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Zhu Y, Narsai R, He C, Štaka Z, Bai C, Berkowitz O, Liew LC, Whelan J. Overexpression of the transcription factor ANAC017 results in a genomes uncoupled phenotype under lincomycin. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39145415 DOI: 10.1111/tpj.16973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 12/18/2023] [Accepted: 07/29/2024] [Indexed: 08/16/2024]
Abstract
Over-expression (OE) lines for the ER-tethered NAC transcription factor ANAC017 displayed de-repression of gun marker genes when grown on lincomycin (lin). RNA-seq revealed that ANAC017OE2 plants constitutively expressed greater than 40% of the genes induced in wild-type with lin treatment, including plastid encoded genes ycf1.2 and the gene cluster ndhH-ndhA-ndhI-ndhG-ndhE-psaC-ndhD, documented as direct RNA targets of GUN1. Genes encoding components involved in organelle translation were enriched in constitutively expressed genes in ANAC017OE2. ANAC017OE resulted in constitutive location in the nucleus and significant constitutive binding of ANAC017 was detected by ChIP-Seq to target genes. ANAC017OE2 lines maintained the ability to green on lin, were more ABA sensitive, did not show photo-oxidative damage after exposure of de-etiolated seedlings to continuous light and the transcriptome response to lin were as much as 80% unique compared to gun1-1. Both double mutants, gun1-1:ANAC017OE and bzip60:ANAC017OE (but not single bzip60), have a gun molecular gene expression pattern and result in variegated and green plants, suggesting that ANAC017OE may act through an independent pathway compared to gun1. Over-expression of ANAC013 or rcd1 did not produce a GUN phenotype or green plants on lin. Thus, constitutive ANAC017OE2 establishes an alternative transcriptional program that likely acts through a number of pathways, that is, maintains plastid gene expression, and induction of a variety of transcription factors involved in reactive oxygen species metabolism, priming plants for lin tolerance to give a gun phenotype.
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Affiliation(s)
- Yanqiao Zhu
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang, 314400, People's Republic of China
| | - Reena Narsai
- Department of Animal, Plant and Soil Science, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, 3086, Victoria, Australia
| | - Cunman He
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang, 314400, People's Republic of China
- Department of Animal, Plant and Soil Science, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, 3086, Victoria, Australia
| | - Zorana Štaka
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Chen Bai
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Science, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, 3086, Victoria, Australia
| | - Lim Chee Liew
- Department of Animal, Plant and Soil Science, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, 3086, Victoria, Australia
| | - James Whelan
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang, 314400, People's Republic of China
- Department of Animal, Plant and Soil Science, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, 3086, Victoria, Australia
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Willems P, Sterck L, Dard A, Huang J, De Smet I, Gevaert K, Van Breusegem F. The Plant PTM Viewer 2.0: in-depth exploration of plant protein modification landscapes. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4611-4624. [PMID: 38872385 DOI: 10.1093/jxb/erae270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 06/13/2024] [Indexed: 06/15/2024]
Abstract
Post-translational modifications (PTMs) greatly increase protein diversity and functionality. To help the plant research community interpret the ever-increasing number of reported PTMs, the Plant PTM Viewer (https://www.psb.ugent.be/PlantPTMViewer) provides an intuitive overview of plant protein PTMs and the tools to assess it. This update includes 62 novel PTM profiling studies, adding a total of 112 000 modified peptides reporting plant PTMs, including 14 additional PTM types and three species (moss, tomato, and soybean). Furthermore, an open modification re-analysis of a large-scale Arabidopsis thaliana mass spectrometry tissue atlas identified previously uncharted landscapes of lysine acylations predominant in seed and flower tissues and 3-phosphoglycerylation on glycolytic enzymes in plants. An extra 'Protein list analysis' tool was developed for retrieval and assessing the enrichment of PTMs in a protein list of interest. We conducted a protein list analysis on nuclear proteins, revealing a substantial number of redox modifications in the nucleus, confirming previous assumptions regarding the redox regulation of transcription. We encourage the plant research community to use PTM Viewer 2.0 for hypothesis testing and new target discovery, and also to submit new data to expand the coverage of conditions, plant species, and PTM types, thereby enriching our understanding of plant biology.
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Affiliation(s)
- Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9052 Ghent, Belgium
- VIB Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
| | - Lieven Sterck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Avilien Dard
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Jingjing Huang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, 9052 Ghent, Belgium
- VIB Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
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3
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Schnabel E, Bashyal S, Corbett C, Kassaw T, Nowak S, Rosales-García RA, Noorai RE, Müller LM, Frugoli J. The Defective in Autoregulation (DAR) gene of Medicago truncatula encodes a protein involved in regulating nodulation and arbuscular mycorrhiza. BMC PLANT BIOLOGY 2024; 24:766. [PMID: 39123119 PMCID: PMC11316349 DOI: 10.1186/s12870-024-05479-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND Legumes utilize a long-distance signaling feedback pathway, termed Autoregulation of Nodulation (AON), to regulate the establishment and maintenance of their symbiosis with rhizobia. Several proteins key to this pathway have been discovered, but the AON pathway is not completely understood. RESULTS We report a new hypernodulating mutant, defective in autoregulation, with disruption of a gene, DAR (Medtr2g450550/MtrunA17_Chr2g0304631), previously unknown to play a role in AON. The dar-1 mutant produces ten-fold more nodules than wild type, similar to AON mutants with disrupted SUNN gene function. As in sunn mutants, suppression of nodulation by CLE peptides MtCLE12 and MtCLE13 is abolished in dar. Furthermore, dar-1 also shows increased root length colonization by an arbuscular mycorrhizal fungus, suggesting a role for DAR in autoregulation of mycorrhizal symbiosis (AOM). However, unlike SUNN which functions in the shoot to control nodulation, DAR functions in the root. CONCLUSIONS DAR encodes a membrane protein that is a member of a small protein family in M. truncatula. Our results suggest that DAR could be involved in the subcellular transport of signals involved in symbiosis regulation, but it is not upregulated during symbiosis. DAR gene family members are also present in Arabidopsis, lycophytes, mosses, and microalgae, suggesting the AON and AOM may use pathway components common to other plants, even those that do not undergo either symbiosis.
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Affiliation(s)
- Elise Schnabel
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA
| | - Sagar Bashyal
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- School of Biological Sciences, University of California San Diego, San Diego, CA, 92093, USA
| | - Cameron Corbett
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA
- Present addresses: Department of Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - Tessema Kassaw
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA
- Present addresses: Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Stephen Nowak
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA
- Present addresses: Center for Technology Licensing, Cornell University, Ithaca, NY, 14850, USA
| | - Ramsés Alejandro Rosales-García
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA
- Clemson University Genomics and Bioinformatics Facility, Clemson University, Clemson, SC, 29634, USA
| | - Rooksana E Noorai
- Clemson University Genomics and Bioinformatics Facility, Clemson University, Clemson, SC, 29634, USA
| | - Lena Maria Müller
- Department of Biology, University of Miami, Coral Gables, FL, 33124, USA
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Julia Frugoli
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA.
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Kopecká R, Černý M. Xylem Sap Proteome Analysis Provides Insight into Root-Shoot Communication in Response to flg22. PLANTS (BASEL, SWITZERLAND) 2024; 13:1983. [PMID: 39065510 PMCID: PMC11281318 DOI: 10.3390/plants13141983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024]
Abstract
Xylem sap proteomics provides crucial insights into plant defense and root-to-shoot communication. This study highlights the sensitivity and reproducibility of xylem sap proteome analyses, using a single plant per sample to track over 3000 proteins in two model crop plants, Solanum tuberosum and Hordeum vulgare. By analyzing the flg22 response, we identified immune response components not detectable through root or shoot analyses. Notably, we discovered previously unknown elements of the plant immune system, including calcium/calmodulin-dependent kinases and G-type lectin receptor kinases. Despite similarities in the metabolic pathways identified in the xylem sap of both plants, the flg22 response differed significantly: S. tuberosum exhibited 78 differentially abundant proteins, whereas H. vulgare had over 450. However, an evolutionarily conserved overlap in the flg22 response proteins was evident, particularly in the CAZymes and lipid metabolism pathways, where lipid transfer proteins and lipases showed a similar response to flg22. Additionally, many proteins without conserved signal sequences for extracellular targeting were found, such as members of the HSP70 family. Interestingly, the HSP70 response to flg22 was specific to the xylem sap proteome, suggesting a unique regulatory role in the extracellular space similar to that reported in mammalians.
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Affiliation(s)
| | - Martin Černý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
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Ceasar SA, Prabhu S, Ebeed HT. Protein research in millets: current status and way forward. PLANTA 2024; 260:43. [PMID: 38958760 DOI: 10.1007/s00425-024-04478-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024]
Abstract
MAIN CONCLUSION Millets' protein studies are lagging behind those of major cereals. Current status and future insights into the investigation of millet proteins are discussed. Millets are important small-seeded cereals majorly grown and consumed by people in Asia and Africa and are considered crops of future food security. Although millets possess excellent climate resilience and nutrient supplementation properties, their research advancements have been lagging behind major cereals. Although considerable genomic resources have been developed in recent years, research on millet proteins and proteomes is currently limited, highlighting a need for further investigation in this area. This review provides the current status of protein research in millets and provides insights to understand protein responses for climate resilience and nutrient supplementation in millets. The reference proteome data is available for sorghum, foxtail millet, and proso millet to date; other millets, such as pearl millet, finger millet, barnyard millet, kodo millet, tef, and browntop millet, do not have any reference proteome data. Many studies were reported on stress-responsive protein identification in foxtail millet, with most studies on the identification of proteins under drought-stress conditions. Pearl millet has a few reports on protein identification under drought and saline stress. Finger millet is the only other millet to have a report on stress-responsive (drought) protein identification in the leaf. For protein localization studies, foxtail millet has a few reports. Sorghum has the highest number of 40 experimentally proven crystal structures, and other millets have fewer or no experimentally proven structures. Further proteomics studies will help dissect the specific proteins involved in climate resilience and nutrient supplementation and aid in breeding better crops to conserve food security.
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Affiliation(s)
- S Antony Ceasar
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, Kerala, 683 104, India.
| | - Srinivasan Prabhu
- Division of Phytochemistry and Drug Design, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, Kerala, 683 104, India
| | - Heba T Ebeed
- Botany and Microbiology Department, Faculty of Science, Damietta University, Damietta, Egypt
- National Biotechnology Network of Expertise (NBNE), Academy of Scientific Research and Technology (ASRT), Cairo, Egypt
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Réthoré E, Pelletier S, Balliau T, Zivy M, Avelange-Macherel MH, Macherel D. Multi-scale analysis of heat stress acclimation in Arabidopsis seedlings highlights the primordial contribution of energy-transducing organelles. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:300-331. [PMID: 38613336 DOI: 10.1111/tpj.16763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 04/14/2024]
Abstract
Much progress has been made in understanding the molecular mechanisms of plant adaptation to heat stress. However, the great diversity of models and stress conditions, and the fact that analyses are often limited to a small number of approaches, complicate the picture. We took advantage of a liquid culture system in which Arabidopsis seedlings are arrested in their development, thus avoiding interference with development and drought stress responses, to investigate through an integrative approach seedlings' global response to heat stress and acclimation. Seedlings perfectly tolerate a noxious heat shock (43°C) when subjected to a heat priming treatment at a lower temperature (38°C) the day before, displaying a thermotolerance comparable to that previously observed for Arabidopsis. A major effect of the pre-treatment was to partially protect energy metabolism under heat shock and favor its subsequent rapid recovery, which was correlated with the survival of seedlings. Rapid recovery of actin cytoskeleton and mitochondrial dynamics were another landmark of heat shock tolerance. The omics confirmed the role of the ubiquitous heat shock response actors but also revealed specific or overlapping responses to priming, heat shock, and their combination. Since only a few components or functions of chloroplast and mitochondria were highlighted in these analyses, the preservation and rapid recovery of their bioenergetic roles upon acute heat stress do not require extensive remodeling of the organelles. Protection of these organelles is rather integrated into the overall heat shock response, thus allowing them to provide the energy required to elaborate other cellular responses toward acclimation.
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Affiliation(s)
- Elise Réthoré
- Univ Angers, Institut Agro Rennes-Angers, INRAE, IRHS-UMR 1345, F-49000, Angers, France
| | - Sandra Pelletier
- Univ Angers, Institut Agro Rennes-Angers, INRAE, IRHS-UMR 1345, F-49000, Angers, France
| | - Thierry Balliau
- INRAE, PAPPSO, UMR/UMR Génétique Végétale, Gif sur Yvette, France
| | - Michel Zivy
- INRAE, PAPPSO, UMR/UMR Génétique Végétale, Gif sur Yvette, France
| | | | - David Macherel
- Univ Angers, Institut Agro Rennes-Angers, INRAE, IRHS-UMR 1345, F-49000, Angers, France
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Kunz HH, Armbruster U, Mühlbauer S, de Vries J, Davis GA. Chloroplast ion homeostasis - what do we know and where should we go? THE NEW PHYTOLOGIST 2024; 243:543-559. [PMID: 38515227 DOI: 10.1111/nph.19661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 02/01/2024] [Indexed: 03/23/2024]
Abstract
Plant yields heavily depend on proper macro- and micronutrient supply from the soil. In the leaf cells, nutrient ions fulfill specific roles in biochemical reactions, especially photosynthesis housed in the chloroplast. Here, a well-balanced ion homeostasis is maintained by a number of ion transport proteins embedded in the envelope and thylakoid membranes. Ten years ago, the first alkali metal transporters from the K+ EFFLUX ANTIPORTER family were discovered in the model plant Arabidopsis. Since then, our knowledge about the physiological importance of these carriers and their substrates has greatly expanded. New insights into the role of alkali ions in plastid gene expression and photoprotective mechanisms, both prerequisites for plant productivity in natural environments, were gained. The discovery of a Cl- channel in the thylakoid and several additional plastid alkali and alkali metal transport proteins have advanced the field further. Nevertheless, scientists still have long ways to go before a complete systemic understanding of the chloroplast's ion transportome will emerge. In this Tansley review, we highlight and discuss the achievements of the last decade. More importantly, we make recommendations on what areas to prioritize, so the field can reach the next milestones. One area, laid bare by our similarity-based comparisons among phototrophs is our lack of knowledge what ion transporters are used by cyanobacteria to buffer photosynthesis fluctuations.
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Affiliation(s)
- Hans-Henning Kunz
- Plant Biochemistry, Biology, LMU Munich, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Ute Armbruster
- Institute of Molecular Photosynthesis, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
- CEPLAS - Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Susanne Mühlbauer
- Plant Biochemistry, Biology, LMU Munich, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), University of Goettingen, Goldschmidtstr. 1, D-37077, Göttingen, Germany
| | - Geoffry A Davis
- Plant Biochemistry, Biology, LMU Munich, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
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8
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Jakoby M, Stephan L, Heinemann B, Hülskamp M. Mutations in RABE1C suppress the spirrig mutant phenotype. PLoS One 2024; 19:e0304001. [PMID: 38885274 PMCID: PMC11182498 DOI: 10.1371/journal.pone.0304001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 05/03/2024] [Indexed: 06/20/2024] Open
Abstract
The plant BEACH-domain protein SPIRRIG (SPI) is involved in regulating cell morphogenesis and salt stress responses in Arabidopsis thaliana, Arabis alpina, and Marchantia polymorpha and was reported to function in the context of two unrelated cellular processes: vesicular trafficking and P-body mediated RNA metabolism. To further explore the molecular function of SPI, we isolated a second-site mutant, specifically rescuing the spi mutant trichome phenotype. The molecular analysis of the corresponding gene revealed a dominant negative mutation in RABE1C, a ras-related small GTP-binding protein that localizes to Golgi. Taken together, our data identified the genetic interaction between RABE1C and SPI, which is beneficial for further dissecting the function of SPI in vesicle trafficking-associated cell morphogenesis.
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Affiliation(s)
- Marc Jakoby
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Lisa Stephan
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Björn Heinemann
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne University, Cologne, Germany
| | - Martin Hülskamp
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
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9
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Schlößer M, Moseler A, Bodnar Y, Homagk M, Wagner S, Pedroletti L, Gellert M, Ugalde JM, Lillig CH, Meyer AJ. Localization of four class I glutaredoxins in the cytosol and the secretory pathway and characterization of their biochemical diversification. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1455-1474. [PMID: 38394181 DOI: 10.1111/tpj.16687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024]
Abstract
Class I glutaredoxins (GRXs) are catalytically active oxidoreductases and considered key proteins mediating reversible glutathionylation and deglutathionylation of protein thiols during development and stress responses. To narrow in on putative target proteins, it is mandatory to know the subcellular localization of the respective GRXs and to understand their catalytic activities and putative redundancy between isoforms in the same compartment. We show that in Arabidopsis thaliana, GRXC1 and GRXC2 are cytosolic proteins with GRXC1 being attached to membranes through myristoylation. GRXC3 and GRXC4 are identified as type II membrane proteins along the early secretory pathway with their enzymatic function on the luminal side. Unexpectedly, neither single nor double mutants lacking both GRXs isoforms in the cytosol or the ER show phenotypes that differ from wild-type controls. Analysis of electrostatic surface potentials and clustering of GRXs based on their electrostatic interaction with roGFP2 mirrors the phylogenetic classification of class I GRXs, which clearly separates the cytosolic GRXC1 and GRXC2 from the luminal GRXC3 and GRXC4. Comparison of all four studied GRXs for their oxidoreductase function highlights biochemical diversification with GRXC3 and GRXC4 being better catalysts than GRXC1 and GRXC2 for the reduction of bis(2-hydroxyethyl) disulfide. With oxidized roGFP2 as an alternative substrate, GRXC1 and GRXC2 catalyze the reduction faster than GRXC3 and GRXC4, which suggests that catalytic efficiency of GRXs in reductive reactions depends on the respective substrate. Vice versa, GRXC3 and GRXC4 are faster than GRXC1 and GRXC2 in catalyzing the oxidation of pre-reduced roGFP2 in the reverse reaction.
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Affiliation(s)
- Michelle Schlößer
- INRES-Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, D-53113, Bonn, Germany
| | - Anna Moseler
- INRES-Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, D-53113, Bonn, Germany
| | - Yana Bodnar
- Institute for Medical Biochemistry and Molecular Biology, University Medicine, University of Greifswald, Ferdinand-Sauerbruch-Straße, D-17475, Greifswald, Germany
| | - Maria Homagk
- INRES-Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, D-53113, Bonn, Germany
| | - Stephan Wagner
- INRES-Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, D-53113, Bonn, Germany
| | - Luca Pedroletti
- INRES-Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, D-53113, Bonn, Germany
| | - Manuela Gellert
- Institute for Medical Biochemistry and Molecular Biology, University Medicine, University of Greifswald, Ferdinand-Sauerbruch-Straße, D-17475, Greifswald, Germany
| | - José M Ugalde
- INRES-Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, D-53113, Bonn, Germany
| | - Christopher H Lillig
- Institute for Medical Biochemistry and Molecular Biology, University Medicine, University of Greifswald, Ferdinand-Sauerbruch-Straße, D-17475, Greifswald, Germany
| | - Andreas J Meyer
- INRES-Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, D-53113, Bonn, Germany
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10
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Miyaji S, Ito T, Kitaiwa T, Nishizono K, Agake SI, Harata H, Aoyama H, Umahashi M, Sato M, Inaba J, Fushinobu S, Yokoyama T, Maruyama-Nakashita A, Hirai MY, Ohkama-Ohtsu N. N 2-Acetylornithine deacetylase functions as a Cys-Gly dipeptidase in the cytosolic glutathione degradation pathway in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1603-1618. [PMID: 38441834 DOI: 10.1111/tpj.16700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/04/2024] [Accepted: 02/20/2024] [Indexed: 05/31/2024]
Abstract
Glutathione (GSH) is required for various physiological processes in plants, including redox regulation and detoxification of harmful compounds. GSH also functions as a repository for assimilated sulfur and is actively catabolized in plants. In Arabidopsis, GSH is mainly degraded initially by cytosolic enzymes, γ-glutamyl cyclotransferase, and γ-glutamyl peptidase, which release cysteinylglycine (Cys-Gly). However, the subsequent enzyme responsible for catabolizing this dipeptide has not been identified to date. In the present study, we identified At4g17830 as a Cys-Gly dipeptidase, namely cysteinylglycine peptidase 1 (CGP1). CGP1 complemented the phenotype of the yeast mutant that cannot degrade Cys-Gly. The Arabidopsis cgp1 mutant had lower Cys-Gly degradation activity than the wild type and showed perturbed concentrations of thiol compounds. Recombinant CGP1 showed reasonable Cys-Gly degradation activity in vitro. Metabolomic analysis revealed that cgp1 exhibited signs of severe sulfur deficiency, such as elevated accumulation of O-acetylserine (OAS) and the decrease in sulfur-containing metabolites. Morphological changes observed in cgp1, including longer primary roots of germinating seeds, were also likely associated with sulfur starvation. Notably, At4g17830 has previously been reported to encode an N2-acetylornithine deacetylase (NAOD) that functions in the ornithine biosynthesis. The cgp1 mutant did not show a decrease in ornithine content, whereas the analysis of CGP1 structure did not rule out the possibility that CGP1 has Cys-Gly dipeptidase and NAOD activities. Therefore, we propose that CGP1 is a Cys-Gly dipeptidase that functions in the cytosolic GSH degradation pathway and may play dual roles in GSH and ornithine metabolism.
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Affiliation(s)
- Shunsuke Miyaji
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Takehiro Ito
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Taisuke Kitaiwa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Kosuke Nishizono
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Shin-Ichiro Agake
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Hiroki Harata
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Haruna Aoyama
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Minori Umahashi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Muneo Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Jun Inaba
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Tadashi Yokoyama
- Institute of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
- Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima, 960-1296, Japan
| | - Akiko Maruyama-Nakashita
- Graduate School of Bioresource and Bioenvironmental Science, Kyushu University, Fukuoka, 819-0395, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Bioagricultural Science, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Naoko Ohkama-Ohtsu
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
- Institute of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
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11
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Cook R, Froehlich JE, Yang Y, Korkmaz I, Kramer DM, Benning C. Chloroplast phosphatases LPPγ and LPPε1 facilitate conversion of extraplastidic phospholipids to galactolipids. PLANT PHYSIOLOGY 2024; 195:1506-1520. [PMID: 38401529 DOI: 10.1093/plphys/kiae100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/08/2024] [Accepted: 01/25/2024] [Indexed: 02/26/2024]
Abstract
Galactolipids comprise the majority of chloroplast membranes in plants, and their biosynthesis requires dephosphorylation of phosphatidic acid at the chloroplast envelope membranes. In Arabidopsis (Arabidopsis thaliana), the lipid phosphate phosphatases LPPγ, LPPε1, and LPPε2 have been previously implicated in chloroplast lipid assembly, with LPPγ being essential, as null mutants were reported to exhibit embryo lethality. Here, we show that lppγ mutants are in fact viable and that LPPγ, LPPε1, and LPPε2 do not appear to have central roles in the plastid pathway of membrane lipid biosynthesis. Redundant LPPγ and LPPε1 activity at the outer envelope membrane is important for plant development, and the respective lppγ lppε1 double mutant exhibits reduced flux through the ER pathway of galactolipid synthesis. While LPPε2 is imported and associated with interior chloroplast membranes, its role remains elusive and does not include basal nor phosphate limitation-induced biosynthesis of glycolipids. The specific physiological roles of LPPγ, LPPε1, and LPPε2 are yet to be uncovered, as does the identity of the phosphatidic acid phosphatase required for plastid galactolipid biosynthesis.
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Affiliation(s)
- Ron Cook
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - John E Froehlich
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Yang Yang
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Ilayda Korkmaz
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - David M Kramer
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Christoph Benning
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
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12
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Hou LY, Sommer F, Poeker L, Dziubek D, Schroda M, Geigenberger P. The impact of light and thioredoxins on the plant thiol-disulfide proteome. PLANT PHYSIOLOGY 2024; 195:1536-1560. [PMID: 38214043 PMCID: PMC11142374 DOI: 10.1093/plphys/kiad669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/22/2023] [Indexed: 01/13/2024]
Abstract
Thiol-based redox regulation is a crucial posttranslational mechanism to acclimate plants to changing light availability. Here, we conducted a biotin switch-based redox proteomics study in Arabidopsis (Arabidopsis thaliana) to systematically investigate dynamics of thiol-redox networks in response to temporal changes in light availability and across genotypes lacking parts of the thioredoxin (Trx) or NADPH-Trx-reductase C (NTRC) systems in the chloroplast. Time-resolved dynamics revealed light led to marked decreases in the oxidation states of many chloroplast proteins with photosynthetic functions during the first 10 min, followed by their partial reoxidation after 2 to 6 h into the photoperiod. This involved f, m, and x-type Trx proteins showing similar light-induced reduction-oxidation dynamics, while NTRC, 2-Cys peroxiredoxins, and Trx y2 showed an opposing pattern, being more oxidized in light than dark. In Arabidopsis trxf1f2, trxm1m2, or ntrc mutants, most proteins showed increased oxidation states in the light compared to wild type, suggesting their light-dependent dynamics were related to NTRC/Trx networks. While NTRC deficiency had a strong influence in all light conditions, deficiencies in f- or m-type Trxs showed differential impacts on the thiol-redox proteome depending on the light environment, being higher in constant or fluctuating light, respectively. The results indicate plant redox proteomes are subject to dynamic changes in reductive and oxidative pathways to cooperatively fine-tune photosynthetic and metabolic processes in the light. The importance of the individual elements of the NTRC/Trx networks mediating these responses depend on the extent of light variability, with NTRC playing a crucial role to balance protein-redox states in rapidly fluctuating light.
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Affiliation(s)
- Liang-Yu Hou
- Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
- Institute of Plant and Microbial Biology, Academia Sinica, 11529 Taipei, Taiwan
| | - Frederik Sommer
- Molekulare Biotechnologie und Systembiologie, TU Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Louis Poeker
- Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Dejan Dziubek
- Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Michael Schroda
- Molekulare Biotechnologie und Systembiologie, TU Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Peter Geigenberger
- Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
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13
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Rugen N, Senkler M, Braun HP. Deep proteomics reveals incorporation of unedited proteins into mitochondrial protein complexes in Arabidopsis. PLANT PHYSIOLOGY 2024; 195:1180-1199. [PMID: 38060994 PMCID: PMC11142381 DOI: 10.1093/plphys/kiad655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/12/2023] [Indexed: 06/02/2024]
Abstract
The mitochondrial proteome consists of numerous types of proteins which either are encoded and synthesized in the mitochondria, or encoded in the cell nucleus, synthesized in the cytoplasm and imported into the mitochondria. Their synthesis in the mitochondria, but not in the nucleus, relies on the editing of the primary transcripts of their genes at defined sites. Here, we present an in-depth investigation of the mitochondrial proteome of Arabidopsis (Arabidopsis thaliana) and a public online platform for the exploration of the data. For the analysis of our shotgun proteomic data, an Arabidopsis sequence database was created comprising all available protein sequences from the TAIR10 and Araport11 databases, supplemented with sequences of proteins translated from edited and nonedited transcripts of mitochondria. Amino acid sequences derived from partially edited transcripts were also added to analyze proteins encoded by the mitochondrial genome. Proteins were digested in parallel with six different endoproteases to obtain maximum proteome coverage. The resulting peptide fractions were finally analyzed using liquid chromatography coupled to ion mobility spectrometry and tandem mass spectrometry. We generated a "deep mitochondrial proteome" of 4,692 proteins. 1,339 proteins assigned to mitochondria by the SUBA5 database (https://suba.live) accounted for >80% of the total protein mass of our fractions. The coverage of proteins by identified peptides was particularly high compared to single-protease digests, allowing the exploration of differential splicing and RNA editing events at the protein level. We show that proteins translated from nonedited transcripts can be incorporated into native mitoribosomes and the ATP synthase complex. We present a portal for the use of our data, based on "proteomaps" with directly linked protein data. The portal is available at www.proteomeexplorer.de.
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Affiliation(s)
- Nils Rugen
- Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Michael Senkler
- Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Hans-Peter Braun
- Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
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14
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Matamoros MA, Romero LC, Tian T, Román Á, Duanmu D, Becana M. Persulfidation of plant and bacteroid proteins is involved in legume nodule development and senescence. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3009-3025. [PMID: 37952184 PMCID: PMC11103110 DOI: 10.1093/jxb/erad436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 11/02/2023] [Indexed: 11/14/2023]
Abstract
Legumes establish symbiosis with rhizobia, forming nitrogen-fixing nodules. The central role of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in nodule biology has been clearly established. Recently, hydrogen sulfide (H2S) and other reactive sulfur species (RSS) have emerged as novel signaling molecules in animals and plants. A major mechanism by which ROS, RNS, and RSS fulfil their signaling role is the post-translational modification of proteins. To identify possible functions of H2S in nodule development and senescence, we used the tag-switch method to quantify changes in the persulfidation profile of common bean (Phaseolus vulgaris) nodules at different developmental stages. Proteomic analyses indicate that persulfidation plays a regulatory role in plant and bacteroid metabolism and senescence. The effect of a H2S donor on nodule functioning and on several proteins involved in ROS and RNS homeostasis was also investigated. Our results using recombinant proteins and nodulated plants support a crosstalk among H2S, ROS, and RNS, a protective function of persulfidation on redox-sensitive enzymes, and a beneficial effect of H2S on symbiotic nitrogen fixation. We conclude that the general decrease of persulfidation levels observed in plant proteins of aging nodules is one of the mechanisms that disrupt redox homeostasis leading to senescence.
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Affiliation(s)
- Manuel A Matamoros
- Departamento de Biología Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Avenida Montañana 1005, 50059 Zaragoza, Spain
| | - Luis C Romero
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas y Universidad de Sevilla, 41092 Sevilla, Spain
| | - Tao Tian
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ángela Román
- Departamento de Biología Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Avenida Montañana 1005, 50059 Zaragoza, Spain
| | - Deqiang Duanmu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Manuel Becana
- Departamento de Biología Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Avenida Montañana 1005, 50059 Zaragoza, Spain
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15
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Mizrahi R, Ostersetzer-Biran O. Mitochondrial RNA Helicases: Key Players in the Regulation of Plant Organellar RNA Splicing and Gene Expression. Int J Mol Sci 2024; 25:5502. [PMID: 38791540 PMCID: PMC11122041 DOI: 10.3390/ijms25105502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Mitochondrial genomes of land plants are large and exhibit a complex mode of gene organization and expression, particularly at the post-transcriptional level. The primary organellar transcripts in plants undergo extensive maturation steps, including endo- and/or exo-nucleolytic cleavage, RNA-base modifications (mostly C-to-U deaminations) and both 'cis'- and 'trans'-splicing events. These essential processing steps rely on the activities of a large set of nuclear-encoded factors. RNA helicases serve as key players in RNA metabolism, participating in the regulation of transcription, mRNA processing and translation. They unwind RNA secondary structures and facilitate the formation of ribonucleoprotein complexes crucial for various stages of gene expression. Furthermore, RNA helicases are involved in RNA metabolism by modulating pre-mRNA maturation, transport and degradation processes. These enzymes are, therefore, pivotal in RNA quality-control mechanisms, ensuring the fidelity and efficiency of RNA processing and turnover in plant mitochondria. This review summarizes the significant roles played by helicases in regulating the highly dynamic processes of mitochondrial transcription, RNA processing and translation in plants. We further discuss recent advancements in understanding how dysregulation of mitochondrial RNA helicases affects the splicing of organellar genes, leading to respiratory dysfunctions, and consequently, altered growth, development and physiology of land plants.
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Affiliation(s)
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus—Givat Ram, Jerusalem 9190401, Israel
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16
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Song C, Hou Y, Li T, Liu Y, Wang XA, Qu W, Li L. Lon1 Inactivation Downregulates Autophagic Flux and Brassinosteroid Biogenesis, Modulating Mitochondrial Proportion and Seed Development in Arabidopsis. Int J Mol Sci 2024; 25:5425. [PMID: 38791463 PMCID: PMC11121791 DOI: 10.3390/ijms25105425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/11/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Mitochondrial protein homeostasis is crucially regulated by protein degradation processes involving both mitochondrial proteases and cytosolic autophagy. However, it remains unclear how plant cells regulate autophagy in the scenario of lacking a major mitochondrial Lon1 protease. In this study, we observed a notable downregulation of core autophagy proteins in Arabidopsis Lon1 knockout mutant lon1-1 and lon1-2, supporting the alterations in the relative proportions of mitochondrial and vacuolar proteins over total proteins in the plant cells. To delve deeper into understanding the roles of the mitochondrial protease Lon1 and autophagy in maintaining mitochondrial protein homeostasis and plant development, we generated the lon1-2atg5-1 double mutant by incorporating the loss-of-function mutation of the autophagy core protein ATG5, known as atg5-1. The double mutant exhibited a blend of phenotypes, characterized by short plants and early senescence, mirroring those observed in the individual single mutants. Accordingly, distinct transcriptome alterations were evident in each of the single mutants, while the double mutant displayed a unique amalgamation of transcriptional responses. Heightened severity, particularly evident in reduced seed numbers and abnormal embryo development, was observed in the double mutant. Notably, aberrations in protein storage vacuoles (PSVs) and oil bodies were evident in the single and double mutants. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of genes concurrently downregulated in lon1-2, atg5-1, and lon1-2atg5-1 unveiled a significant suppression of genes associated with brassinosteroid (BR) biosynthesis and homeostasis. This downregulation likely contributes to the observed abnormalities in seed and embryo development in the mutants.
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Affiliation(s)
| | | | | | | | | | | | - Lei Li
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China; (C.S.); (Y.H.); (T.L.); (Y.L.); (X.-A.W.); (W.Q.)
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17
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Edris R, Sultan LD, Best C, Mizrahi R, Weinstein O, Chen S, Kamennaya NA, Keren N, Zer H, Zhu H, Ostersetzer-Biran O. Root Primordium Defective 1 Encodes an Essential PORR Protein Required for the Splicing of Mitochondria-Encoded Group II Introns and for Respiratory Complex I Biogenesis. PLANT & CELL PHYSIOLOGY 2024; 65:602-617. [PMID: 37702436 DOI: 10.1093/pcp/pcad101] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/19/2023] [Accepted: 09/06/2023] [Indexed: 09/14/2023]
Abstract
Cellular respiration involves complex organellar metabolic activities that are pivotal for plant growth and development. Mitochondria contain their own genetic system (mitogenome, mtDNA), which encodes key elements of the respiratory machinery. Plant mtDNAs are notably larger than their counterparts in Animalia, with complex genome organization and gene expression characteristics. The maturation of the plant mitochondrial transcripts involves extensive RNA editing, trimming and splicing events. These essential processing steps rely on the activities of numerous nuclear-encoded cofactors, which may also play key regulatory roles in mitochondrial biogenesis and function and hence in plant physiology. Proteins that harbor the plant organelle RNA recognition (PORR) domain are represented in a small gene family in plants. Several PORR members, including WTF1, WTF9 and LEFKOTHEA, are known to act in the splicing of organellar group II introns in angiosperms. The AT4G33495 gene locus encodes an essential PORR protein in Arabidopsis, termed ROOT PRIMORDIUM DEFECTIVE 1 (RPD1). A null mutation of At.RPD1 causes arrest in early embryogenesis, while the missense mutant lines, rpd1.1 and rpd1.2, exhibit a strong impairment in root development and retarded growth phenotypes, especially under high-temperature conditions. Here, we further show that RPD1 functions in the splicing of introns that reside in the coding regions of various complex I (CI) subunits (i.e. nad2, nad4, nad5 and nad7), as well as in the maturation of the ribosomal rps3 pre-RNA in Arabidopsis mitochondria. The altered growth and developmental phenotypes and modified respiration activities are tightly correlated with respiratory chain CI defects in rpd1 mutants.
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Affiliation(s)
- Rana Edris
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Laure D Sultan
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Corinne Best
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Ron Mizrahi
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Ofir Weinstein
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Stav Chen
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Nina A Kamennaya
- The French Associates Institute for Agriculture and Biotechnology of Drylands, Bluestein Institutes for Desert Research, Ben Gurion University of the Negev, Sede Boqer Campus, Sede Boqer 8499000, Israel
| | - Nir Keren
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Hagit Zer
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
| | - Hongliang Zhu
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus-Givat Ram, Jerusalem 9190401, Israel
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18
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Jarvis RP, Li J, Lin R, Ling Q, Lyu Y, Sun Y, Yao Z. Reply: Does the polyubiquitination pathway operate inside intact chloroplasts to remove proteins? THE PLANT CELL 2024:koae105. [PMID: 38738499 DOI: 10.1093/plcell/koae105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/19/2024] [Indexed: 05/14/2024]
Affiliation(s)
- R Paul Jarvis
- Section of Molecular Plant Biology, Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Jialong Li
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Qihua Ling
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS-JIC Center of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yuping Lyu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yi Sun
- Section of Molecular Plant Biology, Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Zujie Yao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
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19
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Otulak-Kozieł K, Kozieł E, Treder K, Rusin P. Homogalacturonan Pectins Tuned as an Effect of Susceptible rbohD, Col-0-Reactions, and Resistance rbohF-, rbohD/F-Reactions to TuMV. Int J Mol Sci 2024; 25:5256. [PMID: 38791293 PMCID: PMC11120978 DOI: 10.3390/ijms25105256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/02/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
The plant cell wall is an actively reorganized network during plant growth and triggered immunity in response to biotic stress. While the molecular mechanisms managing perception, recognition, and signal transduction in response to pathogens are well studied in the context of damaging intruders, the current understanding of plant cell wall rebuilding and active defense strategies in response to plant virus infections remains poorly characterized. Pectins can act as major elements of the primary cell wall and are dynamic compounds in response to pathogens. Homogalacturonans (HGs), a main component of pectins, have been postulated as defensive molecules in plant-pathogen interactions and linked to resistance responses. This research focused on examining the regulation of selected pectin metabolism components in susceptible (rbohD-, Col-0-TuMV) and resistance (rbohF-, rbohD/F-TuMV) reactions. Regardless of the interaction type, ultrastructural results indicated dynamic cell wall rebuilding. In the susceptible reaction promoted by RbohF, there was upregulation of AtPME3 (pectin methylesterase) but not AtPME17, confirmed by induction of PME3 protein deposition. Moreover, the highest PME activity along with a decrease in cell wall methylesters compared to resistance interactions in rbohD-TuMV were noticed. Consequently, the susceptible reaction of rbohD and Col-0 to TuMV was characterized by a significant domination of low/non-methylesterificated HGs. In contrast, cell wall changes during the resistance response of rbohF and rbohD/F to TuMV were associated with dynamic induction of AtPMEI2, AtPMEI3, AtGAUT1, and AtGAUT7 genes, confirmed by significant induction of PMEI2, PMEI3, and GAUT1 protein deposition. In both resistance reactions, a dynamic decrease in PME activity was documented, which was most intense in rbohD/F-TuMV. This decrease was accompanied by an increase in cell wall methylesters, indicating that the domination of highly methylesterificated HGs was associated with cell wall rebuilding in rbohF and rbohD/F defense responses to TuMV. These findings suggest that selected PME with PMEI enzymes have a diverse impact on the demethylesterification of HGs and metabolism as a result of rboh-TuMV interactions, and are important factors in regulating cell wall changes depending on the type of interaction, especially in resistance responses. Therefore, PMEI2 and PMEI3 could potentially be important signaling resistance factors in the rboh-TuMV pathosystem.
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Affiliation(s)
- Katarzyna Otulak-Kozieł
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences—SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland
| | - Edmund Kozieł
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences—SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland
- Plant Breeding and Acclimatization Institute—National Research Institute in Radzików, Bonin Division, Department of Potato Protection and Seed Science at Bonin, Bonin Str. 3, 76-009 Bonin, Poland;
| | - Krzysztof Treder
- Plant Breeding and Acclimatization Institute—National Research Institute in Radzików, Bonin Division, Department of Potato Protection and Seed Science at Bonin, Bonin Str. 3, 76-009 Bonin, Poland;
| | - Piotr Rusin
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences—SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland
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20
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Pei S, Tao Q, Li W, Qi G, Wang B, Wang Y, Dai S, Shen Q, Wang X, Wu X, Xu S, Theprungsirikul L, Zhang J, Liang L, Liu Y, Chen K, Shen Y, Crawford BM, Cheng M, Zhang Q, Wang Y, Liu H, Yang B, Krichilsky B, Pei J, Song K, Johnson DM, Jiang Z, Wu F, Swift GB, Yang H, Liu Z, Zou X, Vo-Dinh T, Liu F, Pei ZM, Yuan F. Osmosensor-mediated control of Ca 2+ spiking in pollen germination. Nature 2024; 629:1118-1125. [PMID: 38778102 PMCID: PMC11136663 DOI: 10.1038/s41586-024-07445-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 04/19/2024] [Indexed: 05/25/2024]
Abstract
Higher plants survive terrestrial water deficiency and fluctuation by arresting cellular activities (dehydration) and resuscitating processes (rehydration). However, how plants monitor water availability during rehydration is unknown. Although increases in hypo-osmolarity-induced cytosolic Ca2+ concentration (HOSCA) have long been postulated to be the mechanism for sensing hypo-osmolarity in rehydration1,2, the molecular basis remains unknown. Because osmolarity triggers membrane tension and the osmosensing specificity of osmosensing channels can only be determined in vivo3-5, these channels have been classified as a subtype of mechanosensors. Here we identify bona fide cell surface hypo-osmosensors in Arabidopsis and find that pollen Ca2+ spiking is controlled directly by water through these hypo-osmosensors-that is, Ca2+ spiking is the second messenger for water status. We developed a functional expression screen in Escherichia coli for hypo-osmosensitive channels and identified OSCA2.1, a member of the hyperosmolarity-gated calcium-permeable channel (OSCA) family of proteins6. We screened single and high-order OSCA mutants, and observed that the osca2.1/osca2.2 double-knockout mutant was impaired in pollen germination and HOSCA. OSCA2.1 and OSCA2.2 function as hypo-osmosensitive Ca2+-permeable channels in planta and in HEK293 cells. Decreasing osmolarity of the medium enhanced pollen Ca2+ oscillations, which were mediated by OSCA2.1 and OSCA2.2 and required for germination. OSCA2.1 and OSCA2.2 convert extracellular water status into Ca2+ spiking in pollen and may serve as essential hypo-osmosensors for tracking rehydration in plants.
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Affiliation(s)
- Songyu Pei
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, China
- Department of Biology, Duke University, Durham, NC, USA
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC, USA
- College of Life Sciences, Zhejiang University, Hangzhou, China
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Qi Tao
- College of Life Sciences, Zhejiang University, Hangzhou, China
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Wenke Li
- College of Life Sciences, Zhejiang University, Hangzhou, China
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Guoning Qi
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Borong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yan Wang
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, China
| | - Shiwen Dai
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, China
| | - Qiujing Shen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xi Wang
- College of Life Sciences, Zhejiang University, Hangzhou, China
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xiaomei Wu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Shijian Xu
- Department of Biology, Duke University, Durham, NC, USA
| | | | | | - Liang Liang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yuantao Liu
- College of Life Sciences, Zhejiang University, Hangzhou, China
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Kena Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yang Shen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | | | - Mengjia Cheng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Qi Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, China
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yiqi Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Hongli Liu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Benguang Yang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | | | - Jessica Pei
- Department of Biology, Duke University, Durham, NC, USA
- Fuqua School of Business, Duke University, Durham, NC, USA
| | - Karen Song
- Department of Biology, Duke University, Durham, NC, USA
| | | | | | - Feihua Wu
- Department of Biology, Duke University, Durham, NC, USA
| | - Gary B Swift
- Department of Physics, Duke University, Durham, NC, USA
| | - Huanghe Yang
- Department of Biochemistry, Duke University, Durham, NC, USA
| | - Zhonghua Liu
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, China
| | - Xuexiao Zou
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, China
| | - Tuan Vo-Dinh
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC, USA
| | - Feng Liu
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, China.
- Department of Biology, Duke University, Durham, NC, USA.
| | - Zhen-Ming Pei
- Department of Biology, Duke University, Durham, NC, USA.
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC, USA.
| | - Fang Yuan
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, China.
- Department of Biology, Duke University, Durham, NC, USA.
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China.
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21
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Jorge GL, Kim D, Xu C, Cho SH, Su L, Xu D, Bartley LE, Stacey G, Thelen JJ. Unveiling orphan receptor-like kinases in plants: novel client discovery using high-confidence library predictions in the Kinase-Client (KiC) assay. FRONTIERS IN PLANT SCIENCE 2024; 15:1372361. [PMID: 38633461 PMCID: PMC11021772 DOI: 10.3389/fpls.2024.1372361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/20/2024] [Indexed: 04/19/2024]
Abstract
Plants are remarkable in their ability to adapt to changing environments, with receptor-like kinases (RLKs) playing a pivotal role in perceiving and transmitting environmental cues into cellular responses. Despite extensive research on RLKs from the plant kingdom, the function and activity of many kinases, i.e., their substrates or "clients", remain uncharted. To validate a novel client prediction workflow and learn more about an important RLK, this study focuses on P2K1 (DORN1), which acts as a receptor for extracellular ATP (eATP), playing a crucial role in plant stress resistance and immunity. We designed a Kinase-Client (KiC) assay library of 225 synthetic peptides, incorporating previously identified P2K phosphorylated peptides and novel predictions from a deep-learning phosphorylation site prediction model (MUsite) and a trained hidden Markov model (HMM) based tool, HMMER. Screening the library against purified P2K1 cytosolic domain (CD), we identified 46 putative substrates, including 34 novel clients, 27 of which may be novel peptides, not previously identified experimentally. Gene Ontology (GO) analysis among phosphopeptide candidates revealed proteins associated with important biological processes in metabolism, structure development, and response to stress, as well as molecular functions of kinase activity, catalytic activity, and transferase activity. We offer selection criteria for efficient further in vivo experiments to confirm these discoveries. This approach not only expands our knowledge of P2K1's substrates and functions but also highlights effective prediction algorithms for identifying additional potential substrates. Overall, the results support use of the KiC assay as a valuable tool in unraveling the complexities of plant phosphorylation and provide a foundation for predicting the phosphorylation landscape of plant species based on peptide library results.
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Affiliation(s)
- Gabriel Lemes Jorge
- Division of Biochemistry, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Daewon Kim
- Division of Plant Science & Technology, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Chunhui Xu
- Institute for Data Science and Informatics, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Sung-Hwan Cho
- Division of Plant Science & Technology, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Lingtao Su
- Department of Electrical Engineering and Computer Science, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Shandong University of Science and Technology, Qingdao, Shandong, China
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Laura E. Bartley
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Gary Stacey
- Division of Plant Science & Technology, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Jay J. Thelen
- Division of Biochemistry, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
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22
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The SV, Santiago JP, Pappenberger C, Hammes UZ, Tegeder M. UMAMIT44 is a key player in glutamate export from Arabidopsis chloroplasts. THE PLANT CELL 2024; 36:1119-1139. [PMID: 38092462 PMCID: PMC10980354 DOI: 10.1093/plcell/koad310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/15/2023] [Indexed: 04/01/2024]
Abstract
Selective partitioning of amino acids among organelles, cells, tissues, and organs is essential for cellular metabolism and plant growth. Nitrogen assimilation into glutamine and glutamate and de novo biosynthesis of most protein amino acids occur in chloroplasts; therefore, various transport mechanisms must exist to accommodate their directional efflux from the stroma to the cytosol and feed the amino acids into the extraplastidial metabolic and long-distance transport pathways. Yet, Arabidopsis (Arabidopsis thaliana) transporters functioning in plastidial export of amino acids remained undiscovered. Here, USUALLY MULTIPLE ACIDS MOVE IN AND OUT TRANSPORTER 44 (UMAMIT44) was identified and shown to function in glutamate export from Arabidopsis chloroplasts. UMAMIT44 controls glutamate homeostasis within and outside of chloroplasts and influences nitrogen partitioning from leaves to sinks. Glutamate imbalances in chloroplasts and leaves of umamit44 mutants impact cellular redox state, nitrogen and carbon metabolism, and amino acid (AA) and sucrose supply of growing sinks, leading to negative effects on plant growth. Nonetheless, the mutant lines adjust to some extent by upregulating alternative pathways for glutamate synthesis outside the plastids and by mitigating oxidative stress through the production of other amino acids and antioxidants. Overall, this study establishes that the role of UMAMIT44 in glutamate export from chloroplasts is vital for controlling nitrogen availability within source leaf cells and for sink nutrition, with an impact on growth and seed yield.
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Affiliation(s)
- Samantha Vivia The
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - James P Santiago
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Clara Pappenberger
- Plant Systems Biology, School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Ulrich Z Hammes
- Plant Systems Biology, School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Mechthild Tegeder
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
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23
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Molinelli L, Drula E, Gaillard JC, Navarro D, Armengaud J, Berrin JG, Tron T, Tarrago L. Methionine oxidation of carbohydrate-active enzymes during white-rot wood decay. Appl Environ Microbiol 2024; 90:e0193123. [PMID: 38376171 PMCID: PMC10952391 DOI: 10.1128/aem.01931-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/24/2024] [Indexed: 02/21/2024] Open
Abstract
White-rot fungi employ secreted carbohydrate-active enzymes (CAZymes) along with reactive oxygen species (ROS), like hydrogen peroxide (H2O2), to degrade lignocellulose in wood. H2O2 serves as a co-substrate for key oxidoreductases during the initial decay phase. While the degradation of lignocellulose by CAZymes is well documented, the impact of ROS on the oxidation of the secreted proteins remains unclear, and the identity of the oxidized proteins is unknown. Methionine (Met) can be oxidized to Met sulfoxide (MetO) or Met sulfone (MetO2) with potential deleterious, antioxidant, or regulatory effects. Other residues, like proline (Pro), can undergo carbonylation. Using the white-rot Pycnoporus cinnabarinus grown on aspen wood, we analyzed the Met content of the secreted proteins and their susceptibility to oxidation combining H218O2 with deep shotgun proteomics. Strikingly, their overall Met content was significantly lower (1.4%) compared to intracellular proteins (2.1%), a feature conserved in fungi but not in metazoans or plants. We evidenced that a catalase, widespread in white-rot fungi, protects the secreted proteins from oxidation. Our redox proteomics approach allowed the identification of 49 oxidizable Met and 40 oxidizable Pro residues within few secreted proteins, mostly CAZymes. Interestingly, many of them had several oxidized residues localized in hotspots. Some Met, including those in GH7 cellobiohydrolases, were oxidized up to 47%, with a substantial percentage of sulfone (13%). These Met are conserved in fungal homologs, suggesting important functional roles. Our findings reveal that white-rot fungi safeguard their secreted proteins by minimizing their Met content and by scavenging ROS and pinpoint redox-active residues in CAZymes.IMPORTANCEThe study of lignocellulose degradation by fungi is critical for understanding the ecological and industrial implications of wood decay. While carbohydrate-active enzymes (CAZymes) play a well-established role in lignocellulose degradation, the impact of hydrogen peroxide (H2O2) on secreted proteins remains unclear. This study aims at evaluating the effect of H2O2 on secreted proteins, focusing on the oxidation of methionine (Met). Using the model white-rot fungi Pycnoporus cinnabarinus grown on aspen wood, we showed that fungi protect their secreted proteins from oxidation by reducing their Met content and utilizing a secreted catalase to scavenge exogenous H2O2. The research identified key oxidizable Met within secreted CAZymes. Importantly, some Met, like those of GH7 cellobiohydrolases, undergone substantial oxidation levels suggesting important roles in lignocellulose degradation. These findings highlight the adaptive mechanisms employed by white-rot fungi to safeguard their secreted proteins during wood decay and emphasize the importance of these processes in lignocellulose breakdown.
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Affiliation(s)
- Lise Molinelli
- />Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille Université, Marseille, France
- Centrale Marseille, CNRS, ISM2, Aix Marseille Université, Marseille, France
| | - Elodie Drula
- />Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille Université, Marseille, France
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille Université, Marseille, France
| | - Jean-Charles Gaillard
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, CEA, INRAE, Bagnols-sur-Cèze, France
| | - David Navarro
- />Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille Université, Marseille, France
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, CEA, INRAE, Bagnols-sur-Cèze, France
| | - Jean-Guy Berrin
- />Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille Université, Marseille, France
| | - Thierry Tron
- Centrale Marseille, CNRS, ISM2, Aix Marseille Université, Marseille, France
| | - Lionel Tarrago
- />Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille Université, Marseille, France
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24
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Li J, Zhang BS, Wu HW, Liu CL, Guo HS, Zhao JH. The RNA-binding domain of DCL3 is required for long-distance RNAi signaling. ABIOTECH 2024; 5:17-28. [PMID: 38576436 PMCID: PMC10987413 DOI: 10.1007/s42994-023-00124-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/27/2023] [Indexed: 04/06/2024]
Abstract
Small RNA (sRNA)-mediated RNA silencing (also known as RNA interference, or RNAi) is a conserved mechanism in eukaryotes that includes RNA degradation, DNA methylation, heterochromatin formation and protein translation repression. In plants, sRNAs can move either cell-to-cell or systemically, thereby acting as mobile silencing signals to trigger noncell autonomous silencing. However, whether and what proteins are also involved in noncell autonomous silencing have not been elucidated. In this study, we utilized a previously reported inducible RNAi plant, PDSi, which can induce systemic silencing of the endogenous PDS gene, and we demonstrated that DCL3 is involved in systemic PDS silencing through its RNA binding activity. We confirmed that the C-terminus of DCL3, including the predicted RNA-binding domain, is capable of binding short RNAs. Mutations affecting RNA binding, but not processing activity, reduced systemic PDS silencing, indicating that DCL3 binding to RNAs is required for the induction of systemic silencing. Cucumber mosaic virus infection assays showed that the RNA-binding activity of DCL3 is required for antiviral RNAi in systemically noninoculated leaves. Our findings demonstrate that DCL3 acts as a signaling agent involved in noncell autonomous silencing and an antiviral effect in addition to its previously known function in the generation of 24-nucleotide sRNAs. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-023-00124-6.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Bo-Sen Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Hua-Wei Wu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Cheng-Lan Liu
- Qilu Zhongke Academy of Modern Microbiology Technology, Jinan, 250022 China
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Jian-Hua Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049 China
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25
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Tausta SL, Fontaine K, Hillmer AT, Strobel SA. Fluoride transport in Arabidopsis thaliana plants is impaired in Fluoride EXporter (FEX) mutants. PLANT MOLECULAR BIOLOGY 2024; 114:17. [PMID: 38342783 PMCID: PMC10859346 DOI: 10.1007/s11103-023-01413-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/20/2023] [Indexed: 02/13/2024]
Abstract
Fluoride is an environmental toxin prevalent in water, soil, and air. A fluoride transporter called Fluoride EXporter (FEX) has been discovered across all domains of life, including bacteria, single cell eukaryotes, and all plants, that is required for fluoride tolerance. How FEX functions to protect multicellular plants is unknown. In order to distinguish between different models, the dynamic movement of fluoride in wildtype (WT) and fex mutant plants was monitored using [18F]fluoride with positron emission tomography. Significant differences were observed in the washout behavior following initial fluoride uptake between plants with and without a functioning FEX. [18F]Fluoride traveled quickly up the floral stem and into terminal tissues in WT plants. In contrast, the fluoride did not move out of the lower regions of the stem in mutant plants resulting in clearance rates near zero. The roots were not the primary locus of FEX action, nor did FEX direct fluoride to a specific tissue. Fluoride efflux by WT plants was saturated at high fluoride concentrations resulting in a pattern like the fex mutant. The kinetics of fluoride movement suggested that FEX mediates a fluoride transport mechanism throughout the plant where each individual cell benefits from FEX expression.
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Affiliation(s)
- S Lori Tausta
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06510, USA
- Institute of Biomolecular Design and Discovery, Yale University West Campus, West Haven, CT, 06516, USA
| | - Kathryn Fontaine
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, 330 Cedar Street, New Haven, CT, 06519, USA
- Yale PET Center, Yale University, 801 Howard Avenue, New Haven, CT, 06510, USA
| | - Ansel T Hillmer
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, 330 Cedar Street, New Haven, CT, 06519, USA
- Yale PET Center, Yale University, 801 Howard Avenue, New Haven, CT, 06510, USA
- Department of Biomedical Engineering, Yale University, 17 Hillhouse Avenue, New Haven, CT, 06511, USA
- Department of Psychiatry, Yale School of Medicine, 300 George Street, New Haven, CT, 06510, USA
| | - Scott A Strobel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06510, USA.
- Institute of Biomolecular Design and Discovery, Yale University West Campus, West Haven, CT, 06516, USA.
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26
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Lian Q, Li S, Kan S, Liao X, Huang S, Sloan DB, Wu Z. Association Analysis Provides Insights into Plant Mitonuclear Interactions. Mol Biol Evol 2024; 41:msae028. [PMID: 38324417 PMCID: PMC10875325 DOI: 10.1093/molbev/msae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/17/2024] [Accepted: 02/01/2024] [Indexed: 02/09/2024] Open
Abstract
Cytonuclear interaction refers to the complex and ongoing process of coevolution between nuclear and organelle genomes, which are responsible for cellular respiration, photosynthesis, lipid metabolism, etc. and play a significant role in adaptation and speciation. There have been a large number of studies to detect signatures of cytonuclear interactions. However, identification of the specific nuclear and organelle genetic polymorphisms that are involved in these interactions within a species remains relatively rare. The recent surge in whole genome sequencing has provided us an opportunity to explore cytonuclear interaction from a population perspective. In this study, we analyzed a total of 3,439 genomes from 7 species to identify signals of cytonuclear interactions by association (linkage disequilibrium) analysis of variants in both the mitochondrial and nuclear genomes across flowering plants. We also investigated examples of nuclear loci identified based on these association signals using subcellular localization assays, gene editing, and transcriptome sequencing. Our study provides a novel perspective on the investigation of cytonuclear coevolution, thereby enriching our understanding of plant fitness and offspring sterility.
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Affiliation(s)
- Qun Lian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shuai Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Marine College, Shandong University, Weihai 264209, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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27
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Fuchs P, Feixes-Prats E, Arruda P, Feitosa-Araújo E, Fernie AR, Grefen C, Lichtenauer S, Linka N, de Godoy Maia I, Meyer AJ, Schilasky S, Sweetlove LJ, Wege S, Weber APM, Millar AH, Keech O, Florez-Sarasa I, Barreto P, Schwarzländer M. PLANT UNCOUPLING MITOCHONDRIAL PROTEIN 2 localizes to the Golgi. PLANT PHYSIOLOGY 2024; 194:623-628. [PMID: 37820040 DOI: 10.1093/plphys/kiad540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 10/13/2023]
Abstract
In contrast to its close homolog PLANT UNCOUPLING MITOCHONDRIAL PROTEIN 1 (UCP1), which is an abundant carrier protein in the mitochondria, UCP2 localizes to the Golgi.
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Affiliation(s)
- Philippe Fuchs
- Institute of Plant Biology and Biotechnology (IBBP), Universität Münster, D-48143 Münster, Germany
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, D-53113 Bonn, Germany
| | - Elisenda Feixes-Prats
- Centre for Research in Agricultural Genomics (CRAG), Campus UAB Bellaterra, 08193 Barcelona, Spain
| | - Paulo Arruda
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas, 13083-875 Campinas, Brazil
| | - Elias Feitosa-Araújo
- Institute of Plant Biology and Biotechnology (IBBP), Universität Münster, D-48143 Münster, Germany
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, D-14476 Postdam-Golm, Germany
| | - Christopher Grefen
- Institute of Molecular and Cellular Botany, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Sophie Lichtenauer
- Institute of Plant Biology and Biotechnology (IBBP), Universität Münster, D-48143 Münster, Germany
| | - Nicole Linka
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Ivan de Godoy Maia
- Institute of Biosciences, São Paulo State University (UNESP), 18618-970 Botucatu, Brazil
| | - Andreas J Meyer
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, D-53113 Bonn, Germany
| | - Sören Schilasky
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, D-53113 Bonn, Germany
| | - Lee J Sweetlove
- Department of Biology, South Parks Road, University of Oxford, OX1 3RB Oxford, UK
| | - Stefanie Wege
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, D-53113 Bonn, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, 6009 Perth, Western Australia, Australia
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden
| | - Igor Florez-Sarasa
- Centre for Research in Agricultural Genomics (CRAG), Campus UAB Bellaterra, 08193 Barcelona, Spain
- Institut de Recerca i Tecnología Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Pedro Barreto
- Institute of Plant Biology and Biotechnology (IBBP), Universität Münster, D-48143 Münster, Germany
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology (IBBP), Universität Münster, D-48143 Münster, Germany
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Dziubek D, Poeker L, Siemitkowska B, Graf A, Marino G, Alseekh S, Arrivault S, Fernie AR, Armbruster U, Geigenberger P. NTRC and thioredoxins m1/m2 underpin the light acclimation of plants on proteome and metabolome levels. PLANT PHYSIOLOGY 2024; 194:982-1005. [PMID: 37804523 PMCID: PMC10828201 DOI: 10.1093/plphys/kiad535] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/09/2023]
Abstract
During photosynthesis, plants must manage strong fluctuations in light availability on different time scales, leading to long-term acclimation and short-term responses. However, little is known about the regulation and coordination of these processes and the modulators involved. In this study, we used proteomics, metabolomics, and reverse genetics to investigate how different light environmental factors, such as intensity or variability, affect long-term and short-term acclimation responses of Arabidopsis (Arabidopsis thaliana) and the importance of the chloroplast redox network in their regulation. In the wild type, high light, but not fluctuating light, led to large quantitative changes in the proteome and metabolome, accompanied by increased photosynthetic dynamics and plant growth. This finding supports light intensity as a stronger driver for acclimation than variability. Deficiencies in NADPH-thioredoxin reductase C (NTRC) or thioredoxins m1/m2, but not thioredoxin f1, almost completely suppressed the re-engineering of the proteome and metabolome, with both the induction of proteins involved in stress and redox responses and the repression of those involved in cytosolic and plastid protein synthesis and translation being strongly attenuated. Moreover, the correlations of protein or metabolite levels with light intensity were severely disturbed, suggesting a general defect in the light-dependent acclimation response, resulting in impaired photosynthetic dynamics. These results indicate a previously unknown role of NTRC and thioredoxins m1/m2 in modulating light acclimation at proteome and metabolome levels to control dynamic light responses. NTRC, but not thioredoxins m1/m2 or f1, also improves short-term photosynthetic responses by balancing the Calvin-Benson cycle in fluctuating light.
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Affiliation(s)
- Dejan Dziubek
- Fakultät für Biologie, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, 82152 Martinsried, Germany
| | - Louis Poeker
- Fakultät für Biologie, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, 82152 Martinsried, Germany
| | - Beata Siemitkowska
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alexander Graf
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Giada Marino
- Fakultät für Biologie, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, 82152 Martinsried, Germany
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Departments of Metabolomics and Crop Quantitative Genetics, Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgari
| | - Stéphanie Arrivault
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Departments of Metabolomics and Crop Quantitative Genetics, Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgari
| | - Ute Armbruster
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Institute of Molecular Photosynthesis, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
- CEPLAS—Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Peter Geigenberger
- Fakultät für Biologie, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2-4, 82152 Martinsried, Germany
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29
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Wang S, He B, Wu H, Cai Q, Ramírez-Sánchez O, Abreu-Goodger C, Birch PRJ, Jin H. Plant mRNAs move into a fungal pathogen via extracellular vesicles to reduce infection. Cell Host Microbe 2024; 32:93-105.e6. [PMID: 38103543 PMCID: PMC10872371 DOI: 10.1016/j.chom.2023.11.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/17/2023] [Accepted: 11/20/2023] [Indexed: 12/19/2023]
Abstract
Cross-kingdom small RNA trafficking between hosts and microbes modulates gene expression in the interacting partners during infection. However, whether other RNAs are also transferred is unclear. Here, we discover that host plant Arabidopsis thaliana delivers mRNAs via extracellular vesicles (EVs) into the fungal pathogen Botrytis cinerea. A fluorescent RNA aptamer reporter Broccoli system reveals host mRNAs in EVs and recipient fungal cells. Using translating ribosome affinity purification profiling and polysome analysis, we observe that delivered host mRNAs are translated in fungal cells. Ectopic expression of two transferred host mRNAs in B. cinerea shows that their proteins are detrimental to infection. Arabidopsis knockout mutants of the genes corresponding to these transferred mRNAs are more susceptible. Thus, plants have a strategy to reduce infection by transporting mRNAs into fungal cells. mRNAs transferred from plants to pathogenic fungi are translated to compromise infection, providing knowledge that helps combat crop diseases.
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Affiliation(s)
- Shumei Wang
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Baoye He
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Huaitong Wu
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Qiang Cai
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan, China
| | - Obed Ramírez-Sánchez
- National Laboratory of Genomics for Biodiversity (Langebio), Cinvestav, Irapuato 36821 Guanajuato, Mexico
| | - Cei Abreu-Goodger
- Institute of Ecology and Evolution, School of Biological Sciences, the University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Paul R J Birch
- Division of Plant Sciences, School of Life Science, University of Dundee at James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK; Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Hailing Jin
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA.
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30
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van Wijk KJ, Leppert T, Sun Z, Kearly A, Li M, Mendoza L, Guzchenko I, Debley E, Sauermann G, Routray P, Malhotra S, Nelson A, Sun Q, Deutsch EW. Detection of the Arabidopsis Proteome and Its Post-translational Modifications and the Nature of the Unobserved (Dark) Proteome in PeptideAtlas. J Proteome Res 2024; 23:185-214. [PMID: 38104260 DOI: 10.1021/acs.jproteome.3c00536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
This study describes a new release of the Arabidopsis thaliana PeptideAtlas proteomics resource (build 2023-10) providing protein sequence coverage, matched mass spectrometry (MS) spectra, selected post-translational modifications (PTMs), and metadata. 70 million MS/MS spectra were matched to the Araport11 annotation, identifying ∼0.6 million unique peptides and 18,267 proteins at the highest confidence level and 3396 lower confidence proteins, together representing 78.6% of the predicted proteome. Additional identified proteins not predicted in Araport11 should be considered for the next Arabidopsis genome annotation. This release identified 5198 phosphorylated proteins, 668 ubiquitinated proteins, 3050 N-terminally acetylated proteins, and 864 lysine-acetylated proteins and mapped their PTM sites. MS support was lacking for 21.4% (5896 proteins) of the predicted Araport11 proteome: the "dark" proteome. This dark proteome is highly enriched for E3 ligases, transcription factors, and for certain (e.g., CLE, IDA, PSY) but not other (e.g., THIONIN, CAP) signaling peptides families. A machine learning model trained on RNA expression data and protein properties predicts the probability that proteins will be detected. The model aids in discovery of proteins with short half-life (e.g., SIG1,3 and ERF-VII TFs) and for developing strategies to identify the missing proteins. PeptideAtlas is linked to TAIR, tracks in JBrowse, and several other community proteomics resources.
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Affiliation(s)
- Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Tami Leppert
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Zhi Sun
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Alyssa Kearly
- Boyce Thompson Institute, Ithaca, New York 14853, United States
| | - Margaret Li
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Luis Mendoza
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Isabell Guzchenko
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Erica Debley
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Georgia Sauermann
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Pratyush Routray
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Sagunya Malhotra
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Andrew Nelson
- Boyce Thompson Institute, Ithaca, New York 14853, United States
| | - Qi Sun
- Computational Biology Service Unit, Cornell University, Ithaca, New York 14853, United States
| | - Eric W Deutsch
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
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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. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 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] [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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32
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Seidel T. Detection of Stress-Induced Changes in Subcellular Protein Distribution. Methods Mol Biol 2024; 2832:115-132. [PMID: 38869791 DOI: 10.1007/978-1-0716-3973-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
Proteins often show alterations in their subcellular localization with changing environmental conditions; transcription factors enter the nucleus or are actively removed from the nucleus; some even bind to endo-membranes by conditional membrane anchors; and other proteins and mRNA arrange in RNA granules. These are some examples of the complex regulation of subcellular localization, which often depends on posttranslational modifications and is triggered by environmental stressors. The challenge is the precise identification of the compartments, the quantitative analysis of proteins, which reside in multiple compartments, and their transport dynamics. Therefore, appropriate compartment markers and routines for a reproducible quantitative workflow are required.
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Affiliation(s)
- Thorsten Seidel
- Dynamic Cell Imaging, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
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33
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Jain D, Schmidt W. Protein Phosphorylation Orchestrates Acclimations of Arabidopsis Plants to Environmental pH. Mol Cell Proteomics 2024; 23:100685. [PMID: 38000714 PMCID: PMC10837763 DOI: 10.1016/j.mcpro.2023.100685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 10/18/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
Environment pH (pHe) is a key parameter dictating a surfeit of conditions critical to plant survival and fitness. To elucidate the mechanisms that recalibrate cytoplasmic and apoplastic pH homeostasis, we conducted a comprehensive proteomic/phosphoproteomic inventory of plants subjected to transient exposure to acidic or alkaline pH, an approach that covered the majority of protein-coding genes of the reference plant Arabidopsis thaliana. Our survey revealed a large set-of so far undocumented pHe-dependent phospho-sites, indicative of extensive post-translational regulation of proteins involved in the acclimation to pHe. Changes in pHe altered both electrogenic H+ pumping via P-type ATPases and H+/anion co-transport processes, putatively leading to altered net trans-plasma membrane translocation of H+ ions. In pH 7.5 plants, the transport (but not the assimilation) of nitrogen via NRT2-type nitrate and AMT1-type ammonium transporters was induced, conceivably to increase the cytosolic H+ concentration. Exposure to both acidic and alkaline pH resulted in a marked repression of primary root elongation. No such cessation was observed in nrt2.1 mutants. Alkaline pH decreased the number of root hairs in the wild type but not in nrt2.1 plants, supporting a role of NRT2.1 in developmental signaling. Sequestration of iron into the vacuole via alterations in protein abundance of the vacuolar iron transporter VTL5 was inversely regulated in response to high and low pHe, presumptively in anticipation of associated changes in iron availability. A pH-dependent phospho-switch was also observed for the ABC transporter PDR7, suggesting changes in activity and, possibly, substrate specificity. Unexpectedly, the effect of pHe was not restricted to roots and provoked pronounced changes in the shoot proteome. In both roots and shoots, the plant-specific TPLATE complex components AtEH1 and AtEH2-essential for clathrin-mediated endocytosis-were differentially phosphorylated at multiple sites in response to pHe, indicating that the endocytic cargo protein trafficking is orchestrated by pHe.
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Affiliation(s)
- Dharmesh Jain
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei, Taiwan; Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan; Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Wolfgang Schmidt
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei, Taiwan; Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan; Biotechnology Center, National Chung-Hsing University, Taichun, Taiwan; Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei, Taiwan.
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34
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Kuntz M, Dimnet L, Pullara S, Moyet L, Rolland N. The Main Functions of Plastids. Methods Mol Biol 2024; 2776:89-106. [PMID: 38502499 DOI: 10.1007/978-1-0716-3726-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Plastids are semi-autonomous organelles like mitochondria and derive from a cyanobacterial ancestor that was engulfed by a host cell. During evolution, they have recruited proteins originating from the nuclear genome, and only parts of their ancestral metabolic properties were conserved and optimized to limit functional redundancy with other cell compartments. Furthermore, large disparities in metabolic functions exist among various types of plastids, and the characterization of their various metabolic properties is far from being accomplished. In this review, we provide an overview of the main functions, known to be achieved by plastids or shared by plastids and other compartments of the cell. In short, plastids appear at the heart of all main plant functions.
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Affiliation(s)
- Marcel Kuntz
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble, France.
| | - Laura Dimnet
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble, France
| | - Sara Pullara
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble, France
| | - Lucas Moyet
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble, France
| | - Norbert Rolland
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Univ. Grenoble Alpes, IRIG, CEA Grenoble, Grenoble, France
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35
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Rhodes J, Zipfel C. Identification of Bioactive Phytocytokines Using Transcriptomic Data and Plant Bioassays. Methods Mol Biol 2024; 2731:23-35. [PMID: 38019423 DOI: 10.1007/978-1-0716-3511-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Plant genomes contain thousands of short open reading frames that encode putative peptides. Some of these peptides play important signaling roles in response to environmental stress. Here we describe a pipeline used to identify the CTNIP/SMALL PHYTOCYTOKINES REGULATING DEFENSE AND WATER LOSS (SCREW) family of phytocytokines, based upon their transcriptional upregulation during biotic stress. Moreover, we describe approaches to assay their activity in planta by measuring increases in cytoplasmic calcium concentration, reactive oxygen species production, and mitogen-activated protein kinase phosphorylation.
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Affiliation(s)
- Jack Rhodes
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK.
| | - Cyril Zipfel
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
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36
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Arrivé M, Bruggeman M, Skaltsogiannis V, Coudray L, Quan YF, Schelcher C, Cognat V, Hammann P, Chicher J, Wolff P, Gobert A, Giegé P. A tRNA-modifying enzyme facilitates RNase P activity in Arabidopsis nuclei. NATURE PLANTS 2023; 9:2031-2041. [PMID: 37945696 DOI: 10.1038/s41477-023-01564-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 10/09/2023] [Indexed: 11/12/2023]
Abstract
RNase P is the essential activity that performs the 5' maturation of transfer RNA (tRNA) precursors. Beyond the ancestral form of RNase P containing a ribozyme, protein-only RNase P enzymes termed PRORP were identified in eukaryotes. In human mitochondria, PRORP forms a complex with two protein partners to become functional. In plants, although PRORP enzymes are active alone, we investigate their interaction network to identify potential tRNA maturation complexes. Here we investigate functional interactions involving the Arabidopsis nuclear RNase P PRORP2. We show, using an immuno-affinity strategy, that PRORP2 occurs in a complex with the tRNA methyl transferases TRM1A and TRM1B in vivo. Beyond RNase P, these enzymes can also interact with RNase Z. We show that TRM1A/TRM1B localize in the nucleus and find that their double knockout mutation results in a severe macroscopic phenotype. Using a combination of immuno-detections, mass spectrometry and a transcriptome-wide tRNA sequencing approach, we observe that TRM1A/TRM1B are responsible for the m22G26 modification of 70% of cytosolic tRNAs in vivo. We use the transcriptome wide tRNAseq approach as well as RNA blot hybridizations to show that RNase P activity is impaired in TRM1A/TRM1B mutants for specific tRNAs, in particular, tRNAs containing a m22G modification at position 26 that are strongly downregulated in TRM1A/TRM1B mutants. Altogether, results indicate that the m22G-adding enzymes TRM1A/TRM1B functionally cooperate with nuclear RNase P in vivo for the early steps of cytosolic tRNA biogenesis.
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Affiliation(s)
- Mathilde Arrivé
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Mathieu Bruggeman
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Vasileios Skaltsogiannis
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Léna Coudray
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Yi-Fat Quan
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Cédric Schelcher
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Valérie Cognat
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Philippe Hammann
- Plateforme protéomique Strasbourg Esplanade, FR1589 du CNRS, Strasbourg, France
| | - Johana Chicher
- Plateforme protéomique Strasbourg Esplanade, FR1589 du CNRS, Strasbourg, France
| | - Philippe Wolff
- Plateforme protéomique Strasbourg Esplanade, FR1589 du CNRS, Strasbourg, France
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Anthony Gobert
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Philippe Giegé
- Institut de biologie moléculaire des plantes, UPR2357 du CNRS, Université de Strasbourg, Strasbourg, France.
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37
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Kerbler SML, Armijos-Jaramillo V, Lunn JE, Vicente R. The trehalose 6-phosphate phosphatase family in plants. PHYSIOLOGIA PLANTARUM 2023; 175:e14096. [PMID: 38148193 DOI: 10.1111/ppl.14096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/15/2023] [Accepted: 11/12/2023] [Indexed: 12/28/2023]
Abstract
Trehalose 6-phosphate (Tre6P), the intermediate of trehalose biosynthesis, is an essential signalling metabolite linking plant growth and development to carbon metabolism. While recent work has focused predominantly on the enzymes that produce Tre6P, little is known about the proteins that catalyse its degradation, the trehalose 6-phosphate phosphatases (TPPs). Often occurring in large protein families, TPPs exhibit cell-, tissue- and developmental stage-specific expression patterns, suggesting important regulatory functions in controlling local levels of Tre6P and trehalose as well as Tre6P signalling. Furthermore, growing evidence through gene expression studies and transgenic approaches shows that TPPs play an important role in integrating environmental signals with plant metabolism. This review highlights the large diversity of TPP isoforms in model and crop plants and identifies how modulating Tre6P metabolism in certain cell types, tissues, and at different developmental stages may promote stress tolerance, resilience and increased crop yield.
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Affiliation(s)
- Sandra Mae-Lin Kerbler
- Leibniz-Institute für Gemüse- und Zierpflanzenbau, Groβbeeren, Germany
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Vinicio Armijos-Jaramillo
- Grupo de Bio-Quimioinformática, Carrera de Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, Ecuador
| | - John Edward Lunn
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Rubén Vicente
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Plant Ecophysiology and Metabolism Group, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Huang J, Staes A, Impens F, Demichev V, Van Breusegem F, Gevaert K, Willems P. CysQuant: Simultaneous quantification of cysteine oxidation and protein abundance using data dependent or independent acquisition mass spectrometry. Redox Biol 2023; 67:102908. [PMID: 37793239 PMCID: PMC10562924 DOI: 10.1016/j.redox.2023.102908] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 10/06/2023] Open
Abstract
Protein cysteinyl thiols are susceptible to reduction-oxidation reactions that can influence protein function. Accurate quantification of cysteine oxidation is therefore crucial for decoding protein redox regulation. Here, we present CysQuant, a novel approach for simultaneous quantification of cysteine oxidation degrees and protein abundancies. CysQuant involves light/heavy iodoacetamide isotopologues for differential labeling of reduced and reversibly oxidized cysteines analyzed by data-dependent acquisition (DDA) or data-independent acquisition mass spectrometry (DIA-MS). Using plexDIA with in silico predicted spectral libraries, we quantified an average of 18% cysteine oxidation in Arabidopsis thaliana by DIA-MS, including a subset of highly oxidized cysteines forming disulfide bridges in AlphaFold2 predicted structures. Applying CysQuant to Arabidopsis seedlings exposed to excessive light, we successfully quantified the well-established increased reduction of Calvin-Benson cycle enzymes and discovered yet uncharacterized redox-sensitive disulfides in chloroplastic enzymes. Overall, CysQuant is a highly versatile tool for assessing the cysteine modification status that can be widely applied across various mass spectrometry platforms and organisms.
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Affiliation(s)
- Jingjing Huang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - An Staes
- Department of Biomolecular Medicine, Ghent University, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, 9052, Ghent, Belgium; VIB Proteomics Core, 9052, Ghent, Belgium
| | - Francis Impens
- Department of Biomolecular Medicine, Ghent University, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, 9052, Ghent, Belgium; VIB Proteomics Core, 9052, Ghent, Belgium
| | - Vadim Demichev
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, 9052, Ghent, Belgium.
| | - Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, 9052, Ghent, Belgium.
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Zhang L, Braynen J, Fahey A, Chopra K, Cifani P, Tadesse D, Regulski M, Hu F, van Dam HJJ, Xie M, Ware D, Blaby-Haas CE. Two related families of metal transferases, ZNG1 and ZNG2, are involved in acclimation to poor Zn nutrition in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 14:1237722. [PMID: 37965006 PMCID: PMC10642216 DOI: 10.3389/fpls.2023.1237722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/02/2023] [Indexed: 11/16/2023]
Abstract
Metal homeostasis has evolved to tightly modulate the availability of metals within the cell, avoiding cytotoxic interactions due to excess and protein inactivity due to deficiency. Even in the presence of homeostatic processes, however, low bioavailability of these essential metal nutrients in soils can negatively impact crop health and yield. While research has largely focused on how plants assimilate metals, acclimation to metal-limited environments requires a suite of strategies that are not necessarily involved in metal transport across membranes. The identification of these mechanisms provides a new opportunity to improve metal-use efficiency and develop plant foodstuffs with increased concentrations of bioavailable metal nutrients. Here, we investigate the function of two distinct subfamilies of the nucleotide-dependent metallochaperones (NMCs), named ZNG1 and ZNG2, that are found in plants, using Arabidopsis thaliana as a reference organism. AtZNG1 (AT1G26520) is an ortholog of human and fungal ZNG1, and like its previously characterized eukaryotic relatives, localizes to the cytosol and physically interacts with methionine aminopeptidase type I (AtMAP1A). Analysis of AtZNG1, AtMAP1A, AtMAP2A, and AtMAP2B transgenic mutants are consistent with the role of Arabidopsis ZNG1 as a Zn transferase for AtMAP1A, as previously described in yeast and zebrafish. Structural modeling reveals a flexible cysteine-rich loop that we hypothesize enables direct transfer of Zn from AtZNG1 to AtMAP1A during GTP hydrolysis. Based on proteomics and transcriptomics, loss of this ancient and conserved mechanism has pleiotropic consequences impacting the expression of hundreds of genes, including those involved in photosynthesis and vesicle transport. Members of the plant-specific family of NMCs, ZNG2A1 (AT1G80480) and ZNG2A2 (AT1G15730), are also required during Zn deficiency, but their target protein(s) remain to be discovered. RNA-seq analyses reveal wide-ranging impacts across the cell when the genes encoding these plastid-localized NMCs are disrupted.
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Affiliation(s)
- Lifang Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Janeen Braynen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Audrey Fahey
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Kriti Chopra
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY, United States
| | - Paolo Cifani
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Dimiru Tadesse
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Michael Regulski
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Fangle Hu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Hubertus J. J. van Dam
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Meng Xie
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
- USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY, United States
| | - Crysten E. Blaby-Haas
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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Wrobel TJ, Brilhaus D, Stefanski A, Stühler K, Weber APM, Linka N. Mapping the castor bean endosperm proteome revealed a metabolic interaction between plastid, mitochondria, and peroxisomes to optimize seedling growth. FRONTIERS IN PLANT SCIENCE 2023; 14:1182105. [PMID: 37868318 PMCID: PMC10588648 DOI: 10.3389/fpls.2023.1182105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/07/2023] [Indexed: 10/24/2023]
Abstract
In this work, we studied castor-oil plant Ricinus communis as a classical system for endosperm reserve breakdown. The seeds of castor beans consist of a centrally located embryo with the two thin cotyledons surrounded by the endosperm. The endosperm functions as major storage tissue and is packed with nutritional reserves, such as oil, proteins, and starch. Upon germination, mobilization of the storage reserves requires inter-organellar interplay of plastids, mitochondria, and peroxisomes to optimize growth for the developing seedling. To understand their metabolic interactions, we performed a large-scale organellar proteomic study on castor bean endosperm. Organelles from endosperm of etiolated seedlings were isolated and subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS). Computer-assisted deconvolution algorithms were applied to reliably assign the identified proteins to their correct subcellular localization and to determine the abundance of the different organelles in the heterogeneous protein samples. The data obtained were used to build a comprehensive metabolic model for plastids, mitochondria, and peroxisomes during storage reserve mobilization in castor bean endosperm.
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Affiliation(s)
- Thomas J. Wrobel
- Institute of Plant Biochemistry and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
| | - Dominik Brilhaus
- Institute of Plant Biochemistry and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
| | - Anja Stefanski
- Molecular Proteomics Laboratory, Biologisch-Medizinisches Forschungszentrum (BMFZ), Universitätsklinikum, Düsseldorf, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, Biologisch-Medizinisches Forschungszentrum (BMFZ), Universitätsklinikum, Düsseldorf, Germany
| | - Andreas P. M. Weber
- Institute of Plant Biochemistry and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
| | - Nicole Linka
- Institute of Plant Biochemistry and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
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Schwenkert S, Lo WT, Szulc B, Yip CK, Pratt AI, Cusack SA, Brandt B, Leister D, Kunz HH. Probing the physiological role of the plastid outer-envelope membrane using the oemiR plasmid collection. G3 (BETHESDA, MD.) 2023; 13:jkad187. [PMID: 37572358 PMCID: PMC10542568 DOI: 10.1093/g3journal/jkad187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 07/20/2023] [Accepted: 08/04/2023] [Indexed: 08/14/2023]
Abstract
Plastids are the site of complex biochemical pathways, most prominently photosynthesis. The organelle evolved through endosymbiosis with a cyanobacterium, which is exemplified by the outer envelope membrane that harbors more than 40 proteins in Arabidopsis. Their evolutionary conservation indicates high significance for plant cell function. While a few proteins are well-studied as part of the protein translocon complex the majority of outer envelope protein functions is unclear. Gaining a deeper functional understanding has been complicated by the lack of observable loss-of-function mutant phenotypes, which is often rooted in functional genetic redundancy. Therefore, we designed outer envelope-specific artificial micro RNAs (oemiRs) capable of downregulating transcripts from several loci simultaneously. We successfully tested oemiR function by performing a proof-of-concept screen for pale and cold-sensitive mutants. An in-depth analysis of pale mutant alleles deficient in the translocon component TOC75 using proteomics provided new insights into putative compensatory import pathways. The cold stress screen not only recapitulated 3 previously known phenotypes of cold-sensitive mutants but also identified 4 mutants of additional oemiR outer envelope loci. Altogether our study revealed a role of the outer envelope to tolerate cold conditions and showcasts the power of the oemiR collection to research the significance of outer envelope proteins.
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Affiliation(s)
- Serena Schwenkert
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Wing Tung Lo
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Beata Szulc
- Plant Biochemistry, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Chun Kwan Yip
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Anna I Pratt
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA 99164-4236, USA
| | | | - Benjamin Brandt
- Plant Biochemistry, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
| | - Hans-Henning Kunz
- Plant Biochemistry, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA 99164-4236, USA
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Wan H, Zhang Y, Wu L, Zhou G, Pan L, Fernie AR, Ruan YL. Evolution of cytosolic and organellar invertases empowered the colonization and thriving of land plants. PLANT PHYSIOLOGY 2023; 193:1227-1243. [PMID: 37429000 PMCID: PMC10661998 DOI: 10.1093/plphys/kiad401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/06/2023] [Accepted: 06/12/2023] [Indexed: 07/12/2023]
Abstract
The molecular innovation underpinning efficient carbon and energy metabolism during evolution of land plants remains largely unknown. Invertase-mediated sucrose cleavage into hexoses is central to fuel growth. Why some cytoplasmic invertases (CINs) function in the cytosol, whereas others operate in chloroplasts and mitochondria, is puzzling. We attempted to shed light on this question from an evolutionary perspective. Our analyses indicated that plant CINs originated from a putatively orthologous ancestral gene in cyanobacteria and formed the plastidic CIN (α1 clade) through endosymbiotic gene transfer, while its duplication in algae with a loss of its signal peptide produced the β clade CINs in the cytosol. The mitochondrial CINs (α2) were derived from duplication of the plastidic CINs and coevolved with vascular plants. Importantly, the copy number of mitochondrial and plastidic CINs increased upon the emergence of seed plants, corresponding with the rise of respiratory, photosynthetic, and growth rates. The cytosolic CIN (β subfamily) kept expanding from algae to gymnosperm, indicating its role in supporting the increase in carbon use efficiency during evolution. Affinity purification mass spectrometry identified a cohort of proteins interacting with α1 and 2 CINs, which points to their roles in plastid and mitochondrial glycolysis, oxidative stress tolerance, and the maintenance of subcellular sugar homeostasis. Collectively, the findings indicate evolutionary roles of α1 and α2 CINs in chloroplasts and mitochondria for achieving high photosynthetic and respiratory rates, respectively, which, together with the expanding of cytosolic CINs, likely underpin the colonization of land plants through fueling rapid growth and biomass production.
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Affiliation(s)
- Hongjian Wan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Youjun Zhang
- Center for Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Limin Wu
- Food and Agriculture, CSIRO, ACT, Canberra 2601, Australia
| | - Guozhi Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Luzhao Pan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Alisdair R Fernie
- Center for Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Yong-Ling Ruan
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Horticulture, Northwest A&F University, Xianyang 712100, China
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
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43
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Zhang Y, Jaime SM, Bulut M, Graf A, Fernie AR. The conditional mitochondrial protein complexome in the Arabidopsis thaliana root and shoot. PLANT COMMUNICATIONS 2023; 4:100635. [PMID: 37291828 PMCID: PMC10504587 DOI: 10.1016/j.xplc.2023.100635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 02/23/2023] [Accepted: 06/02/2023] [Indexed: 06/10/2023]
Abstract
Protein complexes are important for almost all biological processes. Hence, to fully understand how cells work, it is also necessary to characterize protein complexes and their dynamics in response to various cellular cues. Moreover, the dynamics of protein interaction play crucial roles in regulating the (dis)association of protein complexes and, in turn, regulating biological processes such as metabolism. Here, mitochondrial protein complexes were investigated by blue native PAGE and size-exclusion chromatography under conditions of oxidative stress in order to monitor their dynamic (dis)associations. Rearrangements of enzyme interactions and changes in protein complex abundance were observed in response to oxidative stress induced by menadione treatment. These included changes in enzymatic protein complexes involving γ-amino butyric acid transaminase (GABA-T), Δ-ornithine aminotransferase (Δ-OAT), or proline dehydrogenase 1 (POX1) that are expected to affect proline metabolism. Menadione treatment also affected interactions between several enzymes of the tricarboxylic acid (TCA) cycle and the abundance of complexes of the oxidative phosphorylation pathway. In addition, we compared the mitochondrial complexes of roots and shoots. Considerable differences between the two tissues were observed in the mitochondrial import/export apparatus, the formation of super-complexes in the oxidative phosphorylation pathway, and specific interactions between enzymes of the TCA cycle that we postulate may be related to the metabolic/energetic requirements of roots and shoots.
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Affiliation(s)
- Youjun Zhang
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria; Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Silvia Martínez Jaime
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Mustafa Bulut
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alexander Graf
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Alisdair R Fernie
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria; Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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Tran HC, Schmitt V, Lama S, Wang C, Launay-Avon A, Bernfur K, Sultan K, Khan K, Brunaud V, Liehrmann A, Castandet B, Levander F, Rasmusson AG, Mireau H, Delannoy E, Van Aken O. An mTRAN-mRNA interaction mediates mitochondrial translation initiation in plants. Science 2023; 381:eadg0995. [PMID: 37651534 DOI: 10.1126/science.adg0995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 08/02/2023] [Indexed: 09/02/2023]
Abstract
Plant mitochondria represent the largest group of respiring organelles on the planet. Plant mitochondrial messenger RNAs (mRNAs) lack Shine-Dalgarno-like ribosome-binding sites, so it is unknown how plant mitoribosomes recognize mRNA. We show that "mitochondrial translation factors" mTRAN1 and mTRAN2 are land plant-specific proteins, required for normal mitochondrial respiration chain biogenesis. Our studies suggest that mTRANs are noncanonical pentatricopeptide repeat (PPR)-like RNA binding proteins of the mitoribosomal "small" subunit. We identified conserved Adenosine (A)/Uridine (U)-rich motifs in the 5' regions of plant mitochondrial mRNAs. mTRAN1 binds this motif, suggesting that it is a mitoribosome homing factor to identify mRNAs. We demonstrate that mTRANs are likely required for translation of all plant mitochondrial mRNAs. Plant mitochondrial translation initiation thus appears to use a protein-mRNA interaction that is divergent from bacteria or mammalian mitochondria.
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Affiliation(s)
| | | | - Sbatie Lama
- Department of Biology, Lund University, Lund, Sweden
| | - Chuande Wang
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Alexandra Launay-Avon
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Katja Bernfur
- Department of Chemistry, Lund University, Lund, Sweden
| | - Kristin Sultan
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Kasim Khan
- Department of Biology, Lund University, Lund, Sweden
| | - Véronique Brunaud
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Arnaud Liehrmann
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
- Université Paris-Saclay, CNRS, Université d'Évry, Laboratoire de Mathématiques et Modélisation d'Évry, 91037 Évry-Courcouronnes, France
| | - Benoît Castandet
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Fredrik Levander
- Department of Immunotechnology, Lund University, Lund, Sweden
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | | | - Hakim Mireau
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Etienne Delannoy
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
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Monti MM, Mancini I, Gualtieri L, Domingo G, Beccaccioli M, Bossa R, Bracale M, Loreto F, Ruocco M. Volatilome and proteome responses to Colletotrichum lindemuthianum infection in a moderately resistant and a susceptible bean genotype. PHYSIOLOGIA PLANTARUM 2023; 175:e14044. [PMID: 37882283 DOI: 10.1111/ppl.14044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/07/2023] [Accepted: 10/02/2023] [Indexed: 10/27/2023]
Abstract
We analyzed the changes in the volatilome, proteome, stomatal conductance, salicylic and jasmonic acid contents of a susceptible and a moderately resistant genotype of common bean, Phaseoulus vulgaris L., challenged with Colletotrichum lindemuthianum, the causal agent of fungal anthracnose. Our results indicate differences at both proteome and volatilome levels between the two genotypes, before and after the infection, and different defense strategies. The moderately resistant genotype hindered pathogen infection, invasion, and replication mainly by maintaining epidermal and cell wall structure. The susceptible genotype was not able to limit the early stages of pathogen infection. Rather, stomatal conductance increased in the infected susceptible genotype, and enhanced synthesis of Green Leaf Volatiles and salicylic acid was observed, together with a strong hypersensitive response. Proteomic investigation provided a general framework for physiological changes, whereas observed variations in the volatilome suggested that volatile organic compounds may principally represent stress markers rather than defensive compounds per se.
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Affiliation(s)
- Maurilia M Monti
- Istituto per la Protezione Sostenibile delle Piante, CNR, Portici, Napoli, Italy
| | - Ilaria Mancini
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Liberata Gualtieri
- Istituto per la Protezione Sostenibile delle Piante, CNR, Portici, Napoli, Italy
| | - Guido Domingo
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Marzia Beccaccioli
- Dipartimento di Biologia Ambientale, Università Sapienza Roma, Roma, Italy
| | - Rosanna Bossa
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Marcella Bracale
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Francesco Loreto
- Istituto per la Protezione Sostenibile delle Piante, CNR, Portici, Napoli, Italy
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Michelina Ruocco
- Istituto per la Protezione Sostenibile delle Piante, CNR, Portici, Napoli, Italy
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Figueroa NE, Franz P, Luzarowski M, Martinez-Seidel F, Moreno JC, Childs D, Ziemblicka A, Sampathkumar A, Andersen TG, Tsiavaliaris G, Chodasiewicz M, Skirycz A. Protein interactome of 3',5'-cAMP reveals its role in regulating the actin cytoskeleton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1214-1230. [PMID: 37219088 DOI: 10.1111/tpj.16313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/24/2023]
Abstract
Identification of protein interactors is ideally suited for the functional characterization of small molecules. 3',5'-cAMP is an evolutionary ancient signaling metabolite largely uncharacterized in plants. To tap into the physiological roles of 3',5'-cAMP, we used a chemo-proteomics approach, thermal proteome profiling (TPP), for the unbiased identification of 3',5'-cAMP protein targets. TPP measures shifts in the protein thermal stability upon ligand binding. Comprehensive proteomics analysis yielded a list of 51 proteins significantly altered in their thermal stability upon incubation with 3',5'-cAMP. The list contained metabolic enzymes, ribosomal subunits, translation initiation factors, and proteins associated with the regulation of plant growth such as CELL DIVISION CYCLE 48. To functionally validate obtained results, we focused on the role of 3',5'-cAMP in regulating the actin cytoskeleton suggested by the presence of actin among the 51 identified proteins. 3',5'-cAMP supplementation affected actin organization by inducing actin-bundling. Consistent with these results, the increase in 3',5'-cAMP levels, obtained either by feeding or by chemical modulation of 3',5'-cAMP metabolism, was sufficient to partially rescue the short hypocotyl phenotype of the actin2 actin7 mutant, severely compromised in actin level. The observed rescue was specific to 3',5'-cAMP, as demonstrated using a positional isomer 2',3'-cAMP, and true for the nanomolar 3',5'-cAMP concentrations reported for plant cells. In vitro characterization of the 3',5'-cAMP-actin pairing argues against a direct interaction between actin and 3',5'-cAMP. Alternative mechanisms by which 3',5'-cAMP would affect actin dynamics, such as by interfering with calcium signaling, are discussed. In summary, our work provides a specific resource, 3',5'-cAMP interactome, as well as functional insight into 3',5'-cAMP-mediated regulation in plants.
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Affiliation(s)
- Nicolás E Figueroa
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Peter Franz
- Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Straße 1, Hannover, 30625, Germany
| | - Marcin Luzarowski
- Max-Planck-Institute of Molecular Plant Physiology, Am Muhlenberg 1, Potsdam-Golm, 14476, Germany
- Core facility for Mass Spectrometry and Proteomics, Zentrum fur Molekulare Biologie der Universitat Heidelberg, Im Neuenheimer Feld 329, Heidelberg, 69120, Germany
| | - Federico Martinez-Seidel
- Max-Planck-Institute of Molecular Plant Physiology, Am Muhlenberg 1, Potsdam-Golm, 14476, Germany
- School of BioSciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Juan C Moreno
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Max-Planck-Institute of Molecular Plant Physiology, Am Muhlenberg 1, Potsdam-Golm, 14476, Germany
| | - Dorothee Childs
- European Molecular Biology Laboratory (EMBL) Heidelberg, Heidelberg, 69117, Germany
| | - Aleksandra Ziemblicka
- Max-Planck-Institute of Molecular Plant Physiology, Am Muhlenberg 1, Potsdam-Golm, 14476, Germany
| | - Arun Sampathkumar
- Max-Planck-Institute of Molecular Plant Physiology, Am Muhlenberg 1, Potsdam-Golm, 14476, Germany
| | - Tonni Grube Andersen
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Georgios Tsiavaliaris
- Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Straße 1, Hannover, 30625, Germany
| | - Monika Chodasiewicz
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Max-Planck-Institute of Molecular Plant Physiology, Am Muhlenberg 1, Potsdam-Golm, 14476, Germany
| | - Aleksandra Skirycz
- Max-Planck-Institute of Molecular Plant Physiology, Am Muhlenberg 1, Potsdam-Golm, 14476, Germany
- Boyce Thompson Institute (BTI), Cornell University, 533 Tower Rd., Ithaca, New York, 14853, USA
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47
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Bhattacharya O, Ortiz I, Hendricks N, Walling LL. The tomato chloroplast stromal proteome compendium elucidated by leveraging a plastid protein-localization prediction Atlas. FRONTIERS IN PLANT SCIENCE 2023; 14:1020275. [PMID: 37701797 PMCID: PMC10493611 DOI: 10.3389/fpls.2023.1020275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 06/22/2023] [Indexed: 09/14/2023]
Abstract
Tomato (Solanum lycopersicum) is a model species for studying fruit development, wounding, herbivory, and pathogen attack. Despite tomato's world-wide economic importance and the role of chloroplasts as metabolic hubs and integrators of environmental cues, little is known about the stromal proteome of tomato. Using a high-yielding protocol for chloroplast and stromal protein isolation, MudPIT nano-LC-MS/MS analyses, a robust in-house protein database (the Atlas) for predicting the plastid localization of tomato proteins, and rigorous selection criteria for inclusion/exclusion in the stromal proteome, we identified 1,278 proteins of the tomato stromal proteome. We provide one of the most robust stromal proteomes available to date with empirical evidence for 545 and 92 proteins not previously described for tomato plastids and the Arabidopsis stroma, respectively. The relative abundance of tomato stromal proteins was determined using the exponentially modified protein abundance index (emPAI). Comparison of the abundance of tomato and Arabidopsis stromal proteomes provided evidence for the species-specific nature of stromal protein homeostasis. The manual curation of the tomato stromal proteome classified proteins into ten functional categories resulting in an accessible compendium of tomato chloroplast proteins. After curation, only 91 proteins remained as unknown, uncharacterized or as enzymes with unknown functions. The curation of the tomato stromal proteins also indicated that tomato has a number of paralogous proteins, not present in Arabidopsis, which accumulated to different levels in chloroplasts. As some of these proteins function in key metabolic pathways or in perceiving or transmitting signals critical for plant adaptation to biotic and abiotic stress, these data suggest that tomato may modulate the bidirectional communication between chloroplasts and nuclei in a novel manner. The stromal proteome provides a fertile ground for future mechanistic studies in the field of tomato chloroplast-nuclear signaling and are foundational for our goal of elucidating the dynamics of the stromal proteome controlled by the solanaceous-specific, stromal, and wound-inducible leucine aminopeptidase A of tomato.
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Affiliation(s)
- Oindrila Bhattacharya
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Irma Ortiz
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Nathan Hendricks
- Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | - Linda L. Walling
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
- Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
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48
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Córdoba SC, Tong H, Burgos A, Zhu F, Alseekh S, Fernie AR, Nikoloski Z. Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism. Nat Commun 2023; 14:4897. [PMID: 37580345 PMCID: PMC10425450 DOI: 10.1038/s41467-023-40644-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 08/04/2023] [Indexed: 08/16/2023] Open
Abstract
Lipids play fundamental roles in regulating agronomically important traits. Advances in plant lipid metabolism have until recently largely been based on reductionist approaches, although modulation of its components can have system-wide effects. However, existing models of plant lipid metabolism provide lumped representations, hindering detailed study of component modulation. Here, we present the Plant Lipid Module (PLM) which provides a mechanistic description of lipid metabolism in the Arabidopsis thaliana rosette. We demonstrate that the PLM can be readily integrated in models of A. thaliana Col-0 metabolism, yielding accurate predictions (83%) of single lethal knock-outs and 75% concordance between measured transcript and predicted flux changes under extended darkness. Genome-wide associations with fluxes obtained by integrating the PLM in diel condition- and accession-specific models identify up to 65 candidate genes modulating A. thaliana lipid metabolism. Using mutant lines, we validate up to 40% of the candidates, paving the way for identification of metabolic gene function based on models capturing natural variability in metabolism.
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Affiliation(s)
- Sandra Correa Córdoba
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.
| | - Hao Tong
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Asdrúbal Burgos
- Department of Zoology and Botany, University of Guadalajara, Guadalajara, Mexico
| | - Feng Zhu
- National R&D Center for Citrus Preservation, Hubei Hongshan Laboratory, National Key Laboratory for Germplasm Innovation and Utilization for Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Saleh Alseekh
- Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Alisdair R Fernie
- Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria.
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49
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Wang C, Quadrado M, Mireau H. Interplay of endonucleolytic and exonucleolytic processing in the 3'-end formation of a mitochondrial nad2 RNA precursor in Arabidopsis. Nucleic Acids Res 2023; 51:7619-7630. [PMID: 37293952 PMCID: PMC10415111 DOI: 10.1093/nar/gkad493] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/17/2023] [Accepted: 05/31/2023] [Indexed: 06/10/2023] Open
Abstract
Initiation and termination of plant mitochondrial transcription are poorly controlled steps. Precursor transcripts are thus often longer than necessary, and 3'-end processing as well as control of RNA stability are essential to produce mature mRNAs in plant mitochondria. Plant mitochondrial 3' ends are determined by 3'-to-5' exonucleolytic trimming until the progression of mitochondrial exonucleases along transcripts is stopped by stable RNA structures or RNA binding proteins. In this analysis, we investigated the function of the endonucleolytic mitochondrial stability factor 1 (EMS1) pentatricopeptide repeat (PPR) protein and showed that it is essential for the production and the stabilization of the mature form of the nad2 exons 1-2 precursor transcript, whose 3' end corresponds to the 5' half of the nad2 trans-intron 2. The accumulation of an extended rather than a truncated form of this transcript in ems1 mutant plants suggests that the role of EMS1 in 3' end formation is not strictly limited to blocking the passage of 3'-5' exonucleolytic activity, but that 3' end formation of the nad2 exons 1-2 transcript involves an EMS1-dependent endonucleolytic cleavage. This study demonstrates that the formation of the 3' end of mitochondrial transcripts may involve an interplay of endonucleolytic and exonucleolytic processing mediated by PPR proteins.
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Affiliation(s)
- Chuande Wang
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Martine Quadrado
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Hakim Mireau
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
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50
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Wang L, Patena W, Van Baalen KA, Xie Y, Singer ER, Gavrilenko S, Warren-Williams M, Han L, Harrigan HR, Hartz LD, Chen V, Ton VTNP, Kyin S, Shwe HH, Cahn MH, Wilson AT, Onishi M, Hu J, Schnell DJ, McWhite CD, Jonikas MC. A chloroplast protein atlas reveals punctate structures and spatial organization of biosynthetic pathways. Cell 2023; 186:3499-3518.e14. [PMID: 37437571 DOI: 10.1016/j.cell.2023.06.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 05/06/2023] [Accepted: 06/11/2023] [Indexed: 07/14/2023]
Abstract
Chloroplasts are eukaryotic photosynthetic organelles that drive the global carbon cycle. Despite their importance, our understanding of their protein composition, function, and spatial organization remains limited. Here, we determined the localizations of 1,034 candidate chloroplast proteins using fluorescent protein tagging in the model alga Chlamydomonas reinhardtii. The localizations provide insights into the functions of poorly characterized proteins; identify novel components of nucleoids, plastoglobules, and the pyrenoid; and reveal widespread protein targeting to multiple compartments. We discovered and further characterized cellular organizational features, including eleven chloroplast punctate structures, cytosolic crescent structures, and unexpected spatial distributions of enzymes within the chloroplast. We also used machine learning to predict the localizations of other nuclear-encoded Chlamydomonas proteins. The strains and localization atlas developed here will serve as a resource to accelerate studies of chloroplast architecture and functions.
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Affiliation(s)
- Lianyong Wang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Weronika Patena
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Kelly A Van Baalen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Yihua Xie
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Emily R Singer
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sophia Gavrilenko
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | | | - Linqu Han
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI 48824, USA
| | - Henry R Harrigan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Linnea D Hartz
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Vivian Chen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Vinh T N P Ton
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Saw Kyin
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Henry H Shwe
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Matthew H Cahn
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Alexandra T Wilson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Masayuki Onishi
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Jianping Hu
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI 48824, USA
| | - Danny J Schnell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Claire D McWhite
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA.
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