The viral transportome (ViTra)

Host factor requirements for many classes of viruses are yet to be unraveled. Replication of the viral genome and synthesis of viral proteins inside the host cell are associated with altered, often enhanced cellular metabolism and increased demand in nutrients and specific molecules. With some 400 identified members in humans, the solute carriers (SLC) represent the largest family of trans-membrane proteins dedicated to the transport of small molecules, such as amino acids, sugars, nucleotides and ions. Thus far, several members of the SLC protein family were described as being viral receptors; however, their role in other parts of the viral life cycle, such as viral uncoating, replication or virion assembly, remains obscure. Given the crucial physiological functions of SLCs, at the interface between metabolism and the environment, the action of these proteins may contribute importantly to the pathology of viral infection. The aim of this project is to characterize the role of host SLCs in viral replication, confirm their function as a new regulatory group of proteins in the antiviral immune response as well as gather knowledge on the cargoes and protein-protein interactions of relevant SLCs. Upon integration of multiple large-scale datasets from recent genome-wide screens, a group of 20 SLC proteins has been identified to have a function linked to viral replication or immune response. We systematically inactivated the genes encoding these SLCs in a human cell line using the CRISPR-Cas9 system. Functional screens using Influenza, Vaccinia and Vesicular Stomatitis Viruses will be performed to define the effect of mutations in the SLC genes on the susceptibility of cells to infection. Preliminary results from a primary screen performed using the Influenza A WSN strain indeed suggest that several of the selected SLCs affect viral infection. We plan to carry on further characterization of the most interesting SLC candidates in order to dissect their role in the context of host-pathogen interplay and host metabolism. Moreover, we will study the protein-protein interactions of their gene products and will try to identify their natural cargo through a combination of experimental (metabolomics, mass spectrometry) and computational (chemoinformatics, modeling) approaches. Together, this viral transportome may offer novel insights into possible strategies to pharmacologically interfere with viral infections.

Host factor requirements for many classes of viruses are yet to be unraveled. Replication of the viral genome and synthesis of viral proteins inside the host cell are associated with altered, often enhanced cellular metabolism and increased demand in nutrients and specific molecules. With some 400 identified members in humans, the solute carriers (SLC) represent the largest family of trans-membrane proteins dedicated to the transport of small molecules, such as amino acids, sugars, nucleotides and ions. Thus far, several members of the SLC protein family were described as being viral receptors; however, their role in other parts of the viral life cycle, such as viral uncoating, replication or virion assembly, remains obscure. Given the crucial physiological functions of SLCs, at the interface between metabolism and the environment, the action of these proteins may contribute importantly to the pathology of viral infection. The aim of this project was to characterize the role of host SLCs in viral replication, confirm their function as a new regulatory group of proteins in the antiviral immune response as well as gather knowledge on the cargoes and protein-protein interactions of relevant SLCs. Upon integration of multiple large-scale datasets from recent genome-wide screens, a group of 20 SLC proteins has been identified to have a function linked to viral replication or immune response. We systematically inactivated the genes encoding these SLCs in a human cell line using the CRISPR-Cas9 system. Functional screens using Influenza, Vaccinia and Vesicular Stomatitis Viruses were performed to define the effect of mutations in the SLC genes on the susceptibility of cells to infection. Moreover, loss-of-function genetic screening approaches using a SLC-focused library expanded the set of interactions with both known as well as novel SLC-virus interactions. Further characterization of the most interesting SLC candidates revealed opposite roles for the zinc transporter SLC30A1 and the sialic acid-CMP transporter SLC35A1 in determining the cellular response to VSV infection. Together, this "viral transportome" may offer novel insights into possible strategies to pharmacologically interfere with viral infections.