Lew Lab

The Lew Lab works with the tractable budding yeast, Saccharomyces cerevisiae, to study the generation, maintenance, and directionality of cell polarity. We also study the relationship between the cell cycle and cell polarity and cell shape.

The Lab studies questions in fundamental cell biology, using fungal models and a mix of experimental and computational approaches. Fungi and animals share conserved molecular strategies to perform many core cell functions, so the tractable yeast Saccharomyces cerevisiae provides a superb model system to gain in-depth understanding that can be translated into computational models. We also study an emerging non-model fungus, Aureobasidium pullulans, that is an ubiquitous poly-extremophile with unconventional growth modes that raise novel questions in cell biology.

Some Questions of Interest:
(*) How do cells regulate cell polarity to achieve different morphologies?
(*) How do cells orient cell polarity in response to extracellular signals?
(*) How do cells distribute their contents, particularly in complex geometries?
(*) How do fungi growing under stringent turgor pressure expand their cell walls without lysing?
(*) How do cell-cell contacts between cell walls communicate mechanical information to the cell?

The Lab address these questions using a combination of genetic, cell biological, and computational approaches. Imaging of various cells (including mutants based on prior knowledge) in different conditions with high spatio-temporal resolution often suggests hypotheses that can be tested by generating other informative mutants. Conceptual models can be translated into computational models to test their plausibility, which can also lead to ideas that can be tested experimentally. By developing custom image analysis tools, we can quantify behaviors for more precise matching between model and experiment.

Cell Polarity: Number and Stability of Polarity Sites: Diverse cell types rely on a common molecular pathway, centered on the conserved GTPase Cdc42, to establish cell polarity and develop cell shapes and contacts that are critical for cell function. Polarization signals act through Cdc42-directed regulators to promote accumulation of membrane-bound active GTP-Cdc42 at the site destined to become the cell’s "front". Cdc42 then organizes cytoskeletal elements through a variety of “effectors”, proteins that bind specifically to GTP-Cdc42. Our work identified a positive feedback mechanism that promotes concentration of active Cdc42 to form a polarity site. Positive feedback concentrates active Cdc42 at a single cortical site, which is critical for budding of yeast cells and directed migration of animal cells. But some cells generate several polarity sites to make more complex morphologies. How is the number of sites encoded in the polarity circuit? Also, when cells need to respond to external cues, they can undergo a search process where they rapidly assemble and disassemble polarity sites in different places. Computational explorations indicate that it is very difficult for a polarity circuit designed to form a stable front to exhibit this searching behavior. So how do cells do it?

Orienting Polarity: How Yeast Cells Find Their Mates: Polarization is often oriented by physical or chemical features or the cell’s environment, and cells are extraordinarily good at detecting and decoding chemical gradients in noisy and complex environments. Micro-organisms track gradients to find food or mates, and gradient detection underlies axon guidance, homing of immune cells towards invaders, chemotaxis of fibroblasts towards wound sites, and guidance of sperm towards the egg. To track a chemical gradient, eukaryotic cells compare concentrations at different points on the cell’s surface. Gradient decoding becomes most challenging when cells are small (so concentrations can only be compared across short distances), when gradients are shallow (so that concentrations differ very little across a short distance), and when chemical concentrations are low (so that molecular noise is significant). Also challenging are situations when there is more than one source of attractant. Yeast cells seeking mates encounter a combination of ALL these challenges, yet remarkably they can decode gradients of pheromones to find mates. How do they perform this astonishing feat?

Mechanobiology of the Fungal Cell Wall: Fungal infections are on the rise, and climate change is predicted to acclimate fungi to human body temperature, potentially creating a surge in fungal disease that we are ill-equipped to treat, because (unlike bacteria) fungi and animals share most of their cell biology. However, a major difference between animals and fungi, and a potential Achilles’ heel, is the fungal cell wall. Fungal cells live in conditions that drive water influx into the cell, leading to an expansion that would catastrophically lyse the cell if it were not protected by a rigid cell wall. The cell wall is composed of a mesh of cross-linked carbohydrate polymers and glycoproteins. In order to grow, this mesh must expand, which involves local wall thinning and remodeling near the polarity site. Small imbalances in wall expansion would easily burst the cells, except that fungi have developed a wall mechanosensing pathway that detects local flaws and rapidly repairs them. How does this pathway detect flaws? How does it pause growth to allow repair? And how do cells silence this pathway when it is safe to remove the cell wall, as happens at contact sites between mating cells?

Cell Biology of an Unconventional Fungus: Tractable yeast model systems have provided much of our molecular understanding of eukaryotic cell biology, because the tools developed to allow rapid and definitive experiments were for decades only available in those systems. However, recent advances have made the path from non-model system to tractable system much faster, allowing investigation into a growing menagerie of “unconventional” systems. One such system that we are developing is the poly-extremophile Aureobasidium pullulans, which has been found in diverse niches including on many trees and terrestrial plants, in the ocean, in salt lakes, and in the Antarctic. The genome of this fungus reveals a capacity for unusual biochemical reactions, stimulating biotechnological interest. Our interest was stimulated by the finding that the A. pullulans lifestyle differs from that of other known budding yeasts. Unlike diverse well-studied yeasts like the baker’s yeast Saccharomyces cerevisiae, the human pathogens Candida albicans and Cryptococcus neoformans, or the plant pathogen Ustilago maydis, which always produce one daughter cell (“bud”) per cell cycle, A. pullulans can produce several buds (>10) simultaneously. This makes A. pullulans a powerful tool for comparative cell biology. How does A. pullulans decide how many buds to make in a given cell cycle? How does it apportion its many nuclei among the buds? How does it distribute organelles between the buds? Are there accurate partitioning systems? If so, how do they work? If not, how do A. pullulans cells tolerate or adjust to variable organelle numbers?