DNA sequence of a gene in Escherichia coli encoding a putative tripartite transcription factor with receiver, ATPase and DNA binding domains.

Abstract

We have sequenced downstream of the last previously sequenced gene of the glucitol operon (gutABDMRQ) in E. coli and have found that gutQ is the last gene of this operon. Downstream of the gutQ gene is found a palindromic unit (PU or REP sequence), followed by a large open reading frame of 1515 (or possibly 1590) bps transcribed in the direction opposite to that of the gut operon. This open reading frame encodes a protein of 504 (or possibly 529) amino acids with a tripartite structure. The N-terminal "receiver" domain of 187 (or possibly 212) residues is homologous to the FhlA protein of E. coli, a transcriptional activator of formate hydrogen lyase. It may possess a short domain at its extreme N-terminus exhibiting sequence similarity to carbohydrate binding proteins. The central ATPase domain (236 residues) exhibits greatest sequence similarity to the HydG protein of E. coli, a transcriptional activator of labile hydrogenase. The C-terminal DNA binding domain (81 residues) is homologous to NtrX of Azorhizobium caulinodans, a protein involved in transcriptional regulation of nitrogen fixation. Sequence comparisons with well-characterized transcription factors suggest that ORF504 encodes a protein that hydrolyzes ATP to generate the open transcriptional initiation complex of sigma 54-dependent promoters, possibly in response to redox conditions and/or ligand binding. We propose that this tripartite transcription factor arose by fusion of gene fragments encoding its three constituent modules.