The alkB gene is one of a group of alkylation-inducible genes in Escherichia coli, and its product protects cells from S N 2-type alkylating agents such as methyl methanesulfonate (MMS). However, the precise biochemical function of the AlkB protein remains unknown. Here, we describe the cloning, sequencing, and characterization of three Saccharomyces cerevisiae genes (YFW1, YFW12, and YFW16) that functionally complement E. coli alkB mutant cells. DNA sequence analysis showed that none of the three gene products have any amino acid sequence homology with the AlkB protein. The YFW1 and YFW12 proteins are highly serine and threonine rich, and YFW1 contains a stretch of 28 hydrophobic residues, indicating that it may be a membrane protein. The YFW16 gene turned out to be allelic with the S. cerevisiae STE11 gene. STE11 is a protein kinase known to be involved in pheromone signal transduction in S. cerevisiae; however, the kinase activity is not required for MMS resistance because mutant STE11 proteins lacking kinase activity could still complement E. coli alkB mutants. Despite the fact that YFW1, YFW12, and YFW16/STE11 each confer substantial MMS resistance upon E. coli alkB cells, S. cerevisiae null mutants for each gene were not MMS sensitive. Whether these three genes provide alkylation resistance in E. coli via an alkB-like mechanism remains to be determined, but protection appears to be specific for AlkB-deficient E. coli because none of the genes protect other alkylation-sensitive E. coli strains from killing by MMS.Various environmental compounds and intermediary metabolites contribute to DNA damage which, if left unrepaired, can be lethal or mutagenic. When DNA is exposed to alkylating agents such as methyl methanesulfonate (MMS) and Nmethyl-NЈ-nitro-N-nitrosoguanidine, more than a dozen different DNA adducts can be formed (37). Some adducts are harmless, but others cause mutations and cell death (37). Escherichia coli constitutively expresses at least two proteins, the Ogt O 6 -methylguanine/O 4 -methylthymine DNA methyltransferase (28) and the Tag 3-methyladenine (3MeA)/3-methylguanine DNA glycosylase (4,30), that specifically repair alkylated DNA lesions. In addition, four genes are induced as part of the adaptive response upon exposure to sublethal levels of an alkylating agent. These are the ada, alkB, alkA, and aidB genes, and their products protect cells against killing and mutation induced by further alkylation damage (22,32,36,40). The ada gene encodes another DNA repair methyltransferase, which transfers the methyl group from either O The E. coli alkB gene lies downstream from, and forms an operon with, the ada gene. The alkB gene is therefore coordinately regulated with the ada gene as part of the adaptive response to alkylating agents (22). E. coli alkB null mutants become extremely sensitive to killing induced by MMS, an S N 2 alkylating agent, marking the alkB pathway as an extremely effective defense mechanism against alkylation toxicity. The fact that MMS-treated phage survives better in wild...