Characterization of the Salmonella enterica Serovar TyphimuriumydcIGene, Which Encodes a Conserved DNA Binding Protein Required for Full Acid Stress Resistance

Abstract

Salmonella enterica serovar Typhimurium possesses a stimulon of genes that are differentially regulated in response to conditions of low fluid shear force that increase bacterial virulence and alter other phenotypes. In this study, we show that a previously uncharacterized member of this stimulon, ydcI or STM1625, encodes a highly conserved DNA binding protein with related homologs present in a range of Gram-negative bacterial genera. Gene expression analysis shows that ydcI is expressed in different bacterial genera and is involved in its autoregulation in S. Typhimurium. We demonstrate that purified YdcI protein specifically binds a DNA probe consisting of its own promoter sequence. We constructed an S. Typhimurium ⌬ydcI mutant strain and show that this strain is more sensitive to both organic and inorganic acid stress than is an isogenic WT strain, and this defect is complemented in trans. Moreover, our data indicate that ydcI is part of the rpoS regulon related to stress resistance. The S. Typhimurium ⌬ydcI mutant was able to invade cultured cells to the same degree as the WT strain, but a strain in which ydcI expression is induced invaded cells at a level 2.8 times higher than that of the WT. In addition, induction of ydcI expression in S. Typhimurium resulted in the formation of a biofilm in stationary-phase cultures. These data indicate the ydcI gene encodes a conserved DNA binding protein involved with aspects of prokaryotic biology related to stress resistance and possibly virulence.Bacterial growth environments characterized by low fluid shear force have been shown to induce a multitude of phenotypic responses, including altered acid, oxidative, thermal, and osmotic stress resistance (7,33,36,41,(52)(53)(54)(55), increased biofilm formation (6, 33, 52), altered protein secretion (14, 15), altered cell surface lipid and polysaccharide profiles (6, 7, 55), and increased survival in cellular and animal hosts (39,(52)(53)(54). Notably, the virulence of Salmonella enterica serovar Typhimurium is increased by low fluid shear growth conditions as measured using murine infection assays and tissue culture models (39,(52)(53)(54). Low fluid shear force (defined here as approximately Ͻ0.01 to 0.2 dynes/cm 2 ) is characterized by a lowturbulence, low-agitation environment, as opposed to high fluid shear (defined here as approximately from 5 to Ͼ50 dynes/cm 2 ) where liquid moves with higher velocity over the cellular surface (3-5, 21, 23, 25, 36). Low fluid shear growth environments include spaceflight, ground-based suspension culture models such as the rotating-wall vessel (RWV) bioreactor, and the spaces between cellular microvilli, the last of which is encountered by numerous pathogens during the natural course of infection (21,23,25,30,40,41). Previous work has shown that bacteria grown in low fluid shear environments induce a molecular response which includes genome-wide changes in gene expression (the low fluid shear stimulon) (6,7,39,48,52,53,55). Since growth under low fluid shear conditions is able to ind...

Systematic discovery of uncharacterized transcription factors inEscherichia coliK-12 MG1655

“…Previous studies showed that YdcI is responsible for acid stress and oxidative stress in Salmonella enterica (55) . We analyzed the protein identity of YdcI among multiple strains across Gram-negative bacteria and found that YdcI is a highly and broadly conserved protein ( Figure 5A).…”

Transcriptional profile of Salmonella enterica subsp. enterica serovar Weltevreden during alfalfa sprout colonization

“…Genes encoding the secretion apparatus of SPI‐2 and motility genes were found to be more transcribed in presence of sprouts. The gene ydcI (SENTW_1576) encoding a conserved DNA‐binding protein is related to stress resistance, and possibly, virulence (Jennings et al ., ) was more transcribed in presence of sprouts. Additional higher transcribed genes in presence of sprouts encode the regulator RcsA (SENTW_1101), which is besides RcsB one of the positive regulators for transcription of capsular polysaccharide synthesis in E. coli (Sledjeski and Gottesman, ) and YdhM (SENTW_1780), which is a putative TetR‐family regulator that mainly regulates biosynthesis of antibiotics, efflux pumps and osmotic stress (Ramos et al ., ).…”

Metabolic Control of the TCA cycle by the YdcI Transcriptional Regulator in Escherichia coli

“…Lozada-Chávez et al [40] analyzed the gene-regulatory network structure using a largescale data set, and proposed that the gene-network hierarchy consists of global and local regulators, as seen in the relationships between E. coli ArcA and YdcI and B. subtilis CcpA and CcpC. Genome-sequence data revealed that E. coli ArcA was well-conserved and E. coli YdcI was partially conserved among γ-proteobacteria [41], whereas the ydcI gene was suggested to be acquired after divergence by gene duplication [40]. The TCA cycle local regulatory system in E. coli is suggested to have evolved in a biologically appropriate manner.…”