Lab research overview – How do cells think and make decisions

Size Control

Underlying the wonderful diversity of natural forms is the ability of an organism to grow into its appropriate shape. It is hard to imagine a mouse the size of a hippopotamus, and, indeed, the laws of physics and physiology will prevent it from attaining such a size without a severe change in form. The regulation of growth ensures that cells grow, divide and select a fate so that the organism and its constitutive parts are properly proportioned and of a size suitable for their function. Although the size-control mechanism active in an individual cell is of fundamental importance to this process, it is difficult to isolate and study in complex multi-cellular systems and remains mysterious.

Often free from the constraints imposed by communal living, unicellular organisms are governed by simpler psychology: proliferate rapidly whenever environmental conditions permit. Cell cycle control then insures that growth is coupled to division and that the genome is duplicated only once before being accurately partitioned into two nascent cells. We study size control in the model organism budding yeast, whose study has often revealed conserved mechanisms, shared by both yeasts and humans.

Size control in budding yeast has been attributed to the G1/S transition known as Start (network diagram shown below). In the last 30 years, advances in our understanding of the molecular details of the cell cycle have been remarkable and many of the genes involved in the G1/S transition have been identified. Yet, in spite of all this molecular detail a fundamental question remains unanswered: where in the sequence of molecular interactions does size control occur? How does a cell measure its own size?

Current Directions / Possible rotation projects

  1. How does the proteome change with increasing cell size? Whi5 and Rb are not unique and many proteins change concentration with cell growth and increased cell size (eg Lanz, Zatulovskiy et al 2022). What are the mechanisms that drive this size scaling?

  2. What are the specific molecular mechanisms that drive the dilution dynamics of the cell cycle inhibitors Whi5 and Rb?

  3. Large cell size can promote senescence (irreversible cell cycle arrest) in mammalian cells grown in culture. What is the mechanism? Why does a dilute genome result in senescence?

  4. How is the proteome in yeast partitioned at different growth rates to optimize cell growth? Can we discover a general model for cell growth with real predictive power?

Systems Biology

Understanding the principles underlying genetic control circuits will be a central aim of biological research in the coming decade. These principles, when found, should provide a unifying framework for understanding disparate natural systems and aid in the design of robust synthetic circuits for medical and engineering purposes.

Previously, the bias of biological research has been toward the identification of novel genes and their interactions; i.e., the construction of networks consisting of nodes and arrows corresponding to genes and interactions respectively. Over the past decade, high-throughput genomic methods have greatly facilitated this line or research and quantitatively minded researchers have mined the newly expanded networks for their statistical properties. Yet, it is becoming increasingly clear that this is not enough. Not all arrows are equal and parameters determine system behavior. In other words, for the same network, varying the strengths of the interactions can radically affect dynamics and function. This is not surprising since even simple systems can be very sensitive to parameter values, in particular, if they are poised near a bifurcation. Therefore, the adequate characterization of a given circuit requires careful quantitative analysis.

We have chosen to make headway on this problem via the in-depth study of a natural circuit: the cell cycle. Our study revealed a novel function of positive feedback, which is likely to exist in other evolutionarily unrelated natural circuits. Hopefully, our result will also prove useful in synthetic circuit design.

Foundational discovery – Cell growth drives division by diluting key cell cycle inhibitors in yeast and human cells.

Our laboratory made a breakthrough discovery in understanding how cell growth triggers division in budding yeast (Schmoller et al, Nature 2015). While it was expected that growth would promote cell division through an increase in the activity of the cyclin-dependent kinase Cdk1, this was not the case. Rather, we found that cell growth acts in the opposite manner. Cell growth triggers division by diluting Whi5, a protein that inhibits cell division. Whi5 is a transcriptional inhibitor so that its dilution activates key cell cycle genes to initiate the cell cycle. We then examined cultured human cells and discovered that cell growth triggers their division by diluting the cell cycle inhibitor RB, the retinoblastoma protein (Zatulovskiy et al, Science 2020). Thus, in both yeast and human cells, growth triggers cell division by diluting a cell cycle inhibitor (Fig. 3)

5. A lot of cell size regulation in mammalian cells is understood through cell culture studies. However, Mimi (Xie et al 2020, 24) showed that size control operates much tighter in vivo in epidermal stem cells. Moreover, in vivo cells are often a fraction of their size when grown in culture. Why is this? What is epithelial cell size optimized for?

6. Much remains to be discovered about the biochemical mechanisms driving cell proliferation. In human cells this primarily takes place at the G1/S transition. We discovered that cyclin D docks the retinoblastoma protein on a C-terminal helix in an otherwise unstructured part of the protein (Topacio et al 2019). Many more interactions regulating cell proliferation, likely important for medicine, remain to be discovered.

7. Many cells in our bodies are terminally differentiated. What are the balances of synthesis and degradation regulating the size of these cells?