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Redox Signaling in Plant Heat Stress Response. Antioxidants (Basel) 2023; 12:antiox12030605. [PMID: 36978852 PMCID: PMC10045013 DOI: 10.3390/antiox12030605] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
The increase in environmental temperature due to global warming is a critical threat to plant growth and productivity. Heat stress can cause impairment in several biochemical and physiological processes. Plants sense and respond to this adverse environmental condition by activating a plethora of defense systems. Among them, the heat stress response (HSR) involves an intricate network of heat shock factors (HSFs) and heat shock proteins (HSPs). However, a growing amount of evidence suggests that reactive oxygen species (ROS), besides potentially being responsible for cellular oxidative damage, can act as signal molecules in HSR, leading to adaptative responses. The role of ROS as toxic or signal molecules depends on the fine balance between their production and scavenging. Enzymatic and non-enzymatic antioxidants represent the first line of defense against oxidative damage and their activity is critical to maintaining an optimal redox environment. However, the HS-dependent ROS burst temporarily oxidizes the cellular environment, triggering redox-dependent signaling cascades. This review provides an overview of the redox-activated mechanisms that participate in the HSR.
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Martí-Guillén JM, Pardo-Hernández M, Martínez-Lorente SE, Almagro L, Rivero RM. Redox post-translational modifications and their interplay in plant abiotic stress tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:1027730. [PMID: 36388514 PMCID: PMC9644032 DOI: 10.3389/fpls.2022.1027730] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/10/2022] [Indexed: 05/27/2023]
Abstract
The impact of climate change entails a progressive and inexorable modification of the Earth's climate and events such as salinity, drought, extreme temperatures, high luminous intensity and ultraviolet radiation tend to be more numerous and prolonged in time. Plants face their exposure to these abiotic stresses or their combination through multiple physiological, metabolic and molecular mechanisms, to achieve the long-awaited acclimatization to these extreme conditions, and to thereby increase their survival rate. In recent decades, the increase in the intensity and duration of these climatological events have intensified research into the mechanisms behind plant tolerance to them, with great advances in this field. Among these mechanisms, the overproduction of molecular reactive species stands out, mainly reactive oxygen, nitrogen and sulfur species. These molecules have a dual activity, as they participate in signaling processes under physiological conditions, but, under stress conditions, their production increases, interacting with each other and modifying and-or damaging the main cellular components: lipids, carbohydrates, nucleic acids and proteins. The latter have amino acids in their sequence that are susceptible to post-translational modifications, both reversible and irreversible, through the different reactive species generated by abiotic stresses (redox-based PTMs). Some research suggests that this process does not occur randomly, but that the modification of critical residues in enzymes modulates their biological activity, being able to enhance or inhibit complete metabolic pathways in the process of acclimatization and tolerance to the exposure to the different abiotic stresses. Given the importance of these PTMs-based regulation mechanisms in the acclimatization processes of plants, the present review gathers the knowledge generated in recent years on this subject, delving into the PTMs of the redox-regulated enzymes of plant metabolism, and those that participate in the main stress-related pathways, such as oxidative metabolism, primary metabolism, cell signaling events, and photosynthetic metabolism. The aim is to unify the existing information thus far obtained to shed light on possible fields of future research in the search for the resilience of plants to climate change.
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Affiliation(s)
- José M. Martí-Guillén
- Department of Plant Nutrition, Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas, Murcia, Spain
- Department of Plant Biology, Faculty of Biology, University of Murcia, Murcia, Spain
| | - Miriam Pardo-Hernández
- Department of Plant Nutrition, Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas, Murcia, Spain
| | - Sara E. Martínez-Lorente
- Department of Plant Nutrition, Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas, Murcia, Spain
| | - Lorena Almagro
- Department of Plant Biology, Faculty of Biology, University of Murcia, Murcia, Spain
| | - Rosa M. Rivero
- Department of Plant Nutrition, Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas, Murcia, Spain
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3
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Zeng M, He S, Hao J, Zhao Y, Zheng C. iTRAQ-based proteomic analysis of heteromorphic leaves reveals eco-adaptability of Populus euphratica Oliv. JOURNAL OF PLANT PHYSIOLOGY 2022; 271:153644. [PMID: 35219031 DOI: 10.1016/j.jplph.2022.153644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 01/28/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Heterophylly is regard as adaptation to different environments in plant, and Populus euphratica is an important heterophyllous woody plant. However, information on its molecular mechanism in eco-adaptability remains obscure. RESULTS In this research, proteins were identified by isobaric tags for relative and absolute quantitation (iTRAQ) technology in lanceolate, ovate, and dentate broad-ovate leaves from adult P. euphratica trees, respectively. Besides, chlorophyll content, net photosynthetic rate, stomatal conductance, transpiration rate and peroxidase activity in these heteromorphic leaves were investigated. A total number of 2,689 proteins were detected in the heteromorphic leaves, of which 56, 73, and 222 differential abundance proteins (DAPs) were determined in ovate/lanceolate, dentate broad-ovate/lanceolate, and dentate broad-ovate/ovate comparison groups. Bioinformatics analysis suggested these altered proteins related to photosynthesis, stress tolerance, respiration and primary metabolism accumulated in dentate broad-ovate and ovate leaves, which were consistent with the results of physiological parameters and Real-time Quantitative PCR experiments. CONCLUSION This research demonstrated the mechanism of the differential abundance proteins in providing an optimal strategy of resource utilization and survival for P. euphratica, that could offer clues for further investigations into eco-adaptability of heterophyllous woody plants.
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Affiliation(s)
- Ming Zeng
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qing Hua Dong Lu, Beijing, 100083, China; Guangdong Academy of Forestry, Guangzhou, 510520, China.
| | - Shuhang He
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qing Hua Dong Lu, Beijing, 100083, China.
| | - Jianqing Hao
- School of Basic Medical Sciences, Shanxi Medical University, No. 56 Xinjian Nan Lu, Taiyuan, 030001, China.
| | - Yuanyuan Zhao
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qing Hua Dong Lu, Beijing, 100083, China.
| | - Caixia Zheng
- College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qing Hua Dong Lu, Beijing, 100083, China.
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4
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Kerchev PI, Van Breusegem F. Improving oxidative stress resilience in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:359-372. [PMID: 34519111 DOI: 10.1111/tpj.15493] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/02/2021] [Accepted: 09/08/2021] [Indexed: 05/22/2023]
Abstract
Originally conceived as harmful metabolic byproducts, reactive oxygen species (ROS) are now recognized as an integral part of numerous cellular programs. Thanks to their diverse physicochemical properties, compartmentalized production, and tight control exerted by the antioxidant machinery they activate signaling pathways that govern plant growth, development, and defense. Excessive ROS levels are often driven by adverse changes in environmental conditions, ultimately causing oxidative stress. The associated negative impact on cellular constituents have been a major focus of decade-long research efforts to improve the oxidative stress resilience by boosting the antioxidant machinery in model and crop species. We highlight the role of enzymatic and non-enzymatic antioxidants as integral factors of multiple signaling cascades beyond their mere function to prevent oxidative damage under adverse abiotic stress conditions.
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Affiliation(s)
- Pavel I Kerchev
- Phytophthora Research Centre, Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300, Brno, Czech Republic
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Gent, Belgium
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5
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Abstract
Biochemical analysis is crucial for determining protein functionality changes during various conditions, including oxidative stress conditions. In this chapter, after giving brief guidelines for experimental design, we provide step-by-step instructions to purify recombinant plant proteins from E. coli, to prepare reduced and oxidized proteins for activity assay, and to characterize the protein under reducing and oxidizing conditions, with a focus on thiol-based oxidative modifications, like S-sulfenylation and disulfide formations.
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Affiliation(s)
- Zeya Chen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Jingjing Huang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- Center for Plant Systems Biology, VIB, Ghent, Belgium.
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Castro B, Citterico M, Kimura S, Stevens DM, Wrzaczek M, Coaker G. Stress-induced reactive oxygen species compartmentalization, perception and signalling. NATURE PLANTS 2021; 7:403-412. [PMID: 33846592 PMCID: PMC8751180 DOI: 10.1038/s41477-021-00887-0] [Citation(s) in RCA: 145] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 02/24/2021] [Indexed: 05/19/2023]
Abstract
Reactive oxygen species (ROS) are essential for life and are involved in the regulation of almost all biological processes. ROS production is critical for plant development, response to abiotic stresses and immune responses. Here, we focus on recent discoveries in ROS biology emphasizing abiotic and biotic stress responses. Recent advancements have resulted in the identification of one of the first sensors for extracellular ROS and highlighted waves of ROS production during stress signalling in Arabidopsis. Enzymes that produce ROS, including NADPH oxidases, exhibit precise regulation through diverse post-translational modifications. Discoveries highlight the importance of both amino- and carboxy-terminal regulation of NADPH oxidases through protein phosphorylation and cysteine oxidation. Here, we discuss advancements in ROS compartmentalization, systemic ROS waves, ROS sensing and post-translational modification of ROS-producing enzymes and identify areas where foundational gaps remain.
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Affiliation(s)
- Bardo Castro
- Department of Plant Pathology, University of California, Davis, Davis, CA, USA
| | - Matteo Citterico
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Sachie Kimura
- Ritsumeikan Global Innovation Research Organization, Ritsumeikan University, Kusatsu, Japan
| | - Danielle M Stevens
- Department of Plant Pathology, University of California, Davis, Davis, CA, USA
| | - Michael Wrzaczek
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
- Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, Davis, CA, USA.
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Mukherjee S. Cysteine modifications (oxPTM) and protein sulphenylation-mediated sulfenome expression in plants: evolutionary conserved signaling networks? PLANT SIGNALING & BEHAVIOR 2021; 16:1831792. [PMID: 33300450 PMCID: PMC7781837 DOI: 10.1080/15592324.2020.1831792] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Plant resilience to oxidative stress possibly operates through the restoration of intracellular redox milieu and the activity of various posttranslationally modified proteins. Among various modes of redox regulation operative in plants cys oxPTMs are brought about by the activity of reactive oxygen species (ROS), reactive nitrogen species (RNS), and hydrogen peroxide. Cysteine oxPTMs are capable of transducing ROS-mediated long-distance hormone signaling (ABA, JA, SA) in plants. S-sulphenylation is an intermediary modification en route to other oxidative states of cysteine. In silico analysis have revealed evolutionary conservation of certain S-sulphenylated proteins across human and plants. Further analysis of protein sulphenylation in plants should be extended to the functional follow-up studies followed by site-specific characterization and case-by-case validation of protein activity. The repertoire of physiological methods (fluorescent conjugates (dimedone) and yeast AP-1 (YAP1)-based genetic probes) in the recent past has been successful in the detection of sulphenylated proteins and other cysteine-based modifications in plants. In view of a better understanding of the sulfur-based redoxome it is necessary to update our timely progress on the methodological advancements for the detection of cysteine-based oxPTM. This substantiative information can extend our investigations on plant-environment interaction thus improving crop manipulation strategies. The simulation-based computational approach has emerged as a new method to determine the directive mechanism of cysteine oxidation in plants. Thus, sulfenome analysis in various plant systems might reflect as a pinnacle of plant redox biology in the future.
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Affiliation(s)
- Soumya Mukherjee
- Department of Botany, Jangipur College, University of Kalyani, West, Bengal, India
- CONTACT Soumya Mukherjee Department of Botany, Jangipur College, University of Kalyani, West, Bengal742213, India
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Integration of MsrB1 and MsrB2 in the Redox Network during the Development of Orthodox and Recalcitrant Acer Seeds. Antioxidants (Basel) 2020; 9:antiox9121250. [PMID: 33316974 PMCID: PMC7763665 DOI: 10.3390/antiox9121250] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023] Open
Abstract
Two related tree species, Norway maple (Acer platanoides L.) and sycamore (Acer pseudoplatanus L.), produce desiccation-tolerant (orthodox) and desiccation-sensitive (recalcitrant) seeds, respectively. We compared the seeds of these two species to characterize the developmentally driven changes in the levels of peptide-bound methionine sulfoxide (MetO) and the abundance of methionine sulfoxide reductases (Msrs) B1 and B2, with respect to the cellular redox environment. Protein oxidation at the Met level was dynamic only in Norway maple seeds, and the reduced MsrB2 form was detected only in this species. Cell redox status, characterized by the levels of reduced and oxidized ascorbate, glutathione, and nicotinamide adenine dinucleotide (NAD)/phosphate (NADP), was clearly more reduced in the Norway maple seeds than in the sycamore seeds. Clear correlations between MetO levels, changes in water content and redox status were reported in orthodox Acer seeds. The abundance of Msrs was correlated in both species with redox determinants, mainly ascorbate and glutathione. Our data suggest that MsrB2 is associated with the acquisition of desiccation tolerance and that ascorbate might be involved in the redox pathway enabling the regeneration of Msr via intermediates that are not known yet.
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9
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Veredas FJ, Urda D, Subirats JL, Cantón FR, Aledo JC. Combining feature engineering and feature selection to improve the prediction of methionine oxidation sites in proteins. Neural Comput Appl 2020. [DOI: 10.1007/s00521-018-3655-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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10
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Farooq MA, Niazi AK, Akhtar J, Farooq M, Souri Z, Karimi N, Rengel Z. Acquiring control: The evolution of ROS-Induced oxidative stress and redox signaling pathways in plant stress responses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 141:353-369. [PMID: 31207496 DOI: 10.1016/j.plaphy.2019.04.039] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/23/2019] [Accepted: 04/30/2019] [Indexed: 05/18/2023]
Abstract
Reactive oxygen species (ROS) - the byproducts of aerobic metabolism - influence numerous aspects of the plant life cycle and environmental response mechanisms. In plants, ROS act like a double-edged sword; they play multiple beneficial roles at low concentrations, whereas at high concentrations ROS and related redox-active compounds cause cellular damage through oxidative stress. To examine the dual role of ROS as harmful oxidants and/or crucial cellular signals, this review elaborates that (i) how plants sense and respond to ROS in various subcellular organelles and (ii) the dynamics of subsequent ROS-induced signaling processes. The recent understanding of crosstalk between various cellular compartments in mediating their redox state spatially and temporally is discussed. Emphasis on the beneficial effects of ROS in maintaining cellular energy homeostasis, regulating diverse cellular functions, and activating acclimation responses in plants exposed to abiotic and biotic stresses are described. The comprehensive view of cellular ROS dynamics covering the breadth and versatility of ROS will contribute to understanding the complexity of apparently contradictory ROS roles in plant physiological responses in less than optimum environments.
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Affiliation(s)
- Muhammad Ansar Farooq
- Institute of Soil & Environmental Sciences, University of Agriculture, Faisalabad, Pakistan.
| | - Adnan Khan Niazi
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Javaid Akhtar
- Institute of Soil & Environmental Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Farooq
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Oman
| | - Zahra Souri
- Laboratory of Plant Physiology, Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | - Naser Karimi
- Laboratory of Plant Physiology, Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | - Zed Rengel
- School of Agriculture and Environment, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
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11
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Zaffagnini M, Fermani S, Marchand CH, Costa A, Sparla F, Rouhier N, Geigenberger P, Lemaire SD, Trost P. Redox Homeostasis in Photosynthetic Organisms: Novel and Established Thiol-Based Molecular Mechanisms. Antioxid Redox Signal 2019; 31:155-210. [PMID: 30499304 DOI: 10.1089/ars.2018.7617] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Significance: Redox homeostasis consists of an intricate network of reactions in which reactive molecular species, redox modifications, and redox proteins act in concert to allow both physiological responses and adaptation to stress conditions. Recent Advances: This review highlights established and novel thiol-based regulatory pathways underlying the functional facets and significance of redox biology in photosynthetic organisms. In the last decades, the field of redox regulation has largely expanded and this work is aimed at giving the right credit to the importance of thiol-based regulatory and signaling mechanisms in plants. Critical Issues: This cannot be all-encompassing, but is intended to provide a comprehensive overview on the structural/molecular mechanisms governing the most relevant thiol switching modifications with emphasis on the large genetic and functional diversity of redox controllers (i.e., redoxins). We also summarize the different proteomic-based approaches aimed at investigating the dynamics of redox modifications and the recent evidence that extends the possibility to monitor the cellular redox state in vivo. The physiological relevance of redox transitions is discussed based on reverse genetic studies confirming the importance of redox homeostasis in plant growth, development, and stress responses. Future Directions: In conclusion, we can firmly assume that redox biology has acquired an established significance that virtually infiltrates all aspects of plant physiology.
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Affiliation(s)
- Mirko Zaffagnini
- 1 Department of Pharmacy and Biotechnology and University of Bologna, Bologna, Italy
| | - Simona Fermani
- 2 Department of Chemistry Giacomo Ciamician, University of Bologna, Bologna, Italy
| | - Christophe H Marchand
- 3 Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226, Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Sorbonne Université, Paris, France
| | - Alex Costa
- 4 Department of Biosciences, University of Milan, Milan, Italy
| | - Francesca Sparla
- 1 Department of Pharmacy and Biotechnology and University of Bologna, Bologna, Italy
| | | | - Peter Geigenberger
- 6 Department Biologie I, Ludwig-Maximilians-Universität München, LMU Biozentrum, Martinsried, Germany
| | - Stéphane D Lemaire
- 3 Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226, Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Sorbonne Université, Paris, France
| | - Paolo Trost
- 1 Department of Pharmacy and Biotechnology and University of Bologna, Bologna, Italy
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12
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Tan K, Huang Z, Ji R, Qiu Y, Wang Z, Liu J. A review of allelopathy on microalgae. MICROBIOLOGY-SGM 2019; 165:587-592. [PMID: 30688632 DOI: 10.1099/mic.0.000776] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Algal blooms have severe impacts on the utilization of water resources. The discovery of allelopathy provides a new dimension to solving this problem due to its high efficiency, safety and economy. Allelopathy can suppress the growth of microalgae by impairing the structure, photosynthesis and enzyme activity of algal cells. In the current work, we first demonstrate the allelopathy and allelochemicals derived from both plants and algae. We then expound the potential mechanisms of allelopathy on microalgae. Next, the potential application of allelochemicals in water environment is proposed. Finally, the key challenge and future perspective are presented.
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Affiliation(s)
- Kaiting Tan
- School of Civil and Transportation Engineering, Guangdong University of Technology, Guangzhou 510006, PR China
| | - Ziqi Huang
- School of Civil and Transportation Engineering, Guangdong University of Technology, Guangzhou 510006, PR China
| | - Ruibo Ji
- School of Civil and Transportation Engineering, Guangdong University of Technology, Guangzhou 510006, PR China
| | - Yongting Qiu
- School of Civil and Transportation Engineering, Guangdong University of Technology, Guangzhou 510006, PR China
| | - Zhihong Wang
- School of Civil and Transportation Engineering, Guangdong University of Technology, Guangzhou 510006, PR China
| | - Junxia Liu
- School of Civil and Transportation Engineering, Guangdong University of Technology, Guangzhou 510006, PR China
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13
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Neves DM, Santana-Vieira DDS, Dória MS, Freschi L, Ferreira CF, Soares Filho WDS, Costa MGC, Coelho Filho MA, Micheli F, Gesteira ADS. Recurrent water deficit causes alterations in the profile of redox proteins in citrus plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 132:497-507. [PMID: 30292982 DOI: 10.1016/j.plaphy.2018.09.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 06/08/2023]
Abstract
Plant acclimation to recurrent stress involves profound alterations in multiple genetic, metabolic and physiological processes. Stressful conditions usually implicate imbalance in reactive oxygen species (ROS) production and removal rates, which may lead to oxidative stress. However, the primary cellular targets of oxidative stress and their relevance in plant acclimation to abiotic stresses remains poorly characterized. By comparing redox proteomic and sugar profiles in citrus Valencia (VO) scions grafted onto two rootstocks with different soil water extraction capacities - Rangpur Lime (RL) and Sunki Maravilha (SM) - here we demonstrate that both ROS-mediated post-translational protein modification and changes in sugar composition are associated with acclimation to recurrent drought in citrus. The redox proteomic analysis of the distinct scion/rootstock combinations exposed to one (WD1), two (WD2) or three (WD3) water deficit episodes revealed a total of 32 and 55 redox protein spots present in VO/RL and VO/SM plants, respectively. Mass spectrometry analysis of these protein spots revealed essential targets of ROS-mediated posttranslational protein modification in citrus plants challenged by recurrent drought. The oxidation of cysteine thiol groups into glyceraldehyde 3-phosphate dehydrogenase (GAPDH) was shown to increase in WD3 samples of the VO/RL combination, whereas the opposite was observed for the VO/SM combination. Similarly, recurrent drought promoted the oxidation of catalase thiol groups in VO/SM, but not in VO/RL. Carbohydrate profiling revealed that glucose, fructose and galactose may also contribute to the phenotypic differences observed between the citrus genotypes exposed to drought. These findings reveal for the first time that recurrent drought differentially affects the profile of redox proteomics of citrus, suggesting that this alteration may be part of the stress memory in perennial plants.
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Affiliation(s)
- Diana Matos Neves
- Departamento de Ciências Biológicas, Centro de Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | | | - Milena Santos Dória
- Departamento de Ciências Biológicas, Centro de Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - Luciano Freschi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Marcio Gilberto Cardoso Costa
- Departamento de Ciências Biológicas, Centro de Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | | | - Fabienne Micheli
- Departamento de Ciências Biológicas, Centro de Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil; CIRAD -UMR AGAP, Montpellier, France
| | - Abelmon da Silva Gesteira
- Departamento de Ciências Biológicas, Centro de Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil; Embrapa - Mandioca e Fruticultura, Cruz das Almas, Bahia, Brazil.
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14
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Takahashi M, Morikawa H. A novel role for PsbO1 in photosynthetic electron transport as suggested by its light-triggered selective nitration in Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2018; 13:e1513298. [PMID: 30230951 PMCID: PMC6259825 DOI: 10.1080/15592324.2018.1513298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 06/08/2023]
Abstract
Exposure of Arabidopsis leaves to nitrogen dioxide (NO2) results in the selective nitration of specific proteins, such as PsbO1. The 9th tyrosine residue (9Tyr) of PsbO1 has been identified as the nitration site. This nitration is triggered by light and inhibited by photosynthetic electron transport inhibitors. During protein nitration, tyrosyl and NO2 radicals are formed concurrently and combine rapidly to form 3-nitrotyrosine. A selective oxidation mechanism for 9Tyr of PsbO1 is required. We postulated that, similar to 161Tyr of D1, 9Tyr of PsbO1 is selectively photo-oxidized by photosynthetic electron transport in response to illumination to a tyrosyl radical. In corroboration, after reappraising our oxygen evolution analysis, the nitration of PsbO1 proved responsible for decreased oxygen evolution from the thylakoid membranes. NO2 is reportedly taken into cells as nitrous acid, which dissociates to form NO2-. NO2- may be oxidized into NO2 by the oxygen-evolving complex. Light may synchronize this reaction with tyrosyl radical formation. These findings suggest a novel role for PsbO1 in photosynthetic electron transport.
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Affiliation(s)
- Misa Takahashi
- Department of Mathematical and Life Sciences, Hiroshima University, Higashi-Hiroshima, Japan
| | - Hiromichi Morikawa
- Department of Mathematical and Life Sciences, Hiroshima University, Higashi-Hiroshima, Japan
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15
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Czarnocka W, Karpiński S. Friend or foe? Reactive oxygen species production, scavenging and signaling in plant response to environmental stresses. Free Radic Biol Med 2018; 122:4-20. [PMID: 29331649 DOI: 10.1016/j.freeradbiomed.2018.01.011] [Citation(s) in RCA: 274] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/17/2017] [Accepted: 01/09/2018] [Indexed: 01/11/2023]
Abstract
In the natural environment, plants are exposed to a variety of biotic and abiotic stress conditions that trigger rapid changes in the production and scavenging of reactive oxygen species (ROS). The production and scavenging of ROS is compartmentalized, which means that, depending on stimuli type, they can be generated and eliminated in different cellular compartments such as the apoplast, plasma membrane, chloroplasts, mitochondria, peroxisomes, and endoplasmic reticulum. Although the accumulation of ROS is generally harmful to cells, ROS play an important role in signaling pathways that regulate acclimatory and defense responses in plants, such as systemic acquired acclimation (SAA) and systemic acquired resistance (SAR). However, high accumulations of ROS can also trigger redox homeostasis disturbance which can lead to cell death, and in consequence, to a limitation in biomass and yield production. Different ROS have various half-lifetimes and degrees of reactivity toward molecular components such as lipids, proteins, and nucleic acids. Thus, they play different roles in intra- and extra-cellular signaling. Despite their possible damaging effect, ROS should mainly be considered as signaling molecules that regulate local and systemic acclimatory and defense responses. Over the past two decades it has been proven that ROS together with non-photochemical quenching (NPQ), hormones, Ca2+ waves, and electrical signals are the main players in SAA and SAR, two physiological processes essential for plant survival and productivity in unfavorable conditions.
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Affiliation(s)
- Weronika Czarnocka
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences (SGGW), Nowoursynowska Street 159, 02-776 Warsaw, Poland; Department of Botany, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska Street 159, 02-776 Warsaw, Poland
| | - Stanisław Karpiński
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences (SGGW), Nowoursynowska Street 159, 02-776 Warsaw, Poland; The Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute, Radzików, 05-870 Błonie, Poland.
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Corpas FJ, Freschi L, Rodríguez-Ruiz M, Mioto PT, González-Gordo S, Palma JM. Nitro-oxidative metabolism during fruit ripening. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3449-3463. [PMID: 29304200 DOI: 10.1093/jxb/erx453] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 12/03/2017] [Indexed: 05/21/2023]
Abstract
Pepper (Capsicum annuum L.) and tomato (Solanum lycopersicum L.), which belong to the Solanaceae family, are among the most cultivated and consumed fleshy fruits worldwide and constitute excellent sources of many essential nutrients, such as vitamins A, C, and E, calcium, and carotenoids. While fruit ripening is a highly regulated and complex process, tomato and pepper have been classified as climacteric and non-climacteric fruits, respectively. These fruits differ greatly in shape, color composition, flavor, and several other features which undergo drastic changes during the ripening process. Such ripening-related metabolic and developmental changes require extensive alterations in many cellular and biochemical processes, which ultimately leads to fully ripe fruits with nutritional and organoleptic features that are attractive to both natural dispersers and human consumers. Recent data show that reactive oxygen and nitrogen species (ROS/RNS) are involved in fruit ripening, during which molecules, such as hydrogen peroxide (H2O2), NADPH, nitric oxide (NO), peroxynitrite (ONOO-), and S-nitrosothiols (SNOs), interact to regulate protein functions through post-translational modifications. In light of these recent discoveries, this review provides an update on the nitro-oxidative metabolism during the ripening of two of the most economically important fruits, discusses the signaling roles played by ROS/RNS in controlling this complex physiological process, and highlights the potential biotechnological applications of these substances to promote further improvements in fruit ripening regulation and nutritional quality. In addition, we suggest that the term 'nitro-oxidative eustress' with regard to fruit ripening would be more appropriate than nitro-oxidative stress, which ultimately favors the consolidation of the plant species.
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Affiliation(s)
- Francisco J Corpas
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Granada, Spain
| | - Luciano Freschi
- Department of Botany, Institute of Biosciences, University of São Paulo (USP), São Paulo, Brazil
| | - Marta Rodríguez-Ruiz
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Granada, Spain
| | - Paulo T Mioto
- Department of Botany, Biological Sciences Center, Universidade Federal de Santa Catarina, Campus Reitor João David Ferreira Lima, s/n, Florianópolis, Brazil
| | - Salvador González-Gordo
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Granada, Spain
| | - José M Palma
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Granada, Spain
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He H, Van Breusegem F, Mhamdi A. Redox-dependent control of nuclear transcription in plants. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3359-3372. [PMID: 29659979 DOI: 10.1093/jxb/ery130] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 03/27/2018] [Indexed: 05/03/2023]
Abstract
Redox-dependent regulatory networks are affected by altered cellular or extracellular levels of reactive oxygen species (ROS). Perturbations of ROS production and scavenging homeostasis have a considerable impact on the nuclear transcriptome. While the regulatory mechanisms by which ROS modulate gene transcription in prokaryotes, lower eukaryotes, and mammalian cells are well established, new insights into the mechanism underlying redox control of gene expression in plants have only recently been known. In this review, we aim to provide an overview of the current knowledge on how ROS and thiol-dependent transcriptional regulatory networks are controlled. We assess the impact of redox perturbations and oxidative stress on transcriptome adjustments using cat2 mutants as a model system and discuss how redox homeostasis can modify the various parts of the transcriptional machinery.
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Affiliation(s)
- Huaming He
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Amna Mhamdi
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
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Aledo JC, Cantón FR, Veredas FJ. A machine learning approach for predicting methionine oxidation sites. BMC Bioinformatics 2017; 18:430. [PMID: 28962549 PMCID: PMC5622526 DOI: 10.1186/s12859-017-1848-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 09/21/2017] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The oxidation of protein-bound methionine to form methionine sulfoxide, has traditionally been regarded as an oxidative damage. However, recent evidences support the view of this reversible reaction as a regulatory post-translational modification. The perception that methionine sulfoxidation may provide a mechanism to the redox regulation of a wide range of cellular processes, has stimulated some proteomic studies. However, these experimental approaches are expensive and time-consuming. Therefore, computational methods designed to predict methionine oxidation sites are an attractive alternative. As a first approach to this matter, we have developed models based on random forests, support vector machines and neural networks, aimed at accurate prediction of sites of methionine oxidation. RESULTS Starting from published proteomic data regarding oxidized methionines, we created a hand-curated dataset formed by 113 unique polypeptides of known structure, containing 975 methionyl residues, 122 of which were oxidation-prone (positive dataset) and 853 were oxidation-resistant (negative dataset). We use a machine learning approach to generate predictive models from these datasets. Among the multiple features used in the classification task, some of them contributed substantially to the performance of the predictive models. Thus, (i) the solvent accessible area of the methionine residue, (ii) the number of residues between the analyzed methionine and the next methionine found towards the N-terminus and (iii) the spatial distance between the atom of sulfur from the analyzed methionine and the closest aromatic residue, were among the most relevant features. Compared to the other classifiers we also evaluated, random forests provided the best performance, with accuracy, sensitivity and specificity of 0.7468±0.0567, 0.6817±0.0982 and 0.7557±0.0721, respectively (mean ± standard deviation). CONCLUSIONS We present the first predictive models aimed to computationally detect methionine sites that may become oxidized in vivo in response to oxidative signals. These models provide insights into the structural context in which a methionine residue become either oxidation-resistant or oxidation-prone. Furthermore, these models should be useful in prioritizing methinonyl residues for further studies to determine their potential as regulatory post-translational modification sites.
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Affiliation(s)
- Juan C. Aledo
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar de Louis Pasteur s/n, Málaga, 29071 Spain
| | - Francisco R. Cantón
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar de Louis Pasteur s/n, Málaga, 29071 Spain
| | - Francisco J. Veredas
- Departamento de Lenguajes y Ciencias de la Computación, Universidad de Málaga, Bulevar de Louis Pasteur s/n, Málaga, 29071 Spain
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Qi J, Wang J, Gong Z, Zhou JM. Apoplastic ROS signaling in plant immunity. CURRENT OPINION IN PLANT BIOLOGY 2017; 38:92-100. [PMID: 28511115 DOI: 10.1016/j.pbi.2017.04.022] [Citation(s) in RCA: 255] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 04/26/2017] [Accepted: 04/28/2017] [Indexed: 05/18/2023]
Abstract
Reactive oxygen species (ROS) are widely produced in different cellular compartments under both biotic and abiotic stress conditions. ROS play a central role in plant signaling and regulate diverse cellular processes. Recent advances are shedding new light on sophisticated mechanisms controlling ROS biogenesis and signaling in plant immunity. In this review, we summarize our current understanding of the regulation of apoplastic ROS production in response to microbial molecular patterns and draw comparison with abscisic acid (ABA)-induced apoplastic ROS. We also discuss how ROS act as signal molecules to regulate cellular activities using stomatal movement as an example.
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Affiliation(s)
- Junsheng Qi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jinlong Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Jian-Min Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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21
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Methionine residues around phosphorylation sites are preferentially oxidized in vivo under stress conditions. Sci Rep 2017; 7:40403. [PMID: 28079140 PMCID: PMC5227694 DOI: 10.1038/srep40403] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/06/2016] [Indexed: 12/22/2022] Open
Abstract
Protein phosphorylation is one of the most prevalent and well-understood protein modifications. Oxidation of protein-bound methionine, which has been traditionally perceived as an inevitable damage derived from oxidative stress, is now emerging as another modification capable of regulating protein activity during stress conditions. However, the mechanism coupling oxidative signals to changes in protein function remains unknown. An appealing hypothesis is that methionine oxidation might serve as a rheostat to control phosphorylation. To investigate this potential crosstalk between phosphorylation and methionine oxidation, we have addressed the co-occurrence of these two types of modifications within the human proteome. Here, we show that nearly all (98%) proteins containing oxidized methionine were also phosphoproteins. Furthermore, phosphorylation sites were much closer to oxidized methionines when compared to non-oxidized methionines. This proximity between modification sites cannot be accounted for by their co-localization within unstructured clusters because it was faithfully reproduced in a smaller sample of structured proteins. We also provide evidence that the oxidation of methionine located within phosphorylation motifs is a highly selective process among stress-related proteins, which supports the hypothesis of crosstalk between methionine oxidation and phosphorylation as part of the cellular defence against oxidative stress.
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22
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Adler G, Konrad Z, Zamir L, Mishra AK, Raveh D, Bar-Zvi D. The Arabidopsis paralogs, PUB46 and PUB48, encoding U-box E3 ubiquitin ligases, are essential for plant response to drought stress. BMC PLANT BIOLOGY 2017; 17:8. [PMID: 28077082 PMCID: PMC5225562 DOI: 10.1186/s12870-016-0963-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 12/21/2016] [Indexed: 05/13/2023]
Abstract
BACKGROUND Plants respond to abiotic stress on physiological, biochemical and molecular levels. This includes a global change in their cellular proteome achieved by changes in the pattern of their protein synthesis and degradation. The ubiquitin-proteasome system (UPS) is a key player in protein degradation in eukaryotes. Proteins are marked for degradation by the proteasome by coupling short chains of ubiquitin polypeptides in a three-step pathway. The last and regulatory stage is catalyzed by a member of a large family of substrate-specific ubiquitin ligases. RESULTS We have identified AtPUB46 and AtPUB48-two paralogous genes that encode ubiquitin ligases (E3s)-to have a role in the plant environmental response. The AtPUB46, -47, and -48 appear as tandem gene copies on chromosome 5, and we present a phylogenetic analysis that traces their evolution from an ancestral PUB-ARM gene. Single homozygous T-DNA insertion mutants of AtPUB46 and AtPUB48 displayed hypersensitivity to water stress; this was not observed for similar mutants of AtPUB47. Although the three genes show a similar spatial expression pattern, the steady state levels of their transcripts are differentially affected by abiotic stresses and plant hormones. CONCLUSIONS AtPUB46 and AtPUB48 encode plant U-Box E3s and are involved in the response to water stress. Our data suggest that despite encoding highly homologous proteins, AtPUB46 and AtPUB48 biological activity does not fully overlap.
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Affiliation(s)
- Guy Adler
- Department of Life Sciences, Ben-Gurion University of the Negev, 1 Ben-Gurion Blvd, Beer-Sheva, 8410501 Israel
- The Doris and Bertie I. Black Center for Bioenergetics in Life Sciences, Ben-Gurion University of the Negev, 1 Ben-Gurion Blvd, Beer-Sheva, 8410501 Israel
| | - Zvia Konrad
- Department of Life Sciences, Ben-Gurion University of the Negev, 1 Ben-Gurion Blvd, Beer-Sheva, 8410501 Israel
- The Doris and Bertie I. Black Center for Bioenergetics in Life Sciences, Ben-Gurion University of the Negev, 1 Ben-Gurion Blvd, Beer-Sheva, 8410501 Israel
| | - Lyad Zamir
- Department of Life Sciences, Ben-Gurion University of the Negev, 1 Ben-Gurion Blvd, Beer-Sheva, 8410501 Israel
- The Doris and Bertie I. Black Center for Bioenergetics in Life Sciences, Ben-Gurion University of the Negev, 1 Ben-Gurion Blvd, Beer-Sheva, 8410501 Israel
| | - Amit Kumar Mishra
- Department of Life Sciences, Ben-Gurion University of the Negev, 1 Ben-Gurion Blvd, Beer-Sheva, 8410501 Israel
- The Doris and Bertie I. Black Center for Bioenergetics in Life Sciences, Ben-Gurion University of the Negev, 1 Ben-Gurion Blvd, Beer-Sheva, 8410501 Israel
| | - Dina Raveh
- Department of Life Sciences, Ben-Gurion University of the Negev, 1 Ben-Gurion Blvd, Beer-Sheva, 8410501 Israel
| | - Dudy Bar-Zvi
- Department of Life Sciences, Ben-Gurion University of the Negev, 1 Ben-Gurion Blvd, Beer-Sheva, 8410501 Israel
- The Doris and Bertie I. Black Center for Bioenergetics in Life Sciences, Ben-Gurion University of the Negev, 1 Ben-Gurion Blvd, Beer-Sheva, 8410501 Israel
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Busche T, Winkler A, Wedderhoff I, Rückert C, Kalinowski J, Ortiz de Orué Lucana D. Deciphering the Transcriptional Response Mediated by the Redox-Sensing System HbpS-SenS-SenR from Streptomycetes. PLoS One 2016; 11:e0159873. [PMID: 27541358 PMCID: PMC4991794 DOI: 10.1371/journal.pone.0159873] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/08/2016] [Indexed: 12/30/2022] Open
Abstract
The secreted protein HbpS, the membrane-embedded sensor kinase SenS and the cytoplasmic response regulator SenR from streptomycetes have been shown to form a novel type of signaling pathway. Based on structural biology as well as different biochemical and biophysical approaches, redox stress-based post-translational modifications in the three proteins were shown to modulate the activity of this signaling pathway. In this study, we show that the homologous system, named here HbpSc-SenSc-SenRc, from the model species Streptomyces coelicolor A3(2) provides this bacterium with an efficient defense mechanism under conditions of oxidative stress. Comparative analyses of the transcriptomes of the Streptomyces coelicolor A3(2) wild-type and the generated hbpSc-senSc-senRc mutant under native and oxidative-stressing conditions allowed to identify differentially expressed genes, whose products may enhance the anti-oxidative defense of the bacterium. Amongst others, the results show an up-regulated transcription of genes for biosynthesis of cysteine and vitamin B12, transport of methionine and vitamin B12, and DNA synthesis and repair. Simultaneously, transcription of genes for degradation of an anti-oxidant compound is down-regulated in a HbpSc-SenSc-SenRc-dependent manner. It appears that HbpSc-SenSc-SenRc controls the non-enzymatic response of Streptomyces coelicolor A3(2) to counteract the hazardous effects of oxidative stress. Binding of the response regulator SenRc to regulatory regions of some of the studied genes indicates that the regulation is direct. The results additionally suggest that HbpSc-SenSc-SenRc may act in concert with other regulatory modules such as a transcriptional regulator, a two-component system and the Streptomyces B12 riboswitch. The transcriptomics data, together with our previous in vitro results, enable a profound characterization of the HbpS-SenS-SenR system from streptomycetes. Since homologues to HbpS-SenS-SenR are widespread in different actinobacteria with ecological and medical relevance, the data presented here will serve as a basis to elucidate the biological role of these homologues.
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Affiliation(s)
- Tobias Busche
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Anika Winkler
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Ina Wedderhoff
- Applied Genetics of Microorganisms, Department of Biology and Chemistry, University of Osnabrueck, Osnabrueck, Barbarastraße 13, 49076, Osnabrueck, Germany
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Darío Ortiz de Orué Lucana
- Applied Genetics of Microorganisms, Department of Biology and Chemistry, University of Osnabrueck, Osnabrueck, Barbarastraße 13, 49076, Osnabrueck, Germany
- * E-mail:
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24
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Zaffagnini M, De Mia M, Morisse S, Di Giacinto N, Marchand CH, Maes A, Lemaire SD, Trost P. Protein S-nitrosylation in photosynthetic organisms: A comprehensive overview with future perspectives. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:952-66. [PMID: 26861774 DOI: 10.1016/j.bbapap.2016.02.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/15/2016] [Accepted: 02/04/2016] [Indexed: 12/20/2022]
Abstract
BACKGROUND The free radical nitric oxide (NO) and derivative reactive nitrogen species (RNS) play essential roles in cellular redox regulation mainly through protein S-nitrosylation, a redox post-translational modification in which specific cysteines are converted to nitrosothiols. SCOPE OF VIEW This review aims to discuss the current state of knowledge, as well as future perspectives, regarding protein S-nitrosylation in photosynthetic organisms. MAJOR CONCLUSIONS NO, synthesized by plants from different sources (nitrite, arginine), provides directly or indirectly the nitroso moiety of nitrosothiols. Biosynthesis, reactivity and scavenging systems of NO/RNS, determine the NO-based signaling including the rate of protein nitrosylation. Denitrosylation reactions compete with nitrosylation in setting the levels of nitrosylated proteins in vivo. GENERAL SIGNIFICANCE Based on a combination of proteomic, biochemical and genetic approaches, protein nitrosylation is emerging as a pervasive player in cell signaling networks. Specificity of protein nitrosylation and integration among different post-translational modifications are among the major challenges for future experimental studies in the redox biology field. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Affiliation(s)
- M Zaffagnini
- Laboratory of Plant Redox Biology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - M De Mia
- Sorbonne Universités, UPMC Univ Paris 06, Centre National de la Recherche Scientifique, UMR8226, Laboratoire de Biologie Moléculaire et Cellulaire and des Eucaryotes, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - S Morisse
- Sorbonne Universités, UPMC Univ Paris 06, Centre National de la Recherche Scientifique, UMR8226, Laboratoire de Biologie Moléculaire et Cellulaire and des Eucaryotes, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - N Di Giacinto
- Laboratory of Plant Redox Biology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - C H Marchand
- Sorbonne Universités, UPMC Univ Paris 06, Centre National de la Recherche Scientifique, UMR8226, Laboratoire de Biologie Moléculaire et Cellulaire and des Eucaryotes, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - A Maes
- Sorbonne Universités, UPMC Univ Paris 06, Centre National de la Recherche Scientifique, UMR8226, Laboratoire de Biologie Moléculaire et Cellulaire and des Eucaryotes, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - S D Lemaire
- Sorbonne Universités, UPMC Univ Paris 06, Centre National de la Recherche Scientifique, UMR8226, Laboratoire de Biologie Moléculaire et Cellulaire and des Eucaryotes, Institut de Biologie Physico-Chimique, 75005 Paris, France.
| | - P Trost
- Laboratory of Plant Redox Biology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.
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25
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Walton A, Tsiatsiani L, Jacques S, Stes E, Messens J, Van Breusegem F, Goormachtig S, Gevaert K. Diagonal chromatography to study plant protein modifications. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:945-51. [PMID: 26772901 DOI: 10.1016/j.bbapap.2016.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/01/2015] [Accepted: 01/04/2016] [Indexed: 10/22/2022]
Abstract
An interesting asset of diagonal chromatography, which we have introduced for contemporary proteome research, is its high versatility concerning proteomic applications. Indeed, the peptide modification or sorting step that is required between consecutive peptide separations can easily be altered and thereby allows for the enrichment of specific, though different types of peptides. Here, we focus on the application of diagonal chromatography for the study of modifications of plant proteins. In particular, we show how diagonal chromatography allows for studying proteins processed by proteases, protein ubiquitination, and the oxidation of protein-bound methionines. We discuss the actual sorting steps needed for each of these applications and the obtained results. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Affiliation(s)
- Alan Walton
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium; Department of Biochemistry, Ghent University, 9000 Ghent, Belgium; Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Liana Tsiatsiani
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Silke Jacques
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium; Department of Biochemistry, Ghent University, 9000 Ghent, Belgium; Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Elisabeth Stes
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium; Department of Biochemistry, Ghent University, 9000 Ghent, Belgium; Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Joris Messens
- Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Brussels Center for Redox Biology, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Sofie Goormachtig
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium; Department of Biochemistry, Ghent University, 9000 Ghent, Belgium.
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26
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Kerchev P, De Smet B, Waszczak C, Messens J, Van Breusegem F. Redox Strategies for Crop Improvement. Antioxid Redox Signal 2015; 23:1186-205. [PMID: 26062101 DOI: 10.1089/ars.2014.6033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
SIGNIFICANCE Recently, the agro-biotech industry has been driven by overcoming the limitations imposed by fluctuating environmental stress conditions on crop productivity. A common theme among (a)biotic stresses is the perturbation of the redox homeostasis. RECENT ADVANCES As a strategy to engineer stress-tolerant crops, many approaches have been centered on restricting the negative impact of reactive oxygen species (ROS) accumulation. CRITICAL ISSUES In this study, we discuss the scientific background of the existing redox-based strategies to improve crop performance and quality. In this respect, a special focus goes to summarizing the current patent landscape because this aspect is very often ignored, despite constituting the forefront of applied research. FUTURE DIRECTIONS The current increased understanding of ROS acting as signaling molecules has opened new avenues to exploit redox biology for crop improvement required for sustainable food security.
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Affiliation(s)
- Pavel Kerchev
- 1 Department of Plant Systems Biology , VIB, Ghent, Belgium .,2 Department of Plant Biotechnology and Bioinformatics, Ghent University , Ghent, Belgium
| | - Barbara De Smet
- 1 Department of Plant Systems Biology , VIB, Ghent, Belgium .,2 Department of Plant Biotechnology and Bioinformatics, Ghent University , Ghent, Belgium .,3 Structural Biology Research Center , VIB, Brussels, Belgium .,4 Brussels Center for Redox Biology , Brussel, Belgium .,5 Structural Biology Brussels, Vrije Universiteit Brussel , Brussel, Belgium
| | - Cezary Waszczak
- 1 Department of Plant Systems Biology , VIB, Ghent, Belgium .,2 Department of Plant Biotechnology and Bioinformatics, Ghent University , Ghent, Belgium .,3 Structural Biology Research Center , VIB, Brussels, Belgium .,4 Brussels Center for Redox Biology , Brussel, Belgium .,5 Structural Biology Brussels, Vrije Universiteit Brussel , Brussel, Belgium
| | - Joris Messens
- 3 Structural Biology Research Center , VIB, Brussels, Belgium .,4 Brussels Center for Redox Biology , Brussel, Belgium .,5 Structural Biology Brussels, Vrije Universiteit Brussel , Brussel, Belgium
| | - Frank Van Breusegem
- 1 Department of Plant Systems Biology , VIB, Ghent, Belgium .,2 Department of Plant Biotechnology and Bioinformatics, Ghent University , Ghent, Belgium
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Peng X, Teng L, Yan X, Zhao M, Shen S. The cold responsive mechanism of the paper mulberry: decreased photosynthesis capacity and increased starch accumulation. BMC Genomics 2015; 16:898. [PMID: 26537770 PMCID: PMC4634900 DOI: 10.1186/s12864-015-2047-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 10/09/2015] [Indexed: 11/10/2022] Open
Abstract
Background Most studies on the paper mulberry are mainly focused on the medicated and pharmacology, fiber quality, leaves feed development, little is known about its mechanism of adaptability to abiotic stress. Physiological measurement, transcriptomics and proteomic analysis were employed to understand its response to cold stress in this study. Methods The second to fourth fully expanded leaves from up to down were harvested at different stress time points forthe transmission electron microscope (TEM) observation. Physiological characteristics measurement included the relative electrolyte leakage (REL), SOD activity assay, soluble sugar content, and Chlorophyll fluorescence parameter measurement. For screening of differentially expressed genes, the expression level of every transcript in each sample was calculated by quantifying the number of Illumina reads. To identify the differentially expressed protein, leaves of plants under 0, 6, 12, 24, 48 and 72 h cold stress wereharvested for proteomic analysis. Finally, real time PCR was used to verify the DEG results of the RNA-seq and the proteomics data. Results Results showed that at the beginning of cold stress, respiratory metabolism was decreased and the transportation and hydrolysis of photosynthetic products was inhibited, leading to an accumulation of starch in the chloroplasts. Total of 5800 unigenes and 38 proteins were affected, including the repressed expression of photosynthesis and the enhanced expression in signal transduction, stress defense pathway as well as secondary metabolism. Although the transcriptional level of a large number of genes has been restored after 12 h, sustained cold stress brought more serious injury to the leaf cells, including the sharp rise of the relative electrolyte leakage, the declined Fv/Fm value, swelled chloroplast and the disintegrated membrane system. Conclusion The starch accumulation and the photoinhibition might be the main adaptive mechanism of the paper mulberry responded to cold stress. Most of important, enhancing the transport and hydrolysis of photosynthetic products could be the potential targets for improving the cold tolerance of the paper mulberry. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2047-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xianjun Peng
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China.
| | - Linhong Teng
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China.
| | - Xueqing Yan
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China.
| | - Meiling Zhao
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China.
| | - Shihua Shen
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China.
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Tuttle JR, Nah G, Duke MV, Alexander DC, Guan X, Song Q, Chen ZJ, Scheffler BE, Haigler CH. Metabolomic and transcriptomic insights into how cotton fiber transitions to secondary wall synthesis, represses lignification, and prolongs elongation. BMC Genomics 2015; 16:477. [PMID: 26116072 PMCID: PMC4482290 DOI: 10.1186/s12864-015-1708-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 06/19/2015] [Indexed: 11/20/2022] Open
Abstract
Background The morphogenesis of single-celled cotton fiber includes extreme elongation and staged cell wall differentiation. Designing strategies for improving cotton fiber for textiles and other uses relies on uncovering the related regulatory mechanisms. In this research we compared the transcriptomes and metabolomes of two Gossypium genotypes, Gossypium barbadense cv Phytogen 800 and G. hirsutum cv Deltapine 90. When grown in parallel, the two types of fiber developed similarly except for prolonged fiber elongation in the G. barbadense cultivar. The data were collected from isolated fibers between 10 to 28 days post anthesis (DPA) representing: primary wall synthesis to support elongation; transitional cell wall remodeling; and secondary wall cellulose synthesis, which was accompanied by continuing elongation only in G. barbadense fiber. Results Of 206 identified fiber metabolites, 205 were held in common between the two genotypes. Approximately 38,000 transcripts were expressed in the fiber of each genotype, and these were mapped to the reference set and interpreted by homology to known genes. The developmental changes in the transcriptomes and the metabolomes were compared within and across genotypes with several novel implications. Transitional cell wall remodeling is a distinct stable developmental stage lasting at least four days (18 to 21 DPA). Expression of selected cell wall related transcripts was similar between genotypes, but cellulose synthase gene expression patterns were more complex than expected. Lignification was transcriptionally repressed in both genotypes. Oxidative stress was lower in the fiber of G. barbadense cv Phytogen 800 as compared to G. hirsutum cv Deltapine 90. Correspondingly, the G. barbadense cultivar had enhanced capacity for management of reactive oxygen species during its prolonged elongation period, as indicated by a 138-fold increase in ascorbate concentration at 28 DPA. Conclusions The parallel data on deep-sequencing transcriptomics and non-targeted metabolomics for two genotypes of single-celled cotton fiber showed that a discrete developmental stage of transitional cell wall remodeling occurs before secondary wall cellulose synthesis begins. The data showed how lignification can be transcriptionally repressed during secondary cell wall synthesis, and they implicated enhanced capacity to manage reactive oxygen species through the ascorbate-glutathione cycle as a positive contributor to fiber length. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1708-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John R Tuttle
- Department of Crop Science, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Gyoungju Nah
- Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA.
| | - Mary V Duke
- USDA ARS Genomics and Bioinformatics Research Unit, Stoneville, MS, 38776, USA.
| | | | - Xueying Guan
- Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA.
| | - Qingxin Song
- Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA.
| | - Z Jeffrey Chen
- Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA.
| | - Brian E Scheffler
- USDA ARS Genomics and Bioinformatics Research Unit, Stoneville, MS, 38776, USA.
| | - Candace H Haigler
- Department of Crop Science, North Carolina State University, Raleigh, NC, 27695, USA. .,Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA.
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Waszczak C, Akter S, Jacques S, Huang J, Messens J, Van Breusegem F. Oxidative post-translational modifications of cysteine residues in plant signal transduction. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2923-34. [PMID: 25750423 DOI: 10.1093/jxb/erv084] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In plants, fluctuation of the redox balance by altered levels of reactive oxygen species (ROS) can affect many aspects of cellular physiology. ROS homeostasis is governed by a diversified set of antioxidant systems. Perturbation of this homeostasis leads to transient or permanent changes in the redox status and is exploited by plants in different stress signalling mechanisms. Understanding how plants sense ROS and transduce these stimuli into downstream biological responses is still a major challenge. ROS can provoke reversible and irreversible modifications to proteins that act in diverse signalling pathways. These oxidative post-translational modifications (Ox-PTMs) lead to oxidative damage and/or trigger structural alterations in these target proteins. Characterization of the effect of individual Ox-PTMs on individual proteins is the key to a better understanding of how cells interpret the oxidative signals that arise from developmental cues and stress conditions. This review focuses on ROS-mediated Ox-PTMs on cysteine (Cys) residues. The Cys side chain, with its high nucleophilic capacity, appears to be the principle target of ROS. Ox-PTMs on Cys residues participate in various signalling cascades initiated by plant stress hormones. We review the mechanistic aspects and functional consequences of Cys Ox-PTMs on specific target proteins in view of stress signalling events.
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Affiliation(s)
- Cezary Waszczak
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Structural Biology Research Center, VIB, 1050 Brussels, Belgium Brussels Center for Redox Biology, 1050 Brussels, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium * Present address: Division of Plant Biology, Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland
| | - Salma Akter
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Structural Biology Research Center, VIB, 1050 Brussels, Belgium Brussels Center for Redox Biology, 1050 Brussels, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium Faculty of Biological Sciences, University of Dhaka, 1000 Dhaka, Bangladesh
| | - Silke Jacques
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Department of Biochemistry, Ghent University, 9000 Gent, Belgium Department of Medical Protein Research, VIB, 9000 Gent, Belgium
| | - Jingjing Huang
- Structural Biology Research Center, VIB, 1050 Brussels, Belgium Brussels Center for Redox Biology, 1050 Brussels, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Joris Messens
- Structural Biology Research Center, VIB, 1050 Brussels, Belgium Brussels Center for Redox Biology, 1050 Brussels, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
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Trapet P, Kulik A, Lamotte O, Jeandroz S, Bourque S, Nicolas-Francès V, Rosnoblet C, Besson-Bard A, Wendehenne D. NO signaling in plant immunity: a tale of messengers. PHYTOCHEMISTRY 2015; 112:72-9. [PMID: 24713571 DOI: 10.1016/j.phytochem.2014.03.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 03/12/2014] [Indexed: 05/05/2023]
Abstract
Nitric oxide (NO) is a free radical gas involved in a myriad of plant physiological processes including immune responses. How NO mediates its biological effects in plant facing microbial pathogen attack is an unresolved question. Insights into the molecular mechanisms by which it propagates signals reveal the contribution of this simple gas in complex signaling pathways shared with reactive oxygen species (ROS) and the second messenger Ca(2+). Understanding of the subtle cross-talks operating between these signals was greatly improved by the recent identification and the functional analysis of proteins regulated through S-nitrosylation, a major NO-dependent post-translational protein modification. Overall, these findings suggest that NO is probably an important component of the mechanism coordinating and regulating Ca(2+) and ROS signaling in plant immunity.
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Affiliation(s)
- Pauline Trapet
- Université de Bourgogne, UMR 1347 Agroécologie, BP 86510, F-21000 Dijon, France; ERL CNRS 6300, BP 86510, 21000 Dijon, France
| | - Anna Kulik
- INRA, UMR 1347 Agroécologie, BP 86510, F-21000 Dijon, France; ERL CNRS 6300, BP 86510, 21000 Dijon, France
| | - Olivier Lamotte
- CNRS, UMR 1347 Agroécologie, BP 86510, F-21000 Dijon, France; ERL CNRS 6300, BP 86510, 21000 Dijon, France
| | - Sylvain Jeandroz
- AgroSup Dijon, UMR 1347 Agroécologie, BP 86510, F-21000 Dijon, France; ERL CNRS 6300, BP 86510, 21000 Dijon, France
| | - Stéphane Bourque
- Université de Bourgogne, UMR 1347 Agroécologie, BP 86510, F-21000 Dijon, France; ERL CNRS 6300, BP 86510, 21000 Dijon, France
| | - Valérie Nicolas-Francès
- Université de Bourgogne, UMR 1347 Agroécologie, BP 86510, F-21000 Dijon, France; ERL CNRS 6300, BP 86510, 21000 Dijon, France
| | - Claire Rosnoblet
- Université de Bourgogne, UMR 1347 Agroécologie, BP 86510, F-21000 Dijon, France; ERL CNRS 6300, BP 86510, 21000 Dijon, France
| | - Angélique Besson-Bard
- Université de Bourgogne, UMR 1347 Agroécologie, BP 86510, F-21000 Dijon, France; ERL CNRS 6300, BP 86510, 21000 Dijon, France
| | - David Wendehenne
- Université de Bourgogne, UMR 1347 Agroécologie, BP 86510, F-21000 Dijon, France; ERL CNRS 6300, BP 86510, 21000 Dijon, France.
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Jacques S, Ghesquière B, De Bock PJ, Demol H, Wahni K, Willems P, Messens J, Van Breusegem F, Gevaert K. Protein Methionine Sulfoxide Dynamics in Arabidopsis thaliana under Oxidative Stress. Mol Cell Proteomics 2015; 14:1217-29. [PMID: 25693801 DOI: 10.1074/mcp.m114.043729] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Indexed: 02/02/2023] Open
Abstract
Reactive oxygen species such as hydrogen peroxide can modify proteins via direct oxidation of their sulfur-containing amino acids, cysteine and methionine. Methionine oxidation, studied here, is a reversible posttranslational modification that is emerging as a mechanism by which proteins perceive oxidative stress and function in redox signaling. Identification of proteins with oxidized methionines is the first prerequisite toward understanding the functional effect of methionine oxidation on proteins and the biological processes in which they are involved. Here, we describe a proteome-wide study of in vivo protein-bound methionine oxidation in plants upon oxidative stress using Arabidopsis thaliana catalase 2 knock-out plants as a model system. We identified over 500 sites of oxidation in about 400 proteins and quantified the differences in oxidation between wild-type and catalase 2 knock-out plants. We show that the activity of two plant-specific glutathione S-transferases, GSTF9 and GSTT23, is significantly reduced upon oxidation. And, by sampling over time, we mapped the dynamics of methionine oxidation and gained new insights into this complex and dynamic landscape of a part of the plant proteome that is sculpted by oxidative stress.
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Affiliation(s)
- Silke Jacques
- From the Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium, Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium, Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium, Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
| | - Bart Ghesquière
- From the Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium, Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Pieter-Jan De Bock
- From the Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium, Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Hans Demol
- From the Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium, Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Khadija Wahni
- VIB Structural Biology Research Center, Vrije Universiteit Brussel (VUB), B-1050 Brussels, Belgium, Brussels Center for Redox Biology, B-1050 Brussels, Belgium, Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Patrick Willems
- From the Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium, Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium, Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium, Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
| | - Joris Messens
- VIB Structural Biology Research Center, Vrije Universiteit Brussel (VUB), B-1050 Brussels, Belgium, Brussels Center for Redox Biology, B-1050 Brussels, Belgium, Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium, Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium,
| | - Kris Gevaert
- From the Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium, Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium,
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Akter S, Huang J, Bodra N, De Smet B, Wahni K, Rombaut D, Pauwels J, Gevaert K, Carroll K, Van Breusegem F, Messens J. DYn-2 Based Identification of Arabidopsis Sulfenomes. Mol Cell Proteomics 2015; 14:1183-200. [PMID: 25693797 DOI: 10.1074/mcp.m114.046896] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Indexed: 01/02/2023] Open
Abstract
Identifying the sulfenylation state of stressed cells is emerging as a strategic approach for the detection of key reactive oxygen species signaling proteins. Here, we optimized an in vivo trapping method for cysteine sulfenic acids in hydrogen peroxide (H2O2) stressed plant cells using a dimedone based DYn-2 probe. We demonstrated that DYn-2 specifically detects sulfenylation events in an H2O2 dose- and time-dependent way. With mass spectrometry, we identified 226 sulfenylated proteins after H2O2 treatment of Arabidopsis cells, residing in the cytoplasm (123); plastid (68); mitochondria (14); nucleus (10); endoplasmic reticulum, Golgi and plasma membrane (7) and peroxisomes (4). Of these, 123 sulfenylated proteins have never been reported before to undergo cysteine oxidative post-translational modifications in plants. All in all, with this DYn-2 approach, we have identified new sulfenylated proteins, and gave a first glance on the locations of the sulfenomes of Arabidopsis thaliana.
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Affiliation(s)
- Salma Akter
- From the Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Brussels Center for Redox Biology, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Faculty of Biological Sciences, University of Dhaka, 1000 Dhaka, Bangladesh
| | - Jingjing Huang
- Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Brussels Center for Redox Biology, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Nandita Bodra
- From the Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Brussels Center for Redox Biology, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Barbara De Smet
- From the Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Brussels Center for Redox Biology, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Khadija Wahni
- Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Brussels Center for Redox Biology, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Debbie Rombaut
- From the Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Jarne Pauwels
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium; Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium; Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Kate Carroll
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Frank Van Breusegem
- From the Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
| | - Joris Messens
- Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Brussels Center for Redox Biology, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium;
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Jorrín-Novo JV, Pascual J, Sánchez-Lucas R, Romero-Rodríguez MC, Rodríguez-Ortega MJ, Lenz C, Valledor L. Fourteen years of plant proteomics reflected in Proteomics: moving from model species and 2DE-based approaches to orphan species and gel-free platforms. Proteomics 2015; 15:1089-112. [PMID: 25487722 DOI: 10.1002/pmic.201400349] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 10/23/2014] [Accepted: 12/04/2014] [Indexed: 12/21/2022]
Abstract
In this article, the topic of plant proteomics is reviewed based on related papers published in the journal Proteomics since publication of the first issue in 2001. In total, around 300 original papers and 41 reviews published in Proteomics between 2000 and 2014 have been surveyed. Our main objective for this review is to help bridge the gap between plant biologists and proteomics technologists, two often very separate groups. Over the past years a number of reviews on plant proteomics have been published . To avoid repetition we have focused on more recent literature published after 2010, and have chosen to rather make continuous reference to older publications. The use of the latest proteomics techniques and their integration with other approaches in the "systems biology" direction are discussed more in detail. Finally we comment on the recent history, state of the art, and future directions of plant proteomics, using publications in Proteomics to illustrate the progress in the field. The review is organized into two major blocks, the first devoted to provide an overview of experimental systems (plants, plant organs, biological processes) and the second one to the methodology.
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Affiliation(s)
- Jesus V Jorrín-Novo
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Cordoba-CeiA3, Cordoba, Spain
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Takáč T, Šamajová O, Vadovič P, Pechan T, Košútová P, Ovečka M, Husičková A, Komis G, Šamaj J. Proteomic and biochemical analyses show a functional network of proteins involved in antioxidant defense of the Arabidopsis anp2anp3 double mutant. J Proteome Res 2014; 13:5347-61. [PMID: 25325904 PMCID: PMC4423761 DOI: 10.1021/pr500588c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Disentanglement of functional complexity associated with plant mitogen-activated protein kinase (MAPK) signaling has benefited from transcriptomic, proteomic, phosphoproteomic, and genetic studies. Published transcriptomic analysis of a double homozygous recessive anp2anp3 mutant of two MAPK kinase kinase (MAPKKK) genes called Arabidopsis thaliana Homologues of Nucleus- and Phragmoplast-localized Kinase 2 (ANP2) and 3 (ANP3) showed the upregulation of stress-related genes. In this study, a comparative proteomic analysis of anp2anp3 mutant against its respective Wassilevskaja ecotype (Ws) wild type background is provided. Such differential proteomic analysis revealed overabundance of core enzymes such as FeSOD1, MnSOD, DHAR1, and FeSOD1-associated regulatory protein CPN20, which are involved in the detoxification of reactive oxygen species in the anp2anp3 mutant. The proteomic results were validated at the level of single protein abundance by Western blot analyses and by quantitative biochemical determination of antioxidant enzymatic activities. Finally, the functional network of proteins involved in antioxidant defense in the anp2anp3 mutant was physiologically linked with the increased resistance of mutant seedlings against paraquat treatment.
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Affiliation(s)
- Tomáš Takáč
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic
| | - Olga Šamajová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic
| | - Pavol Vadovič
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic
| | - Tibor Pechan
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Petra Košútová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic
| | - Miroslav Ovečka
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic
| | - Alexandra Husičková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Biophysics, Faculty of Science, Palacký University, Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic
| | - George Komis
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic
| | - Jozef Šamaj
- Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Cell Biology, Faculty of Science, Palacký University, Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic
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Zagorchev L, Terzieva M, Stoichkova M, Odjakova M. Changes in protein thiols in response to salt stress in embryogenic suspension cultures of Dactylis glomerata L. BIOTECHNOL BIOTEC EQ 2014; 28:616-621. [PMID: 26019548 PMCID: PMC4433836 DOI: 10.1080/13102818.2014.946798] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 06/19/2014] [Indexed: 12/26/2022] Open
Abstract
The aim of the present study is to assess the rate of protein disulphide formation and the activity of NADPH-dependent thioredoxin and glutaredoxin systems, responsible for the reverse reduction of protein and mixed protein-glutathione disulphides, in embryogenic suspension cultures of Dactylis glomerata, subjected to salt stress. Two concentrations of NaCl previously established as enhancing (0.085 mol/L) and inhibiting (0.17 mol/L) somatic embryogenesis were used. The quantitative (by colour reaction with Ellman's reagent) and qualitative (by diagonal gel electrophoresis) analyses showed a significant increase in protein disulphide formation in salt-treated cultures compared to controls. The ratio of disulphides to free thiols is higher in 0.17 mol/L NaCl-treated cultures. The activity of the thioredoxin-thioredoxin reductase system has been increased accordingly in 0.085 mol/L NaCl-treated cultures but decreased at the higher salt concentration. The activity of glutaredoxins was also estimated, by using glutathionylated bovine serum albumin as substrate and following the decrease of NADPH absorbance at 340 nm in the presence of glutathione and glutathione reductase. Mild salt (0.085 mol/L NaCl) treated cultures again showed the highest activity compared to controls and 0.17 mol/L NaCl-treated cultures. Based on these observations it was suggested that salt treatment resulted in increased protein disulphide formation and thioredoxin and glutaredoxin systems are important regulators of this process, strongly involved in salt stress response. The highest activity at 0.085 mol/L NaCl may be also related to the regulatory mechanisms, involved in the potentiating of somatic embryogenesis at this salt concentration.
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Affiliation(s)
- Lyuben Zagorchev
- Department of Biochemistry, Faculty of Biology, Sofia University St. Kliment Ohridski , Sofia, Bulgaria
| | - Miroslava Terzieva
- Department of Biochemistry, Faculty of Biology, Sofia University St. Kliment Ohridski , Sofia, Bulgaria
| | - Marina Stoichkova
- Department of Biochemistry, Faculty of Biology, Sofia University St. Kliment Ohridski , Sofia, Bulgaria
| | - Mariela Odjakova
- Department of Biochemistry, Faculty of Biology, Sofia University St. Kliment Ohridski , Sofia, Bulgaria
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Manai J, Gouia H, Corpas FJ. Redox and nitric oxide homeostasis are affected in tomato (Solanum lycopersicum) roots under salinity-induced oxidative stress. JOURNAL OF PLANT PHYSIOLOGY 2014; 171:1028-35. [PMID: 24974329 DOI: 10.1016/j.jplph.2014.03.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 03/11/2014] [Accepted: 03/11/2014] [Indexed: 05/04/2023]
Abstract
The nicotinamide adenine dinucleotide phosphate (NADPH) and reduced glutathione (GSH) molecules play important roles in the redox homeostasis of plant cells. Using tomato (Solanum lycopersicum) plants grown with 120mM NaCl, we studied the redox state of NADPH and GSH as well as ascorbate, nitric oxide (NO) and S-nitrosoglutathione (GSNO) content and the activity of the principal enzymes involved in the metabolism of these molecules in roots. Salinity caused a significant reduction in growth parameters and an increase in oxidative parameters such as lipid peroxidation and protein oxidation. Salinity also led to an overall decrease in the content of these redox molecules and in the enzymatic activities of the main NADPH-generating dehydrogenases, S-nitrosoglutathione reductase and catalase. However, NO content as well as gluthahione reductase and glutathione peroxidase activity increased under salinity stress. These findings indicate that salinity drastically affects redox and NO homeostasis in tomato roots. In our view, these molecules, which show the interaction between ROS and RNS metabolisms, could be excellent parameters for evaluating the physiological conditions of plants under adverse stress conditions.
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Affiliation(s)
- Jamel Manai
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Apartado 419, E-18080 Granada, Spain; Faculty of Sciences of Tunisia, University Tunis El Manar, Tunis, Tunisia
| | - Houda Gouia
- Faculty of Sciences of Tunisia, University Tunis El Manar, Tunis, Tunisia
| | - Francisco J Corpas
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Apartado 419, E-18080 Granada, Spain.
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37
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Sewelam N, Jaspert N, Van Der Kelen K, Tognetti VB, Schmitz J, Frerigmann H, Stahl E, Zeier J, Van Breusegem F, Maurino VG. Spatial H2O2 signaling specificity: H2O2 from chloroplasts and peroxisomes modulates the plant transcriptome differentially. MOLECULAR PLANT 2014; 7:1191-210. [PMID: 24908268 DOI: 10.1093/mp/ssu070] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Hydrogen peroxide (H2O2) operates as a signaling molecule in eukaryotes, but the specificity of its signaling capacities remains largely unrevealed. Here, we analyzed whether a moderate production of H2O2 from two different plant cellular compartments has divergent effects on the plant transcriptome. Arabidopsis thaliana overexpressing glycolate oxidase in the chloroplast (Fahnenstich et al., 2008; Balazadeh et al., 2012) and plants deficient in peroxisomal catalase (Queval et al., 2007; Inzé et al., 2012) were grown under non-photorespiratory conditions and then transferred to photorespiratory conditions to foster the production of H2O2 in both organelles. We show that H2O2 originating in a specific organelle induces two types of responses: one that integrates signals independently from the subcellular site of H2O2 production and another that is dependent on the H2O2 production site. H2O2 produced in peroxisomes induces transcripts involved in protein repair responses, while H2O2 produced in chloroplasts induces early signaling responses, including transcription factors and biosynthetic genes involved in production of secondary signaling messengers. There is a significant bias towards the induction of genes involved in responses to wounding and pathogen attack by chloroplastic-produced H2O2, including indolic glucosinolates-, camalexin-, and stigmasterol-biosynthetic genes. These transcriptional responses were accompanied by the accumulation of 4-methoxy-indol-3-ylmethyl glucosinolate and stigmasterol.
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Affiliation(s)
- Nasser Sewelam
- Institut of Developmental and Molecular Biology of Plants, Plant Molecular Physiology and Biotechnology Group, Heinrich-Heine-Universität, Universitätsstraße 1, 40225 Düsseldorf, Germany Botany Department, Faculty of Science, Tanta University, 31527, Tanta, Egypt
| | - Nils Jaspert
- Institut of Developmental and Molecular Biology of Plants, Plant Molecular Physiology and Biotechnology Group, Heinrich-Heine-Universität, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Katrien Van Der Kelen
- Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Vanesa B Tognetti
- Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium Present address: Mendel Centre for Plant Genomics and Proteomics, CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Jessica Schmitz
- Institut of Developmental and Molecular Biology of Plants, Plant Molecular Physiology and Biotechnology Group, Heinrich-Heine-Universität, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Henning Frerigmann
- Botanical Institute, Cologne Biocenter, University of Cologne, 50674 Cologne, Germany Cluster of Excellence on Plant Sciences (CEPLAS), 40225 Düsseldorf and 50674 Cologne, Germany
| | - Elia Stahl
- Molecular Ecophysiology of Plants, Heinrich-Heine-Universität, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Jürgen Zeier
- Cluster of Excellence on Plant Sciences (CEPLAS), 40225 Düsseldorf and 50674 Cologne, Germany Molecular Ecophysiology of Plants, Heinrich-Heine-Universität, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Veronica G Maurino
- Institut of Developmental and Molecular Biology of Plants, Plant Molecular Physiology and Biotechnology Group, Heinrich-Heine-Universität, Universitätsstraße 1, 40225 Düsseldorf, Germany Cluster of Excellence on Plant Sciences (CEPLAS), 40225 Düsseldorf and 50674 Cologne, Germany
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Zhou L, Xu H, Mischke S, Meinhardt LW, Zhang D, Zhu X, Li X, Fang W. Exogenous abscisic acid significantly affects proteome in tea plant (Camellia sinensis) exposed to drought stress. HORTICULTURE RESEARCH 2014; 1:14029. [PMID: 27076915 PMCID: PMC4816387 DOI: 10.1038/hortres.2014.29] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 04/21/2014] [Accepted: 04/30/2014] [Indexed: 05/03/2023]
Abstract
Tea [Camellia sinensis (L.) O. Kuntze] is an important economic crop, and drought is the most important abiotic stress affecting yield and quality. Abscisic acid (ABA) is an important phytohormone responsible for activating drought resistance. Increased understanding of ABA effects on tea plant under drought stress is essential to develop drought-tolerant tea genotypes, along with crop management practices that can mitigate drought stress. The objective of the present investigation is evaluation of effects of exogenous ABA on the leaf proteome in tea plant exposed to drought stress. Leaf protein patterns of tea plants under simulated drought stress [(polyethylene glycol (PEG)-treated] and exogenous ABA treatment were analyzed in a time-course experiment using two-dimensional electrophoresis (2-DE), followed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). Among the 72 protein spots identified by MALDI-TOF MS, 16 proteins were downregulated and two were upregulated by exogenous ABA. The upregulated proteins have roles in glycolysis and photosystem II stabilization. Twenty-one protein spots were responsive to drought stress and most participate in carbohydrate and nitrogen metabolism, control of reactive oxygen species (ROS), defense, signaling or nucleic acid metabolism. The combined treatments of exogenous ABA and drought showed upregulation of 10 protein spots at 12 h and upregulation of 11 proteins at 72 h after initiation of drought stress. The results support the importance of the role that ABA plays in the tea plant during drought stress, by improving protein transport, carbon metabolism and expression of resistance proteins.
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Affiliation(s)
- Lin Zhou
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Xu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Sue Mischke
- USDA/ARS, Beltsville Agricultural Research Center, SPCL, Beltsville, MD 20705, USA
| | - Lyndel W Meinhardt
- USDA/ARS, Beltsville Agricultural Research Center, SPCL, Beltsville, MD 20705, USA
| | - Dapeng Zhang
- USDA/ARS, Beltsville Agricultural Research Center, SPCL, Beltsville, MD 20705, USA
| | - Xujun Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinghui Li
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wanping Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- USDA/ARS, Beltsville Agricultural Research Center, SPCL, Beltsville, MD 20705, USA
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Selective chemoprecipitation to enrich nitropeptides from complex proteomes for mass-spectrometric analysis. Nat Protoc 2014; 9:882-95. [PMID: 24651500 DOI: 10.1038/nprot.2014.052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Post-translational protein nitration has attracted interest owing to its involvement in cellular signaling, effects on protein function and potential as biomarker of nitroxidative stress. We describe a procedure for enriching nitropeptides for mass spectrometry (MS)-based proteomics that is a simple and reliable alternative to immunoaffinity-based methods. The starting material for this procedure is a proteolytic digest. The peptides are reacted with formaldehyde and sodium cyanoborohydride to dimethylate all the N-terminal and side chain amino groups. Sodium dithionite is added subsequently to reduce the nitro groups to amines; in theory, the only amino groups present will have originally been nitro groups. The peptide sample is then applied to a solid-phase active ester reagent (SPAER), and those peptides with amino groups will be selectively and covalently captured. Release of the peptides on hydrolysis with trifluoroacetic acid (TFA) results in peptides that have a 4-formyl-benzamido group where the nitro group used to be. In qualitative setups, the procedure can be used to identify proteins modified by reactive nitrogen species and to determine the specific sites of their nitration. Quantitative measurements can be performed by stable-isotope labeling of the peptides in the reductive dimethylation step. Preparation of the SPAER takes about 1 d. Enrichment of nitropeptides requires about 2 d, and sample preparations need 1-30 h, depending on the experimental design. LC-MS/MS assays take from 4 h to several days and data processing can be done in 1-7 d.
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40
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Qin Y, Song W, Xiao S, Yin G, Zhu Y, Yan Y, Hu Y. Stress-related genes distinctly expressed in unfertilized wheat ovaries under both normal and water deficit conditions whereas differed in fertilized ovaries. J Proteomics 2014; 102:11-27. [PMID: 24607492 DOI: 10.1016/j.jprot.2014.02.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 02/16/2014] [Accepted: 02/21/2014] [Indexed: 12/17/2022]
Abstract
UNLABELLED In this study, a proteomic approach was utilized to identify differentially accumulated proteins in developing wheat ovaries before and after fertilization and in response to water deficit. Proteins were extracted, quantified, and resolved by 2-DE at pH4-7. Statistical analysis of spot intensity was performed by using principal component analysis and samples were clustered by using Euclidean distance. In total, 136 differentially accumulated protein spots representing 88 unique proteins were successfully identified by MALDI-TOF/TOF MS. Under normal conditions, stress-related proteins were abundant in unfertilized ovaries while proteins involved in the metabolism of energy and matter were enriched in fertilized ovaries just 48h after fertilization. Similar trends were observed in unfertilized and fertilized wheat ovaries under water deficit conditions, except for increased accumulation of stress-related proteins in fertilized ovaries. Some proteins required for normal development were not present in ovaries subjected to water deficit. Our comprehensive results provide new insights into the biochemical mechanisms involved in ovary development before and after fertilization and in tolerance to water deficit. BIOLOGICAL SIGNIFICANCE Fertilization initiates the most dramatic changes that occur in the life cycle of higher plants; research into differences in gene expression before and after ovary pollination can make a substantial contribution to understanding the physiological and biochemical processes associated with fertilization. To date, a small number of studies have examined changes in transcriptional activity of the developing plant embryo sac before and after fertilization. However, comparative proteomic analysis of wheat ovary development before and after fertilization, and in response to water deficit, has not yet been reported. Our comprehensive results provide new insights into the biochemical mechanisms involved in ovary development before and after fertilization and in tolerance to water deficit.
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Affiliation(s)
- Yajuan Qin
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Wanlu Song
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Shuyang Xiao
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Guangjun Yin
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Yan Zhu
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Yueming Yan
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Yingkao Hu
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
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41
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Venne AS, Kollipara L, Zahedi RP. The next level of complexity: Crosstalk of posttranslational modifications. Proteomics 2014; 14:513-24. [DOI: 10.1002/pmic.201300344] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 11/06/2013] [Accepted: 11/21/2013] [Indexed: 12/22/2022]
Affiliation(s)
- A. Saskia Venne
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V; Dortmund Germany
| | | | - René P. Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V; Dortmund Germany
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42
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Srivastava V, Obudulu O, Bygdell J, Löfstedt T, Rydén P, Nilsson R, Ahnlund M, Johansson A, Jonsson P, Freyhult E, Qvarnström J, Karlsson J, Melzer M, Moritz T, Trygg J, Hvidsten TR, Wingsle G. OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants. BMC Genomics 2013; 14:893. [PMID: 24341908 PMCID: PMC3878592 DOI: 10.1186/1471-2164-14-893] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 11/27/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Reactive oxygen species (ROS) are involved in the regulation of diverse physiological processes in plants, including various biotic and abiotic stress responses. Thus, oxidative stress tolerance mechanisms in plants are complex, and diverse responses at multiple levels need to be characterized in order to understand them. Here we present system responses to oxidative stress in Populus by integrating data from analyses of the cambial region of wild-type controls and plants expressing high-isoelectric-point superoxide dismutase (hipI-SOD) transcripts in antisense orientation showing a higher production of superoxide. The cambium, a thin cell layer, generates cells that differentiate to form either phloem or xylem and is hypothesized to be a major reason for phenotypic perturbations in the transgenic plants. Data from multiple platforms including transcriptomics (microarray analysis), proteomics (UPLC/QTOF-MS), and metabolomics (GC-TOF/MS, UPLC/MS, and UHPLC-LTQ/MS) were integrated using the most recent development of orthogonal projections to latent structures called OnPLS. OnPLS is a symmetrical multi-block method that does not depend on the order of analysis when more than two blocks are analysed. Significantly affected genes, proteins and metabolites were then visualized in painted pathway diagrams. RESULTS The main categories that appear to be significantly influenced in the transgenic plants were pathways related to redox regulation, carbon metabolism and protein degradation, e.g. the glycolysis and pentose phosphate pathways (PPP). The results provide system-level information on ROS metabolism and responses to oxidative stress, and indicate that some initial responses to oxidative stress may share common pathways. CONCLUSION The proposed data evaluation strategy shows an efficient way of compiling complex, multi-platform datasets to obtain significant biological information.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gunnar Wingsle
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183 Umeå, Sweden.
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43
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Salmi ML, Clark G, Roux SJ. Current status and proposed roles for nitric oxide as a key mediator of the effects of extracellular nucleotides on plant growth. FRONTIERS IN PLANT SCIENCE 2013; 4:427. [PMID: 24298275 PMCID: PMC3829461 DOI: 10.3389/fpls.2013.00427] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 10/09/2013] [Indexed: 05/20/2023]
Abstract
Recent data indicate that nucleotides are released into the extracellular matrix during plant cell growth, and that these extracellular nucleotides induce signaling changes that can, in a dose-dependent manner, increase or decrease the cell growth. After activation of a presumed receptor, the earliest signaling change induced by extracellular nucleotides is an increase in the concentration of cytosolic Ca(2+), but rapidly following this change is an increase in the cellular level of nitric oxide (NO). In Arabidopsis, mutants deficient in nitrate reductase activity (nia1nia2) have drastically reduced nitric oxide production and cannot transduce the effects of applied nucleotides into growth changes. Both increased levels of extracellular nucleotides and increased NO production inhibit auxin transport and inhibit growth, and these effects are potentially due to disruption of the localization and/or function of auxin transport facilitators. However, because NO- and auxin-induced signaling pathways can intersect at multiple points, there may be diverse ways by which the induction of NO by extracellular ATP could modulate auxin signaling and thus influence growth. This review will discuss these optional mechanisms and suggest possible regulatory routes based on current experimental data and predictive computational analyses.
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Affiliation(s)
| | | | - Stanley J. Roux
- *Correspondence: Stanley J. Roux, Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A6700, 205 West 24th Street, BIO 16, Austin, TX 78712-0183, USA e-mail:
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Arc E, Galland M, Godin B, Cueff G, Rajjou L. Nitric oxide implication in the control of seed dormancy and germination. FRONTIERS IN PLANT SCIENCE 2013; 4:346. [PMID: 24065970 PMCID: PMC3777103 DOI: 10.3389/fpls.2013.00346] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 08/16/2013] [Indexed: 05/20/2023]
Abstract
Germination ability is regulated by a combination of environmental and endogenous signals with both synergistic and antagonistic effects. Nitric oxide (NO) is a potent dormancy-releasing agent in many species, including Arabidopsis, and has been suggested to behave as an endogenous regulator of this physiological blockage. Distinct reports have also highlighted a positive impact of NO on seed germination under sub-optimal conditions. However, its molecular mode of action in the context of seed biology remains poorly documented. This review aims to focus on the implications of this radical in the control of seed dormancy and germination. The consequences of NO chemistry on the investigations on both its signaling and its targets in seeds are discussed. NO-dependent protein post-translational modifications are proposed as a key mechanism underlying NO signaling during early seed germination.
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Affiliation(s)
- Erwann Arc
- INRA, Institut Jean-Pierre Bourgin (UMR1318 Institut National de la Recherche Agronomique – AgroParisTech), Laboratory of Excellence “Saclay Plant Sciences”, VersaillesFrance
- AgroParisTech, UFR de Physiologie végétaleParis, France
- University of Innsbruck, Institute of BotanyInnsbruck, Austria
- *Correspondence: Erwann Arc and Loïc Rajjou, INRA, Institut Jean-Pierre Bourgin (UMR1318 Institut National de la Recherche Agronomique – AgroParisTech), Laboratory of Excellence “Saclay Plant Sciences”, Route de Saint Cyr (RD10) - Bât 2, F-78026 Versailles Cedex, France e-mail: ;
| | - Marc Galland
- INRA, Institut Jean-Pierre Bourgin (UMR1318 Institut National de la Recherche Agronomique – AgroParisTech), Laboratory of Excellence “Saclay Plant Sciences”, VersaillesFrance
- AgroParisTech, UFR de Physiologie végétaleParis, France
| | - Béatrice Godin
- INRA, Institut Jean-Pierre Bourgin (UMR1318 Institut National de la Recherche Agronomique – AgroParisTech), Laboratory of Excellence “Saclay Plant Sciences”, VersaillesFrance
- AgroParisTech, UFR de Physiologie végétaleParis, France
| | - Gwendal Cueff
- INRA, Institut Jean-Pierre Bourgin (UMR1318 Institut National de la Recherche Agronomique – AgroParisTech), Laboratory of Excellence “Saclay Plant Sciences”, VersaillesFrance
- AgroParisTech, UFR de Physiologie végétaleParis, France
| | - Loïc Rajjou
- INRA, Institut Jean-Pierre Bourgin (UMR1318 Institut National de la Recherche Agronomique – AgroParisTech), Laboratory of Excellence “Saclay Plant Sciences”, VersaillesFrance
- AgroParisTech, UFR de Physiologie végétaleParis, France
- *Correspondence: Erwann Arc and Loïc Rajjou, INRA, Institut Jean-Pierre Bourgin (UMR1318 Institut National de la Recherche Agronomique – AgroParisTech), Laboratory of Excellence “Saclay Plant Sciences”, Route de Saint Cyr (RD10) - Bât 2, F-78026 Versailles Cedex, France e-mail: ;
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Guillas I, Puyaubert J, Baudouin E. Nitric oxide-sphingolipid interplays in plant signalling: a new enigma from the Sphinx? FRONTIERS IN PLANT SCIENCE 2013; 4:341. [PMID: 24062754 PMCID: PMC3770979 DOI: 10.3389/fpls.2013.00341] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 08/13/2013] [Indexed: 05/04/2023]
Abstract
Nitric oxide (NO) emerged as one of the major signaling molecules operating during plant development and plant responses to its environment. Beyond the identification of the direct molecular targets of NO, a series of studies considered its interplay with other actors of signal transduction and the integration of NO into complex signaling networks. Beside the close relationships between NO and calcium or phosphatidic acid signaling pathways that are now well-established, recent reports paved the way for interplays between NO and sphingolipids (SLs). This mini-review summarizes our current knowledge of the influence NO and SLs might exert on each other in plant physiology. Based on comparisons with examples from the animal field, it further indicates that, although SL-NO interplays are common features in signaling networks of eukaryotic cells, the underlying mechanisms and molecular targets significantly differ.
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Affiliation(s)
- Isabelle Guillas
- UR 5, Laboratoire de Physiologie Cellulaire et Moléculaire des Plantes, Université Pierre et Marie Curie - Paris 6Paris, France
- EAC 7180, Laboratoire de Physiologie Cellulaire et Moléculaire des Plantes, Centre National de la Recherche ScientifiqueParis, France
| | - Juliette Puyaubert
- UR 5, Laboratoire de Physiologie Cellulaire et Moléculaire des Plantes, Université Pierre et Marie Curie - Paris 6Paris, France
- EAC 7180, Laboratoire de Physiologie Cellulaire et Moléculaire des Plantes, Centre National de la Recherche ScientifiqueParis, France
| | - Emmanuel Baudouin
- UR 5, Laboratoire de Physiologie Cellulaire et Moléculaire des Plantes, Université Pierre et Marie Curie - Paris 6Paris, France
- EAC 7180, Laboratoire de Physiologie Cellulaire et Moléculaire des Plantes, Centre National de la Recherche ScientifiqueParis, France
- *Correspondence: Emmanuel Baudouin, UR 5, Laboratoire de Physiologie Cellulaire et Moléculaire des Plantes, Université Pierre et Marie Curie - Paris 6, Bâtiment C/3 Boîte courrier 156, 4 place Jussieu, F-75252 Paris Cédex 05, France; EAC 7180, Laboratoire de Physiologie Cellulaire et Moléculaire des Plantes, Centre National de la Recherche Scientifique, Bâtiment C/3 Boîte courrier 156, 4 place Jussieu, F-75252 Paris Cédex 05, France e-mail:
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