The H/ACA RNP assembly factor SHQ1 functions as an RNA mimic

Abstract

SHQ1 is an essential assembly factor for H/ACA ribonucleoproteins (RNPs) required for ribosome biogenesis, premRNA splicing, and telomere maintenance. SHQ1 binds dyskerin/NAP57, the catalytic subunit of human H/ACA RNPs, and this interaction is modulated by mutations causing X-linked dyskeratosis congenita. We report the crystal structure of the C-terminal domain of yeast SHQ1, Shq1p, and its complex with yeast dyskerin/NAP57, Cbf5p, lacking its catalytic domain. The C-terminal domain of Shq1p interacts with the RNA-binding domain of Cbf5p and, through structural mimicry, uses the RNA-protein-binding sites to achieve a specific protein-protein interface. We propose that Shq1p operates as a Cbf5p chaperone during RNP assembly by acting as an RNA placeholder, thereby preventing Cbf5p from nonspecific RNA binding before association with an H/ACA RNA and the other core RNP proteins.

Mechanism of the AAA+ ATPases pontin and reptin in the biogenesis of H/ACA RNPs

“…The CS domain of SHQ1 binds to NAP57 in trans to the SSD Binding of SHQ1 to NAP57 is an essential first step in H/ACA RNP biogenesis and occurs through NAPDcat (Grozdanov et al 2009a,b;Li et al 2011;Walbott et al 2011). The SSD of SHQ1 (Fig.…”

“…Since human SHQ1 functionally complemented that strain (Walbott et al 2011), the yeast counterparts were used for this purpose. Although full-length Shq1p (ySHQ1) provided on a plasmid restored growth to the shq1 null strain, neither the yCS domain nor the ySSD of Shq1p alone were sufficient (Fig.…”

“…1I, lane 4). Because NAP57 is an RNA binding protein and although RNA and SHQ1 binding are mutually exclusive (Li et al 2011;Walbott et al 2011), we ascertained that the protein-protein interactions were direct and not mediated by bacterial RNA that might have copurified. Indeed, RNase treatment of either protein had no effect on NAP57 binding of fulllength SHQ1 or of its CS domain and SSD in trans (Fig.…”

“…B and C; only the long C-terminal extremity is shown in C). The majority of the mostly missense mutations identified in patients with X-DC cluster in the NAPDcat domain (Meier 2006;Ye 2007;Li 2008;Hamma and Ferré-D'amaré 2010) and modulate the interaction with SHQ1 (Grozdanov et al 2009a;Walbott et al 2011).…”

“…1D; Godin et al 2009;Grozdanov et al 2009b;Singh et al 2009). Recently, we and others solved the crystal structures of the yeast orthologs of the SSD alone and in complex with the NAPDcat domain of NAP57, demonstrating that the SSD functions as an RNAmimic hugging the surface of NAP57 that is destined for H/ACA RNAs (Li et al 2011;Walbott et al 2011). Surprisingly, however, this surface in human NAP57 is distant from that harboring most X-DC mutations, leaving one wondering how they modulate the interaction of the two proteins.…”