Structural insights into the signalling mechanisms of two-component systems

Differential size-dependent response patterns and antibiotic resistance development mechanism in anammox consortia

Antibiotic resistance is a global threat to human and animal health. Anaerobic ammonia oxidation (anammox) is an efficient and innovative wastewater treatment technology, which can be served as a promising approach to teat antibiotic wastewater. This study systematically investigated effects of sulfamethazine on the performance, microbial community dynamics and the resistome in anammox systems inoculated with different-sized granular sludge. The activity and performance of small (< 0.5 mm) anammox granules were more susceptible to sulfamethazine stress than those of medium (0.5-1.0 mm) and large (1.0-2.0 mm) granules. Sulfamethazine addition greatly increased the diversity and abundance of mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs). Based on the metagenomic analysis, the horizontal transfer of ARGs in the anammox system was upregulated through bacterial oxidative stress, pili synthesis and type IV secretion system. In addition, two strains of sulfamethazine-resistant bacteria (Pseudomonas asiatica sp. nov. and Pseudomonas shirazica sp. nov.) were isolated from the anammox system. Their whole genome sequencing results showed that the most abundant plasmid was pkF7158B, which mediated the horizontal transfer of two main multidrug resistance genes (cpxR and mexB). This work provides a holistic insight into microbial heterogeneity of different-sized anammox granular sludge and their evolution and resistance development mechanism.

Antibiofilm efficacies and mechanism of perillaldehyde against Shewanella putrefaciens

Shewanella putrefaciens is Gram-negative bacterium and important spoilage organism in aquatic products, negatively impacting the organoleptic properties of aquatic products. S. putrefaciens could form biofilm, which increases persistence and contamination in food system. Efficient antibiofilm strategies are urgently needed to reduce its presence in food environment. This study aimed to explore the impact of perillaldehyde on S. putrefaciens biofilm and the underlying mechanisms using transcriptomic analysis. Perillaldehyde remarkably reduced extracellular polymeric substance contents, inhibited metabolic activity of biofilm cells, disrupted bacterial motility, loose biofilm structure and decreased biofilm formation in food juice and on various surfaces (stainless steel, silicone, glass, razon clam and shrimp). Transcriptome analysis revealed that 553 differentially expressed genes were identified, among which 254 were down-regulated and 299 were up-regulated. The differentially expressed genes included ATP-binding cassette transporters, ribosome, two-component systems, resistance/nodulation/division efflux systems, quorum sensing, amino acid metabolism, biosynthesis and degradation pathways. The findings demonstrate antibiofilm properties of perillaldehyde against S. putrefaciens and indicate that perillaldehyde could be developed as an antibiofilm agent to mitigate existence and contamination of S. putrefaciens and to reduce associated food loss caused by this spoilage bacteria.

Repurposing FDA-approved drugs for combating tigecycline resistance in Acinetobacter baumannii: in silico screening against BaeR protein

Acinetobacter baumannii is becoming a gravely threatening nosocomial infection with a higher mortality rate. The present study targets the BaeR protein that mediates resistance to tigecycline antibiotics. The BaeR protein, along with the aid of BaeS, senses the incoming antibiotics and stimulates the expression of resistance proteins. These resistance proteins efflux the antibiotics and protect the cells from its effect. The main goal of the current study is to determine potential inhibitors from already existing FDA-approved drugs that could mitigate the BaeR protein. A range of in silico approaches, including molecular dynamics, virtual screening, SIFT analysis, ADMET, DFT, MM/GBSA, MMPBSA and per residue interaction analysis, were performed to identify inhibitors against this protein. The screening of FDA-approved compounds against the BaeR protein yielded 620 compounds. These compounds were clustered by SIFT to distinguish related compounds, it resulted in 20 different clusters. The top five clusters that can accommodate the binding site with better interaction and score by fulfilling all criteria were selected. The DFT analysis showed a smaller energy gap among all the compounds, indicating the ability of the compound to form firm interactions. All the compounds showed less binding free energy in both MM/GBSA and MM/PBSA analyses. The compounds were observed to be stable throughout the simulation. The per-residue interaction analysis confirmed that interactions with binding site residues were stable throughout the simulation. As a result of the study, four compounds, namely ZINC000003801919, DB01203, DB11217 and ZINC0000000056652, were identified as efficient candidates to deal with antimicrobial resistance in A. baumannii.

Advanced microbiome therapeutics for oral delivery of peptides and proteins: Advances, challenges, and opportunities

Peptide and protein medicines have changed the therapeutic landscape for many diseases, yet oral delivery remains a significant challenge due to enzymatic degradation, instability, and poor permeability in the gastrointestinal tract. Advanced Microbiome Therapeutics (AMTs) could overcome some of these barriers by producing and releasing therapeutic peptides directly in the gastrointestinal tract. AMTs can localize peptide production at the site of absorption, providing either sustained or controlled release while potentially reducing side effects associated with systemic administration. Here, this review assesses the status of AMTs for oral peptide delivery and discusses the potential integration of enzyme inhibitors, permeation enhancers, and mucoadhesive to improve oral bioavailability further. Combining these approaches could pave the way for more widespread oral delivery strategies for peptide and protein medicines.

Navigating Antibiotic Resistance in Gram-Negative Bacteria: Current Challenges and Emerging Therapeutic Strategies

The rapid rise of antibiotic resistance poses a severe global health crisis, necessitating new approaches to counter this growing threat. The problem is exacerbated in Gram-negative bacterial pathogens as many antibiotics are unable to enter these cells owing to their unique additional outer membrane barrier. In this review, we discuss the challenges of targeting Gram-negative bacteria, including the complexity of the outer membrane, as well as the presence of efflux pumps and β-lactamases that contribute to resistance. We also review solutions proposed to facilitate the entry and accumulation of antibiotics in Gram-negative bacteria. These involve using existing antibiotics in combination with other inhibitors to attack the bacterial cell synergistically. We also highlight approaches to target Gram-negative pathogens via novel modes of action, providing new strategies to tackle antibiotic resistance.

The deletion of the uvrY in Aeromonas veronii disrupted the BarA/UvrY two-component system, decreasing persister formation and bacterial resistance to multiple antibiotics

Antibiotic resistance (AR) is increasingly recognized as a critical global public health threat. Aeromonas species, widely distributed in aquatic environments, have emerged as potential foodborne pathogens. These bacteria are frequently detected in water sources and various ready-to-eat foods, posing a significant risk to food safety and human health. Two-component systems (TCSs) are key regulators of stress tolerance and adaptive behaviors, but the role of the BarA-UvrY TCS in AR is unclear. In our study, multidrug-resistant Aeromonas veronii (A. veronii) strains isolated from the grass carp intestinal contents were used to investigate the role of uvrY in AR, and mutant strain (Δ uvrY) was constructed using homologous recombination. The growth characteristics of wild-type (WT), Δ uvrY, and complemented strains (C-Δ uvrY) were evaluated under various stress conditions. Additionally, prokaryotic transcriptome analysis was performed to identify the downstream stress-factors in WT and Δ uvrY. The results indicated that the Δ uvrY strain exhibited reduced tolerance to osmotic and acid - base stress compared with the WT and C-Δ uvrY. Furthermore, the deletion of uvrY in A. veronii significantly impaired persister formation and decreased resistance to multiple antibiotics, particularly tetracyclines and chloramphenicol. The transcriptome analysis revealed that the increased susceptibility of Δ uvrY to tetracyclines was accompanied by a significant down-regulation of efflux pump genes and NADH dehydrogenase I. STRING network analysis further demonstrated that the BarA-UvrY TCS is associated with genes encoding NADH dehydrogenase I and efflux pump. Additionally, efflux experiments and respiratory rate assays confirmed that the Δ uvrY strain exhibited reduced efflux pump activity and a low respiratory rate, establishing a clear correlation between these two processes. Collectively, BarA-UvrY TCS play a crucial role in AR and persister formation by mediating energy-dependent efflux mechanisms. This study provides mechanistic insights into the regulatory functions of UvrY and offers a theoretical foundation for developing novel strategies to control A. veronii infections and enhance antimicrobial interventions.

Cross-talk between signal transduction systems and metabolic networks in antibiotic resistance and tolerance

The comprehensive antibiotic resistance of pathogens signifies the oneset of the "post-antibiotic era", and the myriad treatment challenges posed by "superbugs" have emerged as the primary threat to human health. Recent studies indicate that bacterial resistance and tolerance development are mediated at the metabolic level by various signalling networks (e.g., quorum sensing systems, second messenger systems, and two-component systems), resulting in metabolic rearrangements and alterations in bacterial community behaviour. This review focuses on current research, highlighting the intrinsic link between signalling and metabolic networks in bacterial resistance and tolerance.

A Staphylococcus aureus Virulence Inhibitor Identified by SaeRS Refactoring and Screening in Bacillus subtilis

Bacteria utilize two-component system (TCS) signal transduction pathways to sense environmental and physiological stimuli and mount appropriate responses. In opportunistic pathogens such as Staphylococcus aureus, TCSs activate virulence programs in response to host defense systems. Due to their critical role in pathogenesis, TCSs are important targets for antivirulence drug discovery campaigns. However, challenges associated with screening TCSs in pathogens and in vitro have limited the output of such efforts to a small number of characterized drug candidates. Here, we functionally express the S. aureus virulence-regulating TCS SaeRS from synthetic gene regulatory elements in the model bacterium Bacillus subtilis to reliably screen this system against a small molecule library under simple culturing conditions. Our approach reveals the compound NSC97920 as a strong inhibitor of SaeRS signaling. We combine in situ, in vivo, in silico, and in vitro characterization to demonstrate that NSC97920 suppresses the critical step of autophosphorylation in the SaeS histidine kinase, resulting in strong antivirulence activity. Our work shows that heterologous expression and screening of TCSs in model bacteria could accelerate the development of therapeutics against antibiotic-resistant pathogens.

Group A Streptococcal asparagine metabolism regulates bacterial virulence

Group A Streptococcus (GAS) causes various human diseases linked to virulome expression predominantly regulated by the two-component system (TCS), CovR/S. Here, we demonstrate that asparagine (Asn) presence in a minimal chemically defined medium increases virulence gene expression in a CovR-dependent fashion. It also decreases the transcription of asparagine synthetase (AsnA), the ABC transporter responsible for Asn uptake (GlnPQ), and that of the hemolysin toxins responsible for scavenging Asn from the host. Metabolomics data show that Asn availability increases intracellular ADP/ATP ratio, which enhances phosphatase activity in structurally related CovS sensors and is probably responsible for the Asn-mediated decrease in CovR phosphorylation. Mutants deficient in AsnA, GlnPQ, asparaginase, (AsnB) activities are attenuated in a mouse model of human GAS invasive soft tissue infection. The similarity between the mechanisms of Asn-mediated regulation of GAS virulence and tumor growth suggests that, as in cancer, components maintaining Asn homeostasis could be targeted for anti-GAS treatments.

Evaluation of protective immune response of live-attenuated candidate vaccines ΔcpxA and ΔcpxR against Vibrio alginolyticus in pearl gentian grouper

The grouper farming industry was severely influenced by vibriosis. In this study, we developed two live-attenuated vaccine (LAV) candidates against Vibrio alginolyticus infection in pearl gentian groupers using cpxA or cpxR mutant strains of V. alginolyticus (ΔcpxA and ΔcpxR). Groupers were administrated with ΔcpxA and ΔcpxR at the dose of 1.0 × 104 CFU/fish (safety dose) to evaluate the immune protect effect of LAV. The increasing median lethal dose (LD50) of ΔcpxA and ΔcpxR indicated the decreased virulence of bacteria to groupers. Our results suggested that two LAVs achieved over 70 % relative percent survival (RPS) after groupers were challenged by V. alginolyticus on 14 days post-immunization. The immune protection was mainly attributed to the up-regulation of immune-related gene expression (IL-6, IL-12, TNF-α, TLR2, TLR5S, CD4, MHC-Iα, IFN-γ2 and NF-κB), the higher activities of catalase (CAT), lysozyme (LZM), superoxide dismutase (SOD), and the increasing production of total protein (TP) in serum. The research indicated that the vaccination of fish with ΔcpxA and ΔcpxR can induce the innate and acquired immunity and survival rate of groupers after bacterial infection, so they can be considered as the promising candidates of vaccine for grouper industry.

Involvement of an orphan response regulator of the two-component regulatory system in the formation of physiologically mature sporangia in Actinoplanes missouriensis

The actinomycete Actinoplanes missouriensis forms terminal sporangia that contain dormant sporangiospores. Upon contact with water, sporangia release zoospores through a process called sporangium dehiscence. In this study, we characterized asfR (AMIS_76070), which encodes an orphan response regulator receiver domain protein of the two-component regulatory system, as one of 136 genes whose transcription was highly activated during sporangium formation. Actinoplanes sporangium formation regulator (AsfR) homologs are conserved among Actinoplanes bacteria. An asfR null mutant (ΔasfR) strain formed normally shaped sporangia containing apparently normal dormant spores, but they exhibited defective sporangium dehiscence; the number of spores released from the sporangia of the ΔasfR strain was four orders of magnitude lower than that from the sporangia of the wild-type strain. This phenotypic change was recovered by introducing asfR with its own promoter into the ΔasfR strain. Based on the amino acid sequence and predicted structure, the function of AsfR appeared to be controlled by the phosphorylation of Asp-72. Consistently, the phenotypic change observed in the ΔasfR strain was not restored by introducing a mutated asfR (D72N) gene. Three orphan histidine kinases (HKs) in A. missouriensis were found to interact with AsfR by screening using a bacterial two-hybrid assay. However, gene disruption experiments revealed that these three HKs were not required for sporangium dehiscence in A. missouriensis. Although the molecular functions of AsfR remain to be elucidated, this study shows that AsfR is involved in the formation of physiologically mature sporangia that are fully prepared to release spores under sporangium dehiscence-inducing conditions.IMPORTANCEActinoplanes missouriensis undergoes a life cycle involving complex morphological development, including mycelial growth, sporangium formation and dehiscence, swimming as zoospores, germination, and outgrowth to mycelial growth. In this study, we revealed that a stand-alone response regulator receiver domain protein, AsfR, is required for the formation of physiologically mature sporangia that can release spores under sporangium dehiscence-inducing conditions. A. missouriensis seems to express genes that are involved in sporangium dehiscence during sporangium formation, considering that an asfR null mutant produced normally shaped sporangia, but these sporangia were deficient in sporangium dehiscence. Although the molecular functions of AsfR, as well as the histidine kinase(s) that phosphorylates AsfR, remain to be elucidated, identification of AsfR as a possible key regulator for the preparation of the onset and progression of sporangium dehiscence is significant, because almost no proteins involved in the early stages of sporangium dehiscence have been identified in A. missouriensis.

Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems

Different microbial communities are impacted disproportionately by environmental disturbances. The degree to which a community can remain unchanged under a disturbance is referred to as resistance1. However, the contributing ecological factors, which infer a community's resistance are unknown. In this study, the impact of historical environmental stability on ecological phenomena and microbial community resistance to shocks was investigated. Three separate methanogenic bioreactor consortia, which were subjected to varying degrees of historical environmental stability, and displayed different levels of resistance to an organic loading rate (OLR) shock were sampled. Their community composition was assessed using high throughput sequencing of 16S rRNA genes and assembly based metagenomics. The effect environmental instability on ecological phenomena such as microbial community assembly, microbial niche breadth and the rare biosphere were assessed in the context of each reactor's demonstrated resistance to an OLR shock. Additionally, metagenome assembled genomes were analysed for functional effects of prolonged stability/instability. The system which was subjected to more environmental instability experienced more temporal variation in community beta diversity and a proliferation of specialists, with more abundant two component regulatory systems. This community was more susceptible to deterministic community assembly and demonstrated a lower degree of resistance, indicating that microbial communities experiencing longer term environmental instability (e.g. variations in pH or temperature) are less able to resist a large disturbance.

A small periplasmic protein governs broad physiological adaptations in Vibrio cholerae via regulation of the DbfRS two-component system

Two-component signaling pathways allow bacteria to sense and respond to environmental changes, yet the sensory mechanisms of many remain poorly understood. In the pathogen Vibrio cholerae, the DbfRS two-component system controls the biofilm lifecycle, a critical process for environmental persistence and host colonization. Here, we identified DbfQ, a small periplasmic protein encoded adjacent to dbfRS, as a direct modulator of pathway activity. DbfQ directly binds the sensory domain of the histidine kinase DbfS, shifting it toward phosphatase activity and promoting biofilm dispersal. In contrast, outer membrane perturbations, caused by mutations in lipopolysaccharide biosynthesis genes or membrane-damaging antimicrobials, activate phosphorylation of the response regulator DbfR. Transcriptomic analyses reveal that DbfR phosphorylation leads to broad transcriptional changes spanning genes involved in biofilm formation, central metabolism, peptidoglycan synthesis, and cellular stress responses. Constitutive DbfR phosphorylation imposes severe fitness costs in an infection model, highlighting this pathway as a potential target for anti-infective therapeutics. We find that dbfQRS-like genetic modules are widely present across bacterial phyla, underscoring their broad relevance in bacterial physiology. Collectively, these findings establish DbfQ as a new class of periplasmic regulator that influences two-component signaling and bacterial adaptation.

The GacS/GacA two-component system strongly regulates antimicrobial competition mechanisms of Pseudomonas fluorescens MFE01 strain

Pseudomonas fluorescens MFE01 is an environmental bacterium characterized by an hyperactive type 6 secretion system (T6SS) and a strong emission of volatile organic compounds (VOCs). In a previous study, a transposition mutant, 3H5, exhibited an inactive T6SS and altered VOC emission. In 3H5, the interruption of trpE gene by the transposon was insufficient to explain these phenotypes. To determine the actual impact of this insertion, a comparative transcriptomic analysis was performed on the two-component system GacS/GacA, known to influence numerous phenotypes in Pseudomonas. The results demonstrated that the gacS gene is less expressed in 3H5 than in MFE01. Phenotypic analysis of a gacS deletion mutant, ΔgacS, confirmed many similarities between ΔgacS and 3H5. Indeed, ΔgacS exhibited an inactive T6SS and an altered VOC emission profile. In-depth analysis of volatilomes and phenotypes correlated with the decrease in gacS transcription, highlighting that the emission of 1-undecene is under the strict control of GacS/GacA. This study confirms that 1-undecene is not the sole volatile molecule responsible for MFE01's inhibition of Legionella. Moreover, MFE01 has antimicrobial activity against the phytopathogenic oomycetes Phytophthora infestans via hydrogen cyanide (HCN) emission, which is also controlled by GacS. In MFE01, GacS/GacA is also a partial positive regulator of other VOC emission, whose reduced emission in 3H5 coincides with the decrease in gacS transcription.

IMPORTANCE

Our model strain Pseudomonas fluorescens MFE01 uses an active type VI secretion system (T6SS) and volatile compounds (VCs) to outcompete other microorganisms in the natural environment. By investigating the cellular mechanism regulating the production of these weapons, we identified the two-component system GacS/GacA. Indeed, GacS cellular membrane sensor plays a crucial role in regulating T6SS activity and VC emission. Among the latter, 1-undecene and hydrogen cyanide are strong aerial inhibitors of the Legionella human pathogen and the Phytophtora infestans major plant pest, respectively. The aim is to improve the understanding of the regulation of these volatile molecule emission and the critical role of a global regulator in both plant and human health.

Signaling molecule alleviates inhibitory impacts of surfactant on methane production during sludge and food waste co-digestion: Insights of electron bifurcation and quorum sensing

Anaerobic co-digestion of food waste (FW) and waste-activated sludge (WAS) is increasingly recognized as a viable solution for managing organic wastes. However, emerging contaminants (ECs), such as surfactant like sodium dodecylbenzene sulfonate (SDBS), can severely inhibit methane production. This study explores the potential of C6-HSL, a quorum sensing (QS) signaling molecule, to mitigate inhibitory effects of SDBS during FW and WAS co-digestion. Results demonstrated that SDBS reduced methane yields from 122.2 mL/g VSS in the control to 18.5 mL/g VSS, but supplementation with C6-HSL alleviated this inhibition, increasing yields to 115.4 mL/g VSS. C6-HSL not only restored suppressed methanogen populations but also promoted bacteria-archaea mutualisms, enhancing system resilience and stability. Additionally, C6-HSL enhanced key electron bifurcation pathways critical for overcoming thermodynamic barriers in methane metabolism, increasing the relative abundance of functional genes involved in four methane metabolism modules. Moreover, C6-HSL enhanced QS system (e.g., SecY and trpE), prompting microorganisms to activate adaptive mechanisms, such as DNA replication (e.g., rfcL and rfcS), efflux pumps (e.g., mdlA and mdlB), and bacterial chemotaxis (e.g., cheB and cheD), to counter SDBS toxicity. Correspondingly, TCA cycle (e.g., fumA and fumB) was also upregulated to ensure sufficient energy and electrons for methane production and microbial adaptation.

Structural and biophysical characterization of the cytoplasmic domains of HprS kinase and its interactions with the cognate regulator HprR

The HprSR constitutes the bacterial two-component regulatory system engaged by Escherichia coli to reduce the damaging effects of reactive chlorine and oxygen species present in its cytosol. Hypochlorous acid (HOCl) has been shown to be the molecule capable of activating of the HprSR system. HOCl is produced upon pathogen invasion by phagocytic cells of the human innate immune system, particularly neutrophils, to take advantage of its powerful antimicrobial attributes. Therefore, comprehensive studies concerning bacterial sensing and regulatory HprSR system are indispensable in understanding and effectively eliminating pathogens. Here we present the first crystal structure, solved at 1.7 Å resolution, of the HprS cytoplasmic domains arranged as a homodimer. In both protomers, the catalytic ATP-binding domain contains a non-hydrolysable ATP analog coordinated by a magnesium ion. This structure allowed us to provide a detailed characterization of kinase-substrate interaction. Furthermore, the structural data are supported by biophysical studies of kinase interaction with cognate response regulator HprR and substrate ATP. The kinase activity is also assessed in the presence or absence of HprR.

RcsF-independent mechanisms of signaling within the Rcs phosphorelay

The Rcs (regulator of capsule synthesis) phosphorelay is a conserved cell envelope stress response mechanism in enterobacteria. It responds to perturbations at the cell surface and the peptidoglycan layer from a variety of sources, including antimicrobial peptides, beta-lactams, and changes in osmolarity. RcsF, an outer membrane lipoprotein, is the sensor for this pathway and activates the phosphorelay by interacting with an inner membrane protein IgaA. IgaA is essential; it negatively regulates the signaling by interacting with the phosphotransferase RcsD. We previously showed that RcsF-dependent signaling does not require the periplasmic domain of the histidine kinase RcsC and identified a dominant negative mutant of RcsD that can block signaling via increased interactions with IgaA. However, how the inducing signals are sensed and how signal is transduced to activate the transcription of the Rcs regulon remains unclear. In this study, we investigated how the Rcs cascade functions without its only known sensor, RcsF, and characterized the underlying mechanisms for three distinct RcsF-independent inducers. Previous reports showed that Rcs activity can be induced in the absence of RcsF by a loss of function mutation in the periplasmic oxidoreductase DsbA or by overexpression of the DnaK cochaperone DjlA. We identified an inner membrane protein, DrpB, as a multicopy RcsF-independent Rcs activator in E. coli. The loss of the periplasmic oxidoreductase DsbA and the overexpression of the DnaK cochaperone DjlA each trigger the Rcs cascade in the absence of RcsF by weakening IgaA-RcsD interactions in different ways. In contrast, the cell-division associated protein DrpB uniquely requires the RcsC periplasmic domain for activation; this domain is not needed for RcsF-dependent signaling. This suggests the possibility that the RcsC periplasmic domain acts as a sensor for some Rcs signals. Overall, the results add new understanding to how this complex phosphorelay can be activated by diverse mechanisms.

Non-antibiotic disinfectant synchronously interferes methane production and antibiotic resistance genes propagation during sludge anaerobic digestion: Activation of microbial adaptation and reconfiguration of bacteria-archaea synergies

Waste activated sludge (WAS) presents both resource recovery potential and pollution risks, making its efficient treatment challenging. Anaerobic digestion is broadly recognized as a green and sustainable approach to WAS treatment, whose efficiency is easily impacted by the exogeneous pollutants in WAS. However, the impact of polyhexamethylene guanidine (PHMG), as a widely-used non-antibiotic disinfectant, on WAS digestion under semi-continuous flow conditions remains unclear. In this study, CH4 production decreased from 16.1 mL/g volatile suspended solids (VSS) in the control to 13.2 mL/g VSS and 0.3 mL/g VSS under low and high PHMG exposure, respectively, while PHMG increased the number of antibiotic resistance gene (ARG) copies per bacterium by 4.6-12.7 %. Molecular docking analysis revealed that PHMG could spontaneously bind to and disintegrate WAS (binding energy:2.35 and -9.62 kcal/mol), increasing the likelihood of microbial exposure to PHMG. This led to an increase in bacterial abundance and a reduction in archaeal populations, resulting in bacterial dominance in ecological niches. The network topology index in PHMG-treated reactors was consistently lower than in the control, with a higher proportion of negatively correlated links, indicating a more antagonistic relationship between bacteria and archaea. Consequently, PHMG significantly interfered with key genes involved in CH4 biosynthesis (e.g., mch and mtd). Interestingly, methanogenic activity and archaeal chemotaxis (e.g., rfk and cheA) partially recovered under low PHMG exposure due to archaeal adaptation through quorum sensing and two-component systems. However, this adaptation process also contributed to the propagation of ARGs through horizontal gene transfer, facilitated by the enhancement of mobile genetic elements and ARGs hosts. These findings confirm the ecological risks of PHMG and highlight the need for effective WAS disposal strategies.

Cryo-EM structures of a bathy phytochrome histidine kinase reveal a unique light-dependent activation mechanism

Phytochromes are photoreceptor proteins in plants, fungi, and bacteria. They can adopt two photochromic states with differential biochemical responses. The structural changes transducing the signal from the chromophore to the biochemical output modules are poorly understood due to challenges in capturing structures of the dynamic, full-length protein. Here, we present cryoelectron microscopy (cryo-EM) structures of the phytochrome from Pseudomonas aeruginosa (PaBphP) in its resting (Pfr) and photoactivated (Pr) state. The kinase-active Pr state has an asymmetric, dimeric structure, whereas the kinase-inactive Pfr state opens up. This behavior is different from other known phytochromes and we explain it with the unusually short connection between the photosensory and output modules. Multiple sequence alignment of this region suggests evolutionary optimization for different modes of signal transduction in sensor proteins. The results establish a new mechanism for light-sensing by phytochrome histidine kinases and provide input for the design of optogenetic phytochrome variants.

Effect of gamma irradiation on the proteogenome of cold-acclimated Kocuria rhizophila PT10

The effects of ionizing radiation (IR) on the protein dynamics of cold-stressed cells of a radioresistant actinobacterium, Kocuria rhizophila PT10, isolated from the rhizosphere of the desert plant Panicum turgidum were investigated using a shotgun methodology based on nanoflow liquid chromatography coupled to tandem mass spectrometry. Overall, 1487 proteins were certified, and their abundances were compared between the irradiated condition and control. IR of cold-acclimated PT10 triggered the over-abundance of proteins involved in (1) a strong transcriptional regulation, (2) amidation of peptidoglycan and preservation of cell envelope integrity, (3) detoxification of reactive electrophiles and regulation of the redox status of proteins, (4) base excision repair and prevention of mutagenesis and (5) the tricarboxylic acid (TCA) cycle and production of fatty acids. Also, one of the more significant findings to emerge from this study is the SOS response of stressed PT10. Moreover, a comparison of top hits radio-modulated proteins of cold-acclimated PT10 with proteomics data from gamma-irradiated Deinococcus deserti showed that stressed PT10 has a specific response characterised by a high over-abundance of NemA, GatD, and UdgB.

The two-component histidine kinase BdHk1 regulates fungal development, virulence and fungicide sensitivity in Botryosphaeria dothidea

Histidine kinases (HKs) allow fungal cells to sense and respond to environmental stimuli. However, the biological role of HKs in Botryosphaeria dothidea, the causal agent of Botryosphaeria canker and apple ring rot, remains unknown. In this study, we identified and characterized the two-component histidine kinase BdHk1 in B. dothidea. Targeted knockout of BdHK1 gene resulted in severe conidiation and pathogenicity defects. In addition, the ΔBdHk1 mutant showed hypersensitivity to osmotic stress, but resistance to phenylpyrrole and dicarboximide fungicides. Moreover, the ΔBdHk1 mutant exhibited significantly increased sensitivity to the cell membrane-damaging agent SDS and high temperature. Comparative transcriptome analysis revealed that inactivation of BdHk1 influenced multiple metabolic pathways in B. dothidea. Taken together, our results suggest that BdHk1 plays an important role in development, virulence and stress tolerance in B. dothidea.

A designed Zn 2+ sensor domain transmits binding information to transmembrane histidine kinases

Generating stimulus-responsive, allosteric signaling de novo is a significant challenge in protein design. In natural systems like bacterial histidine kinases (HKs), signal transduction occurs when ligand binding initiates a signal that is amplified across biological membranes over long distances to induce large-scale rearrangements and phosphorylation relays. Here, we ask whether our understanding of protein design and multi-domain, intramolecular signaling has progressed sufficiently to enable engineering of a HK with tunable de novo components. We generated de novo metal-binding sensor domains and substituted them for the native sensor domain of a transmembrane HK, affording chimeras that transduce signals initiated from a de novo sensor. Signaling depended on the designed sensor's stability and the interdomain linker's phase and length. These results show the usefulness of de novo design to elucidate biochemical mechanisms and principles for design of new signaling systems.

Constitutive activation of two-component systems reveals regulatory network interactions in Streptococcus agalactiae

Bacterial two-component systems (TCSs) are signaling modules that control physiology, adaptation, and host interactions. A typical TCS consists of a histidine kinase (HK) that activates a response regulator via phosphorylation in response to environmental signals. Here, we systematically test the effect of inactivating the conserved phosphatase activity of HKs to activate TCS signaling pathways. Transcriptome analyses of 14 HK mutants in Streptococcus agalactiae, the leading cause of neonatal meningitis, validate the conserved HK phosphatase mechanism and its role in the inhibition of TCS activity in vivo. Constitutive TCS activation, independent of environmental signals, enables high-resolution mapping of the regulons for several TCSs (e.g., SaeRS, BceRS, VncRS, DltRS, HK11030, HK02290) and reveals the functional diversity of TCS signaling pathways, ranging from highly specialized to interconnected global regulatory networks. Targeted analysis shows that the SaeRS-regulated PbsP adhesin acts as a signaling molecule to activate CovRS signaling, thereby linking the major regulators of host-pathogen interactions. Furthermore, constitutive BceRS activation reveals drug-independent activity, suggesting a role in cell envelope homeostasis beyond antimicrobial resistance. This study highlights the versatility of constitutive TCS activation, via phosphatase-deficient HKs, to uncover regulatory networks and biological processes.

The HmrABCX pathway regulates the transition between motile and sessile lifestyles in Caulobacter crescentus by a mechanism independent of hfiA transcription

During its cell cycle, the bacterium Caulobacter crescentus switches from a motile, free-living state, to a sessile surface-attached cell. During this coordinated process, cells undergo irreversible morphological changes, such as shedding of their polar flagellum and synthesis of an adhesive holdfast at the same pole. In this work, we used genetic screens to identify genes involved in the regulation of the transition from the motile to the sessile lifestyle. We identified a predicted hybrid histidine kinase that inhibits biofilm formation and promotes the motile lifestyle: HmrA (holdfast and motility regulator A). Genetic screens and genomic localization led to the identification of additional genes that form a putative phosphorelay pathway with HmrA. We postulate that the Hmr pathway acts as a rheostat to control the proportion of cells harboring a flagellum or a holdfast in the population. Further genetic analysis suggests that the Hmr pathway impacts c-di-GMP synthesis through the diguanylate cyclase DgcB pathway. Our results also indicate that the Hmr pathway is involved in the regulation of motile to sessile lifestyle transition as a function of various environmental factors: biofilm formation is repressed when excess copper is present and derepressed under non-optimal temperatures. Finally, we provide evidence that the Hmr pathway regulates motility and adhesion without modulating the transcription of the holdfast synthesis regulator HfiA.

IMPORTANCE

Complex communities attached to a surface, or biofilms, represent the major lifestyle of bacteria in the environment. Such a sessile state enables the inhabitants to be more resistant to adverse environmental conditions. Thus, having a deeper understanding of the underlying mechanisms that regulate the transition between the motile and the sessile states could help design strategies to improve biofilms when they are beneficial or impede them when they are detrimental. For Caulobacter crescentus motile cells, the transition to the sessile lifestyle is irreversible, and this decision is regulated at several levels. In this work, we describe a putative phosphorelay that promotes the motile lifestyle and inhibits biofilm formation, providing new insights into the control of adhesin production that leads to the formation of biofilms.

Integrated large-scale metagenome assembly and multi-kingdom network analyses identify sex differences in the human nasal microbiome

BACKGROUND

Respiratory diseases impose an immense health burden worldwide. Epidemiological studies have revealed extensive disparities in the incidence and severity of respiratory tract infections between men and women. It has been hypothesized that there might also be a nasal microbiome axis contributing to the observed sex disparities.

RESULTS

Here, we study the nasal microbiome of healthy young adults in the largest cohort to date with 1593 individuals, using shotgun metagenomic sequencing. We compile the most comprehensive reference catalog for the nasal bacterial community containing 4197 metagenome-assembled genomes and integrate the mycobiome, to provide a valuable resource and a more holistic perspective for the understudied human nasal microbiome. We systematically evaluate sex differences and reveal extensive sex-specific features in both taxonomic and functional levels in the nasal microbiome. Through network analyses, we capture markedly higher ecological stability and antagonistic potentials in the female nasal microbiome compared to the male's. The analysis of the keystone bacteria reveals that the sex-dependent evolutionary characteristics might have contributed to these differences.

CONCLUSIONS

In summary, we construct the most comprehensive catalog of metagenome-assembled-genomes for the nasal bacterial community to provide a valuable resource for the understudied human nasal microbiome. On top of that, comparative analysis in relative abundance and microbial co-occurrence networks identify extensive sex differences in the respiratory tract community, which may help to further our understanding of the observed sex disparities in the respiratory diseases.

Engineering two-component systems for advanced biosensing: From architecture to applications in biotechnology

Two-component systems (TCSs) are prevalent signaling pathways in bacteria. These systems mediate phosphotransfer between histidine kinase and a response regulator, facilitating responses to diverse physical, chemical, and biological stimuli. Advancements in synthetic and structural biology have repurposed TCSs for applications in monitoring heavy metals, disease-associated biomarkers, and the production of bioproducts. However, the utility of many TCS biosensors is hindered by undesired performance due to the lack of effective engineering methods. Here, we briefly discuss the architectures and regulatory mechanisms of TCSs. We also summarize the recent advancements in TCS engineering by experimental or computational-based methods to fine-tune the biosensor functional parameters, such as response curve and specificity. Engineered TCSs have great potential in the medical, environmental, and biorefinery fields, demonstrating a crucial role in a wide area of biotechnology.

Signal-sensing triggers the shutdown of HemKR, regulating heme and iron metabolism in the spirochete Leptospira biflexa

Heme and iron metabolic pathways are highly intertwined, both compounds being essential for key biological processes, yet becoming toxic if overabundant. Their concentrations are exquisitely regulated, including via dedicated two-component systems (TCSs) that sense signals and regulate adaptive responses. HemKR is a TCS present in both saprophytic and pathogenic Leptospira species, involved in the control of heme metabolism. However, the molecular means by which HemKR is switched on/off in a signal-dependent way, are still unknown. Moreover, a comprehensive list of HemKR-regulated genes, potentially overlapped with iron-responsive targets, is also missing. Using the saprophytic species Leptospira biflexa as a model, we now show that 5-aminolevulinic acid (ALA) triggers the shutdown of the HemKR pathway in live cells, and does so by stimulating the phosphatase activity of HemK towards phosphorylated HemR. Phospho~HemR dephosphorylation leads to differential expression of multiple genes, including of heme metabolism and transport systems. Besides the heme-biosynthetic genes hemA and the catabolic hmuO, which we had previously reported as phospho~HemR targets, we now extend the regulon identifying additional genes. Finally, we discover that HemR inactivation brings about an iron-deficit tolerant phenotype, synergistically with iron-responsive signaling systems. Future studies with pathogenic Leptospira will be able to confirm whether such tolerance to iron deprivation is conserved among Leptospira spp., in which case HemKR could play a vital role during infection where available iron is scarce. In sum, HemKR responds to abundance of porphyrin metabolites by shutting down and controlling heme homeostasis, while also contributing to integrate the regulation of heme and iron metabolism in the L. biflexa spirochete model.

Structure and distribution of sensor histidine kinases in the fungal kingdom

Two-component systems (TCSs) are diverse cell signaling pathways that play a significant role in coping with a wide range of environmental cues in both prokaryotic and eukaryotic organisms. These transduction circuitries are primarily governed by histidine kinases (HKs), which act as sensing proteins of a broad variety of stressors. To date, nineteen HK groups have been previously described in the fungal kingdom. However, the structure and distribution of these prominent sensing proteins were hitherto investigated in a limited number of fungal species. In this study, we took advantage of recent genomic resources in fungi to refine the fungal HK classification by deciphering the structural diversity and phylogenetic distribution of HKs across a large number of fungal clades. To this end, we browsed the genome of 91 species representative of different fungal clades, which yielded 726 predicted HK sequences. A domain organization analysis, coupled with a robust phylogenomic approach, led to an improved categorization of fungal HKs. While most of the compiled sequences were categorized into previously described fungal HK groups, some new groups were also defined. Overall, this study provides an improved overview of the structure, distribution, and evolution of HKs in the fungal kingdom.

Mechanism of activation and autophosphorylation of a histidine kinase

Histidine kinases (HK) are one of the main prokaryotic signaling systems. Two structurally conserved catalytic domains inside the HK enable autokinase, phosphotransfer, and phosphatase activities. Here, we focus on a detailed mechanistic understanding of the functional cycle of the WalK HK by a multi-scale simulation approach, consisting of classical as well as hybrid QM/MM molecular dynamics simulation. Strikingly, a conformational transition induced solely in DHp leads to the correct activated conformation in CA crucial for autophosphorylation. This finding explains how variable sensor domains induce the transition from inactive to active state. The subsequent autophosphorylation inside DHp proceeds via a penta-coordinated transition state to a protonated phosphohistidine intermediate. This intermediate is consequently deprotonated by a suitable nearby base. The reaction energetics are controlled by the final proton acceptor and presence of a magnesium cation. The slow rates of the process result from the high energy barrier of the conformational transition between inactive and active states. The phosphorylation step exhibits a lower barrier and down-the-hill energetics. Thus, our work suggests a detailed mechanistic model for HK autophosphorylation.

RcsF-independent mechanisms of signaling within the Rcs Phosphorelay

The Rcs (regulator of capsule synthesis) phosphorelay is a conserved cell envelope stress response mechanism in enterobacteria. It responds to perturbations at the cell surface and the peptidoglycan layer from a variety of sources, including antimicrobial peptides, beta-lactams, and changes in osmolarity. RcsF, an outer membrane lipoprotein, is the sensor for this pathway and activates the phosphorelay by interacting with an inner membrane protein IgaA. IgaA is essential; it negatively regulates the signaling by interacting with the phosphotransferase RcsD. We previously showed that RcsF-dependent signaling does not require the periplasmic domain of the histidine kinase RcsC and identified a dominant negative mutant of RcsD that can block signaling via increased interactions with IgaA. However, how the inducting signals are sensed and how signal is transduced to activate the transcription of the Rcs regulon remains unclear. In this study, we investigated how the Rcs cascade functions without its only known sensor, RcsF and characterized the underlying regulatory mechanisms for three distinct RcsF-independent inducers. Previous reports showed that Rcs signaling can be induced in the absence of RcsF by a loss of function mutation in the periplasmic oxidoreductase DsbA or by overexpression of the DnaK cochaperone DjlA. We identified an inner membrane protein, DrpB, as a multicopy RcsF-independent Rcs activator in E. coli. The loss of the periplasmic oxidoreductase DsbA and the overexpression of the DnaK cochaperone DjlA each trigger the Rcs cascade in the absence of RcsF by weakening IgaA-RcsD interactions in different ways. In contrast, the cell-division associated protein DrpB uniquely requires the RcsC periplasmic domain for signaling; this domain is not needed for RcsF-dependent signaling. This suggests the possibility that RcsC acts as a sensor for some Rcs signals. Overall, the results add new understanding to how this complex phosphorelay can be activated by diverse mechanisms.

Unveiling the molecular mechanisms of the type IX secretion system's response regulator: Structural and functional insights

The type IX secretion system (T9SS) is a nanomachinery utilized by bacterial pathogens to facilitate infection. The system is regulated by a signaling cascade serving as its activation switch. A pivotal member in this cascade, the response regulator protein PorX, represents a promising drug target to prevent the secretion of virulence factors. Here, we provide a comprehensive characterization of PorX both in vitro and in vivo. First, our structural studies revealed PorX harbors a unique enzymatic effector domain, which, surprisingly, shares structural similarities with the alkaline phosphatase superfamily, involved in nucleotide and lipid signaling pathways. Importantly, such pathways have not been associated with the T9SS until now. Enzymatic characterization of PorX's effector domain revealed a zinc-dependent phosphodiesterase activity, with active site dimensions suitable to accommodate a large substrate. Unlike typical response regulators that dimerize via their receiver domain upon phosphorylation, we found that zinc can also induce conformational changes and promote PorX's dimerization via an unexpected interface. These findings suggest that PorX can serve as a cellular zinc sensor, broadening our understanding of its regulatory mechanisms. Despite the strict conservation of PorX in T9SS-utilizing bacteria, we demonstrate that PorX is essential for virulence factors secretion in Porphyromonas gingivalis and affects metabolic enzymes secretion in the nonpathogenic Flavobacterium johnsoniae, but not for the secretion of gliding adhesins. Overall, this study advances our structural and functional understanding of PorX, highlighting its potential as a druggable target for intervention strategies aimed at disrupting the T9SS and mitigating virulence in pathogenic species.

Evolution of orphan and atypical histidine kinases and response regulators for microbial signaling diversity

Two-component signaling systems (TCS) are the predominant means of microbes for sensing and responding to environmental stimuli. Typically, TCS is comprised of a sensor histidine kinase (HK) and a cognate response regulator (RR), which might have coevolved together. They usually involve the phosphoryl transfer signaling mechanism. However, there are also some orphan and atypical HK and RR homologs, and their evolutionary origins are still not very clear. They are not associated with cognate pairs or lack the conserved residues for phosphoryl transfer, but they could receive or respond to signals from other regulators. The objective of this study is to reveal the evolutionary history of these orphan and atypical HK and RR homologs. Structural, domain, sequence, and phylogenetic analyses indicated that their evolution process might undergo gene duplication, divergence, and domain shuffling. Meanwhile, lateral gene transfer might also be involved for their gene distribution. Evolution of orphan and atypical HK and RR homologs have increased their signaling diversity, which could be helpful for microbial adaption in complex environments.

Identification of pathways to high-level vancomycin resistance in Clostridioides difficile that incur high fitness costs in key pathogenicity traits

Clostridioides difficile is an important human pathogen, for which there are very limited treatment options, primarily the glycopeptide antibiotic vancomycin. In recent years, vancomycin resistance has emerged as a serious problem in several gram-positive pathogens, but high-level resistance has yet to be reported for C. difficile, although it is not known if this is due to constraints upon resistance evolution in this species. Here, we show that resistance to vancomycin can evolve rapidly under ramping selection but is accompanied by fitness costs and pleiotropic trade-offs, including sporulation defects that would be expected to severely impact transmission. We identified 2 distinct pathways to resistance, both of which are predicted to result in changes to the muropeptide terminal D-Ala-D-Ala that is the primary target of vancomycin. One of these pathways involves a previously uncharacterised D,D-carboxypeptidase, expression of which is controlled by a dedicated two-component signal transduction system. Our findings suggest that while C. difficile is capable of evolving high-level vancomycin resistance, this outcome may be limited clinically due to pleiotropic effects on key pathogenicity traits. Moreover, our data identify potential mutational routes to resistance that should be considered in genomic surveillance.

A conserved inhibitory interdomain interaction regulates DNA-binding activities of hybrid two-component systems in Bacteroides

Hybrid two-component systems (HTCSs) comprise a major class of transcription regulators of polysaccharide utilization genes in Bacteroides. Distinct from classical two-component systems in which signal transduction is carried out by intermolecular phosphotransfer between a histidine kinase (HK) and a cognate response regulator (RR), HTCSs contain the membrane sensor HK and the RR transcriptional regulator within a single polypeptide chain. Tethering the DNA-binding domain (DBD) of the RR with the dimeric HK domain in an HTCS could potentially promote dimerization of the DBDs and would thus require a mechanism to suppress DNA-binding activity in the absence of stimulus. Analysis of phosphorylation and DNA-binding activities of several HTCSs from Bacteroides thetaiotaomicron revealed a DBD suppression mechanism in which an inhibitory interaction between the DBD and the phosphoryl group-accepting receiver domain (REC) decreases autophosphorylation rates of HTCS-RECs and represses DNA-binding activities in the absence of phosphorylation. Sequence analyses and structure predictions identified a highly conserved sequence motif correlated with a conserved inhibitory domain arrangement of REC and DBD. The presence of the motif, as in most HTCSs, or its absence, in a small subset of HTCSs, is likely predictive of two distinct regulatory mechanisms evolved for different glycans. Substitutions within the conserved motif relieve the inhibitory interaction and result in elevated DNA-binding activities in the absence of phosphorylation. Our data suggest a fundamental regulatory mechanism shared by most HTCSs to suppress DBD activities using a conserved inhibitory interdomain arrangement to overcome the challenge of the fused HK and RR components.

IMPORTANCE

Different dietary and host-derived complex carbohydrates shape the gut microbial community and impact human health. In Bacteroides, the prevalent gut bacteria genus, utilization of these diverse carbohydrates relies on different gene clusters that are under sophisticated control by various signaling systems, including the hybrid two-component systems (HTCSs). We have uncovered a highly conserved regulatory mechanism in which the output DNA-binding activity of HTCSs is suppressed by interdomain interactions in the absence of stimulating phosphorylation. A consensus amino acid motif is found to correlate with the inhibitory interaction surface while deviations from the consensus can lead to constitutive activation. Understanding of such conserved HTCS features will be important to make regulatory predictions for individual systems as well as to engineer novel systems with substitutions in the consensus to explore the glycan regulation landscape in Bacteroides.

FapR regulates HssRS-mediated heme homeostasis in Bacillus anthracis

Bacillus anthracis, a Gram-positive facultative anaerobe and the causative agent of anthrax, multiplies to extraordinarily high numbers in vertebrate blood, resulting in considerable heme exposure. Heme is an essential nutrient and the preferred iron source for bacteria during vertebrate colonization, but its high redox potential makes it toxic in excess. To regulate heme homeostasis, many Gram-positive bacteria, including B. anthracis, rely on the two-component signaling system HssRS. HssRS comprises the heme sensing histidine kinase HssS, which modulates the activity of the HssR transcription factor to enable bacteria to circumvent heme toxicity. However, the regulation of the HssRS system remains unclear. Here we identify FapR, the transcriptional regulator of fatty acid biosynthesis, as a key factor in HssRS function. FapR plays an important role in maintaining membrane integrity and the localization of the histidine kinase HssS. Specifically, disruption of fapR leads to increased membrane rigidity, which hinders the penetration of HssRS inducers, resulting in the inactivation of HssRS. Furthermore, deletion of fapR affects the loading of HssS onto the cell membrane, compromising its heme sensing function and subsequently reducing endogenous heme biosynthesis. These findings shed light on the molecular mechanisms governing bacterial adaptation to heme stress and provide potential targets for antimicrobial intervention strategies.

The two-component system TtrRS boosts Vibrio parahaemolyticus colonization by exploiting sulfur compounds in host gut

One of the greatest challenges encountered by enteric pathogens is responding to rapid changes of nutrient availability in host. However, the mechanisms by which pathogens sense gastrointestinal signals and exploit available host nutrients for proliferation remain largely unknown. Here, we identified a two-component system in Vibrio parahaemolyticus, TtrRS, which senses environmental tetrathionate and subsequently activates the transcription of the ttrRS-ttrBCA-tsdBA gene cluster to promote V. parahaemolyticus colonization of adult mice. We demonstrated that TsdBA confers the ability of thiosulfate oxidation to produce tetrathionate which is sensed by TtrRS. TtrRS autoregulates and directly activates the transcription of the ttrBCA and tsdBA gene clusters. Activated TtrBCA promotes bacterial growth under micro-aerobic conditions by inducing the reduction of both tetrathionate and thiosulfate. TtrBCA and TsdBA activation by TtrRS is important for V. parahaemolyticus to colonize adult mice. Therefore, TtrRS and their target genes constitute a tetrathionate-responsive genetic circuit to exploit the host available sulfur compounds, which further contributes to the intestinal colonization of V. parahaemolyticus.

Propionate outperforms conventional acetate as electron donors for highly-sensitive electrochemical active biofilm sensors in water biotoxicity early-warning

With the ability to generate in situ real-time electric signals, electrochemically active biofilm (EAB) sensors have attracted wide attention as a promising water biotoxicity early-warning device. Organic matters serving as the electron donors potentially affect the electric signal's output and the sensitivity of the EAB sensor. To explore the influence of organic matters on EAB sensor's performance, this study tested six different organic matters during the sensor's inoculation. Besides the acetate, a conventional and widely used organic matter, propionate and lactate were also found capable of starting up the sensor. Moreover, the propionate-fed (PF) sensor delivered the highest sensitivity, which are respectively 1.4 times and 2.8 times of acetate-fed (AF) sensor and lactate-fed (LF) sensor. Further analysis revealed that EAB of PF sensor had more vulnerable intracellular metabolism than the others, which manifested as the most severe energy metabolic suppression and reactive oxygen species attack. Regarding the microbial function, a two-component system that was deemed as an environment awareness system was found in the EAB of PF, which also contributed to its high sensitivity. Finally, PF sensor was tested in real water environment to deliver early-warning signals.

Function analysis of transcription factor OSR1 regulating osmotic stress resistance in maize

BACKGROUND

Maize is a major cereal crop world widely, however, the yield of maize is frequently limited by dehydration and even death of plants, which resulted from osmotic stress such as drought and salinity. Dissection of molecular mechanisms controlling stress tolerance will enable plant scientists and breeders to increase crops yield by manipulating key regulatory components.

METHODS

The candidate OSR1 gene was identified by map-based cloning. The expression level of OSR1 was verified by qRT-PCR and digital PCR in WT and osr1 mutant. Electrophoretic mobility shift assay, transactivation activity assay, subcellular localization, transcriptome analysis and physiological characters measurements were conducted to analyze the function of OSR1 in osmotic stress resistance in maize.

RESULTS

The osr1 mutant was significantly less sensitive to osmotic stress than the WT plants and displayed stronger water-holding capacity, and the OSR1 homologous mutant in Arabidopsis showed a phenotype similar with maize osr1 mutant. Differentially expressed genes (DEGs) were identified between WT and osr1 under osmotic stress by transcriptome analysis, the expression levels of many genes, such as LEA, auxin-related factors, PPR family members, and TPR family members, changed notably, which may primarily involve in osmotic stress or promote root development.

CONCLUSIONS

OSR1 may serve as a negative regulatory factor in response to osmotic stress in maize. The present study sheds new light on the molecular mechanisms of osmotic stress in maize.

Molecular Mechanisms of Bacterial Resistance to Antimicrobial Peptides in the Modern Era: An Updated Review

Antimicrobial resistance (AMR) poses a serious global health concern, resulting in a significant number of deaths annually due to infections that are resistant to treatment. Amidst this crisis, antimicrobial peptides (AMPs) have emerged as promising alternatives to conventional antibiotics (ATBs). These cationic peptides, naturally produced by all kingdoms of life, play a crucial role in the innate immune system of multicellular organisms and in bacterial interspecies competition by exhibiting broad-spectrum activity against bacteria, fungi, viruses, and parasites. AMPs target bacterial pathogens through multiple mechanisms, most importantly by disrupting their membranes, leading to cell lysis. However, bacterial resistance to host AMPs has emerged due to a slow co-evolutionary process between microorganisms and their hosts. Alarmingly, the development of resistance to last-resort AMPs in the treatment of MDR infections, such as colistin, is attributed to the misuse of this peptide and the high rate of horizontal genetic transfer of the corresponding resistance genes. AMP-resistant bacteria employ diverse mechanisms, including but not limited to proteolytic degradation, extracellular trapping and inactivation, active efflux, as well as complex modifications in bacterial cell wall and membrane structures. This review comprehensively examines all constitutive and inducible molecular resistance mechanisms to AMPs supported by experimental evidence described to date in bacterial pathogens. We also explore the specificity of these mechanisms toward structurally diverse AMPs to broaden and enhance their potential in developing and applying them as therapeutics for MDR bacteria. Additionally, we provide insights into the significance of AMP resistance within the context of host-pathogen interactions.

Pseudomonas aeruginosa two-component system LadS/PA0034 regulates macrophage phagocytosis via fimbrial protein cupA1

Pseudomonas aeruginosa is one of the most common nosocomial pathogens worldwide, known for its virulence, drug resistance, and elaborate sensor-response network. The primary challenge encountered by pathogens during the initial stages of infection is the immune clearance arising from the host. The resident macrophages of barrier organs serve as the frontline defense against these pathogens. Central to our understanding is the mechanism by which bacteria modify their behavior to circumvent macrophage-mediated clearance, ensuring their persistence and colonization. To successfully evade macrophage-mediated phagocytosis, bacteria must possess an adaptive response mechanism. Two-component systems provide bacteria the agility to navigate diverse environmental challenges, translating external stimuli into cellular adaptive responses. Here, we report that the well-documented histidine kinase, LadS, coupled to a cognate two-component response regulator, PA0034, governs the expression of a vital adhesin called chaperone-usher pathway pilus cupA. The LadS/PA0034 system is susceptible to interference from the reactive oxygen species likely to be produced by macrophages and further lead to a poor adhesive phenotype with scantily cupA pilus, impairing the phagocytosis efficiency of macrophages during acute infection. This dynamic underscores the intriguing interplay: as macrophages deploy reactive oxygen species to combat bacterial invasion, the bacteria recalibrate their exterior to elude these defenses.

IMPORTANCE

The notoriety of Pseudomonas aeruginosa is underscored by its virulence, drug resistance, and elaborate sensor-response network. Yet, the mechanisms by which P. aeruginosa maneuvers to escape phagocytosis during acute infections remain elusive. This study pinpoints a two-component response regulator, PA0034, coupled with the histidine kinase LadS, and responds to macrophage-derived reactive oxygen species. The macrophage-derived reactive oxygen species can impair the LadS/PA0034 system, resulting in reduced expression of cupA pilus in the exterior of P. aeruginosa. Since the cupA pilus is an important adhesin of P. aeruginosa, its deficiency reduces bacterial adhesion and changes their behavior to adopt a planktonic lifestyle, subsequently inhibiting the phagocytosis of macrophages by interfering with bacterial adhesion. Briefly, reactive oxygen species may act as environmental cues for the LadS/PA0034 system. Upon recognition, P. aeruginosa may transition to a poorly adhesive state, efficiently avoiding engulfment by macrophages.

Design of a water-soluble transmembrane receptor kinase with intact molecular function by QTY code

Membrane proteins are critical to biological processes and central to life sciences and modern medicine. However, membrane proteins are notoriously challenging to study, mainly owing to difficulties dictated by their highly hydrophobic nature. Previously, we reported QTY code, which is a simple method for designing water-soluble membrane proteins. Here, we apply QTY code to a transmembrane receptor, histidine kinase CpxA, to render it completely water-soluble. The designed CpxAQTY exhibits expected biophysical properties and highly preserved native molecular function, including the activities of (i) autokinase, (ii) phosphotransferase, (iii) phosphatase, and (iv) signaling receptor, involving a water-solubilized transmembrane domain. We probe the principles underlying the balance of structural stability and activity in the water-solubilized transmembrane domain. Computational approaches suggest that an extensive and dynamic hydrogen-bond network introduced by QTY code and its flexibility may play an important role. Our successful functional preservation further substantiates the robustness and comprehensiveness of QTY code.

How sensor Amt-like proteins integrate ammonium signals

Unlike aquaporins or potassium channels, ammonium transporters (Amts) uniquely discriminate ammonium from potassium and water. This feature has certainly contributed to their repurposing as ammonium receptors during evolution. Here, we describe the ammonium receptor Sd-Amt1, where an Amt module connects to a cytoplasmic diguanylate cyclase transducer module via an HAMP domain. Structures of the protein with and without bound ammonium were determined to 1.7- and 1.9-Ångstrom resolution, depicting the ON and OFF states of the receptor and confirming the presence of a binding site for two ammonium cations that is pivotal for signal perception and receptor activation. The transducer domain was disordered in the crystals, and an AlphaFold2 prediction suggests that the helices linking both domains are flexible. While the sensor domain retains the trimeric fold formed by all Amt family members, the HAMP domains interact as pairs and serve to dimerize the transducer domain upon activation.

Tannic Acid Modulation of Substrate Utilization, Microbial Community, and Metabolic Traits in Sludge Anaerobic Fermentation for Volatile Fatty Acid Promotion

Anaerobic fermentation is a crucial route to realize effective waste activated sludge (WAS) resource recovery and utilization, while the overall efficiency is commonly restrained by undesirable disruptors (i.e., chemical dewatering agents). This work unveiled the unexpectedly positive effects of biodewatering tannic acid (TA) on the volatile fatty acids (VFAs) biosynthesis during WAS anaerobic fermentation. The total VFAs yield was remarkably increased by 15.6 folds with enriched acetate and butyrate in TA-occurred systems. TA was capable to disintegrate extracellular polymeric substances to promote the overall organics release. However, TA further modulated the soluble proteins structure by hydrogen bonding and hydrophobic interactions, resulting in the decrease of proteins bioavailability and consequential alteration of metabolic substrate feature. These changes reshaped the microbial community and stimulated adaptive regulatory systems in hydrolytic-acidogenic bacteria. The keystone species for carbohydrate metabolism (i.e., Solobacterium and Erysipelotrichaceae) were preferentially enriched. Also, the typical quorum sensing (i.e., enhancing substrate transport) and two-component systems (i.e., sustaining high metabolic activity) were activated to promote the microbial networks connectivity and ecological cooperative behaviors in response to TA stress. Additionally, the metabolic functions responsible for carbohydrate hydrolysis, transmembrane transport, and intracellular metabolism as well as VFA biosynthesis showed increased relative abundance, which maintained high microbial activities for VFAs biosynthesis. This study underscored the advantages of biodewatering TA for WAS treatment in the context of resource recovery and deciphered the interactive mechanisms.

Promoting agricultural waste-driven denitrification and nitrogen sequestration with nano-enabled strategy

Nanotechnology and biotechnology offer promising avenues for bolstering food security through the facilitation of soil nitrogen (N) sequestration and the reduction of nitrate leaching. Nonetheless, a comprehensive and mechanistic evaluation of their effectiveness and safety remains unclear. In this study, a soil remediation strategy employing nano-Fe3O4 and straw in N-contaminated soil was developed to elucidate N retention mechanisms via diverse metagenomics techniques. The findings revealed that subsoil amended with straw, particularly in conjunction with nano-Fe3O4, significantly increased subsoil N content (53.2%) and decreased nitrate concentration (74.6%) in leachate. Furthermore, the enrichment of functional genes associated with N-cycling, sulfate, nitrate, and iron uptake, along with chemotaxis, and responses to environmental stimuli or microbial collaboration, effectively mitigates nitrate leaching while enhancing soil N sequestration. This study introduces a pioneering approach utilizing nanomaterials in soil remediation, thereby offering the potential for the cultivation of safe vegetables in high N input greenhouse agriculture.

Molecular Mechanisms of Bacterial Communication and Their Biocontrol

A bacterium's ability to colonize and adapt to an ecological niche is highly dependent on its capacity to perceive and analyze its environment and its ability to interact with its hosts and congeners [...].

Unveiling the Molecular Mechanisms of the Type-IX Secretion System's Response Regulator: Structural and Functional Insights

The Type-IX secretion system (T9SS) is a nanomachinery utilized by bacterial pathogens to facilitate infection. The system is regulated by a signaling cascade serving as its activation switch. A pivotal member in this cascade, the response regulator protein PorX, represents a promising drug target to prevent the secretion of virulence factors. Here, we provide a comprehensive characterization of PorX both in vitro and in vivo . First, our structural studies revealed PorX harbours a unique enzymatic effector domain, which, surprisingly, shares structural similarities with the alkaline phosphatase superfamily, involved in nucleotide and lipid signaling pathways. Importantly, such pathways have not been associated with the T9SS until now. Enzymatic characterization of PorX's effector domain revealed a zinc-dependent phosphodiesterase activity, with active site dimensions suitable to accommodate a large substrate. Unlike typical response regulators that dimerize via their receiver domain upon phosphorylation, we found that zinc can also induce conformational changes and promote PorX's dimerization via an unexpected interface. These findings suggest that PorX can serve as a cellular zinc sensor, broadening our understanding of its regulatory mechanisms. Despite the strict conservation of PorX in T9SS-utilizing bacteria, we demonstrate that PorX is essential for virulence factors secretion in Porphyromonas gingivalis and affects metabolic enzymes secretion in the non-pathogenic Flavobacterium johnsoniae , but not for the secretion of gliding adhesins. Overall, this study advances our structural and functional understanding of PorX, highlighting its potential as a druggable target for intervention strategies aimed at disrupting the T9SS and mitigating virulence in pathogenic species.

Arsenic stress on soil microbial nutrient metabolism interpreted by microbial utilization of dissolved organic carbon

In a 120-day microcosm incubation experiment, we investigated the impact of arsenic contamination on soil microbial nutrient metabolism, focusing on carbon cycling processes. Our study encompassed soil basal respiration, key enzyme activities (particularly, β-1,4-N-acetylglucosaminidase and phosphatases), microbial biomass, and community structure. Results revealed a substantial increase (1.21-2.81 times) in β-1,4-N-acetylglucosaminidase activities under arsenic stress, accompanied by a significant decrease (9.86%-45.20%) in phosphatase activities (sum of acid and alkaline phosphatases). Enzymatic stoichiometry analysis demonstrated the mitigation of microbial C and P requirements in response to arsenic stress. The addition of C-sources alleviated microbial C requirements but exacerbated P requirements, with the interference amplitude increasing with the complexity of the C-source. Network analysis unveiled altered microbial nutrient requirements and an increased resistance process of microbes under arsenic stress. Microbial carbon use efficiency (CUE) and basal respiration significantly increased (1.17-1.59 and 1.18-3.56 times, respectively) under heavy arsenic stress (500 mg kg-1). Arsenic stress influenced the relative abundances of microbial taxa, with Gemmatimonadota increasing (5.5-50.5%) and Bacteroidota/ Nitrospirota decreasing (31.4-47.9% and 31.2-63.7%). Application of C-sources enhanced microbial resistance to arsenic, promoting cohesion among microorganisms. These findings deepen our understanding of microbial nutrient dynamics in arsenic-contaminated areas, which is crucial for developing enzyme-based toxicity assessment systems for soil arsenic contamination.

Determinants of bacterial survival and proliferation in blood

Bloodstream infection is a major public health concern associated with high mortality and high healthcare costs worldwide. Bacteremia can trigger fatal sepsis whose prevention, diagnosis, and management have been recognized as a global health priority by the World Health Organization. Additionally, infection control is increasingly threatened by antimicrobial resistance, which is the focus of global action plans in the framework of a One Health response. In-depth knowledge of the infection process is needed to develop efficient preventive and therapeutic measures. The pathogenesis of bloodstream infection is a dynamic process resulting from the invasion of the vascular system by bacteria, which finely regulate their metabolic pathways and virulence factors to overcome the blood immune defenses and proliferate. In this review, we highlight our current understanding of determinants of bacterial survival and proliferation in the bloodstream and discuss their interactions with the molecular and cellular components of blood.

Investigation into the potential mechanism of Bacillus amyloliquefaciens in the fermentation of broad bean paste by metabolomics and transcriptomics

Pixian broad bean paste is a renowned fermented seasoning. The fermentation of broad bean is the most important process of Pixian broad bean paste. To enhance the flavor of tank-fermented broad bean paste, salt-tolerant Bacillus amyloliquefaciens strain was inoculated, resulting in an increase in total amount of volatile compounds, potentially leading to different flavor characteristics. To investigate the fermentation mechanism, monoculture simulated fermentation systems were designed. Metabolomics and transcriptomics were used to explore Bacillus amyloliquefaciens' transcriptional response to salt stress and potential aroma production mechanisms. The results highlighted different metabolite profiles under salt stress, and the crucial roles of energy metabolism, amino acid metabolism, reaction system, transportation system in Bacillus amyloliquefaciens' hypersaline stress response. This study provides a scientific basis for the industrial application of Bacillus amyloliquefaciens and new insights into addressing the challenges of poor flavor quality in tank fermentation products.

The sensor of the bacterial histidine kinase CpxA is a novel dimer of extracytoplasmic Per-ARNT-Sim domains

Histidine kinases are key bacterial sensors that recognize diverse environmental stimuli. While mechanisms of phosphorylation and phosphotransfer by cytoplasmic kinase domains are relatively well-characterized, the ways in which extracytoplasmic sensor domains regulate activation remain mysterious. The Cpx envelope stress response is a conserved Gram-negative two-component system which is controlled by the sensor kinase CpxA. We report the structure of the Escherichia coli CpxA sensor domain (CpxA-SD) as a globular Per-ARNT-Sim (PAS)-like fold highly similar to that of Vibrio parahaemolyticus CpxA as determined by X-ray crystallography. Because sensor kinase dimerization is important for signaling, we used AlphaFold2 to model CpxA-SD in the context of its connected transmembrane domains, which yielded a novel dimer of PAS domains possessing a distinct dimer organization compared to previously characterized sensor domains. Gain of function cpxA∗ alleles map to the dimer interface, and mutation of other residues in this region also leads to constitutive activation. CpxA activation can be suppressed by mutations that restore inter-monomer interactions, suggesting that inhibitory interactions between CpxA-SD monomers are the major point of control for CpxA activation and signaling. Searching through hundreds of structural homologs revealed the sensor domain of Pseudomonas aeruginosa sensor kinase PfeS as the only PAS structure in the same novel dimer orientation as CpxA, suggesting that our dimer orientation may be utilized by other extracytoplasmic PAS domains. Overall, our findings provide insight into the diversity of the organization of PAS sensory domains and how they regulate sensor kinase activation.