Temporal SILAC-based quantitative proteomics identifies host factors involved in chikungunya virus replication

Area of Science:

• Virology
• Molecular Biology
• Proteomics

Background:

• Chikungunya virus (CHIKV) is a reemerging arthropod-borne pathogen causing severe arthritis.
• CHIKV outbreaks have affected millions globally since 2005.
• Viral replication relies on host cellular factors, presenting potential therapeutic targets.

Purpose of the Study:

• To define the temporal dynamics of the cellular proteome during CHIKV infection.
• To identify host proteins crucial for CHIKV replication.
• To explore potential therapeutic targets against CHIKV.

Main Methods:

• Stable Isotope Labeling by Amino acids in Cell culture (SILAC) coupled with Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) were employed.
• Proteomic analysis was performed on infected cells at 8, 10, and 12 hours postinfection.
• Differential protein expression analysis identified host factors affected by CHIKV.

Main Results:

• Over 4700 proteins were identified, with 2800-3500 quantified per time point.
• A significant number of proteins, including RNA polymerase II subunits, showed decreased abundance over time.
• Downregulation of Rho family GTPase 3 (Rnd3), DEAD box helicase 56 (DDX56), polo-like kinase 1 (Plk1), and ubiquitin-conjugating enzyme E2C (UbcH10) was observed.

Conclusions:

• CHIKV infection leads to host transcriptional shut-off, partly via RNA polymerase II degradation.
• Overexpression of downregulated proteins (Rnd3, DDX56, Plk1, UbcH10) reduced CHIKV susceptibility, indicating their importance for viral replication.
• These host factors represent promising targets for developing CHIKV therapeutics.