Identification of clock and memory genes controlling autophagy in response to cyclic environmental nutritional changes in yeast
Autophagy is a housekeeping process that preserves a functional cell state by balancing cell material degradation and recycling, with nutrient availability, metabolism and growth. For this, cells target damaged organelles and proteins to the lysosomes for degradation into smaller constituents that are then reincorporated back into the cell circuitry.
Autophagy is an intrinsic component of a cell’s adaptive machinery because it maintains cellular homeostasis in a fluctuating environment. For efficient adaptation to occur, the cell must integrate available information from its environment that allows it to make decisions on timing, execution, and resetting of the autophagy program. For instance, unicellular organisms transmit information about nutrient availability through signal transduction pathways to induce coherent metabolic reprogramming. In mammals, these mechanisms have evolved, where the nutritional information and subsequent metabolic rearrangements, align with biological rhythms. Cellular synchronization of metabolic programs with recurrent environmental change is a cost-efficient way of executing repetitive biological behavior. In unicellular organisms, biological rhythms and feedback cycles are simple forms of cell memory stored through clock and memory factors acting as internal oscillators.
Recent studies have pointed out that the desynchronization of biological rhythms affects human health. For instance, changes in the distribution of the food along the day may negatively influence nutrient metabolism and may be associated with metabolic disorders. Likewise, chronic sleep disturbance increases the risk of neurodegenerative diseases. Other studies have reported that both metabolic and neurodegenerative disorders are the consequence of dysfunctional autophagy. Thus, we can hypothesize that disruption of biological rhythms, in turn, may result in deregulated autophagy and consequently metabolic disorders or neurodegenerative diseases.
Given the growing amount of evidence linking biological rhythms, autophagy, and diseases, we are interested in identifying potential clock and memory factors acting as upstream modulators of autophagy response upon cyclic nutritional changes. As a starting point, we have performed a high-content screening with confocal imaging of a collection of single deletion mutants that comprises the whole genome of yeast. As a result, we have identified a set of mutants that represent the yeast network of genes involved in autophagy dynamic control.
As a goal, we will set experimental conditions where we monitor autophagy responses in a selected library of yeast mutants, exposed to periodic cycles of starvation and replenishment of external nutrients. Using this strategy, we will provoke cyclic autophagy rhythms that we will eventually disrupt. Those mutants that fail at coping with a cyclic autophagy response will be potential candidates to act as memory or clock genes in the regulation of the process. The student will also perform protein and gene expression experiments to characterize the cyclic factors that couple to the autophagy machinery to modulate the timing and kinetics of the autophagy response. We will use established methodologies to monitor and measure autophagy such as confocal imaging, tracking of autophagy selective markers by western blotting, and enzymatic assays to monitor degradation.
What we offer the student
The student in this project will get wet lab experience with budding yeast handling, molecular biology and biochemistry methods such as PCR, cloning, western blotting and confocal microscopy. In addition, the student will get experience in data analysis and training in transferrable skills such as scientific oral communication, writing and project planning.
The Cancer Molecular Medicine group is led by Professor Jorrit Enserink and consists of 21 members from 9 different countries. One of our research areas is the study of dynamic behaviours of autophagy control together with the development of computational strategies. The group has extensive experience in the supervision of master and PhD students and offers an excellent international and dynamic research environment. Our group is located at the Department for Molecular Cell Biology at Radiumhospitalet, where we share facilities, reagents, and expertise with other groups working on a variety of research topics. We are also part of the CanCell Centre of Excellence.