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Wang Y, Wang D, Du J, Wang Y, Shao C, Cui C, Xiao J, Wang X. Crucial role of SWL1 in chloroplast biogenesis and development in Arabidopsis thaliana. PLANT CELL REPORTS 2024; 43:135. [PMID: 38704787 DOI: 10.1007/s00299-024-03210-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 04/01/2024] [Indexed: 05/07/2024]
Abstract
KEY MESSAGE The disruption of the SWL1 gene leads to a significant down regulation of chloroplast and secondary metabolites gene expression in Arabidopsis thaliana. And finally results in a dysfunction of chloroplast and plant growth. Although the development of the chloroplast has been a consistent focus of research, the corresponding regulatory mechanisms remain unidentified. In this study, the CRISPR/Cas9 system was used to mutate the SWL1 gene, resulting in albino cotyledons and variegated true leaf phenotype. Confocal microscopy and western blot of chloroplast protein fractions revealed that SWL1 localized in the chloroplast stroma. Electron microscopy indicated chloroplasts in the cotyledons of swl1 lack well-defined grana and internal membrane structures, and similar structures have been detected in the albino region of variegated true leaves. Transcriptome analysis revealed that down regulation of chloroplast and nuclear gene expression related to chloroplast, including light harvesting complexes, porphyrin, chlorophyll metabolism and carbon metabolism in the swl1 compared to wild-type plant. In addition, proteomic analysis combined with western blot analysis, showed that a significant decrease in chloroplast proteins of swl1. Furthermore, the expression of genes associated with secondary metabolites and growth hormones was also reduced, which may be attributed to SWL1 associated with absorption and fixation of inorganic carbon during chloroplast development. Together, the above findings provide valuable information to elucidate the exact function of SWL1 in chloroplast biogenesis and development.
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Affiliation(s)
- Yue Wang
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Dong Wang
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Jingxia Du
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yan Wang
- College of Agriculture and Forestry, Hebei North University, Zhangjiakou, 075000, China
| | - Chunxue Shao
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Chuwen Cui
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Jianwei Xiao
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing, 100083, China.
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
| | - Xinwei Wang
- College of Agriculture and Forestry, Hebei North University, Zhangjiakou, 075000, China.
- SENO Biotechnology Co., Ltd., Zhangjiakou, 075000, China.
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2
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Ezzedine JA, Uwizeye C, Si Larbi G, Villain G, Louwagie M, Schilling M, Hagenmuller P, Gallet B, Stewart A, Petroutsos D, Devime F, Salze P, Liger L, Jouhet J, Dumont M, Ravanel S, Amato A, Valay JG, Jouneau PH, Falconet D, Maréchal E. Adaptive traits of cysts of the snow alga Sanguina nivaloides unveiled by 3D subcellular imaging. Nat Commun 2023; 14:7500. [PMID: 37980360 PMCID: PMC10657455 DOI: 10.1038/s41467-023-43030-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/26/2023] [Indexed: 11/20/2023] Open
Abstract
Sanguina nivaloides is the main alga forming red snowfields in high mountains and Polar Regions. It is non-cultivable. Analysis of environmental samples by X-ray tomography, focused-ion-beam scanning-electron-microscopy, physicochemical and physiological characterization reveal adaptive traits accounting for algal capacity to reside in snow. Cysts populate liquid water at the periphery of ice, are photosynthetically active, can survive for months, and are sensitive to freezing. They harbor a wrinkled plasma membrane expanding the interface with environment. Ionomic analysis supports a cell efflux of K+, and assimilation of phosphorus. Glycerolipidomic analysis confirms a phosphate limitation. The chloroplast contains thylakoids oriented in all directions, fixes carbon in a central pyrenoid and produces starch in peripheral protuberances. Analysis of cells kept in the dark shows that starch is a short-term carbon storage. The biogenesis of cytosolic droplets shows that they are loaded with triacylglycerol and carotenoids for long-term carbon storage and protection against oxidative stress.
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Affiliation(s)
- Jade A Ezzedine
- Laboratoire de Physiologie Cellulaire et Végétale, Centre National de la Recherche Scientifique, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Commissariat à l'Energie Atomique et aux Energies Alternatives, Université Grenoble Alpes; IRIG, CEA-Grenoble, 17 avenue des Martyrs, 38000, Grenoble, France
| | - Clarisse Uwizeye
- Laboratoire de Physiologie Cellulaire et Végétale, Centre National de la Recherche Scientifique, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Commissariat à l'Energie Atomique et aux Energies Alternatives, Université Grenoble Alpes; IRIG, CEA-Grenoble, 17 avenue des Martyrs, 38000, Grenoble, France
| | - Grégory Si Larbi
- Laboratoire de Physiologie Cellulaire et Végétale, Centre National de la Recherche Scientifique, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Commissariat à l'Energie Atomique et aux Energies Alternatives, Université Grenoble Alpes; IRIG, CEA-Grenoble, 17 avenue des Martyrs, 38000, Grenoble, France
| | - Gaelle Villain
- Laboratoire de Physiologie Cellulaire et Végétale, Centre National de la Recherche Scientifique, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Commissariat à l'Energie Atomique et aux Energies Alternatives, Université Grenoble Alpes; IRIG, CEA-Grenoble, 17 avenue des Martyrs, 38000, Grenoble, France
| | - Mathilde Louwagie
- Laboratoire de Physiologie Cellulaire et Végétale, Centre National de la Recherche Scientifique, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Commissariat à l'Energie Atomique et aux Energies Alternatives, Université Grenoble Alpes; IRIG, CEA-Grenoble, 17 avenue des Martyrs, 38000, Grenoble, France
| | - Marion Schilling
- Laboratoire de Physiologie Cellulaire et Végétale, Centre National de la Recherche Scientifique, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Commissariat à l'Energie Atomique et aux Energies Alternatives, Université Grenoble Alpes; IRIG, CEA-Grenoble, 17 avenue des Martyrs, 38000, Grenoble, France
| | - Pascal Hagenmuller
- Centre d'Etudes de la Neige, Université Grenoble Alpes, Université de Toulouse, Météo-France, CNRS, CNRM, 38000, Grenoble, France
| | - Benoît Gallet
- Institut de Biologie Structurale, Centre National de la Recherche Scientifique, Université Grenoble Alpes, Commissariat à l'Energie Atomique et aux Energies Alternatives; IRIG, 71 avenue des Martyrs, 38000, Grenoble, France
| | - Adeline Stewart
- Laboratoire de Physiologie Cellulaire et Végétale, Centre National de la Recherche Scientifique, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Commissariat à l'Energie Atomique et aux Energies Alternatives, Université Grenoble Alpes; IRIG, CEA-Grenoble, 17 avenue des Martyrs, 38000, Grenoble, France
| | - Dimitris Petroutsos
- Laboratoire de Physiologie Cellulaire et Végétale, Centre National de la Recherche Scientifique, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Commissariat à l'Energie Atomique et aux Energies Alternatives, Université Grenoble Alpes; IRIG, CEA-Grenoble, 17 avenue des Martyrs, 38000, Grenoble, France
| | - Fabienne Devime
- Laboratoire de Physiologie Cellulaire et Végétale, Centre National de la Recherche Scientifique, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Commissariat à l'Energie Atomique et aux Energies Alternatives, Université Grenoble Alpes; IRIG, CEA-Grenoble, 17 avenue des Martyrs, 38000, Grenoble, France
| | - Pascal Salze
- Jardin du Lautaret, Université Grenoble-Alpes, Centre National de la Recherche Scientifique; 2233 rue de la piscine, Domaine Universitaire, 38610, Gières, France
| | - Lucie Liger
- Jardin du Lautaret, Université Grenoble-Alpes, Centre National de la Recherche Scientifique; 2233 rue de la piscine, Domaine Universitaire, 38610, Gières, France
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire et Végétale, Centre National de la Recherche Scientifique, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Commissariat à l'Energie Atomique et aux Energies Alternatives, Université Grenoble Alpes; IRIG, CEA-Grenoble, 17 avenue des Martyrs, 38000, Grenoble, France
| | - Marie Dumont
- Centre d'Etudes de la Neige, Université Grenoble Alpes, Université de Toulouse, Météo-France, CNRS, CNRM, 38000, Grenoble, France
| | - Stéphane Ravanel
- Laboratoire de Physiologie Cellulaire et Végétale, Centre National de la Recherche Scientifique, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Commissariat à l'Energie Atomique et aux Energies Alternatives, Université Grenoble Alpes; IRIG, CEA-Grenoble, 17 avenue des Martyrs, 38000, Grenoble, France
| | - Alberto Amato
- Laboratoire de Physiologie Cellulaire et Végétale, Centre National de la Recherche Scientifique, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Commissariat à l'Energie Atomique et aux Energies Alternatives, Université Grenoble Alpes; IRIG, CEA-Grenoble, 17 avenue des Martyrs, 38000, Grenoble, France
| | - Jean-Gabriel Valay
- Jardin du Lautaret, Université Grenoble-Alpes, Centre National de la Recherche Scientifique; 2233 rue de la piscine, Domaine Universitaire, 38610, Gières, France
| | - Pierre-Henri Jouneau
- Laboratoire Modélisation et Exploration des Matériaux, Commissariat à l'Energie Atomique et aux Energies Alternatives, Université Grenoble Alpes; IRIG, CEA-Grenoble, 17 avenue des Martyrs, 38000, Grenoble, France
| | - Denis Falconet
- Laboratoire de Physiologie Cellulaire et Végétale, Centre National de la Recherche Scientifique, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Commissariat à l'Energie Atomique et aux Energies Alternatives, Université Grenoble Alpes; IRIG, CEA-Grenoble, 17 avenue des Martyrs, 38000, Grenoble, France
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale, Centre National de la Recherche Scientifique, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Commissariat à l'Energie Atomique et aux Energies Alternatives, Université Grenoble Alpes; IRIG, CEA-Grenoble, 17 avenue des Martyrs, 38000, Grenoble, France.
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3
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Wickramanayake JS, Czymmek KJ. A conventional fixation volume electron microscopy protocol for plants. Methods Cell Biol 2023; 177:83-99. [PMID: 37451777 DOI: 10.1016/bs.mcb.2023.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Volume electron microscopy techniques play an important role in plant research from understanding organelles and unicellular forms to developmental studies, environmental effects and microbial interactions with large plant structures, to name a few. Due to large air voids central vacuole, cell wall and waxy cuticle, many plant tissues pose challenges when trying to achieve high quality morphology, metal staining and adequate conductivity for high-resolution volume EM studies. Here, we applied a robust conventional chemical fixation strategy to address the special challenges of plant samples and suitable for, but not limited to, serial block-face and focused ion beam scanning electron microscopy. The chemistry of this protocol was modified from an approach developed for improved and uniform staining of large brain volumes. Briefly, primary fixation was in paraformaldehyde and glutaraldehyde with malachite green followed by secondary fixation with osmium tetroxide, potassium ferrocyanide, thiocarbohydrazide, osmium tetroxide and finally uranyl acetate and lead aspartate staining. Samples were then dehydrated in acetone with a propylene oxide transition and embedded in a hard formulation Quetol 651 resin. The samples were trimmed and mounted with silver epoxy, metal coated and imaged via serial block-face scanning electron microscopy and focal charge compensation for charge suppression. High-contrast plant tobacco and duckweed leaf cellular structures were readily visible including mitochondria, Golgi, endoplasmic reticulum and nuclear envelope membranes, as well as prominent chloroplast thylakoid membranes and individual lamella in grana stacks. This sample preparation protocol serves as a reliable starting point for routine plant volume electron microscopy.
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Affiliation(s)
- Janithri S Wickramanayake
- Donald Danforth Plant Science Center, Saint Louis, MO, United States; Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center, Saint Louis, MO, United States
| | - Kirk J Czymmek
- Donald Danforth Plant Science Center, Saint Louis, MO, United States; Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center, Saint Louis, MO, United States.
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4
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Montag K, Ivanov R, Bauer P. Role of SEC14-like phosphatidylinositol transfer proteins in membrane identity and dynamics. FRONTIERS IN PLANT SCIENCE 2023; 14:1181031. [PMID: 37255567 PMCID: PMC10225987 DOI: 10.3389/fpls.2023.1181031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/05/2023] [Indexed: 06/01/2023]
Abstract
Membrane identity and dynamic processes, that act at membrane sites, provide important cues for regulating transport, signal transduction and communication across membranes. There are still numerous open questions as to how membrane identity changes and the dynamic processes acting at the surface of membranes are regulated in diverse eukaryotes in particular plants and which roles are being played by protein interaction complexes composed of peripheral and integral membrane proteins. One class of peripheral membrane proteins conserved across eukaryotes comprises the SEC14-like phosphatidylinositol transfer proteins (SEC14L-PITPs). These proteins share a SEC14 domain that contributes to membrane identity and fulfills regulatory functions in membrane trafficking by its ability to sense, bind, transport and exchange lipophilic substances between membranes, such as phosphoinositides and diverse other lipophilic substances. SEC14L-PITPs can occur as single-domain SEC14-only proteins in all investigated organisms or with a modular domain structure as multi-domain proteins in animals and streptophytes (comprising charales and land plants). Here, we present an overview on the functional roles of SEC14L-PITPs, with a special focus on the multi-domain SEC14L-PITPs of the SEC14-nodulin and SEC14-GOLD group (PATELLINs, PATLs in plants). This indicates that SEC14L-PITPs play diverse roles from membrane trafficking to organism fitness in plants. We concentrate on the structure of SEC14L-PITPs, their ability to not only bind phospholipids but also other lipophilic ligands, and their ability to regulate complex cellular responses through interacting with proteins at membrane sites.
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Affiliation(s)
- Karolin Montag
- Institute of Botany, Heinrich Heine University, Düsseldorf, Germany
| | - Rumen Ivanov
- Institute of Botany, Heinrich Heine University, Düsseldorf, Germany
| | - Petra Bauer
- Institute of Botany, Heinrich Heine University, Düsseldorf, Germany
- Center of Excellence on Plant Sciences (CEPLAS), Germany
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5
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Demurtas OC, Nicolia A, Diretto G. Terpenoid Transport in Plants: How Far from the Final Picture? PLANTS (BASEL, SWITZERLAND) 2023; 12:634. [PMID: 36771716 PMCID: PMC9919377 DOI: 10.3390/plants12030634] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
Contrary to the biosynthetic pathways of many terpenoids, which are well characterized and elucidated, their transport inside subcellular compartments and the secretion of reaction intermediates and final products at the short- (cell-to-cell), medium- (tissue-to-tissue), and long-distance (organ-to-organ) levels are still poorly understood, with some limited exceptions. In this review, we aim to describe the state of the art of the transport of several terpene classes that have important physiological and ecological roles or that represent high-value bioactive molecules. Among the tens of thousands of terpenoids identified in the plant kingdom, only less than 20 have been characterized from the point of view of their transport and localization. Most terpenoids are secreted in the apoplast or stored in the vacuoles by the action of ATP-binding cassette (ABC) transporters. However, little information is available regarding the movement of terpenoid biosynthetic intermediates from plastids and the endoplasmic reticulum to the cytosol. Through a description of the transport mechanisms of cytosol- or plastid-synthesized terpenes, we attempt to provide some hypotheses, suggestions, and general schemes about the trafficking of different substrates, intermediates, and final products, which might help develop novel strategies and approaches to allow for the future identification of terpenoid transporters that are still uncharacterized.
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Affiliation(s)
- Olivia Costantina Demurtas
- Biotechnology and Agro-Industry Division, Biotechnology Laboratory, Casaccia Research Center, ENEA—Italian National Agency for New Technologies, Energy and Sustainable Economic Development, 00123 Rome, Italy
| | - Alessandro Nicolia
- Council for Agricultural Research and Economics, Research Centre for Vegetable and Ornamental Crops, via Cavalleggeri 25, 84098 Pontecagnano Faiano, Italy
| | - Gianfranco Diretto
- Biotechnology and Agro-Industry Division, Biotechnology Laboratory, Casaccia Research Center, ENEA—Italian National Agency for New Technologies, Energy and Sustainable Economic Development, 00123 Rome, Italy
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6
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Kim E, Poudyal RS, Lee K, Yu H, Gi E, Kim HU. Chloroplast-localized PITP7 is essential for plant growth and photosynthetic function in Arabidopsis. PHYSIOLOGIA PLANTARUM 2022; 174:e13760. [PMID: 36004734 PMCID: PMC9546280 DOI: 10.1111/ppl.13760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 07/21/2022] [Accepted: 08/02/2022] [Indexed: 06/02/2023]
Abstract
Recent studies of chloroplast-localized Sec14-like protein (CPSFL1, also known as phosphatidylinositol transfer protein 7, PITP7) showed that CPSFL1 is necessary for photoautotropic growth and chloroplast vesicle formation in Arabidopsis (Arabidopsis thaliana). Here, we investigated the functional roles of CPSFL1/PITP7 using two A. thaliana mutants carrying a putative null allele (pitp7-1) and a weak allele (pitp7-2), respectively. PITP7 transcripts were undetectable in pitp7-1 and less abundant in pitp7-2 than in the wild-type (WT). The severity of mutant phenotypes, such as plant developmental abnormalities, levels of plastoquinone-9 (PQ-9) and chlorophylls, photosynthetic protein complexes, and photosynthetic performance, were well related to PITP7 transcript levels. The pitp7-1 mutation was seedling lethal and was associated with significantly lower levels of PQ-9 and major photosynthetic proteins. pitp7-2 plants showed greater susceptibility to high-intensity light stress than the WT, attributable to defects in nonphotochemical quenching and photosynthetic electron transport. PITP7 is specifically bound to phosphatidylinositol phosphates (PIPs) in lipid-binding assays in vitro, and the point mutations R82, H125, E162, or K233 reduced the binding affinity of PITP7 to PIPs. Further, constitutive expression of PITP7H125Q or PITP7E162K in pitp7-1 homozygous plants restored autotrophic growth in soil but without fully complementing the mutant phenotypes. Consistent with a previous study, our results demonstrate that PITP7 is essential for plant development, particularly the accumulation of PQ-9 and photosynthetic complexes. We propose a possible role for PITP7 in membrane trafficking of hydrophobic ligands such as PQ-9 and carotenoids through chloroplast vesicle formation or direct binding involving PIPs.
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Affiliation(s)
- Eun‐Ha Kim
- Department of Agricultural BiotechnologyNational Institute of Agricultural Sciences, Rural Development AdministrationJeonjuRepublic of Korea
| | - Roshan Sharma Poudyal
- Department of Agricultural BiotechnologyNational Institute of Agricultural Sciences, Rural Development AdministrationJeonjuRepublic of Korea
| | - Kyeong‐Ryeol Lee
- Department of Agricultural BiotechnologyNational Institute of Agricultural Sciences, Rural Development AdministrationJeonjuRepublic of Korea
| | - Hami Yu
- Department of Agricultural BiotechnologyNational Institute of Agricultural Sciences, Rural Development AdministrationJeonjuRepublic of Korea
| | - Eunji Gi
- Department of Agricultural BiotechnologyNational Institute of Agricultural Sciences, Rural Development AdministrationJeonjuRepublic of Korea
| | - Hyun Uk Kim
- Department of Bioindustry and Bioresource EngineeringPlant Engineering Research Institute, Sejong UniversitySeoulRepublic of Korea
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Sun T, Rao S, Zhou X, Li L. Plant carotenoids: recent advances and future perspectives. MOLECULAR HORTICULTURE 2022; 2:3. [PMID: 37789426 PMCID: PMC10515021 DOI: 10.1186/s43897-022-00023-2] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 01/03/2022] [Indexed: 10/05/2023]
Abstract
Carotenoids are isoprenoid metabolites synthesized de novo in all photosynthetic organisms. Carotenoids are essential for plants with diverse functions in photosynthesis, photoprotection, pigmentation, phytohormone synthesis, and signaling. They are also critically important for humans as precursors of vitamin A synthesis and as dietary antioxidants. The vital roles of carotenoids to plants and humans have prompted significant progress toward our understanding of carotenoid metabolism and regulation. New regulators and novel roles of carotenoid metabolites are continuously revealed. This review focuses on current status of carotenoid metabolism and highlights recent advances in comprehension of the intrinsic and multi-dimensional regulation of carotenoid accumulation. We also discuss the functional evolution of carotenoids, the agricultural and horticultural application, and some key areas for future research.
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Affiliation(s)
- Tianhu Sun
- Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Sombir Rao
- Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Xuesong Zhou
- Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, 14853, USA
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Li Li
- Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, 14853, USA.
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
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8
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Sun T, Zhou X, Rao S, Liu J, Li L. Protein–protein interaction techniques to investigate post-translational regulation of carotenogenesis. Methods Enzymol 2022; 671:301-325. [DOI: 10.1016/bs.mie.2022.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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9
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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.
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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.
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10
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Wakao S, Shih PM, Guan K, Schackwitz W, Ye J, Patel D, Shih RM, Dent RM, Chovatia M, Sharma A, Martin J, Wei CL, Niyogi KK. Discovery of photosynthesis genes through whole-genome sequencing of acetate-requiring mutants of Chlamydomonas reinhardtii. PLoS Genet 2021; 17:e1009725. [PMID: 34492001 PMCID: PMC8448359 DOI: 10.1371/journal.pgen.1009725] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 09/17/2021] [Accepted: 07/19/2021] [Indexed: 11/18/2022] Open
Abstract
Large-scale mutant libraries have been indispensable for genetic studies, and the development of next-generation genome sequencing technologies has greatly advanced efforts to analyze mutants. In this work, we sequenced the genomes of 660 Chlamydomonas reinhardtii acetate-requiring mutants, part of a larger photosynthesis mutant collection previously generated by insertional mutagenesis with a linearized plasmid. We identified 554 insertion events from 509 mutants by mapping the plasmid insertion sites through paired-end sequences, in which one end aligned to the plasmid and the other to a chromosomal location. Nearly all (96%) of the events were associated with deletions, duplications, or more complex rearrangements of genomic DNA at the sites of plasmid insertion, and together with deletions that were unassociated with a plasmid insertion, 1470 genes were identified to be affected. Functional annotations of these genes were enriched in those related to photosynthesis, signaling, and tetrapyrrole synthesis as would be expected from a library enriched for photosynthesis mutants. Systematic manual analysis of the disrupted genes for each mutant generated a list of 253 higher-confidence candidate photosynthesis genes, and we experimentally validated two genes that are essential for photoautotrophic growth, CrLPA3 and CrPSBP4. The inventory of candidate genes includes 53 genes from a phylogenomically defined set of conserved genes in green algae and plants. Altogether, 70 candidate genes encode proteins with previously characterized functions in photosynthesis in Chlamydomonas, land plants, and/or cyanobacteria; 14 genes encode proteins previously shown to have functions unrelated to photosynthesis. Among the remaining 169 uncharacterized genes, 38 genes encode proteins without any functional annotation, signifying that our results connect a function related to photosynthesis to these previously unknown proteins. This mutant library, with genome sequences that reveal the molecular extent of the chromosomal lesions and resulting higher-confidence candidate genes, will aid in advancing gene discovery and protein functional analysis in photosynthesis.
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Affiliation(s)
- Setsuko Wakao
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Patrick M. Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Katharine Guan
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Wendy Schackwitz
- Joint Genome Institute, Berkeley, California, United States of America
| | - Joshua Ye
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Dhruv Patel
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Robert M. Shih
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Rachel M. Dent
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Mansi Chovatia
- Joint Genome Institute, Berkeley, California, United States of America
| | - Aditi Sharma
- Joint Genome Institute, Berkeley, California, United States of America
| | - Joel Martin
- Joint Genome Institute, Berkeley, California, United States of America
| | - Chia-Lin Wei
- Joint Genome Institute, Berkeley, California, United States of America
| | - Krishna K. Niyogi
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
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Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging. Nat Commun 2021; 12:1049. [PMID: 33594064 PMCID: PMC7886885 DOI: 10.1038/s41467-021-21314-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 01/12/2021] [Indexed: 01/31/2023] Open
Abstract
Eukaryotic phytoplankton have a small global biomass but play major roles in primary production and climate. Despite improved understanding of phytoplankton diversity and evolution, we largely ignore the cellular bases of their environmental plasticity. By comparative 3D morphometric analysis across seven distant phytoplankton taxa, we observe constant volume occupancy by the main organelles and preserved volumetric ratios between plastids and mitochondria. We hypothesise that phytoplankton subcellular topology is modulated by energy-management constraints. Consistent with this, shifting the diatom Phaeodactylum from low to high light enhances photosynthesis and respiration, increases cell-volume occupancy by mitochondria and the plastid CO2-fixing pyrenoid, and boosts plastid-mitochondria contacts. Changes in organelle architectures and interactions also accompany Nannochloropsis acclimation to different trophic lifestyles, along with respiratory and photosynthetic responses. By revealing evolutionarily-conserved topologies of energy-managing organelles, and their role in phytoplankton acclimation, this work deciphers phytoplankton responses at subcellular scales.
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12
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Mohanta TK, Mishra AK, Khan A, Hashem A, Abd_Allah EF, Al-Harrasi A. Gene Loss and Evolution of the Plastome. Genes (Basel) 2020; 11:E1133. [PMID: 32992972 PMCID: PMC7650654 DOI: 10.3390/genes11101133] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/07/2020] [Accepted: 09/14/2020] [Indexed: 12/13/2022] Open
Abstract
Chloroplasts are unique organelles within the plant cells and are responsible for sustaining life forms on the earth due to their ability to conduct photosynthesis. Multiple functional genes within the chloroplast are responsible for a variety of metabolic processes that occur in the chloroplast. Considering its fundamental role in sustaining life on the earth, it is important to identify the level of diversity present in the chloroplast genome, what genes and genomic content have been lost, what genes have been transferred to the nuclear genome, duplication events, and the overall origin and evolution of the chloroplast genome. Our analysis of 2511 chloroplast genomes indicated that the genome size and number of coding DNA sequences (CDS) in the chloroplasts genome of algae are higher relative to other lineages. Approximately 10.31% of the examined species have lost the inverted repeats (IR) in the chloroplast genome that span across all the lineages. Genome-wide analyses revealed the loss of the Rbcl gene in parasitic and heterotrophic plants occurred approximately 56 Ma ago. PsaM, Psb30, ChlB, ChlL, ChlN, and Rpl21 were found to be characteristic signature genes of the chloroplast genome of algae, bryophytes, pteridophytes, and gymnosperms; however, none of these genes were found in the angiosperm or magnoliid lineage which appeared to have lost them approximately 203-156 Ma ago. A variety of chloroplast-encoded genes were lost across different species lineages throughout the evolutionary process. The Rpl20 gene, however, was found to be the most stable and intact gene in the chloroplast genome and was not lost in any of the analyzed species, suggesting that it is a signature gene of the plastome. Our evolutionary analysis indicated that chloroplast genomes evolved from multiple common ancestors ~1293 Ma ago and have undergone vivid recombination events across different taxonomic lineages.
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Affiliation(s)
- Tapan Kumar Mohanta
- Biotech and Omics Laboratory, Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Oman;
| | | | - Adil Khan
- Biotech and Omics Laboratory, Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Oman;
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
- Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, Giza 12511, Egypt
| | - Elsayed Fathi Abd_Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box. 2460, Riyadh 11451, Saudi Arabia;
| | - Ahmed Al-Harrasi
- Natural Product Laboratory, Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa 616, Oman
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