Daniel Lew

Overview:

Our research interests focus on the control of cell polarity.  Cell polarity is a nearly universal feature of eukaryotic cells. A polarized cell usually has a single, clear axis of asymmetry: a “front” and a “back”.  In the past several years it has become apparent that the highly conserved Rho-family GTPase Cdc42, first discovered in yeast, is a component of a master pathway, employed time and again to promote polarity in different contexts.  

Most cells know which way to polarize.  Concentration gradients of attractants, repellents, nutrients, or pheromones reveal the optimal directions for successful attack, escape, feeding, or mating. However, cells can and do polarize even when deprived of directional cues, choosing a random axis and committing to it as if they knew where they were going.  This process, called "symmetry breaking", reflects the presence of a core internal polarity program.  Our work has uncovered the biochemical basis for this core program, which uses positive feedback loops to reinforce inequalities in the local concentrations of polarity factors, so that stochastic fluctuations are amplified into a single dominating asymmetry.  

We use the tractable budding yeast as a model system.  Because the genes and processes we study are highly conserved, we anticipate that learning the answers to fundamental questions in yeast will be relevant and informative for a wide range of organisms.  Our work combines molecular genetics, cell biology, and mathematical modeling, and addresses questions including:

  • Why is there one and only one “front”?   
  • How is polarity turned on and off?   
  • How does Cdc42 organize the cytoskeleton?  
  • How is polarity guided by pheromone gradients?  

 

Positions:

James B. Duke Distinguished Professor of Pharmacology and Cancer Biology

Pharmacology & Cancer Biology
School of Medicine

Professor of Pharmacology and Cancer Biology

Pharmacology & Cancer Biology
School of Medicine

Professor in Molecular Genetics and Microbiology

Molecular Genetics and Microbiology
School of Medicine

Professor of Cell Biology

Cell Biology
School of Medicine

Member of the Duke Cancer Institute

Duke Cancer Institute
School of Medicine

Education:

Ph.D. 1990

Rockefeller University

Grants:

Studies of cell polarity, chemotropism, and cell-cycle control

Administered By
Pharmacology & Cancer Biology
Awarded By
National Institutes of Health
Role
Principal Investigator
Start Date
End Date

Studies of cell polarity, chemotropism, and cell-cycle control

Administered By
Pharmacology & Cancer Biology
Awarded By
National Institutes of Health
Role
Principal Investigator
Start Date
End Date

Program to Support Student Development and Diversity in Duke Biosciences

Administered By
School of Medicine
Awarded By
National Institutes of Health
Role
Principal Investigator
Start Date
End Date

Mechanisms of cell fusion during mating in Saccharomyces cerevisiae

Administered By
Pharmacology & Cancer Biology
Awarded By
Burroughs Wellcome Fund
Role
Principal Investigator
Start Date
End Date

Spatiotemporal modeling of signal transduction in yeast

Administered By
Pharmacology & Cancer Biology
Awarded By
University of North Carolina - Chapel Hill
Role
Principal Investigator
Start Date
End Date

Publications:

A novel stochastic simulation approach enables exploration of mechanisms for regulating polarity site movement.

Cells polarize their movement or growth toward external directional cues in many different contexts. For example, budding yeast cells grow toward potential mating partners in response to pheromone gradients. Directed growth is controlled by polarity factors that assemble into clusters at the cell membrane. The clusters assemble, disassemble, and move between different regions of the membrane before eventually forming a stable polarity site directed toward the pheromone source. Pathways that regulate clustering have been identified but the molecular mechanisms that regulate cluster mobility are not well understood. To gain insight into the contribution of chemical noise to cluster behavior we simulated clustering using the reaction-diffusion master equation (RDME) framework to account for molecular-level fluctuations. RDME simulations are a computationally efficient approximation, but their results can diverge from the underlying microscopic dynamics. We implemented novel concentration-dependent rate constants that improved the accuracy of RDME-based simulations, allowing us to efficiently investigate how cluster dynamics might be regulated. Molecular noise was effective in relocating clusters when the clusters contained low numbers of limiting polarity factors, and when Cdc42, the central polarity regulator, exhibited short dwell times at the polarity site. Cluster stabilization occurred when abundances or binding rates were altered to either lengthen dwell times or increase the number of polarity molecules in the cluster. We validated key results using full 3D particle-based simulations. Understanding the mechanisms cells use to regulate the dynamics of polarity clusters should provide insights into how cells dynamically track external directional cues.
Authors
Ramirez, SA; Pablo, M; Burk, S; Lew, DJ; Elston, TC
MLA Citation
Ramirez, Samuel A., et al. “A novel stochastic simulation approach enables exploration of mechanisms for regulating polarity site movement.Plos Computational Biology, vol. 17, no. 7, July 2021, p. e1008525. Epmc, doi:10.1371/journal.pcbi.1008525.
URI
https://scholars.duke.edu/individual/pub1488972
PMID
34264926
Source
epmc
Published In
Plos Computational Biology
Volume
17
Published Date
Start Page
e1008525
DOI
10.1371/journal.pcbi.1008525

Chemotactic movement of a polarity site enables yeast cells to find their mates.

How small eukaryotic cells can interpret dynamic, noisy, and spatially complex chemical gradients to orient growth or movement is poorly understood. We address this question using Saccharomyces cerevisiae, where cells orient polarity up pheromone gradients during mating. Initial orientation is often incorrect, but polarity sites then move around the cortex in a search for partners. We find that this movement is biased by local pheromone gradients across the polarity site: that is, movement of the polarity site is chemotactic. A bottom-up computational model recapitulates this biased movement. The model reveals how even though pheromone-bound receptors do not mimic the shape of external pheromone gradients, nonlinear and stochastic effects combine to generate effective gradient tracking. This mechanism for gradient tracking may be applicable to any cell that searches for a target in a complex chemical landscape.
Authors
Ghose, D; Jacobs, K; Ramirez, S; Elston, T; Lew, D
MLA Citation
Ghose, Debraj, et al. “Chemotactic movement of a polarity site enables yeast cells to find their mates.Proc Natl Acad Sci U S A, vol. 118, no. 22, June 2021. Pubmed, doi:10.1073/pnas.2025445118.
URI
https://scholars.duke.edu/individual/pub1484551
PMID
34050026
Source
pubmed
Published In
Proc Natl Acad Sci U S A
Volume
118
Published Date
DOI
10.1073/pnas.2025445118

How cells determine the number of polarity sites.

The diversity of cell morphologies arises, in part, through regulation of cell polarity by Rho-family GTPases. A poorly understood but fundamental question concerns the regulatory mechanisms by which different cells generate different numbers of polarity sites. Mass-conserved activator-substrate (MCAS) models that describe polarity circuits develop multiple initial polarity sites, but then those sites engage in competition, leaving a single winner. Theoretical analyses predicted that competition would slow dramatically as GTPase concentrations at different polarity sites increase toward a 'saturation point', allowing polarity sites to coexist. Here, we test this prediction using budding yeast cells, and confirm that increasing the amount of key polarity proteins results in multiple polarity sites and simultaneous budding. Further, we elucidate a novel design principle whereby cells can switch from competition to equalization among polarity sites. These findings provide insight into how cells with diverse morphologies may determine the number of polarity sites.
Authors
Chiou, J-G; Moran, KD; Lew, DJ
MLA Citation
Chiou, Jian-Geng, et al. “How cells determine the number of polarity sites.Elife, vol. 10, Apr. 2021. Pubmed, doi:10.7554/eLife.58768.
URI
https://scholars.duke.edu/individual/pub1480685
PMID
33899733
Source
pubmed
Published In
Elife
Volume
10
Published Date
DOI
10.7554/eLife.58768

Exploratory polarization facilitates mating partner selection in Saccharomyces cerevisiae.

Yeast decode pheromone gradients to locate mating partners, providing a model for chemotropism. How yeast polarize toward a single partner in crowded environments is unclear. Initially, cells often polarize in unproductive directions, but then they relocate the polarity site until two partners' polarity sites align, whereupon the cells "commit" to each other by stabilizing polarity to promote fusion. Here we address the role of the early mobile polarity sites. We found that commitment by either partner failed if just one partner was defective in generating, orienting, or stabilizing its mobile polarity sites. Mobile polarity sites were enriched for pheromone receptors and G proteins, and we suggest that such sites engage in an exploratory search of the local pheromone landscape, stabilizing only when they detect elevated pheromone levels. Mobile polarity sites were also enriched for pheromone secretion factors, and simulations suggest that only focal secretion at polarity sites would produce high pheromone concentrations at the partner's polarity site, triggering commitment.
Authors
Clark-Cotton, MR; Henderson, NT; Pablo, M; Ghose, D; Elston, TC; Lew, DJ
MLA Citation
Clark-Cotton, Manuella R., et al. “Exploratory polarization facilitates mating partner selection in Saccharomyces cerevisiae.Mol Biol Cell, vol. 32, no. 10, May 2021, pp. 1048–63. Pubmed, doi:10.1091/mbc.E21-02-0068.
URI
https://scholars.duke.edu/individual/pub1475825
PMID
33689470
Source
pubmed
Published In
Molecular Biology of the Cell
Volume
32
Published Date
Start Page
1048
End Page
1063
DOI
10.1091/mbc.E21-02-0068

Mechanisms that ensure monogamous mating in Saccharomyces cerevisiae.

Haploid cells of the budding yeast Saccharomyces cerevisiae communicate using secreted pheromones and mate to form diploid zygotes. Mating is monogamous, resulting in the fusion of precisely one cell of each mating type. Monogamous mating in crowded conditions, where cells have access to more than one potential partner, raises the question of how multiple-mating outcomes are prevented. Here we identify mutants capable of mating with multiple partners, revealing the mechanisms that ensure monogamous mating. Before fusion, cells develop polarity foci oriented toward potential partners. Competition between these polarity foci within each cell leads to disassembly of all but one focus, thus favoring a single fusion event. Fusion promotes the formation of heterodimeric complexes between subunits that are uniquely expressed in each mating type. One complex shuts off haploid-specific gene expression, and the other shuts off the ability to respond to pheromone. Zygotes able to form either complex remain monogamous, but zygotes lacking both can re-mate.
Authors
Robertson, CG; Clark-Cotton, MR; Lew, DJ
MLA Citation
Robertson, Corrina G., et al. “Mechanisms that ensure monogamous mating in Saccharomyces cerevisiae.Mol Biol Cell, vol. 32, no. 8, Apr. 2021, pp. 638–44. Pubmed, doi:10.1091/mbc.E20-12-0757.
URI
https://scholars.duke.edu/individual/pub1474834
PMID
33596113
Source
pubmed
Published In
Molecular Biology of the Cell
Volume
32
Published Date
Start Page
638
End Page
644
DOI
10.1091/mbc.E20-12-0757

Research Areas:

Actin Cytoskeleton
Adaptor Proteins, Signal Transducing
CDC28 Protein Kinase, S cerevisiae
Cell Cycle
Cell Division
Cell Polarity
Cell Shape
Cell Wall
Chemotaxis
Computer Simulation
Cyclin B
Cyclin-Dependent Kinases
Cyclins
Cytokinesis
Cytoskeleton
Feedback, Physiological
Fluorescence Recovery After Photobleaching
GTP-Binding Proteins
GTPase-Activating Proteins
Guanine Nucleotide Exchange Factors
MAP Kinase Signaling System
Microscopy, Confocal
Mitogen-Activated Protein Kinases
Morphogenesis
Phosphothreonine
Polarity
Protein Kinases
Saccharomyces cerevisiae
Saccharomyces cerevisiae Proteins
Septins
Signal Transduction
Systems Biology
Time-Lapse Imaging
Yeast
cdc42 GTP-Binding Protein
cdc42 GTP-Binding Protein, Saccharomyces cerevisiae
p21-Activated Kinases