Riboproteomics of the hepatitis C virus internal ribosomal entry site.
Hepatitis C virus (HCV) protein translation is mediated by a cis-acting RNA, an internal ribosomal entry site (IRES), located in the 5' nontranslated region of the viral RNA. To examine proteins bound to the IRES, which could include proteins important for its function as well as potential drug targets, we used shotgun peptide sequencing to identify proteins in quadruplicate protein affinity extracts of lysed Huh7 cells, obtained using a biotinylated IRES. Twenty-six proteins bound the HCV IRES but not a reversed complementary sequence RNA or vector RNA controls. These included five ribosomal subunits, nine eukaryotic initiation factor 3 subunits, and novel interacting proteins such as the cytoskeletal-related proteins actin, FHOS (formin homologue overexpressed in spleen) and MIP-T3 (microtubule interacting protein that associates with TRAF3). Other novel HCV IRES-binding proteins included UNR (upstream of N-ras), UNR-interacting protein, and the RNA-binding proteins PAI-1 (plasminogen activator inhibitor-1) mRNA binding protein and Ewing sarcoma breakpoint 1 region protein EWS. A large set of additional proteins bound both the HCV IRES and a reversed complementary IRES sequence control, including the known HCV interactors PTB (polypyrimidine tract binding protein), the La autoantigen, and nucleolin. The discovery of these novel HCV IRES-binding proteins suggests links between IRES biology and the cytoskeleton, signal transduction, and other cellular functions.
Rigel, Inc., South San Francisco, California 94066, USA.
Henry
H
Lu
Weiqun
W
Li
William Stafford
WS
Noble
Donald
D
Payan
D C
DC
Anderson
D000595:Amino Acid Sequence; D000604:Amino Acyl-tRNA Synthetases / Q000032:analysis; D001185:Artificial Intelligence; D001665:Binding Sites / Q000235:genetics; D019921:Biotinylation; D045744:Cell Line, Tumor; D003593:Cytoplasm / Q000737:chemistry / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000032:analysis; D004591:Electrophoresis, Polyacrylamide Gel; D016174:Hepacivirus / Q000235:genetics* / Q000378:metabolism; D034441:Heterogeneous-Nuclear Ribonucleoproteins / Q000032:analysis; D006801:Humans; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000032:analysis / Q000737:chemistry; D010448:Peptide Initiation Factors / Q000032:analysis; D010957:Plasmids / Q000235:genetics; D014176:Protein Biosynthesis / Q000235:genetics*; D040901:Proteomics; D012367:RNA, Viral / Q000235:genetics* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000032:analysis* / Q000378:metabolism; D012269:Ribosomal Proteins / Q000032:analysis; D014158:Transcription, Genetic / Q000235:genetics; D014357:Trypsin / Q000378:metabolism
D004268:DNA-Binding Proteins; D034441:Heterogeneous-Nuclear Ribonucleoproteins; D010446:Peptide Fragments; D010448:Peptide Initiation Factors; D012367:RNA, Viral; D016601:RNA-Binding Proteins; D012269:Ribosomal Proteins; D014357:Trypsin; D000604:Amino Acyl-tRNA Synthetases