Selection for tandem stop codons in ciliate species with reassigned stop codons.

Ira Fleming,Andre R O Cavalcanti,Geoffrey M Kapler

doi:10.1371/journal.pone.0225804

Abstract

The failure of mRNA translation machinery to recognize a stop codon as a termination signal and subsequent translation of the 3’ untranslated region (UTR) is referred to as stop codon readthrough, the frequency of which is related to the length, composition, and structure of mRNA sequences downstream of end-of-gene stop codons. Secondary in-frame stop codons within a few positions downstream of the primary stop codons, so-called tandem stop codons (TSCs), serve as backup termination signals, which limit the effects of readthrough: polypeptide product degradation, mislocalization, and aggregation. In this study, ciliate species with UAA and UAG stop codons reassigned to code for glutamine are found to possess statistical excesses of TSCs at the beginning of their 3’ UTRs. The overrepresentation of TSCs in these species is greater than that observed in standard code organisms. Though the overall numbers of TSCs are lower in most species with alternative stop codons because they use fewer than three unique stop codons, the relatively great overrepresentation of TSCs in alternative-code ciliate species suggests that there exist stronger selective pressures to maintain TSCs in these organisms compared to standard code organisms.

Highlights

In the standard model of protein translation in eukaryotes, the stop codons UAA, UAG, and UGA are not recognized by tRNAs bearing amino acids and instead pair with eukaryotic release factors, which trigger the hydrolysis of the ester bond linking the nascent polypeptide to the ribosome-mRNA complex, terminating translation [1]
The most current annotated macronuclear genome sequence and general feature format genome annotation files for the ciliate species Oxytricha trifallax, Ichthyophthirius mutifilis, Tetrahymena borealis, Tetrahymena ellioti, Tetrahymena malaccensis, T. thermophila, Stylonychia lemnae, Selection for tandem stop codons in ciliate species with reassigned stop codons and Stentor coeruleus, were obtained from the ciliates.org database [27].The genome sequence and gff files for the ciliates P. tetraurelia and Pseudocohnilembus persalinus were downloaded from NCBI
Sets of 3’ untranslated region (UTR) were obtained for 86 different eukaryotic organisms (S1 Table), some with the UAR stop codon to Gln reassignment, one with a UGA to Cys reassignment, and the remainder with the standard set of stop codons

Summary

Introduction

In the standard model of protein translation in eukaryotes, the stop codons UAA, UAG, and UGA are not recognized by tRNAs bearing amino acids and instead pair with eukaryotic release factors (eRFs), which trigger the hydrolysis of the ester bond linking the nascent polypeptide to the ribosome-mRNA complex, terminating translation [1]. Part or all of the downstream 3’ UTR of the mRNA transcript is translated, resulting in the addition of extra amino acids onto the C-terminus of the polypeptide, a C-terminal extension [6]. Failure to terminate translation at the end of a gene may be the result of a mutated release factor or nonstop mutations that alter a stop codon

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Conclusion