A Rhodococcal Transcriptional Regulatory Mechanism Detects the Common Lactone Ring of AHL Quorum-Sensing Signals and Triggers the Quorum-Quenching Response

Application of nanomaterials as potential quorum quenchers for disease: Recent advances and challenges

Chemical signal molecules are used by bacteria to interact with one another. Small hormone-like molecules known as autoinducers are produced, released, detected, and responded to during chemical communication. Quorum Sensing (QS) is the word for this procedure; it allows bacterial populations to communicate and coordinate group behavior. Several research has been conducted on using inhibitors to prevent QS and minimize the detrimental consequences. Through the enzymatic breakdown of the autoinducer component, by preventing the formation of autoinducers, or by blocking their reception by adding some compounds (inhibitors) that can mimic the autoinducers, a technique known as "quorum quenching" (QQ) disrupts microbial communication. Numerous techniques, including colorimetry, electrochemistry, bioluminescence, chemiluminescence, fluorescence, chromatography-mass spectroscopy, and many more, can be used to test QS/QQ. They all permit quantitative and qualitative measurements of QS/QQ molecules. The mechanism of QS and QQ, as well as the use of QQ in the prevention of biofilms, are all elaborated upon in this writing, along with the fundamental study of nanoparticle (NP)in QQ. Q.

Pseudomonas fluorescens MFE01 uses 1-undecene as aerial communication molecule

Bacterial communication is a fundamental process used to synchronize gene expression and collective behavior among the bacterial population. The most studied bacterial communication system is quorum sensing, a cell density system, in which the concentration of inductors increases to a threshold level allowing detection by specific receptors. As a result, bacteria can change their behavior in a coordinated way. While in Pseudomonas quorum sensing based on the synthesis of N-acyl homoserine lactone molecules is well studied, volatile organic compounds, although considered to be communication signals in the rhizosphere, are understudied. The Pseudomonas fluorescens MFE01 strain has a very active type six secretion system that can kill some competitive bacteria. Furthermore, MFE01 emits numerous volatile organic compounds, including 1-undecene, which contributes to the aerial inhibition of Legionella pneumophila growth. Finally, MFE01 appears to be deprived of N-acyl homoserine lactone synthase. The main objective of this study was to explore the role of 1-undecene in the communication of MFE01. We constructed a mutant affected in undA gene encoding the enzyme responsible for 1-undecene synthesis to provide further insight into the role of 1-undecene in MFE01. First, we studied the impacts of this mutation both on volatile organic compounds emission, using headspace solid-phase microextraction combined with gas chromatography-mass spectrometry and on L. pneumophila long-range inhibition. Then, we analyzed influence of 1-undecene on MFE01 coordinated phenotypes, including type six secretion system activity and biofilm formation. Next, to test the ability of MFE01 to synthesize N-acyl homoserine lactones in our conditions, we investigated in silico the presence of corresponding genes across the MFE01 genome and we exposed its biofilms to an N-acyl homoserine lactone-degrading enzyme. Finally, we examined the effects of 1-undecene emission on MFE01 biofilm maturation and aerial communication using an original experimental set-up. This study demonstrated that the ΔundA mutant is impaired in biofilm maturation. An exposure of the ΔundA mutant to the volatile compounds emitted by MFE01 during the biofilm development restored the biofilm maturation process. These findings indicate that P. fluorescens MFE01 uses 1-undecene emission for aerial communication, reporting for the first time this volatile organic compound as bacterial intraspecific communication signal.

Rhodococcus strains as a good biotool for neutralizing pharmaceutical pollutants and obtaining therapeutically valuable products: Through the past into the future

Active pharmaceutical ingredients present a substantial risk when they reach the environment and drinking water sources. As a new type of dangerous pollutants with high chemical resistance and pronounced biological effects, they accumulate everywhere, often in significant concentrations (μg/L) in ecological environments, food chains, organs of farm animals and humans, and cause an intense response from the aquatic and soil microbiota. Rhodococcus spp. (Actinomycetia class), which occupy a dominant position in polluted ecosystems, stand out among other microorganisms with the greatest variety of degradable pollutants and participate in natural attenuation, are considered as active agents with high transforming and degrading impacts on pharmaceutical compounds. Many representatives of rhodococci are promising as unique sources of specific transforming enzymes, quorum quenching tools, natural products and novel antimicrobials, biosurfactants and nanostructures. The review presents the latest knowledge and current trends regarding the use of Rhodococcus spp. in the processes of pharmaceutical pollutants’ biodegradation, as well as in the fields of biocatalysis and biotechnology for the production of targeted pharmaceutical products. The current literature sources presented in the review can be helpful in future research programs aimed at promoting Rhodococcus spp. as potential biodegraders and biotransformers to control pharmaceutical pollution in the environment.

Delineation of mechanistic approaches of rhizosphere microorganisms facilitated plant health and resilience under challenging conditions

Sustainable agriculture demands the balanced use of inorganic, organic, and microbial biofertilizers for enhanced plant productivity and soil fertility. Plant growth-enhancing rhizospheric bacteria can be an excellent biotechnological tool to augment plant productivity in different agricultural setups. We present an overview of microbial mechanisms which directly or indirectly contribute to plant growth, health, and development under highly variable environmental conditions. The rhizosphere microbiomes promote plant growth, suppress pathogens and nematodes, prime plants immunity, and alleviate abiotic stress. The prospective of beneficial rhizobacteria to facilitate plant growth is of primary importance, particularly under abiotic and biotic stresses. Such microbe can promote plant health, tolerate stress, even remediate soil pollutants, and suppress phytopathogens. Providing extra facts and a superior understanding of microbial traits underlying plant growth promotion can stir the development of microbial-based innovative solutions for the betterment of agriculture. Furthermore, the application of novel scientific approaches for facilitating the design of crop-specific microbial biofertilizers is discussed. In this context, we have highlighted the exercise of "multi-omics" methods for assessing the microbiome's impact on plant growth, health, and overall fitness via analyzing biochemical, physiological, and molecular facets. Furthermore, the role of clustered regularly interspaced short palindromic repeats (CRISPR) based genome alteration and nanotechnology for improving the agronomic performance and rhizosphere microbiome is also briefed. In a nutshell, the paper summarizes the recent vital molecular processes that underlie the different beneficial plant-microbe interactions imperative for enhancing plant fitness and resilience under-challenged agriculture.

Quorum-Sensing Inhibition by Gram-Positive Bacteria

The modern paradigm assumes that interspecies communication of microorganisms occurs through precise regulatory mechanisms. In particular, antagonism between bacteria or bacteria and fungi can be achieved by direct destruction of the targeted cells through the regulated production of antimicrobial metabolites or by controlling their adaptive mechanisms, such as the formation of biofilms. The quorum-quenching phenomenon provides such a countermeasure strategy. This review discusses quorum-sensing suppression by Gram-positive microorganisms, the underlying mechanisms of this process, and its molecular intermediates. The main focus will be on Gram-positive bacteria that have practical applications, such as starter cultures for food fermentation, probiotics, and other microorganisms of biotechnological importance. The possible evolutionary role of quorum-quenching mechanisms during the development of interspecies interactions of bacteria is also considered. In addition, the review provides possible practical applications for these mechanisms, such as the control of pathogens, improving the efficiency of probiotics, and plant protection.

Responses to Ecopollutants and Pathogenization Risks of Saprotrophic Rhodococcus Species

Under conditions of increasing environmental pollution, true saprophytes are capable of changing their survival strategies and demonstrating certain pathogenicity factors. Actinobacteria of the genus Rhodococcus, typical soil and aquatic biotope inhabitants, are characterized by high ecological plasticity and a wide range of oxidized organic substrates, including hydrocarbons and their derivatives. Their cell adaptations, such as the ability of adhering and colonizing surfaces, a complex life cycle, formation of resting cells and capsule-like structures, diauxotrophy, and a rigid cell wall, developed against the negative effects of anthropogenic pollutants are discussed and the risks of possible pathogenization of free-living saprotrophic Rhodococcus species are proposed. Due to universal adaptation features, Rhodococcus species are among the candidates, if further anthropogenic pressure increases, to move into the group of potentially pathogenic organisms with "unprofessional" parasitism, and to join an expanding list of infectious agents as facultative or occasional parasites.

Biocontrol of Biofilm Formation: Jamming of Sessile-Associated Rhizobial Communication by Rhodococcal Quorum-Quenching

Biofilms are complex structures formed by a community of microbes adhering to a surface and/or to each other through the secretion of an adhesive and protective matrix. The establishment of these structures requires a coordination of action between microorganisms through powerful communication systems such as quorum-sensing. Therefore, auxiliary bacteria capable of interfering with these means of communication could be used to prevent biofilm formation and development. The phytopathogen Rhizobium rhizogenes, which causes hairy root disease and forms large biofilms in hydroponic crops, and the biocontrol agent Rhodococcus erythropolis R138 were used for this study. Changes in biofilm biovolume and structure, as well as interactions between rhizobia and rhodococci, were monitored by confocal laser scanning microscopy with appropriate fluorescent biosensors. We obtained direct visual evidence of an exchange of signals between rhizobia and the jamming of this communication by Rhodococcus within the biofilm. Signaling molecules were characterized as long chain (C₁₄) N-acyl-homoserine lactones. The role of the Qsd quorum-quenching pathway in biofilm alteration was confirmed with an R. erythropolis mutant unable to produce the QsdA lactonase, and by expression of the qsdA gene in a heterologous host, Escherichia coli. Finally, Rhizobium biofilm formation was similarly inhibited by a purified extract of QsdA enzyme.

Biosensors Used for Epifluorescence and Confocal Laser Scanning Microscopies to Study Dickeya and Pectobacterium Virulence and Biocontrol

Promoter-probe vectors carrying fluorescent protein-reporter genes are powerful tools used to study microbial ecology, epidemiology, and etiology. In addition, they provide direct visual evidence of molecular interactions related to cell physiology and metabolism. Knowledge and advances carried out thanks to the construction of soft-rot Pectobacteriaceae biosensors, often inoculated in potato Solanum tuberosum, are discussed in this review. Under epifluorescence and confocal laser scanning microscopies, Dickeya and Pectobacterium-tagged strains managed to monitor in situ bacterial viability, microcolony and biofilm formation, and colonization of infected plant organs, as well as disease symptoms, such as cell-wall lysis and their suppression by biocontrol antagonists. The use of dual-colored reporters encoding the first fluorophore expressed from a constitutive promoter as a cell tag, while a second was used as a regulator-based reporter system, was also used to simultaneously visualize bacterial spread and activity. This revealed the chronology of events leading to tuber maceration and quorum-sensing communication, in addition to the disruption of the latter by biocontrol agents. The promising potential of these fluorescent biosensors should make it possible to apprehend other activities, such as subcellular localization of key proteins involved in bacterial virulence in planta, in the near future.

Effect of a Bacillus subtilis strain on flax protection against Fusarium oxysporum and its impact on the root and stem cell walls

In Normandy, flax is a plant of important economic interest because of its fibres. Fusarium oxysporum, a telluric fungus, is responsible for the major losses in crop yield and fibre quality. Several methods are currently used to limit the use of phytochemicals on crops. One of them is the use of plant growth promoting rhizobacteria (PGPR) occurring naturally in the rhizosphere. PGPR are known to act as local antagonists to soil-borne pathogens and to enhance plant resistance by eliciting the induced systemic resistance (ISR). In this study, we first investigated the cell wall modifications occurring in roots and stems after inoculation with the fungus in two flax varieties. First, we showed that both varieties displayed different cell wall organization and that rapid modifications occurred in roots and stems after inoculation. Then, we demonstrated the efficiency of a Bacillus subtilis strain to limit Fusarium wilt on both varieties with a better efficiency for one of them. Finally, thermo-gravimetry was used to highlight that B. subtilis induced modifications of the stem properties, supporting a reinforcement of the cell walls. Our findings suggest that the efficiency and the mode of action of the PGPR B. subtilis is likely to be flax variety dependent.

Therapeutic applications and biological activities of bacterial bioactive extracts

Bacteria are rich in a wide variety of secondary metabolites, such as pigments, alkaloids, antibiotics, and others. These bioactive microbial products serve a great application in human and animal health. Their molecular diversity allows these natural products to possess several therapeutic attributes and biological functions. That's why the current natural drug industry focuses on uncovering all the possible ailments and diseases that could be combated by bacterial extracts and their secondary metabolites. In this paper, we review the major utilizations of bacterial natural products for the treatment of cancer, inflammatory diseases, allergies, autoimmune diseases, infections and other diseases that threaten public health. We also elaborate on the identified biological activities of bacterial secondary metabolites including antibacterial, antifungal, antiviral and antioxidant activities all of which are essential nowadays with the emergence of drug-resistant microbial pathogens. Throughout this review, we discuss the possible mechanisms of actions in which bacterial-derived biologically active molecular entities could possess healing properties to inspire the development of new therapeutic agents in academia and industry.

The Evanescent GacS Signal

The GacS histidine kinase is the membrane sensor of the major upstream two-component system of the regulatory Gac/Rsm signal transduction pathway. This pathway governs the expression of a wide range of genes in pseudomonads and controls bacterial fitness and motility, tolerance to stress, biofilm formation, and virulence or plant protection. Despite the importance of these roles, the ligands binding to the sensor domain of GacS remain unknown, and their identification is an exciting challenge in this domain. At high population densities, the GacS signal triggers a switch from primary to secondary metabolism and a change in bacterial lifestyle. It has been suggested, based on these observations, that the GacS signal is a marker of the emergence of nutritional stress and competition. Biochemical investigations have yet to characterize the GacS signal fully. However, they portray this cue as a low-molecular weight, relatively simple and moderately apolar metabolite possibly resembling, but nevertheless different, from the aliphatic organic acids acting as quorum-sensing signaling molecules in other Proteobacteria. Significant progress in the development of metabolomic tools and new databases dedicated to Pseudomonas metabolism should help to unlock some of the last remaining secrets of GacS induction, making it possible to control the Gac/Rsm pathway.

Close-up on a bacterial informational war in the geocaulosphere

The geocaulosphere is home to microbes that establish communication between themselves and others that disrupt them. These cell-to-cell communication systems are based on the synthesis and perception of signaling molecules, of which the best known belong to the N-acyl-homoserine lactone (AHL) family. Among indigenous bacteria, certain Gram-positive actinobacteria can sense AHLs produced by soft-rot Gram-negative phytopathogens and can degrade the quorum-sensing AHL signals to impair the expression of virulence factors. We mimicked this interaction by introducing dual-color reporter strains suitable for monitoring both the location of the cells and their quorum-sensing and -quenching activities, in potato tubers. The exchange of AHL signals within the pathogen’s cell quorum was clearly detected by the presence of bright green fluorescence instead of blue in a portion of Pectobacterium-tagged cells. This phenomenon in Rhodococcus cells was accompanied by a change from red fluorescence to orange, showing that the disappearance of signaling molecules is due to rhodococcal AHL degradation rather than the inhibition of AHL production. Rhodococci are victorious in this fight for the control of AHL-based communication, as their jamming activity is powerful enough to prevent the onset of disease symptoms.

Identification of a Second Type of AHL-lactonase from Rhodococcus sp. BH4, belonging to the α/β Hydrolase Superfamily

N-acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) plays a major role in development of biofilms, which contribute to rise in infections and biofouling in water-related industries. Interference in QS, called quorum quenching (QQ), has recieved a lot of attention in recent years. Rhodococcus spp. are known to have prominent quorum quenching activity and in previous reports it was suggested that this genus possesses multiple QQ enzymes, but only one gene, qsdA, which encodes an AHL-lactonase belonging to phosphotriesterase family, has been identified. Therefore, we conducted a whole genome sequencing and analysis of Rhodococcus sp. BH4 isolated from a wastewater treatment plant. The sequencing revealed another gene encoding a QQ enzyme (named jydB) that exhibited a high AHL degrading activity. This QQ enzyme had a 46% amino acid sequence similarity with the AHL-lactonase (AidH) of Ochrobactrum sp. T63. HPLC analysis and AHL restoration experiments by acidification revealed that the jydB gene encodes an AHL-lactonase which shares the known characteristics of the α/β hydrolase family. Purified recombinant JydB demonstrated a high hydrolytic activity against various AHLs. Kinetic analysis of JydB revealed a high catalytic efficiency (k_cat/K_M) against C4-HSL and 3-oxo-C6 HSL, ranging from 1.88 × 10⁶ to 1.45 × 10⁶ M^-1 s^-1, with distinctly low K_M values (0.16 - 0.24 mM). This study affirms that the AHL degrading activity and biofilm inhibition ability of Rhodococcus sp. BH4 may be due to the presence of multiple quorum quenching enzymes, including two types of AHL-lactonases, in addition to AHL-acylase and oxidoreductase, for which the genes have yet to be described.

Quorum sensing mediated response of Achromobacter denitrificans SP1 towards prodigiosin production under phthalate stress

Quorum sensing is a density-dependent chemical process between bacteria, which may be intergenus or intragenus. N-acyl homoserine lactones (HSLs) are a type of small signaling molecules associated with Gram-negative bacteria for monitoring their own population density. The present study unveils the mechanism of HSLs in Achromobacter denitrificans SP1 while transforming di(2-ethylhexyl) phthalate (DEHP) into prodigiosin in a simple basal salt medium. The primary detection of HSLs was done by the colorimetric method. Fourier-transform infrared spectroscopy and liquid chromatography-mass spectrometry-quadrupole time-of-flight confirmed and identified the HSLs. The maximum production of HSLs was observed between 24 and 72 h of incubation, which is noted to be a peak time of DEHP degradation. A total of 57.2% of DEHP was degraded within 30 h and complete degradation was observed within 72 h of incubation. Regulation in the synthesis of various acyl-HSL molecules, viz. 3OC6-HSL in the initial stage of DEHP stress, 3OC8-HSL, and C10-HSL during the time of degradation and 3OC12-HSL on completion of degradation was noticed. The role of HSLs on the production of prodigiosin was confirmed using vanillin as an HSL inhibitor. Through the selective activation of HSL molecules, A. denitrificans SP1 sustain the changing stressful conditions. Supplementation of acyl-HSL signal molecules may boost up the efficacy of A. denitrificans SP1 in both DEHP degradation and prodigiosin production which offers great potential towards the management of DEHP containing plastic wastes.

Profile of the Intervention Potential of the Phylum Actinobacteria Toward Quorum Sensing and Other Microbial Virulence Strategies

The rapid dissemination of antimicrobial resistance amongst microorganisms and their deleterious effect on public health has propelled the exploration of alternative interventions that target microbial virulence rather than viability. In several microorganisms, the expression of virulence factors is controlled by quorum sensing systems. A comprehensive understanding into microbial quorum sensing systems, virulence strategies and pathogenesis has exposed potential targets whose attenuation may alleviate infectious diseases. Such virulence attenuating natural products sourced from the different phyla of bacteria from diverse ecosystems have been identified. In this review, we discuss chemical entities derived from the phylum Actinobacteria that have demonstrated the potential to inhibit microbial biofilms, enzymes, and other virulence factors both in vivo and in vitro. We also review Actinobacteria-derived compounds that can degrade quorum sensing signal molecules, and the genes encoding such molecules. As many Actinobacteria-derived compounds have been translated into pharmaceutically important agents including antibiotics, the identification of virulence attenuating compounds from this phylum exemplifies their significance as a prospective source for anti-virulent drugs.

Biocontrol of Soft Rot: Confocal Microscopy Highlights Virulent Pectobacterial Communication and Its Jamming by Rhodococcal Quorum-Quenching

Confocal laser-scanning microscopy was chosen to observe the colonization and damage caused by the soft rot Pectobacterium atrosepticum and the protection mediated by the biocontrol agent Rhodococcus erythropolis. We developed dual-color reporter strains suited for monitoring quorum-sensing and quorum-quenching activities leading to maceration or biocontrol, respectively. A constitutively expressed cyan or red fluorescent protein served as a cell tag for plant colonization, while an inducible expression reporter system based on the green fluorescent protein gene enabled the simultaneous recording of signaling molecule production, detection, or degradation. The dual-colored pathogen and biocontrol strains were used to coinoculate potato tubers. At cellular quorum, images revealed a strong pectobacterial quorum-sensing activity, especially at the plant cell walls, as well as a concomitant rhodococcal quorum-quenching response, at both the single-cell and microcolony levels. The generated biosensors appear to be promising and complementary tools useful for molecular and cellular studies of bacterial communication and interference.

A Flavor Lactone Mimicking AHL Quorum-Sensing Signals Exploits the Broad Affinity of the QsdR Regulator to Stimulate Transcription of the Rhodococcal qsd Operon Involved in Quorum-Quenching and Biocontrol Activities

In many Gram-negative bacteria, virulence, and social behavior are controlled by quorum-sensing (QS) systems based on the synthesis and perception of N-acyl homoserine lactones (AHLs). Quorum-quenching (QQ) is currently used to disrupt bacterial communication, as a biocontrol strategy for plant crop protection. In this context, the Gram-positive bacterium Rhodococcus erythropolis uses a catabolic pathway to control the virulence of soft-rot pathogens by degrading their AHL signals. This QS signal degradation pathway requires the expression of the qsd operon, encoding the key enzyme QsdA, an intracellular lactonase that can hydrolyze a wide range of substrates. QsdR, a TetR-like family regulator, represses the expression of the qsd operon. During AHL degradation, this repression is released by the binding of the γ-butyrolactone ring of the pathogen signaling molecules to QsdR. We show here that a lactone designed to mimic quorum signals, γ-caprolactone, can act as an effector ligand of QsdR, triggering the synthesis of qsd operon-encoded enzymes. Interaction between γ-caprolactone and QsdR was demonstrated indirectly, by quantitative RT-PCR, molecular docking and transcriptional fusion approaches, and directly, in an electrophoretic mobility shift assay. This broad-affinity regulatory system demonstrates that preventive or curative quenching therapies could be triggered artificially and/or managed in a sustainable way by the addition of γ-caprolactone, a compound better known as cheap food additive. The biostimulation of QQ activity could therefore be used to counteract the lack of consistency observed in some large-scale biocontrol assays.