Transfer RNAs with novel cloverleaf structures
Abstract
We report the identification of novel tRNA species with 12-base pair amino-acid acceptor branches composed of longer acceptor stem and shorter Tstem. While canonical tRNAs have a 7/5 configuration of the branch, the novel tRNAs have either 8/4 or 9/3 structure. They were found during the search for selenocysteine tRNAs in terabytes of genome, metagenome and metatranscriptome sequences. Certain bacteria and their phages employ the 8/4 structure for serine and histidine tRNAs, while minor cysteine and selenocysteine tRNA species may have a modified 8/4 structure with one bulge nucleotide. In Acidobacteria, tRNAs with 8/4 and 9/3 structures may function as missense and nonsense suppressor tRNAs and/or regulatory noncod ing RNAs. In δ-proteobacteria, an additional cysteine tRNA with an 8/4 structure mimics selenocysteine tRNA and may function as opal suppressor. We examined the potential translation function of suppressor tRNA species inEscherichia coli; tRNAs with 8/4 or 9/3 structures efficiently inserted serine, alanine and cysteine in response to stop and sense codons, depending on the identity element and anticodon sequence of the tRNA. These findings expand our view of how tRNA, and possibly the genetic code, is diversified in nature.
- Authors:
-
- Yale Univ., New Haven, CT (United States). Dept. of Molecular Biophysics and Biochemistry
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Yale Univ., New Haven, CT (United States). Dept. of Molecular Biophysics and Biochemistry, Dept. of Chemistry
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1379781
- Grant/Contract Number:
- AC02-05CH11231; FG02-98ER20311
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nucleic Acids Research
- Additional Journal Information:
- Journal Volume: 45; Journal Issue: 5; Journal ID: ISSN 0305-1048
- Publisher:
- Oxford University Press
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; amino acids; allopurinol; anticodon; codon nucleotides; cysteine; genome; proteobacteria; transfer ma; selenocysteine; serine; bacteria; transfer technique
Citation Formats
Mukai, Takahito, Vargas-Rodriguez, Oscar, Englert, Markus, Tripp, H. James, Ivanova, Natalia N., Rubin, Edward M., Kyrpides, Nikos C., and Söll, Dieter. Transfer RNAs with novel cloverleaf structures. United States: N. p., 2016.
Web. doi:10.1093/nar/gkw898.
Mukai, Takahito, Vargas-Rodriguez, Oscar, Englert, Markus, Tripp, H. James, Ivanova, Natalia N., Rubin, Edward M., Kyrpides, Nikos C., & Söll, Dieter. Transfer RNAs with novel cloverleaf structures. United States. https://doi.org/10.1093/nar/gkw898
Mukai, Takahito, Vargas-Rodriguez, Oscar, Englert, Markus, Tripp, H. James, Ivanova, Natalia N., Rubin, Edward M., Kyrpides, Nikos C., and Söll, Dieter. Wed .
"Transfer RNAs with novel cloverleaf structures". United States. https://doi.org/10.1093/nar/gkw898. https://www.osti.gov/servlets/purl/1379781.
@article{osti_1379781,
title = {Transfer RNAs with novel cloverleaf structures},
author = {Mukai, Takahito and Vargas-Rodriguez, Oscar and Englert, Markus and Tripp, H. James and Ivanova, Natalia N. and Rubin, Edward M. and Kyrpides, Nikos C. and Söll, Dieter},
abstractNote = {We report the identification of novel tRNA species with 12-base pair amino-acid acceptor branches composed of longer acceptor stem and shorter Tstem. While canonical tRNAs have a 7/5 configuration of the branch, the novel tRNAs have either 8/4 or 9/3 structure. They were found during the search for selenocysteine tRNAs in terabytes of genome, metagenome and metatranscriptome sequences. Certain bacteria and their phages employ the 8/4 structure for serine and histidine tRNAs, while minor cysteine and selenocysteine tRNA species may have a modified 8/4 structure with one bulge nucleotide. In Acidobacteria, tRNAs with 8/4 and 9/3 structures may function as missense and nonsense suppressor tRNAs and/or regulatory noncod ing RNAs. In δ-proteobacteria, an additional cysteine tRNA with an 8/4 structure mimics selenocysteine tRNA and may function as opal suppressor. We examined the potential translation function of suppressor tRNA species inEscherichia coli; tRNAs with 8/4 or 9/3 structures efficiently inserted serine, alanine and cysteine in response to stop and sense codons, depending on the identity element and anticodon sequence of the tRNA. These findings expand our view of how tRNA, and possibly the genetic code, is diversified in nature.},
doi = {10.1093/nar/gkw898},
journal = {Nucleic Acids Research},
number = 5,
volume = 45,
place = {United States},
year = {Wed Oct 05 00:00:00 EDT 2016},
month = {Wed Oct 05 00:00:00 EDT 2016}
}
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