N-acyl homoserine lactone molecules assisted quorum sensing: effects consequences and monitoring of bacteria talking in real life

Indwelling Urological Device Biofilm Composition and Characteristics in the Presence and Absence of Infection

OBJECTIVE

To characterize microbial biofilms associated with different device types used in the urological field including ureteral stents, sacral neuromodulation (SNM) devices, penile prostheses, and artificial urinary sphincters (AUS).

MATERIALS AND METHODS

Data from 4 studies, each reporting biofilm composition of a particular device type, were pooled and included for inter-device analysis. Studies recruited adults scheduled for ureteral stent, SNM, IPP, or AUS removal/revision. Device (n = 115) biofilms and controls were analyzed with multi-omics approaches, and compositions were compared across device types and clinical factors.

RESULTS

Microbiota present on each device type was distinct from that of perineal, rectal, or urine flora (P <.01). Biofilm microbial counts (P <.001) and diversity (P = .024) differed by device type. Ureteral stents had greater microbial counts than other device types (P <.001). Staphylococcus, Pseudomonas, Lactobacillus, Ureaplasma were commonly detected across devices. Device biofilms harbored a greater proportion of Proteobacteria phylum, and the rectal, perineal, and urine flora harbored a greater proportion of Firmicutes. Unique microbe-metabolite interaction networks were identified in presence and absence of infection. Antibiotic-resistance genes including sul2 (sulfonamide resistance) and rpoB (rifampin resistance) were detected in biofilms across device types. Biofilm reconstitution in vitro differed by device type from which strains were isolated.

CONCLUSION

Ureteral stents, sacral neuromodulation devices, penile prostheses, and artificial urinary sphincters harbored unique microbial and metabolite profiles that differed from those of skin, urine, and rectal flora. The findings of this study set the groundwork for investigation of novel strategies to reduce device-associated infection risk within and outside urology.

Effect of Nicotine on Pulmonary Pathogenic Bacteria

Exposure to cigarette smoke significantly enhances susceptibility to bacterial infections by inducing physiological and structural alterations, including immune system dysregulation. This exposure also augments bacterial virulence including biofilm formation, leading to severe infectious diseases and antibiotic resistance. Notably, cigarette smoke exposure increases the incidence of pneumonia by up to 2.5-fold and tuberculosis by up to 4.1-fold. Nicotine, a primary constituent of cigarette smoke, has been extensively characterized for its immunomodulatory effects. However, despite the wealth of knowledge on nicotine's impact on the host immune response, there is a paucity of data regarding its direct effects on various pulmonary pathogens. In the present review, we discuss the main findings in this field.

Bacterial biofilm-mediated environmental remediation: Navigating strategies to attain Sustainable Development Goals

Bacterial biofilm is a structured bacterial community enclosed within a three-dimensional polymeric matrix, governed by complex signaling pathways, including two-component systems, quorum sensing, and c-di-GMP, which regulate its development and resistance in challenging environments. The genetic configurations within biofilm empower bacteria to exhibit significant pollutant remediation abilities, offering a promising strategy to tackle diverse ecological challenges and expedite progress toward Sustainable Development Goals (SDGs). Biofilm-based technologies offer advantages such as high treatment efficiency, cost-effectiveness, and sustainability compared to conventional methods. They significantly contribute to agricultural improvement, soil fertility, nutrient cycling, and carbon sequestration, thereby supporting SDG 1 (No poverty), SDG 2 (Zero hunger), SDG 13 (Climate action), and SDG 15 (Life on land). In addition, biofilm facilitates the degradation of organic-inorganic pollutants from contaminated environments, aligning with SDG 6 (Clean water and sanitation) and SDG 14 (Life below water). Bacterial biofilm also has potential applications in industrial innovation, aligning SDG 7 (Affordable and clean energy), SDG 8 (Decent work and economic growth), and SDG 9 (Industry, innovation, and infrastructure). Besides, bacterial biofilm prevents several diseases, aligning with SDG 3 (Good health and well-being). Thus, bacterial biofilm-mediated remediation provides advanced opportunities for addressing environmental issues and progressing toward achieving the SDGs. This review explores the potential of bacterial biofilms in addressing soil pollution, wastewater, air quality improvement, and biodiversity conservation, emphasizing their critical role in promoting sustainable development.

Catalytic Redundancies and Conformational Plasticity Drives Selectivity and Promiscuity in Quorum Quenching Lactonases

Several enzymes from the metallo-β-lactamase-like family of lactonases (MLLs) degrade N-acyl L-homoserine lactones (AHLs). They play a role in a microbial communication system known as quorum sensing, which contributes to pathogenicity and biofilm formation. Designing quorum quenching (QQ) enzymes that can interfere with this communication allows them to be used in a range of industrial and biomedical applications. However, tailoring these enzymes for specific communication signals requires a thorough understanding of their mechanisms and the physicochemical properties that determine their substrate specificities. We present here a detailed biochemical, computational, and structural study of GcL, which is a highly proficient and thermostable MLL with broad substrate specificity. We show that GcL not only accepts a broad range of substrates but also hydrolyzes these substrates through at least two different mechanisms. Further, the preferred mechanism appears to depend on both the substrate structure and/or the nature of the residues lining the active site. We demonstrate that other lactonases, such as AiiA and AaL, show similar mechanistic promiscuity, suggesting that this is a shared feature among MLLs. Mechanistic promiscuity has been seen previously in the lactonase/paraoxonase PON1, as well as with protein tyrosine phosphatases that operate via a dual general acid mechanism. The apparent prevalence of this phenomenon is significant from both a biochemical and protein engineering perspective: in addition to optimizing for specific substrates, it may be possible to optimize for specific mechanisms, opening new doors not just for the design of novel quorum quenching enzymes but also of other mechanistically promiscuous enzymes.

Marine-Derived Furanones Targeting Quorum-Sensing Receptors in Pseudomonas aeruginosa: Molecular Insights and Potential Mechanisms of Inhibition

The quorum-sensing (QS) machinery in disease-causing microorganisms is critical in developing antibiotic resistance. In Pseudomonas aeruginosa, QS is involved in biofilm formation, virulence factors production, and general tolerance to antimicrobials. Owing to the major role QS plays, interference in the process is probably a facile route to overcome antimicrobial resistance. Some furanone-derived compounds from marine sources have shown promising anti-QS activity. However, their protein targets and potential mechanisms of action have not been explored. To elucidate their potential protein targets in this study, marine metabolites with furanone backbones similar to their cognitive autoinducers (AIs) were screened against various QS receptors (LasR, RhlR, and PqsR) using molecular docking and molecular dynamics (MD) simulation techniques. The order by which the compounds bind to the receptors follows LasR > RhlR > PqsR. Compounds exhibited remarkable stability against LasR and RhlR, likely because the AIs of these receptors are structural analogs of furanones. Furanones with shorter alkyl side chains bound strongly against RhlR. The presence of halogens improved binding against various receptors. PqsR, with its hydrophobic-binding site and structurally different AIs, showed weaker binding. This study provides a molecular basis for the design of potent antagonists against QS receptors using marine-derived furanones.

Quorum sensing inhibiting dihydropyrrol-2-ones embedded polymer/graphene oxide nanocomposite waterborne antimicrobial coatings

With increasing antibiotic resistance and hospital acquired microbial infections, there has been a growing interest to explore alternate antimicrobial approaches. This is particularly challenging when aiming to protect surfaces over a large area to avoid contact mediated infection transmission. Quorum sensing (QS) inhibition has emerged as an alternate antimicrobial approach overcoming evolutionary stress driven resistance observed in antibiotic treatment. However, specific surface orientation requirements and limited work on delivery of small molecule QS inhibiting compounds have limited their widespread applicability certainly when it comes to coating large surfaces. Here, we report antimicrobial nanocomposite coatings overcoming the dependence on molecular orientation of QS inhibiting dihydropyrrol-2-ones (DHP) analogues and release small molecule analogues. In a systematic study, we developed poly(styrene-stat-n-butyl acrylate)/graphene oxide (GO)/DHP analogue nanocomposite antimicrobial coatings that can be easily applied to surfaces of any length scale and studied their efficacy against Staphylococcus aureus. The polymer nanocomposite was designed to undergo coating formation at ambient temperature. The antimicrobial coatings exhibited DHP dose dependent antimicrobial response both in the supernatant growth media with a ∼7-log10 reduction in cell growth and virtually a complete inhibition in cell adhesion on the surface in the best coating compared to controls. When compared, DHP-Br coatings outperformed other DHP analogues (-F and -Ph) both in limiting the cell growth in the media and cellular adhesion on the coating surface. This is the first example of nanocomposite coatings comprising QS inhibiting compounds, and their exceptional performance is expected to pave the way for further research in the field.

Electrochemical Detection of Pseudomonas aeruginosa Quorum Sensing Molecule (S)-N-Butyryl Homoserine Lactone Using Molecularly Imprinted Polymers

Pseudomonas aeruginosa is a multidrug-resistant Gram-negative bacterium that poses a significant threat to public health, necessitating rapid and on-site detection methods for rapid recognition. The goal of the project is therefore to indirectly detect the presence of P. aeruginosa in environmental water samples targeting one of its quorum-sensing molecules, namely, (S)-N-butyryl homoserine lactone (BHL). To this aim, molecularly imprinted polymers (MIPs) were synthesized via bulk free-radical polymerization using BHL as a template molecule. The obtained MIP particles were immobilized onto screen-printed electrodes (MIP-SPEs), and the BHL rebinding was analyzed via electrochemical impedance spectroscopy (EIS). To study the specificity of the synthesized MIPs, isotherm curves were built after on-point rebinding analysis performed via LC-MS measurements for both MIPs and NIPs (nonimprinted polymers, used as a negative control), obtaining an imprinting factor (IF) of 2.8 (at C f = 0.4 mM). The MIP-SPEs were integrated into an electrochemical biosensor with a linear range of 1 × 101-1 × 103 nM and a limit of detection (LoD) of 31.78 ± 4.08 nM. Selectivity measurements were also performed after choosing specific interferent molecules, such as structural analogs and potential interferents, followed by on-point analysis performed in spiked tap water to prove the sensor's potential to detect the presence of the quorum-sensing molecule in environmentally related real-life samples.

Catalytic Redundancies and Conformational Plasticity Drives Selectivity and Promiscuity in Quorum Quenching Lactonases

Several enzymes from the metallo-β-lactamase-like family of lactonases (MLLs) degrade N- acyl-L-homoserine lactones (AHLs). In doing so, they play a role in a microbial communication system, quorum sensing, which contributes to pathogenicity and biofilm formation. There is currently great interest in designing quorum quenching ( QQ ) enzymes that can interfere with this communication and be used in a range of industrial and biomedical applications. However, tailoring these enzymes for specific targets requires a thorough understanding of their mechanisms and the physicochemical properties that determine their substrate specificities. We present here a detailed biochemical, computational, and structural study of the MLL GcL, which is highly proficient, thermostable, and has broad substrate specificity. Strikingly, we show that GcL does not only accept a broad range of substrates but is also capable of utilizing different reaction mechanisms that are differentially used in function of the substrate structure or the remodeling of the active site via mutations. Comparison of GcL to other lactonases such as AiiA and AaL demonstrates similar mechanistic promiscuity, suggesting this is a shared feature across lactonases in this enzyme family. Mechanistic promiscuity has previously been observed in the lactonase/paraoxonase PON1, as well as with protein tyrosine phosphatases that operate via a dual general-acid mechanism. The apparent prevalence of this phenomenon is significant from both a biochemical and an engineering perspective: in addition to optimizing for specific substrates, it is possible to optimize for specific mechanisms, opening new doors not just for the design of novel quorum quenching enzymes, but also of other mechanistically promiscuous enzymes.

Chitosan oligosaccharide/pluronic F127 micelles exhibiting anti-biofilm effect to treat bacterial keratitis

Mono or dual chitosan oligosaccharide lactate (COL)-conjugated pluronic F127 polymers, FCOL1 and FCOL2 were prepared, self-assembled to form micelles, and loaded with gatifloxacin. The Gati@FCOL1/Gati@FCOL2 micelles preparation process was optimized by QbD analysis. Micelles were characterized thoroughly for size, CMC, drug compatibility, and viscosity by GPC, DLS, SEM, IR, DSC, and XRD. The micelles exhibited good cellular uptake in both monolayers and spheroids of HCEC. The antibacterial and anti-biofilm activities of the micelles were evaluated on P. aeruginosa and S. aureus. The anti-quorum sensing activity was explored in P. aeruginosa by analyzing micelles' ability to produce virulence factors, including AHLs, pyocyanin, and the motility behavior of the organism. Gati@FCOL2 Ms was mucoadhesive, cornea-penetrant, antibacterial, and inhibited the biofilm formation by P. aeruginosa and S. aureus significantly more than Gati@FCOL1. A significant reduction in bacterial load in mice cornea was observed after Gati@FCOL2 Ms-treatment to the P. aeruginosa-induced bacterial keratitis-infected mice.

Rapid eradication of vancomycin and methicillin-resistant Staphylococcus aureus by MDP1 antimicrobial peptide coated on photocrosslinkable chitosan hydrogel: in vitro antibacterial and in silico molecular docking studies

Introduction

Antibiotic resistance and weak bioavailability of antibiotics in the skin due to systemic administration leads to failure in eradication of vancomycin- and methicillin-resistant Staphylococcus aureus (VRSA and MRSA)-associated wound infections and subsequent septicemia and even death. Accordingly, this study aimed at designing a photocrosslinkable methacrylated chitosan (MECs) hydrogel coated by melittin-derived peptide 1 (MDP1) that integrated the antibacterial activity with the promising skin regenerative capacity of the hydrogel to eradicate bacteria by burst release strategy.

Methods

The MECs was coated with MDP1 (MECs-MDP1), characterized, and the hydrogel-peptide interaction was evaluated by molecular docking. Antibacterial activities of MECs-MDP1 were evaluated against VRSA and MRSA bacteria and compared to MECs-vancomycin (MECs-vanco). Antibiofilm activity of MECs-MDP1 was studied by our novel 'in situ biofilm inhibition zone (IBIZ)' assay, and SEM. Biocompatibility with human dermal fibroblast cells (HDFs) was also evaluated.

Results and Discussion

Molecular docking showed hydrogen bonds as the most interactions between MDP1 and MECs at a reasonable affinity. MECs-MDP1 eradicated the bacteria rapidly by burst release strategy whereas MECs-vanco failed to eradicate them at the same time intervals. Antibiofilm activity of MECs-MDP1 were also proved successfully. As a novel report, molecular docking analysis has demonstrated that MDP1 covers the structure of MECs and also binds to lysozyme with a reasonable affinity, which may explain the inhibition of lysozyme. MECs-MDP1 was also biocompatible with human dermal fibroblast skin cells, which indicates its safe future application. The antibacterial properties of a photocrosslinkable methacrylated chitosan-based hydrogel coated with MDP1 antimicrobial peptide were successfully proved against the most challenging antibiotic-resistant bacteria causing nosocomial wound infections; VRSA and MRSA. Molecular docking analysis revealed that MDP1 interacts with MECs mainly through hydrogen bonds with reasonable binding affinity. MECs-MDP1 hydrogels eradicated the planktonic state of bacteria by burst release of MDP1 in just a few hours whereas MECs-vanco failed to eradicate them. inhibition zone assay showed the anti-biofilm activity of the MECs-MDP1 hydrogel too. These findings emphasize that MECs-MDP1 hydrogel would be suggested as a biocompatible wound-dressing candidate with considerable and rapid antibacterial activities to prevent/eradicate VRSA/MRSA bacterial wound infections.

Comprehensive Similarity Algorithm and Molecular Dynamics Simulation-Assisted Terahertz Spectroscopy for Intelligent Matching Identification of Quorum Signal Molecules (N-Acyl-Homoserine Lactones)

To investigate the mechanism of aquatic pathogens in quorum sensing (QS) and decode the signal transmission of aquatic Gram-negative pathogens, this paper proposes a novel method for the intelligent matching identification of eight quorum signaling molecules (N-acyl-homoserine lactones, AHLs) with similar molecular structures, using terahertz (THz) spectroscopy combined with molecular dynamics simulation and spectral similarity calculation. The THz fingerprint absorption spectral peaks of the eight AHLs were identified, attributed, and resolved using the density functional theory (DFT) for molecular dynamics simulation. To reduce the computational complexity of matching recognition, spectra with high peak matching values with the target were preliminarily selected, based on the peak position features of AHL samples. A comprehensive similarity calculation (CSC) method using a weighted improved Jaccard similarity algorithm (IJS) and discrete Fréchet distance algorithm (DFD) is proposed to calculate the similarity between the selected spectra and the targets, as well as to return the matching result with the highest accuracy. The results show that all AHL molecular types can be correctly identified, and the average quantization accuracy of CSC is 98.48%. This study provides a theoretical and data-supported foundation for the identification of AHLs, based on THz spectroscopy, and offers a new method for the high-throughput and automatic identification of AHLs.

Identification of potential natural products derived from fungus growing termite, inhibiting Pseudomonas aeruginosa quorum sensing protein LasR using molecular docking and molecular dynamics simulation approach

Pseudomonas aeruginosa, the most common opportunistic pathogen, is becoming antibiotic-resistant worldwide. The fate of P. aeruginosa, a multidrug-resistant strain, can be determined by multidrug efflux pumps, enzyme synthesis, outer membrane protein depletion, and target alterations. Microbial niches have long used quorum sensing (QS) to synchronize virulence gene expression. Computational methods can aid in the development of novel P. aeruginosa drug-resistant treatments. The tripartite symbiosis in termites that grow fungus may help special microbes find new antimicrobial drugs. To find anti-quorum sensing natural products that could be used as alternative therapies, a library of 376 fungal-growing termite-associated natural products (NPs) was screened for their physicochemical properties, pharmacokinetics, and drug-likeness. Using GOLD, the top 74 NPs were docked to the QS transcriptional regulator LasR protein. The five lead NPs with the highest gold score and drug-like properties were chosen for a 200-ns molecular dynamics simulation to test the competitive activity of different compounds against negative catechin. Fridamycin and Daidzein had stable conformations, with mean RMSDs of 2.48 and 3.67 Å, respectively, which were similar to Catechin's 3.22 Å. Fridamycin and Daidzein had absolute binding energies of -71.186 and -52.013 kcal/mol, respectively, which were higher than the control's -42.75 kcal/mol. All the compounds within the active site of the LasR protein were kept intact by Trp54, Arg55, Asp67, and Ser123. These findings indicate that termite gut and fungus-associated NPs, specifically Fridamycin and Daidzein, are potent QS antagonists that can be used to treat P. aeruginosa's multidrug resistance.Communicated by Ramaswamy H. Sarma.

Study of the biofilm mechanism of C4-HSL and C6-HSL in the degradation of quinoline

Quinoline is a hard-to-degrade organic compound widely found in coal chemical wastewater, that seriously affects the ecological environment and human health. A number of biochemical methods are already available for quinoline degradation, but the use of microbial community sensing for quinoline degradation has not been studied in depth. Therefore, this paper focuses on the enhanced mechanism of quorum-sensing signaling molecules in the biofilm formation process during quinoline degradation by functional strains of bacteria. In this paper, the effects of the signal molecules C4-HSL and C6-HSL on the adhesion ability, colony diameter, biofilm formation ability and biofilm morphology of functional strains of quinoline degrading bacteria (Ochrobactrum sp., LC-1) were investigated, and the results showed that both signal molecules promoted the biofilm formation process during the degradation of quinoline by exhibiting an efficient biofortification effect. Both signal molecules could enhance the colony diameter of strain LC-1, where C4-HSL could enhance the biomass of strain LC-1 and stimulate the secretion of extracellular polysaccharides; and C6-HSL could induce the enhancement of adhesion performance and the secretion of extracellular proteins from strain LC-1; both molecules together enhanced the biofilm formation process of strain LC-1. This study has practical application in the degradation of quinoline in coal chemical wastewater.

Autoinducers modulation as a potential anti-virulence target of bacteria by phenolic compounds

OBJECTIVE

The goal of this study was to determine the effects of phenolic extracts from grape (GrPE), pomegranate (PoPE), and persimmon (PePE) by-products on bacterial virulence activities such as biofilms, motility, energy-dependent efflux pumps, and β-lactamase activity, which are modulated primarily by quorum sensing (QS), defining their potential applications.

METHOD

The microdilution method was used to determine the minimum inhibitory concentration (MIC) and sub-inhibitory concentrations (SICs) of the extracts against reference pathogenic bacteria. The antibacterial mode of action was determined by labelling bacterial cells in in vivo cell-tracking experiments.

RESULTS

Antibiograms showed that PoPE inhibited bacteria at lower concentrations, and PePE had a stronger effect against Klebsiella pneumoniae. Both extracts caused significant cell membrane damage (CMD), whereas GrPE did not. At SICs, all extracts showed anti-QS activity, especially PePE, which inhibited violacein and pyocyanin production at 1/128 × MIC. Additionally, QS autoinducers found in Chromobacterium violaceum and Pseudomonas aeruginosa were modulated by the extracts; PePE showed the highest modulation. Antibiofilm assays revealed that GrPE, at MIC and 2 × MIC, acted as a potent antibiofilm agent against biofilms of Pseudomonas putida, Bacillus cereus, and Staphylococcus aureus, which was related to disruption of swarming motility by GrPE. All extracts, especially PoPE, exerted a potent effect against the activation of efflux pumps of P. aeruginosa as well as β-lactamase activity in K. pneumoniae.

CONCLUSION

Results suggest that the anti-virulence potential of the extracts may be related to their effect as extracellular autoinducer modulators. This study allowed to define potential applications of these extracts.

Effectiveness of metal and metal oxide nanoparticles against bacterial biofilms: Perspectives and limitations

In the last few years, there has been a necessary demand in the pharmaceutical industries for finding a treatment against biofilms formed by different bacterial species. We are aware of the fact that classical processes, which are already there for the removal of bacterial biofilms gives a very low efficiency and consequently antimicrobial resistance makes it even worse. To cope up with the cited problems, scientists from the past few years are inclining toward various types of nanoparticle based treatment procedures as a pharmaceutical agent against bacterial biofilms. Nanoparticles are known for their extremely efficient antimicrobial properties. The current review gives a description of different types of metal oxide nanoparticles and their antibiofilm properties. It also shows a comparative analysis of the nanoparticles and depicts the efficiency rates of biofilm degradation in each of them. It explains the mechanism of the nanoparticles through which the disintegration of bacterial biofilm is carried out. Lastly, the review throws light upon the limitations of different nanoparticles, their safety issues, the mutagenicity, genotoxicity concerns, and toxicity hazards caused by them.

Association of polymicrobial interactions with dental caries development and prevention

Dental caries is a common oral disease. In many cases, disruption of the ecological balance of the oral cavity can result in the occurrence of dental caries. There are many cariogenic microbiota and factors, and their identification allows us to take corresponding prevention and control measures. With the development of microbiology, the caries-causing bacteria have evolved from the traditional single Streptococcus mutans to the discovery of oral symbiotic bacteria. Thus it is necessary to systematically organized the association of polymicrobial interactions with dental caries development. In terms of ecology, caries occurs due to an ecological imbalance of the microbiota, caused by the growth and reproduction of cariogenic microbiota due to external factors or the disruption of homeostasis by one's own factors. To reduce the occurrence of dental caries effectively, and considering the latest scientific viewpoints, caries may be viewed from the perspective of ecology, and preventive measures can be taken; hence, this article systematically summarizes the prevention and treatment of dental caries from the aspects of ecological perspectives, in particular the ecological biofilm formation, bacterial quorum sensing, the main cariogenic microbiota, and preventive measures.

QSP: An open sequence database for quorum sensing related gene analysis with an automatic annotation pipeline

Quorum sensing (QS) has attracted great attention due to its important role in the bacterial interactions and its relevance to water management. With the development of high-throughput sequencing technology, a specific database for QS-related sequence annotation is urgently needed. Here, Hidden Markov Model (HMM) profiles for 38 types of QS-related proteins were built using a total of 4024 collected seed sequences. Based on both homolog search and keywords confirmation against the non-redundant database, we established a QS-related protein (QSP) database, that includes 809,721 protein sequences and 186,133 nucleotide sequences, downloaded available at: https://github.com/chunxiao-dcx/QSP. The entries were classified into 38 types and 315 subtypes among 91 bacterial phyla. Furthermore, an automatic annotation pipeline, named QSAP, was developed for rapid annotation, classification and abundance quantification of QSP-like sequences from sequencing data. This pipeline provided the two homolog alignment strategies offered by Diamond (Blastp) or HMMER (Hmmscan), as well as a data cleansing function for a subset or union set of the hits. The pipeline was tested using 14 metagenomic samples from various water environments, including activated sludge, deep-sea sediments, estuary water, and reservoir water. The QSAP pipeline is freely available for academic use in the code repository at: https://github.com/chunxiao-dcx/QSAP. The establishment of this database and pipeline, provides a useful tool for QS-related sequence annotation in a wide range of projects, and will increase our understanding of QS communication in aquatic environments.

Selection and Molecular Response of AHL-lactonase (aiiA) Producing Bacillus sp. Under Penicillin G-induced Conditions

Quorum sensing (QS) is the process by which microorganisms employ chemicals called autoinducers (AIs) to communicate with their population. The QS mechanism generally controls the expression of the virulence related genes in bacteria. N-acyl homoserine lactones (AHLs) are the most widespread QS molecules. Due to their diverse AHL-lactonase activities, Bacillus species make particularly suitable candidates for procedures such as demolition of pathogenic bacterial QS signals and bioremediation of β-lactam antibiotics from contaminated environments. In this study, seven Bacillus strains with Quorum quenching (QQ) activity were isolated using an enrichment medium supplemented with Penicillin G (PenG). The AHL-lactonase encoding gene (aiiA) was amplified by PCR and sequenced. Amino acid sequences underwent multiple sequence alignment. Docking studies were carried out with both C6HSL and PenG ligand using AutoDock tools. The aiiA amino acid sequences of the isolates were found to be well conserved. Furthermore, amino acid sequence alignment revealed that 74.9% of amino acid sequences were conserved in the genus Bacillus. Docking of the C6HSL to wild type (3DHA) and H97D variant reduced the docking score by only 0.1 kcal/mol for the mutated protein. When PenG docked with a higher (1.5 kcal/mol) score as a ligand to wild-type and mutant receptors, the docking score for the mutated protein likewise decreased by 0.1 kcal/mol. This research contributed to the diversification of organisms with QQ activity and beta-lactam antibiotic resistance. It also clarified the binding score of the PenG ligand to the Bacillus AHL lactonase molecule for the first time.

Multi-omics analysis on seasonal variations of the biofilm microbial community in a full-scale pre-denitrification biofilter

The seasonal variations of biofilm communities in a municipal wastewater treatment plant were investigated using multi-omics techniques. The abundance of the main phyla of microorganisms varied with summer (July 2019) and winter (January 2019) samples considerably, the Bacteroidetes enriched in winter and Chloroflexi in summer. The results of metaproteomic and metagenomic showed that most of the functional microorganisms belonged to the Betaproteobacteria class, and the enrichment of Flavobacteria class in winter guaranteed the stability of denitrification performance to some extent. Seasonal variations affected the proteomic expression profiling, a total of 2835 differentially expressed proteins identified were significantly enriched in quorum sensing, two-component system, ribosome, benzoate degradation, butanoate metabolism, tricarboxylic acid cycle (TCA cycle), and cysteine and methionine metabolism pathways. With the expression of nitrogen metabolic proteins decreases in winter, the overall expression of denitrification-related enzymes in winter was much lower than that in summer, the nitrogen metabolism pathway varied significantly. Seasonal variations also induced the alteration of the biofilm metabolite profile; a total of 66 differential metabolites, 8 potential biomarkers, and 8 perturbed metabolic pathways such as TCA cycle were detected. It was found that most of the perturbed pathways are directly related to nitrogen metabolism, and several amino acids and organic acids associated with the TCA cycle were significantly perturbed, the accumulation of TCA cycle intermediates, ornithine, and L-histidine in winter might be conducive to resisting cold temperatures. Furthermore, the correlation between biofilm microbial communities and metabolites was identified by the combined analysis of metabolomic and metaproteomic. The differences of microbial community structure, function, and metabolism between winter and summer in a full-scale pre-denitrification biofilter were revealed for the first time, strengthening our understanding of the microbial ecology of biofilm communities.

Molecular Mechanisms and Applications of N-Acyl Homoserine Lactone-Mediated Quorum Sensing in Bacteria

Microbial biodiversity includes biotic and abiotic components that support all life forms by adapting to environmental conditions. Climate change, pollution, human activity, and natural calamities affect microbial biodiversity. Microbes have diverse growth conditions, physiology, and metabolism. Bacteria use signaling systems such as quorum sensing (QS) to regulate cellular interactions via small chemical signaling molecules which also help with adaptation under undesirable survival conditions. Proteobacteria use acyl-homoserine lactone (AHL) molecules as autoinducers to sense population density and modulate gene expression. The LuxI-type enzymes synthesize AHL molecules, while the LuxR-type proteins (AHL transcriptional regulators) bind to AHLs to regulate QS-dependent gene expression. Diverse AHLs have been identified, and the diversity extends to AHL synthases and AHL receptors. This review comprehensively explains the molecular diversity of AHL signaling components of Pseudomonas aeruginosa, Chromobacterium violaceum, Agrobacterium tumefaciens, and Escherichia coli. The regulatory mechanism of AHL signaling is also highlighted in this review, which adds to the current understanding of AHL signaling in Gram-negative bacteria. We summarize molecular diversity among well-studied QS systems and recent advances in the role of QS proteins in bacterial cellular signaling pathways. This review describes AHL-dependent QS details in bacteria that can be employed to understand their features, improve environmental adaptation, and develop broad biomolecule-based biotechnological applications.