scholarly journals Contribution of DNA adenine methylation to gene expression heterogeneity in Salmonella enterica

2020 ◽  
Vol 48 (21) ◽  
pp. 11857-11867
Author(s):  
María A Sánchez-Romero ◽  
David R Olivenza ◽  
Gabriel Gutiérrez ◽  
Josep Casadesús
Keyword(s):  
Gene Expression ◽  
Salmonella Enterica ◽  
Transcriptional Control ◽  
Single Cell Analysis ◽  
Environmental Control ◽  
Bioinformatic Analysis ◽  
Growth Conditions ◽  
Dam Methylation ◽  
Gene Expression Heterogeneity ◽  
Dam Methylase

Abstract Expression of Salmonella enterica loci harboring undermethylated GATC sites at promoters or regulatory regions was monitored by single cell analysis. Cell-to-cell differences in expression were detected in ten such loci (carA, dgoR, holA, nanA, ssaN, STM1290, STM3276, STM5308, gtr and opvAB), with concomitant formation of ON and OFF subpopulations. The ON and OFF subpopulation sizes varied depending on the growth conditions, suggesting that the population structure can be modulated by environmental control. All the loci under study except STM5308 displayed altered patterns of expression in strains lacking or overproducing Dam methylase, thereby confirming control by Dam methylation. Bioinformatic analysis identified potential binding sites for transcription factors OxyR, CRP and Fur, and analysis of expression in mutant backgrounds confirmed transcriptional control by one or more of such factors. Surveys of gene expression in pairwise combinations of Dam methylation-dependent loci revealed independent switching, thus predicting the formation of a high number of cell variants. This study expands the list of S. enterica loci under transcriptional control by Dam methylation, and underscores the relevance of the DNA adenine methylome as a source of phenotypic heterogeneity.

scholarly journals Dam and its role in pathogenicity of Salmonella enterica

2009 ◽  
Vol 3 (07) ◽  
pp. 484-490 ◽  
Author(s):  
Mónica N. Giacomodonato ◽  
Sebastián H. Sarnacki ◽  
Mariángeles Noto Llana ◽  
M. Cristina Cerquetti
Keyword(s):  
Gene Expression ◽  
Animal Models ◽  
Salmonella Enterica ◽  
Bacterial Pathogens ◽  
General Strategy ◽  
Essential Factor ◽  
Bacterial Gene ◽  
Bacterial Gene Expression ◽  
Dam Methylation

Dam methylation is an essential factor involved in the virulence of an increasing number of bacterial pathogens including Salmonella enterica. Lack of Dam methylation causes severe attenuation in animal models. It has been proposed that dysregulation of Dam activity is potentially a general strategy for the generation of vaccines against bacterial pathogens. In this review, we focus our attention on the role of methylation by Dam protein in regulating bacterial gene expression and virulence in Salmonella enterica.

scholarly journals DNA Adenine Methylation Regulates Virulence Gene Expression in Salmonella enterica Serovar Typhimurium

2006 ◽  
Vol 188 (23) ◽  
pp. 8160-8168 ◽  
Author(s):  
Roberto Balbontín ◽  
Gary Rowley ◽  
M. Graciela Pucciarelli ◽  
Javier López-Garrido ◽  
Yvette Wormstone ◽  
...  
Keyword(s):  
Gene Expression ◽  
Salmonella Enterica ◽  
Expression Patterns ◽  
Virulence Gene ◽  
Luria Bertani ◽  
Altered Expression ◽  
Virulence Gene Expression ◽  
Adenine Methylation ◽  
Dam Methylation ◽  
Serovar Typhimurium

ABSTRACT Transcriptomic analyses during growth in Luria-Bertani medium were performed in strain SL1344 of Salmonella enterica serovar Typhimurium and in two isogenic derivatives lacking Dam methylase. More genes were repressed than were activated by Dam methylation (139 versus 37). Key genes that were differentially regulated by Dam methylation were verified independently. The largest classes of Dam-repressed genes included genes belonging to the SOS regulon, as previously described in Escherichia coli, and genes of the SOS-inducible Salmonella prophages ST64B, Gifsy-1, and Fels-2. Dam-dependent virulence-related genes were also identified. Invasion genes in pathogenicity island SPI-1 were activated by Dam methylation, while the fimbrial operon std was repressed by Dam methylation. Certain flagellar genes were repressed by Dam methylation, and Dam− mutants of S. enterica showed reduced motility. Altered expression patterns in the absence of Dam methylation were also found for the chemotaxis genes cheR (repressed by Dam) and STM3216 (activated by Dam) and for the Braun lipoprotein gene, lppB (activated by Dam). The requirement for DNA adenine methylation in the regulation of specific virulence genes suggests that certain defects of Salmonella Dam− mutants in the mouse model may be caused by altered patterns of gene expression.

scholarly journals HilE is required for synergistic activation of SPI-1 gene expression in Salmonella enterica serovar Typhimurium

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Selwan Hamed ◽  
Riham M. Shawky ◽  
Mohamed Emara ◽  
James M. Slauch ◽  
Christopher V. Rao
Keyword(s):  
Gene Expression ◽  
Salmonella Enterica ◽  
Salmonella Enterica Serovar Typhimurium ◽  
Growth Conditions ◽  
Intestinal Epithelial ◽  
Synergistic Activation ◽  
Wide Range ◽  
Serovar Typhimurium ◽  
In The Wild ◽  
Intestinal Pathogen

Abstract Background Salmonella enterica serovar Typhimurium is an intestinal pathogen capable of infecting a wide range of animals. It initiates infection by invading intestinal epithelial cells using a type III secretion system encoded within Salmonella pathogenicity island 1 (SPI-1). The SPI-1 genes are regulated by multiple interacting transcription factors. The master regulator is HilD. HilE represses SPI-1 gene expression by binding HilD and preventing it from activating its target promoters. Previous work found that acetate and nutrients synergistically induce SPI-1 gene expression. In the present study, we investigated the role of HilE, nominally a repressor of SPI-1 gene expression, in mediating this response to acetate and nutrients. Results HilE is necessary for activation of SPI-1 gene expression by acetate and nutrients. In mutants lacking hilE, acetate and nutrients no longer increase SPI-1 gene expression but rather repress it. This puzzling response is not due to the BarA/SirA two component system, which governs the response to acetate. To identify the mechanism, we profiled gene expression using RNAseq in the wild type and a ΔhilE mutant under different growth conditions. Analysis of these data suggested that the Rcs system, which regulates gene expression in response to envelope stress, is involved. Consistent with this hypothesis, acetate and nutrients were able to induce SPI-1 gene expression in mutants lacking hilE and the Rcs system. Conclusions While the exact mechanism is unknown, these results demonstrate the HilE, nominally a repressor of SPI-1 gene expression, can also function as an activator under the growth conditions investigated. Collectively, these results provide new insights regarding SPI-1 gene regulation and demonstrate that HilE is more complex than initially envisioned.

scholarly journals Epidermal Wnt signalling regulates transcriptome heterogeneity and proliferative fate in neighbouring cells

2017 ◽  
Author(s):  
Arsham Ghahramani ◽  
Giacomo Donati ◽  
Nicholas M. Luscombe ◽  
Fiona M. Watt
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Cell Fate ◽  
Single Cell Analysis ◽  
Transcriptional Response ◽  
Wnt Signalling ◽  
Beta Catenin ◽  
Dependent Manner ◽  
Self Renewal ◽  
Gene Expression Heterogeneity

AbstractCanonical Wnt/beta-catenin signalling regulates self-renewal and lineage selection within the mouse epidermis. Although the transcriptional response of keratinocytes that receive a Wnt signal is well characterised, little is known about the mechanism by which keratinocytes in proximity to the Wntreceiving cell are co-opted to undergo a change in cell fate. To address this, we performed single-cell mRNA-Seq on mouse keratinocytes co-cultured with and without the presence of beta-catenin activated neighbouring cells. We identified seven distinct cell states in cultures that had not been exposed to the beta-catenin stimulus and show that the stimulus redistributes wild type subpopulation proportions. Using temporal single-cell analysis we reconstruct the cell fate changes induced by neighbour Wnt activation. Gene expression heterogeneity was reduced in neighbouring cells and this effect was most dramatic for protein synthesis associated genes. The changes in gene expression were accompanied by a shift from a quiescent to a more proliferative stem cell state. By integrating imaging and reconstructed sequential gene expression changes during the state transition we identified transcription factors, including Smad4 and Bcl3, that were responsible for effecting the transition in a contact-dependent manner. Our data indicate that non cell-autonomous Wnt/beta-catenin signalling decreases transcriptional heterogeneity and further our understanding of how epidermal Wnt signalling orchestrates regeneration and self-renewal.

scholarly journals Two Tandem Mechanisms Control Bimodal Expression of the Flagellar Genes in Salmonella enterica

2020 ◽  
Vol 202 (13) ◽  
Author(s):  
Xiaoyi Wang ◽  
Santosh Koirala ◽  
Phillip D. Aldridge ◽  
Christopher V. Rao
Keyword(s):  
Gene Expression ◽  
Salmonella Enterica ◽  
Feedback Loop ◽  
Growth Conditions ◽  
Double Negative ◽  
Flagellar Gene ◽  
Content Type ◽  
Motile Cells ◽  
Flagellar Assembly ◽  
Flagellar Genes

ABSTRACT Flagellar gene expression is bimodal in Salmonella enterica. Under certain growth conditions, some cells express the flagellar genes whereas others do not. This results in mixed populations of motile and nonmotile cells. In the present study, we found that two independent mechanisms control bimodal expression of the flagellar genes. One was previously found to result from a double negative-feedback loop involving the flagellar regulators RflP and FliZ. This feedback loop governs bimodal expression of class 2 genes. In this work, a second mechanism was found to govern bimodal expression of class 3 genes. In particular, class 3 gene expression is still bimodal, even when class 2 gene expression is not. Using a combination of experimental and modeling approaches, we found that class 3 bimodality results from the σ28-FlgM developmental checkpoint. IMPORTANCE Many bacterial use flagella to swim in liquids and swarm over surface. In Salmonella enterica, over 50 genes are required to assemble flagella. The expression of these genes is tightly regulated. Previous studies have found that flagellar gene expression is bimodal in S. enterica, which means that only a fraction of cells express flagellar genes and are motile. In the present study, we found that two separate mechanisms induce this bimodal response. One mechanism, which was previously identified, tunes the fraction of motile cells in response to nutrients. The other results from a developmental checkpoint that couples flagellar gene expression to flagellar assembly. Collectively, these results further our understanding of how flagellar gene expression is regulated in S. enterica.

scholarly journals Dam Methylation Controls O-Antigen Chain Length in Salmonella enterica Serovar Enteritidis by Regulating the Expression of Wzz Protein

2009 ◽  
Vol 191 (21) ◽  
pp. 6694-6700 ◽  
Author(s):  
Sebastián H. Sarnacki ◽  
Cristina L. Marolda ◽  
Mariángeles Noto Llana ◽  
Mónica N. Giacomodonato ◽  
Miguel A. Valvano ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chain Length ◽  
Parental Strain ◽  
Salmonella Enterica ◽  
Length Distribution ◽  
Surface Proteins ◽  
Logarithmic Phase ◽  
Chain Length Distribution ◽  
O Antigen ◽  
Dam Methylation

ABSTRACT We reported previously that a Salmonella enterica serovar Enteritidis dam mutant expressing a truncated Dam protein does not agglutinate in the presence of specific antibodies against O9 polysaccharide. Here we investigate the participation of Dam in lipopolysaccharide (LPS) synthesis in Salmonella. The LPS O-antigen profiles of a dam null mutant (SEΔdam) and the Salmonella serovar Enteritidis parental strain were examined by using electrophoresis and silver staining. Compared to the parental strain, SEΔdam produced LPS with shorter O-antigen polysaccharide chains. Since Wzz is responsible for the chain length distribution of the O antigen, we investigated whether Dam methylation is involved in regulating wzz expression. Densitometry analysis showed that the amount of Wzz produced by SEΔdam is threefold lower than the amount of Wzz produced by the parental strain. Concomitantly, the activity of the wzz promoter in SEΔdam was reduced nearly 50% in logarithmic phase and 25% in stationary phase. These results were further confirmed by reverse transcription-PCR showing that wzz gene expression was threefold lower in the dam mutant than in the parental strain. Our results demonstrate that wzz gene expression is downregulated in a dam mutant, indicating that Dam methylation activates expression of this gene. This work indicates that wzz is a new target regulated by Dam methylation and demonstrates that DNA methylation not only affects the production of bacterial surface proteins but also the production of surface polysaccharides.

scholarly journals Two tandem mechanisms control bimodal expression of the flagellar genes in Salmonella enterica

2019 ◽  
Author(s):  
Xiaoyi Wang ◽  
Santosh Koirala ◽  
Phillip D. Aldridge ◽  
Christopher V. Rao
Keyword(s):  
Gene Expression ◽  
Salmonella Enterica ◽  
Feedback Loop ◽  
Growth Conditions ◽  
Double Negative ◽  
Flagellar Gene ◽  
Motile Cells ◽  
Flagellar Assembly ◽  
Mixed Populations ◽  
Flagellar Genes

ABSTRACTFlagellar gene expression is bimodal in Salmonella enterica. Under certain growth conditions, some cells express the flagellar genes whereas others do not. This results in mixed populations of motile and non-motile cells. In the present study, we found that two independent mechanisms control bimodal expression of the flagellar genes. One was previously found to result from a double negative-feedback loop involving the flagellar regulators YdiV and FliZ. This feedback loop governs bimodal expression of class 2 genes. In this work, a second mechanism was found to govern bimodal expression of class 3 genes. In particular, class 3 gene expression is still bimodal even when class 2 gene expression is not. Using a combination of experimental and modeling approaches, we found that class 3 bimodalilty results from the σ28-FlgM developmental checkpoint.IMPORTANCEMany bacterial use flagella to swim in liquids and swarm over surface. In Salmonella enterica, over fifty genes are required to assemble flagella. The expression of these genes is tightly regulated. Previous studies have found that flagella gene expression is bimodal in S. enterica, which means that only a fraction of cells express flagellar genes and are motile. In the present study, we found that two separate mechanisms induce this bimodal response. One mechanism, which was previously identified, tunes the fraction of motile cells in response to nutrients. The other results from a developmental checkpoint that couples flagellar gene expression to flagellar assembly. Collectively, these results further our understanding of how flagellar gene expression is regulated in S. enterica.

Nutrient-regulated gene expression in eukaryotes

2006 ◽  
Vol 73 ◽  
pp. 85-96 ◽  
Author(s):  
Richard J. Reece ◽  
Laila Beynon ◽  
Stacey Holden ◽  
Amanda D. Hughes ◽  
Karine Rébora ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcriptional Control ◽  
Direct Interaction ◽  
Signalling Pathways ◽  
A Cell ◽  
One Step ◽  
Higher Eukaryotes ◽  
Regulated Gene Expression

The recognition of changes in environmental conditions, and the ability to adapt to these changes, is essential for the viability of cells. There are numerous well characterized systems by which the presence or absence of an individual metabolite may be recognized by a cell. However, the recognition of a metabolite is just one step in a process that often results in changes in the expression of whole sets of genes required to respond to that metabolite. In higher eukaryotes, the signalling pathway between metabolite recognition and transcriptional control can be complex. Recent evidence from the relatively simple eukaryote yeast suggests that complex signalling pathways may be circumvented through the direct interaction between individual metabolites and regulators of RNA polymerase II-mediated transcription. Biochemical and structural analyses are beginning to unravel these elegant genetic control elements.

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