Transcriptomic Analysis Reveals Key Roles of (p)ppGpp and DksA in Regulating Metabolism and Chemotaxis in Yersinia enterocolitica

Huang, Can; Li, Wenqian; Chen, Jing Yu

doi:10.3390/ijms24087612

Cited by 7 publications

(7 citation statements)

References 45 publications

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“…vinelandii , in other bacteria, carbon metabolism enzymes of the glycolytic pathway and the tricarboxylic acid (TCA) cycle have been reported as part of the DksA and (p)ppGpp regulon [ 23 ]. Also, in the Enterobacteriaceae , Yersinia enterocolitica , the response to DksA and RelA/SpoT proteins has been studied, revealing the downregulation of genes encoding enzymes of the TCA cycle [ 24 ].…”

Section: Discussionmentioning

confidence: 99%

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The stringent response regulates the poly-β-hydroxybutyrate (PHB) synthesis in Azotobacter vinelandii

Ortiz-Vasco,

Moreno,

Quintero-Navarro

et al. 2024

PLoS ONE

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The stringent response exerted by (p)ppGpp and RNA-polymerase binding protein DksA regulates gene expression in diverse bacterial species. To control gene expression (p)ppGpp, synthesized by enzymes RelA and SpoT, interacts with two sites within the RNA polymerase; site 1, located in the interphase between subunits β’ and ω (rpoZ), and site 2 located in the secondary channel that is dependent on DksA protein. In Escherichia coli, inactivation of dksA results in a reduced sigma factor RpoS expression. In Azotobacter vinelandii the synthesis of polyhydroxybutyrate (PHB) is under RpoS regulation. In this study, we found that the inactivation of relA or dksA, but not rpoZ, resulted in a negative effect on PHB synthesis. We also found that the dksA, but not the relA mutation reduced both rpoS transcription and RpoS protein levels, implying that (p)ppGpp and DksA control PHB synthesis through different mechanisms. Interestingly, despite expressing rpoS from a constitutive promoter in the dksA mutant, PHB synthesis was not restored to wild type levels. A transcriptomic analysis in the dksA mutant, revealed downregulation of genes encoding enzymes needed for the synthesis of acetyl-CoA, the precursor substrate for PHB synthesis. Together, these data indicate that DksA is required for optimal expression of RpoS which in turn activates transcription of genes for PHB synthesis. Additionally, DksA is required for optimal transcription of genes responsible for the synthesis of precursors for PHB synthesis.

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Section: Discussionmentioning

confidence: 99%

“…More recent transcriptomic analysis revealed upregulation of genes coding for ribosomal proteins and ribosome assembly factors in E . coli and Yersinia enterocolitica [ 5 , 24 ]. This study revealed that DksA functions as a repressor of ribosomal synthesis genes in A .…”

Section: Discussionmentioning

confidence: 99%

The stringent response regulates the poly-β-hydroxybutyrate (PHB) synthesis in Azotobacter vinelandii

Ortiz-Vasco,

Moreno,

Quintero-Navarro

et al. 2024

PLoS ONE

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“…The flgA gene is responsible for assembling the basal body of the flagella, and the process requires a substantial amount of energy. The energy requirement of flagella in bacteria is influenced by the proton motive force (PMF) generated by the electron transport chain (ETC) [43]. As protons fall back into the cell via the motor protein complex in the flagellar basal body, rotational energy drives flagellar movement.…”

Section: Discussionmentioning

confidence: 99%

“…However, nutrient starvation can hinder flagellar movement by limiting the availability of ATP and proton motive force, thereby impairing bacterial motility and navigation towards nutrients. Since flagella synthesis is an energy-intensive process [43], the CBD-resistant strains possibly could not operate in the least without any form of energy. In addition, while the CBD-susceptible strains might have utilized CBD as an energy source, the CBD-resistant strains did not have any room for CBD utility.…”

Section: Discussionmentioning

confidence: 99%

Prolonged CBD Pressure Mediates Higher Expression of flgA in <em>Salmonella</em> typhimurium

Ibrahim,

Mathias,

Johnson

et al. 2024

Preprint

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Salmonella Typhimurium is a typical Gram-Negative bacterium associated with food-borne illness threatening public health. This pathogen is reported to have caused millions of infections and thousands of hospitalizations yearly in the United States alone. Salmonella Typhimurium has a sophisticated array of virulent factors, including its flagella, which contributes significantly to its pathogenicity. Cannabidiol (CBD), the non-psychoactive component of the cannabis plant, has attracted the interest of many researchers recently because of its antimicrobial properties. With the growing interest in exploring CBD’s antimicrobial properties, we, in this study, have delved into unravelling how prolonged exposure of Salmonella Typhimurium to CBD influences the expression of the flgA gene. We hypothesized that the exposure of Salmonella Typhimurium to CBD may result in flgA upregulation, causing the bacteria to withstand various stresses and potentially enhance its survival rates and pathogenicity. We have employed several assays, such as mRNA expression, motility assays, pH induction assays, nutrient starvation interventions, and biofilm analysis, to explore the influence of CBD on the pathophysiology of Salmonella Typhimurium. Our findings reveal that CBD-resistant strains exhibit enhanced resilience to extreme pH levels and motility and survive poorly under nutrient starvation, with more robust biofilm formation compared to the susceptible strains. The results contribute to the broader comprehension of CBD resistance mechanisms in bacteria. This work provides insight into the potential therapeutic interventions for controlling CBD-resistant bacterial infections. This study also underscores the essence of exploring novel alternative antimicrobial agents to tackle the ever-persistence of bacterial antibiotic resistance.

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“…We used LEfSE analysis to find species that differed significantly in abundance between groups and to discuss the results. The Yersinia within the Yersiniaceae can cause sepsis in humans and animals ( Huang et al, 2023 ). The results of the study showed a significant increase in Yersiniaceae after infection with IHNV at 12–13°C.…”

Section: Discussionmentioning

confidence: 99%

Metagenomic and metabolomic analysis of changes in intestinal contents of rainbow trout (Oncorhynchus mykiss) infected with infectious hematopoietic necrosis virus at different culture water temperatures

Hai,

Wang,

Kang

et al. 2023

Front. Microbiol.

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Infectious hematopoietic necrosis (IHN) is a major disease that limits the culture of rainbow trout. In practical production, it has been found that the temperature of the culture water is a crucial factor affecting its mortality. Currently, little is known about how temperature affects the immune response of rainbow trout gut microbiota and metabolites to IHNV. In this study, our main objective is to analyze the changes in gut microorganisms of rainbow trout (juvenile fish with a consistent genetic background) after 14 days of infection with IHNV (5 × 105 pfu/fish) at 12–13°C (C: injected with saline, A: injected with IHNV) and 16–17°C (D: injected with saline, B: injected with IHNV) using metagenomic and metabolomic analyses, and to screen for probiotics that are effective against IHNV. The results showed that infection with IHNV at 12–13°C caused Eukaryote loss. Compared to Group C, Group A showed a significant increase in harmful pathogens, such as Yersiniaceae, and a significant alteration of 4,087 gut metabolites. Compared to group D, group B showed a significant increase in the abundance of Streptococcaceae and Lactococcus lactis, along with significant changes in 4,259 intestinal metabolites. Compared with their respective groups, the levels of two immune-related metabolites, 1-Octadecanoyl-glycero-3-phosphoethanolamine and L-Glutamate, were significantly upregulated in groups A and B. Compared to group B, Group A showed significantly higher pathogenic bacteria including Aeromonas, Pseudomonas, and Yersiniaceae, while group B showed a significant increase in Streptococcaceae and Lactococcus lactis. Additionally, there were 4,018 significantly different metabolites between the two groups. Interestingly, 1-Octadecanoyl-sn-glycero-3-phosphoethanolamine and L-Glutamate were significantly higher in group A than in group B. Some of the different metabolites in C vs. A are correlated with Fomitopsis pinicola, while in D vs. B they were correlated with Lactococcus raffinolactis, and in A vs. B they were correlated with Hypsizygus marmoreus. This study exposed how rainbow trout gut microbiota and metabolites respond to IHNV at different temperatures, and screens beneficial bacteria with potential resistance to IHN, providing new insights and scientific basis for the prevention and treatment of IHN.

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Transcriptomic Analysis Reveals Key Roles of (p)ppGpp and DksA in Regulating Metabolism and Chemotaxis in Yersinia enterocolitica

Cited by 7 publications

References 45 publications

The stringent response regulates the poly-β-hydroxybutyrate (PHB) synthesis in Azotobacter vinelandii

The stringent response regulates the poly-β-hydroxybutyrate (PHB) synthesis in Azotobacter vinelandii

Prolonged CBD Pressure Mediates Higher Expression of flgA in <em>Salmonella</em> typhimurium

Metagenomic and metabolomic analysis of changes in intestinal contents of rainbow trout (Oncorhynchus mykiss) infected with infectious hematopoietic necrosis virus at different culture water temperatures

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