A fly trap mechanism provides sequence-specific RNA recognition by CPEB proteins

Abstract

Cytoplasmic changes in polyA tail length is a key mechanism of translational control and is implicated in germline development, synaptic plasticity, cellular proliferation, senescence, and cancer progression. The presence of a U-rich cytoplasmic polyadenylation element (CPE) in the 39 untranslated regions (UTRs) of the responding mRNAs gives them the selectivity to be regulated by the CPE-binding (CPEB) family of proteins, which recognizes RNA via the tandem RNA recognition motifs (RRMs). Here we report the solution structures of the tandem RRMs of two human paralogs (CPEB1 and CPEB4) in their free and RNA-bound states. The structures reveal an unprecedented arrangement of RRMs in the free state that undergo an original closure motion upon RNA binding that ensures high fidelity. Structural and functional characterization of the ZZ domain (zinc-binding domain) of CPEB1 suggests a role in both protein-protein and protein-RNA interactions. Together with functional studies, the structures reveal how RNA binding by CPEB proteins leads to an optimal positioning of the N-terminal and ZZ domains at the 39 UTR, which favors the nucleation of the functional ribonucleoprotein complexes for translation regulation.

RNA-binding profiles of Drosophila CPEB proteins Orb and Orb2

“…Other reports suggest that both CPEB1 and CPEB4 recognize and control at least partially overlapping sets of mRNA targets and bind the same motif (23)(24)(25). Although a small number of fly Orb2 mRNA targets was described (26), the authors could not identify the bound sequence unambiguously.…”

“…Similar problems may occur with the use of in vitro gelshift assays (26). Interestingly, studies on the vertebrate CPEB4 in cell division support a CPE motif as a recognition sequence for this subfamily (23)(24)(25). CPEB4 can substitute functionally for its paralogue CPEB1 as a translational activator during the progress of meiosis (23) and binds a largely overlapping set of RNA targets (24,25).…”

“…Interestingly, studies on the vertebrate CPEB4 in cell division support a CPE motif as a recognition sequence for this subfamily (23)(24)(25). CPEB4 can substitute functionally for its paralogue CPEB1 as a translational activator during the progress of meiosis (23) and binds a largely overlapping set of RNA targets (24,25). Notably even though the canonical CPE motif was identified as a CPEB4-binding motif, its affinity for CPE motif was reduced compared with that of CPEB1 (24); this finding now is supported by the enrichment of distinct motif variants in the Orb and Orb2 datasets ( Fig.…”

Unmasking the U2AF homology motif family: a bona fide protein–protein interaction motif in disguise

“…The N-terminal SAP49 RRM engages a neighboring Cus1 subunit in the activated yeast spliceosome (Yan et al 2016) via a tryptophan-mediated interaction that is qualitatively similar to a UHM. In addition to the SAP49-Cus1 complex (Yan et al 2016), new examples of tryptophan-mediated interactions with RRM-like domains have emerged outside the UHM family, including eIF3b-eIF3j in the translation initiation complex (ElAntak et al 2010), Snu17p-Bud13p in the RES complex (Tripsianes et al 2014), mRNA export complexes of viral proteins with AlyREF (Tunnicliffe et al 2011;Tunnicliffe et al 2014), and an intramolecular interface of CPEB1 (Afroz et al 2014). The exact conformations of the tryptophan-containing ligands differ among these atypical RRMs, which also lack the RXF motif, acidic α1, and C-terminal α-helix of UHMs.…”

“…One of the first RRM structures revealed distinct α-helical and β-sheet surfaces of the U2B ′′ RRM bound to the U2A ′ protein and the U2 small nuclear (sn) RNA (Price et al 1998). Subsequent structures, including the complex of alternative splicing factors PTB with Raver1 (Rideau et al 2006;Joshi et al 2011), intramolecular CPEB1 contacts for polyadenylation (Afroz et al 2014), and the Snu17p RRM bound to Bud13p in the pre-mRNA retention and splicing complex (RES) (Tripsianes et al 2014;Yan et al 2016), establish that separate α-helical and RNP surfaces of the RRMs often bind protein and RNA partners simultaneously.…”