Characterizing Semliki Forest virus non-structural protein 3 interactome during replication with proximity labelling

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Title: Characterizing Semliki Forest virus non-structural protein 3 interactome during replication with proximity labelling
Author: Thiruvaiyaru, Aditya
Contributor: University of Helsinki, Faculty of Agriculture and Forestry
Publisher: Helsingin yliopisto
Date: 2021
Language: eng
Thesis level: master's thesis
Degree program: Mikrobiologian ja mikrobibiotekniikan maisteriohjelma
Master's Programme in Microbiology and Microbial Biotechnology
Magisterprogrammet i mikrobiologi och mikrobibioteknik
Specialisation: ei opintosuuntaa
no specialization
ingen studieinriktning
Abstract: Semliki Forest virus (SFV) is an enveloped virus with positive-sense single-stranded RNA genome that encodes nine proteins, of which four non-structural proteins, nsP1-4, form the replication/transcription complex (RTC) along with several host proteins, which play an important role in the replication of the virus. To establish the interactome of SFV RTC, a promiscuous biotin ligase capable of biotinylating proximal endogenous proteins in the presence of exogenous biotin was genetically fused to nsP3. After establishing the stability, kinetics and functionality of this virus, BHK-21 cells were infected with this mutant SFV at multiplicity of infection of 50 plaque forming units per cell. At an early time point of 2.5 hours post infection, 50 μM biotin was added to medium for 15 minutes. Cells were lysed, and biotinylated proteins were enriched with streptavidin beads, and analyzed through tandem mass-spectrometry. We were able to identify several key host protein interactions, some of which were already established before, but also a several new ones. Many of the host proteins detected were involved with the formation of stress granules, including G3BP’s, or contained a SH3-binding domain (SRC homology 3) like CD2AP, SH3KBP1 and BIN1, and some of them also had RNA binding motifs. In future, we wish to study the role of these identified host proteins in the replication of SFV through gene silencing as well as their co-localization with the RTC and nsP3 with the help of Immunofluorescence.
Subject: Semliki Forest virus
replication/transcription complex
non-structural protein 3
proximity labellings
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