Protein Synthesis in E. coli: Dependence of Codon-Specific Elongation on tRNA Concentration and Codon Usage

Abstract

To synthesize a protein, a ribosome moves along a messenger RNA (mRNA), reads it codon by codon, and takes up the corresponding ternary complexes which consist of aminoacylated transfer RNAs (aa-tRNAs), elongation factor Tu (EF-Tu), and GTP. During this process of translation elongation, the ribosome proceeds with a codon-specific rate. Here, we present a general theoretical framework to calculate codon-specific elongation rates and error frequencies based on tRNA concentrations and codon usages. Our theory takes three important aspects of in-vivo translation elongation into account. First, non-cognate, near-cognate and cognate ternary complexes compete for the binding sites on the ribosomes. Second, the corresponding binding rates are determined by the concentrations of free ternary complexes, which must be distinguished from the total tRNA concentrations as measured in vivo. Third, for each tRNA species, the difference between total tRNA and ternary complex concentration depends on the codon usages of the corresponding cognate and near-cognate codons. Furthermore, we apply our theory to two alternative pathways for tRNA release from the ribosomal E site and show how the mechanism of tRNA release influences the concentrations of free ternary complexes and thus the codon-specific elongation rates. Using a recently introduced method to determine kinetic rates of in-vivo translation from in-vitro data, we compute elongation rates for all codons in Escherichia coli. We show that for some tRNA species only a few tRNA molecules are part of ternary complexes and, thus, available for the translating ribosomes. In addition, we find that codon-specific elongation rates strongly depend on the overall codon usage in the cell, which could be altered experimentally by overexpression of individual genes.

Heterogeneity of Stop Codon Readthrough in Single Bacterial Cells and Implications for Population Fitness

“…Now, our experimentally measured growth rate in absence of Chl is ~1.9 h −1 . With this information and following a recent analysis of TC concentration for various tRNA species under different growth conditions (Rudorf and Lipowsky, 2015), we set [TC] 0 = 3.2 μM. We do not consider here any dependence of [RF2] on [Chl].…”

Síntese proteica em suínos: como fêmeas, machos não castrados e castrados respondem a este processo?

“…O mRNA transcrito no núcleo da célula a partir da fita de DNA, contendo o código para a síntese do polipeptídeo, se liga à subunidade menor do ribossomo e ao aminoacil-tRNA iniciador; a subunidade maior do ribossomo se liga então para formar o complexo de iniciação (Rudorf & Lipowsky, 2015 (Lehninger, 2006).…”

“…Sua atividade é regulada por hormônios e fatores de crescimento, além de ser dependente do status energético da célula e de AA que, na maioria das células, a leucina é o AA mediador (Kimball & Jefferson, 2006, Manjarín et al, 2016. Na fase de alongamento, o polipeptídeo formado é alongado pela adição de unidades sucessivas de AA ligadas covalentemente, oriundas da ligação entre o códon do mRNA e o anticódon do tRNA (Rudorf & Lipowsky, 2015). Este processo requer fatores de alongamento, regulados pela mTOR (Wang & Proud, 2006, You et al, 2015 e hidrólise de GTP.…”

“…A terminação e reciclagem do ribossomo é dada por um códon de parada no mRNA, fazendo com que o novo polipeptídeo seja liberado do ribossomo por ação de fatores de liberação, e o ribossomo é reciclado para uma nova síntese (Rudorf & Lipowsky, 2015). Em condições normais, este processo ocorre com três códons de parada diferentes, UGA, UAA ou UAG (Fernández et al, 2013).…”

Genome stability versus transcript diversity

“…In addition, a significant effort has been made to model the protein translation system, incorporating codon misreading at the ribosome, charged tRNA concentration, tRNA mischarging, etc. [75], [76], [77], [78] and [79]. Recent evidence also demonstrates how tRNA synthetase fidelity is critical for mammalian fitness.…”