A Chemical Genetics Analysis of the Roles of Bypass Polymerase DinB and DNA Repair Protein AlkB in Processing N[superscript 2]-Alkylguanine Lesions In Vivo

DinB, the E. coli translesion synthesis polymerase, has been shown to bypass several N-alkylguanine adducts in vitro, including N-furfurylguanine, the structural analog of the DNA adduct formed by the antibacterial agent nitrofurazone. Recently, it was demonstrated that the Fe(II)and a-ketoglutarate-dependent dioxygenase AlkB, a DNA repair enzyme, can dealkylate in vitro a series of N-alkyguanines, including N-furfurylguanine. The present study explored, head to head, the in vivo relative contributions of these two DNA maintenance pathways (replicative bypass vs. repair) as they processed a series of structurally varied, biologically relevant N-alkylguanine lesions: N-furfurylguanine (FF), 2-tetrahydrofuran-2-ylmethylguanine (HF), 2-methylguanine, and 2-ethylguanine. Each lesion was chemically synthesized and incorporated site-specifically into an M13 bacteriophage genome, which was then replicated in E. coli cells deficient or proficient for DinB and AlkB (4 strains in total). Biochemical tools were employed to analyze the relative replication efficiencies of the phage (a measure of the bypass efficiency of each lesion) and the base composition at the lesion site after replication (a measure of the mutagenesis profile of each lesion). The main findings were: 1) Among the lesions studied, the bulky FF and HF lesions proved to be strong replication blocks when introduced site-specifically on a single-stranded vector in DinB deficient cells. This toxic effect disappeared in the strains expressing physiological levels of DinB. 2) AlkB is known to repair N-alkylguanine lesions in vitro; however, the presence of AlkB showed no relief from the replication blocks induced by FF and HF in vivo. 3) The mutagenic properties of the entire series of N-alkyguanines adducts were investigated in vivo for the first time. None of the adducts were mutagenic under the conditions evaluated, regardless of the DinB or AlkB cellular status. Taken together, the data indicated that the cellular pathway to combat bulky N-alkylguanine DNA adducts was DinB-dependent lesion bypass. Citation: Shrivastav N, Fedeles BI, Li D, Delaney JC, Frick LE, et al. (2014) A Chemical Genetics Analysis of the Roles of Bypass Polymerase DinB and DNA Repair Protein AlkB in Processing N-Alkylguanine Lesions In Vivo. PLoS ONE 9(4): e94716. doi:10.1371/journal.pone.0094716 Editor: Martin G. Marinus, University of Massachusetts Medical School, United States of America Received February 22, 2014; Accepted March 18, 2014; Published April 14, 2014 Copyright: 2014 Shrivastav et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by National Institutes of Health Grants CA080024, CA26731, ES002109 (to J.M.E.), and CA021615 (to G.C.W.). G.C.W. is an American Cancer Society Professor. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: [email protected] ¤a Current address: McKinsey & Company, Philadelphia, Pennsylvania, United States of America ¤b Current address: Visterra Inc., Cambridge, Massachusetts, United States of America ¤c Current address: Agilent Technologies Inc., Wakefield, Massachusetts, United States of America ¤d Current address: Joule Unlimited, Bedford, Massachusetts, United States of America