Chemoproteomic profiling identifies changes in DNA-PK as markers of early dengue virus infection.

Abstract

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.

• Authors: Michael L Vetter, Mary A Rodgers, Matthew P Patricelli, Priscilla L Yang
• Journal: ACS chemical biology (ACS Chem Biol) Vol. 7 Issue 12 Pg. 2019-26 (Dec 21 2012) ISSN: 1554-8937 [Electronic] United States
• PMID: 22999307 (Publication Type: Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't)

Chemical References

• 5' Untranslated Regions
• Biomarkers
• DNA-Activated Protein Kinase

Topics

• 5' Untranslated Regions
• Biomarkers (metabolism)
• Blotting, Western
• Cell Line
• DNA-Activated Protein Kinase (metabolism)
• Dengue (enzymology)
• Humans
• Proteomics
• Signal Transduction