Ongoing Projects

 

Autophagy is the cellular process responsible for removal and recycling of large and stable macromolecular assemblies, such as protein aggregates, organelles, and intracellular pathogens; by engulfing these targets in multi-layered vesicles followed by fusion with and degradation by the lysosome.  Dysfunction of autophagy has been implicated in lysosomal storage diseases like Neimen-Pick and Tay-Sachs diseases; abnormal embryonic and fetal development (due to inefficient remodeling of cells); neurodegenerative diseases like Parkinson’s and Alzheimer’s (due to accumulation of protein aggregates); heart diseases (due to remodeling of cardiac tissue in response to stress condition); cancers and aging (due to inadequate removal of mutant / damaged proteins); and numerous infectious diseases (due to inadequate removal of pathogens).  Many of the proteins that execute this pathway have been identified over the last decade, but others are still being identified.  However, little is known about the mechanism by which these proteins carry out their autophagy function. 
The overarching goal of the research in my laboratory is to understand in atomic detail, the mechanistic bases of the function of autophagy proteins, their interactions with proteins from other pathways, and how the malfunction of these proteins results in autophagy defects and consequently in various diseases. 
This overall goal can be divided into three distinct, yet overlapping, broad sub-goals outlined below:

 

To date, 65 different proteins have been shown to serve as autophagy effectors and regulators in the cell.  These proteins function in multi-protein complexes responsible for autophagy activation, target selection, vesicle nucleation, vesicle elongation, vesicle fusion with the lysosome, and recycling of autophagy proteins. 
In one project, two graduate students, Ms. Yang Mei and Mr. Gaurav Soni are conducting extensive sequence analyses to identify intrinsically disordered domains in all known proteins with roles in autophagy.  Such domains play very important, yet poorly understood roles in the cell.  We are collaborating with Dr. Colbert (Chemistry and Biochemistry) and Dr. Salem (Computer Science) on this project.
An important focus of our research is to investigate proteins known to be involved in vesicle nucleation: Class III phosphatidylinositol-3-kinase, p150, Beclin 1, Atg14, UVRAG, Bif-1, and Ambra1.  We are studying these proteins in isolation, as well as in complex with each other and other proteins.
Previously, we have determined the structure and mechanism of the Beclin 1 BH3 domain and its inhibition by Bcl-2 proteins.  This research, which was funded in part by an NIH R21 grant, was reported in the cover article of the journal Autophagy, and reviewed in the journal Oncogene.  A graduate student, Ms. Yang Mei, is investigating the remaining Beclin 1 domains, and was assisted by Mr. Tom Moulton, a 2011 COBRE REU student.  Ms. Mei was recently selected to present her preliminary results on this project, at the Gordon Research Seminars in March, 2012.  The investigation of another Beclin 1 domain (the coiled-coil domain) is the subject of my NSF CAREER proposal currently in review. 
Another graduate student, Ms. Minfei Su, along with an undergraduate, Ms. Marion Okondo, is investigating the structure and mechanism of UVRAG and its interaction with Bif-1. 
Ms. Mei and Ms. Su will also collaborate to study the interaction of Beclin 1 and UVRAG.  Investigation of the other proteins listed awaits the recruitment of other qualified graduate students and undergraduates.

 

Autophagy plays a critical direct role in protecting cells from intracellular pathogens, like viruses, many bacteria and other microbes.  Therefore, many pathogens have developed methods to inhibit, evade or disrupt autophagy, to allow them to establish intracellular infections.  Currently, we are focusing on how different viruses inhibit the essential autophagy protein Beclin 1. 
We are investigating how g-herpesvirus-encoded Bcl-2 proteins bind to and inhibit Beclin 1.  This research, funded by my ongoing NIH R21 grant, was reported and featured in the journal Autophagy, and an additional article in the journal Molecular Cell.  Subsequent work, aimed at obtaining information useful for the design of drugs targeting the g-herpesviruses, is being completed by my graduate student, Ms. Su, and includes some results from Ms. Mei.  Dr. Colbert (Chemistry & Biochemistry) and Dr. Guo (Pharmaceutical Sciences) have contributed to the design of two different experiments to be included in this paper.  Preliminary results on this project were included in my seminar presented at the Zing Autophagy conference in Nov. 2011.  Ms. Su has also been recently selected to present her preliminary results on this project at the Gordon Research Seminars in March 2012.  In the future we hope to build on these results by collaborating with Drs. Svetlana Kilina (Chemistry and Biochemistry) and Dr. Keith Henry (UND, Grand Forks, ND) to design small molecule inhibitors of the g-herpesvirus Bcl-2s, and with Dr. Cook (Chemistry and Biochemistry) to chemically synthesize these molecules, in order to inhibit g-herpesvirus-encoded Bcl-2s.  In vivo testing of any potential drugs will be done via collaboration with Dr. Beth Levine (UTSW Medical Center, Dallas, TX).

 

Regulation of autophagy, a degradation pathway, is coordinated with apoptosis, another important degradation pathway that causes cell-death.  My collaborator, Dr. Beth Levine, has shown that the anti-apoptotic Bcl-2 proteins also bind to Beclin 1 and inhibit autophagy, and my structural and biochemical studies have elucidated the atomic details of this inhibitory mechanism.  This research was reported in two separate articles in the journal Autophagy.  We reviewed these combined findings in refereed articles in the journals Autophagy and Oncogene.  We are continuing to investigate different nodes of interaction between the autophagy and apoptosis pathways.