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Poretsky E, Andorf CM, Sen TZ. PhosBoost: Improved phosphorylation prediction recall using gradient boosting and protein language models. PLANT DIRECT 2023; 7:e554. [PMID: 38124705 PMCID: PMC10732782 DOI: 10.1002/pld3.554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 12/23/2023]
Abstract
Protein phosphorylation is a dynamic and reversible post-translational modification that regulates a variety of essential biological processes. The regulatory role of phosphorylation in cellular signaling pathways, protein-protein interactions, and enzymatic activities has motivated extensive research efforts to understand its functional implications. Experimental protein phosphorylation data in plants remains limited to a few species, necessitating a scalable and accurate prediction method. Here, we present PhosBoost, a machine-learning approach that leverages protein language models and gradient-boosting trees to predict protein phosphorylation from experimentally derived data. Trained on data obtained from a comprehensive plant phosphorylation database, qPTMplants, we compared the performance of PhosBoost to existing protein phosphorylation prediction methods, PhosphoLingo and DeepPhos. For serine and threonine prediction, PhosBoost achieved higher recall than PhosphoLingo and DeepPhos (.78, .56, and .14, respectively) while maintaining a competitive area under the precision-recall curve (.54, .56, and .42, respectively). PhosphoLingo and DeepPhos failed to predict any tyrosine phosphorylation sites, while PhosBoost achieved a recall score of .6. Despite the precision-recall tradeoff, PhosBoost offers improved performance when recall is prioritized while consistently providing more confident probability scores. A sequence-based pairwise alignment step improved prediction results for all classifiers by effectively increasing the number of inferred positive phosphosites. We provide evidence to show that PhosBoost models are transferable across species and scalable for genome-wide protein phosphorylation predictions. PhosBoost is freely and publicly available on GitHub.
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Affiliation(s)
- Elly Poretsky
- Agricultural Research Service, Crop Improvement and Genetics Research UnitU.S. Department of AgricultureAlbanyCAUnited States
| | - Carson M. Andorf
- Agricultural Research Service, Corn Insects and Crop Genetics ResearchU.S. Department of AgricultureAmesIAUnited States
- Department of Computer ScienceIowa State UniversityAmesIAUnited States
| | - Taner Z. Sen
- Agricultural Research Service, Crop Improvement and Genetics Research UnitU.S. Department of AgricultureAlbanyCAUnited States
- Department of BioengineeringUniversity of CaliforniaBerkeleyCAUnited States
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Robson JK, Ferguson JN, McAusland L, Atkinson JA, Tranchant-Dubreuil C, Cubry P, Sabot F, Wells DM, Price AH, Wilson ZA, Murchie EH. Chlorophyll fluorescence-based high-throughput phenotyping facilitates the genetic dissection of photosynthetic heat tolerance in African (Oryza glaberrima) and Asian (Oryza sativa) rice. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5181-5197. [PMID: 37347829 PMCID: PMC10498015 DOI: 10.1093/jxb/erad239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 06/20/2023] [Indexed: 06/24/2023]
Abstract
Rising temperatures and extreme heat events threaten rice production. Half of the global population relies on rice for basic nutrition, and therefore developing heat-tolerant rice is essential. During vegetative development, reduced photosynthetic rates can limit growth and the capacity to store soluble carbohydrates. The photosystem II (PSII) complex is a particularly heat-labile component of photosynthesis. We have developed a high-throughput chlorophyll fluorescence-based screen for photosynthetic heat tolerance capable of screening hundreds of plants daily. Through measuring the response of maximum PSII efficiency to increasing temperature, this platform generates data for modelling the PSII-temperature relationship in large populations in a small amount of time. Coefficients from these models (photosynthetic heat tolerance traits) demonstrated high heritabilities across African (Oryza glaberrima) and Asian (Oryza sativa, Bengal Assam Aus Panel) rice diversity sets, highlighting valuable genetic variation accessible for breeding. Genome-wide association studies were performed across both species for these traits, representing the first documented attempt to characterize the genetic basis of photosynthetic heat tolerance in any species to date. A total of 133 candidate genes were highlighted. These were significantly enriched with genes whose predicted roles suggested influence on PSII activity and the response to stress. We discuss the most promising candidates for improving photosynthetic heat tolerance in rice.
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Affiliation(s)
- Jordan K Robson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - John N Ferguson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
- School of Life Sciences, University of Essex, Colchester, UK
| | - Lorna McAusland
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Jonathan A Atkinson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | | | - Phillipe Cubry
- Institut de Recherche pour le Developpement, 911 Av. Agropolis, 34394 Montpellier, France
| | - François Sabot
- Institut de Recherche pour le Developpement, 911 Av. Agropolis, 34394 Montpellier, France
| | - Darren M Wells
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Adam H Price
- Institut de Recherche pour le Developpement, 911 Av. Agropolis, 34394 Montpellier, France
| | - Zoe A Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Erik H Murchie
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
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3
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Li W, Lin M, Li J, Liu D, Tan W, Yin X, Zhai Y, Zhou Y, Xing W. Genome-wide association study of drought tolerance traits in sugar beet germplasms at the seedling stage. Front Genet 2023; 14:1198600. [PMID: 37547461 PMCID: PMC10401439 DOI: 10.3389/fgene.2023.1198600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/30/2023] [Indexed: 08/08/2023] Open
Abstract
Introduction: Sugar beets are an important crop for global sugar production. Intense drought and the increasing lack of water resources pose a great threat to sugar beet cultivation. It is a priority to investigate favourable germplasms and functional genes to improve the breeding of drought tolerant plants. Methods: Thus, in this study, 328 sugar beet germplasms were used in a genome-wide association study (GWAS) to identify single nucleotide polymorphism (SNP) markers and candidate genes associated with drought tolerance. Results: The results showed that under drought stress (9% PEG-6000), there were 11 significantly associated loci on chromosomes 2, 3, 5, 7, and 9 from the 108946 SNPs filtered using a mixed linear model (MLM). Genome-wide association analysis combined with qRT-PCR identified 13 genes that were significantly differentially expressed in drought-tolerant extreme materials. Discussion: These candidate genes mainly exhibited functions such as regulating sugar metabolism, maintaining internal environmental stability and participating in photosystem repair. This study provides valuable information for exploring the molecular mechanisms of drought tolerance and improvement in sugar beet.
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Affiliation(s)
- Wangsheng Li
- National Beet Medium-Term Gene Bank, Heilongjiang University, Harbin, China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Ming Lin
- Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Jiajia Li
- National Beet Medium-Term Gene Bank, Heilongjiang University, Harbin, China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Dali Liu
- National Beet Medium-Term Gene Bank, Heilongjiang University, Harbin, China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Wenbo Tan
- National Beet Medium-Term Gene Bank, Heilongjiang University, Harbin, China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Xilong Yin
- National Beet Medium-Term Gene Bank, Heilongjiang University, Harbin, China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Yan Zhai
- National Beet Medium-Term Gene Bank, Heilongjiang University, Harbin, China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Yuanhang Zhou
- Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Wang Xing
- National Beet Medium-Term Gene Bank, Heilongjiang University, Harbin, China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
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Bender KW, Zipfel C. Paradigms of receptor kinase signaling in plants. Biochem J 2023; 480:835-854. [PMID: 37326386 PMCID: PMC10317173 DOI: 10.1042/bcj20220372] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023]
Abstract
Plant receptor kinases (RKs) function as key plasma-membrane localized receptors in the perception of molecular ligands regulating development and environmental response. Through the perception of diverse ligands, RKs regulate various aspects throughout the plant life cycle from fertilization to seed set. Thirty years of research on plant RKs has generated a wealth of knowledge on how RKs perceive ligands and activate downstream signaling. In the present review, we synthesize this body of knowledge into five central paradigms of plant RK signaling: (1) RKs are encoded by expanded gene families, largely conserved throughout land plant evolution; (2) RKs perceive many different kinds of ligands through a range of ectodomain architectures; (3) RK complexes are typically activated by co-receptor recruitment; (4) post-translational modifications fulfill central roles in both the activation and attenuation of RK-mediated signaling; and, (5) RKs activate a common set of downstream signaling processes through receptor-like cytoplasmic kinases (RLCKs). For each of these paradigms, we discuss key illustrative examples and also highlight known exceptions. We conclude by presenting five critical gaps in our understanding of RK function.
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Affiliation(s)
- Kyle W. Bender
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, 8008 Zürich, Switzerland
| | - Cyril Zipfel
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, 8008 Zürich, Switzerland
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, U.K
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Li F, Chen X, Yang R, Zhang K, Shan W, Joosten MHAJ, Du Y. Potato protein tyrosine phosphatase StPTP1a is activated by StMKK1 to negatively regulate plant immunity. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:646-661. [PMID: 36519513 PMCID: PMC9946141 DOI: 10.1111/pbi.13979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/25/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Phytophthora infestans causes severe losses in potato production. The MAPK kinase StMKK1 was previously found to negatively regulate potato immunity to P. infestans. Our results showed that StMKK1 interacts with a protein tyrosine phosphatase, referred to as StPTP1a, and StMKK1 directly phosphorylates StPTP1a at residues Ser-99, Tyr-223 and Thr-290. StPTP1a is a functional phosphatase and the phosphorylation of StPTP1a at these three residues enhances its stability and catalytic activity. StPTP1a negatively regulates potato immunity and represses SA-related gene expression. Furthermore, StPTP1a interacts with, and dephosphorylates, the StMKK1 downstream signalling targets StMPK4 and -7 at their Tyr-203 residue resulting in the repression of salicylic acid (SA)-related immunity. Silencing of NbPTP1a + NbMPK4 or NbPTP1a + NbMPK7 abolished the plant immunity to P. infestans caused by NbPTP1a silencing, indicating that PTP1a functions upstream of NbMPK4 and NbMPK7. StMKK1 requires StPTP1a to negatively regulate SA-related immunity and StPTP1a is phosphorylated and stabilized during immune activation to promote the de-phosphorylation of StMPK4 and -7. Our results reveal that potato StMKK1 activates and stabilizes the tyrosine phosphatase StPTP1a that in its turn de-phosphorylates StMPK4 and -7, thereby repressing plant SA-related immunity.
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Affiliation(s)
- Fangfang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Xiaokang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Ruixin Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Kun Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Weixing Shan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | | | - Yu Du
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
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Kong Y, Chen J, Jiang L, Chen H, Shen Y, Wang L, Yan Y, Zhou H, Zheng H, Yu F, Ming Z. Structural and biochemical basis of Arabidopsis FERONIA receptor kinase-mediated early signaling initiation. PLANT COMMUNICATIONS 2023:100559. [PMID: 36774537 PMCID: PMC10363478 DOI: 10.1016/j.xplc.2023.100559] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/11/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Accumulating evidence indicates that early and essential events for receptor-like kinase (RLK) function involve both autophosphorylation and substrate phosphorylation. However, the structural and biochemical basis for these events is largely unclear. Here, we used RLK FERONIA (FER) as a model and crystallized its core kinase domain (FER-KD) and two FER-KD mutants (K565R, S525A) in complexes with ATP/ADP and Mg2+ in the unphosphorylated state. Unphosphorylated FER-KD was found to adopt an unexpected active conformation in its crystal structure. Moreover, unphosphorylated FER-KD mutants with reduced (S525A) or no catalytic activity (K565R) also adopt similar active conformations. Biochemical studies revealed that FER-KD is a dual-specificity kinase, and its autophosphorylation is accomplished via an intermolecular mechanism. Further investigations confirmed that initiating substrate phosphorylation requires autophosphorylation of the activation segment on T696, S701, and Y704. This study reveals the structural and biochemical basis for the activation and regulatory mechanism of FER, providing a paradigm for the early steps in RLK signaling initiation.
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Affiliation(s)
- Yanqiong Kong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530004, P.R. China
| | - Jia Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Lingli Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Hong Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Yanan Shen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Lifeng Wang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, P.R. China
| | - Yujie Yan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Huan Zhou
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, P.R. China
| | - Heping Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China; State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, P.R. China.
| | - Zhenhua Ming
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530004, P.R. China.
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Sobol G, Chakraborty J, Martin GB, Sessa G. The Emerging Role of PP2C Phosphatases in Tomato Immunity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:737-747. [PMID: 35696659 DOI: 10.1094/mpmi-02-22-0037-cr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The antagonistic effect of plant immunity on growth likely drove evolution of molecular mechanisms that prevent accidental initiation and prolonged activation of plant immune responses. Signaling networks of pattern-triggered and effector-triggered immunity, the two main layers of plant immunity, are tightly regulated by the activity of protein phosphatases that dephosphorylate their protein substrates and reverse the action of protein kinases. Members of the PP2C class of protein phosphatases have emerged as key negative regulators of plant immunity, primarily from research in the model plant Arabidopsis thaliana, revealing the potential to employ PP2C proteins to enhance plant disease resistance. As a first step towards focusing on the PP2C family for both basic and translational research, we analyzed the tomato genome sequence to ascertain the complement of the tomato PP2C family, identify conserved protein domains and signals in PP2C amino acid sequences, and examine domain combinations in individual proteins. We then identified tomato PP2Cs that are candidate regulators of single or multiple layers of the immune signaling network by in-depth analysis of publicly available RNA-seq datasets. These included expression profiles of plants treated with fungal or bacterial pathogen-associated molecular patterns, with pathogenic, nonpathogenic, and disarmed bacteria, as well as pathogenic fungi and oomycetes. Finally, we discuss the possible use of immunity-associated PP2Cs to better understand the signaling networks of plant immunity and to engineer durable and broad disease resistance in crop plants. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Guy Sobol
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, 69978 Tel-Aviv, Israel
| | - Joydeep Chakraborty
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, 69978 Tel-Aviv, Israel
| | - Gregory B Martin
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, U.S.A
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
| | - Guido Sessa
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, 69978 Tel-Aviv, Israel
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8
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Song W, Hu L, Ma Z, Yang L, Li J. Importance of Tyrosine Phosphorylation in Hormone-Regulated Plant Growth and Development. Int J Mol Sci 2022; 23:ijms23126603. [PMID: 35743047 PMCID: PMC9224382 DOI: 10.3390/ijms23126603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/07/2022] [Accepted: 06/11/2022] [Indexed: 02/01/2023] Open
Abstract
Protein phosphorylation is the most frequent post-translational modification (PTM) that plays important regulatory roles in a wide range of biological processes. Phosphorylation mainly occurs on serine (Ser), threonine (Thr), and tyrosine (Tyr) residues, with the phosphorylated Tyr sites accounting for ~1–2% of all phosphorylated residues. Tyr phosphorylation was initially believed to be less common in plants compared to animals; however, recent investigation indicates otherwise. Although they lack typical protein Tyr kinases, plants possess many dual-specificity protein kinases that were implicated in diverse cellular processes by phosphorylating Ser, Thr, and Tyr residues. Analyses of sequenced plant genomes also identified protein Tyr phosphatases and dual-specificity protein phosphatases. Recent studies have revealed important regulatory roles of Tyr phosphorylation in many different aspects of plant growth and development and plant interactions with the environment. This short review summarizes studies that implicated the Tyr phosphorylation in biosynthesis and signaling of plant hormones.
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Affiliation(s)
- Weimeng Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (W.S.); (L.H.); (Z.M.); (L.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Li Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (W.S.); (L.H.); (Z.M.); (L.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Zhihui Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (W.S.); (L.H.); (Z.M.); (L.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Lei Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (W.S.); (L.H.); (Z.M.); (L.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Jianming Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (W.S.); (L.H.); (Z.M.); (L.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence:
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Nicolas-Francès V, Rossi J, Rosnoblet C, Pichereaux C, Hichami S, Astier J, Klinguer A, Wendehenne D, Besson-Bard A. S-Nitrosation of Arabidopsis thaliana Protein Tyrosine Phosphatase 1 Prevents Its Irreversible Oxidation by Hydrogen Peroxide. FRONTIERS IN PLANT SCIENCE 2022; 13:807249. [PMID: 35222471 PMCID: PMC8867174 DOI: 10.3389/fpls.2022.807249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/19/2022] [Indexed: 06/01/2023]
Abstract
Tyrosine-specific protein tyrosine phosphatases (Tyr-specific PTPases) are key signaling enzymes catalyzing the removal of the phosphate group from phosphorylated tyrosine residues on target proteins. This post-translational modification notably allows the regulation of mitogen-activated protein kinase (MAPK) cascades during defense reactions. Arabidopsis thaliana protein tyrosine phosphatase 1 (AtPTP1), the only Tyr-specific PTPase present in this plant, acts as a repressor of H2O2 production and regulates the activity of MPK3/MPK6 MAPKs by direct dephosphorylation. Here, we report that recombinant histidine (His)-AtPTP1 protein activity is directly inhibited by H2O2 and nitric oxide (NO) exogenous treatments. The effects of NO are exerted by S-nitrosation, i.e., the formation of a covalent bond between NO and a reduced cysteine residue. This post-translational modification targets the catalytic cysteine C265 and could protect the AtPTP1 protein from its irreversible oxidation by H2O2. This mechanism of protection could be a conserved mechanism in plant PTPases.
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Affiliation(s)
- Valérie Nicolas-Francès
- Agroécologie, CNRS, INRAE, Institut Agro, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Jordan Rossi
- Agroécologie, CNRS, INRAE, Institut Agro, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Claire Rosnoblet
- Agroécologie, CNRS, INRAE, Institut Agro, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Carole Pichereaux
- Fédération de Recherche (FR3450), Agrobiosciences, Interactions et Biodiversité (FRAIB), CNRS, Toulouse, France
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse UPS, CNRS, Toulouse, France
| | - Siham Hichami
- Agroécologie, CNRS, INRAE, Institut Agro, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Jeremy Astier
- Agroécologie, CNRS, INRAE, Institut Agro, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Agnès Klinguer
- Agroécologie, CNRS, INRAE, Institut Agro, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - David Wendehenne
- Agroécologie, CNRS, INRAE, Institut Agro, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Angélique Besson-Bard
- Agroécologie, CNRS, INRAE, Institut Agro, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
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