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Chaturvedi M, Raj R, Yadav SK, Srivastava T, Devi S, Dharmadana D, Valéry C, Sharma SK, Kumar D, Priya S. Implications of In Vitro Multi-Serine Phosphorylation of Alpha-Synuclein in Aggregation and Cytotoxicity. ACS Chem Neurosci 2023; 14:3103-3112. [PMID: 37562012 DOI: 10.1021/acschemneuro.3c00234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023] Open
Abstract
Post-translational modifications guide the functional diversity and identity of proteins. Phosphorylation is one such post-translational modification that has been reported in pathological proteins related to various neurodegenerative disorders such as α-synuclein (α-syn) phosphorylation in Parkinson's disease and other synucleinopathies. In α-syn, the phosphorylation has mostly been observed at S129; however, the occurrence of other serine modifications at S9, S42, and S87 is partially explored. In pathogenic conditions, where α-syn is phosphorylated by complex kinase pathways, multi-site modifications may happen and alter the mechanism of α-syn aggregation. Here, using Polo-like kinase 2 and G-protein coupled receptor kinase 4, the in vitro phosphorylation of α-syn was performed, which revealed multi-serine phosphorylation. Mass spectrometry with customized proteolytic digestion showed prominent phosphorylation at S129 and modifications at S87 and S42 with PLK2 and S87 with GRK4. The phosphorylation at the identified serine residues was further validated with NMR and western blotting. Multi-serine phosphorylation aggravates the aggregation potential of monomeric α-syn, seeding capacity, and cytotoxicity in the SH-SY5Y cell line. This study proposes evidence for in vitro multi-site phosphorylation and its significance in α-syn aggregation, toxicity, and related pathogenesis.
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Affiliation(s)
- Minal Chaturvedi
- Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan 31, MG Marg, Lucknow 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- School of Health and Biomedical Science, RMIT University, Bundoora, Victoria 3083, Australia
| | - Ritu Raj
- Centre of BioMedical Research, Sanjay Gandhi Post Graduate Institute of Medical Sciences Campus, Raebareli Road, Lucknow 226014, Uttar Pradesh, India
| | - Sanjeev Kumar Yadav
- Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan 31, MG Marg, Lucknow 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Tulika Srivastava
- Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan 31, MG Marg, Lucknow 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shweta Devi
- Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan 31, MG Marg, Lucknow 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Durga Dharmadana
- School of Health and Biomedical Science, RMIT University, Bundoora, Victoria 3083, Australia
| | - Céline Valéry
- School of Health and Biomedical Science, RMIT University, Bundoora, Victoria 3083, Australia
| | - Sandeep K Sharma
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Food, Drug & Chemical Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan 31, MG Marg, Lucknow 226001, Uttar Pradesh, India
| | - Dinesh Kumar
- Centre of BioMedical Research, Sanjay Gandhi Post Graduate Institute of Medical Sciences Campus, Raebareli Road, Lucknow 226014, Uttar Pradesh, India
| | - Smriti Priya
- Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan 31, MG Marg, Lucknow 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Holani R, Rathnayaka C, Blyth GA, Babbar A, Lahiri P, Young D, Dufour A, Hollenberg MD, McKay DM, Cobo ER. Cathelicidins Induce Toll-Interacting Protein Synthesis to Prevent Apoptosis in Colonic Epithelium. J Innate Immun 2022; 15:204-221. [PMID: 36116427 PMCID: PMC10643900 DOI: 10.1159/000526121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 06/27/2022] [Indexed: 11/17/2023] Open
Abstract
Cathelicidin peptides secreted by leukocytes and epithelial cells are microbicidal but also regulate pathogen sensing via toll-like receptors (TLRs) in the colon by mechanisms that are not fully understood. Herein, analyses with the attaching/effacing pathogen Citrobacter rodentium model of colitis in cathelicidin-deficient (Camp-/-) mice, and colonic epithelia demonstrate that cathelicidins prevent apoptosis by sustaining post-transcriptional synthesis of a TLR adapter, toll-interacting protein (TOLLIP). Cathelicidins induced phosphorylation-activation of epidermal growth factor receptor (EGFR)-kinase, which phosphorylated-inactivated miRNA-activating enzyme Argonaute 2 (AGO2), thus reducing availability of the TOLLIP repressor miRNA-31. Cathelicidins promoted stability of TOLLIP protein via a proteosome-dependent pathway. This cathelicidin-induced TOLLIP upregulation prevented apoptosis in the colonic epithelium by reducing levels of caspase-3 and poly (ADP-ribose) polymerase (PARP)-1 in response to the proinflammatory cytokines, interferon-γ (IFNγ) and tumor necrosis factor-α (TNFα). Further, Camp-/- colonic epithelial cells were more susceptible to apoptosis during C. rodentium infection than wild-type cells. This antiapoptotic effect of cathelicidins, maintaining epithelial TOLLIP protein in the gut, provides insight into cathelicidin's ability to regulate TLR signaling and prevent exacerbated inflammation.
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Affiliation(s)
- Ravi Holani
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Chathurika Rathnayaka
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Graham A.D. Blyth
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Anshu Babbar
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Priyoshi Lahiri
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Daniel Young
- Department of Physiology & Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Antoine Dufour
- Department of Physiology & Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Morley D. Hollenberg
- Department of Physiology & Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Calvin, Phoebe and Joan Snyder Institute for Chronic Disease, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Derek M. McKay
- Department of Physiology & Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Calvin, Phoebe and Joan Snyder Institute for Chronic Disease, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Eduardo R. Cobo
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Calvin, Phoebe and Joan Snyder Institute for Chronic Disease, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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Gomathi K, Rohini M, Vairamani M, Selvamurugan N. Identification and characterization of TGF-β1-responsive Runx2 acetylation sites for matrix Metalloproteinase-13 expression in osteoblastic cells. Biochimie 2022; 201:1-6. [PMID: 35779648 DOI: 10.1016/j.biochi.2022.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/26/2022] [Accepted: 06/27/2022] [Indexed: 11/20/2022]
Abstract
In skeletal tissues, transforming growth factor-beta 1 (TGF-β1) serves a number of activities. For example, in osteoblastic cells, TGF-β1 stimulates the expression of matrix metalloproteinase-13 (MMP-13, a bone remodeling gene), which requires the bone transcription factor Runx2. Although TGF-β1 is known to stimulate Runx2 acetylation, the sites involved in MMP-13 gene activation remain unknown. Mass spectrometry analysis revealed that Runx2 was acetylated at one site (K134) and three sites (K24, K134, and K169) following control and TGF-β1-treatment, respectively, in osteoblastic cells. In addition, we mutated the lysine residues in the Runx2 construct into arginine and transfected the construct into mouse mesenchymal stem cells (C3H10T1/2). Wild-type Runx2 expression and acetylation were significantly increased by TGF-β1-treatment, whereas this effect was decreased in the presence of the Runx2 double mutant construct (K24 + K169) in C3H10T1/2 cells. TGF-β1 enhanced MMP-13 promoter activity in cells transfected with the wild-type Runx2 construct, but this effect was considerably reduced in cells transfected with the Runx2 double mutant construct (K24 + K169), according to a luciferase reporter test. Hence, the stability of Runx2 may be mediated by TGF-β1-induced acetylation at K24 and K169 and is required for MMP-13 expression in osteoblastic cells. These findings add to our knowledge of TGF-β1, Runx2, and MMP-13's physiological roles in bone metabolism.
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Affiliation(s)
- Kanagaraj Gomathi
- Department of Biotechnology, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, 603 203, Tamil Nadu, India
| | - Muthukumar Rohini
- Department of Biotechnology, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, 603 203, Tamil Nadu, India
| | - Mariappan Vairamani
- Department of Biotechnology, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, 603 203, Tamil Nadu, India
| | - Nagarajan Selvamurugan
- Department of Biotechnology, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, 603 203, Tamil Nadu, India.
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Bhagat PK, Verma D, Singh K, Badmi R, Sharma D, Sinha AK. Dynamic Phosphorylation of miRNA Biogenesis Factor HYL1 by MPK3 Involving Nuclear-Cytoplasmic Shuttling and Protein Stability in Arabidopsis. Int J Mol Sci 2022; 23:ijms23073787. [PMID: 35409147 PMCID: PMC8998556 DOI: 10.3390/ijms23073787] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 02/25/2022] [Accepted: 03/04/2022] [Indexed: 11/16/2022] Open
Abstract
MicroRNAs (miRNAs) are one of the prime regulators of gene expression. The recruitment of hyponastic leaves 1 (HYL1), a double-stranded RNA binding protein also termed as DRB1, to the microprocessor complex is crucial for accurate primary-miRNA (pri-miRNA) processing and the accumulation of mature miRNA in Arabidopsis thaliana. In the present study, we investigated the role of the MAP kinase-mediated phosphorylation of AtHYL1 and its sub-cellular activity. AtMPK3 specifically phosphorylates AtHYL1 at the evolutionarily conserved serine-42 present at the N-terminal regions and plays an important role in its nuclear-cytosolic shuttling. Additionally, we identified that AtHYL1 is cleaved by trypsin-like proteases into an N-terminal fragment, which renders its subcellular activities. We, for the first time, report that the dimerization of AtHYL1 not only takes place in the nucleus, but also in the cytosol, and the C-terminal of AtHYL1 has a role in regulating its stability, as well as its subcellular localization. AtHYL1 is hyper-phosphorylated in mpk3 mutants, leading to higher stability and reduced degradation. Our data show that AtMPK3 is a negative regulator of AtHYL1 protein stability and that the AtMPK3-induced phosphorylation of AtHYL1 leads to its protein degradation.
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Affiliation(s)
- Prakash Kumar Bhagat
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110065, India
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Deepanjali Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110065, India
- Department of Plant Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08901, USA
| | - Kirti Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110065, India
| | - Raghuram Badmi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110065, India
- Raghu Ram Badmi, School of Biological, Earth and Environmental Sciences, University College Cork, T23TK30 Cork, Ireland
| | - Deepika Sharma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110065, India
| | - Alok Krishna Sinha
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110065, India
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5
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Palanivel C, Chaudhary N, Seshacharyulu P, Cox JL, Yan Y, Batra SK, Ouellette MM. The GSK3 kinase and LZTR1 protein regulate the stability of Ras family proteins and the proliferation of pancreatic cancer cells. Neoplasia 2022; 25:28-40. [PMID: 35114566 PMCID: PMC8814762 DOI: 10.1016/j.neo.2022.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/30/2021] [Accepted: 01/12/2022] [Indexed: 11/24/2022]
Abstract
Ras family proteins are membrane-bound GTPases that control proliferation, survival, and motility. Many forms of cancers are driven by the acquisition of somatic mutations in a RAS gene. In pancreatic cancer (PC), more than 90% of tumors carry an activating mutation in KRAS. Mutations in components of the Ras signaling pathway can also be the cause of RASopathies, a group of developmental disorders. In a subset of RASopathies, the causal mutations are in the LZTR1 protein, a substrate adaptor for E3 ubiquitin ligases that promote the degradation of Ras proteins. Here, we show that the function of LZTR1 is regulated by the glycogen synthase kinase 3 (GSK3). In PC cells, inhibiting or silencing GSK3 led to a decline in the level of Ras proteins, including both wild type Ras proteins and the oncogenic Kras protein. This decline was accompanied by a 3-fold decrease in the half-life of Ras proteins and was blocked by the inhibition of the proteasome or the knockdown of LZTR1. Irrespective of the mutational status of KRAS, the decline in Ras proteins was observed and accompanied by a loss of cell proliferation. This loss of proliferation was blocked by the knockdown of LZTR1 and could be recapitulated by the silencing of either KRAS or GSK3. These results reveal a novel GSK3-regulated LZTR1-dependent mechanism that controls the stability of Ras proteins and proliferation of PC cells. The significance of this novel pathway to Ras signaling and its contribution to the therapeutic properties of GSK3 inhibitors are both discussed.
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6
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Gomathi K, Rohini M, Partridge NC, Selvamurugan N. Regulation of transforming growth factor-β1-stimulation of Runx2 acetylation for matrix metalloproteinase 13 expression in osteoblastic cells. Biol Chem 2022; 403:305-315. [PMID: 34643076 DOI: 10.1515/hsz-2021-0292] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 09/30/2021] [Indexed: 01/12/2023]
Abstract
Transforming growth factor beta 1 (TGF-β1) functions as a coupling factor between bone development and resorption. Matrix metalloproteinase 13 (MMP13) is important in bone remodeling, and skeletal dysplasia is caused by a deficiency in MMP13 expre-ssion. Runx2, a transcription factor is essential for bone development, and MMP13 is one of its target genes. TGF-β1 promoted Runx2 phosphorylation, which was necessary for MMP13 production in osteoblastic cells, as we previously shown. Since the phosphorylation of some proteins causes them to be degraded by the ubiquitin/proteasome pathway, we hypothesized that TGF-β1 might stabilize the phosphorylated Runx2 protein for its activity by other post-translational modification (PTM). This study demonstrated that TGF-β1-stimulated Runx2 acetylation in rat osteoblastic cells. p300, a histone acetyltransferase interacted with Runx2, and it promoted Runx2 acetylation upon TGF-β1-treatment in these cells. Knockdown of p300 decreased the TGF-β1-stimulated Runx2 acetylation and MMP13 expression in rat osteoblastic cells. TGF-β1-treatment stimulated the acetylated Runx2 bound at the MMP13 promoter, and knockdown of p300 reduced this effect in these cells. Overall, our studies identified the transcriptional regulation of MMP13 by TGF-β1 via Runx2 acetylation in rat osteoblastic cells, and these findings contribute to the knowledge of events presiding bone metabolism.
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Affiliation(s)
- Kanagaraj Gomathi
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - Muthukumar Rohini
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - Nicola C Partridge
- Department of Molecular Pathobiology, New York University College Dentistry, New York, NY, USA
| | - Nagarajan Selvamurugan
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
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Roth A, Gihring A, Göser F, Peifer C, Knippschild U, Bischof J. Assessing the Inhibitory Potential of Kinase Inhibitors In Vitro: Major Pitfalls and Suggestions for Improving Comparability of Data Using CK1 Inhibitors as an Example. Molecules 2021; 26:4898. [PMID: 34443486 PMCID: PMC8401859 DOI: 10.3390/molecules26164898] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 11/16/2022] Open
Abstract
Phosphorylation events catalyzed by protein kinases represent one of the most prevalent as well as important regulatory posttranslational modifications, and dysregulation of protein kinases is associated with the pathogenesis of different diseases. Therefore, interest in developing potent small molecule kinase inhibitors has increased enormously within the last two decades. A critical step in the development of new inhibitors is cell-free in vitro testing with the intention to determine comparable parameters like the commonly used IC50 value. However, values described in the literature are often biased as experimental setups used for determination of kinase activity lack comparability due to different readout parameters, insufficient normalization or the sheer number of experimental approaches. Here, we would like to hold a brief for highly sensitive, radioactive-based in vitro kinase assays especially suitable for kinases exhibiting autophosphorylation activity. Therefore, we demonstrate a systematic workflow for complementing and validating results from high-throughput screening as well as increasing the comparability of enzyme-specific inhibitor parameters for radiometric as well as non-radiometric assays. Using members of the CK1 family of serine/threonine-specific protein kinases and established CK1-specific inhibitors as examples, we clearly demonstrate the power of our proposed workflow, which has the potential to support the generation of more comparable data for biological characterization of kinase inhibitors.
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Affiliation(s)
- Aileen Roth
- Department of General and Visceral Surgery, Surgery Center, Ulm University Medical Center, Albert-Einstein-Allee 23, 89081 Ulm, Germany; (A.R.); (A.G.); (F.G.); (J.B.)
| | - Adrian Gihring
- Department of General and Visceral Surgery, Surgery Center, Ulm University Medical Center, Albert-Einstein-Allee 23, 89081 Ulm, Germany; (A.R.); (A.G.); (F.G.); (J.B.)
| | - Florian Göser
- Department of General and Visceral Surgery, Surgery Center, Ulm University Medical Center, Albert-Einstein-Allee 23, 89081 Ulm, Germany; (A.R.); (A.G.); (F.G.); (J.B.)
| | - Christian Peifer
- Institute of Pharmacy, Christian-Albrechts-University of Kiel, Gutenbergstraße 76, 24118 Kiel, Germany;
| | - Uwe Knippschild
- Department of General and Visceral Surgery, Surgery Center, Ulm University Medical Center, Albert-Einstein-Allee 23, 89081 Ulm, Germany; (A.R.); (A.G.); (F.G.); (J.B.)
| | - Joachim Bischof
- Department of General and Visceral Surgery, Surgery Center, Ulm University Medical Center, Albert-Einstein-Allee 23, 89081 Ulm, Germany; (A.R.); (A.G.); (F.G.); (J.B.)
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Armbrust F, Bickenbach K, Koudelka T, Tholey A, Pietrzik C, Becker-Pauly C. Phosphorylation of meprin β controls its cell surface abundance and subsequently diminishes ectodomain shedding. FASEB J 2021; 35:e21677. [PMID: 34125978 DOI: 10.1096/fj.202100271r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/24/2021] [Accepted: 05/04/2021] [Indexed: 12/18/2022]
Abstract
Meprin β is a zinc-dependent metalloprotease exhibiting a unique cleavage specificity with strong preference for acidic amino acids at the cleavage site. Proteomic studies revealed a diverse substrate pool of meprin β including the interleukin-6 receptor (IL-6R) and the amyloid precursor protein (APP). Dysregulation of meprin β is often associated with pathological conditions such as chronic inflammation, fibrosis, or Alzheimer's disease (AD). The extracellular regulation of meprin β including interactors, sheddases, and activators has been intensively investigated while intracellular regulation has been barely addressed in the literature. This study aimed to analyze C-terminal phosphorylation of meprin β with regard to cell surface expression and proteolytic activity. By immunoprecipitation of endogenous meprin β from the colon cancer cell line Colo320 and subsequent LC-MS analysis, we identified several phosphorylation sites in its C-terminal region. Here, T694 in the C-terminus of meprin β was the most preferred residue after phorbol 12-myristate 13-acetate (PMA) stimulation. We further demonstrated the role of protein kinase C (PKC) isoforms for meprin β phosphorylation and identified the involvement of PKC-α and PKC-β. As a result of phosphorylation, the meprin β activity at the cell surface is reduced and, consequently, the extent of substrate cleavage is diminished. Our data indicate that this decrease of the surface activity is caused by the internalization and degradation of meprin β.
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Affiliation(s)
- Fred Armbrust
- Biochemical Institute, Unit for Degradomics of the Protease Web, University of Kiel, Kiel, Germany
| | - Kira Bickenbach
- Biochemical Institute, Unit for Degradomics of the Protease Web, University of Kiel, Kiel, Germany
| | - Tomas Koudelka
- Systematic Proteomics & Bioanalytics, Institute for Experimental Medicine, University of Kiel, Kiel, Germany
| | - Andreas Tholey
- Systematic Proteomics & Bioanalytics, Institute for Experimental Medicine, University of Kiel, Kiel, Germany
| | - Claus Pietrzik
- Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Christoph Becker-Pauly
- Biochemical Institute, Unit for Degradomics of the Protease Web, University of Kiel, Kiel, Germany
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Ferrer I, Andrés-Benito P, Ausín K, Pamplona R, Del Rio JA, Fernández-Irigoyen J, Santamaría E. Dysregulated protein phosphorylation: A determining condition in the continuum of brain aging and Alzheimer's disease. Brain Pathol 2021; 31:e12996. [PMID: 34218486 PMCID: PMC8549032 DOI: 10.1111/bpa.12996] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 01/09/2023] Open
Abstract
Tau hyperphosphorylation is the first step of neurofibrillary tangle (NFT) formation. In the present study, samples of the entorhinal cortex (EC) and frontal cortex area 8 (FC) of cases with NFT pathology classified as stages I-II, III-IV, and V-VI without comorbidities, and of middle-aged (MA) individuals with no NFT pathology, were analyzed by conventional label-free and SWATH-MS (sequential window acquisition of all theoretical fragment ion spectra mass spectrometry) to assess the (phospho)proteomes. The total number of identified dysregulated phosphoproteins was 214 in the EC, 65 of which were dysregulated at the first stages (I-II) of NFT pathology; 167 phosphoproteins were dysregulated in the FC, 81 of them at stages I-II of NFT pathology. A large percentage of dysregulated phosphoproteins were identified in the two regions and at different stages of NFT progression. The main group of dysregulated phosphoproteins was made up of components of the membranes, cytoskeleton, synapses, proteins linked to membrane transport and ion channels, and kinases. The present results show abnormal phosphorylation of proteins at the first stages of NFT pathology in the elderly (in individuals clinically considered representative of normal aging) and sporadic Alzheimer's disease (sAD). Dysregulated protein phosphorylation in the FC precedes the formation of NFTs and SPs. The most active period of dysregulated phosphorylation is at stages III-IV when a subpopulation of individuals might be clinically categorized as suffering from mild cognitive impairment which is a preceding determinant stage in the progression to dementia. Altered phosphorylation of selected proteins, carried out by activation of several kinases, may alter membrane and cytoskeletal functions, among them synaptic transmission and membrane/cytoskeleton signaling. Besides their implications in sAD, the present observations suggest a molecular substrate for "benign" cognitive deterioration in "normal" brain aging.
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Affiliation(s)
- Isidro Ferrer
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Hospitalet de Llobregat, Spain.,CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, Hospitalet de Llobregat, Spain.,Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL, Hospitalet de Llobregat, Spain
| | - Pol Andrés-Benito
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Hospitalet de Llobregat, Spain.,CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, Hospitalet de Llobregat, Spain.,Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL, Hospitalet de Llobregat, Spain
| | - Karina Ausín
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA, IdiSNA, Pamplona, Spain
| | - Reinald Pamplona
- Department of Experimental Medicine, University of Lleida-Biomedical Research Institute of Lleida (UdL-IRBLleida, Lleida, Spain
| | - José Antonio Del Rio
- Molecular and Cellular Neurobiotechnology, Institute of Bioengineering of Catalonia (IBEC), Barcelona Institute for Science and Technology, Science Park Barcelona (PCB, Barcelona, Spain.,Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA, IdiSNA, Pamplona, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA, IdiSNA, Pamplona, Spain
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10
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Cabral AD, Radu TB, de Araujo ED, Gunning PT. Optical chemosensors for the detection of proximally phosphorylated peptides and proteins. RSC Chem Biol 2021; 2:815-829. [PMID: 34458812 PMCID: PMC8341930 DOI: 10.1039/d1cb00055a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/19/2021] [Indexed: 12/31/2022] Open
Abstract
Proximal multi-site phosphorylation is a critical post-translational modification in protein biology. The additive effects of multiple phosphosite clusters in close spatial proximity triggers integrative and cooperative effects on protein conformation and activity. Proximal phosphorylation has been shown to modulate signal transduction pathways and gene expression, and as a result, is implicated in a broad range of disease states through altered protein function and/or localization including enzyme overactivation or protein aggregation. The role of proximal multi-phosphorylation events is becoming increasingly recognized as mechanistically important, although breakthroughs are limited due to a lack of detection technologies. To date, there is a limited selection of facile and robust sensing tools for proximal phosphorylation. Nonetheless, there have been considerable efforts in developing optical chemosensors for the detection of proximal phosphorylation motifs on peptides and proteins in recent years. This review provides a comprehensive overview of optical chemosensors for proximal phosphorylation, with the majority of work being reported in the past two decades. Optical sensors, in the form of fluorescent and luminescent chemosensors, hybrid biosensors, and inorganic nanoparticles, are described. Emphasis is placed on the rationale behind sensor scaffolds, relevant protein motifs, and applications in protein biology.
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Affiliation(s)
- Aaron D Cabral
- Department of Chemical and Physical Sciences, University of Toronto Mississauga 3359 Mississauga Road Mississauga Ontario L5L 1C6 Canada
- Department of Chemistry, University of Toronto 80 St George Street Toronto Ontario M5S 3H6 Canada
| | - Tudor B Radu
- Department of Chemical and Physical Sciences, University of Toronto Mississauga 3359 Mississauga Road Mississauga Ontario L5L 1C6 Canada
- Department of Chemistry, University of Toronto 80 St George Street Toronto Ontario M5S 3H6 Canada
| | - Elvin D de Araujo
- Department of Chemical and Physical Sciences, University of Toronto Mississauga 3359 Mississauga Road Mississauga Ontario L5L 1C6 Canada
| | - Patrick T Gunning
- Department of Chemical and Physical Sciences, University of Toronto Mississauga 3359 Mississauga Road Mississauga Ontario L5L 1C6 Canada
- Department of Chemistry, University of Toronto 80 St George Street Toronto Ontario M5S 3H6 Canada
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11
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Sheynov AA, Tatarskiy VV, Tatarskiy EV, Nabirochkina EN, Georgieva SG, Soshnikova NV. The sequential phosphorylation of PHF10 subunit of the PBAF chromatin-remodeling complex determines different properties of the PHF10 isoforms. Biol Open 2020; 9:bio.043943. [PMID: 31911482 PMCID: PMC6994943 DOI: 10.1242/bio.043943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The mammalian PBAF subfamily of SWI/SNF chromatin remodeling complexes plays a wide role in the regulation of gene expression. PHF10 is a subunit of the signature module of PBAF, responsible for its interaction with chromatin. PHF10 is represented by four different isoforms, which are alternatively incorporated in the complex. Two of PHF10 isoforms lacking C-terminal PHD domains contain a cluster of phosphorylated serine residues, designated as X-cluster. In the present study, we explore the phosphorylation of the X-cluster in detail. We identified additional phosphorylated serine residues and designated them as either frequently or rarely phosphorylated. The X-cluster consists of two independently phosphorylated subclusters. Phosphorylation of the second subcluster depends on phosphorylation of a primary serine 327. These two subclusters surround a sequence, which is predicted to be a nuclear localization sequence (NLS3). The NLS3 does not affect localization of PHF10 isoforms. However, it is essential for X-cluster phosphorylation and increased stability of isoforms that lack PHD. Conversely, the presence of NLS3 signal in isoforms that contain C-terminal PHD domains reduces their stability. Thus, phosphorylation of PHF10 isoforms regulates their cell level, determining the rate of incorporation in PBAF. This may alter the pattern of PBAF regulated genes. Summary: The sequential phosphorylation of the linker domain of PHF10 subunit of PBAF chromatin remodeling complex is triggered by two primarily phosphorylated serines and determines the different properties of PHF10 isoforms.
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Affiliation(s)
- Andrey A Sheynov
- Department of Eukaryotic Transcription Factors, Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, Moscow 119991, Russia
| | - Victor V Tatarskiy
- Department of Eukaryotic Transcription Factors, Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, Moscow 119991, Russia
| | - Eugene V Tatarskiy
- Department of Eukaryotic Transcription Factors, Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, Moscow 119991, Russia
| | - Elena N Nabirochkina
- Department of Eukaryotic Transcription Factors, Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, Moscow 119991, Russia
| | - Sofia G Georgieva
- Department of Eukaryotic Transcription Factors, Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, Moscow 119991, Russia
| | - Nataliya V Soshnikova
- Department of Eukaryotic Transcription Factors, Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, Moscow 119991, Russia
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12
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Stachurska A, Sarna T. Regulation of Melanopsin Signaling: Key Interactions of the Nonvisual Photopigment. Photochem Photobiol 2018; 95:83-94. [DOI: 10.1111/php.12995] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/26/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Anna Stachurska
- Labolatory of Imaging and Force Spectroscopy; Malopolska Centre of Biotechnology; Jagiellonian University; Krakow Poland
| | - Tadeusz Sarna
- Department of Biophysics; Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Krakow Poland
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13
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Xian H, Xie W, Yang S, Liu Q, Xia X, Jin S, Sun T, Cui J. Stratified ubiquitination of RIG-I creates robust immune response and induces selective gene expression. SCIENCE ADVANCES 2017; 3:e1701764. [PMID: 28948228 PMCID: PMC5609842 DOI: 10.1126/sciadv.1701764] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/01/2017] [Indexed: 05/12/2023]
Abstract
The activation of retinoic acid-inducible gene I (RIG-I), an indispensable viral RNA sensor in mammals, is subtly regulated by ubiquitination. Although multiple ubiquitination sites at the amino terminus of RIG-I have been identified, their functional allocations in RIG-I activation remain elusive. We identified a stratified model for RIG-I amino-terminal ubiquitination, in which initiation at either Lys164 or Lys172 allows subsequent ubiquitination at other lysines, to trigger and amplify RIG-I activation. Experimental and mathematical modeling showed that multisite ubiquitination provides robustness in RIG-I-mediated type I interferon (IFN) signaling. Furthermore, the flexibly controlled ultrasensitivity and IFN activation intensity determine the specificity of the IFN-stimulated gene transcription and manipulate cell fate in antiviral immune response. Our work demonstrates that tunable type I IFN signaling can be regulated through multisite RIG-I ubiquitination and elucidates a new paradigm for dynamic regulation in RIG-I-mediated antiviral signaling.
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Affiliation(s)
- Huifang Xian
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Weihong Xie
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Shuai Yang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Qingxiang Liu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xiaojun Xia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Shouheng Jin
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Tingzhe Sun
- School of Life Sciences, Anqing Normal University, Anqing 246011, China
| | - Jun Cui
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
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14
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Huang P, Chen A, He W, Li Z, Zhang G, Liu Z, Liu G, Liu X, He S, Xiao G, Huang F, Stenvang J, Brünner N, Hong A, Wang J. BMP-2 induces EMT and breast cancer stemness through Rb and CD44. Cell Death Discov 2017; 3:17039. [PMID: 28725489 PMCID: PMC5511860 DOI: 10.1038/cddiscovery.2017.39] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/07/2017] [Accepted: 05/11/2017] [Indexed: 12/25/2022] Open
Abstract
Bone morphogenetic protein 2 (BMP-2) has been reported to facilitate epithelial-to-mesenchymal transition (EMT) and bone metastasis in breast cancer xenograft models. To investigate the role of BMP-2 in the development of breast cancer stem cells (BCSCs), and to further elucidate the mechanisms underlying its influence on breast cancer metastasis, we conducted a comprehensive molecular study using breast cancer cell lines and clinical samples. Our results showed that downregulation of Rb by BMP-2 was associated with ubiquitin-mediated degradation activated by phosphorylation of Rb via the PI3K/AKT signal pathway. In addition, the Smad signaling pathways are implicated in upregulation of CD44 protein expression by BMP-2. It was suggested that cross-talk exists between Rb and CD44 signaling pathways, as recombinant human BMP-2 (rhBMP-2) was found to regulate CD44 expression partly through Rb signals. In clinical tissues, BMP-2 was positively and negatively correlated with CD44 and Rb expression, respectively. Based on the in vitro and in vivo results, we have established an integrated mechanism by which rhBMP-2 induces EMT and stemness of breast cancer cells via the Rb and CD44 signaling pathways, which then contribute to breast cancer metastasis. These findings may be helpful for developing new strategies for the treatment and prognosis of advanced breast cancer.
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Affiliation(s)
- Peide Huang
- Institute of Biomedicine, Guangdong Provincial Key Laboratory of Bioengineering Medicine, National Engineering Research Centre of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.,Section for Molecular Disease Biology, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Anan Chen
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kai Yuan Avenue, Science Park Luogang, Guangzhou 510530, China
| | - Weiyi He
- Institute of Biomedicine, Guangdong Provincial Key Laboratory of Bioengineering Medicine, National Engineering Research Centre of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhen Li
- Institute of Biomedicine, Guangdong Provincial Key Laboratory of Bioengineering Medicine, National Engineering Research Centre of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Guanglin Zhang
- Institute of Biomedicine, Guangdong Provincial Key Laboratory of Bioengineering Medicine, National Engineering Research Centre of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhong Liu
- Institute of Biomedicine, Guangdong Provincial Key Laboratory of Bioengineering Medicine, National Engineering Research Centre of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Ge Liu
- Institute of Biomedicine, Guangdong Provincial Key Laboratory of Bioengineering Medicine, National Engineering Research Centre of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xueting Liu
- Institute of Biomedicine, Guangdong Provincial Key Laboratory of Bioengineering Medicine, National Engineering Research Centre of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Shuilian He
- Institute of Biomedicine, Guangdong Provincial Key Laboratory of Bioengineering Medicine, National Engineering Research Centre of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Gang Xiao
- Institute of Biomedicine, Guangdong Provincial Key Laboratory of Bioengineering Medicine, National Engineering Research Centre of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Feicheng Huang
- Department of Chemistry and Institute for Nano-Chemistry, Jinan University, Guangzhou 510632, China
| | - Jan Stenvang
- Section for Molecular Disease Biology, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Nils Brünner
- Section for Molecular Disease Biology, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - An Hong
- Institute of Biomedicine, Guangdong Provincial Key Laboratory of Bioengineering Medicine, National Engineering Research Centre of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Ju Wang
- Institute of Biomedicine, Guangdong Provincial Key Laboratory of Bioengineering Medicine, National Engineering Research Centre of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
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15
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Chiappori F, Mattiazzi L, Milanesi L, Merelli I. A novel molecular dynamics approach to evaluate the effect of phosphorylation on multimeric protein interface: the αB-Crystallin case study. BMC Bioinformatics 2016; 17 Suppl 4:57. [PMID: 26961246 PMCID: PMC4896236 DOI: 10.1186/s12859-016-0909-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Phosphorylation is one of the most important post-translational modifications (PTM) employed by cells to regulate several cellular processes. Studying the effects of phosphorylations on protein structures allows to investigate the modulation mechanisms of several proteins including chaperones, like the small HSPs, which display different multimeric structures according to the phosphorylation of a few serine residues. In this context, the proposed study is aimed at finding a method to correlate different PTM patterns (in particular phosphorylations at the monomers interface of multimeric complexes) with the dynamic behaviour of the complex, using physicochemical parameters derived from molecular dynamics simulations in the timescale of nanoseconds. RESULTS We have developed a methodology relying on computing nine physicochemical parameters, derived from the analysis of short MD simulations, and combined with N identifiers that characterize the PTMs of the analysed protein. The nine general parameters were validated on three proteins, with known post-translational modified conformation and unmodified conformation. Then, we applied this approach to the case study of αB-Crystallin, a chaperone which multimeric state (up to 40 units) is supposed to be controlled by phosphorylation of Ser45 and Ser59. Phosphorylation of serines at the dimer interface induces the release of hexamers, the active state of αB-Crystallin. 30 ns of MD simulation were obtained for each possible combination of dimer phosphorylation state and average values of structural, dynamic, energetic and functional features were calculated on the equilibrated portion of the trajectories. Principal Component Analysis was applied to the parameters and the first five Principal Components, which summed up to 84 % of the total variance, were finally considered. CONCLUSIONS The validation of this approach on multimeric proteins, which structures were known both modified and unmodified, allowed us to propose a new approach that can be used to predict the impact of PTM patterns in multi-modified proteins using data collected from short molecular dynamics simulations. Analysis on the αB-Crystallin case study clusters together all-P dimers with all-P hexamers and no-P dimer with no-P hexamer and results suggest a great influence of Ser59 phosphorylation on chain B.
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Affiliation(s)
- Federica Chiappori
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Segrate, MI, 20090, Italy.
| | - Luca Mattiazzi
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Segrate, MI, 20090, Italy. .,Biotechnology and Biosciences Department, University of Milano-Bicocca, Milan, 20126, Italy.
| | - Luciano Milanesi
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Segrate, MI, 20090, Italy.
| | - Ivan Merelli
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Segrate, MI, 20090, Italy.
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16
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Yue J, Qin Q, Meng S, Jing H, Gou X, Li J, Hou S. TOPP4 Regulates the Stability of PHYTOCHROME INTERACTING FACTOR5 during Photomorphogenesis in Arabidopsis. PLANT PHYSIOLOGY 2016; 170:1381-97. [PMID: 26704640 PMCID: PMC4775132 DOI: 10.1104/pp.15.01729] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/23/2015] [Indexed: 05/18/2023]
Abstract
In plants, photoreceptors transfer light signals to phytochrome-interacting factors (PIFs), inducing the rapid phosphorylation and degradation of PIFs to promote photomorphogenesis. However, the phosphatase responsible for PIF dephosphorylation remains unknown. In this study, we identified a type 1 protein phosphatase, TOPP4, that is essential for PIF5 protein stability in Arabidopsis (Arabidopsis thaliana). Compared with the wild type, the dominant-negative mutant, topp4-1, displayed reduced hypocotyl length and larger apical hook and cotyledon opening angle under red light. Overexpression of topp4-1 in the wild type led to defects that were similar to those in the topp4-1 mutant. Red light induced phytochrome B (phyB)-dependent TOPP4 expression in hypocotyls. The topp4-1 mutation weakened the closed cotyledon angle of phyB-9 and phyA-211 phyB-9, while overexpression of TOPP4 significantly repressed the short hypocotyls of phyB-green fluorescent protein seedlings, indicating that TOPP4 and phyB function in an antagonistic way during photomorphogenesis. Protein interaction assays and phosphorylation studies demonstrate that TOPP4 interacts directly with PIF5 and dephosphorylates it. Furthermore, TOPP4 inhibits the red light-induced ubiquitination and degradation of PIF5. These findings demonstrate that dephosphorylation of PIF5 by TOPP4 inhibits its ubiquitin-mediated degradation during photomorphogenesis. These data outline a novel phytochrome signaling mechanism by which TOPP4-mediated dephosphorylation of PIF5 attenuates phytochrome-dependent light responses.
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Affiliation(s)
- Jing Yue
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Qianqian Qin
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Siyuan Meng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Huiting Jing
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiaoping Gou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jia Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Suiwen Hou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
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17
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Sullivan JM, Havrda MC, Kettenbach AN, Paolella BR, Zhang Z, Gerber SA, Israel MA. Phosphorylation Regulates Id2 Degradation and Mediates the Proliferation of Neural Precursor Cells. Stem Cells 2016; 34:1321-31. [PMID: 26756672 DOI: 10.1002/stem.2291] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 11/23/2015] [Accepted: 12/07/2015] [Indexed: 01/07/2023]
Abstract
Inhibitor of DNA binding proteins (Id1-Id4) function to inhibit differentiation and promote proliferation of many different cell types. Among the Id family members, Id2 has been most extensively studied in the central nervous system (CNS). Id2 contributes to cultured neural precursor cell (NPC) proliferation as well as to the proliferation of CNS tumors such as glioblastoma that are likely to arise from NPC-like cells. We identified three phosphorylation sites near the N-terminus of Id2 in NPCs. To interrogate the importance of Id2 phosphorylation, Id2(-/-) NPCs were modified to express wild type (WT) Id2 or an Id2 mutant protein that could not be phosphorylated at the identified sites. We observed that NPCs expressing this mutant lacking phosphorylation near the N-terminus had higher steady-state levels of Id2 when compared to NPCs expressing WT Id2. This elevated level was the result of a longer half-life and reduced proteasome-mediated degradation. Moreover, NPCs expressing constitutively de-phosphorylated Id2 proliferated more rapidly than NPCs expressing WT Id2, a finding consistent with the well-characterized function of Id2 in driving proliferation. Observing that phosphorylation of Id2 modulates the degradation of this important cell-cycle regulator, we sought to identify a phosphatase that would stabilize Id2 enhancing its activity in NPCs and extended our analysis to include human glioblastoma-derived stem cells (GSCs). We found that expression of the phosphatase PP2A altered Id2 levels. Our findings suggest that inhibition of PP2A may be a novel strategy to regulate the proliferation of normal NPCs and malignant GSCs by decreasing Id2 levels. Stem Cells 2016;34:1321-1331.
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Affiliation(s)
- Jaclyn M Sullivan
- Pharmacology and Toxicology, Norris Cotton Cancer Center, One Medical Center Drive, Lebanon, NH, 03756.,Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Matthew C Havrda
- Pharmacology and Toxicology, Norris Cotton Cancer Center, One Medical Center Drive, Lebanon, NH, 03756.,Department of Pediatrics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Arminja N Kettenbach
- Pharmacology and Toxicology, Norris Cotton Cancer Center, One Medical Center Drive, Lebanon, NH, 03756.,Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Brenton R Paolella
- Pharmacology and Toxicology, Norris Cotton Cancer Center, One Medical Center Drive, Lebanon, NH, 03756.,Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Zhonghua Zhang
- Pharmacology and Toxicology, Norris Cotton Cancer Center, One Medical Center Drive, Lebanon, NH, 03756.,Department of Pediatrics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Scott A Gerber
- Pharmacology and Toxicology, Norris Cotton Cancer Center, One Medical Center Drive, Lebanon, NH, 03756.,Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA.,Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Mark A Israel
- Pharmacology and Toxicology, Norris Cotton Cancer Center, One Medical Center Drive, Lebanon, NH, 03756.,Department of Pediatrics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA.,Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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18
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Zhao H, Cunningham DL, Creese AJ, Heath JK, Cooper HJ. FAIMS and Phosphoproteomics of Fibroblast Growth Factor Signaling: Enhanced Identification of Multiply Phosphorylated Peptides. J Proteome Res 2015; 14:5077-87. [PMID: 26503514 DOI: 10.1021/acs.jproteome.5b00713] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We have applied liquid chromatography high-field asymmetric waveform ion mobility spectrometry tandem mass spectrometry (LC-FAIMS-MS/MS) and liquid chromatography tandem mass spectrometry (LC-MS/MS) to the investigation of site-specific phosphorylation in fibroblast growth factor (FGF) signaling. We have combined a SILAC approach with chemical inhibition by SU5402 (an FGF receptor tyrosine kinase inhibitor) and dasatinib (a Src family kinase inhibitor). The results show that incorporation of FAIMS within the workflow results in (a) an increase in the relative proportion of phosphothreonine and phosphotyrosine sites identified, (b) an increase in phosphopeptide identifications from precursors with charge states ≥ +3 (with an associated increase in peptide length), and (c) an increase in the identification of multiply phosphorylated peptides. Approximately 20% of the phosphorylation sites identified via the FAIMS workflow had not been reported previously, and over 80% of those were from multiply phosphorylated peptides. Moreover, FAIMS provided access to a distinct set of phosphorylation sites regulated in response to SU5402 and dasatinib. The enhanced identification of multiply phosphorylated peptides was particularly striking in the case of sites regulated by SU5402. In addition to providing a compelling example of the complementarity of FAIMS in phosphoproteomics, the results provide a valuable resource of phosphorylation sites for further investigation of FGF signaling and trafficking.
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Affiliation(s)
- Hongyan Zhao
- School of Biosciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Debbie L Cunningham
- School of Biosciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Andrew J Creese
- School of Biosciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, United Kingdom
| | - John K Heath
- School of Biosciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Helen J Cooper
- School of Biosciences, University of Birmingham , Edgbaston, Birmingham B15 2TT, United Kingdom
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19
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Filatov A, Kruglova N, Meshkova T, Mazurov D. Lymphocyte phosphatase-associated phosphoprotein proteoforms analyzed using monoclonal antibodies. Clin Transl Immunology 2015; 4:e44. [PMID: 26682052 PMCID: PMC4673442 DOI: 10.1038/cti.2015.22] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/03/2015] [Accepted: 09/03/2015] [Indexed: 11/09/2022] Open
Abstract
Phosphatase CD45 regulates the activation of lymphocytes by controlling the level of receptor and signal molecule phosphorylation. However, it remains unknown which molecules mediate the phosphatase activity of CD45. A candidate for such a molecule is a small transmembrane adapter protein called lymphocyte phosphatase-associated phosphoprotein (LPAP). LPAP forms a supramolecular complex that consists of not only CD45 molecule but also CD4 and Lck kinase. The function of LPAP has not been defined clearly. In our study, we determined the pattern of LPAP expression in various cell types and characterized its proteoforms using new monoclonal antibodies generated against the intracellular portion of the protein. We show that LPAP is a pan-lymphocyte marker, and its expression in cells correlates with the expression of CD45. The majority of T, B and NK cells express high levels of LPAP, whereas monocytes, granulocytes, monocyte-derived dendritic cells, platelets and red blood cells are negative for LPAP. Using one- and two-dimensional protein gel electrophoresis, we demonstrate that LPAP has at least four sites of phosphorylation. The resting cells express at least six different LPAP phosphoforms representing mono-, di- and tri-phosphorylated LPAP. T and B cells differ in the distribution of the protein between phosphoforms. The activation of lymphocytes with PMA reduces the diversity of phosphorylated forms. Our experiments on Lck-deficient Jurkat cells show that Lck kinase is not involved in LPAP phosphorylation. Thus, LPAP is a dynamically phosphorylated protein, the function of which can be understood, when all phosphosites and kinases involved in its phosphorylation will be identified.
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Affiliation(s)
- Alexander Filatov
- Laboratory of Immunochemistry, Institute of Immunology , Moscow, Russia
| | - Natalia Kruglova
- Faculty of Biology, Lomonosov Moscow State University , Moscow, Russia
| | - Tatiana Meshkova
- Faculty of Biology, Lomonosov Moscow State University , Moscow, Russia
| | - Dmitriy Mazurov
- Laboratory of Immunochemistry, Institute of Immunology , Moscow, Russia
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20
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A systems model of phosphorylation for inflammatory signaling events. PLoS One 2014; 9:e110913. [PMID: 25333362 PMCID: PMC4205014 DOI: 10.1371/journal.pone.0110913] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/19/2014] [Indexed: 12/24/2022] Open
Abstract
Phosphorylation is a fundamental biochemical reaction that modulates protein activity in cells. While a single phosphorylation event is relatively easy to understand, multisite phosphorylation requires systems approaches for deeper elucidation of the underlying molecular mechanisms. In this paper we develop a mechanistic model for single- and multi-site phosphorylation. The proposed model is compared with previously reported studies. We compare the predictions of our model with experiments published in the literature in the context of inflammatory signaling events in order to provide a mechanistic description of the multisite phosphorylation-mediated regulation of Signal Transducer and Activator of Transcription 3 (STAT3) and Interferon Regulatory Factor 5 (IRF-5) proteins. The presented model makes crucial predictions for transcription factor phosphorylation events in the immune system. The model proposes potential mechanisms for T cell phenotype switching and production of cytokines. This study also provides a generic framework for the better understanding of a large number of multisite phosphorylation-regulated biochemical circuits.
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21
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Theillet FX, Binolfi A, Frembgen-Kesner T, Hingorani K, Sarkar M, Kyne C, Li C, Crowley PB, Gierasch L, Pielak GJ, Elcock AH, Gershenson A, Selenko P. Physicochemical properties of cells and their effects on intrinsically disordered proteins (IDPs). Chem Rev 2014; 114:6661-714. [PMID: 24901537 PMCID: PMC4095937 DOI: 10.1021/cr400695p] [Citation(s) in RCA: 338] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Francois-Xavier Theillet
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Andres Binolfi
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Tamara Frembgen-Kesner
- Department
of Biochemistry, University of Iowa, Bowen Science Building, 51 Newton
Road, Iowa City, Iowa 52242, United States
| | - Karan Hingorani
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Mohona Sarkar
- Department
of Chemistry, Department of Biochemistry and Biophysics and Lineberger
Comprehensive Cancer Center, University
of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Ciara Kyne
- School
of Chemistry, National University of Ireland,
Galway, University Road, Galway, Ireland
| | - Conggang Li
- Key Laboratory
of Magnetic Resonance in Biological Systems, State Key Laboratory
of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center
for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P.R. China
| | - Peter B. Crowley
- School
of Chemistry, National University of Ireland,
Galway, University Road, Galway, Ireland
| | - Lila Gierasch
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Gary J. Pielak
- Department
of Chemistry, Department of Biochemistry and Biophysics and Lineberger
Comprehensive Cancer Center, University
of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Adrian H. Elcock
- Department
of Biochemistry, University of Iowa, Bowen Science Building, 51 Newton
Road, Iowa City, Iowa 52242, United States
| | - Anne Gershenson
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Philipp Selenko
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
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22
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Berg EL. Systems biology in drug discovery and development. Drug Discov Today 2013; 19:113-25. [PMID: 24120892 DOI: 10.1016/j.drudis.2013.10.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 09/14/2013] [Accepted: 10/03/2013] [Indexed: 11/25/2022]
Abstract
The complexity of human biology makes it challenging to develop safe and effective new medicines. Systems biology omics-based efforts have led to an explosion of high-throughput data and focus is now shifting to the integration of diverse data types to connect molecular and pathway information to predict disease outcomes. Better models of human disease biology, including more integrated network-based models that can accommodate multiple omics data types, as well as more relevant experimental systems, will help predict drug effects in patients, enabling personalized medicine, improvement of the success rate of new drugs in the clinic, and the finding of new uses for existing drugs.
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Affiliation(s)
- Ellen L Berg
- BioSeek, A Division of DiscoveRx, 310 Utah Avenue, Suite 100, South San Francisco, CA 94080, USA.
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23
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Suwanmajo T, Krishnan J. Biphasic responses in multi-site phosphorylation systems. J R Soc Interface 2013; 10:20130742. [PMID: 24108693 DOI: 10.1098/rsif.2013.0742] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Multi-site phosphorylation systems are repeatedly encountered in cellular biology and multi-site modification is a basic building block of post-translational modification. In this paper, we demonstrate how distributive multi-site modification mechanisms by a single kinase/phosphatase pair can lead to biphasic/partial biphasic dose-response characteristics for the maximally phosphorylated substrate at steady state. We use simulations and analysis to uncover a hidden competing effect which is responsible for this and analyse how it may be accentuated. We build on this to analyse different variants of multi-site phosphorylation mechanisms showing that some mechanisms are intrinsically not capable of displaying this behaviour. This provides both a consolidated understanding of how and under what conditions biphasic responses are obtained in multi-site phosphorylation and a basis for discriminating between different mechanisms based on this. We also demonstrate how this behaviour may be combined with other behaviour such as threshold and bistable responses, demonstrating the capacity of multi-site phosphorylation systems to act as complex molecular signal processors.
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Affiliation(s)
- Thapanar Suwanmajo
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, , South Kensington Campus, London SW7 2AZ, UK
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24
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Tang C, Welty DF. A dynamic view to the modulation of phosphorylation and O-GlcNAcylation by inhibition of O-GlcNAcase. Comput Biol Chem 2013; 45:9-16. [DOI: 10.1016/j.compbiolchem.2013.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 03/05/2013] [Accepted: 03/11/2013] [Indexed: 12/31/2022]
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25
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Ni W, Xu SL, Chalkley RJ, Pham TND, Guan S, Maltby DA, Burlingame AL, Wang ZY, Quail PH. Multisite light-induced phosphorylation of the transcription factor PIF3 is necessary for both its rapid degradation and concomitant negative feedback modulation of photoreceptor phyB levels in Arabidopsis. THE PLANT CELL 2013; 25:2679-98. [PMID: 23903316 PMCID: PMC3753391 DOI: 10.1105/tpc.113.112342] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Revised: 06/26/2013] [Accepted: 07/11/2013] [Indexed: 05/17/2023]
Abstract
Plants constantly monitor informational light signals using sensory photoreceptors, which include the phytochrome (phy) family (phyA to phyE), and adjust their growth and development accordingly. Following light-induced nuclear translocation, photoactivated phy molecules bind to and induce rapid phosphorylation and degradation of phy-interacting basic Helix Loop Helix (bHLH) transcription factors (PIFs), such as PIF3, thereby regulating the expression of target genes. However, the mechanisms underlying the signal-relay process are still not fully understood. Here, using mass spectrometry, we identify multiple, in vivo, light-induced Ser/Thr phosphorylation sites in PIF3. Using transgenic expression of site-directed mutants of PIF3, we provide evidence that a set of these phosphorylation events acts collectively to trigger rapid degradation of the PIF3 protein in response to initial exposure of dark-grown seedlings to light. In addition, we show that phyB-induced PIF3 phosphorylation is also required for the known negative feedback modulation of phyB levels in prolonged light, potentially through codegradation of phyB and PIF3. This mutually regulatory intermolecular transaction thus provides a mechanism with the dual capacity to promote early, graded, or threshold regulation of the primary, PIF3-controlled transcriptional network in response to initial light exposure, and later, to attenuate global sensitivity to the light signal through reductions in photoreceptor levels upon prolonged exposure.
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Affiliation(s)
- Weimin Ni
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
- U.S. Department of Agriculture/Agriculture Research Service, Plant Gene Expression Center, Albany, California 94710
| | - Shou-Ling Xu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Robert J. Chalkley
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143
| | - Thao Nguyen D. Pham
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
- U.S. Department of Agriculture/Agriculture Research Service, Plant Gene Expression Center, Albany, California 94710
| | - Shenheng Guan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143
| | - Dave A. Maltby
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143
| | - Alma L. Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143
| | - Zhi-Yong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Peter H. Quail
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
- U.S. Department of Agriculture/Agriculture Research Service, Plant Gene Expression Center, Albany, California 94710
- Address correspondence to
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26
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Seaton DD, Krishnan J. Effects of multiple enzyme-substrate interactions in basic units of cellular signal processing. Phys Biol 2012; 9:045009. [PMID: 22872009 DOI: 10.1088/1478-3975/9/4/045009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Covalent modification cycles are a ubiquitous feature of cellular signalling networks. In these systems, the interaction of an active enzyme with the unmodified form of its substrate is essential for signalling to occur. However, this interaction is not necessarily the only enzyme-substrate interaction possible. In this paper, we analyse the behaviour of a basic model of signalling in which additional, non-essential enzyme-substrate interactions are possible. These interactions include those between the inactive form of an enzyme and its substrate, and between the active form of an enzyme and its product. We find that these additional interactions can result in increased sensitivity and biphasic responses, respectively. The dynamics of the responses are also significantly altered by the presence of additional interactions. Finally, we evaluate the consequences of these interactions in two variations of our basic model, involving double modification of substrate and scaffold-mediated signalling, respectively. We conclude that the molecular details of protein-protein interactions are important in determining the signalling properties of enzymatic signalling pathways.
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Affiliation(s)
- D D Seaton
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, UK
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27
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Duan DD, Wang G. Double the keys, double the control: coupled phosphorylation sites provide novel molecular targets for precise control of ion channel function. Focus on "Differential regulation of a CLC anion channel by SPAK kinase ortholog-mediated multisite phosphorylation". Am J Physiol Cell Physiol 2012; 302:C1699-701. [PMID: 22496246 DOI: 10.1152/ajpcell.00107.2012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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28
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Barberis M. Sic1 as a timer of Clb cyclin waves in the yeast cell cycle--design principle of not just an inhibitor. FEBS J 2012; 279:3386-410. [PMID: 22356687 DOI: 10.1111/j.1742-4658.2012.08542.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Cellular systems biology aims to uncover design principles that describe the properties of biological networks through interaction of their components in space and time. The cell cycle is a complex system regulated by molecules that are integrated into functional modules to ensure genome integrity and faithful cell division. In budding yeast, cyclin-dependent kinases (Cdk1/Clb) drive cell cycle progression, being activated and inactivated in a precise temporal sequence. In this module, which we refer to as the 'Clb module', different Cdk1/Clb complexes are regulated to generate waves of Clb activity, a functional property of cell cycle control. The inhibitor Sic1 plays a critical role in the Clb module by binding to and blocking Cdk1/Clb activity, ultimately setting the timing of DNA replication and mitosis. Fifteen years of research subsequent to the identification of Sic1 have lead to the development of an integrative approach that addresses its role in regulating the Clb module. Sic1 is an intrinsically disordered protein and achieves its inhibitory function by cooperative binding, where different structural regions stretch on the Cdk1/Clb surface. Moreover, Sic1 promotes S phase entry, facilitating Cdk1/Clb5 nuclear transport, and therefore revealing a double function of inhibitor/activator that rationalizes a mechanism to prevent precocious DNA replication. Interestingly, the investigation of Clb temporal dynamics by mathematical modelling and experimental validation provides evidence that Sic1 acts as a timer to coordinate oscillations of Clb cyclin waves. Here we review these findings, focusing on the design principle underlying the Clb module, which highlights the role of Sic1 in regulating phase-specific Cdk1/Clb activities.
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Affiliation(s)
- Matteo Barberis
- Institute for Biology, Theoretical Biophysics, Humboldt University Berlin, Germany.
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29
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Composite low affinity interactions dictate recognition of the cyclin-dependent kinase inhibitor Sic1 by the SCFCdc4 ubiquitin ligase. Proc Natl Acad Sci U S A 2012; 109:3287-92. [PMID: 22328159 DOI: 10.1073/pnas.1116455109] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ubiquitin ligase SCF(Cdc4) (Skp1/Cul1/F-box protein) recognizes its substrate, the cyclin-dependent kinase inhibitor Sic1, in a multisite phosphorylation-dependent manner. Although short diphosphorylated peptides derived from Sic1 can bind to Cdc4 with high affinity, through systematic mutagenesis and quantitative biophysical analysis we show that individually weak, dispersed Sic1 phospho sites engage Cdc4 in a dynamic equilibrium. The affinities of individual phosphoepitopes serve to tune the overall phosphorylation site threshold needed for efficient recognition. Notably, phosphoepitope affinity for Cdc4 is dramatically weakened in the context of full-length Sic1, demonstrating the importance of regional environment on binding interactions. The multisite nature of the Sic1-Cdc4 interaction confers cooperative dependence on kinase activity for Sic1 recognition and ubiquitination under equilibrium reaction conditions. Composite dynamic interactions of low affinity sites may be a general mechanism to establish phosphorylation thresholds in biological responses.
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30
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Feala JD, Cortes J, Duxbury PM, McCulloch AD, Piermarocchi C, Paternostro G. Statistical properties and robustness of biological controller-target networks. PLoS One 2012; 7:e29374. [PMID: 22235289 PMCID: PMC3250441 DOI: 10.1371/journal.pone.0029374] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Accepted: 11/28/2011] [Indexed: 01/04/2023] Open
Abstract
Cells are regulated by networks of controllers having many targets, and targets affected by many controllers, in a “many-to-many” control structure. Here we study several of these bipartite (two-layer) networks. We analyze both naturally occurring biological networks (composed of transcription factors controlling genes, microRNAs controlling mRNA transcripts, and protein kinases controlling protein substrates) and a drug-target network composed of kinase inhibitors and of their kinase targets. Certain statistical properties of these biological bipartite structures seem universal across systems and species, suggesting the existence of common control strategies in biology. The number of controllers is ∼8% of targets and the density of links is 2.5%±1.2%. Links per node are predominantly exponentially distributed. We explain the conservation of the mean number of incoming links per target using a mathematical model of control networks, which also indicates that the “many-to-many” structure of biological control has properties of efficient robustness. The drug-target network has many statistical properties similar to the biological networks and we show that drug-target networks with biomimetic features can be obtained. These findings suggest a completely new approach to pharmacological control of biological systems. Molecular tools, such as kinase inhibitors, are now available to test if therapeutic combinations may benefit from being designed with biomimetic properties, such as “many-to-many” targeting, very wide coverage of the target set, and redundancy of incoming links per target.
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Affiliation(s)
- Jacob D. Feala
- Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Jorge Cortes
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, United States of America
| | - Phillip M. Duxbury
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan, United States of America
| | - Andrew D. McCulloch
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Carlo Piermarocchi
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan, United States of America
| | - Giovanni Paternostro
- Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
- * E-mail:
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31
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Danchin A, Binder PM, Noria S. Antifragility and Tinkering in Biology (and in Business) Flexibility Provides an Efficient Epigenetic Way to Manage Risk. Genes (Basel) 2011; 2:998-1016. [PMID: 24710302 PMCID: PMC3927596 DOI: 10.3390/genes2040998] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 10/25/2011] [Accepted: 11/16/2011] [Indexed: 12/25/2022] Open
Abstract
The notion of antifragility, an attribute of systems that makes them thrive under variable conditions, has recently been proposed by Nassim Taleb in a business context. This idea requires the ability of such systems to 'tinker', i.e., to creatively respond to changes in their environment. A fairly obvious example of this is natural selection-driven evolution. In this ubiquitous process, an original entity, challenged by an ever-changing environment, creates variants that evolve into novel entities. Analyzing functions that are essential during stationary-state life yield examples of entities that may be antifragile. One such example is proteins with flexible regions that can undergo functional alteration of their side residues or backbone and thus implement the tinkering that leads to antifragility. This in-built property of the cell chassis must be taken into account when considering construction of cell factories driven by engineering principles.
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Affiliation(s)
- Antoine Danchin
- AMAbiotics SAS, CEA/Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France.
| | - Philippe M Binder
- Natural Sciences Division, University of Hawaii, Hilo, HI 96720-4091, USA.
| | - Stanislas Noria
- Fondation Fourmentin-Guilbert, 2 avenue du Pavé Neuf, 93160 Noisy-le-Grand, France.
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32
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Avila-Elchiver M, Nagrath D, Yarmush ML. Optimality and thermodynamics determine the evolution of transcriptional regulatory networks. MOLECULAR BIOSYSTEMS 2011; 8:511-530. [PMID: 22076617 DOI: 10.1039/c1mb05177f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Transcriptional motifs are small regulatory interaction patterns that regulate biological functions in highly-interacting cellular networks. Recently, attempts have been made to explain the significance of transcriptional motifs through dynamic function. However, fundamental questions remain unanswered. Why are certain transcriptional motifs with similar dynamic function abundant while others occur rarely? What are the criteria for topological generalization of these motifs into complex networks? Here, we present a novel paradigm that combines non-equilibrium thermodynamics with multiobjective-optimality for network analysis. We found that energetic cost, defined herein as specific dissipation energy, is minimal at the optimal environmental conditions and it correlates inversely with the abundance of the network motifs obtained experimentally for E. coli and S. cerevisiae. This yields evidence that dissipative energetics is the underlying criteria used during evolution for motif selection and that biological systems during transcription tend towards evolutionary selection of subgraphs which produces minimum specific heat dissipation under optimal conditions, thereby explaining the abundance/rare occurrence of some motifs. We show that although certain motifs had similar dynamical functionality, they had significantly different energetic cost, thus explaining the abundance/rare occurrence of these motifs. The presented insights may establish global thermodynamic analysis as a backbone in designing and understanding complex networks systems, such as metabolic and protein interaction networks.
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Affiliation(s)
- Marco Avila-Elchiver
- Massachusetts General Hospital and the Harvard Medical School, Shriners Hospitals for Children, 51 Blossom Street, Boston, MA 02114
| | - Deepak Nagrath
- Chemical and Biomolecular Engineering Department, Rice University, Houston, TX 77005.
| | - Martin L Yarmush
- Massachusetts General Hospital and the Harvard Medical School, Shriners Hospitals for Children, 51 Blossom Street, Boston, MA 02114
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