1
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Zhang T, Day NJ, Gaffrey M, Weitz KK, Attah K, Mimche PN, Paine R, Qian WJ, Helms MN. Regulation of hyperoxia-induced neonatal lung injury via post-translational cysteine redox modifications. Redox Biol 2022; 55:102405. [PMID: 35872399 PMCID: PMC9307955 DOI: 10.1016/j.redox.2022.102405] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 07/11/2022] [Indexed: 12/17/2022] Open
Abstract
Preterm infants and patients with lung disease often have excess fluid in the lungs and are frequently treated with oxygen, however long-term exposure to hyperoxia results in irreversible lung injury. Although the adverse effects of hyperoxia are mediated by reactive oxygen species, the full extent of the impact of hyperoxia on redox-dependent regulation in the lung is unclear. In this study, neonatal mice overexpressing the beta-subunit of the epithelial sodium channel (β-ENaC) encoded by Scnn1b and their wild type (WT; C57Bl6) littermates were utilized to study the pathogenesis of high fraction inspired oxygen (FiO2)-induced lung injury. Results showed that O2-induced lung injury in transgenic Scnn1b mice is attenuated following chronic O2 exposure. To test the hypothesis that reversible cysteine-redox-modifications of proteins play an important role in O2-induced lung injury, we performed proteome-wide profiling of protein S-glutathionylation (SSG) in both WT and Scnn1b overexpressing mice maintained at 21% O2 (normoxia) or FiO2 85% (hyperoxia) from birth to 11-15 days postnatal. Over 7700 unique Cys sites with SSG modifications were identified and quantified, covering more than 3000 proteins in the lung. In both mouse models, hyperoxia resulted in a significant alteration of the SSG levels of Cys sites belonging to a diverse range of proteins. In addition, substantial SSG changes were observed in the Scnn1b overexpressing mice exposed to hyperoxia, suggesting that ENaC plays a critically important role in cellular regulation. Hyperoxia-induced SSG changes were further supported by the results observed for thiol total oxidation, the overall level of reversible oxidation on protein cysteine residues. Differential analyses reveal that Scnn1b overexpression may protect against hyperoxia-induced lung injury via modulation of specific processes such as cell adhesion, blood coagulation, and proteolysis. This study provides a landscape view of protein oxidation in the lung and highlights the importance of redox regulation in O2-induced lung injury.
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Affiliation(s)
- Tong Zhang
- Integrative Omics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Nicholas J Day
- Integrative Omics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Matthew Gaffrey
- Integrative Omics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karl K Weitz
- Integrative Omics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kwame Attah
- Integrative Omics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Patrice N Mimche
- Division of Microbiology and Immunology, Department of Pathology, University of Utah Molecular Medicine Program, Salt Lake City, UT, USA
| | - Robert Paine
- Pulmonary Division, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Wei-Jun Qian
- Integrative Omics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - My N Helms
- Pulmonary Division, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA.
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2
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Chen Y, Zhu W, Yan T, Chen D, Jiang L, Chen ZH, Wu D. Stomatal morphological variation contributes to global ecological adaptation and diversification of Brassica napus. PLANTA 2022; 256:64. [PMID: 36029339 DOI: 10.1007/s00425-022-03982-4] [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: 06/29/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Stomatal density and guard cell length of 274 global core germplasms of rapeseed reveal that the stomatal morphological variation contributes to global ecological adaptation and diversification of Brassica napus. Stomata are microscopic structures of plants for the regulation of CO2 assimilation and transpiration. Stomatal morphology has changed substantially in the adaptation to the external environment during land plant evolution. Brassica napus is a major crop to produce oil, livestock feed and biofuel in the world. However, there are few studies on the regulatory genes controlling stomatal development and their interaction with environmental factors as well as the genetic mechanism of adaptive variation in B. napus. Here, we characterized stomatal density (SD) and guard cell length (GL) of 274 global core germplasms at seedling stage. It was found that among the significant phenotypic variation, European germplasms are mostly winter rapeseed with high stomatal density and small guard cell length. However, the germplasms from Asia (especially China) are semi-winter rapeseed, which is characterized by low stomatal density and large guard cell length. Through selective sweep analysis and homology comparison, we identified several candidate genes related to stomatal density and guard cell length, including Epidermal Patterning Factor2 (EPF2; BnaA09g23140D), Epidermal Patterning Factor Like4 (EPFL4; BnaC01g22890D) and Suppressor of LLP1 (SOL1 BnaC01g22810D). Haplotype and phylogenetic analysis showed that natural variation in EPF2, EPFL4 and SOL1 is closely associated with the winter, spring, and semi-winter rapeseed ecotypes. In summary, this study demonstrated for the first time the relation between stomatal phenotypic variation and ecological adaptation in rapeseed, which is useful for future molecular breeding of rapeseed in the context of evolution and domestication of key stomatal traits and global climate change.
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Affiliation(s)
- Yeke Chen
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Weizhuo Zhu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Tao Yan
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Danyi Chen
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Lixi Jiang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW, Australia.
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.
| | - Dezhi Wu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China.
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.
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3
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Maszkowska J, Szymańska KP, Kasztelan A, Krzywińska E, Sztatelman O, Dobrowolska G. The Multifaceted Regulation of SnRK2 Kinases. Cells 2021; 10:cells10092180. [PMID: 34571829 PMCID: PMC8465348 DOI: 10.3390/cells10092180] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/12/2021] [Accepted: 08/23/2021] [Indexed: 12/16/2022] Open
Abstract
SNF1-related kinases 2 (SnRK2s) are central regulators of plant responses to environmental cues simultaneously playing a pivotal role in the plant development and growth in favorable conditions. They are activated in response to osmotic stress and some of them also to abscisic acid (ABA), the latter being key in ABA signaling. The SnRK2s can be viewed as molecular switches between growth and stress response; therefore, their activity is tightly regulated; needed only for a short time to trigger the response, it has to be induced transiently and otherwise kept at a very low level. This implies a strict and multifaceted control of SnRK2s in plant cells. Despite emerging new information concerning the regulation of SnRK2s, especially those involved in ABA signaling, a lot remains to be uncovered, the regulation of SnRK2s in an ABA-independent manner being particularly understudied. Here, we present an overview of available data, discuss some controversial issues, and provide our perspective on SnRK2 regulation.
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Affiliation(s)
- Justyna Maszkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (J.M.); (A.K.); (E.K.)
| | - Katarzyna Patrycja Szymańska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (J.M.); (A.K.); (E.K.)
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, ul. Noakowskiego 3, 00-664 Warsaw, Poland;
| | - Adrian Kasztelan
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (J.M.); (A.K.); (E.K.)
| | - Ewa Krzywińska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (J.M.); (A.K.); (E.K.)
| | - Olga Sztatelman
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (J.M.); (A.K.); (E.K.)
- Correspondence: (O.S.); (G.D.); Tel.: +48-22-5925718 (G.D.)
| | - Grażyna Dobrowolska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (J.M.); (A.K.); (E.K.)
- Correspondence: (O.S.); (G.D.); Tel.: +48-22-5925718 (G.D.)
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4
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Montillet JL, Rondet D, Brugière S, Henri P, Rumeau D, Reichheld JP, Couté Y, Leonhardt N, Rey P. Plastidial and cytosolic thiol reductases participate in the control of stomatal functioning. PLANT, CELL & ENVIRONMENT 2021; 44:1417-1435. [PMID: 33537988 DOI: 10.1111/pce.14013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
Stomatal movements via the control of gas exchanges determine plant growth in relation to environmental stimuli through a complex signalling network involving reactive oxygen species that lead to post-translational modifications of Cys and Met residues, and alter protein activity and/or conformation. Thiol-reductases (TRs), which include thioredoxins, glutaredoxins (GRXs) and peroxiredoxins (PRXs), participate in signalling pathways through the control of Cys redox status in client proteins. Their involvement in stomatal functioning remains poorly characterized. By performing a mass spectrometry-based proteomic analysis, we show that numerous thiol reductases, like PRXs, are highly abundant in guard cells. When investigating various Arabidopsis mutants impaired in the expression of TR genes, no change in stomatal density and index was noticed. In optimal growth conditions, a line deficient in cytosolic NADPH-thioredoxin reductases displayed higher stomatal conductance and lower leaf temperature evaluated by thermal infrared imaging. In contrast, lines deficient in plastidial 2-CysPRXs or type-II GRXs exhibited compared to WT reduced conductance and warmer leaves in optimal conditions, and enhanced stomatal closure in epidermal peels treated with abscisic acid or hydrogen peroxide. Altogether, these data strongly support the contribution of thiol redox switches within the signalling network regulating guard cell movements and stomatal functioning.
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Affiliation(s)
- Jean-Luc Montillet
- Plant Protective Proteins Team, Aix Marseille University, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, France
| | - Damien Rondet
- Plant Protective Proteins Team, Aix Marseille University, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, France
- Laboratoire Nixe, Sophia-Antipolis, Valbonne, France
| | - Sabine Brugière
- Laboratoire EDyP, University of Grenoble Alpes, CEA, INSERM, IRIG, BGE, Grenoble, France
| | - Patricia Henri
- Plant Protective Proteins Team, Aix Marseille University, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, France
| | - Dominique Rumeau
- Plant Protective Proteins Team, Aix Marseille University, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, France
| | - Jean-Philippe Reichheld
- Laboratoire Génome et Développement des Plantes, CNRS, Université Perpignan Via Domitia, Perpignan, France
| | - Yohann Couté
- Laboratoire EDyP, University of Grenoble Alpes, CEA, INSERM, IRIG, BGE, Grenoble, France
| | - Nathalie Leonhardt
- SAVE Team, Aix Marseille University, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, France
| | - Pascal Rey
- Plant Protective Proteins Team, Aix Marseille University, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, France
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5
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Zhang T, Gaffrey MJ, Li X, Qian WJ. Characterization of cellular oxidative stress response by stoichiometric redox proteomics. Am J Physiol Cell Physiol 2020; 320:C182-C194. [PMID: 33264075 DOI: 10.1152/ajpcell.00040.2020] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The thiol redox proteome refers to all proteins whose cysteine thiols are subjected to various redox-dependent posttranslational modifications (PTMs) including S-glutathionylation (SSG), S-nitrosylation (SNO), S-sulfenylation (SOH), and S-sulfhydration (SSH). These modifications can impact various aspects of protein function such as activity, binding, conformation, localization, and interactions with other molecules. To identify novel redox proteins in signaling and regulation, it is highly desirable to have robust redox proteomics methods that can provide global, site-specific, and stoichiometric quantification of redox PTMs. Mass spectrometry (MS)-based redox proteomics has emerged as the primary platform for broad characterization of thiol PTMs in cells and tissues. Herein, we review recent advances in MS-based redox proteomics approaches for quantitative profiling of redox PTMs at physiological or oxidative stress conditions and highlight some recent applications. Considering the relative maturity of available methods, emphasis will be on two types of modifications: 1) total oxidation (i.e., all reversible thiol modifications), the level of which represents the overall redox state, and 2) S-glutathionylation, a major form of reversible thiol oxidation. We also discuss the significance of stoichiometric measurements of thiol PTMs as well as future perspectives toward a better understanding of cellular redox regulatory networks in cells and tissues.
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Affiliation(s)
- Tong Zhang
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Matthew J Gaffrey
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Xiaolu Li
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.,Bioproducts Sciences and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, Washington
| | - Wei-Jun Qian
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
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6
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Zhang T, Schneider JD, Lin C, Koh J, Chen S. Proteomics data of SNF1-related protein kinase 2.4 interacting proteins revealed by immunoprecipitation-mass spectrometry. Data Brief 2020; 32:106326. [PMID: 33005707 PMCID: PMC7519261 DOI: 10.1016/j.dib.2020.106326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/05/2020] [Accepted: 09/16/2020] [Indexed: 01/04/2023] Open
Abstract
Identification of kinase substrates is a prerequisite for elucidating the mechanism by which a kinase transduces internal or external stimuli to cellular responses. Conventional methods to profile this type of protein-protein interaction typically deal with one kinase-substrate pair at a time. Mass spectrometry-based proteomics, on the other hand, can determine putative kinase-substrate pairs at a large-scale in an unbiased manner. In this study, we identified the interacting partners of SNF1-related protein kinase 2.4 (SnRK2.4) via immunoprecipitation coupled with mass spectrometry. Proteins from stable transgenic Arabidopsis plants overexpressing a FLAG-tagged SnRK2.4 (cloned from Brassica napus) were pulled down using an anti-FLAG antibody. The protein components were then identified by mass spectrometry. In parallel, proteins from wild type plants were also analyzed, providing a list of nonspecific binding proteins that were further removed from the candidate SnRK2.4-interacting protein list. Our data identified over 30 putative SnRK2.4 interacting partners, which included many key players in stress responses, transport, and cellular metabolic processes.
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Affiliation(s)
- Tong Zhang
- Department of Biology, University of Florida, Gainesville, FL 32610, USA
| | | | - Chuwei Lin
- Department of Biology, University of Florida, Gainesville, FL 32610, USA
| | - Jin Koh
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA
| | - Sixue Chen
- Department of Biology, University of Florida, Gainesville, FL 32610, USA.,Genetics Institute, University of Florida, Gainesville, FL 32610, USA.,Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA.,Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA
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7
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Zhang T, Chhajed S, Schneider JD, Feng G, Song WY, Chen S. Proteomic characterization of MPK4 signaling network and putative substrates. PLANT MOLECULAR BIOLOGY 2019; 101:325-339. [PMID: 31399934 DOI: 10.1007/s11103-019-00908-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/06/2019] [Indexed: 05/21/2023]
Abstract
KEY MESSAGE Combining genetic engineering of MPK4 activity and quantitative proteomics, we established an in planta system that enables rapid study of MPK4 signaling networks and potential substrate proteins. Mitogen activated protein kinase 4 (MPK4) is a multifunctional kinase that regulates various signaling events in plant defense, growth, light response and cytokinesis. The question of how a single protein modulates many distinct processes has spurred extensive research into the physiological outcomes resulting from genetic perturbation of MPK4. However, the mechanism by which MPK4 functions is still poorly understood due to limited data on the MPK4 networks including substrate proteins and downstream pathways. Here we introduce an experimental system that combines genetic engineering of kinase activity and quantitative proteomics to rapidly study the signaling networks of MPK4. First, we transiently expressed a constitutively active (MPK4CA) and an inactive (MPK4IN) version of a Brassica napus MPK4 (BnMPK4) in Nicotiana benthamiana leaves. Proteomics analysis revealed that BnMPK4 activation affects multiple pathways (e.g., metabolism, redox regulation, jasmonic acid biosynthesis and stress responses). Furthermore, BnMPK4 activation also increased protein phosphorylation in the phosphoproteome, from which putative MPK4 substrates were identified. Using protein kinase assay, we validated that a transcription factor TCP8-like (TCP8) and a PP2A regulatory subunit TAP46-like (TAP46) were indeed phosphorylated by BnMPK4. Taken together, we demonstrated the utility of proteomics and phosphoproteomics in elucidating kinase signaling networks and in identification of downstream substrates.
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Affiliation(s)
- Tong Zhang
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Biological Sciences Division, Pacific Northwest National Lab, Richland, WA, 99354, USA
| | - Shweta Chhajed
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | | | - Guanqiao Feng
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32610, USA
| | - Wen-Yuan Song
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32610, USA
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Sixue Chen
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA.
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32610, USA.
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA.
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32610, USA.
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8
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X Cai L, Tanada Y, D Bello G, C Fleming J, F Alkassis F, Ladd T, Golde T, Koh J, Chen S, Kasahara H. Cardiac MLC2 kinase is localized to the Z-disc and interacts with α-actinin2. Sci Rep 2019; 9:12580. [PMID: 31467300 PMCID: PMC6715661 DOI: 10.1038/s41598-019-48884-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/13/2019] [Indexed: 02/07/2023] Open
Abstract
Cardiac contractility is enhanced by phosphorylation of myosin light chain 2 (MLC2) by cardiac-specific MLC kinase (cMLCK), located at the neck region of myosin heavy chain. In normal mouse and human hearts, the level of phosphorylation is maintained relatively constant, at around 30-40% of total MLC2, likely by well-balanced phosphorylation and phosphatase-dependent dephosphorylation. Overexpression of cMLCK promotes sarcomere organization, while the loss of cMLCK leads to cardiac atrophy in vitro and in vivo. In this study, we showed that cMLCK is predominantly expressed at the Z-disc with additional diffuse cytosolic expression in normal adult mouse and human hearts. cMLCK interacts with the Z-disc protein, α-actinin2, with a high-affinity kinetic value of 13.4 ± 0.1 nM through the N-terminus region of cMLCK unique to cardiac-isoform. cMLCK mutant deficient for interacting with α-actinin2 did not promote sarcomeric organization and reduced cardiomyocyte cell size. In contrast, a cMLCK kinase-deficient mutant showed effects similar to wild-type cMLCK on sarcomeric organization and cardiomyocyte cell size. Our results suggest that cMLCK plays a role in sarcomere organization, likely distinct from its role in phosphorylating MLC2, both of which will contribute to the enhancement of cardiac contractility.
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Affiliation(s)
- Lawrence X Cai
- Department of Physiology and Functional Genomics, University of Florida, College of Medicine, Gainesville, FL, 32610, USA
| | - Yohei Tanada
- Department of Physiology and Functional Genomics, University of Florida, College of Medicine, Gainesville, FL, 32610, USA
| | - Gregory D Bello
- Department of Physiology and Functional Genomics, University of Florida, College of Medicine, Gainesville, FL, 32610, USA
| | - James C Fleming
- Department of Physiology and Functional Genomics, University of Florida, College of Medicine, Gainesville, FL, 32610, USA
| | - Fariz F Alkassis
- Department of Physiology and Functional Genomics, University of Florida, College of Medicine, Gainesville, FL, 32610, USA
| | - Thomas Ladd
- Department of Neuroscience, University of Florida, College of Medicine, Gainesville, FL, 32610, USA
| | - Todd Golde
- Department of Neuroscience, University of Florida, College of Medicine, Gainesville, FL, 32610, USA
| | - Jin Koh
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research (ICBR), University of Florida, Gainesville, FL, 32610, USA
| | - Sixue Chen
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research (ICBR), University of Florida, Gainesville, FL, 32610, USA.,Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32610, USA
| | - Hideko Kasahara
- Department of Physiology and Functional Genomics, University of Florida, College of Medicine, Gainesville, FL, 32610, USA.
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9
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Jamsheer K M, Jindal S, Laxmi A. Evolution of TOR-SnRK dynamics in green plants and its integration with phytohormone signaling networks. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2239-2259. [PMID: 30870564 DOI: 10.1093/jxb/erz107] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 02/26/2019] [Indexed: 05/07/2023]
Abstract
The target of rapamycin (TOR)-sucrose non-fermenting 1 (SNF1)-related protein kinase 1 (SnRK1) signaling is an ancient regulatory mechanism that originated in eukaryotes to regulate nutrient-dependent growth. Although the TOR-SnRK1 signaling cascade shows highly conserved functions among eukaryotes, studies in the past two decades have identified many important plant-specific innovations in this pathway. Plants also possess SnRK2 and SnRK3 kinases, which originated from the ancient SnRK1-related kinases and have specialized roles in controlling growth, stress responses and nutrient homeostasis in plants. Recently, an integrative picture has started to emerge in which different SnRKs and TOR kinase are highly interconnected to control nutrient and stress responses of plants. Further, these kinases are intimately involved with phytohormone signaling networks that originated at different stages of plant evolution. In this review, we highlight the evolution and divergence of TOR-SnRK signaling components in plants and their communication with each other as well as phytohormone signaling to fine-tune growth and stress responses in plants.
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Affiliation(s)
- Muhammed Jamsheer K
- Amity Food & Agriculture Foundation, Amity University Uttar Pradesh, Noida, India
| | - Sunita Jindal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Ashverya Laxmi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
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10
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Meng L, Zhang T, Geng S, Scott PB, Li H, Chen S. Comparative proteomics and metabolomics of JAZ7-mediated drought tolerance in Arabidopsis. J Proteomics 2019; 196:81-91. [DOI: 10.1016/j.jprot.2019.02.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 01/29/2019] [Accepted: 02/01/2019] [Indexed: 01/16/2023]
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11
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Zhang T, Schneider JD, Lin C, Geng S, Ma T, Lawrence SR, Dufresne CP, Harmon AC, Chen S. MPK4 Phosphorylation Dynamics and Interacting Proteins in Plant Immunity. J Proteome Res 2019; 18:826-840. [PMID: 30632760 DOI: 10.1021/acs.jproteome.8b00345] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Arabidopsis MAP kinase 4 (MPK4) has been proposed to be a negative player in plant immunity, and it is also activated by pathogen-associated molecular patterns (PAMPs), such as flg22. The molecular mechanisms by which MPK4 is activated and regulates plant defense remain elusive. In this study, we investigated Arabidopsis defense against a bacterial pathogen Pseudomonas syringae pv tomato ( Pst) DC3000 when Brassica napus MPK4 ( BnMPK4) is overexpressed. We showed an increase in pathogen resistance and suppression of jasmonic acid (JA) signaling in the BnMPK4 overexpressing (OE) plants. We also showed that the OE plants have increased sensitivity to flg22-triggered reactive oxygen species (ROS) burst in guard cells, which resulted in enhanced stomatal closure compared to wild-type (WT). During flg22 activation, dynamic phosphorylation events within and outside of the conserved TEY activation loop were observed. To elucidate how BnMPK4 functions during the defense response, we used immunoprecipitation coupled with mass spectrometry (IP-MS) to identify BnMPK4 interacting proteins in the absence and presence of flg22. Quantitative proteomic analysis revealed a shift in the MPK4-associated protein network, providing insight into the molecular functions of MPK4 at the systems level.
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Affiliation(s)
| | | | | | | | | | | | - Craig P Dufresne
- Thermo Fisher Scientific , 1400 Northpoint Parkway , West Palm Beach , Florida 33407 , United States
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12
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Collins J, Dufresne C, Gurley WB, Chen S. Proteomics dataset containing proteins that obscure identification of TOPLESS interactors in Arabidopsis. Data Brief 2018; 20:909-916. [PMID: 30225301 PMCID: PMC6138984 DOI: 10.1016/j.dib.2018.08.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/12/2018] [Accepted: 08/22/2018] [Indexed: 11/18/2022] Open
Abstract
Here we report proteins identified after conducting Tandem Affinity Purification (TAP) of the TOPLESS (TPL) corepressor from Arabidopsis. We generated transgenic plants harboring TPL fused to the GS-TAG, "Boosting tandem affinity purification of plant protein complexes" (Van Leene et al., 2008) [1]. Four independent biological replicates of a selected TPL-GS-TAG line were grown simultaneously, crosslinked with formaldehyde, and proteins were isolated from whole plant tissue via TAP. Purified proteins were treated with trypsin, and the peptides were analyzed via mass spectrometry. Datasets are hosted in the MassIVE public repository (reference number: MSV000082477, https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=f16255fb7080426a9fe1926b4d3d5862). The data in this article has not been published elsewhere and is original to this work.
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Affiliation(s)
- Joe Collins
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, USA
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, USA
| | | | - William B. Gurley
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, USA
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Sixue Chen
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, USA
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, USA
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
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Pang Q, Zhang T, Wang Y, Kong W, Guan Q, Yan X, Chen S. Metabolomics of Early Stage Plant Cell-Microbe Interaction Using Stable Isotope Labeling. FRONTIERS IN PLANT SCIENCE 2018; 9:760. [PMID: 29922325 PMCID: PMC5996122 DOI: 10.3389/fpls.2018.00760] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 05/17/2018] [Indexed: 05/02/2023]
Abstract
Metabolomics has been used in unraveling metabolites that play essential roles in plant-microbe (including pathogen) interactions. However, the problem of profiling a plant metabolome with potential contaminating metabolites from the coexisting microbes has been largely ignored. To address this problem, we implemented an effective stable isotope labeling approach, where the metabolome of a plant bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000 was labeled with heavy isotopes. The labeled bacterial cells were incubated with Arabidopsis thaliana epidermal peels (EPs) with guard cells, and excessive bacterial cells were subsequently removed from the plant tissues by washing. The plant metabolites were characterized by liquid chromatography mass spectrometry using multiple reactions monitoring, which can differentiate plant and bacterial metabolites. Targeted metabolomic analysis suggested that Pst DC3000 infection may modulate stomatal movement by reprograming plant signaling and primary metabolic pathways. This proof-of-concept study demonstrates the utility of this strategy in differentiation of the plant and microbe metabolomes, and it has broad applications in studying metabolic interactions between microbes and other organisms.
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Affiliation(s)
- Qiuying Pang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Tong Zhang
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Yang Wang
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Wenwen Kong
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Qijie Guan
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Xiufeng Yan
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, China
- *Correspondence: Xiufeng Yan, Sixue Chen,
| | - Sixue Chen
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, United States
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research (ICBR), University of Florida, Gainesville, FL, United States
- *Correspondence: Xiufeng Yan, Sixue Chen,
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