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Barros JAS, Chatt EC, Augustine RC, McLoughlin F, Li F, Otegui MS, Vierstra RD. Autophagy during maize endosperm development dampens oxidative stress and promotes mitochondrial clearance. Plant Physiol 2023; 193:1395-1415. [PMID: 37335933 PMCID: PMC10517192 DOI: 10.1093/plphys/kiad340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 06/21/2023]
Abstract
The selective turnover of macromolecules by autophagy provides a critical homeostatic mechanism for recycling cellular constituents and for removing superfluous and damaged organelles, membranes, and proteins. To better understand how autophagy impacts seed maturation and nutrient storage, we studied maize (Zea mays) endosperm in its early and middle developmental stages via an integrated multiomic approach using mutants impacting the core macroautophagy factor AUTOPHAGY (ATG)-12 required for autophagosome assembly. Surprisingly, the mutant endosperm in these developmental windows accumulated normal amounts of starch and Zein storage proteins. However, the tissue acquired a substantially altered metabolome, especially for compounds related to oxidative stress and sulfur metabolism, including increases in cystine, dehydroascorbate, cys-glutathione disulfide, glucarate, and galactarate, and decreases in peroxide and the antioxidant glutathione. While changes in the associated transcriptome were mild, the proteome was strongly altered in the atg12 endosperm, especially for increased levels of mitochondrial proteins without a concomitant increase in mRNA abundances. Although fewer mitochondria were seen cytologically, a heightened number appeared dysfunctional based on the accumulation of dilated cristae, consistent with attenuated mitophagy. Collectively, our results confirm that macroautophagy plays a minor role in the accumulation of starch and storage proteins during maize endosperm development but likely helps protect against oxidative stress and clears unneeded/dysfunctional mitochondria during tissue maturation.
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Affiliation(s)
- Jessica A S Barros
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Elizabeth C Chatt
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Robert C Augustine
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Fionn McLoughlin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Faqiang Li
- Department of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison, WI 53706, USA
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
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Nicolas P, Shinozaki Y, Powell A, Philippe G, Snyder SI, Bao K, Zheng Y, Xu Y, Courtney L, Vrebalov J, Casteel CL, Mueller LA, Fei Z, Giovannoni JJ, Rose JKC, Catalá C. Spatiotemporal dynamics of the tomato fruit transcriptome under prolonged water stress. Plant Physiol 2022; 190:2557-2578. [PMID: 36135793 PMCID: PMC9706477 DOI: 10.1093/plphys/kiac445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/07/2022] [Indexed: 05/04/2023]
Abstract
Water availability influences all aspects of plant growth and development; however, most studies of plant responses to drought have focused on vegetative organs, notably roots and leaves. Far less is known about the molecular bases of drought acclimation responses in fruits, which are complex organs with distinct tissue types. To obtain a more comprehensive picture of the molecular mechanisms governing fruit development under drought, we profiled the transcriptomes of a spectrum of fruit tissues from tomato (Solanum lycopersicum), spanning early growth through ripening and collected from plants grown under varying intensities of water stress. In addition, we compared transcriptional changes in fruit with those in leaves to highlight different and conserved transcriptome signatures in vegetative and reproductive organs. We observed extensive and diverse genetic reprogramming in different fruit tissues and leaves, each associated with a unique response to drought acclimation. These included major transcriptional shifts in the placenta of growing fruit and in the seeds of ripe fruit related to cell growth and epigenetic regulation, respectively. Changes in metabolic and hormonal pathways, such as those related to starch, carotenoids, jasmonic acid, and ethylene metabolism, were associated with distinct fruit tissues and developmental stages. Gene coexpression network analysis provided further insights into the tissue-specific regulation of distinct responses to water stress. Our data highlight the spatiotemporal specificity of drought responses in tomato fruit and indicate known and unrevealed molecular regulatory mechanisms involved in drought acclimation, during both vegetative and reproductive stages of development.
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Affiliation(s)
| | - Yoshihito Shinozaki
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Adrian Powell
- Boyce Thompson Institute, Ithaca, New York 14853, USA
| | - Glenn Philippe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Stephen I Snyder
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Kan Bao
- Boyce Thompson Institute, Ithaca, New York 14853, USA
| | - Yi Zheng
- Boyce Thompson Institute, Ithaca, New York 14853, USA
| | - Yimin Xu
- Boyce Thompson Institute, Ithaca, New York 14853, USA
| | | | | | - Clare L Casteel
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | | | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, New York 14853, USA
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853, USA
| | - James J Giovannoni
- Boyce Thompson Institute, Ithaca, New York 14853, USA
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853, USA
| | - Jocelyn K C Rose
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Carmen Catalá
- Boyce Thompson Institute, Ithaca, New York 14853, USA
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
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Blackburn MR, Minkoff BB, Sussman MR. Mass spectrometry-based technologies for probing the 3D world of plant proteins. Plant Physiol 2022; 189:12-22. [PMID: 35139210 PMCID: PMC9070838 DOI: 10.1093/plphys/kiac039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 12/30/2021] [Indexed: 05/03/2023]
Abstract
Over the past two decades, mass spectrometric (MS)-based proteomics technologies have facilitated the study of signaling pathways throughout biology. Nowhere is this needed more than in plants, where an evolutionary history of genome duplications has resulted in large gene families involved in posttranslational modifications and regulatory pathways. For example, at least 5% of the Arabidopsis thaliana genome (ca. 1,200 genes) encodes protein kinases and protein phosphatases that regulate nearly all aspects of plant growth and development. MS-based technologies that quantify covalent changes in the side-chain of amino acids are critically important, but they only address one piece of the puzzle. A more crucially important mechanistic question is how noncovalent interactions-which are more difficult to study-dynamically regulate the proteome's 3D structure. The advent of improvements in protein 3D technologies such as cryo-electron microscopy, nuclear magnetic resonance, and X-ray crystallography has allowed considerable progress to be made at this level, but these methods are typically limited to analyzing proteins, which can be expressed and purified in milligram quantities. Newly emerging MS-based technologies have recently been developed for studying the 3D structure of proteins. Importantly, these methods do not require protein samples to be purified and require smaller amounts of sample, opening the wider proteome for structural analysis in complex mixtures, crude lysates, and even in intact cells. These MS-based methods include covalent labeling, crosslinking, thermal proteome profiling, and limited proteolysis, all of which can be leveraged by established MS workflows, as well as newly emerging methods capable of analyzing intact macromolecules and the complexes they form. In this review, we discuss these recent innovations in MS-based "structural" proteomics to provide readers with an understanding of the opportunities they offer and the remaining challenges for understanding the molecular underpinnings of plant structure and function.
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Affiliation(s)
- Matthew R Blackburn
- Department of Biochemistry and Center for Genomic Science Innovation, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Benjamin B Minkoff
- Department of Biochemistry and Center for Genomic Science Innovation, University of Wisconsin, Madison, Wisconsin 53706, USA
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Sanclemente MA, Ma F, Liu P, Della Porta A, Singh J, Wu S, Colquhoun T, Johnson T, Guan JC, Koch KE. Sugar modulation of anaerobic-response networks in maize root tips. Plant Physiol 2021; 185:295-317. [PMID: 33721892 PMCID: PMC8133576 DOI: 10.1093/plphys/kiaa029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/28/2020] [Indexed: 05/11/2023]
Abstract
Sugar supply is a key component of hypoxia tolerance and acclimation in plants. However, a striking gap remains in our understanding of mechanisms governing sugar impacts on low-oxygen responses. Here, we used a maize (Zea mays) root-tip system for precise control of sugar and oxygen levels. We compared responses to oxygen (21 and 0.2%) in the presence of abundant versus limited glucose supplies (2.0 and 0.2%). Low-oxygen reconfigured the transcriptome with glucose deprivation enhancing the speed and magnitude of gene induction for core anaerobic proteins (ANPs). Sugar supply also altered profiles of hypoxia-responsive genes carrying G4 motifs (sources of regulatory quadruplex structures), revealing a fast, sugar-independent class followed more slowly by feast-or-famine-regulated G4 genes. Metabolite analysis showed that endogenous sugar levels were maintained by exogenous glucose under aerobic conditions and demonstrated a prominent capacity for sucrose re-synthesis that was undetectable under hypoxia. Glucose abundance had distinctive impacts on co-expression networks associated with ANPs, altering network partners and aiding persistence of interacting networks under prolonged hypoxia. Among the ANP networks, two highly interconnected clusters of genes formed around Pyruvate decarboxylase 3 and Glyceraldehyde-3-phosphate dehydrogenase 4. Genes in these clusters shared a small set of cis-regulatory elements, two of which typified glucose induction. Collective results demonstrate specific, previously unrecognized roles of sugars in low-oxygen responses, extending from accelerated onset of initial adaptive phases by starvation stress to maintenance and modulation of co-expression relationships by carbohydrate availability.
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Affiliation(s)
- Maria-Angelica Sanclemente
- Plant Molecular and Cellular Biology, University of Florida, Gainesville, Florida 32611, USA
- Horticultural Sciences, University of Florida, Gainesville, Florida 32611, USA
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht 3584CH, The Netherlands
- Author for communication:
| | - Fangfang Ma
- Plant Molecular and Cellular Biology, University of Florida, Gainesville, Florida 32611, USA
- Horticultural Sciences, University of Florida, Gainesville, Florida 32611, USA
- Horticultural Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Peng Liu
- Plant Molecular and Cellular Biology, University of Florida, Gainesville, Florida 32611, USA
- Horticultural Sciences, University of Florida, Gainesville, Florida 32611, USA
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Adriana Della Porta
- Plant Molecular and Cellular Biology, University of Florida, Gainesville, Florida 32611, USA
| | - Jugpreet Singh
- Plant Molecular and Cellular Biology, University of Florida, Gainesville, Florida 32611, USA
- Horticultural Sciences, University of Florida, Gainesville, Florida 32611, USA
| | - Shan Wu
- Plant Molecular and Cellular Biology, University of Florida, Gainesville, Florida 32611, USA
| | - Thomas Colquhoun
- Plant Molecular and Cellular Biology, University of Florida, Gainesville, Florida 32611, USA
- Environmental Horticulture, University of Florida, Gainesville, Florida, USA
| | - Timothy Johnson
- Plant Molecular and Cellular Biology, University of Florida, Gainesville, Florida 32611, USA
- Environmental Horticulture, University of Florida, Gainesville, Florida, USA
| | - Jiahn-Chou Guan
- Horticultural Sciences, University of Florida, Gainesville, Florida 32611, USA
| | - Karen E Koch
- Plant Molecular and Cellular Biology, University of Florida, Gainesville, Florida 32611, USA
- Horticultural Sciences, University of Florida, Gainesville, Florida 32611, USA
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