Gene expression profiling of the pH response inShigella flexneri2a

Abstract

The pH response of Shigella flexneri 2a 301 was identified by gene expression profiling. Gene expression profiles of cells grown in pH 4.5 or 8.6 were compared with the profiles of cells grown at pH 7.0. Differential expression was observed for 307 genes: 97 were acid up-regulated, 102 were acid down-regulated, 91 were base up-regulated, and 86 were base down-regulated. Twenty-seven genes were found to be both acid and base up-regulated, and 29 genes were both acid and base down-regulated. This study showed that (1) the most pH-dependent genes regulate energy metabolism; (2) the RpoS-dependent acid-resistance system is induced, while the glutamate-dependent acid resistance system is not; (3) high pH up-regulates some virulence genes, while low pH down-regulates them, consistent with Shigella infection of the low gut; and (4) several cross-stress response genes are induced by pH changes. These results also illustrate that many unknown genes are significantly regulated under acid or basic conditions, providing researchers with important information to characterize their function.

Identification of Campylobacter jejuni Genes Contributing to Acid Adaptation by Transcriptional Profiling and Genome-Wide Mutagenesis

“…Taking our results together, it is tempting to speculate that the translocation of protons across the cytoplasmic membrane during electron transfer contributes significantly to the ability of C. jejuni to survive in mildly acidic environments. In contrast, the expression of succinate dehydrogenase genes in S. flexneri is induced by either acidic or basic growth conditions (18), while in E. coli, succinate and NADH dehydrogenase genes show opposite pH responses under aerobic (induced by acid) and anaerobic (repressed by acid) growth conditions (37,53). Thus, it is possible that the pH-dependent regulation of energy generation systems is dependent on the organism and/or the growth conditions used.…”

“…The growth of E. coli and Shigella under acidic or basic conditions leads to the preferential expression of metabolic systems that are compatible with the bacterium's environment, i.e., that minimize acid production at low pH and maximize it at high pH (17,18,37,53). For instance, growth under acidic conditions leads to the up-regulation of genes encoding products that are involved in amino acid catabolism, which generates amines (decarboxylases) or ammonia (dehydratases) that can buffer the cellular environment and prevent and/or reverse the acidification of the cytoplasm.…”

“…A number of studies have sought to examine the transcriptional profile of bacteria grown under acidic and/or basic conditions (2,16,18,37,53,84). The small degree of overlap between these studies affirms the importance of using multiple approaches to characterize these responses as thoroughly as possible.…”

“…The small degree of overlap between these studies affirms the importance of using multiple approaches to characterize these responses as thoroughly as possible. These studies revealed that low pH changes the expression of genes involved in energy generation and metabolism, reflecting a switch to metabolic processes that minimize acid production (18,37,53). In addition, pH affects the expression of genes involved in motility and chemotaxis (2,16,37,53,84) as well as genes that encode products that take up and/or export H ϩ (e.g., ATPase and electron transport chain components) (2,16,18,37,53).…”

“…These studies revealed that low pH changes the expression of genes involved in energy generation and metabolism, reflecting a switch to metabolic processes that minimize acid production (18,37,53). In addition, pH affects the expression of genes involved in motility and chemotaxis (2,16,37,53,84) as well as genes that encode products that take up and/or export H ϩ (e.g., ATPase and electron transport chain components) (2,16,18,37,53). These studies also have shown that bacterial acid stress responses show some overlap with oxidative stress (16,53,67) and heat shock (2,18,37,67) responses.…”