Fine-tuning of amino sugar homeostasis by EIIA(Ntr) in Salmonella Typhimurium

Multiple regulatory inputs including cell envelope stress orchestrate expression of the Escherichia coli rpoN operon

The rpoN operon, an important regulatory hub in Enterobacteriaceae, includes rpoN encoding sigma factor σ54, hpf involved in ribosome hibernation, rapZ regulating glucosamine-6-phosphate levels, and two genes encoding proteins of the nitrogen-related phosphotransferase system. Little is known about regulatory mechanisms controlling the abundance of these proteins. This study employs transposon mutagenesis and chemical screens to dissect the complex expression of the rpoN operon. We find that envelope stress conditions trigger read-through transcription into the rpoN operon from a promoter located upstream of the preceding lptA-lptB locus. This promoter is controlled by the envelope stress sigma factor E and response regulator PhoP is required for its full response to a subset of stress signals. σE also stimulates ptsN-rapZ-npr expression using an element downstream of rpoN, presumably by interfering with mRNA processing by RNase E. Additionally, we identify a novel promoter in the 3' end of rpoN that directs transcription of the distal genes in response to ethanol. Finally, we show that translation of hpf and ptsN is individually regulated by the RNA chaperone Hfq, perhaps involving small RNAs. Collectively, our work demonstrates that the rpoN operon is subject to complex regulation, integrating signals related to envelope stress and carbon source quality.

Purification mechanism of microbial metabolism in kitchen-oil wastewater enhanced by cationic vacancies on γ-Al2O3

The use of catalyst materials to mediate the enhancement of microbial degradation in wastewater is a new economic and energy saving breakthrough in water treatment technology. In this study, γ-Al2O3, which is commonly used as catalyst/carrier, is used as biological filler to treat kitchen-oil wastewater with low biodegradability, and the COD removal rate is about 50 %. It is found that the complexation of cationic vacancies on Al2O3 surface with extracellular polymeric substance (EPS) secreted by microorganisms in wastewater lead to the polarization of electron distribution on biofilm. The efficient degrading bacteria are enriched on reaction interface and obtain electrons to maintain electron dynamic balance by enhancing the transmembrane metabolism of pollutants. The aluminum vacancies on Al2O3 surface accelerate the microbial degradation of pollutants. The cationic vacancies in the structure of catalyst accelerate the acquisition of exogenous electrons by microorganisms without the addition of external energy, which provides a new idea for catalytic fillers to enhance wastewater degradation.

The phosphotransferase system gene ptsH affects persister formation in Klebsiella pneumoniae by regulating cyclic adenosine monophosphate levels

Klebsiella pneumoniae is one of the most common opportunistic pathogens causing hospital- and community-acquired infections. Antibiotic resistance in K. pneumoniae has emerged as a major clinical and public health threat. Persisters are specific antibiotic-tolerant bacterial cells. Studies on the mechanism underlying their formation mechanism and growth status are scarce. Therefore, it is urgent to explore the key genes and signalling pathways involved in the formation and recovery process of K. pneumoniae persisters to enhance the understanding and develop relevant treatment strategies. In this study, we treated K. pneumoniae with a lethal concentration of levofloxacin. It resulted in a distinct plateau of surviving levofloxacin-tolerant persisters. Subsequently, we obtained bacterial samples at five different time points during the formation and recovery of K. pneumoniae persisters to perform transcriptome analysis. ptsH gene was observed to be upregulated during the formation of persisters, and down-regulated during the recovery of the persisters. Further, we used CRISPR-Cas9 to construct ΔptsH, the ptsH-knockout K. pneumoniae strain, and to investigate the effect of ptsH on the persister formation. We observed that ptsH can promote the formation of persisters, reduce accumulation of reactive oxygen species, and enhance antioxidant capacity by reducing cyclic adenosine monophosphate (cAMP) levels. To the best of our knowledge, this is the first study to report that ptsH plays a vital role in forming K. pneumoniae persisters. This study provided important insights to further explore the mechanism underlying the formation of K. pneumoniae persisters and provided a potential target for treating infection with K. pneumoniae persisters.

Bacterial metabolism and susceptibility to cell wall-active antibiotics

Bacterial infections are increasingly resistant to antimicrobial therapy. Intense research focus has thus been placed on identifying the mechanisms that bacteria use to resist killing or growth inhibition by antibiotics and the ways in which bacteria share these traits with one another. This work has led to the advancement of new drugs, combination therapy regimens, and a deeper appreciation for the adaptability seen in microorganisms. However, while the primary mechanisms of action of most antibiotics are well understood, the more subtle contributions of bacterial metabolic state to repairing or preventing damage caused by antimicrobials (thereby promoting survival) are still understudied. Here, we review a modern viewpoint on a classical system: examining bacterial metabolism's connection to antibiotic susceptibility. We dive into the relationship between metabolism and antibiotic efficacy through the lens of growth rate, energy state, resource allocation, and the infection environment, focusing on cell wall-active antibiotics.

Phyllosphere microbial community of cigar tobacco and its corresponding metabolites

Cigar is made of a typical fermented tobacco where the microbiota inhabits within an alkaline environment. Our current understanding on cigar fermentation is far from thorough. This work employed both high-throughput sequencing and chromatography-mass spectrometric technologies to provide new scientific reference for this specific fermented system. Typical cigar samples from different regions (the Caribbeans, South America, East Asia, and Southeast Asia) were investigated. The results show that Firmicutes, Actinobacteria, Proteobacteria, Ascomycota, and Basidiomycota were the predominant phyla in the cigar samples. Rather than the fungal community, it was the bacterial community structures that played vital roles to differentiate the cigar from different regions: Staphylococcus was the dominant genus in the Americas; Bacillus was the dominant genus in Southeast Asia; while in East Asia, there was no dominant genus. Such differences in community structure then affected the microflora metabolism. The correlation between microbiota and metabolites revealed that Aspergillaceae, Cercospora, and Staphylococcus were significantly correlated with sclareolide; Bacillus were positively associated with isophorone. Alcaligenaceae was significantly and positively correlated with L-nicotine and hexadecanoic acid, methyl ester. GRAPHICAL ABSTRACT.

The role of nitrogen-responsive regulators in controlling inorganic polyphosphate synthesis in Escherichia coli

Inorganic polyphosphate (polyP) is synthesized by bacteria under stressful environmental conditions and acts by a variety of mechanisms to promote cell survival. While the kinase that synthesizes polyP (PPK, encoded by the ppk gene) is well known, ppk transcription is not activated by environmental stress and little is understood about how environmental stress signals lead to polyP accumulation. Previous work has shown that the transcriptional regulators DksA, RpoN (σ54) and RpoE (σ24) positively regulate polyP production, but not ppk transcription, in Escherichia coli. In this work, we examine the role of the alternative sigma factor RpoN and nitrogen starvation stress response pathways in controlling polyP synthesis. We show that the RpoN enhancer binding proteins GlnG and GlrR impact polyP production, and uncover a new role for the nitrogen phosphotransferase regulator PtsN (EIIANtr) as a positive regulator of polyP production, acting upstream of DksA, downstream of RpoN and apparently independently of RpoE. However, neither these regulatory proteins nor common nitrogen metabolites appear to act directly on PPK, and the precise mechanism(s) by which polyP production is modulated after stress remain(s) unclear. Unexpectedly, we also found that the genes that impact polyP production vary depending on the composition of the rich media in which the cells were grown before exposure to polyP-inducing stress. These results constitute progress towards deciphering the regulatory networks driving polyP production under stress, and highlight the remarkable complexity of this regulation and its connections to a broad range of stress-sensing pathways.

Performance and enhancement mechanism of redox mediator for nitrate removal in immobilized bioreactor with preponderant microbes

The acceleration of nitrate removal in wastewater treatment by redox mediator (RM) is greatly weakened due to wash-out loss and mass transfer resistance (low hydrophilia) of RM during operation. In this study, an RM reactor with the fixed 1-Amino-4-hydroxyanthraquinone (AHAQ) and three core strains was established and achieved high nitrate removal efficiency (NRE) under low carbon to nitrogen ratio (C/N) and short hydraulic retention time (HRT) conditions, with the maximum efficiency of 99.41% (14.00 mg L-1 h-1) and average improvement by 11.97% (1.41 mg L-1 h-1). This acceleration led to more proportion of carbon consumption by denitrifying bacteria and improved their competitiveness against others in carbon deficiency, although resulting in nitrite accumulation (NIA) in lower C/N. The RM reactor induced the decorrelation tendencies between NRE and active extracellular organics and more sensitive denitrification toward C/N, which favored the stability of effluent organics and biological activities. The increase of oxidative phosphorylation and ubiquinone and other terpenoid-quinone biosynthesis pathway suggested electron transport activity was potentially enhanced by AHAQ. Although the lower C/N deteriorated the reactor NRE, the abundances of amino acids-, fatty acids- and carbohydrate-related metabolisms (45% of the total up-regulating pathways) were enhanced to utilize carbon source effectively. Meanwhile, the enhanced phosphotransferase system facilitated the balance between carbon and nitrogen metabolism. These indicated the changes in biological strategy to grow better and resist the adverse condition. This study highlighted the superior NRE by AHAQ in an immobilized reactor with core strains and more importantly, extended the RM application in wastewater treatment.

Atomic-Level Investigation of Reactant Recognition Mechanism and Thermodynamic Property in Glucosamine 6-Phosphate Deaminase Catalysis

Glucosamine 6-phosphate deaminase (NagB) influences the direction of N-acetylglucosamine (GlcNAc) metabolism, facilitating the conversion of D-glucosamine 6-phosphate (GlcN6P) to D-fructose 6-phosphate (Fru6P) with the release of ammonia. Here, extensive molecular dynamics simulations combined with various techniques were performed to study the recognition and delivery process of GlcN6P by SmuNagB, due to its guidance of subsequent enzymatic reaction. The key residues Lys194, His130, Arg127, Thr38, and Ser37 stabilize GlcN6P in the active site by hydrogen bond interactions, therein electrostatic and polar solvent effects provide the primary traction. Four delivery channels were identified, with GlcN6P most likely to enter the active site of NagB through a “door” comprising residues 6–10, 122–136, and 222–233. The corresponding mechanism and thermodynamic properties were investigated. An exothermic recognition and delivery process were detected, accompanied by the flipping of GlcN6P and changes in key direct and indirect hydrogen bond interactions, which provide the driving force for the chemical reaction to occur. Furthermore, “the lid motif” was identified that remain open in alkaline condition with different extent of opening at each stage of transfer that induced GlcN6P to move the active site of NagB. The work will assist in the elucidation of the catalytic mechanism of action of NagB, allowing inhibitors to be designed with superior dynamic behavior.

A Nitrogen Metabolic Enzyme Provides Salmonella Fitness Advantage by Promoting Utilization of Microbiota-Derived Carbon Source

Microbes support their growth in vertebrate hosts by exploiting a large variety of dietary components as nutrients, which determines the composition of gut microbiota. A pathogen Salmonella expands by utilizing 1,2-propanediol, a microbiota-fermented product, during mucosal inflammation. However, it remains largely unknown how the pathogen decides which nutrient to consume from the complex mixture in the gut. Here, we show that Salmonella enterica serovar Typhimurium utilizes 1,2-propanediol by EIIANtr (a nitrogen-metabolic PTS component implicated in virulence)-mediated regulation of the pdu operon, thereby expanding in the murine intestine. Propionyl-CoA, a metabolic intermediate produced by 1,2-propanediol catabolism, elevates EIIANtr protein amounts, entailing positive feedback, thereby boosting the 1,2-propanediol-utilization process. EIIANtr promotes pdu expression by enhancing glutathione synthesis. CRP (cAMP receptor protein) induces pdu genes by increasing EIIANtr expression in response to glucose availability. Notably, EIIANtr-mediated 1,2-propanediol-utilization conferred a growth benefit even under high glucose conditions which reduces CRP activity. The EIIANtr-mediated activation is likely conserved in pathogenic enterobacteria including Escherichia coli. Collectively, our findings suggest that Salmonella promotes its fitness by precisely modulating the utilization system for microbiota-derived carbon source. They also suggest that Salmonella may integrate signals, processed via EIIANtr, into its metabolic program as well as virulence circuit.

Comparative transcriptomics analysis of Streptococcus mutans with disruption of LuxS/AI-2 quorum sensing and recovery of methyl cycle

OBJECTIVE

The LuxS/AI-2 quorum sensing (QS) system has critical roles in Streptococcus mutans cariogenicity. Whereas the molecular and cellular mechanisms of the LuxS/AI-2 QS system are not thoroughly understood. Given that LuxS has roles in QS and methyl cycle, its mutation can cause QS deficiency and methyl cycle disruption. The aim of this study was to investigate effects of the LuxS/AI-2 QS system on gene expression in Streptococcus mutans when methyl cycle was recovered with exogenous sahH gene.

METHODS

Our previous study introduced the exogenous sahH gene from Pseudomonas aeruginosa into an S. mutans luxS-null strain to restore the disrupted methyl cycle, and this produced the solely the LuxS/AI-2 QS system deficient strain. Here, we analyzed the transcriptomics of this strain to get insights into the molecular mechanisms of the LuxS/AI-2 QS system applying RNA-seq.

RESULTS

With recovery of methyl cycle, 84 genes didn't change in expression trends in S. mutans luxS-null strain. These genes mainly encode the ABC transporters, sugar transporter EII and enzymes of carbohydrate metabolism, and are rich in the Phosphotransferase system, Fructose and mannose metabolism, Amino sugar and nucleotide sugar metabolism, Galactose metabolism, Glycolysis/Gluconeogenesis, RNA degradation, Lysine biosynthesis, and Glycine, serine and threonine metabolism.

CONCLUSIONS

The LuxS/AI-2 QS system may mainly affect ABC transporters and carbohydrate transport, transformation and metabolism via EII subunits and enzymes to influence virulence-associated traits without effects of methyl cycle inStreptococcus mutans.

Resource sharing between central metabolism and cell envelope synthesis

Synthesis of the bacterial cell envelope requires a regulated partitioning of resources from central metabolism. Here, we consider the key metabolic junctions that provide the precursors needed to assemble the cell envelope. Peptidoglycan synthesis requires redirection of a glycolytic intermediate, fructose-6-phosphate, into aminosugar biosynthesis by the highly regulated branchpoint enzyme GlmS. MurA directs the downstream product, UDP-GlcNAc, specifically into peptidoglycan synthesis. Other shared resources required for cell envelope synthesis include the isoprenoid carrier lipid undecaprenyl phosphate and amino acids required for peptidoglycan cross-bridges. Assembly of the envelope requires a sharing of limited resources between competing cellular pathways and may additionally benefit from scavenging of metabolites released from neighboring cells or the formation of symbiotic relationships with a host.

Global control of bacterial nitrogen and carbon metabolism by a PTSNtr-regulated switch

The nitrogen-related phosphotransferase system (PTS^Ntr) of Rhizobium leguminosarum bv. viciae 3841 transfers phosphate from PEP via PtsP and NPr to two output regulators, ManX and PtsN. ManX controls central carbon metabolism via the tricarboxylic acid (TCA) cycle, while PtsN controls nitrogen uptake, exopolysaccharide production, and potassium homeostasis, each of which is critical for cellular adaptation and survival. Cellular nitrogen status modulates phosphorylation when glutamine, an abundant amino acid when nitrogen is available, binds to the GAF sensory domain of PtsP, preventing PtsP phosphorylation and subsequent modification of ManX and PtsN. Under nitrogen-rich, carbon-limiting conditions, unphosphorylated ManX stimulates the TCA cycle and carbon oxidation, while unphosphorylated PtsN stimulates potassium uptake. The effects are reversed with the phosphorylation of ManX and PtsN, occurring under nitrogen-limiting, carbon-rich conditions; phosphorylated PtsN triggers uptake and nitrogen metabolism, the TCA cycle and carbon oxidation are decreased, while carbon-storage polymers such as surface polysaccharide are increased. Deleting the GAF domain from PtsP makes cells "blind" to the cellular nitrogen status. PTS^Ntr constitutes a switch through which carbon and nitrogen metabolism are rapidly, and reversibly, regulated by protein:protein interactions. PTS^Ntr is widely conserved in proteobacteria, highlighting its global importance.

Small RNA-binding protein RapZ mediates cell envelope precursor sensing and signaling in Escherichia coli

The RNA-binding protein RapZ cooperates with small RNAs (sRNAs) GlmY and GlmZ to regulate the glmS mRNA in Escherichia coli. Enzyme GlmS synthesizes glucosamine-6-phosphate (GlcN6P), initiating cell envelope biosynthesis. GlmZ activates glmS expression by base-pairing. When GlcN6P is ample, GlmZ is bound by RapZ and degraded through ribonuclease recruitment. Upon GlcN6P depletion, the decoy sRNA GlmY accumulates through a previously unknown mechanism and sequesters RapZ, suppressing GlmZ decay. This circuit ensures GlcN6P homeostasis and thereby envelope integrity. In this work, we identify RapZ as GlcN6P receptor. GlcN6P-free RapZ stimulates phosphorylation of the two-component system QseE/QseF by interaction, which in turn activates glmY expression. Elevated GlmY levels sequester RapZ into stable complexes, which prevents GlmZ decay, promoting glmS expression. Binding of GlmY also prevents RapZ from activating QseE/QseF, generating a negative feedback loop limiting the response. When GlcN6P is replenished, GlmY is released from RapZ and rapidly degraded. We reveal a multifunctional sRNA-binding protein that dynamically engages into higher-order complexes for metabolite signaling.

Regulation of Iron Uptake by Fine-Tuning the Iron Responsiveness of the Iron Sensor Fur

Iron is one of most abundant environmental metal ions but is highly limited in organisms. It is an important metal ion as it facilitates various biological processes, including catalysis of metabolic enzymes and DNA biogenesis. In bacteria, the ferric uptake regulator (Fur) protein controls iron uptake by regulating genes coding for iron transporters in response to iron concentration. This iron response is ascribed to Fur's intrinsic affinity for iron because its binding to iron dictates its regulatory function. However, we now report that the pathogen Salmonella achieves a proper response of Fur to changes in environmental iron concentrations via EIIA^Ntr (a nitrogen metabolic phosphotransferase system component). We establish that EIIA^Ntr increases expression of iron transporter-coding genes under low-iron conditions (i.e., nanomolar ranges) in a Fur-dependent manner, which promotes Salmonella growth under such conditions. EIIA^Ntr directly hampers Fur binding to DNA, thereby inducing expression of those genes. This regulation allows Salmonella to express Fur-regulated genes under low-iron conditions. Our findings reveal a potentially widespread control mechanism of bacterial iron uptake systems operating in response to iron availability.IMPORTANCE Iron is a fundamental metal ion for living organisms as it facilitates various biological processes. The ferric uptake regulator (Fur) protein controls iron homeostasis in various bacterial species. It is believed that Fur's iron-dependent regulatory action is sufficient for it to function as an iron sensor. However, we now establish that the bacterial pathogen Salmonella enables Fur to properly reflect changes in surrounding iron availability by fine-tuning its responsiveness to iron. This process requires a protein that hampers Fur DNA binding at low iron concentrations. In this way, Salmonella broadens the range of iron concentrations that Fur responds to. Our findings reveal a potentially widespread control mechanism of bacterial iron homeostasis.

Programmed Delay of a Virulence Circuit Promotes Salmonella Pathogenicity

Signal transduction systems dictate various cellular behaviors in response to environmental changes. To operate cellular programs appropriately, organisms have sophisticated regulatory factors to optimize the signal response. The PhoP/PhoQ master virulence regulatory system of the intracellular pathogen Salmonella enterica is activated inside acidic macrophage phagosomes. Here we report that Salmonella delays the activation of this system inside macrophages using an inhibitory protein, EIIA^Ntr (a component of the nitrogen-metabolic phosphotransferase system). We establish that EIIA^Ntr directly restrains PhoP binding to its target promoter, thereby negatively controlling the expression of PhoP-activated genes. PhoP furthers its activation by promoting Lon-mediated degradation of EIIA^Ntr at acidic pH. These results suggest that Salmonella ensures robust activation of its virulence system by suspending the activation of PhoP until a sufficient level of active PhoP is present to overcome the inhibitory effect of EIIA^Ntr Our findings reveal how a pathogen precisely and efficiently operates its virulence program during infection.IMPORTANCE To accomplish successful infection, pathogens must operate their virulence programs in a precise, time-sensitive, and coordinated manner. A major question is how pathogens control the timing of virulence gene expression during infection. Here we report that the intracellular pathogen Salmonella controls the timing and level of virulence gene expression by using an inhibitory protein, EIIA^Ntr A DNA binding master virulence regulator, PhoP, controls various virulence genes inside acidic phagosomes. Salmonella decreases EIIA^Ntr amounts at acidic pH in a Lon- and PhoP-dependent manner. This, in turn, promotes expression of the PhoP-activated virulence program because EIIA^Ntr hampers activation of PhoP-regulated genes by interfering with PhoP binding to DNA. EIIA^Ntr enables Salmonella to impede the activation of PhoP-regulated gene expression inside macrophages. Our findings suggest that Salmonella achieves programmed delay of virulence gene activation by adjusting levels of an inhibitory factor.

Retrospective application of transposon-directed insertion-site sequencing to investigate niche-specific virulence of Salmonella Typhimurium in cattle

Background

Salmonella enterica subspecies enterica is an animal and zoonotic pathogen of global importance. Cattle are a significant reservoir of human non-typhoidal salmonellosis and can suffer enteric and systemic disease owing to the ability of Salmonella to survive within the bovine lymphatic system and intestines. Contamination of food can occur due to the incorporation of contaminated peripheral lymph nodes or by direct contamination of carcasses with gut contents. It is essential to understand the mechanisms used by Salmonella to enter and persist within the bovine lymphatic system and how they differ from those required for intestinal colonization to minimize zoonotic infections.

Results

Transposon-directed insertion site sequencing (TraDIS) was applied to pools of mutants recovered from mesenteric lymph nodes (MLNs) draining the distal ileum of calves after oral inoculation with a library of 8550 random S. Typhimurium mini-Tn5Km2 mutants in pools of 475 mutants per calf. A total of 8315 mutants representing 2852 different genes were detected in MLNs and their in vivo fitness was calculated. Using the same improved algorithm for analysis of transposon-flanking sequences, the identity and phenotype of mutants recovered from the distal ileal mucosa of the same calves was also defined, enabling comparison with previously published data and of mutant phenotypes across the tissues. Phenotypes observed for the majority of mutants were highly significantly correlated in the two tissues. However, 32 genes were identified in which transposon insertions consistently resulted in differential fitness in the ileal wall and MLNs, suggesting niche-specific roles for these genes in pathogenesis. Defined null mutations affecting ptsN and spvC were confirmed to result in tissue-specific phenotypes in calves, thus validating the TraDIS dataset.

Conclusions

This validation of the role of thousands of Salmonella genes and identification of genes with niche-specific roles in a key target species will inform the design of control strategies for bovine salmonellosis and zoonotic infections, for which efficacious and cross-protective vaccines are currently lacking.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5319-0) contains supplementary material, which is available to authorized users.

Core non-coding RNAs of Piscirickettsia salmonis

Piscirickettsia salmonis, a fastidious Gram-negative intracellular facultative bacterium, is the causative agent o Piscirickettsiosis. P. salmonis has broad host range with a nearly worldwide distribution, causing significant mortality. The molecular regulatory mechanisms of P. salmonis pathogenesis are relatively unknown, mainly due to its difficult in vitro culture and genomic differences between genogroups. Bacterial non-coding RNAs (ncRNAs) are important post-transcriptional regulators of bacterial physiology and virulence that are predominantly transcribed from intergenic regions (trans-acting) or antisense strand of open reading frames (cis-acting). The repertoire of ncRNAs present in the genome of P. salmonis and its possible role in bacterial physiology and pathogenesis are unknown. Here, we predicted and analyzed the core ncRNAs of P. salmonis base on structure and correlate this prediction to RNA sequencing data. We identified a total of 69 ncRNA classes related to tRNAs, rRNA, thermoregulators, antitoxins, ribozymes, riboswitches, miRNAs and antisense-RNAs. Among these ncRNAs, 29 classes of ncRNAs are shared between all P. salmonis genomes, constituting the core ncRNAs of P. salmonis. The ncRNA core of P. salmonis could serve to develop diagnostic tools and explore the role of ncRNA in fish pathogenesis.

Proteome analysis of an Escherichia coli ptsN-null strain under different nitrogen regimes

The carbohydrate-uptake phosphorelay PTS system plays a key role in metabolic regulation in Bacteria controlling the utilization of secondary carbon sources. Some bacteria, such as Escherichia coli, encode a paralogous system named PTS^Ntr (nitrogen related PTS). PTS^Ntr is composed of EI^Ntr (ptsP), NPr (ptsO), and EIIA^Ntr (ptsN). These proteins act as a phosphorelay system from phosphoenolpyruvate to EI^Ntr, NPr and them to EIIA^Ntr. PTS^Ntr is not involved in carbohydrate uptake and it may be dedicated to performing regulatory functions. The phosphorylation state of EI^Ntr is regulated by allosteric binding of glutamine and 2-oxoglutarate, metabolites whose intracellular levels reflect the nitrogen status. Although PTS^Ntr is designated as having nitrogen-sensory properties, no major effect of this system on nitrogen regulation has been described in E. coli. Here we show that an E. coli ptsN deletion mutant has impaired growth in minimal medium. Proteome analysis of the ∆ptsN strain under different nitrogen regimes revealed no involvement in regulation of the canonical nitrogen regulatory (Ntr) system. The proteomic data support the conclusion that ptsN is required to balance the activities of the sigma factors RpoS and RpoD in such way that, in the absence of ptsN, RpoS-dependent genes are preferentially expressed.

SIGNIFICANCE

The nitrogen related PTS^Ntr phosphorelay system has been hypothesized to participate in the control of nitrogen metabolism. Here we used a proteomics approach to show that an Escherichia coli ptsN null strain, which misses the final module of PTS^Ntr phosphorelay, has no significant effects on nitrogen metabolism under different nitrogen regimes. We noted that ptsN is required for fitness under minimal medium and for the proper balance between RpoS and sigma 70 activities in such way that, in the absence of ptsN, RpoS-dependent genes are preferentially expressed.

Non-canonical activation of histidine kinase KdpD by phosphotransferase protein PtsN through interaction with the transmitter domain

The two-component system KdpD/KdpE governs K⁺ homeostasis by controlling synthesis of the high affinity K⁺ transporter KdpFABC. When sensing low environmental K⁺ concentrations, the dimeric kinase KdpD autophosphorylates in trans and transfers the phosphoryl-group to the response regulator KdpE, which subsequently activates kdpFABC transcription. In Escherichia coli, KdpD can also be activated by interaction with the non-phosphorylated form of the accessory protein PtsN. PtsN stimulates KdpD kinase activity thereby increasing phospho-KdpE levels. Here, we analyzed the interplay between KdpD/KdpE and PtsN. PtsN binds specifically to the catalytic DHp domain of KdpD, which is also contacted by KdpE. Accordingly, PtsN and KdpE compete for binding, providing a paradox. Low levels of non-phosphorylated PtsN stimulate, whereas high amounts reduce kdpFABC expression by blocking access of KdpE to KdpD. Ligand fishing experiments provided insight as they revealed ternary complex formation of PtsN/KdpD₂ /KdpE in vivo demonstrating that PtsN and KdpE bind different protomers in the KdpD dimer. PtsN may bind one protomer to stimulate phosphorylation of the second KdpD protomer, which then phosphorylates bound KdpE. Phosphorylation of PtsN prevents its incorporation in ternary complexes. Interaction with the conserved DHp domain enables PtsN to regulate additional kinases such as PhoR.

Enzyme IIANtr Regulates Salmonella Invasion Via 1,2-Propanediol And Propionate Catabolism

Many Proteobacteria possess a nitrogen-metabolic phosphotransferase system (PTS^Ntr) consisting of EI^Ntr, NPr, and EIIA^Ntr (encoded by ptsP, ptsO, and ptsN, respectively). The PTS^Ntr plays diverse regulatory roles, but the substrate phosphorylated by EIIA^Ntr and its primary functions have not yet been identified. To comprehensively understand the roles of PTS^Ntr in Salmonella Typhimurium, we compared the whole transcriptomes of wild-type and a ΔptsN mutant. Genome-wide RNA sequencing revealed that 3.5% of the annotated genes were up- or down-regulated by three-fold or more in the absence of EIIA^Ntr. The ΔptsN mutant significantly down-regulated the expression of genes involved in vitamin B₁₂ synthesis, 1,2-propanediol utilization, and propionate catabolism. Moreover, the invasiveness of the ΔptsN mutant increased about 5-fold when 1,2-propanediol or propionate was added, which was attributable to the increased stability of HilD, the transcriptional regulator of Salmonella pathogenicity island-1. Interestingly, an abundance of 1,2-propanediol or propionate promoted the production of EIIA^Ntr, suggesting the possibility of a positive feedback loop between EIIA^Ntr and two catabolic pathways. These results demonstrate that EIIA^Ntr is a key factor for the utilization of 1,2-propanediol and propionate as carbon and energy sources, and thereby modulates the invasiveness of Salmonella via 1,2-propanediol or propionate catabolism.

Sophisticated Regulation of Transcriptional Factors by the Bacterial Phosphoenolpyruvate: Sugar Phosphotransferase System

The phosphoenolpyruvate:sugar phosphotransferase system (PTS) is a carbohydrate transport and phosphorylation system present in bacteria of all different phyla and in archaea. It is usually composed of three proteins or protein complexes, enzyme I, HPr, and enzyme II, which are phosphorylated at histidine or cysteine residues. However, in many bacteria, HPr can also be phosphorylated at a serine residue. The PTS not only functions as a carbohydrate transporter but also regulates numerous cellular processes either by phosphorylating its target proteins or by interacting with them in a phosphorylation-dependent manner. The target proteins can be catabolic enzymes, transporters, and signal transduction proteins but are most frequently transcriptional regulators. In this review, we will describe how PTS components interact with or phosphorylate proteins to regulate directly or indirectly the activity of transcriptional repressors, activators, or antiterminators. We will briefly summarize the well-studied mechanism of carbon catabolite repression in firmicutes, where the transcriptional regulator catabolite control protein A needs to interact with seryl-phosphorylated HPr in order to be functional. We will present new results related to transcriptional activators and antiterminators containing specific PTS regulation domains, which are the phosphorylation targets for three different types of PTS components. Moreover, we will discuss how the phosphorylation level of the PTS components precisely regulates the activity of target transcriptional regulators or antiterminators, with or without PTS regulation domain, and how the availability of PTS substrates and thus the metabolic status of the cell are connected with various cellular processes, such as biofilm formation or virulence of certain pathogens.