Why is that nucleotide there? Causes and consequences of kinetic and metabolic translational efficiency

Abstract

A variety of sequence features at the levels of DNA, RNA, and protein affect the process of translation and may thus be under selection to increase the efficiency of that process. To ask whether they are and in what ways they might act, I first examine what the sequence-based mechanisms of elongation rate determination are. I show that positive charges in newly-translated peptides are the primary sequence-encoded elements modulating elongation rates, probably via their interaction with the negatively charged ribosomal exit tunnel. Contrary to common expectations, I do not find that codon usage has a significant effect on the velocity of ribosomes under normal in vivo conditions, while mRNA structure has only a marginal effect. That codons do not significantly slow ribosomes compared to the magnitude of the charge effect is seemingly at odds with a large body of literature which purports to show that they in fact do. Reviewing the literature, however, I suggest that these apparently at-odds findings can be reconciled by considering the supply (available tRNA) and demand (transcriptomic codon usage plus translation initiation rates). Taking supply and demand into account reveals that if codons do slow ribosomes, they are likely to do so significantly only under highly non-equilibrium, experimental conditions. That codons may not greatly differ in their translation speeds one to the next under normal in vivo conditions calls into question theories of selection on codon usage bias to modulate translational efficiency in a local, along-transcript fashion, for example the suggestion that codon usage is selected for at the 5’ end of transcripts as a kind of speed ramp to modulate ribosomal traffic just after translation initiation. That codons have similar translation speeds is still, however, consistent with a theory that codon usage is under general selection and even speed selection to increase the global translational efficiency of cells by limiting the number of bound ribosomes on mRNAs. Returning to the matter of positive charges, I ask whether they, instead of codons, might cause the suggested translational-ramping effect, as positive charges tend to be overloaded at the N-termini of proteins across various domains and taxa. I find however that their distribution at the starts of proteins is better explained by a biochemical, structural null rather than the gene regulatory hypothesis of the ramp: the use of positive charges at N-termini can be completely explained in terms of the needs of a subset of proteins to correctly orientate themselves in membranes. I end with an example of how selection for translational efficiency can act not just on the process of translation but on the finished protein product, showing that the need to manufacture metabolically cheap proteins contributes to the anomalous AT skews observed in the Firmicutes.

Date of Award	27 Jan 2014
Original language	English
Awarding Institution	University of Bath
Supervisor	Laurence Hurst (Supervisor)