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.The DNA molecules of living organisms continuously suffer from various types of damage resulting from exposure to endogenous and environmental genotoxic agents. Damage to DNA impairs the faithful propagation of genetic information during replication and transcription, exerting deleterious effects on cells (20). DNA-protein cross-links (DPCs) are unique among DNA lesions in that they are extremely bulky compared to conventional bulky lesions, such as pyrimidine photodimers and the base adducts of aromatic compounds. DPCs are produced by a number of chemical agents, such as aldehydes and heavy metal ions, and also by physical agents such as ionizing radiation and UV light (reviewed in reference 3). DPCs have also been identified in cells or nuclei treated with antitumor agents (4, 10, 44, 62). In addition, we have shown that oxanine, which is produced by nitrosative damage to guanine, mediates the formation of DPCs and polyamine cross-link adducts (49, 50, 52). Thus, understanding the repair and/or damage tolerance mechanism of this ubiquitous and unique class of DNA lesions will provide further insight into how cells maintain genetic integrity and ensure survival in the face of genomic insults. However, the repair and damage tolerance mechanisms of DPCs have long remained elusive, partly because many but not all DPC-inducing agents produce other types of DNA lesions simultaneously, making it rather...