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Hong C, Lee HG, Shim S, Park OS, Kim JH, Lee K, Oh E, Kim J, Jung YJ, Seo PJ. Histone modification-dependent production of peptide hormones facilitates acquisition of pluripotency during leaf-to-callus transition in Arabidopsis. New Phytol 2024; 242:1068-1083. [PMID: 38406998 DOI: 10.1111/nph.19637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/07/2024] [Indexed: 02/27/2024]
Abstract
Chromatin configuration is critical for establishing tissue identity and changes substantially during tissue identity transitions. The crucial scientific and agricultural technology of in vitro tissue culture exploits callus formation from diverse tissue explants and tissue regeneration via de novo organogenesis. We investigated the dynamic changes in H3ac and H3K4me3 histone modifications during leaf-to-callus transition in Arabidopsis thaliana. We analyzed changes in the global distribution of H3ac and H3K4me3 during the leaf-to-callus transition, focusing on transcriptionally active regions in calli relative to leaf explants, defined by increased accumulation of both H3ac and H3K4me3. Peptide signaling was particularly activated during callus formation; the peptide hormones RGF3, RGF8, PIP1 and PIPL3 were upregulated, promoting callus proliferation and conferring competence for de novo shoot organogenesis. The corresponding peptide receptors were also implicated in peptide-regulated callus proliferation and regeneration capacity. The effect of peptide hormones in plant regeneration is likely at least partly conserved in crop plants. Our results indicate that chromatin-dependent regulation of peptide hormone production not only stimulates callus proliferation but also establishes pluripotency, improving the overall efficiency of two-step regeneration in plant systems.
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Affiliation(s)
- Cheljong Hong
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Hong Gil Lee
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
- Research Institute of Basic Science, Seoul National University, Seoul, 08826, Korea
| | - Sangrea Shim
- Department of Forest Resources, College of Forest and Environmental Sciences, Kangwon National University, Chuncheon, 24341, Korea
| | - Ok-Sun Park
- Research Institute of Basic Science, Seoul National University, Seoul, 08826, Korea
| | - Jong Hee Kim
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong, 17579, Korea
| | - Kyounghee Lee
- Research Institute of Basic Science, Seoul National University, Seoul, 08826, Korea
| | - Eunkyoo Oh
- Department of Life Sciences, Korea University, Seoul, 08826, Korea
| | - Jungmook Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 61186, Korea
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, Korea
| | - Yu Jin Jung
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong, 17579, Korea
- Institute of Genetic Engineering, Hankyong National University, Anseong, 17579, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
- Research Institute of Basic Science, Seoul National University, Seoul, 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
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2
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Cai Y, Ping H, Zhao J, Li C, Li Y, Liang G. IRON MAN interacts with Cu-DEFICIENCY INDUCED TRANSCRIPTION FACTOR 1 to maintain copper homeostasis. New Phytol 2024; 242:1206-1217. [PMID: 38031525 DOI: 10.1111/nph.19439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023]
Abstract
Copper (Cu) is essential for plant growth and development. IRON MAN (IMA) is a family of small peptides that can bind both iron (Fe) and Cu ions. It was reported that IMAs mediate Fe homeostasis in Arabidopsis thaliana. However, it remains unclear whether IMAs are involved in Cu homeostasis. The transcript abundance of IMA genes decreased in response to Cu deficiency. The combined disruption of all IMA genes caused enhanced tolerance to Cu deficiency and resulted in an increase in the transcript abundance of Cu uptake genes, whereas the overexpression of IMA1 or IMA3 led to the opposite results. Protein interaction assays indicated that IMAs interact with Cu-DEFICIENCY INDUCED TRANSCRIPTION FACTOR1 (CITF1), which is a positive regulator of the Cu uptake genes. Further studies showed that IMAs not only interfere with the DNA binding of CITF1 but also repress the transcriptional activation activity of CITF1, hence resulting in downregulation of the Cu uptake genes. Genetic analyses indicated that IMAs modulate Cu homeostasis in a CITF1-dependent manner. Our findings indicate that IMAs inhibit the functions of CITF1 in regulating Cu deficiency responses, thereby providing a conceptual framework for comprehending the regulation of Cu homeostasis.
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Affiliation(s)
- Yuerong Cai
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Huaqian Ping
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Junhui Zhao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Chenyang Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Yang Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Gang Liang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
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3
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Poethig RS. Ca 2+ regulates developmental timing in Arabidopsis. New Phytol 2024; 242:829-831. [PMID: 38379438 DOI: 10.1111/nph.19613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
This article is a Commentary on Wang et al. (2024), 242: 1043–1054.
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Affiliation(s)
- R Scott Poethig
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
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4
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Huang PK, Schmitt J, Runcie DE. Exploring the molecular regulation of vernalization-induced flowering synchrony in Arabidopsis. New Phytol 2024; 242:947-959. [PMID: 38509854 DOI: 10.1111/nph.19680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 02/27/2024] [Indexed: 03/22/2024]
Abstract
Many plant populations exhibit synchronous flowering, which can be advantageous in plant reproduction. However, molecular mechanisms underlying flowering synchrony remain poorly understood. We studied the role of known vernalization-response and flower-promoting pathways in facilitating synchronized flowering in Arabidopsis thaliana. Using the vernalization-responsive Col-FRI genotype, we experimentally varied germination dates and daylength among individuals to test flowering synchrony in field and controlled environments. We assessed the activity of flowering regulation pathways by measuring gene expression across leaves produced at different time points during development and through a mutant analysis. We observed flowering synchrony across germination cohorts in both environments and discovered a previously unknown process where flower-promoting and repressing signals are differentially regulated between leaves that developed under different environmental conditions. We hypothesized this mechanism may underlie synchronization. However, our experiments demonstrated that signals originating from sources other than leaves must also play a pivotal role in synchronizing flowering time, especially in germination cohorts with prolonged growth before vernalization. Our results suggest flowering synchrony is promoted by a plant-wide integration of flowering signals across leaves and among organs. To summarize our findings, we propose a new conceptual model of vernalization-induced flowering synchrony and provide suggestions for future research in this field.
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Affiliation(s)
- Po-Kai Huang
- Department of Plant Sciences, University of California, Davis, Davis, CA, 95616, USA
| | - Johanna Schmitt
- Department of Evolution and Ecology, University of California, Davis, Davis, CA, 95616, USA
| | - Daniel E Runcie
- Department of Plant Sciences, University of California, Davis, Davis, CA, 95616, USA
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5
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Bao X, Jia H, Zhang X, Tian S, Zhao Y, Li X, Lin P, Ma C, Wang P, Song CP, Zhu X. Mapping of cytosol-facing organelle outer membrane proximity proteome by proximity-dependent biotinylation in living Arabidopsis cells. Plant J 2024; 118:7-23. [PMID: 38261530 DOI: 10.1111/tpj.16641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/15/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024]
Abstract
The cytosol-facing outer membrane (OM) of organelles communicates with other cellular compartments to exchange proteins, metabolites, and signaling molecules. Cellular surveillance systems also target OM-resident proteins to control organellar homeostasis and ensure cell survival under stress. However, the OM proximity proteomes have never been mapped in plant cells since using traditional approaches to discover OM proteins and identify their dynamically interacting partners remains challenging. In this study, we developed an OM proximity labeling (OMPL) system using biotin ligase-mediated proximity biotinylation to identify the proximity proteins of the OMs of mitochondria, chloroplasts, and peroxisomes in living Arabidopsis (Arabidopsis thaliana) cells. Using this approach, we mapped the OM proximity proteome of these three organelles under normal conditions and examined the effects of the ultraviolet-B (UV-B) or high light (HL) stress on the abundances of OM proximity proteins. We demonstrate the power of this system with the discovery of cytosolic factors and OM receptor candidates potentially involved in local protein translation and translocation. The candidate proteins that are involved in mitochondrion-peroxisome, mitochondrion-chloroplast, or peroxisome-chloroplast contacts, and in the organellar quality control system are also proposed based on OMPL analysis. OMPL-generated OM proximity proteomes are valuable sources of candidates for functional validation and suggest directions for further investigation of important questions in cell biology.
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Affiliation(s)
- Xinyue Bao
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Huifang Jia
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xiaoyan Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Sang Tian
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yanming Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xiangyun Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Ping Lin
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Chongyang Ma
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Pengcheng Wang
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chun-Peng Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xiaohong Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
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6
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Atanasov V, Schumacher J, Muiño JM, Larasati C, Wang L, Kaufmann K, Leister D, Kleine T. Arabidopsis BBX14 is involved in high light acclimation and seedling development. Plant J 2024; 118:141-158. [PMID: 38128030 DOI: 10.1111/tpj.16597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 11/22/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023]
Abstract
The development of photosynthetically competent seedlings requires both light and retrograde biogenic signaling pathways. The transcription factor GLK1 functions at the interface between these pathways and receives input from the biogenic signal integrator GUN1. BBX14 was previously identified, together with GLK1, in a core module that mediates the response to high light (HL) levels and biogenic signals, which was studied by using inhibitors of chloroplast development. Our chromatin immunoprecipitation-Seq experiments revealed that BBX14 is a direct target of GLK1, and RNA-Seq analysis suggests that BBX14 may function as a regulator of the circadian clock. In addition, BBX14 plays a role in chlorophyll biosynthesis during early onset of light. Knockout of BBX14 results in a long hypocotyl phenotype dependent on a retrograde signal. Furthermore, the expression of BBX14 and BBX15 during biogenic signaling requires GUN1. Investigation of the role of BBX14 and BBX15 in GUN-type biogenic (gun) signaling showed that the overexpression of BBX14 or BBX15 caused de-repression of CA1 mRNA levels, when seedlings were grown on norflurazon. Notably, transcripts of the LHCB1.2 marker are not de-repressed. Furthermore, BBX14 is required to acclimate plants to HL stress. We propose that BBX14 is an integrator of biogenic signals and that BBX14 is a nuclear target of retrograde signals downstream of the GUN1/GLK1 module. However, we do not classify BBX14 or BBX15 overexpressors as gun mutants based on a critical evaluation of our results and those reported in the literature. Finally, we discuss a classification system necessary for the declaration of new gun mutants.
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Affiliation(s)
- Vasil Atanasov
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-University München, 82152, Martinsried, Germany
| | - Julia Schumacher
- Chair for Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jose M Muiño
- Chair for Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Catharina Larasati
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-University München, 82152, Martinsried, Germany
| | - Liangsheng Wang
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-University München, 82152, Martinsried, Germany
| | - Kerstin Kaufmann
- Chair for Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dario Leister
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-University München, 82152, Martinsried, Germany
| | - Tatjana Kleine
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-University München, 82152, Martinsried, Germany
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7
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Ohlsson JA, Leong JX, Elander PH, Ballhaus F, Holla S, Dauphinee AN, Johansson J, Lommel M, Hofmann G, Betnér S, Sandgren M, Schumacher K, Bozhkov PV, Minina EA. SPIRO - the automated Petri plate imaging platform designed by biologists, for biologists. Plant J 2024; 118:584-600. [PMID: 38141174 DOI: 10.1111/tpj.16587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/04/2023] [Indexed: 12/25/2023]
Abstract
Phenotyping of model organisms grown on Petri plates is often carried out manually, despite the procedures being time-consuming and laborious. The main reason for this is the limited availability of automated phenotyping facilities, whereas constructing a custom automated solution can be a daunting task for biologists. Here, we describe SPIRO, the Smart Plate Imaging Robot, an automated platform that acquires time-lapse photographs of up to four vertically oriented Petri plates in a single experiment, corresponding to 192 seedlings for a typical root growth assay and up to 2500 seeds for a germination assay. SPIRO is catered specifically to biologists' needs, requiring no engineering or programming expertise for assembly and operation. Its small footprint is optimized for standard incubators, the inbuilt green LED enables imaging under dark conditions, and remote control provides access to the data without interfering with sample growth. SPIRO's excellent image quality is suitable for automated image processing, which we demonstrate on the example of seed germination and root growth assays. Furthermore, the robot can be easily customized for specific uses, as all information about SPIRO is released under open-source licenses. Importantly, uninterrupted imaging allows considerably more precise assessment of seed germination parameters and root growth rates compared with manual assays. Moreover, SPIRO enables previously technically challenging assays such as phenotyping in the dark. We illustrate the benefits of SPIRO in proof-of-concept experiments which yielded a novel insight on the interplay between autophagy, nitrogen sensing, and photoblastic response.
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Affiliation(s)
- Jonas A Ohlsson
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Jia Xuan Leong
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, D-72076, Germany
| | - Pernilla H Elander
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Florentine Ballhaus
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Sanjana Holla
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Adrian N Dauphinee
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | | | - Mark Lommel
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
- Department of Microbiology, Saarland University, Campus A1.5, Saarbrücken, 66123, Germany
| | - Gero Hofmann
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
| | - Staffan Betnér
- Northern Registry Centre, Department of Public Health and Clinical Medicine, Umeå University, Umeå, 90187, Sweden
| | - Mats Sandgren
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Karin Schumacher
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Elena A Minina
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
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8
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Chery M, Berrissou C, Humbert N, Hummel G, Mely Y, Salinas-Giegé T, Drouard L. The Arabidopsis tDR Ala forms G-quadruplex structures that can be unwound by the DExH1 DEA(D/H)-box RNA helicase. Plant J 2024; 118:124-140. [PMID: 38113339 DOI: 10.1111/tpj.16596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/05/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023]
Abstract
As in many other organisms, tRNA-derived RNAs (tDRs) exist in plants and likely have multiple functions. We previously showed that tDRs are present in Arabidopsis under normal growth conditions, and that the ones originating from alanine tRNAs are the most abundant in leaves. We also showed that tDRs Ala of 20 nt produced from mature tRNAAla (AGC) can block in vitro protein translation. Here, we report that first, these tDRs Ala (AGC) can be found within peculiar foci in the cell that are neither P-bodies nor stress granules and, second, that they assemble into intermolecular RNA G-quadruplex (rG4) structures. Such tDR Ala rG4 structures can specifically interact with an Arabidopsis DEA(D/H) RNA helicase, the DExH1 protein, and unwind them. The rG4-DExH1 protein interaction relies on a glycine-arginine domain with RGG/RG/GR/GRR motifs present at the N-terminal extremity of the protein. Mutations on the four guanine residues located at the 5' extremity of the tDR Ala abolish its rG4 structure assembly, association with the DExH1 protein, and foci formation, but they do not prevent protein translation inhibition in vitro. Our data suggest that the sequestration of tDRs Ala into rG4 complexes might represent a way to modulate accessible and functional tDRs for translation inhibition within the plant cell via the activity of a specific RNA helicase, DExH1.
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Affiliation(s)
- Marjorie Chery
- Institut de Biologie Moléculaire des Plantes - CNRS, Université de Strasbourg, 12 rue du général Zimmer, F-67084, Strasbourg, France
| | - Christina Berrissou
- Institut de Biologie Moléculaire des Plantes - CNRS, Université de Strasbourg, 12 rue du général Zimmer, F-67084, Strasbourg, France
| | - Nicolas Humbert
- Laboratoire de Bioimagerie et Pathologies - CNRS, UMR 7021, Faculté de Pharmacie, Université de Strasbourg, 74 route du Rhin, 67401, Illkirch, France
| | - Guillaume Hummel
- Institut de Biologie Moléculaire des Plantes - CNRS, Université de Strasbourg, 12 rue du général Zimmer, F-67084, Strasbourg, France
| | - Yves Mely
- Laboratoire de Bioimagerie et Pathologies - CNRS, UMR 7021, Faculté de Pharmacie, Université de Strasbourg, 74 route du Rhin, 67401, Illkirch, France
| | - Thalia Salinas-Giegé
- Institut de Biologie Moléculaire des Plantes - CNRS, Université de Strasbourg, 12 rue du général Zimmer, F-67084, Strasbourg, France
| | - Laurence Drouard
- Institut de Biologie Moléculaire des Plantes - CNRS, Université de Strasbourg, 12 rue du général Zimmer, F-67084, Strasbourg, France
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9
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Kralemann LEM, van Tol N, Hooykaas PJJ, Tijsterman M. Molecular analysis of the role of polymerase theta in gene targeting in Arabidopsis thaliana. Plant J 2024; 118:255-262. [PMID: 38402589 DOI: 10.1111/tpj.16689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/05/2024] [Accepted: 02/07/2024] [Indexed: 02/27/2024]
Abstract
Precise genetic modification can be achieved via a sequence homology-mediated process known as gene targeting (GT). Whilst established for genome engineering purposes, the application of GT in plants still suffers from a low efficiency for which an explanation is currently lacking. Recently reported reduced rates of GT in A. thaliana deficient in polymerase theta (Polθ), a core component of theta-mediated end joining (TMEJ) of DNA breaks, have led to the suggestion of a direct involvement of this enzyme in the homology-directed process. Here, by monitoring homology-driven gene conversion in plants with CRISPR reagent and donor sequences pre-integrated at random sites in the genome (in planta GT), we demonstrate that Polθ action is not required for GT, but instead suppresses the process, likely by promoting the repair of the DNA break by end-joining. This finding indicates that lack of donor integration explains the previously established reduced GT rates seen upon transformation of Polθ-deficient plants. Our study additionally provides insight into ectopic gene targeting (EGT), recombination events between donor and target that do not map to the target locus. EGT, which occurs at similar frequencies as "true" GT during transformation, was rare in our in planta GT experiments arguing that EGT predominantly results from target locus recombination with nonintegrated T-DNA molecules. By describing mechanistic features of GT our study provides directions for the improvement of precise genetic modification of plants.
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Affiliation(s)
- Lejon E M Kralemann
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Niels van Tol
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Paul J J Hooykaas
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Marcel Tijsterman
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2300 RC, Leiden, The Netherlands
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10
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Bando K, Kushibe R, Kitaoka N, Tamai Y, Narisawa K, Matsuura H. Isolation, structural elucidation, and biological activity of a novel isocoumarin from the dark septate endophytic fungus Phialocephala fortinii. Z NATURFORSCH C 2024; 0:znc-2023-0139. [PMID: 38421614 DOI: 10.1515/znc-2023-0139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/13/2024] [Indexed: 03/02/2024]
Abstract
A novel isocoumarin was isolated from the mycelia of the dark septate endophytic fungus Phialocephala fortinii. The chemical structure was determined to be 8-hydroxy-6-methoxy-3,7-dimethyl-1H-2-benzopyran-1-one based on mass spectrometry, 1H-nuclear magnetic resonance (NMR), and 13C-NMR spectroscopic analyses, including 2D-NMR experiments. The isolated compound inhibited root growth of Arabidopsis thaliana, suggesting its potential as a plant growth regulator.
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Affiliation(s)
- Kei Bando
- Research Faculty of Agriculture, 12810 Hokkaido University , Sapporo, Hokkaido, 060-8589, Japan
| | - Ryoga Kushibe
- Research Faculty of Agriculture, 12810 Hokkaido University , Sapporo, Hokkaido, 060-8589, Japan
| | - Naoki Kitaoka
- Research Faculty of Agriculture, 12810 Hokkaido University , Sapporo, Hokkaido, 060-8589, Japan
| | - Yutaka Tamai
- Research Faculty of Agriculture, 12810 Hokkaido University , Sapporo, Hokkaido, 060-8589, Japan
| | - Kazuhiko Narisawa
- Department of Bioresource Science, College of Agriculture, Ibaraki University, Ami, Inashiki, Ibaraki, 300-0393, Japan
| | - Hideyuki Matsuura
- Research Faculty of Agriculture, 12810 Hokkaido University , Sapporo, Hokkaido, 060-8589, Japan
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11
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Chai X, Wang X, Rong L, Luo M, Yuan L, Li Q, He B, Jiang J, Ji D, Ouyang M, Lu Q, Zhang L, Rochaix JD, Chi W. The translocon protein FtsHi1 is an ATP-dependent DNA/RNA helicase that prevents R-loop accumulation in chloroplasts. New Phytol 2024; 241:2209-2226. [PMID: 38084045 DOI: 10.1111/nph.19470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 11/22/2023] [Indexed: 02/09/2024]
Abstract
R-loops, three-stranded nucleic acid structures consisting of a DNA: RNA hybrid and displaced single-stranded DNA, play critical roles in gene expression and genome stability. How R-loop homeostasis is integrated into chloroplast gene expression remains largely unknown. We found an unexpected function of FtsHi1, an inner envelope membrane-bound AAA-ATPase in chloroplast R-loop homeostasis of Arabidopsis thaliana. Previously, this protein was shown to function as a component of the import motor complex for nuclear-encoded chloroplast proteins. However, this study provides evidence that FtsHi1 is an ATP-dependent helicase that efficiently unwinds both DNA-DNA and DNA-RNA duplexes, thereby preventing R-loop accumulation. Over-accumulation of R-loops could impair chloroplast transcription but not necessarily genome integrity. The dual function of FtsHi1 in both protein import and chloroplast gene expression may be important to coordinate the biogenesis of nuclear- and chloroplast-encoded subunits of multi-protein photosynthetic complexes. This study suggests a mechanical link between protein import and R-loop homeostasis in chloroplasts of higher plants.
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Affiliation(s)
- Xin Chai
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiushun Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liwei Rong
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Manfei Luo
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Yuan
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiuxin Li
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoye He
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jingjing Jiang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Daili Ji
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Min Ouyang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Qingtao Lu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Lixin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun St., Kaifeng, 475001, China
| | - Jean-David Rochaix
- Department of Molecular Biology, University of Geneva, 1211, Geneva, Switzerland
- Department of Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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12
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Kubalová M, Müller K, Dobrev PI, Rizza A, Jones AM, Fendrych M. Auxin co-receptor IAA17/AXR3 controls cell elongation in Arabidopsis thaliana root solely by modulation of nuclear auxin pathway. New Phytol 2024; 241:2448-2463. [PMID: 38308183 DOI: 10.1111/nph.19557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 01/06/2024] [Indexed: 02/04/2024]
Abstract
The nuclear TIR1/AFB-Aux/IAA auxin pathway plays a crucial role in regulating plant growth and development. Specifically, the IAA17/AXR3 protein participates in Arabidopsis thaliana root development, response to auxin and gravitropism. However, the mechanism by which AXR3 regulates cell elongation is not fully understood. We combined genetical and cell biological tools with transcriptomics and determination of auxin levels and employed live cell imaging and image analysis to address how the auxin response pathways influence the dynamics of root growth. We revealed that manipulations of the TIR1/AFB-Aux/IAA pathway rapidly modulate root cell elongation. While inducible overexpression of the AXR3-1 transcriptional inhibitor accelerated growth, overexpression of the dominant activator form of ARF5/MONOPTEROS inhibited growth. In parallel, AXR3-1 expression caused loss of auxin sensitivity, leading to transcriptional reprogramming, phytohormone signaling imbalance and increased levels of auxin. Furthermore, we demonstrated that AXR3-1 specifically perturbs nuclear auxin signaling, while the rapid auxin response remains functional. Our results shed light on the interplay between the nuclear and cytoplasmic auxin pathways in roots, revealing their partial independence but also the dominant role of the nuclear auxin pathway during the gravitropic response of Arabidopsis thaliana roots.
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Affiliation(s)
- Monika Kubalová
- Department of Experimental Plant Biology, Charles University, Prague, 12844, Czech Republic
| | - Karel Müller
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, 16502, Czech Republic
| | - Petre Ivanov Dobrev
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, 16502, Czech Republic
| | - Annalisa Rizza
- Sainsbury Laboratory, Cambridge University, Cambridge, CB2 1LR, UK
| | | | - Matyáš Fendrych
- Department of Experimental Plant Biology, Charles University, Prague, 12844, Czech Republic
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13
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Du X, Gao Y, Zhang H, Xu X, Li Y, Zhao L, Luo M, Wang H. HDA6 modulates Arabidopsis pavement cell morphogenesis through epigenetic suppression of ROP6 GTPase expression and signaling. New Phytol 2024; 241:2523-2539. [PMID: 38214469 DOI: 10.1111/nph.19532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 01/01/2024] [Indexed: 01/13/2024]
Abstract
The transcriptional regulation of Rho-related GTPase from plants (ROPs), which determine cell polarity formation and maintenance during plant development, still remains enigmatic. In this study, we elucidated the epigenetic mechanism of histone deacetylase HDA6 in transcriptional repression of ROP6 and its impact on cell polarity and morphogenesis in Arabidopsis leaf epidermal pavement cells (PCs). We found that the hda6 mutant axe1-4 exhibited impaired jigsaw-shaped PCs and convoluted leaves. This correlated with disruptions in the spatial organizations of cortical microtubules and filamentous actin, which is integral to PC indentation and lobe formation. Further transcriptional analyses and chromatin immunoprecipitation assay revealed that HDA6 specifically represses ROP6 expression through histone H3K9K14 deacetylation. Importantly, overexpression of dominant negative-rop6 in axe1-4 restored interdigitated cell morphology. Our study unveils HDA6 as a key regulator in Arabidopsis PC morphogenesis through epigenetic suppression of ROP6. It reveals the pivotal role of HDA6 in the transcriptional regulation of ROP6 and provides compelling evidence for the functional interplay between histone deacetylation and ROP6-mediated cytoskeletal arrangement in the development of interdigitated PCs.
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Affiliation(s)
- Xiaojuan Du
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yingmiao Gao
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Zhang
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaoyu Xu
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Ying Li
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Lifeng Zhao
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Ming Luo
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Wang
- Department of Cell and Developmental Biology, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
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14
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Canal MV, Mansilla N, Gras DE, Ibarra A, Figueroa CM, Gonzalez DH, Welchen E. Cytochrome c levels affect the TOR pathway to regulate growth and metabolism under energy-deficient conditions. New Phytol 2024; 241:2039-2058. [PMID: 38191763 DOI: 10.1111/nph.19506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/03/2023] [Indexed: 01/10/2024]
Abstract
Mitochondrial function is essential for plant growth, but the mechanisms involved in adjusting growth and metabolism to changes in mitochondrial energy production are not fully understood. We studied plants with reduced expression of CYTC-1, one of two genes encoding the respiratory chain component cytochrome c (CYTc) in Arabidopsis, to understand how mitochondria communicate their status to coordinate metabolism and growth. Plants with CYTc deficiency show decreased mitochondrial membrane potential and lower ATP content, even when carbon sources are present. They also exhibit higher free amino acid content, induced autophagy, and increased resistance to nutritional stress caused by prolonged darkness, similar to plants with triggered starvation signals. CYTc deficiency affects target of rapamycin (TOR)-pathway activation, reducing S6 kinase (S6K) and RPS6A phosphorylation, as well as total S6K protein levels due to increased protein degradation via proteasome and autophagy. TOR overexpression restores growth and other parameters affected in cytc-1 mutants, even if mitochondrial membrane potential and ATP levels remain low. We propose that CYTc-deficient plants coordinate their metabolism and energy availability by reducing TOR-pathway activation as a preventive signal to adjust growth in anticipation of energy exhaustion, thus providing a mechanism by which changes in mitochondrial activity are transduced to the rest of the cell.
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Affiliation(s)
- María Victoria Canal
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Natanael Mansilla
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Diana E Gras
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Agustín Ibarra
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Carlos M Figueroa
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Daniel H Gonzalez
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Elina Welchen
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
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15
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Huang P, El-Soda M, Wolinska KW, Zhao K, Davila Olivas NH, van Loon JJA, Dicke M, Aarts MGM. Genome-wide association analysis reveals genes controlling an antagonistic effect of biotic and osmotic stress on Arabidopsis thaliana growth. Mol Plant Pathol 2024; 25:e13436. [PMID: 38460112 PMCID: PMC10924621 DOI: 10.1111/mpp.13436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 03/11/2024]
Abstract
While the response of Arabidopsis thaliana to drought, herbivory or fungal infection has been well-examined, the consequences of exposure to a series of such (a)biotic stresses are not well studied. This work reports on the genetic mechanisms underlying the Arabidopsis response to single osmotic stress, and to combinatorial stress, either fungal infection using Botrytis cinerea or herbivory using Pieris rapae caterpillars followed by an osmotic stress treatment. Several small-effect genetic loci associated with rosette dry weight (DW), rosette water content (WC), and the projected rosette leaf area in response to combinatorial stress were mapped using univariate and multi-environment genome-wide association approaches. A single-nucleotide polymorphism (SNP) associated with DROUGHT-INDUCED 19 (DI19) was identified by both approaches, supporting its potential involvement in the response to combinatorial stress. Several SNPs were found to be in linkage disequilibrium with known stress-responsive genes such as PEROXIDASE 34 (PRX34), BASIC LEUCINE ZIPPER 25 (bZIP25), RESISTANCE METHYLATED GENE 1 (RMG1) and WHITE RUST RESISTANCE 4 (WRR4). An antagonistic effect between biotic and osmotic stress was found for prx34 and arf4 mutants, which suggests PRX34 and ARF4 play an important role in the response to the combinatorial stress.
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Affiliation(s)
- Pingping Huang
- Laboratory of Genetics, Wageningen University & Research, Wageningen, Netherlands
| | - Mohamed El-Soda
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Katarzyna W Wolinska
- Laboratory of Genetics, Wageningen University & Research, Wageningen, Netherlands
| | - Kaige Zhao
- Laboratory of Genetics, Wageningen University & Research, Wageningen, Netherlands
| | | | - Joop J A van Loon
- Laboratory of Entomology, Wageningen University & Research, Wageningen, Netherlands
| | - Marcel Dicke
- Laboratory of Entomology, Wageningen University & Research, Wageningen, Netherlands
| | - Mark G M Aarts
- Laboratory of Genetics, Wageningen University & Research, Wageningen, Netherlands
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16
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Zhong R, Cui D, Richardson EA, Ye ZH. Acetylation of homogalacturonan and rhamnogalacturonan-I is catalyzed by a suite of trichome birefringence-like proteins. Plant J 2024; 117:1084-1098. [PMID: 37934816 DOI: 10.1111/tpj.16540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/20/2023] [Accepted: 10/29/2023] [Indexed: 11/09/2023]
Abstract
Plant cell wall polysaccharides, including xylan, mannan, xyloglucan, and pectins, are often acetylated and members of the domain of unknown function 231 (DUF231)/trichome birefringence-like (TBL) family have been shown to be O-acetyltransferases mediating the acetylation of xylan, mannan, and xyloglucan. However, little is known about the O-acetyltransferases responsible for pectin acetylation. In this report, we biochemically characterized a suite of Arabidopsis DUF231/TBL proteins for their roles in pectin acetylation. We generated 24 TBL recombinant proteins in mammalian cells and demonstrated that 10 of them were able to transfer acetyl groups from acetyl-CoA onto the pectins homogalacturonan (HG) or rhamnogalacturonan-I (RG-I), and thus were named pectin O-acetyltransferase 1 to 10 (POAT1 to 10). It was found that POAT2,4,9,10 specifically acetylated HG and POAT5,6 acetylated RG-I, whereas POAT1,3,7,8 could act on both HG and RG-I. The acetylation of HG and RG-I by POATs was further corroborated by hydrolysis with pectin acetylesterases and by nuclear magnetic resonance spectroscopy. In addition, mutations of the conserved GDS and DXXH motifs in POAT3 and POAT8 were shown to lead to a loss of their ability to acetylate HG and RG-I. Furthermore, simultaneous RNA interference downregulation of POAT1,3,6,7,8 resulted in reduced cell expansion, impaired plant growth, and decreased pectin acetylation. Together, our findings indicate that these POATs are pectin O-acetyltransferases involved in acetylation of the pectin polysaccharides HG and RG-I.
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Affiliation(s)
- Ruiqin Zhong
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - Dongtao Cui
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, 02138, USA
| | | | - Zheng-Hua Ye
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, USA
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17
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Smith AB, Ganguly DR, Moore M, Bowerman AF, Janapala Y, Shirokikh NE, Pogson BJ, Crisp PA. Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation. Plant J 2024; 117:818-839. [PMID: 37947266 PMCID: PMC10952913 DOI: 10.1111/tpj.16531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 09/20/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023]
Abstract
Transcript stability is an important determinant of its abundance and, consequently, translational output. Transcript destabilisation can be rapid and is well suited for modulating the cellular response. However, it is unclear the extent to which RNA stability is altered under changing environmental conditions in plants. We previously hypothesised that recovery-induced transcript destabilisation facilitated a phenomenon of rapid recovery gene downregulation (RRGD) in Arabidopsis thaliana (Arabidopsis) following light stress, based on mathematical calculations to account for ongoing transcription. Here, we test this hypothesis and investigate processes regulating transcript abundance and fate by quantifying changes in transcription, stability and translation before, during and after light stress. We adapt syringe infiltration to apply a transcriptional inhibitor to soil-grown plants in combination with stress treatments. Compared with measurements in juvenile plants and cell culture, we find reduced stability across a range of transcripts encoding proteins involved in RNA binding and processing. We also observe light-induced destabilisation of transcripts, followed by their stabilisation during recovery. We propose that this destabilisation facilitates RRGD, possibly in combination with transcriptional shut-off that was confirmed for HSP101, ROF1 and GOLS1. We also show that translation remains highly dynamic over the course of light stress and recovery, with a bias towards transcript-specific increases in ribosome association, independent of changes in total transcript abundance, after 30 min of light stress. Taken together, we provide evidence for the combinatorial regulation of transcription and stability that occurs to coordinate translation during light stress and recovery in Arabidopsis.
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Affiliation(s)
- Aaron B. Smith
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Diep R. Ganguly
- CSIRO Synthetic Biology Future Science PlatformCanberraAustralian Capital Territory2601Australia
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Marten Moore
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Andrew F. Bowerman
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Yoshika Janapala
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery InstituteMonash UniversityClaytonVictoria3800Australia
| | - Nikolay E. Shirokikh
- The John Curtin School of Medical Research, The Shine‐Dalgarno Centre for RNA InnovationThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Barry J. Pogson
- Research School of BiologyThe Australian National UniversityCanberraAustralian Capital Territory2601Australia
| | - Peter A. Crisp
- School of Agriculture and Food SciencesThe University of QueenslandBrisbaneQueensland4072Australia
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18
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Schneider M, Van Bel M, Inzé D, Baekelandt A. Leaf growth - complex regulation of a seemingly simple process. Plant J 2024; 117:1018-1051. [PMID: 38012838 DOI: 10.1111/tpj.16558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/08/2023] [Accepted: 11/11/2023] [Indexed: 11/29/2023]
Abstract
Understanding the underlying mechanisms of plant development is crucial to successfully steer or manipulate plant growth in a targeted manner. Leaves, the primary sites of photosynthesis, are vital organs for many plant species, and leaf growth is controlled by a tight temporal and spatial regulatory network. In this review, we focus on the genetic networks governing leaf cell proliferation, one major contributor to final leaf size. First, we provide an overview of six regulator families of leaf growth in Arabidopsis: DA1, PEAPODs, KLU, GRFs, the SWI/SNF complexes, and DELLAs, together with their surrounding genetic networks. Next, we discuss their evolutionary conservation to highlight similarities and differences among species, because knowledge transfer between species remains a big challenge. Finally, we focus on the increase in knowledge of the interconnectedness between these genetic pathways, the function of the cell cycle machinery as their central convergence point, and other internal and environmental cues.
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Affiliation(s)
- Michele Schneider
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Michiel Van Bel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Dirk Inzé
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Alexandra Baekelandt
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
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19
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Kim SH, Lee SH, Park TK, Tian Y, Yu K, Lee BH, Bai MY, Cho SJ, Kim TW. Comparative analysis of BZR1/BES1 family transcription factors in Arabidopsis. Plant J 2024; 117:747-765. [PMID: 37926922 DOI: 10.1111/tpj.16527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 09/26/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023]
Abstract
Brassinazole Resistant 1 (BZR1) and bri1 EMS Suppressor 1 (BES1) are key transcription factors that mediate brassinosteroid (BR)-responsive gene expression in Arabidopsis. The BZR1/BES1 family is composed of BZR1, BES1, and four BES1/BZR1 homologs (BEH1-BEH4). However, little is known about whether BEHs are regulated by BR signaling in the same way as BZR1 and BES1. We comparatively analyzed the functional characteristics of six BZR1/BES1 family members and their regulatory mechanisms in BR signaling using genetic and biochemical analyses. We also compared their subcellular localizations regulated by the phosphorylation status, interaction with GSK3-like kinases, and heterodimeric combination. We found that all BZR1/BES1 family members restored the phenotypic defects of bri1-5 by their overexpression. Unexpectedly, BEH2-overexpressing plants showed the most distinct phenotype with enhanced BR responses. RNA-Seq analysis indicated that overexpression of both BZR1 and BEH2 regulates BR-responsive gene expression, but BEH2 has a much greater proportion of BR-independent gene expression than BZR1. Unlike BZR1 and BES1, the BR-regulated subcellular translocation of the four BEHs was not tightly correlated with their phosphorylation status. Notably, BEH1 and BEH2 are predominantly localized in the nucleus, which induces the nuclear accumulation of other BZR1/BES1 family proteins through heterodimerization. Altogether, our comparative analyses suggest that BEH1 and BEH2 play an important role in the functional interaction between BZR1/BES1 family transcription factors.
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Affiliation(s)
- So-Hee Kim
- Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Convergence of Basic Science, Hanyang University, Seoul, 04763, Republic of Korea
| | - Se-Hwa Lee
- Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Convergence of Basic Science, Hanyang University, Seoul, 04763, Republic of Korea
| | - Tae-Ki Park
- Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea
- Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, 04763, Republic of Korea
| | - Yanchen Tian
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Kyoungjae Yu
- Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Byeong-Ha Lee
- Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Ming-Yi Bai
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Sung-Jin Cho
- School of Biological Sciences, College of Natural Sciences, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Tae-Wuk Kim
- Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Convergence of Basic Science, Hanyang University, Seoul, 04763, Republic of Korea
- Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, 04763, Republic of Korea
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20
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Messant M, Hani U, Lai TL, Wilson A, Shimakawa G, Krieger-Liszkay A. Plastid terminal oxidase (PTOX) protects photosystem I and not photosystem II against photoinhibition in Arabidopsis thaliana and Marchantia polymorpha. Plant J 2024; 117:669-678. [PMID: 37921075 DOI: 10.1111/tpj.16520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/01/2023] [Accepted: 10/21/2023] [Indexed: 11/04/2023]
Abstract
The plastid terminal oxidase PTOX controls the oxidation level of the plastoquinone pool in the thylakoid membrane and acts as a safety valve upon abiotic stress, but detailed characterization of its role in protecting the photosynthetic apparatus is limited. Here we used PTOX mutants in two model plants Arabidopsis thaliana and Marchantia polymorpha. In Arabidopsis, lack of PTOX leads to a severe defect in pigmentation, a so-called variegated phenotype, when plants are grown at standard light intensities. We created a green Arabidopsis PTOX mutant expressing the bacterial carotenoid desaturase CRTI and a double mutant in Marchantia lacking both PTOX isoforms, the plant-type and the alga-type PTOX. In both species, lack of PTOX affected the redox state of the plastoquinone pool. Exposure of plants to high light intensity showed in the absence of PTOX higher susceptibility of photosystem I to light-induced damage while photosystem II was more stable compared with the wild type demonstrating that PTOX plays both, a pro-oxidant and an anti-oxidant role in vivo. Our results shed new light on the function of PTOX in the protection of photosystem I and II.
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Affiliation(s)
- Marine Messant
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette cedex, France
| | - Umama Hani
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette cedex, France
| | - Thanh-Lan Lai
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette cedex, France
| | - Adjélé Wilson
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette cedex, France
| | - Ginga Shimakawa
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette cedex, France
- Department of Bioscience, School of Biological and Environmental Sciences, Kwansei-Gakuin University, 1 Gakuen-Uegahara, Sanda, Hyogo, 669-1330, Japan
| | - Anja Krieger-Liszkay
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette cedex, France
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21
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Felemban A, Moreno JC, Mi J, Ali S, Sham A, AbuQamar SF, Al-Babili S. The apocarotenoid β-ionone regulates the transcriptome of Arabidopsis thaliana and increases its resistance against Botrytis cinerea. Plant J 2024; 117:541-560. [PMID: 37932864 DOI: 10.1111/tpj.16510] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 11/08/2023]
Abstract
Carotenoids are isoprenoid pigments indispensable for photosynthesis. Moreover, they are the precursor of apocarotenoids, which include the phytohormones abscisic acid (ABA) and strigolactones (SLs) as well as retrograde signaling molecules and growth regulators, such as β-cyclocitral and zaxinone. Here, we show that the application of the volatile apocarotenoid β-ionone (β-I) to Arabidopsis plants at micromolar concentrations caused a global reprogramming of gene expression, affecting thousands of transcripts involved in stress tolerance, growth, hormone metabolism, pathogen defense, and photosynthesis. This transcriptional reprogramming changes, along with induced changes in the level of the phytohormones ABA, jasmonic acid, and salicylic acid, led to enhanced Arabidopsis resistance to the widespread necrotrophic fungus Botrytis cinerea (B.c.) that causes the gray mold disease in many crop species and spoilage of harvested fruits. Pre-treatment of tobacco and tomato plants with β-I followed by inoculation with B.c. confirmed the effect of β-I in increasing the resistance to this pathogen in crop plants. Moreover, we observed reduced susceptibility to B.c. in fruits of transgenic tomato plants overexpressing LYCOPENE β-CYCLASE, which contains elevated levels of endogenous β-I, providing a further evidence for its effect on B.c. infestation. Our work unraveled β-I as a further carotenoid-derived regulatory metabolite and indicates the possibility of establishing this natural volatile as an environmentally friendly bio-fungicide to control B.c.
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Affiliation(s)
- Abrar Felemban
- The Bioactives Laboratory, Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Juan C Moreno
- The Bioactives Laboratory, Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Jianing Mi
- The Bioactives Laboratory, Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Shawkat Ali
- Kentville Research and Development Center, Agriculture and Agri-Food Canada, Kentville, Nova Scotia, B4N 1J5, Canada
| | - Arjun Sham
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Synan F AbuQamar
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Salim Al-Babili
- The Bioactives Laboratory, Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
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22
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Launhardt L, Uhlenberg J, Stellmach H, Schomburg M, Hause B, Heilmann I, Heilmann M. Association of the Arabidopsis oleoyl Δ12-desaturase FAD2 with pre-cis-Golgi stacks at endoplasmic reticulum-Golgi-exit sites. Plant J 2024; 117:242-263. [PMID: 37805827 DOI: 10.1111/tpj.16492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/26/2023] [Accepted: 09/26/2023] [Indexed: 10/09/2023]
Abstract
The unsaturation of phospholipids influences the function of membranes. In Arabidopsis thaliana, the oleoyl Δ12-desaturase FAD2 converts oleic (18:1Δ9 ) to linoleic acid (18:2Δ9,12 ) and influences phospholipid unsaturation in different cellular membranes. Despite its importance, the precise localization of Arabidopsis FAD2 has not been unambiguously described. As FAD2 is thought to modify phospholipid-associated fatty acids at the endoplasmic reticulum (ER), from where unsaturates are distributed to other cellular sites, we hypothesized that FAD2 locates to ER subdomains enabling trafficking of lipid intermediates through the secretory pathway. Fluorescent FAD2 fusions used to test this hypothesis were first assessed for functionality by heterologous expression in yeast (Saccharomyces cerevisiae), and in planta by Arabidopsis fad2 mutant rescue upon ectopic expression from an intrinsic FAD2 promoter fragment. Light sheet fluorescence, laser scanning confocal or spinning disc microscopy of roots, leaves, or mesophyll protoplasts showed the functional fluorescence-tagged FAD2 variants in flattened donut-shaped structures of ~0.5-1 μm diameter, in a pattern not resembling mere ER association. High-resolution imaging of coexpressed organellar markers showed fluorescence-tagged FAD2 in a ring-shaped pattern surrounding ER-proximal Golgi particles, colocalizing with pre-cis-Golgi markers. This localization required the unusual C-terminal retention signal of FAD2, and deletion or substitutions in this protein region resulted in relaxed distribution and diffuse association with the ER. The distinct association of FAD2 with pre-cis-Golgi stacks in Arabidopsis root and leaf tissue is consistent with a contribution of FAD2 to membrane lipid homeostasis through the secretory pathway, as verified by an increased plasma membrane liquid phase order in the fad2 mutant.
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Affiliation(s)
- Larissa Launhardt
- Department of Plant Biochemistry, Institute of Biochemistry, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Johanna Uhlenberg
- Department of Plant Biochemistry, Institute of Biochemistry, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Hagen Stellmach
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, 06120, Halle (Saale), Germany
| | - Marie Schomburg
- Department of Plant Biochemistry, Institute of Biochemistry, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Bettina Hause
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, 06120, Halle (Saale), Germany
| | - Ingo Heilmann
- Department of Plant Biochemistry, Institute of Biochemistry, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Mareike Heilmann
- Department of Plant Biochemistry, Institute of Biochemistry, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
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23
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Manosalva Pérez N, Ferrari C, Engelhorn J, Depuydt T, Nelissen H, Hartwig T, Vandepoele K. MINI-AC: inference of plant gene regulatory networks using bulk or single-cell accessible chromatin profiles. Plant J 2024; 117:280-301. [PMID: 37788349 DOI: 10.1111/tpj.16483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/13/2023] [Accepted: 09/16/2023] [Indexed: 10/05/2023]
Abstract
Gene regulatory networks (GRNs) represent the interactions between transcription factors (TF) and their target genes. Plant GRNs control transcriptional programs involved in growth, development, and stress responses, ultimately affecting diverse agricultural traits. While recent developments in accessible chromatin (AC) profiling technologies make it possible to identify context-specific regulatory DNA, learning the underlying GRNs remains a major challenge. We developed MINI-AC (Motif-Informed Network Inference based on Accessible Chromatin), a method that combines AC data from bulk or single-cell experiments with TF binding site (TFBS) information to learn GRNs in plants. We benchmarked MINI-AC using bulk AC datasets from different Arabidopsis thaliana tissues and showed that it outperforms other methods to identify correct TFBS. In maize, a crop with a complex genome and abundant distal AC regions, MINI-AC successfully inferred leaf GRNs with experimentally confirmed, both proximal and distal, TF-target gene interactions. Furthermore, we showed that both AC regions and footprints are valid alternatives to infer AC-based GRNs with MINI-AC. Finally, we combined MINI-AC predictions from bulk and single-cell AC datasets to identify general and cell-type specific maize leaf regulators. Focusing on C4 metabolism, we identified diverse regulatory interactions in specialized cell types for this photosynthetic pathway. MINI-AC represents a powerful tool for inferring accurate AC-derived GRNs in plants and identifying known and novel candidate regulators, improving our understanding of gene regulation in plants.
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Affiliation(s)
- Nicolás Manosalva Pérez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Camilla Ferrari
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Julia Engelhorn
- Molecular Physiology Department, Heinrich-Heine University, 40225, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Thomas Depuydt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Thomas Hartwig
- Molecular Physiology Department, Heinrich-Heine University, 40225, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052, Ghent, Belgium
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24
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Wang Q, De Gernier H, Duan X, Xie Y, Geelen D, Hayashi KI, Xuan W, Geisler M, Ten Tusscher K, Beeckman T, Vanneste S. GH3-mediated auxin inactivation attenuates multiple stages of lateral root development. New Phytol 2023; 240:1900-1912. [PMID: 37743759 DOI: 10.1111/nph.19284] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/19/2023] [Indexed: 09/26/2023]
Abstract
Lateral root (LR) positioning and development rely on the dynamic interplay between auxin production, transport but also inactivation. Nonetheless, how the latter affects LR organogenesis remains largely uninvestigated. Here, we systematically analyze the impact of the major auxin inactivation pathway defined by GRETCHEN HAGEN3-type (GH3) auxin conjugating enzymes and DIOXYGENASE FOR AUXIN OXIDATION1 (DAO1) in all stages of LR development using reporters, genetics and inhibitors in Arabidopsis thaliana. Our data demonstrate that the gh3.1/2/3/4/5/6 hextuple (gh3hex) mutants display a higher LR density due to increased LR initiation and faster LR developmental progression, acting epistatically over dao1-1. Grafting and local inhibitor applications reveal that root and shoot GH3 activities control LR formation. The faster LR development in gh3hex is associated with GH3 expression domains in and around developing LRs. The increase in LR initiation is associated with accelerated auxin response oscillations coinciding with increases in apical meristem size and LR cap cell death rates. Our research reveals how GH3-mediated auxin inactivation attenuates LR development. Local GH3 expression in LR primordia attenuates development and emergence, whereas GH3 effects on pre-initiation stages are indirect, by modulating meristem activities that in turn coordinate root growth with LR spacing.
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Affiliation(s)
- Qing Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Hugues De Gernier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Xingliang Duan
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuanming Xie
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Danny Geelen
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, 9000, Belgium
| | - Ken-Ishiro Hayashi
- Department of Bioscience, Okayama University of Science, Okayama, 700-0005, Japan
| | - Wei Xuan
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Markus Geisler
- Department of Biology, University of Fribourg, Fribourg, CH-1700, Switzerland
| | - Kirsten Ten Tusscher
- Computational Developmental Biology Group, Faculty of Science, Utrecht University, Utrecht, 3584 CH, the Netherlands
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Steffen Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, 9000, Belgium
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25
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Duque-Jaramillo A, Ulmer N, Alseekh S, Bezrukov I, Fernie AR, Skirycz A, Karasov TL, Weigel D. The genetic and physiological basis of Arabidopsis thaliana tolerance to Pseudomonas viridiflava. New Phytol 2023; 240:1961-1975. [PMID: 37667565 DOI: 10.1111/nph.19241] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 08/15/2023] [Indexed: 09/06/2023]
Abstract
The opportunistic pathogen Pseudomonas viridiflava colonizes > 50 agricultural crop species and is the most common Pseudomonas in the phyllosphere of European Arabidopsis thaliana populations. Belonging to the P. syringae complex, it is genetically and phenotypically distinct from well-characterized P. syringae sensu stricto. Despite its prevalence, we lack knowledge of how A. thaliana responds to its native isolates at the molecular level. Here, we characterize the host response in an A. thaliana - P. viridiflava pathosystem. We measured host and pathogen growth in axenic infections and used immune mutants, transcriptomics, and metabolomics to determine defense pathways influencing susceptibility to P. viridiflava infection. Infection with P. viridiflava increased jasmonic acid (JA) levels and the expression of ethylene defense pathway marker genes. The immune response in a susceptible host accession was delayed compared with a tolerant one. Mechanical injury rescued susceptibility, consistent with an involvement of JA. The JA/ethylene pathway is important for suppression of P. viridiflava, yet suppression capacity varies between accessions. Our results shed light on how A. thaliana can suppress the ever-present P. viridiflava, but further studies are needed to understand how P. viridiflava evades this suppression to spread broadly across A. thaliana populations.
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Affiliation(s)
| | - Nina Ulmer
- Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Ilja Bezrukov
- Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Aleksandra Skirycz
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Boyce Thompson Institute, Cornell University, Ithaca, 14850, USA
| | - Talia L Karasov
- Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
- School of Biological Sciences, University of Utah, Salt Lake City, 84112, USA
| | - Detlef Weigel
- Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, 72074, Germany
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26
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Kenchanmane Raju SK, Lensink M, Kliebenstein DJ, Niederhuth C, Monroe G. Epigenomic divergence correlates with sequence polymorphism in Arabidopsis paralogs. New Phytol 2023; 240:1292-1304. [PMID: 37614211 DOI: 10.1111/nph.19227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/26/2023] [Indexed: 08/25/2023]
Abstract
Processes affecting rates of sequence polymorphism are fundamental to the evolution of gene duplicates. The relationship between gene activity and sequence polymorphism can influence the likelihood that functionally redundant gene copies are co-maintained in stable evolutionary equilibria vs other outcomes such as neofunctionalization. Here, we investigate genic variation in epigenome-associated polymorphism rates in Arabidopsis thaliana and consider whether these affect the evolution of gene duplicates. We compared the frequency of sequence polymorphism and patterns of genetic differentiation between genes classified by exon methylation patterns: unmethylated (unM), gene-body methylated (gbM), and transposon-like methylated (teM) states, which reflect divergence in gene expression. We found that the frequency of polymorphism was higher in teM (transcriptionally repressed, tissue-specific) genes and lower in gbM (active, constitutively expressed) genes. Comparisons of gene duplicates were largely consistent with genome-wide patterns - gene copies that exhibit teM accumulate more variation, evolve faster, and are in chromatin states associated with reduced DNA repair. This relationship between expression, the epigenome, and polymorphism may lead to the breakdown of equilibrium states that would otherwise maintain genetic redundancies. Epigenome-mediated polymorphism rate variation may facilitate the evolution of novel gene functions in duplicate paralogs maintained over evolutionary time.
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Affiliation(s)
| | - Mariele Lensink
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | | | - Chad Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- AgBioResearch, Michigan State University, East Lansing, MI, 48824, USA
| | - Grey Monroe
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
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27
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Yonehara K, Kumakura N, Motoyama T, Ishihama N, Dallery J, O'Connell R, Shirasu K. Efficient multiple gene knockout in Colletotrichum higginsianum via CRISPR/Cas9 ribonucleoprotein and URA3-based marker recycling. Mol Plant Pathol 2023; 24:1451-1464. [PMID: 37522511 PMCID: PMC10576178 DOI: 10.1111/mpp.13378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/21/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023]
Abstract
Colletotrichum higginsianum is a hemibiotrophic pathogen that causes anthracnose disease on crucifer hosts, including Arabidopsis thaliana. Despite the availability of genomic and transcriptomic information and the ability to transform both organisms, identifying C. higginsianum genes involved in virulence has been challenging due to recalcitrance to gene targeting and redundancy of virulence factors. To overcome these obstacles, we developed an efficient method for multiple gene disruption in C. higginsianum by combining CRISPR/Cas9 and a URA3-based marker recycling system. Our method significantly increased the efficiency of gene knockout via homologous recombination by introducing genomic DNA double-strand breaks. We demonstrated the applicability of the URA3-based marker recycling system for multiple gene targeting in the same strain. Using our technology, we successfully targeted two melanin biosynthesis genes, SCD1 and PKS1, which resulted in deficiency in melanization and loss of pathogenicity in the mutants. Our findings demonstrate the effectiveness of our methods in analysing virulence factors in C. higginsianum, thus accelerating research on plant-fungus interactions.
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Affiliation(s)
- Katsuma Yonehara
- RIKEN Center for Sustainable Resource ScienceYokohamaJapan
- Department of Biological Science, Graduate School of ScienceThe University of TokyoTokyoJapan
| | | | | | | | | | | | - Ken Shirasu
- RIKEN Center for Sustainable Resource ScienceYokohamaJapan
- Department of Biological Science, Graduate School of ScienceThe University of TokyoTokyoJapan
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28
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Wang LY, Li J, Gong B, Wang RH, Chen YL, Yin J, Yang C, Lin JT, Liu HZ, Yang Y, Li J, Li C, Yao N. Orosomucoid proteins limit endoplasmic reticulum stress in plants. New Phytol 2023; 240:1134-1148. [PMID: 37606093 DOI: 10.1111/nph.19200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/17/2023] [Indexed: 08/23/2023]
Abstract
Sphingolipids are cell membrane components and signaling molecules that induce endoplasmic reticulum (ER) stress responses, but the underlying mechanism is unknown. Orosomucoid proteins (ORMs) negatively regulate serine palmitoyltransferase activity, thus helping maintain proper sphingolipid levels in humans, yeast, and plants. In this report, we explored the roles of ORMs in regulating ER stress in Arabidopsis thaliana. Loss of ORM1 and ORM2 function caused constitutive activation of the unfolded protein response (UPR), as did treatment with the ceramide synthase inhibitor Fumonisin B1 (FB1) or ceramides. FB1 treatment induced the transcription factor bZIP28 to relocate from the ER membrane to the nucleus. The transcription factor WRKY75 positively regulates the UPR and physically interacted with bZIP28. We also found that the orm mutants showed impaired ER-associated degradation (ERAD), blocking the degradation of misfolded MILDEW RESISTANCE LOCUS-O 12 (MLO-12). ORM1 and ORM2 bind to EMS-MUTAGENIZED BRI1 SUPPRESSOR 7 (EBS7), a plant-specific component of the Arabidopsis ERAD complex, and regulate its stability. These data strongly suggest that ORMs in the ER membrane play vital roles in the UPR and ERAD pathways to prevent ER stress in Arabidopsis. Our results reveal that ORMs coordinate sphingolipid homeostasis with ER quality control and play a role in stress responses.
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Affiliation(s)
- Ling-Yan Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jian Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Benqiang Gong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Rui-Hua Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yi-Li Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jian Yin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Chang Yang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jia-Ting Lin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Hao-Zhuo Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yubing Yang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jianfeng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Chunyu Li
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Nan Yao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
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Lindbäck LN, Ji Y, Cervela-Cardona L, Jin X, Pedmale UV, Strand Å. An interplay between bZIP16, bZIP68, and GBF1 regulates nuclear photosynthetic genes during photomorphogenesis in Arabidopsis. New Phytol 2023; 240:1082-1096. [PMID: 37602940 PMCID: PMC10592178 DOI: 10.1111/nph.19219] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 07/20/2023] [Indexed: 08/22/2023]
Abstract
The development of a seedling into a photosynthetically active plant is a crucial process. Despite its importance, we do not fully understand the regulatory mechanisms behind the establishment of functional chloroplasts. We herein provide new insight into the early light response by identifying the function of three basic region/leucine zipper (bZIP) transcription factors: bZIP16, bZIP68, and GBF1. These proteins are involved in the regulation of key components required for the establishment of photosynthetically active chloroplasts. The activity of these bZIPs is dependent on the redox status of a conserved cysteine residue, which provides a mechanism to finetune light-responsive gene expression. The blue light cryptochrome (CRY) photoreceptors provide one of the major light-signaling pathways, and bZIP target genes overlap with one-third of CRY-regulated genes with an enrichment for photosynthesis/chloroplast-associated genes. bZIP16, bZIP68, and GBF1 were demonstrated as novel interaction partners of CRY1. The interaction between CRY1 and bZIP16 was stimulated by blue light. Furthermore, we demonstrate a genetic link between the bZIP proteins and cryptochromes as the cry1cry2 mutant is epistatic to the cry1cry2bzip16bzip68gbf1 mutant. bZIP16, bZIP68, and GBF1 regulate a subset of photosynthesis associated genes in response to blue light critical for a proper greening process in Arabidopsis.
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Affiliation(s)
- Louise Norén Lindbäck
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
| | - Yan Ji
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Luis Cervela-Cardona
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Xu Jin
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Ullas V. Pedmale
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Åsa Strand
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
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Buelbuel S, Sakuraba Y, Sedaghatmehr M, Watanabe M, Hoefgen R, Balazadeh S, Mueller-Roeber B. Arabidopsis BBX14 negatively regulates nitrogen starvation- and dark-induced leaf senescence. Plant J 2023; 116:251-268. [PMID: 37382898 DOI: 10.1111/tpj.16374] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/03/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023]
Abstract
Senescence is a highly regulated process driven by developmental age and environmental factors. Although leaf senescence is accelerated by nitrogen (N) deficiency, the underlying physiological and molecular mechanisms are largely unknown. Here, we reveal that BBX14, a previously uncharacterized BBX-type transcription factor in Arabidopsis, is crucial for N starvation-induced leaf senescence. We find that inhibiting BBX14 by artificial miRNA (amiRNA) accelerates senescence during N starvation and in darkness, while BBX14 overexpression (BBX14-OX) delays it, identifying BBX14 as a negative regulator of N starvation- and dark-induced senescence. During N starvation, nitrate and amino acids like glutamic acid, glutamine, aspartic acid, and asparagine were highly retained in BBX14-OX leaves compared to the wild type. Transcriptome analysis showed a large number of senescence-associated genes (SAGs) to be differentially expressed between BBX14-OX and wild-type plants, including ETHYLENE INSENSITIVE3 (EIN3) which regulates N signaling and leaf senescence. Chromatin immunoprecipitation (ChIP) showed that BBX14 directly regulates EIN3 transcription. Furthermore, we revealed the upstream transcriptional cascade of BBX14. By yeast one-hybrid screen and ChIP, we found that MYB44, a stress-responsive MYB transcription factor, directly binds to the promoter of BBX14 and activates its expression. In addition, Phytochrome Interacting Factor 4 (PIF4) binds to the promoter of BBX14 to repress BBX14 transcription. Thus, BBX14 functions as a negative regulator of N starvation-induced senescence through EIN3 and is directly regulated by PIF4 and MYB44.
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Affiliation(s)
- Selin Buelbuel
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße 24-25, Haus 20, 14476, Potsdam, Germany
| | - Yasuhito Sakuraba
- Graduate School of Agricultural and Life Sciences, Biotechnology Research Center, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Mastoureh Sedaghatmehr
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße 24-25, Haus 20, 14476, Potsdam, Germany
| | - Mutsumi Watanabe
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Rainer Hoefgen
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Salma Balazadeh
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße 24-25, Haus 20, 14476, Potsdam, Germany
| | - Bernd Mueller-Roeber
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße 24-25, Haus 20, 14476, Potsdam, Germany
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31
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Shin D, Perez VC, Dickinson GK, Zhao H, Dai R, Tomiczek B, Cho KH, Zhu N, Koh J, Grenning A, Kim J. Altered methionine metabolism impacts phenylpropanoid production and plant development in Arabidopsis thaliana. Plant J 2023; 116:187-200. [PMID: 37366635 DOI: 10.1111/tpj.16370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/20/2023] [Indexed: 06/28/2023]
Abstract
Phenylpropanoids are specialized metabolites derived from phenylalanine. Glucosinolates are defense compounds derived mainly from methionine and tryptophan in Arabidopsis. It was previously shown that the phenylpropanoid pathway and glucosinolate production are metabolically linked. The accumulation of indole-3-acetaldoxime (IAOx), the precursor of tryptophan-derived glucosinolates, represses phenylpropanoid biosynthesis through accelerated degradation of phenylalanine ammonia lyase (PAL). As PAL functions at the entry point of the phenylpropanoid pathway, which produces indispensable specialized metabolites such as lignin, aldoxime-mediated phenylpropanoid repression is detrimental to plant survival. Although methionine-derived glucosinolates in Arabidopsis are abundant, any impact of aliphatic aldoximes (AAOx) derived from aliphatic amino acids such as methionine on phenylpropanoid production remains unclear. Here, we investigate the impact of AAOx accumulation on phenylpropanoid production using Arabidopsis aldoxime mutants, ref2 and ref5. REF2 and REF5 metabolize aldoximes to respective nitrile oxides redundantly, but with different substrate specificities. ref2 and ref5 mutants have decreased phenylpropanoid contents due to the accumulation of aldoximes. As REF2 and REF5 have high substrate specificity toward AAOx and IAOx, respectively, it was assumed that ref2 accumulates AAOx, not IAOx. Our study indicates that ref2 accumulates both AAOx and IAOx. Removing IAOx partially restored phenylpropanoid content in ref2, but not to the wild-type level. However, when AAOx biosynthesis was silenced, phenylpropanoid production and PAL activity in ref2 were completely restored, suggesting an inhibitory effect of AAOx on phenylpropanoid production. Further feeding studies revealed that the abnormal growth phenotype commonly observed in Arabidopsis mutants lacking AAOx production is a consequence of methionine accumulation.
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Affiliation(s)
- Doosan Shin
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Veronica C Perez
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL, USA
| | - Gabriella K Dickinson
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL, USA
| | - Haohao Zhao
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Ru Dai
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Breanna Tomiczek
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Keun Ho Cho
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Ning Zhu
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32611, USA
| | - Jin Koh
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32611, USA
| | - Alexander Grenning
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Jeongim Kim
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL, USA
- Genetic Institute, University of Florida, Gainesville, FL, USA
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32
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Donà M, Bradamante G, Bogojevic Z, Gutzat R, Streubel S, Mosiolek M, Dolan L, Mittelsten Scheid O. A versatile CRISPR-based system for lineage tracing in living plants. Plant J 2023; 115:1169-1184. [PMID: 37403571 DOI: 10.1111/tpj.16378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/09/2023] [Accepted: 06/22/2023] [Indexed: 07/06/2023]
Abstract
Individual cells give rise to diverse cell lineages during the development of multicellular organisms. Understanding the contribution of these lineages to mature organisms is a central question of developmental biology. Several techniques to document cell lineages have been used, from marking single cells with mutations that express a visible marker to generating molecular bar codes by CRISPR-induced mutations and subsequent single-cell analysis. Here, we exploit the mutagenic activity of CRISPR to allow lineage tracing within living plants with a single reporter. Cas9-induced mutations are directed to correct a frameshift mutation that restores expression of a nuclear fluorescent protein, labelling the initial cell and all progenitor cells with a strong signal without modifying other phenotypes of the plants. Spatial and temporal control of Cas9 activity can be achieved using tissue-specific and/or inducible promoters. We provide proof of principle for the function of lineage tracing in two model plants. The conserved features of the components and the versatile cloning system, allowing for easy exchange of promoters, are expected to make the system widely applicable.
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Affiliation(s)
- Mattia Donà
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
| | - Gabriele Bradamante
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
| | - Zorana Bogojevic
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
| | - Ruben Gutzat
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
| | - Susanna Streubel
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
| | - Magdalena Mosiolek
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
| | - Liam Dolan
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030, Vienna, Austria
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Sharma A, Pridgeon AJ, Liu W, Segers F, Sharma B, Jenkins GI, Franklin KA. ELONGATED HYPOCOTYL5 (HY5) and HY5 HOMOLOGUE (HYH) maintain shade avoidance suppression in UV-B. Plant J 2023; 115:1394-1407. [PMID: 37243898 PMCID: PMC10953383 DOI: 10.1111/tpj.16328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/17/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023]
Abstract
Reductions in red to far-red ratio (R:FR) provide plants with an unambiguous signal of vegetational shade and are monitored by phytochrome photoreceptors. Plants integrate this information with other environmental cues to determine the proximity and density of encroaching vegetation. Shade-sensitive species respond to reductions in R:FR by initiating a suite of developmental adaptations termed shade avoidance. These include the elongation of stems to facilitate light foraging. Hypocotyl elongation is driven by increased auxin biosynthesis promoted by PHYTOCHROME INTERACTING FACTORs (PIF) 4, 5 and 7. UV-B perceived by the UV RESISTANCE LOCUS 8 (UVR8) photoreceptor rapidly inhibits shade avoidance, in part by suppressing PIF4/5 transcript accumulation and destabilising PIF4/5 protein. Here, we show that longer-term inhibition of shade avoidance is sustained by ELONGATED HYPOCOTYL 5 (HY5) and HY5 HOMOLOGUE (HYH), which regulate transcriptional reprogramming of genes involved in hormone signalling and cell wall modification. HY5 and HYH are elevated in UV-B and suppress the expression of XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE (XTH) genes involved in cell wall loosening. They additionally increase expression GA2-OXIDASE1 (GA2ox1) and GA2ox2, encoding gibberellin catabolism enzymes that act redundantly to stabilise the PIF-inhibiting DELLA proteins. UVR8 therefore regulates temporally distinct signalling pathways to first rapidly inhibit and subsequently maintain suppression of shade avoidance following UV-B exposure.
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Affiliation(s)
- Ashutosh Sharma
- School of Biological Sciences, Life Sciences BuildingUniversity of BristolBristolBS8 1TQUK
| | - Ashley J. Pridgeon
- School of Biological Sciences, Life Sciences BuildingUniversity of BristolBristolBS8 1TQUK
| | - Wei Liu
- School of Molecular Biosciences, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - Francisca Segers
- School of Biological Sciences, Life Sciences BuildingUniversity of BristolBristolBS8 1TQUK
| | - Bhavana Sharma
- School of Biological Sciences, Life Sciences BuildingUniversity of BristolBristolBS8 1TQUK
| | - Gareth I. Jenkins
- School of Molecular Biosciences, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - Keara A. Franklin
- School of Biological Sciences, Life Sciences BuildingUniversity of BristolBristolBS8 1TQUK
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34
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Zhai X, Bai J, Xu W, Yang X, Jia Z, Xia W, Wu X, Liang Q, Li B, Jia N. The molecular chaperone mtHSC70-1 interacts with DjA30 to regulate female gametophyte development and fertility in Arabidopsis. The Plant Journal 2023; 115:1677-1698. [PMID: 37294615 DOI: 10.1111/tpj.16347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/26/2023] [Indexed: 06/10/2023]
Abstract
Arabidopsis mitochondria-targeted heat shock protein 70 (mtHSC70-1) plays important roles in the establishment of cytochrome c oxidase-dependent respiration and redox homeostasis during the vegetative growth of plants. Here, we report that knocking out the mtHSC70-1 gene led to a decrease in plant fertility; the fertility defect of the mutant was completely rescued by introducing the mtHSC70-1 gene. mtHSC70-1 mutants also showed defects in female gametophyte (FG) development, including delayed mitosis, abnormal nuclear position, and ectopic gene expression in the embryo sacs. In addition, we found that an Arabidopsis mitochondrial J-protein gene (DjA30) mutant, j30+/- , had defects in FG development and fertility similar to those of mtHSC70-1 mutant. mtHSC70-1 and DjA30 had similar expression patterns in FGs and interacted in vivo, suggesting that these two proteins might cooperate during female gametogenesis. Further, respiratory chain complex IV activity in mtHSC70-1 and DjA30 mutant embryo sacs was markedly downregulated; this led to the accumulation of mitochondrial reactive oxygen species (ROS). Scavenging excess ROS by introducing Mn-superoxide dismutase 1 or catalase 1 gene into the mtHSC70-1 mutant rescued FG development and fertility. Altogether, our results suggest that mtHSC70-1 and DjA30 are essential for the maintenance of ROS homeostasis in the embryo sacs and provide direct evidence for the roles of ROS homeostasis in embryo sac maturation and nuclear patterning, which might determine the fate of gametic and accessory cells.
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Affiliation(s)
- Xiaoting Zhai
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Normal University, Shijiazhuang, 050024, China
- College of Agriculture and Forestry, Hebei North University, Zhangjiakou, 075000, China
| | - Jiaoteng Bai
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Normal University, Shijiazhuang, 050024, China
| | - Wenyan Xu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Normal University, Shijiazhuang, 050024, China
| | - Xiujuan Yang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Normal University, Shijiazhuang, 050024, China
| | - Zichao Jia
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Normal University, Shijiazhuang, 050024, China
| | - Wenxuan Xia
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Normal University, Shijiazhuang, 050024, China
| | - Xiaoqing Wu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Normal University, Shijiazhuang, 050024, China
| | - Qi Liang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Normal University, Shijiazhuang, 050024, China
| | - Bing Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Normal University, Shijiazhuang, 050024, China
| | - Ning Jia
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
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35
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Pikaard CS, Chandrasekhara C, McKinlay A, Enganti R, Fultz D. Reaching for the off switch in nucleolar dominance. Plant J 2023; 115:1185-1192. [PMID: 37228042 PMCID: PMC10524600 DOI: 10.1111/tpj.16318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 05/27/2023]
Abstract
Nucleolus organizer regions (NORs) are eukaryotic chromosomal loci where ribosomal RNA (rRNA) genes are clustered, typically in hundreds to thousands of copies. Transcription of these rRNA genes by RNA polymerase I and processing of their transcripts results in the formation of the nucleolus, the sub-nuclear domain in which ribosomes are assembled. Approximately 90 years ago, cytogenetic observations revealed that NORs inherited from the different parents of an interspecific hybrid sometimes differ in morphology at metaphase. Fifty years ago, those chromosomal differences were found to correlate with differences in rRNA gene transcription and the phenomenon became known as nucleolar dominance. Studies of the past 30 years have revealed that nucleolar dominance results from selective rRNA gene silencing, involving repressive chromatin modifications, and occurs in pure species as well as hybrids. Recent evidence also indicates that silencing depends on the NOR in which an rRNA gene is located, and not on the gene's sequence. In this perspective, we discuss how our thinking about nucleolar dominance has shifted over time from the kilobase scale of individual genes to the megabase scale of NORs and chromosomes and questions that remain unanswered in the search for a genetic and biochemical understanding of the off switch.
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Affiliation(s)
- Craig S Pikaard
- Department of Biology, Indiana University, Bloomington, Indiana, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA
- Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana, USA
| | - Chinmayi Chandrasekhara
- Department of Biology, Indiana University, Bloomington, Indiana, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA
| | - Anastasia McKinlay
- Department of Biology, Indiana University, Bloomington, Indiana, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA
- Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana, USA
| | - Ramya Enganti
- Department of Biology, Indiana University, Bloomington, Indiana, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA
- Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana, USA
| | - Dalen Fultz
- Department of Biology, Indiana University, Bloomington, Indiana, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA
- Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana, USA
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36
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McRae AG, Taneja J, Yee K, Shi X, Haridas S, LaButti K, Singan V, Grigoriev IV, Wildermuth MC. Spray-induced gene silencing to identify powdery mildew gene targets and processes for powdery mildew control. Mol Plant Pathol 2023; 24:1168-1183. [PMID: 37340595 PMCID: PMC10423327 DOI: 10.1111/mpp.13361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 06/22/2023]
Abstract
Spray-induced gene silencing (SIGS) is an emerging tool for crop pest protection. It utilizes exogenously applied double-stranded RNA to specifically reduce pest target gene expression using endogenous RNA interference machinery. In this study, SIGS methods were developed and optimized for powdery mildew fungi, which are widespread obligate biotrophic fungi that infect agricultural crops, using the known azole-fungicide target cytochrome P450 51 (CYP51) in the Golovinomyces orontii-Arabidopsis thaliana pathosystem. Additional screening resulted in the identification of conserved gene targets and processes important to powdery mildew proliferation: apoptosis-antagonizing transcription factor in essential cellular metabolism and stress response; lipid catabolism genes lipase a, lipase 1, and acetyl-CoA oxidase in energy production; and genes involved in manipulation of the plant host via abscisic acid metabolism (9-cis-epoxycarotenoid dioxygenase, xanthoxin dehydrogenase, and a putative abscisic acid G-protein coupled receptor) and secretion of the effector protein, effector candidate 2. Powdery mildew is the dominant disease impacting grapes and extensive powdery mildew resistance to applied fungicides has been reported. We therefore developed SIGS for the Erysiphe necator-Vitis vinifera system and tested six successful targets identified using the G. orontii-A. thaliana system. For all targets tested, a similar reduction in powdery mildew disease was observed between systems. This indicates screening of broadly conserved targets in the G. orontii-A. thaliana pathosystem identifies targets and processes for the successful control of other powdery mildew fungi. The efficacy of SIGS on powdery mildew fungi makes SIGS an exciting prospect for commercial powdery mildew control.
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Affiliation(s)
- Amanda G. McRae
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Jyoti Taneja
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Kathleen Yee
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Xinyi Shi
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Sajeet Haridas
- US Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Kurt LaButti
- US Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Vasanth Singan
- US Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Igor V. Grigoriev
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
- US Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Mary C. Wildermuth
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
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37
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Burke R, McCabe A, Sonawane NR, Rathod MH, Whelan CV, McCabe PF, Kacprzyk J. Arabidopsis cell suspension culture and RNA sequencing reveal regulatory networks underlying plant-programmed cell death. Plant J 2023; 115:1465-1485. [PMID: 37531399 DOI: 10.1111/tpj.16407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/27/2023] [Accepted: 07/20/2023] [Indexed: 08/04/2023]
Abstract
Programmed cell death (PCD) facilitates selective, genetically controlled elimination of redundant, damaged, or infected cells. In plants, PCD is often an essential component of normal development and can mediate responses to abiotic and biotic stress stimuli. However, studying the transcriptional regulation of PCD is hindered by difficulties in sampling small groups of dying cells that are often buried within the bulk of living plant tissue. We addressed this challenge by using RNA sequencing and Arabidopsis thaliana suspension cells, a model system that allows precise monitoring of PCD rates. The use of three PCD-inducing treatments (salicylic acid, heat, and critical dilution), in combination with three cell death modulators (3-methyladenine, lanthanum chloride, and conditioned medium), enabled isolation of candidate core- and stimuli-specific PCD genes, inference of underlying regulatory networks and identification of putative transcriptional regulators of PCD in plants. This analysis underscored a disturbance of the cell cycle and mitochondrial retrograde signaling, and repression of pro-survival stress responses, as key elements of the PCD-associated transcriptional signature. Further, phenotyping of Arabidopsis T-DNA insertion mutants in selected candidate genes validated the potential of generated resources to identify novel genes involved in plant PCD pathways and/or stress tolerance.
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Affiliation(s)
- Rory Burke
- School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Aideen McCabe
- School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Neetu Ramesh Sonawane
- School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Meet Hasmukh Rathod
- School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Conor V Whelan
- School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Paul F McCabe
- School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Joanna Kacprzyk
- School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
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38
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Midorikawa K, Numata K, Kodama Y. Peroxisomes undergo morphological changes in a light-dependent manner with proximity to the nucleus. FEBS Lett 2023; 597:2178-2184. [PMID: 37428521 DOI: 10.1002/1873-3468.14697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/11/2023]
Abstract
The size and shape of organelles can influence the rate of biochemical reactions in cells. Previous studies have suggested that organelle morphology changes due to intra- and extracellular environmental responses, affecting the metabolic efficiency of and signal transduction emanating from neighboring organelles. In this study, we tested the possibility that intracellularly distributed organelles exhibit a heterogeneous response to intra- and extracellular environments. We detected a high correlation between peroxisome morphology and distance to the nucleus in light-exposed cells. Moreover, the proximity area between chloroplasts and peroxisomes varied with distance to the nucleus. These results indicate that peroxisome morphology varies with proximity to the nucleus, suggesting the presence of a nucleus-peroxisome signal transduction cascade mediated by chloroplasts.
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Affiliation(s)
- Keiko Midorikawa
- Center for Bioscience Research and Education, Utsunomiya University, Japan
| | - Keiji Numata
- Department of Material Chemistry, Kyoto University, Japan
- Biomacromoleules Research Team, RIKEN Center for Sustainable Resource Science, Wako-shi, Japan
| | - Yutaka Kodama
- Center for Bioscience Research and Education, Utsunomiya University, Japan
- Biomacromoleules Research Team, RIKEN Center for Sustainable Resource Science, Wako-shi, Japan
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39
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Oakley CG, Schemske DW, McKay JK, Ågren J. Ecological genetics of local adaptation in Arabidopsis: An 8-year field experiment. Mol Ecol 2023; 32:4570-4583. [PMID: 37317048 DOI: 10.1111/mec.17045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/16/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023]
Abstract
There is considerable evidence for local adaptation in nature, yet important questions remain regarding its genetic basis. How many loci are involved? What are their effect sizes? What is the relative importance of conditional neutrality versus genetic trade-offs? Here we address these questions in the self-pollinating, annual plant Arabidopsis thaliana. We used 400 recombinant inbred lines (RILs) derived from two locally adapted populations in Italy and Sweden, grew the RILs and parents at the parental locations, and mapped quantitative trait loci (QTL) for mean fitness (fruits/seedling planted). We previously published results from the first 3 years of the study, and here add five additional years, providing a unique opportunity to assess how temporal variation in selection might affect QTL detection and classification. We found 10 adaptive and one maladaptive QTL in Italy, and six adaptive and four maladaptive QTL in Sweden. The discovery of maladaptive QTL at both sites suggests that even locally adapted populations are not always at their genotypic optimum. Mean effect sizes for adaptive QTL, 0.97 and 0.55 fruits in Italy and Sweden, respectively, were large relative to the mean fitness of the RILs (approximately 8 fruits/seedling planted at both sites). Both genetic trade-offs (four cases) and conditional neutrality (seven cases) contribute to local adaptation in this system. The 8-year dataset provided greater power to detect QTL and to estimate their locations compared to our previous 3-year study, identifying one new genetic trade-off and resolving one genetic trade-off into two conditionally adaptive QTL.
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Affiliation(s)
- Christopher G Oakley
- Department of Botany and Plant Pathology, and the Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Douglas W Schemske
- Department of Plant Biology and W. K. Kellogg Biological Station, Michigan State University, East Lansing, Michigan, USA
| | - John K McKay
- College of Agricultural Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Jon Ågren
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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40
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Nakazato I, Okuno M, Itoh T, Tsutsumi N, Arimura SI. Characterization and development of a plastid genome base editor, ptpTALECD. Plant J 2023; 115:1151-1162. [PMID: 37265080 DOI: 10.1111/tpj.16311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 05/09/2023] [Accepted: 05/15/2023] [Indexed: 06/03/2023]
Abstract
The modification of photosynthesis-related genes in plastid genomes may improve crop yields. Recently, we reported that a plastid-targeting base editor named ptpTALECD, in which a cytidine deaminase DddA functions as the catalytic domain, can homoplasmically substitute a targeted C to T in plastid genomes of Arabidopsis thaliana. However, some target Cs were not substituted. In addition, although ptpTALECD could substitute Cs on the 3' side of T and A, it was unclear whether it could also substitute Cs on the 3' side of G and C. In this study, we identified the preferential positions of the substituted Cs in ptpTALECD-targeting sequences in the Arabidopsis plastid genome. We also found that ptpTALECD could substitute Cs on the 3' side of all four bases in plastid genomes of Arabidopsis. More recently, a base editor containing an improved version of DddA (DddA11) was reported to substitute Cs more efficiently, and to substitute Cs on the 3' side of more varieties of bases in human mitochondrial genomes than a base editor containing DddA. Here, we also show that ptpTALECD_v2, in which a modified version of DddA11 functions as the catalytic domain, more frequently substituted Cs than ptpTALECD in the Arabidopsis plastid genome. We also found that ptpTALECD_v2 tended to substitute Cs at more positions than ptpTALECD. Our results reveal that ptpTALECD can cause a greater variety of codon changes and amino acid substitutions than previously thought, and that ptpTALECD and ptpTALECD_v2 are useful tools for the targeted base editing of plastid genomes.
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Affiliation(s)
- Issei Nakazato
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi Bunkyo-ku, Tokyo, 113-8657, Japan
- Research Fellow of Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo, 102-0083, Japan
| | - Miki Okuno
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Japan, 67, Asahi-machi, Kurume, Fukuoka, 830-0011, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Nobuhiro Tsutsumi
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Shin-Ichi Arimura
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi Bunkyo-ku, Tokyo, 113-8657, Japan
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41
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Kimura S, Vaattovaara A, Ohshita T, Yokoyama K, Yoshida K, Hui A, Kaya H, Ozawa A, Kobayashi M, Mori IC, Ogata Y, Ishino Y, Sugano SS, Nagano M, Fukao Y. Zinc deficiency-induced defensin-like proteins are involved in the inhibition of root growth in Arabidopsis. Plant J 2023; 115:1071-1083. [PMID: 37177878 DOI: 10.1111/tpj.16281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/30/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023]
Abstract
The depletion of cellular zinc (Zn) adversely affects plant growth. Plants have adaptation mechanisms for Zn-deficient conditions, inhibiting growth through the action of transcription factors and metal transporters. We previously identified three defensin-like (DEFL) proteins (DEFL203, DEFL206 and DEFL208) that were induced in Arabidopsis thaliana roots under Zn-depleted conditions. DEFLs are small cysteine-rich peptides involved in defense responses, development and excess metal stress in plants. However, the functions of DEFLs in the Zn-deficiency response are largely unknown. Here, phylogenetic tree analysis revealed that seven DEFLs (DEFL202-DEFL208) were categorized into one subgroup. Among the seven DEFLs, the transcripts of five (not DEFL204 and DEFL205) were upregulated by Zn deficiency, consistent with the presence of cis-elements for basic-region leucine-zipper 19 (bZIP19) or bZIP23 in their promoter regions. Microscopic observation of GFP-tagged DEFL203 showed that DEFL203-sGFP was localized to the apoplast and plasma membrane. Whereas a single mutation of the DEFL202 or DEFL203 genes only slightly affected root growth, defl202 defl203 double mutants showed enhanced root growth under all growth conditions. We also showed that the size of the root meristem was increased in the double mutants compared with the wild type. Our results suggest that DEFL202 and DEFL203 are redundantly involved in the inhibition of root growth under Zn-deficient conditions through a reduction in root meristem length and cell number.
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Affiliation(s)
- Sachie Kimura
- Ritsumeikan Global Innovation Research Organization, Ritsumeikan University, Shiga, 525-8577, Japan
| | - Aleksia Vaattovaara
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, University of Helsinki, Helsinki, FI-00014, Finland
| | - Tomoya Ohshita
- Graduate School of Life Science, Ritsumeikan University, Shiga, 525-8577, Japan
| | - Kotomi Yokoyama
- Graduate School of Life Science, Ritsumeikan University, Shiga, 525-8577, Japan
| | - Kota Yoshida
- Graduate School of Life Science, Ritsumeikan University, Shiga, 525-8577, Japan
| | - Agnes Hui
- Graduate School of Life Science, Ritsumeikan University, Shiga, 525-8577, Japan
| | - Hidetaka Kaya
- Department of Food Production Science, Ehime University, Ehime, 790-8566, Japan
| | - Ai Ozawa
- Graduate School of Life Science, Ritsumeikan University, Shiga, 525-8577, Japan
| | - Mami Kobayashi
- Graduate School of Life Science, Ritsumeikan University, Shiga, 525-8577, Japan
| | - Izumi C Mori
- Institute of Plant Science and Resources, Okayama University, Okayama, 710-0046, Japan
| | - Yoshiyuki Ogata
- Department of Agricultural Biology, Graduate School of Agriculture, Osaka Metropolitan University, Osaka, 599-8531, Japan
| | - Yoko Ishino
- Graduate School of Innovation and Technology Management, Yamaguchi University, Yamaguchi, 755-8611, Japan
| | - Shigeo S Sugano
- Ritsumeikan Global Innovation Research Organization, Ritsumeikan University, Shiga, 525-8577, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, 305-8566, Japan
| | - Minoru Nagano
- Graduate School of Life Science, Ritsumeikan University, Shiga, 525-8577, Japan
| | - Yoichiro Fukao
- Graduate School of Life Science, Ritsumeikan University, Shiga, 525-8577, Japan
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42
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Jia X, Zhang H, Qin H, Li K, Liu X, Wang W, Ye M, Yin H. Protein O-GlcNAcylation impairment caused by N-acetylglucosamine phosphate mutase deficiency leads to growth variations in Arabidopsis thaliana. Plant J 2023; 114:613-635. [PMID: 36799458 DOI: 10.1111/tpj.16156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 05/10/2023]
Abstract
As an essential enzyme in the uridine diphosphate (UDP)-GlcNAc biosynthesis pathway, the significant role of N-acetylglucosamine phosphate mutase (AGM) remains unknown in plants. In the present study, a functional plant AGM (AtAGM) was identified from Arabidopsis thaliana. AtAGM catalyzes the isomerization of GlcNAc-1-P and GlcNAc-6-P, and has broad catalytic activity on different phosphohexoses. UDP-GlcNAc contents were significantly decreased in AtAGM T-DNA insertional mutants, which caused temperature-dependent growth defects in seedlings and vigorous growth in adult plants. Further analysis revealed that protein O-GlcNAcylation but not N-glycosylation was dramatically impaired in Atagm mutants due to UDP-GlcNAc shortage. Combined with the results from O-GlcNAcylation or N-glycosylation deficient mutants, and O-GlcNAcase inhibitor all suggested that protein O-GlcNAcylation impairment mainly leads to the phenotypic variations of Atagm plants. In conclusion, based on the essential role in UDP-GlcNAc biosynthesis, AtAGM is important for plant growth mainly via protein O-GlcNAcylation-level regulation.
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Affiliation(s)
- Xiaochen Jia
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
| | - Hongyan Zhang
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
| | - Hongqiang Qin
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Kuikui Li
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
| | - Xiaoyan Liu
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Wenxia Wang
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
| | - Mingliang Ye
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Heng Yin
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
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43
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Zheng J, Yang X, Huang Y, Yang S, Wuchty S, Zhang Z. Deep learning-assisted prediction of protein-protein interactions in Arabidopsis thaliana. Plant J 2023; 114:984-994. [PMID: 36919205 DOI: 10.1111/tpj.16188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/20/2023] [Accepted: 03/09/2023] [Indexed: 05/27/2023]
Abstract
Currently, the experimentally identified interactome of Arabidopsis (Arabidopsis thaliana) is still far from complete, suggesting that computational prediction methods can complement experimental techniques. Motivated by the prosperity and success of deep learning algorithms and natural language processing techniques, we introduce an integrative deep learning framework, DeepAraPPI, allowing us to predict protein-protein interactions (PPIs) of Arabidopsis utilizing sequence, domain and Gene Ontology (GO) information. Our current DeepAraPPI comprises: (i) a word2vec encoding-based Siamese recurrent convolutional neural network (RCNN) model; (ii) a Domain2vec encoding-based multiple-layer perceptron (MLP) model; and (iii) a GO2vec encoding-based MLP model. Finally, DeepAraPPI combines the prediction results of the three individual predictors through a logistic regression model. Compiling high-quality positive and negative training and test samples by applying strict filtering strategies, DeepAraPPI shows superior performance compared with existing state-of-the-art Arabidopsis PPI prediction methods. DeepAraPPI also provides better cross-species predictive ability in rice (Oryza sativa) than traditional machine learning methods, although the overall performance in cross-species prediction remains to be improved. DeepAraPPI is freely accessible at http://zzdlab.com/deeparappi/. In the meantime, we have also made the source code and data sets of DeepAraPPI available at https://github.com/zjy1125/DeepAraPPI.
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Affiliation(s)
- Jingyan Zheng
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaodi Yang
- Department of Hematology, Peking University First Hospital, Beijing, 100034, China
| | - Yan Huang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Shiping Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Stefan Wuchty
- Department of Computer Science, University of Miami, Miami, FL, 33146, USA
- Department of Biology, University of Miami, Miami, FL, 33146, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, 33136, USA
- Institute of Data Science and Computing, University of Miami, Miami, FL, 33146, USA
| | - Ziding Zhang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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44
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Han WY, Hou BH, Lee WC, Chan TC, Lin TH, Chen HM. Arabidopsis mRNA decay landscape shaped by XRN 5'-3' exoribonucleases. Plant J 2023; 114:895-913. [PMID: 36987558 DOI: 10.1111/tpj.16181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 02/18/2023] [Accepted: 03/03/2023] [Indexed: 05/27/2023]
Abstract
5'-3' exoribonucleases (XRNs) play crucial roles in the control of RNA processing, quality, and quantity in eukaryotes. Although genome-wide profiling of RNA decay fragments is now feasible, how XRNs shape the plant mRNA degradome remains elusive. Here, we profiled and analyzed the RNA degradomes of Arabidopsis wild-type and mutant plants with defects in XRN activity. Deficiency of nuclear XRN3 or cytoplasmic XRN4 activity but not nuclear XRN2 activity greatly altered Arabidopsis mRNA decay profiles. Short excised linear introns and cleaved pre-mRNA fragments downstream of polyadenylation sites were polyadenylated and stabilized in the xrn3 mutant, demonstrating the unique function of XRN3 in the removal of cleavage remnants from pre-mRNA processing. Further analysis of stabilized XRN3 substrates confirmed that pre-mRNA 3' end cleavage frequently occurs after adenosine. The most abundant decay intermediates in wild-type plants include not only the primary substrates of XRN4 but also the products of XRN4-mediated cytoplasmic decay. An increase in decay intermediates with 5' ends upstream of a consensus motif in the xrn4 mutant suggests that there is an endonucleolytic cleavage mechanism targeting the 3' untranslated regions of many Arabidopsis mRNAs. However, analysis of decay fragments in the xrn4 mutant indicated that, except for microRNA-directed slicing, endonucleolytic cleavage events in the coding sequence rarely result in major decay intermediates. Together, these findings reveal the major substrates and products of nuclear and cytoplasmic XRNs along Arabidopsis transcripts and provide a basis for precise interpretation of RNA degradome data.
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Affiliation(s)
- Wan-Yin Han
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University, Taichung 40227, Taiwan, and Academia Sinica, Taipei, 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, 40227, Taiwan
| | - Bo-Han Hou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Wen-Chi Lee
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Tze-Ching Chan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Tzu-Hsiang Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Ho-Ming Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University, Taichung 40227, Taiwan, and Academia Sinica, Taipei, 11529, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung, 40227, Taiwan
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45
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Ramming A, Kappel C, Kanaoka MM, Higashiyama T, Lenhard M. Poly(A) polymerase 1 contributes to competence acquisition of pollen tubes growing through the style in Arabidopsis thaliana. Plant J 2023; 114:651-667. [PMID: 36811355 DOI: 10.1111/tpj.16162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/16/2023] [Indexed: 05/10/2023]
Abstract
Polyadenylation of mRNAs is critical for their export from the nucleus, stability, and efficient translation. The Arabidopsis thaliana genome encodes three isoforms of canonical nuclear poly(A) polymerase (PAPS) that redundantly polyadenylate the bulk of pre-mRNAs. However, previous studies have indicated that subsets of pre-mRNAs are preferentially polyadenylated by either PAPS1 or the other two isoforms. Such functional specialization raises the possibility of an additional level of gene-expression control in plants. Here we test this notion by studying the function of PAPS1 in pollen-tube growth and guidance. Pollen tubes growing through female tissue acquire the competence to find ovules efficiently and upregulate PAPS1 expression at the transcriptional, but not detectably at the protein level compared with in vitro grown pollen tubes. Using the temperature-sensitive paps1-1 allele we show that PAPS1 activity during pollen-tube growth is required for full acquisition of competence, resulting in inefficient fertilization by paps1-1 mutant pollen tubes. While these mutant pollen tubes grow almost at the wild-type rate, they are compromised in locating the micropyles of ovules. Previously identified competence-associated genes are less expressed in paps1-1 mutant than in wild-type pollen tubes. Estimating the poly(A) tail lengths of transcripts suggests that polyadenylation by PAPS1 is associated with reduced transcript abundance. Our results therefore suggest that PAPS1 plays a key role in the acquisition of competence and underline the importance of functional specialization between PAPS isoforms throughout different developmental stages.
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Affiliation(s)
- Anna Ramming
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Christian Kappel
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Masahiro M Kanaoka
- Prefectural University of Hiroshima, Faculty of Life and Environmental Sciences, Faculty of Bioresource Sciences, Shobara, Hiroshima, Japan
| | - Tetsuya Higashiyama
- The University of Tokyo Graduate School of Science, Faculty of Science, Bunkyo-ku, Tokyo, Japan
| | - Michael Lenhard
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
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46
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McQuinn RP, Leroux J, Sierra J, Escobar-Tovar L, Frusciante S, Finnegan EJ, Diretto G, Giuliano G, Giovannoni JJ, León P, Pogson BJ. Deregulation of ζ-carotene desaturase in Arabidopsis and tomato exposes a unique carotenoid-derived redundant regulation of floral meristem identity and function. Plant J 2023; 114:783-804. [PMID: 36861314 DOI: 10.1111/tpj.16168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 02/05/2023] [Accepted: 02/26/2023] [Indexed: 05/27/2023]
Abstract
A level of redundancy and interplay among the transcriptional regulators of floral development safeguards a plant's reproductive success and ensures crop production. In the present study, an additional layer of complexity in the regulation of floral meristem (FM) identity and flower development is elucidated linking carotenoid biosynthesis and metabolism to the regulation of determinate flowering. The accumulation and subsequent cleavage of a diverse array of ζ-carotenes in the chloroplast biogenesis 5 (clb5) mutant of Arabidopsis results in the reprogramming of meristematic gene regulatory networks establishing FM identity mirroring that of the FM identity master regulator, APETALA1 (AP1). The immediate transition to floral development in clb5 requires long photoperiods in a GIGANTEA-independent manner, whereas AP1 is essential for the floral organ development of clb5. The elucidation of this link between carotenoid metabolism and floral development translates to tomato exposing a regulation of FM identity redundant to and initiated by AP1 and proposed to be dependent on the E class floral initiation and organ identity regulator, SEPALLATA3 (SEP3).
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Affiliation(s)
- Ryan P McQuinn
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Julie Leroux
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Julio Sierra
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, Mexico
| | - Lina Escobar-Tovar
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, Mexico
| | - Sarah Frusciante
- Italian National Agency for New Technologies, Energy, and Sustainable Development (ENEA), Casaccia Research Center, Rome, 00196, Italy
| | | | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy, and Sustainable Development (ENEA), Casaccia Research Center, Rome, 00196, Italy
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy, and Sustainable Development (ENEA), Casaccia Research Center, Rome, 00196, Italy
| | - James J Giovannoni
- US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Patricia León
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, Mexico
| | - Barry J Pogson
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
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47
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Ai H, Bellstaedt J, Bartusch KS, Eschen-Lippold L, Babben S, Balcke GU, Tissier A, Hause B, Andersen TG, Delker C, Quint M. Auxin-dependent regulation of cell division rates governs root thermomorphogenesis. EMBO J 2023:e111926. [PMID: 37071525 DOI: 10.15252/embj.2022111926] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 03/16/2023] [Accepted: 03/21/2023] [Indexed: 04/19/2023] Open
Abstract
Roots are highly plastic organs enabling plants to adapt to a changing below-ground environment. In addition to abiotic factors like nutrients or mechanical resistance, plant roots also respond to temperature variation. Below the heat stress threshold, Arabidopsis thaliana seedlings react to elevated temperature by promoting primary root growth, possibly to reach deeper soil regions with potentially better water saturation. While above-ground thermomorphogenesis is enabled by thermo-sensitive cell elongation, it was unknown how temperature modulates root growth. We here show that roots are able to sense and respond to elevated temperature independently of shoot-derived signals. This response is mediated by a yet unknown root thermosensor that employs auxin as a messenger to relay temperature signals to the cell cycle. Growth promotion is achieved primarily by increasing cell division rates in the root apical meristem, depending on de novo local auxin biosynthesis and temperature-sensitive organization of the polar auxin transport system. Hence, the primary cellular target of elevated ambient temperature differs fundamentally between root and shoot tissues, while the messenger auxin remains the same.
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Affiliation(s)
- Haiyue Ai
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Julia Bellstaedt
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Kai Steffen Bartusch
- Department of Biology, Institute of Molecular Plant Biology, ETH Zürich, Zürich, Switzerland
| | - Lennart Eschen-Lippold
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Steve Babben
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Gerd Ulrich Balcke
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Bettina Hause
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | | | - Carolin Delker
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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48
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Stitz M, Kuster D, Reinert M, Schepetilnikov M, Berthet B, Reyes-Hernández J, Janocha D, Artins A, Boix M, Henriques R, Pfeiffer A, Lohmann J, Gaquerel E, Maizel A. TOR acts as a metabolic gatekeeper for auxin-dependent lateral root initiation in Arabidopsis thaliana. EMBO J 2023; 42:e111273. [PMID: 37021425 PMCID: PMC10183831 DOI: 10.15252/embj.2022111273] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 02/27/2023] [Accepted: 03/03/2023] [Indexed: 04/07/2023] Open
Abstract
Plant organogenesis requires matching the available metabolic resources to developmental programs. In Arabidopsis, the root system is determined by primary root-derived lateral roots (LRs), and adventitious roots (ARs) formed from non-root organs. Lateral root formation entails the auxin-dependent activation of transcription factors ARF7, ARF19, and LBD16. Adventitious root formation relies on LBD16 activation by auxin and WOX11. The allocation of shoot-derived sugar to the roots influences branching, but how its availability is sensed for LRs formation remains unknown. We combine metabolic profiling with cell-specific interference to show that LRs switch to glycolysis and consume carbohydrates. The target-of-rapamycin (TOR) kinase is activated in the lateral root domain. Interfering with TOR kinase blocks LR initiation while promoting AR formation. The target-of-rapamycin inhibition marginally affects the auxin-induced transcriptional response of the pericycle but attenuates the translation of ARF19, ARF7, and LBD16. TOR inhibition induces WOX11 transcription in these cells, yet no root branching occurs as TOR controls LBD16 translation. TOR is a central gatekeeper for root branching that integrates local auxin-dependent pathways with systemic metabolic signals, modulating the translation of auxin-induced genes.
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Affiliation(s)
- Michael Stitz
- Center for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - David Kuster
- Center for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Maximilian Reinert
- Center for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | | | - Béatrice Berthet
- Center for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | | | - Denis Janocha
- Center for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Anthony Artins
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Marc Boix
- Centre for Research in Agricultural Genomics, Barcelona, Spain
| | - Rossana Henriques
- Environmental Research Institute, University College Cork, Cork, Ireland
| | - Anne Pfeiffer
- Center for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Jan Lohmann
- Center for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Emmanuel Gaquerel
- Institut de Biologie Moleculaire des Plantes (IBMP), UPR CNRS 2357, Strasbourg, France
| | - Alexis Maizel
- Center for Organismal Studies, Heidelberg University, Heidelberg, Germany
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49
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Liu C, Hao D, Sun R, Zhang Y, Peng Y, Yuan Y, Jiang K, Li W, Wen X, Guo H. Arabidopsis NPF2.13 functions as a critical transporter of bacterial natural compound tunicamycin in plant-microbe interaction. New Phytol 2023; 238:765-780. [PMID: 36653958 DOI: 10.1111/nph.18752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Metabolites including antibiotics, enzymes, and volatiles produced by plant-associated bacteria are key factors in plant-microbiota interaction that regulates various plant biological processes. There should be crucial mediators responsible for their entry into host plants. However, less is known about the identities of these plant transporters. We report that the Arabidopsis Nitrate Transporter1 (NRT1)/NPF protein NPF2.13 functions in plant uptake of tunicamycin (TM), a natural antibiotic produced by several Streptomyces spp., which inhibits protein N-glycosylation. Loss of NPF2.13 function resulted in enhanced TM tolerance, whereas NPF2.13 overexpression led to TM hypersensitivity. Transport assays confirmed that NPF2.13 is a H+ /TM symporter and the transport is not affected by other substrates like nitrate. NPF2.13 exclusively showed TM transport activity among tested NPFs. Tunicamycin uptake from TM-producing Streptomyces upregulated the expression of nitrate-related genes including NPF2.13. Moreover, nitrate allocation to younger leaves was promoted by TM in host plants. Tunicamycin could also benefit plant defense against the pathogen. Notably, the TM effects were significantly repressed in npf2.13 mutant. Overall, this study identifies NPF2.13 protein as an important TM transporter in plant-microbe interaction and provides insights into multiple facets of NPF proteins in modulating plant nutrition and defense by transporting exterior bacterial metabolites.
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Affiliation(s)
- Chuanfa Liu
- Department of Biology, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), 518055, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech, 518055, Shenzhen, China
| | - Dongdong Hao
- Department of Biology, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), 518055, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech, 518055, Shenzhen, China
| | - Ruixue Sun
- Department of Biology, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), 518055, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech, 518055, Shenzhen, China
| | - Yi Zhang
- Department of Biology, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), 518055, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech, 518055, Shenzhen, China
| | - Yang Peng
- Department of Biology, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), 518055, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech, 518055, Shenzhen, China
| | - Yang Yuan
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Centre and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Kai Jiang
- Department of Biology, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), 518055, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech, 518055, Shenzhen, China
- SUSTech Academy for Advanced and Interdisciplinary Studies, SUSTech, 518055, Shenzhen, China
| | - Wenyang Li
- Department of Biology, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), 518055, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech, 518055, Shenzhen, China
| | - Xing Wen
- Department of Biology, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), 518055, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech, 518055, Shenzhen, China
| | - Hongwei Guo
- Department of Biology, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), 518055, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech, 518055, Shenzhen, China
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50
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Waksman T, Suetsugu N, Hermanowicz P, Ronald J, Sullivan S, Łabuz J, Christie JM. Phototropin phosphorylation of ROOT PHOTOTROPISM 2 and its role in mediating phototropism, leaf positioning, and chloroplast accumulation movement in Arabidopsis. Plant J 2023; 114:390-402. [PMID: 36794876 PMCID: PMC10953443 DOI: 10.1111/tpj.16144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/08/2023] [Indexed: 05/10/2023]
Abstract
Directional movements impact the ability of plants to respond and adjust their growth accordingly to the prevailing light environment. The plasma-membrane associated protein, ROOT PHOTOTROPISM 2 (RPT2) is a key signalling component involved in chloroplast accumulation movement, leaf positioning, and phototropism, all of which are regulated redundantly by the ultraviolet/blue light-activated AGC kinases phototropin 1 and 2 (phot1 and phot2). We recently demonstrated that members of the NON-PHOTOTROPIC HYPOCOTYL 3 (NPH3)/RPT2-like (NRL) family in Arabidopsis thaliana, including RPT2, are directly phosphorylated by phot1. However, whether RPT2 is a substrate for phot2, and the biological significance of phot phosphorylation of RPT2 remains to be determined. Here, we show that RPT2 is phosphorylated by both phot1 and phot2 at a conserved serine residue (S591) within the C-terminal region of the protein. Blue light triggered the association of 14-3-3 proteins with RPT2 consistent with S591 acting as a 14-3-3 binding site. Mutation of S591 had no effect on the plasma membrane localization of RPT2 but reduced its functionality for leaf positioning and phototropism. Moreover, our findings indicate that S591 phosphorylation within the C-terminus of RPT2 is required for chloroplast accumulation movement to low level blue light. Taken together, these findings further highlight the importance of the C-terminal region of NRL proteins and how its phosphorylation contributes to phot receptor signalling in plants.
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Affiliation(s)
- Thomas Waksman
- School of Molecular BiosciencesCollege of Medical, Veterinary and Life Sciences, University of GlasgowBower BuildingGlasgowG12 8QQUK
| | - Noriyuki Suetsugu
- School of Molecular BiosciencesCollege of Medical, Veterinary and Life Sciences, University of GlasgowBower BuildingGlasgowG12 8QQUK
- Graduate School of Arts and SciencesThe University of TokyoTokyo153‐8902Japan
| | - Pawel Hermanowicz
- Malopolska Centre of BiotechnologyJagiellonian UniversityGronostajowa 7A30‐387KrakówPoland
| | - James Ronald
- School of Molecular BiosciencesCollege of Medical, Veterinary and Life Sciences, University of GlasgowBower BuildingGlasgowG12 8QQUK
| | - Stuart Sullivan
- School of Molecular BiosciencesCollege of Medical, Veterinary and Life Sciences, University of GlasgowBower BuildingGlasgowG12 8QQUK
| | - Justyna Łabuz
- Malopolska Centre of BiotechnologyJagiellonian UniversityGronostajowa 7A30‐387KrakówPoland
| | - John M. Christie
- School of Molecular BiosciencesCollege of Medical, Veterinary and Life Sciences, University of GlasgowBower BuildingGlasgowG12 8QQUK
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