43 results on '"Kohki Yoshimoto"'
Search Results
2. A proposed role for endomembrane trafficking processes in regulating tonoplast content and vacuole dynamics under ammonium stress conditions in Arabidopsis root cells
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Mako Yagyu, Germán Robert, Hernán Ramiro Lascano, Céline Masclaux-Daubresse, Kohki Yoshimoto, Unidad de estudios agropecuarios (UDEA), Instituto Nacional de Tecnología Agropecuaria (INTA), Universidad Nacional de Córdoba [Argentina], Meiji University [Tokyo], Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Fondo para la Investigación Científica y Tecnológica [FONCyT PICT-2017-2863], Ministry of Education, Culture, Sports, Science and Technology, Program for Strategic Research Foundation at Private Universities [S1411023], Institute of Science and Technology, Meiji University [Research Project Grant], Meiji University, Researcher Mobility Grant [MU-RMG 2019-11], Proyecto INTA [2019-PD-E6-I116-001], and Grant-in-Aid for Scientific Research on Innovative Areas, Research in a Proposed Research Area [19H05713]
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0106 biological sciences ,0301 basic medicine ,inorganic chemicals ,microautophagy ,Short Communication ,Arabidopsis ,Plant Science ,Vacuole ,Endocytosis ,Plant Roots ,01 natural sciences ,03 medical and health sciences ,Stress, Physiological ,Ammonium Compounds ,Autophagy ,endocytosis ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Endomembrane system ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Microautophagy ,cell elongation ,endomembrane trafficking ,biology ,vacuole morphology ,Plant physiology ,food and beverages ,biology.organism_classification ,Adaptation, Physiological ,Cell biology ,Ammonium toxicity ,macroautophagy ,030104 developmental biology ,Vacuoles ,Flux (metabolism) ,010606 plant biology & botany - Abstract
Ammonium (NH(4)(+)) stress has multiple effects on plant physiology, therefore, plant responses are complex, and multiple mechanisms are involved in NH(4)(+) sensitivity and tolerance in plants. Root growth inhibition is an important quantitative readout of the effects of NH(4)(+) stress on plant physiology, and cell elongation appear as the principal growth inhibition target. We recently proposed autophagy as a relevant physiological mechanisms underlying NH(4)(+) sensitivity response in Arabidopsis. In a brief overview, the impaired macro-autophagic flux observed under NH(4)(+) stress conditions has a detrimental impact on the cellular energetic balance, and therefore on the energy-demanding plant growth. In contrast to its inhibitory effect on the autophagosomes flux to vacuole, NH(4)(+) toxicity induced a micro-autophagy-like process. Consistent with the reduced membrane flux to the vacuole related to macro-autophagy inhibition and the increased tonoplast degradation due to enhanced micro-autophagy, the vacuoles of the root cells of the NH(4)(+)-stressed plants showed lower tonoplast content and a decreased perimeter/area ratio. As the endosome-to-vacuole trafficking is another important process that contributes to membrane flux toward the vacuole, we evaluated the effects of NH(4)(+) stress on this process. This allows us to propose that autophagy could contribute to vacuole development as well as possible avenues to follow for future studies.
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- 2021
3. Ammonium stress increases microautophagic activity while impairing macroautophagic flux in Arabidopsis roots
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Céline Masclaux-Daubresse, Germán Robert, Kohki Yoshimoto, Takaya Koizumi, Loreto Naya, Mako Yagyu, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Instituto Nacional de Tecnología Agropecuaria (INTA), Department of Life Sciences, School of Agriculture, Meiji University [Tokyo]-Meiji University [Tokyo], and IJPB's Plant Observatory technological platforms INRA Package program, IJPB Saclay Plant Sciences-SPS ANR-17-EUR-0007National Institute of Agronomical Technology (INTA, Argentina) LabEx Saclay Plant Sciences-SPS ANR-10-LABX-0040-SPSFondo para la Investigacion Cientifica y Tecnologica FONCyT PICT-2017-2863Proyecto Especifico INTA PNCYO112703326484INTA 2019-PD-E6-I116-001Institute of Science and Technology, Meiji University Meiji University, Researcher Mobility Grant MU-RMG 2019-11Ministry of Education, Culture, Sports, Science and Technology, Program for Strategic Research Foundation at Private Universities S1411023INRA Package program (2012-2015) ANR-12-ADAPT-001-01-AUTOADAPT 19H05713
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0106 biological sciences ,0301 basic medicine ,inorganic chemicals ,microautophagy ,Arabidopsis ,CCZ1‐ ,Plant Science ,Vacuole ,Plant Roots ,01 natural sciences ,03 medical and health sciences ,chemistry.chemical_compound ,Stress, Physiological ,Ammonium Compounds ,Genetics ,vacuole fusion ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Ammonium ,Microautophagy ,NH4 (+) toxicity ,biology ,Vesicle ,Autophagy ,vacuole morphology ,Autophagosomes ,food and beverages ,Cell Biology ,biology.organism_classification ,to‐ ,macroautophagy ,030104 developmental biology ,chemistry ,Cytoplasm ,Biophysics ,MON1 ,Flux (metabolism) ,autophagosome‐ ,010606 plant biology & botany - Abstract
International audience; Plant responses to NH4 (+) stress are complex, and multiple mechanisms underlying NH4 (+) sensitivity and tolerance in plants may be involved. Here, we demonstrate that macro- and microautophagic activities are oppositely affected in plants grown under NH4 (+) toxicity conditions. When grown under NH4 (+) stress conditions, macroautophagic activity was impaired in roots. Root cells accumulated autophagosomes in the cytoplasm, but showed less autophagic flux, indicating that late steps of the macroautophagy process are affected under NH4 (+) stress conditions. Under this scenario, we also found that the CCZ1-MON1 complex, a critical factor for vacuole delivery pathways, functions in the late step of the macroautophagic pathway in Arabidopsis. In contrast, an accumulation of tonoplast-derived vesicles was observed in vacuolar lumens of root cells of NH4 (+)-stressed plants, suggesting the induction of a microautophagy-like process. In this sense, some SYP22-, but mainly VAMP711-positive vesicles were observed inside vacuole in roots of NH4 (+)-stressed plants. Consistent with the increased tonoplast degradation and the reduced membrane flow to the vacuole due to the impaired macroautophagic flux, the vacuoles of root cells of NH4 (+)-stressed plants showed a simplified structure and lower tonoplast content. Taken together, this study presents evidence that postulates late steps of the macroautophagic process as a relevant physiological mechanism underlying the NH4 (+) sensitivity response in Arabidopsis, and additionally provides insights into the molecular tools for studying microautophagy in plants.
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- 2021
4. Optimal Distribution of Iron to Sink Organs via Autophagy Is Important for Tolerance to Excess Zinc in Arabidopsis
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Kohki Yoshimoto, Daiki Shinozaki, and Keitaro Tanoi
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Chlorophyll ,Physiology ,Iron ,ATG5 ,Arabidopsis ,chemistry.chemical_element ,Plant Science ,Zinc ,Gene Expression Regulation, Plant ,Stress, Physiological ,Autophagy ,Arabidopsis thaliana ,Chlorosis ,biology ,Chemistry ,food and beverages ,Cell Biology ,General Medicine ,Iron Deficiencies ,Meristem ,biology.organism_classification ,Cell biology ,Plant Leaves ,Sink (computing) ,Reactive Oxygen Species - Abstract
Zinc (Zn) is nutritionally an essential metal element, but excess Zn in the environment is toxic to plants. Autophagy is a major pathway responsible for intracellular degradation. Here, we demonstrate the important role of autophagy in adaptation to excess Zn stress. We found that autophagy-defective Arabidopsis thaliana (atg2 and atg5) exhibited marked excess Zn-induced chlorosis and growth defects relative to wild-type (WT). Imaging and biochemical analyses revealed that autophagic activity was elevated under excess Zn. Interestingly, the excess Zn symptoms of atg5 were alleviated by supplementation of high levels of iron (Fe) to the media. Under excess Zn, in atg5, Fe starvation was especially severe in juvenile true leaves. Consistent with this, accumulation levels of Fe3+ near the shoot apical meristem remarkably reduced in atg5. Furthermore, excision of cotyledons induced severe excess Zn symptoms in WT, similar to those observed in atg5. Our data suggest that Fe3+ supplied from source leaves (cotyledons) via autophagy is distributed to sink leaves (true leaves) to promote healthy growth under excess Zn, revealing a new dimension, the importance of heavy-metal stress responses by the intracellular recycling.
- Published
- 2020
5. Thaumatin-like proteins and a cysteine protease inhibitor secreted by the pine wood nematode Bursaphelenchus xylophilus induce cell death in Nicotiana benthamiana
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Ryoji Shinya, Haru Kirino, and Kohki Yoshimoto
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0106 biological sciences ,0301 basic medicine ,Tylenchida ,Science ,Nicotiana benthamiana ,Bursaphelenchus xylophilus ,Cysteine Proteinase Inhibitors ,Proteomics ,01 natural sciences ,Microbiology ,Host-Parasite Interactions ,03 medical and health sciences ,Tobacco ,Animals ,Pathogen ,Wilt disease ,Nicotiana ,Plant Diseases ,Multidisciplinary ,biology ,Cell Death ,fungi ,food and beverages ,Helminth Proteins ,biology.organism_classification ,Cysteine protease ,030104 developmental biology ,Thaumatin ,Medicine ,010606 plant biology & botany ,Research Article - Abstract
Pine wilt disease (PWD) is an infectious disease of pines that typically kills affected trees. The causal pathogen of PWD is the pine wood nematode (PWN), Bursaphelenchus xylophilus. Understanding of the disease has advanced in recent years through the use of a highly sensitive proteomics procedure and whole genome sequence analysis; in combination, these approaches have enabled identification of proteins secreted by PWNs. However, the roles of these proteins during the onset of parasitism have not yet been elucidated. In this study, we used a leaf-disk assay based on transient overexpression in Nicotiana benthamiana to allow functional screening of 10 candidate pathogenic proteins secreted by PWNs. These proteins were selected based on previous secretome and RNA-seq analyses. We found that five molecules induced significant cell death in tobacco plants relative to a GFP-only control. Three of these proteins (Bx-TH1, Bx-TH2, and Bx-CPI) may have a role in molecular mimicry and likely make important contributions to inducing hypersensitive responses in host plants.
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- 2020
6. Editorial: Organelle Autophagy in Plant Development
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Henri Batoko, Masanori Izumi, and Kohki Yoshimoto
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selective autophagy ,autophagy ,Carbon metabolism ,carbon metabolism ,Autophagy ,Lipid metabolism ,Plant Science ,Biology ,lcsh:Plant culture ,Cell biology ,Selective autophagy ,Plant development ,organelles ,Organelle ,lcsh:SB1-1110 ,plant development ,autophagy receptors - Published
- 2020
7. Importance of non-systemic leaf autophagy for suppression of zinc starvation induced-chlorosis
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Kohki Yoshimoto, Michitaka Notaguchi, and Daiki Shinozaki
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0106 biological sciences ,0301 basic medicine ,Starvation ,Chlorosis ,Short Communication ,Autophagy ,chemistry.chemical_element ,Intracellular zinc ,Plant Science ,Zinc ,Biology ,01 natural sciences ,Cell biology ,Plant Leaves ,03 medical and health sciences ,030104 developmental biology ,chemistry ,medicine ,medicine.symptom ,Rootstock ,010606 plant biology & botany - Abstract
Autophagy, which is one of the self-degradation systems, promotes intracellular zinc (Zn) recycling under Zn deficiency (−Zn) in plants. Therefore, autophagy defective plants show severe chlorosis under −Zn. Root is the plant organ which directly exposed to Zn deficient environment, however, in our recent study, −Zn symptom was prominently observed in leaves as chlorosis. Here, we conducted micrografting to determine which organ’s autophagic activities are important to suppress the −Zn induced chlorosis. Grafted plants that have autophagic activities only in roots or leaves were grown under −Zn and then compared chlorotic phenotypes among them. As a result, regardless of the autophagic activities in rootstocks, −Zn induced-chlorosis in leaves was occurred only when autophagy in scion was defective. This data indicates that Zn resupplied by autophagic degradation in root cells could not contribute to suppress the chlorosis in leaves. Thus, autophagy in the aerial part is critical for controlling −Zn induced-chlorosis in leaves. Taken together, along with our recently reported data, we conclude that the mechanism of Zn resupply by autophagic degradation is not systemic throughout the plant but rather a local system.
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- 2020
8. Autophagy Increases Zinc Bioavailability to Avoid Light-Mediated Reactive Oxygen Species Production under Zinc Deficiency
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Kohki Yoshimoto, Ekaterina A. Merkulova, Céline Masclaux-Daubresse, Yuri Kanno, Tetsuro Horie, Loreto Naya, Yoshinori Ohsumi, Mitsunori Seo, Daiki Shinozaki, Department of Life Science, School of Agriculture, Meiji University [Tokyo]-Meiji University [Tokyo], Life Science Program, Graduate School of Agriculture, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Research Center for Odontology, School of Life Dentistry at Tokyo, The Nippon Dental University-The Nippon Dental University, Research Unit for Cell Biology, Institute of Innovative Research, Tokyo Institute of Technology [Tokyo] (TITECH)-Tokyo Institute of Technology [Tokyo] (TITECH), RIKEN Center for Sustainable Resource Science [Yokohama] (RIKEN CSRS), and RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN)
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0106 biological sciences ,Chloroplasts ,Physiology ,[SDV]Life Sciences [q-bio] ,Mutant ,Arabidopsis ,Plant Science ,01 natural sciences ,chemistry.chemical_compound ,Gene Expression Regulation, Plant ,Zinc deficiency (plant disorder) ,Genetics ,Autophagy ,Arabidopsis thaliana ,Research Articles ,2. Zero hunger ,chemistry.chemical_classification ,Reactive oxygen species ,biology ,Chemistry ,Superoxide ,Arabidopsis Proteins ,biology.organism_classification ,Cell biology ,Chloroplast ,Zinc ,Reactive Oxygen Species ,010606 plant biology & botany - Abstract
Zinc (Zn) is an essential micronutrient for plant growth. Accordingly, Zn deficiency (−Zn) in agricultural fields is a serious problem, especially in developing regions. Autophagy, a major intracellular degradation system in eukaryotes, plays important roles in nutrient recycling under nitrogen and carbon starvation. However, the relationship between autophagy and deficiencies of other essential elements remains poorly understood, especially in plants. In this study, we focused on Zn due to the property that within cells most Zn is tightly bound to proteins, which can be targets of autophagy. We found that autophagy plays a critical role during −Zn in Arabidopsis (Arabidopsis thaliana). Autophagy-defective plants (atg mutants) failed to grow and developed accelerated chlorosis under −Zn. As expected, −Zn induced autophagy in wild-type plants, whereas in atg mutants, various organelle proteins accumulated to high levels. Additionally, the amount of free Zn(2+) was lower in atg mutants than in control plants. Interestingly, −Zn symptoms in atg mutants recovered under low-light, iron-limited conditions. The levels of hydroxyl radicals in chloroplasts were elevated, and the levels of superoxide were reduced in −Zn atg mutants. These results imply that the photosynthesis-mediated Fenton-like reaction, which is responsible for the chlorotic symptom of −Zn, is accelerated in atg mutants. Together, our data indicate that autophagic degradation plays important functions in maintaining Zn pools to increase Zn bioavailability and maintain reactive oxygen species homeostasis under −Zn in plants.
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- 2020
9. Autophagy and Nutrients Management in Plants
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Fabien Chardon, Mathieu Pottier, Michèle Reisdorf-Cren, Daiki Shinozaki, Sébastien Thomine, Kohki Yoshimoto, Céline Masclaux-Daubresse, Marien Havé, Jie Luo, Anne Marmagne, and Qinwu Chen
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0106 biological sciences ,0301 basic medicine ,Nutrient cycle ,leaf senescence ,Plant Development ,Review ,Biology ,01 natural sciences ,nitrogen use efficiency ,03 medical and health sciences ,iron ,Nutrient ,Stress, Physiological ,Autophagy ,Plant Proteins ,2. Zero hunger ,plant proteases ,business.industry ,zinc ,fungi ,food and beverages ,nitrogen remobilization ,Nutrients ,General Medicine ,Plant engineering ,Plants ,15. Life on land ,Biotechnology ,030104 developmental biology ,Metabolic Engineering ,Seeds ,business ,010606 plant biology & botany - Abstract
Nutrient recycling and mobilization from organ to organ all along the plant lifespan is essential for plant survival under changing environments. Nutrient remobilization to the seeds is also essential for good seed production. In this review, we summarize the recent advances made to understand how plants manage nutrient remobilization from senescing organs to sink tissues and what is the contribution of autophagy in this process. Plant engineering manipulating autophagy for better yield and plant tolerance to stresses will be presented.
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- 2019
10. Unveiling the molecular mechanisms of plant autophagy – from autophagosomes to vacuoles in plants
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Kohki Yoshimoto and Yoshinori Ohsumi
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0301 basic medicine ,biology ,Physiology ,Saccharomyces cerevisiae ,Autophagy ,Autophagosomes ,food and beverages ,Cell Biology ,Plant Science ,General Medicine ,Vacuole ,biology.organism_classification ,Phenotype ,Yeast ,Cell biology ,03 medical and health sciences ,030104 developmental biology ,Plant Cells ,Vacuoles ,Identification (biology) ,Gene ,Intracellular ,Plant Proteins - Abstract
Autophagy is an evolutionarily conserved intracellular vacuolar process. Since Christian de Duve first coined the term 'autophagy' in 1963, it had not been well understood at the molecular level until much later, due to limitations in biochemical approaches and/or morphological approaches posed by electron microscopy. An important milestone was achieved with the isolation and identification of autophagy-related (ATG) genes by genetic screening using yeast Saccharomyces cerevisiae. ATG genes are well conserved in most eukaryotic organisms, which allowed the subsequent isolation of ATG gene-knockouts in plants. From the phenotypic analyses of the autophagy-defective plants, the physiological roles of autophagy have been predicted. However, in some cases, all the phenotypes cannot be simply explained by defects in autophagy. Therefore, in order to fully understand the physiological implications of plant autophagy, it is quite important to elucidate the molecular mechanisms involved in each process in macro-/micro-autophagy. Although, until recently, our understanding of the molecular mechanisms of plant autophagy was lagging compared to similar research in yeast and animals, current studies have made many great advances in the plant research field. In this review, we discuss current knowledge of the molecular mechanisms of plant autophagy, from autophagy-induction/autophagosome-formation to vacuolar degradation, comparing these to processes in yeast and mammals. We also review aspects of plant autophagy research that require further investigation in the future.
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- 2018
11. Autophagy controls resource allocation and protein storage accumulation in Arabidopsis seeds
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Gwendal Cueff, Fabien Chardon, Kohki Yoshimoto, Julien Di Berardino, Michèle Reisdorf-Cren, Anne Marmagne, Céline Masclaux-Daubresse, Adeline Berger, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Centre National de la Recherche Scientifique (CNRS), Université Paris Saclay (COmUE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), ANR program [ANR-12-ADAPT-0010-0], Ministere de l'Enseignement Superieur et de la Recherche, and the LabEx Saclay Plant Sciences-SPS [ANR-10-LABX-0040-SPS]
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0106 biological sciences ,0301 basic medicine ,grain protein content ,Physiology ,[SDV]Life Sciences [q-bio] ,ATG5 ,Mutant ,Arabidopsis ,Plant Science ,01 natural sciences ,12S globulin ,03 medical and health sciences ,2S albumin ,Gene Expression Regulation, Plant ,atg5 ,[SDV.IDA]Life Sciences [q-bio]/Food engineering ,Autophagy ,Storage protein ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,[SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering ,seed filling ,2. Zero hunger ,chemistry.chemical_classification ,biology ,Arabidopsis Proteins ,food and beverages ,Embryo ,biology.organism_classification ,Research Papers ,Cell biology ,030104 developmental biology ,chemistry ,Seeds ,Phloem ,seed abortion ,Silique ,010606 plant biology & botany - Abstract
Autophagy takes place in seeds, as evidenced by detection of autophagosomes and high expression of ATG genes in Arabidopsis, and the seeds of the atg5 mutant exhibit early browning as well as low and early accumulation of 12S globulin., Autophagy is essential for nutrient recycling and plays a fundamental role in seed production and grain filling in plants. Autophagy participates in nitrogen remobilization at the whole-plant level, and the seeds of autophagy mutants present abnormal C and N contents relative to wild-type (WT) plants. It is well known that autophagy (ATG) genes are induced in leaves during senescence; however, expression of such genes in seeds has not yet been reported. In this study we show that most of the ATG genes are induced during seed maturation in Arabidopsis siliques. Promoter–ATG8f::UIDA and promoter–ATG8f::GFP fusions showed the strong expression of ATG8f in the phloem companion cells of pericarps and the funiculus, and in the embryo. Expression was especially strong at the late stages of development. The presence of many GFP-ATG8 pre-autophagosomal structures and autophagosomes confirmed the presence of autophagic activity in WT seed embryos. Seeds of atg5 and WT plants grown under low- or high-nitrate conditions were analysed. Nitrate-independent phenotypes were found with higher seed abortion in atg5 and early browing, higher total protein concentrations in the viable seeds of this mutant as compared to the WT. The higher total protein accumulation in atg5 viable seeds was significant from early developmental stages onwards. In addition, relatively low and early accumulation of 12S globulins were found in atg5 seeds. These features led us to the conclusion that atg5 seed development is accelerated and that the protein storage deposition pathway is somehow abnormal or incomplete.
- Published
- 2018
12. Autophagy, plant senescence, and nutrient recycling
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Liliana Avila-Ospina, Céline Masclaux-Daubresse, Kohki Yoshimoto, Michaël Moison, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, CETIOM (Centre Technique des Oleagineux), Biologie et Amelioration des Plantes, INRA, INRA Package programme, European Project: 264394, Avila-Ospina, Liliana, and Moison, Michaël
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0106 biological sciences ,Senescence ,proteolysis ,Chloroplasts ,Nitrogen ,Physiology ,[SDV]Life Sciences [q-bio] ,Proteolysis ,media_common.quotation_subject ,Cell ,Flowers ,Plant Science ,Biology ,proteolyse ,01 natural sciences ,03 medical and health sciences ,Autophagy ,medicine ,vesicular trafficking ,Organism ,030304 developmental biology ,media_common ,Plant senescence ,Nitrogen remobilization ,Rubisco containing bodies ,plant cell death ,0303 health sciences ,medicine.diagnostic_test ,Longevity ,Plants ,Cell biology ,Plant Leaves ,medicine.anatomical_structure ,Adaptation ,010606 plant biology & botany - Abstract
Large numbers of publications have appeared over the last few years, dealing with the molecular details of the regulation and process of the autophagy machinery in animals, plants, and unicellular eukaryotic organisms. This strong interest is caused by the fact that the autophagic process is involved in the adaptation of organisms to their environment and to stressful conditions, thereby contributing to cell and organism survival and longevity. In plants, as in other eukaryotes, autophagy is associated with longevity as mutants display early and strong leaf senescence symptoms, however, the exact role of autophagy as a pro-survival or pro-death process is unclear. Recently, evidence that autophagy participates in nitrogen remobilization has been provided, but the duality of the role of autophagy in leaf longevity and/or nutrient recycling through cell component catabolism remains. This review aims to give an overview of leaf senescence-associated processes from the physiological point of view and to discuss relationships between nutrient recycling, proteolysis, and autophagy. The dual role of autophagy as a pro-survival or pro-death process is discussed.
- Published
- 2014
13. Autophagy machinery controls nitrogen remobilization at the whole‐plant level under both limiting and ample nitrate conditions in Arabidopsis
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Céline Masclaux-Daubresse, Fabienne Soulay, Anne Guiboileau, Marie-Paule Bataillé, Jean-Christophe Avice, Kohki Yoshimoto, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Ecophysiologie Végétale, Agronomie et Nutritions (EVA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Recherche Agronomique (INRA), SAKURA [21124QA], French Ministere des Affaires Etrangeres et Europeennes, Japan Society for the Promotion of Science, Institut Jean-Pierre Bourgin ( IJPB ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Ecophysiologie Végétale, Agronomie et Nutritions ( EVA ), Université de Caen Normandie ( UNICAEN ), and Normandie Université ( NU ) -Normandie Université ( NU ) -Institut National de la Recherche Agronomique ( INRA )
- Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences ,0106 biological sciences ,Physiology ,Mutant ,Arabidopsis ,NATURAL VARIATION ,Plant Science ,Vacuole ,01 natural sciences ,Autophagy-Related Protein 5 ,chemistry.chemical_compound ,Nitrate ,CHLOROPLASTS ,Biomass ,[ SDV.SA ] Life Sciences [q-bio]/Agricultural sciences ,harvest index (HI) ,Cellular Senescence ,2. Zero hunger ,0303 health sciences ,biology ,15N ,food and beverages ,nitrogen remobilization ,Plants, Genetically Modified ,Chloroplast ,Phenotype ,Seeds ,RNA Interference ,RIBULOSE-1 ,autophagy ,Nitrogen ,PROTEINS ,Ribulose-Bisphosphate Carboxylase ,03 medical and health sciences ,Botany ,LEAVES ,LEAF SENESCENCE ,Nitrogen cycle ,030304 developmental biology ,Nitrates ,Nitrogen Isotopes ,THALIANA ,Arabidopsis Proteins ,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE ,Autophagy ,RuBisCO ,DEGRADATION ,yield ,biology.organism_classification ,RUBISCO ,Carbon ,Phosphoric Monoester Hydrolases ,Plant Leaves ,chemistry ,Mutation ,Vacuoles ,biology.protein ,nitrogen use efficiency (NUE) ,STARVATION ,010606 plant biology & botany - Abstract
• Processes allowing the recycling of organic nitrogen and export to young leaves and seeds are important determinants of plant yield, especially when plants are nitrate-limited. Because autophagy is induced during leaf ageing and in response to nitrogen starvation, its role in nitrogen remobilization was suspected. It was recently shown that autophagy participates in the trafficking of Rubisco-containing bodies to the vacuole. • To investigate the role of autophagy in nitrogen remobilization, several autophagy-defective (atg) Arabidopsis mutants were grown under low and high nitrate supplies and labeled with at the vegetative stage in order to determine (15) N partitioning in seeds at harvest. Because atg mutants displayed earlier and more rapid leaf senescence than wild type, we investigated whether their defects in nitrogen remobilization were related to premature leaf cell death by studying the stay-green atg5.sid2 and atg5.NahG mutants. • Results showed that nitrogen remobilization efficiency was significantly lower in all the atg mutants irrespective of biomass defects, harvest index reduction, leaf senescence phenotypes and nitrogen conditions. • We conclude that autophagy core machinery is needed for nitrogen remobilization and seed filling.
- Published
- 2012
14. Autophagy Negatively Regulates Cell Death by Controlling NPR1-Dependent Salicylic Acid Signaling during Senescence and the Innate Immune Response inArabidopsis
- Author
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Yoshinori Ohsumi, Ken Shirasu, Kohki Yoshimoto, Yuji Kamiya, Chiara Consonni, Yusuke Jikumaru, Miyako Kusano, and Ralph Panstruga
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Senescence ,Programmed cell death ,Arabidopsis ,Cyclopentanes ,Plant Science ,Autophagy-Related Protein 5 ,chemistry.chemical_compound ,Plant Growth Regulators ,Gene Expression Regulation, Plant ,Autophagy ,Oxylipins ,Research Articles ,Innate immune system ,biology ,Arabidopsis Proteins ,Jasmonic acid ,Hydrogen Peroxide ,Cell Biology ,Ethylenes ,biology.organism_classification ,Phosphoric Monoester Hydrolases ,Cell biology ,chemistry ,RNA, Plant ,Signal transduction ,Salicylic Acid ,Intracellular ,Signal Transduction - Abstract
Autophagy is an evolutionarily conserved intracellular process for vacuolar degradation of cytoplasmic components. In higher plants, autophagy defects result in early senescence and excessive immunity-related programmed cell death (PCD) irrespective of nutrient conditions; however, the mechanisms by which cells die in the absence of autophagy have been unclear. Here, we demonstrate a conserved requirement for salicylic acid (SA) signaling for these phenomena in autophagy-defective mutants (atg mutants). The atg mutant phenotypes of accelerated PCD in senescence and immunity are SA signaling dependent but do not require intact jasmonic acid or ethylene signaling pathways. Application of an SA agonist induces the senescence/cell death phenotype in SA-deficient atg mutants but not in atg npr1 plants, suggesting that the cell death phenotypes in the atg mutants are dependent on the SA signal transducer NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1. We also show that autophagy is induced by the SA agonist. These findings imply that plant autophagy operates a novel negative feedback loop modulating SA signaling to negatively regulate senescence and immunity-related PCD.
- Published
- 2009
15. OsATG10b, an autophagosome component, is needed for cell survival against oxidative stresses in rice
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Jun-Hye Shin, Jong-Seong Jeon, Gynheung An, Yoshinori Ohsumi, and Kohki Yoshimoto
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DNA, Bacterial ,Paraquat ,Autophagosome ,DNA, Complementary ,Cell Survival ,Molecular Sequence Data ,Mutant ,GUS reporter system ,Sodium Chloride ,Biology ,Genes, Plant ,Gene Expression Regulation, Plant ,Phagosomes ,Gene expression ,Organelle ,Autophagy ,Amino Acid Sequence ,Molecular Biology ,Gene ,Vascular tissue ,Glucuronidase ,Plant Proteins ,Gene Expression Profiling ,Oryza ,Cell Biology ,General Medicine ,Mutagenesis, Insertional ,Oxidative Stress ,Protein Transport ,Biochemistry ,Mutation ,Subcellular Fractions - Abstract
Autophagy degrades toxic materials and old organelles, and recycles nutrients in eukaryotic cells. Whereas the studies on autophagy have been reported in other eukaryotic cells, its functioning in plants has not been well elucidated. We analyzed the roles of OsATG10 genes, which are autophagy-related. Two rice ATG10 genes - OsATG10a and OsATG10b - share significant sequence homology (about 75%), and were ubiquitously expressed in all organs examined here. GUS assay indicated that OsATG10b was highly expressed in the mesophyll cells and vascular tissue of younger leaves, but its level of expression decreased in older leaves. We identified T-DNA insertional mutants in that gene. Those osatg10b mutants were sensitive to treatments with high salt and methyl viologen (MV). Monodansylcadaverine-staining experiments showed that the number of autophagosomes was significantly decreased in the mutants compared with the WT. Furthermore, the amount of oxidized proteins increased in MV-treated mutant seedlings. These results demonstrate that OsATG10b plays an important role in the survival of rice cells against oxidative stresses.
- Published
- 2009
16. Mobilization of Rubisco and Stroma-Localized Fluorescent Proteins of Chloroplasts to the Vacuole by anATGGene-Dependent Autophagic Process
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Hiroyuki Ishida, Amane Makino, Yoshinori Ohsumi, Kohki Yoshimoto, Yuichi Yano, Maureen R. Hanson, Tadahiko Mae, Daniel Reisen, and Masanori Izumi
- Subjects
biology ,Physiology ,Immunoelectron microscopy ,Vacuolar lumen ,fungi ,RuBisCO ,food and beverages ,Plant Science ,Vacuole ,Green fluorescent protein ,Chloroplast ,Biochemistry ,Plant protein ,Genetics ,biology.protein ,Chloroplast Proteins - Abstract
During senescence and at times of stress, plants can mobilize needed nitrogen from chloroplasts in leaves to other organs. Much of the total leaf nitrogen is allocated to the most abundant plant protein, Rubisco. While bulk degradation of the cytosol and organelles in plants occurs by autophagy, the role of autophagy in the degradation of chloroplast proteins is still unclear. We have visualized the fate of Rubisco, stroma-targeted green fluorescent protein (GFP) and DsRed, and GFP-labeled Rubisco in order to investigate the involvement of autophagy in the mobilization of stromal proteins to the vacuole. Using immunoelectron microscopy, we previously demonstrated that Rubisco is released from the chloroplast into Rubisco-containing bodies (RCBs) in naturally senescent leaves. When leaves of transgenic Arabidopsis (Arabidopsis thaliana) plants expressing stroma-targeted fluorescent proteins were incubated with concanamycin A to inhibit vacuolar H+-ATPase activity, spherical bodies exhibiting GFP or DsRed fluorescence without chlorophyll fluorescence were observed in the vacuolar lumen. Double-labeled immunoelectron microscopy with anti-Rubisco and anti-GFP antibodies confirmed that the fluorescent bodies correspond to RCBs. RCBs could also be visualized using GFP-labeled Rubisco directly. RCBs were not observed in leaves of a T-DNA insertion mutant in ATG5, one of the essential genes for autophagy. Stroma-targeted DsRed and GFP-ATG8 fusion proteins were observed together in autophagic bodies in the vacuole. We conclude that Rubisco and stroma-targeted fluorescent proteins can be mobilized to the vacuole through an ATG gene-dependent autophagic process without prior chloroplast destruction.
- Published
- 2008
17. An Arabidopsis Homolog of YeastATG6/VPS30Is Essential for Pollen Germination
- Author
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Yuki Fujiki, Yoshinori Ohsumi, and Kohki Yoshimoto
- Subjects
Genetics ,biology ,Physiology ,Autophagy ,Mutant ,Saccharomyces cerevisiae ,Plant Science ,biology.organism_classification ,Carboxypeptidase ,Yeast ,Transport protein ,Cell biology ,Arabidopsis ,biology.protein ,Arabidopsis thaliana - Abstract
Yeast (Saccharomyces cerevisiae) Atg6/Vps30 is required for autophagy and the sorting of vacuolar hydrolases, such as carboxypeptidase Y. In higher eukaryotes, however, roles for ATG6/VPS30 homologs in vesicle sorting have remained obscure. Here, we show that AtATG6, an Arabidopsis (Arabidopsis thaliana) homolog of yeast ATG6/VPS30, restored both autophagy and vacuolar sorting of carboxypeptidase Y in a yeast atg6/vps30 mutant. In Arabidopsis cells, green fluorescent protein-AtAtg6 protein localized to punctate structures and colocalized with AtAtg8, a marker protein of the preautophagosomal structure. Disruption of AtATG6 by T-DNA insertion resulted in male sterility that was confirmed by reciprocal crossing experiments. Microscopic analyses of AtATG6 heterozygous plants (AtATG6/atatg6) crossed with the quartet mutant revealed that AtATG6-deficient pollen developed normally, but did not germinate. Because other atatg mutants are fertile, AtAtg6 likely mediates pollen germination in a manner independent of autophagy. We propose that Arabidopsis Atg6/Vps30 functions not only in autophagy, but also plays a pivotal role in pollen germination.
- Published
- 2007
18. Autophagy in development and stress responses of plants
- Author
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Yoshinori Ohsumi, Francis Marty, Yuji Moriyasu, Kohki Yoshimoto, Diane C. Bassham, Laura J. Olsen, and Marianne M. Laporte
- Subjects
Autophagosome ,Senescence ,Programmed cell death ,biology ,Arabidopsis Proteins ,Autophagy ,Arabidopsis ,food and beverages ,Cell Biology ,Vacuole ,biology.organism_classification ,Genes, Plant ,Cell biology ,Biochemistry ,Molecular Biology ,Gene ,Function (biology) - Abstract
The uptake and degradation of cytoplasmic material by vacuolar autophagy in plants has been studied extensively by electron microscopy and shown to be involved in developmental processes such as vacuole formation, deposition of seed storage proteins and senescence, and in the response of plants to nutrient starvation and to pathogens. The isolation of genes required for autophagy in yeast has allowed the identification of many of the corresponding Arabidopsis genes based on sequence similarity. Knockout mutations in some of these Arabidopsis genes have revealed physiological roles for autophagy in nutrient recycling during nitrogen deficiency and in senescence. Recently, markers for monitoring autophagy in whole plants have been developed, opening the way for future studies to decipher the mechanisms and pathways of autophagy, and the function of these pathways in plant development and stress responses.
- Published
- 2005
19. The Crystal Structure of Plant ATG12 and its Biological Implication in Autophagy
- Author
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Kohki Yoshimoto, Yoshinori Ohsumi, Yuko Fujioka, Fuyuhiko Inagaki, and Nobuo Suzuki
- Subjects
Models, Molecular ,Protein Folding ,Arabidopsis Proteins ,Molecular Sequence Data ,ATG5 ,Autophagy ,Arabidopsis ,Cell Biology ,Crystal structure ,Biology ,Conjugated system ,Crystallography, X-Ray ,Cell biology ,ATG12 ,Biochemistry ,Plant protein ,Amino Acid Sequence ,Hydrophobic and Hydrophilic Interactions ,Molecular Biology ,Conjugate - Abstract
Atg12 is a post-translational modifier that is activated and conjugated to its single target, Atg5, by a ubiquitin-like conjugation system. The Atg12-Atg5 conjugate is essential for autophagy, the bulk degradation process of cytoplasmic components by the vacuolar/lysosomal system. Here, we demonstrate that the Atg12 conjugation system exists in Arabidopsis and is essential for plant autophagy as well as in yeast and mammals. We also report the crystal structure of Arabidopsis thaliana (At) ATG12 at 1.8 A resolution. Despite no obvious sequence homology with ubiquitin, the structure of AtATG12 shows a ubiquitin fold strikingly similar to those of mammalian homologs of Atg8, the other ubiquitin-like modifier essential for autophagy, which is conjugated to phosphatidylethanolamine. Two types of hydrophobic patches are present on the surface of AtATG12: one is conserved in both Atg12 and Atg8 orthologs, while the other is unique to Atg12 orthologs. Considering that they share Atg7 as an E1-like enzyme, we suggest that the first hydrophobic patch is responsible for the conjugation reaction, while the latter is involved in Atg12-specific functions.
- Published
- 2005
20. Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy
- Author
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Shusei Sato, Kohki Yoshimoto, Satoshi Tabata, Yoshinori Ohsumi, Takeshi Noda, Hideki Hanaoka, and Tomohiko Kato
- Subjects
DNA, Bacterial ,Vacuolar Proton-Translocating ATPases ,Nitrogen ,Recombinant Fusion Proteins ,ATG8 ,Transgene ,Arabidopsis ,Plant Science ,Vacuole ,Plant Roots ,Microscopy, Electron, Transmission ,Gene Expression Regulation, Plant ,Autophagy ,Arabidopsis thaliana ,Enzyme Inhibitors ,Gene ,Research Articles ,biology ,Arabidopsis Proteins ,Ubiquitin ,Genetic Complementation Test ,Gene Expression Regulation, Developmental ,Cell Biology ,Plants, Genetically Modified ,biology.organism_classification ,Cell biology ,Biochemistry ,Cytoplasm ,Mutation ,Vacuoles ,Microtubule-Associated Proteins - Abstract
Autophagy is an intracellular process for vacuolar degradation of cytoplasmic components. Thus far, plant autophagy has been studied primarily using morphological analyses. A recent genome-wide search revealed significant conservation among autophagy genes ( ATG s) in yeast and plants. It has not been proved, however, that Arabidopsis thaliana ATG genes are required for plant autophagy. To evaluate this requirement, we examined the ubiquitination-like Atg8 lipidation system, whose component genes are all found in the Arabidopsis genome. In Arabidopsis, all nine ATG8 genes and two ATG4 genes were expressed ubiquitously and were induced further by nitrogen starvation. To establish a system monitoring autophagy in whole plants, we generated transgenic Arabidopsis expressing each green fluorescent protein–ATG8 fusion (GFP-ATG8). In wild-type plants, GFP-ATG8s were observed as ring shapes in the cytoplasm and were delivered to vacuolar lumens under nitrogen-starved conditions. By contrast, in a T-DNA insertion double mutant of the ATG4 s ( atg4a4b-1 ), autophagosomes were not observed, and the GFP-ATG8s were not delivered to the vacuole under nitrogen-starved conditions. In addition, we detected autophagic bodies in the vacuoles of wild-type roots but not in those of atg4a4b-1 in the presence of concanamycin A, a V-ATPase inhibitor. Biochemical analyses also provided evidence that autophagy in higher plants requires ATG proteins. The phenotypic analysis of atg4a4b-1 indicated that plant autophagy contributes to the development of a root system under conditions of nutrient limitation.
- Published
- 2004
21. A Novel Selection Method Based on the Expression Level of Green Fluorescent Protein Measured with a Quantitative Fluorescence Imager
- Author
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Yasuo Niwa, Shingo Goto, Ryoko Kuruto-Niwa, and Kohki Yoshimoto
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Reporter gene ,Fluorescence-lifetime imaging microscopy ,Plant Science ,Biology ,Molecular biology ,Green fluorescent protein ,Serine ,Transformation (genetics) ,Quantitative fluorescence ,Biophysics ,Threonine ,Agronomy and Crop Science ,Function (biology) ,Biotechnology - Abstract
Green fluorescent protein (GFP) has been used extensively as a novel non-invasive reporter in the investigation of issues such as promoter function, transformation marker recognition, and sub-cellular localization analysis. A plant-optimized synthetic GFP modified via the replacement of the serine to threonine at position 65 [sGFP(S65T)] has achieved high levels of expression with no toxic side-effects in many plants. It would be useful to develop a non-invasive selection system based only upon GFP expression levels. A trapping vector was constructed using an sGFP(S65T) and a quantitative fluorescence imaging system was used for non-invasive screening of trapped tobacco cultured cells. Putative trapped lines could be identified using this system. Moreover, the GFP products from the candidate trapped lines could be quantitatively visualized directly via SDS-PAGE using the fluorescence imaging system. We conclude that the non-invasive selection system described here could be a powerful new tool for plant biotechnology.
- Published
- 2003
22. Plant autophagy is responsible for peroxisomal transition and plays an important role in the maintenance of peroxisomal quality
- Author
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Michitaro Shibata, Kazusato Oikawa, Kenji Yamada, Kohki Yoshimoto, Maki Kondo, Yoshinori Ohsumi, Makoto Hayashi, Shino Goto-Yamada, Wataru Sakamoto, Shoji Mano, Mikio Nishimura, Department of Cell Biology, National Institute for Basic Biology [Okazaki], Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, Department of Applied Biological Chemistry, Niigata University, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Institute of Plant Science and Resources, Okayama University, Frontier Research Center, and Tokyo Institute of Technology [Tokyo] (TITECH)
- Subjects
0106 biological sciences ,Arabidopsis thaliana ,Membrane lipids ,[SDV]Life Sciences [q-bio] ,Arabidopsis ,hydrogen peroxide ,01 natural sciences ,03 medical and health sciences ,Glyoxysome ,Autophagy ,Peroxisomes ,peroxisome ,Molecular Biology ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,Reactive oxygen species ,biology ,glyoxysome leaf peroxisome ,Cell Biology ,Peroxisome ,Plants, Genetically Modified ,biology.organism_classification ,pexophagy ,Autophagic Punctum ,Cell biology ,Plant Leaves ,Metabolic pathway ,Biochemistry ,chemistry ,Photorespiration ,peroxisome transition ,Reactive Oxygen Species ,Oxidation-Reduction ,Metabolic Networks and Pathways ,010606 plant biology & botany - Abstract
In photosynthetic cells, a large amount of hydrogen peroxide is produced in peroxisomes through photorespiration, which is a metabolic pathway related to photosynthesis. Hydrogen peroxide, a reactive oxygen species, oxidizes peroxisomal proteins and membrane lipids, resulting in a decrease in peroxisomal quality. We demonstrate that the autophagic system is responsible for the elimination of oxidized peroxisomes in plant. We isolated Arabidopsis mutants that accumulated oxidized peroxisomes, which formed large aggregates. We revealed that these mutants were defective in autophagy-related (ATG) genes and that the aggregated peroxisomes were selectively targeted by the autophagic machinery. These findings suggest that autophagy plays an important role in the quality control of peroxisomes by the selective degradation of oxidized peroxisomes. In addition, the results suggest that autophagy is also responsible for the functional transition of glyoxysomes to leaf peroxisomes.
- Published
- 2014
23. Stitching together the multiple dimensions of autophagy using metabolomics and transcriptomics reveals impacts on metabolism, development, and plant responses to the environment in arabidopsis
- Author
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Pauline Anne, Jean-Marc Routaboul, Ken Shirasu, Céline Masclaux-Daubresse, Kohki Yoshimoto, Gilles Clément, Fabienne Soulay, Anne Guiboileau, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génomique et Biotechnologie des Fruits (GBF), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Toulouse-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Plant Science Center, RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Ministere de l'Education et de la Recherche of France, Ministry of Education, Culture, Sports, Science, and Technology of Japan [18770040, 19039033, 2020061], French Ministere des Affaires Etrangeres et Europeennes [21124QA], Japan Society for the Promotion of Science [21124QA], and Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP)
- Subjects
2. Zero hunger ,plant responses to the environment ,autophagy ,biology ,[SDV]Life Sciences [q-bio] ,Autophagy ,fungi ,food and beverages ,Cell Biology ,Plant Science ,Vacuole ,biology.organism_classification ,Cell biology ,Metabolic pathway ,arabidopsis ,Flavonoid biosynthesis ,Biochemistry ,Arabidopsis ,Plant defense against herbivory ,Large-Scale Biology Article ,COP9 signalosome ,Functional genomics ,transcriptome ,metabolism - Abstract
Autophagy is a fundamental process in the plant life story, playing a key role in immunity, senescence, nutrient recycling, and adaptation to the environment. Transcriptomics and metabolomics of the rosette leaves of Arabidopsis thaliana autophagy mutants (atg) show that autophagy is essential for cell homeostasis and stress responses and that several metabolic pathways are affected. Depletion of hexoses, quercetins, and anthocyanins parallel the overaccumulation of several amino acids and related compounds, such as glutamate, methionine, glutathione, pipecolate, and 2-aminoadipate. Transcriptomic data show that the pathways for glutathione, methionine, raffinose, galacturonate, and anthocyanin are perturbed. Anthocyanin depletion in atg mutants, which was previously reported as a possible defect in flavonoid trafficking to the vacuole, appears due to the downregulation of the master genes encoding the enzymes and regulatory proteins involved in flavonoid biosynthesis. Overexpression of the PRODUCTION OF ANTHOCYANIN PIGMENT1 transcription factor restores anthocyanin accumulation in vacuoles of atg mutants. Transcriptome analyses reveal connections between autophagy and (1) salicylic acid biosynthesis and response, (2) cytokinin perception, (3) oxidative stress and plant defense, and possible interactions between autophagy and the COP9 signalosome machinery. The metabolic and transcriptomic signatures identified for the autophagy mutants are discussed and show consistencies with the observed phenotypes.
- Published
- 2014
24. Autophagy as a possible mechanism for micronutrient remobilization from leaves to seeds
- Author
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Mathieu Pottier, Céline Masclaux-Daubresse, Sébastien Thomine, Kohki Yoshimoto, Institut des Sciences du Végétal-UPR2355, Saclay Plant Sciences, Centre National de la Recherche Scientifique (CNRS), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Region Ile-de-France, INRA, CNRS, Agence Nationale de la Recherche [ANR 2011 BSV6 004 01], and Thomine, Sébastien
- Subjects
Nutrient cycle ,nutrient fluxes ,leaf senescence ,[SDV]Life Sciences [q-bio] ,Biofortification ,Context (language use) ,autophagie ,Plant Science ,nutrient use efficiency ,lcsh:Plant culture ,Biology ,transition metal ,atg ,fer ,Mini Review Article ,Nutrient ,Botany ,Zn ,lcsh:SB1-1110 ,isotopic labeling ,Nutrient allocation ,2. Zero hunger ,Mechanism (biology) ,zinc ,Autophagy ,food and beverages ,Micronutrient ,Fe - Abstract
Seed formation is an important step of plant development which depends on nutrient allocation. Uptake from soil is an obvious source of nutrients which mainly occurs during vegetative stage. Because seed filling and leaf senescence are synchronized, subsequent mobilization of nutrients from vegetative organs also play an essential role in nutrient use efficiency, providing source-sink relationships. However, nutrient accumulation during the formation of seeds may be limited by their availability in source tissues. While several mechanisms contributing to make leaf macronutrients available were already described, little is known regarding micronutrients such as metals. Autophagy, which is involved in nutrient recycling, was already shown to play a critical role in nitrogen remobilization to seeds during leaf senescence. Because it is a non-specific mechanism, it could also control remobilization of metals. This article reviews actors and processes involved in metal remobilization with emphasis on autophagy and methodology to study metal fluxes inside the plant. A better understanding of metal remobilization is needed to improve metal use efficiency in the context of biofortification.
- Published
- 2014
25. Quality control of plant peroxisomes in organ specific manner via autophagy
- Author
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Michitaro Shibata, Kiminori Toyooka, Mayuko Sato, Yoshinori Ohsumi, Mikio Nishimura, Kohki Yoshimoto, Kazusato Oikawa, Ken Shirasu, and Maki Kondo
- Subjects
biology ,Autophagy ,Cell Biology ,Vacuole ,Peroxisome ,biology.organism_classification ,Cell biology ,Biochemistry ,Catalase ,Arabidopsis ,Organelle ,Glyoxysome ,biology.protein ,Arabidopsis thaliana - Abstract
Peroxisomes are essential organelles characterized by the possession of enzymes that produce hydrogen peroxide (H2O2) as part of their normal catalytic cycle. During the metabolic process, peroxisomal proteins are inevitably damaged by H2O2 and the integrity of the peroxisomes is impaired. Here, we show that autophagy, an intracellular process for vacuolar degradation, selectively degrades dysfunctional peroxisomes. Marked accumulation of peroxisomes was observed in the leaves but not roots of autophagy-related (ATG) gene-knockout Arabidopsis thaliana mutants. The peroxisomes in leaf cells contained markedly increased levels of catalase in an insoluble and inactive aggregate form. The chemically inducible complementation system in ATG5 knockout Arabidopsis provided the evidence that these accumulated peroxisomes were delivered to vacuoles by autophagy for degradation. Interestingly, autophagosomal membrane structures specifically recognized the abnormal peroxisomes at the site of the aggregates. Thus, autophagy is essential for the quality control of peroxisomes in leaves for proper plant development under natural growth conditions.
- Published
- 2014
26. Assessment and optimization of autophagy monitoring methods in Arabidopsis roots indicate direct fusion of autophagosomes with vacuoles
- Author
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Céline Masclaux-Daubresse, Kohki Yoshimoto, Anne Guiboileau, Ekaterina A. Merkulova, Loreto Naya, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Institut National de la Recherche Agronomique (INRA) France [INRA package program]
- Subjects
Autophagosome ,Arabidopsis thaliana ,Monitoring ,Physiology ,ATG8 ,Recombinant Fusion Proteins ,[SDV]Life Sciences [q-bio] ,Cytological Techniques ,Green Fluorescent Proteins ,Arabidopsis ,Plant Science ,Vacuole ,Membrane Fusion ,Plant Roots ,Green fluorescent protein ,Wortmannin ,chemistry.chemical_compound ,Acidotropic dye ,Leucine ,Cadaverine ,Phagosomes ,Plant Cells ,Tobacco ,Autophagy ,Amines ,biology ,Staining and Labeling ,Arabidopsis Proteins ,Cell Biology ,General Medicine ,biology.organism_classification ,Plants, Genetically Modified ,Fusion protein ,Cell biology ,Androstadienes ,Kinetics ,chemistry ,Biochemistry ,Vacuoles ,Lysosomes - Abstract
Autophagy is a degradation pathway that recycles cell materials upon encountering stress conditions or during specific developmental processes. To better understand the physiological roles of autophagy, proper monitoring methods are very important. In mammals and yeast, monitoring of autophagy is often performed with a green fluorescent protein (GFP)-ATG8 fusion protein or with acidotropic dyes such as monodansylcadaverine (MDC) and LysoTracker Red (LTR). To evaluate these monitoring methods, here we examined these systems by inducing autophagy in Arabidopsis thaliana roots as a model for monitoring autophagy in planta. Under carbon- and nitrogen-starved conditions, the number and size of vesicles labeled by GFP-ATG8 was increased for several hours and then gradually decreased to a level higher than that observed before the start of the experiment. We also observed the disappearance of GFP-ATG8-labeled vesicles after treatment with wortmannin, a phosphatidylinositol 3-kinase inhibitor known as an autophagy inhibitor, showing that the GFP-ATG8 transgenic line constitutes an excellent method for monitoring autophagy. These data were compared with plants stained with MDC and LTR. There was no appreciable MDC/LTR staining of small organelles in the root under the induction of autophagy. Some vesicles were eventually observed in the root tip only, but co-localization experiments, as well as experiments with autophagy-deficient atg mutants, provided the evidence that these structures were located in the vacuole and were not manifestly autophagosomes and/or autolysosomes. Extreme caution should therefore be used when monitoring autophagy with the aid of MDC/LTR. Additionally, our observations strongly suggest that autophagosomes fuse directly to vacuoles in Arabidopsis roots.
- Published
- 2014
27. Comparison of Strength of Endogenous and Exogenous Gene Promoters in Arabidopsis Chloroplasts
- Author
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Kohki Yoshimoto, Kyoichi Isono, Mao Sakaiya, and Hirokazu Kobayashi
- Subjects
Nuclear gene ,biology ,Operon ,food and beverages ,Promoter ,Plant Science ,Chimeric gene ,biology.organism_classification ,Molecular biology ,Chloroplast ,Chloroplast DNA ,Arabidopsis ,Agronomy and Crop Science ,Gene ,Biotechnology - Abstract
We have focused on possible stronger promoters in the chloroplast: those of psbA encoding D1 protein of photosystem II reaction center, 16S rDNA in rrn operon, the bacterial fused promoter tac, and the bacteriophage T7 gene φ10 in combination with transgenic T7 RNA polymerase (RNAP). Arabidopsis plants were made transgenic in the nuclear genome with the construct of a chimeric gene for T7 RNAP fused to a chloroplast transit peptide at its N-terminus placed under the control of CaMV 35S promoter. We have transiently expressed gene for β-glucuronidase (GUS) under control of the above promoters in the Arabidopsis chloroplast followed by particle bombardment. Expression in the chloroplast but not in the nucleus was confirmed histochemically and by treatment with α-amanitin. T7 promoter was the strongest among the examined promoters in the Arabidopsis chloroplast, being applicable to higher expression of foreign genes in the chloroplast with managed expression of T7 RNAP.
- Published
- 2001
28. Highly Oxidized Peroxisomes Are Selectively Degraded via Autophagy in Arabidopsis[C][W]
- Author
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Michitaro Shibata, Yoshinori Ohsumi, Mikio Nishimura, Maki Kondo, Kazusato Oikawa, Kenji Yamada, Makoto Hayashi, Kohki Yoshimoto, Wataru Sakamoto, Shoji Mano, Department of Cell Biology, National Institute for Basic Biology [Okazaki], School of Life Science, Department of Basic Biology, The Graduate University for Advanced Studies, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institute of Plant Science and Resources, Okayama University, Frontier Research Center, Tokyo Institute of Technology [Tokyo] (TITECH), Japan Society for the Promotion of Science [5852], and 22120007
- Subjects
0106 biological sciences ,Autophagosome ,ATG8 ,[SDV]Life Sciences [q-bio] ,Mutant ,Arabidopsis ,Plant Science ,01 natural sciences ,In Brief ,03 medical and health sciences ,Stress, Physiological ,Phagosomes ,Autophagy ,Peroxisomes ,Research Articles ,030304 developmental biology ,0303 health sciences ,biology ,Arabidopsis Proteins ,Wild type ,Hydrogen Peroxide ,Cell Biology ,Peroxisome ,biology.organism_classification ,Cell biology ,Biochemistry ,Catalase ,Mutation ,biology.protein ,Oxidation-Reduction ,010606 plant biology & botany - Abstract
The legend for Figure 1B has been corrected; The positioning of peroxisomes in a cell is a regulated process that is closely associated with their functions. Using this feature of the peroxisomal positioning as a criterion, we identified three Arabidopsis thaliana mutants (peroxisome unusual positioning1 [peup1], peup2, and peup4) that contain aggregated peroxisomes. We found that the PEUP1, PEUP2, and PEUP4 were identical to Autophagy-related2 (ATG2), ATG18a, and ATG7, respectively, which are involved in the autophagic system. The number of peroxisomes was increased and the peroxisomal proteins were highly accumulated in the peup1 mutant, suggesting that peroxisome degradation by autophagy (pexophagy) is deficient in the peup1 mutant. These aggregated peroxisomes contained high levels of inactive catalase and were more oxidative than those of the wild type, indicating that peroxisome aggregates comprise damaged peroxisomes. In addition, peroxisome aggregation was induced in wild-type plants by exogenous application of hydrogen peroxide. The cat2 mutant also contained peroxisome aggregates. These findings demonstrate that hydrogen peroxide as a result of catalase inactivation is the inducer of peroxisome aggregation. Furthermore, an autophagosome marker, ATG8, frequently colocalized with peroxisome aggregates, indicating that peroxisomes damaged by hydrogen peroxide are selectively degraded by autophagy in the wild type. Our data provide evidence that autophagy is crucial for quality control mechanisms for peroxisomes in Arabidopsis.
- Published
- 2013
29. Leaf-specifically expressed genes for polypeptides destined for chloroplasts with domains of σ 70 factors of bacterial RNA polymerases in Arabidopsis thaliana
- Author
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Akiho Yokota, Kohki Yoshimoto, Hirokazu Kobayashi, Kyoichi Isono, Masanori Shimizu, Kimiyuki Satoh, and Yasuo Niwa
- Subjects
Chloroplasts ,Molecular Sequence Data ,Arabidopsis ,Sigma Factor ,Genes, Plant ,Genome ,chemistry.chemical_compound ,Bacterial Proteins ,Transcription (biology) ,Sigma factor ,RNA polymerase ,Amino Acid Sequence ,Plastid ,Gene ,Polymerase ,Genetics ,Multidisciplinary ,biology ,Arabidopsis Proteins ,DNA-Directed RNA Polymerases ,Biological Sciences ,biology.organism_classification ,chemistry ,biology.protein ,Peptides ,Sequence Alignment - Abstract
Genes for σ-like factors of bacterial-type RNA polymerase have not been characterized from any multicellular eukaryotes, although they probably play a crucial role in the expression of plastid photosynthesis genes. We have cloned three distinct cDNAs, designated SIG1 , SIG2 , and SIG3 , for polypeptides possessing amino acid sequences for domains conserved in σ 70 factors of bacterial RNA polymerases from the higher plant Arabidopsis thaliana . Each gene is present as one copy per haploid genome without any additional sequences hybridized in the genome. Transient expression assays using green fluorescent protein demonstrated that N-terminal regions of the SIG2 and SIG3 ORFs could function as transit peptides for import into chloroplasts. Transcripts for all three SIG genes were detected in leaves but not in roots, and were induced in leaves of dark-adapted plants in rapid response to light illumination. Together with results of our previous analysis of tissue-specific regulation of transcription of plastid photosynthesis genes, these results indicate that expressed levels of the genes may influence transcription by regulating RNA polymerase activity in a green tissue-specific manner.
- Published
- 1997
30. Physiological and metabolic consequences of autophagy deficiency for the management of nitrogen and protein resources in Arabidopsis leaves depending on nitrate availability
- Author
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Anne Guiboileau, Jérémy Lothier, Marianne Azzopardi, Kohki Yoshimoto, Fabienne Soulay, Céline Masclaux-Daubresse, Anne Marmagne, Liliana Avila-Ospina, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA)
- Subjects
0106 biological sciences ,[SDV.SA]Life Sciences [q-bio]/Agricultural sciences ,Physiology ,leaf senescence ,Arabidopsis ,Plant Science ,01 natural sciences ,AMINO-ACIDS ,Biomass ,2. Zero hunger ,0303 health sciences ,aminopeptidase ,biology ,medicine.diagnostic_test ,PROFILING APPROACH ,nitrogen remobilization ,REMOBILIZATION ,carboxypeptidase ,Biochemistry ,5-BISPHOSPHATE CARBOXYLASE OXYGENASE ,Carbohydrate Metabolism ,RNA Interference ,RIBULOSE-1 ,EUGLENA-GRACILIS ,nitrate availability ,Nitrogen ,Proteolysis ,Blotting, Western ,Protein degradation ,03 medical and health sciences ,Ribosomal protein ,Glutamate-Ammonia Ligase ,GLUTAMINE-SYNTHETASE ,Glutamine synthetase ,medicine ,Autophagy ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,PLANTS ,030304 developmental biology ,selective autophagy ,SENESCING LEAVES ,Nitrates ,Arabidopsis Proteins ,Glutamate dehydrogenase ,RuBisCO ,DEGRADATION ,biology.organism_classification ,Carbon ,Plant Leaves ,Mutation ,biology.protein ,010606 plant biology & botany ,Peptide Hydrolases - Abstract
Article de revue (Article scientifique dans une revue à comité de lecture); International audience; Autophagy is present at a basal level in all plant tissues and is induced during leaf ageing and in response to nitrogen (N) starvation. Nitrogen remobilization from the rosette to the seeds is impaired in autophagy mutants. This report focuses on the role of autophagy in leaf N management and proteolysis during plant ageing.Metabolites, enzyme activities and protein contents were monitored in several autophagy-defective (atg) Arabidopsis mutants grown under low and high nitrate conditions.Results showed that carbon (C) and N statuses were affected in atg mutants before any senescence symptoms appeared. atg mutants accumulated larger amounts of ammonium, amino acids and proteins than wild type, and were depleted in sugars. Over-accumulation of proteins in atg mutants was selective and occurred despite higher endopeptidase and carboxypeptidase activities. Specific over-accumulation of the ribosomal proteins S6 and L13 subunits, and of catalase and glutamate dehydrogenase proteins was observed. atg mutants also accumulated peptides putatively identified as degradation products of the Rubisco large subunit and glutamine synthetase 2 (GS2). Incomplete chloroplast protein degradation resulting from autophagy defects could explain the higher N concentrations measured in atg rosettes and defects in N remobilization.It is concluded that autophagy controls C:N status and protein content in leaves of Arabidopsis.
- Published
- 2013
31. Beginning to Understand Autophagy, an Intracellular Self-Degradation System in Plants
- Author
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Kohki Yoshimoto, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Ministry of Education, Culture, Sports, Science and Technology, Japan [22770049], and INRA, France
- Subjects
0106 biological sciences ,Autophagosome ,[SDV.SA]Life Sciences [q-bio]/Agricultural sciences ,Physiology ,ATG8 ,Saccharomyces cerevisiae ,Arabidopsis ,Plant Science ,Biology ,01 natural sciences ,Plant life ,SACCHAROMYCES-CEREVISIAE ,03 medical and health sciences ,SUCROSE STARVATION CONDITIONS ,organelle degradation ,Plant Cells ,Autophagy ,POLLEN GERMINATION ,SELECTIVE AUTOPHAGY ,Plant Proteins ,030304 developmental biology ,PROTEIN LIPIDATION ,Organelles ,2. Zero hunger ,0303 health sciences ,MONITORING AUTOPHAGY ,Autophagy database ,Protein ,fungi ,CONSTITUTIVE AUTOPHAGY ,food and beverages ,Cell Biology ,General Medicine ,Plants ,biology.organism_classification ,Cell biology ,INNATE IMMUNE-RESPONSE ,ROOT-TIP CELLS ,Starvation ,ARABIDOPSIS-THALIANA ,Intracellular ,010606 plant biology & botany - Abstract
Autophagy is an evolutionarily conserved intracellular process for the vacuolar degradation of cytoplasmic components. There is no doubt that autophagy is very important to plant life, especially because plants are immobile and must survive in environmental extremes. Early studies of autophagy provided our first insights into the structural characteristics of the process in plants, but for a long time the molecular mechanisms and the physiological roles of autophagy were not understood. Genetic analyses of autophagy in the yeast Saccharomyces cerevisiae have greatly expanded our knowledge of the molecular aspects of autophagy in plants as well as in animals. Until recently our knowledge of plant autophagy was in its infancy compared with autophagy research in yeast and animals, but recent efforts by plant researchers have made many advances in our understanding of plant autophagy. Here I will introduce an overview of autophagy in plants, present current findings and discuss the physiological roles of self-degradation.
- Published
- 2012
32. A possible involvement of autophagy in amyloplast degradation in columella cells during hydrotropic response of Arabidopsis roots
- Author
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Ken Shirasu, Hideyuki Takahashi, Yutaka Miyazawa, Mikio Nishimura, Nobuharu Fujii, Kenji Yamada, Hiroyuki Ishida, Mayumi Nakayama, Nahoko Higashitani, Kohki Yoshimoto, Yasuko Kaneko, and Shinya Wada
- Subjects
Autophagosome ,Time Factors ,Recombinant Fusion Proteins ,Gravitropism ,Arabidopsis ,Autophagy-Related Proteins ,Plant Science ,Hydrotropism ,Vacuole ,Endoplasmic Reticulum ,Plant Roots ,Tropism ,Microscopy, Electron, Transmission ,Gene Expression Regulation, Plant ,Stress, Physiological ,Botany ,Genetics ,Autophagy ,Amyloplast ,Plastids ,Cell Nucleus ,Microscopy, Confocal ,biology ,Dehydration ,Arabidopsis Proteins ,Endoplasmic reticulum ,Cell Polarity ,biology.organism_classification ,Plants, Genetically Modified ,Cell biology ,Vacuolization ,Seedlings ,Mutation ,Vacuoles ,Transcription Factors - Abstract
Seedling roots display not only gravitropism but also hydrotropism, and the two tropisms interfere with one another. In Arabidopsis (Arabidopsis thaliana) roots, amyloplasts in columella cells are rapidly degraded during the hydrotropic response. Degradation of amyloplasts involved in gravisensing enhances the hydrotropic response by reducing the gravitropic response. However, the mechanism by which amyloplasts are degraded in hydrotropically responding roots remains unknown. In this study, the mechanistic aspects of the degradation of amyloplasts in columella cells during hydrotropic response were investigated by analyzing organellar morphology, cell polarity and changes in gene expression. The results showed that hydrotropic stimulation or systemic water stress caused dramatic changes in organellar form and positioning in columella cells. Specifically, the columella cells of hydrotropically responding or water-stressed roots lost polarity in the distribution of the endoplasmic reticulum (ER), and showed accelerated vacuolization and nuclear movement. Analysis of ER-localized GFP showed that ER redistributed around the developed vacuoles. Cells often showed decomposing amyloplasts in autophagosome-like structures. Both hydrotropic stimulation and water stress upregulated the expression of AtATG18a, which is required for autophagosome formation. Furthermore, analysis with GFP-AtATG8a revealed that both hydrotropic stimulation and water stress induced the formation of autophagosomes in the columella cells. In addition, expression of plastid marker, pt-GFP, in the columella cells dramatically decreased in response to both hydrotropic stimulation and water stress, but its decrease was much less in the autophagy mutant atg5. These results suggest that hydrotropic stimulation confers water stress in the roots, which triggers an autophagic response responsible for the degradation of amyloplasts in columella cells of Arabidopsis roots.
- Published
- 2011
33. The Rab GTPase RabG3b functions in autophagy and contributes to tracheary element differentiation in Arabidopsis
- Author
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Ohkmae K. Park, Soon Il Kwon, Hong Joo Cho, Jin Hee Jung, Ken Shirasu, and Kohki Yoshimoto
- Subjects
Programmed cell death ,biology ,Cell ,Autophagy ,Mutant ,Wild type ,food and beverages ,Cell Biology ,Plant Science ,biology.organism_classification ,Cell biology ,medicine.anatomical_structure ,Tracheary element differentiation ,Arabidopsis ,Genetics ,medicine ,Rab - Abstract
The tracheary elements (TEs) of the xylem serve as the water-conducting vessels of the plant vascular system. To achieve this, TEs undergo secondary cell wall thickening and cell death, during which the cell contents are completely removed. Cell death of TEs is a typical example of developmental programmed cell death that has been suggested to be autophagic. However, little evidence of autophagy in TE differentiation has been provided. The present study demonstrates that the small GTP binding protein RabG3b plays a role in TE differentiation through its function in autophagy. Differentiating wild type TE cells were found to undergo autophagy in an Arabidopsis culture system. Both autophagy and TE formation were significantly stimulated by overexpression of a constitutively active mutant (RabG3bCA), and were inhibited in transgenic plants overexpressing a dominant negative mutant (RabG3bDN) or RabG3b RNAi (RabG3bRNAi), a brassinosteroid insensitive mutant bri1-301, and an autophagy mutant atg5-1. Taken together, our results suggest that autophagy occurs during TE differentiation, and that RabG3b, as a component of autophagy, regulates TE differentiation.
- Published
- 2010
34. Physiological roles of autophagy in plants: does plant autophagy have a pro-death function?
- Author
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Kohki Yoshimoto
- Subjects
Senescence ,Programmed cell death ,Cell Death ,Mutant ,Autophagy ,fungi ,food and beverages ,Plant Science ,Review ,Biology ,Plants ,Models, Biological ,Cell biology ,Phenotype ,Biochemistry ,Apoptosis ,Plant Cells ,Signal transduction ,Intracellular ,Function (biology) - Abstract
Autophagy is an evolutionarily conserved intracellular process for vacuolar degradation of cytoplasmic components. Early morphological studies suggested that autophagy occurs in plant cells and predicted that autophagy has a variety of functions in plant growth and development. However, it is only since the identification of autophagy genes that the physiological roles of autophagy in plants have become apparent. Recent reverse genetic studies indicate that autophagy defects in higher plants result in early senescence and excessive immunity-related programmed cell death (PCD), irrespective of nutrient conditions, suggesting that plant autophagy has an important pro-survival function during these types of cell death. Further biochemical and pharmacological studies in combination with double mutant analyses revealed that excessive salicylic acid (SA) signaling is a major factor in autophagy-defective plant-dependent cell death and that the SA signal can induce autophagy. These results demonstrate a novel physiological function for plant autophagy that operates a negative feedback loop to modulate SA signaling.
- Published
- 2010
35. Chloroplasts autophagy during senescence of individually darkened leaves
- Author
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Amane Makino, Masanori Izumi, Tadahiko Mae, Kohki Yoshimoto, Hiroyuki Ishida, Shinya Wada, and Yoshinori Ohsumi
- Subjects
Chlorophyll ,DNA, Bacterial ,Chloroplasts ,Physiology ,Ribulose-Bisphosphate Carboxylase ,Population ,Arabidopsis ,Plant Science ,Vacuole ,Photosynthesis ,chemistry.chemical_compound ,Botany ,Autophagy ,Genetics ,Arabidopsis thaliana ,education ,Cellular Senescence ,Plant Proteins ,education.field_of_study ,biology ,Vacuolar lumen ,RuBisCO ,fungi ,food and beverages ,biology.organism_classification ,Article Addendum ,Cell biology ,Plant Leaves ,Chloroplast ,Mutagenesis, Insertional ,Cytosol ,chemistry ,Biochemistry ,biology.protein ,Chloroplast Proteins ,Cell aging ,Research Article - Abstract
We recently reported that autophagy plays a role in chloroplasts degradation in individually-darkened senescing leaves. Chloroplasts contain approximately 80% of total leaf nitrogen, mainly as photosynthetic proteins, predominantly ribulose 1, 5-bisphosphate carboxylase/oxygenase (Rubisco). During leaf senescence, chloroplast proteins are degraded as a major source of nitrogen for new growth. Concomitantly, while decreasing in size, chloroplasts undergo transformation to non-photosynthetic gerontoplasts. Likewise, over time the population of chloroplasts (gerontoplasts) in mesophyll cells also decreases. While bulk degradation of the cytosol and organelles is mediated by autophagy, the role of chloroplast degradation is still unclear. In our latest study, we darkened individual leaves to observe chloroplast autophagy during accelerated senescence. At the end of the treatment period chloroplasts were much smaller in wild-type than in the autophagy defective mutant, atg4a4b-1, with the number of chloroplasts decreasing only in wild-type. Visualizing the chloroplast fractions accumulated in the vacuole, we concluded that chloroplasts were degraded by two different pathways, one was partial degradation by small vesicles containing only stromal-component (Rubisco containing bodies; RCBs) and the other was whole chloroplast degradation. Together, these pathways may explain the morphological attenuation of chloroplasts during leaf senescence and describe the fate of chloroplasts.
- Published
- 2009
36. Role of chloroplasts and other plastids in ageing and death of plants and animals: a tale of Vishnu and Shiva
- Author
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Wouter G. van Doorn and Kohki Yoshimoto
- Subjects
Aging ,Chloroplasts ,Photosynthesis ,Biochemistry ,Algae ,Chromoplast ,Botany ,Animals ,Plastid ,Symbiosis ,Molecular Biology ,Cellular Senescence ,Plant Physiological Phenomena ,Apicoplast ,Endosymbiosis ,biology ,Cell Death ,fungi ,food and beverages ,Eukaryota ,biology.organism_classification ,Anthozoa ,Chloroplast ,Neurology ,Cell aging ,Biotechnology - Abstract
Chloroplasts (chlorophyll-containing plastids) and other plastids are found in all plants and many animals. They are crucial to the survival of plants and most of the animals that harbour them. An example of a non-photosynthesizing plastid in animals is the apicoplast in the malaria-causing Plasmodium species, which is required for survival of the parasite. Many animals (such as sea slugs, sponges, reef corals, and clams) consume prey containing chloroplasts, or feed on algae. Some of these incorporate the chloroplasts from their food, or whole algal cells, into their own cells. Other species from these groups place algal cells between their own cells. Reef-building corals often lose their intracellular algae as a result of environmental changes, resulting in coral bleaching and death. The sensitivity of the chloroplast internal membranes to temperature stress is one of the reasons for coral death. Chloroplasts can also be a causal factor in the processes leading to whole-plant death, as the knockout of a gene encoding a chloroplast protein delayed the yellowing that proceeds death in tobacco plants. It is concluded that chloroplasts and other plastids are essential to individual survival in many species, including animals, and that they also play a role in triggering death in some plant and animal species.
- Published
- 2009
37. Visualization of Rubisco-Containing Bodies Derived from Chloroplasts in Living Cells of Arabidopsis
- Author
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Tadahiko Mae, Amane Makino, Yoshinori Ohsumi, Daniel Reisen, Hiroyuki Ishida, Kohki Yoshimoto, and Maureen R. Hanson
- Subjects
biology ,Chemistry ,Immunoelectron microscopy ,fungi ,RuBisCO ,food and beverages ,Vacuole ,biology.organism_classification ,Green fluorescent protein ,Chloroplast ,Biochemistry ,Plant protein ,Arabidopsis ,Botany ,biology.protein ,Chlorophyll fluorescence - Abstract
During senescence and times of stress, plants can mobilize needed nitrogen from chloroplasts in leaves to other organs. Much of the total leaf nitrogen is allocated to the most abundant plant protein, ribulose-1,5-bisphosphate carboxylase/ oxygenase (Rubisco). Previously by immunoelectron microscopy (IEM), we demonstrated that Rubisco is released from the chloroplast into Rubisco-containing bodies (RCBs) in naturally senescent leaves (Chiba et al. 2003). In this study, we visualized RCBs in living cells of transgenic Arabidopsis plants containing stroma-targeted green fluorescent protein (GFP). When leaves of transgenic Arabidopsis plants were incubated under starvation conditions with a vacuolar-ATPase inhibitor, spherical bodies exhibiting GFP fluorescence without chlorophyll fluorescence were observed. Spherical bodies were not observed when leaves were provided with a sugar and nutrient solution. IEM of concanamycin-A-treated leaves with anti-Rubisco antibodies confirmed the existence of RCBs in the vacuolar compartment. These results suggest the hypothesis that stromal proteins can be mobilized to the vacuole via RCBs by possibly autophagy for the degradation.
- Published
- 2008
38. In vitro reconstitution of plant Atg8 and Atg12 conjugation systems essential for autophagy
- Author
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Kohki Yoshimoto, Yuko Fujioka, Nobuo N. Noda, Fuyuhiko Inagaki, Yoshinori Ohsumi, and Kiyonaga Fujii
- Subjects
Mammals ,biology ,Arabidopsis Proteins ,Ubiquitin ,ATG8 ,Phosphatidylethanolamines ,Saccharomyces cerevisiae ,Arabidopsis ,Ubiquitination ,Cell Biology ,biology.organism_classification ,Biochemistry ,Yeast ,In vitro ,ATG12 ,Autophagy ,Arabidopsis thaliana ,Animals ,Molecular Biology ,Autophagy-Related Protein 12 ,Conjugate - Abstract
Genetic and biochemical analyses using yeast Saccharomyces cerevisiae showed that two ubiquitin-like conjugation systems, the Atg8 and Atg12 systems, exist and play essential roles in autophagy, the bulk degradation system conserved in yeast and mammals. These conjugation systems are also conserved in Arabidopsis thaliana; however, further detailed study of plant ATG (autophagy-related) conjugation systems in relation to those in yeast and mammals is needed. Here, we describe the in vitro reconstitution of Arabidopsis thaliana ATG8 and ATG12 (AtATG8 and AtATG12) conjugation systems using purified recombinant proteins. AtATG12b was conjugated to AtATG5 in a manner dependent on AtATG7, AtATG10, and ATP, whereas AtATG8a was conjugated to phosphatidylethanolamine (PE) in a manner dependent on AtATG7, AtATG3, and ATP. Other AtATG8 homologs (AtATG8b–8i) were similarly conjugated to PE. The AtATG8 conjugates were deconjugated by AtATG4a and AtATG4b. These results support the hypothesis that the ATG conjugation systems in Arabidopsis are very similar to those in yeast and mammals. Intriguingly, in vitro analyses showed that AtATG12-AtATG5 conjugates accelerated the formation of AtATG8-PE, whereas AtATG3 inhibited the formation of AtATG12-AtATG5 conjugates. The in vitro conjugation systems reported here will afford a tool with which to investigate the cross-talk mechanism between two conjugation systems.
- Published
- 2007
39. AtATG genes, homologs of yeast autophagy genes, are involved in constitutive autophagy in Arabidopsis root tip cells
- Author
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Masaki Hattori, Takao Suzuki, Yuji Moriyasu, Yuko Inoue, Yoshinori Ohsumi, and Kohki Yoshimoto
- Subjects
Sucrose ,Physiology ,Mutant ,Meristem ,Arabidopsis ,Autophagy-Related Proteins ,Plant Science ,Vacuole ,medicine.disease_cause ,Genes, Plant ,Aminopeptidases ,Autophagy-Related Protein 5 ,Gene Expression Regulation, Plant ,medicine ,Autophagy ,Gene ,Mutation ,biology ,Arabidopsis Proteins ,Adenine ,Cell Biology ,General Medicine ,biology.organism_classification ,Phosphoric Monoester Hydrolases ,Cell biology ,Biochemistry ,Cytoplasm ,Vacuoles - Abstract
In Arabidopsis root tips cultured in medium containing sufficient nutrients and the membrane-permeable protease inhibitor E-64d, parts of the cytoplasm accumulated in the vacuoles of the cells from the meristematic zone to the elongation zone. Also in barley root tips treated with E-64, parts of the cytoplasm accumulated in autolysosomes and pre-existing central vacuoles. These results suggest that vacuolar and/or lysosomal autophagy occurs constitutively in these regions of cells. 3-Methyladenine, an inhibitor of autophagy, inhibited the accumulation of such inclusions in Arabidopsis root tip cells. Such inclusions were also not observed in root tips prepared from Arabidopsis T-DNA mutants in which AtATG2 or AtATG5, an Arabidopsis homolog of yeast ATG genes essential for autophagy, is disrupted. In contrast, an atatg9 mutant, in which another homolog of ATG is disrupted, accumulated a significant number of vacuolar inclusions in the presence of E-64d. These results suggest that both AtAtg2 and AtAtg5 proteins are essential for autophagy whereas AtAtg9 protein contributes to, but is not essential for, autophagy in Arabidopsis root tip cells. Autophagy that is sensitive to 3-methyladenine and dependent on Atg proteins constitutively occurs in the root tip cells of Arabidopsis.
- Published
- 2006
40. Plant autophagy puts the brakes on cell death by controlling salicylic acid signaling
- Author
-
Kohki Yoshimoto
- Subjects
Feedback, Physiological ,Senescence ,Physiological function ,Programmed cell death ,Cell Death ,Acclimatization ,Autophagy ,food and beverages ,Cell Biology ,Plants ,Biology ,Plants, Genetically Modified ,Cell biology ,chemistry.chemical_compound ,chemistry ,Salicylic Acid ,Molecular Biology ,Gene ,Plant Physiological Phenomena ,Salicylic acid ,Plant Diseases ,Signal Transduction - Abstract
It has long been recognized that autophagy in plants is important for nutrient recycling and plays a critical role in the ability of plants to adapt to environmental extremes such as nutrient deprivation. Recent reverse genetic studies, however, hint at other roles for autophagy, showing that autophagy defects in higher plants result in early senescence and excessive immunity-related programmed cell death (PCD), irrespective of nutrient conditions. Until now, the mechanisms by which cells die in the absence of autophagy were unclear. In our study, using biochemical, pharmacological and genetic approaches, we reveal that excessive salicylic acid (SA) signaling is a major factor in autophagy-defective plant-dependent cell death and that the SA signal can induce autophagy. These findings suggest a novel physiological function for plant autophagy that operates via a negative feedback loop to modulate proper SA signaling.
- Published
- 2010
41. Non-invasive quantitative detection and applications of non-toxic, S65T-type green fluorescent protein in living plants
- Author
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Yasuo Niwa, Masanori Shimizu, Hirokazu Kobayashi, Kohki Yoshimoto, and Takanori Hirano
- Subjects
Light ,Transgene ,Mutant ,Genetic Vectors ,Green Fluorescent Proteins ,Arabidopsis ,Plant Science ,medicine.disease_cause ,Green fluorescent protein ,Protein targeting ,Botany ,Tobacco ,Genetics ,medicine ,Arabidopsis thaliana ,Plastid ,DNA Primers ,biology ,Base Sequence ,fungi ,food and beverages ,Cell Biology ,biology.organism_classification ,Plants, Genetically Modified ,Cell biology ,Luminescent Proteins ,Plants, Toxic ,Organelle biogenesis - Abstract
Green fluorescent protein (GFP) has emerged as a powerful new tool in a variety of organisms. An engineered sGFP(S65T) sequence containing optimized codons of highly expressed eukaryotic proteins has provided up to 100-fold brighter fluorescence signals than the original jellyfish GFP sequence in plant and mammalian cells. It would be useful to establish a non-invasive, quantitative detection system which is optimized for S65T-type GFP, one of the brightest chromophore mutants among the various GFPs. We demonstrate here that highly fluorescent transgenic Arabidopsis can be generated, and the fluorescence intensity of whole plants can be measured under non-disruptive, sterile conditions using a quantitative fluorescent imaging system with blue laser excitation. Homozygous plants can be distinguished from heterozygous plants and fully fertile progenies can be obtained from the analyzed plants. In the case of cultured tobacco cells, GFP-positive cells can be quantitatively distinguished from non-transformed cells under non-selective conditions. This system will be useful in applications such as mutant screening, analysis of whole-body phenomena, including gene silencing and quantitative assessments of colonies from microorganisms to cultured eukaryotic cells. To facilitate the elucidation of protein targeting and organelle biogenesis in planta, we also generated transgenic Arabidopsis that stably express the plastid- or mitochondria-targeted sGFP(S65T). Etioplasts in dark-grown cotyledons and mitochondria in dry seed embryos could be visualized for the first time in transgenic Arabidopsis plants under normal growing conditions.
- Published
- 1999
42. Chloroplasts are partially mobilized to the vacuole by autophagy
- Author
-
Kohki Yoshimoto and Hiroyuki Ishida
- Subjects
Chloroplasts ,biology ,Arabidopsis Proteins ,Ribulose-Bisphosphate Carboxylase ,Green Fluorescent Proteins ,fungi ,RuBisCO ,Autophagy ,Arabidopsis ,food and beverages ,Cell Biology ,Vacuole ,Photosynthesis ,Cell biology ,Chloroplast ,Cytosol ,Biochemistry ,Vacuoles ,Organelle ,biology.protein ,Chloroplast Proteins ,Molecular Biology - Abstract
Excluding the central vacuole, chloroplasts constitute the largest compartment within the leaf cells of plants and contain approximately 80 percent of the total leaf nitrogen, mainly as proteins. Much of this nitrogen is allocated to the carbon-fixing enzyme in photosynthesis, Rubisco. During senescence, plants can mobilize nitrogen from chloroplasts in older leaves to other organs, such as developing seeds. Whereas bulk degradation of the cytosol and organelles in plants occurs by autophagy, the role of autophagy in the degradation of chloroplast proteins is still unclear. We have recently demonstrated that stroma-targeted green fluorescent protein (GFP), DsRed, and GFP-labeled Rubisco can be mobilized to the vacuole of living cells via Rubisco-containing bodies, in an ATG gene-dependent manner. Our results indicate the presence of a specific autophagic pathway for chloroplast stromal proteins, which does not cause chloroplast lysis. Here, we also discuss the involvement of stroma-filled tubules, stromules, which are important for the structural flexibility of the organelle, on the autophagic transfer of stromal proteins to the vacuole.
- Published
- 2008
43. Several Strategies for Dissecting and Controlling Functions in Plant Cells
- Author
-
Yasuo Niwa, Jen Sheen, Yoshihiro Narusaka, Hirokazu Kobayashi, Mao Sakaiya, and Kohki Yoshimoto
- Subjects
biology ,Transgene ,Gene expression ,food and beverages ,Arabidopsis thaliana ,RNA ,Mutagenesis (molecular biology technique) ,biology.organism_classification ,Molecular biology ,Gene ,Genome ,Green fluorescent protein ,Cell biology - Abstract
The strengths of gene promoters functional in chloroplasts have been evaluated for transient expression by particle bombardment to facilitate engineering of the chloroplast genome of Arabidopsis thaliana. The T7 RNA polymerase-recognized promoter was the most active in transgenic A. thaliana with T7 RNA polymcrase destined for chloroplasts. As a vital reporter of gene expression, an improved gene for green fluorescent protein (GFP) was chemically synthesized and resulted in approx. 100 times higher fluorescence intensity in A. thaliana. To overcome the limitations of experimentally designing of engineered proteins, we employed in vitro random mutagenesis of genes and subsequent selection of their transformants under certain conditions. The strategy was successfully applied to the photosystem II reaction center D1 protein to confer phototolerance on it.
- Published
- 1998
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