Mechanism of β-actin mRNA Recognition by ZBP1

• Published in: Cell reports (Cambridge) 2017-01, Vol.18 (5), p.1187-1199
• Main Authors: Nicastro, Giuseppe, Candel, Adela M., Uhl, Michael, Oregioni, Alain, Hollingworth, David, Backofen, Rolf, Martin, Stephen R., Ramos, Andres
• Format: Article
• Language: English
• Subjects: Actins - metabolism; Amino Acid Sequence; Animals; Avian Proteins - metabolism; binding mechanism; Chickens - metabolism; Embryonic Development - physiology; IMP1; mRNA local translation; neuronal development; neuronal mRNA granules; NMR; protein-RNA interactions; RNA - metabolism; RNA, Messenger - metabolism; RNA-Binding Proteins - metabolism; ZBP1
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2016.12.091

Zipcode binding protein 1 (ZBP1) is an oncofetal RNA-binding protein that mediates the transport and local translation of β-actin mRNA by the KH3-KH4 di-domain, which is essential for neuronal development. The high-resolution structures of KH3-KH4 with their respective target sequences show that KH4 recognizes a non-canonical GGA sequence via an enlarged and dynamic hydrophobic groove, whereas KH3 binding to a core CA sequence occurs with low specificity. A data-informed kinetic simulation of the two-step binding reaction reveals that the overall reaction is driven by the second binding event and that the moderate affinities of the individual interactions favor RNA looping. Furthermore, the concentration of ZBP1, but not of the target RNA, modulates the interaction, which explains the functional significance of enhanced ZBP1 expression during embryonic development. [Display omitted] •The dynamic groove of ZBP1’s KH4 domain allows recognition of a G-rich RNA sequence•ZBP1’s KH3 and KH4 domains bind their target RNA sequences with similar affinities•RNA looping drives the ZBP1-β-actin interaction•The protein, rather than the RNA, concentration regulates ZBP1-β-actin mRNA binding The interaction of β-actin mRNA with the RNA-binding protein ZBP1 regulates mRNA transport and translation and is necessary for neuronal development. Using NMR and biophysics, Nicastro et al. have shown that the interaction is driven by RNA looping and regulated by the protein, rather than the RNA, concentration.