Network rewiring: physiological consequences of reciprocally exchanging the physical locations and growth-phase-dependent expression patterns of theSalmonella fisanddpsgenes

Abstract

ABSTRACTThe Fis nucleoid-associated protein controls the expression of a large and diverse regulon of genes in Gram-negative bacteria. Fis production is normally maximal in bacteria during the early exponential phase of batch culture growth, becoming almost undetectable by the onset of stationary phase. We tested the effect on the Fis regulatory network inSalmonellaof moving the completefisgene from its usual location near the origin of chromosomal replication to the position normally occupied by thedpsgene in the Right macrodomain of the chromosome, andvice versa, creating the strain GX. In a parallel experiment, we tested the effect of rewiring the Fis regulatory network by placing thefisopen reading frame under the control of the stationary-phase-activateddpspromoter at thedpsgenetic location within Ter, andvice versa, creating the strain OX. ChIP-seq was used to measure global Fis protein binding and gene expression patterns. Strain GX showed few changes when compared with the wild type, although we did detect increased Fis binding at Ter, accompanied by reduced binding at Ori. Strain OX displayed a more pronounced version of this distorted Fis protein-binding pattern together with numerous alterations in the expression of genes in the Fis regulon. OX, but not GX, had a reduced ability to infect cultured mammalian cells. These findings illustrate the inherent robustness of the Fis regulatory network to rewiring based on gene repositioning alone and emphasise the importance offisexpression signals in phenotypic determination.IMPORTANCEWe assessed the impacts onSalmonellaphysiology of reciprocally translocating the genes encoding the Fis and Dps nucleoid-associated proteins (NAPs), and of inverting their growth phase production patterns such that Fis is produced in stationary phase (like Dps) and Dps is produced in exponential phase (like Fis). Changes to peak binding of Fis were detected by ChIP-seq on the chromosome, as were widespread impacts on the transcriptome, especially when Fis production mimicked Dps. Virulence gene expression and the expression of a virulence phenotype were altered. Overall, these radical changes to NAP gene expression were well tolerated, revealing the robust and well-buffered nature of global gene regulation networks in the bacterium.