Identification of PhoB binding sites of the yibD and ytfK promoter regions in Escherichia coli

Abstract

By using a lacZ operon fusion genomic library of the Escherichia coli 0157:H7 Sakai, we identified phosphate-starvation-inducible (psi) promoters located upstream of the yibD and ytfK genes. They have been previously proposed to belong to the phosphate regulon (pho regulon) by Beak and Lee (2006), based on the DNA array and in vivo transcriptional experiments. However, the direct interaction of these promoters with the activator protein of the pho regulon, PhoB, has not been determined. We determined the binding regions of PhoB in these promoter regions by DNase I footprinting. Both regions contained two pho boxes similar to the consensus sequence for PhoB binding.

Novel members of the phosphate regulon in Escherichia coli O157:H7 identified using a whole-genome shotgun approach

“…This observation agrees well with the reported findings of the systematic mutation analysis of the pho box (Makino et al, 1998). All previously identified pho regulon promoters have −10 promoter sequences exactly 10-bp downstream from the pho box consensus sequence (Makino et al, 1998;Yoshida et al, 2010Yoshida et al, , 2011. Accordingly, we also identified putative −10 promoter sequences 10-bp downstream from the pho box sequences identified here (Table 2).…”

“…Notably, the protected regions within inserts S7 and Y6 included two pho box sequences. Tandemly arranged pho box sequences in the pstS, ugp, psiE, yibD, and ytfK promoter regions have also been reported (Kasahara et al, 1991;Kim et al, 2000;Kimura et al, 1989;Yoshida et al, 2011). Based on these novel and previously identified pho box sequences, we generated a sequence logo.…”

Control of the phoBR Regulon in Escherichia coli

“…Two genes that encode cell envelope modification enzymes have been identified as being regulated by PhoB. They are waaH and mipA (44,55). waaH (also known as yibD) encodes an enzyme for the modification of lipopolysaccharide (LPS) in which a phosphate on the inner core region of LPS is replaced by glucuronic acid (56), allowing maintenance of a negative charge at the site.…”

Molecular and Structural Basis of Inner Core Lipopolysaccharide Alterations in Escherichia coli

“…Thus, the presence of predicted PhoB boxes in the promoter region of the waaH gene (33) supports our results. After the completion of this work, direct PhoB-binding sites have been found upstream of the waaH (yibD) gene, although the function of the gene remained elusive (38).…”