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Koletti A, Skliros D, Kalloniati C, Marka S, Zografaki ME, Infante C, Mantecón L, Flemetakis E. Global omics study of Tetraselmis chuii reveals time-related metabolic adaptations upon oxidative stress. Appl Microbiol Biotechnol 2024; 108:138. [PMID: 38229403 DOI: 10.1007/s00253-023-12936-z] [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: 08/03/2023] [Revised: 11/26/2023] [Accepted: 12/01/2023] [Indexed: 01/18/2024]
Abstract
Microalgae species encounter oxidative stress in their natural environments, prompting the development of species-specific adaptation mechanisms. Understanding these mechanisms can offer valuable insights for biotechnological applications in microalgal metabolic manipulation. In this study, we investigated the response of Tetraselmis chuii, an industrially important microalga, to H2O2-induced oxidative stress. Exposure to 0.5-mM H2O2 resulted in reduced cell viability, and higher concentrations led to a drastic decline. After 1 h of exposure to H2O2, photosynthetic capacity (Qy) was negatively impacted, and this reduction intensified after 6 h of continuous stress. Global multi-omics analysis revealed that T. chuii rapidly responded to H2O2-induced oxidative stress within the first hour, causing significant changes in both transcriptomic and metabolomic profiles. Among the cellular functions negatively affected were carbon and energy flow, with photosynthesis-related PSBQ having a 2.4-fold downregulation, pyruvate kinase decreased by 1.5-fold, and urea content reduced by threefold. Prolonged exposure to H2O2 incurred a high energy cost, leading to unsuccessful attempts to enhance carbon metabolism, as depicted, for example, by the upregulation of photosystems-related PETC and PETJ by more than twofold. These findings indicate that T. chuii quickly responds to oxidative stress, but extended exposure can have detrimental effects on its cellular functions. KEY POINTS: • 0.5-mM H2O2-induced oxidative stress strongly affects T. chuii • Distinct short- and long-term adaptation mechanisms are induced • Major metabolic adaptations occur within the first hour of exposure.
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Affiliation(s)
- Aikaterini Koletti
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855, Athens, Greece
| | - Dimitrios Skliros
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855, Athens, Greece
| | - Chrysanthi Kalloniati
- Department of Marine Sciences, University of the Aegean, University Hill 81100, Mytilene, Greece
| | - Sofia Marka
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855, Athens, Greece
| | - Maria-Eleftheria Zografaki
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855, Athens, Greece
| | - Carlos Infante
- Fitoplancton Marino, S.L., Dársena Comercial S/N (Muelle Pesquero), 11500, El Puerto de Santa María (Cádiz), Spain
| | - Lalia Mantecón
- Fitoplancton Marino, S.L., Dársena Comercial S/N (Muelle Pesquero), 11500, El Puerto de Santa María (Cádiz), Spain
| | - Emmanouil Flemetakis
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855, Athens, Greece.
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2
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Wright ZJ, Bartel B. Hormonal control of underwater germination in rice. Dev Cell 2024; 59:1361-1362. [PMID: 38834032 DOI: 10.1016/j.devcel.2024.04.016] [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: 04/05/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 06/06/2024]
Abstract
The ability to germinate, develop, and thrive underwater is key to efficient rice cultivation. In this issue of Developmental Cell, Wang et al. (2024) illuminate a hormone synthesis and inactivation cascade that promotes germination of submerged rice seeds and may allow improved germination in the field.
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Affiliation(s)
- Zachary J Wright
- Department of Biosciences, Rice University, Houston, TX 77005, USA
| | - Bonnie Bartel
- Department of Biosciences, Rice University, Houston, TX 77005, USA.
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3
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Skowyra ML, Feng P, Rapoport TA. Towards solving the mystery of peroxisomal matrix protein import. Trends Cell Biol 2024; 34:388-405. [PMID: 37743160 PMCID: PMC10957506 DOI: 10.1016/j.tcb.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023]
Abstract
Peroxisomes are vital metabolic organelles that import their lumenal (matrix) enzymes from the cytosol using mobile receptors. Surprisingly, the receptors can even import folded proteins, but the underlying mechanism has been a mystery. Recent results reveal how import receptors shuttle cargo into peroxisomes. The cargo-bound receptors move from the cytosol across the peroxisomal membrane completely into the matrix by a mechanism that resembles transport through the nuclear pore. The receptors then return to the cytosol through a separate retrotranslocation channel, leaving the cargo inside the organelle. This cycle concentrates imported proteins within peroxisomes, and the energy for cargo import is supplied by receptor export. Peroxisomal protein import thus fundamentally differs from other previously known mechanisms for translocating proteins across membranes.
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Affiliation(s)
- Michael L Skowyra
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Peiqiang Feng
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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4
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Ji X, Wang N, Wang J, Wang T, Huang X, Hao H. Non-destructive real-time monitoring and investigation of the self-assembly process using fluorescent probes. Chem Sci 2024; 15:3800-3830. [PMID: 38487216 PMCID: PMC10935763 DOI: 10.1039/d3sc06527h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/22/2024] [Indexed: 03/17/2024] Open
Abstract
Self-assembly has been considered as a strategy to construct superstructures with specific functions, which has been widely used in many different fields, such as bionics, catalysis, and pharmacology. A detailed and in-depth analysis of the self-assembly mechanism is beneficial for directionally and accurately regulating the self-assembly process of substances. Fluorescent probes exhibit unique advantages of sensitivity, non-destructiveness, and real-time self-assembly tracking, compared with traditional methods. In this work, the design principle of fluorescent probes with different functions and their applications for the detection of thermodynamic and kinetic parameters during the self-assembly process were systematically reviewed. Their efficiency, limitations and advantages are also discussed. Furthermore, the promising perspectives of fluorescent probes for investigating the self-assembly process are also discussed and suggested.
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Affiliation(s)
- Xiongtao Ji
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China
| | - Na Wang
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin 300072 China
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China +86-22-27374971 +86-22-27405754
| | - Jingkang Wang
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin 300072 China
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China +86-22-27374971 +86-22-27405754
| | - Ting Wang
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin 300072 China
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China +86-22-27374971 +86-22-27405754
| | - Xin Huang
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin 300072 China
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China +86-22-27374971 +86-22-27405754
| | - Hongxun Hao
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin 300072 China
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin 300072 China +86-22-27374971 +86-22-27405754
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5
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Cadena-Ramos AI, De-la-Peña C. Picky eaters: selective autophagy in plant cells. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:364-384. [PMID: 37864806 DOI: 10.1111/tpj.16508] [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: 07/14/2023] [Revised: 09/21/2023] [Accepted: 10/10/2023] [Indexed: 10/23/2023]
Abstract
Autophagy, a fundamental cellular process, plays a vital role in maintaining cellular homeostasis by degrading damaged or unnecessary components. While selective autophagy has been extensively studied in animal cells, its significance in plant cells has only recently gained attention. In this review, we delve into the intriguing realm selective autophagy in plants, with specific focus on its involvement in nutrient recycling, organelle turnover, and stress response. Moreover, recent studies have unveiled the interesting interplay between selective autophagy and epigenetic mechanisms in plants, elucidating the significance of epigenetic regulation in modulating autophagy-related gene expression and finely tuning the selective autophagy process in plants. By synthesizing existing knowledge, this review highlights the emerging field of selective autophagy in plant cells, emphasizing its pivotal role in maintaining nutrient homeostasis, facilitating cellular adaptation, and shedding light on the epigenetic regulation that governs these processes. Our comprehensive study provides the way for a deeper understanding of the dynamic control of cellular responses to nutrient availability and stress conditions, opening new avenues for future research in this field of autophagy in plant physiology.
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Affiliation(s)
- Alexis I Cadena-Ramos
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34 Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34 Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
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Jiang H, Nair V, Sun Y, Ding C. The diverse roles of peroxisomes in the interplay between viruses and mammalian cells. Antiviral Res 2024; 221:105780. [PMID: 38092324 DOI: 10.1016/j.antiviral.2023.105780] [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: 07/30/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/26/2023]
Abstract
Peroxisomes are ubiquitous organelles found in eukaryotic cells that play a critical role in the oxidative metabolism of lipids and detoxification of reactive oxygen species (ROS). Recently, the role of peroxisomes in viral infections has been extensively studied. Although several studies have reported that peroxisomes exert antiviral activity, evidence indicates that viruses have also evolved diverse strategies to evade peroxisomal antiviral signals. In this review, we summarize the multiple roles of peroxisomes in the interplay between viruses and mammalian cells. Focus is given on the peroxisomal regulation of innate immune response, lipid metabolism, ROS production, and viral regulation of peroxisomal biosynthesis and degradation. Understanding the interactions between peroxisomes and viruses provides novel insights for the development of new antiviral strategies.
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Affiliation(s)
- Hui Jiang
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute. Chinese Academy of Agricultural Science, Shanghai, China
| | - Venugopal Nair
- Avian Oncogenic Viruses Group, UK-China Centre of Excellence in Avian Disease Research, The Pirbright Institute, Pirbright, Guildford, Surrey, United Kingdom
| | - Yingjie Sun
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute. Chinese Academy of Agricultural Science, Shanghai, China.
| | - Chan Ding
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute. Chinese Academy of Agricultural Science, Shanghai, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu Province, China.
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7
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Borek S, Stefaniak S, Nuc K, Wojtyla Ł, Ratajczak E, Sitkiewicz E, Malinowska A, Świderska B, Wleklik K, Pietrowska-Borek M. Sugar Starvation Disrupts Lipid Breakdown by Inducing Autophagy in Embryonic Axes of Lupin ( Lupinus spp.) Germinating Seeds. Int J Mol Sci 2023; 24:11773. [PMID: 37511532 PMCID: PMC10380618 DOI: 10.3390/ijms241411773] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Under nutrient deficiency or starvation conditions, the mobilization of storage compounds during seed germination is enhanced to primarily supply respiratory substrates and hence increase the potential of cell survival. Nevertheless, we found that, under sugar starvation conditions in isolated embryonic axes of white lupin (Lupinus albus L.) and Andean lupin (Lupinus mutabilis Sweet) cultured in vitro for 96 h, the disruption of lipid breakdown occurs, as was reflected in the higher lipid content in the sugar-starved (-S) than in the sucrose-fed (+S) axes. We postulate that pexophagy (autophagic degradation of the peroxisome-a key organelle in lipid catabolism) is one of the reasons for the disruption in lipid breakdown under starvation conditions. Evidence of pexophagy can be: (i) the higher transcript level of genes encoding proteins of pexophagy machinery, and (ii) the lower content of the peroxisome marker Pex14p and its increase caused by an autophagy inhibitor (concanamycin A) in -S axes in comparison to the +S axes. Additionally, based on ultrastructure observation, we documented that, under sugar starvation conditions lipophagy (autophagic degradation of whole lipid droplets) may also occur but this type of selective autophagy seems to be restricted under starvation conditions. Our results also show that autophagy occurs at the very early stages of plant growth and development, including the cells of embryonic seed organs, and allows cell survival under starvation conditions.
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Affiliation(s)
- Sławomir Borek
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Szymon Stefaniak
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Katarzyna Nuc
- Department of Biochemistry and Biotechnology, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Łukasz Wojtyla
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Ewelina Ratajczak
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Ewa Sitkiewicz
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Agata Malinowska
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Bianka Świderska
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Karolina Wleklik
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Małgorzata Pietrowska-Borek
- Department of Biochemistry and Biotechnology, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
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8
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Traver MS, Bartel B. The ubiquitin-protein ligase MIEL1 localizes to peroxisomes to promote seedling oleosin degradation and lipid droplet mobilization. Proc Natl Acad Sci U S A 2023; 120:e2304870120. [PMID: 37410814 PMCID: PMC10629534 DOI: 10.1073/pnas.2304870120] [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: 03/28/2023] [Accepted: 06/02/2023] [Indexed: 07/08/2023] Open
Abstract
Lipid droplets are organelles conserved across eukaryotes that store and release neutral lipids to regulate energy homeostasis. In oilseed plants, fats stored in seed lipid droplets provide fixed carbon for seedling growth before photosynthesis begins. As fatty acids released from lipid droplet triacylglycerol are catabolized in peroxisomes, lipid droplet coat proteins are ubiquitinated, extracted, and degraded. In Arabidopsis seeds, the predominant lipid droplet coat protein is OLEOSIN1 (OLE1). To identify genes modulating lipid droplet dynamics, we mutagenized a line expressing mNeonGreen-tagged OLE1 expressed from the OLE1 promoter and isolated mutants with delayed oleosin degradation. From this screen, we identified four miel1 mutant alleles. MIEL1 (MYB30-interacting E3 ligase 1) targets specific MYB transcription factors for degradation during hormone and pathogen responses [D. Marino et al., Nat. Commun. 4, 1476 (2013); H. G. Lee and P. J. Seo, Nat. Commun. 7, 12525 (2016)] but had not been implicated in lipid droplet dynamics. OLE1 transcript levels were unchanged in miel1 mutants, indicating that MIEL1 modulates oleosin levels posttranscriptionally. When overexpressed, fluorescently tagged MIEL1 reduced oleosin levels, causing very large lipid droplets. Unexpectedly, fluorescently tagged MIEL1 localized to peroxisomes. Our data suggest that MIEL1 ubiquitinates peroxisome-proximal seed oleosins, targeting them for degradation during seedling lipid mobilization. The human MIEL1 homolog (PIRH2; p53-induced protein with a RING-H2 domain) targets p53 and other proteins for degradation and promotes tumorigenesis [A. Daks et al., Cells 11, 1515 (2022)]. When expressed in Arabidopsis, human PIRH2 also localized to peroxisomes, hinting at a previously unexplored role for PIRH2 in lipid catabolism and peroxisome biology in mammals.
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Affiliation(s)
- Melissa S. Traver
- Department of Biosciences, Biochemistry and Cell Biology Program, Rice University, Houston, TX77005
| | - Bonnie Bartel
- Department of Biosciences, Biochemistry and Cell Biology Program, Rice University, Houston, TX77005
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Liu F, Sun X, Wang L, Zhou K, Yao Q, Zhan RL. Transcriptomic and proteomic analyses of Mangifera indica in response to Xanthomonas critis pv. mangiferaeindicae. Front Microbiol 2023; 14:1220101. [PMID: 37469435 PMCID: PMC10352610 DOI: 10.3389/fmicb.2023.1220101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
Mango is an important tropical fruit with the reputation of "Tropical Fruit King." It is widely cultivated in tropical and subtropical regions. Mango bacterial leaf spot, which is caused by Xanthomonas critis pv. mangiferaeindicae (Xcm), poses a great threat to the development of mango planting industry. In this study, we used RNA sequencing and data-independent acquisition techniques to compare the transcriptome and proteome of the highly resistant cultivar "Renong No.1" (RN) and the highly susceptible cultivar "Keitt" (KT) in response to Xcm infection at different stages (0, 2, and 6 days). A total of 14,397 differentially expressed genes (DEGs) were identified in the transcriptome of the two varieties, and 4,400 and 8,926 genes were differentially expressed in RN and KT, respectively. Among them, 217 DEGs were related to plant hormone signaling pathway, and 202 were involved in the maintenance of cellular redox homeostasis. A total of 3,438 differentially expressed proteins (DEPs) were identified in the proteome of the two varieties. Exactly 1,542 and 1,700 DEPs were detected in RN and KT, respectively. In addition, 39 DEPs were related to plant hormone signaling pathway, whereas 68 were involved in the maintenance of cellular redox homeostasis. Through cross-validation of the two omics, 1,470 genes were found to be expressed in both groups, and a large number of glutathione metabolism-related genes, such as HSP26-A, G6PD4, and GPX2, were up-regulated in both omics. Peroxisome-related genes, such as LACS6, LACS9, PED1, GLO4, and HACL, were up-regulated or down-regulated in both omics. ABCB11, SAPK2, MYC2, TAG7, PYL1, and other genes related to indole-3-acetic acid and abscisic acid signal transduction and plant-pathogen interaction were up-regulated or down-regulated in both omics. We also used weighted gene co-expression network analysis to combine physiological and biochemical data (superoxide dismutase and catalase activity changes) with transcriptome and proteome data and finally identified three hub genes/proteins (SAG113, SRK2A, and ABCB1) that play an important role in plant hormone signal transduction. This work was the first study of gene/protein changes in resistant and susceptible mango varieties, and its results improved our understanding of the molecular mechanism of mango resistance to Xcm.
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Affiliation(s)
- Feng Liu
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Xin Sun
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Lulu Wang
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Kaibing Zhou
- College of Horticulture, Hainan University, Haikou, China
| | - Quansheng Yao
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Ru-lin Zhan
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
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10
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Luzarowska U, Ruß AK, Joubès J, Batsale M, Szymański J, P Thirumalaikumar V, Luzarowski M, Wu S, Zhu F, Endres N, Khedhayir S, Schumacher J, Jasinska W, Xu K, Correa Cordoba SM, Weil S, Skirycz A, Fernie AR, Li-Beisson Y, Fusari CM, Brotman Y. Hello darkness, my old friend: 3-KETOACYL-COENZYME A SYNTHASE4 is a branch point in the regulation of triacylglycerol synthesis in Arabidopsis thaliana. THE PLANT CELL 2023; 35:1984-2005. [PMID: 36869652 DOI: 10.1093/plcell/koad059] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 05/30/2023]
Abstract
Plant lipids are important as alternative sources of carbon and energy when sugars or starch are limited. Here, we applied combined heat and darkness or extended darkness to a panel of ∼300 Arabidopsis (Arabidopsis thaliana) accessions to study lipid remodeling under carbon starvation. Natural allelic variation at 3-KETOACYL-COENZYME A SYNTHASE4 (KCS4), a gene encoding an enzyme involved in very long chain fatty acid (VLCFA) synthesis, underlies the differential accumulation of polyunsaturated triacylglycerols (puTAGs) under stress. Ectopic expression of KCS4 in yeast and plants proved that KCS4 is a functional enzyme localized in the endoplasmic reticulum with specificity for C22 and C24 saturated acyl-CoA. Allelic mutants and transient overexpression in planta revealed the differential role of KCS4 alleles in VLCFA synthesis and leaf wax coverage, puTAG accumulation, and biomass. Moreover, the region harboring KCS4 is under high selective pressure and allelic variation at KCS4 correlates with environmental parameters from the locales of Arabidopsis accessions. Our results provide evidence that KCS4 plays a decisive role in the subsequent fate of fatty acids released from chloroplast membrane lipids under carbon starvation. This work sheds light on both plant response mechanisms and the evolutionary events shaping the lipidome under carbon starvation.
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Affiliation(s)
- Urszula Luzarowska
- Department of Life Sciences, Ben Gurion University of the Negev, 8410501 Beer-Sheva, Israel
| | - Anne-Kathrin Ruß
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jérôme Joubès
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, University Bordeaux, F-33140 Villenave d'Ornon, France
| | - Marguerite Batsale
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, University Bordeaux, F-33140 Villenave d'Ornon, France
| | - Jędrzej Szymański
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, 06466 Seeland, Germany
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany
| | | | - Marcin Luzarowski
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Si Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Feng Zhu
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Niklas Endres
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Sarah Khedhayir
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Julia Schumacher
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Philippstraße 13, 10115 Berlin, Germany
| | - Weronika Jasinska
- Department of Life Sciences, Ben Gurion University of the Negev, 8410501 Beer-Sheva, Israel
| | - Ke Xu
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | | | - Simy Weil
- Department of Life Sciences, Ben Gurion University of the Negev, 8410501 Beer-Sheva, Israel
| | - Aleksandra Skirycz
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair Robert Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Yonghua Li-Beisson
- CEA, CNRS, BIAM, Institute de Biosciences et Biotechnologies Aix-Marseille, Aix Marseille Univ., F-13108 Saint Paul-Lez-Durance, France
| | - Corina M Fusari
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET-UNR), Suipacha 570, S2000LRJ Rosario, Argentina
| | - Yariv Brotman
- Department of Life Sciences, Ben Gurion University of the Negev, 8410501 Beer-Sheva, Israel
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Ninck S, Halder V, Krahn JH, Beisser D, Resch S, Dodds I, Scholtysik R, Bormann J, Sewald L, Gupta MD, Heilmann G, Bhandari DD, Morimoto K, Buscaill P, Hause B, van der Hoorn RAL, Kaschani F, Kaiser M. Chemoproteomics Reveals the Pan-HER Kinase Inhibitor Neratinib To Target an Arabidopsis Epoxide Hydrolase Related to Phytohormone Signaling. ACS Chem Biol 2023; 18:1076-1088. [PMID: 37115018 DOI: 10.1021/acschembio.2c00322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Plant phytohormone pathways are regulated by an intricate network of signaling components and modulators, many of which still remain unknown. Here, we report a forward chemical genetics approach for the identification of functional SA agonists in Arabidopsis thaliana that revealed Neratinib (Ner), a covalent pan-HER kinase inhibitor drug in humans, as a modulator of SA signaling. Instead of a protein kinase, chemoproteomics unveiled that Ner covalently modifies a surface-exposed cysteine residue of Arabidopsis epoxide hydrolase isoform 7 (AtEH7), thereby triggering its allosteric inhibition. Physiologically, the Ner application induces jasmonate metabolism in an AtEH7-dependent manner as an early response. In addition, it modulates PATHOGENESIS RELATED 1 (PR1) expression as a hallmark of SA signaling activation as a later effect. AtEH7, however, is not the exclusive target for this physiological readout induced by Ner. Although the underlying molecular mechanisms of AtEH7-dependent modulation of jasmonate signaling and Ner-induced PR1-dependent activation of SA signaling and thus defense response regulation remain unknown, our present work illustrates the powerful combination of forward chemical genetics and chemical proteomics for identifying novel phytohormone signaling modulatory factors. It also suggests that marginally explored metabolic enzymes such as epoxide hydrolases may have further physiological roles in modulating signaling.
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Affiliation(s)
- Sabrina Ninck
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Vivek Halder
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
- Chemical Biology Laboratory, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Jan H Krahn
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Daniela Beisser
- Department of Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, 45117 Essen, Germany
| | - Sarah Resch
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Isobel Dodds
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
| | - René Scholtysik
- Genomics and Transcriptomics Facility, Institute for Cell Biology (Tumour Research), University of Duisburg-Essen, Virchowstr. 173, 45122 Essen, Germany
| | - Jenny Bormann
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Leonard Sewald
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Mainak D Gupta
- Department of Molecular Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Geronimo Heilmann
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Deepak D Bhandari
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne 50829, Germany
| | - Kyoko Morimoto
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
| | - Pierre Buscaill
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
| | - Bettina Hause
- Department of Metabolic and Cell Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Renier A L van der Hoorn
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
| | - Farnusch Kaschani
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Markus Kaiser
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
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12
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Wang B, Yang R, Zhang Z, Huang S, Ji Z, Zheng W, Zhang H, Zhang Y, Feng F. Integration of miRNA and mRNA analysis reveals the role of ribosome in to anti-artificial aging in sweetcorn. Int J Biol Macromol 2023; 240:124434. [PMID: 37062384 DOI: 10.1016/j.ijbiomac.2023.124434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/03/2023] [Accepted: 03/31/2023] [Indexed: 04/18/2023]
Abstract
Sweetcorn is a kind of maize with high sugar content and has poor seed aging tolerance, which seriously limits its production. However, few studies have explored the artificial aging (AA) tolerance by miRNA-mRNA integration analysis in sweetcorn. Here, we characterized the physiological, biochemical and transcriptomic changes of two contrasting lines K62 and K107 treated with AA during time series. Both the germination indexes and antioxidant enzymes showed significant difference between two lines. The MDA content of AA-tolerant genotype K62 was significantly lower than that of K107 on the fourth and sixth day. Subsequently, 157 differentially expressed miRNAs (DEMIs) and 8878 differentially expressed mRNAs (DEMs) were identified by RNA-seq analysis under aging stress. The "ribosome" and "peroxisome" pathways were enriched to respond to aging stress, genes for both large units and small ribosomal subunits were significantly upregulated expressed and higher translation efficiency might exist in K62. Thirteen pairs of miRNA-target genes were obtained, and 8 miRNA-mRNA pairs might involve in ribosome protein and translation process. Our results elucidate the mechanism of sweetcorn response to AA at miRNA-mRNA level, and provide a new insight into sweetcorn AA response to stress.
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Affiliation(s)
- Bo Wang
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Ruichun Yang
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Zili Zhang
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Silin Huang
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Zhaoqian Ji
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Wenbo Zheng
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Huaxing Zhang
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Yafeng Zhang
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Faqiang Feng
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China.
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13
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Skowyra ML, Rapoport TA. Cell-free reconstitution of peroxisomal matrix protein import using Xenopus egg extract. STAR Protoc 2023; 4:102111. [PMID: 36853666 PMCID: PMC9947420 DOI: 10.1016/j.xpro.2023.102111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/08/2022] [Accepted: 01/20/2023] [Indexed: 02/13/2023] Open
Abstract
Peroxisomes are vital metabolic organelles whose matrix enzymes are imported from the cytosol in a folded state by the soluble receptor PEX5. The import mechanism has been challenging to decipher because of the lack of suitable in vitro systems. Here, we present a protocol for reconstituting matrix protein import using Xenopus egg extract. We describe how extract is prepared, how to replace endogenous PEX5 with recombinant versions, and how to perform and interpret a peroxisomal import reaction using a fluorescent cargo. For complete details on the use and execution of this protocol, please refer to Skowyra and Rapoport (2022).1.
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Affiliation(s)
- Michael L Skowyra
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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14
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Sandalio LM, Collado-Arenal AM, Romero-Puertas MC. Deciphering peroxisomal reactive species interactome and redox signalling networks. Free Radic Biol Med 2023; 197:58-70. [PMID: 36642282 DOI: 10.1016/j.freeradbiomed.2023.01.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/19/2022] [Accepted: 01/12/2023] [Indexed: 01/15/2023]
Abstract
Plant peroxisomes are highly dynamic organelles with regard to metabolic pathways, number and morphology and participate in different metabolic processes and cell responses to their environment. Peroxisomes from animal and plant cells house a complex system of reactive oxygen species (ROS) production associated to different metabolic pathways which are under control of an important set of enzymatic and non enzymatic antioxidative defenses. Nitric oxide (NO) and its derivate reactive nitrogen species (RNS) are also produced in these organelles. Peroxisomes can regulate ROS and NO/RNS levels to allow their role as signalling molecules. The metabolism of other reactive species such as carbonyl reactive species (CRS) and sulfur reactive species (SRS) in peroxisomes and their relationship with ROS and NO have not been explored in depth. In this review, we define a peroxisomal reactive species interactome (PRSI), including all reactive species ROS, RNS, CRS and SRS, their interaction and effect on target molecules contributing to the dynamic redox/ROS homeostasis and plasticity of peroxisomes, enabling fine-tuned regulation of signalling networks associated with peroxisome-dependent H2O2. Particular attention will be paid to update the information available on H2O2-dependent peroxisomal retrograde signalling and to discuss a specific peroxisomal footprint.
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Affiliation(s)
- Luisa M Sandalio
- Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín (EEZ), Consejo Superior de Investigaciones Científicas (CSIC), C/ Profesor Albareda 1, 18008, Granada, Spain.
| | - Aurelio M Collado-Arenal
- Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín (EEZ), Consejo Superior de Investigaciones Científicas (CSIC), C/ Profesor Albareda 1, 18008, Granada, Spain
| | - María C Romero-Puertas
- Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín (EEZ), Consejo Superior de Investigaciones Científicas (CSIC), C/ Profesor Albareda 1, 18008, Granada, Spain
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15
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Xiang F, Liu WC, Liu X, Song Y, Zhang Y, Zhu X, Wang P, Guo S, Song CP. Direct balancing of lipid mobilization and reactive oxygen species production by the epoxidation of fatty acid catalyzed by a cytochrome P450 protein during seed germination. THE NEW PHYTOLOGIST 2023; 237:2104-2117. [PMID: 36495066 DOI: 10.1111/nph.18669] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Fatty acid (FA) β-oxidation provides energy for oil seed germination but also produces massive byproduct reactive oxygen species (ROS), posing potential oxidative damage to plant cells. How plants overcome the contradiction between energy supply and ROS production during seed germination remains unclear. In this study, we identified an Arabidopsis mvs1 (methylviologen-sensitive) mutant that was hypersensitive to ROS and caused by a missense mutation (G1349 substituted as A) of a cytochrome P450 gene, CYP77A4. CYP77A4 was highly expressed in germinating seedling cotyledons, and its protein is localized in the endoplasmic reticulum. As CYP77A4 catalyzes the epoxidation of unsaturated FA, disruption of CYP77A4 resulted in increased unsaturated FA abundance and over accumulated ROS in the mvs1 mutant. Consistently, scavenging excess ROS or blocking FA β-oxidation could repress the ROS overaccumulation and hypersensitivity in the mvs1 mutant. Furthermore, H2 O2 transcriptionally upregulated CYP77A4 expression and post-translationally modified CYP77A4 by sulfenylating its Cysteine-456, which is necessary for CYP77A4's role in modulating FA abundance and ROS production. Together, our study illustrates that CYP77A4 mediates direct balancing of lipid mobilization and ROS production by the epoxidation of FA during seed germination.
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Affiliation(s)
- Fuyou Xiang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, College of Agriculture, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, Henan, 475004, China
| | - Wen-Cheng Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, College of Agriculture, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, Henan, 475004, China
| | - Xin Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, College of Agriculture, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, Henan, 475004, China
| | - Yuwei Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, College of Agriculture, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, Henan, 475004, China
- College of Life Sciences and Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, China
| | - Yu Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, College of Agriculture, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, Henan, 475004, China
| | - Xiaojing Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, College of Agriculture, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, Henan, 475004, China
| | - Pengtao Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, College of Agriculture, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, Henan, 475004, China
| | - Siyi Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, College of Agriculture, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, Henan, 475004, China
| | - Chun-Peng Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, College of Agriculture, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, Henan, 475004, China
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16
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Akhter D, Zhang Y, Hu J, Pan R. Protein ubiquitination in plant peroxisomes. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:371-380. [PMID: 35975710 DOI: 10.1111/jipb.13346] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Protein ubiquitination regulates diverse cellular processes in eukaryotic organisms, from growth and development to stress response. Proteins subjected to ubiquitination can be found in virtually all subcellular locations and organelles, including peroxisomes, single-membrane and highly dynamic organelles ubiquitous in eukaryotes. Peroxisomes contain metabolic functions essential to plants and animals such as lipid catabolism, detoxification of reactive oxygen species (ROS), biosynthesis of vital hormones and cofactors, and photorespiration. Plant peroxisomes possess a complex proteome with functions varying among different tissue types and developmental stages, and during plant response to distinct environmental cues. However, how these diverse functions are regulated at the post-translational level is poorly understood, especially in plants. In this review, we summarized current knowledge of the involvement of protein ubiquitination in peroxisome protein import, remodeling, pexophagy, and metabolism, focusing on plants, and referencing discoveries from other eukaryotic systems when relevant. Based on previous ubiquitinomics studies, we compiled a list of 56 ubiquitinated Arabidopsis peroxisomal proteins whose functions are associated with all the major plant peroxisomal metabolic pathways. This discovery suggests a broad impact of protein ubiquitination on plant peroxisome functions, therefore substantiating the need to investigate this significant regulatory mechanism in peroxisomes at more depths.
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Affiliation(s)
- Delara Akhter
- State Key Laboratory of Rice Biology, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310058/311200, China
- Zhejiang Laboratory, Hangzhou, 311121, China
- Department of Genetics and Plant Breeding, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Yuchan Zhang
- State Key Laboratory of Rice Biology, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310058/311200, China
- Zhejiang Laboratory, Hangzhou, 311121, China
| | - Jianping Hu
- Department of Energy Plant Research Laboratory and Plant Biology Department, Michigan State University, East Lansing,, Michigan, USA
- Department of Plant Biology, Michigan State University, East Lansing,, Michigan, USA
| | - Ronghui Pan
- State Key Laboratory of Rice Biology, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310058/311200, China
- Zhejiang Laboratory, Hangzhou, 311121, China
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17
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Kong B, Ma J, Zhang P, Chen T, Liu Y, Che Z, Shahinnia F, Yang D. Deciphering key genomic regions controlling flag leaf size in wheat via integration of meta-QTL and in silico transcriptome assessment. BMC Genomics 2023; 24:33. [PMID: 36658498 PMCID: PMC9854125 DOI: 10.1186/s12864-023-09119-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/05/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Grain yield is a complex and polygenic trait influenced by the photosynthetic source-sink relationship in wheat. The top three leaves, especially the flag leaf, are considered the major sources of photo-assimilates accumulated in the grain. Determination of significant genomic regions and candidate genes affecting flag leaf size can be used in breeding for grain yield improvement. RESULTS With the final purpose of understanding key genomic regions for flag leaf size, a meta-analysis of 521 initial quantitative trait loci (QTLs) from 31 independent QTL mapping studies over the past decades was performed, where 333 loci eventually were refined into 64 meta-QTLs (MQTLs). The average confidence interval (CI) of these MQTLs was 5.28 times less than that of the initial QTLs. Thirty-three MQTLs overlapped the marker trait associations (MTAs) previously reported in genome-wide association studies (GWAS) for flag leaf traits in wheat. A total of 2262 candidate genes for flag leaf size, which were involved in the peroxisome, basal transcription factor, and tyrosine metabolism pathways were identified in MQTL regions by the in silico transcriptome assessment. Of these, the expression analysis of the available genes revealed that 134 genes with > 2 transcripts per million (TPM) were highly and specifically expressed in the leaf. These candidate genes could be critical to affect flag leaf size in wheat. CONCLUSIONS The findings will make further insight into the genetic determinants of flag leaf size and provide some reliable MQTLs and putative candidate genes for the genetic improvement of flag leaf size in wheat.
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Affiliation(s)
- Binxue Kong
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jingfu Ma
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Peipei Zhang
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China
| | - Tao Chen
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuan Liu
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zhuo Che
- Plant Seed Master Station of Gansu Province, Lanzhou, 730000, China
| | - Fahimeh Shahinnia
- Bavarian State Research Centre for Agriculture, Institute for Crop Science and Plant Breeding, 85354, Freising, Germany
| | - Delong Yang
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China.
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
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18
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Bauwe H. Photorespiration - Rubisco's repair crew. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153899. [PMID: 36566670 DOI: 10.1016/j.jplph.2022.153899] [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: 11/15/2022] [Revised: 12/11/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
The photorespiratory repair pathway (photorespiration in short) was set up from ancient metabolic modules about three billion years ago in cyanobacteria, the later ancestors of chloroplasts. These prokaryotes developed the capacity for oxygenic photosynthesis, i.e. the use of water as a source of electrons and protons (with O2 as a by-product) for the sunlight-driven synthesis of ATP and NADPH for CO2 fixation in the Calvin cycle. However, the CO2-binding enzyme, ribulose 1,5-bisphosphate carboxylase (known under the acronym Rubisco), is not absolutely selective for CO2 and can also use O2 in a side reaction. It then produces 2-phosphoglycolate (2PG), the accumulation of which would inhibit and potentially stop the Calvin cycle and subsequently photosynthetic electron transport. Photorespiration removes the 2-PG and in this way prevents oxygenic photosynthesis from poisoning itself. In plants, the core of photorespiration consists of ten enzymes distributed over three different types of organelles, requiring interorganellar transport and interaction with several auxiliary enzymes. It goes together with the release and to some extent loss of freshly fixed CO2. This disadvantageous feature can be suppressed by CO2-concentrating mechanisms, such as those that evolved in C4 plants thirty million years ago, which enhance CO2 fixation and reduce 2PG synthesis. Photorespiration itself provided a pioneer variant of such mechanisms in the predecessors of C4 plants, C3-C4 intermediate plants. This article is a review and update particularly on the enzyme components of plant photorespiration and their catalytic mechanisms, on the interaction of photorespiration with other metabolism and on its impact on the evolution of photosynthesis. This focus was chosen because a better knowledge of the enzymes involved and how they are embedded in overall plant metabolism can facilitate the targeted use of the now highly advanced methods of metabolic network modelling and flux analysis. Understanding photorespiration more than before as a process that enables, rather than reduces, plant photosynthesis, will help develop rational strategies for crop improvement.
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Affiliation(s)
- Hermann Bauwe
- University of Rostock, Plant Physiology, Albert-Einstein-Straße 3, D-18051, Rostock, Germany.
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19
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Li M, Yuan C, Zhang X, Pang W, Zhang P, Xie R, Lian C, Zhang T. The Transcriptional Responses of Ectomycorrhizal Fungus, Cenococcum geophilum, to Drought Stress. J Fungi (Basel) 2022; 9:jof9010015. [PMID: 36675836 PMCID: PMC9864566 DOI: 10.3390/jof9010015] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
With global warming, drought has become one of the major environmental pressures that threaten the development of global agricultural and forestry production. Cenococcum geophilum (C. geophilum) is one of the most common ectomycorrhizal fungi in nature, which can form mycorrhiza with a large variety of host trees of more than 200 tree species from 40 genera of both angiosperms and gymnosperms. In this study, six C. geophilum strains with different drought tolerance were selected to analyze their molecular responses to drought stress with treatment of 10% polyethylene glycol. Our results showed that drought-sensitive strains absorbed Na and K ions to regulate osmotic pressure and up-regulated peroxisome pathway genes to promote the activity of antioxidant enzymes to alleviate drought stress. However, drought-tolerant strains responded to drought stress by up-regulating the functional genes involved in the ubiquinone and other terpenoid-quinone biosynthesis and sphingolipid metabolism pathways. The results provided a foundation for studying the mechanism of C. geophilum response to drought stress.
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Affiliation(s)
- Mingtao Li
- International Joint Laboratory of Forest Symbiology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chao Yuan
- International Joint Laboratory of Forest Symbiology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaohui Zhang
- International Joint Laboratory of Forest Symbiology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenbo Pang
- International Joint Laboratory of Forest Symbiology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Panpan Zhang
- International Joint Laboratory of Forest Symbiology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Rongzhang Xie
- Forestry Bureau, Sanyuan District, Sanming 365000, China
| | - Chunlan Lian
- Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo, Tokyo 188-0002, Japan
- Correspondence: (C.L.); (T.Z.); Tel.: +86-80-7456-1286 (C.L.); +86-180-0691-1945 (T.Z.)
| | - Taoxiang Zhang
- International Joint Laboratory of Forest Symbiology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (C.L.); (T.Z.); Tel.: +86-80-7456-1286 (C.L.); +86-180-0691-1945 (T.Z.)
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20
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Feng P, Skowyra ML, Rapoport TA. Structure and function of the peroxisomal ubiquitin ligase complex. Biochem Soc Trans 2022; 50:1921-1930. [PMID: 36421406 PMCID: PMC9788354 DOI: 10.1042/bst20221393] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 09/26/2023]
Abstract
Peroxisomes are membrane-bounded organelles that exist in most eukaryotic cells and are involved in the oxidation of fatty acids and the destruction of reactive oxygen species. Depending on the organism, they house additional metabolic reactions that range from glycolysis in parasitic protozoa to the production of ether lipids in animals and antibiotics in fungi. The importance of peroxisomes for human health is revealed by various disorders - notably the Zellweger spectrum - that are caused by defects in peroxisome biogenesis and are often fatal. Most peroxisomal metabolic enzymes reside in the lumen, but are synthesized in the cytosol and imported into the organelle by mobile receptors. The receptors accompany cargo all the way into the lumen and must return to the cytosol to start a new import cycle. Recycling requires receptor monoubiquitination by a membrane-embedded ubiquitin ligase complex composed of three RING finger (RF) domain-containing proteins: PEX2, PEX10, and PEX12. A recent cryo-electron microscopy (cryo-EM) structure of the complex reveals its function as a retro-translocation channel for peroxisomal import receptors. Each subunit of the complex contributes five transmembrane segments that assemble into an open channel. The N terminus of a receptor likely inserts into the pore from the lumenal side, and is then monoubiquitinated by one of the RFs to enable extraction into the cytosol. If recycling is compromised, receptors are polyubiquitinated by the concerted action of the other two RFs and ultimately degraded. The new data provide mechanistic insight into a crucial step of peroxisomal protein import.
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Affiliation(s)
- Peiqiang Feng
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, U.S.A
| | - Michael L. Skowyra
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, U.S.A
| | - Tom A. Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, U.S.A
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21
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Gao Y, Skowyra ML, Feng P, Rapoport TA. Protein import into peroxisomes occurs through a nuclear pore-like phase. Science 2022; 378:eadf3971. [PMID: 36520918 PMCID: PMC9795577 DOI: 10.1126/science.adf3971] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Peroxisomes are ubiquitous organelles whose dysfunction causes fatal human diseases. Most peroxisomal proteins are imported from the cytosol in a folded state by the soluble receptor PEX5. How folded cargo crosses the membrane is unknown. Here, we show that peroxisomal import is similar to nuclear transport. The peroxisomal membrane protein PEX13 contains a conserved tyrosine (Y)- and glycine (G)-rich YG domain, which forms a selective phase resembling that formed by phenylalanine-glycine (FG) repeats within nuclear pores. PEX13 resides in the membrane in two orientations that oligomerize and suspend the YG meshwork within the lipid bilayer. Purified YG domains form hydrogels into which PEX5 selectively partitions, by using conserved aromatic amino acid motifs, bringing cargo along. The YG meshwork thus forms an aqueous conduit through which PEX5 delivers folded proteins into peroxisomes.
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Affiliation(s)
- Yuan Gao
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Michael L. Skowyra
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Peiqiang Feng
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Tom A. Rapoport
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA.,Corresponding author.
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22
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Nonconventional Yeasts Engineered Using the CRISPR-Cas System as Emerging Microbial Cell Factories. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8110656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Because the petroleum-based chemical synthesis of industrial products causes serious environmental and societal issues, biotechnological production using microorganisms is an alternative approach to achieve a more sustainable economy. In particular, the yeast Saccharomyces cerevisiae is widely used as a microbial cell factory to produce biofuels and valuable biomaterials. However, product profiles are often restricted due to the Crabtree-positive nature of S. cerevisiae, and ethanol production from lignocellulose is possibly enhanced by developing alternative stress-resistant microbial platforms. With desirable metabolic pathways and regulation in addition to strong resistance to diverse stress factors, nonconventional yeasts (NCY) may be considered an alternative microbial platform for industrial uses. Irrespective of their high industrial value, the lack of genetic information and useful gene editing tools makes it challenging to develop metabolic engineering-guided scaled-up applications using yeasts. The recently developed clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (Cas) system is a powerful gene editing tool for NCYs. This review describes the current status of and recent advances in promising NCYs in terms of industrial and biotechnological applications, highlighting CRISPR-Cas9 system-based metabolic engineering strategies. This will serve as a basis for the development of novel yeast applications.
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23
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Viñegra de la Torre N, Vayssières A, Obeng-Hinneh E, Neumann U, Zhou Y, Lázaro A, Roggen A, Sun H, Stolze SC, Nakagami H, Schneeberger K, Timmers T, Albani MC. FLOWERING REPRESSOR AAA + ATPase 1 is a novel regulator of perennial flowering in Arabis alpina. THE NEW PHYTOLOGIST 2022; 236:729-744. [PMID: 35832005 DOI: 10.1111/nph.18374] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Arabis alpina is a polycarpic perennial, in which PERPETUAL FLOWERING1 (PEP1) regulates flowering and perennial traits in a vernalization-dependent manner. Mutagenesis screens of the pep1 mutant established the role of other flowering time regulators in PEP1-parallel pathways. Here we characterized three allelic enhancers of pep1 (eop002, 085 and 091) which flower early. We mapped the causal mutations and complemented mutants with the identified gene. Using quantitative reverse transcriptase PCR and reporter lines, we determined the protein spatiotemporal expression patterns and localization within the cell. We also characterized its role in Arabidopsis thaliana using CRISPR and in A. alpina by introgressing mutant alleles into a wild-type background. These mutants carried lesions in an AAA+ ATPase of unknown function, FLOWERING REPRESSOR AAA+ ATPase 1 (AaFRAT1). AaFRAT1 was detected in the vasculature of young leaf primordia and the rib zone of flowering shoot apical meristems. At the subcellular level, AaFRAT1 was localized at the interphase between the endoplasmic reticulum and peroxisomes. Introgression lines carrying Aafrat1 alleles required less vernalization to flower and reduced number of vegetative axillary branches. By contrast, A. thaliana CRISPR lines showed weak flowering phenotypes. AaFRAT1 contributes to flowering time regulation and the perennial growth habit of A. alpina.
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Affiliation(s)
- Natanael Viñegra de la Torre
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225, Düsseldorf, Germany
| | - Alice Vayssières
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225, Düsseldorf, Germany
| | - Evelyn Obeng-Hinneh
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225, Düsseldorf, Germany
| | - Ulla Neumann
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Yanhao Zhou
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225, Düsseldorf, Germany
| | - Ana Lázaro
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225, Düsseldorf, Germany
| | - Adrian Roggen
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Hequan Sun
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Sara C Stolze
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Hirofumi Nakagami
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Korbinian Schneeberger
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Ton Timmers
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Maria C Albani
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225, Düsseldorf, Germany
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Photosynthetic Efficiency and Glyco-Metabolism Changes in Artificial Triploid Loquats Contribute to Heterosis Manifestation. Int J Mol Sci 2022; 23:ijms231911337. [PMID: 36232635 PMCID: PMC9570370 DOI: 10.3390/ijms231911337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
Previous studies indicated that extensive genetic variations could be generated due to polyploidy, which is considered to be closely associated with the manifestation of polyploid heterosis. Our previous studies confirmed that triploid loquats demonstrated significant heterosis, other than the ploidy effect, but the underlying mechanisms are largely unknown. This study aimed to overcome the narrow genetic distance of loquats, increase the genetic variation level of triploid loquats, and systematically illuminate the heterosis mechanisms of triploid loquats derived from two cross combinations. Here, inter-simple sequence repeats (ISSRs) and simple sequence repeats (SSRs) were adopted for evaluating the genetic diversity, and transcriptome sequencing (RNA-Seq) was performed to investigate gene expression as well as pathway changes in the triploids. We found that extensive genetic variations were produced during the formation of triploid loquats. The polymorphism ratios of ISSRs and SSRs were 43.75% and 19.32%, respectively, and almost all their markers had a PIC value higher than 0.5, suggesting that both ISSRs and SSRs could work well in loquat assisted breeding. Furthermore, our results revealed that by broadening the genetic distance between the parents, genetic variations in triploids could be promoted. Additionally, RNA-Seq results suggested that numerous genes differentially expressed between the triploids and parents were screened out. Moreover, KEGG analyses revealed that “photosynthetic efficiency” and “glyco-metabolism” were significantly changed in triploid loquats compared with the parents, which was consistent with the results of physiological indicator analyses, leaf micro-structure observations, and qRT-PCR validation. Collectively, our results suggested that extensive genetic variations occurred in the triploids and that the changes in the “photosynthetic efficiency” as well as “glyco-metabolism” of triploids might have further resulted in heterosis manifestation in the triploid loquats.
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Arabidopsis Ubiquitin-Conjugating Enzymes UBC4, UBC5, and UBC6 Have Major Functions in Sugar Metabolism and Leaf Senescence. Int J Mol Sci 2022; 23:ijms231911143. [PMID: 36232444 PMCID: PMC9569852 DOI: 10.3390/ijms231911143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 11/23/2022] Open
Abstract
The ubiquitin-conjugating enzyme (E2) is required for protein ubiquitination. Arabidopsis has 37 E2s grouped into 14 subfamilies and the functions for many of them are unknown. We utilized genetic and biochemical methods to study the roles of Arabidopsis UBC4, UBC5, and UBC6 of the E2 subfamily IV. The Arabidopsis ubc4/5/6 triple mutant plants had higher levels of glucose, sucrose, and starch than the control plants, as well as a higher protein level of a key gluconeogenic enzyme, cytosolic fructose 1,6-bisphosphatase 1 (cyFBP). In an in vitro assay, the proteasome inhibitor MG132 inhibited the degradation of recombinant cyFBP whereas ATP promoted cyFBP degradation. In the quadruple mutant ubc4/5/6 cyfbp, the sugar levels returned to normal, suggesting that the increased sugar levels in the ubc4/5/6 mutant were due to an increased cyFBPase level. In addition, the ubc4/5/6 mutant plants showed early leaf senescence at late stages of plant development as well as accelerated leaf senescence using detached leaves. Further, the leaf senescence phenotype remained in the quadruple ubc4/5/6 cyfbp mutant. Our results suggest that UBC4/5/6 have two lines of important functions, in sugar metabolism through regulating the cyFBP protein level and in leaf senescence likely through a cyFBP-independent mechanism.
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Liu X, Zheng X, Zhang L, Li J, Li Y, Huang H, Fan Z. Joint toxicity mechanisms of binary emerging PFAS mixture on algae (Chlorella pyrenoidosa) at environmental concentration. JOURNAL OF HAZARDOUS MATERIALS 2022; 437:129355. [PMID: 35716567 DOI: 10.1016/j.jhazmat.2022.129355] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/04/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Since traditional Per- and polyfluoroalkyl substances (PFAS) were banned in 2009 due to their bioaccumulation, persistence and biological toxicity, the emerging PFAS have been widely used as their substitutes and entered the aquatic environment in the form of mixtures. However, the joint toxicity mechanisms of these emerging PFAS mixtures to aquatic organisms remain largely unknown. Then, based on the testing of growth inhibition, cytotoxicity, photosynthesis and oxidative stress, and the toxicity mechanism of PFAS mixture (Perfluorobutane sulfonate and Perfluorobutane sulfonamide) to algae was explored using the Gene set enrichment analysis (GSEA). The results revealed that all three emerging PFAS treatments had a certain growth inhibitory effect on Chlorella pyrenoidosa (C. pyrenoidosa), but the toxicity of PFAS mixture was stronger than that of individual PFAS and showed a significant synergistic effect at environmental concentration. The joint toxicity mechanisms of binary PFAS mixture to C. pyrenoidosa were related to the damage of photosynthetic system, obstruction of ROS metabolism, and inhibition of DNA replication. Our findings are conductive to adding knowledge in understanding the joint toxicity mechanisms and provide a basis for assessing the environmental risk of emerging PFAS.
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Affiliation(s)
- Xianglin Liu
- Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Xiaowei Zheng
- Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Liangliang Zhang
- Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Jue Li
- Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Yanyao Li
- Laboratory of Industrial Water and Ecotechnology, Department of Green Chemistry and Technology, Ghent University, 8500 Kortrijk, Belgium
| | - Honghui Huang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou 510300, China
| | - Zhengqiu Fan
- Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China.
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27
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Skowyra ML, Rapoport TA. PEX5 translocation into and out of peroxisomes drives matrix protein import. Mol Cell 2022; 82:3209-3225.e7. [PMID: 35931083 PMCID: PMC9444985 DOI: 10.1016/j.molcel.2022.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/30/2022] [Accepted: 07/08/2022] [Indexed: 12/12/2022]
Abstract
Peroxisomes are ubiquitous organelles whose dysfunction causes fatal human diseases. Most peroxisomal enzymes are imported from the cytosol by the receptor PEX5, which interacts with a docking complex in the peroxisomal membrane and then returns to the cytosol after monoubiquitination by a membrane-embedded ubiquitin ligase. The mechanism by which PEX5 shuttles between cytosol and peroxisomes and releases cargo inside the lumen is unclear. Here, we use Xenopus egg extract to demonstrate that PEX5 accompanies cargo completely into the lumen, utilizing WxxxF/Y motifs near its N terminus that bind a lumenal domain of the docking complex. PEX5 recycling is initiated by an amphipathic helix that binds to the lumenal side of the ubiquitin ligase. The N terminus then emerges in the cytosol for monoubiquitination. Finally, PEX5 is extracted from the lumen, resulting in the unfolding of the receptor and cargo release. Our results reveal the unique mechanism by which PEX5 ferries proteins into peroxisomes.
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Affiliation(s)
- Michael L Skowyra
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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28
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Terrón-Camero LC, Peláez-Vico MÁ, Rodríguez-González A, del Val C, Sandalio LM, Romero-Puertas MC. Gene network downstream plant stress response modulated by peroxisomal H 2O 2. FRONTIERS IN PLANT SCIENCE 2022; 13:930721. [PMID: 36082297 PMCID: PMC9445673 DOI: 10.3389/fpls.2022.930721] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Reactive oxygen species (ROS) act as secondary messengers that can be sensed by specific redox-sensitive proteins responsible for the activation of signal transduction culminating in altered gene expression. The subcellular site, in which modifications in the ROS/oxidation state occur, can also act as a specific cellular redox network signal. The chemical identity of ROS and their subcellular origin is actually a specific imprint on the transcriptome response. In recent years, a number of transcriptomic studies related to altered ROS metabolism in plant peroxisomes have been carried out. In this study, we conducted a meta-analysis of these transcriptomic findings to identify common transcriptional footprints for plant peroxisomal-dependent signaling at early and later time points. These footprints highlight the regulation of various metabolic pathways and gene families, which are also found in plant responses to several abiotic stresses. Major peroxisomal-dependent genes are associated with protein and endoplasmic reticulum (ER) protection at later stages of stress while, at earlier stages, these genes are related to hormone biosynthesis and signaling regulation. Furthermore, in silico analyses allowed us to assign human orthologs to some of the peroxisomal-dependent proteins, which are mainly associated with different cancer pathologies. Peroxisomal footprints provide a valuable resource for assessing and supporting key peroxisomal functions in cellular metabolism under control and stress conditions across species.
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Affiliation(s)
- Laura C. Terrón-Camero
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín (EEZ), Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - M. Ángeles Peláez-Vico
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín (EEZ), Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - A. Rodríguez-González
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín (EEZ), Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Coral del Val
- Department of Artificial Intelligence, University of Granada, Granada, Spain
- Andalusian Data Science and Computational Intelligence (DaSCI) Research Institute, University of Granada, Granada, Spain
| | - Luisa M. Sandalio
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín (EEZ), Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - María C. Romero-Puertas
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín (EEZ), Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
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Muhammad D, Smith KA, Bartel B. Plant peroxisome proteostasis-establishing, renovating, and dismantling the peroxisomal proteome. Essays Biochem 2022; 66:229-242. [PMID: 35538741 PMCID: PMC9375579 DOI: 10.1042/ebc20210059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 12/28/2022]
Abstract
Plant peroxisomes host critical metabolic reactions and insulate the rest of the cell from reactive byproducts. The specialization of peroxisomal reactions is rooted in how the organelle modulates its proteome to be suitable for the tissue, environment, and developmental stage of the organism. The story of plant peroxisomal proteostasis begins with transcriptional regulation of peroxisomal protein genes and the synthesis, trafficking, import, and folding of peroxisomal proteins. The saga continues with assembly and disaggregation by chaperones and degradation via proteases or the proteasome. The story concludes with organelle recycling via autophagy. Some of these processes as well as the proteins that facilitate them are peroxisome-specific, while others are shared among organelles. Our understanding of translational regulation of plant peroxisomal protein transcripts and proteins necessary for pexophagy remain based in findings from other models. Recent strides to elucidate transcriptional control, membrane dynamics, protein trafficking, and conditions that induce peroxisome turnover have expanded our knowledge of plant peroxisomal proteostasis. Here we review our current understanding of the processes and proteins necessary for plant peroxisome proteostasis-the emergence, maintenance, and clearance of the peroxisomal proteome.
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Affiliation(s)
| | - Kathryn A Smith
- Department of BioSciences, Rice University, Houston, TX 77005, U.S.A
| | - Bonnie Bartel
- Department of BioSciences, Rice University, Houston, TX 77005, U.S.A
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Koletti A, Dervisi I, Kalloniati C, Zografaki ME, Rennenberg H, Roussis A, Flemetakis E. Selenium-binding Protein 1 (SBD1): A stress response regulator in Chlamydomonas reinhardtii. PLANT PHYSIOLOGY 2022; 189:2368-2381. [PMID: 35579367 PMCID: PMC9342975 DOI: 10.1093/plphys/kiac230] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/04/2022] [Indexed: 05/20/2023]
Abstract
Selenium-binding proteins (SBPs) represent a ubiquitous protein family implicated in various environmental stress responses, although the exact molecular and physiological role of the SBP family remains elusive. In this work, we report the identification and characterization of CrSBD1, an SBP homolog from the model microalgae Chlamydomonas reinhardtii. Growth analysis of the C. reinhardtii sbd1 mutant strain revealed that the absence of a functional CrSBD1 resulted in increased growth under mild oxidative stress conditions, although cell viability rapidly declined at higher hydrogen peroxide (H2O2) concentrations. Furthermore, a combined global transcriptomic and metabolomic analysis indicated that the sbd1 mutant exhibited a dramatic quenching of the molecular and biochemical responses upon H2O2-induced oxidative stress when compared to the wild-type. Our results indicate that CrSBD1 represents a cell regulator, which is involved in the modulation of C. reinhardtii early responses to oxidative stress. We assert that CrSBD1 acts as a member of an extensive and conserved protein-protein interaction network including Fructose-bisphosphate aldolase 3, Cysteine endopeptidase 2, and Glutaredoxin 6 proteins, as indicated by yeast two-hybrid assays.
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Affiliation(s)
- Aikaterini Koletti
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens 11855, Greece
| | - Irene Dervisi
- Department of Botany, Faculty of Biology, National & Kapodistrian University of Athens, Athens 15784, Greece
| | - Chrysanthi Kalloniati
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens 11855, Greece
| | - Maria-Eleftheria Zografaki
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens 11855, Greece
| | - Heinz Rennenberg
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Chongqing 400715, China
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31
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Llinas RJ, Xiong JQ, Clark NM, Burkhart SE, Bartel B. An Arabidopsis pre-RNA processing8a (prp8a) missense allele restores splicing of a subset of mis-spliced mRNAs. PLANT PHYSIOLOGY 2022; 189:2175-2192. [PMID: 35608297 PMCID: PMC9342983 DOI: 10.1093/plphys/kiac221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
Eukaryotic precursor mRNAs often harbor noncoding introns that must be removed prior to translation. Accurate splicing of precursor messenger RNA depends on placement and assembly of small nuclear ribonucleoprotein (snRNP) sub-complexes of the spliceosome. Yeast (Saccharomyces cerevisiae) studies established a role in splice-site selection for PRE-RNA PROCESSING8 (PRP8), a conserved spliceosome scaffolding protein of the U5 snRNP. However, analogous splice-site selection studies in multicellular eukaryotes are lacking. Such studies are crucial for a comprehensive understanding of alternative splicing, which is extensive in plants and animals but limited in yeast. In this work, we describe an Arabidopsis (Arabidopsis thaliana) prp8a mutant that modulates splice-site selection. We isolated prp8a-14 from a screen for suppressors of pex14-6, which carries a splice-site mutation in the PEROXIN14 (PEX14) peroxisome biogenesis gene. To elucidate Arabidopsis PRP8A function in spliceosome fidelity, we combined prp8a-14 with various pex14 splice-site mutations and monitored the double mutants for physiological and molecular consequences of dysfunctional and functional peroxisomes that correspond to impaired and recovered splicing, respectively. prp8a-14 restored splicing and PEX14 function to alleles with mutations in the exonic guanine of the 5'-splice site but did not restore splicing or function to alleles with mutations in the intronic guanine of 5'- or 3'-splice sites. We used RNA-seq to reveal the systemic impact of prp8a-14 and found hundreds of differentially spliced transcripts and thousands of transcripts with significantly altered levels. Among differentially spliced transcripts, prp8a-14 significantly altered 5'- and 3'-splice-site utilization to favor sites resulting in shorter introns. This study provides a genetic platform for probing splicing in plants and hints at a role for plant PRP8 in splice-site selection.
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Affiliation(s)
- Roxanna J Llinas
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
| | | | - Natalie M Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - Sarah E Burkhart
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
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Johnston C, García Navarrete LT, Ortiz E, Romsdahl TB, Guzha A, Chapman KD, Grotewold E, Alonso AP. Effective Mechanisms for Improving Seed Oil Production in Pennycress ( Thlaspi arvense L.) Highlighted by Integration of Comparative Metabolomics and Transcriptomics. FRONTIERS IN PLANT SCIENCE 2022; 13:943585. [PMID: 35909773 PMCID: PMC9330397 DOI: 10.3389/fpls.2022.943585] [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: 05/13/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Pennycress is a potentially lucrative biofuel crop due to its high content of long-chain unsaturated fatty acids, and because it uses non-conventional pathways to achieve efficient oil production. However, metabolic engineering is required to improve pennycress oilseed content and make it an economically viable source of aviation fuel. Research is warranted to determine if further upregulation of these non-conventional pathways could improve oil production within the species even more, which would indicate these processes serve as promising metabolic engineering targets and could provide the improvement necessary for economic feasibility of this crop. To test this hypothesis, we performed a comparative biomass, metabolomic, and transcriptomic analyses between a high oil accession (HO) and low oil accession (LO) of pennycress to assess potential factors required to optimize oil content. An evident reduction in glycolysis intermediates, improved oxidative pentose phosphate pathway activity, malate accumulation in the tricarboxylic acid cycle, and an anaplerotic pathway upregulation were noted in the HO genotype. Additionally, higher levels of threonine aldolase transcripts imply a pyruvate bypass mechanism for acetyl-CoA production. Nucleotide sugar and ascorbate accumulation also were evident in HO, suggesting differential fate of associated carbon between the two genotypes. An altered transcriptome related to lipid droplet (LD) biosynthesis and stability suggests a contribution to a more tightly-packed LD arrangement in HO cotyledons. In addition to the importance of central carbon metabolism augmentation, alternative routes of carbon entry into fatty acid synthesis and modification, as well as transcriptionally modified changes in LD regulation, are key aspects of metabolism and storage associated with economically favorable phenotypes of the species.
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Affiliation(s)
- Christopher Johnston
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, United States
| | | | - Emmanuel Ortiz
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, United States
| | - Trevor B. Romsdahl
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, United States
| | - Athanas Guzha
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, United States
| | - Kent D. Chapman
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, United States
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Ana Paula Alonso
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, United States
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Liu J, Bi B, Tian G, Li Z, Wang W, Ma F, Shi H, Liu W. Crystal idioblasts are involved in the anther dehiscence of Nicotiana tabacum. PHYSIOLOGIA PLANTARUM 2022; 174:e13753. [PMID: 36004735 DOI: 10.1111/ppl.13753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/08/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
In Nicotiana tabacum, the degeneration of connective tissue and stomium tissue (the stomium and circular cell cluster [CCC]) is essential for anther dehiscence. Both connective cells and CCC cells are crystal idioblasts, and these cells will undergo degeneration after accumulating calcium oxalate (CaOx) crystals. However, detailed data concerning this process are minimal. Therefore, this study used cellular biological and physiological methods to illustrate this relationship. Results demonstrated that tobacco anther dehiscence is a series of timed programmed cell death (PCD) processes that include the CCC, connective tissue, and stomium. The degenerating crystal idioblasts of the tobacco anther were found to possess two hallmark characteristics that distinguished them from normal PCD cells, namely dynamic changes in CaOx crystals and the appearance of numerous peroxisomes. The accumulation of CaOx and the production of H2 O2 occurred simultaneously or successively before PCD. The peak H2 O2 content was found to appear after the insoluble oxalate. Further, CeCl3 cytochemistry staining was used to detect subcellular H2 O2 , and the precipitate of H2 O2 was primarily present in peroxisomes and around CaOx crystals. These results show that anther dehiscence in N. tabacum is a PCD process in which crystal idioblasts play a vital role in CaOx degradation and H2 O2 production.
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Affiliation(s)
- Jing Liu
- School of Life Science, Northwest University, Xi'an, China
- School of Life Science, Northwest Normal University, Lanzhou, China
| | - Baoxia Bi
- School of Life Science, Northwest University, Xi'an, China
| | - Guanghua Tian
- School of Life Science, Northwest University, Xi'an, China
| | - Ziwei Li
- School of Life Science, Northwest University, Xi'an, China
| | - Weirui Wang
- School of Life Science, Northwest University, Xi'an, China
| | - Fang Ma
- School of Life Science, Northwest University, Xi'an, China
- Institute of Ethnic Preparatory, Ningxia University, Yinchuan, China
| | - Hongyong Shi
- School of Life Science, Guangzhou University, Guangzhou, China
| | - Wenzhe Liu
- School of Life Science, Northwest University, Xi'an, China
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Ma D, Lai Z, Ding Q, Zhang K, Chang K, Li S, Zhao Z, Zhong F. Identification, Characterization and Function of Orphan Genes Among the Current Cucurbitaceae Genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:872137. [PMID: 35599909 PMCID: PMC9114813 DOI: 10.3389/fpls.2022.872137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
Orphan genes (OGs) that are missing identifiable homologs in other lineages may potentially make contributions to a variety of biological functions. The Cucurbitaceae family consists of a wide range of fruit crops of worldwide or local economic significance. To date, very few functional mechanisms of OGs in Cucurbitaceae are known. In this study, we systematically identified the OGs of eight Cucurbitaceae species using a comparative genomics approach. The content of OGs varied widely among the eight Cucurbitaceae species, ranging from 1.63% in chayote to 16.55% in wax gourd. Genetic structure analysis showed that OGs have significantly shorter protein lengths and fewer exons in Cucurbitaceae. The subcellular localizations of OGs were basically the same, with only subtle differences. Except for aggregation in some chromosomal regions, the distribution density of OGs was higher near the telomeres and relatively evenly distributed on the chromosomes. Gene expression analysis revealed that OGs had less abundantly and highly tissue-specific expression. Interestingly, the largest proportion of these OGs was significantly more tissue-specific expressed in the flower than in other tissues, and more detectable expression was found in the male flower. Functional prediction of OGs showed that (1) 18 OGs associated with male sterility in watermelon; (2) 182 OGs associated with flower development in cucumber; (3) 51 OGs associated with environmental adaptation in watermelon; (4) 520 OGs may help with the large fruit size in wax gourd. Our results provide the molecular basis and research direction for some important mechanisms in Cucurbitaceae species and domesticated crops.
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Affiliation(s)
- Dongna Ma
- College of Horticulture, Fujian Agriculture and Forestry University, Fujian, China
- College of the Environment and Ecology, Xiamen University, Fujian, China
| | - Zhengfeng Lai
- Subtropical Agricultural Research Institute, Fujian Academy of Agriculture Sciences, Fujian, China
| | - Qiansu Ding
- College of the Environment and Ecology, Xiamen University, Fujian, China
| | - Kun Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fujian, China
| | - Kaizhen Chang
- College of Horticulture, Fujian Agriculture and Forestry University, Fujian, China
| | - Shuhao Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fujian, China
| | - Zhizhu Zhao
- College of the Environment and Ecology, Xiamen University, Fujian, China
| | - Fenglin Zhong
- College of Horticulture, Fujian Agriculture and Forestry University, Fujian, China
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Goto-Yamada S, Oikawa K, Yamato KT, Kanai M, Hikino K, Nishimura M, Mano S. Image-Based Analysis Revealing the Molecular Mechanism of Peroxisome Dynamics in Plants. Front Cell Dev Biol 2022; 10:883491. [PMID: 35592252 PMCID: PMC9110829 DOI: 10.3389/fcell.2022.883491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/15/2022] [Indexed: 11/13/2022] Open
Abstract
Peroxisomes are present in eukaryotic cells and have essential roles in various biological processes. Plant peroxisomes proliferate by de novo biosynthesis or division of pre-existing peroxisomes, degrade, or replace metabolic enzymes, in response to developmental stages, environmental changes, or external stimuli. Defects of peroxisome functions and biogenesis alter a variety of biological processes and cause aberrant plant growth. Traditionally, peroxisomal function-based screening has been employed to isolate Arabidopsis thaliana mutants that are defective in peroxisomal metabolism, such as lipid degradation and photorespiration. These analyses have revealed that the number, subcellular localization, and activity of peroxisomes are closely related to their efficient function, and the molecular mechanisms underlying peroxisome dynamics including organelle biogenesis, protein transport, and organelle interactions must be understood. Various approaches have been adopted to identify factors involved in peroxisome dynamics. With the development of imaging techniques and fluorescent proteins, peroxisome research has been accelerated. Image-based analyses provide intriguing results concerning the movement, morphology, and number of peroxisomes that were hard to obtain by other approaches. This review addresses image-based analysis of peroxisome dynamics in plants, especially A. thaliana and Marchantia polymorpha.
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Affiliation(s)
- Shino Goto-Yamada
- Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Kazusato Oikawa
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Katsuyuki T. Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Masatake Kanai
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Kazumi Hikino
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Mikio Nishimura
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan
| | - Shoji Mano
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
- *Correspondence: Shoji Mano
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Jurdak R, Rodrigues GDAG, Chaumont N, Schivre G, Bourbousse C, Barneche F, Bou Dagher Kharrat M, Bailly C. Intracellular reactive oxygen species trafficking participates in seed dormancy alleviation in Arabidopsis seeds. THE NEW PHYTOLOGIST 2022; 234:850-866. [PMID: 35175638 DOI: 10.1111/nph.18038] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Reactive oxygen species (ROS) release seed dormancy through an unknown mechanism. We used different seed dormancy-breaking treatments to decipher the dynamics and localization of ROS production during seed germination. We studied the involvement of ROS in the breaking of Arabidopsis seed dormancy by cold stratification, gibberellic acid (GA3 ) and light. We characterized the effects of these treatments on abscisic acid and gibberellins biosynthesis and signalling pathways. ROS, mitochondrial redox status and peroxisomes were visualized and/or quantified during seed imbibition. Finally, we performed a cytogenetic characterization of the nuclei from the embryonic axes during seed germination. We show that mitochondria participate in the early ROS production during seed imbibition and that a possible involvement of peroxisomes in later stages should still be analysed. At the time of radicle protrusion, ROS accumulated within the nucleus, which correlated with nuclear expansion and chromatin decompaction. Taken together, our results provide evidence of the role of ROS trafficking between organelles and of the nuclear redox status in the regulation of seed germination by dormancy.
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Affiliation(s)
- Rana Jurdak
- IBPS, CNRS, UMR 7622 Biologie du Développement, Sorbonne Université, Paris, F-75005, France
- Biodiversity and Functional Genomics Laboratory, Université Saint-Joseph de Beyrouth, Beyrouth, 1107 2050, Lebanon
| | - Guilherme de Almeida Garcia Rodrigues
- IBPS, CNRS, UMR 7622 Biologie du Développement, Sorbonne Université, Paris, F-75005, France
- Plant Physiology Lab, Federal University of Santa Catarina (UFSC), Florianópolis, SC, 88040-900, Brazil
| | - Nicole Chaumont
- IBPS, CNRS, UMR 7622 Biologie du Développement, Sorbonne Université, Paris, F-75005, France
| | - Geoffrey Schivre
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, F-75005, France
- Université Paris-Saclay, Orsay, F-91405, France
| | - Clara Bourbousse
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, F-75005, France
| | - Fredy Barneche
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, F-75005, France
| | - Magda Bou Dagher Kharrat
- Biodiversity and Functional Genomics Laboratory, Université Saint-Joseph de Beyrouth, Beyrouth, 1107 2050, Lebanon
| | - Christophe Bailly
- IBPS, CNRS, UMR 7622 Biologie du Développement, Sorbonne Université, Paris, F-75005, France
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37
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Kataya A, Gautam N, Jamshed M, Muench DG, Samuel MA, Thelen JJ, Moorhead GB. Identification of Arabidopsis Protein Kinases That Harbor Functional Type 1 Peroxisomal Targeting Signals. Front Cell Dev Biol 2022; 10:745883. [PMID: 35242755 PMCID: PMC8886021 DOI: 10.3389/fcell.2022.745883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 01/25/2022] [Indexed: 12/25/2022] Open
Abstract
Peroxisomes are eukaryotic specific organelles that perform diverse metabolic functions including fatty acid β-oxidation, reactive species metabolism, photorespiration, and responses to stress. However, the potential regulation of these functions by post-translational modifications, including protein phosphorylation, has had limited study. Recently, we identified and catalogued a large number of peroxisomal phosphorylated proteins, implicating the presence of protein kinases in this organelle. Here, we employed available prediction models coupled with sequence conservation analysis to identify 31 protein kinases from the Arabidopsis kinome (all protein kinases) that contain a putative, non-canonical peroxisomal targeting signal type 1 (PTS1). From this, twelve C-terminal domain-PTS1s were demonstrated to be functional in vivo, targeting enhanced yellow fluorescent protein to peroxisomes, increasing the list of presumptive peroxisomal protein kinases to nineteen. Of the twelve protein kinases with functional PTS1s, we obtained full length clones for eight and demonstrated that seven target to peroxisomes in vivo. Screening homozygous mutants of the presumptive nineteen protein kinases revealed one candidate (GPK1) that harbors a sugar-dependence phenotype, suggesting it is involved in regulating peroxisomal fatty acid β-oxidation. These results present new opportunities for investigating the regulation of peroxisome functions.
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Affiliation(s)
- Amr Kataya
- Department of Chemistry, Bioscience, and Environmental Engineering, University of Stavanger, Stavanger, Norway.,Department of Biological Sciences, University of Calgary, Calgary, AB, Canada.,Christopher S. Bond Life Sciences Center, Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Nitija Gautam
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Muhammad Jamshed
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Marcus A Samuel
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Jay J Thelen
- Christopher S. Bond Life Sciences Center, Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Greg B Moorhead
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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38
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Ning N, Xie X, Yu H, Mei J, Li Q, Zuo S, Wu H, Liu W, Li Z. Plant Peroxisome-Targeting Effector MoPtep1 Is Required for the Virulence of Magnaporthe oryzae. Int J Mol Sci 2022; 23:2515. [PMID: 35269662 PMCID: PMC8910473 DOI: 10.3390/ijms23052515] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 02/01/2023] Open
Abstract
Rice blast caused by Magnaporthe oryzae is one of the most serious fungous diseases in rice. In the past decades, studies have reported that numerous M. oryzae effectors were secreted into plant cells to facilitate inoculation. Effectors target host proteins to assist the virulence of pathogens via the localization of specific organelles, such as the nucleus, endoplasmic reticulum, chloroplast, etc. However, studies on the pathogenesis of peroxisome-targeting effectors are still limited. In our previous study, we analyzed the subcellular localization of candidate effectors from M. oryzae using the agrobacterium-mediated transient expression system in tobacco and found that MoPtep1 (peroxisomes-targeted effector protein 1) localized in plant peroxisomes. Here, we proved that MoPtep1 was induced in the early stage of the M. oryzae infection and positively regulated the pathogenicity, while it did not affect the vegetative growth of mycelia. Subcellular localization results showed that MoPtep1 was localized in the plant peroxisomes with a signal peptide and a cupredoxin domain. Sequence analysis indicated that the homologous protein of MoPtep1 in plant-pathogenic fungi was evolutionarily conserved. Furthermore, MoPtep1 could suppress INF1-induced cell death in tobacco, and the targeting host proteins were identified using the Y2H system. Our results suggested that MoPtep1 is an important pathogenic effector in rice blast.
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Affiliation(s)
- Na Ning
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, China; (N.N.); (X.X.)
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (J.M.); (H.W.)
| | - Xin Xie
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, China; (N.N.); (X.X.)
| | - Haiyue Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (J.M.); (H.W.)
| | - Jie Mei
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (J.M.); (H.W.)
| | - Qianqian Li
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;
| | - Shimin Zuo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China;
| | - Hanxiang Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (J.M.); (H.W.)
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (J.M.); (H.W.)
| | - Zhiqiang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.Y.); (J.M.); (H.W.)
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Traver MS, Bradford SE, Olmos JL, Wright ZJ, Miller MD, Xu W, Phillips GN, Bartel B. The Structure of the Arabidopsis PEX4-PEX22 Peroxin Complex-Insights Into Ubiquitination at the Peroxisomal Membrane. Front Cell Dev Biol 2022; 10:838923. [PMID: 35300425 PMCID: PMC8922245 DOI: 10.3389/fcell.2022.838923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 01/28/2022] [Indexed: 01/11/2023] Open
Abstract
Peroxisomes are eukaryotic organelles that sequester critical oxidative reactions and process the resulting reactive oxygen species into less toxic byproducts. Peroxisome function and formation are coordinated by peroxins (PEX proteins) that guide peroxisome biogenesis and division and shuttle proteins into the lumen and membrane of the organelle. Despite the importance of peroxins in plant metabolism and development, no plant peroxin structures have been reported. Here we report the X-ray crystal structure of the PEX4-PEX22 peroxin complex from the reference plant Arabidopsis thaliana. PEX4 is a ubiquitin-conjugating enzyme (UBC) that ubiquitinates proteins associated with the peroxisomal membrane, and PEX22 is a peroxisomal membrane protein that anchors PEX4 to the peroxisome and facilitates PEX4 activity. We co-expressed Arabidopsis PEX4 as a translational fusion with the soluble PEX4-interacting domain of PEX22 in E. coli. The fusion was linked via a protease recognition site, allowing us to separate PEX4 and PEX22 following purification and solve the structure of the complex. We compared the structure of the PEX4-PEX22 complex to the previously published structures of yeast orthologs. Arabidopsis PEX4 displays the typical UBC structure expected from its sequence. Although Arabidopsis PEX22 lacks notable sequence identity to yeast PEX22, it maintains a similar Rossmann fold-like structure. Several salt bridges are positioned to contribute to the specificity of PEX22 for PEX4 versus other Arabidopsis UBCs, and the long unstructured PEX22 tether would allow PEX4-mediated ubiquitination of distant peroxisomal membrane targets without dissociation from PEX22. The Arabidopsis PEX4-PEX22 structure also revealed that the residue altered in pex4-1 (P123L), a mutant previously isolated via a forward-genetic screen for peroxisomal dysfunction, is near the active site cysteine of PEX4. We demonstrated in vitro UBC activity for the PEX4-PEX22 complex and found that the pex4-1 enzyme has reduced in vitro ubiquitin-conjugating activity and altered specificity compared to PEX4. Our findings illuminate the role of PEX4 and PEX22 in peroxisome structure and function and provide tools for future exploration of ubiquitination at the peroxisome surface.
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Affiliation(s)
- Melissa S. Traver
- Department of Biosciences, Rice University, Houston, TX, United States
| | - Sarah E. Bradford
- Department of Biosciences, Rice University, Houston, TX, United States
| | - Jose Luis Olmos
- Department of Biosciences, Rice University, Houston, TX, United States
| | - Zachary J. Wright
- Department of Biosciences, Rice University, Houston, TX, United States
| | | | - Weijun Xu
- Department of Biosciences, Rice University, Houston, TX, United States
| | - George N. Phillips
- Department of Biosciences, Rice University, Houston, TX, United States
- Department of Chemistry, Rice University, Houston, TX, United States
| | - Bonnie Bartel
- Department of Biosciences, Rice University, Houston, TX, United States
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40
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Romero-Puertas MC, Peláez-Vico MÁ, Pazmiño DM, Rodríguez-Serrano M, Terrón-Camero L, Bautista R, Gómez-Cadenas A, Claros MG, León J, Sandalio LM. Insights into ROS-dependent signalling underlying transcriptomic plant responses to the herbicide 2,4-D. PLANT, CELL & ENVIRONMENT 2022; 45:572-590. [PMID: 34800292 DOI: 10.1111/pce.14229] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
The synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D) functions as an agronomic weed control herbicide. High concentrations of 2,4-D induce plant growth defects, particularly leaf epinasty and stem curvature. Although the 2,4-D triggered reactive oxygen species (ROS) production, little is known about its signalling. In this study, by using a null mutant in peroxisomal acyl CoA oxidase 1 (acx1-2), we identified acyl-coenzyme A oxidase 1 (ACX1) as one of the main sources of ROS production and, in part, also causing the epinastic phenotype following 2,4-D application. Transcriptomic analyses of wild type (WT) plants after treatment with 2,4-D revealed a ROS-related peroxisomal footprint in early plant responses, while other organelles, such as mitochondria and chloroplasts, are involved in later responses. Interestingly, a group of 2,4-D-responsive ACX1-dependent transcripts previously associated with epinasty is related to auxin biosynthesis, metabolism, and signalling. We found that the auxin receptor auxin signalling F-box 3 (AFB3), a component of Skp, Cullin, F-box containing complex (SCF) (ASK-cullin-F-box) E3 ubiquitin ligase complexes, which mediates auxin/indole acetic acid (AUX/IAA) degradation by the 26S proteasome, acts downstream of ACX1 and is involved in the epinastic phenotype induced by 2,4-D. We also found that protein degradation associated with ubiquitin E3-RING and E3-SCF-FBOX in ACX1-dependent signalling in plant responses to 2,4-D is significantly regulated over longer treatment periods.
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Affiliation(s)
- María C Romero-Puertas
- Departamento de Bioquímica, Biología Celular y Molecular de Plantas, EEZ, CSIC, Granada, Spain
| | | | - Diana M Pazmiño
- Departamento de Bioquímica, Biología Celular y Molecular de Plantas, EEZ, CSIC, Granada, Spain
| | - María Rodríguez-Serrano
- Departamento de Bioquímica, Biología Celular y Molecular de Plantas, EEZ, CSIC, Granada, Spain
| | | | - Rocío Bautista
- Plataforma Andaluza de Bioinformática-SCBI, Universidad de Málaga, Málaga, Spain
| | - Aurelio Gómez-Cadenas
- Department Ciències Agràries i del Medi Natural, Universitat Jaume I, Castelló de la Plana, Spain
| | - M Gonzalo Claros
- Plataforma Andaluza de Bioinformática-SCBI, Universidad de Málaga, Málaga, Spain
- Departamento de Biología Molecular y Bioquímica, Ciencias, Univ. de Málaga, Málaga, Spain
- Institute for Mediterranean and Subtropical Horticulture "La Mayora" (IHSM-UMA-CSIC), Málaga, Spain
| | - José León
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Univ. Valencia), CPI Edificio 8E, Valencia, Spain
| | - Luisa M Sandalio
- Departamento de Bioquímica, Biología Celular y Molecular de Plantas, EEZ, CSIC, Granada, Spain
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41
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Kang BH, Anderson CT, Arimura SI, Bayer E, Bezanilla M, Botella MA, Brandizzi F, Burch-Smith TM, Chapman KD, Dünser K, Gu Y, Jaillais Y, Kirchhoff H, Otegui MS, Rosado A, Tang Y, Kleine-Vehn J, Wang P, Zolman BK. A glossary of plant cell structures: Current insights and future questions. THE PLANT CELL 2022; 34:10-52. [PMID: 34633455 PMCID: PMC8846186 DOI: 10.1093/plcell/koab247] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/29/2021] [Indexed: 05/03/2023]
Abstract
In this glossary of plant cell structures, we asked experts to summarize a present-day view of plant organelles and structures, including a discussion of outstanding questions. In the following short reviews, the authors discuss the complexities of the plant cell endomembrane system, exciting connections between organelles, novel insights into peroxisome structure and function, dynamics of mitochondria, and the mysteries that need to be unlocked from the plant cell wall. These discussions are focused through a lens of new microscopy techniques. Advanced imaging has uncovered unexpected shapes, dynamics, and intricate membrane formations. With a continued focus in the next decade, these imaging modalities coupled with functional studies are sure to begin to unravel mysteries of the plant cell.
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Affiliation(s)
- Byung-Ho Kang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Charles T Anderson
- Department of Biology and Center for Lignocellulose Structure and Formation, The Pennsylvania State University, University Park, Pennsylvania 16802 USA
| | - Shin-ichi Arimura
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Emmanuelle Bayer
- Université de Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire, UMR 5200, Villenave d'Ornon F-33140, France
| | - Magdalena Bezanilla
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA
| | - Miguel A Botella
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortifruticultura Subtropical y Mediterránea “La Mayora,” Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga 29071, Spain
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, Michigan 48824 USA
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824, USA
| | - Tessa M Burch-Smith
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Kent D Chapman
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, Texas 76203, USA
| | - Kai Dünser
- Faculty of Biology, Chair of Molecular Plant Physiology (MoPP) University of Freiburg, Freiburg 79104, Germany
- Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg 79104, Germany
| | - Yangnan Gu
- Department of Plant and Microbial Biology, Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes (RDP), Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France
| | - Helmut Kirchhoff
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, USA
| | - Marisa S Otegui
- Department of Botany and Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Wisconsin 53706, USA
| | - Abel Rosado
- Department of Botany, University of British Columbia, Vancouver V6T1Z4, Canada
| | - Yu Tang
- Department of Plant and Microbial Biology, Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Jürgen Kleine-Vehn
- Faculty of Biology, Chair of Molecular Plant Physiology (MoPP) University of Freiburg, Freiburg 79104, Germany
- Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg 79104, Germany
| | - Pengwei Wang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Bethany Karlin Zolman
- Department of Biology, University of Missouri, St. Louis, St. Louis, Missouri 63121, USA
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González-Gordo S, Palma JM, Corpas FJ. Peroxisomal Proteome Mining of Sweet Pepper ( Capsicum annuum L.) Fruit Ripening Through Whole Isobaric Tags for Relative and Absolute Quantitation Analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:893376. [PMID: 35615143 PMCID: PMC9125320 DOI: 10.3389/fpls.2022.893376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/21/2022] [Indexed: 05/05/2023]
Abstract
Peroxisomes are ubiquitous organelles from eukaryotic cells characterized by an active nitro-oxidative metabolism. They have a relevant metabolic plasticity depending on the organism, tissue, developmental stage, or physiological/stress/environmental conditions. Our knowledge of peroxisomal metabolism from fruits is very limited but its proteome is even less known. Using sweet pepper (Capsicum annuum L.) fruits at two ripening stages (immature green and ripe red), it was analyzed the proteomic peroxisomal composition by quantitative isobaric tags for relative and absolute quantitation (iTRAQ)-based protein profiling. For this aim, it was accomplished a comparative analysis of the pepper fruit whole proteome obtained by iTRAQ versus the identified peroxisomal protein profile from Arabidopsis thaliana. This allowed identifying 57 peroxisomal proteins. Among these proteins, 49 were located in the peroxisomal matrix, 36 proteins had a peroxisomal targeting signal type 1 (PTS1), 8 had a PTS type 2, 5 lacked this type of peptide signal, and 8 proteins were associated with the membrane of this organelle. Furthermore, 34 proteins showed significant differences during the ripening of the fruits, 19 being overexpressed and 15 repressed. Based on previous biochemical studies using purified peroxisomes from pepper fruits, it could be said that some of the identified peroxisomal proteins were corroborated as part of the pepper fruit antioxidant metabolism (catalase, superoxide dismutase, ascorbate peroxidase, monodehydroascorbate reductase, dehydroascorbate reductaseglutathione reductase, 6-phosphogluconate dehydrogenase and NADP-isocitrate dehydrogenase), the β-oxidation pathway (acyl-coenzyme A oxidase, 3-hydroxyacyl-CoA dehydrogenase, enoyl-CoA hydratase), while other identified proteins could be considered "new" or "unexpected" in fruit peroxisomes like urate oxidase (UO), sulfite oxidase (SO), 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase (METE1), 12-oxophytodienoate reductase 3 (OPR3) or 4-coumarate-CoA ligase (4CL), which participate in different metabolic pathways such as purine, sulfur, L-methionine, jasmonic acid (JA) or phenylpropanoid metabolisms. In summary, the present data provide new insights into the complex metabolic machinery of peroxisomes in fruit and open new windows of research into the peroxisomal functions during fruit ripening.
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Mehlhorn DG, Asseck LY, Grefen C. Looking for a safe haven: tail-anchored proteins and their membrane insertion pathways. PLANT PHYSIOLOGY 2021; 187:1916-1928. [PMID: 35235667 PMCID: PMC8644595 DOI: 10.1093/plphys/kiab298] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/05/2021] [Indexed: 06/14/2023]
Abstract
Insertion of membrane proteins into the lipid bilayer is a crucial step during their biosynthesis. Eukaryotic cells face many challenges in directing these proteins to their predestined target membrane. The hydrophobic signal peptide or transmembrane domain (TMD) of the nascent protein must be shielded from the aqueous cytosol and its target membrane identified followed by transport and insertion. Components that evolved to deal with each of these challenging steps range from chaperones to receptors, insertases, and sophisticated translocation complexes. One prominent translocation pathway for most proteins is the signal recognition particle (SRP)-dependent pathway which mediates co-translational translocation of proteins across or into the endoplasmic reticulum (ER) membrane. This textbook example of protein insertion is stretched to its limits when faced with secretory or membrane proteins that lack an amino-terminal signal sequence or TMD. Particularly, a large group of so-called tail-anchored (TA) proteins that harbor a single carboxy-terminal TMD require an alternative, post-translational insertion route into the ER membrane. In this review, we summarize the current research in TA protein insertion with a special focus on plants, address challenges, and highlight future research avenues.
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Affiliation(s)
- Dietmar G Mehlhorn
- Faculty of Biology and Biotechnology, Molecular and Cellular Botany, University of Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Lisa Y Asseck
- Faculty of Biology and Biotechnology, Molecular and Cellular Botany, University of Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Christopher Grefen
- Faculty of Biology and Biotechnology, Molecular and Cellular Botany, University of Bochum, Universitätsstraße 150, 44780 Bochum, Germany
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Calace P, Tonetti T, Margarit E, Figueroa CM, Lobertti C, Andreo CS, Gerrard Wheeler MC, Saigo M. The C4 cycle and beyond: diverse metabolic adaptations accompany dual-cell photosynthetic functions in Setaria. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7876-7890. [PMID: 34402880 DOI: 10.1093/jxb/erab381] [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: 04/05/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
C4 photosynthesis is typically characterized by the spatial compartmentalization of the photosynthetic reactions into mesophyll (M) and bundle sheath (BS) cells. Initial carbon fixation within M cells gives rise to C4 acids, which are transported to the BS cells. There, C4 acids are decarboxylated so that the resulting CO2 is incorporated into the Calvin cycle. This work is focused on the study of Setaria viridis, a C4 model plant, closely related to several major feed and bioenergy grasses. First, we performed the heterologous expression and biochemical characterization of Setaria isoforms for chloroplastic NADP-malic enzyme (NADP-ME) and mitochondrial NAD-malic enzyme (NAD-ME). The kinetic parameters obtained agree with a major role for NADP-ME in the decarboxylation of the C4 acid malate in the chloroplasts of BS cells. In addition, mitochondria-located NAD-ME showed regulatory properties that could be important in the context of the operation of the C4 carbon shuttle. Secondly, we compared the proteomes of M and BS compartments and found 825 differentially accumulated proteins that could support different metabolic scenarios. Most interestingly, we found evidence of metabolic strategies to insulate the C4 core avoiding the leakage of intermediates by either up-regulation or down-regulation of chloroplastic, mitochondrial, and peroxisomal proteins. Overall, the results presented in this work provide novel data concerning the complexity of C4 metabolism, uncovering future lines of research that will undoubtedly contribute to the expansion of knowledge on this topic.
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Affiliation(s)
- Paula Calace
- Grupo de Metabolismo del Carbono y Producción Vegetal, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Tomás Tonetti
- Instituto de Agrobiotecnología del Litoral (IAL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Ezequiel Margarit
- Grupo de Calidad de Frutos Cítricos, Bayas y Mejoramiento Forestal, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Carlos M Figueroa
- Instituto de Agrobiotecnología del Litoral (IAL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Carlos Lobertti
- Grupo de Metabolismo del Carbono y Producción Vegetal, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- Laboratorio de Patogénesis Bacteriana, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Centro Científico Tecnológico Rosario, Rosario, Argentina
| | - Carlos S Andreo
- Grupo de Metabolismo del Carbono y Producción Vegetal, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Mariel C Gerrard Wheeler
- Grupo de Metabolismo del Carbono y Producción Vegetal, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Mariana Saigo
- Grupo de Metabolismo del Carbono y Producción Vegetal, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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Sun Y, Wang X, Chen Z, Qin L, Li B, Ouyang L, Peng X, He H. Quantitative Proteomics and Transcriptomics Reveals Differences in Proteins During Anthers Development in Oryza longistaminata. FRONTIERS IN PLANT SCIENCE 2021; 12:744792. [PMID: 34868129 PMCID: PMC8640343 DOI: 10.3389/fpls.2021.744792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/22/2021] [Indexed: 06/07/2023]
Abstract
Oryza longistaminata is an African wild rice species that possesses special traits for breeding applications. Self-incompatibility is the main cause of sterility in O. longistaminata, but here we demonstrated that its pollen vitality are normal. Lipid and carbohydrate metabolism were active throughout pollen development. In this study, we used I2-KI staining and TTC staining to investigate pollen viability. Aniline-blue-stained semithin sections were used to investigate important stages of pollen development. Tandem mass tags (TMT)-based quantitative analysis was used to investigate the profiles of proteins related to lipid and carbohydrate metabolism in 4-, 6-, and 8.5-mm O. longistaminata spikelets before flowering. Pollen was found to germinate normally in vitro and in vivo. We documented cytological changes throughout important stages of anther development, including changes in reproductive cells as they formed mature pollen grains through meiosis and mitosis. A total of 31,987 RNA transcripts and 8,753 proteins were identified, and 6,842 of the proteins could be quantified. RNA-seq and proteome association analysis indicated that fatty acids were converted to sucrose after the 6-mm spikelet stage, based on the abundance of most key enzymes of the glyoxylate cycle and gluconeogenesis. The abundance of proteins involved in pollen energy metabolism was further confirmed by combining quantitative real-time PCR with parallel reaction monitoring (PRM) analyses. In conclusion, our study provides novel insights into the pollen viability of O. longistaminata at the proteome level, which can be used to improve the efficiency of male parent pollination in hybrid rice breeding applications.
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Rehman NU, Zeng P, Mo Z, Guo S, Liu Y, Huang Y, Xie Q. Conserved and Diversified Mechanism of Autophagy between Plants and Animals upon Various Stresses. Antioxidants (Basel) 2021; 10:1736. [PMID: 34829607 PMCID: PMC8615172 DOI: 10.3390/antiox10111736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 01/01/2023] Open
Abstract
Autophagy is a highly conserved degradation mechanism in eukaryotes, executing the breakdown of unwanted cell components and subsequent recycling of cellular material for stress relief through vacuole-dependence in plants and yeast while it is lysosome-dependent in animal manner. Upon stress, different types of autophagy are stimulated to operate certain biological processes by employing specific selective autophagy receptors (SARs), which hijack the cargo proteins or organelles to the autophagy machinery for subsequent destruction in the vacuole/lysosome. Despite recent advances in autophagy, the conserved and diversified mechanism of autophagy in response to various stresses between plants and animals still remain a mystery. In this review, we intend to summarize and discuss the characterization of the SARs and their corresponding processes, expectantly advancing the scope and perspective of the evolutionary fate of autophagy between plants and animals.
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Affiliation(s)
- Naveed Ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (N.U.R.); (P.Z.); (Z.M.); (S.G.)
| | - Peichun Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (N.U.R.); (P.Z.); (Z.M.); (S.G.)
| | - Zulong Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (N.U.R.); (P.Z.); (Z.M.); (S.G.)
| | - Shaoying Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (N.U.R.); (P.Z.); (Z.M.); (S.G.)
| | - Yunfeng Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences and Technology, Guangxi University, Nanning 530004, China;
| | - Yifeng Huang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou 310001, China
| | - Qingjun Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (N.U.R.); (P.Z.); (Z.M.); (S.G.)
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Metabolomics for Crop Breeding: General Considerations. Genes (Basel) 2021; 12:genes12101602. [PMID: 34680996 PMCID: PMC8535592 DOI: 10.3390/genes12101602] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 12/16/2022] Open
Abstract
The development of new, more productive varieties of agricultural crops is becoming an increasingly difficult task. Modern approaches for the identification of beneficial alleles and their use in elite cultivars, such as quantitative trait loci (QTL) mapping and marker-assisted selection (MAS), are effective but insufficient for keeping pace with the improvement of wheat or other crops. Metabolomics is a powerful but underutilized approach that can assist crop breeding. In this review, basic methodological information is summarized, and the current strategies of applications of metabolomics related to crop breeding are explored using recent examples. We briefly describe classes of plant metabolites, cellular localization of metabolic pathways, and the strengths and weaknesses of the main metabolomics technique. Among the commercialized genetically modified crops, about 50 with altered metabolic enzyme activities have been identified in the International Service for the Acquisition of Agri-biotech Applications (ISAAA) database. These plants are reviewed as encouraging examples of the application of knowledge of biochemical pathways. Based on the recent examples of metabolomic studies, we discuss the performance of metabolic markers, the integration of metabolic and genomic data in metabolic QTLs (mQTLs) and metabolic genome-wide association studies (mGWAS). The elucidation of metabolic pathways and involved genes will help in crop breeding and the introgression of alleles of wild relatives in a more targeted manner.
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Piacentini D, Della Rovere F, Bertoldi I, Massimi L, Sofo A, Altamura MM, Falasca G. Peroxisomal PEX7 Receptor Affects Cadmium-Induced ROS and Auxin Homeostasis in Arabidopsis Root System. Antioxidants (Basel) 2021; 10:antiox10091494. [PMID: 34573126 PMCID: PMC8471170 DOI: 10.3390/antiox10091494] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/15/2021] [Accepted: 09/15/2021] [Indexed: 12/18/2022] Open
Abstract
Peroxisomes are important in plant physiological functions and stress responses. Through the production of reactive oxygen and nitrogen species (ROS and RNS), and antioxidant defense enzymes, peroxisomes control cellular redox homeostasis. Peroxin (PEX) proteins, such as PEX7 and PEX5, recognize peroxisome targeting signals (PTS1/PTS2) important for transporting proteins from cytosol to peroxisomal matrix. pex7-1 mutant displays reduced PTS2 protein import and altered peroxisomal metabolism. In this research we analyzed the role of PEX7 in the Arabidopsis thaliana root system exposed to 30 or 60 μM CdSO4. Cd uptake and translocation, indole-3-acetic acid (IAA) and indole-3-butyric acid (IBA) levels, and reactive oxygen species (ROS) and reactive nitrogen species (RNS) levels and catalase activity were analyzed in pex7-1 mutant primary and lateral roots in comparison with the wild type (wt). The peroxisomal defect due to PEX7 mutation did not reduce Cd-uptake but reduced its translocation to the shoot and the root cell peroxisomal signal detected by 8-(4-Nitrophenyl) Bodipy (N-BODIPY) probe. The trend of nitric oxide (NO) and peroxynitrite in pex7-1 roots, exposed/not exposed to Cd, was as in wt, with the higher Cd-concentration inducing higher levels of these RNS. By contrast, PEX7 mutation caused changes in Cd-induced hydrogen peroxide (H2O2) and superoxide anion (O2●-) levels in the roots, delaying ROS-scavenging. Results show that PEX7 is involved in counteracting Cd toxicity in Arabidopsis root system by controlling ROS metabolism and affecting auxin levels. These results add further information to the important role of peroxisomes in plant responses to Cd.
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Affiliation(s)
- Diego Piacentini
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (D.P.); (F.D.R.); (I.B.); (L.M.); (M.M.A.)
| | - Federica Della Rovere
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (D.P.); (F.D.R.); (I.B.); (L.M.); (M.M.A.)
| | - Ilaria Bertoldi
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (D.P.); (F.D.R.); (I.B.); (L.M.); (M.M.A.)
| | - Lorenzo Massimi
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (D.P.); (F.D.R.); (I.B.); (L.M.); (M.M.A.)
| | - Adriano Sofo
- Department of European and Mediterranean Cultures: Architecture, Environment, and Cultural Heritage (DICEM), University of Basilicata, Via San Rocco 3, 75100 Matera, Italy;
| | - Maria Maddalena Altamura
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (D.P.); (F.D.R.); (I.B.); (L.M.); (M.M.A.)
| | - Giuseppina Falasca
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (D.P.); (F.D.R.); (I.B.); (L.M.); (M.M.A.)
- Correspondence: ; Tel.: +39-(0)6-4992-2839
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Levis NA, Kelly PW, Harmon EA, Ehrenreich IM, McKay DJ, Pfennig DW. Transcriptomic bases of a polyphenism. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 336:482-495. [PMID: 34142757 DOI: 10.1002/jez.b.23066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 03/22/2021] [Accepted: 05/22/2021] [Indexed: 11/06/2022]
Abstract
Polyphenism-in which multiple distinct phenotypes are produced from a single genotype owing to differing environmental conditions-is commonplace, but its molecular bases are poorly understood. Here, we examine the transcriptomic bases of a polyphenism in Mexican spadefoot toads (Spea multiplicata). Depending on their environment, their tadpoles develop into either a default "omnivore" morph or a novel "carnivore" morph. We compared patterns of gene expression among sibships that exhibited high versus low production of carnivores when reared in conditions that induce the carnivore morph versus those that do not. We found that production of the novel carnivore morph actually involved changes in fewer genes than did the maintenance of the default omnivore morph in the inducing environment. However, only body samples showed this pattern; head samples showed the opposite pattern. We also found that changes to lipid metabolism (especially cholesterol biosynthesis) and peroxisome contents and function might be crucial for establishing and maintaining differences between the morphs. Thus, our findings suggest that carnivore phenotype might have originally evolved following the breakdown of robustness mechanisms that maintain the default omnivore phenotype, and that the carnivore morph is developmentally regulated by lipid metabolism and peroxisomal form, function, and/or signaling. This study also serves as a springboard for further exploration into the nature and causes of plasticity in an emerging model system.
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Affiliation(s)
- Nicholas A Levis
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA.,Current affiliation: Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Patrick W Kelly
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Emily A Harmon
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Ian M Ehrenreich
- Molecular and Computational Biology Section, University of Southern, Los Angeles, California, USA
| | - Daniel J McKay
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - David W Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
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50
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Emenecker RJ, Holehouse AS, Strader LC. Biological Phase Separation and Biomolecular Condensates in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:17-46. [PMID: 33684296 PMCID: PMC8221409 DOI: 10.1146/annurev-arplant-081720-015238] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A surge in research focused on understanding the physical principles governing the formation, properties, and function of membraneless compartments has occurred over the past decade. Compartments such as the nucleolus, stress granules, and nuclear speckles have been designated as biomolecular condensates to describe their shared property of spatially concentrating biomolecules. Although this research has historically been carried out in animal and fungal systems, recent work has begun to explore whether these same principles are relevant in plants. Effectively understanding and studying biomolecular condensates require interdisciplinary expertise that spans cell biology, biochemistry, and condensed matter physics and biophysics. As such, some involved concepts may be unfamiliar to any given individual. This review focuses on introducing concepts essential to the study of biomolecular condensates and phase separation for biologists seeking to carry out research in this area and further examines aspects of biomolecular condensates that are relevant to plant systems.
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Affiliation(s)
- Ryan J Emenecker
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
- Center for Science and Engineering of Living Systems, Washington University, St. Louis, Missouri 63130, USA
- Center for Engineering MechanoBiology, Washington University, St. Louis, Missouri 63130, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
- Center for Science and Engineering of Living Systems, Washington University, St. Louis, Missouri 63130, USA
| | - Lucia C Strader
- Center for Science and Engineering of Living Systems, Washington University, St. Louis, Missouri 63130, USA
- Center for Engineering MechanoBiology, Washington University, St. Louis, Missouri 63130, USA
- Department of Biology, Duke University, Durham, North Carolina 27708, USA;
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