A pair of non-optimal codons are necessary for the correct biosynthesis of the Aspergillus nidulans urea transporter, UreA

Abstract

In both prokaryotic and eukaryotic genomes, synonymous codons are unevenly used. Such differential usage of optimal or non-optimal codons has been suggested to play a role in the control of translation initiation and elongation, as well as at the level of transcription and mRNA stability. In the case of membrane proteins, codon usage has been proposed to assist in the establishment of a pause necessary for the correct targeting of the nascent chains to the translocon. By using as a model UreA, the Aspergillus nidulans urea transporter, we revealed that a pair of non-optimal codons encoding amino acids situated at the boundary between the N-terminus and the first transmembrane segment are necessary for proper biogenesis of the protein at 37°C. These codons presumably regulate the translation rate in a previously undescribed fashion, possibly contributing to the correct interaction of ureA-translating ribosome-nascent chain complexes with the signal recognition particle and/or other factors, while the polypeptide has not yet emerged from the ribosomal tunnel. Our results suggest that the presence of the pair of non-optimal codons would not be functionally important in all cellular conditions. Whether this mechanism would affect other proteins remains to be determined.

A code within the genetic code: codon usage regulates co-translational protein folding

“…In Aspergillus nidulans, a pair of rare codons in the gene encoding the urea transporter are important for the production and localization of the UreA protein [102].…”

“…In human cells, co-translational arginylation of γ-actin, which regulates stability of the protein by influencing ubiquitination, is influenced by rare codons that slow elongation rate in the 5′ end of the gene [ 101 ]. In Aspergillus nidulans , a pair of rare codons in the gene encoding the urea transporter are important for the production and localization of the UreA protein [ 102 ].…”

Synonymous but Not Silent: The Codon Usage Code for Gene Expression and Protein Folding

“…Moreover, rare codons downstream of the region encoding the signal recognition particle (SRP) binding site in some yeast genes encoding membrane proteins are proposed to promote protein translocation by regulating the interaction between nascent polypeptides and the SRP (154). A pair of rare codons in the gene encoding the urea transporter is important for the production and localization of the UreA protein in Aspergillus nidulans (155). Together, these studies suggest that codon usage has diverse physiological roles in regulating cotranslational folding-related processes.…”

Substrate Recognition Properties from an Intermediate Structural State of the UreA Transporter

“…Paradigmatic structure-function studies have allowed for unveiling relevant aspects of the biology of different membrane transporters [15]. In this way, we have focused on the study of UreA (UniProt Q5BGB2), the only high-affinity urea transport system in A. nidulans [4,16,17] as a representative of the fungi and plant urea/H + symporters. UreA was isolated and named by Pateman et al [18] more than 40 years ago to refer to mutants isolated as resistant to 2-thiourea and shown by transport assays and growth tests to be specifically impaired in urea transport.…”