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PMID: 24049072 Published · ppublish 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.

Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria.

Nucleic acids research ·Vol. 42 ·No. 1 ·2014-01-00 ·Pages 499-508

Ling J, Daoud R, Lajoie MJ, Church GM, Söll D, Lang BF

Abstract

The discovery of diverse codon reassignment events has demonstrated that the canonical genetic code is not universal. Studying coding reassignment at the molecular level is critical for understanding genetic code evolution, and provides clues to genetic code manipulation in synthetic biology. Here we report a novel reassignment event in the mitochondria of Ashbya (Eremothecium) gossypii, a filamentous-growing plant pathogen related to yeast (Saccharomycetaceae). Bioinformatics studies of conserved positions in mitochondrial DNA-encoded proteins suggest that CUU and CUA codons correspond to alanine in A. gossypii, instead of leucine in the standard code or threonine in yeast mitochondria. Reassignment of CUA to Ala was confirmed at the protein level by mass spectrometry. We further demonstrate that a predicted tRNA(Ala)UAG is transcribed and accurately processed in vivo, and is responsible for Ala reassignment. Enzymatic studies reveal that tRNA(Ala)UAG is efficiently recognized by A. gossypii mitochondrial alanyl-tRNA synthetase (AgAlaRS). AlaRS typically recognizes the G3:U70 base pair of tRNA(Ala); a G3A change in Ashbya tRNA(Ala)UAG abolishes its recognition by AgAlaRS. Conversely, an A3G mutation in Saccharomyces cerevisiae tRNA(Thr)UAG confers tRNA recognition by AgAlaRS. Our work highlights the dynamic feature of natural genetic codes in mitochondria, and the relative simplicity by which tRNA identity may be switched.

MeSH Terms
Alanine/metabolism Alanine-tRNA Ligase/metabolism Amino Acid Sequence Base Sequence Codon Eremothecium/enzymology,genetics Leucine/metabolism Mitochondria/enzymology,genetics Mitochondrial Proteins/chemistry,genetics Molecular Sequence Data RNA, Transfer/chemistry,metabolism RNA, Transfer, Ala/chemistry,metabolism
Chemicals
Codon Mitochondrial Proteins RNA, Transfer, Ala RNA, Transfer Alanine-tRNA Ligase Leucine Alanine
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Ling Jiqiang
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA, Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, 2900 Boulevard Edouard Montpetit, Montréal, Québec, H3C 3J7, Canada, Program in Chemical Biology, Harvard University, Cambridge, MA 02138, USA, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA and Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA.
Daoud Rachid
Lajoie Marc J
Church George M
Söll Dieter
Lang B Franz
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkt842
Published
2014-01-00
Epub
2013-00-17
Pages
499-508
Language
English
Region
England
NLM ID
0411011
PMCID
PMC3874161
Subset
IM
Grants
NIGMS NIH HHS · R01 GM022854 · United States
NIGMS NIH HHS · GM022854 · United States
External Links
PubMed source DOI: 10.1093/nar/gkt842 PMC Full Text View journal details
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