mRNA length-sensing in eukaryotic translation: reconsidering the "closed loop" and its implications for translational control

Abstract

Most eukaryotic mRNAs are recruited to the ribosome by recognition of a 5' m⁷GpppN cap. 30 years of genetic and biochemical evidence point to a role for interaction between the 5' cap-interacting factors and the 3' poly(A)-binding protein in bringing the ends of the mRNA into close proximity and promoting both translation and stability of the mRNA, in a form known as the "closed loop". However, the results of recent RNA-protein interaction studies suggest that not all mRNAs have equal access to the closed loop factors. Furthermore, association with closed loop factors appears to be highly biased towards mRNAs with short open reading frames, echoing the trend for higher translation of short mRNAs that has been observed in many eukaryotes. We recently reported that the ribosomal signaling scaffold protein RACK1 promotes the efficient translation of short mRNAs that strongly associate with the closed loop factors. Here, we discuss the implications of these observations with respect to translational control and suggest avenues through which the universality of the closed loop in eukaryotic translation could be revisited.

Keywords: Closed loop; RACK1; Ribosome; Translation.

Fig. 1

mRNAs that associate highly with the closed loop complex (Costello et al. 2015) have short open reading frames and are highly translated. Wild type translation efficiency data is taken from (Thompson et al. 2016). The Spearman correlation coefficient for each group is indicated (r=-0.50 for all mRNAs and r=-0.40 for strong closed loop mRNAs). The Mann-Whitney U test one-sided p-values for differences between strong closed loop mRNAs and other mRNAs is p<10^-134 for ORF length and p<10^-131 for wild type translation efficiency.

Fig. 2

Translational enhancement and regulation via the closed loop. a Closed loop mRNAs may be more highly translated than linear mRNAs due to higher de novo initiation rates and/or intrapolysomal ribosome recycling. The mutually reinforcing network of interactions between the cap, eIF4E, eIF4G, and PABP on closed loop mRNAs decreases the dissociation rate of the complex. b During activating conditions, eIF4E phosphorylation reduces the affinity of eIF4E for the cap, which could repress translation of linear mRNAs because eIF4E-cap binding is not stabilized by the eIF4G-PABP interaction. eIF4E binding to closed loop mRNAs is stabilized by protein-protein interactions. Closed loop mRNAs may benefit from reduced competition for limiting translation factors. c Under repressing conditions, 4E-BPs disrupt translation in a graded manner. Sub-saturating levels of 4E-BPs repress translation of linear mRNAs, but do not affect closed loop mRNAs because of the low dissociation rate of eIF4E from eIF4G-PABP in the closed loop complex. At saturating 4E-BP concentrations, 4E-BP concentration overcomes the high affinity of the closed loop complex for closed loop mRNAs leading to their translational repression.