Divide and conquer: the Pseudomonas aeruginosa two-component hybrid SagS enables biofilm formation and recalcitrance of biofilm cells to antimicrobial agents via distinct regulatory circuits

The role of extracellular structures in Clostridioides difficile biofilm formation

C. difficile infection (CDI) is a costly and increasing burden on the healthcare systems of many developed countries due to the high rates of nosocomial infections. Despite the availability of several antibiotics with high response rates, effective treatment is hampered by recurrent infections. One potential mechanism for recurrence is the existence of C. difficile biofilms in the gut which persist through the course of antibiotics. In this review, we describe current developments in understanding the molecular mechanisms by which C. difficile biofilms form and are stabilized through extracellular biomolecular interactions.

Maltodextrin-binding protein as a key factor in Cronobacter sakazakii survival under desiccation stress

Cronobacter sakazakii (C. sakazakii) is a notorious pathogen responsible for infections in infants and newborns, often transmitted through contaminated infant formula. Despite the use of traditional pasteurization methods, which can reduce microbial contamination, there remains a significant risk of pathogenic C. sakazakii surviving due to its exceptional stress tolerance. In our study, we employed a comparative proteomic approach by comparing wild-type strains with gene knockout strains to identify the essential genes crucial for the successful survival of C. sakazakii during desiccation. Our investigation revealed the significance of envZ-ompR, recA, and flhD gene cassettes in contributing to desiccation tolerance in C. sakazakii. Furthermore, through our comparative proteomic profiling, we identified the maltodextrin-binding protein encoded by ESA_03421 as a potential factor influencing dry tolerance. This protein is regulated by EnvZ-OmpR, RecA, and FlhD. Notably, the knockout of ESA_03421 resulted in a 150% greater reduction in Log CFU compared to the wild-type C. sakazakii. Overall, our findings offer valuable insights into the mechanisms underlying C. sakazakii desiccation tolerance and provide potential targets for the development of new antimicrobial strategies aimed at reducing the risk of infections in infants and newborns.

Structure based virtual screening and molecular dynamics of natural anti-biofilm compounds against SagS response regulator/sensor kinase in Pseudomonas aeruginosa

SagS sensor regulator plays a vital role in biofilm development of Pseudomonas aeruginosa which subsequently makes the cells more tolerant to various antimicrobials. The multidrug resistance (MDR) issue has risen substantially in recent years and is considered a global threat. Therefore, alternative compounds should be unearthed immediately to address the issues related to P. aeruginosa drug resistance for which SagS could be a candidate. The present study is an attempt to screen natural anti-biofilm compounds as the potent inhibitors of SagS. Twenty natural anti-biofilm/quorum sensing inhibiting compounds were retrieved from various literatures with significant inhibitory effects against P. aeruginosa biofilm from in-vitro experiments which were screened using various pharmacokinetic parameters. The screened and three standard drugs were docked against SagS-HisKA using AutoDock 4.2 tool, which were further analysed by MD simulations to understand the binding mode of compounds and dynamic behaviour of the complexes. Two potential anti-biofilm natural compounds, pinocembrin with binding affinity (-7.19 kcal/mol), vestitol (-7.18 kcal/mol) and the standard drug ceftazidime (-8.89 kcal/mol) were selected based on filtered parameters and better binding affinity. The trajectory analysis of MD simulations reflected Pinocembrin in stabilizing the system compared to ceftazidime. The existing reports state that the natural products represent promising source of therapy with least or almost nil adverse effect compared to synthetic drugs which is well collated with our in-silico findings. This investigation can save both time and cost required for in-vitro and in-vivo analysis for designing of a novel anti-biofilm agent against P. aeruginosa biofilm-associated infections.Communicated by Ramaswamy H. Sarma.

Manganese Acts as an Environmental Inhibitor of Pseudomonas aeruginosa Biofilm Development by Inducing Dispersion and Modulating c-di-GMP and Exopolysaccharide Production via RbdA

The opportunistic human pathogen Pseudomonas aeruginosa causes chronic infections that involve multicellular aggregates called biofilms. Biofilm formation is modulated by the host environment and the presence of cues and/or signals, likely affecting the pool of the bacterial second messenger cyclic diguanylate monophosphate (c-di-GMP). The manganese ion Mn2+ is a divalent metal cation that is essential for pathogenic bacterial survival and replication during the infection in a host organism. In this study, we investigated how Mn2+ alters P. aeruginosa biofilm formation via the regulation of c-di-GMP levels. Exposure to Mn2+ was found to temporally enhance attachment but impair subsequent biofilm development, apparent by reduced biofilm biomass accumulation and lack of microcolony formation due to the induction of dispersion. Moreover, exposure to Mn2+ coincided with reduced production of the exopolysaccharides Psl and Pel, decreased transcriptional abundance of pel and psl, and decreased levels of c-di-GMP. To determine whether the effect of Mn2+ was linked to the activation of phosphodiesterases (PDEs), we screened several PDE mutants for Mn2+-dependent phenotypes (attachment and polysaccharide production) as well as PDE activity. The screen revealed that the PDE RbdA is activated by Mn2+ and is responsible for Mn2+-dependent attachment, inhibition of Psl production, and dispersion. Taken together, our findings suggest Mn2+ is an environmental inhibitor of P. aeruginosa biofilm development that acts through the PDE RbdA to modulate c-di-GMP levels, thereby impeding polysaccharide production and biofilm formation but enhancing dispersion. IMPORTANCE While diverse environmental conditions such as the availability of metal ions have been shown to affect biofilm development, little is known about the mechanism. Here, we demonstrate that Mn2+ affects Pseudomonas aeruginosa biofilm development by stimulating phosphodiesterase RbdA activity to reduce the signaling molecule c-di-GMP levels, thereby hindering polysaccharide production and biofilm formation but enhancing dispersion. Our findings demonstrate that Mn2+ acts as an environmental inhibitor of P. aeruginosa biofilms, further suggesting manganese to be a promising new antibiofilm factor.

MoaB1 Homologs Contribute to Biofilm Formation and Motility by Pseudomonas aeruginosa and Escherichia coli

moaB homologs, encoding the molybdopterin biosynthetic protein B1, have been reported to be expressed under anoxic conditions and during biofilm growth in various microorganisms; however, little is known about MoaB's function. Here, we demonstrate that in Pseudomonas aeruginosa, MoaB1 (PA3915) contributes to biofilm-related phenotypes. Specifically, moaB1 expression is induced in biofilms, and insertional inactivation of moaB1 reduced biofilm biomass accumulation and pyocyanin production while enhancing swarming motility, and pyoverdine abundance without affecting attachment, swimming motility, or c-di-GMP levels. Inactivation of the highly conserved E. coli homolog of moaB1, moaBEc, likewise coincided with reduced biofilm biomass accumulation. In turn, heterologous expression of moaBEc restored biofilm formation and swarming motility by the P. aeruginosa moaB1 mutant to wild-type levels. Moreover, MoaB1 was found to interact with other conserved biofilm-associated proteins, PA2184 and PA2146, as well as the sensor-kinase SagS. However, despite the interaction, MoaB1 failed to restore SagS-dependent expression of brlR encoding the transcriptional regulator BrlR, and inactivation of moaB1 or moaBEc had no effect on the antibiotic susceptibility phenotype of biofilms formed by P. aeruginosa and E. coli, respectively. While our findings did not establish a link between MoaB1 and molybdenum cofactor biosynthesis, they suggest that MoaB1 homologs contribute to biofilm-associated phenotypes across species boundaries, possibly hinting at the existence of a previously undescribed conserved biofilm pathway. IMPORTANCE Proteins contributing to the biogenesis of molybdenum cofactors have been characterized; however, the role of the molybdopterin biosynthetic protein B1 (MoaB1) has remained elusive, and solid evidence to support its role in biosynthesis of molybdenum cofactor is lacking. Here, we demonstrate that, in Pseudomonas aeruginosa, MoaB1 (PA3915) contributes to biofilm-related phenotypes in a manner that does not support a role of MoaB1 in the biosynthesis of molybdenum cofactors.

The biofilm life cycle: expanding the conceptual model of biofilm formation

Bacterial biofilms are often defined as communities of surface-attached bacteria and are typically depicted with a classic mushroom-shaped structure characteristic of Pseudomonas aeruginosa. However, it has become evident that this is not how all biofilms develop, especially in vivo, in clinical and industrial settings, and in the environment, where biofilms often are observed as non-surface-attached aggregates. In this Review, we describe the origin of the current five-step biofilm development model and why it fails to capture many aspects of bacterial biofilm physiology. We aim to present a simplistic developmental model for biofilm formation that is flexible enough to include all the diverse scenarios and microenvironments where biofilms are formed. With this new expanded, inclusive model, we hereby introduce a common platform for developing an understanding of biofilms and anti-biofilm strategies that can be tailored to the microenvironment under investigation.

A previously uncharacterized gene, PA2146, contributes to biofilm formation and drug tolerance across the ɣ-Proteobacteria

Transcriptomic studies have revealed a large number of uncharacterized genes that are differentially expressed in biofilms, which may be important in regulating biofilm phenotypes such as resistance to antimicrobial agents. To identify biofilm genes of unknown function in P. aeruginosa, we made use of RNA-seq and selected 27 uncharacterized genes that were induced upon biofilm growth. Biofilms by respective mutants were subsequently analyzed for two biofilm characteristics, the biofilm architecture and drug susceptibility. The screen revealed 12 out of 27 genes to contribute to biofilm formation and 13 drug susceptibility, with 8 genes affecting both biofilm phenotypes. Amongst the genes affecting both biofilm phenotypes was PA2146, encoding a small hypothetical protein that exhibited some of the most substantial increases in transcript abundance during biofilm growth by P. aeruginosa PAO1 and clinical isolates. PA2146 is highly conserved in ɣ-proteobacteria. Inactivation of PA2146 affected both biofilm phenotypes in P. aeruginosa PAO1, with inactivation of homologs in Klebsiella pneumoniae and Escherichia coli having similar effects. Heterologous expression of PA2146 homologs complemented the P. aeruginosa ∆PA2146, suggesting that PA2146 homologs substitute for and play a similar role as PA2146 in P. aeruginosa.

Targeting the Holy Triangle of Quorum Sensing, Biofilm Formation, and Antibiotic Resistance in Pathogenic Bacteria

Chronic and recurrent bacterial infections are frequently associated with the formation of biofilms on biotic or abiotic materials that are composed of mono- or multi-species cultures of bacteria/fungi embedded in an extracellular matrix produced by the microorganisms. Biofilm formation is, among others, regulated by quorum sensing (QS) which is an interbacterial communication system usually composed of two-component systems (TCSs) of secreted autoinducer compounds that activate signal transduction pathways through interaction with their respective receptors. Embedded in the biofilms, the bacteria are protected from environmental stress stimuli, and they often show reduced responses to antibiotics, making it difficult to eradicate the bacterial infection. Besides reduced penetration of antibiotics through the intricate structure of the biofilms, the sessile biofilm-embedded bacteria show reduced metabolic activity making them intrinsically less sensitive to antibiotics. Moreover, they frequently express elevated levels of efflux pumps that extrude antibiotics, thereby reducing their intracellular levels. Some efflux pumps are involved in the secretion of QS compounds and biofilm-related materials, besides being important for removing toxic substances from the bacteria. Some efflux pump inhibitors (EPIs) have been shown to both prevent biofilm formation and sensitize the bacteria to antibiotics, suggesting a relationship between these processes. Additionally, QS inhibitors or quenchers may affect antibiotic susceptibility. Thus, targeting elements that regulate QS and biofilm formation might be a promising approach to combat antibiotic-resistant biofilm-related bacterial infections.

Search for a Shared Genetic or Biochemical Basis for Biofilm Tolerance to Antibiotics across Bacterial Species

Is there a universal genetically programmed defense providing tolerance to antibiotics when bacteria grow as biofilms? A comparison between biofilms of three different bacterial species by transcriptomic and metabolomic approaches uncovered no evidence of one. Single-species biofilms of three bacterial species (Pseudomonas aeruginosa, Staphylococcus aureus, and Acinetobacter baumannii) were grown in vitro for 3 days and then challenged with respective antibiotics (ciprofloxacin, daptomycin, and tigecycline) for an additional 24 h. All three microorganisms displayed reduced susceptibility in biofilms compared to planktonic cultures. Global transcriptomic profiling of gene expression comparing biofilm to planktonic and antibiotic-treated biofilm to untreated biofilm was performed. Extracellular metabolites were measured to characterize the utilization of carbon sources between biofilms, treated biofilms, and planktonic cells. While all three bacteria exhibited a species-specific signature of stationary phase, no conserved gene, gene set, or common functional pathway could be identified that changed consistently across the three microorganisms. Across the three species, glucose consumption was increased in biofilms compared to planktonic cells, and alanine and aspartic acid utilization were decreased in biofilms compared to planktonic cells. The reasons for these changes were not readily apparent in the transcriptomes. No common shift in the utilization pattern of carbon sources was discerned when comparing untreated to antibiotic-exposed biofilms. Overall, our measurements do not support the existence of a common genetic or biochemical basis for biofilm tolerance against antibiotics. Rather, there are likely myriad genes, proteins, and metabolic pathways that influence the physiological state of individual microorganisms in biofilms and contribute to antibiotic tolerance.

Controlling Biofilm Development Through Cyclic di-GMP Signaling

The cyclic di-GMP (c-di-GMP) second messenger represents a signaling system that regulates many bacterial behaviors and is of key importance for driving the lifestyle switch between motile loner cells and biofilm formers. This review provides an up-to-date summary of c-di-GMP pathways connected to biofilm formation by the opportunistic pathogen P. aeruginosa. Emphasis will be on the timing of c-di-GMP production over the course of biofilm formation, to highlight non-uniform and hierarchical increases in c-di-GMP levels, as well as biofilm growth conditions that do not conform with our current model of c-di-GMP.

Role of Two-Component System Networks in Pseudomonas aeruginosa Pathogenesis

Two-component systems (TCS) are the largest family of signaling systems in the bacterial kingdom. They enable bacteria to cope with a wide range of environmental conditions via the sensing of stimuli and the transduction of the signal into an appropriate cellular adaptation response. Pseudomonas aeruginosa possesses one of the richest arrays of TCSs in bacteria and they have been the subject of intense investigation for more than 20 years. Most of the P. aeruginosa TCSs characterized to date affect its pathogenesis, via the regulation of virulence factors expression, modulation of the synthesis of antibiotic/antimicrobial resistance mechanisms, and/or via linking virulence to energy metabolism. Here, we give an overview of the current knowledge on P. aeruginosa TCSs, citing key examples for each of the above-mentioned regulatory actions. We then conclude by mentioning few small molecule inhibitors of P. aeruginosa TCSs that have shown an antimicrobial action in vitro.

Phylogenetic Analysis with Prediction of Cofactor or Ligand Binding for Pseudomonas aeruginosa PAS and Cache Domains

PAS domains are omnipresent building blocks of multidomain proteins in all domains of life. Bacteria possess a variety of PAS domains in intracellular proteins and the related Cache domains in periplasmic or extracellular proteins. PAS and Cache domains are predominant in sensory systems, often carry cofactors or bind ligands, and serve as dimerization domains in protein association. To aid our understanding of the wide distribution of these domains, we analyzed the proteome of the opportunistic human pathogen Pseudomonas aeruginosa PAO1 in silico. The ability of this bacterium to survive under different environmental conditions, to switch between planktonic and sessile/biofilm lifestyle, or to evade stresses, notably involves c-di-GMP regulatory proteins or depends on sensory pathways involving multidomain proteins that possess PAS or Cache domains. Maximum likelihood phylogeny was used to group PAS and Cache domains on the basis of amino acid sequence. Conservation of cofactor- or ligand-coordinating amino acids aided by structure-based comparison was used to inform function. The resulting classification presented here includes PAS domains that are candidate binders of carboxylic acids, amino acids, fatty acids, flavin adenine dinucleotide (FAD), 4-hydroxycinnamic acid, and heme. These predictions are put in context to previously described phenotypic data, often generated from deletion mutants. The analysis predicts novel functions for sensory proteins and sheds light on functional diversification in a large set of proteins with similar architecture. IMPORTANCE To adjust to a variety of life conditions, bacteria typically use multidomain proteins, where the modular structure allows functional differentiation. Proteins responding to environmental cues and regulating physiological responses are found in chemotaxis pathways that respond to a wide range of stimuli to affect movement. Environmental cues also regulate intracellular levels of cyclic-di-GMP, a universal bacterial secondary messenger that is a key determinant of bacterial lifestyle and virulence. We study Pseudomonas aeruginosa, an organism known to colonize a broad range of environments that can switch lifestyle between the sessile biofilm and the planktonic swimming form. We have investigated the PAS and Cache domains, of which we identified 101 in 70 Pseudomonas aeruginosa PAO1 proteins, and have grouped these by phylogeny with domains of known structure. The resulting data set integrates sequence analysis and structure prediction to infer ligand or cofactor binding. With this data set, functional predictions for PAS and Cache domain-containing proteins are made.

SagS and its unorthodox contributions to Pseudomonas aeruginosa biofilm development

The Pseudomonas aeruginosa orphan sensor SagS (PA2824) was initially reported as one of three orphan sensor kinases capable of activating HptB, a component of the HptB signaling pathway that intersects with the Gac/Rsm signaling pathway and fine-tunes P. aeruginosa motility and pathogenesis. Since then, this orphan sensor has been reported to be involved in other, unorthodox signaling pathways serving additional functions. The present review is aimed at summarizing the various functions of SagS, with an emphasis on its toggle or dual switch functions, and highlighting the role of SagS as a hub at which the various signaling pathways intersect, to regulate the transition from the planktonic to the sessile mode of growth, as well as the transition of surface-associated cells to a drug tolerant state.

Glucose-6-Phosphate Acts as an Extracellular Signal of SagS To Modulate Pseudomonas aeruginosa c-di-GMP Levels, Attachment, and Biofilm Formation

In Pseudomonas aeruginosa, the orphan two-component sensor SagS contributes both to transition to biofilm formation and to biofilm cells gaining their heightened tolerance to antimicrobials. However, little is known about the identity of the signals or conditions sensed by SagS to induce the switch to the sessile, drug-tolerant mode of growth. Using a modified Biolog phenotype assay to screen for compounds that modulate attachment in a SagS-dependent manner, we identified glucose-6-phosphate to enhance attachment in a manner dependent on the glucose-6-phosphate concentration and SagS. The stimulatory effect was not limited to the attachment since glucose-6-phosphate likewise enhanced biofilm formation and also enhanced the expression of select biofilm marker genes. Moreover, exposure to glucose-6-phosphate coincided with decreased swarming motility but increased cellular cyclic-di-GMP (c-di-GMP) levels in biofilms. No such response was noted for compounds modulating attachment and biofilm formation in a manner independent of SagS. Modulation of c-di-GMP in response to glucose-6-phosphate was due to the diguanylate cyclase NicD, with NicD also being required for enhanced biofilm formation. The latter was independent of the sensory domain of NicD but dependent on NicD activity, SagS, and the interaction between NicD and SagS. Our findings indicate that glucose-6-phosphate likely mimics a signal or conditions sensed by SagS to activate its motile-sessile switch function. In addition, our findings provide new insight into the interfaces between the ligand-mediated two-component system signaling pathway and c-di-GMP levels.IMPORTANCE Pathogens sense and respond to signals and cues present in their environment, including host-derived small molecules to modulate the expression of their virulence repertoire. Here, we demonstrate that the opportunistic pathogen Pseudomonas aeruginosa responds to glucose-6-phosphate. Since glucose-6-phosphate is primarily made available due to cell lysis, it is likely that glucose-6-phosphate represents a cross-kingdom cell-to-cell signal that enables P. aeruginosa to adapt to the (nutrient-poor) host environment by enhancing biofilm formation, cyclic-di-GMP, and the expression of genes linked to biofilm formation in a concentration- and SagS-dependent manner.

Biofilm dispersion

The formation of microbial biofilms enables single planktonic cells to assume a multicellular mode of growth. During dispersion, the final step of the biofilm life cycle, single cells egress from the biofilm to resume a planktonic lifestyle. As the planktonic state is considered to be more vulnerable to antimicrobial agents and immune responses, dispersion is being considered a promising avenue for biofilm control. In this Review, we discuss conditions that lead to dispersion and the mechanisms by which native and environmental cues contribute to dispersion. We also explore recent findings on the role of matrix degradation in the dispersion process, and the distinct phenotype of dispersed cells. Last, we discuss the translational and therapeutic potential of dispersing bacteria during infection.

Microbial biofilm ecology, in silico study of quorum sensing receptor-ligand interactions and biofilm mediated bioremediation

Biofilms are structured microbial communities of single or multiple populations in which microbial cells adhere to a surface and get embedded in extracellular polymeric substances (EPS). This review attempts to explain biofilm architecture, development phases, and forces that drive bacteria to promote biofilm mode of growth. Bacterial chemical communication, also known as Quorum sensing (QS), which involves the production, detection, and response to small molecules called autoinducers, is highlighted. The review also provides a brief outline of interspecies and intraspecies cell-cell communication. Additionally, we have performed docking studies using Discovery Studio 4.0, which has enabled our understanding of the prominent interactions between autoinducers and their receptors in different bacterial species while also scoring their interaction energies. Receptors, such as LuxN (Phosphoreceiver domain and RecA domain), LuxP, and LuxR, interacted with their ligands (AI-1, AI-2, and AHL) with a CDocker interaction energy of - 31.6083 kcal/mole; - 34.5821 kcal/mole, - 48.2226 kcal/mole and - 41.5885 kcal/mole, respectively. Since biofilms are ideal for the remediation of contaminants due to their high microbial biomass and their potential to immobilize pollutants, this article also provides an overview of biofilm-mediated bioremediation.

Signal Sensing and Transduction Are Conserved between the Periplasmic Sensory Domains of BifA and SagS

The hybrid sensor kinase SagS of Pseudomonas aeruginosa plays a key role in the transition from the planktonic to the biofilm mode of growth. Recently, we have shown that distinct sets of residues in its periplasmic HmsP sensory domain are involved in the regulation of biofilm formation or antibiotic tolerance. Interestingly, the HmsP domain of the phosphodiesterase BifA shows great predicted structural similarity to that of SagS, despite moderate sequence conservation and only a number of residues involved in SagS signaling being conserved between both proteins. Based on this observation, we hypothesized that BifA and SagS may use similar mechanisms to sense and transduce signals perceived at their periplasmic HmsP domains and, therefore, may be interchangeable. To test this hypothesis, we constructed SagS hybrids in which the HmsP domain of SagS was replaced by that of BifA (and vice versa) or by the DISMED2 sensory domain of NicD. The SagS-BifA hybrid restored attachment and biofilm formation by the ΔbifA mutant. Likewise, while the NicD-SagS hybrid was nonfunctional, the BifA-SagS hybrid partially restored pathways leading to biofilm formation and antibiotic tolerance in a ΔsagS mutant background. Furthermore, alanine substitution of key residues previously associated with the biofilm formation and antibiotic tolerance pathways of SagS impaired signal transduction by the BifA-SagS hybrid in a similar way to SagS. In conclusion, our data indicate that the nature of the sensory domain is important for proper functionality of the cytoplasmic effector domains and that signal sensing and transduction are likely conserved in SagS and BifA.IMPORTANCE Biofilms have been associated with more than 60% of all recalcitrant and chronic infections and can render bacterial cells up to a thousand times more resistant to antibiotics than planktonic cells. Although it is known that the transition from the planktonic to the biofilm mode of growth involves two-component regulatory systems, increased c-di-GMP levels, and quorum sensing systems among others, the exact signaling events that lead to biofilm formation remain unknown. In the opportunistic pathogen Pseudomonas aeruginosa, the hybrid sensor kinase SagS regulates biofilm formation and antibiotic tolerance through two independent pathways via distinct residues in its periplasmic sensory domain. Interestingly, the sensory domains of SagS and BifA show great predicted structural similarity despite moderate sequence conservation. Here we show that the sensory domains of BifA and SagS are functionally interchangeable and that they use a similar mechanism of signal sensing and transduction, which broadens our understanding of how bacteria perceive and transduce signals when transitioning to the biofilm mode of growth.

Multikinase Networks: Two-Component Signaling Networks Integrating Multiple Stimuli

Bacteria depend on two-component systems to detect and respond to threats. Simple pathways comprise a single sensor kinase (SK) that detects a signal and activates a response regulator protein to mediate an appropriate output. These simple pathways with only a single SK are not well suited to making complex decisions where multiple different stimuli need to be evaluated. A recently emerging theme is the existence of multikinase networks (MKNs) where multiple SKs collaborate to detect and integrate numerous different signals to regulate a major lifestyle switch, e.g., between virulence, sporulation, biofilm formation, and cell division. In this review, the role of MKNs and the phosphosignaling mechanisms underpinning their signal integration and decision making are explored.

Roles of two-component regulatory systems in antibiotic resistance

Two-component regulatory systems (TCSs) are a major mechanism by which bacteria sense and respond to changes in their environment. TCSs typically consist of two proteins that bring about major regulation of the cell genome through coordinated action mediated by phosphorylation. Environmental conditions that activate TCSs are numerous and diverse and include exposure to antibiotics as well as conditions inside a host. The resulting regulatory action often involves activation of antibiotic defenses and changes to cell physiology that increase antibiotic resistance. Examples of resistance mechanisms enacted by TCSs contained in this review span those found in both Gram-negative and Gram-positive species and include cell surface modifications, changes in cell permeability, increased biofilm formation, and upregulation of antibiotic-degrading enzymes.

Controlling chronic Pseudomonas aeruginosa infections by strategically interfering with the sensory function of SagS

The hybrid sensor SagS plays a central role in the formation of Pseudomonas aeruginosa biofilms, by enabling the switch from the planktonic to the biofilm mode of growth and by facilitating the transition of biofilm cells to a highly tolerant state. In this study, we examined the importance of the SagS key amino acid residues associated with biofilm formation (L154) and antibiotic tolerance (D105) in P. aeruginosa virulence. Recombinant P. aeruginosa ΔsagS and ΔsagS chromosomally expressing wild-type sagS, or its two variants D105A and L154A, were tested for their potential to form biofilms and cause virulence in plants and mouse models of acute and chronic pneumonia. Although mutation of sagS did not alter P. aeruginosa virulence during acute infections, a significant difference in pathogenicity of sagS mutants was observed during chronic infections, with the L154A variant showing reduced bacterial loads in the chronic pneumonia model, while interference with the D105 residue enhanced the susceptibility of P. aeruginosa biofilms during tobramycin treatment. Our findings suggest that interference with the biofilm or tolerance regulatory circuits of SagS affects P. aeruginosa pathogenicity in chronic but not acute infections, and reveal SagS to be a promising new target to treat P. aeruginosa biofilm infections.

Connected partner-switches control the life style of Pseudomonas aeruginosa through RpoS regulation

Biofilm formation is a complex process resulting from the action of imbricated pathways in response to environmental cues. In this study, we showed that biofilm biogenesis in the opportunistic pathogen Pseudomonas aeruginosa depends on the availability of RpoS, the sigma factor regulating the general stress response in bacteria. Moreover, it was demonstrated that RpoS is post-translationally regulated by the HsbR-HsbA partner switching system as has been demonstrated for its CrsR-CrsA homolog in Shewanella oneidensis. Finally, it was established that HsbA, the anti-sigma factor antagonist, has a pivotal role depending on its phosphorylation state since it binds HsbR, the response regulator, when phosphorylated and FlgM, the anti-sigma factor of FliA, when non-phosphorylated. The phosphorylation state of HsbA thus drives the switch between the sessile and planktonic way of life of P. aeruginosa by driving the release or the sequestration of one or the other of these two sigma factors.

Pyruvate-depleting conditions induce biofilm dispersion and enhance the efficacy of antibiotics in killing biofilms in vitro and in vivo

The formation of biofilms is a developmental process initiated by planktonic cells transitioning to the surface, which comes full circle when cells disperse from the biofilm and transition to the planktonic mode of growth. Considering that pyruvate has been previously demonstrated to be required for the formation of P. aeruginosa biofilms, we asked whether pyruvate likewise contributes to the maintenance of the biofilm structure, with depletion of pyruvate resulting in dispersion. Here, we demonstrate that the enzymatic depletion of pyruvate coincided with the dispersion of established biofilms by S. aureus and laboratory and clinical P. aeruginosa isolates. The dispersion response was dependent on pyruvate fermentation pathway components but independent of proteins previously described to contribute to P. aeruginosa biofilm dispersion. Using porcine second-degree burn wounds infected with P. aeruginosa biofilm cells, we furthermore demonstrated that pyruvate depletion resulted in a reduction of biofilm biomass in vivo. Pyruvate-depleting conditions enhanced the efficacy of tobramycin killing of the resident wound biofilms by up to 5-logs. Our findings strongly suggest the management of pyruvate availability to be a promising strategy to combat biofilm-related infections by two principal pathogens associated with wound and cystic fibrosis lung infections.

Recent Advances and Current Trends in Nucleotide Second Messenger Signaling in Bacteria

The "International Symposium on Nucleotide Second Messenger Signaling in Bacteria" (September 30-October 3, 2018, Berlin), which was organized within the framework of DFG Priority Programme 1879 (www.spp1879.de), brought together 125 participants from 20 countries to discuss recent progress and future trends in this field. Even 50 years after its discovery, (p)ppGpp is venturing into exciting new fields, especially in gram-positive bacteria. After triggering the current renaissance in bacterial second messenger research, c-di-GMP is becoming ever more global with abounding new molecular mechanisms of action and physiological functions. The more recently discovered c-di-AMP is rapidly catching up and has now been found even in archaea, with its function in osmotic homeostasis being conserved across kingdom boundaries. Small modules associated with mobile genetic elements, which make and react to numerous novel mixed cyclic dinucleotides, seem to roam around rather freely in the bacterial world. Finally, many novel and old nucleotide molecules are still lurking around in search of a function. Across many talks it became apparent that (p)ppGpp, c-di-GMP and GTP/ATP can share and compete for binding sites (e.g., the Walker A motif in GTP/ATPases) with intriguing regulatory consequences, thus contributing to the emergent trend of systemwide networks that interconnect diverse signaling nucleotides. Overall, this inspiring conference made it clear that second messenger signaling is currently one of the most dynamic and exciting areas in microbial molecular biology and physiology, with major impacts ranging from microbial systems biology and ecology to infection biology.

The PA3177 Gene Encodes an Active Diguanylate Cyclase That Contributes to Biofilm Antimicrobial Tolerance but Not Biofilm Formation by Pseudomonas aeruginosa

A hallmark of biofilms is their heightened resistance to antimicrobial agents. Recent findings suggested a role for bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) in the susceptibility of bacteria to antimicrobial agents; however, no c-di-GMP modulating enzyme(s) contributing to the drug tolerance phenotype of biofilms has been identified. The goal of this study was to determine whether c-di-GMP modulating enzyme(s) specifically contributes to the biofilm drug tolerance of Pseudomonas aeruginosa Using transcriptome sequencing combined with biofilm susceptibility assays, we identified PA3177 encoding a probable diguanylate cyclase. PA3177 was confirmed to be an active diguanylate cyclase, with overexpression affecting swimming and swarming motility, and inactivation affecting cellular c-di-GMP levels of biofilm but not planktonic cells. Inactivation of PA3177 rendered P. aeruginosa PAO1 biofilms susceptible to tobramycin and hydrogen peroxide. Inactivation of PA3177 also eliminated the recalcitrance of biofilms to killing by tobramycin, with multicopy expression of PA3177 but not PA3177_GGAAF harboring substitutions in the active site, restoring tolerance to wild-type levels. Susceptibility was linked to BrlR, a previously described transcriptional regulator contributing to biofilm tolerance, with inactivation of PA3177 negatively impacting BrlR levels and BrlR-DNA binding. While PA3177 contributed to biofilm drug tolerance, inactivation of PA3177 had no effect on attachment and biofilm formation. Our findings demonstrate for the first time that biofilm drug tolerance by P. aeruginosa is linked to a specific c-di-GMP modulating enzyme, PA3177, with the pool of PA3177-generated c-di-GMP only contributing to biofilm drug tolerance but not to biofilm formation.

The Yin and Yang of SagS: Distinct Residues in the HmsP Domain of SagS Independently Regulate Biofilm Formation and Biofilm Drug Tolerance

The formation of inherently drug-tolerant biofilms by the opportunistic pathogen Pseudomonas aeruginosa requires the sensor-regulator hybrid SagS, with ΔsagS biofilms being unstructured and exhibiting increased antimicrobial susceptibility. Recent findings indicated SagS to function as a switch to control biofilm formation and drug tolerance independently. Moreover, findings suggested the periplasmic sensory HmsP domain of SagS is likely to be the control point in the regulation of biofilm formation and biofilm cells transitioning to a drug-tolerant state. We thus asked whether specific amino acid residues present in the HmsP domain contribute to the switch function of SagS. HmsP domain residues were therefore subjected to alanine replacement mutagenesis to identify substitutions that block the sensory function(s) of SagS, which is apparent by attached cells being unable to develop mature biofilms and/or prevent transition to an antimicrobial-resistant state. Mutant analyses revealed 32 residues that only contribute to blocking one sensory function. Moreover, amino acid residues affecting attachment and subsequent biofilm formation but not biofilm tolerance also impaired histidine kinase signaling via BfiS. In contrast, residues affecting biofilm drug tolerance but not attachment and subsequent biofilm formation negatively impacted BrlR transcription factor levels. Structure prediction suggested the two sets of residues affecting sensory functions are located in distinct areas that were previously described as being involved in ligand binding interactions. Taken together, these studies identify the molecular basis for the dual regulatory function of SagS.IMPORTANCE The membrane-bound sensory protein SagS plays a pivotal role in P. aeruginosa biofilm formation and biofilm cells gaining their heightened resistance to antimicrobial agents, with SagS being the control point at which both pathways diverge. Here, we demonstrate for the first time that the two distinct pathways leading to biofilm formation and biofilm drug tolerance are under the control of two sets of amino acid residues located within the HmsP sensory domain of SagS. The respective amino acids are likely part of ligand binding interaction sites. Thus, our findings have the potential not only to enable the manipulation of SagS function but also to enable research of biofilm drug tolerance in a manner independent of biofilm formation (and vice versa). Moreover, the manipulation of SagS function represents a promising target/avenue open for biofilm control.

The ABC of Biofilm Drug Tolerance: the MerR-Like Regulator BrlR Is an Activator of ABC Transport Systems, with PA1874-77 Contributing to the Tolerance of Pseudomonas aeruginosa Biofilms to Tobramycin

A hallmark of biofilms is their tolerance to killing by antimicrobial agents. In Pseudomonas aeruginosa, biofilm drug tolerance requires the c-di-GMP-responsive MerR transcriptional regulator BrlR. However, the mechanism by which BrlR mediates biofilm drug tolerance has not been elucidated. Here, we demonstrate that BrlR activates the expression of at least 7 ABC transport systems, including the PA1874-PA1875-PA1876-PA1877 (PA1874-77) operon, with chromatin immunoprecipitation and DNA binding assays confirming BrlR binding to the promoter region of PA1874-77. Insertional inactivation of the 7 ABC transport systems rendered P. aeruginosa PAO1 biofilms susceptible to tobramycin or norfloxacin. Susceptibility was linked to drug accumulation, with BrlR contributing to norfloxacin accumulation in a manner dependent on multidrug efflux pumps and the PA1874-77 ABC transport system. Inactivation of the respective ABC transport system, furthermore, eliminated the recalcitrance of biofilms to killing by tobramycin but not norfloxacin, indicating that drug accumulation is not linked to biofilm drug tolerance. Our findings indicate for the first time that BrlR, a MerR-type transcriptional activator, activates genes encoding several ABC transport systems, in addition to multiple multidrug efflux pump genes. Moreover, our data confirm a BrlR target contributing to drug tolerance, likely countering the prevailing dogma that biofilm tolerance arises from a multiplicity of factors.

Two-component systems required for virulence in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a versatile opportunistic pathogen capable of infecting a broad range of hosts, in addition to thriving in a broad range of environmental conditions outside of hosts. With this versatility comes the need to tightly regulate its genome to optimise its gene expression and behaviour to the prevailing conditions. Two-component systems (TCSs) comprising sensor kinases and response regulators play a major role in this regulation. This minireview discusses the growing number of TCSs that have been implicated in the virulence of P. aeruginosa, with a special focus on the emerging theme of multikinase networks, which are networks comprising multiple sensor kinases working together, sensing and integrating multiple signals to decide upon the best response. The networks covered in depth regulate processes such as the switch between acute and chronic virulence (GacS network), the Cup fimbriae (Roc network and Rcs/Pvr network), the aminoarabinose modification of lipopolysaccharide (a network involving the PhoQP and PmrBA TCSs), twitching motility and virulence (a network formed from the Chp chemosensory pathway and the FimS/AlgR TCS), and biofilm formation (Wsp chemosensory pathway). In addition, we highlight the important interfaces between these systems and secondary messenger signals such as cAMP and c-di-GMP.