BMBDG Seminar - Carolina Tropini

“Differential transporter utilization facilitates nutrient crosstalk and creates a targetable metabolic niche in cancer,” by Seth Parke, Post-Doctoral Fellow, New York University School of Medicine, Alec Kimmelman Lab.

Department of Biochemistry and Molecular Biology and BC Children’s Hospital presents Seth Parker, candidate for joint Faculty position in BMB and BCCHRI.

Seth Parker received his B.S. in Chemical and Biological Engineering from the University of Colorado at Boulder. He completed his Ph.D. in Bioengineering at the University of California, San Diego where he developed quantitative methods to study cancer metabolism under the supervision of Dr. Christian Metallo. He is currently a postdoctoral fellow at New York University School of Medicine in the laboratory of Dr. Alec Kimmelman where he studies alanine transport in pancreatic cancer. He is interested in understanding how specific transporters permit acquisition of nutrients from the tumor microenvironment, and how targeting these transporters may restrict tumor growth by limiting access to anabolic substrates.

Friday, September 6th at 9:00 am
Michael Smith Laboratories, Lecture Theatre, Room 102
2185 East Mall

“Characterization of Interaction between Ty1 Integrase and RNA Polymerase III For Ty1 Retrotransposon Insertion Into the Yeast Genome“, by Stephanie Cheung, PhD candidate in the Measday Lab.

Thursday, August 15, 2019 at 12:30 in Room 203, Graduate Student Centre, 6371 Crescent Road.

Abstract
Retrotransposons are eukaryotic mobile genetic elements that transpose by reverse transcription of an RNA intermediate and are derived from retroviruses. The Ty1 retrotransposon of Saccharomyces cerevisiae (S. cerevisiae) belongs to the Ty1-copia superfamily. Ty1 integration into the S. cerevisiae genome occurs within a 1 kb window upstream of genes transcribed by RNA Polymerase (Pol) III, including tRNA genes, 5S rRNA genes, and other small non-coding RNA genes. A Ty1-encoded protein, integrase (IN), is needed for catalyzing the insertion of Ty1 cDNA into the genome. The functional domains of INs among retrotransposons and retroviruses are also strikingly similar although the host genome target site selection is different. We seek to identify the S. cerevisiae host factors that mediate the specificity of Ty1 integration target site selection. We find that Ty1-IN interacts in vivo and in vitro with Pol III-specific subunits using mass spectrometry and co-purification approaches. The interaction with Pol III is specific as Ty1-IN does not interact with Pol II or the transcription complexes that recruit Pol III to promoters. Next, we narrow down the region required for interaction with Pol III to the Ty1-IN C-terminal (Ct) 75 amino acids. Using a purified version of the Ty1-IN Ct we demonstrate using single-particle electron microscopy that Ty1-IN docks onto the RNA Pol III complex in a region that maps to the Pol III jaw and clamp domains. We test a panel of Pol III subunit mutant strains for Ty1 integration, and find mutations in the Rpc34, Rpc53 and Rpc160 Pol III subunits that abrogate Ty1 insertion upstream of tGLY genes. We also optimize a whole genome Ty1 mapping protocol and analyze de novo Ty1 integration sites in a subset of these Pol III mutant strains. We find that rpc34 mutants are less efficient at targeting the Ty1 element upstream of all tRNA genes whereas an rpc53 mutant has no effect. Taken together, we establish that RNA Pol III is the host factor that tethers the Ty1 intasome to insertion target sites at Pol III-transcribed genes.

“Adipocyte Control of Energy Balance” by Lawrence Kazak, Assistant Professor, Department of Biochemistry, McGill University, Rosalind and Morris Goodman Cancer Research Centre

The obesity pandemic has precipitated a steep rise in metabolic diseases such as type 2 diabetes, heart disease, and many cancers. Globally, 40% of adults are overweight and 15% are obese. Obesity occurs when energy intake exceeds energy expenditure (energy imbalance). Thus, obesity can be caused by increased energy intake, decreased energy expenditure, or a combination of the two. Adipose tissue plays a central role in regulating whole-body energy homeostasis. Specifically, thermogenic (brown and beige) adipocytes can catabolize stored energy to generate heat. This capacity for thermogenesis holds tremendous promise as a therapy for metabolic diseases. The major focus of my lab is to identify the molecular mechanisms that drive adipocyte thermogenesis. By elucidating the genetic and metabolic pathways that control thermogenesis, we aim to recapitulate the positive effects of brown fat energy expenditure on health. To accomplish this, my lab uses molecular biology, bioenergetics, and stable isotope tracing to understand how adipocytes dissipate energy, at the level of cells and organelles. The physiological relevance of our findings is then examined using mice with engineered mutations in putative energy consuming pathways to test if these animals become obese (or not) when exposed to high calorie foods. Our research program will inform the development of therapies that support energy expenditure to combat obesity and related metabolic disorders.

Monday, April 8, 2019 @3:00 pm, LSC#3, 2350 Health Sciences Mall.

Host: Dr. Christian Kastrup

“Characterizing the assembly and molecular interactions of the fission yeast Atg1 autophagy regulatory complex”,  by Tamiza Nanji, PhD Candidate, Yip Lab.

Abstract: Macroautophagy, often referred to as autophagy, is a non-selective degradation mechanism used by eukaryotic cells to recycle cytoplasmic material and maintain homeostasis. Upregulated under starvation to generate molecular building blocks for ongoing cellular processes, this pathway requires the coordinated action of six multi-protein complexes, the Atg1/ULK1 complex being the first. Although, the Atg1 complex has been extensively studied in Saccharomyces cerevisiae, far less is known about the biochemical and structural properties of its mammalian counterpart, the ULK1 complex. Unlike the S. cerevisiae Atg1 complex which contains five subunits (Atg1, Atg13, Atg17, Atg29, and Atg31), the ULK1 complex consists of four proteins (ULK1, FIP200/RB1CC1, ATG13, and ATG101) that are technically more challenging to study. In this study, I characterized the Atg1 complex from fission yeast, Schizosaccharomyces pombe, as the composition of proteins resembles the mammalian ULK1 complex but is more amenable to biochemical analyses. The Atg1 complex in S. pombe is composed of Atg1 (ULK1 counterpart), Atg13, Atg17 (FIP200 counterpart) and Atg101. We found that the interactions between Atg1, Atg17, and Atg13 are conserved while Atg101 does not replace Atg29 and Atg31. Instead, Atg101 binds to Atg1 and the HORMA domain of Atg13. Furthermore, Atg101 was previously shown to contain a conserved loop, termed the WF finger, postulated to bind and recruit downstream autophagy-related proteins and effectors. Using affinity purification mass spectrometry, we further investigated the potential interacting partners of S. pombe Atg101 under autophagy-inducing and non-inducing conditions. We obtained 625 proteins that co-purified with Atg101-GFP from cells grown in defined media. We used in vitro pairwise studies to confirm the interaction between Atg101 and prey proteins. 9 of the 16 proteins tested were confirmed including Fkh1, an FKBP-type peptidyl-prolyl cis-trans isomerase. We further explored the interaction interface between Atg101 and Fkh1 and found that the WF finger is required for the interaction in vitro. Although the S. cerevisiae Fkh1 homologue, FKBP12, interacts with rapamycin; Fkh1 it is not thought to be directly involved in autophagy. Collectively, our results give new insights into an Atg101-containing Atg1/ULK1 complex and reveals that Atg101’s function may span beyond autophagy.

Host: Calvin Yip
Monday, March 18, 2019 at 3:00 pm. LSC#3, 2350 Health Sciences Mall.