Alu RNA regulates the cellular pool of active ribosomes by targeted delivery of SRP9/14 to 40S subunits

Ivanova, Elena; Berger, Audrey; Scherrer, Anne; Alkalaeva, Elena; Strub, Katharina

The essential feature in the protein for 40S-binding and for initiation inhibition is the C-terminal pentapeptide of SRP14 ( Figure 2E and F). Short basic oligopeptides are frequently present in ribosomal and ribosome-binding proteins and have been shown to bind ribosomal RNA (38, 39) (Supplementary Figure S9) . The three residues K60, K61 and K64 in SRP9 are essential for the elongation arrest function of SRP (21) and are also required for 40S subunit inactivation ( Figure 2E and F). However, they are not required for 40S binding. Interestingly, in SRP-ribosomenascent chain complex these residues are located in close proximity to 40S (40) . Further studies will be required to determine the binding sites of SRP9/14 on the 40S subunit and whether the protein uses the same binding site in either function. Our data showed that SRP9/14 can be delivered to the 43S complex ( Figures 1I and 5D ) but not to the 80S ribosome ( Figure 5C ). This suggests that protein-binding site is not occupied by the ternary complex, eIF3, eIF1 and 1A but is blocked by the presence of the 60S subunit. The protein SRP9/14 alone had no inhibitory activity, which is consistent with earlier observations that high levels of SRP9/14 are well tolerated in primate cells (11, 41) Only few regulatory factors acting directly on the 40S subunit have so far been described: the acute respiratory syndrome coronavirus nsp1 protein and the proapoptotic protein Reaper (42, 43) . As for SRP9/14, the binding sites of these proteins in the 40S subunit remain to be revealed.