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

• Final Report Year: 2023

Final Report Abstract

Viruses are the cause of numerous diseases and cause considerable morbidity and mortality worldwide. Genome-based studies are well advanced and provide insights into evolution, host adaptation and virulence. Critical to the success of viral infection in the infected cell are proteins produced by the virus that interact with cellular proteins (known as protein-protein interactions, PPIs) to enable viral replication. Despite the importance of understanding these interactions in combating viral infections, comparatively little is known to date about these PPIs in intact infected cells. This can at least partly be attributed to a lack of suitable high-throughput methods at the PPI level. In this work, a method was established to overcome these limitations and systematically map virus-host interactions at the molecular level. This was achieved by combining pulse labeling using bioorthogonal amino acids and the use of cross-linking mass spectrometry (XL-MS) (method named SHVIP for Structural Host Virus Interactome Profiling). While XL-MS provides insights into the structural configuration of PPIs, bioorthogonal pulse labeling allows selective enrichment of the viral proteome, which can then be sensitively measured in the mass spectrometer. Thus, SHVIP allows sensitive discovery and structural characterization of virus-host PPIs in intact infected cells. Using this method, a global network of PPIs in cells infected with the medically relevant herpes simplex virus type I was created. SHVIP was able to detect interactions in all cellular compartments and is particularly suitable for mapping interactions at the host membrane system. Systematic comparison with other approaches (AP-MS) and by AI-assisted modeling supports the validity of SHVIP and enabled the creation of a compendium of virus-host models supported by structural data. Selected models were examined by targeted mutagenesis of relevant amino acids in the viral genome. Several interactions could be disrupted by point mutations, including the PPIs of the alkaline nuclease UL12 with 14-3-3 proteins or the DNA-damage relevant kinase MAPK8, and the viral tegument proteins UL47 and UL48. With the increasing global threat of viral diseases and the constant emergence of new infectious viruses, there is an urgent need to deepen our understanding of the interactions between viruses and host cells. SHVIP provides scientists with a crucial tool to address current and future challenges posed by viral infections.

Publications

• Combining Metabolic Pulse Labeling and Quantitative Proteomics to Monitor Protein Synthesis Upon Viral Infection. Methods in Molecular Biology, 149-165. Springer US.
  Bogdanow, Boris; Katsimani, Niki; Liu, Fan & Selbach, Matthias
  
• Enhancing Inter-link Coverage in Cross-Linking Mass Spectrometry through Context-Sensitive Subgrouping and Decoy Fusion. Cold Spring Harbor Laboratory.
  Bogdanow, Boris; Wang, Cong; Ruwolt, Max; Ruta, Julia; Mühlberg, Lars; Zeng, Wen-feng; Elofsson, Arne & Liu, Fan
  
• Spatially resolved protein map of intact human cytomegalovirus virions. Nature Microbiology, 8(9), 1732-1747.
  Bogdanow, Boris; Gruska, Iris; Mühlberg, Lars; Protze, Jonas; Hohensee, Svea; Vetter, Barbara; Bosse, Jens B.; Lehmann, Martin; Sadeghi, Mohsen; Wiebusch, Lüder & Liu, Fan