Abstract
The synthesis of protein from messenger RNA during translation is a highly dynamic process that plays a key role in controlling the efficiency and fidelity of genome-wide protein expression. The availability of aminoacylated transfer RNA (tRNA) is a major factor influencing the speed of ribosomal movement, which depending on codon choices, varies considerably along a transcript. Furthermore, it has been shown experimentally that tRNA availability can vary significantly under different growth and stress conditions, offering the cell a way to adapt translational dynamics across the genome. Existing models of translation have neglected fluctuations of tRNA pools, instead assuming fixed tRNA availabilities over time. This has lead to an incomplete understanding of this process. Here, we show for the entire Escherichia coli genome how and to what extent translational speed profiles, which capture local aspects of translational elongation, respond to measured shifts in tRNA availability. We find that translational profiles across the genome are affected to differing degrees, with genes that are essential or related to fundamental processes such as translation, being more robust than those linked to regulation. Furthermore, we reveal how fluctuating tRNA availability influences profiles of specific sequences known to play a significant role in translational control of gene expression.
Highlights
Protein translation is one of the most important cellular processes during bacterial replication and growth, dynamics of this process are still barely understood
With the aim to understand the influence that such fluctuations can have on translational dynamics, we developed a generalized computational workflow (Figure 1) to estimate the translational speed at individual codons and generated translational speed profiles for every transcript in the Escherichia coli genome
Availability of transfer RNA (tRNA) was obtained from two experimental data sets: (i) tRNA concentrations measured at different growth rates [12]—in this data set, the concentrations for Gly1 and Gly2 as well as the concentrations for Ile1 and Ile2 are treated collectively, and to obtain the individual concentrations, the values were split according to the ratio of the gene copy numbers for the two isoacceptors (Gly1:Gly2 = 1:1, Ile1:Ile2 = 3:1) and (ii) tRNA charging values at different times after leucine starvation [11]—absolute concentrations were obtained by multiplying the charging values with the concentrations at a growth rate of 2.5 doublings per hour, taken from [12]
Summary
Protein translation is one of the most important cellular processes during bacterial replication and growth, dynamics of this process are still barely understood. There is growing realization that post-transcriptional modifications of tRNAs by uridine methyl-transferases at wobble position 34 play an important role in both the recognition and sensitivity of particular codon-anticodon pairings [13,14]. All of these factors can affect the speed at which a ribosome can join and move along a transcript. A better understanding of the contribution that these mechanisms have on protein expression is essential to provide a clearer picture of how these features have evolved and become used for regulation purposes by organisms and to enable the improved design of bioengineered systems where protein synthesis plays an important role, e.g. recombinant protein production
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