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Mosbacher M, Lee SS, Yaakov G, Nadal-Ribelles M, de Nadal E, van Drogen F, Posas F, Peter M, Claassen M. Positive feedback induces switch between distributive and processive phosphorylation of Hog1. Nat Commun 2023; 14:2477. [PMID: 37120434 PMCID: PMC10148820 DOI: 10.1038/s41467-023-37430-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 03/16/2023] [Indexed: 05/01/2023] Open
Abstract
Cellular decision making often builds on ultrasensitive MAPK pathways. The phosphorylation mechanism of MAP kinase has so far been described as either distributive or processive, with distributive mechanisms generating ultrasensitivity in theoretical analyses. However, the in vivo mechanism of MAP kinase phosphorylation and its activation dynamics remain unclear. Here, we characterize the regulation of the MAP kinase Hog1 in Saccharomyces cerevisiae via topologically different ODE models, parameterized on multimodal activation data. Interestingly, our best fitting model switches between distributive and processive phosphorylation behavior regulated via a positive feedback loop composed of an affinity and a catalytic component targeting the MAP kinase-kinase Pbs2. Indeed, we show that Hog1 directly phosphorylates Pbs2 on serine 248 (S248), that cells expressing a non-phosphorylatable (S248A) or phosphomimetic (S248E) mutant show behavior that is consistent with simulations of disrupted or constitutively active affinity feedback and that Pbs2-S248E shows significantly increased affinity to Hog1 in vitro. Simulations further suggest that this mixed Hog1 activation mechanism is required for full sensitivity to stimuli and to ensure robustness to different perturbations.
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Affiliation(s)
- Maximilian Mosbacher
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Sung Sik Lee
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- Scientific Center for Optical and Electron Microscopy, ETH Zurich, Zurich, Switzerland
| | - Gilad Yaakov
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Mariona Nadal-Ribelles
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Eulàlia de Nadal
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Frank van Drogen
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Francesc Posas
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Matthias Peter
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.
| | - Manfred Claassen
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
- Department of Computer Science, University of Tübingen, Tübingen, Germany.
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.
- Department of Internal Medicine I, Faculty of Medicine, University Hospital Tübingen, University of Tübingen, Tübingen, Germany.
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2
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Zhang W, Leng X, Qi Y, Yang X, Jiang R, Yang X, Hu X, Tan Y, Zhong H. Electrophoresis of Phosphoproteins on a Tandem Polymerized Gel. Anal Chem 2022; 94:7466-7474. [PMID: 35536683 DOI: 10.1021/acs.analchem.1c04404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A substrate with n phosphorylated sites may have 2n phosphor-forms for temporal-spatial regulation of biological events. Because phosphates do not significantly change molecular masses but net charges of proteins, those isoforms cannot be separated by regular mass-based sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE). A tandem polymerized gel was developed to resolve phosphor-isoforms with different masses, charges, and posttranslational modifications. Without the usage of SDS, the electrophoresis was primarily performed on three adjacent acidic polyacrylamide gels. After being concentrated on a stacking gel, protonated proteins were then separated on the Zr4+ immobilized gel through the coordination of metal ions with phosphates followed by further charge and mass (z/m)-based electrophoretic separation on a TiO2 containing gel. The presence of TiO2 nanoparticles in the third gel is aimed for the initiation of the polymerization of acrylamide in acidic conditions upon ultraviolet irradiation. Distinct isoforms of α-S1-casein, α-S2-casein, β-casein, and κ casein model proteins located on 11, 8, 8, and 7 different bands of the tandem gel were unambiguously identified, respectively. With the tandem polymerized gel electrophoresis, new phosphorylation events that may occur simultaneously or sequentially were discovered in not only model proteins but also complex biological samples including human saliva, chicken egg, and sprouting maize. This provides a new tool to dissect complex biological processes that are triggered by dynamic phosphorylation events.
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Affiliation(s)
- Wenyang Zhang
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, Wuhan, Hubei 430079, P. R. China.,Guangdong Key Laboratory for Crop Germplasm Resources Prevention and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640, P. R. China
| | - Xiebin Leng
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, Wuhan, Hubei 430079, P. R. China
| | - Yinghua Qi
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, Wuhan, Hubei 430079, P. R. China
| | - Xiaojie Yang
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, Wuhan, Hubei 430079, P. R. China
| | - Ruowei Jiang
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, Wuhan, Hubei 430079, P. R. China
| | - Xiaoyu Yang
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, Wuhan, Hubei 430079, P. R. China
| | - Xuewen Hu
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, Wuhan, Hubei 430079, P. R. China
| | - Ying Tan
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, Wuhan, Hubei 430079, P. R. China
| | - Hongying Zhong
- Laboratory of Mass Spectrometry, College of Chemistry, Central China Normal University, Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, Wuhan, Hubei 430079, P. R. China.,Center for Instrumental Analysis, College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, Guangxi 530004, P. R. China
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3
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Conradi C, Obatake N, Shiu A, Tang X. Dynamics of ERK regulation in the processive limit. J Math Biol 2021; 82:32. [PMID: 33694015 DOI: 10.1007/s00285-021-01574-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 09/01/2020] [Accepted: 02/13/2021] [Indexed: 10/21/2022]
Abstract
We consider a model of extracellular signal-regulated kinase regulation by dual-site phosphorylation and dephosphorylation, which exhibits bistability and oscillations, but loses these properties in the limit in which the mechanisms underlying phosphorylation and dephosphorylation become processive. Our results suggest that anywhere along the way to becoming processive, the model remains bistable and oscillatory. More precisely, in simplified versions of the model, precursors to bistability and oscillations (specifically, multistationarity and Hopf bifurcations, respectively) exist at all "processivity levels". Finally, we investigate whether bistability and oscillations can exist together.
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Affiliation(s)
| | - Nida Obatake
- Department of Mathematics, Texas A&M University, College Station, USA
| | - Anne Shiu
- Department of Mathematics, Texas A&M University, College Station, USA
| | - Xiaoxian Tang
- Department of Mathematics, Texas A&M University, College Station, USA. .,School of Mathematical Sciences, Beihang University, Beijing, China.
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Abstract
Extracellular polysaccharides and glycoproteins of pathogenic bacteria assist in adherence, autoaggregation, biofilm formation, and host immune system evasion. As a result, considerable research in the field of glycobiology is dedicated to study the composition and function of glycans associated with virulence, as well as the enzymes involved in their biosynthesis with the aim to identify novel antibiotic targets. Especially, insights into the enzyme mechanism, substrate binding, and transition-state structures are valuable as a starting point for rational inhibitor design. An intriguing aspect of enzymes that generate or process polysaccharides and glycoproteins is the level of processivity. The existence of enzymatic processivity reflects the need for regulation of the final glycan/glycoprotein length and structure, depending on the role they perform. In this Review, we describe the currently reported examples of various processive enzymes involved in polymerization and transfer of sugar moieties, predominantly in bacterial pathogens, with a focus on the biochemical methods, to showcase the importance of studying processivity for understanding the mechanism.
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Affiliation(s)
- Liubov Yakovlieva
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Marthe T. C. Walvoort
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
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5
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Rashkov P, Barrett IP, Beardmore RE, Bendtsen C, Gudelj I. Kinase Inhibition Leads to Hormesis in a Dual Phosphorylation-Dephosphorylation Cycle. PLoS Comput Biol 2016; 12:e1005216. [PMID: 27898662 PMCID: PMC5127489 DOI: 10.1371/journal.pcbi.1005216] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 10/21/2016] [Indexed: 01/07/2023] Open
Abstract
Many antimicrobial and anti-tumour drugs elicit hormetic responses characterised by low-dose stimulation and high-dose inhibition. While this can have profound consequences for human health, with low drug concentrations actually stimulating pathogen or tumour growth, the mechanistic understanding behind such responses is still lacking. We propose a novel, simple but general mechanism that could give rise to hormesis in systems where an inhibitor acts on an enzyme. At its core is one of the basic building blocks in intracellular signalling, the dual phosphorylation-dephosphorylation motif, found in diverse regulatory processes including control of cell proliferation and programmed cell death. Our analytically-derived conditions for observing hormesis provide clues as to why this mechanism has not been previously identified. Current mathematical models regularly make simplifying assumptions that lack empirical support but inadvertently preclude the observation of hormesis. In addition, due to the inherent population heterogeneities, the presence of hormesis is likely to be masked in empirical population-level studies. Therefore, examining hormetic responses at single-cell level coupled with improved mathematical models could substantially enhance detection and mechanistic understanding of hormesis. Hormesis is a highly controversial and poorly understood phenomenon. It describes the idea that an inhibitor molecule, like an anti-cancer or anti-microbial drug, can inadvertently stimulate cell growth instead of suppressing it. This can have a profound effect on human health leading to failures in clinical treatments. Therefore, getting at the mechanistic basis of hormesis is critical for drug development and clinical practice, however molecular mechanisms underpinning hormesis remain poorly understood. In this paper we use a mathematical model to propose a simple and yet general mechanism that could explain why we find hormesis so widely in living systems. In particular, we discover that hormesis is present within a fundamental structure that forms a basic building block of many intracellular signalling pathways found in diverse processes including control of cell reproduction and programmed cell death. The benefits of our study are two-fold. Having simple molecular understanding of the causes of hormetic responses can greatly improve the design of new drug compounds that avoid such responses. Moreover, due to the fundamental nature of the newly proposed mechanism, our findings have a potential broad applicability to both anti-cancer and anti-microbial drugs.
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Affiliation(s)
- Peter Rashkov
- School of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Ian P. Barrett
- Discovery Sciences, Innovative Medicines and Early Development, AstraZeneca, Cambridge, United Kingdom
| | | | - Claus Bendtsen
- Discovery Sciences, Innovative Medicines and Early Development, AstraZeneca, Cambridge, United Kingdom
- * E-mail: (CB); (IG)
| | - Ivana Gudelj
- School of Biosciences, University of Exeter, Exeter, United Kingdom
- * E-mail: (CB); (IG)
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6
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Mathematical modeling reveals the mechanisms of feedforward regulation in cell fate decisions in budding yeast. QUANTITATIVE BIOLOGY 2015. [DOI: 10.1007/s40484-015-0043-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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7
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Zhang XP, Liu F, Wang W. Interplay between Mdm2 and HIPK2 in the DNA damage response. J R Soc Interface 2014; 11:rsif.2014.0319. [PMID: 24829283 DOI: 10.1098/rsif.2014.0319] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The tumour suppressor p53 is activated to induce cell-cycle arrest or apoptosis in the DNA damage response (DDR). p53 phosphorylation at Ser46 by HIPK2 (homeodomain-interacting protein kinase 2) is a critical event in apoptosis induction. Interestingly, HIPK2 is degraded by Mdm2 (a negative regulator of p53), whereas Mdm2 is downregulated by HIPK2 through several mechanisms. Here, we develop a four-module network model for the p53 pathway to clarify the role of interplay between Mdm2 and HIPK2 in the DDR evoked by ultraviolet radiation. By numerical simulations, we reveal that Mdm2-dependent HIPK2 degradation promotes cell survival after mild DNA damage and that inhibition of HIPK2 degradation is sufficient to trigger apoptosis. In response to severe damage, p53 phosphorylation at Ser46 is promoted by the accumulation of HIPK2 due to downregulation of nuclear Mdm2 in the later phase of the response. Meanwhile, the concentration of p53 switches from moderate to high levels, contributing to apoptosis induction. We show that the presence of three mechanisms for Mdm2 downregulation, i.e. repression of mdm2 expression, inhibition of its nuclear entry and HIPK2-induced degradation, guarantees the apoptosis of irreparably damaged cells. Our results agree well with multiple experimental observations, and testable predictions are also made. This work advances our understanding of the regulation of p53 activity in the DDR and suggests that HIPK2 should be a significant target for cancer therapy.
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Affiliation(s)
- Xiao-Peng Zhang
- National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, People's Republic of China Kuang Yaming Honors School, Nanjing University, Nanjing 210093, People's Republic of China
| | - Feng Liu
- National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, People's Republic of China
| | - Wei Wang
- National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, People's Republic of China
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