Mechanism of β-actin mRNA Recognition by ZBP1

Abstract

SummaryZipcode 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.

The structural basis for RNA selectivity by the IMP family of RNA binding proteins

“…3b, e, f). This result was consistent with ZBP1 KH domain/RNA interaction where the highly conserved GXXG motif faces the phosphate backbone and the variable loops face the nucleobases 13,34 . Together the two form a vice like structure that binds to the RNA 5 .…”

Combinatorial recognition of clustered RNA elements by a multidomain RNA-binding protein, IMP3

“…Analogously, there is evidence that the KH1-2 and KH3-4 tandem domains represent pre-arranged RNA-binding modules for recognition of bipartite RNA sequence motifs. Structures of the human IMP1 KH3-4 14 , as well as the KH3-4 di-domains of the chicken ortholog ZBP1 16 proved the existence of an extended domain interface between KH3 and 4. These structures suggest target RNA motifs to require a minimal spacing to be recognized by the tandem RBDs.…”

“…This "caging" of mRNAs ranges in its functional spectrum from packaging for cytoplasmic transport 5 , delayed translation within stable mRNPs [6][7][8] , cytoplasmic storage, and protection against pre-mature miRNA-directed mRNA regulation 3,[9][10][11][12] . Several target mRNAs have been suggested 3,13 , with IMP1 associating with the ACTB mRNA zipcode element and all three IMPs regulating HMGA2 stability via the 3´-UTR as the currently best-studied examples [9][10][11][12][14][15][16] .…”

Joining the dots – protein‐RNA interactions mediating local mRNA translation in neurons

“…Please note the structural representation on the left has been obtained by superimposing the structures of the KH 3‐ RNA bound and KH 4‐ RNA bound KH 34 complexes as described in Ref. . Right: blow‐up of the protein‐ RNA contacts present in the two structures.…”

“…ZBP1 recognition of β‐actin mRNAs is mediated by the recognition of two specific sequences by KH3 and KH4 (ACA and CGGAC respectively) within the β‐actin mRNA Zipcode . The two RNA sequences bind on opposite sides of the KH3KH4 di‐domain (Fig. ), and biophysical and functional data indicate that these interactions are coupled .…”