Two-Component Signal Transduction Systems of Pathogenic Bacteria As Targets for Antimicrobial Therapy: An Overview

Human neutrophil defensin-1 binding increases histidine kinase activity of SaeS in Staphylococcus aureus

Human neutrophil defensin-1 (HNP-1) can specifically activate the SaeRS two-component system(TCS), which is essential for controlling virulence and immune evasion factors in Staphylococcus aureus. The reaction to HNP1 requires the transmembrane domain of SaeS (SaeS™), however the precise mechanism is yet unknown. In this work, we reconstructed the SaeS™ protein into bicelles and discovered that HNP1 can interact directly with SaeS™ using BiacoreT200, their binding significantly increases SaeS kinase activity and activated the SaeRS system subsequently. Staphylococcus aureus may exploit host-derived factors released by human immune cells to activate its two-component signal transduction system, thereby enhancing antimicrobial peptide resistance.

Evaluating the Link between Efflux Pump Expression and Motility Phenotypes in Pseudomonas aeruginosa Treated with Virulence Inhibitors

Antibiotic resistance continues to rise as a global health threat. Novel antivirulence strategies diminish the drive for evolutionary pressure but still hinder a pathogen's ability to infect a host. Treatment of the highly virulent Pseudomonas aeruginosa strain PA14 with virulence inhibitors (R-2 and R-6) elicited widely varying transcriptional profiles. Of interest, the expression of a family of resistance-nodulation-division (RND) efflux pumps implicated in the intrinsic drug resistance of P. aeruginosa was significantly altered by R-2 and R-6 treatment. While structurally similar, these inhibitors caused differential expression of various RND efflux pumps within the Mex family─the R-2 treatment stimulated the expression of mexEF-oprN, while the R-6 treatment led to increased mexAB-oprM expression. Further expansion into a small library of virulence inhibitors revealed chemical motifs that trigger increases in the level of RND efflux pump expression. Additionally, activation of these efflux pumps suggests a low accumulation of virulence inhibitors in WT PA14. Treatment of an efflux pump-deficient strain with R-2 or R-6 resulted in inhibition of several virulence factors; for example, R-2 was found to abolish swimming motility. Collectively, treatment with either R-2 or R-6 gives rise to a convoluted transcriptomic response confounded by the impact of efflux pump expression on the system. However, understanding the moieties that lead to high expression of the efflux pumps enables the further rational design of novel virulence inhibitors that do not cause RND efflux pump activation.

Physical communication pathways in bacteria: an extra layer to quorum sensing

Bacterial communication is essential for survival, adaptation, and collective behavior. While chemical signaling, such as quorum sensing, has been extensively studied, physical cues play a significant role in bacterial interactions. This review explores the diverse range of physical stimuli, including mechanical forces, electromagnetic fields, temperature, acoustic vibrations, and light that bacteria may experience with their environment and within a community. By integrating these diverse communication pathways, bacteria can coordinate their activities and adapt to changing environmental conditions. Furthermore, we discuss how these physical stimuli modulate bacterial growth, lifestyle, motility, and biofilm formation. By understanding the underlying mechanisms, we can develop innovative strategies to combat bacterial infections and optimize industrial processes.

Photoheterotrophic extracellular reduction of ferrihydrite activates diverse intracellular metabolic pathways in Rhodopseudomonas palustris for enhanced antibiotic degradation

Anoxygenic photosynthetic bacteria (APB) have been frequently detected as a photoautotrophic Fe-carbon cycling drivers in photic and anoxic environment. However, the potential capacity of these bacteria for photoheterotrophic extracellular reduction of iron-containing minerals and their impact on the transformation of organic pollutants remain currently unknown. This study investigated the capacity of R. palustris, a purple non-sulfur anoxygenic photosynthetic bacterium, to reduce ferrihydrite (Fh) and its correlation with sulfamethazine (SDZ) degradation were firstly investigated. The results revealed that R. palustris could undergo photoheterotrophic extracellular reduction of Fh to form goethite through direct contact, facilitating the formation of conductive bands and enter the interior of cells with a maximum Fe(II)/Fe(T) ratio of up to 39 % within 8 days which led to 13 % increase in assimilation rate of acetate carbon and 53.2 % increase in SDZ degradation rates, as compared with those by R. palustris alone. Moreover, the intermediates generated during the degradation of SDZ by R. palustris-Fh exhibited relatively lower developmental toxicity compared with the original SDZ molecule. The extracellular reduction of Fh significantly up-regulated the expression of genes related to photosynthetic metabolic enzymes, extracellular electron transporters, and extracellular degrading enzymes in R. palustris. This enhancement promoted the photoheterotrophic metabolism and extracellular secretion of photosensitive active compounds in R. palustris, thereby enhancing both the biodegradation and photosensitive degradation of SDZ.

Lasso peptides sviceucin and siamycin I exhibit anti-virulence activity and restore vancomycin effectiveness in vancomycin-resistant pathogens

Antibiotic resistance is a major threat to human health and new drugs are urgently needed. Ideally, these drugs should have several cellular targets in pathogens, decreasing the risk of resistance development. We show here that two natural ribosomally synthesized lasso peptides (LPs), sviceucin and siamycin I, (1) abolish bacterial virulence of pathogenic enterococci, (2) restore vancomycin clinical susceptibility of vancomycin-resistant (VR) enterococci in vitro and in a surrogate animal model, and (3) re-sensitize VR Staphylococcus aureus. Mode of action (MoA) analyses showed that they do so by inhibiting the histidine kinases (HKs) FsrC and VanS controlling these phenotypes. Strains resistant to the vancomycin/LP combination were difficult to obtain, and were still fully susceptible to the anti-virulence effect of the LPs, highlighting the advantage of multiple targets. Together with the highly sought-after MoA as HK inhibitors, such properties make these lasso peptides promising candidates for the development of next generation antibiotics.

Silver Nanoparticles: A Versatile Tool Against Infectious and Non-Infectious Diseases

Silver nanoparticles possess remarkable properties that render them highly beneficial for medical applications in both infectious and non-infectious diseases. Among their most renowned attributes is their antimicrobial activity. They have demonstrated efficacy against a wide range of bacteria, fungi, protozoa, and viruses. Additionally, the antitumor and anti-diabetic properties of silver nanoparticles, along with their ability to promote wound healing and their application as biosensors, underscore their therapeutic potential for various non-infectious conditions. As silver nanoparticles are employed for medical purposes, their potential toxicity must be considered. While silver nanoparticles present a promising alternative in the therapeutic domain, further research is needed to elucidate their precise mechanisms of action, optimize their efficacy, and mitigate any potential health risks associated with their use.

An Overview of the Genetic Mechanisms of Colistin-Resistance in Bacterial Pathogens: An Indian Perspective

Colistin resistance in bacteria is a growing global issue, given its role as a critical last-resort antibiotic, particularly for treating Gram-negative bacterial infections. Pathogens adopt multiple resistance mechanisms, mediated either by plasmids or chromosomal changes. Some of the most frequently observed strategies include the occurrence of plasmid-borne mobile colistin resistance (mcr) genes, enhanced efflux pump activity, mutations in the regulatory systems, and alterations in the lipid A structure. This article provides an overview of the studies investigating the genetic mechanisms underlying colistin resistance in nosocomial Gram-negative bacteria from India. A total of 37 studies were identified through online searches across various databases, including PubMed, ScienceDirect, and Web of Science. These studies were reviewed to examine bacterial species and their mechanisms of colistin resistance. Over 26 (70.27%) studies were focused on Klebsiella pneumoniae. The most commonly reported mechanism of colistin resistance involved mutations in the two-component systems pmrAB and phoPQ. Plasmid-mediated colistin-resistant mcr genes were identified in 22 studies (18.18%). Four studies reported the overexpression of efflux pump genes as a mechanism of colistin resistance. This article provides a comprehensive summary of these studies, emphasizing the presence of diverse resistance mechanisms across various pathogens. It underscores the necessity for future genomic research on a broader range of pathogens to investigate the prevalence of different mechanisms of colistin resistance in the various regions of India.

Cpx-signalling in Yersinia pseudotuberculosis modulates Lipid-A remodelling and resistance to last-resort antimicrobials

Antibiotic resistance is a global healthcare crisis. Bacteria are highly adaptable and can rapidly acquire mechanisms of resistance towards conventional antibiotics. The permeability barrier conferred by the Gram-negative bacteria cell envelope constitutes a first line of defence against the action of antibiotics. Exposure to extracytoplasmic stresses can negatively affect cell envelope homoeostasis and this causes localised protein misfolding, compromised envelope integrity and impairs barrier function. The CpxA-CpxR two-component regulatory system has evolved to sense extracytoplasmic stresses and to regulate processes that restore homoeostasis of the cell envelope. Hence, controlled Cpx-signalling assists bacteria in adapting, surviving and proliferating in harsh environments, including exposure to antibiotics. Herein, we determined that an intact Cpx-signalling is key to maintaining the Yersinia pseudotuberculosis resistance to colistin and polymyxin B. The susceptibility displayed by Cpx-signalling defective mutants, correlated with cell-envelope deformity and specific modifications of Lipid-A. In vivo transcriptional analysis and in vitro protein-DNA binding studies demonstrated that these modifications were dependent on the direct regulation of Lipid-A biogenesis and modifications of operons by the active phosphorylated CpxR~P isoform. Altogether, our work defines the regulatory mechanism that enables Cpx-signalling to actively control cell envelope remodelling and the permeability of antibiotics in the clinically relevant enteropathogen Y. pseudotuberculosis.

Biogenic metallic nanoparticles: from green synthesis to clinical translation

Biogenic metallic nanoparticles (NPs) have garnered significant attention in recent years due to their unique properties and various applications in different fields. NPs, including gold, silver, zinc oxide, copper, titanium, and magnesium oxide NPs, have attracted considerable interest. Green synthesis approaches, utilizing natural products, offer advantages such as sustainability and environmental friendliness. The theranostics applications of these NPs hold immense significance in the fields of medicine and diagnostics. The review explores intricate cellular uptake pathways, internalization dynamics, reactive oxygen species generation, and ensuing inflammatory responses, shedding light on the intricate mechanisms governing their behaviour at a molecular level. Intriguingly, biogenic metallic NPs exhibit a wide array of applications in medicine, including but not limited to anti-inflammatory, anticancer, anti-diabetic, anti-plasmodial, antiviral properties and radical scavenging efficacy. Their potential in personalized medicine stands out, with a focus on tailoring treatments to individual patients based on these NPs' unique attributes and targeted delivery capabilities. The article culminates in emphasizing the role of biogenic metallic NPs in shaping the landscape of personalized medicine. Harnessing their unique properties for tailored therapeutics, diagnostics and targeted interventions, these NPs pave the way for a paradigm shift in healthcare, promising enhanced efficacy and reduced adverse effects.

Histidine Kinase QseC in Glaesserella parasuis Enhances the Secretion of Proinflammatory Cytokines by Macrophages via the p38 and NF-κB Signaling Pathways

The qseC gene is a two-component system that encodes a histidine protein kinase and is highly conserved among different Glaesserella parasuis strains. In this study, we used qRT-PCR and enzyme-linked immunosorbent assay to confirm that Toll-like receptor 4 (TLR4) plays a role in the expression of proinflammatory cytokines interleukin (IL)-1β and IL-6 by stimulating RAW 264.7 macrophages with QseC. Furthermore, we revealed that blocking the p38 and NF-κB pathways that regulate signaling can significantly reduce the production of proinflammatory cytokines induced by QseC. In summary, our data suggest that QseC is a novel proinflammatory mediator that induces TLR4-dependent proinflammatory activity in RAW 264.7 macrophages through the p38 and NF-κB pathways.

Recent advances in the development of bacterial response regulators inhibitors as antibacterial and/or antibiotic adjuvant agent: A new approach to combat bacterial resistance

The number of new antibacterial agents currently being discovered is insufficient to combat bacterial resistance. It is extremely challenging to find new antibiotics and to introduce them to the pharmaceutical market. Therefore, special attention must be given to find new strategies to combat bacterial resistance and prevent bacteria from developing resistance. Two-component system is a transduction system and the most prevalent mechanism employed by bacteria to respond to environmental changes. This signaling system consists of a membrane sensor histidine kinase that perceives environmental stimuli and a response regulator which acts as a transcription factor. The approach consisting of developing response regulators inhibitors with antibacterial activity or antibiotic adjuvant activity is a novel approach that has never been previously reviewed. In this review we report for the first time, the importance of targeting response regulators and summarizing all existing studies carried out from 2008 until now on response regulators inhibitors as antibacterial agents or / and antibiotic adjuvants. Moreover, we describe the antibacterial activity and/or antibiotic adjuvants activity against the studied bacterial strains and the mechanism of different response regulator inhibitors when it's possible.

Sensing for survival: specialised regulatory mechanisms of Type III secretion systems in Gram-negative pathogens

For centuries, Gram-negative pathogens have infected the human population and been responsible for numerous diseases in animals and plants. Despite advancements in therapeutics, Gram-negative pathogens continue to evolve, with some having developed multi-drug resistant phenotypes. For the successful control of infections caused by these bacteria, we need to widen our understanding of the mechanisms of host-pathogen interactions. Gram-negative pathogens utilise an array of effector proteins to hijack the host system to survive within the host environment. These proteins are secreted into the host system via various secretion systems, including the integral Type III secretion system (T3SS). The T3SS spans two bacterial membranes and one host membrane to deliver effector proteins (virulence factors) into the host cell. This multifaceted process has multiple layers of regulation and various checkpoints. In this review, we highlight the multiple strategies adopted by these pathogens to regulate or maintain virulence via the T3SS, encompassing the regulation of small molecules to sense and communicate with the host system, as well as master regulators, gatekeepers, chaperones, and other effectors that recognise successful host contact. Further, we discuss the regulatory links between the T3SS and other systems, like flagella and metabolic pathways including the tricarboxylic acid (TCA) cycle, anaerobic metabolism, and stringent cell response.

Anti-quorum sensing activity of poly-amidoamine dendrimer generation 5 dendrimer loaded kinase inhibitor peptide against methicillin-resistant Staphylococcus aureus

Methicillin-resistant Staphylococcus aureus (MRSA) is a significant concern in both healthcare and community settings, as it causes numerous infections worldwide with high morbidity and mortality rates. One promising strategy is to target the quorum sensing (QS) system of MRSA using a dendrimer loaded with kinase inhibitor peptide. The present investigation has formulated a poly-amidoamine dendrimer (PAMAM) G5 dendrimer that is loaded with Quorum Quencher (QQ) peptide, which functions as a histidine kinase inhibitor. The particle average size of the formulated G5-QQ3 complex was determined to be 276 nm, and polydispersity index values of 0.33. The MIC50 for the formulated nanoparticles was 18 μM as demonstrated by a growth assay. Furthermore, the G5-QQ3 complex was able to inhibit the hemolysis activity of the MRSA with a concentration of 10 μM, and for Staphylococcus aureus was 3 μM. The G5-QQ3 complex possesses the ability to inhibit, penetrate, and eradicate biofilm in MRSA, Staphylococcus aureus, and different agr mutants with inhibition percentages ranging from 60 to 72%. Furthermore, live/dead viability assay confirmed the ability of the formulated nanoparticles to effectively kill all strains within the biofilm structure as evidenced by a confocal microscope, and the cytotoxicity of the G5-QQ3 complex was dose-dependent (p < 0.05). against RAW 264.7 cells. In general, the study confirmed that encapsulating QQ3 peptide within PAMAM G5 dendrimer results in a potent anti-virulence and anti-bacterial action and suggests a synergistic effect. The findings of this study have significant implications for the development of new treatments for MRSA infections, which are a major public health concern.

A bacterial sensor taxonomy across earth ecosystems for machine learning applications

Microbial communities have evolved to colonize all ecosystems of the planet, from the deep sea to the human gut. Microbes survive by sensing, responding, and adapting to immediate environmental cues. This process is driven by signal transduction proteins such as histidine kinases, which use their sensing domains to bind or otherwise detect environmental cues and "transduce" signals to adjust internal processes. We hypothesized that an ecosystem's unique stimuli leave a sensor "fingerprint," able to identify and shed insight on ecosystem conditions. To test this, we collected 20,712 publicly available metagenomes from Host-associated, Environmental, and Engineered ecosystems across the globe. We extracted and clustered the collection's nearly 18M unique sensory domains into 113,712 similar groupings with MMseqs2. We built gradient-boosted decision tree machine learning models and found we could classify the ecosystem type (accuracy: 87%) and predict the levels of different physical parameters (R2 score: 83%) using the sensor cluster abundance as features. Feature importance enables identification of the most predictive sensors to differentiate between ecosystems which can lead to mechanistic interpretations if the sensor domains are well annotated. To demonstrate this, a machine learning model was trained to predict patient's disease state and used to identify domains related to oxygen sensing present in a healthy gut but missing in patients with abnormal conditions. Moreover, since 98.7% of identified sensor domains are uncharacterized, importance ranking can be used to prioritize sensors to determine what ecosystem function they may be sensing. Furthermore, these new predictive sensors can function as targets for novel sensor engineering with applications in biotechnology, ecosystem maintenance, and medicine.IMPORTANCEMicrobes infect, colonize, and proliferate due to their ability to sense and respond quickly to their surroundings. In this research, we extract the sensory proteins from a diverse range of environmental, engineered, and host-associated metagenomes. We trained machine learning classifiers using sensors as features such that it is possible to predict the ecosystem for a metagenome from its sensor profile. We use the optimized model's feature importance to identify the most impactful and predictive sensors in different environments. We next use the sensor profile from human gut metagenomes to classify their disease states and explore which sensors can explain differences between diseases. The sensors most predictive of environmental labels here, most of which correspond to uncharacterized proteins, are a useful starting point for the discovery of important environment signals and the development of possible diagnostic interventions.

Evaluation of Expanded 2-Aminobenzothiazole Library for Inhibition of Pseudomonas aeruginosa Virulence Phenotypes

Bacterial resistance to antibiotics is a rapidly increasing threat to human health. New strategies to combat resistant organisms are desperately needed. One potential avenue is targeting two-component systems, which are the main bacterial signal transduction pathways used to regulate development, metabolism, virulence, and antibiotic resistance. These systems consist of a homodimeric membrane-bound sensor histidine kinase, and a cognate effector, the response regulator. The high sequence conservation in the catalytic and adenosine triphosphate-binding (CA) domain of histidine kinases and their essential role in bacterial signal transduction could enable broad-spectrum antibacterial activity. Through this signal transduction, histidine kinases regulate multiple virulence mechanisms including toxin production, immune evasion, and antibiotic resistance. Targeting virulence, as opposed to development of bactericidal compounds, could reduce evolutionary pressure for acquired resistance. Additionally, compounds targeting the CA domain have the potential to impair multiple two-component systems that regulate virulence in one or more pathogens. We conducted structure-activity relationship studies of 2-aminobenzothiazole-based inhibitors designed to target the CA domain of histidine kinases. We found these compounds have anti-virulence activities in Pseudomonas aeruginosa, reducing motility phenotypes and toxin production associated with the pathogenic functions of this bacterium.

The two-component system WalKR provides an essential link between cell wall homeostasis and DNA replication in Staphylococcus aureus

IMPORTANCE

The opportunistic human pathogen Staphylococcus aureus uses an array of protein sensing systems called two-component systems (TCS) to sense environmental signals and adapt its physiology in response by regulating different genes. This sensory network is key to S. aureus versatility and success as a pathogen. Here, we reveal for the first time the full extent of the regulatory network of WalKR, the only staphylococcal TCS that is indispensable for survival under laboratory conditions. We found that WalKR is a master regulator of cell growth, coordinating the expression of genes from multiple, fundamental S. aureus cellular processes, including those involved in maintaining cell wall metabolism, protein biosynthesis, nucleotide metabolism, and the initiation of DNA replication.

REC protein family expansion by the emergence of a new signaling pathway

IMPORTANCE

We explore when and why large classes of proteins expand into new sequence space. We used an unsupervised machine learning approach to observe the sequence landscape of REC domains of bacterial response regulator proteins. We find that within-gene recombination can switch effector domains and, consequently, change the regulatory context of the duplicated protein.

The phage-encoded PIT4 protein affects multiple two-component systems of Pseudomonas aeruginosa

IMPORTANCE

More and more Pseudomonas aeruginosa isolates have become resistant to antibiotics like carbapenem. As a consequence, P. aeruginosa ranks in the top three of pathogens for which the development of novel antibiotics is the most crucial. The pathogen causes both acute and chronic infections, especially in patients who are the most vulnerable. Therefore, efforts are urgently needed to develop alternative therapies. One path explored in this article is the use of bacteriophages and, more specifically, phage-derived proteins. In this study, a phage-derived protein was studied that impacts key virulence factors of the pathogen via interaction with multiple histidine kinases of TCSs. The fundamental insights gained for this protein can therefore serve as inspiration for the development of an anti-virulence compound that targets the bacterial TCS.

Type I Photosensitizer Targeting Glycans: Overcoming Biofilm Resistance by Inhibiting the Two-Component System, Quorum Sensing, and Multidrug Efflux

Stubborn biofilm infections pose serious threats to human health due to the persistence, recurrence, and dramatically magnified antibiotic resistance. Photodynamic therapy has emerged as a promising approach to combat biofilm. Nevertheless, how to inhibit the bacterial signal transduction system and the efflux pump to conquer biofilm recurrence and resistance remains a challenging and unaddressed issue. Herein, a boric acid-functionalized lipophilic cationic type I photosensitizer, ACR-DMP, is developed, which efficiently generates •OH to overcome the hypoxic microenvironment and photodynamically eradicates methicillin-resistant Staphylococcus aureus (MRSA) and biofilms. Furthermore, it not only alters membrane potential homeostasis and osmotic pressure balance due to its strong binding ability with plasma membrane but also inhibits quorum sensing and the two-component system, reduces virulence factors, and regulates the activity of the drug efflux pump attributed to the glycan-targeting ability, helping to prevent biofilm recurrence and conquer biofilm resistance. In vivo, ACR-DMP successfully obliterates MRSA biofilms attached to implanted medical catheters, alleviates inflammation, and promotes vascularization, thereby combating infections and accelerating wound healing. This work not only provides an efficient strategy to combat stubborn biofilm infections and bacterial multidrug resistance but also offers systematic guidance for the rational design of next-generation advanced antimicrobial materials.

PmrAB controls virulence-associated traits and outer membrane vesicle biogenesis in Acinetobacter baumannii

The PmrAB two-component system modulates colistin resistance in Acinetobacter baumannii, but its association with the virulence traits of this bacterium remains uncharacterized. This study explored the role of A. baumannii PmrAB in surface motility, biofilm formation, and outer membrane vesicle (OMV) biogenesis using wild-type (WT) A. baumannii 17978 and ΔpmrA and ΔpmrB mutant strains. The two mutant strains exhibited significantly decreased surface motility compared with that of WT strain by the low expression of abaI, abaR, A1S_0113, A1S_0115, and A1S_0116. Biofilm mass also significantly decreased in the two mutant strains at 12 h of incubation, but restored at 24 h. Under static culture conditions for 12 h, the two mutant strains showed low pgaA expression. However, the other biofilm-associated genes, such as csuC, csuE, ompA, and bap, showed different expression between the two mutant strains. Although the size of OMVs was similar among the three strains, the number of OMVs secreted from the two mutant strains slightly decreased compared with that secreted from the WT strain. Protein concentrations in the OMVs of ΔpmrA mutant significantly decreased compared with those in the OMVs of WT and ΔpmrB strains. Overall, PmrAB modulates virulence traits and OMV biogenesis in A. baumannii.

Expanding our grasp of two-component signaling in Clostridioides difficile

The intestinal pathogen Clostridioides difficile encodes roughly 50 TCS, but very few have been characterized in terms of their activating signals or their regulatory roles. A. G. Pannullo, B. R. Zbylicki, and C. D. Ellermeier (J Bacteriol 205:e00164-23, 2023, https://doi.org/10.1128/jb.00164-23) have identified both for the novel C. difficile TCD DraRS. DraRS responds to antibiotics that target lipid-II molecules in the bacterial cell envelope, and regulates the production of a novel glycolipid necessary for bacitracin and daptomycin resistance in C. difficile.

Multi-omics analysis revealed the selective enrichment of partial denitrifying bacteria for the stable coupling of partial-denitrification and anammox process under the influence of low strength magnetic field

The microbial consortium involving anaerobic ammonium oxidation (anammox) and partial denitrification (PD), known as PD-anammox, is an emerging energy-efficient and lower carbon nitrogen removal process from wastewater. However, maintaining a stable PD process by locking nitrate reduction until nitrite was challenging. This study established the first stable connection of anammox with constant nitrite generation by PD bacteria under a low-strength (1.3 mT) magnetic field (MF). When the nitrogen loading rate was 1.81 kg-N/m3/d, the nitrogen removal efficiency of the control reactor (R1) was 75%, lower than that of the experimental reactor (R2), which was 85%. The expression of Thauera and Zoogloea, potential PD bacteria was substantially lower in R1 (5.75% and 1.21%, respectively) than in R2 (10.25 and 6.61%, respectively), according to a meta-transcriptomic analysis. At the same time, the mRNA expression of anammox genera Candidatus Brocadia and Candidatus Kuenenia was 33.53% and 3.83% in R1 and 22.86% and 1.87% in R2. Moreover, carbon and nitrogen metabolism pathways were more abundant under the influence of low-strength MF. The selective enrichment of PD bacteria can be attributed to the increased expression of carbon metabolic pathways like the citrate cycle, glycolysis/gluconeogenesis, and pyruvate metabolism. Interestingly, the control reactor was dominated by a hydroxylamine-dependent anammox process while a low-strength MF-enhanced nitric-oxide-dependent anammox process. For successful anammox-centered nitrogen removal from wastewater, this study demonstrated that low-strength MF is a convenient and applicable technique to lock the nitrate reduction until nitrite.

Transcriptomics of Lactobacillus paracasei: metabolism patterns and cellular responses under high-density culture conditions

Lactobacillus paracasei has significant potential for development and application in the environmental field, particularly in addressing malodor pollution. This study aims to investigate the cellular response of L. paracasei B1 under high-density culture conditions. The selected strain has previously shown effective deodorizing and bacteriostatic abilities. Transcriptomics techniques are employed to dissect the nutrient metabolism pattern of L. paracasei B1 and its response mechanism under environmental stress. The study characterizes the functions of key differentially expressed genes during growth before and after optimizing the culture conditions. The optimization of fermentation culture conditions provides a suitable growth environment for L. paracasei B1, inducing an enhancement of its phosphotransferase system for sugar source uptake and maintaining high levels of glycolysis and pyruvate metabolism. Consequently, the strain is able to grow and multiply rapidly. Under acid stress conditions, glycolysis and pyruvate metabolism are inhibited, and L. paracasei B1 generates additional energy through aerobic respiration to meet the energy demand. The two-component system and quorum sensing play roles in the response and regulation of L. paracasei B1 to adverse environments. The strain mitigates oxygen stress damage through glutathione metabolism, cysteine and methionine metabolism, base excision repair, and purine and pyrimidine metabolism. Additionally, the strain enhances lysine synthesis, the alanine, aspartate, and glutamate metabolic pathways, and relies on the ABC transport system to accumulate amino acid-compatible solutes to counteract acid stress and osmotic stress during pH regulation. These findings establish a theoretical basis for the further development and application of L. paracasei B1 for its productive properties.

Considerations for defining +80 Da mass shifts in mass spectrometry-based proteomics: phosphorylation and beyond

Post-translational modifications (PTMs) are ubiquitous and key to regulating protein function. Understanding the dynamics of individual PTMs and their biological roles requires robust characterisation. Mass spectrometry (MS) is the method of choice for the identification and quantification of protein modifications. This article focusses on the MS-based analysis of those covalent modifications that induce a mass shift of +80 Da, notably phosphorylation and sulfation, given the challenges associated with their discrimination and pinpointing the sites of modification on a polypeptide chain. Phosphorylation in particular is highly abundant, dynamic and can occur on numerous residues to invoke specific functions, hence robust characterisation is crucial to understanding biological relevance. Showcasing our work in the context of other developments in the field, we highlight approaches for enrichment and site localisation of phosphorylated (canonical and non-canonical) and sulfated peptides, as well as modification analysis in the context of intact proteins (top down proteomics) to explore combinatorial roles. Finally, we discuss the application of native ion-mobility MS to explore the effect of these PTMs on protein structure and ligand binding.

Using next generation antimicrobials to target the mechanisms of infection

The remarkable impact of antibiotics on human health is being eroded at an alarming rate by the emergence of multidrug resistant pathogens. There is a recognised consensus that new strategies to tackle infection are urgently needed to limit the devasting impact of antibiotic resistance on our global healthcare infrastructure. Next generation antimicrobials (NGAs) are compounds that target bacterial virulence factors to disrupt pathogenic potential without impacting bacterial viability. By disabling the key virulence factors required to establish and maintain infection, NGAs make pathogens more vulnerable to clearance by the immune system and can potentially render them more susceptible to traditional antibiotics. In this review, we discuss the developing field of NGAs and how advancements in this area could offer a viable standalone alternative to traditional antibiotics or an effective means to prolong antibiotic efficacy when used in combination.

N-Acetylglucosamine and its dimer ameliorate inflammation in murine colitis by strengthening the gut barrier function

Ulcerative colitis (UC) is a chronic gastrointestinal disease whose incidence is increasing rapidly worldwide. Anti-inflammatory medications, including 5-aminosalicylic acid (5-ASA), corticosteroids, and immunosuppressants, are used for its treatment; however, new alternatives would be required due to the serious side effects of some of these medications. N-Acetylglucosamine (NAG) is an amino sugar composed of mucin that is secreted by intestinal epithelial cells. It is also used to promote the growth of intestinal bacteria. The current study aimed to determine the efficacy of NAG against dextran sulfate sodium (DSS)-induced chronic colitis and elucidate its mechanism of action. Mice were randomly divided into control, DSS, 0.1% sulfasalazine, 0.1% NAG, 0.3% NAG, and 0.3% NAG-dimer (NAG-D) groups, and results showed that colitis-induced body weight loss, disease activity, colonic tissue damage, colon length shortening, and the loss of mucin-secreting area were significantly improved in the NAG-D group. The intestinal permeability indicator, serum CD 14 level, and expression of the tight junction protein, occludin, were both improved in the 0.3% NAG group. Inflammatory biomarkers, including GATA3, IFN-γ, p-IκBα, COX2, TGF-β1, and Smad7, were significantly lower in the 0.3% NAG and NAG-D groups than in the DSS group. The intestinal microbial composition was most significantly altered in the 0.3% NAG group, showing decreased ratios of pathogenic bacteria, such as Betaproteobacteria, especially Burkholderiales. The results overall suggested that NAG or NAG-D supplementation can alleviate inflammation by strengthening the intestinal barrier function and maintaining gut microbiota homeostasis in a DSS-induced colitis mouse model.

Virtual Screening of Potential RoxS Inhibitors and Evaluation of Their Antimicrobial Activity in Combination with Antibiotics against Clinically Resistant Bacteria

Pseudomonas aeruginosa with difficult-to-treat resistance has been designated as an urgent or serious threat by the CDC in the United States; therefore, novel antibacterial drugs and combination strategies are urgently needed. The sensor kinase RoxS is necessary for the aerobic growth of Pseudomonas aeruginosa. This study aimed to screen candidate RoxS inhibitors and evaluate their efficacy in treating multi-drug-resistant and extensively drug-resistant Pseudomonas aeruginosa in combination with meropenem and amikacin to identify promising combination strategies. RoxS protein structures were constructed using homology modeling and potential RoxS inhibitors, including Ezetimibe, Deferasirox, and Posaconazole, were screened from the FDA-approved ZINC drug database using molecular docking and molecular dynamics simulations. MIC and checkerboard assays were used to determine the in vitro antimicrobial efficacy of the three drugs in combination with antibiotics. The results of in vitro experiments showed an additive effect of 100 μg/mL Deferasirox or 16 μg/mL Posaconazole in combination with meropenem and a synergistic effect of 1.5 μg/mL Deferasirox and amikacin. In summary, these three drugs are potential inhibitors of RoxS, and their combination with meropenem or amikacin is expected to reverse the resistance of P. aeruginosa, providing new combination strategies for the treatment of clinically difficult-to-treat Pseudomonas aeruginosa.

Roles of two-component regulatory systems in Klebsiella pneumoniae: Regulation of virulence, antibiotic resistance, and stress responses

Klebsiella pneumoniae is an opportunistic pathogen belonging to the Enterobacteriaceae family, which is the leading cause of nosocomial infections. The emergence of hypervirulent and multi-drug resistant K. pneumoniae is a serious health threat. In the process of infection, K. pneumoniae needs to adapt to different environmental conditions, and the two-component regulatory system (TCS) composed of a sensor histidine kinase and response regulator is an important bacterial regulatory system in response to external stimuli. Understanding how K. pneumoniae perceives and responds to complex environmental stimuli provides insights into TCS regulation mechanisms and new targets for drug design. In this review, we analyzed the TCS composition and summarized the regulation mechanisms of TCSs, focusing on the regulation of genes involved in virulence, antibiotic resistance, and stress response. Collectively, these studies demonstrated that several TCSs play important roles in the regulation of virulence, antibiotic resistance and stress responses of K. pneumoniae. A single two-component regulatory system can participate in the regulation of several stress responses, and one stress response process may include several TCSs, forming a complex regulatory network. However, the function and regulation mechanism of some TCSs require further study. Hence, future research endeavors are required to enhance the understanding of TCS regulatory mechanisms and networks in K. pneumoniae, which is essential for the design of novel drugs targeting TCSs.

OmpR (TCS response regulator) of Aeromonas veronii plays a major role in drug resistance, stress resistance and virulence by regulating biofilm formation

Aeromonas veronii (A. veronii), a highly pathogenic bacteria with a wide range of hosts, widely exists in the environment of humans, animals and aquatic animals, and can cause a variety of diseases. In this study, the receptor regulator ompR in the envZ/ompR of two-component system was selected to construct a mutant strain (Δ ompR) and a complement strain (C-ompR) to explore the regulatory effect of ompR on the biological characteristics and virulence of TH0426. The results showed that the ability of biofilm formation and osmotic stress of TH0426 were significantly reduced (P < 0.001), the resistance to ceftriaxone and neomycin were slightly down-regulate when the ompR gene was deleted. At the same time, animal pathogenicity experiments showed that the virulence of TH0426 was significantly down-regulated (P < 0.001). These results indicated that ompR gene regulates the biofilm formation of TH0426, and regulates some biological characteristics of TH0426, including drug sensitivity, resistance to osmotic stress, and also affects its virulence.

Targeting multidrug resistant Staphylococcus infections with bacterial histidine kinase inhibitors

The emergence of drug-resistant bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA), which are not susceptible to current antibiotics has necessitated the development of novel approaches and targets to tackle this growing challenge. Bacterial two-component systems (TCSs) play a central role in the adaptative response of bacteria to their ever-changing environment. They are linked to antibiotic resistance and bacterial virulence making the proteins of the TCSs, histidine kinases and response regulators, attractive for the development of novel antibacterial drugs. Here, we developed a suite of maleimide-based compounds that we evaluated against a model histidine kinase, HK853, in vitro and in silico. The most potent leads were then assessed for their ability to decrease the pathogenicity and virulence of MRSA, resulting in the identification of a molecule that decreased the lesion size caused by a methicillin-resistant S. aureus skin infection by 65% in a murine model.

Acinetobacter baumannii under Acidic Conditions Induces Colistin Resistance through PmrAB Activation and Lipid A Modification

Colistin is a last-resort antimicrobial agent for treating carbapenem-resistant Acinetobacter baumannii infections. The activation of PmrAB by several environmental signals induces colistin resistance in Gram-negative bacteria. This study investigated the molecular mechanisms of colistin resistance in A. baumannii under acidic conditions using wild-type (WT) A. baumannii 17978, ΔpmrA and ΔpmrB mutants, and pmrA-complemented strains. The pmrA or pmrB deletion did not affect the growth of A. baumannii under acidic or aerobic conditions. A. baumannii under acidic (pH 5.5) and high-iron (1 mM) conditions showed 32- and 8-fold increases in the minimum inhibitory concentrations (MICs) of colistin, respectively. The ΔpmrA and ΔpmrB mutants at pH 5.5 showed a significant decrease in colistin MICs compared to the WT strain at pH 5.5. No difference in colistin MICs was observed between WT and mutant strains under high-iron conditions. The pmrCAB expression significantly increased in the WT strain at pH 5.5 compared to the WT strain at pH 7.0. The pmrC expression significantly decreased in two mutant strains at pH 5.5 compared to the WT strain at pH 5.5. The PmrA protein was expressed in the ΔpmrA strain carrying ppmrA_FLAG plasmids at pH 5.5 but not at pH 7.0. Lipid A modification by the addition of phosphoethanolamine was observed in the WT strain at pH 5.5. In conclusion, this study demonstrated that A. baumannii under acidic conditions induces colistin resistance via the activation of pmrCAB operon and subsequent lipid A modification.

Expression patterns and influence of the two-component system in Vibrio parahaemolyticus of different genotypes

Vibrio parahaemolyticus is a foodborne pathogen that threatens global food security and human health. The two-component system (TCS) is a primary method for bacteria self-regulate and adapt to the environment. Previous studies have shown that V. parahaemolyticus has four hemolytic genotypes with diverse biological phenotypes and environmental adaptability, but the mechanism is unclear. In this study, we investigated TCS expression patterns in V. parahaemolyticus with different genotypes for the first time and explored the differences in TCS between strains. The results showed similarities in the TCS expression pattern between VPC17 (tdh+/trh-) and VPC44 (tdh-/trh-), while VPC85(tdh-/trh+) had the least similar TCS expression pattern to the other three strains. Analysis of biological information revealed that different regulations of C4 dicarboxylate transport, tetrathionate uptake, antibiotic resistance, and flagellar synthesis involved in the TCS might influence strains' growth, antibiotic resistance, biofilm, and virulence. The different TCS regulatory abilities of strains might be one of the reasons for diverse biological characteristics and different environmental adaptations. This work provides a theoretical basis and a new research direction for the strain variability of V. parahaemolyticus.

A Review of the Bacterial Phosphoproteomes of Beneficial Microbes

The number and variety of protein post-translational modifications (PTMs) found and characterized in bacteria over the past ten years have increased dramatically. Compared to eukaryotic proteins, most post-translational protein changes in bacteria affect relatively few proteins because the majority of modified proteins exhibit substoichiometric modification levels, which makes structural and functional analyses challenging. In addition, the number of modified enzymes in bacterial species differs widely, and degrees of proteome modification depend on environmental conditions. Nevertheless, evidence suggests that protein PTMs play essential roles in various cellular processes, including nitrogen metabolism, protein synthesis and turnover, the cell cycle, dormancy, spore germination, sporulation, persistence, and virulence. Additional investigations on protein post-translational changes will undoubtedly close knowledge gaps in bacterial physiology and create new means of treating infectious diseases. Here, we describe the role of the post-translation phosphorylation of major bacterial proteins and review the progress of research on phosphorylated proteins depending on bacterial species.

A Survey of Two-Component Systems in Coxiella burnetii Reveals Redundant Regulatory Schemes and a Requirement for an Atypical PhoBR System in Mammalian Cell Infection

Coxiella burnetii is an obligate intracellular bacterium and the etiological agent of Q fever in humans. C. burnetii transitions between a replicative, metabolically active large-cell variant (LCV) and a spore-like, quiescent small-cell variant (SCV) as a likely mechanism to ensure survival between host cells and mammalian hosts. C. burnetii encodes three canonical two-component systems, four orphan hybrid histidine kinases, five orphan response regulators, and a histidine phosphotransfer protein, which have been speculated to play roles in the signaling required for C. burnetii morphogenesis and virulence. However, very few of these systems have been characterized. By employing a CRISPR interference system for genetic manipulation of C. burnetii, we created single- and multigene transcriptional knockdown strains targeting most of these signaling genes. Through this, we revealed a role for the C. burnetii PhoBR canonical two-component system in virulence, regulation of [Pi] maintenance, and Pi transport. We also outline a novel mechanism by which PhoBR function may be regulated by an atypical PhoU-like protein. We also determined that the GacA.2/GacA.3/GacA.4/GacS orphan response regulators coordinately and disparately regulate expression of SCV-associated genes in C. burnetii LCVs. These foundational results will inform future studies on the role of C. burnetii two-component systems in virulence and morphogenesis. IMPORTANCE C. burnetii is an obligate intracellular bacterium with a spore-like stability allowing it to survive long periods of time in the environment. This stability is likely due to its biphasic developmental cycle, whereby it can transition from an environmentally stable small-cell variant (SCV) to a metabolically active large-cell variant (LCV). Here, we define the role of two-component phosphorelay systems (TCS) in C. burnetii's ability to survive within the harsh environment contained in the phagolysosome of host cells. We show that the canonical PhoBR TCS has an important role in C. burnetii virulence and phosphate sensing. Further examination of the regulons controlled by orphan regulators indicated a role in modulating gene expression of SCV-associated genes, including genes essential for cell wall remodeling.

The AtoC family response regulator upregulates an operon encoding putative outer membrane proteins sorted by type IX secretion system in Porphyromonas gingivalis

OBJECTIVES

Porphyromonas gingivalis, a keystone periodontopathogen, has multiple two-component systems that are thought to modulate virulence. In this study, we focused on PGN_0775 response regulator (RR), an AtoC homolog, and attempted to identify the target gene that it regulates in P. gingivalis.

METHODS

Comparative proteomic analyses comprising two-dimensional electrophoresis and peptide mass fingerprinting were applied to total protein samples from parent (WT) and atoC gene knockout (KO) strains to screen for affected protein spots. Fluctuations in the expression of corresponding genes were further confirmed using relative quantitative real-time polymerase chain reaction (RQPCR).

RESULTS

Five protein spots with fluctuating expression levels were identified in pgn_0775 KO strains along with their masses and physiological features, which contained two hypothetical proteins with higher expression levels in the WT than in the KO strains. RQPCR analysis confirmed that mRNA levels were consistently decreased in KO and recovered in pgn_0775-complemented KO strains. The two hypothetical proteins appeared to be the products of an operon that comprises four genes encoding three hypothetical but putative type IX secretion system sorting domain-containing proteins and an N-terminal region of the C25 cysteine peptidase.

CONCLUSIONS

The AtoC RR homolog in P. gingivalis upregulates the expression of the operon encoding potentially antigenic proteins retained on the cell surface; thus, it could be a promising target for P. gingivalis-specific antivirulence therapy.

The Biofilm Regulatory Network from Bacillus subtilis: A Structure-Function Analysis

Bacterial biofilms are notorious for their ability to protect bacteria from environmental challenges, most importantly the action of antibiotics. Bacillus subtilis is an extensively studied model organism used to understand the process of biofilm formation. A complex network of principal regulatory proteins including Spo0A, AbrB, AbbA, Abh, SinR, SinI, SlrR, and RemA, work in concert to transition B. subtilis from the free-swimming planktonic state to the biofilm state. In this review, we explore, connect, and summarize decades worth of structural and biochemical studies that have elucidated this protein signaling network. Since structure dictates function, unraveling aspects of protein molecular mechanisms will allow us to devise ways to exploit critical features of the biofilm regulatory pathway, such as possible therapeutic intervention. This review pools our current knowledge base of B. subtilis biofilm regulatory proteins and highlights potential therapeutic intervention points.

Regulation of Staphylococcus aureus Virulence and Application of Nanotherapeutics to Eradicate S. aureus Infection

Staphylococcus aureus is a versatile pathogen known to cause hospital- and community-acquired, foodborne, and zoonotic infections. The clinical infections by S. aureus cause an increase in morbidity and mortality rates and treatment costs, aggravated by the emergence of drug-resistant strains. As a multi-faceted pathogen, it is imperative to consolidate the knowledge on its pathogenesis, including the mechanisms of virulence regulation, development of antimicrobial resistance, and biofilm formation, to make it amenable to different treatment strategies. Nanomaterials provide a suitable platform to address this challenge, with the potential to control intracellular parasitism and multidrug resistance where conventional therapies show limited efficacy. In a nutshell, the first part of this review focuses on the impact of S. aureus on human health and the role of virulence factors and biofilms during pathogenesis. The second part discusses the large diversity of nanoparticles and their applications in controlling S. aureus infections, including combination with antibiotics and phytochemicals and the incorporation of antimicrobial coatings for biomaterials. Finally, the limitations and prospects using nanomaterials are highlighted, aiming to foster the development of novel nanotechnology-driven therapies against multidrug-resistant S. aureus.

CzcR Is Essential for Swimming Motility in Pseudomonas aeruginosa during Zinc Stress

Two-component system (TCS) plays a vital role in modulating target gene expression in response to the changing environments. Pseudomonas aeruginosa is a ubiquitous opportunistic pathogen that can survive under diverse stress conditions. The great adaptability of P. aeruginosa relies heavily on the abundant TCSs encoded by its genome. However, most TCSs in P. aeruginosa have not been well-characterized. CzcS/CzcR is a metal responsive TCS which displays multiple regulatory functions associated with metal hemostasis, quorum sensing activity and antibiotic resistance. In this study, we found that swimming motility of P. aeruginosa was completely abolished during zinc (Zn2+) stress when the czcR gene from the TCS CzcS/CzcR was deleted. Noticeably, CzcR was dispensable for swimming without the stress of Zn2+ excess. CzcR was shown to be activated by Zn2+ stress possibly through inducing its expression level and triggering its phosphorylation to positively regulate swimming which was abolished by Zn2+ stress in a CzcR-independent manner. Further TEM analyses and promoter activity examinations revealed that CzcR was required for the expression of genes involved in flagellar biosynthesis during Zn2+ stress. In vitro protein-DNA interaction assay showed that CzcR was capable of specifically recognizing and binding to the promoters of operons flgBCDE, flgFGHIJK, and PA1442/FliMNOPQR/flhB. Together, this study demonstrated a novel function of CzcR in regulating flagellar gene expression and motility in P. aeruginosa when the pathogen encounters Zn2+ stress conditions. IMPORTANCE The fitness of bacterial cells depends largely on their ability to sense and respond quickly to the changing environments. P. aeruginosa expresses a great number of signal sensing and transduction systems that enable the pathogen to grow and survive under diverse stress conditions and cause serious infections at different sites in many hosts. In addition to the previously characterized functions to regulate metal homeostasis, quorum sensing activity, and antibiotic resistance, here we report that CzcR is a novel regulator essential for flagellar gene expression and swimming motility in P. aeruginosa during Zn2+ stress. Since swimming motility is important for the virulence of P. aeruginosa, findings in this study might provide a new target for the treatment of P. aeruginosa infections with Zn2+-based antimicrobial agents in the future.

An Evolutionary Paradigm Favoring Cross Talk between Bacterial Two-Component Signaling Systems

The prevalent paradigm governing bacterial two-component signaling systems (TCSs) is specificity, wherein the histidine kinase (HK) of a TCS exclusively activates its cognate response regulator (RR). Cross talk, where HKs activate noncognate RRs, is considered evolutionarily disadvantageous because it can compromise adaptive responses by leaking signals. Yet cross talk is observed in several bacteria. Here, to resolve this paradox, we propose an alternative paradigm where cross talk can be advantageous. We envisioned programmed environments, wherein signals appear in predefined sequences. In such environments, cross talk that primes bacteria to upcoming signals may improve adaptive responses and confer evolutionary benefits. To test this hypothesis, we employed mathematical modeling of TCS signaling networks and stochastic evolutionary dynamics simulations. We considered the comprehensive set of bacterial phenotypes, comprising thousands of distinct cross talk patterns competing in varied signaling environments. Our simulations predicted that in programmed environments phenotypes with cross talk facilitating priming would outcompete phenotypes without cross talk. In environments where signals appear randomly, bacteria without cross talk would dominate, explaining the specificity widely seen. Additionally, a testable prediction was that the phenotypes selected in programmed environments would display one-way cross talk, ensuring priming to future signals. Interestingly, the cross talk networks we deduced from available data on TCSs of Mycobacterium tuberculosis all displayed one-way cross talk, which was consistent with our predictions. Our study thus identifies potential evolutionary underpinnings of cross talk in bacterial TCSs, suggests a reconciliation of specificity and cross talk, makes testable predictions of the nature of cross talk patterns selected, and has implications for understanding bacterial adaptation and the response to interventions. IMPORTANCE Bacteria use two-component signaling systems (TCSs) to sense and respond to environmental changes. The prevalent paradigm governing TCSs is specificity, where signal flow through TCSs is insulated; leakage to other TCSs is considered evolutionarily disadvantageous. Yet cross talk between TCSs is observed in many bacteria. Here, we present a potential resolution of this paradox. We envision programmed environments, wherein stimuli appear in predefined sequences. Cross talk that primes bacteria to upcoming stimuli could then confer evolutionary benefits. We demonstrate this benefit using mathematical modeling and evolutionary simulations. Interestingly, we found signatures of predicted cross talk patterns in Mycobacterium tuberculosis. Furthermore, specificity was selected in environments where stimuli occurred randomly, thus reconciling specificity and cross talk. Implications follow for understanding bacterial evolution and for interventions.

The two-component system histidine kinase EnvZ contributes to Avian pathogenic Escherichia coli pathogenicity by regulating biofilm formation and stress responses

EnvZ, the histidine kinase (HK) of OmpR/EnvZ, transduces osmotic signals in Escherichia coli K12 and affects the pathogenicity of Shigella flexneri and Vibrio cholera. Avian pathogenic E. coli (APEC) is an extra-intestinal pathogenic E. coli (ExPEC), causing acute and sudden death in poultry and leading to severe economic losses to the global poultry industry. How the functions of EnvZ correlate with APEC pathogenicity was still unknown. In this study, we successfully constructed the envZ mutant strain AE17ΔenvZ and the inactivation of envZ significantly reduced biofilms and altered red, dry, and rough (rdar) morphology. In addition, AE17ΔenvZ was significantly less resistant to acid, alkali, osmotic, and oxidative stress conditions. Deletion of envZ significantly enhanced sensitivity to specific pathogen-free (SPF) chicken serum and increased adhesion to chicken embryonic fibroblast DF-1 cells and elevated inflammatory cytokine IL-1β, IL6, and IL8 expression levels. Also, when compared with the WT strain, AE17ΔenvZ attenuated APEC pathogenicity in chickens. To explore the molecular mechanisms underpinning envZ in APEC17, we compared the WT and envZ-deletion strains using transcriptome analyses. RNA-Seq results identified 711 differentially expressed genes (DEGs) in the envZ mutant strain and DEGs were mainly enriched in outer membrane proteins, stress response systems, and TCSs. Quantitative real-time reverse transcription PCR (RT-qPCR) showed that EnvZ influenced the expression of biofilms and stress responses genes, including ompC, ompT, mlrA, basR, hdeA, hdeB, adiY, and uspB. We provided compelling evidence showing EnvZ contributed to APEC pathogenicity by regulating biofilms and stress response expression.

Two-component systems regulate bacterial virulence in response to the host gastrointestinal environment and metabolic cues

Two-component systems are ubiquitous signaling mechanisms in bacteria that enable intracellular changes from extracellular cues. These bacterial regulatory systems couple external stimuli to control genetic expression via an autophosphorylation cascade that transduces membrane signals to intracellular locations, thereby allowing bacteria to rapidly adapt to the changing environmental conditions. Well known to control basic cellular processes, it is evident that two-component systems also exercise control over virulence traits, such as motility, secretion systems, and stress responses that impact the complex cascade of networks that alter virulence traits. In the gastrointestinal system, cues for activation of virulence-related two-component systems include metal ions, host-derived metabolites, and gut conditions. The diversity and origin of these cues suggest that the host can exert control over enteric pathogenicity via regulation in the gastrointestinal system. With the rise in multi-drug resistant pathogens, the potential control of pathogenicity with host cues via two-component systems presents a potential alternative to antimicrobials. Though the signaling mechanism itself is well studied, to date there is no systematic review compiling the host-associated cues of two-component systems and virulence traits. This review highlights the direct link between the host gastrointestinal environment and pathogenicity by focusing on two-component systems that are associated with the genetic expression of virulence traits, and that are activated by host-derived cues. The direct link between the host gastrointestinal environment, metabolites, and pathogenicity established in this review both underscores the importance of host-derived cues on bacterial activity and presents an enticing therapeutic target in the fight against antimicrobial resistant pathogens.

Targeting virulence regulation to disarm Acinetobacter baumannii pathogenesis

The development of anti-virulence drug therapy against Acinetobacter baumannii infections would provide an alternative to traditional antibacterial therapy that are increasingly failing. Here, we demonstrate that the OmpR transcriptional regulator plays a pivotal role in the pathogenesis of diverse A. baumannii clinical strains in multiple murine and G. mellonella invertebrate infection models. We identified OmpR-regulated genes using RNA sequencing and further validated two genes whose expression can be used as robust biomarker to quantify OmpR inhibition in A. baumannii. Moreover, the determination of the structure of the OmpR DNA binding domain of A. baumannii and the development of in vitro protein-DNA binding assays enabled the identification of an OmpR small molecule inhibitor. We conclude that OmpR is a valid and unexplored target to fight A. baumannii infections and we believe that the described platform combining in silico methods, in vitro OmpR inhibitory assays and in vivo G. mellonella surrogate infection model will facilitate future drug discovery programs.

Meta-analysis of caries microbiome studies can improve upon disease prediction outcomes

As one of the most prevalent infective diseases worldwide, it is crucial that we not only know the constituents of the oral microbiome in dental caries but also understand its functionality. Herein, we present a reproducible meta-analysis to effectively report the key components and the associated functional signature of the oral microbiome in dental caries. Publicly available sequencing data were downloaded from online repositories and subjected to a standardized analysis pipeline before analysis. Meta-analyses identified significant differences in alpha and beta diversities of carious microbiomes when compared to healthy ones. Additionally, machine learning and receiver operator characteristic analysis showed an ability to discriminate between healthy and disease microbiomes. We identified from importance values, as derived from random forest analyses, a group of genera, notably containing Selenomonas, Aggregatibacter, Actinomyces and Treponema, which can be predictive of dental caries. Finally, we propose the most appropriate study design for investigating the microbiome of dental caries by synthesizing the studies, which had the most accurate differentiation based on random forest modelling. In conclusion, we have developed a non-biased, reproducible pipeline, which can be applied to microbiome meta-analyses of multiple diseases, but importantly we have derived from our meta-analysis a key group of organisms that can be used to identify individuals at risk of developing dental caries based on oral microbiome inhabitants.

Lactate causes downregulation of Helicobacter pylori adhesin genes sabA and labA while dampening the production of proinflammatory cytokines

Chronic inflammation induced by Helicobacter pylori is strongly associated with gastric cancer development, which is influenced by both bacterial virulence and host genetics. The sialic acid-binding adhesin SabA and the MUC5AC-binding adhesin LabA are important H. pylori virulence factors that facilitate adhesion of the bacterium, which is a crucial step in colonization. Lactate utilization has been reported to play a key role in the pathogenicity of different bacterial species. However, this is poorly understood in H. pylori. In this study, we investigated the effect of lactate on H. pylori adhesin gene expression and the regulation of host inflammatory cytokines. We show that the bacterial adhesins SabA and LabA were downregulated at the transcriptional level during incubation of H. pylori with lactate. Downregulation of sabA required the involvement of the two-component system ArsRS, while labA was regulated via the CheA/CheY system, indicating differences in the regulation of these genes in response to lactate. The levels of the proinflammatory cytokines TNF and IL-6 in H. pylori-stimulated macrophages were reduced when lactate was present. Interestingly, glucose did not prevent the secretion of these cytokines. Taken together, our data suggest that lactate affects H. pylori adhesin gene expression and the host response upon infection.

Combined transcriptomic and metabolomic analysis of Salmonella in the presence or absence of PhoP-PhoQ system under low Mg2+ conditions

INTRODUCTION

Previous reports revealed the role played by Salmonella PhoP-PhoQ system in virulence activation, antimicrobial tolerance and intracellular survival, the impact of PhoP-PhoQ on cell metabolism has been less extensively described.

OBJECTIVES

The aim of this study is to address whether and how the PhoP-PhoQ system affects the cell metabolism of Salmonella.

METHODS

We constructed a Salmonella phoP deletion mutant strain TT-81 (PhoP-OFF), a Salmonella PhoP constitutively expressed strain TT-82 (PhoP-ON) and a wild-type Salmonella PhoP strain TT-80 (PhoP-N), using P22-mediated generalized transduction or λ Red-mediated targeted mutagenesis. We then measured the in vitro growth kinetics of all test strains and determined their metabolomic and transcriptomic profiles using gas chromatography coupled with tandem mass spectrometry (GC-MS/MS) and RNA-seq technique, respectively.

RESULTS

Low-Mg²⁺ conditions impaired the growth of the phoP deletion mutant strain TT-81 (PhoP-OFF) dramatically. 42 metabolites in the wild-type PhoP strain TT-80 (PhoP-N) and 28 metabolites in the PhoP constitutively expressed strain TT-82 (PhoP-ON) changed by the absence of phoP. In contrast, the level of 19 compounds in TT-80 (PhoP-N) changed comparing to the PhoP constitutively expressed strain TT-82 (PhoP-N). The mRNA level of 95 genes in TT-80 (PhoP-N) changed when phoP was disrupted, wherein 78 genes downregulated and 17 genes upregulated. 106 genes were determined to be differentially expressed between TT-81 (PhoP-OFF) and TT-82 (PhoP-ON). While only 16 genes were found to differentially expressed between TT-82 (PhoP-ON) and TT-80 (PhoP-N).

CONCLUSION

Our findings confirmed the impact of PhoP-PhoQ system on lipopolysaccharide (LPS) modification, energy metabolism, and the biosynthesis or transport of amino acids. Most importantly, we demonstrated that the turnover of a given metabolite could respond differentially to the level of phoP. Taken together, the present study provided new insights into the adaptation of Salmonella to the host environment and helped to characterize the impact of the PhoP-PhoQ system on the cell metabolism.

Membrane Vesicles Derived from Gut Microbiota and Probiotics: Cutting-Edge Therapeutic Approaches for Multidrug-Resistant Superbugs Linked to Neurological Anomalies

Multidrug-resistant (MDR) superbugs can breach the blood-brain barrier (BBB), leading to a continuous barrage of pro-inflammatory modulators and induction of severe infection-related pathologies, including meningitis and brain abscess. Both broad-spectrum or species-specific antibiotics (β-lactamase inhibitors, polymyxins, vancomycin, meropenem, plazomicin, and sarecycline) and biocompatible poly (lactic-co-glycolic acid) (PLGA) nanoparticles have been used to treat these infections. However, new therapeutic platforms with a broad impact that do not exert off-target deleterious effects are needed. Membrane vesicles or extracellular vesicles (EVs) are lipid bilayer-enclosed particles with therapeutic potential owing to their ability to circumvent BBB constraints. Bacteria-derived EVs (bEVs) from gut microbiota are efficient transporters that can penetrate the central nervous system. In fact, bEVs can be remodeled via surface modification and CRISPR/Cas editing and, thus, represent a novel platform for conferring protection against infections breaching the BBB. Here, we discuss the latest scientific research related to gut microbiota- and probiotic-derived bEVs, and their therapeutic modifications, in terms of regulating neurotransmitters and inhibiting quorum sensing, for the treatment of neurodegenerative diseases, such as Parkinson's and Alzheimer's diseases. We also emphasize the benefits of probiotic-derived bEVs to human health and propose a novel direction for the development of innovative heterologous expression systems to combat BBB-crossing pathogens.

Insights into the structure and function of the histidine kinase ComP from Bacillus amyloliquefaciens based on molecular modeling

The ComPA two-component signal transduction system (TCS) is essential in Bacillus spp. However, the molecular mechanism of the histidine kinase ComP remains unclear. Here, we predicted the structure of ComP from Bacillus amyloliquefaciens Q-426 (BaComP) using an artificial intelligence approach, analyzed the structural characteristics based on the molecular docking results and compared homologous proteins, and then investigated the biochemical properties of BaComP. We obtained a truncated ComPS protein with high purity and correct folding in solution based on the predicted structures. The expression and purification of BaComP proteins suggested that the subdomains in the cytoplasmic region influenced the expression and stability of the recombinant proteins. ComPS is a bifunctional enzyme that exhibits the activity of both histidine kinase and phosphotransferase. We found that His571 played an obligatory role in the autophosphorylation of BaComP based on the analysis of the structures and mutagenesis studies. The molecular docking results suggested that the HATPase_c domain contained an ATP-binding pocket, and the ATP molecule was coordinated by eight conserved residues from the N, G1, and G2 boxes. Our study provides novel insight into the histidine kinase BaComP and its homologous proteins.