Pausing on Polyribosomes: Make Way for Elongation in Translational Control

Abstract

Among the three phases of mRNA translation-initiation, elongation, and termination-initiation has traditionally been considered to be rate limiting and thus the focus of regulation. Emerging evidence, however, demonstrates that control of ribosome translocation (polypeptide elongation) can also be regulatory and indeed exerts a profound influence on development, neurologic disease, and cell stress. The correspondence of mRNA codon usage and the relative abundance of their cognate tRNAs is equally important for mediating the rate of polypeptide elongation. Here, we discuss recent results showing that ribosome pausing is a widely used mechanism for controlling translation and, as a result, biological transitions in health and disease.

Figure 1

Translational elongation at a glance. Shown are the four basic steps of translational elongation. The ribosome has three major tRNA pockets, the A, P, and E sites. The first step of polypeptide elongation is the recognition and accommodation of the cognate tRNA, as directed by a mRNA codon, within the ribosomal A-site (i). The cognate tRNA is brought into the ribosome as a complex with elongation factor 1 (EF-TU in bacteria) and GTP. Recognition of the cognate tRNA catalyzes the hydrolysis of GTP and the eviction of EF1 from the A-site (ii). At this point, the deacylated tRNA in the E-site is also thought to be evicted. The A-site tRNA and the P-site tRNA move into close proximity for the peptidyl transfer reaction where the growing polypeptide chain is added to the amino acid on the A-site tRNA (iii). Elongation factor 2 (EF-G in bacteria) then enters the A-site and completes ribosome translocation by moving the A-site tRNA to the P-site, and the P-site deacylated tRNA into the E-site (iv). The process then repeats itself over and over again.

Figure 2

Three examples of regulated polypeptide elongation. FMRP is proposed to bind both the ribosome and the engaged mRNA to impede ribosome translocation. FMRP is not produced when the Fmr1 gene is inactivated, which results in an elevated rate of polypeptide elongation and the Fragile X syndrome (top). In the brain, a mutated tissue-specific tRNA causes ribosome stalling at its corresponding codon. Neurodegeneration occurs if GTPBP2 is also mutated (middle). During proteotoxic stress, the chaperone HSC70, which normally binds the nascent peptide as it emerges from the ribosome, is titrated by misfolded proteins and causes ribosome stalling after reading about 50 codons (bottom).

Figure 3

(A) Illustration of codon optimality showing two hypothetical mRNAs. The green circles represent optimal codons while the red circles represent non-optimal codons. Designation of codons as optimal or non-optimal is a function of the concentration of tRNA in the cell. The green tRNA concentrations are high while the red tRNA concentrations are low; this difference impacts the speed of elongation. (B) Differentiated and proliferative cells have varied concentrations of tRNAs that are tailored to the decoding requirements of the expressed mRNAs. In this example, differentiated cells have an abundance of certain types of tRNAs (depicted in blue) because the mRNAs they express require similarly high levels of the corresponding codons. Conversely, proliferating cells contain different sets of tRNAs (in orange) to match the codons in mRNAs enriched in these cells (see Gingold et al, 2014).