IMP1 KH1 and KH2 domains create a structural platform with unique RNA recognition and re-modelling properties.

Robert Dagil,Neil J Ball,Ian A Taylor,Andrew G Purkiss,Stephen R Martin,Fruzsina Hobor,Roksana W Ogrodowicz,Geoff Kelly,Andres Ramos

doi:10.1093/nar/gkz136

Robert Dagil, Neil J Ball + Show 7 more

Open Access

https://doi.org/10.1093/nar/gkz136

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Abstract

IGF2 mRNA-binding protein 1 (IMP1) is a key regulator of messenger RNA (mRNA) metabolism and transport in organismal development and, in cancer, its mis-regulation is an important component of tumour metastasis. IMP1 function relies on the recognition of a diverse set of mRNA targets that is mediated by the combinatorial action of multiple RNA-binding domains. Here, we dissect the structure and RNA-binding properties of two key RNA-binding domains of IMP1, KH1 and KH2, and we build a kinetic model for the recognition of RNA targets. Our data and model explain how the two domains are organized as an intermolecular pseudo-dimer and that the important role they play in mRNA target recognition is underpinned by the high RNA-binding affinity and fast kinetics of this KH1KH2–RNA recognition unit. Importantly, the high-affinity RNA-binding by KH1KH2 is achieved by an inter-domain coupling 50-fold stronger than that existing in a second pseudo-dimer in the protein, KH3KH4. The presence of this strong coupling supports a role of RNA re-modelling in IMP1 recognition of known cancer targets.

Highlights

IGF2 messenger RNA (mRNA)-binding protein 1 (IMP1) is a conserved RNA-binding protein that plays a key role in regulating cell motility, morphology and differentiation in the embryo, reviewed by Yisraeli [1]
IGF2 mRNA-binding protein 1 (IMP1) increases the stability of the mRNAs encoding the oncoprotein c-Myc [9,10] and the cell-surface glycoprotein CD44 [11] amongst others, and is itself down-regulated by Let-7 miRNA [12]
The structure shows that the KH1 and KH2 domains fold into an intra-molecular pseudo-dimer, (Figure 2A), an arrangement found in a number of KH and RNA-recognition motifs (RRMs)-containing proteins including the IMP1 KH3KH4 di-domain

Summary

Introduction

IGF2 mRNA-binding protein 1 (IMP1) is a conserved RNA-binding protein that plays a key role in regulating cell motility, morphology and differentiation in the embryo, reviewed by Yisraeli [1]. IMP1 regulates the transport, translation and stability of a diverse ensemble of messenger RNAs (mRNAs). The best-studied function of IMP1 is its role in mediating the transport and controlled translation of ␤-actin mRNA [5,6]. IMP1 increases the stability of the mRNAs encoding the oncoprotein c-Myc [9,10] and the cell-surface glycoprotein CD44 [11] amongst others, and is itself down-regulated by Let-7 miRNA [12]. More recent studies have shown a role for IMP1 in the stabilization of numerous non-coding RNAs [13]

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