Profiling of rotavirus 3'UTR-binding proteins reveals the ATP synthase subunit ATP5B as a host factor that supports late-stage virus replication

J Biol Chem. 2019 Apr 12;294(15):5993-6006. doi: 10.1074/jbc.RA118.006004. Epub 2019 Feb 15.


Genome replication and virion assembly of segmented RNA viruses are highly coordinated events, tightly regulated by sequence and structural elements in the UTRs of viral RNA. This process is poorly defined and likely requires the participation of host proteins in concert with viral proteins. In this study, we employed a proteomics-based approach, named RNA-protein interaction detection (RaPID), to comprehensively screen for host proteins that bind to a conserved motif within the rotavirus (RV) 3' terminus. Using this assay, we identified ATP5B, a core subunit of the mitochondrial ATP synthase, as having high affinity to the RV 3'UTR consensus sequences. During RV infection, ATP5B bound to the RV 3'UTR and co-localized with viral RNA and viroplasm. Functionally, siRNA-mediated genetic depletion of ATP5B or other ATP synthase subunits such as ATP5A1 and ATP5O reduced the production of infectious viral progeny without significant alteration of intracellular viral RNA levels or RNA translation. Chemical inhibition of ATP synthase diminished RV yield in both conventional cell culture and in human intestinal enteroids, indicating that ATP5B positively regulates late-stage RV maturation in primary intestinal epithelial cells. Collectively, our results shed light on the role of host proteins in RV genome assembly and particle formation and identify ATP5B as a novel pro-RV RNA-binding protein, contributing to our understanding of how host ATP synthases may galvanize virus growth and pathogenesis.

Keywords: ATP synthase; RNA virus; RNA-binding protein; RNA–protein interaction; biotin proximity ligation; nonenveloped double-stranded RNA virus; proteomics; rotavirus; viral gastroenteritis; virology; virus assembly; virus–host interaction.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • 3' Untranslated Regions*
  • Genome, Viral
  • HEK293 Cells
  • Humans
  • Mitochondrial Proton-Translocating ATPases / genetics
  • Mitochondrial Proton-Translocating ATPases / metabolism*
  • RNA, Viral / genetics
  • RNA, Viral / metabolism*
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism*
  • Rotavirus / physiology*
  • Viral Proteins / genetics
  • Viral Proteins / metabolism*
  • Virus Assembly / physiology*


  • 3' Untranslated Regions
  • ATP5F1B protein, human
  • RNA, Viral
  • RNA-Binding Proteins
  • Viral Proteins
  • Mitochondrial Proton-Translocating ATPases

Associated data

  • PDB/2R7R
  • PDB/2XND
  • PDB/4HXI
  • PDB/1KNZ
  • PDB/3MIW