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PMID: 29760453 Published · epublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Evolutionary instability of CUG-Leu in the genetic code of budding yeasts.

Nature communications ·Vol. 9 ·No. 1 ·2018-00-14 ·Pages 1887

Krassowski T, Coughlan AY, Shen XX, Zhou X, Kominek J, Opulente DA, Riley R, Grigoriev IV, Maheshwari N, Shields DC, Kurtzman CP, Hittinger CT, Rokas A, Wolfe KH

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).

MeSH Terms
Alanine/genetics,metabolism Codon Evolution, Molecular Genetic Code Genome, Fungal Leucine/genetics,metabolism Nucleic Acid Conformation Phylogeny Protein Biosynthesis RNA, Fungal/genetics,metabolism RNA, Transfer, Ala/genetics,metabolism RNA, Transfer, Leu/genetics,metabolism RNA, Transfer, Ser/genetics,metabolism Saccharomycetales/classification,genetics,metabolism Selection, Genetic Serine/genetics,metabolism
Chemicals
Codon RNA, Fungal RNA, Transfer, Ala RNA, Transfer, Leu RNA, Transfer, Ser Serine Leucine Alanine
Authors & Affiliations
14 authors, click to expand affiliations / ORCID
Krassowski Tadeusz
Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland.
Coughlan Aisling Y
Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland.
Shen Xing-Xing ORCID
Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA.
Zhou Xiaofan
Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA. | Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China.
Kominek Jacek ORCID
Laboratory of Genetics, Genome Center of Wisconsin, J.F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, 53706, USA. | DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Opulente Dana A
Laboratory of Genetics, Genome Center of Wisconsin, J.F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Riley Robert
United States Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA. | Amyris, 5885 Hollis Street, Suite 100, Emeryville, CA, 94608, USA.
Grigoriev Igor V ORCID
United States Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA.
Maheshwari Nikunj ORCID
Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland.
Shields Denis C
Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland.
Kurtzman Cletus P
U.S. Department of Agriculture, Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, Peoria, IL, 61604, USA.
Hittinger Chris Todd ORCID
Laboratory of Genetics, Genome Center of Wisconsin, J.F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, 53706, USA. | DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Rokas Antonis ORCID
Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA.
Wolfe Kenneth H ORCID
Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland. [email protected].
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Article Info
Journal
Nature communications
Abbr.
Nat Commun
ISSN
2041-1723
DOI
10.1038/s41467-018-04374-7
Email
[email protected]
Published
2018-00-14
Epub
2018-00-14
Pages
1887
Language
English
Region
England
NLM ID
101528555
PMCID
PMC5951914
Subset
IM
Grants
Wellcome Trust · United Kingdom
NIAID NIH HHS · R21 AI105619 · United States
External Links
PubMed source DOI: 10.1038/s41467-018-04374-7 PMC Full Text View journal details
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