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Journal of Bacteriology, September 2009, p. 5657-5668, Vol. 191, No. 18
0021-9193/09/$08.00+0 doi:10.1128/JB.00417-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
Genetic Analysis of Repair and Damage Tolerance Mechanisms for DNA-Protein Cross-Links in Escherichia coli
,
Amir M. H. Salem,1
Toshiaki Nakano,1
Minako Takuwa,1
Nagisa Matoba,1
Tomohiro Tsuboi,1
Hiroaki Terato,1,
Kazuo Yamamoto,2
Masami Yamada,3
Takehiko Nohmi,3 and
Hiroshi Ide1*
Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan,1 Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Japan,2 Division of Genetics and Mutagenesis, National Institute of Health Sciences, Tokyo 158-8501, Japan3
Received 27 March 2009/ Accepted 9 July 2009
DNA-protein cross-links (DPCs) are unique among DNA lesions in their unusually bulky nature. We have recently shown that nucleotide excision repair (NER) and RecBCD-dependent homologous recombination (HR) collaboratively alleviate the lethal effect of DPCs in Escherichia coli. In this study, to gain further insight into the damage-processing mechanism for DPCs, we assessed the sensitivities of a panel of repair-deficient E. coli mutants to DPC-inducing agents, including formaldehyde (FA) and 5-azacytidine (azaC). We show here that the damage tolerance mechanism involving HR and subsequent replication restart (RR) provides the most effective means of cell survival against DPCs. Translesion synthesis does not serve as an alternative damage tolerance mechanism for DPCs in cell survival. Elimination of DPCs from the genome relies primarily on NER, which provides a second and moderately effective means of cell survival against DPCs. Interestingly, Cho rather than UvrC seems to be an effective nuclease for the NER of DPCs. Together with the genes responsible for HR, RR, and NER, the mutation of genes involved in several aspects of DNA repair and transactions, such as recQ, xth nfo, dksA, and topA, rendered cells slightly but significantly sensitive to FA but not azaC, possibly reflecting the complexity of DPCs or cryptic lesions induced by FA. UvrD may have an additional role outside NER, since the uvrD mutation conferred a slight azaC sensitivity on cells. Finally, DNA glycosylases mitigate azaC toxicity, independently of the repair of DPCs, presumably by removing 5-azacytosine or its degradation product from the chromosome.
* Corresponding author. Mailing address: Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan. Phone and fax: 81-82-424-7457. E-mail: ideh{at}hiroshima-u.ac.jp
Published ahead of print on 17 July 2009.
Supplemental material for this article may be found at http://jb.asm.org/.
Present address: Analytical Research Center for Experimental Sciences, Saga University, Nabeshima, Saga 849-8501, Japan.
Journal of Bacteriology, September 2009, p. 5657-5668, Vol. 191, No. 18
0021-9193/09/$08.00+0 doi:10.1128/JB.00417-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
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