Background
Autophagy preserves cellular function by degradation and recycling cellular material in response to nutrient availability, metabolism, and growth. Cells target damaged organelles and proteins to lysosomes for degradation, which are then reincorporated back into the cell circuitry.
As an intrinsic part of a cell's adaptive machinery, autophagy maintains cellular homeostasis in a fluctuating environment. For efficient adaptation, cells integrate environmental information to make decisions on the timing, execution, and resetting of the autophagy program. Unicellular organisms use signal transduction pathways to reprogram metabolism based on nutrient availability. Mammals align nutritional information and metabolic rearrangements with biological rhythms, efficiently synchronizing metabolic programs with environmental changes. Cellular synchronization of metabolic programs with recurrent environmental change is a cost-efficient way of optimizing their functions and adapting over time, demonstrating their ability to "remember" past experiences and use that information to navigate their environment more effectively.
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.
In unicellular organisms, the concept of cell memory takes on a fascinating simplicity. Instead of relying on complex multicellular sensory and signaling mechanisms, these organisms leverage biochemical rhythms and feedback cycles as their basic forms of memory, stored through clock and memory factors acting as internal oscillators. While, most unicellular model organisms do not possess a circadian clock, simple forms of memory and ultradian cell oscillations can be triggered experimentally in certain growth conditions.
By combining these ideas, the study of cellular memory in unicellular organisms provides valuable insights into the fundamental processes underlying cellular adaptability and autophagy regulation.
Goal
Given the growing amount of evidence linking biological rhythms, autophagy, and disease, we are interested in identifying potential clock and memory factors acting as upstream modulators of autophagy upon cyclic nutritional changes. As a starting point, we have performed a high-content microscopy screening of temporal changes in autophagy in a genome-wide collection of single gene deletion mutants in yeast. As a result, we have identified a set of mutants that represent the yeast network of genes involved in autophagy dynamic control.
In this project, we will set experimental conditions where we monitor autophagy dynamics in a selected library of yeast mutants, exposed to periodic cycles of starvation and replenishment. Using this strategy, we can provoke cyclic autophagy responses and monitor kinetic changes based on the nutritional history of the cells. Mutants that exhibit dysregulated autophagy dynamics will be potential candidates to act as memory or clock genes in regulation of the process. The student will also perform protein and gene expression experiments to characterize the mechanisms by which the factors modulate the timing and kinetics of autophagy through the core machinery. 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 protein 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.
Our group
The Cancer Molecular Medicine group is led by Professor Jorrit Enserink and consists of several members from 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, which offer the opportunity to share your results with a broader scientific audience and grow your professional network.
Supervisors
Nathalia Chica n.c.balaguera@ncmm.uio.no
Jorrit Enserink jorrit.enserink@ibv.uio.no