Effect of Correlated tRNA Abundances on Translation Errors and Evolution of Codon Usage Bias

Despite the fact that tRNA abundances are thought to play a major role in determining translation error rates, their distribution across the genetic code and the resulting implications have received little attention. In general, studies of codon usage bias (CUB) assume that codons with higher tRNA abundance have lower missense error rates. Using a model of protein translation based on tRNA competition and intra-ribosomal kinetics, we show that this assumption can be violated when tRNA abundances are positively correlated across the genetic code. Examining the distribution of tRNA abundances across 73 bacterial genomes from 20 different genera, we find a consistent positive correlation between tRNA abundances across the genetic code. This work challenges one of the fundamental assumptions made in over 30 years of research on CUB that codons with higher tRNA abundances have lower missense error rates and that missense errors are the primary selective force responsible for CUB

Thermal sensitivity of cellular energy budgets in Antarctic fish hepatocytes

Oxygen demand elicited by the main cellular energy consumers was examined in isolated hepatocytes of sub-Antarctic and high-Antarctic notothenioid and zoarcid (Pachycara brachycephalum) fish with respect to the role of cellular metabolism in co-defining thermal tolerance. The relative proportions of energy allocated to protein and RNA/DNA synthesis, ion regulation and ATP synthesis were quantified between 0 and 15°C by analysis of inhibitor sensitive cellular respiration. In all investigated species, protein synthesis constituted 25-37%, RNA synthesis 24-35%, Na+/K+-ATPase 40-45% and mitochondrial ATP synthesis 57-65% of total respiration. The sub-Antarctic nototheniid Lepidonotothen larseni displayed lower cellular protein synthesis rates but somewhat higher active ion regulation activities than its high-Antarctic confamilials, as is typical for more eurythermal species. Assumed thermal optima were mirrored in minimized overall cellular energy demand. Onset of thermal stress indicated by elevated energy turnover became visible between 3 and 0°C as well as beyond 6°C in the sub-Antarctic L. larseni and P. brachycephalum; whereas the high-Antarctic species displayed progressively rising respiration rates during warming with a cellular energetic minimum at 0°C.Sub-Antarctic fish showed signs of cold-eurythermy and appear to live close to their lower limit of thermal tolerance, while high-Antarctic notothenioids show high degrees of energetic efficiency at 0°C. All cellular preparations maintained energy budgets over a wide thermal range, supporting the recent concept that thermal limits are set by oxygen and associated energy limitations at the whole organism level