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Kong Y, Guo P, Xu J, Li J, Wu M, Zhang Z, Wang Y, Liu X, Yang L, Liu M, Zhang H, Wang P, Zhang Z. MoMkk1 and MoAtg1 dichotomously regulating autophagy and pathogenicity through MoAtg9 phosphorylation in Magnaporthe oryzae. mBio 2024; 15:e0334423. [PMID: 38501872 PMCID: PMC11005334 DOI: 10.1128/mbio.03344-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Autophagy is a central biodegradation pathway critical in eliminating intracellular cargo to maintain cellular homeostasis and improve stress resistance. At the same time, the key component of the mitogen-activated protein kinase cascade regulating cell wall integrity signaling MoMkk1 has an essential role in the autophagy of the rice blast fungus Magnaporthe oryzae. Still, the mechanism of how MoMkk1 regulates autophagy is unclear. Interestingly, we found that MoMkk1 regulates the autophagy protein MoAtg9 through phosphorylation. MoAtg9 is a transmembrane protein subjected to phosphorylation by autophagy-related protein kinase MoAtg1. Here, we provide evidence demonstrating that MoMkk1-dependent MoAtg9 phosphorylation is required for phospholipid translocation during isolation membrane stages of autophagosome formation, an autophagic process essential for the development and pathogenicity of the fungus. In contrast, MoAtg1-dependent phosphorylation of MoAtg9 negatively regulates this process, also impacting growth and pathogenicity. Our studies are the first to demonstrate that MoAtg9 is subject to MoMkk1 regulation through protein phosphorylation and that MoMkk1 and MoAtg1 dichotomously regulate autophagy to underlie the growth and pathogenicity of M. oryzae.IMPORTANCEMagnaporthe oryzae utilizes multiple signaling pathways to promote colonization of host plants. MoMkk1, a cell wall integrity signaling kinase, plays an essential role in autophagy governed by a highly conserved autophagy kinase MoAtg1-mediated pathway. How MoMkk1 regulates autophagy in coordination with MoAtg1 remains elusive. Here, we provide evidence that MoMkk1 phosphorylates MoAtg9 to positively regulate phospholipid translocation during the isolation membrane or smaller membrane structures stage of autophagosome formation. This is in contrast to the negative regulation of MoAtg9 by MoAtg1 for the same process. Intriguingly, MoMkk1-mediated MoAtg9 phosphorylation enhances the fungal infection of rice, whereas MoAtg1-dependant MoAtg9 phosphorylation significantly attenuates it. Taken together, we revealed a novel mechanism of autophagy and virulence regulation by demonstrating the dichotomous functions of MoMkk1 and MoAtg1 in the regulation of fungal autophagy and pathogenicity.
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Affiliation(s)
- Yun Kong
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Pusheng Guo
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Jiayun Xu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Jiaxu Li
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Miao Wu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Ziqi Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Yifan Wang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Xinyu Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Leiyun Yang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Muxing Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Haifeng Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Ping Wang
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Zhengguang Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
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Wei Y, Zhu B, Zhang Y, Ma G, Wu J, Tang L, Shi H. CPK1-HSP90 phosphorylation and effector XopC2-HSP90 interaction underpin the antagonism during cassava defense-pathogen infection. New Phytol 2024. [PMID: 38581188 DOI: 10.1111/nph.19739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 03/21/2024] [Indexed: 04/08/2024]
Abstract
Cassava is one of the most important tropical crops, but it is seriously affected by cassava bacteria blight (CBB) caused by the bacterial pathogen Xanthomonas phaseoli pv manihotis (Xam). So far, how pathogen Xam infects and how host cassava defends during pathogen-host interaction remains elusive, restricting the prevention and control of CBB. Here, the illustration of HEAT SHOCK PROTEIN 90 kDa (MeHSP90.9) interacting proteins in both cassava and bacterial pathogen revealed the dual roles of MeHSP90.9 in cassava-Xam interaction. On the one hand, calmodulin-domain protein kinase 1 (MeCPK1) directly interacted with MeHSP90.9 to promote its protein phosphorylation at serine 175 residue. The protein phosphorylation of MeHSP90.9 improved the transcriptional activation of MeHSP90.9 clients (SHI-RELATED SEQUENCE 1 (MeSRS1) and MeWRKY20) to the downstream target genes (avrPphB Susceptible 3 (MePBS3) and N-aceylserotonin O-methyltransferase 2 (MeASMT2)) and immune responses. On the other hand, Xanthomonas outer protein C2 (XopC2) physically associated with MeHSP90.9 to inhibit its interaction with MeCPK1 and the corresponding protein phosphorylation by MeCPK1, so as to repress host immune responses and promote bacterial pathogen infection. In summary, these results provide new insights into genetic improvement of cassava disease resistance and extend our understanding of cassava-bacterial pathogen interaction.
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Affiliation(s)
- Yunxie Wei
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Hainan Province, 572025, China
| | - Binbin Zhu
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Hainan Province, 572025, China
| | - Ye Zhang
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Hainan Province, 572025, China
| | - Guowen Ma
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Hainan Province, 572025, China
| | - Jingyuan Wu
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Hainan Province, 572025, China
| | - Luzhi Tang
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Hainan Province, 572025, China
| | - Haitao Shi
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Hainan Province, 572025, China
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Zeng H, Chen H, Zhang M, Ding M, Xu F, Yan F, Kinoshita T, Zhu Y. Plasma membrane H +-ATPases in mineral nutrition and crop improvement. Trends Plant Sci 2024:S1360-1385(24)00052-9. [PMID: 38582687 DOI: 10.1016/j.tplants.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 04/08/2024]
Abstract
Plasma membrane H+-ATPases (PMAs) pump H+ out of the cytoplasm by consuming ATP to generate a membrane potential and proton motive force for the transmembrane transport of nutrients into and out of plant cells. PMAs are involved in nutrient acquisition by regulating root growth, nutrient uptake, and translocation, as well as the establishment of symbiosis with arbuscular mycorrhizas. Under nutrient stresses, PMAs are activated to pump more H+ and promote organic anion excretion, thus improving nutrient availability in the rhizosphere. Herein we review recent progress in the physiological functions and the underlying molecular mechanisms of PMAs in the efficient acquisition and utilization of various nutrients in plants. We also discuss perspectives for the application of PMAs in improving crop production and quality.
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Affiliation(s)
- Houqing Zeng
- College of Life and Environmental Sciences, Kharkiv Institute at Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China.
| | - Huiying Chen
- College of Life and Environmental Sciences, Kharkiv Institute at Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Maoxing Zhang
- International Research Centre for Environmental Membrane Biology, Department of Horticulture, Foshan University, Foshan 528000, China
| | - Ming Ding
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
| | - Feiyun Xu
- Center for Plant Water-Use and Nutrition Regulation, College of JunCao Science and Ecology (College of Carbon Neutrality), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Feng Yan
- Institute of Agronomy and Plant Breeding, Justus Liebig University of Giessen, Giessen, Germany
| | - Toshinori Kinoshita
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya 4660824, Japan.
| | - Yiyong Zhu
- College of Resource and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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Kannon T, Murashige S, Nishioka T, Amano M, Funahashi Y, Tsuboi D, Yamahashi Y, Nagai T, Kaibuchi K, Yoshimoto J. KANPHOS: Kinase-associated neural phospho-signaling database for data-driven research. Front Mol Neurosci 2024; 17:1379089. [PMID: 38628370 PMCID: PMC11018961 DOI: 10.3389/fnmol.2024.1379089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/11/2024] [Indexed: 04/19/2024] Open
Abstract
Protein phosphorylation, a key regulator of cellular processes, plays a central role in brain function and is implicated in neurological disorders. Information on protein phosphorylation is expected to be a clue for understanding various neuropsychiatric disorders and developing therapeutic strategies. Nonetheless, existing databases lack a specific focus on phosphorylation events in the brain, which are crucial for investigating the downstream pathway regulated by neurotransmitters. To overcome the gap, we have developed a web-based database named "Kinase-Associated Neural PHOspho-Signaling (KANPHOS)." This paper presents the design concept, detailed features, and a series of improvements for KANPHOS. KANPHOS is designed to support data-driven research by fulfilling three key objectives: (1) enabling the search for protein kinases and their substrates related to extracellular signals or diseases; (2) facilitating a consolidated search for information encompassing phosphorylated substrate genes, proteins, mutant mice, diseases, and more; and (3) offering integrated functionalities to support pathway and network analysis. KANPHOS is also equipped with API functionality to interact with external databases and analysis tools, enhancing its utility in data-driven investigations. Those key features represent a critical step toward unraveling the complex landscape of protein phosphorylation in the brain, with implications for elucidating the molecular mechanisms underlying neurological disorders. KANPHOS is freely accessible to all researchers at https://kanphos.jp.
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Affiliation(s)
- Takayuki Kannon
- Department of Biomedical Data Science, Fujita Health University School of Medicine, Toyoake, Japan
- Division of Computational Science, International Center for Brain Science, Fujita Health University, Toyoake, Japan
| | - Satoshi Murashige
- Department of Biomedical Data Science, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tomoki Nishioka
- Division of Cell Biology, International Center for Brain Science, Fujita Health University, Toyoake, Japan
| | - Mutsuki Amano
- Department of Cell Pharmacology, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Yasuhiro Funahashi
- Division of Cell Biology, International Center for Brain Science, Fujita Health University, Toyoake, Japan
| | - Daisuke Tsuboi
- Division of Cell Biology, International Center for Brain Science, Fujita Health University, Toyoake, Japan
| | - Yukie Yamahashi
- Division of Cell Biology, International Center for Brain Science, Fujita Health University, Toyoake, Japan
| | - Taku Nagai
- Division of Behavioral Neuropharmacology, International Center for Brain Science, Fujita Health University, Toyoake, Japan
| | - Kozo Kaibuchi
- Division of Cell Biology, International Center for Brain Science, Fujita Health University, Toyoake, Japan
| | - Junichiro Yoshimoto
- Department of Biomedical Data Science, Fujita Health University School of Medicine, Toyoake, Japan
- Division of Computational Science, International Center for Brain Science, Fujita Health University, Toyoake, Japan
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5
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Levin G, Yasmin M, Pieńko T, Yehishalom N, Hanna R, Kleifeld O, Glaser F, Schuster G. The protein phosphorylation landscape in photosystem I of the desert algae Chlorella sp. New Phytol 2024; 242:544-557. [PMID: 38379464 DOI: 10.1111/nph.19603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/28/2024] [Indexed: 02/22/2024]
Abstract
The phosphorylation of photosystem II (PSII) and its antenna (LHCII) proteins has been studied, and its involvement in state transitions and PSII repair is known. Yet, little is known about the phosphorylation of photosystem I (PSI) and its antenna (LHCI) proteins. Here, we applied proteomics analysis to generate a map of the phosphorylation sites of the PSI-LHCI proteins in Chlorella ohadii cells that were grown under low or extreme high-light intensities (LL and HL). Furthermore, we analyzed the content of oxidized tryptophans and PSI-LHCI protein degradation products in these cells, to estimate the light-induced damage to PSI-LHCI. Our work revealed the phosphorylation of 17 of 22 PSI-LHCI subunits. The analyses detected the extensive phosphorylation of the LHCI subunits Lhca6 and Lhca7, which is modulated by growth light intensity. Other PSI-LHCI subunits were phosphorylated to a lesser extent, including PsaE, where molecular dynamic simulation proposed that a phosphoserine stabilizes ferredoxin binding. Additionally, we show that HL-grown cells accumulate less oxidative damage and degradation products of PSI-LHCI proteins, compared with LL-grown cells. The significant phosphorylation of Lhca6 and Lhca7 at the interface with other LHCI subunits suggests a physiological role during photosynthesis, possibly by altering light-harvesting characteristics and binding of other subunits.
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Affiliation(s)
- Guy Levin
- Faculty of Biology, Technion, Haifa, 32000, Israel
| | | | - Tomasz Pieńko
- Schulich Faculty of Chemistry, Technion, Haifa, 32000, Israel
| | | | - Rawad Hanna
- Faculty of Biology, Technion, Haifa, 32000, Israel
| | | | - Fabian Glaser
- The Lorry I. Lokey Center for Life Sciences and Engineering, Technion, Haifa, 32000, Israel
| | - Gadi Schuster
- Faculty of Biology, Technion, Haifa, 32000, Israel
- Grand Technion Energy Program, Technion, Haifa, 32000, Israel
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Cayuela A, Villasante-Fernández A, Corbalán-Acedo A, Baena-González E, Ferrando A, Belda-Palazón B. An Escherichia coli-Based Phosphorylation System for Efficient Screening of Kinase Substrates. Int J Mol Sci 2024; 25:3813. [PMID: 38612623 PMCID: PMC11011427 DOI: 10.3390/ijms25073813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 02/29/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Posttranslational modifications (PTMs), particularly phosphorylation, play a pivotal role in expanding the complexity of the proteome and regulating diverse cellular processes. In this study, we present an efficient Escherichia coli phosphorylation system designed to streamline the evaluation of potential substrates for Arabidopsis thaliana plant kinases, although the technology is amenable to any. The methodology involves the use of IPTG-inducible vectors for co-expressing kinases and substrates, eliminating the need for radioactive isotopes and prior protein purification. We validated the system's efficacy by assessing the phosphorylation of well-established substrates of the plant kinase SnRK1, including the rat ACETYL-COA CARBOXYLASE 1 (ACC1) and FYVE1/FREE1 proteins. The results demonstrated the specificity and reliability of the system in studying kinase-substrate interactions. Furthermore, we applied the system to investigate the phosphorylation cascade involving the A. thaliana MKK3-MPK2 kinase module. The activation of MPK2 by MKK3 was demonstrated to phosphorylate the Myelin Basic Protein (MBP), confirming the system's ability to unravel sequential enzymatic steps in phosphorylation cascades. Overall, this E. coli phosphorylation system offers a rapid, cost-effective, and reliable approach for screening potential kinase substrates, presenting a valuable tool to complement the current portfolio of molecular techniques for advancing our understanding of kinase functions and their roles in cellular signaling pathways.
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Affiliation(s)
- Andrés Cayuela
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, 46022 Valencia, Spain; (A.C.); (A.V.-F.); (A.C.-A.)
| | - Adela Villasante-Fernández
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, 46022 Valencia, Spain; (A.C.); (A.V.-F.); (A.C.-A.)
| | - Antonio Corbalán-Acedo
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, 46022 Valencia, Spain; (A.C.); (A.V.-F.); (A.C.-A.)
| | | | - Alejandro Ferrando
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, 46022 Valencia, Spain; (A.C.); (A.V.-F.); (A.C.-A.)
| | - Borja Belda-Palazón
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, 46022 Valencia, Spain; (A.C.); (A.V.-F.); (A.C.-A.)
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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. J Exp Bot 2024; 75:2127-2142. [PMID: 38066636 DOI: 10.1093/jxb/erad490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Deichsel S, Gahr BM, Mastel H, Preiss A, Nagel AC. Numerous Serine/Threonine Kinases Affect Blood Cell Homeostasis in Drosophila melanogaster. Cells 2024; 13:576. [PMID: 38607015 PMCID: PMC11011202 DOI: 10.3390/cells13070576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/13/2024] Open
Abstract
Blood cells in Drosophila serve primarily innate immune responses. Various stressors influence blood cell homeostasis regarding both numbers and the proportion of blood cell types. The principle molecular mechanisms governing hematopoiesis are conserved amongst species and involve major signaling pathways like Notch, Toll, JNK, JAK/Stat or RTK. Albeit signaling pathways generally rely on the activity of protein kinases, their specific contribution to hematopoiesis remains understudied. Here, we assess the role of Serine/Threonine kinases with the potential to phosphorylate the transcription factor Su(H) in crystal cell homeostasis. Su(H) is central to Notch signal transduction, and its inhibition by phosphorylation impedes crystal cell formation. Overall, nearly twenty percent of all Drosophila Serine/Threonine kinases were studied in two assays, global and hemocyte-specific overexpression and downregulation, respectively. Unexpectedly, the majority of kinases influenced crystal cell numbers, albeit only a few were related to hematopoiesis so far. Four kinases appeared essential for crystal cell formation, whereas most kinases restrained crystal cell development. This group comprises all kinase classes, indicative of the complex regulatory network underlying blood cell homeostasis. The rather indiscriminative response we observed opens the possibility that blood cells measure their overall phospho-status as a proxy for stress-signals, and activate an adaptive immune response accordingly.
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Affiliation(s)
- Sebastian Deichsel
- Department of Molecular Genetics, Institute of Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Bernd M. Gahr
- Department of Molecular Genetics, Institute of Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Helena Mastel
- Department of Molecular Genetics, Institute of Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Anette Preiss
- Institute of Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Anja C. Nagel
- Department of Molecular Genetics, Institute of Biology, University of Hohenheim, 70599 Stuttgart, Germany
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Sun Q, Sun Y, Liu X, Li M, Li Q, Xiao J, Xu P, Zhang S, Ding X. Regulation of plant resistance to salt stress by the SnRK1-dependent splicing factor SRRM1L. New Phytol 2024. [PMID: 38511255 DOI: 10.1111/nph.19699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
Most splicing factors are extensively phosphorylated but their physiological functions in plant salt resistance are still elusive. We found that phosphorylation by SnRK1 kinase is essential for SRRM1L nuclear speckle formation and its splicing factor activity in plant cells. In Arabidopsis, loss-of-function of SRRM1L leads to the occurrence of alternative pre-mRNA splicing events and compromises plant resistance to salt stress. In Arabidopsis srrm1l mutant line, we identified an intron-retention Nuclear factor Y subunit A 10 (NFYA10) mRNA variant by RNA-Seq and found phosphorylation-dependent RNA-binding of SRRM1L is indispensable for its alternative splicing activity. In the wild-type Arabidopsis, salt stress can activate SnRK1 to phosphorylate SRRM1L, triggering enrichment of functional NFYA10.1 variant to enhance plant salt resistance. By contrast, the Arabidopsis srrm1l mutant accumulates nonfunctional NFYA10.3 variant, sensitizing plants to salt stress. In summary, this work deciphered the molecular mechanisms and physiological functions of SnRK1-SRRM1L-NFYA10 module, shedding light on a regulatory pathway to fine-tune plant adaptation to abiotic stress at the post-transcriptional and post-translational levels.
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Affiliation(s)
- Qi Sun
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, China
| | - Yixin Sun
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
| | - Xin Liu
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
| | - Minglong Li
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
| | - Qiang Li
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, China
| | - Jialei Xiao
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, China
| | - Pengfei Xu
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, China
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shuzhen Zhang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, China
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaodong Ding
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, China
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, China
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10
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Hsiao Y, Zhang H, Li GX, Deng Y, Yu F, Kahrood HV, Steele JR, Schittenhelm RB, Nesvizhskii AI. Analysis and visualization of quantitative proteomics data using FragPipe-Analyst. bioRxiv 2024:2024.03.05.583643. [PMID: 38496650 PMCID: PMC10942459 DOI: 10.1101/2024.03.05.583643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The FragPipe computational proteomics platform is gaining widespread popularity among the proteomics research community because of its fast processing speed and user-friendly graphical interface. Although FragPipe produces well-formatted output tables that are ready for analysis, there is still a need for an easy-to-use and user-friendly downstream statistical analysis and visualization tool. FragPipe-Analyst addresses this need by providing an R shiny web server to assist FragPipe users in conducting downstream analyses of the resulting quantitative proteomics data. It supports major quantification workflows including label-free quantification, tandem mass tags, and data-independent acquisition. FragPipe-Analyst offers a range of useful functionalities, such as various missing value imputation options, data quality control, unsupervised clustering, differential expression (DE) analysis using Limma, and gene ontology and pathway enrichment analysis using Enrichr. To support advanced analysis and customized visualizations, we also developed FragPipeAnalystR, an R package encompassing all FragPipe-Analyst functionalities that is extended to support site-specific analysis of post-translational modifications (PTMs). FragPipe-Analyst and FragPipeAnalystR are both open-source and freely available.
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Affiliation(s)
- Yi Hsiao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Haijian Zhang
- Monash Proteomics & Metabolomics Platform, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Ginny Xiaohe Li
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yamei Deng
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hossein Valipour Kahrood
- Monash Proteomics & Metabolomics Platform, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Monash Genomics & Bioinformatics Platform, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Joel R. Steele
- Monash Proteomics & Metabolomics Platform, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Ralf B. Schittenhelm
- Monash Proteomics & Metabolomics Platform, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Alexey I. Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
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11
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Li X, Hou C, Yang M, Luo B, Mao N, Chen K, Chen Z, Bai Y. The effect of phosphorylation on the conformational dynamics and allostery of the association of death-associated protein kinase with calmodulin. J Biomol Struct Dyn 2024:1-9. [PMID: 38457488 DOI: 10.1080/07391102.2024.2316763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/05/2024] [Indexed: 03/10/2024]
Abstract
Protein phosphorylation plays an important role in the signal transduction and is capable of regulation of cell activity. The death-associated protein kinase 1 (DAPK1), as a Ser/Thr kinase, interacts with calmodulin (CaM) to regulate apoptotic and autophagic signaling. Autophosphorylation of DAPK1 at Ser308 located at the autoregulatory domain (ARD) blocks CaM binding and inhibits kinase catalytic activity. However, the mechanism underlying the influence of Ser308 phosphorylation (pS308) on the DAPK1 activity remains unclear. Here, we performed multiple, microsecond length molecular dynamics (MD) simulations, the molecular mechanics generalized Born/surface area (MM-GBSA) binding free energy calculations, principal component analysis, and dynamic cross-correlation analysis to unravel the conformational dynamics and allostery of the DAPK1 - CaM interaction triggered by the pS308 at the ARD. MD simulations showed that pS308 affected the conformational stability of the DAPK1 - CaM complex. Further energetic and structural exploration revealed that pS308 weakened the association of the phosphorylated DAPK1 to CaM, which lowered the susceptibility of DAPK1 to be activated by CaM. This result can provide mechanistic insights into the molecular underpinning through which the DAPK1 kinase activity is modulated by the auto-phosphorylation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xiaolong Li
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
| | - Canglong Hou
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
| | - Mingyuan Yang
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
| | - Beier Luo
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
| | - Ningfang Mao
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
| | - Kai Chen
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
| | - Ziqiang Chen
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
| | - Yushu Bai
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
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12
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Shen T, Xu F, Chen D, Yan R, Wang Q, Li K, Zhang G, Ni L, Jiang M. A B-box transcription factor OsBBX17 regulates saline-alkaline tolerance through the MAPK cascade pathway in rice. New Phytol 2024; 241:2158-2175. [PMID: 38098211 DOI: 10.1111/nph.19480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/24/2023] [Indexed: 02/09/2024]
Abstract
Rice OsBBX17 encodes a B-box zinc finger transcription factor in which the N-terminal B-box structural domain interacts with OsMPK1. In addition, it directly binds to the G-box of OsHAK2 and OsHAK7 promoters and represses their transcription. Under saline-alkaline conditions, the expression of OsBBX17 was inhibited. Meanwhile, activation of the OsMPK1-mediated mitogen-activated protein kinase cascade pathway caused OsMPK1 to interact with OsBBX17 and phosphorylate OsBBX17 at the Thr-95 site. It reduced OsBBX17 DNA-binding activity and enhanced saline-alkaline tolerance by deregulating transcriptional repression of OsHAK2 and OsHAK7. Genetic assays showed that the osbbx17-KO had an excellent saline-alkaline tolerance, whereas the opposite was in OsBBX17-OE. In addition, overexpression of OsMPK1 significantly improved saline-alkaline tolerance, but knockout of OsMPK1 caused an increased sensitivity. Further overexpression of OsBBX17 in the osmpk1-KO caused extreme saline-alkaline sensitivity, even a quick death. OsBBX17 was validated in saline-alkaline tolerance from two independent aspects, transcriptional level and post-translational protein modification, unveiling a mechanistic framework by which OsMPK1-mediated phosphorylation of OsBBX17 regulates the transcription of OsHAK2 and OsHAK7 to enhance the Na+ /K+ homeostasis, which partially explains light on the molecular mechanisms of rice responds to saline-alkaline stress via B-box transcription factors for the genetic engineering of saline-alkaline tolerant crops.
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Affiliation(s)
- Tao Shen
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fengjuan Xu
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dan Chen
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Runjiao Yan
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qingwen Wang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
| | - Kaiyue Li
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Gang Zhang
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lan Ni
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mingyi Jiang
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
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13
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Suskiewicz MJ. The logic of protein post-translational modifications (PTMs): Chemistry, mechanisms and evolution of protein regulation through covalent attachments. Bioessays 2024; 46:e2300178. [PMID: 38247183 DOI: 10.1002/bies.202300178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024]
Abstract
Protein post-translational modifications (PTMs) play a crucial role in all cellular functions by regulating protein activity, interactions and half-life. Despite the enormous diversity of modifications, various PTM systems show parallels in their chemical and catalytic underpinnings. Here, focussing on modifications that involve the addition of new elements to amino-acid sidechains, I describe historical milestones and fundamental concepts that support the current understanding of PTMs. The historical survey covers selected key research programmes, including the study of protein phosphorylation as a regulatory switch, protein ubiquitylation as a degradation signal and histone modifications as a functional code. The contribution of crucial techniques for studying PTMs is also discussed. The central part of the essay explores shared chemical principles and catalytic strategies observed across diverse PTM systems, together with mechanisms of substrate selection, the reversibility of PTMs by erasers and the recognition of PTMs by reader domains. Similarities in the basic chemical mechanism are highlighted and their implications are discussed. The final part is dedicated to the evolutionary trajectories of PTM systems, beginning with their possible emergence in the context of rivalry in the prokaryotic world. Together, the essay provides a unified perspective on the diverse world of major protein modifications.
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Affiliation(s)
- Marcin J Suskiewicz
- Centre de Biophysique Moléculaire, CNRS - Orléans, UPR 4301, affiliated with Université d'Orléans, Orléans, France
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14
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Cilek N, Ugurel E, Goksel E, Yalcin O. Signaling mechanisms in red blood cells: A view through the protein phosphorylation and deformability. J Cell Physiol 2024; 239:e30958. [PMID: 36748950 DOI: 10.1002/jcp.30958] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/07/2023] [Accepted: 01/19/2023] [Indexed: 02/08/2023]
Abstract
Intracellular signaling mechanisms in red blood cells (RBCs) involve various protein kinases and phosphatases and enable rapid adaptive responses to hypoxia, metabolic requirements, oxidative stress, or shear stress by regulating the physiological properties of the cell. Protein phosphorylation is a ubiquitous mechanism for intracellular signal transduction, volume regulation, and cytoskeletal organization in RBCs. Spectrin-based cytoskeleton connects integral membrane proteins, band 3 and glycophorin C to junctional proteins, ankyrin and Protein 4.1. Phosphorylation leads to a conformational change in the protein structure, weakening the interactions between proteins in the cytoskeletal network that confers a more flexible nature for the RBC membrane. The structural organization of the membrane and the cytoskeleton determines RBC deformability that allows cells to change their ability to deform under shear stress to pass through narrow capillaries. The shear stress sensing mechanisms and oxygenation-deoxygenation transitions regulate cell volume and mechanical properties of the membrane through the activation of ion transporters and specific phosphorylation events mediated by signal transduction. In this review, we summarize the roles of Protein kinase C, cAMP-Protein kinase A, cGMP-nitric oxide, RhoGTPase, and MAP/ERK pathways in the modulation of RBC deformability in both healthy and disease states. We emphasize that targeting signaling elements may be a therapeutic strategy for the treatment of hemoglobinopathies or channelopathies. We expect the present review will provide additional insights into RBC responses to shear stress and hypoxia via signaling mechanisms and shed light on the current and novel treatment options for pathophysiological conditions.
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Affiliation(s)
- Neslihan Cilek
- Research Center for Translational Medicine (KUTTAM), Koc University, Istanbul, Turkey
- School of Medicine, Koc University, Istanbul, Turkey
- Graduate School of Health Sciences, Koc University, Istanbul, Turkey
| | - Elif Ugurel
- Research Center for Translational Medicine (KUTTAM), Koc University, Istanbul, Turkey
- School of Medicine, Koc University, Istanbul, Turkey
| | - Evrim Goksel
- Research Center for Translational Medicine (KUTTAM), Koc University, Istanbul, Turkey
- School of Medicine, Koc University, Istanbul, Turkey
- Graduate School of Health Sciences, Koc University, Istanbul, Turkey
| | - Ozlem Yalcin
- Research Center for Translational Medicine (KUTTAM), Koc University, Istanbul, Turkey
- School of Medicine, Koc University, Istanbul, Turkey
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15
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Wu ZH, He LL, Wang CC, Liang C, Li HY, Zhong DW, Dong ZX, Zhang LJ, Zhang XQ, Ge LF, Chen S. Unveiling unique alternative splicing responses to low temperature in Zoysia japonica through ZjRTD1.0, a high-quality reference transcript dataset. Physiol Plant 2024; 176:e14280. [PMID: 38644527 DOI: 10.1111/ppl.14280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/29/2024] [Accepted: 03/09/2024] [Indexed: 04/23/2024]
Abstract
Inadequate reference databases in RNA-seq analysis can hinder data utilization and interpretation. In this study, we have successfully constructed a high-quality reference transcript dataset, ZjRTD1.0, for Zoysia japonica, a widely-used turfgrass with exceptional tolerance to various abiotic stress, including low temperatures and salinity. This dataset comprises 113,089 transcripts from 57,143 genes. BUSCO analysis demonstrates exceptional completeness (92.4%) in ZjRTD1.0, with reduced proportions of fragmented (3.3%) and missing (4.3%) orthologs compared to prior datasets. ZjRTD1.0 enables more precise analyses, including transcript quantification and alternative splicing assessments using public datasets, which identified a substantial number of differentially expressed transcripts (DETs) and differential alternative splicing (DAS) events, leading to several novel findings on Z. japonica's responses to abiotic stresses. First, spliceosome gene expression influenced alternative splicing significantly under abiotic stress, with a greater impact observed during low-temperature stress. Then, a significant positive correlation was found between the number of differentially expressed genes (DEGs) encoding protein kinases and the frequency of DAS events, suggesting the role of protein phosphorylation in regulating alternative splicing. Additionally, our results suggest possible involvement of serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs) in generating inclusion/exclusion isoforms under low-temperature stress. Furthermore, our investigation revealed a significantly enhanced overlap between DEGs and differentially alternatively spliced genes (DASGs) in response to low-temperature stress, suggesting a unique co-regulatory mechanism governing transcription and splicing in the context of low-temperature response. In conclusion, we have proven that ZjRTD1.0 will serve as a reliable and useful resource for future transcriptomic analyses in Z. japonica.
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Affiliation(s)
- Zhi-Hao Wu
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Liang-Liang He
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Cong-Cong Wang
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Chen Liang
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Han-Ying Li
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Dan-Wen Zhong
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Zhao-Xia Dong
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Li-Juan Zhang
- Shenzhen Tourism College of Jinan University, Shenzhen, Guangdong, China
| | - Xiang-Qian Zhang
- College of Food Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - Liang-Fa Ge
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Shu Chen
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
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16
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Doering LN, Gerling N, Linnenbrügger L, Lansing H, Baune MC, Fischer K, von Schaewen A. Evidence for dual targeting control of Arabidopsis 6-phosphogluconate dehydrogenase isoforms by N-terminal phosphorylation. J Exp Bot 2024:erae077. [PMID: 38412416 DOI: 10.1093/jxb/erae077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Indexed: 02/29/2024]
Abstract
The oxidative pentose-phosphate pathway (OPPP) retrieves NADPH from glucose-6-phosphate, which is important in chloroplasts at night and in plastids of heterotrophic tissues. We previously studied how OPPP enzymes may transiently locate to peroxisomes, but how this is achieved for the 3rd enzyme remained unclear. By extending our genetic approach, we could demonstrate that Arabidopsis isoform 6-phosphogluconate dehydrogenase 2 (PGD2) is indispensable in peroxisomes during fertilization, and then studied why all PGD-reporter fusions show a mostly cytosolic pattern. Previously published interaction of a plant PGD with thioredoxin m was confirmed using Trxm2 for yeast-2-hybrid (Y2H) and bimolecular fluorescent complementation (BiFC) assays, and medial reporter fusions (with both ends accessible) turned out to be beneficial for studying peroxisomal targeting of PGD2. Of special importance were phosphomimetic changes at Thr6, resulting in a clear targeting switch to peroxisomes, while a similar change at position Ser7 in PGD1 conferred plastid import. Apparently, efficient subcellular localization can be achieved by activating an unknown kinase, either early after or during translation. N-terminal phosphorylation of PGD2 interfered with dimerization in the cytosol, thus allowing accessibility of the C-terminal peroxisomal targeting signal (PTS1). Notably, we identified amino-acid positions that are conserved among plant PGD homologs, with PTS1 motifs first appearing in ferns, suggesting a functional link to fertilization during the evolution of seed plants.
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Affiliation(s)
- Lennart Nico Doering
- University of Münster, Department of Biology, Institute of Plant Biology and Biotechnology, Molecular Physiology of Plants, Schlossplatz 7, D-48149 Münster, Germany
| | - Niklas Gerling
- University of Münster, Department of Biology, Institute of Plant Biology and Biotechnology, Molecular Physiology of Plants, Schlossplatz 7, D-48149 Münster, Germany
| | - Loreen Linnenbrügger
- University of Münster, Department of Biology, Institute of Plant Biology and Biotechnology, Molecular Physiology of Plants, Schlossplatz 7, D-48149 Münster, Germany
| | - Hannes Lansing
- University of Münster, Department of Biology, Institute of Plant Biology and Biotechnology, Molecular Physiology of Plants, Schlossplatz 7, D-48149 Münster, Germany
| | - Marie-Christin Baune
- University of Münster, Department of Biology, Institute of Plant Biology and Biotechnology, Molecular Physiology of Plants, Schlossplatz 7, D-48149 Münster, Germany
| | - Kerstin Fischer
- University of Münster, Department of Biology, Institute of Plant Biology and Biotechnology, Molecular Physiology of Plants, Schlossplatz 7, D-48149 Münster, Germany
| | - Antje von Schaewen
- University of Münster, Department of Biology, Institute of Plant Biology and Biotechnology, Molecular Physiology of Plants, Schlossplatz 7, D-48149 Münster, Germany
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17
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Lee E, May H, Kazmierczak K, Liang J, Nguyen N, Hill JA, Gillette TG, Szczesna-Cordary D, Chang AN. The MYPT2-regulated striated muscle-specific myosin light chain phosphatase limits cardiac myosin phosphorylation in vivo. J Biol Chem 2024; 300:105652. [PMID: 38224947 PMCID: PMC10851227 DOI: 10.1016/j.jbc.2024.105652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 01/17/2024] Open
Abstract
The physiological importance of cardiac myosin regulatory light chain (RLC) phosphorylation by its dedicated cardiac myosin light chain kinase has been established in both humans and mice. Constitutive RLC-phosphorylation, regulated by the balanced activities of cardiac myosin light chain kinase and myosin light chain phosphatase (MLCP), is fundamental to the biochemical and physiological properties of myofilaments. However, limited information is available on cardiac MLCP. In this study, we hypothesized that the striated muscle-specific MLCP regulatory subunit, MYPT2, targets the phosphatase catalytic subunit to cardiac myosin, contributing to the maintenance of cardiac function in vivo through the regulation of RLC-phosphorylation. To test this hypothesis, we generated a floxed-PPP1R12B mouse model crossed with a cardiac-specific Mer-Cre-Mer to conditionally ablate MYPT2 in adult cardiomyocytes. Immunofluorescence microscopy using the gene-ablated tissue as a control confirmed the localization of MYPT2 to regions where it overlaps with a subset of RLC. Biochemical analysis revealed an increase in RLC-phosphorylation in vivo. The loss of MYPT2 demonstrated significant protection against pressure overload-induced hypertrophy, as evidenced by heart weight, qPCR of hypertrophy-associated genes, measurements of myocyte diameters, and expression of β-MHC protein. Furthermore, mantATP chase assays revealed an increased ratio of myosin heads distributed to the interfilament space in MYPT2-ablated heart muscle fibers, confirming that RLC-phosphorylation regulated by MLCP, enhances cardiac performance in vivo. Our findings establish MYPT2 as the regulatory subunit of cardiac MLCP, distinct from the ubiquitously expressed canonical smooth muscle MLCP. Targeting MYPT2 to increase cardiac RLC-phosphorylation in vivo may improve baseline cardiac performance, thereby attenuating pathological hypertrophy.
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Affiliation(s)
- Eunyoung Lee
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Herman May
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Katarzyna Kazmierczak
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Jingsheng Liang
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Nhu Nguyen
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Joseph A Hill
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Thomas G Gillette
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Danuta Szczesna-Cordary
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Audrey N Chang
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Pak Center for Mineral Metabolism and Clinical Research, UTSW Medical Center, Dallas, Texas, USA.
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18
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Li C, Li X, Deng Z, Song Y, Liu X, Tang XA, Li Z, Zhang Y, Zhang B, Tang W, Shang JX, Sun Y. EGR1 and EGR2 positively regulate plant ABA signaling by modulating the phosphorylation of SnRK2.2. New Phytol 2024; 241:1492-1509. [PMID: 38095247 DOI: 10.1111/nph.19458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 11/17/2023] [Indexed: 01/26/2024]
Abstract
During abscisic acid (ABA) signaling, reversible phosphorylation controls the activity and accumulation of class III SNF1-RELATED PROTEIN KINASE 2s (SnRK2s). While protein phosphatases that negatively regulate SnRK2s have been identified, those that positively regulate ABA signaling through SnRK2s are less understood. In this study, Arabidopsis thaliana mutants of Clade E Growth-Regulating 1 and 2 (EGR1/2), which belong to the protein phosphatase 2C family, exhibited reduced ABA sensitivity in terms of seed germination, cotyledon greening, and ABI5 accumulation. Conversely, overexpression increased these ABA-induced responses. Transcriptomic data revealed that most ABA-regulated genes in egr1 egr2 plants were expressed at reduced levels compared with those in Col-0 after ABA treatment. Abscisic acid up-regulated EGR1/2, which interact directly with SnRK2.2 through its C-terminal domain I. Genetic analysis demonstrated that EGR1/2 function through SnRK2.2 during ABA response. Furthermore, SnRK2.2 de-phosphorylation by EGR1/2 was identified at serine 31 within the ATP-binding pocket. A phospho-mimic mutation confirmed that phosphorylation at serine 31 inhibited SnRK2.2 activity and reduced ABA responsiveness in plants. Our findings highlight the positive role of EGR1/2 in regulating ABA signaling, they reveal a new mechanism for modulating SnRK2.2 activity, and provide novel insight into how plants fine-tune their responses to ABA.
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Affiliation(s)
- Chuanling Li
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture and Rural Affairs, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China
| | - Xuetong Li
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Zhiping Deng
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Yuning Song
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Xinye Liu
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Xiaohan Alex Tang
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong Special Administrative Region, China
| | - Ziye Li
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Ya Zhang
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Baowen Zhang
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Wenqiang Tang
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Jian-Xiu Shang
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Yu Sun
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
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19
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Song T, Yang Q, Qu P, Qiao L, Wang X. Attenphos: General Phosphorylation Site Prediction Model Based on Attention Mechanism. Int J Mol Sci 2024; 25:1526. [PMID: 38338804 PMCID: PMC10855885 DOI: 10.3390/ijms25031526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Phosphorylation site prediction has important application value in the field of bioinformatics. It can act as an important reference and help with protein function research, protein structure research, and drug discovery. So, it is of great significance to propose scientific and effective calculation methods to accurately predict phosphorylation sites. In this study, we propose a new method, Attenphos, based on the self-attention mechanism for predicting general phosphorylation sites in proteins. The method not only captures the long-range dependence information of proteins but also better represents the correlation between amino acids through feature vector encoding transformation. Attenphos takes advantage of the one-dimensional convolutional layer to reduce the number of model parameters, improve model efficiency and prediction accuracy, and enhance model generalization. Comparisons between our method and existing state-of-the-art prediction tools were made using balanced datasets from human proteins and unbalanced datasets from mouse proteins. We performed prediction comparisons using independent test sets. The results showed that Attenphos demonstrated the best overall performance in the prediction of Serine (S), Threonine (T), and Tyrosine (Y) sites on both balanced and unbalanced datasets. Compared to current state-of-the-art methods, Attenphos has significantly higher prediction accuracy. This proves the potential of Attenphos in accelerating the identification and functional analysis of protein phosphorylation sites and provides new tools and ideas for biological research and drug discovery.
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Affiliation(s)
| | | | | | | | - Xun Wang
- Qingdao Institute of Software, College of Computer Science and Technology, China University of Petroleum, Qingdao 266555, China; (T.S.); (Q.Y.); (P.Q.); (L.Q.)
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20
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Kuhn A, Roosjen M, Mutte S, Dubey SM, Carrillo Carrasco VP, Boeren S, Monzer A, Koehorst J, Kohchi T, Nishihama R, Fendrych M, Sprakel J, Friml J, Weijers D. RAF-like protein kinases mediate a deeply conserved, rapid auxin response. Cell 2024; 187:130-148.e17. [PMID: 38128538 PMCID: PMC10783624 DOI: 10.1016/j.cell.2023.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 06/29/2023] [Accepted: 11/18/2023] [Indexed: 12/23/2023]
Abstract
The plant-signaling molecule auxin triggers fast and slow cellular responses across land plants and algae. The nuclear auxin pathway mediates gene expression and controls growth and development in land plants, but this pathway is absent from algal sister groups. Several components of rapid responses have been identified in Arabidopsis, but it is unknown if these are part of a conserved mechanism. We recently identified a fast, proteome-wide phosphorylation response to auxin. Here, we show that this response occurs across 5 land plant and algal species and converges on a core group of shared targets. We found conserved rapid physiological responses to auxin in the same species and identified rapidly accelerated fibrosarcoma (RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation across species. Genetic analysis connects this kinase to both auxin-triggered protein phosphorylation and rapid cellular response, thus identifying an ancient mechanism for fast auxin responses in the green lineage.
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Affiliation(s)
- Andre Kuhn
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands
| | - Mark Roosjen
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands
| | - Sumanth Mutte
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands
| | - Shiv Mani Dubey
- Department of Experimental Plant Biology, Charles University, Prague, Czech Republic
| | | | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands
| | - Aline Monzer
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Jasper Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Ryuichi Nishihama
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Matyáš Fendrych
- Department of Experimental Plant Biology, Charles University, Prague, Czech Republic
| | - Joris Sprakel
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands
| | - Jiří Friml
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, the Netherlands.
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21
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Wong MM, Huang XJ, Bau YC, Verslues PE. AT Hook-Like 10 phosphorylation determines ribosomal RNA processing 6-like 1 (RRP6L1) chromatin association and growth suppression during water stress. Plant Cell Environ 2024; 47:24-37. [PMID: 37727952 DOI: 10.1111/pce.14725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 09/21/2023]
Abstract
Phosphorylation of AT Hook-Like 10 (AHL10), one of the AT-hook family of plant-specific DNA binding proteins, is critical for growth suppression during moderate severity drought (low water potential, ψw ) stress. To understand how AHL10 phosphorylation determines drought response, we identified putative AHL10 interacting proteins and further characterized interaction with RRP6L1, a protein involved in epigenetic regulation. RRP6L1 and AHL10 mutants, as well as ahl10-1rrp6l1-2, had similar phenotypes of increased growth maintenance during low ψw . Chromatin precipitation demonstrated that RRP6L1 chromatin association increased during low ψw stress and was dependent upon AHL10 phosphorylation. Transcriptome analyses showed that AHL10 and RRP6L1 have concordant effects on expression of stress- and development-related genes. Together these results indicate that stress signalling can act via AHL10 phosphorylation to control the chromatin association of the key regulatory protein RRP6L1. AHL10 and RRP6L1 interaction in meristem cells is part of a mechanism to downregulate growth during low ψw stress. Interestingly, the loss of AHL13, which is homologous to AHL10 and phosphorylated at a similar C-terminal site, blocked the enhanced growth maintenance of ahl10-1. Thus, AHL10 and AHL13, despite their close homology, are not redundant but rather have distinct roles, likely related to the formation of AHL hetero-complexes.
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Affiliation(s)
- Min May Wong
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Xin-Jie Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Chiuan Bau
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Paul E Verslues
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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22
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Wu WC, Chen IH, Hou PY, Wang LH, Tsai CH, Cheng CP. The phosphorylation of the movement protein TGBp1 regulates the accumulation of the Bamboo mosaic virus. J Gen Virol 2024; 105. [PMID: 38189334 DOI: 10.1099/jgv.0.001945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024] Open
Abstract
Phosphorylation and dephosphorylation of viral movement proteins plays a crucial role in regulating virus movement. Our study focused on investigating the movement protein TGBp1 of Bamboo mosaic virus (BaMV), which is a single-stranded positive-sense RNA virus. Specifically, we examined four potential phosphorylation sites (S15, S18, T58, and S247) within the TGBp1 protein. To study the impact of phosphorylation, we introduced amino acid substitutions at the selected sites. Alanine substitutions were used to prevent phosphorylation, while aspartate substitutions were employed to mimic phosphorylation. Our findings suggest that mimicking phosphorylation at S15, S18 and T58 of TGBp1 might be linked to silencing suppressor activities. The phosphorylated form at these sites exhibits a loss of silencing suppressor activity, leading to reduced viral accumulation in the inoculated leaves. Furthermore, mimicking phosphorylation at residues S15 and S18 could diminish viral accumulation at the single-cell level, while doing so at residue T58 could influence virus movement. However, mimicking phosphorylation at residue S247 does not appear to be relevant to both functions of TGBp1. Overall, our study provides insights into the functional significance of specific phosphorylation sites in BaMV TGBp1, illuminating the regulatory mechanisms involved in virus movement and silencing suppression.
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Affiliation(s)
- Wan-Chen Wu
- Department of Biomedical Sciences and Engineering, Tzu Chi University, Hualien, 970, Taiwan, ROC
| | - I-Hsuan Chen
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan, ROC
- Advanced Plant and Food Crop Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Pei-Yu Hou
- Department of Biomedical Sciences and Engineering, Tzu Chi University, Hualien, 970, Taiwan, ROC
| | - Lan-Hui Wang
- Department of Biomedical Sciences and Engineering, Tzu Chi University, Hualien, 970, Taiwan, ROC
| | - Ching-Hsiu Tsai
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan, ROC
- Advanced Plant and Food Crop Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - Chi-Ping Cheng
- Department of Biomedical Sciences and Engineering, Tzu Chi University, Hualien, 970, Taiwan, ROC
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23
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Gandhi A, Tseng YH, Oelmüller R. The damage-associated molecular pattern cellotriose alters the phosphorylation pattern of proteins involved in cellulose synthesis and trans-Golgi trafficking in Arabidopsis thaliana. Plant Signal Behav 2023; 18:2184352. [PMID: 36913771 PMCID: PMC10026868 DOI: 10.1080/15592324.2023.2184352] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We have recently demonstrated that the cellulose breakdown product cellotriose is a damage-associated molecular pattern (DAMP) which induces responses related to the integrity of the cell wall. Activation of downstream responses requires the Arabidopsis malectin domain-containing CELLOOLIGOMER RECEPTOR KINASE1 (CORK1)1. The cellotriose/CORK1 pathway induces immune responses, including NADPH oxidase-mediated reactive oxygen species production, mitogen-activated protein kinase 3/6 phosphorylation-dependent defense gene activation, and the biosynthesis of defense hormones. However, apoplastic accumulation of cell wall breakdown products should also activate cell wall repair mechanisms. We demonstrate that the phosphorylation pattern of numerous proteins involved in the accumulation of an active cellulose synthase complex in the plasma membrane and those for protein trafficking to and within the trans-Golgi network (TGN) are altered within minutes after cellotriose application to Arabidopsis roots. The phosphorylation pattern of enzymes involved in hemicellulose or pectin biosynthesis and the transcript levels for polysaccharide-synthesizing enzymes responded barely to cellotriose treatments. Our data show that the phosphorylation pattern of proteins involved in cellulose biosynthesis and trans-Golgi trafficking is an early target of the cellotriose/CORK1 pathway.
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Affiliation(s)
- Akanksha Gandhi
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Department of Plant Physiology, Friedrich-Schiller-University, Jena, Germany
| | - Yu-Heng Tseng
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Department of Plant Physiology, Friedrich-Schiller-University, Jena, Germany
| | - Ralf Oelmüller
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Department of Plant Physiology, Friedrich-Schiller-University, Jena, Germany
- CONTACT Ralf Oelmüller Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Department of Plant Physiology, Friedrich-Schiller-University, Jena, Germany
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Smith MA, Benidickson KH, Plaxton WC. In Vivo Phosphorylation of the Cytosolic Glucose-6-Phosphate Dehydrogenase Isozyme G6PD6 in Phosphate-Resupplied Arabidopsis thaliana Suspension Cells and Seedlings. Plants (Basel) 2023; 13:31. [PMID: 38202338 PMCID: PMC10780934 DOI: 10.3390/plants13010031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024]
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) catalyzes the first committed step of the oxidative pentose phosphate pathway (OPPP). Our recent phosphoproteomics study revealed that the cytosolic G6PD6 isozyme became hyperphosphorylated at Ser12, Thr13 and Ser18, 48 h following phosphate (Pi) resupply to Pi-starved (-Pi) Arabidopsis thaliana cell cultures. The aim of the present study was to assess whether G6PD6 phosphorylation also occurs in shoots or roots following Pi resupply to -Pi Arabidopsis seedlings, and to investigate its relationship with G6PD activity. Interrogation of phosphoproteomic databases indicated that N-terminal, multi-site phosphorylation of G6PD6 and its orthologs is quite prevalent. However, the functions of these phosphorylation events remain unknown. Immunoblotting with an anti-(pSer18 phosphosite-specific G6PD6) antibody confirmed that G6PD6 from Pi-resupplied, but not -Pi, Arabidopsis cell cultures or seedlings (i.e., roots) was phosphorylated at Ser18; this correlated with a significant increase in extractable G6PD activity, and biomass accumulation. Peptide kinase assays of Pi-resupplied cell culture extracts indicated that G6PD6 phosphorylation at Ser18 is catalyzed by a Ca2+-dependent protein kinase (CDPK), which correlates with the 'CDPK-like' targeting motif that flanks Ser18. Our results support the hypothesis that N-terminal phosphorylation activates G6PD6 to enhance OPPP flux and thus the production of reducing power (i.e., NADPH) and C-skeletons needed to establish the rapid resumption of growth that ensures Pi-resupply to -Pi Arabidopsis.
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Affiliation(s)
| | | | - William C. Plaxton
- Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada; (M.A.S.); (K.H.B.)
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25
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Xu X, Li M, Su Y, Wang Q, Qin P, Huang H, Zhang Y, Zhou Y, Yan J. Cdk5 phosphorylation-dependent C9orf72 degradation promotes neuronal death in Parkinson's disease models. CNS Neurosci Ther 2023; 29:3952-3966. [PMID: 37353944 PMCID: PMC10651984 DOI: 10.1111/cns.14319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 04/08/2023] [Accepted: 05/22/2023] [Indexed: 06/25/2023] Open
Abstract
AIMS Chromosome 9 open reading frame 72 (C9orf72) is one of the most dazzling molecules in neurodegenerative diseases, albeit that its role in Parkinson's disease (PD) remains unknown. This article aimed to explore the potential mechanism of C9orf72 involved in the pathogenesis of PD. METHODS The expression and phosphorylation levels of C9orf72 were examined by Western blotting, RT-PCR, and immunoprecipitation using PD models. Multiple bioinformatics software was used to predict the potential phosphorylation sites of C9orf72 by Cdk5, followed by verification of whether Cdk5-inhibitor ROSCOVITINE could reverse the degradation of C9orf72 in PD. By constructing the sh-C9orf72-knockdown adenovirus and overexpressing the FLAG-C9orf72 plasmid, the effects of C9orf72 knockdown and overexpression, respectively, were determined. A short peptide termed Myr-C9orf72 was used to verify whether interfering with Cdk5 phosphorylation at the Ser9 site of the C9orf72 protein could alleviate autophagy disorder, neuronal death, and movement disorder in PD models. RESULTS The expression level of the C9orf72 protein was significantly reduced, albeit the mRNA expression was not changed in the PD models. Moreover, the phosphorylation level was enhanced, and its reduction was mainly degraded by the ubiquitin-proteasome pathway. The key nervous system kinase Cdk5 directly phosphorylated the S9 site of the C9orf72 protein, which promoted the degradation of the C9orf72 protein. The knockdown of C9orf72 aggravated autophagy dysfunction and increased neuronal loss and motor dysfunction in substantia nigra neurons of PD mice. The overexpression of C9orf72 alleviated autophagy dysfunction in PD neurons. Specifically, interference with Cdk5 phosphorylation at the S9 site of C9orf72 alleviated autophagy dysfunction, neuronal death, and motor dysfunction mediated by C9orf72 protein degradation during PD. CONCLUSIONS Cumulatively, our findings illustrate the importance of the role of C9orf72 in the regulation of neuronal death during PD progression via the Cdk5-dependent degradation.
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Affiliation(s)
- Xingfeng Xu
- Department of PhysiologyGuilin Medical UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Brain and Cognitive NeuroscienceGuilin Medical UniversityGuilinGuangxiChina
| | - Mao Li
- Department of PhysiologyGuilin Medical UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Brain and Cognitive NeuroscienceGuilin Medical UniversityGuilinGuangxiChina
| | - Yan Su
- Department of PhysiologyGuilin Medical UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Brain and Cognitive NeuroscienceGuilin Medical UniversityGuilinGuangxiChina
| | - Qi Wang
- Department of PhysiologyGuilin Medical UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Brain and Cognitive NeuroscienceGuilin Medical UniversityGuilinGuangxiChina
| | - Peifang Qin
- Department of MicrobiologyGuilin Medical UniversityGuilinGuangxiChina
| | - Haitao Huang
- Department of MicrobiologyGuilin Medical UniversityGuilinGuangxiChina
| | - Yuting Zhang
- Department of MicrobiologyGuilin Medical UniversityGuilinGuangxiChina
| | - Yali Zhou
- Department of MicrobiologyGuilin Medical UniversityGuilinGuangxiChina
| | - Jianguo Yan
- Department of PhysiologyGuilin Medical UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Brain and Cognitive NeuroscienceGuilin Medical UniversityGuilinGuangxiChina
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26
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Chen F, Di H, Wang Y, Peng C, Chen R, Pan H, Yang CG, Liang H, Lan L. The enzyme activity of sortase A is regulated by phosphorylation in Staphylococcus aureus. Virulence 2023; 14:2171641. [PMID: 36694285 PMCID: PMC9928477 DOI: 10.1080/21505594.2023.2171641] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
In many Gram-positive bacteria, the transpeptidase enzyme sortase A (SrtA) anchors surface proteins to cell wall and plays a critical role in the bacterial pathogenesis. Here, we show that in Staphylococcus aureus, an important human pathogen, the SrtA is phosphorylated by serine/threonine protein kinase Stk1. S. aureus SrtA can also be phosphorylated by small-molecule phosphodonor acetyl phosphate (AcP) in vitro. We determined that various amino acid residues of S. aureus SrtA are subject to phosphorylation, primarily on its catalytic site residue cysteine-184 in the context of a bacterial cell lysate. Both Stk1 and AcP-mediated phosphorylation inhibited the enzyme activity of SrtA in vitro. Consequently, deletion of gene (i.e. stp1) encoding serine/threonine phosphatase Stp1, the corresponding phosphatase of Stk1, caused an increase in the phosphorylation level of SrtA. The stp1 deletion mutant mimicked the phenotypic traits of srtA deletion mutant (i.e. attenuated growth where either haemoglobin or haem as a sole iron source and reduced liver infections in a mouse model of systemic infection). Importantly, the phenotypic defects of the stp1 deletion mutant can be alleviated by overexpressing srtA. Taken together, our finding suggests that phosphorylation plays an important role in modulating the activity of SrtA in S. aureus.
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Affiliation(s)
- Feifei Chen
- College of Life Science, Northwest University, Xi’an, China,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China,Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Hongxia Di
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China,University of Chinese Academy of Sciences, Beijing, China
| | - Yanhui Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China,University of Chinese Academy of Sciences, Beijing, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, China
| | - Rongrong Chen
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China,University of Chinese Academy of Sciences, Beijing, China
| | - Huiwen Pan
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China,University of Chinese Academy of Sciences, Beijing, China
| | - Cai-Guang Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China,Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China,University of Chinese Academy of Sciences, Beijing, China
| | - Haihua Liang
- College of Life Science, Northwest University, Xi’an, China,School of Medicine, Southern University of Science and Technology, Shenzhen, China,Haihua Liang School of Medicine Southern University of Science and Technology, Shenzhen, China
| | - Lefu Lan
- College of Life Science, Northwest University, Xi’an, China,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China,Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China,University of Chinese Academy of Sciences, Beijing, China,CONTACT Lefu Lan
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27
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de Mojana di Cologna N, Andresen S, Samaddar S, Archer-Hartmann S, Rogers AM, Kajfasz JK, Ganguly T, Garcia BA, Saengpet I, Peterson AM, Azadi P, Szymanski CM, Lemos JA, Abranches J. Post-translational modification by the Pgf glycosylation machinery modulates Streptococcus mutans OMZ175 physiology and virulence. Mol Microbiol 2023. [PMID: 37972006 DOI: 10.1111/mmi.15190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023]
Abstract
Streptococcus mutans is commonly associated with dental caries and the ability to form biofilms is essential for its pathogenicity. We recently identified the Pgf glycosylation machinery of S. mutans, responsible for the post-translational modification of the surface-associated adhesins Cnm and WapA. Since the four-gene pgf operon (pgfS-pgfM1-pgfE-pgfM2) is part of the S. mutans core genome, we hypothesized that the scope of the Pgf system goes beyond Cnm and WapA glycosylation. In silico analyses and tunicamycin sensitivity assays suggested a functional overlap between the Pgf machinery and the rhamnose-glucose polysaccharide synthesis pathway. Phenotypic characterization of pgf mutants (ΔpgfS, ΔpgfE, ΔpgfM1, ΔpgfM2, and Δpgf) revealed that the Pgf system is important for biofilm formation, surface charge, membrane stability, and survival in human saliva. Moreover, deletion of the entire pgf operon (Δpgf strain) resulted in significantly impaired colonization in a rat oral colonization model. Using Cnm as a model, we showed that Cnm is heavily modified with N-acetyl hexosamines but it becomes heavily phosphorylated with the inactivation of the PgfS glycosyltransferase, suggesting a crosstalk between these two post-translational modification mechanisms. Our results revealed that the Pgf machinery contributes to multiple aspects of S. mutans pathobiology that may go beyond Cnm and WapA glycosylation.
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Affiliation(s)
| | - Silke Andresen
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Sandip Samaddar
- Department of Oral Biology, University of Florida, College of Dentistry, Gainesville, Florida, USA
| | | | - Ashley Marie Rogers
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Jessica K Kajfasz
- Department of Oral Biology, University of Florida, College of Dentistry, Gainesville, Florida, USA
| | - Tridib Ganguly
- Department of Oral Biology, University of Florida, College of Dentistry, Gainesville, Florida, USA
| | - Bruna A Garcia
- Department of Oral Biology, University of Florida, College of Dentistry, Gainesville, Florida, USA
| | - Irene Saengpet
- Department of Oral Biology, University of Florida, College of Dentistry, Gainesville, Florida, USA
| | - Alexandra M Peterson
- Department of Oral Biology, University of Florida, College of Dentistry, Gainesville, Florida, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Christine M Szymanski
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - José A Lemos
- Department of Oral Biology, University of Florida, College of Dentistry, Gainesville, Florida, USA
| | - Jacqueline Abranches
- Department of Oral Biology, University of Florida, College of Dentistry, Gainesville, Florida, USA
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Wang W, Lopez McDonald MC, Kim C, Ma M, Pan Z(T, Kaufmann C, Frank DA. The complementary roles of STAT3 and STAT1 in cancer biology: insights into tumor pathogenesis and therapeutic strategies. Front Immunol 2023; 14:1265818. [PMID: 38022653 PMCID: PMC10663227 DOI: 10.3389/fimmu.2023.1265818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
STATs are a family of transcription factors that regulate many critical cellular processes such as proliferation, apoptosis, and differentiation. Dysregulation of STATs is frequently observed in tumors and can directly drive cancer pathogenesis. STAT1 and STAT3 are generally viewed as mediating opposite roles in cancer development, with STAT1 suppressing tumorigenesis and STAT3 promoting oncogenesis. In this review, we investigate the specific roles of STAT1 and STAT3 in normal physiology and cancer biology, explore their interactions with each other, and offer insights into therapeutic strategies through modulating their transcriptional activity.
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Affiliation(s)
| | | | | | | | | | | | - David A. Frank
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, United States
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Zhao Y, Namei E, Yang B, Bao X, Sun W, Subudeng G, Cao G, Li H, Wang G. Cyclic AMP mediates ovine cumulus-oocyte gap junctional function via balancing connexin 43 expression and phosphorylation. Endocr Connect 2023; 12:e230337. [PMID: 37855365 PMCID: PMC10620458 DOI: 10.1530/ec-23-0337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 09/18/2023] [Indexed: 09/19/2023]
Abstract
Gap junction channels in cumulus-oocyte complexes (COCs) enable the transmission and communication of small molecular signals between adjacent cells, such as cAMP. However, the regulation of gap junction function (GJF) by cAMP and the underlying mechanisms involved are not fully clarified. This study investigated the effect of cAMP on connexin 43 (CX43) expression and GJF in ovine COCs using immunofluorescence, quantitative real-time PCR (qRT-PCR), western blotting, and GJF detection. The CX43 was only found in the cumulus cells (CCs) side of ovine COC. The intra-oocyte cAMP showed a significant increase at 30 min, while the intra-CC cAMP exhibited two peaks at 10 min and 1 h during in vitro maturation (IVM). Phosphorylated CX43 protein exhibited an immediate increase at 10 min, and CX43 protein displayed two peaks at 10 min and 1 h during IVM. The duration of pre-IVM exposure to forskolin and IBMX significantly enhanced phosphorylated and total CX43, as well as Gja1 and Creb genes, for 10 min; these effects were counteracted by Rp-cAMP. Both pre-IVM with forskolin and IBMX for 1 h and the GJF and CX43/p-CX43 ratio were elevated. The closure of gap junction channels caused by phosphorylated CX43 to prevent cAMP outflow from oocytes in early IVM of COC. Cyclic AMP upregulated phosphorylated and total CX43 via genomic and non-genomic pathways, but its functional regulation was dependent on the balance of the two proteins. This study provides a new insight into the regulatory mechanism between cAMP and GJF, which would improve IVM in animal and clinical research.
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Affiliation(s)
- Yufen Zhao
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, PR China
- Key Laboratory of Animal Embryo and Development Engineering of Autonomous Region Universities, Inner Mongolia Agricultural University, Hohhot, PR China
| | - Erge Namei
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, PR China
- Key Laboratory of Animal Embryo and Development Engineering of Autonomous Region Universities, Inner Mongolia Agricultural University, Hohhot, PR China
| | - Bingxue Yang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, PR China
- Key Laboratory of Animal Embryo and Development Engineering of Autonomous Region Universities, Inner Mongolia Agricultural University, Hohhot, PR China
| | - Xiangnan Bao
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, PR China
- National Center of Technology Innovation for Dairy Industry, Hohhot, PR China
| | - Wei Sun
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, PR China
| | - Gerile Subudeng
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, PR China
- Key Laboratory of Animal Embryo and Development Engineering of Autonomous Region Universities, Inner Mongolia Agricultural University, Hohhot, PR China
| | - Guifang Cao
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, PR China
- Key Laboratory of Animal Embryo and Development Engineering of Autonomous Region Universities, Inner Mongolia Agricultural University, Hohhot, PR China
| | - Haijun Li
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, PR China
- Key Laboratory of Animal Embryo and Development Engineering of Autonomous Region Universities, Inner Mongolia Agricultural University, Hohhot, PR China
| | - Gui Wang
- Animal Genetic Breeding and Reproduction Research Center, Hetao College, Bayannur, PR China
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Ma G, Zhu B, Zhang Y, Cheng X, Wei Y, Shi H. CPK1-mediated ERF72 protein phosphorylation confers improved disease resistance to cassava bacterial blight. Plant Biotechnol J 2023; 21:2166-2168. [PMID: 37525992 PMCID: PMC10579701 DOI: 10.1111/pbi.14151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 08/02/2023]
Affiliation(s)
- Guowen Ma
- Sanya Nanfan Research Institute of Hainan University, Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Nanfan, School of Tropical Agriculture and ForestryHainan UniversityHaikouHainan ProvinceChina
- National Key Laboratory for Tropical Crop BreedingHainan UniversityHaikouHainan ProvinceChina
- Hainan Yazhou Bay Seed LaboratorySanyaHainan ProvinceChina
| | - Binbin Zhu
- Sanya Nanfan Research Institute of Hainan University, Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Nanfan, School of Tropical Agriculture and ForestryHainan UniversityHaikouHainan ProvinceChina
- National Key Laboratory for Tropical Crop BreedingHainan UniversityHaikouHainan ProvinceChina
- Hainan Yazhou Bay Seed LaboratorySanyaHainan ProvinceChina
| | - Ye Zhang
- Sanya Nanfan Research Institute of Hainan University, Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Nanfan, School of Tropical Agriculture and ForestryHainan UniversityHaikouHainan ProvinceChina
- National Key Laboratory for Tropical Crop BreedingHainan UniversityHaikouHainan ProvinceChina
- Hainan Yazhou Bay Seed LaboratorySanyaHainan ProvinceChina
| | - Xiao Cheng
- Sanya Nanfan Research Institute of Hainan University, Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Nanfan, School of Tropical Agriculture and ForestryHainan UniversityHaikouHainan ProvinceChina
- National Key Laboratory for Tropical Crop BreedingHainan UniversityHaikouHainan ProvinceChina
- Hainan Yazhou Bay Seed LaboratorySanyaHainan ProvinceChina
| | - Yunxie Wei
- Sanya Nanfan Research Institute of Hainan University, Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Nanfan, School of Tropical Agriculture and ForestryHainan UniversityHaikouHainan ProvinceChina
- National Key Laboratory for Tropical Crop BreedingHainan UniversityHaikouHainan ProvinceChina
- Hainan Yazhou Bay Seed LaboratorySanyaHainan ProvinceChina
| | - Haitao Shi
- Sanya Nanfan Research Institute of Hainan University, Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Nanfan, School of Tropical Agriculture and ForestryHainan UniversityHaikouHainan ProvinceChina
- National Key Laboratory for Tropical Crop BreedingHainan UniversityHaikouHainan ProvinceChina
- Hainan Yazhou Bay Seed LaboratorySanyaHainan ProvinceChina
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Barske T, Spät P, Schubert H, Walke P, Maček B, Hagemann M. The Role of Serine/Threonine-Specific Protein Kinases in Cyanobacteria - SpkB Is Involved in Acclimation to Fluctuating Conditions in Synechocystis sp. PCC 6803. Mol Cell Proteomics 2023; 22:100656. [PMID: 37797745 PMCID: PMC10651672 DOI: 10.1016/j.mcpro.2023.100656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 08/31/2023] [Accepted: 10/01/2023] [Indexed: 10/07/2023] Open
Abstract
Protein phosphorylation via serine/threonine protein kinases (Spk) is a widespread mechanism to adjust cellular processes toward changing environmental conditions. To study their role(s) in cyanobacteria, we investigated a collection of 11 completely segregated spk mutants among the 12 annotated Spks in the model cyanobacterium Synechocystis sp. PCC 6803. Screening of the mutant collection revealed that especially the mutant defective in SpkB encoded by slr1697 showed clear deviations regarding carbon metabolism, that is, reduced growth rates at low CO2 or in the presence of glucose, and different glycogen accumulation patterns compared to WT. Alterations in the proteome of ΔspkB indicated changes of the cell surface but also metabolic functions. A phospho-proteome analysis revealed the absence of any phosphorylation in two proteins, while decreased phosphorylation of the carboxysome-associated protein CcmM and increased phosphorylation of the allophycocyanin alpha subunit ApcA was detected in ΔspkB. Furthermore, the regulatory PII protein appeared less phosphorylated in the mutant compared to WT, which was verified in Western blot experiments, indicating a clearly delayed PII phosphorylation in cells shifted from nitrate-containing to nitrate-free medium. Our results indicate that SpkB is an important regulator in Synechocystis that is involved in phosphorylation of the PII protein and additional proteins.
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Affiliation(s)
- Thomas Barske
- Department of Plant Physiology, Institute of Biosciences, University of Rostock, Rostock, Germany
| | - Philipp Spät
- Department of Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany; Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Hendrik Schubert
- Department of Aquatic Ecology, Institute of Biosciences, University of Rostock, Rostock, Germany
| | - Peter Walke
- Department of Plant Physiology, Institute of Biosciences, University of Rostock, Rostock, Germany
| | - Boris Maček
- Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Martin Hagemann
- Department of Plant Physiology, Institute of Biosciences, University of Rostock, Rostock, Germany; Interdisciplinary Faculty, Department Life, Light and Matter, University of Rostock, Rostock, Germany.
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Ren C, Song X, Dong Y, Hou C, Chen L, Wang Z, Li X, Schroyen M, Zhang D. Protein Phosphorylation Induced by Pyruvate Kinase M2 Inhibited Myofibrillar Protein Degradation in Post-Mortem Muscle. J Agric Food Chem 2023; 71:15280-15286. [PMID: 37776280 DOI: 10.1021/acs.jafc.3c03930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/02/2023]
Abstract
Myofibrillar protein degradation is primarily related to meat tenderness through protein phosphorylation regulation. Pyruvate kinase M2 (PKM2), a glycolytic rate-limiting enzyme, is also regarded as a protein kinase to catalyze phosphorylation. The objective of this study was to investigate the relationship between myofibrillar protein degradation and phosphorylation induced by PKM2. Myofibrillar proteins were incubated with PKM2 at 4, 25, and 37 °C. The global phosphorylation level of myofibrillar proteins in the PKM2 group was significantly increased, but it was sensitive to temperature (P < 0.05). Compared with 4 and 25 °C, PKM2 significantly increased the myofibrillar protein phosphorylation level from 0.5 to 6 h at 37 °C (P < 0.05). In addition, the degradation of desmin and actin was inhibited after they were phosphorylated by PKM2 when incubated at 37 °C. These results demonstrate that phosphorylation of myofibrillar proteins catalyzed by PKM2 inhibited protein degradation and provided a possible pathway for meat tenderization through glycolytic enzyme regulation.
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Affiliation(s)
- Chi Ren
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agra-products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
- Precision Livestock and Nutrition Unit, Gembloux Agra-Bio Tech, University of LièGe, Passage des Déport́s 2, Gembloux 5030, Belgium
| | - Xubo Song
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agra-products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Yu Dong
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agra-products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Chengli Hou
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agra-products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Li Chen
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agra-products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Zhenyu Wang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agra-products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Xin Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agra-products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Martine Schroyen
- Precision Livestock and Nutrition Unit, Gembloux Agra-Bio Tech, University of LièGe, Passage des Déport́s 2, Gembloux 5030, Belgium
| | - Dequan Zhang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agra-products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
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Rawat A, Völz R, Sheikh A, Mariappan KG, Kim SK, Rayapuram N, Alwutayd KM, Alidrissi LK, Benhamed M, Blilou I, Hirt H. Salinity stress-induced phosphorylation of INDETERMINATE-DOMAIN 4 (IDD4) by MPK6 regulates plant growth adaptation in Arabidopsis. Front Plant Sci 2023; 14:1265687. [PMID: 37881611 PMCID: PMC10595144 DOI: 10.3389/fpls.2023.1265687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/25/2023] [Indexed: 10/27/2023]
Abstract
The INDETERMINATE DOMAIN (IDD) family belongs to a group of plant-specific transcription factors that coordinates plant growth/development and immunity. However, the function and mode of action of IDDs during abiotic stress, such as salt, are poorly understood. We used idd4 transgenic lines and screened them under salt stress to find the involvement of IDD4 in salinity stress tolerance The genetic disruption of IDD4 increases salt-tolerance, characterized by sustained plant growth, improved Na+/K+ ratio, and decreased stomatal density/aperture. Yet, IDD4 overexpressing plants were hypersensitive to salt-stress with an increase in stomatal density and pore size. Transcriptomic and ChIP-seq analyses revealed that IDD4 directly controls an important set of genes involved in abiotic stress/salinity responses. Interestingly, using anti-IDD4-pS73 antibody we discovered that IDD4 is specifically phosphorylated at serine-73 by MPK6 in vivo under salinity stress. Analysis of plants expressing the phospho-dead and phospho-mimicking IDD4 versions proved that phosphorylation of IDD4 plays a crucial role in plant transcriptional reprogramming of salt-stress genes. Altogether, we show that salt stress adaption involves MPK6 phosphorylation of IDD4 thereby regulating IDD4 DNA-binding and expression of target genes.
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Affiliation(s)
- Anamika Rawat
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ronny Völz
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Arsheed Sheikh
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Kiruthiga G. Mariappan
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Soon-Kap Kim
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Naganand Rayapuram
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Khairiah M. Alwutayd
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Louai K. Alidrissi
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Orsay, France
| | - Ikram Blilou
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Heribert Hirt
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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Herting JR, König JH, Hadova K, Heinick A, Müller FU, Pauls P, Seidl MD, Soppa C, Kirchhefer U. Hypercontractile cardiac phenotype in mice overexpressing the regulatory subunit PR72 of protein phosphatase 2A. Front Cardiovasc Med 2023; 10:1239555. [PMID: 37868783 PMCID: PMC10590119 DOI: 10.3389/fcvm.2023.1239555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/22/2023] [Indexed: 10/24/2023] Open
Abstract
Background The activity, localization, and substrate specificity of the protein phosphatase 2A (PP2A) heterotrimer are controlled by various regulatory B subunits. PR72 belongs to the B'' gene family and has been shown to be upregulated in human heart failure. However, little is known about the functions of PR72 in the myocardium. Methods To address this issue, we generated a transgenic mouse model with heart-specific overexpression of PP2A-PR72. Biochemical and physiological methods were used to determine contractility, Ca2+ cycling parameters, and protein phosphorylation. Results A 2.5-fold increase in PR72 expression resulted in moderate cardiac hypertrophy. Maximal ventricular pressure was increased in catheterized transgenic mice (TG) compared to wild-type (WT) littermates. This was accompanied by an increased shortening of sarcomere length and faster relaxation at the single-cell level in TG. In parallel with these findings, the peak amplitude of Ca2+ transients was increased, and the decay in intracellular Ca2+ levels was shortened in TG compared to WT. The changes in Ca2+ cycling in TG were also evident from an increase in the full duration and width at half maximum of Ca2+ sparks. Consistent with the contractile data, phosphorylation of phospholamban at threonine-17 was higher in TG hearts. The lower expression of the Na+/Ca2+ exchanger may also contribute to the hypercontractile state in transgenic myocardium. Conclusion Our results suggest that PP2A-PR72 plays an important role in regulating cardiac contractile function and Ca2+ cycling, indicating that the upregulation of PR72 in heart failure is an attempt to compensate functionally.
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Affiliation(s)
- Julius R. Herting
- Institut für Pharmakologie und Toxikologie, Universitätsklinikum Münster, Universität Münster, Münster, Germany
| | - Jule H. König
- Institut für Pharmakologie und Toxikologie, Universitätsklinikum Münster, Universität Münster, Münster, Germany
| | - Katarina Hadova
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia
| | - Alexander Heinick
- Institut für Pharmakologie und Toxikologie, Universitätsklinikum Münster, Universität Münster, Münster, Germany
| | - Frank U. Müller
- Institut für Pharmakologie und Toxikologie, Universitätsklinikum Münster, Universität Münster, Münster, Germany
| | - Paul Pauls
- Institut für Pharmakologie und Toxikologie, Universitätsklinikum Münster, Universität Münster, Münster, Germany
| | - Matthias D. Seidl
- Institut für Pharmakologie und Toxikologie, Universitätsklinikum Münster, Universität Münster, Münster, Germany
| | - Carolina Soppa
- Institut für Pharmakologie und Toxikologie, Universitätsklinikum Münster, Universität Münster, Münster, Germany
| | - Uwe Kirchhefer
- Institut für Pharmakologie und Toxikologie, Universitätsklinikum Münster, Universität Münster, Münster, Germany
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Ma Q, Zhao C, Hu S, Zuo K. Arabidopsis calcium-dependent protein kinase CPK6 regulates drought tolerance under high nitrogen by the phosphorylation of NRT1.1. J Exp Bot 2023; 74:5682-5693. [PMID: 37463320 DOI: 10.1093/jxb/erad277] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/14/2023] [Indexed: 07/20/2023]
Abstract
Nitrogen (N) is an essential macronutrient for plant growth and development, and its availability is regulated to some extent by drought stress. Calcium-dependent protein kinases (CPKs) are a unique family of Ca2+ sensors with diverse functions in N uptake and drought-tolerance signaling pathways; however, how CPKs are involved in the crosstalk between drought stress and N transportation remains largely unknown. Here, we identify the drought-tolerance function of Arabidopsis CPK6 under high N conditions. CPK6 expression was induced by ABA and drought treatments. The mutant cpk6 was insensitive to ABA treatment and low N, but was sensitive to drought only under high N conditions. CPK6 interacted with the NRT1.1 (CHL1) protein and phosphorylated the Thr447 residue, which then repressed the NO3- transporting activity of Arabidopsis under high N and drought stress. Taken together, our results show that CPK6 regulates Arabidopsis drought tolerance through changing the phosphorylation state of NRT1.1, and improve our knowledge of N uptake in plants during drought stress.
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Affiliation(s)
- Qijun Ma
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunyan Zhao
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shi Hu
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kaijing Zuo
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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36
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VanZeeland NE, Schultz KM, Klug CS, Kristich CJ. Multisite Phosphorylation Regulates GpsB Function in Cephalosporin Resistance of Enterococcus faecalis. J Mol Biol 2023; 435:168216. [PMID: 37517789 PMCID: PMC10528945 DOI: 10.1016/j.jmb.2023.168216] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/01/2023]
Abstract
Enterococci are normal human commensals and major causes of hospital-acquired infections. Enterococcal infections can be difficult to treat because enterococci harbor intrinsic and acquired antibiotic resistance, such as resistance to cephalosporins. In Enterococcus faecalis, the transmembrane kinase IreK, a member of the bacterial PASTA kinase family, is essential for cephalosporin resistance. The activity of IreK is boosted by the cytoplasmic protein GpsB, which promotes IreK autophosphorylation and signaling to drive cephalosporin resistance. A previous phosphoproteomics study identified eight putative IreK-dependent phosphorylation sites on GpsB, but the functional importance of GpsB phosphorylation was unknown. Here we used genetic and biochemical approaches to define three sites of phosphorylation on GpsB that functionally impact IreK activity and cephalosporin resistance. Phosphorylation at two sites (S80 and T84) serves to impair the ability of GpsB to activate IreK in vivo, suggesting phosphorylation of these sites acts as a means of negative feedback for IreK. The third site of phosphorylation (T133) occurs in a segment of GpsB termed the C-terminal extension that is unique to enterococcal GpsB homologs. The C-terminal extension is highly mobile in solution, suggesting it is largely unstructured, and phosphorylation of T133 appears to enable efficient phosphorylation at S80 / T84. Overall our results are consistent with a model in which multisite phosphorylation of GpsB impairs its ability to activate IreK, thereby diminishing signal transduction through the IreK-dependent pathway and modulating phenotypic cephalosporin resistance.
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Affiliation(s)
- Nicole E VanZeeland
- Department of Microbiology and Immunology, Center for Infectious Disease Research, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226, USA
| | - Kathryn M Schultz
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226, USA
| | - Candice S Klug
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226, USA
| | - Christopher J Kristich
- Department of Microbiology and Immunology, Center for Infectious Disease Research, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226, USA.
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Xin X, Wei D, Lei L, Zheng H, Wallace IS, Li S, Gu Y. CALCIUM-DEPENDENT PROTEIN KINASE32 regulates cellulose biosynthesis through post-translational modification of cellulose synthase. New Phytol 2023; 239:2212-2224. [PMID: 37431066 DOI: 10.1111/nph.19106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/05/2023] [Indexed: 07/12/2023]
Abstract
Cellulose is an essential component of plant cell walls and an economically important source of food, paper, textiles, and biofuel. Despite its economic and biological significance, the regulation of cellulose biosynthesis is poorly understood. Phosphorylation and dephosphorylation of cellulose synthases (CESAs) were shown to impact the direction and velocity of cellulose synthase complexes (CSCs). However, the protein kinases that phosphorylate CESAs are largely unknown. We conducted research in Arabidopsis thaliana to reveal protein kinases that phosphorylate CESAs. In this study, we used yeast two-hybrid, protein biochemistry, genetics, and live-cell imaging to reveal the role of calcium-dependent protein kinase32 (CPK32) in the regulation of cellulose biosynthesis in A. thaliana. We identified CPK32 using CESA3 as a bait in a yeast two-hybrid assay. We showed that CPK32 phosphorylates CESA3 while it interacts with both CESA1 and CESA3. Overexpressing functionally defective CPK32 variant and phospho-dead mutation of CESA3 led to decreased motility of CSCs and reduced crystalline cellulose content in etiolated seedlings. Deregulation of CPKs impacted the stability of CSCs. We uncovered a new function of CPKs that regulates cellulose biosynthesis and a novel mechanism by which phosphorylation regulates the stability of CSCs.
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Affiliation(s)
- Xiaoran Xin
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Donghui Wei
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Lei Lei
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Haiyan Zheng
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, 08854, USA
| | - Ian S Wallace
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, 89557, USA
| | - Shundai Li
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Ying Gu
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
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Jiang Z, Lin Z, Gan Q, Wu P, Zhang X, Xiao Y, She Q, Ni J, Shen Y, Huang Q. The FHA domain protein ArnA functions as a global DNA damage response repressor in the hyperthermophilic archaeon Saccharolobus islandicus. mBio 2023; 14:e0094223. [PMID: 37389462 PMCID: PMC10470591 DOI: 10.1128/mbio.00942-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/18/2023] [Indexed: 07/01/2023] Open
Abstract
Forkhead-associated (FHA) domain proteins specifically recognize phosphorylated threonine via the FHA domain and are involved in signal transduction in various processes especially DNA damage response (DDR) and cell cycle regulation in eukaryotes. Although FHA domain proteins are found in prokaryotes, archaea, and bacteria, their functions are far less clear as compared to the eukaryotic counterparts, and it has not been studied whether archaeal FHA proteins play a role in DDR. Here, we have characterized an FHA protein from the hyperthermophilic Crenarchaeon Saccharolobus islandicus (SisArnA) by genetic, biochemical, and transcriptomic approaches. We find that ΔSisarnA exhibits higher resistance to DNA damage agent 4-nitroquinoline 1-oxide (NQO). The transcription of ups genes, encoding the proteins for pili-mediated cell aggregation and cell survival after DDR, is elevated in ΔSisarnA. The interactions of SisArnA with two predicted partners, SisvWA1 (SisArnB) and SisvWA2 (designated as SisArnE), were enhanced by phosphorylation in vitro. ΔSisarnB displays higher resistance to NQO than the wild type. In addition, the interaction between SisArnA and SisArnB, which is reduced in the NQO-treated cells, is indispensable for DNA binding in vitro. These indicate that SisArnA and SisArnB work together to inhibit the expression of ups genes in vivo. Interestingly, ΔSisarnE is more sensitive to NQO than the wild type, and the interaction between SisArnA and SisArnE is strengthened after NQO treatment, suggesting a positive role of SisArnE in DDR. Finally, transcriptomic analysis reveals that SisArnA represses a number of genes, implying that archaea apply the FHA/phospho-peptide recognition module for extensive transcriptional regulation. IMPORTANCE Cellular adaption to diverse environmental stresses requires a signal sensor and transducer for cell survival. Protein phosphorylation and its recognition by forkhead-associated (FHA) domain proteins are widely used for signal transduction in eukaryotes. Although FHA proteins exist in archaea and bacteria, investigation of their functions, especially those in DNA damage response (DDR), is limited. Therefore, the evolution and functional conservation of FHA proteins in the three domains of life is still a mystery. Here, we find that an FHA protein from the hyperthermophilic Crenarchaeon Saccharolobus islandicus (SisArnA) represses the transcription of pili genes together with its phosphorylated partner SisArnB. SisArnA derepression facilitates DNA exchange and repair in the presence of DNA damage. The fact that more genes including a dozen of those involved in DDR are found to be regulated by SisArnA implies that the FHA/phosphorylation module may serve as an important signal transduction pathway for transcriptional regulation in archaeal DDR.
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Affiliation(s)
- Zhichao Jiang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Zijia Lin
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Qi Gan
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Pengju Wu
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Xuemei Zhang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yuanxi Xiao
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Jinfeng Ni
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yulong Shen
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Qihong Huang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
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Partscht P, Schiebel E. The diverging role of CDC14B: from mitotic exit in yeast to cell fate control in humans. EMBO J 2023; 42:e114364. [PMID: 37493185 PMCID: PMC10425841 DOI: 10.15252/embj.2023114364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/22/2023] [Accepted: 07/07/2023] [Indexed: 07/27/2023] Open
Abstract
CDC14, originally identified as crucial mediator of mitotic exit in budding yeast, belongs to the family of dual-specificity phosphatases (DUSPs) that are present in most eukaryotes. Contradicting data have sparked a contentious discussion whether a cell cycle role is conserved in the human paralogs CDC14A and CDC14B but possibly masked due to redundancy. Subsequent studies on CDC14A and CDC14B double knockouts in human and mouse demonstrated that CDC14 activity is dispensable for mitotic progression in higher eukaryotes and instead suggested functional specialization. In this review, we provide a comprehensive overview of our current understanding of how faithful cell division is linked to phosphorylation and dephosphorylation and compare functional similarities and divergences between the mitotic phosphatases CDC14, PP2A, and PP1 from yeast and higher eukaryotes. Furthermore, we review the latest discoveries on CDC14B, which identify this nuclear phosphatase as a key regulator of gene expression and reveal its role in neuronal development. Finally, we discuss CDC14B functions in meiosis and possible implications in other developmental processes.
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Affiliation(s)
- Patrick Partscht
- Zentrum für Molekulare BiologieUniversität Heidelberg, DKFZ‐ZMBH AllianzHeidelbergGermany
| | - Elmar Schiebel
- Zentrum für Molekulare BiologieUniversität Heidelberg, DKFZ‐ZMBH AllianzHeidelbergGermany
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Butova X, Myachina T, Simonova R, Kochurova A, Mukhlynina E, Kopylova G, Shchepkin D, Khokhlova A. The inter-chamber differences in the contractile function between left and right atrial cardiomyocytes in atrial fibrillation in rats. Front Cardiovasc Med 2023; 10:1203093. [PMID: 37608813 PMCID: PMC10440706 DOI: 10.3389/fcvm.2023.1203093] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/24/2023] [Indexed: 08/24/2023] Open
Abstract
Introduction The left and right atria (LA, RA) work under different mechanical and metabolic environments that may cause an intrinsic inter-chamber diversity in structure and functional properties between atrial cardiomyocytes (CM) in norm and provoke their different responsiveness to pathological conditions. In this study, we assessed a LA vs. RA difference in CM contractility in paroxysmal atrial fibrillation (AF) and underlying mechanisms. Methods We investigated the contractile function of single isolated CM from LA and RA using a 7-day acetylcholine (ACh)-CaCl2 AF model in rats. We compared auxotonic force, sarcomere length dynamics, cytosolic calcium ([Ca2+]i) transients, intracellular ROS and NO production in LA and RA CM, and analyzed the phosphorylation levels of contractile proteins and actin-myosin interaction using an in vitro motility assay. Results AF resulted in more prominent structural and functional changes in LA myocardium, reducing sarcomere shortening amplitude, and velocity of sarcomere relengthening in mechanically non-loaded LA CM, which was associated with the increased ROS production, decreased NO production, reduced myofibrillar content, and decreased phosphorylation of cardiac myosin binding protein C and troponin I. However, in mechanically loaded CM, AF depressed the auxotonic force amplitude and kinetics in RA CM, while force characteristics were preserved in LA CM. Discussion Thus, inter-atrial differences are increased in paroxysmal AF and affected by the mechanical load that may contribute to the maintenance and progression of AF.
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Affiliation(s)
- Xenia Butova
- Institute of Immunology and Physiology, Ural Branch of Russian Academy of Sciences, Yekaterinburg, Russian Federation
| | - Tatiana Myachina
- Institute of Immunology and Physiology, Ural Branch of Russian Academy of Sciences, Yekaterinburg, Russian Federation
| | - Raisa Simonova
- Institute of Immunology and Physiology, Ural Branch of Russian Academy of Sciences, Yekaterinburg, Russian Federation
| | - Anastasia Kochurova
- Institute of Immunology and Physiology, Ural Branch of Russian Academy of Sciences, Yekaterinburg, Russian Federation
| | - Elena Mukhlynina
- Institute of Immunology and Physiology, Ural Branch of Russian Academy of Sciences, Yekaterinburg, Russian Federation
- Institute of Natural Sciences and Mathematics, Ural Federal University, Yekaterinburg, Russian Federation
| | - Galina Kopylova
- Institute of Immunology and Physiology, Ural Branch of Russian Academy of Sciences, Yekaterinburg, Russian Federation
| | - Daniil Shchepkin
- Institute of Immunology and Physiology, Ural Branch of Russian Academy of Sciences, Yekaterinburg, Russian Federation
- Institute of Natural Sciences and Mathematics, Ural Federal University, Yekaterinburg, Russian Federation
| | - Anastasia Khokhlova
- Institute of Immunology and Physiology, Ural Branch of Russian Academy of Sciences, Yekaterinburg, Russian Federation
- Institute of Physics and Technology, Ural Federal University, Yekaterinburg, Russian Federation
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Nguyen H, Kettenbach AN. Substrate and phosphorylation site selection by phosphoprotein phosphatases. Trends Biochem Sci 2023; 48:713-725. [PMID: 37173206 PMCID: PMC10523993 DOI: 10.1016/j.tibs.2023.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 05/15/2023]
Abstract
Dynamic protein phosphorylation and dephosphorylation are essential regulatory mechanisms that ensure proper cellular signaling and biological functions. Deregulation of either reaction has been implicated in several human diseases. Here, we focus on the mechanisms that govern the specificity of the dephosphorylation reaction. Most cellular serine/threonine dephosphorylation is catalyzed by 13 highly conserved phosphoprotein phosphatase (PPP) catalytic subunits, which form hundreds of holoenzymes by binding to regulatory and scaffolding subunits. PPP holoenzymes recognize phosphorylation site consensus motifs and interact with short linear motifs (SLiMs) or structural elements distal to the phosphorylation site. We review recent advances in understanding the mechanisms of PPP site-specific dephosphorylation preference and substrate recruitment and highlight examples of their interplay in the regulation of cell division.
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Affiliation(s)
- Hieu Nguyen
- Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - Arminja N Kettenbach
- Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA; Dartmouth Cancer Center, Lebanon, NH 03756, USA.
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Rumpf M, Pautz S, Drebes B, Herberg FW, Müller HAJ. Microtubule-Associated Serine/Threonine (MAST) Kinases in Development and Disease. Int J Mol Sci 2023; 24:11913. [PMID: 37569286 PMCID: PMC10419289 DOI: 10.3390/ijms241511913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023] Open
Abstract
Microtubule-Associated Serine/Threonine (MAST) kinases represent an evolutionary conserved branch of the AGC protein kinase superfamily in the kinome. Since the discovery of the founding member, MAST2, in 1993, three additional family members have been identified in mammals and found to be broadly expressed across various tissues, including the brain, heart, lung, liver, intestine and kidney. The study of MAST kinases is highly relevant for unraveling the molecular basis of a wide range of different human diseases, including breast and liver cancer, myeloma, inflammatory bowel disease, cystic fibrosis and various neuronal disorders. Despite several reports on potential substrates and binding partners of MAST kinases, the molecular mechanisms that would explain their involvement in human diseases remain rather obscure. This review will summarize data on the structure, biochemistry and cell and molecular biology of MAST kinases in the context of biomedical research as well as organismal model systems in order to provide a current profile of this field.
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Affiliation(s)
- Marie Rumpf
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
| | - Sabine Pautz
- Department of Biochemistry, Institute of Biology, University of Kassel, 34321 Kassel, Germany
| | - Benedikt Drebes
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
| | - Friedrich W. Herberg
- Department of Biochemistry, Institute of Biology, University of Kassel, 34321 Kassel, Germany
| | - Hans-Arno J. Müller
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
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Zittlau K, Nashier P, Cavarischia-Rega C, Macek B, Spät P, Nalpas N. Recent progress in quantitative phosphoproteomics. Expert Rev Proteomics 2023; 20:469-482. [PMID: 38116637 DOI: 10.1080/14789450.2023.2295872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 12/12/2023] [Indexed: 12/21/2023]
Abstract
INTRODUCTION Protein phosphorylation is a critical post-translational modification involved in the regulation of numerous cellular processes from signal transduction to modulation of enzyme activities. Knowledge of dynamic changes of phosphorylation levels during biological processes, under various treatments or between healthy and disease models is fundamental for understanding the role of each phosphorylation event. Thereby, LC-MS/MS based technologies in combination with quantitative proteomics strategies evolved as a powerful strategy to investigate the function of individual protein phosphorylation events. AREAS COVERED State-of-the-art labeling techniques including stable isotope and isobaric labeling provide precise and accurate quantification of phosphorylation events. Here, we review the strengths and limitations of recent quantification methods and provide examples based on current studies, how quantitative phosphoproteomics can be further optimized for enhanced analytic depth, dynamic range, site localization, and data integrity. Specifically, reducing the input material demands is key to a broader implementation of quantitative phosphoproteomics, not least for clinical samples. EXPERT OPINION Despite quantitative phosphoproteomics is one of the most thriving fields in the proteomics world, many challenges still have to be overcome to facilitate even deeper and more comprehensive analyses as required in the current research, especially at single cell levels and in clinical diagnostics.
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Affiliation(s)
- Katharina Zittlau
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Payal Nashier
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Claudia Cavarischia-Rega
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Boris Macek
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Philipp Spät
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Nicolas Nalpas
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
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Lototskaja E, Liblekas L, Piirsoo M, Laaneväli A, Ibragimov R, Piirsoo A. Phosphorylation of E2 Serine Residue 402 Is Required for the Transcription and Replication of the HPV5 Genome. J Virol 2023; 97:e0064323. [PMID: 37272841 PMCID: PMC10308906 DOI: 10.1128/jvi.00643-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 05/13/2023] [Indexed: 06/06/2023] Open
Abstract
Cutaneous human papillomavirus type 5 (HPV5) belongs to the supposedly oncogenic β-HPVs associated with specific types of skin and oral cavity cancers. Three viral proteins, namely, helicase E1 and transcription factors E2 and E8^E2, are master regulators of the viral life cycle. HPV5 E2 is a transcriptional activator that also participates in the E1-dependent replication and nuclear retention of the viral genome, whereas E8^E2 counterbalances the activity of E2 and inhibits HPV transcription and replication. In the present study, we demonstrate that the HPV5 E2 protein is extensively phosphorylated by cellular protein kinases, and serine residue 402 (S402) is the highest scoring phosphoacceptor site. This residue is located within a motif conserved among many β-HPVs and in the oncogenic HPV31 α-type. Using the nonphosphorylatable and phosphomimetic mutants, we demonstrate that phosphorylation of the E2 S402 residue is required for the transcription and replication of the HPV5 genome in U2OS cells and human primary keratinocytes. Mechanistically, the E2-S402-phopshodeficient protein is unable to trigger viral gene transcription and has an impaired ability to support E1-dependent replication, but the respective E8^E2-S213 mutant displays no phenotype. However, phosphorylation of the E2 S402 residue has no impact on the E2 stability, subcellular localization, self-assembly, DNA-binding capacity, and affinity to the E1 and BRD4 proteins. Further studies are needed to identify the protein kinase(s) responsible for this phosphorylation. IMPORTANCE Human papillomavirus type 5 (HPV5) may play a role in the development of specific types of cutaneous and head and neck cancers. The persistence of the HPV genome in host cells depends on the activity of its proteins, namely, a helicase E1 and transcription/replication factor E2. The latter also facilitates the attachment of episomal viral genomes to host cell chromosomes. In the present study, we show that the HPV5 E2 protein is extensively phosphorylated by host cell protein kinases, and we identify serine residue 402 as the highest scoring phosphoacceptor site of E2. We demonstrate that the replication of the HPV5 genome may be blocked by a single point mutation that prevents phosphorylation of this serine residue and switches off the transcriptional activity of the E2 protein. The present study contributes to a better understanding of β-HPV5 replication and its regulation by host cell protein kinases.
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Affiliation(s)
| | - Lisett Liblekas
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Marko Piirsoo
- Institute of Technology, University of Tartu, Tartu, Estonia
| | | | | | - Alla Piirsoo
- Institute of Technology, University of Tartu, Tartu, Estonia
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Pérez-López J, Feria AB, Gandullo J, de la Osa C, Jiménez-Guerrero I, Echevarría C, Monreal JA, García-Mauriño S. Silencing of Sb PPCK1-3 Negatively Affects Development, Stress Responses and Productivity in Sorghum. Plants (Basel) 2023; 12:2426. [PMID: 37446987 DOI: 10.3390/plants12132426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) plays central roles in photosynthesis, respiration, amino acid synthesis, and seed development. PEPC is regulated by different post-translational modifications. Between them, the phosphorylation by PEPC-kinase (PEPCk) is widely documented. In this work, we simultaneously silenced the three sorghum genes encoding PEPCk (SbPPCK1-3) by RNAi interference, obtaining 12 independent transgenic lines (Ppck1-12 lines), showing different degrees of SbPPCK1-3 silencing. Among them, two T2 homozygous lines (Ppck-2 and Ppck-4) were selected for further evaluation. Expression of SbPPCK1 was reduced by 65% and 83% in Ppck-2 and Ppck-4 illuminated leaves, respectively. Expression of SbPPCK2 was higher in roots and decreased by 50% in Ppck-2 and Ppck-4 in this tissue. Expression of SbPPCK3 was low and highly variable. Despite the incomplete gene silencing, it decreased the degree of phosphorylation of PEPC in illuminated leaves, P-deficient plants, and NaCl-treated plants. Both leaves and seeds of Ppck lines had altered metabolic profiles and a general decrease in amino acid content. In addition, Ppck lines showed delayed flowering, and 20% of Ppck-4 plants did not produce flowers at all. The total amount of seeds was lowered by 50% and 36% in Ppck-2 and Ppck-4 lines, respectively. The quality of seeds was lower in Ppck lines: lower amino acid content, including Lys, and higher phytate content. These data confirm the relevance of the phosphorylation of PEPC in sorghum development, stress responses, yield, and quality of seeds.
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Affiliation(s)
- Jesús Pérez-López
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
| | - Ana B Feria
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
| | - Jacinto Gandullo
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
| | - Clara de la Osa
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
| | - Irene Jiménez-Guerrero
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
| | - Cristina Echevarría
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
| | - José A Monreal
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
| | - Sofía García-Mauriño
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes nº 6, 41012 Seville, Spain
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Nishikubo K, Hasegawa M, Izumi Y, Fujii K, Matsuo K, Matsumoto Y, Yokoya A. Structural study of wild-type and phospho-mimic XRCC4 dimer and multimer proteins using circular dichroism spectroscopy. Int J Radiat Biol 2023; 99:1684-1691. [PMID: 37171809 DOI: 10.1080/09553002.2023.2214210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 05/05/2023] [Indexed: 05/13/2023]
Abstract
PURPOSE To investigate the structural features of wild-type and phospho-mimicking mutated XRCC4 protein, a protein involved in DNA double-strand break repair. MATERIALS AND METHODS XRCC4 with a HisTag were expressed by E. coli harboring plasmid DNA and purified. Phospho-mimicking mutants in which one phosphorylation site was replaced with aspartic acid were also prepared in order to reproduce the negative charge resulting from phosphorylation. The proteins were separated into dimers and multimers by gel filtration chromatography. Circular dichroism (CD) spectroscopy was performed in the region from ultraviolet to vacuum-ultraviolet. The CD spectra were analyzed with two analysis programs to evaluate the secondary structures of the wild-type and phospho-mimicked dimers and multimers. RESULT AND DISCUSSION The proportion of β-strand in the wild-type dimers was very low, particularly in their C-terminal region, including the five phosphorylation sites. The secondary structure of the phospho-mimic hardly changed in the dimeric form. In contrast, the β-strand content increased and the α-helix content decreased upon multimerization of the wild-type protein. The structural change of multimers slightly depended on the phospho-mimic site. These results suggest that the β-strand structure stabilizes the multimerization of XRCC4 and it is regulated by phosphorylation at the C-terminal site in living cells. CONCLUSION An increase in the β-strand content in XRCC4 is essential for stabilization of the multimeric form through C-terminal phosphorylation, allowing the formation of the large double-strand break repair machinery.
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Affiliation(s)
- Kai Nishikubo
- Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki, Japan
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes of Quantum Sciences and Technology (QST), Tokai, Ibaraki, Japan
| | - Maho Hasegawa
- Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki, Japan
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes of Quantum Sciences and Technology (QST), Tokai, Ibaraki, Japan
| | - Yudai Izumi
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes of Quantum Sciences and Technology (QST), Tokai, Ibaraki, Japan
| | - Kentaro Fujii
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes of Quantum Sciences and Technology (QST), Tokai, Ibaraki, Japan
| | - Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Yoshihisa Matsumoto
- Laboratory for Zero-Carbon Energy, Institute of Innovative Research, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Akinari Yokoya
- Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki, Japan
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes of Quantum Sciences and Technology (QST), Tokai, Ibaraki, Japan
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Thompson RE, Edmonds K, Dutch RE. Specific Residues in the C-Terminal Domain of the Human Metapneumovirus Phosphoprotein Are Indispensable for Formation of Viral Replication Centers and Regulation of the Function of the Viral Polymerase Complex. J Virol 2023; 97:e0003023. [PMID: 37092993 PMCID: PMC10231248 DOI: 10.1128/jvi.00030-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/30/2023] [Indexed: 04/25/2023] Open
Abstract
Human metapneumovirus (HMPV) is a negative-strand RNA virus that frequently causes respiratory tract infections in infants, the elderly, and the immunocompromised. A hallmark of HMPV infection is the formation of membraneless, liquid-like replication and transcription centers in the cytosol termed inclusion bodies (IBs). The HMPV phosphoprotein (P) and nucleoprotein (N) are the minimal viral proteins necessary to form IB-like structures, and both proteins are required for the viral polymerase to synthesize RNA during infection. HMPV P is a homotetramer with regions of intrinsic disorder and has several known and predicted phosphorylation sites of unknown function. In this study, we found that the P C-terminal intrinsically disordered domain (CTD) must be present to facilitate IB formation with HMPV N, while either the N-terminal intrinsically disordered domain or the central oligomerization domain was dispensable. Alanine substitution at a single tyrosine residue within the CTD abrogated IB formation and reduced coimmunoprecipitation with HMPV N. Mutations to C-terminal phosphorylation sites revealed a potential role for phosphorylation in regulating RNA synthesis and P binding partners within IBs. Phosphorylation mutations which reduced RNA synthesis in a reporter assay produced comparable results in a recombinant viral rescue system, measured as an inability to produce infectious viral particles with genomes containing these single P mutations. This work highlights the critical role HMPV P plays in facilitating a key step of the viral life cycle and reveals the potential role for phosphorylation in regulating the function of this significant viral protein. IMPORTANCE Human metapneumovirus (HMPV) infects global populations, with severe respiratory tract infections occurring in infants, the elderly, and the immunocompromised. There are currently no FDA-approved therapeutics available to prevent or treat HMPV infection. Therefore, understanding how HMPV replicates is vital for the identification of novel targets for therapeutic development. During HMPV infection, viral RNA synthesis proteins localize to membraneless structures called inclusion bodies (IBs), which are sites of genome replication and transcription. The HMPV phosphoprotein (P) is necessary for IBs to form and for the virus to synthesize RNA, but it is not known how this protein contributes to IB formation or if it is capable of regulating viral replication. We show that the C-terminal domain of P is the location of a molecular interaction driving IB formation and contains potential phosphorylation sites where amino acid charge regulates the function of the viral polymerase complex.
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Affiliation(s)
- Rachel Erin Thompson
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Kearstin Edmonds
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Rebecca Ellis Dutch
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky, USA
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48
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Tishchenko A, Van Waesberghe C, Favoreel HW. On-Slide Lambda Protein Phosphatase-Mediated Dephosphorylation of Fixed Samples. Methods Protoc 2023; 6:55. [PMID: 37367999 DOI: 10.3390/mps6030055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
Protein phosphorylation is a ubiquitous post-translational modification that regulates a plethora of intracellular processes, making its analysis crucial for understanding intracellular dynamics. The commonly used methods, such as radioactive labeling and gel electrophoresis, do not provide information about subcellular localization. Immunofluorescence using phospho-specific antibodies and subsequent analysis via microscopy allows researchers to assess subcellular localization, but it typically lacks validation whether the observed fluorescent signal is phosphorylation specific. In this study, an on-slide dephosphorylation assay coupled with immunofluorescence staining using phospho-specific antibodies on fixed samples is proposed as a fast and simple approach to validate phosphorylated proteins in their native subcellular context. The assay was validated using antibodies against two different phosphorylated target proteins, connexin 43 phosphorylated at serine 373, and phosphorylated substrates of protein kinase A, with a dramatic reduction in the signal upon dephosphorylation. The proposed approach provides a convenient way to validate phosphorylated proteins without the need for additional sample preparation steps, reducing the time and effort required for analysis, while minimizing the risk of protein loss or alteration.
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Affiliation(s)
- Alexander Tishchenko
- Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Cliff Van Waesberghe
- Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Herman W Favoreel
- Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
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49
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Spät P, Krauspe V, Hess WR, Maček B, Nalpas N. Deep Proteogenomics of a Photosynthetic Cyanobacterium. J Proteome Res 2023. [PMID: 37146978 DOI: 10.1021/acs.jproteome.3c00065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Cyanobacteria, the evolutionary ancestors of plant chloroplasts, contribute substantially to the Earth's biogeochemical cycles and are of great interest for a sustainable economy. Knowledge of protein expression is the key to understanding cyanobacterial metabolism; however, proteome studies in cyanobacteria are limited and cover only a fraction of the theoretical proteome. Here, we performed a comprehensive proteogenomic analysis of the model cyanobacterium Synechocystis sp. PCC 6803 to characterize the expressed (phospho)proteome, re-annotate known and discover novel open reading frames (ORFs). By mapping extensive shotgun mass spectrometry proteomics data onto a six-frame translation of the Synechocystis genome, we refined the genomic annotation of 64 ORFs, including eight completely novel ORFs. Our study presents the largest reported (phospho)proteome dataset for a unicellular cyanobacterium, covering the expression of about 80% of the theoretical proteome under various cultivation conditions, such as nitrogen or carbon limitation. We report 568 phosphorylated S/T/Y sites that are present on numerous regulatory proteins, including the transcriptional regulators cyAbrB1 and cyAbrB2. We also catalogue the proteins that have never been detected under laboratory conditions and found that a large portion of them is plasmid-encoded. This dataset will serve as a resource, providing dedicated information on growth condition-dependent protein expression and phosphorylation.
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Affiliation(s)
- Philipp Spät
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Vanessa Krauspe
- Genetics & Experimental Bioinformatics, Institute of Biology III, University of Freiburg, Schänzlestraße 1, 79104 Freiburg im Breisgau, Germany
| | - Wolfgang R Hess
- Genetics & Experimental Bioinformatics, Institute of Biology III, University of Freiburg, Schänzlestraße 1, 79104 Freiburg im Breisgau, Germany
| | - Boris Maček
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Nicolas Nalpas
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
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50
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Martínez-Alonso E, Escobar-Peso A, Guerra-Pérez N, Roca M, Masjuan J, Alcázar A. Dihydropyrimidinase-Related Protein 2 Is a New Partner in the Binding between 4E-BP2 and eIF4E Related to Neuronal Death after Cerebral Ischemia. Int J Mol Sci 2023; 24:ijms24098246. [PMID: 37175950 PMCID: PMC10179276 DOI: 10.3390/ijms24098246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 04/23/2023] [Accepted: 04/29/2023] [Indexed: 05/15/2023] Open
Abstract
Transient cerebral ischemia induces neuronal degeneration, followed in time by secondary delayed neuronal death that is strongly correlated with a permanent inhibition of protein synthesis in vulnerable brain regions, while protein translational rates are recovered in resistant areas. In the translation-regulation initiation step, the eukaryotic initiation factor (eIF) 4E is a key player regulated by its association with eIF4E-binding proteins (4E-BPs), mostly 4E-BP2 in brain tissue. In a previous work, we identified dihydropyrimidinase-related protein 2 (DRP2) as a 4E-BP2-interacting protein. Here, using a proteomic approach in a model of transient cerebral ischemia, a detailed study of DRP2 was performed in order to address the challenge of translation restoration in vulnerable regions. In this report, several DRP2 isoforms that have a specific interaction with both 4E-BP2 and eIF4E were identified, showing significant and opposite differences in this association, and being differentially detected in resistant and vulnerable regions in response to ischemia reperfusion. Our results provide the first evidence of DRP2 isoforms as potential regulators of the 4E-BP2-eIF4E association that would have consequences in the delayed neuronal death under ischemic-reperfusion stress. The new knowledge reported here identifies DRP2 as a new target to promote neuronal survival after cerebral ischemia.
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Affiliation(s)
- Emma Martínez-Alonso
- Department of Research, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain
- Proteomics Unit, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain
| | - Alejandro Escobar-Peso
- Department of Research, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain
| | - Natalia Guerra-Pérez
- Department of Genetics, Physiology and Microbiology, Faculty of Biological Sciences, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Marcel Roca
- Department of Research, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain
| | - Jaime Masjuan
- Department of Neurology, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain
- Department of Neurology, Facultad de Medicina, Universidad de Alcalá, 28871 Alcalá de Henares, Spain
| | - Alberto Alcázar
- Department of Research, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain
- Proteomics Unit, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain
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