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Wei Y, Zhang D, Shi H, Qian H, Chen H, Zeng Q, Jin F, Ye Y, Ou Z, Guo M, Guo B, Chen T. PDK1 promotes breast cancer progression by enhancing the stability and transcriptional activity of HIF-1α. Genes Dis 2024; 11:101041. [PMID: 38560503 PMCID: PMC10978537 DOI: 10.1016/j.gendis.2023.06.013] [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: 03/02/2023] [Revised: 05/14/2023] [Accepted: 06/04/2023] [Indexed: 04/04/2024] Open
Abstract
Pyruvate dehydrogenase kinase 1 (PDK1) phosphorylates the pyruvate dehydrogenase complex, which inhibits its activity. Inhibiting pyruvate dehydrogenase complex inhibits the tricarboxylic acid cycle and the reprogramming of tumor cell metabolism to glycolysis, which plays an important role in tumor progression. This study aims to elucidate how PDK1 promotes breast cancer progression. We found that PDK1 was highly expressed in breast cancer tissues, and PDK1 knockdown reduced the proliferation, migration, and tumorigenicity of breast cancer cells and inhibited the HIF-1α (hypoxia-inducible factor 1α) pathway. Further investigation showed that PDK1 promoted the protein stability of HIF-1α by reducing the level of ubiquitination of HIF-1α. The HIF-1α protein levels were dependent on PDK1 kinase activity. Furthermore, HIF-1α phosphorylation at serine 451 was detected in wild-type breast cancer cells but not in PDK1 knockout breast cancer cells. The phosphorylation of HIF-1α at Ser 451 stabilized its protein levels by inhibiting the interaction of HIF-1α with von Hippel-Lindau and prolyl hydroxylase domain. We also found that PDK1 enhanced HIF-1α transcriptional activity. In summary, PDK1 enhances HIF-1α protein stability by phosphorylating HIF-1α at Ser451 and promotes HIF-1α transcriptional activity by enhancing the binding of HIF-1α to P300. PDK1 and HIF-1α form a positive feedback loop to promote breast cancer progression.
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Affiliation(s)
- Yu Wei
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Dian Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - He Shi
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Husun Qian
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Hongling Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Qian Zeng
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Fangfang Jin
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yan Ye
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Zuli Ou
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Minkang Guo
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Bianqin Guo
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Tingmei Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
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2
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Domingo G, Marsoni M, Davide E, Fortunato S, de Pinto MC, Bracale M, Molla G, Gehring C, Vannini C. The cAMP-dependent phosphorylation footprint in response to heat stress. Plant Cell Rep 2024; 43:137. [PMID: 38713285 PMCID: PMC11076351 DOI: 10.1007/s00299-024-03213-y] [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: 02/28/2024] [Accepted: 04/01/2024] [Indexed: 05/08/2024]
Abstract
KEY MESSAGE cAMP modulates the phosphorylation status of highly conserved phosphosites in RNA-binding proteins crucial for mRNA metabolism and reprogramming in response to heat stress. In plants, 3',5'-cyclic adenosine monophosphate (3',5'-cAMP) is a second messenger that modulates multiple cellular targets, thereby participating in plant developmental and adaptive processes. Although its role in ameliorating heat-related damage has been demonstrated, mechanisms that govern cAMP-dependent responses to heat have remained elusive. Here we analyze the role cAMP-dependent phosphorylation during prolonged heat stress (HS) with a view to gain insight into processes that govern plant responses to HS. To do so, we performed quantitative phosphoproteomic analyses in Nicotiana tabacum Bright Yellow-2 cells grown at 27 °C or 35 °C for 3 days overexpressing a molecular "sponge" that reduces free intracellular cAMP levels. Our phosphorylation data and analyses reveal that the presence of cAMP is an essential factor that governs specific protein phosphorylation events that occur during prolonged HS in BY-2 cells. Notably, cAMP modulates HS-dependent phosphorylation of proteins that functions in mRNA processing, transcriptional control, vesicular trafficking, and cell cycle regulation and this is indicative for a systemic role of the messenger. In particular, changes of cAMP levels affect the phosphorylation status of highly conserved phosphosites in 19 RNA-binding proteins that are crucial during the reprogramming of the mRNA metabolism in response to HS. Furthermore, phosphorylation site motifs and molecular docking suggest that some proteins, including kinases and phosphatases, are conceivably able to directly interact with cAMP thus further supporting a regulatory role of cAMP in plant HS responses.
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Affiliation(s)
- Guido Domingo
- Biotechnology and Life Science Department, University of Insubria, Via Dunant 3, 21100, Varese, Italy.
| | - Milena Marsoni
- Biotechnology and Life Science Department, University of Insubria, Via Dunant 3, 21100, Varese, Italy
| | - Eleonora Davide
- Biotechnology and Life Science Department, University of Insubria, Via Dunant 3, 21100, Varese, Italy
| | - Stefania Fortunato
- Department of Biology, University of Bari "Aldo Moro", Piazza Umberto I, 70121, Bari, Italy
| | | | - Marcella Bracale
- Biotechnology and Life Science Department, University of Insubria, Via Dunant 3, 21100, Varese, Italy
| | - Gianluca Molla
- Biotechnology and Life Science Department, University of Insubria, Via Dunant 3, 21100, Varese, Italy
| | - Chris Gehring
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Borgo XX Giugno, 74, 06121, Perugia, Italy
| | - Candida Vannini
- Biotechnology and Life Science Department, University of Insubria, Via Dunant 3, 21100, Varese, Italy.
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Montserrat-Gomez M, Gogl G, Carrasco K, Betzi S, Durbesson F, Cousido-Siah A, Kostmann C, Essig DJ, Strømgaard K, Østergaard S, Morelli X, Trave G, Vincentelli R, Bailly E, Borg JP. PDZome-wide and structural characterization of the PDZ-binding motif of VANGL2. Biochim Biophys Acta Proteins Proteom 2024; 1872:140989. [PMID: 38142947 DOI: 10.1016/j.bbapap.2023.140989] [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] [Received: 09/06/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 12/26/2023]
Abstract
VANGL2 is a core component of the non-canonical Wnt/Planar Cell Polarity signaling pathway that uses its highly conserved carboxy-terminal type 1 PDZ-binding motif (PBM) to bind a variety of PDZ proteins. In this study, we characterize and quantitatively assess the largest VANGL2 PDZome-binding profile documented so far, using orthogonal methods. The results of our holdup approach support VANGL2 interactions with a large panel of both long-recognized and unprecedented PDZ domains. Truncation and point mutation analyses of the VANGL2 PBM establish that, beyond the strict requirement of the P-0 / V521 and P-2 / T519 amino acids, upstream residues, including E518, Q516 and R514 at, respectively, P-3, P-5 and P-7 further contribute to the robustness of VANGL2 interactions with two distinct PDZ domains, SNX27 and SCRIBBLE-PDZ3. In agreement with these data, incremental amino-terminal deletions of the VANGL2 PBM causes its overall affinity to progressively decline. Moreover, the holdup data establish that the PDZome binding repertoire of VANGL2 starts to diverge significantly with the truncation of E518. A structural analysis of the SYNJ2BP-PDZ/VANGL2 interaction with truncated PBMs identifies a major conformational change in the binding direction of the PBM peptide after the P-2 position. Finally, we report that the PDZome binding profile of VANGL2 is dramatically rearranged upon phosphorylation of S517, T519 and S520. Our crystallographic approach illustrates how SYNJ2BP accommodates a S520-phosphorylated PBM peptide through the ideal positioning of two basic residues, K48 and R86. Altogether our data provides a comprehensive view of the VANGL2 PDZ network and how this network specifically responds to the post-translation modification of distinct PBM residues. These findings should prove useful in guiding future functional and molecular studies of the key PCP component VANGL2.
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Affiliation(s)
- Marta Montserrat-Gomez
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue 'Cell polarity, cell signaling and cancer', Marseille, France
| | - Gergo Gogl
- Universite de Strasbourg, INSERM, CNRS, IGBMC, Department of Integrated Structural Biology, Illkirch, France
| | - Kendall Carrasco
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe Integrative Structural & Chemical Biology, Marseille, France
| | - Stephane Betzi
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe Integrative Structural & Chemical Biology, Marseille, France
| | - Fabien Durbesson
- Aix Marseille Université, CNRS, Architecture et fonction des macromolécules biologiques (AFMB), Marseille, France
| | - Alexandra Cousido-Siah
- Universite de Strasbourg, INSERM, CNRS, IGBMC, Department of Integrated Structural Biology, Illkirch, France
| | - Camille Kostmann
- Universite de Strasbourg, INSERM, CNRS, IGBMC, Department of Integrated Structural Biology, Illkirch, France
| | - Dominic J Essig
- Center for Biopharmaceuticals, Jagtvej 162, 2100 Copenhagen, Denmark; Global Research Technologies, Novo Nordisk Research Park, 2760 Maaloev, Denmark
| | | | - Søren Østergaard
- Global Research Technologies, Novo Nordisk Research Park, 2760 Maaloev, Denmark
| | - Xavier Morelli
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe Integrative Structural & Chemical Biology, Marseille, France
| | - Gilles Trave
- Universite de Strasbourg, INSERM, CNRS, IGBMC, Department of Integrated Structural Biology, Illkirch, France
| | - Renaud Vincentelli
- Aix Marseille Université, CNRS, Architecture et fonction des macromolécules biologiques (AFMB), Marseille, France.
| | - Eric Bailly
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue 'Cell polarity, cell signaling and cancer', Marseille, France.
| | - Jean-Paul Borg
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue 'Cell polarity, cell signaling and cancer', Marseille, France; Institut Universitaire de France (IUF), France.
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Zang S, Yang X, Ye J, Mo X, Zhou G, Fang Y. Quantitative phosphoproteomics explain cryopreservation-induced reductions in ram sperm motility. J Proteomics 2024; 298:105153. [PMID: 38438079 DOI: 10.1016/j.jprot.2024.105153] [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: 11/30/2023] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Sperm cryopreservation decreases motility, probably due to changes in protein phosphorylation. Our objective was to use quantitative phosphoproteomics for systematic comparative analyses of fresh versus frozen-thawed sperm to identify factors causing cryo-injury. Ejaculates were collected (artificial vagina) from six Dorper rams, pooled, extended, and frozen over liquid nitrogen. Overall, 915, 3382, and 6875 phosphorylated proteins, phosphorylated peptides, and phosphorylation sites, respectively, were identified. At least two modified sites were present in 57.94% of the 6875 phosphosites identified, of which AKAP4 protein contained up to 331 modified sites. There were 732 phosphorylated peptides significantly up-regulated and 909 significantly down-regulated in frozen-thawed versus fresh sperm. Moreover, the conserved motif [RxxS] was significantly down-regulated in frozen-thawed sperm. Phosphorylation of sperm-specific proteins, e.g., AKAP3/4, CABYR, FSIP2, GSK3A/B, GPI, and ODF1/2 make them potential biomarkers to assess the quality of frozen-thawed ram sperm. Furthermore, these differentially phosphorylated proteins and modification sites were implicated in cryopreservation-induced changes in sperm energy production, fiber sheath composition, and various biological processes. We concluded that abnormal protein phosphorylation modifications are key regulators of reduced sperm motility. These novel findings implicated specific protein phosphorylation modifications in sperm cryo-injury. SIGNIFICANCE: This study used phosphorylated TMT quantitative proteomics to explore regulation of epigenetic modifications in frozen-thawed ram sperm. This experiment demonstrated that ram sperm freezing affects phosphorylation site modifications of proteins, especially those related to functions such as sperm motility and energy production. Furthermore, it is important to link functions of phosphorylated proteins with changes in sperm quality after freezing and thawing, and to clarify intrinsic reasons for sperm quality changes, which is of great importance for elucidating mechanisms of sperm freezing damage. Based on these protein markers and combined with cryoprotectant design theory, it provides a theoretical basis and data reference to study sperm cryoprotectants.
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Affiliation(s)
- Shengqin Zang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu 611130, PR China
| | - Xiaorui Yang
- Key Laboratory of Animal Production, Product Quality and Security, Ministry of Education, College of Animal Science and Technology, Jilin Agricultural University, Jilin, Changchun 130118, China
| | - Jiangfeng Ye
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu 611130, PR China
| | - Xianhong Mo
- College of Chemistry and Life Science, Chifeng University, Chifeng 024000, PR China
| | - Guangbin Zhou
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu 611130, PR China
| | - Yi Fang
- Key Laboratory of Animal Production, Product Quality and Security, Ministry of Education, College of Animal Science and Technology, Jilin Agricultural University, Jilin, Changchun 130118, China.
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5
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Yao YB, Xiao CF, Wu JW, Meng LY, Liu W, Lu JG, Wang C. Yiqi Kaimi prescription regulates protein phosphorylation to promote intestinal motility in slow transit constipation. J Ethnopharmacol 2024; 329:118118. [PMID: 38614261 DOI: 10.1016/j.jep.2024.118118] [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: 12/02/2023] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/15/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The clinical efficacy of the Yiqi Kaimi prescription has been confirmed in slow transit constipation. However, the effects and biological mechanism of Yiqi Kaimi prescription are still unclear. AIMS OF THE STUDY To identify the effects of Yiqi Kaimi prescription on intestinal motility; To reveal the potential key targets and pathways of Yiqi Kaimi prescription for the treatment of slow transit constipation. MATERIALS AND METHODS The effects of Yiqi Kaimi prescription on slow transit constipation were investigated in a mouse model. The terminal ink propulsion experiment and fecal indocyanine green imaging was used to measure the intestinal transit time. Protein phosphorylation changes in colon tissues treated with Yiqi Kaimi prescription were detected using a Phospho Explorer antibody microarray. Bioinformatic analyses were performed using the Database for Annotation Visualization and Integrated Discovery (DAVID) and the Search Tool for the Retrieval of Interacting Genes (STRING). Western blot analysis and immunohistochemistry confirmed the observed changes in phosphorylation. RESULT s: Yiqi Kaimi prescription significantly increased the intestinal transit rate (P < 0.05 vs. model) and reduced the time to first discharge of feces containing fecal indocyanine green imaging in mice (P < 0.05 vs. model). The administration of Yiqi Kaimi prescription induced phosphorylation changes in 41 proteins, with 9 upregulated proteins and 32 downregulated proteins. Functional classification of the phosphorylated proteins with DAVID revealed that the critical biological processes included tyrosine protein kinases, positive regulation of calcium-mediated signaling and response to muscle stretch. The phosphorylation of the spleen tyrosine kinase (SYK) at Tyr348 increased 2.19-fold, which was the most significant change. The phosphorylation level of the transcription factor p65 (RELA) at Thr505 was decreased 0.57-fold. SYK was a hub protein in the protein-protein interaction network and SYK and RELA formed the core of the secondary subnetwork. The key protein phosphorylation after treatment with Yiqi Kaimi prescription were verified by Western blot analysis and immunohistochemistry. CONCLUSION Yiqi Kaimi prescription significantly enhanced intestinal motility. This effect was attributed to alterations in the phosphorylation levels of various target proteins. The observed changes in protein phosphorylation, including SYK and RELA, may serve as crucial factors in the treatment of slow transit constipation.
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Affiliation(s)
- Yi-Bo Yao
- Department of Anorectal Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China.
| | - Chang-Fang Xiao
- Department of Anorectal Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
| | - Jing-Wen Wu
- Department of Anorectal Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
| | - Ling-Yun Meng
- Department of Anorectal Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
| | - Wei Liu
- Department of Pharmacy, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jin-Gen Lu
- Institute of Chinese Traditional Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Chen Wang
- Department of Anorectal Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China.
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Glebov-McCloud AGP, Saide WS, Gaine ME, Strack S. Protein Kinase A in neurological disorders. J Neurodev Disord 2024; 16:9. [PMID: 38481146 PMCID: PMC10936040 DOI: 10.1186/s11689-024-09525-0] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/29/2024] [Indexed: 03/17/2024] Open
Abstract
Cyclic adenosine 3', 5' monophosphate (cAMP)-dependent Protein Kinase A (PKA) is a multi-functional serine/threonine kinase that regulates a wide variety of physiological processes including gene transcription, metabolism, and synaptic plasticity. Genomic sequencing studies have identified both germline and somatic variants of the catalytic and regulatory subunits of PKA in patients with metabolic and neurodevelopmental disorders. In this review we discuss the classical cAMP/PKA signaling pathway and the disease phenotypes that result from PKA variants. This review highlights distinct isoform-specific cognitive deficits that occur in both PKA catalytic and regulatory subunits, and how tissue-specific distribution of these isoforms may contribute to neurodevelopmental disorders in comparison to more generalized endocrine dysfunction.
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Affiliation(s)
- Alexander G P Glebov-McCloud
- Department of Neuroscience and Pharmacology, Bowen Science Building, University of Iowa, Carver College of Medicine, 51 Newton Road, Iowa City, IA, 52242, USA
| | - Walter S Saide
- Department of Neuroscience and Pharmacology, Bowen Science Building, University of Iowa, Carver College of Medicine, 51 Newton Road, Iowa City, IA, 52242, USA
| | - Marie E Gaine
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy Building, College of Pharmacy, University of Iowa, 180 S. Grand Ave, Iowa City, IA, 52242, USA
- Iowa Neuroscience Institute, Intellectual and Developmental Disabilities Research Center, Iowa City, IA, USA
| | - Stefan Strack
- Department of Neuroscience and Pharmacology, Bowen Science Building, University of Iowa, Carver College of Medicine, 51 Newton Road, Iowa City, IA, 52242, USA.
- Iowa Neuroscience Institute, Intellectual and Developmental Disabilities Research Center, Iowa City, IA, USA.
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Katagiri S, Kamiyama Y, Yamashita K, Iizumi S, Suzuki R, Aoi Y, Takahashi F, Kasahara H, Kinoshita T, Umezawa T. Accumulation of Phosphorylated SnRK2 Substrate 1 Promotes Drought Escape in Arabidopsis. Plant Cell Physiol 2024; 65:259-268. [PMID: 37971366 DOI: 10.1093/pcp/pcad146] [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: 10/13/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
Plants adopt optimal tolerance strategies depending on the intensity and duration of stress. Retaining water is a priority under short-term drought conditions, whereas maintaining growth and reproduction processes takes precedence over survival under conditions of prolonged drought. However, the mechanism underlying changes in the stress response depending on the degree of drought is unclear. Here, we report that SNF1-related protein kinase 2 (SnRK2) substrate 1 (SNS1) is involved in this growth regulation under conditions of drought stress. SNS1 is phosphorylated and stabilized by SnRK2 protein kinases reflecting drought conditions. It contributes to the maintenance of growth and promotion of flowering as drought escape by repressing stress-responsive genes and inducing FLOWERING LOCUS T (FT) expression, respectively. SNS1 interacts with the histone methylation reader proteins MORF-related gene 1 (MRG1) and MRG2, and the SNS1-MRG1/2 module cooperatively regulates abscisic acid response. Taken together, these observations suggest that the phosphorylation and accumulation of SNS1 in plants reflect the intensity and duration of stress and can serve as a molecular scale for maintaining growth and adopting optimal drought tolerance strategies under stress conditions.
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Affiliation(s)
- Sotaro Katagiri
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, 184-8588 Japan
| | - Yoshiaki Kamiyama
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, 184-8588 Japan
| | - Kota Yamashita
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, 184-8588 Japan
| | - Sara Iizumi
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, 184-8588 Japan
| | - Risa Suzuki
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, 184-8588 Japan
| | - Yuki Aoi
- INRAE, UR1268 BIA, 3 impasse Yvette Cauchois, CS71627, 44316 Cedex3, Nantes F06160, France
| | - Fuminori Takahashi
- Graduate School of Industrial Science and Technology, Tokyo University of Science, 1-3, Kagurazaka, Shinjuku, 125-8585 Japan
| | - Hiroyuki Kasahara
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, 183-0054 Japan
| | - Toshinori Kinoshita
- Graduate School of Science, Nagoya University, Furocho, Nagoya, 464-8602 Japan
| | - Taishi Umezawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, 184-8588 Japan
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, 183-0054 Japan
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Gergs U, Wackerhagen S, Fuhrmann T, Schäfer I, Neumann J. Further investigations on the influence of protein phosphatases on the signaling of muscarinic receptors in the atria of mouse hearts. Naunyn Schmiedebergs Arch Pharmacol 2024:10.1007/s00210-024-02973-4. [PMID: 38308688 DOI: 10.1007/s00210-024-02973-4] [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: 08/30/2023] [Accepted: 01/21/2024] [Indexed: 02/05/2024]
Abstract
The vagal regulation of cardiac function involves acetylcholine (ACh) receptor activation followed by negative chronotropic and negative as well as positive inotropic effects. The resulting signaling pathways may include Gi/o protein-coupled reduction in adenylyl cyclase (AC) activity, direct Gi/o protein-coupled activation of ACh-activated potassium current (IKACh), inhibition of L-type calcium ion channels, and/or the activation of protein phosphatases. Here, we studied the role of the protein phosphatases 1 (PP1) and 2A (PP2A) for muscarinic receptor signaling in isolated atrial preparations of transgenic mice with cardiomyocyte-specific overexpression of either the catalytic subunit of PP2A (PP2A-TG) or the inhibitor-2 (I2) of PP1 (I2-TG) or in double transgenic mice overexpressing both PP2A and I2 (DT). In mouse left atrial preparations, carbachol (CCh), cumulatively applied (1 nM-10 µM), exerted at low concentrations a negative inotropic effect followed by a positive inotropic effect at higher concentrations. This biphasic effect was noted with CCh alone as well as when CCh was added after β-adrenergic pre-stimulation with isoprenaline (1 µM). Whereas the response to stimulation of β-adrenoceptors or adenosine receptors (used as controls) was changed in PP2A-TG, the response to CCh was unaffected in atrial preparations from all transgenic models studied here. Therefore, the present data tentatively indicate that neither PP2A nor PP1, but possibly other protein phosphatases, is involved in the muscarinic receptor-induced inotropic and chronotropic effects in the mouse heart.
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Affiliation(s)
- Ulrich Gergs
- Institut Für Pharmakologie Und Toxikologie, Medizinische Fakultät, Martin-Luther-Universität Halle-Wittenberg, D-06097, Magdeburger Str. 4, 06112, Halle, Germany.
| | - Silke Wackerhagen
- Institut Für Pharmakologie Und Toxikologie, Medizinische Fakultät, Martin-Luther-Universität Halle-Wittenberg, D-06097, Magdeburger Str. 4, 06112, Halle, Germany
| | - Tobias Fuhrmann
- Institut Für Pharmakologie Und Toxikologie, Medizinische Fakultät, Martin-Luther-Universität Halle-Wittenberg, D-06097, Magdeburger Str. 4, 06112, Halle, Germany
| | - Inka Schäfer
- Institut Für Pharmakologie Und Toxikologie, Medizinische Fakultät, Martin-Luther-Universität Halle-Wittenberg, D-06097, Magdeburger Str. 4, 06112, Halle, Germany
| | - Joachim Neumann
- Institut Für Pharmakologie Und Toxikologie, Medizinische Fakultät, Martin-Luther-Universität Halle-Wittenberg, D-06097, Magdeburger Str. 4, 06112, Halle, Germany
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Ren C, Chen L, Bai Y, Hou C, Li X, Schroyen M, Zhang D. Comparative effects of phosphorylation and acetylation on glycolysis and myofibrillar proteins degradation in postmortem muscle. Int J Biol Macromol 2024; 257:128567. [PMID: 38061521 DOI: 10.1016/j.ijbiomac.2023.128567] [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: 09/05/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023]
Abstract
The study investigated the different effects between protein phosphorylation and acetylation on glycolytic enzyme activity and myofibrillar protein degradation. Lamb longissimus thoracis lumborum muscles were homogenized and then inhibitors were added for incubation at 4 °C. Phosphatase inhibitor was added to produce a high phosphorylation level (PI group) and lysine deacetylase inhibitor was added to produce a high acetylation level (DI group). The lactate and ATP content in the PI group was inhibited compared with that in the DI group (P < 0.05). Phosphofructokinase (PFK) activity was negatively related with the phosphorylation level and was positively related with the acetylation level in the DI group (P < 0.05). The degradation of troponin T and desmin of the DI group were restrained when compared to that in the PI group (P < 0.05). Compared with initial PFK and desmin, the simulation of phosphorylation and acetylation of PFK and desmin showed different electrostatic potential at the surface and a more unstable structure. The phosphorylation level of the DI group was increased, suggesting that the changes of protein acetylation altered protein phosphorylation. In conclusion, compared with protein phosphorylation, protein acetylation had a greater effect on promoting glycolysis and inhibiting protein degradation.
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Affiliation(s)
- Chi Ren
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China; Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, Gembloux, Belgium
| | - Li Chen
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China
| | - Yuqiang Bai
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China
| | - Chengli Hou
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China
| | - Xin Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China.
| | - Martine Schroyen
- Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, Gembloux, Belgium
| | - Dequan Zhang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China
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10
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Fransen M, Lismont C. Peroxisomal hydrogen peroxide signaling: A new chapter in intracellular communication research. Curr Opin Chem Biol 2024; 78:102426. [PMID: 38237354 DOI: 10.1016/j.cbpa.2024.102426] [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: 10/28/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 02/09/2024]
Abstract
Hydrogen peroxide (H2O2), a natural metabolite commonly found in aerobic organisms, plays a crucial role in numerous cellular signaling processes. One of the key organelles involved in the cell's metabolism of H2O2 is the peroxisome. In this review, we first provide a concise overview of the current understanding of H2O2 as a molecular messenger in thiol redox signaling, along with the role of peroxisomes as guardians and modulators of cellular H2O2 balance. Next, we direct our focus toward the recently identified primary protein targets of H2O2 originating from peroxisomes, emphasizing their importance in unraveling the complex interplay between peroxisomal H2O2 and cell signaling. We specifically focus on three areas: signaling through peroxiredoxin redox relay complexes, calcium signaling, and phospho-signaling. Finally, we highlight key research directions that warrant further investigation to enhance our comprehension of the molecular and biochemical mechanisms linking alterations in peroxisomal H2O2 metabolism with disease.
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Affiliation(s)
- Marc Fransen
- Laboratory of Peroxisome Biology and Intracellular Signaling, Department of Cellular and Molecular Medicine, Katholieke Universiteit Leuven, Herestraat 49 Box 901, 3000 Leuven, Belgium.
| | - Celien Lismont
- Laboratory of Peroxisome Biology and Intracellular Signaling, Department of Cellular and Molecular Medicine, Katholieke Universiteit Leuven, Herestraat 49 Box 901, 3000 Leuven, Belgium
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11
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Liu Z, Hou S, He P. Detection of Ligand-Induced Receptor Kinase and Signaling Component Phosphorylation with Mn 2+-Phos-Tag SDS-PAGE. Methods Mol Biol 2024; 2731:205-214. [PMID: 38019436 DOI: 10.1007/978-1-0716-3511-7_15] [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: 11/30/2023]
Abstract
Plasma membrane-resident receptor kinases (RKs) are crucial for plants to sense endogenous and exogenous signals in regulating growth, development, and stress response. Upon perception of ligands by the extracellular domain, RKs are usually activated by auto- and/or trans-phosphorylation of the cytoplasmic kinase domain, which in turn phosphorylates downstream substrates to relay the signaling. Therefore, monitoring ligand-induced in vivo phosphorylation dynamics of RKs and their associated proteins provides mechanistic insight into RK activation and downstream signal transduction. Phos-tag specifically binds phosphomonoester dianions of phosphorylated serine, threonine, and tyrosine residues, which enables Phos-tag-containing SDS-PAGE gels to separate phosphorylated proteins from non-phosphorylated form. Here, we describe a detailed method of Mn2+-Phos-tag SDS-PAGE analysis to detect the ligand-induced in vivo phosphorylation of RKs and associated proteins.
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Affiliation(s)
- Zunyong Liu
- Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Shuguo Hou
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
| | - Ping He
- Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
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12
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Wang J, Zhao X, Zhang H, Chen Y, Bie Z. In situ digestion-assisted multi-template imprinted nanoparticles for efficient analysis of protein phosphorylation. Mikrochim Acta 2023; 190:490. [PMID: 38030869 DOI: 10.1007/s00604-023-06081-7] [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: 07/27/2023] [Accepted: 10/29/2023] [Indexed: 12/01/2023]
Abstract
A new general approach called in situ digestion-assisted multi-template imprinting is proposed for preparation of phospho-specific molecularly imprinted nanoparticles. Through the novel templating strategy and controllable imprinting process, imprinted nanoparticles specific to the intact phosphoprotein and its phosphopeptides were synthesized. The prepared imprinted nanoparticles exhibited excellent specificity (cross reactivity < 10%), high affinity (10-6 M), high efficiency (47.5%), and good generality (both intact phosphoprotein and phosphopeptides). We also realized the fine tuning of the recognition at peptide level of the imprinted nanoparticles by adjusting the imprinting time. Based on the selective enrichment of the imprinted nanoparticles, the MS identification of both the intact phosphoprotein (Tau) and phosphopeptides (angiotensin II and peptides of Tau) in real complex samples could be achieved. Therefore, we believe that the in situ digestion-assisted multi-template imprinting strategy holds promising future in both phosphorylation analysis and proteomics applications.
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Affiliation(s)
- Jie Wang
- Department of Chemistry, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, 233030, China
| | - Xiuling Zhao
- School of Pharmacy, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, 233000, China
| | - Hui Zhang
- Department of Chemistry, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, 233030, China
| | - Yang Chen
- Department of Chemistry, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, 233030, China
- School of Pharmacy, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, 233000, China
| | - Zijun Bie
- Department of Chemistry, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, 233030, China.
- School of Pharmacy, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, 233000, China.
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13
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Chen L, Yang J, Hu H, Jiang Y, Feng L, Liu J, Zhong K, Liu P, Ma Y, Chen M, Yang J. Large-scale phosphoproteome analysis in wheat seedling leaves provides evidence for extensive phosphorylation of regulatory proteins during CWMV infection. BMC Plant Biol 2023; 23:532. [PMID: 37914991 PMCID: PMC10621099 DOI: 10.1186/s12870-023-04559-3] [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: 04/17/2023] [Accepted: 10/25/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND Chinese wheat mosaic virus (CWMV) often causes severe damage to wheat (Triticum aestivum L.) growth and yield. It is well known that a successful infection in plants depends on a complex interaction between the host plant and the pathogen. Post-translational modification (PTM) of proteins is considered to be one of the main processes that decides the outcome of the plant-pathogen arms race during this interaction. Although numerous studies have investigated PTM in various organisms, there has been no large-scale phosphoproteomic analysis of virus-infected wheat plants. We therefore aimed to investigate the CWMV infection-induced phosphoproteomics changes in wheat by high-resolution liquid chromatography-tandem mass spectroscopy (LC-MS/MS) using affinity-enriched peptides followed by comprehensive bioinformatics analysis. RESULTS Through this study, a total of 4095 phosphorylation sites have been identified in 1968 proteins, and 11.6% of the phosphorylated proteins exhibited significant changes (PSPCs) in their phosphorylation levels upon CWMV infection. The result of Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that most of the PSPCs were associated with photosynthesis, plant-pathogen interactions, and MAPK signaling pathways. The protein-protein interaction (PPI) network analysis result showed that these PSPCs were mainly participated in the regulation of biosynthesis and metabolism, protein kinase activities, and transcription factors. Furthermore, the phosphorylation levels of TaChi1 and TaP5CS, two plant immunity-related enzymes, were significantly changed upon CWMV infection, resulting in a significant decrease in CWMV accumulation in the infected plants. CONCLUSIONS Our results indicate that phosphorylation modification of protein plays a critical role in wheat resistance to CWMV infection. Upon CWMV infection, wheat plants will regulate the levels of extra- and intra-cellular signals and modifications of enzyme activities via protein phosphorylation. This novel information about the strategies used by wheat to resist CWMV infection will help researchers to breed new CWMV-resistant cultivars and to better understand the arms race between wheat and CWMV.
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Affiliation(s)
- Lu Chen
- Institute of Crop Sciences, State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jin Yang
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Haichao Hu
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yaoyao Jiang
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Lixiao Feng
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jiaqian Liu
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Kaili Zhong
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Peng Liu
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Youzhi Ma
- Institute of Crop Sciences, State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Ming Chen
- Institute of Crop Sciences, State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Jian Yang
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
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14
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Yegambaram M, Kumar S, Wu X, Lu Q, Sun X, Garcia Flores A, Meadows ML, Barman S, Fulton D, Wang T, Fineman JR, Black SM. Endothelin-1 acutely increases nitric oxide production via the calcineurin mediated dephosphorylation of Caveolin-1. Nitric Oxide 2023; 140-141:50-57. [PMID: 37659679 DOI: 10.1016/j.niox.2023.08.004] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/22/2023] [Accepted: 08/30/2023] [Indexed: 09/04/2023]
Abstract
Endothelin (ET)-1 is an endothelial-derived peptide that exerts biphasic effects on nitric oxide (NO) levels in endothelial cells such that acute exposure stimulates-while sustained exposure attenuates-NO production. Although the mechanism involved in the decrease in NO generation has been identified but the signaling involved in the acute increase in NO is still unresolved. This was the focus of this study. Our data indicate that exposing pulmonary arterial endothelial cells (PAEC) to ET-1 led to an increase in NO for up to 30min after which levels declined. These effects were attenuated by ET receptor antagonists. The increase in NO correlated with significant increases in pp60Src activity and increases in eNOS phosphorylation at Tyr83 and Ser1177. The ET-1 mediated increase in phosphorylation and NO generation were attenuated by the over-expression of a pp60Src dominant negative mutant. The increase in pp60Src activity correlated with a reduction in the interaction of Caveolin-1 with pp60Src and the calcineurin-mediated dephosphorylation of caveolin-1 at three previously unidentified sites: Thr91, Thr93, and Thr95. The calcineurin inhibitor, Tacrolimus, attenuated the acute increase in pp60Src activity induced by ET-1 and a calcineurin siRNA attenuated the ET-1 mediated increase in eNOS phosphorylation at Tyr83 and Ser1177 as well as the increase in NO. By using a Caveolin-1 celluSpot peptide array, we identified a peptide targeting a sequence located between aa 41-56 as the pp60Src binding region. This peptide fused to the TAT sequence was found to decrease caveolin-pp60Src interaction, increased pp60Src activity, increased eNOS pSer1177 and NO levels in PAEC and induce vasodilation in isolated aortic rings in wildtype but not eNOS knockout mice. Together, our data identify a novel mechanism by which ET-1 acutely increases NO via a calcineurin-mediated dephosphorylation of caveolin-1 and the subsequent stimulation of pp60Src activity, leading to increases in phosphorylation of eNOS at Tyr83 and Ser1177.
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Affiliation(s)
- Manivannan Yegambaram
- Center of Translational Science, Florida International University, Port St. Lucie, FL, 34987, USA; Department of Environmental Health Sciences, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL, USA
| | - Sanjiv Kumar
- Department of Medicine, Augusta University, Augusta, GA, USA; Vascular Biology Center, Augusta University, Augusta, GA, USA
| | - Xiaomin Wu
- Department of Medicine, University of Arizona, Tucson, AZ, 33174, USA
| | - Qing Lu
- Center of Translational Science, Florida International University, Port St. Lucie, FL, 34987, USA; Department of Environmental Health Sciences, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL, USA
| | - Xutong Sun
- Center of Translational Science, Florida International University, Port St. Lucie, FL, 34987, USA; Department of Environmental Health Sciences, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL, USA
| | - Alejandro Garcia Flores
- Center of Translational Science, Florida International University, Port St. Lucie, FL, 34987, USA; Department of Environmental Health Sciences, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL, USA
| | | | - Scott Barman
- Department of Pharmacology, Augusta University, Augusta, GA, USA
| | - David Fulton
- Vascular Biology Center, Augusta University, Augusta, GA, USA; Department of Pharmacology, Augusta University, Augusta, GA, USA
| | - Ting Wang
- Center of Translational Science, Florida International University, Port St. Lucie, FL, 34987, USA; Department of Environmental Health Sciences, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL, USA
| | - Jeffrey R Fineman
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Stephen M Black
- Center of Translational Science, Florida International University, Port St. Lucie, FL, 34987, USA; Department of Environmental Health Sciences, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL, USA; Department of Cellular Biology & Pharmacology, Howard Wertheim College of Medicine, Florida International University, Miami, FL, 33174, USA.
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15
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Anandakrishnan M, Ross KE, Chen C, Shanker V, Cowart J, Wu CH. KSFinder-a knowledge graph model for link prediction of novel phosphorylated substrates of kinases. PeerJ 2023; 11:e16164. [PMID: 37818330 PMCID: PMC10561642 DOI: 10.7717/peerj.16164] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 09/01/2023] [Indexed: 10/12/2023] Open
Abstract
Background Aberrant protein kinase regulation leading to abnormal substrate phosphorylation is associated with several human diseases. Despite the promise of therapies targeting kinases, many human kinases remain understudied. Most existing computational tools predicting phosphorylation cover less than 50% of known human kinases. They utilize local feature selection based on protein sequences, motifs, domains, structures, and/or functions, and do not consider the heterogeneous relationships of the proteins. In this work, we present KSFinder, a tool that predicts kinase-substrate links by capturing the inherent association of proteins in a network comprising 85% of the known human kinases. We also postulate the potential role of two understudied kinases based on their substrate predictions from KSFinder. Methods KSFinder learns the semantic relationships in a phosphoproteome knowledge graph using a knowledge graph embedding algorithm and represents the nodes in low-dimensional vectors. A multilayer perceptron (MLP) classifier is trained to discern kinase-substrate links using the embedded vectors. KSFinder uses a strategic negative generation approach that eliminates biases in entity representation and combines data from experimentally validated non-interacting protein pairs, proteins from different subcellular locations, and random sampling. We assess KSFinder's generalization capability on four different datasets and compare its performance with other state-of-the-art prediction models. We employ KSFinder to predict substrates of 68 "dark" kinases considered understudied by the Illuminating the Druggable Genome program and use our text-mining tool, RLIMS-P along with manual curation, to search for literature evidence for the predictions. In a case study, we performed functional enrichment analysis for two dark kinases - HIPK3 and CAMKK1 using their predicted substrates. Results KSFinder shows improved performance over other kinase-substrate prediction models and generalized prediction ability on different datasets. We identified literature evidence for 17 novel predictions involving an understudied kinase. All of these 17 predictions had a probability score ≥0.7 (nine at >0.9, six at 0.8-0.9, and two at 0.7-0.8). The evaluation of 93,593 negative predictions (probability ≤0.3) identified four false negatives. The top enriched biological processes of HIPK3 substrates relate to the regulation of extracellular matrix and epigenetic gene expression, while CAMKK1 substrates include lipid storage regulation and glucose homeostasis. Conclusions KSFinder outperforms the current kinase-substrate prediction tools with higher kinase coverage. The strategically developed negatives provide a superior generalization ability for KSFinder. We predicted substrates of 432 kinases, 68 of which are understudied, and hypothesized the potential functions of two dark kinases using their predicted substrates.
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Affiliation(s)
- Manju Anandakrishnan
- Center for Bioinformatics and Computational Biology, University of Delware, Newark, DE, United States of America
| | - Karen E. Ross
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, United States of America
| | - Chuming Chen
- Center for Bioinformatics and Computational Biology, University of Delware, Newark, DE, United States of America
| | - Vijay Shanker
- Center for Bioinformatics and Computational Biology, University of Delware, Newark, DE, United States of America
| | - Julie Cowart
- Center for Bioinformatics and Computational Biology, University of Delware, Newark, DE, United States of America
| | - Cathy H. Wu
- Center for Bioinformatics and Computational Biology, University of Delware, Newark, DE, United States of America
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, United States of America
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Wang Q, Xia C, Zhu A, Bao Y, Lu J, Chen Y, Xu J, Wang B, Naman CB, Li L, Wang Q, Liu H, Liang H, Cui W. Discrepancy of synaptic and microtubular protein phosphorylation in the hippocampus of APP/PS1 and MAPT×P301S transgenic mice at the early stage of Alzheimer's disease. Metab Brain Dis 2023; 38:1983-1997. [PMID: 37160613 DOI: 10.1007/s11011-023-01209-3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/02/2023] [Indexed: 05/11/2023]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder, and is caused by multiple pathological factors, such as the overproduction of β-amyloid (Aβ) and the hyperphosphorylation of tau. However, there is limited knowledge of the mechanisms underlying AD pathogenesis and no effective biomarker for the early diagnosis of this disorder. Thus in this study, a quantitative phosphoproteomics analysis was performed to evaluate global protein phosphorylation in the hippocampus of Aβ overexpressing APP/PS1 transgenic mice and tau overexpressing MAPT×P301S transgenic mice, two in vivo AD model systems. These animals, up to ten weeks old, do not exhibit cognitive dysfunctions and are widely used to simulate early-stage AD patients. The number of differentially phosphorylated proteins (DPPs) was greater for APP/PS1 transgenic mice than for MAPT×P301S transgenic mice. The function of the DPPs in APP/PS1 transgenic mice was mainly related to synapses, while the function of the DPPs in MAPT×P301S transgenic mice was mainly related to microtubules. In addition, an AD core network was established including seven phosphoproteins differentially expressed in both animal models, and the function of this core network was related to synapses and oxidative stress. The results of this study suggest that Aβ and tau induce different protein phosphorylation profiles in the early stage of AD, leading to the dysfunctions in synapses and microtubule, respectively. And the detection of same DPPs in these animal models might be used for early AD diagnosis.
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Affiliation(s)
- Qiyao Wang
- Translational Medicine Center of Pain, Emotion and Cognition, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, 315211, China
| | - Chenglong Xia
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - An Zhu
- Translational Medicine Center of Pain, Emotion and Cognition, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, 315211, China
| | - Yongjie Bao
- Translational Medicine Center of Pain, Emotion and Cognition, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, 315211, China
| | - Jiani Lu
- Translational Medicine Center of Pain, Emotion and Cognition, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, 315211, China
| | - Yuan Chen
- Translational Medicine Center of Pain, Emotion and Cognition, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, 315211, China
| | - Jiayi Xu
- Translational Medicine Center of Pain, Emotion and Cognition, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, 315211, China
| | - Binbin Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - C Benjamin Naman
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo, 315211, China
| | - Liping Li
- Translational Medicine Center of Pain, Emotion and Cognition, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, 315211, China
| | - Qinwen Wang
- Translational Medicine Center of Pain, Emotion and Cognition, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, 315211, China
| | - Hao Liu
- Translational Medicine Center of Pain, Emotion and Cognition, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, 315211, China
| | - Hongze Liang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China.
| | - Wei Cui
- Translational Medicine Center of Pain, Emotion and Cognition, Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, 315211, China.
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315211, China.
- Ningbo Kangning Hospital, Ningbo University, Ningbo, 315211, China.
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17
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Bardwell L, Thorner J. Mitogen-activated protein kinase (MAPK) cascades-A yeast perspective. Enzymes 2023; 54:137-170. [PMID: 37945169 DOI: 10.1016/bs.enz.2023.07.001] [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: 11/12/2023]
Abstract
Discovery of the class of protein kinase now dubbed a mitogen (or messenger)-activated protein kinase (MAPK) is an illustrative example of how disparate lines of investigation can converge and reveal an enzyme family universally conserved among eukaryotes, from single-celled microbes to humans. Moreover, elucidation of the circuitry controlling MAPK function defined a now overarching principle in enzyme regulation-the concept of an activation cascade mediated by sequential phosphorylation events. Particularly ground-breaking for this field of exploration were the contributions of genetic approaches conducted using several model organisms, but especially the budding yeast Saccharomyces cerevisiae. Notably, examination of how haploid yeast cells respond to their secreted peptide mating pheromones was crucial in pinpointing genes encoding MAPKs and their upstream activators. Fully contemporaneous biochemical analysis of the activities elicited upon stimulation of mammalian cells by insulin and other growth- and differentiation-inducing factors lead eventually to the demonstration that components homologous to those in yeast were involved. Continued studies of these pathways in yeast were integral to other foundational discoveries in MAPK signaling, including the roles of tethering, scaffolding and docking interactions.
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Affiliation(s)
- Lee Bardwell
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA, United States
| | - Jeremy Thorner
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, College of Letters and Science, University of California, Berkeley, Berkeley, CA, United States.
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18
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Wang Y, Liao G, Wu Y, Wang R, Tang DD. The intermediate filament protein nestin serves as a molecular hub for smooth muscle cytoskeletal signaling. Respir Res 2023; 24:157. [PMID: 37316833 DOI: 10.1186/s12931-023-02473-8] [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: 05/02/2023] [Accepted: 06/08/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND The recruitment of the actin-regulatory proteins cortactin and profilin-1 (Pfn-1) to the membrane is important for the regulation of actin cytoskeletal reorganization and smooth muscle contraction. Polo-like kinase 1 (Plk1) and the type III intermediate filament protein vimentin are involved in smooth muscle contraction. Regulation of complex cytoskeletal signaling is not entirely elucidated. The aim of this study was to evaluate the role of nestin (a type VI intermediate filament protein) in cytoskeletal signaling in airway smooth muscle. METHODS Nestin expression in human airway smooth muscle (HASM) was knocked down by specific shRNA or siRNA. The effects of nestin knockdown (KD) on the recruitment of cortactin and Pfn-1, actin polymerization, myosin light chain (MLC) phosphorylation, and contraction were evaluated by cellular and physiological approaches. Moreover, we assessed the effects of non-phosphorylatable nestin mutant on these biological processes. RESULTS Nestin KD reduced the recruitment of cortactin and Pfn-1, actin polymerization, and HASM contraction without affecting MLC phosphorylation. Moreover, contractile stimulation enhanced nestin phosphorylation at Thr-315 and the interaction of nestin with Plk1. Nestin KD also diminished phosphorylation of Plk1 and vimentin. The expression of T315A nestin mutant (alanine substitution at Thr-315) reduced the recruitment of cortactin and Pfn-1, actin polymerization, and HASM contraction without affecting MLC phosphorylation. Furthermore, Plk1 KD diminished nestin phosphorylation at this residue. CONCLUSIONS Nestin is an essential macromolecule that regulates actin cytoskeletal signaling via Plk1 in smooth muscle. Plk1 and nestin form an activation loop during contractile stimulation.
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Affiliation(s)
- Yinna Wang
- Department of Molecular and Cellular Physiology, Albany Medical College, 47 New Scotland Avenue, MC-8, Albany, NY, 12208, USA
| | - Guoning Liao
- Department of Molecular and Cellular Physiology, Albany Medical College, 47 New Scotland Avenue, MC-8, Albany, NY, 12208, USA
| | - Yidi Wu
- Department of Molecular and Cellular Physiology, Albany Medical College, 47 New Scotland Avenue, MC-8, Albany, NY, 12208, USA
| | - Ruping Wang
- Department of Molecular and Cellular Physiology, Albany Medical College, 47 New Scotland Avenue, MC-8, Albany, NY, 12208, USA
| | - Dale D Tang
- Department of Molecular and Cellular Physiology, Albany Medical College, 47 New Scotland Avenue, MC-8, Albany, NY, 12208, USA.
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19
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Kilburn R, Fedosejevs ET, Mehta D, Soleimani F, Ghahremani M, Monaghan J, Thelen JJ, Uhrig RG, Snedden WA, Plaxton WC. Substrate profiling of the Arabidopsis Ca 2+-dependent protein kinase AtCPK4 and its Ricinus communis ortholog RcCDPK1. Plant Sci 2023; 331:111675. [PMID: 36931565 DOI: 10.1016/j.plantsci.2023.111675] [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] [Received: 09/30/2022] [Revised: 03/10/2023] [Accepted: 03/12/2023] [Indexed: 06/18/2023]
Abstract
AtCPK4 and AtCPK11 are Arabidopsis thaliana Ca2+-dependent protein kinase (CDPK) paralogs that have been reported to positively regulate abscisic acid (ABA) signal transduction by phosphorylating ABA-responsive transcription factor-4 (AtABF4). By contrast, RcCDPK1, their closest Ricinus communis ortholog, participates in the control of anaplerotic carbon flux in developing castor oil seeds by catalyzing inhibitory phosphorylation of bacterial-type phosphoenolpyruvate carboxylase at Ser451. LC-MS/MS revealed that AtCPK4 and RcCDPK1 transphosphorylated several common, conserved residues of AtABF4 and its castor ortholog, TRANSCRIPTION FACTOR RESPONSIBLE FOR ABA REGULATON. Arabidopsis atcpk4/atcpk11 mutants displayed an ABA-insensitive phenotype that corroborated the involvement of AtCPK4/11 in ABA signaling. A kinase-client assay was employed to identify additional AtCPK4/RcCDPK1 targets. Both CDPKs were separately incubated with a library of 2095 peptides representative of Arabidopsis protein phosphosites; five overlapping targets were identified including PLANT INTRACELLULAR RAS-GROUP-RELATED LEUCINE-RICH REPEAT PROTEIN-9 (AtPIRL9) and the E3-ubiquitin ligase ARABIDOPSIS TOXICOS EN LEVADURA 6 (AtATL6). AtPIRL9 and AtATL6 residues phosphorylated by AtCPK4/RcCDPK1 conformed to a CDPK recognition motif that was conserved amongst their respective orthologs. Collectively, this study provides evidence for novel AtCPK4/RcCDPK1 substrates, which may help to expand regulatory networks linked to Ca2+- and ABA-signaling, immune responses, and central carbon metabolism.
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Affiliation(s)
- Ryan Kilburn
- Department of Biology, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - Eric T Fedosejevs
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65211, USA
| | - Devang Mehta
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, Alberta, Canada T6G 2E9
| | - Faranak Soleimani
- Department of Biology, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - Mina Ghahremani
- Department of Biology, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - Jacqueline Monaghan
- Department of Biology, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - Jay J Thelen
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65211, USA
| | - R Glen Uhrig
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, Alberta, Canada T6G 2E9
| | - Wayne A Snedden
- Department of Biology, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - William C Plaxton
- Department of Biology, Queen's University, Kingston, Ontario, Canada K7L 3N6.
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20
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Bar-Cohen S, Martínez Quiles ML, Baskin A, Dawud R, Jennings BH, Paroush Z. Normal cell cycle progression requires negative regulation of E2F1 by Groucho during S-phase and its relief at G2-phase. Development 2023:310177. [PMID: 37184159 DOI: 10.1242/dev.201041] [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: 06/15/2022] [Accepted: 05/04/2023] [Indexed: 05/16/2023]
Abstract
The cell cycle depends on a sequence of steps that are triggered and terminated via the synthesis and degradation of phase-specific transcripts and proteins. While much is known about how stage-specific transcription is activated, less is understood about how inappropriate gene expression is suppressed. In this paper we demonstrate that Groucho, the Drosophila orthologue of TLE1 and other related human transcriptional corepressors, regulates normal cell cycle progression in vivo. We show that although Groucho is expressed throughout the cell cycle, its activity is selectively inactivated by phosphorylation, except in S-phase when it negatively regulates E2F1. Constitutive Groucho activity, as well as its depletion and the consequent derepression of e2f1, cause cell cycle phenotypes. Our results suggest that Cdk1 contributes to phase-specific phosphorylation of Groucho in vivo. We propose that Groucho and its orthologues play a role in the metazoan cell cycle that may explain the links between TLE corepressors and several types of human cancer.
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Affiliation(s)
- Shaked Bar-Cohen
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel
| | | | - Alexey Baskin
- Department of Biological Chemistry, The Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ruba Dawud
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel
| | - Barbara H Jennings
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Ze'ev Paroush
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel
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21
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Gunell S, Lempiäinen T, Rintamäki E, Aro EM, Tikkanen M. Enhanced function of non-photoinhibited photosystem II complexes upon PSII photoinhibition. Biochim Biophys Acta Bioenerg 2023; 1864:148978. [PMID: 37100340 DOI: 10.1016/j.bbabio.2023.148978] [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] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 04/28/2023]
Abstract
Light induced photosystem (PS)II photoinhibition inactivates and irreversibly damages the reaction center protein(s) but the light harvesting complexes continue the collection of light energy. Here we addressed the consequences of such a situation on thylakoid light harvesting and electron transfer reactions. For this purpose, Arabidopsis thaliana leaves were subjected to investigation of the function and regulation of the photosynthetic machinery after a distinct portion of PSII centers had experienced photoinhibition in the presence and absence of Lincomycin (Lin), a commonly used agent to block the repair of damaged PSII centers. In the absence of Lin, photoinhibition increased the relative excitation of PSII and decreased NPQ, together enhancing the electron transfer from still functional PSII centers to PSI. In contrast, in the presence of Lin, PSII photoinhibition increased the relative excitation of PSI and led to strong oxidation of the electron transfer chain. We hypothesize that plants are able to minimize the detrimental effects of high-light illumination on PSII by modulating the energy and electron transfer, but lose such a capability if the repair cycle is arrested. It is further hypothesized that dynamic regulation of the LHCII system has a pivotal role in the control of excitation energy transfer upon PSII damage and repair cycle to maintain the photosynthesis safe and efficient.
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Affiliation(s)
- Sanna Gunell
- Molecular Plant Biology, Department of Life Technologies, University of Turku, FI-20014, Turku, Finland
| | - Tapio Lempiäinen
- Molecular Plant Biology, Department of Life Technologies, University of Turku, FI-20014, Turku, Finland
| | - Eevi Rintamäki
- Molecular Plant Biology, Department of Life Technologies, University of Turku, FI-20014, Turku, Finland
| | - Eva-Mari Aro
- Molecular Plant Biology, Department of Life Technologies, University of Turku, FI-20014, Turku, Finland
| | - Mikko Tikkanen
- Molecular Plant Biology, Department of Life Technologies, University of Turku, FI-20014, Turku, Finland.
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22
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Uliana F, Ciuffa R, Mishra R, Fossati A, Frommelt F, Keller S, Mehnert M, Birkeland ES, van Drogen F, Srejic N, Peter M, Tapon N, Aebersold R, Gstaiger M. Phosphorylation-linked complex profiling identifies assemblies required for Hippo signal integration. Mol Syst Biol 2023; 19:e11024. [PMID: 36896621 PMCID: PMC10090947 DOI: 10.15252/msb.202211024] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/11/2023] Open
Abstract
While several computational methods have been developed to predict the functional relevance of phosphorylation sites, experimental analysis of the interdependency between protein phosphorylation and Protein-Protein Interactions (PPIs) remains challenging. Here, we describe an experimental strategy to establish interdependencies between protein phosphorylation and complex formation. This strategy is based on three main steps: (i) systematically charting the phosphorylation landscape of a target protein; (ii) assigning distinct proteoforms of the target protein to different protein complexes by native complex separation (AP-BNPAGE) and protein correlation profiling; and (iii) analyzing proteoforms and complexes in cells lacking regulators of the target protein. We applied this strategy to YAP1, a transcriptional co-activator for the control of organ size and tissue homeostasis that is highly phosphorylated and among the most connected proteins in human cells. We identified multiple YAP1 phosphosites associated with distinct complexes and inferred how both are controlled by Hippo pathway members. We detected a PTPN14/LATS1/YAP1 complex and suggest a model how PTPN14 inhibits YAP1 via augmenting WW domain-dependent complex formation and phosphorylation by LATS1/2.
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Affiliation(s)
- Federico Uliana
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Rodolfo Ciuffa
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ranjan Mishra
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Andrea Fossati
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA
| | - Fabian Frommelt
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Sabrina Keller
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Martin Mehnert
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | | - Frank van Drogen
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Nevena Srejic
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Matthias Peter
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Nicolas Tapon
- Apoptosis and Proliferation Control Laboratory, The Francis Crick Institute, London, UK
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
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23
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Kataya A, Mitchell S, Etman R, Samuel M, Moorhead GB. Peroxisomal protein phosphatase PP2A-B' theta interacts with and piggybacks SINA-like 10 E3 ligase into peroxisomes. Biochem Biophys Res Commun 2023; 644:34-39. [PMID: 36623396 DOI: 10.1016/j.bbrc.2022.12.083] [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: 12/15/2022] [Accepted: 12/30/2022] [Indexed: 01/02/2023]
Abstract
Protein phosphatase 2A (PP2A) is targeted to the plant peroxisome via a C-terminal SSL sequence on its regulatory B' theta (θ) subunit. To date the substrates of peroxisomal PP2A are unknown but are thought to be recruited by the regulatory B'θ subunit. Employing yeast two hybrid screening, we have identified Arabidopsis E3 ligase SINA-like 10 as a B'θ binding partner. The E3 ligase SINA-like 10 was found to harbor the PP2A B'-binding Short Linear interaction Motif or SLiM, LxxIxE. This interaction was further verified both in vitro and in vivo using direct pulldown assays and bimolecular fluorescence complementation. Utilizing peroxisomal targeted and a cytosolic version of B'θ (lacking its C-terminal peroxisomal targeting sequence SSL>) bimolecular fluorescence complementation suggests an interaction to occur in the cytosol followed by piggybacking E3 ligase SINA-like 10 into peroxisomes. These results identify a first peroxisomal PP2A interactor, which also obtains a PP2A B'-binding SLiM.
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Affiliation(s)
- Amr Kataya
- Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada; Department of Chemistry, Bioscience, and Environmental Engineering, University of Stavanger, Stavanger, Norway.
| | - Sierra Mitchell
- Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada
| | - Rasha Etman
- Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada
| | - Marcus Samuel
- Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada
| | - Greg B Moorhead
- Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada.
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24
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Lovinger DM, Roberto M. Synaptic Effects Induced by Alcohol. Curr Top Behav Neurosci 2023:10.1007/7854_2022_412. [PMID: 36765015 PMCID: PMC11104446 DOI: 10.1007/7854_2022_412] [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] [Indexed: 02/12/2023]
Abstract
Ethanol (EtOH) has effects on numerous cellular molecular targets, and alterations in synaptic function are prominent among these effects. Acute exposure to EtOH activates or inhibits the function of proteins involved in synaptic transmission, while chronic exposure often produces opposing and/or compensatory/homeostatic effects on the expression, localization, and function of these proteins. Interactions between different neurotransmitters (e.g., neuropeptide effects on release of small molecule transmitters) can also influence both acute and chronic EtOH actions. Studies in intact animals indicate that the proteins affected by EtOH also play roles in the neural actions of the drug, including acute intoxication, tolerance, dependence, and the seeking and drinking of EtOH. The present chapter is an update of our previous Lovinger and Roberto (Curr Top Behav Neurosci 13:31-86, 2013) chapter and reviews the literature describing these acute and chronic synaptic effects of EtOH with a focus on adult animals and their relevance for synaptic transmission, plasticity, and behavior.
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Affiliation(s)
- David M Lovinger
- Laboratory for Integrative Neuroscience, National Institute on Alcohol Abuse and Alcoholism (NIAAA), Rockville, MD, USA
| | - Marisa Roberto
- Molecular Medicine Department, Scripps Research Institute, La Jolla, CA, USA.
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25
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Arang N, Lubrano S, Rigiracciolo DC, Nachmanson D, Lippman SM, Mali P, Harismendy O, Gutkind JS. Whole-genome CRISPR screening identifies PI3K/AKT as a downstream component of the oncogenic GNAQ-focal adhesion kinase signaling circuitry. J Biol Chem 2023; 299:102866. [PMID: 36596361 DOI: 10.1016/j.jbc.2022.102866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 01/01/2023] Open
Abstract
G proteins and G protein-coupled receptors activate a diverse array of signal transduction pathways that promote cell growth and survival. Indeed, hot spot-activating mutations in GNAQ/GNA11, encoding Gαq proteins, are known to be driver oncogenes in uveal melanoma (UM), for which there are limited effective therapies currently available. Focal adhesion kinase (FAK) has been recently shown to be a central mediator of Gαq-driven signaling in UM, and as a result, is being explored clinically as a therapeutic target for UM, both alone and in combination therapies. Despite this, the repertoire of Gαq/FAK-regulated signaling mechanisms have not been fully elucidated. Here, we used a whole-genome CRISPR screen in GNAQ-mutant UM cells to identify mechanisms that, when overactivated, lead to reduced sensitivity to FAK inhibition. In this way, we found that the PI3K/AKT signaling pathway represented a major resistance driver. Our dissection of the underlying mechanisms revealed that Gαq promotes PI3K/AKT activation via a conserved signaling circuitry mediated by FAK. Further analysis demonstrated that FAK activates PI3K through the association and tyrosine phosphorylation of the p85 regulatory subunit of PI3K and that UM cells require PI3K/AKT signaling for survival. These findings establish a novel link between Gαq-driven signaling and the stimulation of PI3K as well as demonstrate aberrant activation of signaling networks underlying the growth and survival of UM and other Gαq-driven malignancies.
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26
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Mehta V, Decan N, Ooi S, Gaudreau-Lapierre A, Copeland JW, Trinkle-Mulcahy L. SPECC1L binds the myosin phosphatase complex MYPT1/PP1β and can regulate its distribution between microtubules and filamentous actin. J Biol Chem 2023; 299:102893. [PMID: 36634848 PMCID: PMC9929477 DOI: 10.1016/j.jbc.2023.102893] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 01/11/2023] Open
Abstract
The subcellular localization, activity , and substrate specificity of the serine/threonine protein phosphatase 1 catalytic subunit (PP1cat) is mediated through its dynamic association with regulatory subunits in holoenzyme complexes. While some functional overlap is observed for the three human PP1cat isoforms, they also show distinct targeting based on relative preferences for specific regulatory subunits. A well-known example is the preferential association of MYPT1 with PP1β in the myosin phosphatase complex. In smooth muscle, MYPT1/PP1β counteracts the muscle contraction induced by phosphorylation of the light chains of myosin by the myosin light chain kinase. This phosphatase complex is also found in nonmuscle cells, where it is targeted to both myosin and nonmyosin substrates and contributes to regulation of the balance of cytoskeletal structure and motility during cell migration and division. Although it remains unclear how MYPT1/PP1β traffics between microtubule- and actin-associated substrates, our identification of the microtubule- and actin-binding protein SPECC1L in both the PP1β and MYPT1 interactomes suggests that it is the missing link. Our validation of their association using coimmunoprecipitation and proximity biotinylation assays, together with the strong overlap that we observed for the SPECC1L and MYPT1 interactomes, confirmed that they exist in a stable complex in the cell. We further showed that SPECC1L binds MYPT1 directly and that it can impact the balance of the distribution of the MYPT1/PP1β complex between the microtubule and filamentous actin networks.
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Affiliation(s)
- Virja Mehta
- Department of Cellular and Molecular Medicine, University of Ottawa, Faculty of Medicine, Ottawa, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Nathalie Decan
- Department of Cellular and Molecular Medicine, University of Ottawa, Faculty of Medicine, Ottawa, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Sarah Ooi
- Department of Cellular and Molecular Medicine, University of Ottawa, Faculty of Medicine, Ottawa, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Antoine Gaudreau-Lapierre
- Department of Cellular and Molecular Medicine, University of Ottawa, Faculty of Medicine, Ottawa, Canada,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - John W. Copeland
- Department of Cellular and Molecular Medicine, University of Ottawa, Faculty of Medicine, Ottawa, Canada
| | - Laura Trinkle-Mulcahy
- Department of Cellular and Molecular Medicine, University of Ottawa, Faculty of Medicine, Ottawa, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada.
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27
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Chen J, Huang Y, Gan WB, Tsai YH. Selective Inhibition of Kinase Activity in Mammalian Cells by Bioorthogonal Ligand Tethering. Methods Mol Biol 2023; 2676:215-232. [PMID: 37277636 DOI: 10.1007/978-1-0716-3251-2_16] [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: 06/07/2023]
Abstract
Enzymes are critical for cellular functions, and malfunction of enzymes is closely related to many human diseases. Inhibition studies can help in deciphering the physiological roles of enzymes and guide conventional drug development programs. In particular, chemogenetic approaches enabling rapid and selective inhibition of enzymes in mammalian cells have unique advantages. Here, we describe the procedure for rapid and selective inhibition of a kinase in mammalian cells by bioorthogonal ligand tethering (iBOLT). Briefly, a non-canonical amino acid bearing a bioorthogonal group is genetically incorporated into the target kinase by genetic code expansion. The sensitized kinase can react with a conjugate containing a complementary biorthogonal group linked with a known inhibitory ligand. As a result, tethering of the conjugate to the target kinase allows selective inhibition of protein function. Here, we demonstrate this method by using cAMP-dependent protein kinase catalytic subunit alpha (PKA-Cα) as the model enzyme. The method should be applicable to other kinases, enabling their rapid and selective inhibition.
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Affiliation(s)
- Jinghao Chen
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Shenzhen, China
| | - Yang Huang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Wen-Biao Gan
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yu-Hsuan Tsai
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China.
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28
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Chen L. Emerging roles of protein phosphorylation in regulation of stomatal development. J Plant Physiol 2023; 280:153882. [PMID: 36493667 DOI: 10.1016/j.jplph.2022.153882] [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] [Received: 07/28/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Stomata, tiny epidermal spores, control gas exchange between plants and their external environment, thereby playing essential roles in plant development and physiology. Stomatal development requires rapid regulation of components in signaling pathways to respond flexibly to numerous intrinsic and extrinsic signals. In support of this, reversible phosphorylation, which is particularly suitable for rapid signal transduction, has been implicated in this process. This review highlights the current understanding of the essential roles of reversible phosphorylation in the regulation of stomatal development, most of which comes from the dicot Arabidopsis thaliana. Protein phosphorylation tightly controls the activity of SPEECHLESS (SPCH)-SCREAM (SCRM), the stomatal lineage switch, and the activity of several mitogen-activated protein kinases and receptor kinases upstream of SPCH-SCRM, thereby regulating stomatal cell differentiation and patterning. In addition, protein phosphorylation is involved in the establishment of cell polarity during stomatal asymmetric cell division. Finally, cyclin-dependent kinase-mediated protein phosphorylation plays essential roles in cell cycle control during stomatal development.
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Affiliation(s)
- Liang Chen
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, PR China.
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29
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Broucke E, Rolland F, Crepin N. Fast Identification of In Vivo Protein Phosphorylation Events Using Transient Expression in Leaf Mesophyll Protoplasts and Phos-tag TM SDS-PAGE. Methods Mol Biol 2023; 2642:215-231. [PMID: 36944881 DOI: 10.1007/978-1-0716-3044-0_12] [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: 03/23/2023]
Abstract
Phosphorylation/dephosphorylation is a key posttranslational mechanism for signal transduction and amplification. Several techniques exist for assessing protein phosphorylation status, but each has its own drawbacks. The fast, straightforward, and low-tech approach described here uses transient overexpression of peptide-tagged proteins in Arabidopsis leaf mesophyll protoplasts and immunoblotting with Phos-tag™ SDS-PAGE and commercial anti-tag antibodies. We illustrate this with two relevant examples related to the SnRK1 protein kinase, which mediates metabolic stress signaling: Arabidopsis thaliana SnRK1 activation by T-loop (auto-)phosphorylation and SnRK1 phosphorylation of the Arabidopsis RAV1 transcription factor, which is involved in seed germination and early seedling development.
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Affiliation(s)
- Ellen Broucke
- Plant Metabolic Signaling Lab, Biology Department, KU Leuven, Heverlee, Leuven, Belgium.
- KU Leuven Plant Institute (LPI), KU Leuven, Heverlee, Leuven, Belgium.
| | - Filip Rolland
- Plant Metabolic Signaling Lab, Biology Department, KU Leuven, Heverlee, Leuven, Belgium.
- KU Leuven Plant Institute (LPI), KU Leuven, Heverlee, Leuven, Belgium.
| | - Nathalie Crepin
- Plant Metabolic Signaling Lab, Biology Department, KU Leuven, Heverlee, Leuven, Belgium.
- KU Leuven Plant Institute (LPI), KU Leuven, Heverlee, Leuven, Belgium.
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Xu C, Zhu M, Zhao S, Zhang X, Wang Y, Liu M. Mutation of S461, in the GOLGA3 phosphorylation site, does not affect mouse spermatogenesis. PeerJ 2023; 11:e15133. [PMID: 37090114 PMCID: PMC10117384 DOI: 10.7717/peerj.15133] [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: 12/08/2022] [Accepted: 03/06/2023] [Indexed: 04/25/2023] Open
Abstract
Background Golgin subfamily A member 3 (Golga3), a member of the golgin subfamily A, is highly expressed in mouse testis. The GOLGA3 protein, which contains eight phosphorylation sites, is involved in protein transport, cell apoptosis, Golgi localization, and spermatogenesis. Although it has been previously reported that nonsense mutations in Golga3 cause multiple defects in spermatogenesis, the role of Golga3 in the testis is yet to be clarified. Methods Immunofluorescence co-localization in cells and protein dephosphorylation experiments were performed. Golga3 S461L/S461Lmice were generated using cytosine base editors. Fertility tests as well as computer-assisted sperm analysis (CASA) were then performed to investigate sperm motility within caudal epididymis. Histological and immunofluorescence staining were used to analyze testis and epididymis phenotypes and TUNEL assays were used to measure germ cell apoptosis in spermatogenic tubules. Results Immunofluorescence co-localization showed reduced Golgi localization of GOLGA3S465L with some protein scattered in the cytoplasm of HeLa cells .In addition, protein dephosphorylation experiments indicated a reduced band shift of the dephosphorylated GOLGA3S465L, confirming S461 as the phosphorylation site. Golga3 is an evolutionarily conserved gene and Golga3 S461L/S461Lmice were successfully generated using cytosine base editors. These mice had normal fertility and spermatozoa, and did not differ significantly from wild-type mice in terms of spermatogenesis and apoptotic cells in tubules. Conclusions Golga3 was found to be highly conserved in the testis, and GOLGA3 was shown to be involved in spermatogenesis, especially in apoptosis and Golgi complex-mediated effects. Infertility was also observed in Golga3 KO male mice. Although GOLGA3S465Lshowed reduced localization in the Golgi with some expression in the cytoplasm, this abnormal localization did not adversely affect fertility or spermatogenesis in male C57BL/6 mice. Therefore, mutation of the S461 GOLGA3 phosphorylation site did not affect mouse spermatogenesis.
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Affiliation(s)
- Changtong Xu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Mingcong Zhu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Shuqin Zhao
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Xin Zhang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Ying Wang
- State Key Laboratory of Reproductive Medicine, Department of Reproduction, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Mingxi Liu
- State Key Laboratory of Reproductive Medicine, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Nanjing, China
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Orlando E, Medo M, Bensimon A, Quintin A, Riedo R, Roth SM, Riether C, Marti TM, Aebersold DM, Medová M, Aebersold R, Zimmer Y. An oncogene addiction phosphorylation signature and its derived scores inform tumor responsiveness to targeted therapies. Cell Mol Life Sci 2022; 80:6. [PMID: 36494469 DOI: 10.1007/s00018-022-04634-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 11/08/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022]
Abstract
PURPOSE Oncogene addiction provides important therapeutic opportunities for precision oncology treatment strategies. To date the cellular circuitries associated with driving oncoproteins, which eventually establish the phenotypic manifestation of oncogene addiction, remain largely unexplored. Data suggest the DNA damage response (DDR) as a central signaling network that intersects with pathways associated with deregulated addicting oncoproteins with kinase activity in cancer cells. EXPERIMENTAL DESIGN: We employed a targeted mass spectrometry approach to systematically explore alterations in 116 phosphosites related to oncogene signaling and its intersection with the DDR following inhibition of the addicting oncogene alone or in combination with irradiation in MET-, EGFR-, ALK- or BRAF (V600)-positive cancer models. An NSCLC tissue pipeline combining patient-derived xenografts (PDXs) and ex vivo patient organotypic cultures has been established for treatment responsiveness assessment. RESULTS We identified an 'oncogene addiction phosphorylation signature' (OAPS) consisting of 8 protein phosphorylations (ACLY S455, IF4B S422, IF4G1 S1231, LIMA1 S490, MYCN S62, NCBP1 S22, P3C2A S259 and TERF2 S365) that are significantly suppressed upon targeted oncogene inhibition solely in addicted cell line models and patient tissues. We show that the OAPS is present in patient tissues and the OAPS-derived score strongly correlates with the ex vivo responses to targeted treatments. CONCLUSIONS We propose a score derived from OAPS as a quantitative measure to evaluate oncogene addiction of cancer cell samples. This work underlines the importance of protein phosphorylation assessment for patient stratification in precision oncology and corresponding identification of tumor subtypes sensitive to inhibition of a particular oncogene.
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Paulson JR, Vander Mause ER, Dillinger E, Luedeman ME, Usman B. Ellman's reagent prevents dephosphorylation of histones during isolation of mitotic chromosomes. Chromosome Res 2022; 30:351-359. [PMID: 36399199 DOI: 10.1007/s10577-022-09709-1] [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: 08/16/2022] [Revised: 10/21/2022] [Accepted: 10/27/2022] [Indexed: 11/19/2022]
Abstract
Histones H1 and H3 are highly phosphorylated in mitotic HeLa cells but are rapidly dephosphorylated by endogenous protein phosphatases during the isolation of metaphase chromosomes. We show that this dephosphorylation can be prevented by including the sulfhydryl reagent 5,5'-dithiobis-(2-nitrobenzoate) (Ellman's reagent, or DTNB) in the isolation buffer. The minimal amount of DTNB required is approximately stoichiometric with the number of sulfhydryl groups in the lysate. Inhibition of the protein phosphatases can subsequently be reversed by treatment with dithiothreitol or 2-mercaptoethanol. DTNB is compatible with the isolation of either metaphase chromosome clusters or individual metaphase chromosomes. It should be useful in investigations of the structure and biochemistry of chromatin and chromosomes and in the study of possible functions for mitotic histone phosphorylation.
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Affiliation(s)
- James R Paulson
- Department of Chemistry, University of Wisconsin Oshkosh, Oshkosh, WI, 54901, USA.
| | - Erica R Vander Mause
- Department of Chemistry, University of Wisconsin Oshkosh, Oshkosh, WI, 54901, USA
- , A2 Biotherapeutics, Agoura Hills, CA, 91301, USA
| | - Elizabeth Dillinger
- Department of Chemistry, University of Wisconsin Oshkosh, Oshkosh, WI, 54901, USA
- Division of Nephrology and Hypertension, Mayo Clinic College of Medicine and Science, 200 First Street SW, Rochester, MN, 55905, USA
| | - Megan E Luedeman
- Department of Chemistry, University of Wisconsin Oshkosh, Oshkosh, WI, 54901, USA
- 32-038 Lineberger Comprehensive Cancer Center, 450 West Drive, Chapel Hill, NC, 27599, USA
| | - Bakhtawar Usman
- Department of Chemistry, University of Wisconsin Oshkosh, Oshkosh, WI, 54901, USA
- Clarity Clinic-Lakeview, 3665 N. Broadway, Chicago, IL, 60613, USA
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Chrispell JD, Xiong Y, Weiss ER. Grk7 but not Grk1 undergoes cAMP-dependent phosphorylation in zebrafish cone photoreceptors and mediates cone photoresponse recovery to elevated cAMP. J Biol Chem 2022; 298:102636. [PMID: 36273582 PMCID: PMC9692042 DOI: 10.1016/j.jbc.2022.102636] [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: 07/19/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 11/07/2022] Open
Abstract
In the vertebrate retina, phosphorylation of photoactivated visual pigments in rods and cones by G protein-coupled receptor kinases (GRKs) is essential for sustained visual function. Previous in vitro analysis demonstrated that GRK1 and GRK7 are phosphorylated by PKA, resulting in a reduced capacity to phosphorylate rhodopsin. In vivo observations revealed that GRK phosphorylation occurs in the dark and is cAMP dependent. In many vertebrates, including humans and zebrafish, GRK1 is expressed in both rods and cones while GRK7 is expressed only in cones. However, mice express only GRK1 in both rods and cones and lack GRK7. We recently generated a mutation in Grk1 that deletes the phosphorylation site, Ser21. This mutant demonstrated delayed dark adaptation in mouse rods but not in cones in vivo, suggesting GRK1 may serve a different role depending upon the photoreceptor cell type in which it is expressed. Here, zebrafish were selected to evaluate the role of cAMP-dependent GRK phosphorylation in cone photoreceptor recovery. Electroretinogram analyses of larvae treated with forskolin show that elevated intracellular cAMP significantly decreases recovery of the cone photoresponse, which is mediated by Grk7a rather than Grk1b. Using a cone-specific dominant negative PKA transgene, we show for the first time that PKA is required for Grk7a phosphorylation in vivo. Lastly, immunoblot analyses of rod grk1a-/- and cone grk1b-/- zebrafish and Nrl-/- mouse show that cone-expressed Grk1 does not undergo cAMP-dependent phosphorylation in vivo. These results provide a better understanding of the function of Grk phosphorylation relative to cone adaptation and recovery.
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Meyers CMG, Burciaga SD, Faulkner B, Kazemi P, Cohn JM, Mansky KC, Jensen ED. Histone deacetylase 5 is a phosphorylation substrate of protein kinase D in osteoclasts. Bone 2022; 159:116393. [PMID: 35318161 PMCID: PMC9035101 DOI: 10.1016/j.bone.2022.116393] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 03/11/2022] [Accepted: 03/16/2022] [Indexed: 11/24/2022]
Abstract
Protein kinase D (PRKD) family kinases are required for formation and function of osteoclasts. However, the substrates of PRKD in osteoclasts are unknown. To identify PRKD-dependent protein phosphorylation in osteoclasts, we performed a quantitative LC-MS/MS phosphoproteomics screen for proteins showing differential phosphorylation in osteoclasts after treatment with the PRKD inhibitor CRT0066101. We identified 757 phosphopeptides showing significant changes following PRKD inhibition. Among the changes, we found a group of 13 proteins showing decreased phosphorylation at PRKD consensus phosphorylation motifs. This group includes histone deacetylase 5 (HDAC5), which is a previously validated PRKD target. Considering this known interaction, work suggesting HDACs may be important regulators of osteoclasts, and studies suggesting potential functional redundancy between HDACs, we further investigated the relationship between PRKD and class IIa HDACs in osteoclasts. We confirmed that CRT0066101 inhibits phosphorylation of endogenous HDAC5 and to a lesser extent HDAC4, whereas HDAC7 phosphorylation was not affected. Osteoclast cultures from Hdac5 global knockout mice displayed impaired differentiation and reduced ability to resorb bone, while conditional knockout of Hdac4 in osteoclasts showed no phenotype in vitro or in vivo. The inhibitory effect of CRT0066101 was reduced in Hdac5 KO osteoclasts. Together these data indicate that the PRKD/HDAC5 axis contributes to osteoclast formation in vitro and suggest that this pathway may contribute to regulation of skeletal dynamics in vivo.
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Affiliation(s)
- Carina Mello Guimaraes Meyers
- Department of Diagnostic & Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, MN 55455, USA
| | - Samuel D Burciaga
- Department of Diagnostic & Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, MN 55455, USA
| | - Bora Faulkner
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Parandis Kazemi
- Department of Diagnostic & Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, MN 55455, USA
| | - Jacob M Cohn
- Department of Diagnostic & Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, MN 55455, USA
| | - Kim C Mansky
- Department of Developmental and Surgical Sciences, University of Minnesota School of Dentistry, Minneapolis, MN 55455, USA
| | - Eric D Jensen
- Department of Diagnostic & Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, MN 55455, USA.
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Lyons SP, Wilson RJ, Muoio DM, Grimsrud PA. Proteomics and phosphoproteomics datasets of a muscle-specific STIM1 loss-of-function mouse model. Data Brief 2022; 42:108051. [PMID: 35345842 PMCID: PMC8956960 DOI: 10.1016/j.dib.2022.108051] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/04/2022] [Indexed: 11/01/2022] Open
Abstract
STIM1 is an ER/SR transmembrane protein that interacts with ORAI1 to activate store operated Ca2+ entry (SOCE) upon ER/SR depletion of calcium. Normally highly expressed in skeletal muscle, STIM1 deficiency causes significant changes to mitochondrial ultrastructure that do not occur with loss of ORAI1 or other components of SOCE. The datasets in this article are from large-scale proteomics and phosphoproteomics experiments in an inducible mouse model of skeletal muscle-specific STIM1 knock out (KO). These data reveal statistically significant changes in the relative abundance of specific proteins and sites of protein phosphorylation in STIM1 KO gastrocnemius. Protein samples from five biological replicates of each condition (+/- STIM1) were enzymatically digested, the resulting peptides labeled with tandem mass tag (TMT) reagents, mixed, and fractionated. Phosphopeptides were enriched and a small amount of each input retained for protein abundance analysis. All phosphopeptide and input fractions were analyzed by nano LC-MS/MS on a Q Exactive Plus Orbitrap mass spectrometer, searched with Proteome Discoverer software, and processed with in-house R-scripts for data normalization and statistical analysis. Article published in Molecular Metabolism [1].
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Affiliation(s)
- Scott P. Lyons
- Duke Molecular Physiology Institute, and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, NC 27701, USA
| | - Rebecca J. Wilson
- Duke Molecular Physiology Institute, and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, NC 27701, USA
| | - Deborah M. Muoio
- Duke Molecular Physiology Institute, and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, NC 27701, USA
- Department of Medicine, Division of Endocrinology, Metabolism and Nutrition, Duke University School of Medicine, Durham, NC 27701, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27701, USA
| | - Paul A. Grimsrud
- Duke Molecular Physiology Institute, and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, NC 27701, USA
- Department of Medicine, Division of Endocrinology, Metabolism and Nutrition, Duke University School of Medicine, Durham, NC 27701, USA
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Horemans S, Pitoulias M, Holland A, Pateau E, Lechaplais C, Ekaterina D, Perret A, Soultanas P, Janniere L. Pyruvate kinase, a metabolic sensor powering glycolysis, drives the metabolic control of DNA replication. BMC Biol 2022; 20:87. [PMID: 35418203 PMCID: PMC9009071 DOI: 10.1186/s12915-022-01278-3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/11/2022] [Indexed: 12/04/2022] Open
Abstract
Background In all living organisms, DNA replication is exquisitely regulated in a wide range of growth conditions to achieve timely and accurate genome duplication prior to cell division. Failures in this regulation cause DNA damage with potentially disastrous consequences for cell viability and human health, including cancer. To cope with these threats, cells tightly control replication initiation using well-known mechanisms. They also couple DNA synthesis to nutrient richness and growth rate through a poorly understood process thought to involve central carbon metabolism. One such process may involve the cross-species conserved pyruvate kinase (PykA) which catalyzes the last reaction of glycolysis. Here we have investigated the role of PykA in regulating DNA replication in the model system Bacillus subtilis. Results On analysing mutants of the catalytic (Cat) and C-terminal (PEPut) domains of B. subtilis PykA we found replication phenotypes in conditions where PykA is dispensable for growth. These phenotypes are independent from the effect of mutations on PykA catalytic activity and are not associated with significant changes in the metabolome. PEPut operates as a nutrient-dependent inhibitor of initiation while Cat acts as a stimulator of replication fork speed. Disruption of either PEPut or Cat replication function dramatically impacted the cell cycle and replication timing even in cells fully proficient in known replication control functions. In vitro, PykA modulates activities of enzymes essential for replication initiation and elongation via functional interactions. Additional experiments showed that PEPut regulates PykA activity and that Cat and PEPut determinants important for PykA catalytic activity regulation are also important for PykA-driven replication functions. Conclusions We infer from our findings that PykA typifies a new family of cross-species replication control regulators that drive the metabolic control of replication through a mechanism involving regulatory determinants of PykA catalytic activity. As disruption of PykA replication functions causes dramatic replication defects, we suggest that dysfunctions in this new family of universal replication regulators may pave the path to genetic instability and carcinogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01278-3.
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Affiliation(s)
- Steff Horemans
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Matthaios Pitoulias
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Alexandria Holland
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Emilie Pateau
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Christophe Lechaplais
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Dariy Ekaterina
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Alain Perret
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Panos Soultanas
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - Laurent Janniere
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France.
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Ji L, Wang Z, Ji Y, Wang H, Guo M, Zhang L, Wang P, Xiao H. Proteomics and phosphoproteomics analysis of tissues for the reoccurrence prediction of colorectal cancer. Expert Rev Proteomics 2022; 19:263-277. [PMID: 36308708 DOI: 10.1080/14789450.2022.2142566] [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: 12/24/2022]
Abstract
BACKGROUND Many stage II/III colorectal cancer (CRC) patients may relapse after routine treatments. Aberrant phosphorylation can regulate pathophysiological processes of tumors, and finding characteristic protein phosphorylation is an efficient approach for the prediction of CRC relapse. RESEARCH DESIGN AND METHODS We compared the tissue proteome and phosphoproteome of stage II/III CRC patients between the relapsed group (n = 5) and the non-relapsed group (n = 5). Phosphopeptides were enriched with Ti4+-IMAC material. We utilized label-free quantification-based proteomics to screen differentially expressed proteins and phosphopeptides between the two groups. Gene Ontology (GO) analysis and Ingenuity Pathway Analysis (IPA) were used for bioinformatics analysis. RESULTS The immune response of the relapsed group (Z-score -2.229) was relatively poorer than that of the non-relapsed group (Z-score 1.982), while viability of tumor was more activated (Z-score 2.895) in the relapsed group, which might cause increased relapse risk. The phosphorylation degrees of three phosphosites (phosphosite 1362 of TP53BP1, phosphosite 809 of VCL and phosphosite 438 of STK10) might be reliable prognostic biomarkers. CONCLUSIONS Some promising proteins and phosphopeptides were discovered to predict the relapse risk in postoperative follow-ups.
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Affiliation(s)
- Liyun Ji
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 200240, Shanghai, China
| | - Zeyuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 200240, Shanghai, China
| | - Yin Ji
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Pharmaceutical Co Ltd 210042, Nanjing, China
| | - Huiyu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 200240, Shanghai, China
| | - Miao Guo
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 200240, Shanghai, China
| | - Lu Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 200240, Shanghai, China
| | - Peng Wang
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Pharmaceutical Co Ltd 210042, Nanjing, China
| | - Hua Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 200240, Shanghai, China
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Weng K, Li Y, Huo W, Zhang Y, Cao Z, Zhang Y, Xu Q, Chen G. Comparative phosphoproteomic provides insights into meat quality differences between slow- and fast-growing broilers. Food Chem 2022; 373:131408. [PMID: 34710681 DOI: 10.1016/j.foodchem.2021.131408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 06/29/2021] [Revised: 09/29/2021] [Accepted: 10/12/2021] [Indexed: 11/29/2022]
Abstract
The selection of broilers for augmented growth rate and breast yield has been accompanied by deterioration in meat quality. To characterise the meat quality differences between slow- (SG) and fast-growing broilers (FG), Xueshan and Ross 308 chickens were employed to determine the mechanisms causing these differences. SG meat was found to display more redness and yellowness, higher shear force, pH24h, and protein content, with lower intramuscular fat (IMF) content than FG meat. Further, based on comparative phosphoproteomic analysis (SG/FG), upregulated phosphorylated myofibrillar proteins resulted in larger fibres, which contributed to lower pressing loss and tenderness. The phosphoproteins of glycolytic enzymes, phosphorylase kinases, and calcium-related proteins were significantly downregulated, which reduced the acidity of the meat. SLC7A5 at Ser21, MRC2 at Ser1359 and CRAT at Ser341, AUP1 at Ser377 positively affected protein and IMF deposition, respectively. Together, these phosphoproteins elicit vital information for the genetic improvement of chicken meat quality.
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Affiliation(s)
- Kaiqi Weng
- Jiangsu Key Laboratory for Animal Genetic, Breeding and Molecular Design, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yi Li
- Jiangsu Key Laboratory for Animal Genetic, Breeding and Molecular Design, Yangzhou University, Yangzhou, Jiangsu, China
| | - Weiran Huo
- Jiangsu Key Laboratory for Animal Genetic, Breeding and Molecular Design, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yu Zhang
- Jiangsu Key Laboratory for Animal Genetic, Breeding and Molecular Design, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhengfeng Cao
- Jiangsu Key Laboratory for Animal Genetic, Breeding and Molecular Design, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yang Zhang
- Jiangsu Key Laboratory for Animal Genetic, Breeding and Molecular Design, Yangzhou University, Yangzhou, Jiangsu, China
| | - Qi Xu
- Jiangsu Key Laboratory for Animal Genetic, Breeding and Molecular Design, Yangzhou University, Yangzhou, Jiangsu, China.
| | - Guohong Chen
- Jiangsu Key Laboratory for Animal Genetic, Breeding and Molecular Design, Yangzhou University, Yangzhou, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Jiangsu, Yangzhou, China.
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Pan J, Zhao S, He L, Zhang M, Li C, Huang S, Wang J, Jin G. Promotion effect of salt on intramuscular neutral lipid hydrolysis during dry-salting process of porcine (biceps femoris) muscles by inducing phosphorylation of ATGL, HSL and their regulatory proteins of Perilipin1, ABHD5 and G0S2. Food Chem 2022; 373:131597. [PMID: 34815115 DOI: 10.1016/j.foodchem.2021.131597] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 09/22/2021] [Revised: 10/21/2021] [Accepted: 11/10/2021] [Indexed: 12/16/2022]
Abstract
Towards a better understanding of the formation mechanism of salt on intramuscular triglyceride (TG) hydrolysis occurring in biceps femoris (BF) muscles during dry-salting process, the changes of TG hydrolysis, TG hydrolysis activity and phosphorylation of adipose triglyceride lipase (ATGL) and hormone sensitive lipase (HSL) as well as their regulatory proteins (Perilipin1, ABHD5, G0S2) with different salt content (0%, 1%, 3%, 5%) and salting time (the first and third day) were analyzed. The results showed that dry-salting significantly increased the TG hydrolase activity and hydrolysis extent with salting process proceed (P < 0.05), especially upon the treatment with 3% amount of salt. The SDS-PAGE and Western-blot results further demonstrated that the promotion of salt on TG hydrolysis in intramuscular adipocytes was mainly attributed to the activation of protein kinase activity and protein phosphorylation process. Accordingly, the ATGL and HSL were activated, and meanwhile, the TG hydrolysis pivotal switch perilipin1 was also turned on by phosphorylation modification.
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Affiliation(s)
- Jiajing Pan
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China; College of Food Science and Technology of Huazhong Agricultural University, Wuhan 430070, China
| | - Shilin Zhao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China; College of Food Science and Technology of Huazhong Agricultural University, Wuhan 430070, China
| | - Lichao He
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China; College of Food and Biotechnology, Wuhan Institute of Design and Science, Wuhan 430205, China
| | - Min Zhang
- College of Food Science and Technology of Huazhong Agricultural University, Wuhan 430070, China
| | - Chengliang Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China; College of Food Science and Technology of Huazhong Agricultural University, Wuhan 430070, China
| | - Shuangjia Huang
- College of Food Science and Technology of Huazhong Agricultural University, Wuhan 430070, China
| | - Jiamei Wang
- College of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Guofeng Jin
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China; College of Food Science and Technology of Huazhong Agricultural University, Wuhan 430070, China.
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Jiang D, Lv S, Qi R, Han X, Duan L, Liu J. Layer-by-layer assembly of multilayered double hydroxides/polyoxometalate-coated magnetic nanoparticles for highly efficient phosphopeptide enrichment. Mikrochim Acta 2022; 189:156. [PMID: 35347436 DOI: 10.1007/s00604-022-05258-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 03/03/2022] [Indexed: 01/07/2023]
Abstract
A layer-by-layer (LbL) assembly strategy was developed to prepare multilayered double hydroxide/polyoxometalate shell-coated magnetic nanoparticles. The introduction of functional shells not only offered abundant affinity sites of metal oxide and metal ions but also increased the surface area for the contact with targets. By combining the enrichment strategies of immobilized metal ion affinity chromatography and metal oxide affinity chromatography, the nanomaterial can capture phosphopeptides via a synergistic effect. The method presented a low detection limit of 0.1 fmol in combination with matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) analysis. The nanomaterial showed satisfactory selectivity (1:1:5000 M ratio of α-/β-casein/bovine serum albumin), good recovery (92.07%), high adsorption capacity (117.6 mg g-1), and ten times reusability for capturing phosphopeptides.
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Sun X, Li L, Zhang T, Chen L, Zheng Y, Zhou L, Wu B, Liu Z. Identification and characterization of phosphoproteins in the striated and smooth adductor muscles of Yesso scallop Patinopecten yessoensis. Food Chem 2022; 372:131242. [PMID: 34818726 DOI: 10.1016/j.foodchem.2021.131242] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/08/2021] [Accepted: 09/24/2021] [Indexed: 12/17/2022]
Abstract
Many proteins are known to be phosphorylated, affecting important regulatory factors of muscle quality in the aquatic animals. The striated and smooth adductor muscles of Yesso scallop Patinopecten yessoensis were used to investigate muscle texture and identify phosphoproteins by histological methods and phosphoproteomic analysis. Our present study reveals that muscle fiber density is in relation to meat texture of the striated and smooth adductor muscles. The phosphoproteomic analysis has identified 764 down-regulated and 569 up-regulated phosphosites on 743 phosphoproteins in the smooth muscle compared to the striated part. The identification of unique phosphorylation sites in glycolytic enzymes may increase the activity of glycolytic enzymes and the rate of glycolysis in the striated adductor muscle. The present findings will provide new evidences on the role of muscle structure and protein phosphorylation in scallop muscle quality and thus help to develop strategies for improving meat quality of scallop products.
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Kinoshita-Kikuta E, Koike T, Kinoshita E. Recent advances in the Phos-tag technique focused on the analysis of phosphoproteins in a bacterial two-component system. J Proteomics 2022; 252:104429. [PMID: 34813946 DOI: 10.1016/j.jprot.2021.104429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/06/2021] [Accepted: 11/15/2021] [Indexed: 11/21/2022]
Abstract
In a bacterial two-component system (TCS), signals are generally conveyed by means of a His-Asp phosphorelay. Each system consists of a histidine kinase (HK) and its cognate response regulator (RR). The His- and Asp-bound phosphate groups are extremely unstable under acidic conditions easily to be hydrolyzed within a few hours. Because of the labile nature of phosphorylated His and Asp residues, few approaches are available that permit a quantitative analysis of their phosphorylation states in the TCS. Here, we describe that Phos-tag technique is suitable for the quantitative analysis of His- and Asp-phosphorylated proteins. The dynamics of the His-Asp phosphorelay of recombinant TCS derived from Escherichia coli, was examined by Phos-tag SDS-PAGE or Phos-tag fluorescent dye gel staining. The technique permitted not only the quantitative monitoring of the autophosphorylation reactions of HK and RR in the presence of ATP or acetyl phosphate, respectively, but also that of the phosphotransfer reaction from HK to RR in the presence of ATP. Furthermore, we demonstrate profiling of waldiomycin, an HK inhibitor, by using the Phos-tag fluorescent dye gel staining. Consequently, Phos-tag technique provides a simple and convenient approach for screening of HK inhibitors that have potential as new antimicrobial agents. SIGNIFICANCE: Bacterial cells have unique phosphotransfer signaling mechanisms known as two-component systems (TCSs) that permit the organism to sense and respond to various environmental conditions. Each system consists of a histidine kinase (HK) and a response regulator (RR). A typical HK contains an invariant His residue that is autophosphorylated in an ATP-dependent manner. A typical RR has a conserved Asp residue that can acquire a phosphoryl group from its cognate HK. In general, TCS has this type of a His-Asp phosphorelay scheme. Because TCS is also involved in the virulence of pathogens, it is potential targets for novel antibiotics and antivirulence agents. It is, thus, very important to determine HK activity in the bacterial TCS. We believe that our Phos-tag technique provides a simple and convenient approach for drug discovery targeting the bacterial TCS.
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Kinoshita E, Kinoshita-Kikuta E, Koike T. History of Phos-tag technology for phosphoproteomics. J Proteomics 2022; 252:104432. [PMID: 34818585 DOI: 10.1016/j.jprot.2021.104432] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 09/01/2021] [Revised: 11/06/2021] [Accepted: 11/15/2021] [Indexed: 12/14/2022]
Abstract
Phos-tag is a functional molecule that selectively captures a phosphate monoester dianion in neutral aqueous solutions. The affinity of Phos-tag for phosphate monoester dianions is more than 10,000 times greater than that for other anions present in living organisms, such as carboxylic acid anions. We have developed and applied useful techniques for phosphoproteomics based on Phos-tag. This review describes the history of Phos-tag development and outlines three main technologies that have been put to practical use. The first is a technique to separate and concentrate phosphopeptides and phosphoproteins using a Phos-tag derivative with a hydrophilic chromatography carrier (Phos-tag polymer beads). The second is a technology to detect phosphopeptides and phosphoproteins on various arrays using Phos-tag biotin. The third is a technique to separate and detect phosphoproteins by electrophoresis using Phos-tag acrylamide. We hope that these three technologies will make a significant contribution to phosphoproteomics and, ultimately, to life science research. SIGNIFICANCE: The authors found that a dinuclear metal complex of 1,3-bis[bis(pyridin-2-ylmethyl)-amino]propan-2-olato acted as a novel phosphate-binding tag nanomolecule, Phos-tag, in an aqueous solution under near physiological conditions. The metal complex having a vacancy on two metal ions is suitable for the access of a phosphomonoester dianion (R-OPO32-) as a bridging ligand. A dinuclear zinc(II) complex (Zn2+-Phos-tag) strongly binds to a p-nitrophenyl phosphate dianion (Kd = 2.5 × 10-8 M) at a neutral pH. The anion selectivity indexes against SO42-, CH3COO-, Cl-, and the bisphenyl phosphate monoanion at 25 °C are 5.2 × 103, 1.6 × 104, 8.0 × 105, and > 2 × 106, respectively. We have been involved in developing technologies by using the Phos-tag molecule and its derivatives to permit the analysis of phosphorylated biomolecules. To date, Phos-tag technology has contributed to the development of several procedures for phosphoproteomics, including a phosphate-affinity chromatography technique for the separation and enrichment of phosphopeptides and phosphoproteins, a wide variety of microarray/on-chip techniques for the detection of protein phosphorylation, and a phosphate-affinity electrophoresis technique for the detection of shifts in the mobilities of phosphoproteins. In this review article, the authors introduce the impact of Phos-tag-based technological advances for phosphoproteomics.
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Affiliation(s)
- Eiji Kinoshita
- Department of Human Nutrition, Faculty of Human Sciences, Hiroshima Bunkyo University, Kabehigashi 1-2-1, Asakita-ku, Hiroshima 731-0295, Japan.
| | - Emiko Kinoshita-Kikuta
- Department of Functional Molecular Science, Graduate School of Biomedical & Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8553, Japan
| | - Tohru Koike
- Department of Functional Molecular Science, Graduate School of Biomedical & Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8553, Japan
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Pascual J, Kangasjärvi S. Targeted Mass Spectrometry Analysis of Protein Phosphorylation by Selected Ion Monitoring Coupled to Parallel Reaction Monitoring (tSIM/PRM). Methods Mol Biol 2022; 2526:227-240. [PMID: 35657524 DOI: 10.1007/978-1-0716-2469-2_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 06/15/2023]
Abstract
Recent developments in targeted mass spectrometry-based proteomics have provided new methodological solutions for accurate and quantitative analysis of proteins and their posttranslational control, which has significantly advanced our understanding of stress responses in different plant species. Instrumentation allowing high-resolution, accurate-mass (HR/AM) analysis has provided new acquisition strategies for targeted quantitative proteomic analysis by targeted selected ion monitoring (tSIM) and parallel reaction monitoring (PRM). Here we report a sensitive and accurate method for targeted analysis of protein phosphorylation by tSIM coupled to PRM (tSIM/PRM). The tSIM/PRM method takes advantage of HR/AM mass spectrometers and benefits from the combination of highly sensitive precursor ion quantification by tSIM and highly confident peptide identification by spectral library matching in PRM. The detailed protocol describes tSIM/PRM analysis of Arabidopsis thaliana foliar proteins, from the building of a spectral library to sample preparation, mass spectrometry, and data analysis, and provides a methodological approach for specifying the molecular mechanisms of interest.
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Affiliation(s)
- Jesús Pascual
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Saijaliisa Kangasjärvi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FIN-00014 University of Helsinki, Helsinki, Finland.
- Department of Agricultural Sciences, Faculty of Agriculture and Forestry, FIN-00014 University of Helsinki, Helsinki, Finland.
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Yamashita K, Umezawa T. Phosphoproteomic Approaches to Evaluate ABA Signaling. Methods Mol Biol 2022; 2462:163-179. [PMID: 35152388 DOI: 10.1007/978-1-0716-2156-1_13] [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: 06/14/2023]
Abstract
Abscisic acid (ABA) is a major phytohormone that regulates various processes in plants (e.g., seed dormancy/germination, abiotic/biotic stress responses). As protein phosphorylation is involved in the major pathways of ABA signaling, it is necessary to elucidate the phosphosignaling pathway involved in the ABA response. Phosphoproteomics enables determination of the proteins phosphorylated in vivo, and recent studies have applied a comparative phosphoproteomic approach to analyze ABA signaling in plants. For example, ABA-responsive phosphoproteins were identified in barley embryos. Furthermore, a phosphoproteomic approach is useful for screening protein kinase substrates by comparative analysis using kinase knockout mutants. Here, some technical points regarding phosphoproteomic analyses of ABA responses in plants are described.
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Affiliation(s)
- Kota Yamashita
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Taishi Umezawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan.
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan.
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Arumugam K, Shanker RR. Text Mining and Machine Learning Protocol for Extracting Human-Related Protein Phosphorylation Information from PubMed. Methods Mol Biol 2022; 2496:159-177. [PMID: 35713864 DOI: 10.1007/978-1-0716-2305-3_9] [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: 06/15/2023]
Abstract
In the modern health care research, protein phosphorylation has gained an enormous attention from the researchers across the globe and requires automated approaches to process a huge volume of data on proteins and their modifications at the cellular level. The data generated at the cellular level is unique as well as arbitrary, and an accumulation of massive volume of information is inevitable. Biological research has revealed that a huge array of cellular communication aided by protein phosphorylation and other similar mechanisms imply different and diverse meanings. This led to a collection of huge volume of data to understand the biological functions of human evolution, especially for combating diseases in a better way. Text mining, an automated approach to mine the information from an unstructured data, finds its application in extracting protein phosphorylation information from the biomedical literature databases such as PubMed. This chapter outlines a recent text mining protocol that applies natural language parsing (NLP) for named entity recognition and text processing, and support vector machines (SVM), a machine learning algorithm for classifying the processed text related human protein phosphorylation. We discuss on evaluating the text mining system which is the outcome of the protocol on three corpora, namely, human Protein Phosphorylation (hPP) corpus, Integrated Protein Literature Information and Knowledge corpus (iProLink), and Phosphorylation Literature corpus (PLC). We also present a basic understanding on the chemistry and biology that drive the protein phosphorylation process in a human body. We believe that this basic understanding will be useful to advance the existing text mining systems for extracting protein phosphorylation information from PubMed.
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Affiliation(s)
- Krishnamurthy Arumugam
- Department of Management Studies, Coimbatore Institute of Engineering and Technology, Coimbatore, Tamilnadu, India.
| | - Raja Ravi Shanker
- International Business Unit, Alembic Pharmaceuticals Limited, Vadodara, Gujarat, India
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Blea MN, Wallace IS. Analysis of Posttranslational Modifications in Arabidopsis Proteins and Metabolic Pathways Using the FAT-PTM Database. Methods Mol Biol 2022; 2499:145-154. [PMID: 35696079 DOI: 10.1007/978-1-0716-2317-6_7] [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: 06/15/2023]
Abstract
Posttranslational modifications (PTMs) are critical regulators of protein behavior, and over 200 different types of PTMs have been identified. Recent developments in mass spectrometry technology and sample enrichment approaches have led to a massive expansion in the number of identified PTM types and sites within eukaryotic proteins. As these types of data become increasingly available, it is important to develop additional analysis tools and data repositories to investigate PTM cross talk and larger networks of PTMs. Recently, we developed the Functional Analysis Tools for Post-translational Modifications (FAT-PTM) database, which supports data from publicly available proteomic analyses encompassing eight different types of PTMs and over 49,000 PTM sites. In this chapter, we describe the utility of FAT-PTM for analysis of posttranslationally modified proteins in three different contexts. First, a simple protein search tool is available that allows users to investigate proteins in the Arabidopsis proteome to identify types of PTMs that are associated with the query protein as well as quantitative phosphorylation site changes associated with ten different experimental conditions. Second, FAT-PTM contains a metabolic pathway analysis tool to investigate PTMs in the broader context of over 600 different metabolic pathways compiled from the Plant Metabolic Network. Finally, FAT-PTM contains a comodification tool that can be used to identify groups of proteins that are subject to two or more user-defined PTMs. Overall, FAT-PTM provides a user-friendly platform to visualize posttranslationally modified proteins at the individual, metabolic pathway, and PTM cross-talk levels.
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Affiliation(s)
- Madison N Blea
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV, USA
| | - Ian S Wallace
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV, USA.
- Department of Chemistry, University of Nevada, Reno, Reno, NV, USA.
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Duan G, Ma X, Shi Z, Yang Y, Chen H, Huang Q, Yang J. MoSDT1 triggers defense response through modulating phosphorylated proteins in rice. Plant Mol Biol 2022; 108:15-30. [PMID: 34622380 DOI: 10.1007/s11103-021-01201-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 07/05/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
MoSDT1, a rice blast fungus transcription factor, is as an inducer to activate defense response through mainly mediating phosphorylated proteins in rice. Pathogen effector proteins play a dual role in infecting the host or triggering a defense response. Our previous research found a Magnaporthe oryzae effector, MoSDT1, which could activate the rice defense response when it was overexpressed in rice. However, we still know little about the mechanisms on how MoSDT1 in vivo or in vitro influences the resistance ability of rice. Our results showed that decreased ROS and increased lignin contents appeared along with significant upregulation of defense-related genes, raffinose synthesis gene, and phenylalanine ammonialyase gene. Moreover, we revealed that the contents of lignin were increased, which was in accordance with the upregulation of its precursor phenylalanine gene despite the fact that the glutamate-/thiamine-responsive genes were inhibited in MoSDT1 transgenic rice, and these indicated that MoSDT1 triggered the defense system of rice in vivo. Interestingly, in vitro studies, we further found that MoSDT1 induced the defense system by ROS synthesis, callose deposition, PR gene expression and SA/JA synthesis/signal genes using the purified prokaryotic expression system in rice plants. In addition, this defense response was confirmed to be activated by the zinc finger domain of MoSDT1 via prokaryotic expression of MoSDT1 truncated mutants in rice plants. To elucidate the regulative effects of MoSDT1 on protein phosphorylation in rice, phosphoproteome analysis was performed in both MoSDT1-transgenic and wild type rice. We found that MoSDT1 specifically up-regulated the expression levels of a few phosphorylated proteins, which were involved in multiple functions, such as biotic/abiotic stress and growth. In addition, the motifs in these specific proteins ranked the top among the top-five conserved motifs in the MoSDT1-transgenic rice. MoSDT1 played a crucial role in enhancing rice resistance by modulating several genes and signaling pathways.
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Affiliation(s)
- Guihua Duan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, People's Republic of China
- Key Laboratory of Agro-Biodiversity and Pest Management of the Ministry of Education, Yunnan Agricultural University, Kunming, People's Republic of China
| | - Xiaoqing Ma
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, People's Republic of China
- Key Laboratory of Agro-Biodiversity and Pest Management of the Ministry of Education, Yunnan Agricultural University, Kunming, People's Republic of China
| | - Zhufeng Shi
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, People's Republic of China
- Key Laboratory of Agro-Biodiversity and Pest Management of the Ministry of Education, Yunnan Agricultural University, Kunming, People's Republic of China
| | - Yaqiong Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, People's Republic of China
- Key Laboratory of Agro-Biodiversity and Pest Management of the Ministry of Education, Yunnan Agricultural University, Kunming, People's Republic of China
| | - Hongfeng Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, People's Republic of China
- Key Laboratory of Agro-Biodiversity and Pest Management of the Ministry of Education, Yunnan Agricultural University, Kunming, People's Republic of China
| | - Qiong Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, People's Republic of China.
- Key Laboratory of Agro-Biodiversity and Pest Management of the Ministry of Education, Yunnan Agricultural University, Kunming, People's Republic of China.
| | - Jing Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, People's Republic of China.
- Key Laboratory of Agro-Biodiversity and Pest Management of the Ministry of Education, Yunnan Agricultural University, Kunming, People's Republic of China.
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Guevara A, Lugo C, Montilla AJ, Calabokis M, Ferreira J, Martínez JC, Bubis J. Cloning, expression, solubilization, and purification of a functionally active recombinant cAMP-dependent protein kinase catalytic subunit-like protein PKAC1 from Trypanosoma equiperdum. Protein Expr Purif 2021; 192:106041. [PMID: 34953978 DOI: 10.1016/j.pep.2021.106041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/12/2021] [Accepted: 12/20/2021] [Indexed: 11/22/2022]
Abstract
The gene encoding the cAMP-dependent protein kinase (PKA) catalytic subunit-like protein PKAC1 from the Venezuelan TeAp-N/D1 strain of Trypanosoma equiperdum was cloned, and the recombinant TeqPKAC1 protein was overexpressed in bacteria. A major polypeptide with an apparent molecular mass of ∼38 kDa was detected by SDS-polyacrylamide gel electrophoresis, and immunoblotting using antibodies against the human PKA catalytic subunit α. Unfortunately, most of the expressed TeqPKAC1 was highly insoluble. Polypeptides of 36-38 kDa and 45-50 kDa were predominantly seen by immunoblotting in the bacterial particulate and cytosolic fractions, respectively. Since the incorporation of either 4% Triton X-100 or 3% sarkosyl or a mixture of 10 mM MgCl2 and 1 mM ATP (MgATP) improved the solubilization of TeqPKAC1, we used a combination of Triton X-100, sarkosyl and MgATP to solubilize the recombinant protein. TeqPKAC1 was purified by first reconstituting a hybrid holoenzyme between the recombinant protein and a mammalian poly-His-tagged PKA regulatory subunit that was immobilized on a Ni2+-chelating affinity resin, and then by eluting TeqPKAC1 using cAMP. TeqPKAC1 was functional given that it was capable of phosphorylating PKA catalytic subunit substrates, such as kemptide (LRRASLG), histone type II-AS, and the peptide SP20 (TTYADFIASGRTGRRNSIHD), and was inhibited by the peptide IP20 (TTYADFIASGRTGRRNAIHD), which contains the inhibitory motif of the PKA-specific heat-stable inhibitor PKI-α. Optimal enzymatic activity was obtained at 37 °C and pH 8.0-9.0; and the order of effectiveness of nucleotide triphosphates and divalent cations was ATP » GTP ≅ ITP and Mg2+ ≅ Mn2+ ≅ Fe2+ » Ca2+ ≅ Zn2, respectively.
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He P, Jiang F, Wu LF, Zhou X, Lei SF, Deng FY. Why SNP rs3755955 is associated with human bone mineral density? A molecular and cellular study in bone cells. Mol Cell Biochem 2021. [PMID: 34783964 DOI: 10.1007/s11010-021-04292-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 11/04/2021] [Indexed: 11/26/2022]
Abstract
SNP rs3755955 (major/minor allele: G/A) located in Iduronidase-Alpha-L- (IDUA) gene was reported to be significant for human bone mineral density (BMD). This follow-up study was to uncover the underlying association mechanism through molecular and cellular functional assays relevant to bone. We tested the effects of single nucleotide polymorphisms (SNP) rs3755955 (defined allele G as wild-type and allele A as variant-type) on osteoblastic and osteoclastic functions, as well as protein phosphorylation in stably transfected human fetal osteoblast (hFOB) cell and mononuclear-macrophage (RAW264.7) cell. In hFOB cells, transfection with variant-type IDUA significantly decreased osteoblastic gene expression (OPN, COL1A1 and RANKL) (p < 0.01), impeded cell proliferation (p < 0.05), stimulated cell apoptosis (p < 0.001) and decreased ALP enzyme activity, as compared with that of wild-type IDUA transfection. In RAW264.7 cells, transfection with variant-type IDUA significantly inhibited cell apoptosis (p < 0.01), promoted osteoclastic precursor cell migration (p < 0.0001), growth (p < 0.01), osteoclastic gene expression (TRAP, RANK, Inte-αv and Cath-K) (p < 0.05) and TRAP enzyme activity (p < 0.001), as compared with that of wild-type IDUA transfection. In both hFOB and RAW264.7 cells, the total protein and IDUA protein-specific phosphorylation levels were significantly reduced by variant IDUA transfection, as compared with that of wild-type IDUA transfection (p < 0.05). Variant allele A of phosSNP rs3755955 in IDUA gene regulates protein phosphorylation, inhibits osteoblast function and promotes osteoclastic activity. The SNP rs3755955 could alter IDUA protein phosphorylation, significantly regulates human osteoblastic and osteoclastic gene expression, and influences the growth, differentiation and activity of osteoblast and osteoclast, hence to affect BMD.
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