Use of a promiscuous, constitutively-active bacterial enhancer-binding protein to define the σ54 (RpoN) regulon of Salmonella Typhimurium LT2

Samuels, David; Frye, Jonathan G.; Porwollik, Steffen; McClelland, Michael; Mrázek, Jan; Hoover, Timothy R.; Karls, Anna C.

doi:10.1186/1471-2164-14-602

Cited by 33 publications

(71 citation statements)

References 71 publications

(105 reference statements)

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“…2D, E and F). Presence of sense and antisense intragenic binding sites for RpoN is in accordance with what been previously found for S. Typhimurium and E. coli (27,28). The function and mechanisms of RpoN intragenic binding are generally unknown, but there are examples where this binding can drive transcription of downstream genes with long 5´ UTRs (27,34).…”

Section: Rpon Binds To Multiple Sites On the Y Pseudotuberculosis Chsupporting

confidence: 88%

“…This identified 119 ChIP-seq peaks representing putative sites for RpoN binding. The number of peaks was in the range previously shown for E. coli, Salmonella Typhimurium, and V. cholerae (8,27,28). Some of the peaks were narrow and distinct, covering 200-300 nucleotides, whereas others were relatively broad and covered 300-800 nucleotides (Table S1).…”

Section: Rpon Binds To Multiple Sites On the Y Pseudotuberculosis Chsupporting

confidence: 58%

“…2C; Table 1 and 2). There were relatively few ChIP-seq peaks without motifs (16 out of 119; Table S2) compared with the findings in some other studies (23,27,28). This probably reflects the high-stringency analysis used, which limits the number of false positives commonly found in ChIP data from highly transcribed regions (31,32).…”

Section: Rpon Binds To Multiple Sites On the Y Pseudotuberculosis Chmentioning

confidence: 60%

“…To check the conservation of RpoN-regulated genes, cross-species homology prediction was done by comparing Y.pseudotuberculosis YPIII, V. cholerae 037, E. coli 0157, and S. Typhimurium LT2 using OrthologueDB(58). Yersinia genes having orthologs in at least one of the species mentioned above were checked for previous ChIP-seq studies(23,27,28).Figures are plotted using the ggplot2 package in R (linux version 4.0.2). Ethics statement.…”

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confidence: 99%

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Genome-scale mapping reveals complex regulatory activities of RpoN inYersinia pseudotuberculosis

Mahmud

Nilsson

Fahlgren

et al. 2020

Preprint

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RpoN, an alternative sigma factor commonly known as sigma 54, is implicated in persistent stages of Yersinia pseudotuberculosis infections in which genes associated with this regulator are upregulated. We here combined phenotypic and genomic assays to provide insight into its role and function in this pathogen. RpoN was found essential for Y. pseudotuberculosis virulence in mice, and in vitro functional assays showed that it controls biofilm formation and motility. Mapping genome-wide associations of Y. pseudotuberculosis RpoN using chromatin immunoprecipitation coupled with next-generation sequencing identified an RpoN-binding motif located at 103 inter- and intragenic sites on both sense and anti-sense strands. Deletion of rpoN had a large impact on gene expression, including down-regulation of genes encoding proteins involved in flagellar assembly, chemotaxis, and quorum sensing. There were also clear indications of cross talk with other sigma factors, together with indirect effects due to altered expression of other regulators. Matching differential gene expression with locations of the binding sites implicated around 130 genes or operons potentially activated or repressed by RpoN. Mutagenesis of selected intergenic binding sites confirmed both positive and negative regulatory effects of RpoN binding. Corresponding mutations of intragenic sense sites had less impact on associated gene expression. Surprisingly, mutating intragenic sites on the anti-sense strand commonly reduced expression of genes encoded by the corresponding sense strand

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Section: Rpon Binds To Multiple Sites On the Y Pseudotuberculosis Chsupporting

confidence: 88%

Section: Rpon Binds To Multiple Sites On the Y Pseudotuberculosis Chsupporting

confidence: 58%

Section: Rpon Binds To Multiple Sites On the Y Pseudotuberculosis Chmentioning

confidence: 60%

mentioning

confidence: 99%

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Genome-scale mapping reveals complex regulatory activities of RpoN inYersinia pseudotuberculosis

Mahmud

Nilsson

Fahlgren

et al. 2020

Preprint

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“…The S. Typhimurium gfrABCDEF operon was previously predicted to be under the control of the alternative sigma factor RpoN ( 54 ) (13,14). Transcription from RpoN-dependent promoters requires an activator to stimulate isomerization of a closed complex between 54 -RNA polymerase holoenzyme and the promoter to an open complex that is competent to initiate transcription (15).…”

mentioning

confidence: 99%

A Mannose Family Phosphotransferase System Permease and Associated Enzymes Are Required for Utilization of Fructoselysine and Glucoselysine in Salmonella enterica Serovar Typhimurium

et al. 2015

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Salmonella enteric serovar Typhimurium, a major cause of food-borne illness, is capable of using a variety of carbon and nitrogen sources. Fructoselysine and glucoselysine are Maillard reaction products formed by the reaction of glucose or fructose, respectively, with the -amine group of lysine. We report here that S. Typhimurium utilizes fructoselysine and glucoselysine as carbon and nitrogen sources via a mannose family phosphotransferase (PTS) encoded by gfrABCD (glucoselysine/fructoselysine PTS components EIIA, EIIB, EIIC, and EIID; locus numbers STM14_5449 to STM14_5454 in S. Typhimurium 14028s). Genes coding for two predicted deglycases within the gfr operon, gfrE and gfrF, were required for growth with glucoselysine and fructoselysine, respectively. GfrF demonstrated fructoselysine-6-phosphate deglycase activity in a coupled enzyme assay. The biochemical and genetic analyses were consistent with a pathway in which fructoselysine and glucoselysine are phosphorylated at the C-6 position of the sugar by the GfrABCD PTS as they are transported across the membrane. The resulting fructoselysine-6-phosphate and glucoselysine-6-phosphate subsequently are cleaved by GfrF and GfrE to form lysine and glucose-6-phosphate or fructose-6-phosphate. Interestingly, although S. Typhimurium can use lysine derived from fructoselysine or glucoselysine as a sole nitrogen source, it cannot use exogenous lysine as a nitrogen source to support growth. Expression of gfrABCDEF was dependent on the alternative sigma factor RpoN ( 54 ) and an RpoN-dependent LevR-like activator, which we designated GfrR. IMPORTANCESalmonella physiology has been studied intensively, but there is much we do not know regarding the repertoire of nutrients these bacteria are able to use for growth. This study shows that a previously uncharacterized PTS and associated enzymes function together to transport and catabolize fructoselysine and glucoselysine. Knowledge of the range of nutrients that Salmonella utilizes is important, as it could lead to the development of new strategies for reducing the load of Salmonella in food animals, thereby mitigating its entry into the human food supply. Salmonella enterica serovar Typhimurium is one of the leading causes of food-borne illness. Salmonella causes 11% of all infections caused by bacterial food-borne pathogens in the United States and is responsible for an estimated 1 million cases of salmonellosis in the United States each year, which result in approximately 19,000 hospitalizations and 400 deaths (1). S. Typhimurium causes gastroenteritis in humans but is capable of colonizing a wide range of animals with few or no disease symptoms. S. Typhimurium utilizes a broad array of carbon and nitrogen sources (2), which may contribute to the wide host range of this bacterium. Chadhuri and coworkers found that genes encoding enzymes in a variety of catabolic processes appear to be important for S. Typhimurium colonization of the chicken, pig, and calf (3). Among those catabolic genes, some encoded phosphoenolp...

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Regulation of CRISPR‐Cas Expression and Function

Smith

Campa

Fineran

2022

Crispr

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Use of a promiscuous, constitutively-active bacterial enhancer-binding protein to define the σ54 (RpoN) regulon of Salmonella Typhimurium LT2

Cited by 33 publications

References 71 publications

Genome-scale mapping reveals complex regulatory activities of RpoN inYersinia pseudotuberculosis

Genome-scale mapping reveals complex regulatory activities of RpoN inYersinia pseudotuberculosis

A Mannose Family Phosphotransferase System Permease and Associated Enzymes Are Required for Utilization of Fructoselysine and Glucoselysine in Salmonella enterica Serovar Typhimurium

Regulation of CRISPR‐Cas Expression and Function

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