Structures of translationally inactive mammalian ribosomes

Abstract

The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. Here, we use electron cryomicroscopy to analyze inactive ribosomes isolated from mammalian reticulocytes, the penultimate stage of red blood cell differentiation. We identify two types of ribosomes that are translationally repressed by protein interactions. The first comprises ribosomes sequestered with elongation factor 2 (eEF2) by SERPINE mRNA binding protein 1 (SERBP1) occupying the ribosomal mRNA entrance channel. The second type are translationally repressed by a novel ribosome-binding protein, interferon-related developmental regulator 2 (IFRD2), which spans the P and E sites and inserts a C-terminal helix into the mRNA exit channel to preclude translation. IFRD2 binds ribosomes with a tRNA occupying a noncanonical binding site, the ‘Z site’, on the ribosome. These structures provide functional insights into how ribosomal interactions may suppress translation to regulate gene expression.

The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs

“…By perfectly mimicking a canonical P site tRNA, the IAPV‐IRES in a post‐translocated state is able to position the VLR, a flexible element of its structure, in contacting distance with the E site of the 40S subunit. This is accomplished even with a fully closed P site gate (Fig E): Sliding through the P site gate, the single‐stranded VLR can contact the ribosomal protein uS7, normally involved in stabilizing E site tRNAs (Fig E; Brown et al , ). The VLR thus undergoes a marked remodeling as the IAPV‐IRES transitions from the pre‐translocation to the post‐translocation state.…”

Structure and function of yeast Lso2 and human CCDC124 bound to hibernating ribosomes

“…In addition to a type-II tRNA displaying an extended V-loop in the E site, it contains eEF2 and SERBP1 ( Figure 4). Like Stm1, SERBP1 together with eEF2 binds in the mRNA entry channel and prevents mRNA binding in the A and P sites (Anger et al, 2013;Balagopal and Parker, 2011;Ben-Shem et al, 2011;Brown et al, 2018;Van Dyke et al, 2013). Importantly, binding of SERBP1 and CCDC124 is mutually exclusive.…”

“…As a result, bacterial hibernation factors protect the crucial active sites of the ribosome and inhibit binding of both mRNA and tRNA, blocking translation altogether (Prossliner et al, 2018). Several types of inactive or hibernating ribosomes have also been observed in eukaryotes (Brown et al, 2018;Krokowski et al, 2011). In general, idle 80S ribosomes accumulate after exposure to various stresses like amino acid shortage (Krokowski et al, 2011;Tzamarias et al, in proximity to tRNA, and to rRNA helices H43 and H44 based on chemical crosslinking studies (Wang et al, 2018).…”

A memory of RPS25 loss drives resistance phenotypes

“…Given that the CrPV IGR IRES represents a mechanistically unique IRES type, which mimics an elongation rather than initiation state and utilizes no initiation factors , dependence on eS25 should perhaps not be extrapolated to other IRESs. Instead, if eS25 has a direct regulatory role on the translation mechanism, it might be expected to instead function in elongation rather than in the initiation stage, as hinted at by eS25's demonstrated interaction with Z-site tRNA, a likely E-site tRNA ejection intermediate (Brown et al, 2018). The finding that RPS25 loss does not obviously affect flavivirus translation further argues against assuming a direct role of eS25 on specialized translation events (Figures 4-5).…”