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Recent developments in the engineering of Rubisco activase for enhanced crop yield. Biochem Soc Trans 2023; 51:627-637. [PMID: 36929563 DOI: 10.1042/bst20221281] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/18/2023]
Abstract
Rubisco activase (RCA) catalyzes the release of inhibitory sugar phosphates from ribulose-1,6-biphosphate carboxylase/oxygenase (Rubisco) and can play an important role in biochemical limitations of photosynthesis under dynamic light and elevated temperatures. There is interest in increasing RCA activity to improve crop productivity, but a lack of understanding about the regulation of photosynthesis complicates engineering strategies. In this review, we discuss work relevant to improving RCA with a focus on advances in understanding the structural cause of RCA instability under heat stress and the regulatory interactions between RCA and components of photosynthesis. This reveals substantial variation in RCA thermostability that can be influenced by single amino acid substitutions, and that engineered variants can perform better in vitro and in vivo under heat stress. In addition, there are indications RCA activity is controlled by transcriptional, post-transcriptional, post-translational, and spatial regulation, which may be important for balancing between carbon fixation and light capture. Finally, we provide an overview of findings from recent field experiments and consider the requirements for commercial validation as part of efforts to increase crop yields in the face of global climate change.
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Wu L, Meng X, Huang H, Liu Y, Jiang W, Su X, Wang Z, Meng F, Wang L, Peng D, Xing S. Comparative Proteome and Phosphoproteome Analyses Reveal Different Molecular Mechanism Between Stone Planting Under the Forest and Greenhouse Planting of Dendrobium huoshanense. FRONTIERS IN PLANT SCIENCE 2022; 13:937392. [PMID: 35873990 PMCID: PMC9301318 DOI: 10.3389/fpls.2022.937392] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
The highly esteemed Chinese herb, Dendrobium huoshanense, whose major metabolites are polysaccharides and alkaloids, is on the verge of extinction. The stone planting under the forest (SPUF) and greenhouse planting (GP) of D. huoshanense are two different cultivation methods of pharmaceutical Dendrobium with significantly differences in morphology, metabolites content and composition, and medication efficacy. Here, we conducted proteomics and phosphoproteomics analyses to reveal differences in molecular mechanisms between SPUF and GP. We identified 237 differentially expressed proteins (DEPs) between the two proteomes, and 291 modification sites belonging to 215 phosphoproteins with a phosphorylation level significantly changed (PLSC) were observed. GO, KEGG pathway, protein domain, and cluster analyses revealed that these DEPs were mainly localized in the chloroplast; involved in processes such as posttranslational modification, carbohydrate transport and metabolism, and secondary metabolite biosynthesis; and enriched in pathways mainly including linoleic acid metabolism, plant-pathogen interactions, and phenylpropanoid, cutin, suberin, and wax biosynthesis. PLSC phosphoproteins were mainly located in the chloroplast, and highly enriched in responses to different stresses and signal transduction mechanisms through protein kinase and phosphotransferase activities. Significant differences between SPUF and GP were observed by mapping the DEPs and phosphorylated proteins to photosynthesis and polysaccharide and alkaloid biosynthesis pathways. Phosphorylation characteristics and kinase categories in D. huoshanense were also clarified in this study. We analyzed different molecular mechanisms between SPUF and GP at proteomic and phosphoproteomic levels, providing valuable information for the development and utilization of D. huoshanense.
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Affiliation(s)
- Liping Wu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Xiaoxi Meng
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, United States
| | - Huizhen Huang
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences and Environment, Hengyang Normal University, Hengyang, China
| | - Yingying Liu
- College of Humanities and International Education Exchange, Anhui University of Chinese Medicine, Hefei, China
| | - Weimin Jiang
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences and Environment, Hengyang Normal University, Hengyang, China
| | - Xinglong Su
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Zhaojian Wang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Fei Meng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Longhai Wang
- School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Daiyin Peng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, China
- MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, China
| | - Shihai Xing
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, China
- Anhui Province Key Laboratory of Research and Development of Chinese Medicine, Hefei, China
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Matiolli CC, Soares RC, Alves HLS, Abreu IA. Turning the Knobs: The Impact of Post-translational Modifications on Carbon Metabolism. FRONTIERS IN PLANT SCIENCE 2022; 12:781508. [PMID: 35087551 PMCID: PMC8787203 DOI: 10.3389/fpls.2021.781508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
Plants rely on the carbon fixed by photosynthesis into sugars to grow and reproduce. However, plants often face non-ideal conditions caused by biotic and abiotic stresses. These constraints impose challenges to managing sugars, the most valuable plant asset. Hence, the precise management of sugars is crucial to avoid starvation under adverse conditions and sustain growth. This review explores the role of post-translational modifications (PTMs) in the modulation of carbon metabolism. PTMs consist of chemical modifications of proteins that change protein properties, including protein-protein interaction preferences, enzymatic activity, stability, and subcellular localization. We provide a holistic view of how PTMs tune resource distribution among different physiological processes to optimize plant fitness.
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Xia L, Kong X, Song H, Han Q, Zhang S. Advances in proteome-wide analysis of plant lysine acetylation. PLANT COMMUNICATIONS 2022; 3:100266. [PMID: 35059632 PMCID: PMC8760137 DOI: 10.1016/j.xplc.2021.100266] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/21/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Lysine acetylation (LysAc) is a conserved and important post-translational modification (PTM) that plays a key role in plant physiological and metabolic processes. Based on advances in Lys-acetylated protein immunoenrichment and mass-spectrometric technology, LysAc proteomics studies have been performed in many species. Such studies have made substantial contributions to our understanding of plant LysAc, revealing that Lys-acetylated histones and nonhistones are involved in a broad spectrum of plant cellular processes. Here, we present an extensive overview of recent research on plant Lys-acetylproteomes. We provide in-depth insights into the characteristics of plant LysAc modifications and the mechanisms by which LysAc participates in cellular processes and regulates metabolism and physiology during plant growth and development. First, we summarize the characteristics of LysAc, including the properties of Lys-acetylated sites, the motifs that flank Lys-acetylated lysines, and the dynamic alterations in LysAc among different tissues and developmental stages. We also outline a map of Lys-acetylated proteins in the Calvin-Benson cycle and central carbon metabolism-related pathways. We then introduce some examples of the regulation of plant growth, development, and biotic and abiotic stress responses by LysAc. We discuss the interaction between LysAc and Nα-terminal acetylation and the crosstalk between LysAc and other PTMs, including phosphorylation and succinylation. Finally, we propose recommendations for future studies in the field. We conclude that LysAc of proteins plays an important role in the regulation of the plant life cycle.
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Shao Y, Li S, Gao L, Sun C, Hu J, Ullah A, Gao J, Li X, Liu S, Jiang D, Cao W, Tian Z, Dai T. Magnesium Application Promotes Rubisco Activation and Contributes to High-Temperature Stress Alleviation in Wheat During the Grain Filling. FRONTIERS IN PLANT SCIENCE 2021; 12:675582. [PMID: 34177993 PMCID: PMC8231710 DOI: 10.3389/fpls.2021.675582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/21/2021] [Indexed: 06/01/2023]
Abstract
Inhibited photosynthesis caused by post-anthesis high-temperature stress (HTS) leads to decreased wheat grain yield. Magnesium (Mg) plays critical roles in photosynthesis; however, its function under HTS during wheat grain filling remains poorly understood. Therefore, in this study, we investigated the effects of Mg on the impact of HTS on photosynthesis during wheat grain filling by conducting pot experiments in controlled-climate chambers. Plants were subjected to a day/night temperature cycle of 32°C/22°C for 5 days during post-anthesis; the control temperature was set at 26°C/16°C. Mg was applied at the booting stage, with untreated plants used as a control. HTS reduced the yield and net photosynthetic rate (P n ) of wheat plants. The maximum carboxylation rate (V Cmax ), which is limited by Rubisco activity, decreased earlier than the light-saturated potential electron transport rate. This decrease in V Cmax was caused by decreased Rubisco activation state under HTS. Mg application reduced yield loss by stabilizing P n . Rubisco activation was enhanced by increasing Rubisco activase activity following Mg application, thereby stabilizing P n . We conclude that Mg maintains Rubisco activation, thereby helping to stabilize P n under HTS.
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Affiliation(s)
- Yuhang Shao
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Shiyu Li
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Lijun Gao
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Chuanjiao Sun
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Jinling Hu
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Attiq Ullah
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Jingwen Gao
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Xinxin Li
- Rural Energy and Environment Agency, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Sixi Liu
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
- Chengdu Agricultural Technology Extension Station, Chengdu, China
| | - Dong Jiang
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Weixing Cao
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Zhongwei Tian
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
| | - Tingbo Dai
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, China
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Turek I, Gehring C, Irving H. Arabidopsis Plant Natriuretic Peptide Is a Novel Interactor of Rubisco Activase. Life (Basel) 2020; 11:life11010021. [PMID: 33396438 PMCID: PMC7823470 DOI: 10.3390/life11010021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/22/2020] [Accepted: 12/29/2020] [Indexed: 11/16/2022] Open
Abstract
Plant natriuretic peptides (PNPs) are a group of systemically acting peptidic hormones affecting solute and solvent homeostasis and responses to biotrophic pathogens. Although an increasing body of evidence suggests PNPs modulate plant responses to biotic and abiotic stress, which could lead to their potential biotechnological application by conferring increased stress tolerance to plants, the exact mode of PNPs action is still elusive. In order to gain insight into PNP-dependent signalling, we set out to identify interactors of PNP present in the model plant Arabidopsis thaliana, termed AtPNP-A. Here, we report identification of rubisco activase (RCA), a central regulator of photosynthesis converting Rubisco catalytic sites from a closed to an open conformation, as an interactor of AtPNP-A through affinity isolation followed by mass spectrometric identification. Surface plasmon resonance (SPR) analyses reveals that the full-length recombinant AtPNP-A and the biologically active fragment of AtPNP-A bind specifically to RCA, whereas a biologically inactive scrambled peptide fails to bind. These results are considered in the light of known functions of PNPs, PNP-like proteins, and RCA in biotic and abiotic stress responses.
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Affiliation(s)
- Ilona Turek
- Biomolecular Laboratory, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Department of Pharmacy and Biomedical Sciences, La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC 3552, Australia
| | - Chris Gehring
- Biomolecular Laboratory, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06121 Perugia, Italy
| | - Helen Irving
- Department of Pharmacy and Biomedical Sciences, La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC 3552, Australia
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Na 2CO 3-responsive Photosynthetic and ROS Scavenging Mechanisms in Chloroplasts of Alkaligrass Revealed by Phosphoproteomics. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:271-288. [PMID: 32683046 PMCID: PMC7801222 DOI: 10.1016/j.gpb.2018.10.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/08/2018] [Accepted: 10/23/2018] [Indexed: 12/27/2022]
Abstract
Alkali-salinity exerts severe osmotic, ionic, and high-pH stresses to plants. To understand the alkali-salinity responsive mechanisms underlying photosynthetic modulation and reactive oxygen species (ROS) homeostasis, physiological and diverse quantitative proteomics analyses of alkaligrass (Puccinellia tenuiflora) under Na2CO3 stress were conducted. In addition, Western blot, real-time PCR, and transgenic techniques were applied to validate the proteomic results and test the functions of the Na2CO3-responsive proteins. A total of 104 and 102 Na2CO3-responsive proteins were identified in leaves and chloroplasts, respectively. In addition, 84 Na2CO3-responsive phosphoproteins were identified, including 56 new phosphorylation sites in 56 phosphoproteins from chloroplasts, which are crucial for the regulation of photosynthesis, ion transport, signal transduction, and energy homeostasis. A full-length PtFBA encoding an alkaligrass chloroplastic fructose-bisphosphate aldolase (FBA) was overexpressed in wild-type cells of cyanobacterium Synechocystis sp. Strain PCC 6803, leading to enhanced Na2CO3 tolerance. All these results indicate that thermal dissipation, state transition, cyclic electron transport, photorespiration, repair of photosystem (PS) II, PSI activity, and ROS homeostasis were altered in response to Na2CO3 stress, which help to improve our understanding of the Na2CO3-responsive mechanisms in halophytes.
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Shaki F, Ebrahimzadeh Maboud H, Niknam V. Differential proteomics: Effect of growth regulators on salt stress responses in safflower seedlings. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2020; 164:149-155. [PMID: 32284121 DOI: 10.1016/j.pestbp.2020.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/17/2020] [Accepted: 01/18/2020] [Indexed: 06/11/2023]
Abstract
Productivity of safflower (Carthamus tinctorius L.) is markedly reduced by salt stress. This study is based on analysis of proteins profile of safflower plants treated with 200 mM NaCl, with exogenously applied salicylic acid (SA) and penconazole (PEN), as growth regulators. Plants were investigated through a gel-based proteomic approach, which resulted in the identification of 17 salt-responsive proteins related to different metabolic modifications. Of these, seven different proteins were up or down regulated by both SA and PEN, suggesting the synergistic and antagonistic effects of SA and PEN. The classification of differentially expressed proteins showed that salt-responsive proteins were mainly involved in photosynthesis, ion homeostasis, and oxidative stress response, as well as nitrogen, protein, and carbohydrate metabolism. The identified stress-responsive proteins in this study could pave the way to develop salt tolerance in safflower, thus sustaining its productivity under salinity. In addition, SA and PEN may be considered as a foliar application to ameliorate salinity effects, due to their low price and availability.
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Affiliation(s)
- Fatemeh Shaki
- Department of Plant Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
| | - Hasan Ebrahimzadeh Maboud
- Department of Plant Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
| | - Vahid Niknam
- Department of Plant Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
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Probing the rice Rubisco-Rubisco activase interaction via subunit heterooligomerization. Proc Natl Acad Sci U S A 2019; 116:24041-24048. [PMID: 31712424 DOI: 10.1073/pnas.1914245116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
During photosynthesis the AAA+ protein and essential molecular chaperone Rubisco activase (Rca) constantly remodels inhibited active sites of the CO2-fixing enzyme Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase) to release tightly bound sugar phosphates. Higher plant Rca is a crop improvement target, but its mechanism remains poorly understood. Here we used structure-guided mutagenesis to probe the Rubisco-interacting surface of rice Rca. Mutations in Ser-23, Lys-148, and Arg-321 uncoupled adenosine triphosphatase and Rca activity, implicating them in the Rubisco interaction. Mutant doping experiments were used to evaluate a suite of known Rubisco-interacting residues for relative importance in the context of the functional hexamer. Hexamers containing some subunits that lack the Rubisco-interacting N-terminal domain displayed a ∼2-fold increase in Rca function. Overall Rubisco-interacting residues located toward the rim of the hexamer were found to be less critical to Rca function than those positioned toward the axial pore. Rca is a key regulator of the rate-limiting CO2-fixing reactions of photosynthesis. A detailed functional understanding will assist the ongoing endeavors to enhance crop CO2 assimilation rate, growth, and yield.
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Szuba A, Marczak Ł, Karliński L, Mucha J, Tomaszewski D. Regulation of the leaf proteome by inoculation of Populus × canescens with two Paxillus involutus isolates differing in root colonization rates. MYCORRHIZA 2019; 29:503-517. [PMID: 31456074 DOI: 10.1007/s00572-019-00910-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 08/09/2019] [Indexed: 06/10/2023]
Abstract
During ectomycorrhizal symbioses, up to 30% of the carbon produced in leaves may be translocated to the fungal partner. Given that the leaf response to root colonization is largely unknown, we performed a leaf proteome analysis of Populus × canescens inoculated in vitro with two isolates of Paxillus involutus significantly differing in root colonization rates (65 ± 7% vs 14 ± 7%), together with plant growth and leaf biochemistry analyses to determine the response of plant leaves to ectomycorrhizal root colonization. The isolate that more efficiently colonized roots (isolate H) affected 9.1% of the leaf proteome compared with control plants. Simultaneously, ectomycorrhiza in isolate H-inoculated plants led to improved plant growth and an increased abundance of leaf proteins involved in protein turnover, stress response, carbohydrate metabolism, and photosynthesis. The protein increment was also correlated with increases in chlorophyll, foliar carbon, and carbohydrate contents. Although inoculation of P. × canescens roots with the other P. involutus isolate (isolate L, characterized by a low root colonization ratio) affected 6.8% of the leaf proteome compared with control plants, most proteins were downregulated. The proteomic signals of increased carbohydrate biosynthesis were not detected, and carbohydrate, carbon, and leaf pigment levels and plant biomass did not differ from the noninoculated plants. Our results revealed that the upregulation of the photosynthetic protein abundance and levels of leaf carbohydrate are positively related to rates of root colonization. Upregulation of photosynthetic proteins, chlorophyll, and leaf carbohydrate levels in ectomycorrhizal plants was positively related to root colonization rates and resulted in increased carbon translocation and sequestration underground.
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Affiliation(s)
- Agnieszka Szuba
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035, Kórnik, Poland.
| | - Łukasz Marczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Leszek Karliński
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035, Kórnik, Poland
| | - Joanna Mucha
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035, Kórnik, Poland
| | - Dominik Tomaszewski
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035, Kórnik, Poland
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In vivo evidence for a regulatory role of phosphorylation of Arabidopsis Rubisco activase at the Thr78 site. Proc Natl Acad Sci U S A 2019; 116:18723-18731. [PMID: 31451644 DOI: 10.1073/pnas.1812916116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Arabidopsis Rubisco activase (Rca) is phosphorylated at threonine-78 (Thr78) in low light and in the dark, suggesting a potential regulatory role in photosynthesis, but this has not been directly tested. To do so, we transformed an rca-knockdown mutant largely lacking redox regulation with wild-type Rca-β or Rca-β with Thr78-to-Ala (T78A) or Thr78-to-Ser (T78S) site-directed mutations. Interestingly, the T78S mutant was hyperphosphorylated at the Ser78 site relative to Thr78 of the Rca-β wild-type control, as evidenced by immunoblotting with custom antibodies and quantitative mass spectrometry. Moreover, plants expressing the T78S mutation had reduced photosynthesis and quantum efficiency of photosystem II (ϕPSII) and reduced growth relative to control plants expressing wild-type Rca-β under all conditions tested. Gene expression was also altered in a manner consistent with reduced growth. In contrast, plants expressing Rca-β with the phospho-null T78A mutation had faster photosynthetic induction kinetics and increased ϕPSII relative to Rca-β controls. While expression of the wild-type Rca-β or the T78A mutant fully rescued the slow-growth phenotype of the rca-knockdown mutant grown in a square-wave light regime, the T78A mutants grew faster than the Rca-β control plants at low light (30 µmol photons m-2 s-1) and in a fluctuating low-light/high-light environment. Collectively, these results suggest that phosphorylation of Thr78 (or Ser78 in the T78S mutant) plays a negative regulatory role in vivo and provides an explanation for the absence of Ser at position 78 in terrestrial plant species.
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Zhang C, Guo X, Xie H, Li J, Liu X, Zhu B, Liu S, Li H, Li M, He M, Chen P. Quantitative phosphoproteomics of lectin receptor-like kinase VI.4 dependent abscisic acid response in Arabidopsis thaliana. PHYSIOLOGIA PLANTARUM 2019; 165:728-745. [PMID: 29797451 DOI: 10.1111/ppl.12763] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 05/14/2018] [Accepted: 05/15/2018] [Indexed: 06/08/2023]
Abstract
Lectin receptor-like kinases (LecRKs) play important roles in the responses to adverse environment stress. Abscisic acid (ABA) is a plant hormone involved in plant growth, development and adverse environmental stress responses. Although some studies of ABA response LecRK genes have been reported, the molecular mechanisms of LecRKs regulation of downstream pathways under ABA induction are not well understood. The present study showed that LecRK-VI.4 responded to ABA and negatively regulated stomatal closure. Here, a quantitative phosphoproteomics approach based on mass spectrometry was employed to study the roles of LecRK-VI.4 in the ABA signaling pathway. Metal oxide affinity beads and C18 chromatography were used for phosphopeptide enrichment and separation. The isobaric tags for relative and absolute quantitation were used for profiling the phosphoproteome of mutant lecrk-vi.4-1 and wild-type Col-0 Arabidopsis under normal growth conditions or ABA treatments. In total, 475 unique phosphopeptides were quantified, including 81 phosphopeptides related to LecRK-VI.4 regulation. Gene ontology, protein-protein interaction and motif analysis were performed. The bioinformatics data showed that phosphorylated proteins regulated by LecRK-VI.4 had close relations with factors of stomatal function, which included aquaporin activity, H+ pump activity and the Ca2+ concentration in the cytoplasm. These data have expanded our understanding of how LecRK-VI.4 regulates ABA-mediated stomatal movements.
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Affiliation(s)
- Cheng Zhang
- College of Life Sciences, Hunan University, Changsha, 410082, China
| | - Xinhong Guo
- College of Life Sciences, Hunan University, Changsha, 410082, China
| | - Huali Xie
- Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, Hunan Normal University, Changsha, 410081, China
| | - Jinyan Li
- College of Life Sciences, Hunan University, Changsha, 410082, China
| | - Xiaoqian Liu
- Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, Hunan Normal University, Changsha, 410081, China
| | - Baode Zhu
- Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, Hunan Normal University, Changsha, 410081, China
| | - Shucan Liu
- College of Life Sciences, Hunan University, Changsha, 410082, China
| | - Huili Li
- College of Life Sciences, Hunan University, Changsha, 410082, China
| | - Meiling Li
- College of Life Sciences, Hunan University, Changsha, 410082, China
| | - Mingqi He
- College of Life Sciences, Hunan University, Changsha, 410082, China
| | - Ping Chen
- Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, Hunan Normal University, Changsha, 410081, China
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Liu GT, Jiang JF, Liu XN, Jiang JZ, Sun L, Duan W, Li RM, Wang Y, Lecourieux D, Liu CH, Li SH, Wang LJ. New insights into the heat responses of grape leaves via combined phosphoproteomic and acetylproteomic analyses. HORTICULTURE RESEARCH 2019; 6:100. [PMID: 31666961 PMCID: PMC6804945 DOI: 10.1038/s41438-019-0183-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 05/04/2023]
Abstract
Heat stress is a serious and widespread threat to the quality and yield of many crop species, including grape (Vitis vinifera L.), which is cultivated worldwide. Here, we conducted phosphoproteomic and acetylproteomic analyses of leaves of grape plants cultivated under four distinct temperature regimes. The phosphorylation or acetylation of a total of 1011 phosphoproteins with 1828 phosphosites and 96 acetyl proteins with 148 acetyl sites changed when plants were grown at 35 °C, 40 °C, and 45 °C in comparison with the proteome profiles of plants grown at 25 °C. The greatest number of changes was observed at the relatively high temperatures. Functional classification and enrichment analysis indicated that phosphorylation, rather than acetylation, of serine/arginine-rich splicing factors was involved in the response to high temperatures. This finding is congruent with previous observations by which alternative splicing events occurred more frequently in grapevine under high temperature. Changes in acetylation patterns were more common than changes in phosphorylation patterns in photosynthesis-related proteins at high temperatures, while heat-shock proteins were associated more with modifications involving phosphorylation than with those involving acetylation. Nineteen proteins were identified with changes associated with both phosphorylation and acetylation, which is consistent with crosstalk between these posttranslational modification types.
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Affiliation(s)
- Guo-Tian Liu
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- College of Horticulture, Northwest A&F University, Yangling, 712100 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - Jian-Fu Jiang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 China
| | - Xin-Na Liu
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - Jin-Zhu Jiang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - Lei Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 China
| | - Wei Duan
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
| | - Rui-Min Li
- College of Horticulture, Northwest A&F University, Yangling, 712100 China
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - David Lecourieux
- Universite´ de Bordeaux, ISVV, Ecophysiologie et Ge´nomique Fonctionnelle de la Vigne, UMR 1287, F-33140 Villenave d’Ornon, France
- INRA, ISVV, Ecophysiologie et Ge´nomique Fonctionnelle de la Vigne, UMR 1287, F-33140 Villenave d’Ornon, France
| | - Chong-Huai Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 China
| | - Shao-Hua Li
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - Li-Jun Wang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
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14
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Pan D, Wang L, Chen S, Lv X, Lu S, Cheng CL, Tan F, Chen W. Protein acetylation as a mechanism for Kandelia candel's adaption to daily flooding. TREE PHYSIOLOGY 2018; 38:895-910. [PMID: 29301031 DOI: 10.1093/treephys/tpx162] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 12/07/2017] [Indexed: 06/07/2023]
Abstract
To explore the adaptation mechanisms of Kandelia candel (L.) Druce in response to daily flooding, a large-scale quantitative lysine acetylome was carried out using immunoaffinity enrichment of Lys-acetylated peptides and liquid chromatography linked to tandem mass spectrometry. A total of 1041 lysine acetylation (LysAc) sites, 1021 Lys-acetylated peptides and 617 Lys-acetylated proteins were identified. Six conserved sequence motifs of the LysAc sites, including a new motif KxxxxK, were detected. Among these proteins, 260 were differentially acetylated in response to flooding, which were preferentially predicted to participate in carbon metabolism and photosynthesis pathways based on KEGG pathway category enrichment analysis. Consistently, the transcriptional level of acetyltransferase and the consumption of acetyl-CoA were up-regulated under flooding conditions. Most of physiological parameters and mRNA expression levels related to carbon metabolism and photosynthesis were found to be insignificantly affected by flooding. Taken together, reversible protein LysAc is likely to be a post-translational mechanism contributing to the mangrove K. candel's adaptation to daily flooding.
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Affiliation(s)
- Dezhuo Pan
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Lingxia Wang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
- College of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Shipin Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Xiaojie Lv
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Si Lu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Chi-Lien Cheng
- Department of Biology, The University of Iowa, 210 Biology Building, Iowa City, IA 52242, USA
| | - Fanlin Tan
- Fujian Academy of Forestry, Fuzhou 350012, PR China
| | - Wei Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
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15
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Pan D, Wang L, Tan F, Lu S, Lv X, Zaynab M, Cheng CL, Abubakar YS, Chen S, Chen W. Phosphoproteomics unveils stable energy supply as key to flooding tolerance in Kandelia candel. J Proteomics 2018; 176:1-12. [DOI: 10.1016/j.jprot.2018.01.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/30/2017] [Accepted: 01/10/2018] [Indexed: 12/23/2022]
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16
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Mueller-Cajar O. The Diverse AAA+ Machines that Repair Inhibited Rubisco Active Sites. Front Mol Biosci 2017; 4:31. [PMID: 28580359 PMCID: PMC5437159 DOI: 10.3389/fmolb.2017.00031] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 04/29/2017] [Indexed: 11/13/2022] Open
Abstract
Gaseous carbon dioxide enters the biosphere almost exclusively via the active site of the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco). This highly conserved catalyst has an almost universal propensity to non-productively interact with its substrate ribulose 1,5-bisphosphate, leading to the formation of dead-end inhibited complexes. In diverse autotrophic organisms this tendency has been counteracted by the recruitment of dedicated AAA+ (ATPases associated with various cellular activities) proteins that all use the energy of ATP hydrolysis to remodel inhibited Rubisco active sites leading to release of the inhibitor. Three evolutionarily distinct classes of these Rubisco activases (Rcas) have been discovered so far. Green and red-type Rca are mostly found in photosynthetic eukaryotes of the green and red plastid lineage respectively, whereas CbbQO is associated with chemoautotrophic bacteria. Ongoing mechanistic studies are elucidating how the various motors are utilizing both similar and contrasting strategies to ultimately perform their common function of cracking the inhibited Rubisco active site. The best studied mechanism utilized by red-type Rca appears to involve transient threading of the Rubisco large subunit C-terminal peptide, reminiscent of the action performed by Clp proteases. As well as providing a fascinating example of convergent molecular evolution, Rca proteins can be considered promising crop-improvement targets. Approaches aiming to replace Rubisco in plants with improved enzymes will need to ensure the presence of a compatible Rca protein. The thermolability of the Rca protein found in crop plants provides an opportunity to fortify photosynthesis against high temperature stress. Photosynthesis also appears to be limited by Rca when light conditions are fluctuating. Synthetic biology strategies aiming to enhance the autotrophic CO2 fixation machinery will need to take into consideration the requirement for Rubisco activases as well as their properties.
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Affiliation(s)
- Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological UniversitySingapore, Singapore
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17
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Grabsztunowicz M, Koskela MM, Mulo P. Post-translational Modifications in Regulation of Chloroplast Function: Recent Advances. FRONTIERS IN PLANT SCIENCE 2017; 8:240. [PMID: 28280500 PMCID: PMC5322211 DOI: 10.3389/fpls.2017.00240] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 02/08/2017] [Indexed: 05/08/2023]
Abstract
Post-translational modifications (PTMs) of proteins enable fast modulation of protein function in response to metabolic and environmental changes. Phosphorylation is known to play a major role in regulating distribution of light energy between the Photosystems (PS) I and II (state transitions) and in PSII repair cycle. In addition, thioredoxin-mediated redox regulation of Calvin cycle enzymes has been shown to determine the efficiency of carbon assimilation. Besides these well characterized modifications, recent methodological progress has enabled identification of numerous other types of PTMs in various plant compartments, including chloroplasts. To date, at least N-terminal and Lys acetylation, Lys methylation, Tyr nitration and S-nitrosylation, glutathionylation, sumoylation and glycosylation of chloroplast proteins have been described. These modifications impact DNA replication, control transcriptional efficiency, regulate translational machinery and affect metabolic activities within the chloroplast. Moreover, light reactions of photosynthesis as well as carbon assimilation are regulated at multiple levels by a number of PTMs. It is likely that future studies will reveal new metabolic pathways to be regulated by PTMs as well as detailed molecular mechanisms of PTM-mediated regulation.
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Affiliation(s)
| | | | - Paula Mulo
- Molecular Plant Biology, Department of Biochemistry, University of TurkuTurku, Finland
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18
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Yousuf PY, Ahmad A, Aref IM, Ozturk M, Ganie AH, Iqbal M. Salt-stress-responsive chloroplast proteins in Brassica juncea genotypes with contrasting salt tolerance and their quantitative PCR analysis. PROTOPLASMA 2016; 253:1565-1575. [PMID: 26638208 DOI: 10.1007/s00709-015-0917-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 11/23/2015] [Indexed: 05/21/2023]
Abstract
Brassica juncea is mainly cultivated in the arid and semi-arid regions of India where its production is significantly affected by soil salinity. Adequate knowledge of the mechanisms underlying the salt tolerance at sub-cellular levels must aid in developing the salt-tolerant plants. A proper functioning of chloroplasts under salinity conditions is highly desirable to maintain crop productivity. The adaptive molecular mechanisms offered by plants at the chloroplast level to cope with salinity stress must be a prime target in developing the salt-tolerant plants. In the present study, we have analyzed differential expression of chloroplast proteins in two Brassica juncea genotypes, Pusa Agrani (salt-sensitive) and CS-54 (salt-tolerant), under the effect of sodium chloride. The chloroplast proteins were isolated and resolved using 2DE, which facilitated identification and quantification of 12 proteins that differed in expression in the salt-tolerant and salt-sensitive genotypes. The identified proteins were related to a variety of chloroplast-associated molecular processes, including oxygen-evolving process, PS I and PS II functioning, Calvin cycle and redox homeostasis. Expression analysis of genes encoding differentially expressed proteins through real time PCR supported our findings with proteomic analysis. The study indicates that modulating the expression of chloroplast proteins associated with stabilization of photosystems and oxidative defence plays imperative roles in adaptation to salt stress.
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Affiliation(s)
- Peerzada Yasir Yousuf
- Department of Botany, Molecular Ecology Laboratory, Jamia Hamdard, New Delhi, 110062, India
| | - Altaf Ahmad
- Department of Botany, Aligarh Muslim University, Aligarh, 202002, India
| | - Ibrahim M Aref
- Department of Plant Production, College of Food and Agricultural Science, King Saud University, Post Box 2460, Riyadh, 11451, Saudi Arabia
| | - Munir Ozturk
- Department of Biology, Ege University, Izmir, 350000, Turkey
| | - Arshid Hussain Ganie
- Department of Botany, Molecular Ecology Laboratory, Jamia Hamdard, New Delhi, 110062, India
| | - Muhammad Iqbal
- Department of Botany, Molecular Ecology Laboratory, Jamia Hamdard, New Delhi, 110062, India.
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Luís IM, Alexandre BM, Oliveira MM, Abreu IA. Selection of an Appropriate Protein Extraction Method to Study the Phosphoproteome of Maize Photosynthetic Tissue. PLoS One 2016; 11:e0164387. [PMID: 27727304 PMCID: PMC5058499 DOI: 10.1371/journal.pone.0164387] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/23/2016] [Indexed: 12/14/2022] Open
Abstract
Often plant tissues are recalcitrant and, due to that, methods relying on protein precipitation, such as TCA/acetone precipitation and phenol extraction, are usually the methods of choice for protein extraction in plant proteomic studies. However, the addition of precipitation steps to protein extraction methods may negatively impact protein recovery, due to problems associated with protein re-solubilization. Moreover, we show that when working with non-recalcitrant plant tissues, such as young maize leaves, protein extraction methods with precipitation steps compromise the maintenance of some labile post-translational modifications (PTMs), such as phosphorylation. Therefore, a critical issue when studying PTMs in plant proteins is to ensure that the protein extraction method is the most appropriate, both at qualitative and quantitative levels. In this work, we compared five methods for protein extraction of the C4-photosynthesis related proteins, in the tip of fully expanded third-leaves. These included: TCA/Acetone Precipitation; Phenol Extraction; TCA/Acetone Precipitation followed by Phenol Extraction; direct extraction in Lysis Buffer (a urea-based buffer); and direct extraction in Lysis Buffer followed by Cleanup with a commercial kit. Protein extraction in Lysis Buffer performed better in comparison to the other methods. It gave one of the highest protein yields, good coverage of the extracted proteome and phosphoproteome, high reproducibility, and little protein degradation. This was also the easiest and fastest method, warranting minimal sample handling. We also show that this method is adequate for the successful extraction of key enzymes of the C4-photosynthetic metabolism, such as PEPC, PPDK, PEPCK, and NADP-ME. This was confirmed by MALDI-TOF/TOF MS analysis of excised spots of 2DE analyses of the extracted protein pools. Staining for phosphorylated proteins in 2DE revealed the presence of several phosphorylated isoforms of PEPC, PPDK, and PEPCK.
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Affiliation(s)
- Inês M. Luís
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Oeiras, Portugal
| | | | - M. Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Oeiras, Portugal
| | - Isabel A. Abreu
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Oeiras, Portugal
- Instituto Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal
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20
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Baginsky S. Protein phosphorylation in chloroplasts - a survey of phosphorylation targets. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3873-82. [PMID: 26969742 DOI: 10.1093/jxb/erw098] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The development of new software tools, improved mass spectrometry equipment, a suite of optimized scan types, and better-quality phosphopeptide affinity capture have paved the way for an explosion of mass spectrometry data on phosphopeptides. Because phosphoproteomics achieves good sensitivity, most studies use complete cell extracts for phosphopeptide enrichment and identification without prior enrichment of proteins or subcellular compartments. As a consequence, the phosphoproteome of cell organelles often comes as a by-product from large-scale studies and is commonly assembled from these in meta-analyses. This review aims at providing some guidance on the limitations of meta-analyses that combine data from analyses with different scopes, reports on the current status of knowledge on chloroplast phosphorylation targets, provides initial insights into phosphorylation site conservation in different plant species, and highlights emerging information on the integration of gene expression with metabolism and photosynthesis by means of protein phosphorylation.
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Affiliation(s)
- Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany
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21
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Liu Z, Li Y, Cao H, Ren D. Comparative phospho-proteomics analysis of salt-responsive phosphoproteins regulated by the MKK9-MPK6 cascade in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 241:138-50. [PMID: 26706066 DOI: 10.1016/j.plantsci.2015.10.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 10/09/2015] [Accepted: 10/10/2015] [Indexed: 05/20/2023]
Abstract
Mitogen-activated protein kinase (MAPK) cascades are involved in the salt stress response in plants. However, the identities of specific proteins operating downstream of MAPKs in the salt stress response remain unclear. Our studies showed that mkk9 and mpk6 null mutant seedlings are hyposensitive to salt stress. Moreover, we showed that MPK6 was activated by salt stress, indicating that the MKK9-MPK6 cascade mediated the salt stress response in Arabidopsis. To identify phosphoproteins downstream of the MKK9-MPK6 cascade in the salt stress response pathway, we performed two-dimensional electrophoresis (2-DE) with Pro-Q phosphoprotein staining and matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) to identify phosphoproteins induced by salt treatment in mkk9, mpk6, and wild-type seedlings. Phosphorylation of 4 proteins, including Rubisco activase (RCA), plastid ribosomal protein S 1 (PRPS1), plastid division protein (FtsZ2-2), and tortifolia2 (TOR2), was found to be regulated by activation of MKK9-MPK6 cascade. Further Phospho-proteomics analysis of MKK9(DD) mutant seedlings revealed that RCA phosphorylation was up-regulated as a result of MKK9 activation. The finding that the MKK9-MPK6 cascade functions in the salt stress response by regulating phosphorylation of RCA, PRPS1, FtsZ2-2, and TOR2, provides a novel insight into the MAPK-related mechanisms underlying the salt stress response in plants.
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Affiliation(s)
- Zhenbin Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yuan Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hanwei Cao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Dongtao Ren
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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22
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Lin PC, Hu WC, Lee SC, Chen YL, Lee CY, Chen YR, Liu LYD, Chen PY, Lin SS, Chang YC. Application of an Integrated Omics Approach for Identifying Host Proteins That Interact With Odontoglossum ringspot virus Capsid Protein. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:711-26. [PMID: 25625820 DOI: 10.1094/mpmi-08-14-0246-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The glutamic acid at position 100 (E(100)) in the capsid protein (CP) of Odontoglossum ringspot virus (ORSV) plays an important role in long-distance viral movement in Nicotiana benthamiana. The ORSV(E100A) mutant, which has a glutamic acid to alanine substitution, shows a loss of systemic infectivity in N. benthamiana. Transmission electron microscopy and size-exclusion chromatography assays showed that E(100) is essential for CP-CP interaction and viral particle assembly. To identify the ORSV triggering or response genes and CP-interacting proteins (CP-IP), an integrated omics approach based on next-generation sequencing and proteomics profiling was used in this study. The whole-transcriptomes of healthy and ORSV-infected leaves of N. benthamiana were analyzed, and the gene information was used to create a N. benthamiana protein database that was used for protein identification following mass spectrometry analysis. The integrated omics approach identified several putative host proteins that interact with ORSV CP(WT) and were categorized as photosystem subunits, defense-associated proteins, and cell division components. The expression pattern and CP interaction of these CP-IP were examined by semiquantitative reverse transcription polymerase chain reaction and an in vitro binding assay, respectively, to verify the in silico data. Among these proteins, a proteinase inhibitor of N. benthamiana (NbPI2) was highly associated with CP(E100A) as compared with CP(WT), and NbPI1 and NbPI2 were highly induced in ORSV-infected plants. NbPI1- and NbPI2-silenced plants (via a Tobacco rattle virus-induced gene-silencing system) did not exhibit a difference in ORSV infection. Thus, whether NbPI1 and NbPI2 play a role in plant immunity requires further investigation. In summary, the integrated omics approach provides massive and valuable information to identify the ORSV CP-IP and these CP-IP will help us to understand the movement of this virus and plant-virus interaction.
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Affiliation(s)
- Pin-Chun Lin
- 1 Department of Plant Pathology and Microbiology, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
- 2 Institute of Biotechnology, National Taiwan University, 81, Chang-Xing St., Taipei, Taiwan
| | - Wen-Chi Hu
- 1 Department of Plant Pathology and Microbiology, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
| | - Shu-Chuan Lee
- 1 Department of Plant Pathology and Microbiology, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
| | - Ying-Lan Chen
- 4 Agricultural Biotechnology Research Center, Academia Sinica, 128, Academia Rd, Sec. 2, Taipei, Taiwan
- 5 Institute of Plant Biology and Department of Life Science, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
| | - Chi-Ying Lee
- 4 Agricultural Biotechnology Research Center, Academia Sinica, 128, Academia Rd, Sec. 2, Taipei, Taiwan
| | - Yet-Ran Chen
- 4 Agricultural Biotechnology Research Center, Academia Sinica, 128, Academia Rd, Sec. 2, Taipei, Taiwan
| | - Li-Yu Daisy Liu
- 6 Department of Agronomy, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
| | - Po-Yen Chen
- 1 Department of Plant Pathology and Microbiology, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
| | - Shih-Shun Lin
- 2 Institute of Biotechnology, National Taiwan University, 81, Chang-Xing St., Taipei, Taiwan
- 3 Genome and Systems Biology Degree Program, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
- 4 Agricultural Biotechnology Research Center, Academia Sinica, 128, Academia Rd, Sec. 2, Taipei, Taiwan
| | - Ya-Chun Chang
- 1 Department of Plant Pathology and Microbiology, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
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Arabidopsis proteome responses to the smoke-derived growth regulator karrikin. J Proteomics 2015; 120:7-20. [PMID: 25746380 DOI: 10.1016/j.jprot.2015.02.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 02/19/2015] [Accepted: 02/23/2015] [Indexed: 12/19/2022]
Abstract
UNLABELLED Karrikins are butenolide plant growth regulators in smoke from burning plant material that have proven ability to promote germination and seedling photomorphogenesis. However, the molecular mechanisms underlying these processes are unclear. Here we provide the first proteome-wide analysis of early responses to karrikin in plants (Arabidopsis seedlings). Image analysis of two-dimensionally separated proteins, Rubisco-depleted proteomes and phosphoproteomes, together with LC-MS profiling, detected >1900 proteins, 113 of which responded to karrikin treatment. All the differentially abundant proteins (except HSP70-3) are novel karrikin-responders, and most are involved in photosynthesis, carbohydrate metabolism, redox homeostasis, transcription control, proteosynthesis, protein transport and processing, or protein degradation. Our data provide functionally complementary information to previous identifications of karrikin-responsive genes and evidence for a novel karrikin signalling pathway originating in chloroplasts. We present an updated model of karrikin signalling that integrates proteomic data and is supported by growth response observations. BIOLOGICAL SIGNIFICANCE Karrikin has shown promising potential in agricultural applications, yet this process is poorly understood at the molecular level. To the best of our knowledge, this is the first survey of early global proteomic responses to karrikin in plants (Arabidopsis seedlings). The combination of label-free LC-MS profiling and 2-DE analyses provided highly sensitive snapshots of protein abundance and quantitative information on proteoform-level changes. These results present evidence of proteasome-independent karrikin signalling pathways and provide novel targets for detailed mechanistic studies using, e.g., mutants and transgenic plants.
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