1
|
Di X, Ortega-Alarcon D, Kakumanu R, Iglesias-Fernandez J, Diaz L, Baidoo EEK, Velazquez-Campoy A, Rodríguez-Concepción M, Perez-Gil J. MEP pathway products allosterically promote monomerization of deoxy-D-xylulose-5-phosphate synthase to feedback-regulate their supply. PLANT COMMUNICATIONS 2023; 4:100512. [PMID: 36575800 DOI: 10.1016/j.xplc.2022.100512] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/11/2022] [Accepted: 12/22/2022] [Indexed: 05/11/2023]
Abstract
Isoprenoids are a very large and diverse family of metabolites required by all living organisms. All isoprenoids derive from the double-bond isomers isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), which are produced by the methylerythritol 4-phosphate (MEP) pathway in bacteria and plant plastids. It has been reported that IPP and DMAPP feedback-regulate the activity of deoxyxylulose 5-phosphate synthase (DXS), a dimeric enzyme that catalyzes the main flux-controlling step of the MEP pathway. Here we provide experimental insights into the underlying mechanism. Isothermal titration calorimetry and dynamic light scattering approaches showed that IPP and DMAPP can allosterically bind to DXS in vitro, causing a size shift. In silico ligand binding site analysis and docking calculations identified a potential allosteric site in the contact region between the two monomers of the active DXS dimer. Modulation of IPP and DMAPP contents in vivo followed by immunoblot analyses confirmed that high IPP/DMAPP levels resulted in monomerization and eventual aggregation of the enzyme in bacterial and plant cells. Loss of the enzymatically active dimeric conformation allows a fast and reversible reduction of DXS activity in response to a sudden increase or decrease in IPP/DMAPP supply, whereas aggregation and subsequent removal of monomers that would otherwise be available for dimerization appears to be a more drastic response in the case of persistent IPP/DMAPP overabundance (e.g., by a blockage in their conversion to downstream isoprenoids). Our results represent an important step toward understanding the regulation of the MEP pathway and rational design of biotechnological endeavors aimed at increasing isoprenoid contents in microbial and plant systems.
Collapse
Affiliation(s)
- Xueni Di
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-Universitat Politècnica de València, 46022 Valencia, Spain; Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, 08193 Barcelona, Spain
| | - David Ortega-Alarcon
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Ramu Kakumanu
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Lucia Diaz
- Nostrum Biodiscovery SL, 08029 Barcelona, Spain
| | - Edward E K Baidoo
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Adrian Velazquez-Campoy
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Investigación Sanitaria de Aragón (IIS Aragon), 50009 Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Manuel Rodríguez-Concepción
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-Universitat Politècnica de València, 46022 Valencia, Spain; Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, 08193 Barcelona, Spain.
| | - Jordi Perez-Gil
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, 08193 Barcelona, Spain.
| |
Collapse
|
2
|
Winckler LI, Dissmeyer N. Molecular determinants of protein half-life in chloroplasts with focus on the Clp protease system. Biol Chem 2023; 404:499-511. [PMID: 36972025 DOI: 10.1515/hsz-2022-0320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/09/2023] [Indexed: 03/29/2023]
Abstract
Abstract
Proteolysis is an essential process to maintain cellular homeostasis. One pathway that mediates selective protein degradation and which is in principle conserved throughout the kingdoms of life is the N-degron pathway, formerly called the ‘N-end rule’. In the cytosol of eukaryotes and prokaryotes, N-terminal residues can be major determinants of protein stability. While the eukaryotic N-degron pathway depends on the ubiquitin proteasome system, the prokaryotic counterpart is driven by the Clp protease system. Plant chloroplasts also contain such a protease network, which suggests that they might harbor an organelle specific N-degron pathway similar to the prokaryotic one. Recent discoveries indicate that the N-terminal region of proteins affects their stability in chloroplasts and provides support for a Clp-mediated entry point in an N-degron pathway in plastids. This review discusses structure, function and specificity of the chloroplast Clp system, outlines experimental approaches to test for an N-degron pathway in chloroplasts, relates these aspects into general plastid proteostasis and highlights the importance of an understanding of plastid protein turnover.
Collapse
Affiliation(s)
- Lioba Inken Winckler
- Department of Plant Physiology and Protein Metabolism Laboratory, University of Osnabruck, Barbarastrasse 11, D-49076 Osnabruck, Germany
- Center of Cellular Nanoanalytics (CellNanOs), Barbarastrasse 11, D-49076 Osnabruck, Germany
- Faculty of Biology, University of Osnabruck, Barbarastrasse 11, D-49076 Osnabruck, Germany
| | - Nico Dissmeyer
- Department of Plant Physiology and Protein Metabolism Laboratory, University of Osnabruck, Barbarastrasse 11, D-49076 Osnabruck, Germany
- Center of Cellular Nanoanalytics (CellNanOs), Barbarastrasse 11, D-49076 Osnabruck, Germany
- Faculty of Biology, University of Osnabruck, Barbarastrasse 11, D-49076 Osnabruck, Germany
| |
Collapse
|
3
|
Strand DD, Karcher D, Ruf S, Schadach A, Schöttler MA, Sandoval-Ibañez O, Hall D, Kramer DM, Bock R. Characterization of mutants deficient in N-terminal phosphorylation of the chloroplast ATP synthase subunit β. PLANT PHYSIOLOGY 2023; 191:1818-1835. [PMID: 36635853 PMCID: PMC10022623 DOI: 10.1093/plphys/kiad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Understanding the regulation of photosynthetic light harvesting and electron transfer is of great importance to efforts to improve the ability of the electron transport chain to supply downstream metabolism. A central regulator of the electron transport chain is ATP synthase, the molecular motor that harnesses the chemiosmotic potential generated from proton-coupled electron transport to synthesize ATP. ATP synthase is regulated both thermodynamically and post-translationally, with proposed phosphorylation sites on multiple subunits. In this study we focused on two N-terminal serines on the catalytic subunit β in tobacco (Nicotiana tabacum), previously proposed to be important for dark inactivation of the complex to avoid ATP hydrolysis at night. Here we show that there is no clear role for phosphorylation in the dark inactivation of ATP synthase. Instead, mutation of one of the two phosphorylated serine residues to aspartate to mimic constitutive phosphorylation strongly decreased ATP synthase abundance. We propose that the loss of N-terminal phosphorylation of ATPβ may be involved in proper ATP synthase accumulation during complex assembly.
Collapse
Affiliation(s)
| | - Daniel Karcher
- Max-Planck-Institut für Molecular Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Stephanie Ruf
- Max-Planck-Institut für Molecular Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Anne Schadach
- Max-Planck-Institut für Molecular Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Mark A Schöttler
- Max-Planck-Institut für Molecular Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Omar Sandoval-Ibañez
- Max-Planck-Institut für Molecular Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - David Hall
- DOE Plant Research Laboratory, Michigan State University, 612 Wilson Rd 106, East Lansing, Michigan, 48824, USA
| | - David M Kramer
- DOE Plant Research Laboratory, Michigan State University, 612 Wilson Rd 106, East Lansing, Michigan, 48824, USA
| | | |
Collapse
|
4
|
Moloi SJ, Ngara R. The roles of plant proteases and protease inhibitors in drought response: a review. FRONTIERS IN PLANT SCIENCE 2023; 14:1165845. [PMID: 37143877 PMCID: PMC10151539 DOI: 10.3389/fpls.2023.1165845] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/30/2023] [Indexed: 05/06/2023]
Abstract
Upon exposure to drought, plants undergo complex signal transduction events with concomitant changes in the expression of genes, proteins and metabolites. For example, proteomics studies continue to identify multitudes of drought-responsive proteins with diverse roles in drought adaptation. Among these are protein degradation processes that activate enzymes and signalling peptides, recycle nitrogen sources, and maintain protein turnover and homeostasis under stressful environments. Here, we review the differential expression and functional activities of plant protease and protease inhibitor proteins under drought stress, mainly focusing on comparative studies involving genotypes of contrasting drought phenotypes. We further explore studies of transgenic plants either overexpressing or repressing proteases or their inhibitors under drought conditions and discuss the potential roles of these transgenes in drought response. Overall, the review highlights the integral role of protein degradation during plant survival under water deficits, irrespective of the genotypes' level of drought resilience. However, drought-sensitive genotypes exhibit higher proteolytic activities, while drought-tolerant genotypes tend to protect proteins from degradation by expressing more protease inhibitors. In addition, transgenic plant biology studies implicate proteases and protease inhibitors in various other physiological functions under drought stress. These include the regulation of stomatal closure, maintenance of relative water content, phytohormonal signalling systems including abscisic acid (ABA) signalling, and the induction of ABA-related stress genes, all of which are essential for maintaining cellular homeostasis under water deficits. Therefore, more validation studies are required to explore the various functions of proteases and their inhibitors under water limitation and their contributions towards drought adaptation.
Collapse
|
5
|
Rowland E, Kim J, Friso G, Poliakov A, Ponnala L, Sun Q, van Wijk KJ. The CLP and PREP protease systems coordinate maturation and degradation of the chloroplast proteome in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2022; 236:1339-1357. [PMID: 35946374 DOI: 10.1111/nph.18426] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
A network of peptidases governs proteostasis in plant chloroplasts and mitochondria. This study reveals strong genetic and functional interactions in Arabidopsis between the chloroplast stromal CLP chaperone-protease system and the PREP1,2 peptidases, which are dually localized to chloroplast stroma and the mitochondrial matrix. Higher order mutants defective in CLP or PREP proteins were generated and analyzed by quantitative proteomics and N-terminal proteomics (terminal amine isotopic labeling of substrates (TAILS)). Strong synergistic interactions were observed between the CLP protease system (clpr1-2, clpr2-1, clpc1-1, clpt1, clpt2) and both PREP homologs (prep1, prep2) resulting in embryo lethality or growth and developmental phenotypes. Synergistic interactions were observed even when only one of the PREP proteins was lacking, suggesting that PREP1 and PREP2 have divergent substrates. Proteome phenotypes were driven by the loss of CLP protease capacity, with little impact from the PREP peptidases. Chloroplast N-terminal proteomes showed that many nuclear encoded chloroplast proteins have alternatively processed N-termini in prep1prep2, clpt1clpt2 and prep1prep2clpt1clpt2. Loss of chloroplast protease capacity interferes with stromal processing peptidase (SPP) activity due to folding stress and low levels of accumulated cleaved cTP fragments. PREP1,2 proteolysis of cleaved cTPs is complemented by unknown proteases. A model for CLP and PREP activity within a hierarchical chloroplast proteolysis network is proposed.
Collapse
Affiliation(s)
- Elden Rowland
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY, 14853, USA
| | - Jitae Kim
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY, 14853, USA
- S-Korea Bioenergy Research Center, Chonnam National University, Gwangju, 61186, South Korea
| | - Giulia Friso
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY, 14853, USA
| | - Anton Poliakov
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY, 14853, USA
| | | | - Qi Sun
- Computational Biology Service Unit, Cornell University, Ithaca, NY, 14853, USA
| | - Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY, 14853, USA
| |
Collapse
|
6
|
Loiacono FV, Walther D, Seeger S, Thiele W, Gerlach I, Karcher D, Schöttler MA, Zoschke R, Bock R. Emergence of Novel RNA-Editing Sites by Changes in the Binding Affinity of a Conserved PPR Protein. Mol Biol Evol 2022; 39:6760358. [PMID: 36227729 PMCID: PMC9750133 DOI: 10.1093/molbev/msac222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/23/2022] [Accepted: 10/07/2022] [Indexed: 01/07/2023] Open
Abstract
RNA editing converts cytidines to uridines in plant organellar transcripts. Editing typically restores codons for conserved amino acids. During evolution, specific C-to-U editing sites can be lost from some plant lineages by genomic C-to-T mutations. By contrast, the emergence of novel editing sites is less well documented. Editing sites are recognized by pentatricopeptide repeat (PPR) proteins with high specificity. RNA recognition by PPR proteins is partially predictable, but prediction is often inadequate for PPRs involved in RNA editing. Here we have characterized evolution and recognition of a recently gained editing site. We demonstrate that changes in the RNA recognition motifs that are not explainable with the current PPR code allow an ancient PPR protein, QED1, to uniquely target the ndhB-291 site in Brassicaceae. When expressed in tobacco, the Arabidopsis QED1 edits 33 high-confident off-target sites in chloroplasts and mitochondria causing a spectrum of mutant phenotypes. By manipulating the relative expression levels of QED1 and ndhB-291, we show that the target specificity of the PPR protein depends on the RNA:protein ratio. Finally, our data suggest that the low expression levels of PPR proteins are necessary to ensure the specificity of editing site selection and prevent deleterious off-target editing.
Collapse
Affiliation(s)
- F Vanessa Loiacono
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Dirk Walther
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Stefanie Seeger
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Wolfram Thiele
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ines Gerlach
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Daniel Karcher
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Mark Aurel Schöttler
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Reimo Zoschke
- Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | | |
Collapse
|
7
|
Proteolytic regulation of mitochondrial oxidative phosphorylation components in plants. Biochem Soc Trans 2022; 50:1119-1132. [PMID: 35587610 PMCID: PMC9246333 DOI: 10.1042/bst20220195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/07/2022] [Accepted: 05/03/2022] [Indexed: 11/28/2022]
Abstract
Mitochondrial function relies on the homeostasis and quality control of their proteome, including components of the oxidative phosphorylation (OXPHOS) pathway that generates energy in form of ATP. OXPHOS subunits are under constant exposure to reactive oxygen species due to their oxidation-reduction activities, which consequently make them prone to oxidative damage, misfolding, and aggregation. As a result, quality control mechanisms through turnover and degradation are required for maintaining mitochondrial activity. Degradation of OXPHOS subunits can be achieved through proteomic turnover or modular degradation. In this review, we present multiple protein degradation pathways in plant mitochondria. Specifically, we focus on the intricate turnover of OXPHOS subunits, prior to protein import via cytosolic proteasomal degradation and post import and assembly via intra-mitochondrial proteolysis involving multiple AAA+ proteases. Together, these proteolytic pathways maintain the activity and homeostasis of OXPHOS components.
Collapse
|
8
|
Abdel-Ghany SE, LaManna LM, Harroun HT, Maliga P, Sloan DB. Rapid sequence evolution is associated with genetic incompatibilities in the plastid Clp complex. PLANT MOLECULAR BIOLOGY 2022; 108:277-287. [PMID: 35039977 DOI: 10.1007/s11103-022-01241-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
KEY MESSAGE Replacing the native clpP1 gene in the Nicotiana plastid genome with homologs from different donor species showed that the extent of genetic incompatibilities depended on the rate of sequence evolution. The plastid caseinolytic protease (Clp) complex plays essential roles in maintaining protein homeostasis and comprises both plastid-encoded and nuclear-encoded subunits. Despite the Clp complex being retained across green plants with highly conserved protein sequences in most species, examples of extremely accelerated amino acid substitution rates have been identified in numerous angiosperms. The causes of these accelerations have been the subject of extensive speculation but still remain unclear. To distinguish among prevailing hypotheses and begin to understand the functional consequences of rapid sequence divergence in Clp subunits, we used plastome transformation to replace the native clpP1 gene in tobacco (Nicotiana tabacum) with counterparts from another angiosperm genus (Silene) that exhibits a wide range in rates of Clp protein sequence evolution. We found that antibiotic-mediated selection could drive a transgenic clpP1 replacement from a slowly evolving donor species (S. latifolia) to homoplasmy but that clpP1 copies from Silene species with accelerated evolutionary rates remained heteroplasmic, meaning that they could not functionally replace the essential tobacco clpP1 gene. These results suggest that observed cases of rapid Clp sequence evolution are a source of epistatic incompatibilities that must be ameliorated by coevolutionary responses between plastid and nuclear subunits.
Collapse
Affiliation(s)
- Salah E Abdel-Ghany
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Lisa M LaManna
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Haleakala T Harroun
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Pal Maliga
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854, USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| |
Collapse
|
9
|
Zimmer D, Swart C, Graf A, Arrivault S, Tillich M, Proost S, Nikoloski Z, Stitt M, Bock R, Mühlhaus T, Boulouis A. Topology of the redox network during induction of photosynthesis as revealed by time-resolved proteomics in tobacco. SCIENCE ADVANCES 2021; 7:eabi8307. [PMID: 34919428 PMCID: PMC8682995 DOI: 10.1126/sciadv.abi8307] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Photosynthetically produced electrons provide energy for various metabolic pathways, including carbon reduction. Four Calvin-Benson cycle enzymes and several other plastid proteins are activated in the light by reduction of specific cysteines via thioredoxins, a family of electron transporters operating in redox regulation networks. How does this network link the photosynthetic chain with cellular metabolism? Using a time-resolved redox proteomic method, we have investigated the redox network in vivo during the dark–to–low light transition. We show that redox states of some thioredoxins follow the photosynthetic linear electron transport rate. While some redox targets have kinetics compatible with an equilibrium with one thioredoxin (TRXf), reduction of other proteins shows specific kinetic limitations, allowing fine-tuning of each redox-regulated step of chloroplast metabolism. We identified five new redox-regulated proteins, including proteins involved in Mg2+ transport and 1O2 signaling. Our results provide a system-level functional view of the photosynthetic redox regulation network.
Collapse
Affiliation(s)
- David Zimmer
- Computational Systems Biology, TU Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Corné Swart
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Alexander Graf
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Stéphanie Arrivault
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Michael Tillich
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Sebastian Proost
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, TU Kaiserslautern, 67663 Kaiserslautern, Germany
- Corresponding author. (A.B.); (T.M.)
| | - Alix Boulouis
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany
- Laboratory of Chloroplast Biology and Light-sensing in Microalgae, UMR7141, CNRS, Sorbonne Université, Institut de Biologie Physico-Chimique, 75005 Paris, France
- Corresponding author. (A.B.); (T.M.)
| |
Collapse
|
10
|
Torres-Montilla S, Rodriguez-Concepcion M. Making extra room for carotenoids in plant cells: New opportunities for biofortification. Prog Lipid Res 2021; 84:101128. [PMID: 34530006 DOI: 10.1016/j.plipres.2021.101128] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/06/2021] [Accepted: 09/09/2021] [Indexed: 12/22/2022]
Abstract
Plant carotenoids are essential for photosynthesis and photoprotection and provide colors in the yellow to red range to non-photosynthetic organs such as petals and ripe fruits. They are also the precursors of biologically active molecules not only in plants (including hormones and retrograde signals) but also in animals (including retinoids such as vitamin A). A carotenoid-rich diet has been associated with improved health and cognitive capacity in humans, whereas the use of carotenoids as natural pigments is widespread in the agrofood and cosmetic industries. The nutritional and economic relevance of carotenoids has spurred a large number of biotechnological strategies to enrich plant tissues with carotenoids. Most of such approaches to alter carotenoid contents in plants have been focused on manipulating their biosynthesis or degradation, whereas improving carotenoid sink capacity in plant tissues has received much less attention. Our knowledge on the molecular mechanisms influencing carotenoid storage in plants has substantially grown in the last years, opening new opportunities for carotenoid biofortification. Here we will review these advances with a particular focus on those creating extra room for carotenoids in plant cells either by promoting the differentiation of carotenoid-sequestering structures within plastids or by transferring carotenoid production to the cytosol.
Collapse
Affiliation(s)
- Salvador Torres-Montilla
- Institute for Plant Molecular and Cell Biology (IBMCP), Agencia Estatal Consejo Superior de Investigaciones Cientificas - Universitat Politècnica de València, 46022 Valencia, Spain
| | - Manuel Rodriguez-Concepcion
- Institute for Plant Molecular and Cell Biology (IBMCP), Agencia Estatal Consejo Superior de Investigaciones Cientificas - Universitat Politècnica de València, 46022 Valencia, Spain.
| |
Collapse
|
11
|
Zhang Y, Xia G, Zhu Q. Conserved and Unique Roles of Chaperone-Dependent E3 Ubiquitin Ligase CHIP in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:699756. [PMID: 34305988 PMCID: PMC8299108 DOI: 10.3389/fpls.2021.699756] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/17/2021] [Indexed: 05/09/2023]
Abstract
Protein quality control (PQC) is essential for maintaining cellular homeostasis by reducing protein misfolding and aggregation. Major PQC mechanisms include protein refolding assisted by molecular chaperones and the degradation of misfolded and aggregated proteins using the proteasome and autophagy. A C-terminus of heat shock protein (Hsp) 70-interacting protein [carboxy-terminal Hsp70-interacting protein (CHIP)] is a chaperone-dependent and U-box-containing E3 ligase. CHIP is a key molecule in PQC by recognizing misfolded proteins through its interacting chaperones and targeting their degradation. CHIP also ubiquitinates native proteins and plays a regulatory role in other cellular processes, including signaling, development, DNA repair, immunity, and aging in metazoans. As a highly conserved ubiquitin ligase, plant CHIP plays an important role in response to a broad spectrum of biotic and abiotic stresses. CHIP protects chloroplasts by coordinating chloroplast PQC both outside and inside the important photosynthetic organelle of plant cells. CHIP also modulates the activity of protein phosphatase 2A (PP2A), a crucial component in a network of plant signaling, including abscisic acid (ABA) signaling. In this review, we discuss the structure, cofactors, activities, and biological function of CHIP with an emphasis on both its conserved and unique roles in PQC, stress responses, and signaling in plants.
Collapse
Affiliation(s)
| | | | - Qianggen Zhu
- Department of Landscape and Horticulture, Ecology College, Lishui University, Lishui, China
| |
Collapse
|
12
|
Malinova I, Zupok A, Massouh A, Schöttler MA, Meyer EH, Yaneva-Roder L, Szymanski W, Rößner M, Ruf S, Bock R, Greiner S. Correction of frameshift mutations in the atpB gene by translational recoding in chloroplasts of Oenothera and tobacco. THE PLANT CELL 2021; 33:1682-1705. [PMID: 33561268 PMCID: PMC8254509 DOI: 10.1093/plcell/koab050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/02/2021] [Indexed: 05/10/2023]
Abstract
Translational recoding, also known as ribosomal frameshifting, is a process that causes ribosome slippage along the messenger RNA, thereby changing the amino acid sequence of the synthesized protein. Whether the chloroplast employs recoding is unknown. I-iota, a plastome mutant of Oenothera (evening primrose), carries a single adenine insertion in an oligoA stretch [11A] of the atpB coding region (encoding the β-subunit of the ATP synthase). The mutation is expected to cause synthesis of a truncated, nonfunctional protein. We report that a full-length AtpB protein is detectable in I-iota leaves, suggesting operation of a recoding mechanism. To characterize the phenomenon, we generated transplastomic tobacco lines in which the atpB reading frame was altered by insertions or deletions in the oligoA motif. We observed that insertion of two adenines was more efficiently corrected than insertion of a single adenine, or deletion of one or two adenines. We further show that homopolymeric composition of the oligoA stretch is essential for recoding, as an additional replacement of AAA lysine codon by AAG resulted in an albino phenotype. Our work provides evidence for the operation of translational recoding in chloroplasts. Recoding enables correction of frameshift mutations and can restore photoautotrophic growth in the presence of a mutation that otherwise would be lethal.
Collapse
Affiliation(s)
- Irina Malinova
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Arkadiusz Zupok
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Amid Massouh
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Mark Aurel Schöttler
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Etienne H Meyer
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Liliya Yaneva-Roder
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Witold Szymanski
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Margit Rößner
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Stephanie Ruf
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Stephan Greiner
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| |
Collapse
|
13
|
Bouchnak I, van Wijk KJ. Structure, function, and substrates of Clp AAA+ protease systems in cyanobacteria, plastids, and apicoplasts: A comparative analysis. J Biol Chem 2021; 296:100338. [PMID: 33497624 PMCID: PMC7966870 DOI: 10.1016/j.jbc.2021.100338] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 02/08/2023] Open
Abstract
ATPases Associated with diverse cellular Activities (AAA+) are a superfamily of proteins that typically assemble into hexameric rings. These proteins contain AAA+ domains with two canonical motifs (Walker A and B) that bind and hydrolyze ATP, allowing them to perform a wide variety of different functions. For example, AAA+ proteins play a prominent role in cellular proteostasis by controlling biogenesis, folding, trafficking, and degradation of proteins present within the cell. Several central proteolytic systems (e.g., Clp, Deg, FtsH, Lon, 26S proteasome) use AAA+ domains or AAA+ proteins to unfold protein substrates (using energy from ATP hydrolysis) to make them accessible for degradation. This allows AAA+ protease systems to degrade aggregates and large proteins, as well as smaller proteins, and feed them as linearized molecules into a protease chamber. This review provides an up-to-date and a comparative overview of the essential Clp AAA+ protease systems in Cyanobacteria (e.g., Synechocystis spp), plastids of photosynthetic eukaryotes (e.g., Arabidopsis, Chlamydomonas), and apicoplasts in the nonphotosynthetic apicomplexan pathogen Plasmodium falciparum. Recent progress and breakthroughs in identifying Clp protease structures, substrates, substrate adaptors (e.g., NblA/B, ClpS, ClpF), and degrons are highlighted. We comment on the physiological importance of Clp activity, including plastid biogenesis, proteostasis, the chloroplast Protein Unfolding Response, and metabolism, across these diverse lineages. Outstanding questions as well as research opportunities and priorities to better understand the essential role of Clp systems in cellular proteostasis are discussed.
Collapse
Affiliation(s)
- Imen Bouchnak
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York, USA
| | - Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York, USA.
| |
Collapse
|
14
|
Coelho AC, Pires R, Schütz G, Santa C, Manadas B, Pinto P. Disclosing proteins in the leaves of cork oak plants associated with the immune response to Phytophthora cinnamomi inoculation in the roots: A long-term proteomics approach. PLoS One 2021; 16:e0245148. [PMID: 33481834 PMCID: PMC7822296 DOI: 10.1371/journal.pone.0245148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/22/2020] [Indexed: 02/06/2023] Open
Abstract
The pathological interaction between oak trees and Phytophthora cinnamomi has implications in the cork oak decline observed over the last decades in the Iberian Peninsula. During host colonization, the phytopathogen secretes effector molecules like elicitins to increase disease effectiveness. The objective of this study was to unravel the proteome changes associated with the cork oak immune response triggered by P. cinnamomi inoculation in a long-term assay, through SWATH-MS quantitative proteomics performed in the oak leaves. Using the Arabidopis proteome database as a reference, 424 proteins were confidently quantified in cork oak leaves, of which 80 proteins showed a p-value below 0.05 or a fold-change greater than 2 or less than 0.5 in their levels between inoculated and control samples being considered as altered. The inoculation of cork oak roots with P. cinnamomi increased the levels of proteins associated with protein-DNA complex assembly, lipid oxidation, response to endoplasmic reticulum stress, and pyridine-containing compound metabolic process in the leaves. In opposition, several proteins associated with cellular metabolic compound salvage and monosaccharide catabolic process had significantly decreased abundances. The most significant abundance variations were observed for the Ribulose 1,5-Bisphosphate Carboxylase small subunit (RBCS1A), Heat Shock protein 90–1 (Hsp90-1), Lipoxygenase 2 (LOX2) and Histone superfamily protein H3.3 (A8MRLO/At4G40030) revealing a pertinent role for these proteins in the host-pathogen interaction mechanism. This work represents the first SWATH-MS analysis performed in cork oak plants inoculated with P. cinnamomi and highlights host proteins that have a relevant action in the homeostatic states that emerge from the interaction between the oomycete and the host in the long term and in a distal organ.
Collapse
Affiliation(s)
- Ana Cristina Coelho
- Center for Electronic, Optoelectronic and Telecommunications (CEOT), University of Algarve, Faro, Portugal
- Escola Superior de Educação e Comunicação (ESEC), University of Algarve, Faro, Portugal
- * E-mail:
| | - Rosa Pires
- Center for Electronic, Optoelectronic and Telecommunications (CEOT), University of Algarve, Faro, Portugal
| | - Gabriela Schütz
- Center for Electronic, Optoelectronic and Telecommunications (CEOT), University of Algarve, Faro, Portugal
- Instituto Superior de Engenharia, University of Algarve, Faro, Portugal
| | - Cátia Santa
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Patrícia Pinto
- Center for Marine Sciences (CCMAR), University of Algarve, Faro, Portugal
| |
Collapse
|
15
|
Sun JL, Li JY, Wang MJ, Song ZT, Liu JX. Protein Quality Control in Plant Organelles: Current Progress and Future Perspectives. MOLECULAR PLANT 2021; 14:95-114. [PMID: 33137518 DOI: 10.1016/j.molp.2020.10.011] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 10/09/2020] [Accepted: 10/28/2020] [Indexed: 05/20/2023]
Abstract
The endoplasmic reticulum, chloroplasts, and mitochondria are major plant organelles for protein synthesis, photosynthesis, metabolism, and energy production. Protein homeostasis in these organelles, maintained by a balance between protein synthesis and degradation, is essential for cell functions during plant growth, development, and stress resistance. Nucleus-encoded chloroplast- and mitochondrion-targeted proteins and ER-resident proteins are imported from the cytosol and undergo modification and maturation within their respective organelles. Protein folding is an error-prone process that is influenced by both developmental signals and environmental cues; a number of mechanisms have evolved to ensure efficient import and proper folding and maturation of proteins in plant organelles. Misfolded or damaged proteins with nonnative conformations are subject to degradation via complementary or competing pathways: intraorganelle proteases, the organelle-associated ubiquitin-proteasome system, and the selective autophagy of partial or entire organelles. When proteins in nonnative conformations accumulate, the organelle-specific unfolded protein response operates to restore protein homeostasis by reducing protein folding demand, increasing protein folding capacity, and enhancing components involved in proteasome-associated protein degradation and autophagy. This review summarizes recent progress on the understanding of protein quality control in the ER, chloroplasts, and mitochondria in plants, with a focus on common mechanisms shared by these organelles during protein homeostasis.
Collapse
Affiliation(s)
- Jing-Liang Sun
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Jin-Yu Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Mei-Jing Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Ze-Ting Song
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China.
| |
Collapse
|
16
|
Moreno JC, Martinez-Jaime S, Kosmacz M, Sokolowska EM, Schulz P, Fischer A, Luzarowska U, Havaux M, Skirycz A. A Multi-OMICs Approach Sheds Light on the Higher Yield Phenotype and Enhanced Abiotic Stress Tolerance in Tobacco Lines Expressing the Carrot lycopene β -cyclase1 Gene. FRONTIERS IN PLANT SCIENCE 2021; 12:624365. [PMID: 33613605 PMCID: PMC7893089 DOI: 10.3389/fpls.2021.624365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 01/18/2021] [Indexed: 05/17/2023]
Abstract
Recently, we published a set of tobacco lines expressing the Daucus carota (carrot) DcLCYB1 gene with accelerated development, increased carotenoid content, photosynthetic efficiency, and yield. Because of this development, DcLCYB1 expression might be of general interest in crop species as a strategy to accelerate development and increase biomass production under field conditions. However, to follow this path, a better understanding of the molecular basis of this phenotype is essential. Here, we combine OMICs (RNAseq, proteomics, and metabolomics) approaches to advance our understanding of the broader effect of LCYB expression on the tobacco transcriptome and metabolism. Upon DcLCYB1 expression, the tobacco transcriptome (~2,000 genes), proteome (~700 proteins), and metabolome (26 metabolites) showed a high number of changes in the genes involved in metabolic processes related to cell wall, lipids, glycolysis, and secondary metabolism. Gene and protein networks revealed clusters of interacting genes and proteins mainly involved in ribosome and RNA metabolism and translation. In addition, abiotic stress-related genes and proteins were mainly upregulated in the transgenic lines. This was well in line with an enhanced stress (high light, salt, and H2O2) tolerance response in all the transgenic lines compared with the wild type. Altogether, our results show an extended and coordinated response beyond the chloroplast (nucleus and cytosol) at the transcriptome, proteome, and metabolome levels, supporting enhanced plant growth under normal and stress conditions. This final evidence completes the set of benefits conferred by the expression of the DcLCYB1 gene, making it a very promising bioengineering tool to generate super crops.
Collapse
Affiliation(s)
- Juan C. Moreno
- Max Planck Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
- Biological and Environmental Science and Engineering Division, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- *Correspondence: Juan C. Moreno
| | | | - Monika Kosmacz
- Max Planck Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
- Biological and Environmental Science and Engineering Division, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - Philipp Schulz
- Max Planck Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
| | - Axel Fischer
- Max Planck Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
| | - Urszula Luzarowska
- Max Planck Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
| | - Michel Havaux
- Aix-Marseille Univ., CEA, CNRS UMR7265, BIAM, CEA/Cadarache, Saint-Paul-lez-Durance, France
| | - Aleksandra Skirycz
- Max Planck Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
- Aleksandra Skirycz
| |
Collapse
|
17
|
Ameztoy K, Sánchez-López ÁM, Muñoz FJ, Bahaji A, Almagro G, Baroja-Fernández E, Gámez-Arcas S, De Diego N, Doležal K, Novák O, Pěnčík A, Alpízar A, Rodríguez-Concepción M, Pozueta-Romero J. Proteostatic Regulation of MEP and Shikimate Pathways by Redox-Activated Photosynthesis Signaling in Plants Exposed to Small Fungal Volatiles. FRONTIERS IN PLANT SCIENCE 2021; 12:637976. [PMID: 33747018 PMCID: PMC7973468 DOI: 10.3389/fpls.2021.637976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/28/2021] [Indexed: 05/07/2023]
Abstract
Microorganisms produce volatile compounds (VCs) with molecular masses of less than 300 Da that promote plant growth and photosynthesis. Recently, we have shown that small VCs of less than 45 Da other than CO2 are major determinants of plant responses to fungal volatile emissions. However, the regulatory mechanisms involved in the plants' responses to small microbial VCs remain unclear. In Arabidopsis thaliana plants exposed to small fungal VCs, growth promotion is accompanied by reduction of the thiol redox of Calvin-Benson cycle (CBC) enzymes and changes in the levels of shikimate and 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway-related compounds. We hypothesized that plants' responses to small microbial VCs involve post-translational modulation of enzymes of the MEP and shikimate pathways via mechanisms involving redox-activated photosynthesis signaling. To test this hypothesis, we compared the responses of wild-type (WT) plants and a cfbp1 mutant defective in a redox-regulated isoform of the CBC enzyme fructose-1,6-bisphosphatase to small VCs emitted by the fungal phytopathogen Alternaria alternata. Fungal VC-promoted growth and photosynthesis, as well as metabolic and proteomic changes, were substantially weaker in cfbp1 plants than in WT plants. In WT plants, but not in cfbp1 plants, small fungal VCs reduced the levels of both transcripts and proteins of the stromal Clp protease system and enhanced those of plastidial chaperonins and co-chaperonins. Consistently, small fungal VCs promoted the accumulation of putative Clp protease clients including MEP and shikimate pathway enzymes. clpr1-2 and clpc1 mutants with disrupted plastidial protein homeostasis responded weakly to small fungal VCs, strongly indicating that plant responses to microbial volatile emissions require a finely regulated plastidial protein quality control system. Our findings provide strong evidence that plant responses to fungal VCs involve chloroplast-to-nucleus retrograde signaling of redox-activated photosynthesis leading to proteostatic regulation of the MEP and shikimate pathways.
Collapse
Affiliation(s)
- Kinia Ameztoy
- Instituto de Agrobiotecnología (Consejo Superior de Investigaciones Científicas/Gobierno de Navarra), Mutilva, Spain
| | - Ángela María Sánchez-López
- Instituto de Agrobiotecnología (Consejo Superior de Investigaciones Científicas/Gobierno de Navarra), Mutilva, Spain
| | - Francisco José Muñoz
- Instituto de Agrobiotecnología (Consejo Superior de Investigaciones Científicas/Gobierno de Navarra), Mutilva, Spain
| | - Abdellatif Bahaji
- Instituto de Agrobiotecnología (Consejo Superior de Investigaciones Científicas/Gobierno de Navarra), Mutilva, Spain
| | - Goizeder Almagro
- Instituto de Agrobiotecnología (Consejo Superior de Investigaciones Científicas/Gobierno de Navarra), Mutilva, Spain
| | - Edurne Baroja-Fernández
- Instituto de Agrobiotecnología (Consejo Superior de Investigaciones Científicas/Gobierno de Navarra), Mutilva, Spain
| | - Samuel Gámez-Arcas
- Instituto de Agrobiotecnología (Consejo Superior de Investigaciones Científicas/Gobierno de Navarra), Mutilva, Spain
| | - Nuria De Diego
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Karel Doležal
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
- Laboratory of Growth Regulators, Faculty of Science of Palackı University and Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science of Palackı University and Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Ales Pěnčík
- Laboratory of Growth Regulators, Faculty of Science of Palackı University and Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Adán Alpízar
- Unidad de Proteómica Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | - Javier Pozueta-Romero
- Instituto de Agrobiotecnología (Consejo Superior de Investigaciones Científicas/Gobierno de Navarra), Mutilva, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC) Campus de Teatinos, Málaga, Spain
- *Correspondence: Javier Pozueta-Romero,
| |
Collapse
|
18
|
Pacheco TG, Lopes ADS, Welter JF, Yotoko KSC, Otoni WC, Vieira LDN, Guerra MP, Nodari RO, Balsanelli E, Pedrosa FDO, de Souza EM, Rogalski M. Plastome sequences of the subgenus Passiflora reveal highly divergent genes and specific evolutionary features. PLANT MOLECULAR BIOLOGY 2020; 104:21-37. [PMID: 32533420 DOI: 10.1007/s11103-020-01020-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/07/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Juliana Fátima Welter
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Karla Suemy Clemente Yotoko
- Laboratório de Bioinformática e Evolução, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Wagner Campos Otoni
- Laboratório de Cultura de Tecidos Vegetais, Departamento de Biologia Vegetal, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Leila do Nascimento Vieira
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Miguel Pedro Guerra
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Rubens Onofre Nodari
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio de Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
| |
Collapse
|
19
|
Moreno JC, Mi J, Agrawal S, Kössler S, Turečková V, Tarkowská D, Thiele W, Al-Babili S, Bock R, Schöttler MA. Expression of a carotenogenic gene allows faster biomass production by redesigning plant architecture and improving photosynthetic efficiency in tobacco. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1967-1984. [PMID: 32623777 DOI: 10.1111/tpj.14909] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/23/2020] [Indexed: 05/11/2023]
Abstract
Because carotenoids act as accessory pigments in photosynthesis, play a key photoprotective role and are of major nutritional importance, carotenogenesis has been a target for crop improvement. Although carotenoids are important precursors of phytohormones, previous genetic manipulations reported little if any effects on biomass production and plant development, but resulted in specific modifications in carotenoid content. Unexpectedly, the expression of the carrot lycopene β-cyclase (DcLCYB1) in Nicotiana tabacum cv. Xanthi not only resulted in increased carotenoid accumulation, but also in altered plant architecture characterized by longer internodes, faster plant growth, early flowering and increased biomass. Here, we have challenged these transformants with a range of growth conditions to determine the robustness of their phenotype and analyze the underlying mechanisms. Transgenic DcLCYB1 lines showed increased transcript levels of key genes involved in carotenoid, chlorophyll, gibberellin (GA) and abscisic acid (ABA) biosynthesis, but also in photosynthesis-related genes. Accordingly, their carotenoid, chlorophyll, ABA and GA contents were increased. Hormone application and inhibitor experiments confirmed the key role of altered GA/ABA contents in the growth phenotype. Because the longer internodes reduce shading of mature leaves, induction of leaf senescence was delayed, and mature leaves maintained a high photosynthetic capacity. This increased total plant assimilation, as reflected in higher plant yields under both fully controlled constant and fluctuating light, and in non-controlled conditions. Furthermore, our data are a warning that engineering of isoprenoid metabolism can cause complex changes in phytohormone homeostasis and therefore plant development, which have not been sufficiently considered in previous studies.
Collapse
Affiliation(s)
- Juan C Moreno
- Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Jianing Mi
- King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Shreya Agrawal
- Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Stella Kössler
- Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Veronika Turečková
- Laboratory of Growth Regulators, The Czech Academy of Sciences, Institute of Experimental Botany & Palacký University, Šlechtitelů 27, Olomouc, CZ-78371, Czech Republic
| | - Danuše Tarkowská
- Laboratory of Growth Regulators, The Czech Academy of Sciences, Institute of Experimental Botany & Palacký University, Šlechtitelů 27, Olomouc, CZ-78371, Czech Republic
| | - Wolfram Thiele
- Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Salim Al-Babili
- King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ralph Bock
- Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Mark Aurel Schöttler
- Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| |
Collapse
|
20
|
Mamaeva A, Taliansky M, Filippova A, Love AJ, Golub N, Fesenko I. The role of chloroplast protein remodeling in stress responses and shaping of the plant peptidome. THE NEW PHYTOLOGIST 2020; 227:1326-1334. [PMID: 32320487 DOI: 10.1111/nph.16620] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/15/2020] [Indexed: 06/11/2023]
Abstract
In addition to photosynthesis, chloroplasts perform a variety of important cellular functions in the plant cell, which can, for example, regulate plant responses to abiotic and biotic stress conditions. Under stress, intensive chloroplast protein remodeling and degradation can occur, releasing large numbers of endogenous peptides. These protein-derived peptides can be found intracellularly, but also in the plant secretome. Although the pathways of chloroplast protein degradation and the types of chloroplast proteases implicated in this process have received much attention, the role of the resulting peptides is less well understood. In this review we summarize the data on peptide generation processes during the remodeling of the chloroplast proteome under stress conditions and discuss the mechanisms leading to these changes. We also review the experimental evidence which supports the concept that peptides derived from chloroplast proteins can function as regulators of plant responses to (a)biotic stresses.
Collapse
Affiliation(s)
- Anna Mamaeva
- Laboratory of Plant Functional Genomics and Proteomics, Laboratory of Molecular Basis of Plant Stress Resistance, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russian Federation
| | - Michael Taliansky
- Laboratory of Plant Functional Genomics and Proteomics, Laboratory of Molecular Basis of Plant Stress Resistance, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russian Federation
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Anna Filippova
- Laboratory of Plant Functional Genomics and Proteomics, Laboratory of Molecular Basis of Plant Stress Resistance, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russian Federation
| | - Andrew J Love
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Nina Golub
- Laboratory of Plant Functional Genomics and Proteomics, Laboratory of Molecular Basis of Plant Stress Resistance, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russian Federation
| | - Igor Fesenko
- Laboratory of Plant Functional Genomics and Proteomics, Laboratory of Molecular Basis of Plant Stress Resistance, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russian Federation
| |
Collapse
|
21
|
Petereit J, Duncan O, Murcha MW, Fenske R, Cincu E, Cahn J, Pružinská A, Ivanova A, Kollipara L, Wortelkamp S, Sickmann A, Lee J, Lister R, Millar AH, Huang S. Mitochondrial CLPP2 Assists Coordination and Homeostasis of Respiratory Complexes. PLANT PHYSIOLOGY 2020; 184:148-164. [PMID: 32571844 PMCID: PMC7479914 DOI: 10.1104/pp.20.00136] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 06/12/2020] [Indexed: 05/04/2023]
Abstract
Protein homeostasis in eukaryotic organelles and their progenitor prokaryotes is regulated by a series of proteases including the caseinolytic protease (CLPP). CLPP has essential roles in chloroplast biogenesis and maintenance, but the significance of the plant mitochondrial CLPP remains unknown and factors that aid coordination of nuclear- and mitochondrial-encoded subunits for complex assembly in mitochondria await discovery. We generated knockout lines of the single gene for the mitochondrial CLP protease subunit, CLPP2, in Arabidopsis (Arabidopsis thaliana). Mutants showed a higher abundance of transcripts from mitochondrial genes encoding oxidative phosphorylation protein complexes, whereas nuclear genes encoding other subunits of the same complexes showed no change in transcript abundance. By contrast, the protein abundance of specific nuclear-encoded subunits in oxidative phosphorylation complexes I and V increased in CLPP2 knockouts, without accumulation of mitochondrial-encoded counterparts in the same complex. Complexes with subunits mainly or entirely encoded in the nucleus were unaffected. Analysis of protein import and function of complex I revealed that while function was retained, protein homeostasis was disrupted, leading to accumulation of soluble subcomplexes of nuclear-encoded subunits. Therefore, CLPP2 contributes to the mitochondrial protein degradation network through supporting coordination and homeostasis of protein complexes encoded across mitochondrial and nuclear genomes.
Collapse
Affiliation(s)
- Jakob Petereit
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Washington 6009, Australia
| | - Owen Duncan
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Washington 6009, Australia
| | - Monika W Murcha
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Washington 6009, Australia
| | - Ricarda Fenske
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Washington 6009, Australia
| | - Emilia Cincu
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Washington 6009, Australia
| | - Jonathan Cahn
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Washington 6009, Australia
| | - Adriana Pružinská
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Washington 6009, Australia
| | - Aneta Ivanova
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Washington 6009, Australia
| | - Laxmikanth Kollipara
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44139 Dortmund, Germany
| | - Stefanie Wortelkamp
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44139 Dortmund, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44139 Dortmund, Germany
- Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen AB24 3FX, Scotland, United Kingdom
- Medizinische Fakultät, Medizinische Proteom-Center, Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Jiwon Lee
- Centre for advanced Microscopy, The Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Ryan Lister
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Washington 6009, Australia
- The Harry Perkins Institute of Medical Research, Perth, Washington 6009, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Washington 6009, Australia
| | - Shaobai Huang
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Washington 6009, Australia
| |
Collapse
|
22
|
Li HM, Schnell D, Theg SM. Protein Import Motors in Chloroplasts: On the Role of Chaperones. THE PLANT CELL 2020; 32:536-542. [PMID: 31932485 PMCID: PMC7054032 DOI: 10.1105/tpc.19.00300] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/01/2019] [Accepted: 01/08/2020] [Indexed: 05/09/2023]
Affiliation(s)
- Hsou-Min Li
- Institute of Molecular Biology Academia Sinica Taipei 11529, Taiwan
| | - Danny Schnell
- Department of Plant Biology Michigan State University East Lansing, Michigan 48824
| | - Steven M Theg
- Department of Plant Biology University of California Davis, California 95616
| |
Collapse
|
23
|
Wang JZ, Lei Y, Xiao Y, He X, Liang J, Jiang J, Dong S, Ke H, Leon P, Zerbe P, Xiao Y, Dehesh K. Uncovering the functional residues of Arabidopsis isoprenoid biosynthesis enzyme HDS. Proc Natl Acad Sci U S A 2020; 117:355-361. [PMID: 31879352 PMCID: PMC6955319 DOI: 10.1073/pnas.1916434117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The methylerythritol phosphate (MEP) pathway is responsible for producing isoprenoids, metabolites with essential functions in the bacterial kingdom and plastid-bearing organisms including plants and Apicomplexa. Additionally, the MEP-pathway intermediate methylerythritol cyclodiphosphate (MEcPP) serves as a plastid-to-nucleus retrograde signal. A suppressor screen of the high MEcPP accumulating mutant plant (ceh1) led to the isolation of 3 revertants (designated Rceh1-3) resulting from independent intragenic substitutions of conserved amino acids in the penultimate MEP-pathway enzyme, hydroxymethylbutenyl diphosphate synthase (HDS). The revertants accumulate varying MEcPP levels, lower than that of ceh1, and exhibit partial or full recovery of MEcPP-mediated phenotypes, including stunted growth and induced expression of stress response genes and the corresponding metabolites. Structural modeling of HDS and ligand docking spatially position the substituted residues at the MEcPP binding pocket and cofactor binding domain of the enzyme. Complementation assays confirm the role of these residues in suppressing the ceh1 mutant phenotypes, albeit to different degrees. In vitro enzyme assays of wild type and HDS variants exhibit differential activities and reveal an unanticipated mismatch between enzyme kinetics and the in vivo MEcPP levels in the corresponding Rceh lines. Additional analyses attribute the mismatch, in part, to the abundance of the first and rate-limiting MEP-pathway enzyme, DXS, and further suggest MEcPP as a rheostat for abundance of the upstream enzyme instrumental in fine-tuning of the pathway flux. Collectively, this study identifies critical residues of a key MEP-pathway enzyme, HDS, valuable for synthetic engineering of isoprenoids, and as potential targets for rational design of antiinfective drugs.
Collapse
Affiliation(s)
- Jin-Zheng Wang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Yongxing Lei
- Chinese Academy of Sciences (CAS) Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032 Shanghai, China
| | - Yanmei Xiao
- Department of Plant Biology, University of California, Davis, CA 95616
| | - Xiang He
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Jiubo Liang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Jishan Jiang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Shangzhi Dong
- Chinese Academy of Sciences (CAS) Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032 Shanghai, China
| | - Haiyan Ke
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Patricia Leon
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62210 Cuernavaca, México
| | - Philipp Zerbe
- Department of Plant Biology, University of California, Davis, CA 95616
| | - Youli Xiao
- Chinese Academy of Sciences (CAS) Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032 Shanghai, China;
| | - Katayoon Dehesh
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521;
| |
Collapse
|
24
|
Loiacono FV, Thiele W, Schöttler MA, Tillich M, Bock R. Establishment of a Heterologous RNA Editing Event in Chloroplasts. PLANT PHYSIOLOGY 2019; 181:891-900. [PMID: 31519789 PMCID: PMC6836845 DOI: 10.1104/pp.19.00922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 08/31/2019] [Indexed: 05/18/2023]
Abstract
In chloroplasts and plant mitochondria, specific cytidines in mRNAs are posttranscriptionally converted to uridines by RNA editing. Editing sites are recognized by nucleus-encoded RNA-binding proteins of the pentatricopeptide repeat (PPR) family, which bind upstream of the editing site in a sequence-specific manner and direct the editing activity to the target position. Editing sites have been lost many times during evolution by C-to-T mutations. Loss of an editing site is thought to be accompanied by loss or degeneration of its cognate PPR protein. Consequently, foreign editing sites are usually not recognized when introduced into species lacking the site. Previously, the spinach (Spinacia oleracea) psbF-26 editing site was introduced into the tobacco (Nicotiana tabacum) plastid genome. Tobacco lacks the psbF-26 site and cannot edit it. Expression of the "unedited" PsbF protein resulted in impaired PSII function. In Arabidopsis (Arabidopsis thaliana), the PPR protein LPA66 is required for editing at psbF-26. Here, we show that introduction of the Arabidopsis LPA66 reconstitutes editing of the spinach psbF-26 site in tobacco and restores a wild-type-like phenotype. Our findings define the minimum requirements for establishing new RNA editing sites and suggest that the evolutionary dynamics of editing patterns is largely explained by coevolution of editing sites and PPR proteins.
Collapse
Affiliation(s)
- Filomena Vanessa Loiacono
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Wolfram Thiele
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Mark Aurel Schöttler
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Michael Tillich
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| |
Collapse
|
25
|
Ali MS, Baek KH. Co-suppression of NbClpC1 and NbClpC2 alters plant morphology with changed hormone levels in Nicotiana benthamiana. PLANT CELL REPORTS 2019; 38:1317-1328. [PMID: 31385037 DOI: 10.1007/s00299-019-02452-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
KEY MESSAGE Co-suppression of chaperonic ClpC1 and ClpC2 in Nicotiana benthamiana significantly affect the development and exogenous application of gibberellin partially rescue the developmental defects. Over the past decade, the Clp protease complex has been identified as being implicated in plastid protein quality control in plant cells. CLPC1 and CLPC2 proteins form the chaperone subunits of the Clp protease complex and unfold protein substrates to thread them into the ClpP complex. Here, using the technique of virus-induced gene silencing (VIGS), we suppressed both Nicotiana benthamiana ClpC1 and ClpC2 (NbClpC1/C2) functioning as chaperone subunits in the protease complex. Co-suppression of NbClpC1/C2 caused chlorosis and retarded-growth phenotype with no seed formation and significantly reduced root length. We found that co-suppression of NbClpC1/C2 also affected stomata and trichome formation and vascular bundle differentiation and patterning. Analysis of phytohormones revealed significant alteration and imbalance of major hormones in the leaves of NbClpC1/C2 co-suppressed plant. We also found that application of gibberellin (GA3) partially rescued the developmental defects. Co-suppression of NbClpC1/C2 significantly affected the development of N. benthamiana and exogenous application of GA3 partially rescued the developmental defects. Overall, our findings demonstrate that CLPC1 and CLPC2 proteins have a pivotal role in plant growth and development.
Collapse
Affiliation(s)
- Md Sarafat Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea
| | - Kwang-Hyun Baek
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea.
| |
Collapse
|
26
|
Chen X, Chen Z, Huang W, Fu H, Wang Q, Wang Y, Cao J. Proteomic analysis of gametophytic sex expression in the fern Ceratopteris thalictroides. PLoS One 2019; 14:e0221470. [PMID: 31425560 PMCID: PMC6699692 DOI: 10.1371/journal.pone.0221470] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 08/08/2019] [Indexed: 01/25/2023] Open
Abstract
Ceratopteris thalictroides, a model fern, has two kinds of gametophytes with different sex expression: male and hermaphrodite. Hermaphroditic gametophytes have one or several archegonia beneath the growing point and a few antheridia at the base or margin. Male gametophytes show a spoon-like shape with much longer than the width and produce many antheridia at the margin and surface. The results of chlorophyll fluorescence detection showed that the photochemical efficiency of hermaphrodites was higher than that of males. By using two-dimensional electrophoresis and mass spectrometry, the differentially abundant proteins in hermaphroditic and male gametophytes were identified. A total of 1136 ± 55 protein spots were detected in Coomassie-stained gels of proteins from hermaphroditic gametophytes, and 1130 ± 65 spots were detected in gels of proteins from male gametophytes. After annotation, 33 spots representing differentially abundant proteins were identified. Among these, proteins involved in photosynthesis and chaperone proteins were over-represented in hermaphrodites, whereas several proteins involved in metabolism were increased in male gametophytes in order to maintain their development under relatively nutritionally deficient conditions. Furthermore, the differentially abundant cytoskeletal proteins detected in this study, such as centrin and actin, may be involved in the formation of sexual organs and are directly related to sex expression. These differentially abundant proteins are important for maintaining the development of gametophytes of different sexes in C. thalictroides.
Collapse
Affiliation(s)
- Xuefei Chen
- College of Life Science, East China Normal University, Shanghai, China
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Zhiyi Chen
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Wujie Huang
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Huanhuan Fu
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Quanxi Wang
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Youfang Wang
- College of Life Science, East China Normal University, Shanghai, China
- * E-mail: (YW); (JC)
| | - Jianguo Cao
- College of Life Science, Shanghai Normal University, Shanghai, China
- * E-mail: (YW); (JC)
| |
Collapse
|
27
|
Montandon C, Friso G, Liao JYR, Choi J, van Wijk KJ. In Vivo Trapping of Proteins Interacting with the Chloroplast CLPC1 Chaperone: Potential Substrates and Adaptors. J Proteome Res 2019; 18:2585-2600. [DOI: 10.1021/acs.jproteome.9b00112] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Cyrille Montandon
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Giulia Friso
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Jui-Yun Rei Liao
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Junsik Choi
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Klaas J. van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| |
Collapse
|
28
|
Rodriguez-Concepcion M, D'Andrea L, Pulido P. Control of plastidial metabolism by the Clp protease complex. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2049-2058. [PMID: 30576524 DOI: 10.1093/jxb/ery441] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/29/2018] [Indexed: 05/23/2023]
Abstract
Plant metabolism is strongly dependent on plastids. Besides hosting the photosynthetic machinery, these endosymbiotic organelles synthesize starch, fatty acids, amino acids, nucleotides, tetrapyrroles, and isoprenoids. Virtually all enzymes involved in plastid-localized metabolic pathways are encoded by the nuclear genome and imported into plastids. Once there, protein quality control systems ensure proper folding of the mature forms and remove irreversibly damaged proteins. The Clp protease is the main machinery for protein degradation in the plastid stroma. Recent work has unveiled an increasing number of client proteins of this proteolytic complex in plants. Notably, a substantial proportion of these substrates are required for normal chloroplast metabolism, including enzymes involved in the production of essential tetrapyrroles and isoprenoids such as chlorophylls and carotenoids. The Clp protease complex acts in coordination with nuclear-encoded plastidial chaperones for the control of both enzyme levels and proper folding (i.e. activity). This communication involves a retrograde signaling pathway, similarly to the unfolded protein response previously characterized in mitochondria and endoplasmic reticulum. Coordinated Clp protease and chaperone activities appear to further influence other plastid processes, such as the differentiation of chloroplasts into carotenoid-accumulating chromoplasts during fruit ripening.
Collapse
Affiliation(s)
| | - Lucio D'Andrea
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Pablo Pulido
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
| |
Collapse
|
29
|
Rei Liao JY, van Wijk KJ. Discovery of AAA+ Protease Substrates through Trapping Approaches. Trends Biochem Sci 2019; 44:528-545. [PMID: 30773324 DOI: 10.1016/j.tibs.2018.12.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 12/17/2018] [Indexed: 12/27/2022]
Abstract
Proteases play essential roles in cellular proteostasis. Mechanisms through which proteases recognize their substrates are often hard to predict and therefore require experimentation. In vivo trapping allows systematic identification of potential substrates of proteases, their adaptors, and chaperones. This combines in vivo genetic modifications of proteolytic systems, stabilized protease-substrate interactions, affinity enrichments of trapped substrates, and mass spectrometry (MS)-based identification. In vitro approaches, in which immobilized protease components are incubated with isolated cellular proteome, complement this in vivo approach. Both approaches can provide information about substrate recognition signals, degrons, and conditional effects. This review summarizes published trapping studies and their biological outcomes, and provides recommendations for substrate trapping of the processive AAA+ Clp, Lon, and FtsH chaperone proteolytic systems.
Collapse
Affiliation(s)
- Jui-Yun Rei Liao
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY 14853, USA
| | - Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
30
|
Liao JR, Friso G, Kim J, van Wijk KJ. Consequences of the loss of catalytic triads in chloroplast CLPPR protease core complexes in vivo. PLANT DIRECT 2018; 2:e00086. [PMID: 31245686 PMCID: PMC6508832 DOI: 10.1002/pld3.86] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 09/20/2018] [Accepted: 09/22/2018] [Indexed: 05/23/2023]
Abstract
The essential chloroplast CLP protease system consists of a tetradecameric proteolytic core with catalytic P (P1, 3-6) and non-catalytic R (R1-4) subunits, CLP chaperones and adaptors. The chloroplast CLP complex has a total of ten catalytic sites,but it is not known how many of these catalytic sites can be inactivated before plants lose viability. Here we show that CLPP3 and the catalytically inactive variant CLPP3S164A fully complement the developmental arrest of the clpp3-1 null mutant, even under environmental stress. In contrast, whereas the inactive variant CLPP5S193A assembled into the CLP core, it cannot rescue the embryo lethal phenotype of the clpp5-1 null mutant. This shows that CLPP3 makes a unique structural contribution but its catalytic site is dispensable, whereas the catalytic activity of CLPP5 is essential. Mass spectrometry of affinity-purified CLP cores of the complemented lines showed highly enriched CLP cores. Other chloroplast proteins were co-purified with the CLP cores and are candidate substrates. A strong overlap of co-purified proteins between the CLP core complexes with active and inactive subunits indicates that CLP cores with reduced number of catalytic sites do not over-accumulate substrates, suggesting that the bottle-neck for degradation is likely substrate recognition and unfolding by CLP adaptors and chaperones, upstream of the CLP core.
Collapse
Affiliation(s)
- Jui‐Yun Rei Liao
- Section of Plant BiologySchool of Integrative Plant Sciences (SIPS)Cornell UniversityIthacaNew York
| | - Giulia Friso
- Section of Plant BiologySchool of Integrative Plant Sciences (SIPS)Cornell UniversityIthacaNew York
| | - Jitae Kim
- Section of Plant BiologySchool of Integrative Plant Sciences (SIPS)Cornell UniversityIthacaNew York
| | - Klaas J. van Wijk
- Section of Plant BiologySchool of Integrative Plant Sciences (SIPS)Cornell UniversityIthacaNew York
| |
Collapse
|
31
|
Nakai M. New Perspectives on Chloroplast Protein Import. PLANT & CELL PHYSIOLOGY 2018; 59:1111-1119. [PMID: 29684214 DOI: 10.1093/pcp/pcy083] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/13/2018] [Indexed: 05/21/2023]
Abstract
Virtually all chloroplasts in extant photosynthetic eukaryotes derive from a single endosymbiotic event that probably occurred more than a billion years ago between a host eukaryotic cell and a cyanobacterium-like ancestor. Many endosymbiont genes were subsequently transferred to the host nuclear genome, concomitant with the establishment of a system for protein transport through the chloroplast double-membrane envelope. Presently, 2,000-3,000 different nucleus-encoded chloroplast proteins must be imported into the chloroplast following their synthesis in the cytosol. The TOC (translocon at the outer envelope membrane of chloroplasts) and TIC (translocon at the inner envelope membrane of chloroplasts) complexes are protein translocation machineries at the outer and inner envelope membranes, respectively, that facilitate this chloroplast protein import with the aid of a TIC-associated ATP-driven import motor. All the essential components of this protein import system seemed to have been identified through biochemical analyses and subsequent genetic studies that initiated in the late 1990s. However, in 2013, the Nakai group reported a novel inner envelope membrane TIC complex, for which a novel ATP-driven import motor associated with this TIC complex is likely to exist. In this mini review, I will summarize these recent discoveries together with new, or reanalyzed, data presented by other groups in recent years. Whereas the precise concurrent view of chloroplast protein import is still a matter of some debate, it is anticipated that the entire TOC/TIC/ATP motor system, including any novel components, will be conclusively established in the next decade. Such findings may lead to an extensively revised view of the evolution and molecular mechanisms of chloroplast protein import.
Collapse
Affiliation(s)
- Masato Nakai
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871 Japan
| |
Collapse
|