Structural Interactomics of virus host relationships

• Applicant: Dr.-Ing. Boris Bogdanow
• Subject Area: Virology ; Analytical Chemistry ; Cell Biology
• Term: from 2021 to 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 454970352

Protein-protein interactions (PPIs) facilitate essential processes during viral infections. Despite their significant importance, a method to globally study host-virus PPIs and corresponding interaction interfaces from intact infected cells is lacking. I am here planning to address this shortcoming by using cross-linking reagents on infected cells followed by mass-spectrometry of cross-linked peptides. I will combine this method with pulse labeling using biorthogonal amino acids, which increases the sensitivity of the approach towards detecting interactions of viral proteins with host proteins. As a model system, I chose Herpes-simplex virus type 1 due to its medical relevance, complex proteome, numerous interactions with host cellular proteins and its ability to induce shutoff of host cellular protein synthesis.The method I am proposing has numerous advantages compared to current approaches to systematically study virus-host interactions. First, since crosslinks are only formed between proteins that are in proximity, identified crosslinks hint towards interaction interfaces. Second, the use of membrane permissive crosslinking reagents allows to capture interactions in intact cells. Third, the approach works with genetically unaltered viruses and captures interactions of proteins in their native cellular environment. The overarching focus of the presented research proposal is to establish a valuable method for the systematic discovery of direct PPIs based on combining bio-orthogonal labeling and XL-MS. My preliminary data revealed an extensive interaction network involving hundreds of host and virus proteins based on thousands of crosslinks. I will build on these preliminary data and aim to further increase the depth and sensitivity of detecting PPIs in order to achieve near-comprehensive coverage of virus-host interactions. Further, I aim to assess how virus-host and virus-virus interactions dynamically change in the infected cell. Therefore, I will establish a proteomic and bioinformatics pipeline, allowing me to quantitatively capture the dynamics of PPIs during HSV-1 infection. Novel interactions will be validated and the functional importance of notable interactions will be demonstrated. The presented project thus integrates crosslinking mass-spectrometry with functional studies and integrative bioinformatics analyses. The results will deliver unmatched insights into the structural complexity of virus-host protein interactions for an important human pathogen.

• DFG Programme: WBP Position