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.