The dual role of DksA protein in the regulation of<i>Escherichia coli</i>pArgX promoter

Łyżeń, Robert; Maitra, Amarnath; Milewska, Klaudia; Kochanowska-Łyżen, Maja; Hernandez, V. James; Szalewska-Pałasz, Agnieszka

doi:10.1093/nar/gkw912

Cited by 20 publications

(15 citation statements)

References 42 publications

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“…In fact, a 50% loss of promoter activity is observed at ~400 µM of (p)ppGpp and the hns transcription declines as much as 5–10% for higher (p)ppGpp concentrations. These amounts of (p)ppGpp are very close to those used in other in vitro studies [ 11 , 52 , 53 ] and consistent with the value (~0.9–1 mM) measured in vivo during the stringent response [ 42 , 54 ].…”

Section: Discussionsupporting

confidence: 90%

The hns Gene of Escherichia coli Is Transcriptionally Down-Regulated by (p)ppGpp

et al. 2020

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Second messenger nucleotides, such as guanosine penta- or tetra-phosphate, commonly referred to as (p)ppGpp, are powerful signaling molecules, used by all bacteria to fine-tune cellular metabolism in response to nutrient availability. Indeed, under nutritional starvation, accumulation of (p)ppGpp reduces cell growth, inhibits stable RNAs synthesis, and selectively up- or down- regulates the expression of a large number of genes. Here, we show that the E. colihns promoter responds to intracellular level of (p)ppGpp. hns encodes the DNA binding protein H-NS, one of the major components of bacterial nucleoid. Currently, H-NS is viewed as a global regulator of transcription in an environment-dependent mode. Combining results from relA (ppGpp synthetase) and spoT (ppGpp synthetase/hydrolase) null mutants with those from an inducible plasmid encoded RelA system, we have found that hns expression is inversely correlated with the intracellular concentration of (p)ppGpp, particularly in exponential phase of growth. Furthermore, we have reproduced in an in vitro system the observed in vivo (p)ppGpp-mediated transcriptional repression of hns promoter. Electrophoretic mobility shift assays clearly demonstrated that this unusual nucleotide negatively affects the stability of RNA polymerase-hns promoter complex. Hence, these findings demonstrate that the hns promoter is subjected to an RNA polymerase-mediated down-regulation by increased intracellular levels of (p)ppGpp.

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Section: Discussionsupporting

confidence: 90%

The hns Gene of Escherichia coli Is Transcriptionally Down-Regulated by (p)ppGpp

et al. 2020

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“…In accordance with this, we identified several promoter sequences highly similar to host promoters (both Salmonella spp. and Cronobacter spp., Supplementary Material) and a DksA C4-type domain-containing protein that phage S144 might use to direct the RNA polymerase to its own specific promoters [28,29]. Likewise, during translation, S144 exploits the host' tRNA pool, since no tRNA synthesis genes has been detected in its genome and the predicted compatibility of phage codon usage with the hosts' tRNA pools.…”

Section: Discussionmentioning

confidence: 99%

“…Several promoters precede the lysis cassette (see below ORFs 34-37) and the clusters A and B, in the same directions as the ORFs (Figure 2, Supplementary material), indicating that these clusters form also transcriptional operons. While the early promoters may be solely recognized by the host transcription machinery, later expressed genes may be controlled by ORF38 (cluster C) encoding a DksA C4-type domain-containing protein, known as an activator of transcription initiation [28,29]. The translation also relies on the host tRNAs pool, since no tRNA synthesis genes have been identified in S144 genome.…”

Section: Product Functional Category Clustermentioning

confidence: 99%

Phage S144, a New Polyvalent Phage Infecting Salmonella spp. and Cronobacter sakazakii

Gambino

Sørensen

Ahern

et al. 2020

IJMS

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Phages are generally considered species- or even strain-specific, yet polyvalent phages are able to infect bacteria from different genera. Here, we characterize the novel polyvalent phage S144, a member of the Loughboroughvirus genus. By screening 211 Enterobacteriaceae strains, we found that phage S144 forms plaques on specific serovars of Salmonella enterica subsp. enterica and on Cronobacter sakazakii. Analysis of phage resistant mutants suggests that the O-antigen of lipopolysaccharide is the phage receptor in both bacterial genera. The S144 genome consists of 53,628 bp and encodes 80 open reading frames (ORFs), but no tRNA genes. In total, 32 ORFs coding for structural proteins were confirmed by ESI-MS/MS analysis, whereas 45 gene products were functionally annotated within DNA metabolism, packaging, nucleotide biosynthesis and phage morphogenesis. Transmission electron microscopy showed that phage S144 is a myovirus, with a prolate head and short tail fibers. The putative S144 tail fiber structure is, overall, similar to the tail fiber of phage Mu and the C-terminus shows amino acid similarity to tail fibers of otherwise unrelated phages infecting Cronobacter. Since all phages in the Loughboroughvirus genus encode tail fibers similar to S144, we suggest that phages in this genus infect Cronobacter sakazakii and are polyvalent.

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“…In contrast, E. coli Δ relA Δ spoT mutant called (p)ppGpp 0 cells failed to sediment in a similar experimental condition and the adhesion phenotype is not affected upon overexpression of DksA ( Magnusson et al, 2007 ). In addition, transcription of the argX operon containing argX , hisR , leuT , and proM genes is activated by DksA but inhibited in the presence of (p)ppGpp and DksA ( Lyzen et al, 2016 ).…”

Section: Introductionmentioning

confidence: 99%

(p)ppGpp Metabolism and Antimicrobial Resistance in Bacterial Pathogens

Das

Bhadra

2020

Front. Microbiol.

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Single cell microorganisms including pathogens relentlessly face myriads of physicochemical stresses in their living environment. In order to survive and multiply under such unfavorable conditions, microbes have evolved with complex genetic networks, which allow them to sense and respond against these stresses. Stringent response is one such adaptive mechanism where bacteria can survive under nutrient starvation and other related stresses. The effector molecules for the stringent response are guanosine-5'-triphosphate 3'-diphosphate (pppGpp) and guanosine-3', 5'-bis(diphosphate) (ppGpp), together called (p)ppGpp. These effector molecules are now emerging as master regulators for several physiological processes of bacteria including virulence, persistence, and antimicrobial resistance. (p)ppGpp may work independently or along with its cofactor DksA to modulate the activities of its prime target RNA polymerase and other metabolic enzymes, which are involved in different biosynthetic pathways. Enzymes involved in (p)ppGpp metabolisms are ubiquitously present in bacteria and categorized them into three classes, i.e., canonical (p)ppGpp synthetase (RelA), (p)ppGpp hydrolase/synthetase (SpoT/Rel/RSH), and small alarmone synthetases (SAS). While RelA gets activated in response to amino acid starvation, enzymes belonging to SpoT/Rel/RSH and SAS family can synthesize (p)ppGpp in response to glucose starvation and several other stress conditions. In this review, we will discuss about the current status of the following aspects: (i) diversity of (p)ppGpp biosynthetic enzymes among different bacterial species including enteropathogens, (ii) signals that modulate the activity of (p)ppGpp synthetase and hydrolase, (iii) effect of (p)ppGpp in the production of antibiotics, and (iv) role of (p)ppGpp in the emergence of antibiotic resistant pathogens. Emphasis has been given to the cholera pathogen Vibrio cholerae due to its sophisticated and complex (p)ppGpp metabolic pathways, rapid mutational rate, and acquisition of antimicrobial resistance determinants through horizontal gene transfer. Finally, we discuss the prospect of (p)ppGpp metabolic enzymes as potential targets for developing antibiotic adjuvants and tackling persistence of infections.

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The dual role of DksA protein in the regulation ofEscherichia colipArgX promoter

Cited by 20 publications

References 42 publications

The hns Gene of Escherichia coli Is Transcriptionally Down-Regulated by (p)ppGpp

The hns Gene of Escherichia coli Is Transcriptionally Down-Regulated by (p)ppGpp

Phage S144, a New Polyvalent Phage Infecting Salmonella spp. and Cronobacter sakazakii

(p)ppGpp Metabolism and Antimicrobial Resistance in Bacterial Pathogens

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