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Ghosh B, Sarma U, Sourjik V, Legewie S. Sharing of Phosphatases Promotes Response Plasticity in Phosphorylation Cascades. Biophys J 2019; 114:223-236. [PMID: 29320690 DOI: 10.1016/j.bpj.2017.10.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 10/06/2017] [Accepted: 10/17/2017] [Indexed: 01/06/2023] Open
Abstract
Sharing of positive or negative regulators between multiple targets is frequently observed in cellular signaling cascades. For instance, phosphatase sharing between multiple kinases is ubiquitous within the MAPK pathway. Here we investigate how such phosphatase sharing could shape robustness and evolvability of the phosphorylation cascade. Through modeling and evolutionary simulations, we demonstrate that 1) phosphatase sharing dramatically increases robustness of a bistable MAPK response, and 2) phosphatase-sharing cascades evolve faster than nonsharing cascades. This faster evolution is particularly pronounced when evolving from a monostable toward a bistable phenotype, whereas the transition speed of a population from a bistable to monostable response is not affected by phosphatase sharing. This property may enable the phosphatase-sharing design to adapt better in a changing environment. Analysis of the respective mutational landscapes reveal that phosphatase sharing reduces the number of limiting mutations required for transition from monostable to bistable responses, hence facilitating a faster transition to such response types. Taken together, using MAPK cascade as an example, our study offers a general theoretical framework to explore robustness and evolutionary plasticity of signal transduction cascades.
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Affiliation(s)
- Bhaswar Ghosh
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; LOEWE Research Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
| | - Uddipan Sarma
- Modelling of Biological Networks Group, Institute of Molecular Biology (IMB), Mainz, Germany.
| | - Victor Sourjik
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; LOEWE Research Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
| | - Stefan Legewie
- Modelling of Biological Networks Group, Institute of Molecular Biology (IMB), Mainz, Germany.
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Biesiadecki BJ, Westfall MV. Troponin I modulation of cardiac performance: Plasticity in the survival switch. Arch Biochem Biophys 2019; 664:9-14. [PMID: 30684464 DOI: 10.1016/j.abb.2019.01.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/11/2018] [Accepted: 01/22/2019] [Indexed: 01/21/2023]
Abstract
Signaling complexes targeting the myofilament are essential in modulating cardiac performance. A central target of this signaling is cardiac troponin I (cTnI) phosphorylation. This review focuses on cTnI phosphorylation as a model for myofilament signaling, discussing key gaps and future directions towards understanding complex myofilament modulation of cardiac performance. Human heart cTnI is phosphorylated at 14 sites, giving rise to a complex modulatory network of varied functional responses. For example, while classical Ser23/24 phosphorylation mediates accelerated relaxation, protein kinase C phosphorylation of cTnI serves as a brake on contractile function. Additionally, the functional response of cTnI multi-site phosphorylation cannot necessarily be predicted from the response of individual sites alone. These complexities underscore the need for systematically evaluating single and multi-site phosphorylation on myofilament cellular and in vivo contractile function. Ultimately, a complete understanding of these multi-site responses requires work to establish site occupancy and dominance, kinase/phosphatase signaling balance, and the function of adaptive secondary phosphorylation. As cTnI phosphorylation is essential for modulating cardiac performance, future insight into the complex role of cTnI phosphorylation is important to establish sarcomere signaling in the healthy heart as well as identification of novel myofilament targets in the treatment of disease.
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Affiliation(s)
- Brandon J Biesiadecki
- Department of Physiology and Cell Biology, The Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA.
| | - Margaret V Westfall
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI, 48109, USA.
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Long non-coding RNA Gm2199 rescues liver injury and promotes hepatocyte proliferation through the upregulation of ERK1/2. Cell Death Dis 2018; 9:602. [PMID: 29789577 PMCID: PMC5964236 DOI: 10.1038/s41419-018-0595-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 02/06/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a new class of regulators of various human diseases. This study was designed to explore the potential role of lncRNAs in experimental hepatic damage. In vivo hepatic damage in mice and in vitro hepatocyte damage in AML12 and NCTC1469 cells were induced by carbon tetrachloride (CCl4) treatments. Expression profiles of lncRNAs and mRNAs were analyzed by microarray. Bioinformatics analyses were conducted to predict the potential functions of differentially expressed lncRNAs with respect to hepatic damage. Overexpression of lncRNA Gm2199 was achieved by transfection of the pEGFP-N1-Gm2199 plasmid in vitro and adeno-associated virus-Gm2199 in vivo. Cell proliferation and viability was detected by cell counting kit-8 and 5-ethynyl-2′-deoxyuridine assay. Protein and mRNA expressions of extracellular signal-regulated kinase-1/2 (ERK1/2) were detected by western blot and quantitative real-time reverse-transcription PCR (qRT-PCR). Microarray analysis identified 190 and 148 significantly differentially expressed lncRNAs and mRNAs, respectively. The analyses of lncRNA-mRNA co-expression and lncRNA-biological process networks unraveled potential roles of the differentially expressed lncRNAs including Gm2199 in the pathophysiological processes leading to hepatic damage. Gm2199 was downregulated in both damaged livers and hepatocyte lines. Overexpression of Gm2199 restored the reduced proliferation of damaged hepatocyte lines and increased the expression of ERK1/2. Overexpression of Gm2199 also promoted the proliferation and viability of normal hepatocyte lines and increased the level of p-ERK1/2. Overexpression of Gm2199 in vivo also protected mouse liver injury induced by CCl4, evidenced by more proliferating hepatocytes, less serum alanine aminotransferase, less serum aspartate aminotransferase, and decreased hepatic hydroxyproline. The ability of Gm2199 to maintain hepatic proliferation capacity indicates it as a novel anti-liver damage lncRNA.
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Lang SE, Stevenson TK, Schatz TM, Biesiadecki BJ, Westfall MV. Functional communication between PKC-targeted cardiac troponin I phosphorylation sites. Arch Biochem Biophys 2017; 627:1-9. [PMID: 28587770 DOI: 10.1016/j.abb.2017.05.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/16/2017] [Accepted: 05/31/2017] [Indexed: 11/18/2022]
Abstract
Increased protein kinase C (PKC) activity is associated with heart failure, and can target multiple cardiac troponin I (cTnI) residues in myocytes, including S23/24, S43/45 and T144. In earlier studies, cTnI-S43D and/or -S45D augmented S23/24 and T144 phosphorylation, which suggested there is communication between clusters. This communication is now explored by evaluating the impact of phospho-mimetic cTnI S43/45D combined with S23/24D (cTnIS4D) or T144D (cTnISDTD). Gene transfer of epitope-tagged cTnIS4D and cTnISDTD into adult cardiac myocytes progressively replaced endogenous cTnI. Partial replacement with cTnISDTD or cTnIS4D accelerated the time to peak (TTP) shortening and time to 50% re-lengthening (TTR50%) on day 2, but peak shortening was only diminished by cTnIS4D. Extensive cTnIS4D replacement continued to accelerate TTP, and decrease shortening amplitude, while TTR50% returned to baseline levels on day 4. In contrast, cTnISDTD modestly reduced shortening amplitude and continued to accelerate myocyte TTP and TTR50%. These results indicate cTnIS43/45 communicates with S23/24 and T144, with S23/24 exacerbating and T144 attenuating the S43/45D-dependent functional deficit. In addition, more severe functional alterations in cTnIS4D myocytes were accompanied by higher levels of secondary phosphorylation compared to cTnISDTD. These results suggest that secondary phosphorylation helps to maintain steady-state contractile function during chronic cTnI phosphorylation at PKC sites.
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Affiliation(s)
- Sarah E Lang
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI 48109, United States; Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Tamara K Stevenson
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI 48109, United States
| | - Tabea M Schatz
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI 48109, United States
| | - Brandon J Biesiadecki
- Department of Physiology and Cell Biology and Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, United States
| | - Margaret V Westfall
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI 48109, United States; Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, United States.
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McGee RL, Krisenko MO, Geahlen RL, Rundell AE, Buzzard GT. A Computational Study of the Effects of Syk Activity on B Cell Receptor Signaling Dynamics. Processes (Basel) 2015; 3:75-97. [PMID: 26525178 PMCID: PMC4627698 DOI: 10.3390/pr3010075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The kinase Syk is intricately involved in early signaling events in B cells and is required for proper response when antigens bind to B cell receptors (BCRs). Experiments using an analog-sensitive version of Syk (Syk-AQL) have better elucidated its role, but have not completely characterized its behavior. We present a computational model for BCR signaling, using dynamical systems, which incorporates both wild-type Syk and Syk-AQL. Following the use of sensitivity analysis to identify significant reaction parameters, we screen for parameter vectors that produced graded responses to BCR stimulation as is observed experimentally. We demonstrate qualitative agreement between the model and dose response data for both mutant and wild-type kinases. Analysis of our model suggests that the level of NF-κB activation, which is reduced in Syk-AQL cells relative to wild-type, is more sensitive to small reductions in kinase activity than Erkp activation, which is essentially unchanged. Since this profile of high Erkp and reduced NF-κB is consistent with anergy, this implies that anergy is particularly sensitive to small changes in catalytic activity. Also, under a range of forward and reverse ligand binding rates, our model of Erkp and NF-κB activation displays a dependence on a power law affinity: the ratio of the forward rate to a non-unit power of the reverse rate. This dependence implies that B cells may respond to certain details of binding and unbinding rates for ligands rather than simple affinity alone.
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Affiliation(s)
- Reginald L. McGee
- Department of Mathematics, Purdue University, 150 N. University St., West Lafayette, IN 47907, USA
- Author to whom correspondence should be addressed; ; Tel.: +1-765–494–1901
| | - Mariya O. Krisenko
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University Street, West Lafayette, IN 47907, USA
| | - Robert L. Geahlen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University Street, West Lafayette, IN 47907, USA
| | - Ann E. Rundell
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Drive, West Lafayette, IN 47907, USA
| | - Gregery T. Buzzard
- Department of Mathematics, Purdue University, 150 N. University St., West Lafayette, IN 47907, USA
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6
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Padwal MK, Sarma U, Saha B. Comprehensive logic based analyses of Toll-like receptor 4 signal transduction pathway. PLoS One 2014; 9:e92481. [PMID: 24699232 PMCID: PMC3974726 DOI: 10.1371/journal.pone.0092481] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 02/22/2014] [Indexed: 12/19/2022] Open
Abstract
Among the 13 TLRs in the vertebrate systems, only TLR4 utilizes both Myeloid differentiation factor 88 (MyD88) and Toll/Interleukin-1 receptor (TIR)-domain-containing adapter interferon-β-inducing Factor (TRIF) adaptors to transduce signals triggering host-protective immune responses. Earlier studies on the pathway combined various experimental data in the form of one comprehensive map of TLR signaling. But in the absence of adequate kinetic parameters quantitative mathematical models that reveal emerging systems level properties and dynamic inter-regulation among the kinases/phosphatases of the TLR4 network are not yet available. So, here we used reaction stoichiometry-based and parameter independent logical modeling formalism to build the TLR4 signaling network model that captured the feedback regulations, interdependencies between signaling kinases and phosphatases and the outcome of simulated infections. The analyses of the TLR4 signaling network revealed 360 feedback loops, 157 negative and 203 positive; of which, 334 loops had the phosphatase PP1 as an essential component. The network elements' interdependency (positive or negative dependencies) in perturbation conditions such as the phosphatase knockout conditions revealed interdependencies between the dual-specific phosphatases MKP-1 and MKP-3 and the kinases in MAPK modules and the role of PP2A in the auto-regulation of Calmodulin kinase-II. Our simulations under the specific kinase or phosphatase gene-deficiency or inhibition conditions corroborated with several previously reported experimental data. The simulations to mimic Yersinia pestis and E. coli infections identified the key perturbation in the network and potential drug targets. Thus, our analyses of TLR4 signaling highlights the role of phosphatases as key regulatory factors in determining the global interdependencies among the network elements; uncovers novel signaling connections; identifies potential drug targets for infections.
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Affiliation(s)
| | - Uddipan Sarma
- Lab-5, National Center for Cell Science, Pune, Maharashtra, India
| | - Bhaskar Saha
- Lab-5, National Center for Cell Science, Pune, Maharashtra, India
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7
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Mobashir M, Madhusudhan T, Isermann B, Beyer T, Schraven B. Negative interactions and feedback regulations are required for transient cellular response. Sci Rep 2014; 4:3718. [PMID: 24430195 PMCID: PMC3893651 DOI: 10.1038/srep03718] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 12/19/2013] [Indexed: 12/21/2022] Open
Abstract
Signal transduction is a process required to conduct information from a receptor to the nucleus. This process is vital for the control of cellular function and fate. The dynamics of signaling activation and inhibition determine processes such as apoptosis, proliferation, and differentiation. Thus, it is important to understand the factors modulating transient and sustained response. To address this question, by applying mathematical approach we have studied the factors which can alter the activation nature of downstream signaling molecules. The factors which we have investigated are loops (feed forward and feedback loops), cross-talk of signal transduction pathways, and the change in the concentration of the signaling molecules. Based on our results we conclude that among these factors feedback loop and the cross-talks which directly inhibit the target protein dominantly controls the transient cellular response.
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Affiliation(s)
- Mohammad Mobashir
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, 39120, Magdeburg, Germany
| | - Thati Madhusudhan
- Institute of Clinical Chemistry and Pathobiochemistry, Otto-von-Guericke University, 39120, Magdeburg, Germany
| | - Berend Isermann
- Institute of Clinical Chemistry and Pathobiochemistry, Otto-von-Guericke University, 39120, Magdeburg, Germany
| | - Tilo Beyer
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, 39120, Magdeburg, Germany
| | - Burkhart Schraven
- 1] Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, 39120, Magdeburg, Germany [2] Department of Immune Control, Helmholtz Centre for Infectious Disease (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
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8
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Identification of a novel Ser/Thr protein phosphatase Ppq1 as a negative regulator of mating MAP kinase pathway in Saccharomyces cerevisiae. Biochem Biophys Res Commun 2014; 443:252-8. [DOI: 10.1016/j.bbrc.2013.11.110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 11/24/2013] [Indexed: 11/22/2022]
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9
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Agonist activated PKCβII translocation and modulation of cardiac myocyte contractile function. Sci Rep 2013; 3:1971. [PMID: 23756828 PMCID: PMC3679501 DOI: 10.1038/srep01971] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 05/22/2013] [Indexed: 11/26/2022] Open
Abstract
Elevated protein kinase C βII (PKCβII) expression develops during heart failure and yet the role of this isoform in modulating contractile function remains controversial. The present study examines the impact of agonist-induced PKCβII activation on contractile function in adult cardiac myocytes. Diminished contractile function develops in response to low dose phenylephrine (PHE, 100 nM) in controls, while function is preserved in response to PHE in PKCβII-expressing myocytes. PHE also caused PKCβII translocation and a punctate distribution pattern in myocytes expressing this isoform. The preserved contractile function and translocation responses to PHE are blocked by the inhibitor, LY379196 (30 nM) in PKCβII-expressing myocytes. Further analysis showed downstream protein kinase D (PKD) phosphorylation and phosphatase activation are associated with the LY379196-sensitive contractile response. PHE also triggered a complex pattern of end-target phosphorylation in PKCβII-expressing myocytes. These patterns are consistent with bifurcated activation of downstream signaling activity by PKCβII.
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10
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Biarc J, Chalkley RJ, Burlingame AL, Bradshaw RA. Dissecting the roles of tyrosines 490 and 785 of TrkA protein in the induction of downstream protein phosphorylation using chimeric receptors. J Biol Chem 2013; 288:16606-16618. [PMID: 23589303 DOI: 10.1074/jbc.m113.475285] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Receptor tyrosine kinases generally act by forming phosphotyrosine-docking sites on their own endodomains that propagate signals through cascades of post-translational modifications driven by the binding of adaptor/effector proteins. The pathways that are stimulated in any given receptor tyrosine kinase are a function of the initial docking sites that are activated and the availability of downstream participants. In the case of the Trk receptors, which are activated by nerve growth factor, there are only two established phosphotyrosine-docking sites (Tyr-490 and Tyr-785 on TrkA) that are known to be directly involved in signal transduction. Taking advantage of this limited repertoire of docking sites and the availability of PC12 cell lines stably transfected with chimeric receptors composed of the extracellular domain of the PDGF receptor and the transmembrane and intracellular domains of TrkA, the downstream TrkA-induced phosphoproteome was assessed for the "native" receptor and mutants lacking Tyr-490 or both Tyr-490 and Tyr-785. Basal phosphorylation levels were compared with those formed after 20 min of stimulation with PDGF. Several thousand phosphopeptides were identified after TiO2 enrichment, and many were up- or down-regulated by receptor activation. The modified proteins in the native sample contained many of the well established participants in TrkA signaling. The results from the mutant receptors allowed grouping of these downstream targets by their dependence on the two characterized docking site(s). A clear subset that was not dependent on either Tyr-490 or Tyr-785 emerged, providing direct evidence that there are other sites on TrkA that are involved in downstream signaling.
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Affiliation(s)
- Jordane Biarc
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158
| | - Robert J Chalkley
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158.
| | - A L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158
| | - Ralph A Bradshaw
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158; Department of Physiology and Biophysics, University of California, Irvine, California 92697
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11
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Äijö T, Granberg K, Lähdesmäki H. Sorad: a systems biology approach to predict and modulate dynamic signaling pathway response from phosphoproteome time-course measurements. ACTA ACUST UNITED AC 2013; 29:1283-91. [PMID: 23505293 DOI: 10.1093/bioinformatics/btt130] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION Signaling networks mediate responses to different stimuli using a multitude of feed-forward, feedback and cross-talk mechanisms, and malfunctions in these mechanisms have an important role in various diseases. To understand a disease and to help discover novel therapeutic approaches, we have to reveal the molecular mechanisms underlying signal transduction and use that information to design targeted perturbations. RESULTS We have pursued this direction by developing an efficient computational approach, Sorad, which can estimate the structure of signal transduction networks and the associated continuous signaling dynamics from phosphoprotein time-course measurements. Further, Sorad can identify experimental conditions that modulate the signaling toward a desired response. We have analyzed comprehensive phosphoprotein time-course data from a human hepatocellular liver carcinoma cell line and demonstrate here that Sorad provides more accurate predictions of phosphoprotein responses to given stimuli than previously presented methods and, importantly, that Sorad can estimate experimental conditions to achieve a desired signaling response. Because Sorad is data driven, it has a high potential to generate novel hypotheses for further research. Our analysis of the hepatocellular liver carcinoma data predict a regulatory connection where AKT activity is dependent on IKK in TGFα stimulated cells, which is supported by the original data but not included in the original model. AVAILABILITY An implementation of the proposed computational methods will be available at http://research.ics.aalto.fi/csb/software/. CONTACT tarmo.aijo@aalto.fi or harri.lahdesmaki@aalto.fi SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tarmo Äijö
- Department of Information and Computer Science, Aalto University, FI-00076 AALTO, Finland.
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12
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Tian T, Song J. Mathematical modelling of the MAP kinase pathway using proteomic datasets. PLoS One 2012; 7:e42230. [PMID: 22905119 PMCID: PMC3414524 DOI: 10.1371/journal.pone.0042230] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 07/04/2012] [Indexed: 12/29/2022] Open
Abstract
The advances in proteomics technologies offer an unprecedented opportunity and valuable resources to understand how living organisms execute necessary functions at systems levels. However, little work has been done up to date to utilize the highly accurate spatio-temporal dynamic proteome data generated by phosphoprotemics for mathematical modeling of complex cell signaling pathways. This work proposed a novel computational framework to develop mathematical models based on proteomic datasets. Using the MAP kinase pathway as the test system, we developed a mathematical model including the cytosolic and nuclear subsystems; and applied the genetic algorithm to infer unknown model parameters. Robustness property of the mathematical model was used as a criterion to select the appropriate rate constants from the estimated candidates. Quantitative information regarding the absolute protein concentrations was used to refine the mathematical model. We have demonstrated that the incorporation of more experimental data could significantly enhance both the simulation accuracy and robustness property of the proposed model. In addition, we used the MAP kinase pathway inhibited by phosphatases with different concentrations to predict the signal output influenced by different cellular conditions. Our predictions are in good agreement with the experimental observations when the MAP kinase pathway was inhibited by phosphatase PP2A and MKP3. The successful application of the proposed modeling framework to the MAP kinase pathway suggests that our method is very promising for developing accurate mathematical models and yielding insights into the regulatory mechanisms of complex cell signaling pathways.
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Affiliation(s)
- Tianhai Tian
- School of Mathematical Sciences, Faculty of Science, Monash University, Clayton, Victoria, Australia.
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13
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Sarma U, Sareen A, Maiti M, Kamat V, Sudan R, Pahari S, Srivastava N, Roy S, Sinha S, Ghosh I, Chande AG, Mukhopadhyaya R, Saha B. Modeling and experimental analyses reveals signaling plasticity in a bi-modular assembly of CD40 receptor activated kinases. PLoS One 2012; 7:e39898. [PMID: 22815717 PMCID: PMC3399835 DOI: 10.1371/journal.pone.0039898] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 05/28/2012] [Indexed: 12/20/2022] Open
Abstract
Depending on the strength of signal dose, CD40 receptor (CD40) controls ERK-1/2 and p38MAPK activation. At low signal dose, ERK-1/2 is maximally phosphorylated but p38MAPK is minimally phosphorylated; as the signal dose increases, ERK-1/2 phosphorylation is reduced whereas p38MAPK phosphorylation is reciprocally enhanced. The mechanism of reciprocal activation of these two MAPKs remains un-elucidated. Here, our computational model, coupled to experimental perturbations, shows that the observed reciprocity is a system-level behavior of an assembly of kinases arranged in two modules. Experimental perturbations with kinase inhibitors suggest that a minimum of two trans-modular negative feedback loops are required to reproduce the experimentally observed reciprocity. The bi-modular architecture of the signaling pathways endows the system with an inherent plasticity which is further expressed in the skewing of the CD40-induced productions of IL-10 and IL-12, the respective anti-inflammatory and pro-inflammatory cytokines. Targeting the plasticity of CD40 signaling significantly reduces Leishmania major infection in a susceptible mouse strain. Thus, for the first time, using CD40 signaling as a model, we show how a bi-modular assembly of kinases imposes reciprocity to a receptor signaling. The findings unravel that the signalling plasticity is inherent to a reciprocal system and that the principle can be used for designing a therapy.
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Affiliation(s)
- Uddipan Sarma
- National Centre for Cell Science, Ganeshkhind, Pune, India
| | - Archana Sareen
- National Centre for Cell Science, Ganeshkhind, Pune, India
| | | | - Vanita Kamat
- National Centre for Cell Science, Ganeshkhind, Pune, India
| | - Raki Sudan
- National Centre for Cell Science, Ganeshkhind, Pune, India
| | | | | | - Somenath Roy
- Vidyasagar University, Midnapore, West Bengal, India
| | - Sitabhra Sinha
- Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai, India
| | - Indira Ghosh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Ajit G. Chande
- Advanced Centre for Training, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
| | - Robin Mukhopadhyaya
- Advanced Centre for Training, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
| | - Bhaskar Saha
- National Centre for Cell Science, Ganeshkhind, Pune, India
- * E-mail:
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14
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Sarma U, Ghosh I. Different designs of kinase-phosphatase interactions and phosphatase sequestration shapes the robustness and signal flow in the MAPK cascade. BMC SYSTEMS BIOLOGY 2012; 6:82. [PMID: 22748295 PMCID: PMC3508828 DOI: 10.1186/1752-0509-6-82] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 05/09/2012] [Indexed: 02/08/2023]
Abstract
Background The three layer mitogen activated protein kinase (MAPK) signaling cascade exhibits different designs of interactions between its kinases and phosphatases. While the sequential interactions between the three kinases of the cascade are tightly preserved, the phosphatases of the cascade, such as MKP3 and PP2A, exhibit relatively diverse interactions with their substrate kinases. Additionally, the kinases of the MAPK cascade can also sequester their phosphatases. Thus, each topologically distinct interaction design of kinases and phosphatases could exhibit unique signal processing characteristics, and the presence of phosphatase sequestration may lead to further fine tuning of the propagated signal. Results We have built four architecturally distinct types of models of the MAPK cascade, each model with identical kinase-kinase interactions but unique kinases-phosphatases interactions. Our simulations unravelled that MAPK cascade’s robustness to external perturbations is a function of nature of interaction between its kinases and phosphatases. The cascade’s output robustness was enhanced when phosphatases were sequestrated by their target kinases. We uncovered a novel implicit/hidden negative feedback loop from the phosphatase MKP3 to its upstream kinase Raf-1, in a cascade resembling the B cell MAPK cascade. Notably, strength of the feedback loop was reciprocal to the strength of phosphatases’ sequestration and stronger sequestration abolished the feedback loop completely. An experimental method to verify the presence of the feedback loop is also proposed. We further showed, when the models were activated by transient signal, memory (total time taken by the cascade output to reach its unstimulated level after removal of signal) of a cascade was determined by the specific designs of interaction among its kinases and phosphatases. Conclusions Differences in interaction designs among the kinases and phosphatases can differentially shape the robustness and signal response behaviour of the MAPK cascade and phosphatase sequestration dramatically enhances the robustness to perturbations in each of the cascade. An implicit negative feedback loop was uncovered from our analysis and we found that strength of the negative feedback loop is reciprocally related to the strength of phosphatase sequestration. Duration of output phosphorylation in response to a transient signal was also found to be determined by the individual cascade’s kinase-phosphatase interaction design.
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Affiliation(s)
- Uddipan Sarma
- National Centre for Cell Science, Ganeshkhind, Pune-7, India.
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Sarma U, Ghosh I. Oscillations in MAPK cascade triggered by two distinct designs of coupled positive and negative feedback loops. BMC Res Notes 2012; 5:287. [PMID: 22694947 PMCID: PMC3532088 DOI: 10.1186/1756-0500-5-287] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 04/30/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Feedback loops, both positive and negative are embedded in the Mitogen Activated Protein Kinase (MAPK) cascade. In the three layer MAPK cascade, both feedback loops originate from the terminal layer and their sites of action are either of the two upstream layers. Recent studies have shown that the cascade uses coupled positive and negative feedback loops in generating oscillations. Two plausible designs of coupled positive and negative feedback loops can be elucidated from the literature; in one design the positive feedback precedes the negative feedback in the direction of signal flow and vice-versa in another. But it remains unexplored how the two designs contribute towards triggering oscillations in MAPK cascade. Thus it is also not known how amplitude, frequency, robustness or nature (analogous/digital) of the oscillations would be shaped by these two designs. RESULTS We built two models of MAPK cascade that exhibited oscillations as function of two underlying designs of coupled positive and negative feedback loops. Frequency, amplitude and nature (digital/analogous) of oscillations were found to be differentially determined by each design. It was observed that the positive feedback emerging from an oscillating MAPK cascade and functional in an external signal processing module can trigger oscillations in the target module, provided that the target module satisfy certain parametric requirements. The augmentation of the two models was done to incorporate the nuclear-cytoplasmic shuttling of cascade components followed by induction of a nuclear phosphatase. It revealed that the fate of oscillations in the MAPK cascade is governed by the feedback designs. Oscillations were unaffected due to nuclear compartmentalization owing to one design but were completely abolished in the other case. CONCLUSION The MAPK cascade can utilize two distinct designs of coupled positive and negative feedback loops to trigger oscillations. The amplitude, frequency and robustness of the oscillations in presence or absence of nuclear compartmentalization were differentially determined by two designs of coupled positive and negative feedback loops. A positive feedback from an oscillating MAPK cascade was shown to induce oscillations in an external signal processing module, uncovering a novel regulatory aspect of MAPK signal processing.
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Affiliation(s)
- Uddipan Sarma
- National Centre for Cell Science, Ganeshkhind, Pune, India.
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Chatterjee S, Kumar D. Unraveling the design principle for motif organization in signaling networks. PLoS One 2011; 6:e28606. [PMID: 22164309 PMCID: PMC3228783 DOI: 10.1371/journal.pone.0028606] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 11/11/2011] [Indexed: 11/21/2022] Open
Abstract
Cellular signaling networks display complex architecture. Defining the design principle of this architecture is crucial for our understanding of various biological processes. Using a mathematical model for three-node feed-forward loops, we identify that the organization of motifs in specific manner within the network serves as an important regulator of signal processing. Further, incorporating a systemic stochastic perturbation to the model we could propose a possible design principle, for higher-order organization of motifs into larger networks in order to achieve specific biological output. The design principle was then verified in a large, complex human cancer signaling network. Further analysis permitted us to classify signaling nodes of the network into robust and vulnerable nodes as a result of higher order motif organization. We show that distribution of these nodes within the network at strategic locations then provides for the range of features displayed by the signaling network.
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Affiliation(s)
- Samrat Chatterjee
- Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Dhiraj Kumar
- Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- * E-mail:
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A novel mechanism for ERK-dependent regulation of IL4 transcription during human Th2-cell differentiation. Immunol Cell Biol 2011; 90:676-87. [PMID: 21989417 PMCID: PMC3419974 DOI: 10.1038/icb.2011.87] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We demonstrate that the mitogen-activated protein kinases extracellular signal-regulated kinase (ERK)-1 and ERK-2 have a central role in mediating T-cell receptor-dependent induction of IL4 expression in human CD4+ T cells. Significantly, this involved a novel mechanism wherein receptor cross-linking induced activated ERK to physically associate with a promoter element on the IL4 gene. The proximally localized ERK then facilitated recruitment of the key transcription factors necessary for initiating IL4 gene transcription. Although both ERK-1 and ERK-2 bound to the promoter, recruitment of either one alone was found to be sufficient. We thus identify a novel mode of function for ERK wherein its physical association with the promoter serves as a prerequisite for enhanceosome assembly. This unusual pathway is also indispensable for human Th2-cell differentiation.
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