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Nucleic Acids Research Advance Access originally published online on March 13, 2009
Nucleic Acids Research 2009 37(9):2894-2909; doi:10.1093/nar/gkp152
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Nucleic Acids Research, 2009, Vol. 37, No. 9 2894-2909
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA

Basma El Yacoubi1, Benjamin Lyons1, Yulien Cruz1, Robert Reddy2, Brian Nordin2, Fabio Agnelli2, James R. Williamson2, Paul Schimmel2, Manal A. Swairjo2 and Valérie de Crécy-Lagard1,*

1Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, P.O. Box 110700, Gainesville, FL 32611-0700 and 2Department of Chemistry and Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA

*To whom correspondence should be addressed. Tel: +1 352 392 9416; Fax: +1 352 392 5922; Email: vcrecy{at}ufl.edu

Received November 4, 2008. Revised February 3, 2009. Accepted February 24, 2009.

Threonylcarbamoyladenosine (t6A) is a universal modification found at position 37 of ANN decoding tRNAs, which imparts a unique structure to the anticodon loop enhancing its binding to ribosomes in vitro. Using a combination of bioinformatic, genetic, structural and biochemical approaches, the universal protein family YrdC/Sua5 (COG0009) was shown to be involved in the biosynthesis of this hypermodified base. Contradictory reports on the essentiality of both the yrdC wild-type gene of Escherichia coli and the SUA5 wild-type gene of Saccharomyces cerevisiae led us to reconstruct null alleles for both genes and prove that yrdC is essential in E. coli, whereas SUA5 is dispensable in yeast but results in severe growth phenotypes. Structural and biochemical analyses revealed that the E. coli YrdC protein binds ATP and preferentially binds RNAThr lacking only the t6A modification. This work lays the foundation for elucidating the function of a protein family found in every sequenced genome to date and understanding the role of t6A in vivo.

Present addresses: Brian Nordin, ActivX Biosciences, Inc. 11025 North Torrey Pines Road, La Jolla, CA 92037, USA.

Manal A. Swairjo, Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.


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