Functional analysis of a novel viral RNA binding protein

Background: Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that re-emerged in 2004 and has spread from the Indian Ocean region to other areas of the world including Europe and America. In many cases it causes highly debilitating chronic musculoskeletal pain and is thus a major public health issue. Effective treatment strategies are hampered by a lack of knowledge of virus biology, in particular little is known about the functions of viral proteins such as the non-structural protein, nsp3.
Objectives: nsp3 is reported to be an RNA binding protein, yet this hypothesis is only supported by one limited study. The RNA specificity or selectivity of nsp3, and the nature of the RNA binding motif(s) within the protein remain undetermined.
Novelty: The CHIKV nsp3 protein is poorly studied yet is absolutely required for virus replication.
Timeliness: As a re-emerging virus that has infected many millions of people across the world in the past decade CHIKV represents a key target for the development of new therapeutic options that are urgently needed.
Experimental approach: We have developed tagged versions of nsp3 within both replicons and infectious virus. These will be used in an iCLIP in vivo RNA binding approach to determine the RNA species that interact with nsp3 in a physiologically relevant context. Following this, mutagenesis and in vitro and in-cell SHAPE analysis will interrogate the interactions in more detail. As CHIKV grows in both humans and mosquitos this affords further opportunities to generate comparative datasets.