Network Rewiring: Physiological Consequences of Reciprocally Exchanging the Physical Locations and Growth-Phase-Dependent Expression Patterns of the <italic toggle="yes">Salmonella fis</italic> and <italic toggle="yes">dps</italic> Genes

ABSTRACT The 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 p...

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Autores principales:	Marina M. Bogue, Aalap Mogre, Michael C. Beckett, Nicholas R. Thomson, Charles J. Dorman
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	nucleoid-associated protein Fis Dps ChIP-seq RNA-seq transcriptome Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/064ca93dbcdb47179fd853a518f0f58e
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spelling	oai:doaj.org-article:064ca93dbcdb47179fd853a518f0f58e2021-11-15T16:19:09ZNetwork Rewiring: Physiological Consequences of Reciprocally Exchanging the Physical Locations and Growth-Phase-Dependent Expression Patterns of the <italic toggle="yes">Salmonella fis</italic> and <italic toggle="yes">dps</italic> Genes10.1128/mBio.02128-202150-7511https://doaj.org/article/064ca93dbcdb47179fd853a518f0f58e2020-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.02128-20https://doaj.org/toc/2150-7511ABSTRACT The 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 in Salmonella of moving the complete fis gene from its usual location near the origin of chromosomal replication to the position normally occupied by the dps gene in the right macrodomain of the chromosome, and vice versa, creating the gene exchange (GX) strain. In a parallel experiment, we tested the effect of rewiring the Fis regulatory network by placing the fis open reading frame under the control of the stationary-phase-activated dps promoter at the dps genetic location within the right macrodomain, and vice versa, creating the open reading frame exchange (OX) strain. Chromatin immunoprecipitation sequencing (ChIP-seq) was used to measure global Fis protein binding levels and to determine gene expression patterns. Strain GX showed few changes 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 with respect to the effects of rewiring based on gene repositioning alone and emphasize the importance of fis expression signals in phenotypic determination. IMPORTANCE We assessed the impact on Salmonella physiology 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 was produced in stationary phase (like Dps) and Dps was 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 production. 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.Marina M. BogueAalap MogreMichael C. BeckettNicholas R. ThomsonCharles J. DormanAmerican Society for Microbiologyarticlenucleoid-associated proteinFisDpsChIP-seqRNA-seqtranscriptomeMicrobiologyQR1-502ENmBio, Vol 11, Iss 5 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	nucleoid-associated protein Fis Dps ChIP-seq RNA-seq transcriptome Microbiology QR1-502
spellingShingle	nucleoid-associated protein Fis Dps ChIP-seq RNA-seq transcriptome Microbiology QR1-502 Marina M. Bogue Aalap Mogre Michael C. Beckett Nicholas R. Thomson Charles J. Dorman Network Rewiring: Physiological Consequences of Reciprocally Exchanging the Physical Locations and Growth-Phase-Dependent Expression Patterns of the <italic toggle="yes">Salmonella fis</italic> and <italic toggle="yes">dps</italic> Genes
description	ABSTRACT The 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 in Salmonella of moving the complete fis gene from its usual location near the origin of chromosomal replication to the position normally occupied by the dps gene in the right macrodomain of the chromosome, and vice versa, creating the gene exchange (GX) strain. In a parallel experiment, we tested the effect of rewiring the Fis regulatory network by placing the fis open reading frame under the control of the stationary-phase-activated dps promoter at the dps genetic location within the right macrodomain, and vice versa, creating the open reading frame exchange (OX) strain. Chromatin immunoprecipitation sequencing (ChIP-seq) was used to measure global Fis protein binding levels and to determine gene expression patterns. Strain GX showed few changes 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 with respect to the effects of rewiring based on gene repositioning alone and emphasize the importance of fis expression signals in phenotypic determination. IMPORTANCE We assessed the impact on Salmonella physiology 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 was produced in stationary phase (like Dps) and Dps was 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 production. 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.
format	article
author	Marina M. Bogue Aalap Mogre Michael C. Beckett Nicholas R. Thomson Charles J. Dorman
author_facet	Marina M. Bogue Aalap Mogre Michael C. Beckett Nicholas R. Thomson Charles J. Dorman
author_sort	Marina M. Bogue
title	Network Rewiring: Physiological Consequences of Reciprocally Exchanging the Physical Locations and Growth-Phase-Dependent Expression Patterns of the <italic toggle="yes">Salmonella fis</italic> and <italic toggle="yes">dps</italic> Genes
title_short	Network Rewiring: Physiological Consequences of Reciprocally Exchanging the Physical Locations and Growth-Phase-Dependent Expression Patterns of the <italic toggle="yes">Salmonella fis</italic> and <italic toggle="yes">dps</italic> Genes
title_full	Network Rewiring: Physiological Consequences of Reciprocally Exchanging the Physical Locations and Growth-Phase-Dependent Expression Patterns of the <italic toggle="yes">Salmonella fis</italic> and <italic toggle="yes">dps</italic> Genes
title_fullStr	Network Rewiring: Physiological Consequences of Reciprocally Exchanging the Physical Locations and Growth-Phase-Dependent Expression Patterns of the <italic toggle="yes">Salmonella fis</italic> and <italic toggle="yes">dps</italic> Genes
title_full_unstemmed	Network Rewiring: Physiological Consequences of Reciprocally Exchanging the Physical Locations and Growth-Phase-Dependent Expression Patterns of the <italic toggle="yes">Salmonella fis</italic> and <italic toggle="yes">dps</italic> Genes
title_sort	network rewiring: physiological consequences of reciprocally exchanging the physical locations and growth-phase-dependent expression patterns of the <italic toggle="yes">salmonella fis</italic> and <italic toggle="yes">dps</italic> genes
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/064ca93dbcdb47179fd853a518f0f58e
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Network Rewiring: Physiological Consequences of Reciprocally Exchanging the Physical Locations and Growth-Phase-Dependent Expression Patterns of the <italic toggle="yes">Salmonella fis</italic> and <italic toggle="yes">dps</italic> Genes

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