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Qiu M, Sun Y, Tu S, Li H, Yang X, Zhao H, Yin M, Li Y, Ye W, Wang M, Wang Y. Mining oomycete proteomes for phosphatome leads to the identification of specific expanded phosphatases in oomycetes. MOLECULAR PLANT PATHOLOGY 2024; 25:e13425. [PMID: 38462784 PMCID: PMC10925823 DOI: 10.1111/mpp.13425] [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: 07/30/2023] [Revised: 12/23/2023] [Accepted: 01/11/2024] [Indexed: 03/12/2024]
Abstract
Phosphatases are important regulators of protein phosphorylation and various cellular processes, and they serve as counterparts to kinases. In this study, our comprehensive analysis of oomycete complete proteomes unveiled the presence of approximately 3833 phosphatases, with most species estimated to have between 100 and 300 putative phosphatases. Further investigation of these phosphatases revealed a significant increase in protein serine/threonine phosphatases (PSP) within oomycetes. In particular, we extensively studied the metallo-dependent protein phosphatase (PPM) within the PSP family in the model oomycete Phytophthora sojae. Our results showed notable differences in the expression patterns of PPMs throughout 10 life stages of P. sojae, indicating their vital roles in various stages of oomycete pathogens. Moreover, we identified 29 PPMs in P. sojae, and eight of them possessed accessory domains in addition to phosphate domains. We investigated the biological function of one PPM protein with an extra PH domain (PPM1); this protein exhibited high expression levels in both asexual developmental and infectious stages. Our analysis confirmed that PPM1 is indeed an active protein phosphatase, and its accessory domain does not affect its phosphatase activity. To delve further into its function, we generated knockout mutants of PPM1 and validated its essential roles in mycelial growth, sporangia and oospore production, as well as infectious stages. To the best of our knowledge, this study provides the first comprehensive inventory of phosphatases in oomycetes and identifies an important phosphatase within the expanded serine/threonine phosphatase group in oomycetes.
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Affiliation(s)
- Min Qiu
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
- The Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingJiangsuChina
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Yaru Sun
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
| | - Siqun Tu
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
| | - Huaibo Li
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
| | - Xin Yang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
| | - Haiyang Zhao
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
| | - Maozhu Yin
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
| | - Yaning Li
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
| | - Wenwu Ye
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
- The Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingJiangsuChina
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Ming Wang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
- The Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingJiangsuChina
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs)Nanjing Agricultural UniversityNanjingJiangsuChina
| | - Yuanchao Wang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsuChina
- The Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingJiangsuChina
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs)Nanjing Agricultural UniversityNanjingJiangsuChina
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2
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Romanowska-Duda Z, Janas R, Grzesik M, van Duijn B. Valorization of sorghum ash with digestate and biopreparations in the development biomass of plants in a closed production system of energy. Sci Rep 2023; 13:18604. [PMID: 37903894 PMCID: PMC10616079 DOI: 10.1038/s41598-023-45733-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 10/23/2023] [Indexed: 11/01/2023] Open
Abstract
Replacing chemical fertilizers with non-toxic waste that meet all fertilizing purposes, including ash from plant biomass and their management is becoming the important goal of sustainable agriculture concerning energy plants production in a closed system. This study aims to explore a novel strategy for utilizing natural sorghum ash together with digestate and ecological compounds, to replace synthetic fertilizers, for the energy plant development improvement and thus reduction of the environment pollution. Sorghum, as an energy plant, cultivated in low quality sandy and podzolic soils, in Central and North Poland climate, was fertilized with different doses of YaraMila Complex, a synthetic fertilizer (0, 150, 300 kg ha-1 Each dose was supplemented with different amounts of sorghum ash (0.5, 1, 2 and 4 t ha-1), used alone or with addition of APOL-HUMUS (soil improver; 10 L ha-1), biogas plant digestate (30 m3 ha-1) and Stymjod (nano-organic leaf fertilizer; 5 L ha-1). Added to each YaraMila Complex dose, the applied ash amounts (optimally 2-4 t ha-1), increased growth of plants, crop biomass, index of chlorophyll content, net photosynthesis, transpiration, stomatal conductance, content of intercellular CO2, activity of acid and alkaline phosphatase, RNase and dehydrogenase and energy properties. Sorghum ash used with the lesser YaraMila Complex doses of 0 or 150 kg ha-1 caused the enhanced growth of plants more than the doubled YaraMila Complex amounts applied alone (150 or 300 kg ha-1, correspondingly). Additionally, applied biogas plant digestate, APOL-HUMUS and Stymjod further increased the plant growth. This indicates that the application of natural sorghum ash accelerates energy plant development, can reduce by half the recommended synthetic fertilizer doses on poor and marginal soil and enables the cultivation of sorghum in a closed production cycle.
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Affiliation(s)
- Zdzisława Romanowska-Duda
- University of Lodz, Faculty of Biology and Environmental Protection, Banacha 12/16, 90-237, Lodz, Poland.
| | - Regina Janas
- Cultivar Testing, Nursery and Gene Bank Resources Department, The National Institute of Horticultural Research, Konstytucji 3 Maja 1/3, 96-100, Skierniewice, Poland
| | - Mieczysław Grzesik
- Cultivar Testing, Nursery and Gene Bank Resources Department, The National Institute of Horticultural Research, Konstytucji 3 Maja 1/3, 96-100, Skierniewice, Poland
| | - Bert van Duijn
- Plant Biodynamics Laboratory, Institute of Biology Leiden, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Fytagoras, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
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3
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Saini LK, Bheri M, Pandey GK. Protein phosphatases and their targets: Comprehending the interactions in plant signaling pathways. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 134:307-370. [PMID: 36858740 DOI: 10.1016/bs.apcsb.2022.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Protein phosphorylation is a vital reversible post-translational modification. This process is established by two classes of enzymes: protein kinases and protein phosphatases. Protein kinases phosphorylate proteins while protein phosphatases dephosphorylate phosphorylated proteins, thus, functioning as 'critical regulators' in signaling pathways. The eukaryotic protein phosphatases are classified as phosphoprotein phosphatases (PPP), metallo-dependent protein phosphatases (PPM), protein tyrosine (Tyr) phosphatases (PTP), and aspartate (Asp)-dependent phosphatases. The PPP and PPM families are serine (Ser)/threonine (Thr) specific phosphatases (STPs) that dephosphorylate Ser and Thr residues. The PTP family dephosphorylates Tyr residues while dual-specificity phosphatases (DsPTPs/DSPs) dephosphorylate Ser, Thr, and Tyr residues. The composition of these enzymes as well as their substrate specificity are important determinants of their functional significance in a number of cellular processes and stress responses. Their role in animal systems is well-understood and characterized. The functional characterization of protein phosphatases has been extensively covered in plants, although the comprehension of their mechanistic basis is an ongoing pursuit. The nature of their interactions with other key players in the signaling process is vital to our understanding. The substrates or targets determine their potential as well as magnitude of the impact they have on signaling pathways. In this article, we exclusively overview the various substrates of protein phosphatases in plant signaling pathways, which are a critical determinant of the outcome of various developmental and stress stimuli.
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Affiliation(s)
- Lokesh K Saini
- Department of Plant Molecular Biology, University of Delhi South Campus, Dhaula Kuan, New Delhi, India
| | - Malathi Bheri
- Department of Plant Molecular Biology, University of Delhi South Campus, Dhaula Kuan, New Delhi, India
| | - Girdhar K Pandey
- Department of Plant Molecular Biology, University of Delhi South Campus, Dhaula Kuan, New Delhi, India.
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4
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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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Xin J, Guo S, Zhang X, Tian J, Sun Y, Shang JX. AtPFA-DSP5 interacts with MPK3/MPK6 and negatively regulates plant salt responses. PLANT SIGNALING & BEHAVIOR 2021; 16:2000808. [PMID: 34839796 PMCID: PMC9208770 DOI: 10.1080/15592324.2021.2000808] [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: 08/31/2021] [Revised: 10/23/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
Protein tyrosine phosphatases play essential roles in plant growth and development and in plant responses to biotic or abiotic stresses. We recently demonstrated that an atypical dual-specificity protein tyrosine phosphatase in plants, AtPFA-DSP3 (DSP3), negatively regulates plant salt tolerance. Here, we report that a homolog of DSP3, AtPFA-DSP5 (DSP5), affects the response of plants to high-salt conditions. A loss-of-function mutant of DSP5 showed reduced sensitivity to salt treatment at the seed germination and vegetative stages of development while a gain-of-function mutant of DSP5 showed increased sensitivity to salt stress. The salt responses of dsp3dsp5 double-mutant plants were similar to those of dsp3 and dsp5 single-mutant plants. Gel overlay and firefly luciferase complementation assays showed that DSP5 interacts with MPK3 and MPK6 in vitro and in vivo. These results indicate that DSP5 is a novel negative regulator of salt responses in Arabidopsis that interacts directly with MPK3 and MPK6.
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Affiliation(s)
- Jing Xin
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Shanshan Guo
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Xiaolei Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Jiahui Tian
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Yu Sun
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Jian-Xiu Shang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
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6
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Pinto-Almeida A, Mendes TMF, Ferreira P, Abecasis AB, Belo S, Anibal FF, Allegretti SM, Galinaro CA, Carrilho E, Afonso A. A Comparative Proteomic Analysis of Praziquantel-Susceptible and Praziquantel-Resistant Schistosoma mansoni Reveals Distinct Response Between Male and Female Animals. FRONTIERS IN TROPICAL DISEASES 2021. [DOI: 10.3389/fitd.2021.664642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Schistosomiasis is a chronic neglected tropical disease saddling millions of people in the world, mainly children living in poor rural areas. Praziquantel (PZQ) is currently the only drug used for the treatment and control of this disease. However, the extensive use of this drug has brought concern about the emergence of PZQ-resistance/tolerance by Schistosoma mansoni. Studies of Schistosoma spp. genome, transcriptome, and proteome are crucial to better understand this situation. In this in vitro study, we compare the proteomes of a S. mansoni variant strain stably resistant to PZQ and isogenic to its fully susceptible parental counterpart, identifying proteins from male and female adult parasites of PZQ-resistant and PZQ-susceptible strains, exposed and not exposed to PZQ. A total of 60 Schistosoma spp. proteins were identified, some of which present or absent in either strain, which may putatively be involved in the PZQ-resistance phenomenon. These proteins were present in adult parasites not exposed to PZQ, but some of them disappeared when these adult parasites were exposed to the drug. Understanding the development of PZQ-resistance in S. mansoni is crucial to prolong the efficacy of the current drug and develop markers for monitoring the potential emergence of drug resistance.
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7
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Praat M, De Smet I, van Zanten M. Protein kinase and phosphatase control of plant temperature responses. JOURNAL OF EXPERIMENTAL BOTANY 2021:erab345. [PMID: 34283227 DOI: 10.1093/jxb/erab345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Indexed: 06/13/2023]
Abstract
Plants must cope with ever-changing temperature conditions in their environment. Suboptimal high and low temperatures, and stressful extreme temperatures, induce adaptive mechanisms that allow optimal performance and survival, respectively. These processes have been extensively studied at the physiological, transcriptional and (epi)genetic level. Cellular temperature signalling cascades and tolerance mechanisms also involve post-translational modifications (PTMs), particularly protein phosphorylation. Many protein kinases are known to be involved in cold acclimation and heat stress responsiveness but research on the role and importance of kinases and phosphatases in triggering responses to mild changes in temperature such as thermomorphogenesis is inadequately understood. In this review, we summarize the current knowledge on the roles of kinases and phosphatases in plant temperature responses. We discuss how kinases can function over a range of temperatures in different signalling pathways and provide an outlook to the application of PTM-modifying factors for the development of thermotolerant crops.
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Affiliation(s)
- Myrthe Praat
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University. Padualaan 8, 3584CH Utrecht, the Netherlands
| | - Ive De Smet
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Martijn van Zanten
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University. Padualaan 8, 3584CH Utrecht, the Netherlands
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8
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Phosphoproteomics Analysis of Plant Root Tissue. Methods Mol Biol 2021. [PMID: 34270051 DOI: 10.1007/978-1-0716-1625-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Plants absorb water and nutrients from soil through roots and transmit these resources through the xylem to the shoot. Roots therefore participate in information and material transduction as well as signal communication with the shoot. The importance of reversible protein phosphorylation in the regulation of plant growth and development has been amply demonstrated through decades of research. Here, we present a simple mass spectrometry-based shotgun phosphoproteomics protocol for Arabidopsis root tissue. Through this method, we can profile the Arabidopsis root phosphoproteome and construct signal networks of key proteins to better understand their roles in plant growth and development.
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Pandey R, Gupta P, Mohmmed A, Malhotra P, Gupta D. A Plasmodium falciparum protein tyrosine phosphatase inhibitor identified from the ChEMBL-NTD database blocks parasite growth. FEBS Open Bio 2021; 11:1921-1929. [PMID: 33934569 PMCID: PMC8255846 DOI: 10.1002/2211-5463.13171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/31/2021] [Indexed: 02/03/2023] Open
Abstract
Post‐translational modifications, especially reversible phosphorylation, are among the most common mechanisms that regulate protein function and biological processes in Plasmodium species. Of the Plasmodium phosphatases, phosphatase of regenerating liver (PfPRL) is secreted and is an essential phosphatase. Here, we expressed PfPRL in a heterologous expression system, and then purified and characterized its phosphatase activity. We found that Novartis_003209, a previously identified inhibitor, inhibited the PfPRL phosphatase activity of recombinant PfPRL and blocked in vitro parasite growth in a dose‐dependent manner. Further, in silico docking analysis of Novartis_003209 with all four P. falciparum tyrosine phosphatases (PTP) demonstrated that Novartis_003209 is a Plasmodium PTP inhibitor. Overall, our results identify a scaffold as a potential starting point to design a PTP‐specific inhibitor.
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Affiliation(s)
- Rajan Pandey
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Priya Gupta
- Malaria Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Asif Mohmmed
- Parasite Cell Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Pawan Malhotra
- Malaria Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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10
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Xin J, Li C, Ning K, Qin Y, Shang JX, Sun Y. AtPFA-DSP3, an atypical dual-specificity protein tyrosine phosphatase, affects salt stress response by modulating MPK3 and MPK6 activity. PLANT, CELL & ENVIRONMENT 2021; 44:1534-1548. [PMID: 33464564 DOI: 10.1111/pce.14002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/03/2021] [Accepted: 01/05/2021] [Indexed: 06/12/2023]
Abstract
Protein phosphorylation, especially serine/threonine and tyrosine phosphorylation, plays significant roles in signalling during plant growth and development as well as plant responses to biotic or abiotic stresses. Dual-specificity protein tyrosine phosphatases dephosphorylate components of these signalling pathways. Here, we report that an atypical dual-specificity protein tyrosine phosphatase, AtPFA-DSP3 (DSP3), negatively affects the response of plants to high-salt conditions. A DSP3 loss-of-function mutant showed reduced sensitivity to salt treatment. DSP3 was primarily localized in nuclei and was degraded during salt treatment. Compared to wild type, the level of ROS was lower in the dsp3 mutant and higher in plants ectopically expressing DSP3, indicating that higher DSP3 level was associated with increased ROS production. DSP3 interacted with and dephosphorylated MPK3 and MPK6. Genetic analyses of a dsp3mpk3 double mutant revealed that DSP3's effect on salt stress depends on MPK3. Moreover, the phosphatase activity of DSP3 was required for its role in salt signalling. These results indicate that DSP3 is a negative regulator of salt responses in Arabidopsis by directly modulating the accumulation of phosphorylated MPK3 and MPK6.
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Affiliation(s)
- Jing Xin
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Chuanling Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Kexin Ning
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Yuan Qin
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Jian-Xiu Shang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Yu Sun
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
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11
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Cossa G, Parua PK, Eilers M, Fisher RP. Protein phosphatases in the RNAPII transcription cycle: erasers, sculptors, gatekeepers, and potential drug targets. Genes Dev 2021; 35:658-676. [PMID: 33888562 PMCID: PMC8091971 DOI: 10.1101/gad.348315.121] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In this review, Cossa et al. discuss the current knowledge and outstanding questions about phosphatases in the context of the RNAPII transcription cycle. The transcription cycle of RNA polymerase II (RNAPII) is governed at multiple points by opposing actions of cyclin-dependent kinases (CDKs) and protein phosphatases, in a process with similarities to the cell division cycle. While important roles of the kinases have been established, phosphatases have emerged more slowly as key players in transcription, and large gaps remain in understanding of their precise functions and targets. Much of the earlier work focused on the roles and regulation of sui generis and often atypical phosphatases—FCP1, Rtr1/RPAP2, and SSU72—with seemingly dedicated functions in RNAPII transcription. Decisive roles in the transcription cycle have now been uncovered for members of the major phosphoprotein phosphatase (PPP) family, including PP1, PP2A, and PP4—abundant enzymes with pleiotropic roles in cellular signaling pathways. These phosphatases appear to act principally at the transitions between transcription cycle phases, ensuring fine control of elongation and termination. Much is still unknown, however, about the division of labor among the PPP family members, and their possible regulation by or of the transcriptional kinases. CDKs active in transcription have recently drawn attention as potential therapeutic targets in cancer and other diseases, raising the prospect that the phosphatases might also present opportunities for new drug development. Here we review the current knowledge and outstanding questions about phosphatases in the context of the RNAPII transcription cycle.
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Affiliation(s)
- Giacomo Cossa
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Pabitra K Parua
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Martin Eilers
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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12
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Juarez-Escobar J, Elizalde-Contreras JM, Loyola-Vargas VM, Ruiz-May E. A Phosphoproteomic Analysis Pipeline for Peels of Tropical Fruits. Methods Mol Biol 2021; 2139:179-196. [PMID: 32462587 DOI: 10.1007/978-1-0716-0528-8_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Phosphorylation is a posttranslational reversible modification related to signaling and regulatory mechanisms. Protein phosphorylation is linked to structural changes that modulate protein activity, interaction, or localization and therefore the cell signaling pathways. The use of techniques for phosphoprotein enrichment along with mass spectrometry has become a powerful tool for the characterization of signal transduction in model organisms. However, limited efforts have focused on the establishment of protocols for the analysis of the phosphoproteome in nonmodel organisms such as tropical fruits. This chapter describes a potential pipeline for sample preparation and enrichment of phosphorylated proteins/peptides before MS analysis of peels of some species of tropical fruits.
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Affiliation(s)
- Janet Juarez-Escobar
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Veracruz, Mexico
| | - José M Elizalde-Contreras
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Veracruz, Mexico
| | - Víctor M Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán (CICY), Mérida, Yucatán, Mexico
| | - Eliel Ruiz-May
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Veracruz, Mexico.
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13
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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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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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15
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PhosPhAt 4.0: An Updated Arabidopsis Database for Searching Phosphorylation Sites and Kinase-Target Interactions. Methods Mol Biol 2021; 2358:189-202. [PMID: 34270056 DOI: 10.1007/978-1-0716-1625-3_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The PhosPhAt 4.0 database contains information on Arabidopsis phosphorylation sites identified by mass spectrometry in large-scale experiments from different research groups. So far PhosPhAt 4.0 has been one of the most significant large-scale data resources for plant phosphorylation studies. Functionalities of the web application, besides display of phosphorylation sites, include phosphorylation site prediction and kinase-target relationships retrieval. Here, we present an overview and user instructions for the PhosPhAt 4.0 database, with strong emphasis on recent renewals regarding protein annotation by SUBA4.0 and Mapman4, and additional phosphorylation site information imported from other databases, such as UniProt. Here, we provide a user guide for the retrieval of phosphorylation motifs from the kinase-target database and how to visualize these results. The improvements incorporated into the PhosPhAt 4.0 database have produced much more functionality and user flexibility for phosphoproteomic analysis.
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16
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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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17
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Liu Y, Yan J, Qin Q, Zhang J, Chen Y, Zhao L, He K, Hou S. Type one protein phosphatases (TOPPs) contribute to the plant defense response in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:360-377. [PMID: 31125159 DOI: 10.1111/jipb.12845] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 05/22/2019] [Indexed: 05/27/2023]
Abstract
Plant immunity must be tightly controlled to avoid activation of defense mechanisms in the absence of pathogen attack. Protein phosphorylation is a common mechanism regulating immune signaling. In Arabidopsis thaliana, nine members of the type one protein phosphatase (TOPP) family (also known as protein phosphatase 1, PP1) have been identified. Here, we characterized the autoimmune phenotype of topp4-1, a previously identified dominant-negative mutant of TOPP4. Epistasis analysis showed that defense activation in topp4-1 depended on NON-RACE-SPECIFIC DISEASE RESISTANCE1, PHYTOALEXIN DEFICIENT4, and the salicylic acid pathway. We generated topp1/4/5/6/7/8/9 septuple mutants to investigate the function of TOPPs in plant immunity. Elevated defense gene expression and enhanced resistance to Pseudomonas syringae pv. tomato (Pst) DC3000 in the septuple mutant indicate that TOPPs function in plant defense responses. Furthermore, TOPPs physically interacted with mitogen-activated protein kinases (MAPKs) and affected the MAPK-mediated downstream defense pathway. Thus, our study reveals that TOPPs are important regulators of plant immunity.
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Affiliation(s)
- Yaqiong Liu
- MOE Key Laboratoryof Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jia Yan
- MOE Key Laboratoryof Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Qianqian Qin
- MOE Key Laboratoryof Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jing Zhang
- MOE Key Laboratoryof Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yan Chen
- MOE Key Laboratoryof Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Lulu Zhao
- MOE Key Laboratoryof Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Kai He
- MOE Key Laboratoryof Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Suiwen Hou
- MOE Key Laboratoryof Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, 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: 133] [Impact Index Per Article: 26.6] [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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