Fig. 12.

Collinear control results in more uniform particle densities than non-collinear control. a Collinear control. The upper, high translation rate (TR) mRNA has multiple small mRNA stem/loops, no uORFs, a short CDS, and optimal codon frequency. The bottom, low TR mRNA has multiple larger mRNA stem/loops, uORFs, a long CDS, and non-optimal codon frequency. As a result, both mRNAs have relatively even densities of translational complexes along their length. The CDS length-dependent rate of ribosome subunit recycling also matches their respective translation rates. b Non-collinear control. Both mRNAs have multiple small mRNA stem/loops and no uORFs resulting in a high density of preinitiation complexes on the 5′UTR. The top mRNA has a short CDS and optimal codon frequency, which results in a high density of ribosomes along the CDS and efficient ribosome subunit recycling. The bottom mRNA has a suboptimal ribosomal contacts at the iAUG, which reduces the efficiency with which preinitiation complexes convert to active ribosomes. As a result, the density of ribosomes along the CDS and in the recycling step is lower than that directed by the 5′UTR. The density of translational complexes along this mRNA is thus uneven. The rates of translation of mRNAs in a and b are the same. The total number of translation machinery complexes needed in a cell, however, is greater in the non-collinear scenario than in a cell employing collinear control