1
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Sayyed A, Chen B, Wang Y, Cao SK, Tan BC. PPR596 Is Required for nad2 Intron Splicing and Complex I Biogenesis in Arabidopsis. Int J Mol Sci 2024; 25:3542. [PMID: 38542518 PMCID: PMC10971677 DOI: 10.3390/ijms25063542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/15/2024] [Accepted: 03/16/2024] [Indexed: 04/04/2024] Open
Abstract
Mitochondria are essential organelles that generate energy via oxidative phosphorylation. Plant mitochondrial genome encodes some of the respiratory complex subunits, and these transcripts require accurate processing, including C-to-U RNA editing and intron splicing. Pentatricopeptide repeats (PPR) proteins are involved in various organellar RNA processing events. PPR596, a P-type PPR protein, was previously identified to function in the C-to-U editing of mitochondrial rps3 transcripts in Arabidopsis. Here, we demonstrate that PPR596 functions in the cis-splicing of nad2 intron 3 in mitochondria. Loss of the PPR596 function affects the editing at rps3eU1344SS, impairs nad2 intron 3 splicing and reduces the mitochondrial complex I's assembly and activity, while inducing alternative oxidase (AOX) gene expression. This defect in nad2 intron splicing provides a plausible explanation for the slow growth of the ppr595 mutants. Although a few P-type PPR proteins are involved in RNA C-to-U editing, our results suggest that the primary function of PPR596 is intron splicing.
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Affiliation(s)
| | | | | | | | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (A.S.); (B.C.); (Y.W.); (S.-K.C.)
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2
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Kendrick R, Chotewutmontri P, Belcher S, Barkan A. Correlated retrograde and developmental regulons implicate multiple retrograde signals as coordinators of chloroplast development in maize. THE PLANT CELL 2022; 34:4897-4919. [PMID: 36073948 PMCID: PMC9709983 DOI: 10.1093/plcell/koac276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/02/2022] [Indexed: 05/09/2023]
Abstract
Signals emanating from chloroplasts influence nuclear gene expression, but roles of retrograde signals during chloroplast development are unclear. To address this gap, we analyzed transcriptomes of non-photosynthetic maize mutants and compared them to transcriptomes of stages of normal leaf development. The transcriptomes of two albino mutants lacking plastid ribosomes resembled transcriptomes at very early stages of normal leaf development, whereas the transcriptomes of two chlorotic mutants with thylakoid targeting or plastid transcription defects resembled those at a slightly later stage. We identified ∼2,700 differentially expressed genes, which fall into six major categories based on the polarity and mutant-specificity of the change. Downregulated genes were generally expressed late in normal development and were enriched in photosynthesis genes, whereas upregulated genes act early and were enriched for functions in chloroplast biogenesis and cytosolic translation. We showed further that target-of-rapamycin (TOR) signaling was elevated in mutants lacking plastid ribosomes and declined in concert with plastid ribosome buildup during normal leaf development. Our results implicate three plastid signals as coordinators of photosynthetic differentiation. One signal requires plastid ribosomes and activates photosynthesis genes. A second signal reflects attainment of chloroplast maturity and represses chloroplast biogenesis genes. A third signal, the consumption of nutrients by developing chloroplasts, represses TOR, promoting termination of cell proliferation during leaf development.
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Affiliation(s)
- Rennie Kendrick
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | | | - Susan Belcher
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
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3
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Honkanen S, Small I. The GENOMES UNCOUPLED1 protein has an ancient, highly conserved role but not in retrograde signalling. THE NEW PHYTOLOGIST 2022; 236:99-113. [PMID: 35708656 PMCID: PMC9545484 DOI: 10.1111/nph.18318] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 06/07/2022] [Indexed: 06/01/2023]
Abstract
The pentatricopeptide repeat protein GENOMES UNCOUPLED1 (GUN1) is required for chloroplast-to-nucleus signalling when plastid translation becomes inhibited during chloroplast development in Arabidopsis thaliana, but its exact molecular function remains unknown. We analysed GUN1 sequences in land plants and streptophyte algae. We tested functional conservation by complementation of the Arabidopsis gun1 mutant with GUN1 genes from the streptophyte alga Coleochate orbicularis or the liverwort Marchantia polymorpha. We also analysed the transcriptomes of M. polymorpha gun1 knockout mutant lines during chloroplast development. GUN1 evolved within the streptophyte algal ancestors of land plants and is highly conserved among land plants but missing from the Rafflesiaceae that lack chloroplast genomes. GUN1 genes from C. orbicularis and M. polymorpha suppress the cold-sensitive phenotype of the Arabidopsis gun1 mutant and restore typical retrograde responses to treatments with inhibitors of plastid translation, even though M. polymorpha responds very differently to such treatments. Our findings suggest that GUN1 is an ancient protein that evolved within the streptophyte algal ancestors of land plants before the first plants colonized land more than 470 million years ago. Its primary role is likely to be in chloroplast gene expression and its role in chloroplast retrograde signalling probably evolved more recently.
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Affiliation(s)
- Suvi Honkanen
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular SciencesThe University of Western AustraliaCrawleyWA6009Australia
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular SciencesThe University of Western AustraliaCrawleyWA6009Australia
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4
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Gao Y, Thiele W, Saleh O, Scossa F, Arabi F, Zhang H, Sampathkumar A, Kühn K, Fernie A, Bock R, Schöttler MA, Zoschke R. Chloroplast translational regulation uncovers nonessential photosynthesis genes as key players in plant cold acclimation. THE PLANT CELL 2022; 34:2056-2079. [PMID: 35171295 PMCID: PMC9048916 DOI: 10.1093/plcell/koac056] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/12/2022] [Indexed: 05/04/2023]
Abstract
Plants evolved efficient multifaceted acclimation strategies to cope with low temperatures. Chloroplasts respond to temperature stimuli and participate in temperature sensing and acclimation. However, very little is known about the involvement of chloroplast genes and their expression in plant chilling tolerance. Here we systematically investigated cold acclimation in tobacco seedlings over 2 days of exposure to low temperatures by examining responses in chloroplast genome copy number, transcript accumulation and translation, photosynthesis, cell physiology, and metabolism. Our time-resolved genome-wide investigation of chloroplast gene expression revealed substantial cold-induced translational regulation at both the initiation and elongation levels, in the virtual absence of changes at the transcript level. These cold-triggered dynamics in chloroplast translation are widely distinct from previously described high light-induced effects. Analysis of the gene set responding significantly to the cold stimulus suggested nonessential plastid-encoded subunits of photosynthetic protein complexes as novel players in plant cold acclimation. Functional characterization of one of these cold-responsive chloroplast genes by reverse genetics demonstrated that the encoded protein, the small cytochrome b6f complex subunit PetL, crucially contributes to photosynthetic cold acclimation. Together, our results uncover an important, previously underappreciated role of chloroplast translational regulation in plant cold acclimation.
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Affiliation(s)
- Yang Gao
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Wolfram Thiele
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Omar Saleh
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Federico Scossa
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Council for Agricultural Research and Economics, Research Center for Genomics and Bioinformatics (CREA-GB), Rome, 00178, Italy
| | - Fayezeh Arabi
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Hongmou Zhang
- Institute of Optical Sensor Systems, German Aerospace Center (DLR), Berlin, 12489, Germany
| | - Arun Sampathkumar
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Kristina Kühn
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Alisdair Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Mark A Schöttler
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
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5
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Gao Y, Thiele W, Saleh O, Scossa F, Arabi F, Zhang H, Sampathkumar A, Kühn K, Fernie A, Bock R, Schöttler MA, Zoschke R. Chloroplast translational regulation uncovers nonessential photosynthesis genes as key players in plant cold acclimation. THE PLANT CELL 2022; 34:2056-2079. [PMID: 35171295 DOI: 10.1093/plcell/koac056%jtheplantcell] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/12/2022] [Indexed: 05/28/2023]
Abstract
Plants evolved efficient multifaceted acclimation strategies to cope with low temperatures. Chloroplasts respond to temperature stimuli and participate in temperature sensing and acclimation. However, very little is known about the involvement of chloroplast genes and their expression in plant chilling tolerance. Here we systematically investigated cold acclimation in tobacco seedlings over 2 days of exposure to low temperatures by examining responses in chloroplast genome copy number, transcript accumulation and translation, photosynthesis, cell physiology, and metabolism. Our time-resolved genome-wide investigation of chloroplast gene expression revealed substantial cold-induced translational regulation at both the initiation and elongation levels, in the virtual absence of changes at the transcript level. These cold-triggered dynamics in chloroplast translation are widely distinct from previously described high light-induced effects. Analysis of the gene set responding significantly to the cold stimulus suggested nonessential plastid-encoded subunits of photosynthetic protein complexes as novel players in plant cold acclimation. Functional characterization of one of these cold-responsive chloroplast genes by reverse genetics demonstrated that the encoded protein, the small cytochrome b6f complex subunit PetL, crucially contributes to photosynthetic cold acclimation. Together, our results uncover an important, previously underappreciated role of chloroplast translational regulation in plant cold acclimation.
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Affiliation(s)
- Yang Gao
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Wolfram Thiele
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Omar Saleh
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Federico Scossa
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Council for Agricultural Research and Economics, Research Center for Genomics and Bioinformatics (CREA-GB), Rome, 00178, Italy
| | - Fayezeh Arabi
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Hongmou Zhang
- Institute of Optical Sensor Systems, German Aerospace Center (DLR), Berlin, 12489, Germany
| | - Arun Sampathkumar
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Kristina Kühn
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Alisdair Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Mark A Schöttler
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
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6
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CAF Proteins Help SOT1 Regulate the Stability of Chloroplast ndhA Transcripts. Int J Mol Sci 2021; 22:ijms222312639. [PMID: 34884441 PMCID: PMC8657633 DOI: 10.3390/ijms222312639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/20/2021] [Accepted: 11/20/2021] [Indexed: 12/26/2022] Open
Abstract
Protein-mediated RNA stabilization plays profound roles in chloroplast gene expression. Genetic studies have indicated that chloroplast ndhA transcripts, encoding a key subunit of the NADH dehydrogenase-like complex that mediates photosystem I cyclic electron transport and facilitates chlororespiration, are stabilized by PPR53 and its orthologs, but the underlying mechanisms are unclear. Here, we report that CHLOROPLAST RNA SPLICING 2 (CRS2)-ASSOCIATED FACTOR (CAF) proteins activate SUPPRESSOR OF THYLAKOID FORMATION 1 (SOT1), an ortholog of PPR53 in Arabidopsis thaliana, enhancing their affinity for the 5' ends of ndhA transcripts to stabilize these molecules while inhibiting the RNA endonuclease activity of the SOT1 C-terminal SMR domain. In addition, we established that SOT1 improves the splicing efficiency of ndhA by facilitating the association of CAF2 with the ndhA intron, which may be due to the SOT1-mediated stability of the ndhA transcripts. Our findings shed light on the importance of PPR protein interaction partners in moderating RNA metabolism.
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7
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Manavski N, Mathieu S, Rojas M, Méteignier LV, Brachmann A, Barkan A, Hammani K. In vivo stabilization of endogenous chloroplast RNAs by customized artificial pentatricopeptide repeat proteins. Nucleic Acids Res 2021; 49:5985-5997. [PMID: 34037778 PMCID: PMC8191804 DOI: 10.1093/nar/gkab390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/05/2021] [Accepted: 04/28/2021] [Indexed: 12/17/2022] Open
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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Affiliation(s)
- Nikolay Manavski
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Sébastien Mathieu
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Margarita Rojas
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403 USA
| | - Louis-Valentin Méteignier
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Andreas Brachmann
- Genetics, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried Germany
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403 USA
| | - Kamel Hammani
- To whom correspondence should be addressed. Tel: +33 367155281; Fax: +33 367155300;
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8
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Loudya N, Mishra P, Takahagi K, Uehara-Yamaguchi Y, Inoue K, Bogre L, Mochida K, López-Juez E. Cellular and transcriptomic analyses reveal two-staged chloroplast biogenesis underpinning photosynthesis build-up in the wheat leaf. Genome Biol 2021; 22:151. [PMID: 33975629 PMCID: PMC8111775 DOI: 10.1186/s13059-021-02366-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 04/26/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The developmental gradient in monocot leaves has been exploited to uncover leaf developmental gene expression programs and chloroplast biogenesis processes. However, the relationship between the two is barely understood, which limits the value of transcriptome data to understand the process of chloroplast development. RESULTS Taking advantage of the developmental gradient in the bread wheat leaf, we provide a simultaneous quantitative analysis for the development of mesophyll cells and of chloroplasts as a cellular compartment. This allows us to generate the first biologically-informed gene expression map of this leaf, with the entire developmental gradient from meristematic to fully differentiated cells captured. We show that the first phase of plastid development begins with organelle proliferation, which extends well beyond cell proliferation, and continues with the establishment and then the build-up of the plastid genetic machinery. The second phase is marked by the development of photosynthetic chloroplasts which occupy the available cellular space. Using a network reconstruction algorithm, we predict that known chloroplast gene expression regulators are differentially involved across those developmental stages. CONCLUSIONS Our analysis generates both the first wheat leaf transcriptional map and one of the most comprehensive descriptions to date of the developmental history of chloroplasts in higher plants. It reveals functionally distinct plastid and chloroplast development stages, identifies processes occurring in each of them, and highlights our very limited knowledge of the earliest drivers of plastid biogenesis, while providing a basis for their future identification.
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Affiliation(s)
- Naresh Loudya
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Priyanka Mishra
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Kotaro Takahagi
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Japan
| | | | - Komaki Inoue
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Japan
| | - Laszlo Bogre
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Japan.
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, Japan.
- RIKEN Baton Zone Program, Tsurumi-ku, Yokohama, Japan.
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan.
| | - Enrique López-Juez
- Department of Biological Sciences, Royal Holloway University of London, Egham, UK.
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9
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The Arabidopsis NOT4A E3 ligase promotes PGR3 expression and regulates chloroplast translation. Nat Commun 2021; 12:251. [PMID: 33431870 PMCID: PMC7801604 DOI: 10.1038/s41467-020-20506-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 11/30/2020] [Indexed: 12/14/2022] Open
Abstract
Chloroplast function requires the coordinated action of nuclear- and chloroplast-derived proteins, including several hundred nuclear-encoded pentatricopeptide repeat (PPR) proteins that regulate plastid mRNA metabolism. Despite their large number and importance, regulatory mechanisms controlling PPR expression are poorly understood. Here we show that the Arabidopsis NOT4A ubiquitin-ligase positively regulates the expression of PROTON GRADIENT REGULATION 3 (PGR3), a PPR protein required for translating several thylakoid-localised photosynthetic components and ribosome subunits within chloroplasts. Loss of NOT4A function leads to a strong depletion of cytochrome b6f and NAD(P)H dehydrogenase (NDH) complexes, as well as plastid 30 S ribosomes, which reduces mRNA translation and photosynthetic capacity, causing pale-yellow and slow-growth phenotypes. Quantitative transcriptome and proteome analysis of the not4a mutant reveal it lacks PGR3 expression, and that its molecular defects resemble those of a pgr3 mutant. Furthermore, we show that normal plastid function is restored to not4a through transgenic PGR3 expression. Our work identifies NOT4A as crucial for ensuring robust photosynthetic function during development and stress-response, through promoting PGR3 production and chloroplast translation.
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10
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Zhao X, Wang H, Li H, Wu Y, Wang G. Identifying Plant Pentatricopeptide Repeat Proteins Using a Variable Selection Method. FRONTIERS IN PLANT SCIENCE 2021; 12:506681. [PMID: 33732270 PMCID: PMC7957076 DOI: 10.3389/fpls.2021.506681] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/08/2021] [Indexed: 05/05/2023]
Abstract
Motivation: Pentatricopeptide repeat (PPR), which is a triangular pentapeptide repeat domain, plays an important role in plant growth. Features extracted from sequences are applicable to PPR protein identification using certain classification methods. However, which components of a multidimensional feature (namely variables) are more effective for protein discrimination has never been discussed. Therefore, we seek to select variables from a multidimensional feature for identifying PPR proteins. Method: A framework of variable selection for identifying PPR proteins is proposed. Samples representing PPR positive proteins and negative ones are equally split into a training and a testing set. Variable importance is regarded as scores derived from an iteration of resampling, training, and scoring step on the training set. A model selection method based on Gaussian mixture model is applied to automatic choice of variables which are effective to identify PPR proteins. Measurements are used on the testing set to show the effectiveness of the selected variables. Results: Certain variables other than the multidimensional feature they belong to do work for discrimination between PPR positive proteins and those negative ones. In addition, the content of methionine may play an important role in predicting PPR proteins.
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Affiliation(s)
- Xudong Zhao
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Hanxu Wang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Hangyu Li
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Yiming Wu
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Guohua Wang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- *Correspondence: Guohua Wang
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11
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Zhang J, Guo Y, Fang Q, Zhu Y, Zhang Y, Liu X, Lin Y, Barkan A, Zhou F. The PPR-SMR Protein ATP4 Is Required for Editing the Chloroplast rps8 mRNA in Rice and Maize. PLANT PHYSIOLOGY 2020; 184:2011-2021. [PMID: 32928899 PMCID: PMC7723101 DOI: 10.1104/pp.20.00849] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/01/2020] [Indexed: 05/20/2023]
Abstract
Chloroplast gene expression involves the participation of hundreds of pentatricopeptide repeat (PPR) RNA binding proteins, and proteins in the PLS subfamily typically specify sites of RNA editing, whereas those in the P-subfamily typically stabilize RNA, activate translation, or promote intron splicing. Several P-type PPR proteins include a small MutS-related (SMR) domain, but the biochemical contribution of the SMR domain remains enigmatic. Here, we describe a rice (Oryza sativa) mutant, osatp4, lacking the ortholog of ATP4, a PPR-SMR protein in maize (Zea mays). osatp4 mutants were chlorotic and had a plastid-ribosome deficiency when grown in the cold. Like maize ATP4, OsATP4 was required for the accumulation of dicistronic rpl16-rpl14 transcripts. Surprisingly, OsATP4 was also required for the editing of a specific nucleotide in the ribosomal protein S8 transcripts, rps8, and this function was conserved in maize. By contrast, rps8 RNA was edited normally in the maize PROTON gradient regulation3 mutant, pgr3, which also lacks rpl16-rpl14 transcripts, indicating that the editing defect in atp4 mutants is not a secondary effect of altered rpl16-rpl14 RNA metabolism. Expression of the edited rps8 isoform in transgenic osatp4 mutants complemented the cold-sensitive phenotype, indicating that a rps8 expression defect accounts for the cold-sensitivity. We suggest that ATP4 stimulates rps8 editing by facilitating access of a previously characterized PLS-type RNA editing factor to its cognate cis-element upstream of the edited nucleotide.
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Affiliation(s)
- Jinghong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yipo Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qian Fang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongli Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuejiao Liu
- Institute of Crop Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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12
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The Chloroplast RNA Binding Protein CP31A Has a Preference for mRNAs Encoding the Subunits of the Chloroplast NAD(P)H Dehydrogenase Complex and Is Required for Their Accumulation. Int J Mol Sci 2020; 21:ijms21165633. [PMID: 32781615 PMCID: PMC7460601 DOI: 10.3390/ijms21165633] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/16/2020] [Accepted: 08/04/2020] [Indexed: 01/15/2023] Open
Abstract
Chloroplast RNA processing requires a large number of nuclear-encoded RNA binding proteins (RBPs) that are imported post-translationally into the organelle. Most of these RBPs are highly specific for one or few target RNAs. By contrast, members of the chloroplast ribonucleoprotein family (cpRNPs) have a wider RNA target range. We here present a quantitative analysis of RNA targets of the cpRNP CP31A using digestion-optimized RNA co-immunoprecipitation with deep sequencing (DO-RIP-seq). This identifies the mRNAs coding for subunits of the chloroplast NAD(P)H dehydrogenase (NDH) complex as main targets for CP31A. We demonstrate using whole-genome gene expression analysis and targeted RNA gel blot hybridization that the ndh mRNAs are all down-regulated in cp31a mutants. This diminishes the activity of the NDH complex. Our findings demonstrate how a chloroplast RNA binding protein can combine functionally related RNAs into one post-transcriptional operon.
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13
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Castandet B, Germain A, Hotto AM, Stern DB. Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana reveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures. Nucleic Acids Res 2020; 47:11889-11905. [PMID: 31732725 PMCID: PMC7145512 DOI: 10.1093/nar/gkz1059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 10/02/2019] [Accepted: 11/05/2019] [Indexed: 12/23/2022] Open
Abstract
Chloroplast transcription requires numerous quality control steps to generate the complex but selective mixture of accumulating RNAs. To gain insight into how this RNA diversity is achieved and regulated, we systematically mapped transcript ends by developing a protocol called Terminome-seq. Using Arabidopsis thaliana as a model, we catalogued >215 primary 5′ ends corresponding to transcription start sites (TSS), as well as 1628 processed 5′ ends and 1299 3′ ends. While most termini were found in intergenic regions, numerous abundant termini were also found within coding regions and introns, including several major TSS at unexpected locations. A consistent feature was the clustering of both 5′ and 3′ ends, contrasting with the prevailing description of discrete 5′ termini, suggesting an imprecision of the transcription and/or RNA processing machinery. Numerous termini correlated with the extremities of small RNA footprints or predicted stem-loop structures, in agreement with the model of passive RNA protection. Terminome-seq was also implemented for pnp1–1, a mutant lacking the processing enzyme polynucleotide phosphorylase. Nearly 2000 termini were altered in pnp1–1, revealing a dominant role in shaping the transcriptome. In summary, Terminome-seq permits precise delineation of the roles and regulation of the many factors involved in organellar transcriptome quality control.
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Affiliation(s)
- Benoît Castandet
- Boyce Thompson Institute, Ithaca, NY 14853, USA.,Institut des Sciences des Plantes de Paris Saclay (IPS2), UEVE, INRA, CNRS, Univ. Paris Sud, Université Paris-Saclay, F-91192 Gif sur Yvette, France.,Université de Paris, IPS2, F-91192 Gif sur Yvette, France
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14
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Chardon F, Cueff G, Delannoy E, Aubé F, Lornac A, Bedu M, Gilard F, Pateyron S, Rogniaux H, Gargaros A, Mireau H, Rajjou L, Martin-Magniette ML, Budar F. The Consequences of a Disruption in Cyto-Nuclear Coadaptation on the Molecular Response to a Nitrate Starvation in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2020; 9:E573. [PMID: 32369924 PMCID: PMC7285260 DOI: 10.3390/plants9050573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 12/04/2022]
Abstract
Mitochondria and chloroplasts are important actors in the plant nutritional efficiency. So, it could be expected that a disruption of the coadaptation between nuclear and organellar genomes impact plant response to nutrient stresses. We addressed this issue using two Arabidopsis accessions, namely Ct1 and Jea, and their reciprocal cytolines possessing the nuclear genome from one parent and the organellar genomes of the other one. We measured gene expression, and quantified proteins and metabolites under N starvation and non-limiting conditions. We observed a typical response to N starvation at the phenotype and molecular levels. The phenotypical response to N starvation was similar in the cytolines compared to the parents. However, we observed an effect of the disruption of genomic coadaptation at the molecular levels, distinct from the previously described responses to organellar stresses. Strikingly, genes differentially expressed in cytolines compared to parents were mainly repressed in the cytolines. These genes encoded more mitochondrial and nuclear proteins than randomly expected, while N starvation responsive ones were enriched in genes for chloroplast and nuclear proteins. In cytolines, the non-coadapted cytonuclear genomic combination tends to modulate the response to N starvation observed in the parental lines on various biological processes.
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Affiliation(s)
- Fabien Chardon
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
| | - Gwendal Cueff
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, 91405 Orsay, France; (E.D.); (F.G.); (S.P.); (M.-L.M.-M.)
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91405 Orsay, France
| | - Fabien Aubé
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
| | - Aurélia Lornac
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
| | - Magali Bedu
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
| | - Françoise Gilard
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, 91405 Orsay, France; (E.D.); (F.G.); (S.P.); (M.-L.M.-M.)
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91405 Orsay, France
| | - Stéphanie Pateyron
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, 91405 Orsay, France; (E.D.); (F.G.); (S.P.); (M.-L.M.-M.)
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91405 Orsay, France
| | - Hélène Rogniaux
- INRAE, UR BIA, F-44316 Nantes, France; (H.R.); (A.G.)
- INRAE, BIBS Facility, F-44316 Nantes, France
| | - Audrey Gargaros
- INRAE, UR BIA, F-44316 Nantes, France; (H.R.); (A.G.)
- INRAE, BIBS Facility, F-44316 Nantes, France
| | - Hakim Mireau
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
| | - Loïc Rajjou
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
| | - Marie-Laure Martin-Magniette
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, 91405 Orsay, France; (E.D.); (F.G.); (S.P.); (M.-L.M.-M.)
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91405 Orsay, France
- UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, 75005 Paris, France
| | - Françoise Budar
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
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15
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Ozawa SI, Cavaiuolo M, Jarrige D, Kuras R, Rutgers M, Eberhard S, Drapier D, Wollman FA, Choquet Y. The OPR Protein MTHI1 Controls the Expression of Two Different Subunits of ATP Synthase CFo in Chlamydomonas reinhardtii. THE PLANT CELL 2020; 32:1179-1203. [PMID: 31988263 PMCID: PMC7145495 DOI: 10.1105/tpc.19.00770] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/02/2020] [Accepted: 01/27/2020] [Indexed: 05/19/2023]
Abstract
In the green alga Chlamydomonas (Chlamydomonas r einhardtii), chloroplast gene expression is tightly regulated posttranscriptionally by gene-specific trans-acting protein factors. Here, we report the identification of the octotricopeptide repeat protein MTHI1, which is critical for the biogenesis of chloroplast ATP synthase oligomycin-sensitive chloroplast coupling factor. Unlike most trans-acting factors characterized so far in Chlamydomonas, which control the expression of a single gene, MTHI1 targets two distinct transcripts: it is required for the accumulation and translation of atpH mRNA, encoding a subunit of the selective proton channel, but it also enhances the translation of atpI mRNA, which encodes the other subunit of the channel. MTHI1 targets the 5' untranslated regions of both the atpH and atpI genes. Coimmunoprecipitation and small RNA sequencing revealed that MTHI1 binds specifically a sequence highly conserved among Chlorophyceae and the Ulvale clade of Ulvophyceae at the 5' end of triphosphorylated atpH mRNA. A very similar sequence, located ∼60 nucleotides upstream of the atpI initiation codon, was also found in some Chlorophyceae and Ulvale algae species and is essential for atpI mRNA translation in Chlamydomonas. Such a dual-targeted trans-acting factor provides a means to coregulate the expression of the two proton hemi-channels.
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Affiliation(s)
- Shin-Ichiro Ozawa
- Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique and Sorbonne Université, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Marina Cavaiuolo
- Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique and Sorbonne Université, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Domitille Jarrige
- Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique and Sorbonne Université, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Richard Kuras
- Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique and Sorbonne Université, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Mark Rutgers
- Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique and Sorbonne Université, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Stephan Eberhard
- Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique and Sorbonne Université, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Dominique Drapier
- Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique and Sorbonne Université, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Francis-André Wollman
- Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique and Sorbonne Université, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Yves Choquet
- Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique and Sorbonne Université, Institut de Biologie Physico-Chimique, F-75005 Paris, France
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16
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Wang X, Zhao L, Man Y, Li X, Wang L, Xiao J. PDM4, a Pentatricopeptide Repeat Protein, Affects Chloroplast Gene Expression and Chloroplast Development in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2020; 11:1198. [PMID: 32849743 PMCID: PMC7432182 DOI: 10.3389/fpls.2020.01198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 07/23/2020] [Indexed: 05/10/2023]
Abstract
Extensive studies have been carried out on chloroplast gene expression and chloroplast development; however, the regulatory mechanism is still largely unknown. Here, we characterized Pigment-Defective Mutant4 (PDM4), a P-type PPR protein localized in chloroplast. The pdm4 mutant showed seedling-lethal and albino phenotype under heterotrophic growth conditions. Transmission electron microscopic analysis revealed that thylakoid structure was totally disrupted in pdm4 mutant and eventually led to the breakdown of chloroplasts. The levels of several chloroplast- and nuclear-encoded proteins are strongly reduced in pdm4 mutant. Besides, transcript profile analysis detected that, in pdm4 mutant, the expression of plastid-encoded RNA polymerase-dependent genes was markedly affected, and deviant chloroplast rRNA processing was also observed. In addition, we found that PDM4 functions in the splicing of group II introns and may also be involved in the assembly of the 50S ribosomal particle. Our results demonstrate that PDM4 plays an important role in chloroplast gene expression and chloroplast development in Arabidopsis.
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Affiliation(s)
- Xinwei Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Lirong Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yi Man
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xiaojuan Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Li Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Jianwei Xiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- *Correspondence: Jianwei Xiao,
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17
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McDermott JJ, Watkins KP, Williams-Carrier R, Barkan A. Ribonucleoprotein Capture by in Vivo Expression of a Designer Pentatricopeptide Repeat Protein in Arabidopsis. THE PLANT CELL 2019; 31:1723-1733. [PMID: 31123048 PMCID: PMC6713294 DOI: 10.1105/tpc.19.00177] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/01/2019] [Accepted: 05/14/2019] [Indexed: 05/15/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins bind RNA via a mechanism that facilitates the customization of sequence specificity. However, natural PPR proteins have irregular features that limit the degree to which their specificity can be predicted and customized. We demonstrate here that artificial PPR proteins built from consensus PPR motifs selectively bind the intended RNA in vivo, and we use this property to develop a new tool for ribonucleoprotein characterization. We show by RNA coimmunoprecipitation sequencing (RIP-seq) that artificial PPR proteins designed to bind the Arabidopsis (Arabidopsis thaliana) chloroplast psbA mRNA bind with high specificity to psbA mRNA in vivo. Analysis of coimmunoprecipitating proteins by mass spectrometry showed the psbA translational activator HCF173 and two RNA binding proteins of unknown function (CP33C and SRRP1) to be highly enriched. RIP-seq revealed that these proteins are bound primarily to psbA RNA in vivo, and precise mapping of the HCF173 and CP33C binding sites placed them in different locations on psbA mRNA. These results demonstrate that artificial PPR proteins can be tailored to bind specific endogenous RNAs in vivo, add to the toolkit for characterizing native ribonucleoproteins, and open the door to other applications that rely on the ability to target a protein to a specified RNA sequence.
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Affiliation(s)
- James J McDermott
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Kenneth P Watkins
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | | | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
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18
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Zhang Y, Lu C. The Enigmatic Roles of PPR-SMR Proteins in Plants. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1900361. [PMID: 31380188 PMCID: PMC6662315 DOI: 10.1002/advs.201900361] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/03/2019] [Indexed: 05/21/2023]
Abstract
The pentatricopeptide repeat (PPR) protein family, with more than 400 members, is one of the largest and most diverse protein families in land plants. A small subset of PPR proteins contain a C-terminal small MutS-related (SMR) domain. Although there are relatively few PPR-SMR proteins, they play essential roles in embryo development, chloroplast biogenesis and gene expression, and plastid-to-nucleus retrograde signaling. Here, recent advances in understanding the roles of PPR-SMR proteins and the SMR domain based on a combination of genetic, biochemical, and physiological analyses are described. In addition, the potential of the PPR-SMR protein SOT1 to serve as a tool for RNA manipulation is highlighted.
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Affiliation(s)
- Yi Zhang
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTaianShandong271018P. R. China
| | - Congming Lu
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTaianShandong271018P. R. China
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19
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Jiang J, Chai X, Manavski N, Williams-Carrier R, He B, Brachmann A, Ji D, Ouyang M, Liu Y, Barkan A, Meurer J, Zhang L, Chi W. An RNA Chaperone-Like Protein Plays Critical Roles in Chloroplast mRNA Stability and Translation in Arabidopsis and Maize. THE PLANT CELL 2019; 31:1308-1327. [PMID: 30962391 PMCID: PMC6588297 DOI: 10.1105/tpc.18.00946] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/19/2019] [Accepted: 04/07/2019] [Indexed: 05/18/2023]
Abstract
A key characteristic of chloroplast gene expression is the predominance of posttranscriptional control via numerous nucleus-encoded RNA binding factors. Here, we explored the essential roles of the S1-domain-containing protein photosynthetic electron transfer B (petB)/ petD Stabilizing Factor (BSF) in the stabilization and translation of chloroplast mRNAs. BSF binds to the intergenic region of petB-petD, thereby stabilizing 3' processed petB transcripts and stimulating petD translation. BSF also binds to the 5' untranslated region of petA and activates its translation. BSF displayed nucleic-acid-melting activity in vitro, and its absence induces structural changes to target RNAs in vivo, suggesting that BSF functions as an RNA chaperone to remodel RNA structure. BSF physically interacts with the pentatricopeptide repeat protein Chloroplast RNA Processing 1 (AtCRP1) and the ribosomal release factor-like protein Peptide chain Release Factor 3 (PrfB3), whose established RNA ligands overlap with those of BSF. In addition, PrfB3 stimulated the RNA binding ability of BSF in vitro. We propose that BSF and PrfB3 cooperatively reduce the formation of secondary RNA structures within target mRNAs and facilitate AtCRP1 binding. The translation activation function of BSF for petD is conserved in Arabidopsis (Arabidopsis thaliana) and maize (Zea mays), but that for petA operates specifically in Arabidopsis. Our study sheds light on the mechanisms by which RNA binding proteins cooperatively regulate mRNA stability and translation in chloroplasts.
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Affiliation(s)
- Jingjing Jiang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Chai
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nikolay Manavski
- Biozentrum der Ludwig-Maximilians-Universität, Plant Molecular Biology, 82152 Planegg-Martinsried, Germany
| | | | - Baoye He
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Andreas Brachmann
- Genetics, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Daili Ji
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Min Ouyang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yini Liu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Jörg Meurer
- Biozentrum der Ludwig-Maximilians-Universität, Plant Molecular Biology, 82152 Planegg-Martinsried, Germany
| | - Lixin Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Qu K, Wei L, Yu J, Wang C. Identifying Plant Pentatricopeptide Repeat Coding Gene/Protein Using Mixed Feature Extraction Methods. FRONTIERS IN PLANT SCIENCE 2019; 9:1961. [PMID: 30687359 PMCID: PMC6335366 DOI: 10.3389/fpls.2018.01961] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 12/17/2018] [Indexed: 05/04/2023]
Abstract
Motivation: Pentatricopeptide repeat (PPR) is a triangular pentapeptide repeat domain that plays a vital role in plant growth. In this study, we seek to identify PPR coding genes and proteins using a mixture of feature extraction methods. We use four single feature extraction methods focusing on the sequence, physical, and chemical properties as well as the amino acid composition, and mix the features. The Max-Relevant-Max-Distance (MRMD) technique is applied to reduce the feature dimension. Classification uses the random forest, J48, and naïve Bayes with 10-fold cross-validation. Results: Combining two of the feature extraction methods with the random forest classifier produces the highest area under the curve of 0.9848. Using MRMD to reduce the dimension improves this metric for J48 and naïve Bayes, but has little effect on the random forest results. Availability and Implementation: The webserver is available at: http://server.malab.cn/MixedPPR/index.jsp.
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Affiliation(s)
- Kaiyang Qu
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Leyi Wei
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Jiantao Yu
- College of Information Engineering, North-West A&F University, Yangling, China
| | - Chunyu Wang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, United States
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McDermott JJ, Civic B, Barkan A. Effects of RNA structure and salt concentration on the affinity and kinetics of interactions between pentatricopeptide repeat proteins and their RNA ligands. PLoS One 2018; 13:e0209713. [PMID: 30576379 PMCID: PMC6303017 DOI: 10.1371/journal.pone.0209713] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 12/10/2018] [Indexed: 11/19/2022] Open
Abstract
Pentatricopeptide repeat (PPR) proteins are helical repeat proteins that bind specific RNA sequences via modular 1-repeat:1-nucleotide interactions. Binding specificity is dictated, in part, by hydrogen bonds between the amino acids at two positions in each PPR motif and the Watson-Crick face of the aligned nucleobase. There is evidence that PPR-RNA interactions can compete with RNA-RNA interactions in vivo, and that this competition underlies some effects of PPR proteins on gene expression. Conversely, RNA secondary structure can inhibit the binding of a PPR protein to its specific binding site. The parameters that influence whether PPR-RNA or RNA-RNA interactions prevail are unknown. Understanding these parameters will be important for understanding the functions of natural PPR proteins and for the design of engineered PPR proteins for synthetic biology purposes. We addressed this question by analyzing the effects of RNA structures of varying stability and position on the binding of the model protein PPR10 to its atpH RNA ligand. Our results show that even very weak RNA structures (ΔG° ~ 0 kcal/mol) involving only one nucleotide at either end of the minimal binding site impede PPR10 binding. Analysis of binding kinetics using Surface Plasmon Resonance showed that RNA structures reduce PPR10’s on-rate and increase its off-rate. Complexes between the PPR proteins PPR10 and HCF152 and their respective RNA ligands have long half-lives (one hour or more), correlating with their functions as barriers to exonucleolytic RNA decay in vivo. The effects of salt concentration on PPR10-RNA binding kinetics showed that electrostatic interactions play an important role in establishing PPR10-RNA interactions but play a relatively small role in maintaining specific interactions once established.
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Affiliation(s)
- James J. McDermott
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Bryce Civic
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
- * E-mail:
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