Chemoproteomic Profiling Identifies Changes in DNA-PK as Markers of Early Dengue Virus Infection

• Published in: ACS chemical biology Vol. 7; no. 12; pp. 2019 - 2026
• Main Authors: Vetter, Michael L, Rodgers, Mary A, Patricelli, Matthew P, Yang, Priscilla L
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 21.12.2012
• Subjects: 5' Untranslated Regions; Biomarkers - metabolism; Blotting, Western; Cell Line; Dengue - enzymology; DNA-Activated Protein Kinase - metabolism; Humans; Proteomics; Signal Transduction
• ISSN: 1554-8929; 1554-8937
• DOI: 10.1021/cb300420z

Many cellular factors are regulated via mechanisms affecting protein conformation, localization, and function that may be undetected by most commonly used RNA- and protein-based profiling methods that monitor steady-state gene expression. Mass-spectrometry-based chemoproteomic profiling provides alternatives for interrogating changes in the functional properties of proteins that occur in response to biological stimuli, such as viral infection. Taking dengue virus 2 (DV2) infection as a model system, we utilized reactive ATP- and ADP-acyl phosphates as chemical proteomic probes to detect changes in host kinase function that occur within the first hour of infection. The DNA-dependent protein kinase (DNA-PK) was discovered as a host enzyme with significantly elevated probe labeling within 60 min of DV2 infection. Increased probe labeling was associated with increased DNA-PK activity in nuclear lysates and localization of DNA-PK in nucleoli. These effects on DNA-PK were found to require a postfusion step of DV2 entry and were recapitulated by transfection of cells with RNA corresponding to stem loop B of the DV2 5′ untranslated region. Upon investigation of the potential downstream consequences of these phenomena, we detected a modest but significant reduction in the interferon response induced by DV2 in cells partially depleted of the Ku80 subunit of DNA-PK. These findings identify changes in DNA-PK localization and activity as very early markers of DV2 infection. More broadly, these results highlight the utility of chemoproteomic profiling as a tool to detect changes in protein function associated with different cell states and that may occur on very short time scales.