1
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Li Z, Na Wu X, Jacquot A, Chaput V, Adamo M, Neuhäuser B, Straub T, Lejay L, Schulze WX. Phosphoregulation in the N-terminus of NRT2.1 affects nitrate uptake by controlling the interaction of NRT2.1 with NAR2.1 and kinase HPCAL1 in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2127-2142. [PMID: 38066636 DOI: 10.1093/jxb/erad490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/06/2023] [Indexed: 03/28/2024]
Abstract
NRT2.1, the major high affinity nitrate transporter in roots, can be phosphorylated at five different sites within the N- and the C-terminus. Here, we characterized the functional relationship of two N-terminal phosphorylation sites, S21 and S28, in Arabidopsis. Based on a site-specific correlation network, we identified a receptor kinase (HPCAL1, AT5G49770), phosphorylating NRT2.1 at S21 and resulting in active nitrate uptake. HPCAL1 itself was regulated by phosphorylation at S839 and S870 within its kinase domain. In the active state, when S839 was dephosphorylated and S870 was phosphorylated, HPCAL1 was found to interact with the N-terminus of NRT2.1, mainly when S28 was dephosphorylated. Phosphorylation of NRT2.1 at S21 resulted in a reduced interaction of NRT2.1 with its activator NAR2.1, but nitrate transport activity remained. By contrast, phosphorylated NRT2.1 at S28 enhanced the interaction with NAR2.1, but reduced the interaction with HPCAL1. Here we identified HPCAL1 as the kinase affecting this phospho-switch through phosphorylation of NRT2.1 at S21.
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Affiliation(s)
- Zhi Li
- Department of Plant Systems Biology, University of Hohenheim, D-70593, Stuttgart, Germany
| | - Xu Na Wu
- Department of Plant Systems Biology, University of Hohenheim, D-70593, Stuttgart, Germany
| | - Aurore Jacquot
- BPMP, University Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Valentin Chaput
- BPMP, University Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Mattia Adamo
- BPMP, University Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Benjamin Neuhäuser
- Department of Crop Physiology, University of Hohenheim, D-70593, Stuttgart, Germany
| | - Tatsiana Straub
- Department of Plant Systems Biology, University of Hohenheim, D-70593, Stuttgart, Germany
| | - Laurence Lejay
- BPMP, University Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, D-70593, Stuttgart, Germany
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2
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Van den Broeck L, Bhosale DK, Song K, Fonseca de Lima CF, Ashley M, Zhu T, Zhu S, Van De Cotte B, Neyt P, Ortiz AC, Sikes TR, Aper J, Lootens P, Locke AM, De Smet I, Sozzani R. Functional annotation of proteins for signaling network inference in non-model species. Nat Commun 2023; 14:4654. [PMID: 37537196 PMCID: PMC10400656 DOI: 10.1038/s41467-023-40365-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 07/25/2023] [Indexed: 08/05/2023] Open
Abstract
Molecular biology aims to understand cellular responses and regulatory dynamics in complex biological systems. However, these studies remain challenging in non-model species due to poor functional annotation of regulatory proteins. To overcome this limitation, we develop a multi-layer neural network that determines protein functionality directly from the protein sequence. We annotate kinases and phosphatases in Glycine max. We use the functional annotations from our neural network, Bayesian inference principles, and high resolution phosphoproteomics to infer phosphorylation signaling cascades in soybean exposed to cold, and identify Glyma.10G173000 (TOI5) and Glyma.19G007300 (TOT3) as key temperature regulators. Importantly, the signaling cascade inference does not rely upon known kinase motifs or interaction data, enabling de novo identification of kinase-substrate interactions. Conclusively, our neural network shows generalization and scalability, as such we extend our predictions to Oryza sativa, Zea mays, Sorghum bicolor, and Triticum aestivum. Taken together, we develop a signaling inference approach for non-model species leveraging our predicted kinases and phosphatases.
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Affiliation(s)
- Lisa Van den Broeck
- Plant and Microbial Biology Department and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Dinesh Kiran Bhosale
- Electrical and Computer Engineering Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Kuncheng Song
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Cássio Flavio Fonseca de Lima
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Michael Ashley
- Electrical and Computer Engineering Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Tingting Zhu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Shanshuo Zhu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Brigitte Van De Cotte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Pia Neyt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Anna C Ortiz
- USDA-ARS Soybean & Nitrogen Fixation Research Unit, Raleigh, NC, 27607, Belgium
| | - Tiffany R Sikes
- USDA-ARS Soybean & Nitrogen Fixation Research Unit, Raleigh, NC, 27607, Belgium
| | - Jonas Aper
- Protealis NV, Technologiepark-Zwijnaarde 94, 9052, Ghent, Belgium
| | - Peter Lootens
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9090, Melle, Belgium
| | - Anna M Locke
- USDA-ARS Soybean & Nitrogen Fixation Research Unit, Raleigh, NC, 27607, Belgium
- Department of Crop and Soil Sciences and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC, 27695, USA
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Rosangela Sozzani
- Plant and Microbial Biology Department and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC, 27695, USA.
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3
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Chong L, Hsu CC, Zhu Y. Advances in mass spectrometry-based phosphoproteomics for elucidating abscisic acid signaling and plant responses to abiotic stress. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6547-6557. [PMID: 35959917 DOI: 10.1093/jxb/erac324] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/23/2022] [Indexed: 06/15/2023]
Abstract
Abiotic stresses have significant impacts on crop yield and quality. Even though significant efforts during the past decade have been devoted to uncovering the core signaling pathways associated with the phytohormone abscisic acid (ABA) and abiotic stress in plants, abiotic stress signaling mechanisms in most crops remain largely unclear. The core components of the ABA signaling pathway, including early events in the osmotic stress-induced phosphorylation network, have recently been elucidated in Arabidopsis with the aid of phosphoproteomics technologies. We now know that SNF1-related kinases 2 (SnRK2s) are not only inhibited by the clade A type 2C protein phosphatases (PP2Cs) through dephosphorylation, but also phosphorylated and activated by upstream mitogen-activated protein kinase kinase kinases (MAP3Ks). Through describing the course of studies to elucidate abiotic stress and ABA signaling, we will discuss how we can take advantage of the latest innovations in mass-spectrometry-based phosphoproteomics and structural proteomics to boost our investigation of plant regulation and responses to ABA and abiotic stress.
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Affiliation(s)
- Leelyn Chong
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Chuan-Chih Hsu
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Yingfang Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Sanya Institute of Henan University, Sanya, Hainan, China
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4
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Li W, Han X, Lan P. Emerging roles of protein phosphorylation in plant iron homeostasis. TRENDS IN PLANT SCIENCE 2022; 27:908-921. [PMID: 35414480 DOI: 10.1016/j.tplants.2022.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 03/08/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Remarkable progress has been made in dissecting the molecular mechanisms involved in iron (Fe) homeostasis in plants, especially the identification of key transporter and transcriptional regulatory networks. But how the protein activity of these master players is regulated by Fe status remains underexplored. Recent studies show that major players toggle switch their properties by protein phosphorylation under different Fe conditions and consequently control the signaling cascade and metabolic adjustment. Moreover, Fe deficiency causes changes of multiple kinases and phosphatases. Here, we discuss how these findings highlight the emergence of the protein phosphorylation-dependent regulation for rapid and precise responses to Fe status to attain Fe homeostasis. Further studies will be needed to fully understand the regulation of these intricate networks.
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Affiliation(s)
- Wenfeng Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Xiuwen Han
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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5
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Du Y, Xie S, Wang Y, Ma Y, Jia B, Liu X, Rong J, Li R, Zhu X, Song CP, Tao WA, Wang P. Low molecular weight protein phosphatase APH mediates tyrosine dephosphorylation and ABA response in Arabidopsis. STRESS BIOLOGY 2022; 2:23. [PMID: 35935594 PMCID: PMC9345830 DOI: 10.1007/s44154-022-00041-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/17/2022] [Indexed: 02/02/2023]
Abstract
Low molecular weight protein tyrosine phosphatase (LWM-PTP), also known as acid phosphatase, is a highly conserved tyrosine phosphatase in living organisms. However, the function of LWM-PTP homolog has not been reported yet in plants. Here, we revealed a homolog of acid phosphatase, APH, in Arabidopsis plants, is a functional protein tyrosine phosphatase. The aph mutants are hyposensitive to ABA in post-germination growth. We performed an anti-phosphotyrosine antibody-based quantitative phosphoproteomics in wild-type and aph mutant and identified hundreds of putative targets of APH, including multiple splicing factors and other transcriptional regulators. Consistently, RNA-seq analysis revealed that the expression of ABA-highly-responsive genes is suppressed in aph mutants. Thus, APH regulates the ABA-responsive gene expressions by regulating the tyrosine phosphorylation of multiple splicing factors and other post-transcriptional regulators. We also revealed that Tyr383 in RAF9, a member of B2 and B3 RAF kinases that phosphorylate and activate SnRK2s in the ABA signaling pathway, is a direct target site of APH. Phosphorylation of Tyr383 is essential for RAF9 activity. Our results uncovered a crucial function of APH in ABA-induced tyrosine phosphorylation in Arabidopsis. Supplementary Information The online version contains supplementary material available at 10.1007/s44154-022-00041-6.
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Affiliation(s)
- Yanyan Du
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, West Lafayette, IN 47907 USA
| | - Yubei Wang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yu Ma
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Bei Jia
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Xue Liu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Jingkai Rong
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Rongxia Li
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Xiaohong Zhu
- State Key Laboratory of Crop Stress Adaption and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004 China
| | - Chun-Peng Song
- State Key Laboratory of Crop Stress Adaption and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004 China
| | - W. Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907 USA
| | - Pengcheng Wang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- State Key Laboratory of Crop Stress Adaption and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004 China
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6
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He M, Li X, Mang M, Li Z, Ludewig U, Schulze WX. A systems-biology approach identifies co-expression modules in response to low phosphate supply in maize lines of different breeding history. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1249-1270. [PMID: 34897849 DOI: 10.1111/tpj.15630] [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: 10/14/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Plants cope with low phosphorus availability by adjusting growth and metabolism through transcriptomic and proteomic adaptations. We hypothesize that selected genotypes with distinct phosphorous (P) use efficiency covering the breeding history of European Flint heterotic pool provide a tool to reveal general and genotype-specific molecular responses to P limitation. We reconstructed protein and gene co-expression networks by weighted correlation network analysis and related these to phosphate deficiency-induced traits. In roots, low phosphate supply resulted in a decreasing abundance of proteins in the oxidative pentose phosphate pathway and a negative correlation with root and shoot phosphate content. We observed an increase in abundance and positive correlation with root and shoot phosphate content for proteins in sucrose biosynthesis, lipid metabolism, respiration and RNA processing. Purple acid phosphatases, superoxide dismutase and phenylalanine ammonia lyase were identified as being upregulated under low phosphate in all genotypes. Overall, correlations between protein and mRNA abundance changes were limited, with ribosomal proteins and the ubiquitin protein degradation pathway exclusively responding with protein abundance changes. Carbohydrate, phospho- and sulfo-lipid metabolism showed abundance changes at the protein and mRNA levels. These partially non-overlapping proteomic and transcriptomic adjustments to low phosphate suggest sugar and lipid metabolism as metabolic processes associated with improved P use efficiency specifically in Founder Flint lines. We identified a mitogen-activated protein kinase-kinase as a potential genotype-specific regulator of sucrose metabolism at low phosphate in Founder Flint line EP1. We conclude that, during breedingt of Elite Flint lines, regulation of primary metabolism has changed to result in a distinct low phosphate response in Founder lines.
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Affiliation(s)
- Mingjie He
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Xuelian Li
- Department of Nutritional Crop Physiology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Melissa Mang
- Department of Nutritional Crop Physiology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Zhi Li
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Uwe Ludewig
- Department of Nutritional Crop Physiology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, 70593, Germany
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7
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Metabolomics for Crop Breeding: General Considerations. Genes (Basel) 2021; 12:genes12101602. [PMID: 34680996 PMCID: PMC8535592 DOI: 10.3390/genes12101602] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 12/16/2022] Open
Abstract
The development of new, more productive varieties of agricultural crops is becoming an increasingly difficult task. Modern approaches for the identification of beneficial alleles and their use in elite cultivars, such as quantitative trait loci (QTL) mapping and marker-assisted selection (MAS), are effective but insufficient for keeping pace with the improvement of wheat or other crops. Metabolomics is a powerful but underutilized approach that can assist crop breeding. In this review, basic methodological information is summarized, and the current strategies of applications of metabolomics related to crop breeding are explored using recent examples. We briefly describe classes of plant metabolites, cellular localization of metabolic pathways, and the strengths and weaknesses of the main metabolomics technique. Among the commercialized genetically modified crops, about 50 with altered metabolic enzyme activities have been identified in the International Service for the Acquisition of Agri-biotech Applications (ISAAA) database. These plants are reviewed as encouraging examples of the application of knowledge of biochemical pathways. Based on the recent examples of metabolomic studies, we discuss the performance of metabolic markers, the integration of metabolic and genomic data in metabolic QTLs (mQTLs) and metabolic genome-wide association studies (mGWAS). The elucidation of metabolic pathways and involved genes will help in crop breeding and the introgression of alleles of wild relatives in a more targeted manner.
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8
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Xi L, Schulze WX, Wu XN. Phosphoproteomic Analysis of Plant Membranes. Methods Mol Biol 2021; 2200:441-451. [PMID: 33175392 DOI: 10.1007/978-1-0716-0880-7_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Mass spectrometry (MS) is a powerful tool to investigate plant phosphorylation dynamics on a system-wide scale (phosphoproteomics). Plant membrane phosphoproteomics enables elucidating regulatory patterns in membranes, such as kinase-target relationships in different signaling pathways. Here, we present "ShortPhos," an efficient and simple phosphoproteomics protocol for research on plant membrane proteins, which allows fast and efficient identification and quantification of phosphopeptides from small amounts of starting plant material and/or membrane proteins. This method improves upon the efficiency of plant membrane phosphoproteomics profiling and can be applied to the study of membrane-based signaling networks.
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Affiliation(s)
- Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Xu Na Wu
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany.
- School of Life Sciences, Center for Life Sciences, Yunnan University, Kunming, China.
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9
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Xi L, Zhang Z, Herold S, Kassem S, Wu XN, Schulze WX. Phosphorylation Site Motifs in Plant Protein Kinases and Their Substrates. Methods Mol Biol 2021; 2358:1-16. [PMID: 34270043 DOI: 10.1007/978-1-0716-1625-3_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Protein phosphorylation is an important cellular regulatory mechanism affecting the activity, localization, conformation, and interaction of proteins. Protein phosphorylation is catalyzed by kinases, and thus kinases are the enzymes regulating cellular signaling cascades. In the model plant Arabidopsis, 940 genes encode for kinases. The substrate proteins of kinases are phosphorylated at defined sites, which consist of common patterns around the phosphorylation site, known as phosphorylation motifs. The discovery of kinase specificity with a preference of phosphorylation of certain motifs and application of such motifs in deducing signaling cascades helped to reveal underlying regulation mechanisms, and facilitated the prediction of kinase-target pairs. In this mini-review, we took advantage of retrieved data as examples to present the functions of kinase families along with their commonly found phosphorylation motifs from their substrates.
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Affiliation(s)
- Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany.
| | - Zhaoxia Zhang
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Sandra Herold
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Sarah Kassem
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Xu Na Wu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
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10
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Lu D, Gao T, Xi L, Krall L, Wu XN. Phosphoproteomics Profiling of Receptor Kinase Mutants. Methods Mol Biol 2021; 2358:73-82. [PMID: 34270046 DOI: 10.1007/978-1-0716-1625-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The transmembrane receptor kinase family is the largest protein kinase family in Arabidopsis. Many members of this family play critical roles in plant signaling pathways. However, many of these kinases have yet uncharacterized functions and very little is known about the direct substrates of these kinases. We have developed the "ShortPhos" method, an efficient and simple mass spectrometry (MS)-based phosphoproteomics protocol to perform comparative phosphopeptide profiling of knockout mutants of receptor-like kinases. Through this method, we are able to better understand the functional roles of plant kinases in the context of their signaling networks.
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Affiliation(s)
- Dandan Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Ting Gao
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China
| | - Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Leonard Krall
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China
| | - Xu Na Wu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China.
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11
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Aono AH, Pimenta RJG, Garcia ALB, Correr FH, Hosaka GK, Carrasco MM, Cardoso-Silva CB, Mancini MC, Sforça DA, dos Santos LB, Nagai JS, Pinto LR, Landell MGDA, Carneiro MS, Balsalobre TW, Quiles MG, Pereira WA, Margarido GRA, de Souza AP. The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns. FRONTIERS IN PLANT SCIENCE 2021; 12:668623. [PMID: 34305969 PMCID: PMC8294386 DOI: 10.3389/fpls.2021.668623] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/17/2021] [Indexed: 05/11/2023]
Abstract
The protein kinase (PK) superfamily is one of the largest superfamilies in plants and the core regulator of cellular signaling. Despite this substantial importance, the kinomes of sugarcane and sorghum have not been profiled. Here, we identified and profiled the complete kinomes of the polyploid Saccharum spontaneum (Ssp) and Sorghum bicolor (Sbi), a close diploid relative. The Sbi kinome was composed of 1,210 PKs; for Ssp, we identified 2,919 PKs when disregarding duplications and allelic copies, and these were related to 1,345 representative gene models. The Ssp and Sbi PKs were grouped into 20 groups and 120 subfamilies and exhibited high compositional similarities and evolutionary divergences. By utilizing the collinearity between the species, this study offers insights into Sbi and Ssp speciation, PK differentiation and selection. We assessed the PK subfamily expression profiles via RNA-Seq and identified significant similarities between Sbi and Ssp. Moreover, coexpression networks allowed inference of a core structure of kinase interactions with specific key elements. This study provides the first categorization of the allelic specificity of a kinome and offers a wide reservoir of molecular and genetic information, thereby enhancing the understanding of Sbi and Ssp PK evolutionary history.
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Affiliation(s)
- Alexandre Hild Aono
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Ricardo José Gonzaga Pimenta
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Ana Letycia Basso Garcia
- Department of Genetics, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Fernando Henrique Correr
- Department of Genetics, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Guilherme Kenichi Hosaka
- Department of Genetics, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Marishani Marin Carrasco
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | | | - Melina Cristina Mancini
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Danilo Augusto Sforça
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Lucas Borges dos Santos
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - James Shiniti Nagai
- Faculty of Medicine, Institute for Computational Genomics, RWTH Aachen University, Aachen, Germany
| | - Luciana Rossini Pinto
- Advanced Center of Sugarcane Agrobusiness Technological Research, Agronomic Institute of Campinas (IAC), Ribeirão Preto, Brazil
| | | | - Monalisa Sampaio Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Thiago Willian Balsalobre
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Marcos Gonçalves Quiles
- Instituto de Ciência e Tecnologia (ICT), Universidade Federal de São Paulo (Unifesp), São José dos Campos, Brazil
| | | | | | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- *Correspondence: Anete Pereira de Souza,
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12
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Li P, Liu J. Protein Phosphorylation in Plant Cell Signaling. Methods Mol Biol 2021; 2358:45-71. [PMID: 34270045 DOI: 10.1007/978-1-0716-1625-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Owing to their sessile nature, plants have evolved sophisticated sensory mechanisms to respond quickly and precisely to the changing environment. The extracellular stimuli are perceived and integrated by diverse receptors, such as receptor-like protein kinases (RLKs) and receptor-like proteins (RLPs), and then transmitted to the nucleus by complex cellular signaling networks, which play vital roles in biological processes including plant growth, development, reproduction, and stress responses. The posttranslational modifications (PTMs) are important regulators for the diversification of protein functions in plant cell signaling. Protein phosphorylation is an important and well-characterized form of the PTMs, which influences the functions of many receptors and key components in cellular signaling. Protein phosphorylation in plants predominantly occurs on serine (Ser) and threonine (Thr) residues, which is dynamically and reversibly catalyzed by protein kinases and protein phosphatases, respectively. In this review, we focus on the function of protein phosphorylation in plant cell signaling, especially plant hormone signaling, and highlight the roles of protein phosphorylation in plant abiotic stress responses.
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Affiliation(s)
- Ping Li
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China
| | - Junzhong Liu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China.
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Millar AH, Heazlewood JL, Giglione C, Holdsworth MJ, Bachmair A, Schulze WX. The Scope, Functions, and Dynamics of Posttranslational Protein Modifications. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:119-151. [PMID: 30786234 DOI: 10.1146/annurev-arplant-050718-100211] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Assessing posttranslational modification (PTM) patterns within protein molecules and reading their functional implications present grand challenges for plant biology. We combine four perspectives on PTMs and their roles by considering five classes of PTMs as examples of the broader context of PTMs. These include modifications of the N terminus, glycosylation, phosphorylation, oxidation, and N-terminal and protein modifiers linked to protein degradation. We consider the spatial distribution of PTMs, the subcellular distribution of modifying enzymes, and their targets throughout the cell, and we outline the complexity of compartmentation in understanding of PTM function. We also consider PTMs temporally in the context of the lifetime of a protein molecule and the need for different PTMs for assembly, localization, function, and degradation. Finally, we consider the combined action of PTMs on the same proteins, their interactions, and the challenge ahead of integrating PTMs into an understanding of protein function in plants.
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Affiliation(s)
- A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia;
| | - Joshua L Heazlewood
- School of BioSciences, University of Melbourne, Melbourne, Victoria 3010, Australia;
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell, CNRS UMR9198, F-91198 Gif-sur-Yvette Cedex, France;
| | - Michael J Holdsworth
- School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom;
| | - Andreas Bachmair
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria;
| | - Waltraud X Schulze
- Systembiologie der Pflanze, Universität Hohenheim, 70599 Stuttgart, Germany;
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Tunc-Ozdemir M, Urano D, Jaiswal DK, Clouse SD, Jones AM. Direct Modulation of Heterotrimeric G Protein-coupled Signaling by a Receptor Kinase Complex. J Biol Chem 2016; 291:13918-13925. [PMID: 27235398 DOI: 10.1074/jbc.c116.736702] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Indexed: 01/17/2023] Open
Abstract
Plants and some protists have heterotrimeric G protein complexes that activate spontaneously without canonical G protein-coupled receptors (GPCRs). In Arabidopsis, the sole 7-transmembrane regulator of G protein signaling 1 (AtRGS1) modulates the G protein complex by keeping it in the resting state (GDP-bound). However, it remains unknown how a myriad of biological responses is achieved with a single G protein modulator. We propose that in complete contrast to G protein activation in animals, plant leucine-rich repeat receptor-like kinases (LRR RLKs), not GPCRs, provide this discrimination through phosphorylation of AtRGS1 in a ligand-dependent manner. G protein signaling is directly activated by the pathogen-associated molecular pattern flagellin peptide 22 through its LRR RLK, FLS2, and co-receptor BAK1.
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Affiliation(s)
- Meral Tunc-Ozdemir
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Daisuke Urano
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Dinesh Kumar Jaiswal
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Steven D Clouse
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina 27695-7609
| | - Alan M Jones
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599; Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599.
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