The DEAH-box RNA helicase Dhr1 contains a remarkable carboxyl terminal domain essential for small ribosomal subunit biogenesis

Abstract

Ribosome biogenesis is an essential process in all living cells, which entails countless highly sequential and dynamic structural reorganization events. These include formation of dozens RNA helices through Watson-Crick base-pairing within ribosomal RNAs (rRNAs) and between rRNAs and small nucleolar RNAs (snoRNAs), transient association of hundreds of proteinaceous assembly factors to nascent precursor (pre-)ribosomes, and stable assembly of ribosomal proteins. Unsurprisingly, the largest group of ribosome assembly factors are energy-consuming proteins (NTPases) including 25 RNA helicases in budding yeast. Among these, the DEAH-box Dhr1 is essential to displace the box C/D snoRNA U3 from the pre-rRNAs where it is bound in order to prevent premature formation of the central pseudoknot, a dramatic irreversible long-range interaction essential to the overall folding of the small ribosomal subunit. Here, we report the crystal structure of the Dhr1 helicase module, revealing the presence of a remarkable carboxyl-terminal domain essential for Dhr1 function in ribosome biogenesis in vivo and important for its interaction with its coactivator Utp14 in vitro. Furthermore, we report the functional consequences on ribosome biogenesis of DHX37 (human Dhr1) mutations found in patients suffering from microcephaly and other neurological diseases.

Bud23 promotes the final disassembly of the small subunit Processome in Saccharomyces cerevisiae

“…Dhr1 also contains an N-terminal domain (NTD) that interacts with Bud23 [ 40 , 46 ] and a unique C-terminal domain (CTD) that enhances its interaction with its activator Utp14 [ 30 – 32 ]. Recent crystal structures of recombinant yeast Dhr1 [ 31 ] and its murine homolog DHX37 [ 32 ] lacking the NTD allow us to map most of the mutated residues to structure ( Fig 5B ). Consistent with our previous report [ 46 ], the overwhelming majority of the substitutions mapped to residues on the surface of the RecA1 and RecA2 domains ( Fig 5C ), and fully complemented the loss of DHR1 ( S7 Fig ).…”

“…Because U3 blocks CPK formation, the release of U3 is a critical, irreversible step in the maturation of the SSU [14,28]. The unwinding of U3 is catalyzed by the DEAH/RHA helicase Dhr1 [29] which is activated by the SSU Processome factor Utp14 [30][31][32]. Mutational analysis identified a short loop of Utp14 that is necessary and sufficient for the activation of Dhr1 in vitro [30,32], and deletion or mutation in this loop phenocopies a catalytic dhr1 mutant in vivo [30].…”

RNA Binding Motif Protein RBM45 Regulates Expression of the 11-Kilodalton Protein of Parvovirus B19 through Binding to Novel Intron Splicing Enhancers

“…We next asked whether knockdown of the expression of these ISE2interacting proteins affected expression of the VP2 and 11-kDa proteins. As hnRNP proteins function as negative regulators of mRNA splicing (48), we excluded all hnRNP proteins during the knockdown procedures, as well as SF3B1, which is an essential U2 snRNP component (49), and DHX37, which plays a role in ribosome biogenesis (50). We found the presence of lentivirally expressed short hairpin RNA (shRNA) specifically targeting RBM6, KHSRP, DDX21, LARP7, PURA, or RBM45 (Table S2; see also Fig.…”

Systematic Immunotherapy Target Discovery Using Genome-Scale In Vivo CRISPR Screens in CD8 T Cells

“…Tumor-Infiltrating Lymphocytes by Single-Cell RNA-Seq Dhx37 is a highly conserved DEAH box RNA helicase that has been reported to be involved with biogenesis of the small ribosomal subunit through its release of U3 small nucleolar RNA (snoRNA) (Roychowdhury et al, 2019). Its homologs have also been found to regulate escape behavior via glycine receptor expression in zebrafish (Hirata et al, 2013) and cause microcephaly in rare gene variants (Karaca et al, 2015).…”