the PPR cells to a maximum of about 1.8- and in PGR cells to 1.5-fold. In PGR cells treated only with 1.5nM or 3nM bortezomib, VCP RNA rose to 1.4- and 2-fold respectively. Drug combination led to a 1.4-fold increase of VCP RNA in PPR compared to untreated cells, whereas RNA was reduced compared to single gc-treated cells. Protein levels of VCP in PPR cells remained high during drug treatment. VCP increased to a maximum of 1.6-fold in the cytosol of PGR cells, using bortezomib only. In the combination experiments, the amount doubled within 48h and thence decreased to initial levels. Single gc treatment caused a VCP increase to 1.5-fold within 24h. In the wcl, we found the VCP levels for the PGR cells converted to the cytosolic patterns. The results of IF staining supported the different VCP concentrations and exposed formation of aggresome-like complexes in the PPR cell line. The results of this study suggest that the multiagent chemotherapy resistance is indicated by differentially expressed VCP and related to the deregulation of the UPDP. Using inhibitors appears to chemisensitize the PPR for gc treatment. Therefore, drug targeting the proteasome, as in other hematological cancer therapies, might improve the overall therapy outcome.

APA, Harvard, Vancouver, ISO, and other styles

25

Okuda, H., Y. Sudo, M. Mishima, M. Sato, M. Demura, K. Nitta, N. Kamo, and C. Kojima. "Solution NMR of seven transmembrane protein, phR and ppR." Seibutsu Butsuri 43, supplement (2003): S183. http://dx.doi.org/10.2142/biophys.43.s183_3.

Full text

APA, Harvard, Vancouver, ISO, and other styles

26

Spåhr, Henrik, Agata Rozanska, Xinping Li, Ilian Atanassov, Robert N. Lightowlers, Zofia M. A. Chrzanowska-Lightowlers, Oliver Rackham, and Nils-Göran Larsson. "SLIRP stabilizes LRPPRC via an RRM–PPR protein interface." Nucleic Acids Research 44, no. 14 (June 28, 2016): 6868–82. http://dx.doi.org/10.1093/nar/gkw575.

Full text

APA, Harvard, Vancouver, ISO, and other styles

27

Chukwudi, Ijeoma Chekwube, Kenneth Ikejiofor Ogbu, Pam Dachung Luka, Refiloe Petunia Malesa, Livio Edward Heath, Emmanuel Ikenna Ugochukwu, and Kennedy Foinkfu Chah. "Comparison of colorimetric loop-mediated isothermal amplification kit and reverse transcription-polymerase chain reaction in the diagnosis of peste des petits ruminants in sheep and goats in Southeast Nigeria." November-2020 13, no. 11 (2020): 2358–63. http://dx.doi.org/10.14202/vetworld.2020.2358-2363.

Full text

Abstract:

Background and Aim: Peste des petits ruminants (PPR) is an acute, extremely contagious transboundary viral disease of small ruminants with severe economic consequences, caused by PPR virus. Cost-effective and rapid diagnosis of the disease is essential for prompt management and control. This study aimed to compare the application of a commercial colorimetric loop-mediated isothermal amplification (cLAMP) kit and reverse transcriptase-polymerase chain reaction (RT-PCR) in the diagnosis of PPR in sheep and goats in Southeast Nigeria. Materials and Methods: Nasal swab samples were collected from West African Dwarf sheep and goats showing clinical signs suggestive of PPR (n=80) and those without any clinical signs (n=140) of the disease. The diagnosis was achieved through detection of PPR viral genome in the samples using a cLAMP kit and RT-PCR. cLAMP assay was done directly on nasal swab samples without ribosomal nucleic acid extraction. A set of six primers targeting the matrix gene protein was used for the cLAMP assay. Results: PPR viral genome was detected by both cLAMP and RT-PCR in 51 (63.8%) of the 80 samples from sheep and goats with signs suggestive of PPR while 14 (10%) of those without signs tested positive for PPR by both assay methods. There was a 100% agreement in the cLAMP and RT-PCR results. However, cLAMP was a faster, easier, and less expensive method compared to RT-PCR. Conclusion: The cLAMP assay demonstrates the potential for a point of care diagnosis in the field and a valuable diagnostic tool in areas with poor electricity supply as well as in a less equipped diagnostic laboratory. Since the reagents are affordable, cLAMP can be a diagnostic tool of choice in the detection and surveillance of PPR virus in countries with limited resources.

APA, Harvard, Vancouver, ISO, and other styles

28

Lerner, Danica L., and John H. Elder. "Expanded Host Cell Tropism and Cytopathic Properties of Feline Immunodeficiency Virus Strain PPR Subsequent to Passage through Interleukin-2-Independent T Cells." Journal of Virology 74, no. 4 (February 15, 2000): 1854–63. http://dx.doi.org/10.1128/jvi.74.4.1854-1863.2000.

Full text

Abstract:

ABSTRACT A cytopathic variant of feline immunodeficiency virus (FIV) strain PPR emerged after passage of wild-type virus on an interleukin-2-independent cell line. The virus, termed FIV-PPRglial, displayed a phenotype markedly different from the parental virus, including the ability to productively infect previously refractory cell lines, induction of large syncytia, and accelerated kinetic properties. A chimeric molecular clone, FIV-PPRchim42, containing the FIV-PPRglial envelope within the backbone of FIV-PPR, exhibited all the characteristics of the FIV-PPRglial phenotype, demonstrating that the viral envelope was responsible for the acquired traits. Subsequent molecular characterization revealed that the FIV-PPRglial envelope contained five amino acid substitutions relative to wild-type FIV-PPR. Mutagenic analyses further demonstrated that the acquired phenotype was minimally attributable to a combination of three mutations, specifically, a glutamine-to-proline change within the second constant domain of the surface protein (SU); a threonine-to-proline change within the V4 loop, also in the SU; and a premature stop codon in the cytoplasmic tail of the transmembrane protein. All three changes were required to produce the FIV-PPRglial phenotype. Cotransfection studies with mutant viruses in combination with each other and with FIV-PPR indicated that the truncated cytoplasmic tail was responsible for the induction of syncytium formation. Receptor usage analyses were pursued, and distinctions were observed between FIV-PPR and FIV-PPRglial. In vitro infections with FIV-PPR, FIV-PPRglial, and FIV-34TF10 on two adherent cell lines were ablated in the presence of SDF1α, the natural ligand for CXCR4. In contrast, viral infection of T cells was not limited to CXCR4 usage, and inhibition studies indicate the potential involvement of a CC chemokine receptor.

APA, Harvard, Vancouver, ISO, and other styles

29

Yang, Yang, Xiaodong Qin, Xuelian Meng, Xueliang Zhu, Xiangle Zhang, Yanmin Li, and Zhidong Zhang. "MicroRNA Expression Profile in Peripheral Blood Lymphocytes of Sheep Vaccinated with Nigeria 75/1 Peste Des Petits Ruminants Virus." Viruses 11, no. 11 (November 5, 2019): 1025. http://dx.doi.org/10.3390/v11111025.

Full text

Abstract:

Peste des petits ruminants (PPR) is one of the highly contagious transboundary viral diseases of small ruminants. Host microRNA (miRNA) expression patterns may change in response to virus infection, and it mainly works as a post-transcriptional moderator in gene expression and affects viral pathogenesis and replication. In this study, the change of miRNA expression profile in peripheral blood lymphocyte (PBMC) from sheep inoculated with PPR vaccine virus in vivo as well as primary sheep testicular (ST) cells inoculated with PPR vaccine virus in vitro were determined via deep sequencing technology. In PBMC cells, 373 and 115 differentially expressed miRNAs (DEmiRNAs) were identified 3 days and 5 days post inoculated (dpi), respectively. While, 575 DEmiRNAs were identified when comparing miRNA profiles on 5 dpi with 3 dpi. Some of the DEmiRNAs were found to change significantly via time-course during PPR vaccine virus inoculated. Similarly, in ST cells, 136 DEmiRNAs were identified at 3 dpi in comparison with mock-inoculation. A total of 12 DEmiRNAs were validated by real-time quantitative PCR (RT-qPCR). The oar-miR-150, oar-miR-370-3p and oar-miR-411b-3p were found common differentially expressed in both PPR vaccine virus-inoculated PBMC cells and ST cells. Targets prediction and functional analysis of the DEmiRNAs uncovered mainly gathering in antigen processing and presentation pathways, protein processing in endoplasmic reticulum pathways and cell adhesion molecules pathways. Our study supplies information about the DEmiRNAs in PPR vaccine virus-inoculated PBMC cells and ST cells, and provides clues for further understanding the function of miRNAs in PPR vaccine virus replication.

APA, Harvard, Vancouver, ISO, and other styles

30

Pusnik, Mascha, and André Schneider. "A Trypanosomal Pentatricopeptide Repeat Protein Stabilizes the Mitochondrial mRNAs of Cytochrome Oxidase Subunits 1 and 2." Eukaryotic Cell 11, no. 1 (November 4, 2011): 79–87. http://dx.doi.org/10.1128/ec.05213-11.

Full text

Abstract:

ABSTRACT The pentatricopeptide repeat (PPR) protein family consists of organellar proteins predicted to bind to specific RNA sequences. Plants have hundreds of distinct PPR proteins, whereas other eukaryotes generally have many fewer. The genome of the parasitic protozoon Trypanosoma brucei is predicted to encode more than 30 different PPR proteins, which is an extraordinarily high number for a nonplant organism. Here we report the characterization T. brucei PPR9 (TbPPR9). Epitope tagging shows that the protein is exclusively mitochondrially localized. Interestingly, while in induced RNA interference cell lines TbPPR9 is efficiently downregulated, the level of its mRNA is not affected. Ablation of TbPPR9 selectively abolishes oxidative but not mitochondrial substrate-level phosphorylation. The molecular basis of this phenotype is the fact that TbPPR9 is required for the stability of the cytochrome oxidase subunit 1 (COX1) and COX2 mRNAs. This is supported by the observation that ablation of TbPPR9 destabilizes the COX complex but not the cytochrome bc 1 or the ATP synthase complex. Moreover, it was shown by blue native gel electrophoresis that TbPPR9 is present in a large complex of unknown composition.

APA, Harvard, Vancouver, ISO, and other styles

31

Gutmann, Bernard, Michael Millman, Lilian Vincis Pereira Sanglard, Ian Small, and Catherine Colas des Francs-Small. "The Pentatricopeptide Repeat Protein MEF100 Is Required for the Editing of Four Mitochondrial Editing Sites in Arabidopsis." Cells 10, no. 2 (February 22, 2021): 468. http://dx.doi.org/10.3390/cells10020468.

Full text

Abstract:

In Arabidopsis thaliana there are more than 600 C-to-U RNA editing events in the mitochondria and at least 44 in the chloroplasts. Pentatricopeptide repeat (PPR) proteins provide the specificity for these reactions. They recognize RNA sequences in a partially predictable fashion via key amino acids at the fifth and last position in each PPR motif that bind to individual ribonucleotides. A combined approach of RNA-Seq, mutant complementation, electrophoresis of mitochondrial protein complexes and Western blotting allowed us to show that MEF100, a PPR protein identified in a genetic screen for mutants resistant to an inhibitor of γ -glutamylcysteine synthetase, is required for the editing of nad1-493, nad4-403, nad7-698 and ccmFN2-356 sites in Arabidopsis mitochondria. The absence of editing in mef100 leads to a decrease in mitochondrial Complex I activity, which probably explains the physiological phenotype. Some plants have lost the requirement for MEF100 at one or more of these sites through mutations in the mitochondrial genome. We show that loss of the requirement for MEF100 editing leads to divergence in the MEF100 binding site.

APA, Harvard, Vancouver, ISO, and other styles

32

Dai, Dawei, Lifang Jin, Zhenzhen Huo, Shumei Yan, Zeyang Ma, Weiwei Qi, and Rentao Song. "Maize pentatricopeptide repeat protein DEK53 is required for mitochondrial RNA editing at multiple sites and seed development." Journal of Experimental Botany 71, no. 20 (July 25, 2020): 6246–61. http://dx.doi.org/10.1093/jxb/eraa348.

Full text

Abstract:

Abstract Pentatricopeptide repeat (PPR) proteins were identified as site-specific recognition factors for RNA editing in plant mitochondria and plastids. In this study, we characterized maize (Zea mays) kernel mutant defective kernel 53 (dek53), which has an embryo lethal and collapsed endosperm phenotype. Dek53 encodes an E-subgroup PPR protein, which possesses a short PLS repeat region of only seven repeats. Subcellular localization analysis indicated that DEK53 is localized in the mitochondrion. Strand- and transcript-specific RNA-seq analysis showed that the dek53 mutation affected C-to-U RNA editing at more than 60 mitochondrial C targets. Biochemical analysis of mitochondrial protein complexes revealed a significant reduction in the assembly of mitochondrial complex III in dek53. Transmission electron microscopic examination showed severe morphological defects of mitochondria in dek53 endosperm cells. In addition, yeast two-hybrid and luciferase complementation imaging assays indicated that DEK53 can interact with the mitochondrion-targeted non-PPR RNA editing factor ZmMORF1, suggesting that DEK53 might be a functional component of the organellar RNA editosome.

APA, Harvard, Vancouver, ISO, and other styles

33

Zhu, Chenguang, Guangpu Jin, Peng Fang, Yan Zhang, Xuzhen Feng, Yuanping Tang, Weiwei Qi, and Rentao Song. "Maize pentatricopeptide repeat protein DEK41 affects cis-splicing of mitochondrial nad4 intron 3 and is required for normal seed development." Journal of Experimental Botany 70, no. 15 (April 25, 2019): 3795–808. http://dx.doi.org/10.1093/jxb/erz193.

Full text

Abstract:

Abstract The splicing of organelle-encoded mRNA in plants requires proteins encoded in the nucleus. The mechanism of splicing and the factors involved are not well understood. Pentatricopeptide repeat (PPR) proteins are known to participate in such RNA–protein interactions. Maize defective kernel 41 (dek41) is a seedling-lethal mutant that causes developmental defects. In this study, the Dek41 gene was cloned by Mutator tag isolation and allelic confirmation, and was found to encode a P-type PPR protein that targets mitochondria. Analysis of the mitochondrial RNA transcript profile revealed that dek41 mutations cause reduced splicing efficiency of mitochondrial nad4 intron 3. Immature dek41 kernels exhibited severe reductions in complex I assembly and NADH dehydrogenase activity. Up-regulated expression of alternative oxidase genes and deformed inner cristae of mitochondria in dek41, as revealed by TEM, indicated that proper splicing of nad4 is essential for correct mitochondrial functioning and morphology. Consistent with this finding, differentially expressed genes in the dek41 endosperm included those related to mitochondrial function and activity. Our results indicate that DEK41 is a PPR protein that affects cis-splicing of mitochondrial nad4 intron 3 and is required for correct mitochondrial functioning and maize kernel development.

APA, Harvard, Vancouver, ISO, and other styles

34

Dotsenko, G. S., and A. S. Dotsenko. "Conserved Peptides Recognition by Ensemble of Neural Networks for Mining Protein Data – LPMO Case Study." Mathematical Biology and Bioinformatics 15, no. 2 (December 22, 2020): 429–40. http://dx.doi.org/10.17537/2020.15.429.

Full text

Abstract:

Mining protein data is a recent promising area of modern bioinformatics. In this work, we suggested a novel approach for mining protein data – conserved peptides recognition by ensemble of neural networks (CPRENN). This approach was applied for mining lytic polysaccharide monooxygenases (LPMOs) in 19 ascomycete, 18 basidiomycete, and 18 bacterial proteomes. LPMOs are recently discovered enzymes and their mining is of high relevance for biotechnology of lignocellulosic materials. CPRENN was compared with two conventional bioinformatic methods for mining protein data – profile hidden Markov models (HMMs) search (HMMER program) and peptide pattern recognition (PPR program combined with Hotpep application). The maximum number of hypothetical LPMO amino acid sequences was discovered by HMMER. Profile HMMs search proved to be more sensitive method for mining LPMOs than conserved peptides recognition. Totally, CPRENN found 76 %, 67 %, and 65 % of hypothetical ascomycete, basidiomycete, and bacterial LPMOs discovered by HMMER, respectively. For AA9, AA10, and AA11 families which contain the major part of all LPMOs in the carbohydrate-active enzymes database (CAZy), CPRENN and PPR + Hotpep found 69–98 % and 62–95 % of amino acid sequences discovered by HMMER, respectively. In contrast with PPR + Hotpep, CPRENN possessed perfect precision and provided more complete mining of basidiomycete and bacterial LPMOs.

APA, Harvard, Vancouver, ISO, and other styles

35

Wang, Fei, James McD Stewart, and Jinfa Zhang. "Molecular markers linked to the Rf2 fertility restorer gene in cotton." Genome 50, no. 9 (September 2007): 818–24. http://dx.doi.org/10.1139/g07-061.

Full text

Abstract:

Cytoplasmic male sterility (CMS) is a maternally inherited trait in which plants do not produce viable pollen. Fertility in plants with CMS can be recovered by nuclear restorer genes. Most restorer genes cloned so far are members of the pentatricopeptide repeat (PPR) protein family. The objective of our study was to use the CMS-D8 and restoration (Rf2) system of cotton ( Gossypium hirsutum L.) to develop more DNA markers for the Rf2 gene. In a backcross population with 112 plants, segregation of male fertility was 1 fertile : 1 sterile. Three new RAPD markers were identified for Rf2, one of which was converted to a CAPS marker. In addition, 2 AFLP markers and 1 SSR marker were identified to be linked to the fertility restorer gene (Rf2). PPR motif primers were designed based on the conserved PPR motifs and used in combination with AFLP primers to test the mapping population, and 1 PPR-AFLP marker was identified. A linkage map with 9 flanking markers including 1 from a previous study was constructed.

APA, Harvard, Vancouver, ISO, and other styles

36

Berger, Michael, Nathalie Stahl, Giannino Del Sal, and Ygal Haupt. "Mutations in Proline 82 of p53 Impair Its Activation by Pin1 and Chk2 in Response to DNA Damage." Molecular and Cellular Biology 25, no. 13 (July 1, 2005): 5380–88. http://dx.doi.org/10.1128/mcb.25.13.5380-5388.2005.

Full text

Abstract:

ABSTRACT Tumor suppression by the p53 protein largely depends on the elimination of damaged cells by apoptosis. Mutations in the polyproline region (PPR) of p53 impair its apoptotic function. Deletion of the PPR renders p53 more sensitive to inhibition by Mdm2 via an unknown mechanism. We have explored the mechanism by which the PPR modulates the p53/Mdm2 loop. Proline 82 of p53 was identified to be essential for its interaction with the checkpoint kinase 2 (Chk2) and consequent phosphorylation of p53 on serine 20, following DNA damage. These physical and functional interactions are regulated by Pin1 through cis-trans isomerization of proline 82. Our study unravels the pathway by which Pin1 activates p53 in response to DNA damage and explains how Pin1 protects p53 from Mdm2. Further, we propose a role for Pin1-dependent induction of p53 conformational change as a mechanism responsible for the enhanced interaction between p53 and Chk2 following DNA damage. Importantly, our findings elucidate the selection for mutations in the Pin1 target Thr81/Pro82 motif within the PPR of p53 in human cancer.

APA, Harvard, Vancouver, ISO, and other styles

37

Morozova, D. Yu, A. R. Imatdinov, S. P. Zhivoderov, I. A. Titov, V. M. Lyska, A. V. Lunitsyn, and A. D. Sereda. "OBTAINING RECOMBINANT NUCLEOCAPSID PROTEIN OF PPR VIRUS FOR DISEASE SERODIAGNOSTIC." sel'skokhozyaistvennaya Biologiya 54, no. 2 (May 2019): 337–46. http://dx.doi.org/10.15389/agrobiology.2019.2.337eng.

Full text

APA, Harvard, Vancouver, ISO, and other styles

38

Williams, Pascale M., and Alice Barkan. "A chloroplast-localized PPR protein required for plastid ribosome accumulation." Plant Journal 36, no. 5 (November 18, 2003): 675–86. http://dx.doi.org/10.1046/j.1365-313x.2003.01915.x.

Full text

APA, Harvard, Vancouver, ISO, and other styles

39

Ren, Zhenjing, Kaijian Fan, Ting Fang, Jiaojiao Zhang, Li Yang, Jianhua Wang, Guoying Wang, and Yunjun Liu. "Maize Empty Pericarp602 Encodes a P-Type PPR Protein That Is Essential for Seed Development." Plant and Cell Physiology 60, no. 8 (May 10, 2019): 1734–46. http://dx.doi.org/10.1093/pcp/pcz083.

Full text

Abstract:

Abstract Pentatricopeptide repeat (PPR) proteins play crucial roles in intron splicing, which is important for RNA maturation. Identification of novel PPR protein with the function of intron splicing would help to understand the RNA splicing mechanism. In this study, we identified the maize empty pericarp602 (emp602) mutants, the mature kernels of which showed empty pericarp phenotype. We cloned the Emp602 gene from emp602 mutants and revealed that Emp602 encodes a mitochondrial-localized P-type PPR protein. We further revealed that Emp602 is specific for the cis-splicing of mitochondrial Nad4 intron 1 and intron 3, and mutation of Emp602 led to the loss of mature Nad4 transcripts. The loss of function of Emp602 nearly damaged the assembly and accumulation of complex I and arrested mitochondria formation, which arrested the seed development. The failed assembly of complex I triggers significant upregulation of Aox expression in emp602 mutants. Transcriptome analysis showed that the expression of mitochondrial-related genes, e.g. the genes associated with mitochondrial inner membrane presequence translocase complex and electron carrier activity, were extensively upregulated in emp602 mutant. These results demonstrate that EMP602 functions in the splicing of Nad4 intron 1 and intron 3, and the loss of function of Emp602 arrested maize seed development by disrupting the mitochondria complex I assembly.

APA, Harvard, Vancouver, ISO, and other styles

40

Prikryl, Jana, Margarita Rojas, Gadi Schuster, and Alice Barkan. "Mechanism of RNA stabilization and translational activation by a pentatricopeptide repeat protein." Proceedings of the National Academy of Sciences 108, no. 1 (December 20, 2010): 415–20. http://dx.doi.org/10.1073/pnas.1012076108.

Full text

Abstract:

Pentatricopeptide repeat (PPR) proteins comprise a large family of helical repeat proteins that bind RNA and modulate organellar RNA metabolism. The mechanisms underlying the functions attributed to PPR proteins are unknown. We describe in vitro studies of the maize protein PPR10 that clarify how PPR10 modulates the stability and translation of specific chloroplast mRNAs. We show that recombinant PPR10 bound to its native binding site in the chloroplast atpI–atpH intergenic region (i) blocks both 5′→3′ and 3′→ 5 exoribonucleases in vitro; (ii) is sufficient to define the native processed atpH mRNA 5′-terminus in conjunction with a generic 5′→3′ exoribonuclease; and (iii) remodels the structure of the atpH ribosome-binding site in a manner that can account for PPR10’s ability to enhance atpH translation. In addition, we show that the minimal PPR10-binding site spans 17 nt. We propose that the site-specific barrier and RNA remodeling activities of PPR10 are a consequence of its unusually long, high-affinity interface with single-stranded RNA, that this interface provides a functional mimic to bacterial small RNAs, and that analogous activities underlie many of the biological functions that have been attributed to PPR proteins.

APA, Harvard, Vancouver, ISO, and other styles

41

Dedow, Lauren K., and Julia Bailey-Serres. "Searching for a Match: Structure, Function and Application of Sequence-Specific RNA-Binding Proteins." Plant and Cell Physiology 60, no. 9 (May 7, 2019): 1927–38. http://dx.doi.org/10.1093/pcp/pcz072.

Full text

Abstract:

Abstract Plants encode over 1800 RNA-binding proteins (RBPs) that modulate a myriad of steps in gene regulation from chromatin organization to translation, yet only a small number of these proteins and their target transcripts have been functionally characterized. Two classes of eukaryotic RBPs, pentatricopeptide repeat (PPR) and pumilio/fem-3 binding factors (PUF), recognize and bind to specific sequential RNA sequences through protein–RNA interactions. These modular proteins possess helical structural units containing key residues with high affinity for specific nucleotides, whose sequential order determines binding to a specific target RNA sequence. PPR proteins are nucleus-encoded, but largely regulate post-transcriptional gene regulation within plastids and mitochondria, including splicing, translation and RNA editing. Plant PUFs are involved in gene regulatory processes within the cell nucleus and cytoplasm. The modular structures of PPRs and PUFs that determine sequence specificity has facilitated identification of their RNA targets and biological functions. The protein-based RNA-targeting of PPRs and PUFs contrasts to the prokaryotic cluster regularly interspaced short palindromic repeats (CRISPR)-associated proteins (Cas) that target RNAs in prokaryotes. Together the PPR, PUF and CRISPR-Cas systems provide varied opportunities for RNA-targeted engineering applications.

APA, Harvard, Vancouver, ISO, and other styles

42

Marchetti, Fernanda, Maximiliano Cainzos, Sofía Shevtsov, Juan Pablo Córdoba, Laure Dora Sultan, Axel Brennicke, Mizuki Takenaka, Gabriela Pagnussat, Oren Ostersetzer-Biran, and Eduardo Zabaleta. "Mitochondrial Pentatricopeptide Repeat Protein, EMB2794, Plays a Pivotal Role in NADH Dehydrogenase Subunit nad2 mRNA Maturation in Arabidopsis thaliana." Plant and Cell Physiology 61, no. 6 (March 12, 2020): 1080–94. http://dx.doi.org/10.1093/pcp/pcaa028.

Full text

Abstract:

Abstract The Arabidopsis genome encodes >450 proteins containing the pentatricopeptide repeat (PPR) motif. The PPR proteins are classified into two groups, termed as P and P Long-Short (PLS) classes. Typically, the PLS subclass proteins are mainly involved in the RNA editing of mitochondrial and chloroplast transcripts, whereas most of the analyzed P subclass proteins have been mainly implicated in RNA metabolism, such as 5′ or 3′ transcript stabilization and processing, splicing and translation. Mutations of PPR genes often result in embryogenesis and altered seedling developmental defect phenotypes, but only a limited number of ppr mutants have been characterized in detail. In this report, we show that null mutations in the EMB2794 gene result in embryo arrest, due to altered splicing of nad2 transcripts in the Arabidopsis mitochondria. In angiosperms, nad2 has five exons that are transcribed individually from two mitochondrial DNA regions. Biochemical and in vivo analyses further indicate that recombinant or transgenic EMB2794 proteins bind to the nad2 pre-mRNAs in vitro as well as in vivo, suggesting a role for this protein in trans-splicing of nad2 intron 2 and possibly in the stability of the second pre-mRNA of nad2. Homozygous emb2794 lines, showing embryo-defective phenotypes, can be partially rescued by the addition of sucrose to the growth medium. Mitochondria of rescued homozygous mutant plants contain only traces of respiratory complex I, which lack the NADH-dehydrogenase activity.

APA, Harvard, Vancouver, ISO, and other styles

43

Wang, Haojie, Jinhao Bi, Na Feng, Yongkun Zhao, Tiecheng Wang, Yuetao Li, Feihu Yan, Songtao Yang, and Xianzhu Xia. "Construction of Recombinant Rabies Virus Vectors Expressing H or F Protein of Peste des Petits Ruminants Virus." Veterinary Sciences 9, no. 10 (October 10, 2022): 555. http://dx.doi.org/10.3390/vetsci9100555.

Full text

Abstract:

Peste des petits ruminants (PPR) is one of the most contagious and fatal diseases of small ruminants in the world and is classified as a category A epidemic disease. It is the target of a global eradication campaign led by the Office International des Epizooties (OIE) and Food and Agriculture Organization of the United Nations (FAO). The PPR live attenuated vaccine is currently the most widely used and approved vaccine, but the use of this vaccine interferes with the serological testing of the PPR elimination program, and there is a potential safety risk. Viral vector vaccines are one of the most promising methods to solve this dilemma. In this study, the full-length infectious clone plasmid of rabies virus (RABV), pD-SRV9-PM-LASV, was used as the backbone, and the envelope glycoprotein H (hemagglutinin protein) or F (fusion protein) gene of PPRV was inserted into the backbone plasmid to construct the infectious clones pD-SRV9-PM-PPRV-H and pD-SRV9-PM-PPRV-F, which express the PPRV H and PPRV F genes, respectively. The correct construction of these infectious clones was verified after sequencing and double digestion. The infectious clones were transfected with a helper plasmid into BSR/T7 cells, and recombinant viruses were successfully rescued by direct immunofluorescence, indirect immunofluorescence, Western blotting, and transmission electron microscopy and named rSRV9-H and rSRV9-F. The results of growth kinetics studies indicated that the inserted gene did not affect virus proliferation. Stability studies revealed that the inserted target gene was stably expressed in recombinant RABV for at least 15 generations. In this study, the recombinant viruses rSRV9-H and rSRV9-F were successfully rescued. The constructed viruses had good proliferative activity and stability and provided potential bivalent inactivated vaccine candidate strains for the prevention of PPR and livestock rabies.

APA, Harvard, Vancouver, ISO, and other styles

44

Liu, Rui, Shi-Kai Cao, Aqib Sayyed, Huan-Huan Yang, Jiao Zhao, Xiaomin Wang, Ru-Xue Jia, Feng Sun, and Bao-Cai Tan. "The DYW-subgroup pentatricopeptide repeat protein PPR27 interacts with ZmMORF1 to facilitate mitochondrial RNA editing and seed development in maize." Journal of Experimental Botany 71, no. 18 (June 12, 2020): 5495–505. http://dx.doi.org/10.1093/jxb/eraa273.

Full text

Abstract:

Abstract C-to-U RNA editing in plant mitochondria requires the participation of many nucleus-encoded factors, most of which are pentatricopeptide repeat (PPR) proteins. There is a large number of PPR proteins and the functions many of them are unknown. Here, we report a mitochondrion-localized DYW-subgroup PPR protein, PPR27, which functions in the editing of multiple mitochondrial transcripts in maize. The ppr27 mutant is completely deficient in C-to-U editing at the ccmFN-1357 and rps3-707 sites, and editing at six other sites is substantially reduced. The lack of editing at ccmFN-1357 causes a deficiency of CcmFN protein. As CcmFN functions in the maturation pathway of cytochrome proteins that are subunits of mitochondrial complex III, its deficiency results in an absence of cytochrome c1 and cytochrome c proteins. Consequently, the assembly of mitochondrial complex III and super-complex I+III2 is decreased, which impairs the electron transport chain and respiration, leading to arrests in embryogenesis and endosperm development in ppr27. In addition, PPR27 was found to physically interact with ZmMORF1, which interacts with ZmMORF8, suggesting that these three proteins may facilitate C-to-U RNA editing via the formation of a complex in maize mitochondria. This RNA editing is essential for complex III assembly and seed development in maize.

APA, Harvard, Vancouver, ISO, and other styles

45

Selvaraj, Muneeswaran, Mana Mahapatra, and Satya Parida. "Exchange of C-Terminal Variable Sequences within Morbillivirus Nucleocapsid Protein Are Tolerated: Development and Evaluation of Two Marker (DIVA) Vaccines (Sungri/96 DIVA, Nigeria/75/1 DIVA) against PPR." Viruses 13, no. 11 (November 21, 2021): 2320. http://dx.doi.org/10.3390/v13112320.

Full text

Abstract:

Across Africa, the Middle East, and Asia, peste des petits ruminants virus (PPRV) places a huge disease burden on agriculture, affecting, in particular, small ruminant production. The recent PPR outbreaks in Northern Africa, the European part of Turkey, and Bulgaria represent a significant threat to mainland Europe, as a source of disease. Although two safe and efficacious live attenuated vaccines (Sungri/96 and Nigeria/75/1) are available for the control of PPR, current serological tests do not enable the differentiation between naturally infected and vaccinated animals (DIVA). The vaccinated animals develop a full range of immune responses to viral proteins and, therefore, cannot be distinguished serologically from those that have recovered from a natural infection. This poses a serious problem for the post-vaccinal sero-surveillance during the ongoing PPR eradication program. Furthermore, during the latter stages of any eradication program, vaccination is only possible if the vaccine used is fully DIVA compliant. Using reverse genetics, we have developed two live attenuated PPR DIVA vaccines (Sungri/96 DIVA and Nigeria/75/1 DIVA), in which the C-terminal variable region of the PPRV N-protein has been replaced with dolphin morbillivirus (DMV). As a proof of principle, both the DIVA vaccines were evaluated in goats in pilot studies for safety and efficacy, and all the animals were clinically protected against the intranasal virulent virus challenge, similar to the parent vaccines. Furthermore, it is possible to differentiate between infected animals and vaccinated animals using two newly developed ELISAs. Therefore, these DIVA vaccines and associated tests can facilitate the sero-monitoring process and speed up the implementation of global PPR eradication through vaccination.

APA, Harvard, Vancouver, ISO, and other styles

46

Mahapatra, Mana, Martin Mayora Neto, Asha Khunti, Felix Njeumi, and Satya Parida. "Development and Evaluation of a Nested PCR for Improved Diagnosis and Genetic Analysis of Peste des Petits Ruminants Virus (PPRV) for Future Use in Nascent PPR Eradication Programme." Animals 11, no. 11 (November 5, 2021): 3170. http://dx.doi.org/10.3390/ani11113170.

Full text

Abstract:

Peste des petits ruminants (PPR) is a highly contagious viral disease of small ruminants caused by PPR virus (PPRV). PPR is endemic in Asia, the Middle East and across large areas of Africa and is currently targeted for global eradication by 2030. The virus exists as four different lineages that are usually limited to specific geographical areas. However, recent reports of spread of PPRV, in particular of lineage IV viruses to infection-free countries and previously PPR endemic areas are noteworthy. A rapid and accurate laboratory diagnosis and reports on its epidemiological linkage for virus spread play a major role in the effective control and eradication of the disease. Currently, molecular assays, including conventional reverse transcription-polymerase chain reaction (RT-PCR) and real-time RT-PCR (RT-qPCR) are usually used for diagnosis of PPR while the sequencing of part of the nucleocapsid gene is usually carried out for the viral lineage identification. However, it is difficult to diagnose and sequence the genetic material if the animal excreted a low level of virus at the initial stage of infection or if the PPRV is degraded during the long-distance transportation of samples to the reference laboratories. This study describes the development of a novel nested RT-PCR assay for the detection of the PPRV nucleic acid by targeting the N-protein gene, compares the performance of the assay with the existing conventional RT-PCR and also provides good-quality DNA suitable for sequencing in order to identify circulating lineages. The assay was evaluated using cell culture propagated PPRVs, field samples from clinically infected animals and samples from experimentally infected animals encompassing all four lineages (I–IV) of PPRV. This assay provides a solution with an easy, accurate, rapid and cost-effective PPR diagnostic and partial genome sequencing for use in resource-limited settings.

APA, Harvard, Vancouver, ISO, and other styles

47

Mahapatra, Howson, Fowler, Batten, Flannery, Selvaraj, and Parida. "Rapid Detection of Peste des Petits Ruminants Virus (PPRV) Nucleic Acid Using a Novel Low-Cost Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Assay for Future Use in Nascent PPR Eradication Programme." Viruses 11, no. 8 (July 31, 2019): 699. http://dx.doi.org/10.3390/v11080699.

Full text

Abstract:

Peste des petits ruminants (PPR) is a disease of small ruminants caused by peste des petits ruminants virus (PPRV), and is endemic in Asia, the Middle East and Africa. Effective control combines the application of early warning systems, accurate laboratory diagnosis and reporting, animal movement restrictions, suitable vaccination and surveillance programs, and the coordination of all these measures by efficient veterinary services. Molecular assays, including conventional reverse transcription-polymerase chain reaction (RT-PCR) and real-time RT-PCR (RT-qPCR) have improved the sensitivity and rapidity of diagnosing PPR. However, currently these assays are only performed within laboratory settings; therefore, the development of field diagnostics for PPR would improve the fast implementation of control policies, particularly when PPR has been targeted to be eradicated by 2030. Loop-mediated isothermal amplification (LAMP) assays are simple to use, rapid, and have sensitivity and specificity within the range of RT-qPCR; and can be performed in the field using disposable consumables and portable equipment. This study describes the development of a novel RT-LAMP assay for the detection of PPRV nucleic acid by targeting the N-protein gene. The RT-LAMP assay was evaluated using cell culture propagated PPRVs, field samples from clinically infected animals and samples from experimentally infected animals encompassing all four lineages (I-IV) of PPRV. The test displayed 100% concordance with RT-qPCR when considering an RT-qPCR cut-off value of CT >40. Further, the RT-LAMP assay was evaluated using experimental and outbreak samples without prior RNA extraction making it more time and cost-effective. This assay provides a solution for a pen-side, rapid and inexpensive PPR diagnostic for use in the field in nascent PPR eradication programme.

APA, Harvard, Vancouver, ISO, and other styles

48

Yang, Yan-Zhuo, Shuo Ding, Yong Wang, Hong-Chun Wang, Xin-Yuan Liu, Feng Sun, Chunhui Xu, Baohui Liu, and Bao-Cai Tan. "PPR20 Is Required for the cis-Splicing of Mitochondrial nad2 Intron 3 and Seed Development in Maize." Plant and Cell Physiology 61, no. 2 (October 31, 2019): 370–80. http://dx.doi.org/10.1093/pcp/pcz204.

Full text

Abstract:

Abstract Pentatricopeptide repeat (PPR) proteins are helical repeat RNA-binding proteins that function in RNA processing by conferring sequence-specific RNA-binding activity. Owing to the lethality of PPR mutants, functions of many PPR proteins remain obscure. In this study, we report the function of PPR20 in intron splicing in mitochondria and its role in maize seed development. PPR20 is a P-type PPR protein targeted to mitochondria. The ppr20 mutants display slow embryo and endosperm development. Null mutation of PPR20 severely reduces the cis-splicing of mitochondrial nad2 intron 3, resulting in reduction in the assembly and activity of mitochondrial complex I. The ppr20-35 allele with a Mu insertion in the N-terminal region shows a much weaker phenotype. Molecular analyses revealed that the mutant produces a truncated transcript, coding for PPR20ΔN120 lacking the N-terminal 120 amino acids. Subcellular localization revealed that PPR20ΔN120:GFP is able to target to mitochondria as well, suggesting the sequence diversity of the mitochondrial targeting peptides. Another mutant zm_mterf15 was also found to be impaired in the splicing of mitochondrial nad2 intron 3. Further analyses are required to identify the exact function of PPR20 and Zm_mTERF15 in the splicing of nad2 intron 3.

APA, Harvard, Vancouver, ISO, and other styles

49

Zhu, Zixiang, Xiaocui Zhang, Gulizhati Adili, Jiong Huang, Xiaoli Du, Xiangle Zhang, Pengfei Li, et al. "Genetic Characterization of a Novel Mutant of Peste Des Petits Ruminants Virus Isolated fromCapra ibexin China during 2015." BioMed Research International 2016 (2016): 1–9. http://dx.doi.org/10.1155/2016/7632769.

Full text

Abstract:

Peste des petits ruminants virus (PPRV) is the causative agent of peste des petits ruminants (PPR). The spread of PPR often causes severe economic losses. Therefore, special attention should be paid to the surveillance of PPR emergence, spread, and geographic distribution. Here we describe a novel mutant of PPRV China/XJBZ/2015 that was isolated fromCapra ibexin Xinjiang province in China 2015. The sequence analysis and phylogenetic assessment indicate that China/XJBZ/2015 belongs to lineage IV, being closely related to China/XJYL/2013 strain. Interestingly, the V protein sequence of China/XJBZ/2015 showed lower homology with other Chinese PPRVs isolated during 2013 to 2014 (94%~95%), whereas it shared 100% identity with three Tibet strains isolated in China 2007. The 3′ UTR, V gene, and C gene were determined to be highly variable. Besides, 29 PPR genomic sequences available in GenBank were analyzed in this study. It is the first time to use PPRV genomic sequences to classify the different lineages which confirmed the lineage clustering of PPRVs using N gene 255 bp fragments and F gene 322 bp fragments. In conclusion, our findings indicate that the PPRVs continue to evolve in China, and some new mutations have emerged.

APA, Harvard, Vancouver, ISO, and other styles

50

Hammani, Kamel, Anthony Gobert, Ian Small, and Philippe Giegé. "A PPR protein involved in regulating nuclear genes encoding mitochondrial proteins?" Plant Signaling & Behavior 6, no. 5 (May 2011): 748–50. http://dx.doi.org/10.4161/psb.6.5.15148.

Full text

APA, Harvard, Vancouver, ISO, and other styles

Journal articles on the topic 'PPR-Protein'

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles