d-Galactonate, an aldonic sugar acid, is used as a carbon source by Escherichia coli, and the structural dgo genes involved in its metabolism have previously been investigated. Here, using genetic, biochemical and bioinformatics approaches, we present the first detailed molecular and functional insights into the regulation of d-galactonate metabolism in E. coli K-12 by the transcriptional regulator DgoR. We found that dgoR deletion accelerates the growth of E. coli in d-galactonate concomitant with the strong constitutive expression of dgo genes. In the dgo locus, sequence upstream of dgoR alone harbors the d-galactonate-inducible promoter that likely drives the expression of all dgo genes. DgoR exerts repression on the dgo operon by binding two inverted repeats overlapping the dgo promoter. Binding of d-galactonate induces a conformational change in DgoR to derepress the dgo operon. The findings from our work firmly place DgoR in the GntR family of transcriptional regulators: DgoR binds an operator sequence [5′-TTGTA(G/C)TACA(A/T)-3′] matching the signature of GntR family members that recognize inverted repeats [5′-(N)yGT(N)xAC(N)y-3′, where x and y indicate the number of nucleotides, which varies], and it shares critical protein-DNA contacts. We also identified features in DgoR that are otherwise less conserved in the GntR family. Recently, missense mutations in dgoR were recovered in a natural E. coli isolate adapted to the mammalian gut. Our results show these mutants to be DNA binding defective, emphasizing that mutations in the dgo-regulatory elements are selected in the host to allow simultaneous induction of dgo genes. The present study sets the basis to explore the regulation of dgo genes in additional enterobacterial strains where they have been implicated in host-bacterium interactions. IMPORTANCE d-Galactonate is a widely prevalent aldonic sugar acid. Despite the proposed significance of the d-galactonate metabolic pathway in the interaction of enteric bacteria with their hosts, there are no details on its regulation even in Escherichia coli, which has been known to utilize d-galactonate since the 1970s. Here, using multiple methodologies, we identified the promoter, operator, and effector of DgoR, the transcriptional repressor of d-galactonate metabolism in E. coli. We establish DgoR as a GntR family transcriptional regulator. Recently, a human urinary tract isolate of E. coli introduced in the mouse gut was found to accumulate missense mutations in dgoR. Our results show these mutants to be DNA binding defective, hence emphasizing the role of the d-galactonate metabolic pathway in bacterial colonization of the mammalian gut.

The GntR family of transcriptional regulators (TRs), named after the Bacillus subtilis gluconate operon repressor (Haydon and Guest, 1991), represents one of the largest family of TRs with members present in all three domains of life (El-Gebali et al., 2019;Hoskisson and Rigali, 2009). The members of this family are characterized by the presence of an N-terminal winged helix-turn-helix (wHTH) DNA-binding domain (Pfam, PF00392) and a C-terminal effector-binding and oligomerization (E-O) domain (El-Gebali et al., 2019;Rigali et al., 2002). Generally, a specific effector, a small organic molecule, binds the E-O domain and elicits an allosteric change in the TR, which alters its affinity for the cognate operator, resulting in transcriptional activation or repression of the regulon members (Resch et al., 2010; van Aalten et al., 2001).On the basis of diversity in the secondary structure and topology of the C-terminal E-O domain, the GntR family is categorized into seven