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Kochel B. Negative feedback systems for modelling NF-κB transcription factor oscillatory activity. Transcription 2024:1-32. [PMID: 38739365 DOI: 10.1080/21541264.2024.2331887] [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: 10/27/2023] [Accepted: 03/13/2024] [Indexed: 05/14/2024] Open
Abstract
Low-dimensional negative feedback systems (NFSs) were developed within a signal flow model to describe the oscillatory activities of NF-κB caused by interactions with its inhibitor IκBα. The NFSs were established as 3rd- and 4th-order linear systems containing unperturbed and perturbed negative feedback (NF) loops with constant or time-varying NF strengths and a feed-forward loop. NF-related analytical solutions to the NFSs representing the time courses of NF-κB and IκBα were determined and their exact mathematical relationship was found. The NFS's parameters were determined to fit the experimental time courses of NF-κB in TNF-α-stimulated embryonic fibroblasts, rela-/- embryonic fibroblasts reconstituted with RelA, C9L cells, GFP-p65 knock-in embryonic fibroblasts and embryogenic fibroblasts lacking Iκβ and IκBε, LPS-stimulated IC-21 macrophages treated or not with DCPA, and anti-IgM-stimulated DT40 B-lymphocytes. The unperturbed and perturbed NFSs describing the above biosystems generated isochronous and non-isochronous solutions, depending on a constant or time-varying NF strength, respectively. The oscillation period of the NF-coupled solutions, the phase difference between them and the time delays in the appearance of cytoplasmic IκBα after stimulation of NF-κB were determined. A significant divergence between the IκBα solutions to the NFSs and the IκBα experimental courses led to a rejection of the NF coupling between NF-κB and IκBα in the above biosystems. It was shown that neither the linearity nor the low dimensionality of the NFSs altered the NF relationship and the divergence between the IκBα solutions to the NFS and IκBα experimental time courses. Although the NF relationship between IκBα and NF-κB was not confirmed in all the experimental data analyzed, delayed negative feedback was found in some cases.
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Affiliation(s)
- Bonawentura Kochel
- Immunotherapy Central Europe, Wroclaw Medical University, Wrocław, Poland
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Andrews SS, Kochen M, Smith L, Feng S, Wiley HS, Sauro HM. Signal integration and integral feedback control with biochemical reaction networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591337. [PMID: 38746178 PMCID: PMC11092504 DOI: 10.1101/2024.04.26.591337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Biochemical reaction networks perform a variety of signal processing functions, one of which is computing the integrals of signal values. This is often used in integral feedback control, where it enables a system's output to respond to changing inputs, but to then return exactly back to some pre-determined setpoint value afterward. To gain a deeper understanding of how biochemical networks are able to both integrate signals and perform integral feedback control, we investigated these abilities for several simple reaction networks. We found imperfect overlap between these categories, with some networks able to perform both tasks, some able to perform integration but not integral feedback control, and some the other way around. Nevertheless, networks that could either integrate or perform integral feedback control shared key elements. In particular, they included a chemical species that was neutrally stable in the open loop system (no feedback), meaning that this species does not have a unique stable steady-state concentration. Neutral stability could arise from zeroth order decay reactions, binding to a partner that was produced at a constant rate (which occurs in antithetic control), or through a long chain of covalent cycles. Mathematically, it arose from rate equations for the reaction network that were underdetermined when evaluated at steady-state.
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Andrews SS, Wiley HS, Sauro HM. Design patterns of biological cells. Bioessays 2024; 46:e2300188. [PMID: 38247191 PMCID: PMC10922931 DOI: 10.1002/bies.202300188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/03/2023] [Accepted: 12/14/2023] [Indexed: 01/23/2024]
Abstract
Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to cell biology to lend a new perspective on the evolved designs of cells' underlying reaction networks. We present a catalog of 21 design patterns divided into three categories: creational patterns describe processes that build the cell, structural patterns describe the layouts of reaction networks, and behavioral patterns describe reaction network function. Applying this pattern language to the E. coli central metabolic reaction network, the yeast pheromone response signaling network, and other examples lends new insights into these systems.
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Affiliation(s)
- Steven S. Andrews
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - H. Steven Wiley
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Herbert M. Sauro
- Department of Bioengineering, University of Washington, Seattle, WA, USA
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Ram A, Murphy D, DeCuzzi N, Patankar M, Hu J, Pargett M, Albeck JG. A guide to ERK dynamics, part 2: downstream decoding. Biochem J 2023; 480:1909-1928. [PMID: 38038975 PMCID: PMC10754290 DOI: 10.1042/bcj20230277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 12/02/2023]
Abstract
Signaling by the extracellular signal-regulated kinase (ERK) pathway controls many cellular processes, including cell division, death, and differentiation. In this second installment of a two-part review, we address the question of how the ERK pathway exerts distinct and context-specific effects on multiple processes. We discuss how the dynamics of ERK activity induce selective changes in gene expression programs, with insights from both experiments and computational models. With a focus on single-cell biosensor-based studies, we summarize four major functional modes for ERK signaling in tissues: adjusting the size of cell populations, gradient-based patterning, wave propagation of morphological changes, and diversification of cellular gene expression states. These modes of operation are disrupted in cancer and other related diseases and represent potential targets for therapeutic intervention. By understanding the dynamic mechanisms involved in ERK signaling, there is potential for pharmacological strategies that not only simply inhibit ERK, but also restore functional activity patterns and improve disease outcomes.
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Affiliation(s)
- Abhineet Ram
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - Devan Murphy
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - Nicholaus DeCuzzi
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - Madhura Patankar
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - Jason Hu
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
| | - John G. Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, CA, U.S.A
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5
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Qiao L, Ghosh P, Rangamani P. Design principles of improving the dose-response alignment in coupled GTPase switches. NPJ Syst Biol Appl 2023; 9:3. [PMID: 36720885 PMCID: PMC9889403 DOI: 10.1038/s41540-023-00266-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/17/2023] [Indexed: 02/02/2023] Open
Abstract
"Dose-response alignment" (DoRA), where the downstream response of cellular signaling pathways closely matches the fraction of activated receptor, can improve the fidelity of dose information transmission. The negative feedback has been experimentally identified as a key component for DoRA, but numerical simulations indicate that negative feedback is not sufficient to achieve perfect DoRA, i.e., perfect match of downstream response and receptor activation level. Thus a natural question is whether there exist design principles for signaling motifs within only negative feedback loops to improve DoRA to near-perfect DoRA. Here, we investigated several model formulations of an experimentally validated circuit that couples two molecular switches-mGTPase (monomeric GTPase) and tGTPase (heterotrimeric GTPases) - with negative feedback loops. In the absence of feedback, the low and intermediate mGTPase activation levels benefit DoRA in mass action and Hill-function models, respectively. Adding negative feedback has versatile roles on DoRA: it may impair DoRA in the mass action model with low mGTPase activation level and Hill-function model with intermediate mGTPase activation level; in other cases, i.e., the mass action model with a high mGTPase activation level or the Hill-function model with a non-intermediate mGTPase activation level, it improves DoRA. Furthermore, we found that DoRA in a longer cascade (i.e., tGTPase) can be obtained using Hill-function kinetics under certain conditions. In summary, we show how ranges of activity of mGTPase, reaction kinetics, the negative feedback, and the cascade length affect DoRA. This work provides a framework for improving the DoRA performance in signaling motifs with negative feedback.
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Affiliation(s)
- Lingxia Qiao
- Department of Mechanical and Aerospace Engineering, Jacob's School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Moores Comprehensive Cancer Center, University of California San Diego, La Jolla, CA, USA.
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, Jacob's School of Engineering, University of California San Diego, La Jolla, CA, USA.
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Dynamics and Sensitivity of Signaling Pathways. CURRENT PATHOBIOLOGY REPORTS 2022; 10:11-22. [PMID: 36969954 PMCID: PMC10035447 DOI: 10.1007/s40139-022-00230-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Purpose of Review Signaling pathways serve to communicate information about extracellular conditions into the cell, to both the nucleus and cytoplasmic processes to control cell responses. Genetic mutations in signaling network components are frequently associated with cancer and can result in cells acquiring an ability to divide and grow uncontrollably. Because signaling pathways play such a significant role in cancer initiation and advancement, their constituent proteins are attractive therapeutic targets. In this review, we discuss how signaling pathway modeling can assist with identifying effective drugs for treating diseases, such as cancer. An achievement that would facilitate the use of such models is their ability to identify controlling biochemical parameters in signaling pathways, such as molecular abundances and chemical reaction rates, because this would help determine effective points of attack by therapeutics. Recent Findings We summarize the current state of understanding the sensitivity of phosphorylation cycles with and without sequestration. We also describe some basic properties of regulatory motifs including feedback and feedforward regulation. Summary Although much recent work has focused on understanding the dynamics and particularly the sensitivity of signaling networks in eukaryotic systems, there is still an urgent need to build more scalable models of signaling networks that can appropriately represent their complexity across different cell types and tumors.
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Ji F, Wang S, Shao S, Sarkar P, Xue M. Real-Time Analysis of AKT Signaling Activities at Single-Cell Resolution Using Cyclic Peptide-Based Probes. Methods Mol Biol 2022; 2394:65-80. [PMID: 35094322 DOI: 10.1007/978-1-0716-1811-0_5] [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: 06/14/2023]
Abstract
Here we present a protocol for interrogating AKT signaling activities in living single cells, using a pair of cyclic peptide-based fluorescent probes. These probes are encapsulated in liposomes and delivered into cells, where they continuously report on AKT signaling activities through a Föster resonance energy transfer mechanism. We describe the use of a microwell chip to achieve single-cell resolution and demonstrate the procedure for on-chip immunostaining. Finally, we provide a method for data extraction, correction, and processing.
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Affiliation(s)
- Fei Ji
- Department of Chemistry, University of California, Riverside, Riverside, CA, USA
| | - Siwen Wang
- Department of Chemistry, University of California, Riverside, Riverside, CA, USA
| | - Shiqun Shao
- Department of Chemistry, University of California, Riverside, Riverside, CA, USA
| | - Priyanka Sarkar
- Department of Chemistry, University of California, Riverside, Riverside, CA, USA
| | - Min Xue
- Department of Chemistry, University of California, Riverside, Riverside, CA, USA.
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Salinas Castellanos LC, Uchitel OD, Weissmann C. Signaling Pathways in Proton and Non-proton ASIC1a Activation. Front Cell Neurosci 2021; 15:735414. [PMID: 34675777 PMCID: PMC8523820 DOI: 10.3389/fncel.2021.735414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/09/2021] [Indexed: 11/13/2022] Open
Abstract
Acid-sensing ion channels (ASICs) regulate synaptic activities and play important roles in neurodegenerative diseases as well as pain conditions. Classically, ASICs are described as transiently activated by a reduced pH, followed by desensitization; the activation allows sodium influx, and in the case of ASIC1a-composed channels, also calcium to some degree. Several factors are emerging and extensively analyzed as modulators, activating, inhibiting, and potentiating specific channel subunits. However, the signaling pathways triggered by channel activation are only starting to be revealed.The channel has been recently shown to be activated through a mechanism other than proton-mediated. Indeed, the large extracellular loop of these channels opens the possibility that other non-proton ligands might exist. One such molecule discovered was a toxin present in the Texas coral snake venom. The finding was associated with the activation of the channel at neutral pH via the toxin and causing intense and unremitting pain.By using different pharmacological tools, we analyzed the downstream signaling pathway triggered either by the proton and non-proton activation for human, mouse, and rat ASIC1a-composed channels in in vitro models. We show that for all species analyzed, the non-protonic mode of activation determines the activation of the ERK signaling cascade at a higher level and duration compared to the proton mode.This study adds to the growing evidence of the important role ASIC1a channels play in different physiological and pathological conditions and also hints at a possible pathological mechanism for a sustained effect.
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Affiliation(s)
| | | | - Carina Weissmann
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE—UBA CONICET), Facultad de Ciencias, Exactas y Naturales de la Universidad de Buenos Aires, Buenos Aires, Argentina
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9
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Gillies TE, Pargett M, Silva JM, Teragawa CK, McCormick F, Albeck JG. Oncogenic mutant RAS signaling activity is rescaled by the ERK/MAPK pathway. Mol Syst Biol 2021; 16:e9518. [PMID: 33073539 PMCID: PMC7569415 DOI: 10.15252/msb.20209518] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 09/02/2020] [Accepted: 09/21/2020] [Indexed: 12/22/2022] Open
Abstract
Activating mutations in RAS are present in ~ 30% of human tumors, and the resulting aberrations in ERK/MAPK signaling play a central role in oncogenesis. However, the form of these signaling changes is uncertain, with activating RAS mutants linked to both increased and decreased ERK activation in vivo. Rationally targeting the kinase activity of this pathway requires clarification of the quantitative effects of RAS mutations. Here, we use live‐cell imaging in cells expressing only one RAS isoform to quantify ERK activity with a new level of accuracy. We find that despite large differences in their biochemical activity, mutant KRAS isoforms within cells have similar ranges of ERK output. We identify roles for pathway‐level effects, including variation in feedback strength and feedforward modulation of phosphatase activity, that act to rescale pathway sensitivity, ultimately resisting changes in the dynamic range of ERK activity while preserving responsiveness to growth factor stimuli. Our results reconcile seemingly inconsistent reports within the literature and imply that the signaling changes induced by RAS mutations early in oncogenesis are subtle.
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Affiliation(s)
- Taryn E Gillies
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
| | - Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
| | - Jillian M Silva
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Carolyn K Teragawa
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
| | - Frank McCormick
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA.,Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - John G Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
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10
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Wang S, Perkins NG, Ji F, Chaudhuri R, Guo Z, Sarkar P, Shao S, Li Z, Xue M. Digitonin-facilitated delivery of imaging probes enables single-cell analysis of AKT signalling activities in suspension cells. Analyst 2021; 146:5307-5315. [PMID: 34351328 DOI: 10.1039/d1an00751c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Analyzing intracellular signalling protein activities in living cells promises a better understanding of the signalling cascade and related biological processes. We have previously developed cyclic peptide-based probes for analyzing intracellular AKT signalling activities, but these peptide probes were not cell-permeable. Implementing fusogenic liposomes as delivery vehicles could circumvent the problem when analyzing adherent cells, but it remained challenging to study suspension cells using similar approaches. Here, we present a method for delivering these imaging probes into suspension cells using digitonin, which could transiently perforate the cell membrane. Using U87, THP-1, and Jurkat cells as model systems representing suspended adherent cells, myeloid cells, and lymphoid cells, we demonstrated that low concentrations of digitonin enabled a sufficient amount of probes to enter the cytosol without affecting cell viability. We further combined this delivery method with a microwell single-cell chip and interrogated the AKT signalling dynamics in THP-1 and Jurkat cells, followed by immunofluorescence-based quantitation of AKT expression levels. We resolved the cellular heterogeneity in AKT signalling activities and showed that the kinetic patterns of AKT signalling and the AKT expression levels were related in THP-1 cells, but decoupled in Jurkat cells. We expect that our approach can be adapted to study other suspension cells.
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Affiliation(s)
- Siwen Wang
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, USA.
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11
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Azizoglu A, Brent R, Rudolf F. A precisely adjustable, variation-suppressed eukaryotic transcriptional controller to enable genetic discovery. eLife 2021; 10:69549. [PMID: 34342575 PMCID: PMC8421071 DOI: 10.7554/elife.69549] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/02/2021] [Indexed: 11/13/2022] Open
Abstract
Conditional expression of genes and observation of phenotype remain central to biological discovery. Current methods enable either on/off or imprecisely controlled graded gene expression. We developed a 'well-tempered' controller, WTC846, for precisely adjustable, graded, growth condition independent expression of genes in Saccharomyces cerevisiae. Controlled genes are expressed from a strong semisynthetic promoter repressed by the prokaryotic TetR, which also represses its own synthesis; with basal expression abolished by a second, 'zeroing' repressor. The autorepression loop lowers cell-to-cell variation while enabling precise adjustment of protein expression by a chemical inducer. WTC846 allelic strains in which the controller replaced the native promoters recapitulated known null phenotypes (CDC42, TPI1), exhibited novel overexpression phenotypes (IPL1), showed protein dosage-dependent growth rates and morphological phenotypes (CDC28, TOR2, PMA1 and the hitherto uncharacterized PBR1), and enabled cell cycle synchronization (CDC20). WTC846 defines an 'expression clamp' allowing protein dosage to be adjusted by the experimenter across the range of cellular protein abundances, with limited variation around the setpoint.
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Affiliation(s)
| | - Roger Brent
- Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
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12
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Qiao L, Sinha S, El-hafeez AAA, Lo I, Midde KK, Ngo T, Aznar N, Lopez-sanchez I, Gupta V, Farquhar MG, Rangamani P, Ghosh P. A Circuit for Secretion-coupled Cellular Autonomy in Multicellular Eukaryotes.. [DOI: 10.1101/2021.03.18.436048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
ABSTRACTCancers represent complex autonomous systems, displaying self-sufficiency in growth signaling. Autonomous growth is fueled by a cancer cell’s ability to ‘secrete-and-sense’ growth factors: a poorly understood phenomenon. Using an integrated systems and experimental approach, here we dissect the impact of a feedback-coupled GTPase circuit within the secretory pathway that imparts secretion-coupled autonomy. The circuit is assembled when the Ras-superfamily monomeric GTPase Arf1, and the heterotrimeric GTPase Giαβγ and their corresponding GAPs and GEFs are coupled by GIV/Girdin, a protein that is known to fuel aggressive traits in diverse cancers. One forward and two key negative feedback loops within the circuit create closed-loop control (CLC), allow the two GTPases to coregulate each other, and convert the expected switch-like behavior of Arf1-dependent secretion into an unexpected dose response alignment behavior of sensing and secretion. Such behavior translates into cell survival that is self-sustained by stimulus-proportionate secretion. Proteomic studies and protein-protein interaction network analyses pinpoint growth factors (e.g., the epidermal growth factor; EGF) as a key stimuli for such self-sustenance. Findings highlight how enhanced coupling of two biological switches in cancer cells is critical for multiscale feedback control to achieve secretion-coupled autonomy of growth factors.SYNOPSIS IMAGESTANDFIRST TEXTThis work defines the inner workings of a Golgi-localized molecular circuitry comprised of coupled GTPases, which empowers cells to achieve self-sufficiency in growth factor signaling by creating a secrete-and-sense autocrine loop.HIGHLIGHTS/MAIN FINDINGSModeling and experimental approaches were used to dissect a coupled GTPase circuit.Coupling enables closed loop feedback and mutual control of GTPases.Coupling generates dose response alignment behavior of sensing and secretion of growth factors.Coupling is critical for multiscale feedback control to achieve secretion-coupled autonomy.
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Molecular switch architecture determines response properties of signaling pathways. Proc Natl Acad Sci U S A 2021; 118:2013401118. [PMID: 33688042 DOI: 10.1073/pnas.2013401118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Many intracellular signaling pathways are composed of molecular switches, proteins that transition between two states-on and off Typically, signaling is initiated when an external stimulus activates its cognate receptor that, in turn, causes downstream switches to transition from off to on using one of the following mechanisms: activation, in which the transition rate from the off state to the on state increases; derepression, in which the transition rate from the on state to the off state decreases; and concerted, in which activation and derepression operate simultaneously. We use mathematical modeling to compare these signaling mechanisms in terms of their dose-response curves, response times, and abilities to process upstream fluctuations. Our analysis elucidates several operating principles for molecular switches. First, activation increases the sensitivity of the pathway, whereas derepression decreases sensitivity. Second, activation generates response times that decrease with signal strength, whereas derepression causes response times to increase with signal strength. These opposing features allow the concerted mechanism to not only show dose-response alignment, but also to decouple the response time from stimulus strength. However, these potentially beneficial properties come at the expense of increased susceptibility to upstream fluctuations. We demonstrate that these operating principles also hold when the models are extended to include additional features, such as receptor removal, kinetic proofreading, and cascades of switches. In total, we show how the architecture of molecular switches govern their response properties. We also discuss the biological implications of our findings.
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14
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Properties of cell signaling pathways and gene expression systems operating far from steady-state. Sci Rep 2018; 8:17035. [PMID: 30451879 PMCID: PMC6242903 DOI: 10.1038/s41598-018-34766-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/23/2018] [Indexed: 11/10/2022] Open
Abstract
Ligand-receptor systems, covalent modification cycles, and transcriptional networks are basic units of signaling systems and their steady-state properties are well understood. However, the behavior of such systems before steady-state is poorly characterized. Here, we analyzed the properties of input-output curves for each of these systems as they approach steady-state. In ligand-receptor systems, the EC50 (concentration of the ligand that occupies 50% of the receptors) is higher before the system reaches steady-state. Based on this behavior, we have previously defined PRESS (for pre-equilibrium sensing and signaling), a general “systems level” mechanism cells may use to overcome input saturation. Originally, we showed that, given a step stimulation, PRESS operates when the kinetics of ligand-receptor binding are slower than the downstream signaling steps. Now, we show that, provided the input increases slowly, it is not essential for the ligand binding reaction itself to be slow. In addition, we demonstrate that covalent modification cycles and gene expression systems may also operate in PRESS mode. Thus, nearly all biochemical processes may operate in PRESS mode, suggesting that this mechanism may be ubiquitous in cell signaling systems.
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15
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Experimental and engineering approaches to intracellular communication. Essays Biochem 2018; 62:515-524. [PMID: 30139878 DOI: 10.1042/ebc20180024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/10/2018] [Accepted: 08/14/2018] [Indexed: 11/17/2022]
Abstract
Communication between and within cells is essential for multicellular life. While intracellular signal transduction pathways are often specified in molecular terms, the information content they transmit remains poorly defined. Here, we review research efforts to merge biological experimentation with concepts of communication that emerge from the engineering disciplines of signal processing and control theory. We discuss the challenges of performing experiments that quantitate information transfer at the molecular level, and we highlight recent studies that have advanced toward a clearer definition of the information content carried by signaling molecules. Across these studies, we emphasize a theme of increasingly well-matched experimental and theoretical approaches to decode the data streams directing cellular behavior.
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Andrews SS, Brent R, Balázsi G. Transferring information without distortion. eLife 2018; 7:41894. [PMID: 30358530 PMCID: PMC6202050 DOI: 10.7554/elife.41894] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 01/05/2023] Open
Abstract
Despite employing diverse molecular mechanisms, many different cell signaling systems avoid losing information by transmitting it in a linear manner.
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Affiliation(s)
- Steven S Andrews
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States.,Department of Physics, Seattle University, Seattle, United States
| | - Roger Brent
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Gábor Balázsi
- Louis and Beatrice Laufer Center for Physical & Quantitative Biology, Stony Brook University, Stony Brook, United States.,Department of Biomedical Engineering, Stony Brook University, Stony Brook, United States
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17
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Abstract
One challenge in biology is to make sense of the complexity of biological networks. A good system to approach this is signaling pathways, whose well-characterized molecular details allow us to relate the internal processes of each pathway to their input-output behavior. In this study, we analyzed mathematical models of three metazoan signaling pathways: the canonical Wnt, MAPK/ERK, and Tgfβ pathways. We find an unexpected convergence: the three pathways behave in some physiological contexts as linear signal transmitters. Testing the results experimentally, we present direct measurements of linear input-output behavior in the Wnt and ERK pathways. Analytics from each model further reveal that linearity arises through different means in each pathway, which we tested experimentally in the Wnt and ERK pathways. Linearity is a desired property in engineering where it facilitates fidelity and superposition in signal transmission. Our findings illustrate how cells tune different complex networks to converge on the same behavior.
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Affiliation(s)
- Harry Nunns
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
| | - Lea Goentoro
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
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Pesce CG, Zdraljevic S, Peria WJ, Bush A, Repetto MV, Rockwell D, Yu RC, Colman-Lerner A, Brent R. Single-cell profiling screen identifies microtubule-dependent reduction of variability in signaling. Mol Syst Biol 2018; 14:e7390. [PMID: 29618636 PMCID: PMC5884679 DOI: 10.15252/msb.20167390] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/25/2018] [Accepted: 02/06/2018] [Indexed: 01/01/2023] Open
Abstract
Populations of isogenic cells often respond coherently to signals, despite differences in protein abundance and cell state. Previously, we uncovered processes in the Saccharomyces cerevisiae pheromone response system (PRS) that reduced cell-to-cell variability in signal strength and cellular response. Here, we screened 1,141 non-essential genes to identify 50 "variability genes". Most had distinct, separable effects on strength and variability of the PRS, defining these quantities as genetically distinct "axes" of system behavior. Three genes affected cytoplasmic microtubule function: BIM1, GIM2, and GIM4 We used genetic and chemical perturbations to show that, without microtubules, PRS output is reduced but variability is unaffected, while, when microtubules are present but their function is perturbed, output is sometimes lowered, but its variability is always high. The increased variability caused by microtubule perturbations required the PRS MAP kinase Fus3 and a process at or upstream of Ste5, the membrane-localized scaffold to which Fus3 must bind to be activated. Visualization of Ste5 localization dynamics demonstrated that perturbing microtubules destabilized Ste5 at the membrane signaling site. The fact that such microtubule perturbations cause aberrant fate and polarity decisions in mammals suggests that microtubule-dependent signal stabilization might also operate throughout metazoans.
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Affiliation(s)
| | - Stefan Zdraljevic
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | | | - Alan Bush
- IFIBYNE-UBA-CONICET and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Victoria Repetto
- IFIBYNE-UBA-CONICET and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | | | - Alejandro Colman-Lerner
- IFIBYNE-UBA-CONICET and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Roger Brent
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Winters MJ, Pryciak PM. Analysis of the thresholds for transcriptional activation by the yeast MAP kinases Fus3 and Kss1. Mol Biol Cell 2018; 29:669-682. [PMID: 29321252 PMCID: PMC6004581 DOI: 10.1091/mbc.e17-10-0578] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 12/19/2017] [Accepted: 01/03/2018] [Indexed: 12/31/2022] Open
Abstract
Signaling in the pheromone response pathway of budding yeast activates two distinct MAP kinases (MAPKs), Fus3 and Kss1. Either MAPK alone can mediate pheromone-induced transcription, but it has been unclear to what degree each one contributes to transcriptional output in wild-type cells. Here, we report that transcription reflects the ratio of active to inactive MAPK, and not simply the level of active MAPK. For Kss1 the majority of MAPK molecules must be converted to the active form, whereas for Fus3 only a small minority must be activated. These different activation thresholds reflect two opposing effects of each MAPK, in which the inactive forms inhibit transcription, whereas the active forms promote transcription. Moreover, negative feedback from Fus3 limits activation of Kss1 so that it does not meet its required threshold in wild-type cells but does so only when hyperactivated in cells lacking Fus3. The results suggest that the normal transcriptional response involves asymmetric contributions from the two MAPKs, in which pheromone signaling reduces the negative effect of Kss1 while increasing the positive effect of Fus3. These findings reveal new functional distinctions between these MAPKs, and help illuminate how inhibitory functions shape positive pathway outputs in both pheromone and filamentation pathways.
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Affiliation(s)
- Matthew J Winters
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Peter M Pryciak
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
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Bush A, Vasen G, Constantinou A, Dunayevich P, Patop IL, Blaustein M, Colman-Lerner A. Yeast GPCR signaling reflects the fraction of occupied receptors, not the number. Mol Syst Biol 2016; 12:898. [PMID: 28034910 PMCID: PMC5199120 DOI: 10.15252/msb.20166910] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
According to receptor theory, the effect of a ligand depends on the amount of agonist-receptor complex. Therefore, changes in receptor abundance should have quantitative effects. However, the response to pheromone in Saccharomyces cerevisiae is robust (unaltered) to increases or reductions in the abundance of the G-protein-coupled receptor (GPCR), Ste2, responding instead to the fraction of occupied receptor. We found experimentally that this robustness originates during G-protein activation. We developed a complete mathematical model of this step, which suggested the ability to compute fractional occupancy depends on the physical interaction between the inhibitory regulator of G-protein signaling (RGS), Sst2, and the receptor. Accordingly, replacing Sst2 by the heterologous hsRGS4, incapable of interacting with the receptor, abolished robustness. Conversely, forcing hsRGS4:Ste2 interaction restored robustness. Taken together with other results of our work, we conclude that this GPCR pathway computes fractional occupancy because ligand-bound GPCR-RGS complexes stimulate signaling while unoccupied complexes actively inhibit it. In eukaryotes, many RGSs bind to specific GPCRs, suggesting these complexes with opposing activities also detect fraction occupancy by a ratiometric measurement. Such complexes operate as push-pull devices, which we have recently described.
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Affiliation(s)
- Alan Bush
- Department of Physiology, Molecular and Cellular Biology, University of Buenos Aires, Buenos Aires, Argentina.,Institute of Physiology, Molecular Biology and Neurosciences, National Research Council (CONICET), Buenos Aires, Argentina
| | - Gustavo Vasen
- Department of Physiology, Molecular and Cellular Biology, University of Buenos Aires, Buenos Aires, Argentina.,Institute of Physiology, Molecular Biology and Neurosciences, National Research Council (CONICET), Buenos Aires, Argentina
| | - Andreas Constantinou
- Department of Physiology, Molecular and Cellular Biology, University of Buenos Aires, Buenos Aires, Argentina.,Institute of Physiology, Molecular Biology and Neurosciences, National Research Council (CONICET), Buenos Aires, Argentina
| | - Paula Dunayevich
- Department of Physiology, Molecular and Cellular Biology, University of Buenos Aires, Buenos Aires, Argentina.,Institute of Physiology, Molecular Biology and Neurosciences, National Research Council (CONICET), Buenos Aires, Argentina
| | - Inés Lucía Patop
- Department of Physiology, Molecular and Cellular Biology, University of Buenos Aires, Buenos Aires, Argentina.,Institute of Physiology, Molecular Biology and Neurosciences, National Research Council (CONICET), Buenos Aires, Argentina
| | - Matías Blaustein
- Department of Physiology, Molecular and Cellular Biology, University of Buenos Aires, Buenos Aires, Argentina.,Institute of Physiology, Molecular Biology and Neurosciences, National Research Council (CONICET), Buenos Aires, Argentina
| | - Alejandro Colman-Lerner
- Department of Physiology, Molecular and Cellular Biology, University of Buenos Aires, Buenos Aires, Argentina .,Institute of Physiology, Molecular Biology and Neurosciences, National Research Council (CONICET), Buenos Aires, Argentina
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21
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Weiße AY, Mannan AA, Oyarzún DA. Signaling Tug-of-War Delivers the Whole Message. Cell Syst 2016; 3:414-416. [PMID: 27883887 DOI: 10.1016/j.cels.2016.11.003] [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
How do cells transmit biochemical signals accurately? It turns out, pushing and pulling can go a long way.
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Affiliation(s)
- Andrea Y Weiße
- SynthSys - Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Ahmad A Mannan
- Department of Mathematics, Imperial College London, London, SW7 2AZ, UK
| | - Diego A Oyarzún
- Department of Mathematics, Imperial College London, London, SW7 2AZ, UK.
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