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Gene repression by sigmaS: sigma competition for binding to RNA polymerase or more?

ABSTRACT: The alternative subunit of RNA polymerase RpoS/M-OM-^CS controls a global adaptive response allowing many Gram-negative bacteria to survive nutrient deprivation and various stresses and contributes to biofilm formation and virulence of Salmonella enterica serovar Typhimurium. We have addressed an important but poorly understood aspect of M-OM-^CS-dependent control; that of a repressor. The general assumption is that negative regulation of gene expression by M-OM-^CS is mainly a passive phenomenon, due to competition between M-OM-^CS and other sigma factors for binding to a limited amount of core RNA polymerase (RNAP). Genome expression profiling and physiological characterization of mutants of Salmonella ser. Typhimurium deleted for rpoS or producing a M-OM-^CS protein efficient for binding to RNAP, but not to the -10 promoter element, revealed that gene repression by M-OM-^CS requires its binding to DNA. Therefore, gene repression by M-OM-^CS is an active phenomenon rather than the sole cause of M-OM-^CS competing with other sigma factors for RNAP binding. RNA profiles of the wild type strain and two rpoS mutants of Salmonella enterica serotype Typhimurium were generated by RNA sequencing, using three biological replicates. One rpoS mutant is deleted for rpoS (delta-rpoS), while the other (rpoSdb) contains two point mutations in rpoS (C421A and G469A) and produces an M-OM-^CS protein inefficient for binding to the -10 promoter element.

ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium

SUBMITTER: Monot Marc

PROVIDER: E-GEOD-46380 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene repression by sigmaS: sigma competition for binding to RNA polymerase or more?

Project description:The alternative subunit of RNA polymerase RpoS/σS controls a global adaptive response allowing many Gram-negative bacteria to survive nutrient deprivation and various stresses and contributes to biofilm formation and virulence of Salmonella enterica serovar Typhimurium. We have addressed an important but poorly understood aspect of σS-dependent control; that of a repressor. The general assumption is that negative regulation of gene expression by σS is mainly a passive phenomenon, due to competition between σS and other sigma factors for binding to a limited amount of core RNA polymerase (RNAP). Genome expression profiling and physiological characterization of mutants of Salmonella ser. Typhimurium deleted for rpoS or producing a σS protein efficient for binding to RNAP, but not to the -10 promoter element, revealed that gene repression by σS requires its binding to DNA. Therefore, gene repression by σS is an active phenomenon rather than the sole cause of σS competing with other sigma factors for RNAP binding.

2014-05-05 | GSE46380 | GEO

ChIP-chip of RNA Polymerase (RNAP) and RpoD in Salmonella enterica serovar Typhimurium strain SL1344

Project description:ChIP-on-chip analysis of RNAP and RpoD binding to the Salmonella enterica serovar Typhimurium chromosome demonstrated a high degree of overlap between RNAP and RpoD binding and provided us with important insights into the global distribution of these factors. Furthermore this data was correlated with information on the location of 1873 transcription start sites identified by RNA-Seq technology, thereby providing a detailed transcriptional map of Salmonella Typhimurium.

2012-02-16 | GSE35827 | GEO

ChIP-chip of RNA Polymerase (RNAP) and RpoD in Salmonella enterica serovar Typhimurium strain SL1344

2012-02-16 | E-GEOD-35827 | biostudies-arrayexpress

ChIP-chip analysis of RNAP and Sigma factor binding to the Salmonella enterica serovar Typhimurium chromosome

Project description:ChIP-chip analysis of RNA Polymerase (RNAP), RpoD, RpoE, RpoH and RpoN in exponential phase (OD 0.2) and early stationary phase (OD 2.0) Salmonella enterica serovar Typhimurium SL1344 cultures

2017-04-01 | GSE97283 | GEO

ChIP-chip of LeuO, H-NS and RNA Polymerase (RNAP) in Salmonella enterica serovar Typhimurium strain SL1344

Project description:The LysR family transcription factor LeuO is believed to antagonize the global repressor H-NS. ChIP-on-chip analysis of LeuO, H-NS and RNAP binding to the Salmonella enterica serovar Typhimurium chromosome demonstrated a high degree of overlap between LeuO and H-NS regulated genes. Furthermore LeuO binding was associated with RNA polymerase recruitment, indicating a role for LeuO in activating transcription.

2012-02-16 | GSE35826 | GEO

ChIP-chip of LeuO, H-NS and RNA Polymerase (RNAP) in Salmonella enterica serovar Typhimurium strain SL1344

2012-02-16 | E-GEOD-35826 | biostudies-arrayexpress

Quantitative analysis of differential proteome expression in wild-type and mutants strains of Salmonella enterica serovar Typhimurium

Project description:The ability to adapt quickly to changing environmental conditions is crucial for growth and survival of bacteria in their natural environment. The common strategy that bacteria utilize to increase their survival under stressful conditions, including antibiotic treatment, is the entry into a non-actively growing state (quiescence). In the wide host-range pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) and other Gram negative bacteria, this temporary arrest of proliferation induces the expression of the alternative sigma subunit σS/RpoS of RNA polymerase (RNAP) which remodels global gene expression to reshape the cell physiology and ensure survival in various stress conditions and nutritional deficiencies (i.e. general stress resistance) and long-term cell persistence. σS is also required for virulence and biofilm formation. Our work aims at understanding key molecular and physiological determinants responsible for persistence of non-growing bacteria, using the ubiquitous pathogen S. Typhimurium as a working system. We expect to identify novel functional proteins that are both physiologically important and of wide biological significance. One approach to characterize those proteins is to compare mutant proteome to that of the wild-type strain to unravel potential effects of the mutations on the expression and/or stability of proteins.

2018-10-26 | PXD005256 | Pride

ChIP-on-chip of OmpR binding in Salmonella enterica serovar Typhimurium strain SL1344 and E.scherichia coli strain CSH50 at pH 7 and pH 4.5 including analysis of OmpR binding in SL1344 in the absence and presence of novobiocin (25 μg/ml)

Project description:OmpR is a DNA binding protein belonging to the OmpR/EnvZ two component system. This system is known to sense changes in osmolarity in Escherichia coli. Recently, OmpR in Salmonella enterica serovar Typhimurium was found to be activated by acidic pH and DNA relaxation. In this study, ChIP-on-chip was employed to ascertain the genome-wide distribution of OmpR in Salmonella Typhimurium and Escherichia coli in acidic and neutral pH. In addition we investigated the affect of DNA relaxation on OmpR binding in Salmonella Typhimurium.

2014-03-27 | GSE49914 | GEO

Expression analysis of Salmonella enterica serovar Typhimurium UK1 delta-iacP mutant

Project description:Investigation of whole genome gene expression level changes in a Salmonella enterica serovar Typhimurium UK1 delta-iacP mutant, compared to the wild-type strain. IacP is resoponsible for the secretion of virulence effector proteins via the type III secretion system, thereby contributing the virulence of S. Typhimurium. The mutants analyzed in this study are further described in Kim et al. 2011. Role of Salmonella Pathogenicity Island 1 Protein IacP in Salmonella enterica Serovar Typhimurium Pathogenesis. Infection and Immunity 79(4):1440-1450 (PMID 21263021). A chip study using total RNA recovered from two separate wild-type cultures of Salmonella enterica serovar Typhimurium UK1 and two separate cultures of a mutant strain, Salmonella enterica serovar Typhimurium UK1 delta-iacP. Each chip measures the expression level of 4,302 genes from Salmonella enterica serovar Typhimurium.

2012-04-29 | E-GEOD-34663 | biostudies-arrayexpress

Role of DksA in nitrosative stress

Project description:Transcriptional profiles of wt and dksA minus Salmonella enterica sv Typhimurium 14028S in E salts minimal medium in response to 5 mM DETANONOate for 30 min Total RNA was harvested from three biological replicates of wt and dksA mutant cultures exposed or unexposed to 5mM DETANONOate for 30min in E salts minimal medium.

2014-03-31 | E-GEOD-33529 | biostudies-arrayexpress

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