As cells age, they accumulate intracellular, misfolded protein aggregates. The Denic laboratory focuses on fundamental cell biological processes such as very long-chain fatty acid (VLCFA) synthesis, post-translational insertion of tail-anchored (TA) proteins, cellular aging due to protein aggregation, and autophagy. To study these mechanisms, scientists in the Denic lab have developed in vitro systems in yeast that can be extended to the study of homologous mechanisms in human cells. In addition, they use quantitative genetic screening by high-throughput flow cytometry to identify new components of various cell biological processes. Furthermore, their studies on quality control pathways (e.g. chaperone-assisted folding) in aging cells will yield important insights for the development of small molecules to modulate the toxicity of aggregating substrates such as the Alzheimer aggregating peptide. Together, the multi-pronged approach taken by the Denic lab will enable them to develop in vitro assays for mechanistic investigations and drug target discovery.

• Study the mechanism of tail-anchored (TA) protein insertion into the endoplasmic reticulum (ER) membrane.
• Uncover the identity of proteins that become aggregation prone as cells age.
• Investigate the mechanism of autophagosome formation by biochemical reconstitution approaches.
• Elucidate molecular principles enabling structural diversification of Very Long-Chain Fatty Acids (VLCFAs).

The Denic laboratory has focused on fundamental cell biological processes and molecular mechanisms that govern them. They are interested in the synthesis of a structurally diverse class of lipid molecules called very long-chain fatty acids (VLCFAs). Variation in VLCFA chain length across different species and different tissues has enabled the numerous functional specializations of these lipids. They are required for a variety of membrane-based processes, including the formation of GPI lipid anchors and protein trafficking in the secretory pathway. For example, in mammals, VLCFAs with lengths greater than C30 allow the formation of a permeability barrier that is critical for normal structure and function of the skin. Finally, VLCFAs and their derivatives act as signaling molecules such as arachidonic acid, and are dominant lipid constituents of certain tissues in animals like photoreceptor cells and myelin. Using genetic and biochemical approaches in the budding yeast Saccharomyces cerevisiae, the Denic group identified several endoplasmic reticulum (ER) membrane proteins required for VLCFA production. This enabled them to uncover an adjustable, caliper-like mechanism that generates the repertoire of cellular VLCFAs.

Tail-anchored (TA) proteins are defined by the presence of a single C-terminal transmembrane domain (TMD) and play numerous critical roles throughout the secretory pathway. The Denic lab has used complementing in vivo and in vitro approaches in yeast to uncover a chaperone cascade in the cytoplasm that efficiently and accurately sorts tail-anchored (TA) proteins (away from other membrane proteins with related targeting signals) for insertion into the ER. Importantly, this sorting mechanism is conserved in humans where ~5% of the genome encodes TA proteins. Their study now paves the way for biochemical efforts to define the mechanism by which other membrane components of this pathway insert the TMD into the membrane.

In addition, the Denic lab is interested in aging and its effects on the quality control of cellular proteins. The team measures age-induced changes in the ability of certain chaperone systems to handle diverse structural challenges presented by a variety of model aggregating substrates (e.g., polyglutamine-based aggregates versus misfolded globular protein aggregates). Furthermore, they use unbiased global methods (e.g., mass spectrometry) to identify endogenous cellular clients of quality control pathways in aging cells. Collectively, these approaches will help address the fundamental issues of how aging influences the ability of proteins to fold into their native states and what cellular processes are hypersensitive to aging.

The Denic lab also studies how under certain conditions cells engulf large regions of their cytoplasm with intracellular double-membrane structures called autophagosomes. This process of autophagy is essential for providing cells with metabolic building blocks during starvation by breaking down and recycling the contents of autophagosomes. Furthermore, research over the last decade has revealed a role for autophagy in the clearance of intracellular pathogens, cellular defense against neurodegenerative protein aggregates, suppression of tumor formation through activation of non-classical apoptosis, and life-span extension. The Denic group is focused on developing cell-free in vitro assays for monitoring the individual steps leading to autophagosome formation. Together with targeted biochemical reconstitution approaches that make use of the known components, their efforts should provide a more mechanistic understanding of this important cell biological process.

Biological Mechanisms and Pathways

• Aging •
• Chaperones •
• Chaperones •
• Chaperones •
• Fatty acids •
• Proteasome •
• Proteasome •
• Proteasome •
• Protein folding •
• Protein trafficking •
• Proteostasis •
• Secretory pathway •
• Yeast genetics
•  

Cancer

• Autophagy •
• Cancer
•  

Disease Mechanisms

• Cancer •
• Diabetes •
• Neurodegeneration
•  

Metabolism; Metabolic Disease and Aging

• Aging
•  

Research Tools and Instrumentation

• Flow cytometry •
• S. cerevisiae
•  

Therapeutic Discovery Tools and Assays

• Cancer
•  

Therapeutics

• Small molecule screens
•