Abstract
A recent study has shown that archaeal L7Ae binds to a putative k-turn structure in the 5′-leader of the mRNA of its structural gene to regulate translation. To function as a regulator, the RNA should be unstructured in the absence of protein, but it should adopt a k-turn-containing stem–loop on binding L7Ae. Sequence analysis of UTR sequences indicates that their k-turn elements will be unable to fold in the absence of L7Ae, and we have demonstrated this experimentally in solution using FRET for the Archaeoglobus fulgidus sequence. We have solved the X-ray crystal structure of the complex of the A. fulgidus RNA bound to its cognate L7Ae protein. The RNA adopts a standard k-turn conformation that is specifically recognized by the L7Ae protein, so stabilizing the stem–loop. In-line probing of the natural-sequence UTR shows that the RNA is unstructured in the absence of L7Ae binding, but folds on binding the protein such that the ribosome binding site is occluded. Thus, L7Ae regulates its own translation by switching the conformation of the RNA to alter accessibility.
Highlights
In addition to spectroscopic and crystallographic studies, we have investigated the structural change in the k-turn-carrying stem–loop structure formed by the A. fulgidus l7ae 5′-untranslated region (UTR) stem–loop RNA using chemical probing
We have shown that A. fulgidus L7Ae binds to the 5′-UTR of the mRNA of its structural gene, stabilizing the standard k-turn conformation that should occlude the ribosome binding site
L7Ae has been shown to have multiple targets for regulation. In their RIP-Seq analysis of S. acidocaldarius, Daume et al (2017) found that L7Ae lowered translation of the structural gene for NOP5, another protein involved in the assembly of the box C/D snoRNP
Summary
This is a member of a family of structure-selective RNA binding proteins that includes yeast L30e and the human 15.5K protein (Koonin et al 1994; Watkins et al 2000) These proteins fulfill a number of roles; they are important components in the large ribosomal subunit (Ban et al 2000), box C/D (Kuhn et al 2002; Szewczak et al 2002; Watkins et al 2002), and H/ACA (Rozhdestvensky et al 2003; Hamma and Ferré-D’Amaré 2004; Li and Ye 2006) snoRNPs and U4 snRNA in the spliceosome cycle (Nottrott et al 1999; Vidovic et al 2000). L7Ae-family proteins are essential in many cellular processes includ-
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