Genome-wide identification of host functions in RNA virus replication.

Poster number: 0

Paul Ahlquist

  1. Institute for Molecular Virology and Howard Hughes Medical Institute, University of Wisconsin - Madison, USA

Positive-strand RNA ((+)RNA) viruses are the largest genetic class of viruses, encompassing over one-third of virus genera and many important pathogens. (+)RNA viruses amplify their genomes in membrane-bounded RNA replication complexes whose structure, assembly and function share parallels with the replicative cores of reverse-transcribing and dsRNA virus virions, revealing intriguing functional and potentially evolutionary links. In addition to virus functions, host interactions are crucial determinants of (+)RNA virus replication, host range, tissue tropism and pathology. As one approach to identify and characterize host genes and functions in virus replication, we showed that the yeast S. cerevisiae supports genome replication, gene expression and virion assembly by two well-studied (+)RNA viruses: the model alphavirus-like virus, brome mosaic virus (BMV) and the nodavirus, flock house virus. Using classical yeast genetics and genome-wide functional genomics, including systematic analysis of 4500 strains of an ordered yeast single-gene-deletion library (~80% of yeast genes), we have identified over 100 host genes whose absence inhibited or enhanced BMV RNA replication >3- to >30-fold. For many of these host genes, we have identified the viral replication step(s) affected and characterized the associated effects, revealing insights to virus and host. The results show that unexpectedly diverse host functions control viral translation, recruitment of viral RNA templates from translation to RNA replication, chaperone-mediated activation of RNA replication complexes, viral RNA and protein stability, membrane characteristics essential for RNA replication, and other steps. Most of these are common, unifying themes among (+)RNA viruses, and all are potential antiviral targets. Further analyses are revealing contributions from additional host genes. The growing picture of virus replication and host interactions provides rich opportunities for modeling and integration with other functional genomics databases.