Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 87
Filter
Add more filters

Country/Region as subject
Publication year range
1.
Crit Rev Microbiol ; 49(3): 334-349, 2023 May.
Article in English | MEDLINE | ID: mdl-35389761

ABSTRACT

Clostridioides difficile (CD), a nosocomial gut pathogen, produces two major exotoxins, TcdA and TcdB, which disrupt the gut epithelial barrier and induce inflammatory/immune responses, leading to symptoms ranging from mild diarrhoea to pseudomembranous colitis and potentially to death. The expression of toxins is regulated by various transcription factors (TFs) which are induced in response to CD physiological life stages, nutritional availability, and host environment. This review summarises our current understanding on the regulation of toxin expression by TFs that interconnect with pathways of flagellar synthesis, quorum sensing, motility, biofilm formation, sporulation, and phase variation. The pleiotropic roles of some key TFs suggest that toxin production is tightly linked to other cellular processes of the CD physiology.


This review summarises the current knowledge of the transcription factors involved in regulation of toxin production, which is affected by C. difficile physiological life stages, nutritional availability, and host environment in the gut.


Subject(s)
Bacterial Toxins , Clostridioides difficile , Bacterial Toxins/genetics , Bacterial Toxins/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , Clostridioides difficile/genetics , Clostridioides/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism
2.
Proc Natl Acad Sci U S A ; 117(9): 4921-4930, 2020 03 03.
Article in English | MEDLINE | ID: mdl-32071223

ABSTRACT

Antibiotic-resistant superbug bacteria represent a global health problem with no imminent solutions. Here we demonstrate that the combination (termed AB569) of acidified nitrite (A-NO2-) and Na2-EDTA (disodium ethylenediaminetetraacetic acid) inhibited all Gram-negative and Gram-positive bacteria tested. AB569 was also efficacious at killing the model organism Pseudomonas aeruginosa in biofilms and in a murine chronic lung infection model. AB569 was not toxic to human cell lines at bactericidal concentrations using a basic viability assay. RNA-Seq analyses upon treatment of P. aeruginosa with AB569 revealed a catastrophic loss of the ability to support core pathways encompassing DNA, RNA, protein, ATP biosynthesis, and iron metabolism. Electrochemical analyses elucidated that AB569 produced more stable SNO proteins, potentially explaining one mechanism of bacterial killing. Our data implicate that AB569 is a safe and effective means to kill pathogenic bacteria, suggesting that simple strategies could be applied with highly advantageous therapeutic/toxicity index ratios to pathogens associated with a myriad of periepithelial infections and related disease scenarios.


Subject(s)
Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/pharmacology , Bacteria/drug effects , Edetic Acid/pharmacology , Sodium Nitrite/pharmacology , Animals , Anti-Bacterial Agents/therapeutic use , Biofilms/drug effects , Disease Models, Animal , Down-Regulation , Drug Resistance, Bacterial/drug effects , Edetic Acid/chemistry , Lung Diseases/drug therapy , Lung Diseases/microbiology , Metabolic Networks and Pathways , Mice , Nitrites/chemistry , Nitrites/pharmacology , Pseudomonas aeruginosa/drug effects
3.
Infect Immun ; 89(11): e0033621, 2021 10 15.
Article in English | MEDLINE | ID: mdl-34424744

ABSTRACT

Cutaneous thermal injuries from burns/explosives are a major cause of morbidity and mortality and represent a monumental burden on our current health care system. Injury severity is predominantly due to potentially lethal sepsis caused by multidrug-resistant (MDR) bacteria such as Pseudomonas aeruginosa (MDR-PA). Thus, there is a critical need to develop novel and effective antimicrobials for the (i) prevention, (ii) treatment, and (iii) healing of such wounds that are complicated by MDR-P. aeruginosa and other bacterial infections. AB569 is a novel bactericidal tandem consisting of acidified NaNO2 (A-NO2-) and Na2-EDTA. Here, we first show that AB569 acts synergistically to kill all human burn wound strains of P. aeruginosa in vitro. This was found to be due, in part, to the generation of A-NO2--mediated nitric oxide (NO) formation coupled with the metal chelating properties of Na2-EDTA. Using a murine scald burn wound model of P. aeruginosa infection, an AB569-Solosite gel formulation eradicated all bacteria. Futher, we also demonstrate enhanced AB569-mediated wound healing by not only accelerating wound contraction, but also by reducing levels of the proinflammatory cytokines interleukin-6 (IL-6) and IL-1ß while increasing the levels of anti-inflammatory cytokine, IL-10, and granulocyte-colony-stimulating factor (G-CSF). We also observed better epidermal restoration in AB569-treated wounds. Taken together, we conclude that this study provides solid foundational evidence that AB569 can be used topically to treat highly problematic dermal insults, including wound, burn, blast, and likely, diabetic infections in civilian and military populations, and help relieve the economical burden that MDR organisms have on the global health care system.


Subject(s)
Anti-Bacterial Agents/pharmacology , Burns/drug therapy , Edetic Acid/pharmacology , Nitrites/pharmacology , Pseudomonas aeruginosa/drug effects , Wound Healing/drug effects , Animals , Body Weight/drug effects , Burns/complications , Burns/microbiology , Collagen/genetics , Disease Models, Animal , Edetic Acid/therapeutic use , Gels , Nitric Oxide/biosynthesis , Nitrites/therapeutic use , Pseudomonas Infections/drug therapy
4.
J Ind Microbiol Biotechnol ; 45(2): 103-109, 2018 Feb.
Article in English | MEDLINE | ID: mdl-29288437

ABSTRACT

Pseudomonas aeruginosa is a metabolically voracious bacterium that is easily manipulated genetically. We have previously shown that the organism is also highly electrogenic in microbial fuel cells (MFCs). Polarization studies were performed in MFCs with wild-type strain PAO1 and three mutant strains (pilT, bdlA and pilT bdlA). The pilT mutant was hyperpiliated, while the bdlA mutant was suppressed in biofilm dispersion chemotaxis. The double pilT bdlA mutant was expected to have properties of both mutations. Polarization data indicate that the pilT mutant showed 5.0- and 3.2-fold increases in peak power compared to the wild type and the pilT bdlA mutant, respectively. The performance of the bdlA mutant was surprisingly the lowest, while the pilT bdlA electrogenic performance fell between the pilT mutant and wild-type bacteria. Measurements of biofilm thickness and bacterial viability showed equal viability among the different strains. The thickness of the bdlA mutant, however, was twice that of wild-type strain PAO1. This observation implicates the presence of dead or dormant bacteria in the bdlA mutant MFCs, which increases biofilm internal resistance as confirmed by electrochemical measurements.


Subject(s)
Bioelectric Energy Sources , Biofilms , Pseudomonas aeruginosa/genetics , Mutation
5.
PLoS Pathog ; 10(6): e1004168, 2014 Jun.
Article in English | MEDLINE | ID: mdl-24901523

ABSTRACT

The human pathogen Pseudomonas aeruginosa is capable of causing both acute and chronic infections. Differences in virulence are attributable to the mode of growth: bacteria growing planktonically cause acute infections, while bacteria growing in matrix-enclosed aggregates known as biofilms are associated with chronic, persistent infections. While the contribution of the planktonic and biofilm modes of growth to virulence is now widely accepted, little is known about the role of dispersion in virulence, the active process by which biofilm bacteria switch back to the planktonic mode of growth. Here, we demonstrate that P. aeruginosa dispersed cells display a virulence phenotype distinct from those of planktonic and biofilm cells. While the highest activity of cytotoxic and degradative enzymes capable of breaking down polymeric matrix components was detected in supernatants of planktonic cells, the enzymatic activity of dispersed cell supernatants was similar to that of biofilm supernatants. Supernatants of non-dispersing ΔbdlA biofilms were characterized by a lack of many of the degradative activities. Expression of genes contributing to the virulence of P. aeruginosa was nearly 30-fold reduced in biofilm cells relative to planktonic cells. Gene expression analysis indicated dispersed cells, while dispersing from a biofilm and returning to the single cell lifestyle, to be distinct from both biofilm and planktonic cells, with virulence transcript levels being reduced up to 150-fold compared to planktonic cells. In contrast, virulence gene transcript levels were significantly increased in non-dispersing ΔbdlA and ΔdipA biofilms compared to wild-type planktonic cells. Despite this, bdlA and dipA inactivation, resulting in an inability to disperse in vitro, correlated with reduced pathogenicity and competitiveness in cross-phylum acute virulence models. In contrast, bdlA inactivation rendered P. aeruginosa more persistent upon chronic colonization of the murine lung, overall indicating that dispersion may contribute to both acute and chronic infections.


Subject(s)
Bacterial Proteins/metabolism , Biofilms/growth & development , Gene Expression Regulation, Bacterial , Phosphoric Diester Hydrolases/metabolism , Pneumonia, Bacterial/microbiology , Pseudomonas Infections/microbiology , Pseudomonas aeruginosa/physiology , Acute Disease , Animals , Bacterial Proteins/genetics , Cells, Immobilized/enzymology , Cells, Immobilized/physiology , Chronic Disease , Gene Deletion , Host-Pathogen Interactions , Lung/microbiology , Mice , Microbial Interactions , Opportunistic Infections/microbiology , Phosphoric Diester Hydrolases/genetics , Plankton/growth & development , Plankton/pathogenicity , Plankton/physiology , Pseudomonas aeruginosa/enzymology , Pseudomonas aeruginosa/growth & development , Pseudomonas aeruginosa/pathogenicity , Virulence , Virulence Factors/genetics , Virulence Factors/metabolism
6.
J Ind Microbiol Biotechnol ; 43(1): 103-7, 2016 Jan.
Article in English | MEDLINE | ID: mdl-26660316

ABSTRACT

This report documents the first observation of a urine-powered microbial fuel cell operating with a genetically engineered bacterial strain. Under identical conditions, a pilT mutant of the Gram-negative bacterium Pseudomonas aeruginosa showed a 2.7-fold increase in peak power density compared to the wild-type strain, PAO1. The reduced twitching motility and hyperpiliation of the pilT mutant enhances the formation of electrogenic biofilms. For both strains, the observed high internal resistance near open-circuit voltage is attributed to sluggish redox reactions on the anode surface and not to slow bacterial metabolism. This work lays the groundwork for optimization of multiple bacterial traits leading to increased electroactive properties and opens new opportunities for urine-based mini-devices.


Subject(s)
Bacterial Proteins/metabolism , Bioelectric Energy Sources/microbiology , Mutant Proteins/metabolism , Pseudomonas aeruginosa/genetics , Pseudomonas aeruginosa/metabolism , Urine/chemistry , Bacterial Proteins/genetics , Biofilms , Mutant Proteins/genetics , Oxidation-Reduction , Pseudomonas aeruginosa/physiology
7.
Am J Physiol Gastrointest Liver Physiol ; 308(6): G510-24, 2015 Mar 15.
Article in English | MEDLINE | ID: mdl-25552581

ABSTRACT

The majority of antibiotic-induced diarrhea is caused by Clostridium difficile (C. difficile). Hospitalizations for C. difficile infection (CDI) have tripled in the last decade, emphasizing the need to better understand how the organism colonizes the intestine and maintain infection. The mucus provides an interface for bacterial-host interactions and changes in intestinal mucus have been linked host health. To assess mucus production and composition in healthy and CDI patients, the main mucins MUC1 and MUC2 and mucus oligosaccharides were examined. Compared with healthy subjects, CDI patients demonstrated decreased MUC2 with no changes in surface MUC1. Although MUC1 did not change at the level of the epithelia, MUC1 was the primary constituent of secreted mucus in CDI patients. CDI mucus also exhibited decreased N-acetylgalactosamine (GalNAc), increased N-acetylglucosamine (GlcNAc), and increased terminal galactose residues. Increased galactose in CDI specimens is of particular interest since terminal galactose sugars are known as C. difficile toxin A receptor in animals. In vitro, C. difficile is capable of metabolizing fucose, mannose, galactose, GlcNAc, and GalNAc for growth under healthy stool conditions (low Na(+) concentration, pH 6.0). Injection of C. difficile into human intestinal organoids (HIOs) demonstrated that C. difficile alone is sufficient to reduce MUC2 production but is not capable of altering host mucus oligosaccharide composition. We also demonstrate that C. difficile binds preferentially to mucus extracted from CDI patients compared with healthy subjects. Our results provide insight into a mechanism of C. difficile colonization and may provide novel target(s) for the development of alternative therapeutic agents.


Subject(s)
Clostridioides difficile/metabolism , Colon/metabolism , Colon/microbiology , Enterocolitis, Pseudomembranous/metabolism , Enterocolitis, Pseudomembranous/microbiology , Mucus/metabolism , Acetylgalactosamine/metabolism , Acetylglucosamine/metabolism , Adult , Aged , Case-Control Studies , Cells, Cultured , Clostridioides difficile/growth & development , Clostridioides difficile/isolation & purification , Feces/microbiology , Female , Galactose/analogs & derivatives , Galactose/metabolism , Host-Pathogen Interactions , Humans , Intestinal Mucosa/metabolism , Intestinal Mucosa/microbiology , Male , Middle Aged , Mucin-1/metabolism , Mucin-2/metabolism , Organoids , Pluripotent Stem Cells/metabolism , Pluripotent Stem Cells/microbiology
8.
Am J Physiol Gastrointest Liver Physiol ; 308(6): G497-509, 2015 Mar 15.
Article in English | MEDLINE | ID: mdl-25552580

ABSTRACT

Clostridium difficile infection (CDI) is principally responsible for hospital acquired, antibiotic-induced diarrhea and colitis and represents a significant financial burden on our healthcare system. Little is known about C. difficile proliferation requirements, and a better understanding of these parameters is critical for development of new therapeutic targets. In cell lines, C. difficile toxin B has been shown to inhibit Na(+)/H(+) exchanger 3 (NHE3) and loss of NHE3 in mice results in an altered intestinal environment coupled with a transformed gut microbiota composition. However, this has yet to be established in vivo in humans. We hypothesize that C. difficile toxin inhibits NHE3, resulting in alteration of the intestinal environment and gut microbiota. Our results demonstrate that CDI patient biopsy specimens have decreased NHE3 expression and CDI stool has elevated Na(+) and is more alkaline compared with stool from healthy individuals. CDI stool microbiota have increased Bacteroidetes and Proteobacteria and decreased Firmicutes phyla compared with healthy subjects. In vitro, C. difficile grows optimally in the presence of elevated Na(+) and alkaline pH, conditions that correlate to changes observed in CDI patients. To confirm that inhibition of NHE3 was specific to C. difficile, human intestinal organoids (HIOs) were injected with C. difficile or healthy and CDI stool supernatant. Injection of C. difficile and CDI stool decreased NHE3 mRNA and protein expression compared with healthy stool and control HIOs. Together these data demonstrate that C. difficile inhibits NHE3 in vivo, which creates an altered environment favored by C. difficile.


Subject(s)
Clostridioides difficile/growth & development , Colon/metabolism , Colon/microbiology , Enterocolitis, Pseudomembranous/metabolism , Enterocolitis, Pseudomembranous/microbiology , Microbiota , Sodium-Hydrogen Exchangers/metabolism , Adult , Aged , Bacterial Proteins/metabolism , Bacterial Toxins/metabolism , Case-Control Studies , Cells, Cultured , Clostridioides difficile/isolation & purification , Clostridioides difficile/metabolism , Down-Regulation , Feces/microbiology , Female , Host-Pathogen Interactions , Humans , Hydrogen-Ion Concentration , Intestinal Mucosa/metabolism , Intestinal Mucosa/microbiology , Male , Middle Aged , Organoids , Pluripotent Stem Cells/metabolism , Pluripotent Stem Cells/microbiology , RNA, Messenger/metabolism , Sodium/metabolism , Sodium-Hydrogen Exchanger 3 , Sodium-Hydrogen Exchangers/genetics
9.
Analyst ; 140(12): 4277-83, 2015 Jun 21.
Article in English | MEDLINE | ID: mdl-25939879

ABSTRACT

There is a large global effort to improve microbial fuel cell (MFC) techniques and advance their translational potential toward practical, real-world applications. Significant boosts in MFC performance can be achieved with the development of new techniques in synthetic biology that can regulate microbial metabolic pathways or control their gene expression. For these new directions, a high-throughput and rapid screening tool for microbial biopower production is needed. In this work, a 48-well, paper-based sensing platform was developed for the high-throughput and rapid characterization of the electricity-producing capability of microbes. 48 spatially distinct wells of a sensor array were prepared by patterning 48 hydrophilic reservoirs on paper with hydrophobic wax boundaries. This paper-based platform exploited the ability of paper to quickly wick fluid and promoted bacterial attachment to the anode pads, resulting in instant current generation upon loading of the bacterial inoculum. We validated the utility of our MFC array by studying how strategic genetic modifications impacted the electrochemical activity of various Pseudomonas aeruginosa mutant strains. Within just 20 minutes, we successfully determined the electricity generation capacity of eight isogenic mutants of P. aeruginosa. These efforts demonstrate that our MFC array displays highly comparable performance characteristics and identifies genes in P. aeruginosa that can trigger a higher power density.


Subject(s)
Bioelectric Energy Sources , Electricity , Paper , Pseudomonas aeruginosa/isolation & purification , Mutation , Pseudomonas aeruginosa/genetics , Pseudomonas aeruginosa/metabolism
10.
Am J Physiol Gastrointest Liver Physiol ; 305(10): G697-711, 2013 Nov 15.
Article in English | MEDLINE | ID: mdl-24072680

ABSTRACT

Changes in the intestinal microbiota have been linked to diabetes, obesity, inflammatory bowel disease, and Clostridium difficile (C. difficile)-associated disease. Despite this, it remains unclear how the intestinal environment, set by ion transport, affects luminal and mucosa-associated bacterial composition. Na(+)/H(+)-exchanger isoform 3 (NHE3), a target of C. difficile toxin B, plays an integral role in intestinal Na(+) absorption. Thus the NHE3-deficient mouse model was chosen to examine the effect of pH and ion composition on bacterial growth. We hypothesized that ion transport-induced change in the intestinal environment would lead to alteration of the microbiota. Region-specific changes in ion composition and pH correlated with region-specific alteration of luminal and mucosal-associated bacteria with general decreases in Firmicutes and increases in Bacteroidetes members. Bacteroides thetaiotaomicron (B. thetaiotaomicron) increased in NHE3(-/-) terminal ileum and was examined in vitro to determine whether altered Na(+) was sufficient to affect growth. Increased in vitro growth of B. thetaiotaomicron occurred in 43 mM Na(+) correlating with the NHE3(-/-) mouse terminal ileum [Na(+)]. NHE3(-/-) terminal ileum displayed increased fut2 mRNA and fucosylation correlating with B. thetaiotaomicron growth. Inoculation of B. thetaiotaomicron in wild-type and NHE3(-/-) terminal ileum organoids displayed increased fut2 and fucosylation, indicating that B. thetaiotaomicron alone is sufficient for the increased fucosylation seen in vivo. These data demonstrate that loss of NHE3 alters the intestinal environment, leading to region-specific changes in bacteria, and shed light on the growth requirements of some gut microbiota members, which is vital for creating better treatments of complex diseases with an altered gut microbiota.


Subject(s)
Bacteroides/classification , Bacteroides/growth & development , Sodium-Hydrogen Exchangers/metabolism , Animals , Culture Media , Hydrogen-Ion Concentration , Intestines/microbiology , Intestines/physiology , Mice , Sodium , Sodium-Hydrogen Exchanger 3 , Sodium-Hydrogen Exchangers/genetics
11.
Microbiology (Reading) ; 159(Pt 8): 1736-1747, 2013 Aug.
Article in English | MEDLINE | ID: mdl-23782801

ABSTRACT

The opportunistic pathogen Pseudomomas aeruginosa produces multiple pigments during in vitro culture and in vivo during colonization of burn wounds and in the airways of cystic fibrosis (CF) patients. One pigment is a deep 'merlot'-coloured compound known as aeruginosin A (AA). However, the red pigment(s) of P. aeruginosa are often collectively called pyorubrin, of which there is no known chemical composition. Here, we purified and confirmed by MS and assessed the physicochemical properties of AA (2-amino-6-carboxy-10-methylphenazinium betaine) by first focusing on its ability to redox-cycle using cyclic voltammetry and its spectroscopic (as well as fluorescent) properties, experiments that were conducted at physiological pH. AA exhibited reversible electrochemistry at a glassy carbon electrode within a potential range of -500 to -200 mV. Electrochemical anodic and cathodic peak currents were observed at -327 and -360 mV, respectively, with a low formal reduction potential of -343.5 mV versus Ag/AgCl. AA absorbed at 516 nm and fluoresced at 606 nm. Results from the spectro-electrochemistry of pyorubrin revealed that its strongest fluorescence was in its parent or oxidized form. Production of AA by P. aeruginosa was found to be controlled by the rhl component of the intercellular signalling system known as quorum sensing and was produced maximally during the stationary growth phase. However, unlike its downstream blue redox-active toxin, pyocyanin, AA had no adverse effects on methicillin-resistant Staphylococcus aureus USA300, Escherichia coli DH5-α or human keratinocytes. We close with some thoughts on the potential commercial use(s) of AA.


Subject(s)
Organic Chemicals/chemistry , Organic Chemicals/metabolism , Pigments, Biological/chemistry , Pigments, Biological/metabolism , Pseudomonas aeruginosa/chemistry , Pseudomonas aeruginosa/physiology , Cells, Cultured , Electrochemistry , Escherichia coli/drug effects , Fluorescence , Humans , Keratinocytes/drug effects , Mass Spectrometry , Organic Chemicals/isolation & purification , Oxidation-Reduction , Pigments, Biological/isolation & purification , Quorum Sensing , Staphylococcus aureus/drug effects
12.
Appl Microbiol Biotechnol ; 97(20): 9029-41, 2013 Oct.
Article in English | MEDLINE | ID: mdl-23852642

ABSTRACT

Here, we constructed stable, constitutively expressed, chromosomal green (GFP) and red fluorescent (RFP) reporters in the genome of the surrogate strain, Francisella tularensis spp. holarctica LVS (herein LVS), and the select agent, F. tularensis Schu S4. A bioinformatic approach was used to identify constitutively expressed genes. Two promoter regions upstream of the FTT1794 and rpsF(FTT1062) genes were selected and fused with GFP and RFP reporter genes in pMP815, respectively. While the LVS strains with chromosomally integrated reporter fusions exhibited fluorescence, we were unable to deliver the same fusions into Schu S4. Neither a temperature-sensitive Francisella replicon nor a pBBR replicon in the modified pMP815 derivatives facilitated integration. However, a mini-Tn7 integration system was successful at integrating the reporter fusions into the Schu S4 genome. Finally, fluorescent F. tularensis LVS and a mutant lacking MglA were assessed for growth in monocyte-derived macrophages (MDMs). As expected, when compared to wild-type bacteria, replication of an mglA mutant was significantly diminished, and the overall level of fluorescence dramatically decreased with infection time. The utility of the fluorescent Schu S4 strain was also examined within infected MDMs treated with clarithromycin and enrofloxacin. Taken together, this study describes the development of an important reagent for F. tularensis research, especially since the likelihood of engineered antibiotic resistant strains will emerge with time. Such strains will be extremely useful in high-throughput screens for novel compounds that could interfere with critical virulence processes in this important bioweapons agent and during infection of alveolar macrophages.


Subject(s)
Francisella tularensis/genetics , Gene Expression , Green Fluorescent Proteins/genetics , Luminescent Proteins/genetics , Tularemia/microbiology , Bacterial Vaccines/genetics , Bacterial Vaccines/metabolism , Chromosomes, Bacterial/genetics , Chromosomes, Bacterial/metabolism , Francisella tularensis/growth & development , Francisella tularensis/metabolism , Genes, Reporter , Genetic Engineering , Green Fluorescent Proteins/metabolism , Humans , Luminescent Proteins/metabolism , Macrophages/microbiology , Red Fluorescent Protein
13.
Nucleic Acids Res ; 39(3): 795-807, 2011 Feb.
Article in English | MEDLINE | ID: mdl-20870748

ABSTRACT

Rapid and accurate identification of new essential genes in under-studied microorganisms will significantly improve our understanding of how a cell works and the ability to re-engineer microorganisms. However, predicting essential genes across distantly related organisms remains a challenge. Here, we present a machine learning-based integrative approach that reliably transfers essential gene annotations between distantly related bacteria. We focused on four bacterial species that have well-characterized essential genes, and tested the transferability between three pairs among them. For each pair, we trained our classifier to learn traits associated with essential genes in one organism, and applied it to make predictions in the other. The predictions were then evaluated by examining the agreements with the known essential genes in the target organism. Ten-fold cross-validation in the same organism yielded AUC scores between 0.86 and 0.93. Cross-organism predictions yielded AUC scores between 0.69 and 0.89. The transferability is likely affected by growth conditions, quality of the training data set and the evolutionary distance. We are thus the first to report that gene essentiality can be reliably predicted using features trained and tested in a distantly related organism. Our approach proves more robust and portable than existing approaches, significantly extending our ability to predict essential genes beyond orthologs.


Subject(s)
Artificial Intelligence , Genes, Bacterial , Genes, Essential , Acinetobacter/genetics , Bacillus subtilis/genetics , Chromosome Mapping/methods , Classification/methods , Escherichia coli/genetics , Genome, Bacterial , Genomics/methods , Molecular Sequence Annotation , Pseudomonas aeruginosa/genetics
14.
Am J Physiol Lung Cell Mol Physiol ; 302(10): L1044-56, 2012 May 15.
Article in English | MEDLINE | ID: mdl-22345574

ABSTRACT

Pyocyanin (1-hydroxy-N-methylphenazine, PCN) is a cytotoxic pigment and virulence factor secreted by the human bacterial pathogen, Pseudomonas aeruginosa. Here, we report that exposure of PCN to airway peroxidases, hydrogen peroxide (H(2)O(2)), and NaNO(2) generates unique mononitrated PCN metabolites (N-PCN) as revealed by HPLC/mass spectrometry analyses. N-PCN, in contrast to PCN, was devoid of antibiotic activity and failed to kill Escherichia coli and Staphylococcus aureus. Furthermore, in contrast to PCN, intratracheal instillation of N-PCN into murine lungs failed to induce a significant inflammatory response. Surprisingly, at a pH of ∼7, N-PCN was more reactive than PCN with respect to NADH oxidation but resulted in a similar magnitude of superoxide production as detected by electron paramagnetic resonance and spin trapping experiments. When incubated with Escherichia coli or lung A549 cells, PCN and N-PCN both led to superoxide formation, but lesser amounts were detected with N-PCN. Our results demonstrate that PCN that has been nitrated by peroxidase/H(2)O(2)/NO(2)(-) systems possesses less cytotoxic/proinflammatory activity than native PCN. Yield of N-PCN was decreased by the presence of the competing physiological peroxidase substrates (thiocyonate) SCN(-) (myeloperoxidase, MPO, and lactoperoxidase, LPO) and Cl(-) (MPO), which with Cl(-) yielded chlorinated PCNs. These reaction products also showed decreased proinflammatory ability when instilled into the lungs of mice. These observations add important insights into the complexity of the pathogenesis of lung injury associated with Pseudomonas aeruginosa infections and provide additional rationale for exploring the efficacy of NO(2)(-) in the therapy of chronic Pseudomonas aeruginosa airway infection in cystic fibrosis.


Subject(s)
Peroxidases/metabolism , Pseudomonas Infections/metabolism , Pseudomonas aeruginosa/pathogenicity , Pyocyanine/metabolism , Sodium Nitrite/metabolism , Trachea/metabolism , Animals , Cells, Cultured , Chromatography, High Pressure Liquid , Electron Spin Resonance Spectroscopy , Humans , Hydrogen Peroxide/metabolism , Instillation, Drug , Lactoperoxidase/metabolism , Mass Spectrometry , Mice , Mice, Inbred C57BL , Peroxidase/metabolism , Pseudomonas Infections/microbiology , Pseudomonas aeruginosa/metabolism , Pyocyanine/pharmacology , Respiratory Mucosa/cytology , Respiratory Mucosa/drug effects , Respiratory Mucosa/metabolism , Superoxides/metabolism , Trachea/microbiology
15.
Mol Microbiol ; 79(5): 1220-35, 2011 Mar.
Article in English | MEDLINE | ID: mdl-21205009

ABSTRACT

Surfactant protein-A (SP-A) is an important antimicrobial protein that opsonizes and permeabilizes membranes of microbial pathogens in mammalian lungs. Previously, we have shown that Pseudomonas aeruginosa flagellum-deficient mutants are preferentially cleared in the lungs of wild-type mice by SP-A-mediated membrane permeabilization, and not by opsonization. In this study, we report a flagellum-mediated mechanism of P. aeruginosa resistance to SP-A. We discovered that flagellum-deficient (ΔfliC) bacteria are unable to produce adequate amounts of exoproteases to degrade SP-A in vitro and in vivo, leading to its preferential clearance in the lungs of SP-A(+/+) mice. In addition, ΔfliC bacteria failed to degrade another important lung antimicrobial protein lysozyme. Detailed analyses showed that ΔfliC bacteria are unable to upregulate the transcription of lasI and rhlI genes, impairing the production of homoserine lactones necessary for quorum-sensing, an important virulence process that regulates the production of multiple exoproteases. Thus, reduced ability of ΔfliC bacteria to quorum-sense attenuates production of exoproteases and limits degradation of SP-A, thereby conferring susceptibility to this major pulmonary host defence protein.


Subject(s)
Bacterial Proteins/immunology , Exopeptidases/immunology , Flagella/immunology , Lung/immunology , Pseudomonas Infections/immunology , Pseudomonas aeruginosa/enzymology , Pulmonary Surfactant-Associated Protein A/immunology , Quorum Sensing , Animals , Bacterial Proteins/genetics , Exopeptidases/genetics , Female , Flagella/genetics , Humans , Lung/microbiology , Male , Mice , Mice, Knockout , Pseudomonas Infections/genetics , Pseudomonas Infections/microbiology , Pseudomonas aeruginosa/genetics , Pseudomonas aeruginosa/immunology , Pseudomonas aeruginosa/physiology , Pulmonary Surfactant-Associated Protein A/genetics
16.
PLoS Pathog ; 6(1): e1000712, 2010 Jan 08.
Article in English | MEDLINE | ID: mdl-20072604

ABSTRACT

Microbes are subjected to selective pressures during chronic infections of host tissues. Pseudomonas aeruginosa isolates with inactivating mutations in the transcriptional regulator LasR are frequently selected within the airways of people with cystic fibrosis (CF), and infection with these isolates has been associated with poorer lung function outcomes. The mechanisms underlying selection for lasR mutation are unknown but have been postulated to involve the abundance of specific nutrients within CF airway secretions. We characterized lasR mutant P. aeruginosa strains and isolates to identify conditions found in CF airways that select for growth of lasR mutants. Relative to wild-type P. aeruginosa, lasR mutants exhibited a dramatic metabolic shift, including decreased oxygen consumption and increased nitrate utilization, that is predicted to confer increased fitness within the nutrient conditions known to occur in CF airways. This metabolic shift exhibited by lasR mutants conferred resistance to two antibiotics used frequently in CF care, tobramycin and ciprofloxacin, even under oxygen-dependent growth conditions, yet selection for these mutants in vitro did not require preceding antibiotic exposure. The selection for loss of LasR function in vivo, and the associated adverse clinical impact, could be due to increased bacterial growth in the oxygen-poor and nitrate-rich CF airway, and from the resulting resistance to therapeutic antibiotics. The metabolic similarities among diverse chronic infection-adapted bacteria suggest a common mode of adaptation and antibiotic resistance during chronic infection that is primarily driven by bacterial metabolic shifts in response to nutrient availability within host tissues.


Subject(s)
Adaptation, Physiological , Cystic Fibrosis/microbiology , Drug Resistance, Microbial/genetics , Lung/microbiology , Pseudomonas Infections/metabolism , Pseudomonas aeruginosa/metabolism , Bacterial Proteins/genetics , Food , Humans , Mutation , Pseudomonas Infections/genetics , Pseudomonas aeruginosa/genetics , Reactive Nitrogen Species/metabolism , Selection, Genetic , Trans-Activators/genetics
17.
Proc Natl Acad Sci U S A ; 105(49): 19456-61, 2008 Dec 09.
Article in English | MEDLINE | ID: mdl-19047636

ABSTRACT

Hospital-acquired bacterial infections are an increasingly important cause of morbidity and mortality worldwide. Staphylococcal species are responsible for the majority of hospital-acquired infections, which are often complicated by the ability of staphylococci to grow as biofilms. Biofilm formation by Staphylococcus epidermidis and Staphylococcus aureus requires cell-surface proteins (Aap and SasG) containing sequence repeats known as G5 domains; however, the precise role of these proteins in biofilm formation is unclear. We show here, using analytical ultracentrifugation (AUC) and circular dichroism (CD), that G5 domains from Aap are zinc (Zn(2+))-dependent adhesion modules analogous to mammalian cadherin domains. The G5 domain dimerizes in the presence of Zn(2+), incorporating 2-3 Zn(2+) ions in the dimer interface. Tandem G5 domains associate in a modular fashion, suggesting a "zinc zipper" mechanism for G5 domain-based intercellular adhesion in staphylococcal biofilms. We demonstrate, using a biofilm plate assay, that Zn(2+) chelation specifically prevents biofilm formation by S. epidermidis and methicillin-resistant S. aureus (MRSA). Furthermore, individual soluble G5 domains inhibit biofilm formation in a dose-dependent manner. Thus, the complex three-dimensional architecture of staphylococcal biofilms results from the self-association of a single type of protein domain. Surface proteins with tandem G5 domains are also found in other bacterial species, suggesting that this mechanism for intercellular adhesion in biofilms may be conserved among staphylococci and other Gram-positive bacteria. Zn(2+) chelation represents a potential therapeutic approach for combating biofilm growth in a wide range of bacterial biofilm-related infections.


Subject(s)
Bacterial Adhesion/physiology , Bacterial Proteins/metabolism , Biofilms , Cell Adhesion Molecules/metabolism , Staphylococcus aureus/metabolism , Staphylococcus epidermidis/metabolism , Zinc/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Cell Adhesion Molecules/chemistry , Cell Adhesion Molecules/genetics , Chelating Agents/pharmacology , Circular Dichroism , Dimerization , Protein Structure, Tertiary , Staphylococcus aureus/pathogenicity , Staphylococcus epidermidis/pathogenicity , Virulence
18.
Front Microbiol ; 12: 639362, 2021.
Article in English | MEDLINE | ID: mdl-34220733

ABSTRACT

The life-threatening pandemic concerning multi-drug resistant (MDR) bacteria is an evolving problem involving increased hospitalizations, billions of dollars in medical costs and a remarkably high number of deaths. Bacterial pathogens have demonstrated the capacity for spontaneous or acquired antibiotic resistance and there is virtually no pool of organisms that have not evolved such potentially clinically catastrophic properties. Although many diseases are linked to such organisms, three include cystic fibrosis (CF), burn/blast wounds and urinary tract infections (UTIs), respectively. Thus, there is a critical need to develop novel, effective antimicrobials for the prevention and treatment of such problematic infections. One of the most formidable, naturally MDR bacterial pathogens is Pseudomonas aeruginosa (PA) that is particularly susceptible to nitric oxide (NO), a component of our innate immune response. This susceptibility sets the translational stage for the use of NO-based therapeutics during the aforementioned human infections. First, we discuss how such NO therapeutics may be able to target problematic infections in each of the aforementioned infectious scenarios. Second, we describe a recent discovery based on years of foundational information, a novel drug known as AB569. AB569 is capable of forming a "time release" of NO from S-nitrosothiols (RSNO). AB569, a bactericidal tandem consisting of acidified NaNO2 (A-NO2 -) and Na2-EDTA, is capable of killing all pathogens that are associated with the aforementioned disorders. Third, we described each disease state in brief, the known or predicted effects of AB569 on the viability of PA, its potential toxicity and highly remote possibility for resistance to develop. Finally, we conclude that AB569 can be a viable alternative or addition to conventional antibiotic regimens to treat such highly problematic MDR bacterial infections for civilian and military populations, as well as the economical burden that such organisms pose.

19.
Front Bioeng Biotechnol ; 9: 808614, 2021.
Article in English | MEDLINE | ID: mdl-35096795

ABSTRACT

Exosomes are natural cell-derived nanovesicles of endocytic origin that enable cellular crosstalk by transferring encapsulated molecular cargos across biological barriers, thereby holding significantly complex implications in the etiology and progression of diverse disease states. Consequently, the development of exosomes-based nano-theranostic strategies has received immense consideration for advancing therapeutic interventions and disease prognosis. Their favorable biopharmaceutical properties make exosomes a unique nanoparticulate carrier for pharmaceutical drug delivery. This review provides an update on the contemporary strategies utilizing exosomes for theranostic applications in nanomedicine. In addition, we provide a synopsis of exosomal features and insights into strategic modifications that control in vivo biodistribution. We further discuss their opportunities, merits and pitfalls for cell/tissue targeted drug delivery in personalized nanotherapy.

20.
JCI Insight ; 6(10)2021 05 24.
Article in English | MEDLINE | ID: mdl-34027898

ABSTRACT

There is an emerging need for accurate and rapid identification of bacteria in the human body to achieve diverse biomedical objectives. Copper homeostasis is vital for the survival of bacterial species owing to the roles of the metal as a nutrient, respiratory enzyme cofactor, and a toxin. Here, we report the development of a copper-64-labeled bacterial metal chelator, yersiniabactin, to exploit a highly conserved metal acquisition pathway for noninvasive and selective imaging of bacteria. Compared with traditional techniques used to manufacture probes, our strategy simplifies the process considerably by combining the function of metal attachment and cell recognition to the same molecule. We demonstrate, for the first time to our knowledge, how a copper-64 PET probe can be used to identify specific bacterial populations, monitor antibiotic treatment outcomes, and track bacteria in diverse niches in vivo.


Subject(s)
Bacterial Infections , Copper/metabolism , Phenols , Positron-Emission Tomography/methods , Siderophores , Thiazoles , Animals , Bacteria/chemistry , Bacteria/metabolism , Bacterial Infections/diagnostic imaging , Bacterial Infections/microbiology , Disease Models, Animal , Echocardiography , Female , Mice , Mice, Inbred BALB C , Molecular Imaging , Phenols/analysis , Phenols/chemistry , Phenols/metabolism , Siderophores/analysis , Siderophores/chemistry , Siderophores/metabolism , Thiazoles/analysis , Thiazoles/chemistry , Thiazoles/metabolism
SELECTION OF CITATIONS
SEARCH DETAIL