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ARS Home » Midwest Area » Peoria, Illinois » National Center for Agricultural Utilization Research » Mycotoxin Prevention and Applied Microbiology Research » Research » Publications at this Location » Publication #343732
Title: Evolutionary instability of CUG-Leu in the genetic code of budding yeasts

Author
item KRASSOWSKI, TADEUSZ - University College Dublin
item COUGHLAN, AISLING - University College Dublin
item SHEN, XING-XING - Vanderbilt University
item ZHOU, XIAOFAN - Vanderbilt University
item KOMINEK, JACEK - University Of Wisconsin
item OPULENTE, DANA - University Of Wisconsin
item RILEY, ROBERT - Department Of Energy Joint Genome
item GRIGORIEV, IGOR - Department Of Energy Joint Genome
item MAHESHWARI, NIKUNJ - University College Dublin
item SHIELDS, DENIS - University College Dublin
item Kurtzman, Cletus
item HITTINGER, CHRIS - University Of Wisconsin
item ROKAS, ANTONIS - Vanderbilt University
item WOLFE, KENNETH - University College Dublin

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/14/2018
Publication Date: 5/14/2018
Citation: Krassowski, T., Coughlan, A.Y., Shen, X.-X., Zhou, X., Kominek, J., Opulente, D.A., Riley, R., Grigoriev, I.V., Maheshwari, N., Shields, D.C., Kurtzman, C.P., Hittinger, C.T., Rokas, A., Wolfe, K.H. 2018. Evolutionary instability of CUG-Leu in the genetic code of budding yeasts. Nature Communications. Article 1887. https://doi.org/10.1038/s41467-018-04374-7.
DOI: https://doi.org/10.1038/s41467-018-04374-7

Interpretive Summary: We examined the genome sequences from selected groups of yeasts to determine if all used the universal genetic code for production of enzymes and other proteins. This project was initiated because we had found earlier that the biotechnologically important yeast Pachysolen tannophilus uses the CUG DNA sequence (codon) to code for the amino acid alanine rather than the expected leucine, which resulted in altered protein sequences. In the present study, 52 yeast genomes were examined for genetic changes that lead to altered protein structures. Species in two additional genera were discovered to have altered use of the CUG codon. At present, the only known modification of the universal genetic code of life is found in budding yeasts. Many of the yeasts exhibiting these changes are of agricultural and biotechnological importance and work to improve their properties using recombinant DNA modification must take into account the likelihood that expressed proteins may differ in the expected amino acid sequences.

Technical Abstract: The genetic code used in nuclear genes is almost universal, but here we report that it changed three times in parallel during the evolution of budding yeasts. All three changes were reassignments of the codon CUG, which is translated as serine (in 2 yeast clades), alanine (1 clade), or the ‘universal’ leucine (2 clades). The newly discovered Ser2 clade is in the final stages of a genetic code transition. Most species in this clade have genes for both a novel tRNASer(CAG) and an ancestral tRNALeu(CAG) to read CUG, but only tRNASer(CAG) is used in standard growth conditions. The coexistence of these alloacceptor tRNA genes indicates that the genetic code transition occurred via an ambiguous translation phase. We propose that the three parallel reassignments of CUG were not driven by natural selection in favor of their effects on the proteome, but by selection to eliminate the ancestral tRNALeu(CAG).