Physical map location of a set of Escherichia coli genes (hde) whose expression is affected by the nucleoid protein H-NS.

was recently demonstrated that the expression of numerous E. coli proteins is greatly enhanced in an hns deletion background compared with their levels in wild-type cells (8). H-NS thus appears to function as a global DNA-binding transcriptional regulator (7). In a previous study, we purified a subset of proteins whose expression is affected by H-NS and cloned the genes coding for some of these proteins (9). During these studies, an E. coli DNA segment encoding two hns-dependent genes (encoding proteins named 10K-S and 1OK-L) was cloned from X4D9 phage (number 607 in the sets of 476 selected E. coli genomic clones constructed by Kohara et al. [4]). The nucleotide sequences for these contiguous genes have been determined (9). Here, we report the complete nucleotide sequence for the adjacent third gene, whose expression is also affected by H-NS. The positions of these hns-dependent genes have been unambiguously mapped on the E. coli physical map (Fig. 1), proposed by Kohara et al. (4). The restriction map of the E. coli genomic DNA carried on X4D9 is schematically presented in Fig. 1. The physical map of the sequenced region was confirmed by Southern hybridization with appropriate DNA probes. In this EcoRI-PvuII region (corresponding to 77.3 min of the E. coli genetic map [1, 5]), three complete open reading frames (orf-a for 1OK-S, orf-b for 1OK-L, and orf-d) were identified, in addition to two partial open reading frames (orf-c and orf-e). It should be emphasized that the expression of orf-a, orf-b, and orf-d is greatly derepressed in an hns deletion background (9). Thus, we tentatively propose the name hde (hns-dependent expression) for these genes (hdeA, hdeB, and hdeD, respectively [Fig. 1]). The hdeA and hdeB genes seem to constitute a operon (9), although this must be verified. Sequence similarity search against the sequence banks (GenBank, EMBL, and DDBJ) revealed no significant sequence homology with these sequences. However, it is worth mentioning that the homology search revealed that the N-terminal amino acid sequence predicted for orf-c is highly homologous to that of Mg2+ transport ATPase protein C (MgtC), reported previously for Salmonella typhimurium (6), i.e., 49 amino acids within the N-terminal 114-amino-acid sequence of ORF-C and MgtC are identical. Finally, it should be noted that very few genetic loci have been mapped in the region covered by X4D9 (1, 5). According to the compilation of E. coli DNA sequences of Kroger et al. (5), the DNA sequence specifying the gor gene, ECOGOR