Authors: Ashish Patil, Madhu Dyavaiah, Fraulin Joseph, John P. Rooney, Clement T.Y. Chan, Peter C. Dedon and Thomas J. Begley

Ashish Patil

College of Nanoscale Science and Engineering; University at Albany; State University of New York; Albany, NY USA; Department of Biomedical Sciences; University at Albany; State University of New York; Rensselaer, NY USA; Cancer Research Center; University at Albany; State University of New York; Rensselaer, NY USA

Madhu Dyavaiah

College of Nanoscale Science and Engineering; University at Albany; State University of New York; Albany, NY USA; Cancer Research Center; University at Albany; State University of New York; Rensselaer, NY USA

Fraulin Joseph

College of Nanoscale Science and Engineering; University at Albany; State University of New York; Albany, NY USA; Cancer Research Center; University at Albany; State University of New York; Rensselaer, NY USA

John P. Rooney

Department of Biomedical Sciences; University at Albany; State University of New York; Rensselaer, NY USA; Cancer Research Center; University at Albany; State University of New York; Rensselaer, NY USA
Current affiliation: Nicholas School of the Environment; Duke University; Durham, NC USA

Clement T.Y. Chan

Department of Chemistry; Massachusetts Institute of Technology; Cambridge, MA USA

Peter C. Dedon

Department of Biological Engineering; Massachusetts Institute of Technology; Cambridge, MA USA; Center for Environmental Health Sciences; Massachusetts Institute of Technology; Cambridge, MA USA

Thomas J. Begley

Corresponding author: tbegley@albany.edu
College of Nanoscale Science and Engineering; University at Albany; State University of New York; Albany, NY USA; Cancer Research Center; University at Albany; State University of New York; Rensselaer, NY USA

Abstract:
S-phase and DNA damage promote increased ribonucleotide reductase (RNR) activity. Translation of RNR1 has been linked to the wobble uridine modifying enzyme tRNA methyltransferase 9 (Trm9). We predicted that changes in tRNA modification would translationally regulate RNR1 after DNA damage to promote cell cycle progression. In support, we demonstrate that the Trm9-dependent tRNA modification 5-methoxycarbonylmethyluridine (mcm⁵U) is increased in hydroxyurea (HU)-induced S-phase cells, relative to G₁ and G₂, and that mcm⁵U is one of 16 tRNA modifications whose levels oscillate during the cell cycle. Codon-reporter data matches the mcm⁵U increase to Trm9 and the efficient translation of AGA codons and RNR1. Further, we show that in trm9Δ cells reduced Rnr1 protein levels cause delayed transition into S-phase after damage. Codon re-engineering of RNR1 increased the number of trm9Δ cells that have transitioned into S-phase 1 h after DNA damage and that have increased Rnr1 protein levels, similar to that of wild-type cells expressing native RNR1. Our data supports a model in which codon usage and tRNA modification are regulatory components of the DNA damage response, with both playing vital roles in cell cycle progression.

Received: August 17, 2012; Accepted: August 21, 2012; Published Online: August 30, 2012

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