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Mandal D, Köhrer C, Su D, Babu IR, Chan CT, Liu Y, Söll D, Blum P, Kuwahara M, Dedon PC, RajBhandary UL. Identification and codon reading properties of 5-cyanomethyl uridine, a new modified nucleoside found in the anticodon wobble position of mutant haloarchaeal isoleucine tRNAs. RNA 2014; 20:177-88. [PMID: 24344322 PMCID: PMC3895270 DOI: 10.1261/rna.042358.113] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Most archaea and bacteria use a modified C in the anticodon wobble position of isoleucine tRNA to base pair with A but not with G of the mRNA. This allows the tRNA to read the isoleucine codon AUA without also reading the methionine codon AUG. To understand why a modified C, and not U or modified U, is used to base pair with A, we mutated the C34 in the anticodon of Haloarcula marismortui isoleucine tRNA (tRNA2(Ile)) to U, expressed the mutant tRNA in Haloferax volcanii, and purified and analyzed the tRNA. Ribosome binding experiments show that although the wild-type tRNA2(Ile) binds exclusively to the isoleucine codon AUA, the mutant tRNA binds not only to AUA but also to AUU, another isoleucine codon, and to AUG, a methionine codon. The G34 to U mutant in the anticodon of another H. marismortui isoleucine tRNA species showed similar codon binding properties. Binding of the mutant tRNA to AUG could lead to misreading of the AUG codon and insertion of isoleucine in place of methionine. This result would explain why most archaea and bacteria do not normally use U or a modified U in the anticodon wobble position of isoleucine tRNA for reading the codon AUA. Biochemical and mass spectrometric analyses of the mutant tRNAs have led to the discovery of a new modified nucleoside, 5-cyanomethyl U in the anticodon wobble position of the mutant tRNAs. 5-Cyanomethyl U is present in total tRNAs from euryarchaea but not in crenarchaea, eubacteria, or eukaryotes.
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MESH Headings
- Anticodon/genetics
- Base Pairing
- Base Sequence
- Codon/genetics
- Escherichia coli/genetics
- Haloarcula marismortui/genetics
- Haloferax/genetics
- Molecular Structure
- Point Mutation
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Bacterial/genetics
- RNA, Fungal/genetics
- RNA, Transfer, Ile/chemistry
- RNA, Transfer, Ile/genetics
- RNA, Transfer, Ile/metabolism
- Ribosomes/chemistry
- Saccharomyces cerevisiae/genetics
- Sulfolobus/genetics
- Transfer RNA Aminoacylation
- Uridine/analogs & derivatives
- Uridine/chemistry
- Uridine/genetics
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Affiliation(s)
- Debabrata Mandal
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Caroline Köhrer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Dan Su
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - I. Ramesh Babu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Clement T.Y. Chan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Yuchen Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Paul Blum
- School of Biological Sciences, University of Nebraska–Lincoln, Lincoln, Nebraska 68508, USA
| | - Masayasu Kuwahara
- Graduate School of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - Peter C. Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Uttam L. RajBhandary
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Corresponding authorE-mail
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