A rationally engineered decoder of transient intracellular signals

AbstractCells can encode information about their environment by modulating signaling dynamics and responding accordingly. Yet, the mechanisms cells use to decode these dynamics remain unknown when cells respond exclusively to transient signals. Here, we approach design principles underlying such decoding by rationally engineering a synthetic short-pulse decoder in budding yeast. A computational method for rapid prototyping, TopoDesign, allowed us to explore 4122 possible circuit architectures, design targeted experiments, and then rationally select a single circuit for implementation. This circuit demonstrates short-pulse decoding through incoherent feedforward and positive feedback. We predict incoherent feedforward to be essential for decoding transient signals, thereby complementing proposed design principles of temporal filtering, the ability to respond to sustained signals, but not to transient signals. More generally, we anticipate TopoDesign to help designing other synthetic circuits with non-intuitive dynamics, simply by assembling available biological components.

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Design principles of stripe-forming motifs: the role of positive feedback

Scientific Reports ◽

10.1038/srep05003 ◽

2014 ◽

Vol 4 (1) ◽

Cited By ~ 9

Author(s):

Andreea Munteanu ◽

James Cotterell ◽

Ricard V. Solé ◽

James Sharpe

Keyword(s):

Positive Feedback ◽

Design Principles

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Digital signaling network drives the assembly of the AIM2-ASC inflammasome

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1712860115 ◽

2018 ◽

Vol 115 (9) ◽

pp. E1963-E1972 ◽

Cited By ~ 16

Author(s):

Mariusz Matyszewski ◽

Seamus R. Morrone ◽

Jungsan Sohn

Keyword(s):

Host Defense ◽

Positive Feedback ◽

Signal Amplification ◽

Molecular Level ◽

Design Principles ◽

Digital Circuit ◽

Quantitative Model ◽

Feedback Loops ◽

Signaling Network

The AIM2-ASC inflammasome is a filamentous signaling platform essential for mounting host defense against cytoplasmic dsDNA arising not only from invading pathogens but also from damaged organelles. Currently, the design principles of its underlying signaling network remain poorly understood at the molecular level. We show here that longer dsDNA is more effective in inducing AIM2 assembly, its self-propagation, and downstream ASC polymerization. This observation is related to the increased probability of forming the base of AIM2 filaments, and indicates that the assembly discerns small dsDNA as noise at each signaling step. Filaments assembled by receptor AIM2, downstream ASC, and their joint complex all persist regardless of dsDNA, consequently generating sustained signal amplification and hysteresis. Furthermore, multiple positive feedback loops reinforce the assembly, as AIM2 and ASC filaments accelerate the assembly of nascent AIM2 with or without dsDNA. Together with a quantitative model of the assembly, our results indicate that an ultrasensitive digital circuit drives the assembly of the AIM2-ASC inflammasome.

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Anisotropy of plasmalemmal sterols and cell mating require StARkin domain proteins Ysp2 and Lam4

10.1101/2021.09.30.462584 ◽

2021 ◽

Author(s):

Neha Chauhan ◽

Gregory D. Fairn

Keyword(s):

Plasma Membrane ◽

Map Kinase ◽

Cell Polarity ◽

Positive Feedback ◽

Feedback Loop ◽

Budding Yeast ◽

Mapk Signaling ◽

Polarized Growth ◽

Positive Feedback Loop ◽

Mating Efficiency

AbstractIn the budding yeast S. cerevisiae Cdc42 is required for polarized growth and the formation of mating projections (shmoos). Negatively charged lipids including phosphatidylserine and phosphatidylinositol 4,5-bisphosphate support a positive feedback loop that recruits Cdc42 effectors and MAP kinase scaffolds, many of which contain polybasic patches that directly interact with the membrane. Here, using genetically encoded sterol sensor ALOD4 we find that ergosterol is accumulated in the cytosolic leaflet of buds and shmoos. The accumulation of ergosterol in the plasma membrane requires both Osh and Lam proteins however cells lacking Ysp2/Lam2 and Lam4 displayed a reversal in the polarity of ergosterol. The redistribution of ergosterol impairs the polarization of phosphatidylserine and phosphatidylinositol 4,5-bisphophate which further impacts shmoo formation, MAPK signaling and mating efficiency. Our observations demonstrate that the ability of Lam proteins to deliver ergosterol from the plasma membrane to the ER helps maintain a gradient of ergosterol which in turn supports robust cell polarity.SummaryThe sterol sensor ALOD4 is enriched at sites of polarized growth. Elimination of the Osh proteins solubilized the ALOD4 whereas elimination of Ysp2 and Lam4 reversed ALOD4 polarization. Cells lacking Ysp2 and Lam4 have defects in mating and MAP kinase signaling.

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Faculty Opinions recommendation of Regulation of ras signaling dynamics by Sos-mediated positive feedback.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1048353.500263 ◽

2006 ◽

Author(s):

Deborah Morrison

Keyword(s):

Positive Feedback ◽

Ras Signaling ◽

Signaling Dynamics

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Regulation of Ras Signaling Dynamics by Sos-Mediated Positive Feedback

Current Biology ◽

10.1016/j.cub.2006.09.033 ◽

2006 ◽

Vol 16 (21) ◽

pp. 2173-2179 ◽

Cited By ~ 79

Author(s):

Sean Boykevisch ◽

Chen Zhao ◽

Holger Sondermann ◽

Polyxeni Philippidou ◽

Simon Halegoua ◽

...

Keyword(s):

Positive Feedback ◽

Ras Signaling ◽

Signaling Dynamics

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Cell cycle entry triggers a switch between two modes of Cdc42 activation during yeast polarization

eLife ◽

10.7554/elife.26722 ◽

2017 ◽

Vol 6 ◽

Cited By ~ 33

Author(s):

Kristen Witte ◽

Devin Strickland ◽

Michael Glotzer

Keyword(s):

Cell Cycle ◽

Positive Feedback ◽

Budding Yeast ◽

Induce Polarization ◽

Cell Polarization ◽

Cell Cycle Stage ◽

Cell Cycle Entry ◽

Local Perturbations ◽

Polarity Establishment ◽

Local Recruitment

Cell polarization underlies many cellular and organismal functions. The GTPase Cdc42 orchestrates polarization in many contexts. In budding yeast, polarization is associated with a focus of Cdc42•GTP which is thought to self sustain by recruiting a complex containing Cla4, a Cdc42-binding effector, Bem1, a scaffold, and Cdc24, a Cdc42 GEF. Using optogenetics, we probe yeast polarization and find that local recruitment of Cdc24 or Bem1 is sufficient to induce polarization by triggering self-sustaining Cdc42 activity. However, the response to these perturbations depends on the recruited molecule, the cell cycle stage, and existing polarization sites. Before cell cycle entry, recruitment of Cdc24, but not Bem1, induces a metastable pool of Cdc42 that is sustained by positive feedback. Upon Cdk1 activation, recruitment of either Cdc24 or Bem1 creates a stable site of polarization that induces budding and inhibits formation of competing sites. Local perturbations have therefore revealed unexpected features of polarity establishment.

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A light-inducible organelle-targeting system for dynamically activating and inactivating signaling in budding yeast

Molecular Biology of the Cell ◽

10.1091/mbc.e13-03-0126 ◽

2013 ◽

Vol 24 (15) ◽

pp. 2419-2430 ◽

Cited By ~ 70

Author(s):

Xiaojing Yang ◽

Anna Payne-Tobin Jost ◽

Orion D. Weiner ◽

Chao Tang

Keyword(s):

Cell Biology ◽

Mammalian Cells ◽

Temporal Dynamics ◽

Budding Yeast ◽

Protein Localization ◽

Nuclear Fission ◽

General Strategy ◽

Intracellular Signals ◽

Sites Of Action ◽

Organelle Targeting

Protein localization plays a central role in cell biology. Although powerful tools exist to assay the spatial and temporal dynamics of proteins in living cells, our ability to control these dynamics has been much more limited. We previously used the phytochrome B– phytochrome-interacting factor light-gated dimerization system to recruit proteins to the plasma membrane, enabling us to control the activation of intracellular signals in mammalian cells. Here we extend this approach to achieve rapid, reversible, and titratable control of protein localization for eight different organelles/positions in budding yeast. By tagging genes at the endogenous locus, we can recruit proteins to or away from their normal sites of action. This system provides a general strategy for dynamically activating or inactivating proteins of interest by controlling their localization and therefore their availability to binding partners and substrates, as we demonstrate for galactose signaling. More importantly, the temporal and spatial precision of the system make it possible to identify when and where a given protein's activity is necessary for function, as we demonstrate for the mitotic cyclin Clb2 in nuclear fission and spindle stabilization. Our light-inducible organelle-targeting system represents a powerful approach for achieving a better understanding of complex biological systems.

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