Comparison of characteristics and function of translation termination signals between and within prokaryotic and eukaryotic organisms

Six diverse prokaryotic and five eukaryotic genomes were compared to deduce whether the protein synthesis termination signal has common determinants within and across both kingdoms. Four of the six prokaryotic and all of the eukaryotic genomes investigated demonstrated a similar pattern of nucleotide bias both 5′ and 3′ of the stop codon. A preferred core signal of 4 nt was evident, encompassing the stop codon and the following nucleotide. Codons decoded by hyper-modified tRNAs were over-represented in the region 5′ to the stop codon in genes from both kingdoms. The origin of the 3′ bias was more variable particularly among the prokaryotic organisms. In both kingdoms, genes with the highest expression index exhibited a strong bias but genes with the lowest expression showed none. Absence of bias in parasitic prokaryotes may reflect an absence of pressure to evolve more efficient translation. Experiments were undertaken to determine if a correlation existed between bias in signal abundance and termination efficiency. In Escherichia coli signal abundance correlated with termination efficiency for UAA and UGA stop codons, but not in mammalian cells. Termination signals that were highly inefficient could be made more efficient by increasing the concentration of the cognate decoding release factor

Termination efficiency of the UAA, UGA and UAG ‘abundant’ and ‘rare’ termination signals in

<p><b>Copyright information:</b></p><p>Taken from "Comparison of characteristics and function of translation termination signals between and within prokaryotic and eukaryotic organisms"</p><p>Nucleic Acids Research 2006;34(7):1959-1973.</p><p>Published online 13 Apr 2006</p><p>PMCID:PMC1435984.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> Termination efficiency was derived from the 3A′ protein synthesis termination assay (). Readthrough (%) was calculated by comparison of readthrough protein (3A′) to total protein (3A′ + 2A′). Constructs were assayed in specific strains of XAc wild-type strain (dark grey), XA105 UAA suppressor strain (light grey), CDJ64 UGA suppressor strain (light grey) and XA101 UAG suppressor strain (light grey). The mean values from six experiments are presented. Error bars are ±SEM

Termination efficiency of the eukaryotic UAA, UGA and UAG ‘abundant’ and ‘rare’ termination signals and

<p><b>Copyright information:</b></p><p>Taken from "Comparison of characteristics and function of translation termination signals between and within prokaryotic and eukaryotic organisms"</p><p>Nucleic Acids Research 2006;34(7):1959-1973.</p><p>Published online 13 Apr 2006</p><p>PMCID:PMC1435984.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> Termination efficiency was derived from a dual luciferase protein synthesis termination assay (–) and using COS-7 cells (–). Readthrough (%) was calculated by comparison to a control construct (UGG). The mean values from three experiments are presented. Error bars are ±SEM