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Wang X, Ji D, Ma J, Chi W. Function of plastid translation in plant temperature acclimation: Retrograde signalling or extraribosomal 'moonlighting' functions? PLANT, CELL & ENVIRONMENT 2024. [PMID: 39101459 DOI: 10.1111/pce.15074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/06/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024]
Abstract
Summary StatementSpecific components of the plastid ribosome could act as pivotal limiting factors in plant temperature acclimation. We endeavour to elucidate the molecular nexus between plastid translation and temperature acclimation by incorporating the concept of extraribosomal ‘moonlighting’ functions of plastid ribosome proteins.
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Affiliation(s)
- Xiushun Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Daili Ji
- Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jinfang Ma
- Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Wei Chi
- College of Life Sciences, Nanjing Normal University, Nanjing, China
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2
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Bhattacharya O, Ortiz I, Hendricks N, Walling LL. The tomato chloroplast stromal proteome compendium elucidated by leveraging a plastid protein-localization prediction Atlas. FRONTIERS IN PLANT SCIENCE 2023; 14:1020275. [PMID: 37701797 PMCID: PMC10493611 DOI: 10.3389/fpls.2023.1020275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 06/22/2023] [Indexed: 09/14/2023]
Abstract
Tomato (Solanum lycopersicum) is a model species for studying fruit development, wounding, herbivory, and pathogen attack. Despite tomato's world-wide economic importance and the role of chloroplasts as metabolic hubs and integrators of environmental cues, little is known about the stromal proteome of tomato. Using a high-yielding protocol for chloroplast and stromal protein isolation, MudPIT nano-LC-MS/MS analyses, a robust in-house protein database (the Atlas) for predicting the plastid localization of tomato proteins, and rigorous selection criteria for inclusion/exclusion in the stromal proteome, we identified 1,278 proteins of the tomato stromal proteome. We provide one of the most robust stromal proteomes available to date with empirical evidence for 545 and 92 proteins not previously described for tomato plastids and the Arabidopsis stroma, respectively. The relative abundance of tomato stromal proteins was determined using the exponentially modified protein abundance index (emPAI). Comparison of the abundance of tomato and Arabidopsis stromal proteomes provided evidence for the species-specific nature of stromal protein homeostasis. The manual curation of the tomato stromal proteome classified proteins into ten functional categories resulting in an accessible compendium of tomato chloroplast proteins. After curation, only 91 proteins remained as unknown, uncharacterized or as enzymes with unknown functions. The curation of the tomato stromal proteins also indicated that tomato has a number of paralogous proteins, not present in Arabidopsis, which accumulated to different levels in chloroplasts. As some of these proteins function in key metabolic pathways or in perceiving or transmitting signals critical for plant adaptation to biotic and abiotic stress, these data suggest that tomato may modulate the bidirectional communication between chloroplasts and nuclei in a novel manner. The stromal proteome provides a fertile ground for future mechanistic studies in the field of tomato chloroplast-nuclear signaling and are foundational for our goal of elucidating the dynamics of the stromal proteome controlled by the solanaceous-specific, stromal, and wound-inducible leucine aminopeptidase A of tomato.
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Affiliation(s)
- Oindrila Bhattacharya
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Irma Ortiz
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Nathan Hendricks
- Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | - Linda L. Walling
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
- Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
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3
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Jin HL, Duan S, Zhang P, Yang Z, Zeng Y, Chen Z, Hong L, Li M, Luo L, Chang Z, Hu J, Wang HB. Dual roles for CND1 in maintenance of nuclear and chloroplast genome stability in plants. Cell Rep 2023; 42:112268. [PMID: 36933214 DOI: 10.1016/j.celrep.2023.112268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 12/19/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023] Open
Abstract
The coordination of chloroplast and nuclear genome status is critical for plant cell function. Here, we report that Arabidopsis CHLOROPLAST AND NUCLEUS DUAL-LOCALIZED PROTEIN 1 (CND1) maintains genome stability in the chloroplast and the nucleus. CND1 localizes to both compartments, and complete loss of CND1 results in embryo lethality. Partial loss of CND1 disturbs nuclear cell-cycle progression and photosynthetic activity. CND1 binds to nuclear pre-replication complexes and DNA replication origins and regulates nuclear genome stability. In chloroplasts, CND1 interacts with and facilitates binding of the regulator of chloroplast genome stability WHY1 to chloroplast DNA. The defects in nuclear cell-cycle progression and photosynthesis of cnd1 mutants are respectively rescued by compartment-restricted CND1 localization. Light promotes the association of CND1 with HSP90 and its import into chloroplasts. This study provides a paradigm of the convergence of genome status across organelles to coordinately regulate cell cycle to control plant growth and development.
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Affiliation(s)
- Hong-Lei Jin
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China; Guangzhou Key Laboratory of Chinese Medicine Research on Prevention and Treatment of Osteoporosis, The Third Affiliated Hospital of Guangzhou University of Chinese Medicine, No. 263, Longxi Avenue, Guangzhou, China.
| | - Sujuan Duan
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Pengxiang Zhang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Ziyue Yang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Yunping Zeng
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Ziqi Chen
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Liu Hong
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Mengshu Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Lujun Luo
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Zhenyi Chang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Jiliang Hu
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Hong-Bin Wang
- Institute of Medical Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China; Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, China; State Key Laboratory of Dampness Syndrome of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China.
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4
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He C, Berkowitz O, Hu S, Zhao Y, Qian K, Shou H, Whelan J, Wang Y. Co-regulation of mitochondrial and chloroplast function: Molecular components and mechanisms. PLANT COMMUNICATIONS 2023; 4:100496. [PMID: 36435968 PMCID: PMC9860188 DOI: 10.1016/j.xplc.2022.100496] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/20/2022] [Accepted: 11/23/2022] [Indexed: 06/16/2023]
Abstract
The metabolic interdependence, interactions, and coordination of functions between chloroplasts and mitochondria are established and intensively studied. However, less is known about the regulatory components that control these interactions and their responses to external stimuli. Here, we outline how chloroplastic and mitochondrial activities are coordinated via common components involved in signal transduction pathways, gene regulatory events, and post-transcriptional processes. The endoplasmic reticulum emerges as a point of convergence for both transcriptional and post-transcriptional pathways that coordinate chloroplast and mitochondrial functions. Although the identification of molecular components and mechanisms of chloroplast and mitochondrial signaling increasingly suggests common players, this raises the question of how these allow for distinct organelle-specific downstream pathways. Outstanding questions with respect to the regulation of post-transcriptional pathways and the cell and/or tissue specificity of organelle signaling are crucial for understanding how these pathways are integrated at a whole-plant level to optimize plant growth and its response to changing environmental conditions.
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Affiliation(s)
- Cunman He
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China; Department of Animal, Plant and Soil Science, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Science, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Shanshan Hu
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China; International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang 314400, P.R. China
| | - Yang Zhao
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China; Department of Animal, Plant and Soil Science, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Kun Qian
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China; Department of Animal, Plant and Soil Science, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Huixia Shou
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China; International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang 314400, P.R. China
| | - James Whelan
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China; Department of Animal, Plant and Soil Science, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, VIC 3086, Australia; International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang 314400, P.R. China
| | - Yan Wang
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China; Department of Animal, Plant and Soil Science, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, VIC 3086, Australia.
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5
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Liebers M, Cozzi C, Uecker F, Chambon L, Blanvillain R, Pfannschmidt T. Biogenic signals from plastids and their role in chloroplast development. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7105-7125. [PMID: 36002302 DOI: 10.1093/jxb/erac344] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Plant seeds do not contain differentiated chloroplasts. Upon germination, the seedlings thus need to gain photoautotrophy before storage energies are depleted. This requires the coordinated expression of photosynthesis genes encoded in nuclear and plastid genomes. Chloroplast biogenesis needs to be additionally coordinated with the light regulation network that controls seedling development. This coordination is achieved by nucleus to plastid signals called anterograde and plastid to nucleus signals termed retrograde. Retrograde signals sent from plastids during initial chloroplast biogenesis are also called biogenic signals. They have been recognized as highly important for proper chloroplast biogenesis and for seedling development. The molecular nature, transport, targets, and signalling function of biogenic signals are, however, under debate. Several studies disproved the involvement of a number of key components that were at the base of initial models of retrograde signalling. New models now propose major roles for a functional feedback between plastid and cytosolic protein homeostasis in signalling plastid dysfunction as well as the action of dually localized nucleo-plastidic proteins that coordinate chloroplast biogenesis with light-dependent control of seedling development. This review provides a survey of the developments in this research field, summarizes the unsolved questions, highlights several recent advances, and discusses potential new working modes.
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Affiliation(s)
- Monique Liebers
- Gottfried-Wilhelm-Leibniz-Universität Hannover, Naturwissenschaftliche Fakultät, Institut für Botanik, Pflanzenphysiologie, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Carolina Cozzi
- Gottfried-Wilhelm-Leibniz-Universität Hannover, Naturwissenschaftliche Fakultät, Institut für Botanik, Pflanzenphysiologie, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Finia Uecker
- Gottfried-Wilhelm-Leibniz-Universität Hannover, Naturwissenschaftliche Fakultät, Institut für Botanik, Pflanzenphysiologie, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Louise Chambon
- Université Grenoble-Alpes, CNRS, CEA, INRA, IRIG-LPCV, F-38000 Grenoble, France
| | - Robert Blanvillain
- Université Grenoble-Alpes, CNRS, CEA, INRA, IRIG-LPCV, F-38000 Grenoble, France
| | - Thomas Pfannschmidt
- Gottfried-Wilhelm-Leibniz-Universität Hannover, Naturwissenschaftliche Fakultät, Institut für Botanik, Pflanzenphysiologie, Herrenhäuser Str. 2, D-30419 Hannover, Germany
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6
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PAP8/pTAC6 Is Part of a Nuclear Protein Complex and Displays RNA Recognition Motifs of Viral Origin. Int J Mol Sci 2022; 23:ijms23063059. [PMID: 35328480 PMCID: PMC8954402 DOI: 10.3390/ijms23063059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/09/2022] [Accepted: 03/09/2022] [Indexed: 12/13/2022] Open
Abstract
Chloroplast biogenesis depends on a complex transcriptional program involving coordinated expression of plastid and nuclear genes. In particular, photosynthesis-associated plastid genes are expressed by the plastid-encoded polymerase (PEP) that undergoes a structural rearrangement during chloroplast formation. The prokaryotic-type core enzyme is rebuilt into a larger complex by the addition of nuclear-encoded PEP-associated proteins (PAP1 to PAP12). Among the PAPs, some have been detected in the nucleus (PAP5 and PAP8), where they could serve a nuclear function required for efficient chloroplast biogenesis. Here, we detected PAP8 in a large nuclear subcomplex that may include other subunits of the plastid-encoded RNA polymerase. We have made use of PAP8 recombinant proteins in Arabidopsis thaliana to decouple its nucleus- and chloroplast-associated functions and found hypomorphic mutants pointing at essential amino acids. While the origin of the PAP8 gene remained elusive, we have found in its sequence a micro-homologous domain located within a large structural homology with a rhinoviral RNA-dependent RNA polymerase, highlighting potential RNA recognition motifs in PAP8. PAP8 in vitro RNA binding activity suggests that this domain is functional. Hence, we propose that the acquisition of PAPs may have occurred during evolution by different routes, including lateral gene transfer.
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7
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Lamelas L, Valledor L, López-Hidalgo C, Cañal MJ, Meijón M. Nucleus and chloroplast: A necessary understanding to overcome heat stress in Pinus radiata. PLANT, CELL & ENVIRONMENT 2022; 45:446-458. [PMID: 34855991 DOI: 10.1111/pce.14238] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
The recovery and maintenance of plant homeostasis under stressful environments are complex processes involving organelle crosstalk for a coordinated cellular response. Here, we revealed through nuclear and chloroplast subcellular proteomics, biochemical cell profiles and targeted transcriptomics how chloroplasts and nuclei developed their responses under increased temperatures in a long-lived species (Pinus radiata). Parallel to photosynthetic impairment and reactive oxygen species production in the chloroplast, a DNA damage response was triggered in the nucleus followed by an altered chromatin conformation. In addition, in the nuclei, we found several proteins, such as HEMERA or WHIRLY, which change their locations from the chloroplasts to the nuclei carrying the stress message. Additionally, our data showed a deep rearrangement of RNA metabolism in both organelles, revealing microRNAs and AGO1 as potential regulators of the acclimation mechanisms. Altogether, our study highlights the synchronisation among the different stages required for thermotolerance acquisition in P. radiata, pointing out the role of chromatin conformation and posttranscriptional gene regulation in overcoming heat stress and assuring plant survival for the following years.
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Affiliation(s)
- Laura Lamelas
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, Biotechnology Institute of Asturias, Oviedo, Asturias, Spain
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, Biotechnology Institute of Asturias, Oviedo, Asturias, Spain
| | - Cristina López-Hidalgo
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, Biotechnology Institute of Asturias, Oviedo, Asturias, Spain
| | - María Jesús Cañal
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, Biotechnology Institute of Asturias, Oviedo, Asturias, Spain
| | - Mónica Meijón
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, Biotechnology Institute of Asturias, Oviedo, Asturias, Spain
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8
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Gawroński P, Burdiak P, Scharff LB, Mielecki J, Górecka M, Zaborowska M, Leister D, Waszczak C, Karpiński S. CIA2 and CIA2-LIKE are required for optimal photosynthesis and stress responses in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:619-638. [PMID: 33119927 DOI: 10.1111/tpj.15058] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 10/05/2020] [Accepted: 10/12/2020] [Indexed: 05/22/2023]
Abstract
Chloroplast-to-nucleus retrograde signaling is essential for cell function, acclimation to fluctuating environmental conditions, plant growth and development. The vast majority of chloroplast proteins are nuclear-encoded, and must be imported into the organelle after synthesis in the cytoplasm. This import is essential for the development of fully functional chloroplasts. On the other hand, functional chloroplasts act as sensors of environmental changes and can trigger acclimatory responses that influence nuclear gene expression. Signaling via mobile transcription factors (TFs) has been recently recognized as a way of communication between organelles and the nucleus. In this study, we performed a targeted reverse genetic screen to identify dual-localized TFs involved in chloroplast retrograde signaling during stress responses. We found that CHLOROPLAST IMPORT APPARATUS 2 (CIA2) has a functional plastid transit peptide, and can be located both in chloroplasts and the nucleus. Further, we found that CIA2, along with its homolog CIA2-like (CIL) are involved in the regulation of Arabidopsis responses to UV-AB, high light and heat shock. Finally, our results suggest that both CIA2 and CIL are crucial for chloroplast translation. Our results contribute to a deeper understanding of signaling events in the chloroplast-nucleus cross-talk.
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Affiliation(s)
- Piotr Gawroński
- Department of Plant Genetics, Breeding, and Biotechnology, Warsaw University of Life Sciences, Warsaw, 02-776, Poland
| | - Paweł Burdiak
- Department of Plant Genetics, Breeding, and Biotechnology, Warsaw University of Life Sciences, Warsaw, 02-776, Poland
| | - Lars B Scharff
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, 1871, Denmark
| | - Jakub Mielecki
- Department of Plant Genetics, Breeding, and Biotechnology, Warsaw University of Life Sciences, Warsaw, 02-776, Poland
| | - Magdalena Górecka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
| | - Magdalena Zaborowska
- Department of Plant Genetics, Breeding, and Biotechnology, Warsaw University of Life Sciences, Warsaw, 02-776, Poland
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhadernerstraße 2-4, Planegg-Martinsried, 82152, Germany
| | - Cezary Waszczak
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
| | - Stanisław Karpiński
- Department of Plant Genetics, Breeding, and Biotechnology, Warsaw University of Life Sciences, Warsaw, 02-776, Poland
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9
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Liebers M, Gillet FX, Israel A, Pounot K, Chambon L, Chieb M, Chevalier F, Ruedas R, Favier A, Gans P, Boeri Erba E, Cobessi D, Pfannschmidt T, Blanvillain R. Nucleo-plastidic PAP8/pTAC6 couples chloroplast formation with photomorphogenesis. EMBO J 2020; 39:e104941. [PMID: 33001465 DOI: 10.15252/embj.2020104941] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 09/02/2020] [Accepted: 09/09/2020] [Indexed: 12/29/2022] Open
Abstract
The initial greening of angiosperms involves light activation of photoreceptors that trigger photomorphogenesis, followed by the development of chloroplasts. In these semi-autonomous organelles, construction of the photosynthetic apparatus depends on the coordination of nuclear and plastid gene expression. Here, we show that the expression of PAP8, an essential subunit of the plastid-encoded RNA polymerase (PEP) in Arabidopsis thaliana, is under the control of a regulatory element recognized by the photomorphogenic factor HY5. PAP8 protein is localized and active in both plastids and the nucleus, and particularly required for the formation of late photobodies. In the pap8 albino mutant, phytochrome-mediated signalling is altered, degradation of the chloroplast development repressors PIF1/PIF3 is disrupted, HY5 is not stabilized, and the expression of the photomorphogenesis regulator GLK1 is impaired. PAP8 translocates into plastids via its targeting pre-sequence, interacts with the PEP and eventually reaches the nucleus, where it can interact with another PEP subunit pTAC12/HMR/PAP5. Since PAP8 is required for the phytochrome B-mediated signalling cascade and the reshaping of the PEP activity, it may coordinate nuclear gene expression with PEP-driven chloroplastic gene expression during chloroplast biogenesis.
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Affiliation(s)
- Monique Liebers
- CNRS, CEA, INRA, IRIG-LPCV, Univ. Grenoble-Alpes, Grenoble, France
| | | | - Abir Israel
- CNRS, CEA, INRA, IRIG-LPCV, Univ. Grenoble-Alpes, Grenoble, France
| | - Kevin Pounot
- CNRS, CEA, INRA, IRIG-LPCV, Univ. Grenoble-Alpes, Grenoble, France
| | - Louise Chambon
- CNRS, CEA, INRA, IRIG-LPCV, Univ. Grenoble-Alpes, Grenoble, France
| | - Maha Chieb
- CNRS, CEA, INRA, IRIG-LPCV, Univ. Grenoble-Alpes, Grenoble, France
| | - Fabien Chevalier
- CNRS, CEA, INRA, IRIG-LPCV, Univ. Grenoble-Alpes, Grenoble, France
| | - Rémi Ruedas
- CEA, CNRS, IBS, Univ. Grenoble Alpes, Grenoble, France
| | - Adrien Favier
- CEA, CNRS, IBS, Univ. Grenoble Alpes, Grenoble, France
| | - Pierre Gans
- CEA, CNRS, IBS, Univ. Grenoble Alpes, Grenoble, France
| | | | - David Cobessi
- CEA, CNRS, IBS, Univ. Grenoble Alpes, Grenoble, France
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10
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Pfannschmidt T, Terry MJ, Van Aken O, Quiros PM. Retrograde signals from endosymbiotic organelles: a common control principle in eukaryotic cells. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190396. [PMID: 32362267 DOI: 10.1098/rstb.2019.0396] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Endosymbiotic organelles of eukaryotic cells, the plastids, including chloroplasts and mitochondria, are highly integrated into cellular signalling networks. In both heterotrophic and autotrophic organisms, plastids and/or mitochondria require extensive organelle-to-nucleus communication in order to establish a coordinated expression of their own genomes with the nuclear genome, which encodes the majority of the components of these organelles. This goal is achieved by the use of a variety of signals that inform the cell nucleus about the number and developmental status of the organelles and their reaction to changing external environments. Such signals have been identified in both photosynthetic and non-photosynthetic eukaryotes (known as retrograde signalling and retrograde response, respectively) and, therefore, appear to be universal mechanisms acting in eukaryotes of all kingdoms. In particular, chloroplasts and mitochondria both harbour crucial redox reactions that are the basis of eukaryotic life and are, therefore, especially susceptible to stress from the environment, which they signal to the rest of the cell. These signals are crucial for cell survival, lifespan and environmental adjustment, and regulate quality control and targeted degradation of dysfunctional organelles, metabolic adjustments, and developmental signalling, as well as induction of apoptosis. The functional similarities between retrograde signalling pathways in autotrophic and non-autotrophic organisms are striking, suggesting the existence of common principles in signalling mechanisms or similarities in their evolution. Here, we provide a survey for the newcomers to this field of research and discuss the importance of retrograde signalling in the context of eukaryotic evolution. Furthermore, we discuss commonalities and differences in retrograde signalling mechanisms and propose retrograde signalling as a general signalling mechanism in eukaryotic cells that will be also of interest for the specialist. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.
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Affiliation(s)
- Thomas Pfannschmidt
- Institute of Botany, Plant Physiology, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
| | - Matthew J Terry
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Olivier Van Aken
- Department of Biology, Lund University, Sölvegatan 35, 223 62 Lund, Sweden
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11
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Krupinska K, Blanco NE, Oetke S, Zottini M. Genome communication in plants mediated by organelle-n-ucleus-located proteins. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190397. [PMID: 32362260 PMCID: PMC7209962 DOI: 10.1098/rstb.2019.0397] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
An increasing number of eukaryotic proteins have been shown to have a dual localization in the DNA-containing organelles, mitochondria and plastids, and/or the nucleus. Regulation of dual targeting and relocation of proteins from organelles to the nucleus offer the most direct means for communication between organelles as well as organelles and nucleus. Most of the mitochondrial proteins of animals have functions in DNA repair and gene expression by modelling of nucleoid architecture and/or chromatin. In plants, such proteins can affect replication and early development. Most plastid proteins with a confirmed or predicted second location in the nucleus are associated with the prokaryotic core RNA polymerase and are required for chloroplast development and light responses. Few plastid–nucleus-located proteins are involved in pathogen defence and cell cycle control. For three proteins, it has been clearly shown that they are first targeted to the organelle and then relocated to the nucleus, i.e. the nucleoid-associated proteins HEMERA and Whirly1 and the stroma-located defence protein NRIP1. Relocation to the nucleus can be experimentally demonstrated by plastid transformation leading to the synthesis of proteins with a tag that enables their detection in the nucleus or by fusions with fluoroproteins in different experimental set-ups. This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.
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Affiliation(s)
- Karin Krupinska
- Institute of Botany, Christian-Albrechts-University of Kiel, Olshausenstraße 40, 24098 Kiel, Germany
| | - Nicolás E Blanco
- Centre of Photosynthetic and Biochemical Studies, Faculty of Biochemical Science and Pharmacy, National University of Rosario (CEFOBI/UNR-CONICET), Rosario, Argentina
| | - Svenja Oetke
- Institute of Botany, Christian-Albrechts-University of Kiel, Olshausenstraße 40, 24098 Kiel, Germany
| | - Michela Zottini
- Department of Biology, University of Padova, Via U. Bassi 58B, 35131 Padova, Italy
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12
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Seo SY, Wi SJ, Park KY. Functional switching of NPR1 between chloroplast and nucleus for adaptive response to salt stress. Sci Rep 2020; 10:4339. [PMID: 32152424 PMCID: PMC7062895 DOI: 10.1038/s41598-020-61379-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 02/13/2020] [Indexed: 02/02/2023] Open
Abstract
Salt stress causes rapid accumulation of nonexpressor of pathogenesis-related genes 1 (NPR1) protein, known as the redox-sensitive transcription coactivator, which in turn elicits many adaptive responses. The NPR1 protein transiently accumulates in chloroplast stroma under salt stress, which attenuates stress-triggered down-regulation of photosynthetic capability. We observed that oligomeric NPR1 in chloroplasts and cytoplasm had chaperone activity, whereas monomeric NPR1 in the nucleus did not. Additionally, NPR1 overexpression resulted in reinforcement of morning-phased and evening-phased circadian clock. NPR1 overexpression also enhanced antioxidant activity and reduced stress-induced reactive oxygen species (ROS) generation at early stage, followed with transcription levels for ROS detoxification. These results suggest a functional switch from a molecular chaperone to a transcriptional coactivator, which is dependent on subcellular localization. Our findings imply that dual localization of NPR1 is related to proteostasis and redox homeostasis in chloroplasts for emergency restoration as well as transcriptional coactivator in the nucleus for adaptation to stress.
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Affiliation(s)
- So Yeon Seo
- Department of Biology, Sunchon National University, Sunchon, Chonnam, Republic of Korea
| | - Soo Jin Wi
- Department of Biology, Sunchon National University, Sunchon, Chonnam, Republic of Korea
| | - Ky Young Park
- Department of Biology, Sunchon National University, Sunchon, Chonnam, Republic of Korea.
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13
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Ge Q, Zhang Y, Xu Y, Bai M, Luo W, Wang B, Niu Y, Zhao Y, Li S, Weng Y, Wang Z, Qian Q, Chong K. Cyclophilin OsCYP20-2 with a novel variant integrates defense and cell elongation for chilling response in rice. THE NEW PHYTOLOGIST 2020; 225:2453-2467. [PMID: 31736073 PMCID: PMC7064896 DOI: 10.1111/nph.16324] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/31/2019] [Indexed: 05/20/2023]
Abstract
Coordinating stress defense and plant growth is a survival strategy for adaptation to different environments that contains a series of processes, such as, cell growth, division and differentiation. However, little is known about the coordination mechanism for protein conformation change. A cyclophilin OsCYP20-2 with a variant interacts with SLENDER RICE1 (SLR1) and OsFSD2 in the nucleus and chloroplasts, respectively, to integrate chilling tolerance and cell elongation in rice (Oryza sativa) (FSD2, Fe-superoxide dismutase 2). Mass spectrum assay showed that OsNuCYP20-2 localized at the nucleus (nuclear located OsCYP20-2) was a new variant of OsCYP20-2 that truncated 71 amino-acid residues in N-terminal. The loss-of function OsCYP20-2 mutant showed sensitivity to chilling stress with accumulation of extra reactive oxygen species (ROS). In chloroplasts, the full-length OsCYP20-2 promotes OsFSD2 forming homodimers which enhance its activity, eliminating the accumulation of ROS under chilling stress. However, the mutant had shorter epidermal cells in comparison with wild-type Hwayoung (HY). In the nucleus, OsCYP20-2 caused conformation change of SLR1 to promote its degradation for cell elongation. Our data reveal a cyclophilin with a variant with dual-localization in chloroplasts and the nucleus, which mediate chilling tolerance and cell elongation.
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Affiliation(s)
- Qiang Ge
- Key Laboratory of Plant Molecular PhysiologyInstitute of BotanyChinese Academy of SciencesBeijing100093China
- University of Chinese Academy of SciencesBeijing100049China
| | - Yuanyuan Zhang
- Key Laboratory of Plant Molecular PhysiologyInstitute of BotanyChinese Academy of SciencesBeijing100093China
| | - Yunyuan Xu
- Key Laboratory of Plant Molecular PhysiologyInstitute of BotanyChinese Academy of SciencesBeijing100093China
- Innovation Academy for Seed DesignChinese Academy of SciencesBeijing100101China
| | - Mingyi Bai
- The Key Laboratory of Plant Cell Engineering and Germplasm InnovationMinistry of EducationSchool of Life SciencesShandong UniversityJinan250100China
| | - Wei Luo
- Key Laboratory of Plant Molecular PhysiologyInstitute of BotanyChinese Academy of SciencesBeijing100093China
| | - Bo Wang
- Key Laboratory of Plant Molecular PhysiologyInstitute of BotanyChinese Academy of SciencesBeijing100093China
- University of Chinese Academy of SciencesBeijing100049China
| | - Yuda Niu
- Key Laboratory of Plant Molecular PhysiologyInstitute of BotanyChinese Academy of SciencesBeijing100093China
| | - Yuan Zhao
- Key Laboratory of Plant Molecular PhysiologyInstitute of BotanyChinese Academy of SciencesBeijing100093China
- University of Chinese Academy of SciencesBeijing100049China
| | - Shanshan Li
- Laboratory of Soft Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
| | - Yuxiang Weng
- Laboratory of Soft Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijing100190China
| | - Zhiyong Wang
- Department of Plant BiologyCarnegie Institution for ScienceStanfordCA94305USA
| | - Qian Qian
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhou310006China
| | - Kang Chong
- Key Laboratory of Plant Molecular PhysiologyInstitute of BotanyChinese Academy of SciencesBeijing100093China
- University of Chinese Academy of SciencesBeijing100049China
- Innovation Academy for Seed DesignChinese Academy of SciencesBeijing100101China
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Abolhassani Rad S, Clayton EJ, Cornelius EJ, Howes TR, Kohalmi SE. Moonlighting proteins: putting the spotlight on enzymes. PLANT SIGNALING & BEHAVIOR 2018; 13:e1517075. [PMID: 30252596 PMCID: PMC6204816 DOI: 10.1080/15592324.2018.1517075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 06/11/2018] [Accepted: 07/13/2018] [Indexed: 06/08/2023]
Abstract
AROGENATE DEHAYDRATASE2 (ADT2) is a member of the Arabidopsis thaliana ADT family. All members of this family act as arogenate dehydratases in phenylalanine biosynthesis, decarboxylating/dehydrating arogenate to phenylalanine. ADT2 is detected in stromules, and as a ring around the equatorial plane of dividing chloroplasts, indicating it has a second, non-enzymatic function in chloroplast division. Here, we provide further evidence for this alternative role of ADT2. First, we demonstrate that ADT2 and FtsZ co-localize around the equatorial plane at the same time. Second, FtsZ expression in an adt2 mutant was analyzed, as well as ADT2 expression in three Arabidopsis chloroplast division mutants, ACCUMULATION AND REPLICATION OF CHLOROPLASTS3 (ARC3), ARC5 and ARC6. In arc3 and arc6 mutants, ADT2 is misexpressed and resembles the expression of FtsZ in the same mutants. However, in the arc5 mutant, ADT2 ring positioning is observed at constriction points indicating proper relative timing. ADT2 expression in the arc mutants shows that the role of ADT2 in chloroplast division occurs prior to ARC5, but is dependent on ARC3 and ARC6. Abbreviations used: ADT: arogenate dehydratase, ARC: accumulation and replication of chloroplasts, CFP: cyan fluorescent protein, dpi: days post infiltration, FtsZ: filamentous temperature sensitive Z, PD: plastid division, Phe: phenylalanine, YFP: yellow fluorescent protein.
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15
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Lichocka M, Rymaszewski W, Morgiewicz K, Barymow-Filoniuk I, Chlebowski A, Sobczak M, Samuel MA, Schmelzer E, Krzymowska M, Hennig J. Nucleus- and plastid-targeted annexin 5 promotes reproductive development in Arabidopsis and is essential for pollen and embryo formation. BMC PLANT BIOLOGY 2018; 18:183. [PMID: 30189843 PMCID: PMC6127919 DOI: 10.1186/s12870-018-1405-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 08/30/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Pollen development is a strictly controlled post-meiotic process during which microspores differentiate into microgametophytes and profound structural and functional changes occur in organelles. Annexin 5 is a calcium- and lipid-binding protein that is highly expressed in pollen grains and regulates pollen development and physiology. To gain further insights into the role of ANN5 in Arabidopsis development, we performed detailed phenotypic characterization of Arabidopsis plants with modified ANN5 levels. In addition, interaction partners and subcellular localization of ANN5 were analyzed to investigate potential functions of ANN5 at cellular level. RESULTS Here, we report that RNAi-mediated suppression of ANN5 results in formation of smaller pollen grains, enhanced pollen lethality, and delayed pollen tube growth. ANN5 RNAi knockdown plants also displayed aberrant development during the transition from the vegetative to generative phase and during embryogenesis, reflected by delayed bolting time and reduced embryo size, respectively. At the subcellular level, ANN5 was delivered to the nucleus, nucleolus, and cytoplasm, and was frequently localized in plastid nucleoids, suggesting a likely role in interorganellar communication. Furthermore, ANN5-YFP co-immunoprecipitated with RABE1b, a putative GTPase, and interaction in planta was confirmed in plastidial nucleoids using FLIM-FRET analysis. CONCLUSIONS Our findings let us to propose that ANN5 influences basal cell homeostasis via modulation of plastid activity during pollen maturation. We hypothesize that the role of ANN5 is to orchestrate the plastidial and nuclear genome activities via protein-protein interactions however not only in maturing pollen but also during the transition from the vegetative to the generative growth and seed development.
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Affiliation(s)
- Malgorzata Lichocka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Wojciech Rymaszewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Karolina Morgiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Izabela Barymow-Filoniuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Aleksander Chlebowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Miroslaw Sobczak
- Department of Botany, Warsaw University of Life Sciences (SGGW), Warsaw, Poland
| | - Marcus A. Samuel
- Department of Biological Sciences, University of Calgary, Calgary, AB Canada
| | - Elmon Schmelzer
- Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Magdalena Krzymowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Jacek Hennig
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
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16
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Sun Q, Li YY, Wang Y, Zhao HH, Zhao TY, Zhang ZY, Li DW, Yu JL, Wang XB, Zhang YL, Han CG. Brassica yellows virus P0 protein impairs the antiviral activity of NbRAF2 in Nicotiana benthamiana. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3127-3139. [PMID: 29659986 PMCID: PMC5972614 DOI: 10.1093/jxb/ery131] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/24/2018] [Indexed: 05/29/2023]
Abstract
In interactions between poleroviruses and their hosts, few cellular proteins have been identified that directly interact with the multifunctional virus P0 protein. To help explore the functions of P0, we identified a Brassica yellows virus genotype A (BrYV-A) P0BrA-interacting protein from Nicotiana benthamiana, Rubisco assembly factor 2 (NbRAF2), which localizes in the nucleus, cell periphery, chloroplasts, and stromules. We found that its C-terminal domain (amino acids 183-211) is required for self-interaction. A split ubiquitin membrane-bound yeast two-hybrid system and co-immunoprecipitation assays showed that NbRAF2 interacted with P0BrA, and co-localized in the nucleus and at the cell periphery. Interestingly, the nuclear pool of NbRAF2 decreased in the presence of P0BrA and during BrYV-A infection, and the P0BrA-mediated reduction of nuclear NbRAF2 required dual localization of NbRAF2 in the chloroplasts and nucleus. Tobacco rattle virus-based virus-induced gene silencing of NbRAF2 promoted BrYV-A infection in N. benthamiana, and the overexpression of nuclear NbRAF2 inhibited BrYV-A accumulation. Potato leafroll virus P0PL also interacted with NbRAF2 and decreased its nuclear accumulation, indicating that NbRAF2 may be a common target of poleroviruses. These results suggest that nuclear NbRAF2 possesses antiviral activity against BrYV-A infection, and that BrYV-A P0BrA interacts with NbRAF2 and alters its localization pattern to facilitate virus infection.
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Affiliation(s)
- Qian Sun
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory of Plant Pathology, China Agricultural University, Beijing, P. R. China
| | - Yuan-Yuan Li
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory of Plant Pathology, China Agricultural University, Beijing, P. R. China
| | - Ying Wang
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory of Plant Pathology, China Agricultural University, Beijing, P. R. China
| | - Hang-Hai Zhao
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory of Plant Pathology, China Agricultural University, Beijing, P. R. China
| | - Tian-Yu Zhao
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory of Plant Pathology, China Agricultural University, Beijing, P. R. China
| | - Zong-Ying Zhang
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory of Plant Pathology, China Agricultural University, Beijing, P. R. China
| | - Da-Wei Li
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, P. R., China
| | - Jia-Lin Yu
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, P. R., China
| | - Xian-Bing Wang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, P. R., China
| | - Yong-Liang Zhang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, P. R., China
| | - Cheng-Gui Han
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory of Plant Pathology, China Agricultural University, Beijing, P. R. China
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17
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Dissecting the chloroplast proteome of chickpea ( Cicer arietinum L.) provides new insights into classical and non-classical functions. J Proteomics 2017. [DOI: 10.1016/j.jprot.2017.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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18
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Dorrell RG, Gile G, McCallum G, Méheust R, Bapteste EP, Klinger CM, Brillet-Guéguen L, Freeman KD, Richter DJ, Bowler C. Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome. eLife 2017; 6. [PMID: 28498102 PMCID: PMC5462543 DOI: 10.7554/elife.23717] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 05/08/2017] [Indexed: 12/18/2022] Open
Abstract
Plastids are supported by a wide range of proteins encoded within the nucleus and imported from the cytoplasm. These plastid-targeted proteins may originate from the endosymbiont, the host, or other sources entirely. Here, we identify and characterise 770 plastid-targeted proteins that are conserved across the ochrophytes, a major group of algae including diatoms, pelagophytes and kelps, that possess plastids derived from red algae. We show that the ancestral ochrophyte plastid proteome was an evolutionary chimera, with 25% of its phylogenetically tractable nucleus-encoded proteins deriving from green algae. We additionally show that functional mixing of host and plastid proteomes, such as through dual-targeting, is an ancestral feature of plastid evolution. Finally, we detect a clear phylogenetic signal from one ochrophyte subgroup, the lineage containing pelagophytes and dictyochophytes, in plastid-targeted proteins from another major algal lineage, the haptophytes. This may represent a possible serial endosymbiosis event deep in eukaryotic evolutionary history. DOI:http://dx.doi.org/10.7554/eLife.23717.001 The cells of most plants and algae contain compartments called chloroplasts that enable them to capture energy from sunlight in a process known as photosynthesis. Chloroplasts are the remnants of photosynthetic bacteria that used to live freely in the environment until they were consumed by a larger cell. “Complex” chloroplasts can form if a cell that already has a chloroplast is swallowed by another cell. The most abundant algae in the oceans are known as diatoms. These algae belong to a group called the stramenopiles, which also includes giant seaweeds such as kelp. The stramenopiles have a complex chloroplast that they acquired from a red alga (a relative of the seaweed used in sushi). However, some of the proteins in their chloroplasts are from other sources, such as the green algal relatives of plants, and it was not clear how these chloroplast proteins have contributed to the evolution of this group. Many of the proteins that chloroplasts need to work properly are produced by the host cell and are then transported into the chloroplasts. Dorrell et al. studied the genetic material of many stramenopile species and identified 770 chloroplast-targeted proteins that are predicted to underpin the origins of this group. Experiments in a diatom called Phaeodactylum confirmed these predictions and show that many of these chloroplast-targeted proteins have been recruited from green algae, bacteria, and other compartments within the host cell to support the chloroplast. Further experiments suggest that another major group of algae called the haptophytes once had a stramenopile chloroplast. The current haptophyte chloroplast does not come from the stramenopiles so the haptophytes appear to have replaced their chloroplasts at least once in their evolutionary history. The findings show that algal chloroplasts are mosaics, supported by proteins from many different species. This helps us understand why certain species succeed in the wild and how they may respond to environmental changes in the oceans. In the future, these findings may help researchers to engineer new species of algae and plants for food and fuel production. DOI:http://dx.doi.org/10.7554/eLife.23717.002
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Affiliation(s)
- Richard G Dorrell
- IBENS, Département de Biologie, École Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Gillian Gile
- School of Life Sciences, Arizona State University, Tempe, United States
| | - Giselle McCallum
- IBENS, Département de Biologie, École Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Raphaël Méheust
- Institut de Biologie Paris-Seine, Université Pierre et Marie Curie, Paris, France
| | - Eric P Bapteste
- Institut de Biologie Paris-Seine, Université Pierre et Marie Curie, Paris, France
| | | | | | | | - Daniel J Richter
- Sorbonne Universités, Université Pierre et Marie Curie, CNRS UMR 7144.,Adaptation et Diversité en Milieu Marin, Équipe EPEP, Station Biologique de Roscoff, Roscoff, France
| | - Chris Bowler
- IBENS, Département de Biologie, École Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
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19
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Nevarez PA, Qiu Y, Inoue H, Yoo CY, Benfey PN, Schnell DJ, Chen M. Mechanism of Dual Targeting of the Phytochrome Signaling Component HEMERA/pTAC12 to Plastids and the Nucleus. PLANT PHYSIOLOGY 2017; 173:1953-1966. [PMID: 28232584 PMCID: PMC5373053 DOI: 10.1104/pp.16.00116] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 02/21/2017] [Indexed: 05/20/2023]
Abstract
HEMERA (HMR) is a nuclear and plastidial dual-targeted protein. While it functions in the nucleus as a transcriptional coactivator in phytochrome signaling to regulate a distinct set of light-responsive, growth-relevant genes, in plastids it is known as pTAC12, which associates with the plastid-encoded RNA polymerase, and is essential for inducing the plastomic photosynthetic genes and initiating chloroplast biogenesis. However, the mechanism of targeting HMR to the nucleus and plastids is still poorly understood. Here, we show that HMR can be directly imported into chloroplasts through a transit peptide residing in the N-terminal 50 amino acids. Upon cleavage of the transit peptide and additional proteolytic processing, mature HMR, which begins from Lys-58, retains its biochemical properties in phytochrome signaling. Unexpectedly, expression of mature HMR failed to rescue not only the plastidial but also the nuclear defects of the hmr mutant. This is because the predicted nuclear localization signals of HMR are nonfunctional, and therefore mature HMR is unable to accumulate in either plastids or the nucleus. Surprisingly, fusing the transit peptide of the small subunit of Rubisco with mature HMR rescues both its plastidial and nuclear localization and functions. These results, combined with the observation that the nuclear form of HMR has the same reduced molecular mass as plastidial HMR, support a retrograde protein translocation mechanism in which HMR is targeted first to plastids, processed to the mature form, and then relocated to the nucleus.
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Affiliation(s)
- P Andrew Nevarez
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, California 92521 (Y.Q., C.Y., M.C.)
- Department of Biology, Duke University, Durham, North Carolina 27708 (P.A.N., Y.Q., C.Y., P.N.B., M.C.); and
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (H.I., D.J.S.)
| | - Yongjian Qiu
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, California 92521 (Y.Q., C.Y., M.C.)
- Department of Biology, Duke University, Durham, North Carolina 27708 (P.A.N., Y.Q., C.Y., P.N.B., M.C.); and
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (H.I., D.J.S.)
| | - Hitoshi Inoue
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, California 92521 (Y.Q., C.Y., M.C.)
- Department of Biology, Duke University, Durham, North Carolina 27708 (P.A.N., Y.Q., C.Y., P.N.B., M.C.); and
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (H.I., D.J.S.)
| | - Chan Yul Yoo
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, California 92521 (Y.Q., C.Y., M.C.)
- Department of Biology, Duke University, Durham, North Carolina 27708 (P.A.N., Y.Q., C.Y., P.N.B., M.C.); and
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (H.I., D.J.S.)
| | - Philip N Benfey
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, California 92521 (Y.Q., C.Y., M.C.)
- Department of Biology, Duke University, Durham, North Carolina 27708 (P.A.N., Y.Q., C.Y., P.N.B., M.C.); and
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (H.I., D.J.S.)
| | - Danny J Schnell
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, California 92521 (Y.Q., C.Y., M.C.)
- Department of Biology, Duke University, Durham, North Carolina 27708 (P.A.N., Y.Q., C.Y., P.N.B., M.C.); and
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (H.I., D.J.S.)
| | - Meng Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, California 92521 (Y.Q., C.Y., M.C.);
- Department of Biology, Duke University, Durham, North Carolina 27708 (P.A.N., Y.Q., C.Y., P.N.B., M.C.); and
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (H.I., D.J.S.)
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20
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Bross CD, Howes TR, Abolhassani Rad S, Kljakic O, Kohalmi SE. Subcellular localization of Arabidopsis arogenate dehydratases suggests novel and non-enzymatic roles. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1425-1440. [PMID: 28338876 PMCID: PMC5444438 DOI: 10.1093/jxb/erx024] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Arogenate dehydratases (ADTs) catalyze the final step in phenylalanine biosynthesis in plants. The Arabidopsis thaliana genome encodes a family of six ADTs capable of decarboxylating/dehydrating arogenate into phenylalanine. Using cyan fluorescent protein (CFP)-tagged proteins, the subcellular localization patterns of all six A. thaliana ADTs were investigated in intact Nicotiana benthamiana and A. thaliana leaf cells. We show that A. thaliana ADTs localize to stroma and stromules (stroma-filled tubules) of chloroplasts. This localization pattern is consistent with the enzymatic function of ADTs as many enzymes required for amino acid biosynthesis are primarily localized to chloroplasts, and stromules are thought to increase metabolite transport from chloroplasts to other cellular compartments. Furthermore, we provide evidence that ADTs have additional, non-enzymatic roles. ADT2 localizes in a ring around the equatorial plane of chloroplasts or to a chloroplast pole, which suggests that ADT2 is a component of the chloroplast division machinery. In addition to chloroplasts, ADT5 was also found in nuclei, again suggesting a non-enzymatic role for ADT5. We also show evidence that ADT5 is transported to the nucleus via stromules. We propose that ADT2 and ADT5 are moonlighting proteins that play an enzymatic role in phenylalanine biosynthesis and a second role in chloroplast division or transcriptional regulation, respectively.
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Affiliation(s)
- Crystal D Bross
- Department of Biology, Western University, 1151 Richmond Street North, London Ontario, N6A 5B7, Canada
| | - Travis R Howes
- Department of Biology, Western University, 1151 Richmond Street North, London Ontario, N6A 5B7, Canada
| | - Sara Abolhassani Rad
- Department of Biology, Western University, 1151 Richmond Street North, London Ontario, N6A 5B7, Canada
| | - Ornela Kljakic
- Department of Biology, Western University, 1151 Richmond Street North, London Ontario, N6A 5B7, Canada
| | - Susanne E Kohalmi
- Department of Biology, Western University, 1151 Richmond Street North, London Ontario, N6A 5B7, Canada
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21
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Daher Z, Recorbet G, Solymosi K, Wienkoop S, Mounier A, Morandi D, Lherminier J, Wipf D, Dumas-Gaudot E, Schoefs B. Changes in plastid proteome and structure in arbuscular mycorrhizal roots display a nutrient starvation signature. PHYSIOLOGIA PLANTARUM 2017; 159:13-29. [PMID: 27558913 DOI: 10.1111/ppl.12505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/17/2016] [Accepted: 07/18/2016] [Indexed: 05/21/2023]
Abstract
During arbuscular mycorrhizal symbiosis, arbuscule-containing root cortex cells display a proliferation of plastids, a feature usually ascribed to an increased plant anabolism despite the lack of studies focusing on purified root plastids. In this study, we investigated mycorrhiza-induced changes in plastidic pathways by performing a label-free comparative subcellular quantitative proteomic analysis targeted on plastid-enriched fractions isolated from Medicago truncatula roots, coupled to a cytological analysis of plastid structure. We identified 490 root plastid protein candidates, among which 79 changed in abundance upon mycorrhization, as inferred from spectral counting. According to cross-species sequence homology searches, the mycorrhiza-responsive proteome was enriched in proteins experimentally localized in thylakoids, whereas it was depleted of proteins ascribed predominantly to amyloplasts. Consistently, the analysis of plastid morphology using transmission electron microscopy indicated that starch depletion associated with the proliferation of membrane-free and tubular membrane-containing plastids was a feature specific to arbusculated cells. The loss of enzymes involved in carbon/nitrogen assimilation and provision of reducing power, coupled to macromolecule degradation events in the plastid-enriched fraction of mycorrhizal roots that paralleled lack of starch accumulation in arbusculated cells, lead us to propose that arbuscule functioning elicits a nutrient starvation and an oxidative stress signature that may prime arbuscule breakdown.
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Affiliation(s)
- Zeina Daher
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, Pôle Interactions Plantes Microrganismes, Dijon cedex 21065, France
| | - Ghislaine Recorbet
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, Pôle Interactions Plantes Microrganismes, Dijon cedex 21065, France
| | - Katalin Solymosi
- Department of Plant Anatomy, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Stefanie Wienkoop
- Department of Molecular System Biology, University of Vienna, Vienna 1090, Austria
| | - Arnaud Mounier
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, Pôle Interactions Plantes Microrganismes, Dijon cedex 21065, France
| | - Dominique Morandi
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, Pôle Interactions Plantes Microrganismes, Dijon cedex 21065, France
| | - Jeannine Lherminier
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, Pôle Interactions Plantes Microrganismes, Dijon cedex 21065, France
| | - Daniel Wipf
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, Pôle Interactions Plantes Microrganismes, Dijon cedex 21065, France
| | - Eliane Dumas-Gaudot
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, Pôle Interactions Plantes Microrganismes, Dijon cedex 21065, France
| | - Benoît Schoefs
- MicroMar, Mer, Molécules, Santé, UBL, Université du Maine, Le Mans Cedex 9 72085, France
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22
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Erickson JL, Kantek M, Schattat MH. Plastid-Nucleus Distance Alters the Behavior of Stromules. FRONTIERS IN PLANT SCIENCE 2017; 8:1135. [PMID: 28729870 PMCID: PMC5498514 DOI: 10.3389/fpls.2017.01135] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/13/2017] [Indexed: 05/20/2023]
Abstract
Plastids send "retrograde" signals to the nucleus to deliver information regarding their physiological status. One open question concerning this signal transfer is how the signal bridges the cytoplasm. Based on individual reports of plastid derived tubular membrane extensions connecting to nuclei, these so-called stromules have been suggested to function as communication routes between plastids and nuclei in response to biotic stress. However, based on the data currently available it is unclear whether interactions between stromules and nuclei are truly intentional or observed as a result of an inflated stromule frequency throughout the cell, and are thus a random event. The source of this uncertainty stems from missing information regarding the relative distribution of all plastids and stromules within a given cell. A comprehensive analysis of the upper epidermis of Arabidopsis thaliana rosette leaves was performed via a combination of still images and time-lapse movies of stromule formation in the context of the whole cell. This analysis could definitively confirm that stromule formation is not evenly distributed. Stromules are significantly more frequent within 8 μm of the nucleus, and approximately 90% of said stromules formed facing the nucleus. Time-lapse movies revealed that this enrichment of stromules is achieved via a 10-fold higher frequency of stromule initiation events within this 8 μm zone compared to the cell periphery. Following the movement of plastids and nuclei it became evident that movement and formation of stromules is correlated to nucleus movement. Observations suggest that stromules "connecting" to the nucleus are not necessarily the result of plastids sensing the nucleus and reaching out toward it, but are rather pulled out of the surface of nucleus associated plastids during opposing movement of these two organelles. This finding does not exclude the possibility that stromules could be transferring signals to the nucleus. However, this work provides support for an alternative hypothesis to explain stromule-nuclear interactions, suggesting that the main purpose of nucleus associated stromules may be to ensure a certain number of plastids maintain contact with the constantly moving nucleus.
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23
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Multifunctionality of plastid nucleoids as revealed by proteome analyses. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1016-38. [PMID: 26987276 DOI: 10.1016/j.bbapap.2016.03.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/25/2016] [Accepted: 03/09/2016] [Indexed: 01/08/2023]
Abstract
Protocols aimed at the isolation of nucleoids and transcriptionally active chromosomes (TACs) from plastids of higher plants have been established already decades ago, but only recent improvements in the mass spectrometry methods enabled detailed proteomic characterization of their components. Here we present a comprehensive analysis of the protein compositions obtained from two proteomic studies of TAC fractions isolated from Arabidopsis/mustard and spinach chloroplasts, respectively, as well as nucleoid fractions from Arabidopsis, maize and pea. Interestingly, different approaches as well as the use of diverse starting materials resulted in the detection of varying protein catalogues with a number of shared proteins. Possible reasons for the discrepancies between the protein repertoires and for missing out some of the nucleoid proteins that have been identified previously by other means than mass spectrometry as well as the repeated identification of "unexpected" proteins indicating potential links between DNA/RNA-associated nucleoid core functions and energy metabolism as well as biosynthetic activities of plastids will be discussed. In accordance with the nucleoid association of proteins involved in key functions of plastids including photosynthesis, the phenotypes of mutants lacking one or the other plastid nucleoid-associated protein (ptNAP) show the importance of nucleoid proteins for overall plant development and growth. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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24
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Zhang ZW, Zhang GC, Zhu F, Zhang DW, Yuan S. The roles of tetrapyrroles in plastid retrograde signaling and tolerance to environmental stresses. PLANTA 2015; 242:1263-76. [PMID: 26297452 DOI: 10.1007/s00425-015-2384-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 07/20/2015] [Indexed: 05/19/2023]
Abstract
This review provides new insights that tetrapyrrole signals play important roles in nuclear gene expression, chloroplast development and plant's resistance to environmental stresses. Higher plants contain many tetrapyrroles, including chlorophyll (Chl), heme, siroheme, phytochromobilin and some of their precursors, all of which have important biological functions. Genetic and physiological studies indicated that tetrapyrrole (mainly Mg-protoporphyrin IX) retrograde signals control photosynthesis-associated nuclear gene (PhANG) expression. Recent studies have shown that tetrapyrrole-derived signals may correlate with plant resistance to environmental stresses such as drought, high-light stress, water stress, osmotic stress, salinity and heavy metals. Signaling and physiological roles of Mg-protoIX-binding proteins (such as PAPP5, CRD and HSP90) and heme-binding proteins (such as HO and TSPO) and tetrapyrrole-signaling components (such as GUN1, ABI4 and CBFA) are summarized. Some of them positively regulate plant development and response to environmental stresses. The intermediate signaling components (such as PTM, HSP70-HSP90-HAP1 complex and PAPP5) between the nucleus and the plastid also positively regulate plant resistance to environmental stresses. This review provides new insights that genetically modified plants with enhanced tetrapyrrole levels have improved resistance to environmental stresses.
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Affiliation(s)
- Zhong-Wei Zhang
- College of Resources, Sichuan Agricultural University, 211 Huimin Road, Chengdu, 611130, China
| | - Gong-Chang Zhang
- College of Resources, Sichuan Agricultural University, 211 Huimin Road, Chengdu, 611130, China
| | - Feng Zhu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Da-Wei Zhang
- College of Life Science, Sichuan University, Chengdu, 610064, China
| | - Shu Yuan
- College of Resources, Sichuan Agricultural University, 211 Huimin Road, Chengdu, 611130, China.
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25
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Zhang H, Cui F, Wu Y, Lou L, Liu L, Tian M, Ning Y, Shu K, Tang S, Xie Q. The RING finger ubiquitin E3 ligase SDIR1 targets SDIR1-INTERACTING PROTEIN1 for degradation to modulate the salt stress response and ABA signaling in Arabidopsis. THE PLANT CELL 2015; 27:214-27. [PMID: 25616872 PMCID: PMC4330582 DOI: 10.1105/tpc.114.134163] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 12/17/2014] [Accepted: 01/06/2015] [Indexed: 05/18/2023]
Abstract
The plant hormone abscisic acid (ABA) regulates many aspects of plant development and the stress response. The intracellular E3 ligase SDIR1 (SALT- AND DROUGHT-INDUCED REALLY INTERESTING NEW GENE FINGER1) plays a key role in ABA signaling, regulating ABA-related seed germination and the stress response. In this study, we found that SDIR1 is localized on the endoplasmic reticulum membrane in Arabidopsis thaliana. Using cell biology, molecular biology, and biochemistry approaches, we demonstrated that SDIR1 interacts with and ubiquitinates its substrate, SDIRIP1 (SDIR1-INTERACTING PROTEIN1), to modulate SDIRIP1 stability through the 26S proteasome pathway. SDIRIP1 acts genetically downstream of SDIR1 in ABA and salt stress signaling. In detail, SDIRIP1 selectively regulates the expression of the downstream basic region/leucine zipper motif transcription factor gene ABA-INSENSITIVE5, rather than ABA-RESPONSIVE ELEMENTS BINDING FACTOR3 (ABF3) or ABF4, to regulate ABA-mediated seed germination and the plant salt response. Overall, the SDIR1/SDIRIP1 complex plays a vital role in ABA signaling through the ubiquitination pathway.
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Affiliation(s)
- Huawei Zhang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Feng Cui
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yaorong Wu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lijuan Lou
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lijing Liu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Miaomiao Tian
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuese Ning
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kai Shu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Sanyuan Tang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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26
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Kalderon B, Pines O. Protein folding as a driving force for dual protein targeting in eukaryotes. Front Mol Biosci 2014; 1:23. [PMID: 25988164 PMCID: PMC4428415 DOI: 10.3389/fmolb.2014.00023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 10/28/2014] [Indexed: 01/19/2023] Open
Abstract
It is well documented that in eukaryotic cells molecules of one protein can be located in several subcellular locations, a phenomenon termed dual targeting, dual localization, or dual distribution. The differently localized identical or nearly identical proteins are termed “echoforms.” Our conventional definition of dual targeted proteins refers to situations in which one of the echoforms is translocated through/into a membrane. Thus, dual targeted proteins are recognized by at least one organelle's receptors and translocation machineries within the lipid bilayer. In this review we attempt to evaluate mechanisms and situations in which protein folding is the major determinant of dual targeting and of the relative distribution levels of echoforms in the subcellular compartments of the eukaryotic cell. We show that the decisive folding step can occur prior, during or after translocation through the bilayer of a biological membrane. This phenomenon involves folding catalysts in the cell such as chaperones, proteases and modification enzymes, and targeting processes such as signal recognition, translocation through membranes, trapping, retrotranslocation and reverse translocation.
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Affiliation(s)
- Bella Kalderon
- Department of Microbiology and Molecular Genetics, Faculty of Medicine, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem Jerusalem, Israel
| | - Ophry Pines
- Department of Microbiology and Molecular Genetics, Faculty of Medicine, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem Jerusalem, Israel ; CREATE-NUS-HUJ Cellular and Molecular Mechanisms of Inflammation Program, National University of Singapore Singapore, Singapore
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27
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Abstract
In addition to their contribution to metabolism, chloroplasts emit signals that influence the expression of nuclear genes that contribute to numerous plastidic and extraplastidic processes. Plastid-to-nucleus signalling optimizes chloroplast function, regulates growth and development, and affects responses to environmental cues. An incomplete list of plastid signals is available and particular plastid-to-nucleus signalling mechanisms are partially understood. The plastid-to-nucleus signalling that depends on the GENOMES UNCOUPLED (GUN) genes couples the expression of nuclear genes to the functional state of the chloroplast. Analyses of gun mutants provided insight into the mechanisms and biological functions of plastid-to-nucleus signalling. GUN genes contribute to chloroplast biogenesis, the circadian rhythm, stress tolerance, light signalling and development. Some have criticized the gun mutant screen for employing inhibitors of chloroplast biogenesis and suggested that gun alleles do not disrupt significant plastid-to-nucleus signalling mechanisms. Here, I briefly review GUN-dependent plastid-to-nucleus signalling, explain the flaws in the major criticisms of the gun mutant screen and review the influence of plastids on light signalling and development.
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Affiliation(s)
- Robert M. Larkin
- Michigan State University-Department of Energy Plant Research Laboratory, Michigan State University, Room 106 Plant Biology Building, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, Room 106 Plant Biology Building, East Lansing, MI 48824, USA
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28
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Larkin RM. Chloroplast Signaling in Plants. Mol Biol 2014. [DOI: 10.1007/978-1-4614-7570-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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29
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Szechyńska-Hebda M, Karpiński S. Light intensity-dependent retrograde signalling in higher plants. JOURNAL OF PLANT PHYSIOLOGY 2013; 170:1501-16. [PMID: 23850030 DOI: 10.1016/j.jplph.2013.06.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 06/07/2013] [Accepted: 06/10/2013] [Indexed: 05/23/2023]
Abstract
Plants are able to acclimate to highly fluctuating light environment and evolved a short- and long-term light acclimatory responses, that are dependent on chloroplasts retrograde signalling. In this review we summarise recent evidences suggesting that the chloroplasts act as key sensors of light intensity changes in a wide range (low, high and excess light conditions) as well as sensors of darkness. They also participate in transduction and synchronisation of systemic retrograde signalling in response to differential light exposure of distinct leaves. Regulation of intra- and inter-cellular chloroplast retrograde signalling is dependent on the developmental and functional stage of the plastids. Therefore, it is discussed in following subsections: firstly, chloroplast biogenic control of nuclear genes, for example, signals related to photosystems and pigment biogenesis during early plastid development; secondly, signals in the mature chloroplast induced by changes in photosynthetic electron transport, reactive oxygen species, hormones and metabolite biosynthesis; thirdly, chloroplast signalling during leaf senescence. Moreover, with a help of meta-analysis of multiple microarray experiments, we showed that the expression of the same set of genes is regulated specifically in particular types of signals and types of light conditions. Furthermore, we also highlight the alternative scenarios of the chloroplast retrograde signals transduction and coordination linked to the role of photo-electrochemical signalling.
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Affiliation(s)
- Magdalena Szechyńska-Hebda
- Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Kraków, Poland; Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, 02-776 Warszawa, Poland
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30
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Scranton MA, Fowler JH, Girke T, Walling LL. Microarray analysis of tomato's early and late wound response reveals new regulatory targets for Leucine aminopeptidase A. PLoS One 2013; 8:e77889. [PMID: 24205013 PMCID: PMC3812031 DOI: 10.1371/journal.pone.0077889] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 09/04/2013] [Indexed: 11/22/2022] Open
Abstract
Wounding due to mechanical injury or insect feeding causes a wide array of damage to plant cells including cell disruption, desiccation, metabolite oxidation, and disruption of primary metabolism. In response, plants regulate a variety of genes and metabolic pathways to cope with injury. Tomato (Solanum lycopersicum) is a model for wound signaling but few studies have examined the comprehensive gene expression profiles in response to injury. A cross-species microarray approach using the TIGR potato 10-K cDNA array was analyzed for large-scale temporal (early and late) and spatial (locally and systemically) responses to mechanical wounding in tomato leaves. These analyses demonstrated that tomato regulates many primary and secondary metabolic pathways and this regulation is dependent on both timing and location. To determine if LAP-A, a known modulator of wound signaling, influences gene expression beyond the core of late wound-response genes, changes in RNAs from healthy and wounded Leucine aminopeptidase A-silenced (LapA-SI) and wild-type (WT) leaves were examined. While most of the changes in gene expression after wounding in LapA-SI leaves were similar to WT, overall responses were delayed in the LapA-SI leaves. Moreover, two pathogenesis-related 1 (PR-1c and PR-1a2) and two dehydrin (TAS14 and Dhn3) genes were negatively regulated by LAP-A. Collectively, this study has shown that tomato wound responses are complex and that LAP-A's role in modulation of wound responses extends beyond the well described late-wound gene core.
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Affiliation(s)
- Melissa A. Scranton
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California Riverside, Riverside, California, United States of America
| | - Jonathan H. Fowler
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California Riverside, Riverside, California, United States of America
| | - Thomas Girke
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California Riverside, Riverside, California, United States of America
| | - Linda L. Walling
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California Riverside, Riverside, California, United States of America
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31
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Larkin RM. Cytoplasm: Chloroplast Signaling. Mol Biol 2013. [DOI: 10.1007/978-1-4939-0263-7_10-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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32
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Scranton MA, Fowler JH, Girke T, Walling LL. Microarray analysis of tomato's early and late wound response reveals new regulatory targets for Leucine aminopeptidase A. PLoS One 2013. [PMID: 24205013 DOI: 10.1371/journal.pone.007788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
Wounding due to mechanical injury or insect feeding causes a wide array of damage to plant cells including cell disruption, desiccation, metabolite oxidation, and disruption of primary metabolism. In response, plants regulate a variety of genes and metabolic pathways to cope with injury. Tomato (Solanum lycopersicum) is a model for wound signaling but few studies have examined the comprehensive gene expression profiles in response to injury. A cross-species microarray approach using the TIGR potato 10-K cDNA array was analyzed for large-scale temporal (early and late) and spatial (locally and systemically) responses to mechanical wounding in tomato leaves. These analyses demonstrated that tomato regulates many primary and secondary metabolic pathways and this regulation is dependent on both timing and location. To determine if LAP-A, a known modulator of wound signaling, influences gene expression beyond the core of late wound-response genes, changes in RNAs from healthy and wounded Leucine aminopeptidase A-silenced (LapA-SI) and wild-type (WT) leaves were examined. While most of the changes in gene expression after wounding in LapA-SI leaves were similar to WT, overall responses were delayed in the LapA-SI leaves. Moreover, two pathogenesis-related 1 (PR-1c and PR-1a2) and two dehydrin (TAS14 and Dhn3) genes were negatively regulated by LAP-A. Collectively, this study has shown that tomato wound responses are complex and that LAP-A's role in modulation of wound responses extends beyond the well described late-wound gene core.
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Affiliation(s)
- Melissa A Scranton
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California Riverside, Riverside, California, United States of America
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33
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León P, Gregorio J, Cordoba E. ABI4 and its role in chloroplast retrograde communication. FRONTIERS IN PLANT SCIENCE 2012; 3:304. [PMID: 23335930 PMCID: PMC3541689 DOI: 10.3389/fpls.2012.00304] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 12/18/2012] [Indexed: 05/17/2023]
Abstract
The acquisition of plastids is a landmark event in plant evolution. The proper functionality of these organelles depends on strict and continuous communication between the plastids and the nucleus to precisely adjust gene expression in response to the organelle's requirements. Signals originating from the plastids impact the expression of a variety of nuclear genes, and this retrograde communication is essential to couple the nuclear expression of plastid-localized products with organelle gene expression and, ultimately, functionality. Major advances have been made in this field over the past few years with the characterization of independent retrograde signaling pathways and the identification of some of their components. One such factor is the nuclear transcriptional factor ABI4 (ABA-INSENTIVE 4). ABI4, together with the plastid PPR GUN1 protein, has been proposed to function as a node of convergence for multiple plastid retrograde signaling pathways. ABI4 is conserved among plants and also plays important roles in various critical developmental and metabolic processes. ABI4 is a versatile regulator that positively and negatively modulates the expression of many genes, including other transcriptional factors. However, its mode of action during plastid retrograde signaling is not fully understood. In this review, we describe the current evidence that supports the participation of ABI4 in different retrograde communication pathways. ABI4 is regulated at the transcriptional and post-transcriptional level. A known regulator of ABI4 includes the PTM transcription factor, which moves from the chloroplast to the nucleus. This transcription factor is a candidate for the transmission of retrograde signals between the plastid and ABI4.
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Affiliation(s)
- Patricia León
- *Correspondence: Patricia León, Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, México. e-mail:
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34
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Estavillo GM, Chan KX, Phua SY, Pogson BJ. Reconsidering the nature and mode of action of metabolite retrograde signals from the chloroplast. FRONTIERS IN PLANT SCIENCE 2012; 3:300. [PMID: 23316207 PMCID: PMC3539676 DOI: 10.3389/fpls.2012.00300] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 12/12/2012] [Indexed: 05/18/2023]
Abstract
Plant organelles produce retrograde signals to alter nuclear gene expression in order to coordinate their biogenesis, maintain homeostasis, or optimize their performance under adverse conditions. Many signals of different chemical nature have been described in the past decades, including chlorophyll intermediates, reactive oxygen species (ROS), and adenosine derivatives. While the effects of retrograde signaling on gene expression are well understood, the initiation and transport of the signals and their mode of action have either not been resolved, or are a matter of speculation. Moreover, retrograde signaling should be considered as part of a broader cellular network, instead of as separate pathways, required to adjust to changing physiologically relevant conditions. Here we summarize current plastid retrograde signaling models in plants, with a focus on new signaling pathways, SAL1-PAP, methylerythritol cyclodiphosphate (MEcPP), and β-cyclocitral (β-CC), and outline missing links or future areas of research that we believe need to be addressed to have a better understanding of plant intracellular signaling networks.
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Affiliation(s)
| | | | | | - Barry J. Pogson
- *Correspondence: Barry J. Pogson, ARC Centre of Excellence in Plant Energy of Biology, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia. e-mail:
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