Structure of the PCBP2/stem–loop IV complex underlying translation initiation mediated by the poliovirus type I IRES

• Published in: Nucleic acids research Vol. 48; no. 14; pp. 8006 - 8021
• Main Authors: Beckham, Simone A, Matak, Mehdi Y, Belousoff, Matthew J, Venugopal, Hariprasad, Shah, Neelam, Vankadari, Naveen, Elmlund, Hans, Nguyen, Joseph H C, Semler, Bert L, Wilce, Matthew C J, Wilce, Jacqueline A
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 20.08.2020
• Subjects: Cryoelectron Microscopy; Models, Molecular; Nucleic Acid Conformation; Peptide Chain Initiation, Translational; Poliovirus - genetics; Protein Conformation; RNA and RNA-protein complexes; RNA, Viral - chemistry; RNA, Viral - metabolism; RNA-Binding Proteins - chemistry; RNA-Binding Proteins - metabolism; Scattering, Small Angle; X-Ray Diffraction
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkaa519

Abstract The poliovirus type I IRES is able to recruit ribosomal machinery only in the presence of host factor PCBP2 that binds to stem–loop IV of the IRES. When PCBP2 is cleaved in its linker region by viral proteinase 3CD, translation initiation ceases allowing the next stage of replication to commence. Here, we investigate the interaction of PCBP2 with the apical region of stem–loop IV (SLIVm) of poliovirus RNA in its full-length and truncated form. CryoEM structure reconstruction of the full-length PCBP2 in complex with SLIVm solved to 6.1 Å resolution reveals a compact globular complex of PCBP2 interacting with the cruciform RNA via KH domains and featuring a prominent GNRA tetraloop. SEC-SAXS, SHAPE and hydroxyl-radical cleavage establish that PCBP2 stabilizes the SLIVm structure, but upon cleavage in the linker domain the complex becomes more flexible and base accessible. Limited proteolysis and REMSA demonstrate the accessibility of the linker region in the PCBP2/SLIVm complex and consequent loss of affinity of PCBP2 for the SLIVm upon cleavage. Together this study sheds light on the structural features of the PCBP2/SLIV complex vital for ribosomal docking, and the way in which this key functional interaction is regulated following translation of the poliovirus genome.