Nevan Krogan


Email: nevan.krogan / ucsf, edu

1700 4th Street, MC 2530
Byers Hall, Room 308D
San Francisco, CA 94158-2530

Phone: 415 476-2980

Assistant Director
Nikki Treacy
415 514-6109
nikki.treacy / ucsf, edu

My research group is involved in the generation and analysis of large-scale, quantitative genetic and protein-protein interaction maps in a variety of different organisms, including S. cerevisiae, S. pombe and E. coli. We primarily employ a systematic affinity tagging/purification/mass spectrometry approach to identify protein complexes and our E-MAP (epistatic miniarray profile) methodology is utilized to generate quantitative genetic interaction maps. We integrate this information together using a variety of analytical tools that we have developed and are also involved in creating appropriate software that allows for visualization of these large datasets.

We use this information to generate testable hypotheses on a number of different processes, including RNA processing, DNA replication and chromatin function. These unbiased approaches have led to the discovery of many exciting and unanticipated connections between many different functional pathways and biological processes. We are also applying global and unbiased approaches and methodologies to the study of pathogenic organisms to further understand how they “hijack” human cells. It is being increasingly recognized that such approaches may be necessary for breakthroughs in effective anti-pathogen strategies, where host-pathogen interactions have proven to be multifunctional and more complicated than expected. Initially, we are focusing our attention on two organisms that are becoming more problematic worldwide: HIV and Mycobacterium tuberculosis (TB). For instance, using our affinity tagging/purification mass spectrometry strategy, we are systematically identifying all HIV-human protein-protein interactions. To this end, we have purified all 18 proteins and polyproteins associated with this virus from two different cell lines (HEK293 and Jurkat).

Using a novel scoring system, we have identified 497 high confidence HIV-human protein-protein interactions, the vast majority of which have not been previously described. We are also following up on several unanticipated, interesting connections between HIV factors and the pathways they hijack. For example, we have found that HIV protease cleaves several host factors, including a component of a translational initiation complex, which is involved in inhibiting HIV replication. Furthermore, we have found a new component of the Cul5 ubiquitin ligase complex that is hijacked by the HIV accessory factor Vif, which is required for its function and HIV infectivity, and has allowed us to reconstitute an active hexameric protein complex. Furthermore, we are transferring our genetic approach, termed E-MAP, to the study of infectious disease. To this end, we are developing methodology that will allow, for the first time, generation of cross-species, host-pathogen genetic interaction maps. This approach will identify which factors are functioning together within the pathogenic organism and which set of genes are re-wired in the host after infection. Since these unbiased and systematic approaches often identify key proteins that link together different processes, we feel these proteins would be enriched for being suitable drug targets. Identifying these proteins using traditional, hypothesis-driven research, in many cases, would be incredibly difficult.