Analysis of Hepatitis C virus-host protein interactions

Patrick T Dolan, Purdue University

Abstract

Hepatitis C virus (HCV) alters the global behavior of its host cell to create an environment conducive to its own replication. The phenotypic changes in the infected cell are often brought about by interactions between viral and host proteins, but much remains unknown about how only HCV proteins elicit these changes. This dissertation focuses on the question of how viral proteins perturb the host cell through virus-host protein-protein interactions. The studies reported herein address this question from two key perspectives: the biological functions of cellular targets, and the biophysical features of viral proteins that allow them to interact with numerous cellular binding partners. In the first study reported here, we describe the results of a large-scale yeast two-hybrid screen to identify protein-protein interactions between HCV genotype 2a (strain JFH1) and cellular factors. Our study identified 112 unique interactions between 7 HCV and 94 human proteins, over 40% of which have been linked to HCV infection by other studies. These interactions develop a more complete picture of HCV infection, providing insight into HCV manipulation of pathways, such as lipid and cholesterol metabolism, that were previously linked to HCV infection and implicating novel targets within microtubule-organizing centers, the complement system and cell cycle regulatory machinery. In an effort to understand the relationship between HCV and related viruses, we compared the HCV 2a interactome to those of other HCV genotypes and to the related dengue virus. Greater overlap was observed between HCV and dengue virus targets than between HCV genotypes, demonstrating the value of parallel screening approaches when comparing virus-host cell interactomes. Using siRNAs to inhibit expression of cellular proteins, we found that five of the ten shared targets tested (CUL7, PCM1, RILPL2, RNASET2, and TCF7L2) were required for replication of both HCV and dengue virus. These shared interactions provide insight into common features of the viral life cycles of the family Flaviviridae. In the second study, we investigate the hypothesis that viral proteins employ intrinsic disordered regions to mediate interaction with host proteins. We employed a combination of bioinformatic, genetic and computational approaches to analyze the function of two computationally-predicted molecular recognition features within the HCV Core protein. Our results suggest that these features are critical to the interaction with multiple host proteins, including known cofactors of HCV infection. Phylogenetic modeling revealed that these features are undergoing significant purifying selection, providing independent support for an important biological role for the features. This study has established that molecular recognition via intrinsic disorder is one strategy by which viral proteins interact with their host cell. Finally, we describe a new approach to mapping the binding surfaces of protein-protein interactions. The technique, known as the kinetic split luciferase assay, allows for the rapid quantification of relative binding kinetics across libraries of mutants. Focusing on two model systems, we show that we can successfully identify the key residues required for binding. In the future, this technique could be useful in the high-throughput mapping of protein interactions as part of a rational peptide mimetic drug design pipeline.

Degree

Ph.D.

Advisors

LaCount, Purdue University.

Subject Area

Systematic biology|Virology|Biophysics

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