Molecular characterization of the RNA-protein complex directing −2/−1 programmed ribosomal frameshifting during arterivirus replicase expression

Journal of Biological Chemistry, vol. 295, pp. 17904–17921

Abstract

Programmed ribosomal frameshifting (PRF) is a mechanism used by arteriviruses like porcine reproductive and respiratory syndrome virus (PRRSV) to generate multiple proteins from overlapping reading frames within its RNA genome. PRRSV employs -1 PRF directed by RNA secondary and tertiary structures within its viral genome (canonical PRF), as well as a noncanonical -1 and -2 PRF that are stimulated by the interactions of PRRSV nonstructural protein 1β (nsp1β) and host protein poly(C)-binding protein (PCBP) 1 or 2 with the viral genome. Together, nsp1β and one of the PCBPs act as transactivators that bind a C-rich motif near the shift site to stimulate -1 and -2 PRF, thereby enabling the ribosome to generate two frameshift products that are implicated in viral immune evasion. How nsp1β and PCBP associate with the viral RNA genome remains unclear. Here, we describe the purification of the nsp1β:PCBP2:viral RNA complex on a scale sufficient for structural analysis using small-angle X-ray scattering and stochiometric analysis by analytical ultracentrifugation. The proteins associate with the RNA C-rich motif as a 1:1:1 complex. The monomeric form of nsp1β within the complex differs from previously reported homodimer identified by X-ray crystallography. Functional analysis of the complex via mutational analysis combined with RNA-binding assays and cell-based frameshifting reporter assays reveal a number of key residues within nsp1β and PCBP2 that are involved in complex formation and function. Our results suggest that nsp1β and PCBP2 both interact directly with viral RNA during formation of the complex to coordinate this unusual PRF mechanism.

Authors 7

1. Ankoor Patel

   University of Manitoba

   Affiliation as printed

   Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada

2. Emmely E. Treffers Aachen Molecular Virology Laboratory Department of Medical Microbiology

   Leiden University Medical Center

   Affiliation as printed

   Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands

3. Markus Meier

   University of Manitoba

   Affiliation as printed

   Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada

4. Trushar R. Patel

   University of Lethbridge

   Affiliation as printed

   Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada

5. Jörg Stetefeld

   University of Manitoba

   Affiliation as printed

   Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada

6. Eric J. Snijder Aachen Molecular Virology Laboratory Department of Medical Microbiology

   Leiden University Medical Center

   Affiliation as printed

   Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands

7. Brian L. Mark corresponding

   University of Manitoba

   Affiliation as printed

   Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada. Electronic address: brian.mark@umanitoba.ca

   Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada