Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p

Abstract

The SAM domain of the Saccharomyces cerevisiae post-transcriptional regulator Vts1p epitomizes a subfamily of SAM domains conserved from yeast to humans that function as sequence-specific RNA-binding domains. Here we report the 2.0-A X-ray structure of the Vts1p SAM domain bound to a high-affinity RNA ligand. Specificity of RNA binding arises from the association of a guanosine loop base with a shallow pocket on the SAM domain and from multiple SAM domain contacts to the unique backbone structure of the loop, defined in part by a nonplanar base pair within the loop. We have validated NNF1 as an endogenous target of Vts1p among 79 transcripts that copurify with Vts1p. Bioinformatic analysis of these mRNAs demonstrates that the RNA-binding specificity of Vts1p in vivo is probably more stringent than that of the isolated SAM domain in vitro.

Towards deciphering the principles underlying an mRNA recognition code

“…The protein is a homolog of the Drosophila protein Smaug, a translational repressor that mediates body pattering during embryogenesis by binding to a mRNA hairpin termed Smaug recognition element (SRE) [41]. The SRE hairpin exhibits consensus sequences 5′-UNGA-N and 5′-GNGC-N which are targeted by α-helical sterile alpha motif (SAM) domain of Vts1p, a domain also implicated in protein-protein and DNAprotein interactions [42]. Three structures of the Vts1p-SAM domain bound to two SRE variants show parallels with SelB-SECIS recognition, such as shape recognition of the loop region and base-specific binding to an unpaired nucleotide, guanosine in this case [42][43][44].…”

“…The SRE hairpin exhibits consensus sequences 5′-UNGA-N and 5′-GNGC-N which are targeted by α-helical sterile alpha motif (SAM) domain of Vts1p, a domain also implicated in protein-protein and DNAprotein interactions [42]. Three structures of the Vts1p-SAM domain bound to two SRE variants show parallels with SelB-SECIS recognition, such as shape recognition of the loop region and base-specific binding to an unpaired nucleotide, guanosine in this case [42][43][44]. In contrast to the SelB-SECIS complex, the bulged out nucleotide does not play a significant role in recognition by Vts1p-SAM.…”

Mutation of mouse Samd4 causes leanness, myopathy, uncoupled mitochondrial respiration, and dysregulated mTORC1 signaling

“…Sterile alpha motifs (SAM) have been shown to directly bind mRNA with stem-loop structures known as Smaug recognition elements (SRE) having the consensus sequence CNGG or CNGGN (3)(4)(5). Several studies have investigated the function of Samd4 in cultured mammalian cells.…”

Structure determination and dynamics of protein–RNA complexes by NMR spectroscopy

“…Another example illustrating the accuracy of NMR structures is the structure of the protein Vts1 in its complex with RNA. Three structures of this complex were solved independently and at the same time, two by NMR [21,29] and one by X-ray crystallography at 2.0Å resolution [333] (Fig. 27A).…”

“…Spectra were recorded at 900 MHz. A: Structures of the different Vts1p-RNA complexes [21,29,333]. Vts1 is represented as a ribbon structure in grey, RNA is represented as a stick structure in yellow.…”