TIA-1 RRM23 binding and recognition of target oligonucleotides

Abstract

TIA-1 (T-cell restricted intracellular antigen-1) is an RNA-binding protein involved in splicing and translational repression. It mainly interacts with RNA via its second and third RNA recognition motifs (RRMs), with specificity for U-rich sequences directed by RRM2. It has recently been shown that RRM3 also contributes to binding, with preferential binding for C-rich sequences. Here we designed UC-rich and CU-rich 10-nt sequences for engagement of both RRM2 and RRM3 and demonstrated that the TIA-1 RRM23 construct preferentially binds the UC-rich RNA ligand (5΄-UUUUUACUCC-3΄). Interestingly, this binding depends on the presence of Lys274 that is C-terminal to RRM3 and binding to equivalent DNA sequences occurs with similar affinity. Small-angle X-ray scattering was used to demonstrate that, upon complex formation with target RNA or DNA, TIA-1 RRM23 adopts a compact structure, showing that both RRMs engage with the target 10-nt sequences to form the complex. We also report the crystal structure of TIA-1 RRM2 in complex with DNA to 2.3 Å resolution providing the first atomic resolution structure of any TIA protein RRM in complex with oligonucleotide. Together our data support a specific mode of TIA-1 RRM23 interaction with target oligonucleotides consistent with the role of TIA-1 in binding RNA to regulate gene expression.

RNA-binding proteins in tumor progression

“…ARE is the most studied structure related to mRNA stability [165]. The most common RBPs that can stabilize mRNA are human antigen R (HuR), T cell intracellular antigen 1 (TIA-1), and TIA-1-related protein (TIAR) [166]. The abnormal increase and extension of ARE-encoded mRNAs are related to cancer (Fig.…”

RNA Binding Protein Regulation and Cross-Talk in the Control of AU-rich mRNA Fate

“…RRM2 drives the interaction with RNA, and shows the highest affinities for pyrimidine rich sequences. In turn, RRM3 enhances the overall TIA-1 binding affinity for RNA, preferentially interacting with C-rich motifs (Cruz-Gallardo et al, 2014 ; Wang et al, 2014 ; Waris et al, 2017 ). Moreover, HuR and TIAR interact with U- and AU-rich mRNAs in vitro , with greater affinity (≈10-fold) for the former ones.…”

“…Some ARE-RBPs also have the ability to bind to DNA. Importantly, in the case of TIA-1 and TIAR, it occurs with a markedly higher affinity than both RBPs show for their mRNA targets (Suswam et al, 2005 ; Waris et al, 2017 ). In fact, it has been hypothesized that the formation of the RBP-mRNA complexes would require the direct displacement of the RBP from its DNA-binding site by the polymerase.…”

“…In fact, it has been hypothesized that the formation of the RBP-mRNA complexes would require the direct displacement of the RBP from its DNA-binding site by the polymerase. This dual binding capacity of TIA-1 and TIAR could be potentially providing a link between transcription and splicing (Suswam et al, 2005 ; Mcalinden et al, 2007 ; Waris et al, 2017 ).…”

A putative RNA binding protein from Plasmodium vivax apicoplast

“…In addition, its RNP1 module is not fully conserved, whereas RNP2 is partly occluded by a 3 -helix. Eukaryotic RRMs are often found as multiple copies within a protein, and together with other protein domains, they confer different affinity and specificity for the RNA sequences [45][46][47][48][49][50][51][52][53]. RRMs are also found in prokaryotes, where they tend to occur as single domains in small proteins, typically around 100 amino acids in length (Pfam ID PF0076 and InterPro ID IPR000504 [54,55]).…”