Identification of genes negatively regulated by Fis: Fis and RpoS comodulate growth-phase-dependent gene expression in Escherichia coli

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Abstract
Fis is a nucleoid-associated protein in Escherichia coli that has been shown to regulate recombination, replication, and transcription reactions. It is expressed in a transient manner under batch culturing conditions such that high levels are present during early exponential phase and low levels are present during late exponential phase and stationary phase. We have screened a random collection of transposon-induced lac fusions for those which give decreased expression in the presence of Fis. Thirteen different Fis-repressed genes were identified, including glnQ (glutamine high-affinity transport), mglA (methyl-galactoside transport), xylF (D-xylose-binding protein), sdhA (succinate dehydrogenase flavoprotein subunit), and a newly identified aldehyde dehydrogenase, aldB. The LacZ expression patterns revealed that many of the fusions were maximally expressed at different stages of growth, including early log phase, mid- to late log phase, and stationary phase. The expression of some of the late-exponential- and stationary-phase genes was dependent on the RpoS sigma factor, whereas that of others was affected negatively by RpoS. We conclude that Fis negatively regulates a diverse set of genes and that RpoS can function to both activate and inhibit the expression of specific genes.