We carried out DNA microarray-based global transcript profiling of Escherichia coli in response to 4,5-dihydroxy-2-cyclopenten-1-one to explore the manifestation of its antibacterial activity. We show that it has widespread effects in E. coli affecting genes encoding proteins involved in cell metabolism and membrane synthesis and functions. Genes belonging to the regulon involved in synthesis of Cys are upregulated. In addition, rpoS and RpoS-regulated genes responding to various stresses and a number of genes responding to oxidative stress are upregulated.A number of antibiotics are available against a variety of bacteria; however, in recent years, the emergence of multipledrug-resistant bacteria has been a primary concern. This has provided an incentive to search for newer and more effective antibacterial compounds. Previously we described one such compound, 4,5-dihydroxy-2-cyclopenten-1-one (DHCP), having antibacterial activity against a variety of gram-negative and -positive bacteria, such as Escherichia coli and Salmonella, Bacillus, and Staphylococcus spp., etc. DHCP is prepared by the heat treatment of uronic acid or its derivatives (12). It is also produced from roasted or parched vegetables, fruits, cereals, mushrooms, sea algae, cortex, or cartilage. It has been shown elsewhere to have potential applications as a therapeutic or preventive agent against cancer and also as an antibacterial agent in antiseptics, dentifrices, cosmetics, and bathing agents (12). We isolated a multicopy suppressor of DHCP toxicity from an E. coli genomic library. The gene encoding this suppressor was designated dep, and the putative protein encoded by this gene was designated Dep. The Dep protein showed high homology to known efflux proteins conferring resistance to a number of antibiotics including chloramphenicol, bicyclomycin, and tetracycline. However, it did not confer cross-resistance to any of the antibiotics tested (15). The exact mechanism of action of DHCP is not known.In the present study, we analyzed the global transcriptional pattern of E. coli in response to DHCP by DNA microarraybased technology to explore the manifestation of the antibacterial activity of DHCP. We show that DHCP has widespread effects in E. coli affecting genes encoding proteins involved in cell metabolism and membrane synthesis and functions.DNA microarray-based global transcription profiling of E. coli in response to DHCP treatment. Previously we showed that the growth of E. coli strain JM83 [F Ϫ ara⌬(lac-proAB) rpsL(Str r )] (22) was impaired in the presence of DHCP (250 M) after 3 h of incubation and that cells stopped growing after 5 h (15). Our main objective in the present study was to identify all of the E. coli open reading frames that exhibited a significant increase or decrease in mRNA abundance caused by the DHCP treatment. The cells were grown in the presence of 250 M DHCP as described previously (15). In brief, cells grown overnight in Luria-Bertani medium were diluted into fresh Luria-Bertani medium. After the growth reached 50...