Synergic interplay of the La motif, RRM1 and the interdomain linker of LARP6 in the recognition of collagen mRNA expands the RNA binding repertoire of the La module

Abstract

The La-related proteins (LARPs) form a diverse group of RNA-binding proteins characterized by the possession of a composite RNA binding unit, the La module. The La module comprises two domains, the La motif (LaM) and the RRM1, which together recognize and bind to a wide array of RNA substrates. Structural information regarding the La module is at present restricted to the prototypic La protein, which acts as an RNA chaperone binding to 3′ UUUOH sequences of nascent RNA polymerase III transcripts. In contrast, LARP6 is implicated in the regulation of collagen synthesis and interacts with a specific stem-loop within the 5′ UTR of the collagen mRNA. Here, we present the structure of the LaM and RRM1 of human LARP6 uncovering in both cases considerable structural variation in comparison to the equivalent domains in La and revealing an unprecedented fold for the RRM1. A mutagenic study guided by the structures revealed that RNA recognition requires synergy between the LaM and RRM1 as well as the participation of the interdomain linker, probably in realizing tandem domain configurations and dynamics required for substrate selectivity. Our study highlights a considerable complexity and plasticity in the architecture of the La module within LARPs.

The role of LARP1 in translation and beyond

“…Slf1p and Sro9p are RBPs and their LAM is required for their function, and appear to contribute to selective mRNA‐binding . However, the LAM is not able to bind RNA by itself, and additional cis ‐domains that would cooperate with the LAM in S. cerevisiae LARPs have not been detected so far . Hence, how Slf1p and Sro9p bind RNA remains a challenging enigma.…”

“…26 Although absolutely necessary, the LAM is not able to bind RNA alone and cooperates with an adjacent RNA recognition motif (RRM1) and the interdomain linker to form the RNA-binding pocket known as the La-Module. [26][27][28][29] La and related proteins form a superfamily of eukaryotic factors, which classify into five clusters: the genuine La and four LARP subfamilies: LARP1, 4, 6 and 7 15 (Figure 1). Most LARPs retained a La-module organization, but unlike the LAM which diverged very little, the RRM1 and interdomain linker are specific to each subfamily.…”

“…Most LARPs retained a La-module organization, but unlike the LAM which diverged very little, the RRM1 and interdomain linker are specific to each subfamily. 15,26 The genuine La and LARP7 proteins share a related canonical RRM1 (adopting the typical sandwich fold and bearing the RNP1 and RNP2 aromatic patches 30 ), while the other LARP families have specific non-canonical RRM1 15 (Figure 1). Members of a subfamily share additional motifs likely to be key actors of the proteins' functions.…”

Recombinant expression and purification of the RNA-binding LARP6 proteins from fish genetic model organisms

“…Only one endogenous ligand has been identified: in mammals, LARP6 binds to a secondary structure element in the 5′ untranslated region (5′UTR) of type I collagen mRNAs [8,9]. Recently, the high-resolution structures of the individual La motif domain and the RRM domain of human LARP6 protein were solved by solution NMR [10]. The biochemical experiments that accompanied these structures demonstrated that the interdomain linker between the La motif and the RRM plays a critical role in the RNA binding activity [10].…”

“…Recently, the high-resolution structures of the individual La motif domain and the RRM domain of human LARP6 protein were solved by solution NMR [10]. The biochemical experiments that accompanied these structures demonstrated that the interdomain linker between the La motif and the RRM plays a critical role in the RNA binding activity [10]. …”