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Frontiers in Microbiology 2021Pseudomonas species are ubiquitous in nature and include numerous medically, agriculturally and technologically beneficial strains of which the interspecific...
Pseudomonas species are ubiquitous in nature and include numerous medically, agriculturally and technologically beneficial strains of which the interspecific interactions are of great interest for biotechnologies. Specifically, co-cultures containing have been used for bioremediation, biocontrol, aquaculture management and wastewater denitrification. Furthermore, the use of biofilms, in combination with consortia-based approaches, may offer advantages for these processes. Understanding the interspecific interaction within biofilm co-cultures or consortia provides a means for improvement of current technologies. However, the investigation of biofilm-based consortia has been limited. We present an adaptable and scalable method for the analysis of macroscopic interactions (colony morphology, inhibition, and invasion) between colony-forming bacterial strains using an automated printing method followed by analysis of the genes and metabolites involved in the interactions. Using Biofilm Interaction Mapping and Analysis (BIMA), these interactions were investigated between strain RCH2, a denitrifier isolated from chromium (VI) contaminated soil, and 13 other species of pseudomonas isolated from non-contaminated soil. One interaction partner, Pseudomonas fluorescens N1B4 was selected for mutant fitness profiling of a DNA-barcoded mutant library; with this approach four genes of importance were identified and the effects on interactions were evaluated with deletion mutants and mass spectrometry based metabolomics.
PubMed: 34956122
DOI: 10.3389/fmicb.2021.757856 -
MBio Jan 2016Cytochrome c oxidases (CcOs), members of the heme-copper containing oxidase (HCO) superfamily, are the terminal enzymes of aerobic respiratory chains. The cbb3-type...
UNLABELLED
Cytochrome c oxidases (CcOs), members of the heme-copper containing oxidase (HCO) superfamily, are the terminal enzymes of aerobic respiratory chains. The cbb3-type cytochrome c oxidases (cbb3-CcO) form the C-family and have only the central catalytic subunit in common with the A- and B-family HCOs. In Pseudomonas stutzeri, two cbb3 operons are organized in a tandem repeat. The atomic structure of the first cbb3 isoform (Cbb3-1) was determined at 3.2 Å resolution in 2010 (S. Buschmann, E. Warkentin, H. Xie, J. D. Langer, U. Ermler, and H. Michel, Science 329:327-330, 2010, http://dx.doi.org/10.1126/science.1187303). Unexpectedly, the electron density map of Cbb3-1 revealed the presence of an additional transmembrane helix (TMH) which could not be assigned to any known protein. We now identified this TMH as the previously uncharacterized protein PstZoBell_05036, using a customized matrix-assisted laser desorption ionization (MALDI)-tandem mass spectrometry setup. The amino acid sequence matches the electron density of the unassigned TMH. Consequently, the protein was renamed CcoM. In order to identify the function of this new subunit in the cbb3 complex, we generated and analyzed a CcoM knockout strain. The results of the biochemical and biophysical characterization indicate that CcoM may be involved in CcO complex assembly or stabilization. In addition, we found that CcoM plays a role in anaerobic respiration, as the ΔCcoM strain displayed altered growth rates under anaerobic denitrifying conditions.
IMPORTANCE
The respiratory chain has recently moved into the focus for drug development against prokaryotic human pathogens, in particular, for multiresistant strains (P. Murima, J. D. McKinney, and K. Pethe, Chem Biol 21:1423-1432, 2014, http://dx.doi.org/10.1016/j.chembiol.2014.08.020). cbb3-CcO is an essential enzyme for many different pathogenic bacterial species, e.g., Helicobacter pylori, Vibrio cholerae, and Pseudomonas aeruginosa, and represents a promising drug target. In order to develop compounds targeting these proteins, a detailed understanding of the molecular architecture and function is required. Here we identified and characterized a novel subunit, CcoM, in the cbb3-CcO complex and thereby completed the crystal structure of the Cbb3 oxidase from Pseudomonas stutzeri, a bacterium closely related to the human pathogen Pseudomonas aeruginosa.
Topics: Electron Transport Complex IV; Gene Knockout Techniques; Protein Subunits; Pseudomonas stutzeri; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Tandem Mass Spectrometry
PubMed: 26814183
DOI: 10.1128/mBio.01921-15 -
PloS One 2014The presence of nitrogen fixers within the genus Pseudomonas has been established and so far most isolated strains are phylogenetically affiliated to Pseudomonas...
The presence of nitrogen fixers within the genus Pseudomonas has been established and so far most isolated strains are phylogenetically affiliated to Pseudomonas stutzeri. A gene ortholog neighborhood analysis of the nitrogen fixation island (NFI) in four diazotrophic P. stutzeri strains and Pseudomonas azotifigens revealed that all are flanked by genes coding for cobalamin synthase (cobS) and glutathione peroxidise (gshP). The putative NFIs lack all the features characterizing a mobilizable genomic island. Nevertheless, bioinformatic analysis P. stutzeri DSM 4166 NFI demonstrated the presence of short inverted and/or direct repeats within both flanking regions. The other P. stutzeri strains carry only one set of repeats. The genetic diversity of eleven diazotrophic Pseudomonas isolates was also investigated. Multilocus sequence typing grouped nine isolates along with P. stutzeri and two isolates are grouped in a separate clade. A Rep-PCR fingerprinting analysis grouped the eleven isolates into four distinct genotypes. We also provided evidence that the putative NFI in our diazotrophic Pseudomonas isolates is flanked by cobS and gshP genes. Furthermore, we demonstrated that the putative NFI of Pseudomonas sp. Gr65 is flanked by inverted repeats identical to those found in P. stutzeri DSM 4166 and while the other P. stutzeri isolates harbor the repeats located in the intergenic region between cobS and glutaredoxin genes as in the case of P. stutzeri A1501. Taken together these data suggest that all putative NFIs of diazotrophic Pseudomonas isolates are anchored in an intergenic region between cobS and gshP genes and their flanking regions are designated by distinct repeats patterns. Moreover, the presence of almost identical NFIs in diazotrophic Pseudomonas strains isolated from distal geographical locations around the world suggested that this horizontal gene transfer event may have taken place early in the evolution.
Topics: Bacterial Proteins; Base Sequence; China; DNA, Bacterial; Evolution, Molecular; Genetic Variation; Genomic Islands; Geography; Germany; Greece; Models, Genetic; Molecular Sequence Data; Nitrogen Fixation; Phylogeny; Pseudomonas; Pseudomonas stutzeri; RNA, Ribosomal, 16S; Repetitive Sequences, Nucleic Acid; Sequence Analysis, DNA; Sequence Homology, Nucleic Acid; Species Specificity
PubMed: 25251496
DOI: 10.1371/journal.pone.0105837 -
IDCases 2016is infrequently isolated from clinical specimens, and if isolated, more likely represents colonization or contamination rather than infection. Despite this, there are...
is infrequently isolated from clinical specimens, and if isolated, more likely represents colonization or contamination rather than infection. Despite this, there are dozens of case reports which describe clinically significant infections at variable sites. A 69-year-old man had a infection of a prosthetic vascular graft infection, which he received in Panama City. He was successfully treated with a single antipseudomonal agent for 6 weeks and the removal of the infected vascular graft. A 70-year-old man had a infection of a prosthetic joint, which was successfully treated with a single anti-pseudomonal agent for 6 weeks. There is only one other documented case of a prosthetic vascular graft infection secondary to . There are 5 documented cases of prosthetic joint infections. The previous cases were treated with antibiotics and variably, source control with the removal of prosthetic material. Most cases of infection are due to exposure in health care settings. Immunocompromised states such as HIV or hematological and solid tumor malignancies are risk factors for infection. Infections caused by are far less frequent and less fatal than those caused by P. aeruginosa. The etiology of a infection could be exposure to soil and water, but also contaminated material in the health care setting or an immunocompromised state. Iatrogenic infections that are secondary to health care tourism are a potential cause of fever in the returned traveler.
PubMed: 27942461
DOI: 10.1016/j.idcr.2016.10.009 -
Applied and Environmental Microbiology Oct 2021The reaction sequence for aerobic degradation of bile salts by environmental bacteria resembles degradation of other steroid compounds. Recent findings show that...
Comparative Analysis of Bile-Salt Degradation in sp. Strain Chol11 and Pseudomonas stutzeri Strain Chol1 Reveals Functional Diversity of Proteobacterial Steroid Degradation Enzymes and Suggests a Novel Pathway for Side Chain Degradation.
The reaction sequence for aerobic degradation of bile salts by environmental bacteria resembles degradation of other steroid compounds. Recent findings show that bacteria belonging to the use a pathway variant for bile-salt degradation. This study addresses this so-called Δ-variant by comparative analysis of unknown degradation steps in sp. strain Chol11 with known reactions found in Pseudomonas stutzeri Chol1. Investigations of strain Chol11 revealed an essential function of the acyl-CoA dehydrogenase (ACAD) Scd4AB for growth with bile salts. Growth of the deletion mutant was restored with a metabolite containing a double bond within the side chain which was produced by the Δ-ACAD Scd1AB from P. stutzeri Chol1. Expression of in the deletion mutant fully restored growth with bile salts, while expression of only enabled constricted growth in P. stutzeri Chol1 or deletion mutants. Strain Chol11 Δ accumulated hydroxylated steroid metabolites which were degraded and activated with coenzyme A by the wild type. Activities of five Rieske type monooxygenases of strain Chol11 were screened by heterologous expression and compared to the B-ring cleaving KshAB from P. stutzeri Chol1. Three of the Chol11 enzymes catalyzed B-ring cleavage of only Δ-steroids, while KshAB was more versatile. Expression of a fourth KshA homolog, Nov2c228, led to production of metabolites with hydroxylations at an unknown position. These results indicate functional diversity of proteobacterial enzymes for bile-salt degradation and suggest a novel side chain degradation pathway involving an essential ACAD reaction and a steroid hydroxylation step. This study highlights the biochemical diversity of bacterial degradation of steroid compounds in different aspects. First, it further elucidates an unexplored variant in the degradation of bile-salt side chains by sphingomonads, a group of environmental bacteria that is well-known for their broad metabolic capabilities. Moreover, it adds a so far unknown hydroxylation of steroids to the reactions Rieske monooxygenases can catalyze with steroids. Additionally, it analyzes a proteobacterial ketosteroid-9α-hydroxylase and shows that this enzyme is able to catalyze side reactions with nonnative substrates.
Topics: Acyl-CoA Dehydrogenase; Bacterial Proteins; Bile Acids and Salts; Mixed Function Oxygenases; Pseudomonas stutzeri; Sphingomonadaceae; Steroids
PubMed: 34469190
DOI: 10.1128/AEM.01453-21 -
3 Biotech May 2020Textile industry is one of the anthropogenic activities that consume a large amount of water and pollute water bodies. It uses a massive amount of dyes, which is one of...
Textile industry is one of the anthropogenic activities that consume a large amount of water and pollute water bodies. It uses a massive amount of dyes, which is one of the main constituents of polluting textile effluent. In the present research, biodegradation of Acid Blue 113 dye, a commonly used textile di-azo dye, has been studied exploiting , strain AK6. The dye (300 ppm) was decolorized up to 86.2% within 96 h. The metabolites of Acid Blue 113 obtained after biodegradation were identified by various analytical techniques viz. HPLC (high-performance liquid chromatography) and GC-MS (gas chromatography-mass spectrometry). Genome analysis of isolate AK6 using IMG/M (Integrated Microbial Genomes and Microbiomes) system supported the role of azoreductase and laccase for the decolorization and degradation of azo dye. The ability of AK6 to tolerate high amount of dye makes it a potential candidate for bioremediation and pre-processing to remove dyes from textile effluents.
PubMed: 32351872
DOI: 10.1007/s13205-020-02205-5 -
Environmental Pollution (Barking, Essex... Jan 2023Atmospheric particulate matter (PM) contains a mixture of chemical and biological elements that pose threat to human health by increasing susceptibility to respiratory...
Atmospheric particulate matter (PM) contains a mixture of chemical and biological elements that pose threat to human health by increasing susceptibility to respiratory diseases. Although the identification of the microorganisms composing the PM has been assessed, their immunological impacts are still questionable. Here, we examined the mechanisms responsible for the pathogenicity of Pseudomonas stutzeri PM101005 (PMPS), a bacterium isolated from fine dust, in lung epithelial cells, alveolar cells, and macrophages. Relative to its comparative strain Pseudomonas stutzeri (PS), infections with PMPS induced higher production of inflammatory cytokines and chemokines, mediated by the activation of NF-κB and MAPK signaling pathways. Additionally, with three-dimensional (3D) airway spheroids which mimic the human bronchial epithelium, we confirmed that PMPS infections lead to relatively higher induction of pro-inflammatory cytokines than PM infections. Consistent results were observed in murine models as the infections with PMPS provoked greater inflammatory responses than the infections with PS. These PMPS-induced responses were mediated by the signaling pathways of the Toll-like receptors (TLRs), which regulated PMPS infection and played an important role in the expression of the antibiotic peptide β-defensin 3 (BD3) that suppressed PMPS proliferation. Moreover, PM pretreatment enhanced inflammatory responses and tissue damage of PMPS, while reducing BD3 expression. Overall, these results indicate that PM-isolated PMPS induce TLR-mediated inflammatory responses in lung tissues, and contributes to the understanding of the etiology of PM-induced respiratory damage.
Topics: Mice; Humans; Animals; Particulate Matter; Pseudomonas stutzeri; Lung; Cytokines; Signal Transduction
PubMed: 36435285
DOI: 10.1016/j.envpol.2022.120741 -
Journal of Bacteriology Jan 1983Cells of Pseudomonas stutzeri are naturally transformed by homologous chromosomal DNA; they do not require chemical treatment to become competent. This capacity to...
Cells of Pseudomonas stutzeri are naturally transformed by homologous chromosomal DNA; they do not require chemical treatment to become competent. This capacity to undergo natural transformation was found to be shared by the closely related species P. mendocina, P. alcaligenes, and P. pseudoalcaligenes, but was not detectable in strains of P. aeruginosa, P. perfectomarinus, P. putida, P. fluorescens, or P. syringae. P. stutzeri could be transformed either on plates or in liquid medium. Only double-stranded chromosomal DNA was effective; single-stranded DNA and plasmid DNA were not. DNA fragments larger than 10 kilobase pairs were more effective than smaller fragments. The transformation frequency was proportional to DNA concentration from 1 ng/ml to 1 microgram/ml; higher concentrations were saturating. The maximum frequency, about 10(-4) transformants per recipient cell, was obtained with cells from a culture in the early stationary growth phase. A variety of chromosomal mutations have been transformed, including mutations to auxotrophy and to antibiotic resistance. Other systems for genetic exchange in P. stutzeri have not yet been found; transformation offers a means for the genetic analysis of this metabolically versatile organism.
Topics: Chromosomes, Bacterial; DNA, Bacterial; DNA, Single-Stranded; Genetic Markers; Plasmids; Pseudomonas; Species Specificity; Transformation, Bacterial
PubMed: 6571730
DOI: 10.1128/jb.153.1.93-99.1983 -
Journal of Environmental Health Science... Dec 2022A consortium of bacteria capable of decomposing oily hydrocarbons was isolated from tarballs on the beaches of Terengganu, Malaysia, and classified as , , and . The...
UNLABELLED
A consortium of bacteria capable of decomposing oily hydrocarbons was isolated from tarballs on the beaches of Terengganu, Malaysia, and classified as , , and . The Taguchi design was used to optimize the biodegradation of diesel using these bacteria as a consortium. The highest biodegradation of diesel-oil in the experimental tests was 93.6%, and the individual n-alkanes decomposed 87.6-97.6% over 30 days. Optimal settings were inoculum size of 2.5 mL (1.248 OD); 12% (v/v) the initial diesel-oil in a minimal salt medium of pH 7.0, 30.0 gL NaCl and 2.0 gL NHNO concentration, incubated at 42 °C temperature and 150 rpm agitation speed. Parameters significantly improved diesel-oil removal by consortium as shown by the model determination coefficient (R = 90.89%; < 0.001) with a synergistic effect of agitation speed significantly contributing 81.03%. Taguchi design determined the optimal settings for the parameters under study, which significantly improved diesel-oil removal by consortium. This can be used to design a novel bioremediation strategy that can achieve optimal decontamination of oil pollution in a shorter time.
SUPPLEMENTARY INFORMATION
The online version contains supplementary material available at 10.1007/s40201-022-00812-3.
PubMed: 36406595
DOI: 10.1007/s40201-022-00812-3 -
Journal of Infection in Developing... Nov 2012The emergence and rapid spread of blaIMP and blaVIM metallo-beta-lactamase (MBL) producing Gram-negative bacteria causing nosocomial infections are of concern worldwide...
INTRODUCTION
The emergence and rapid spread of blaIMP and blaVIM metallo-beta-lactamase (MBL) producing Gram-negative bacteria causing nosocomial infections are of concern worldwide due to limited treatment options.
METHODOLOGY
A total of 179 nonreplicate, consecutive, carbapenem resistant Pseudomonas aeruginosa (61), Acinetobacter baumannii (116), Acinetobacter lwoffii (1) and Pseudomonas stutzeri (1) isolated from patients hospitalized for 48 hours or more were included in the study. The minimum inhibitory concentrations (MIC) to imipenem and meropenem were determined and interpreted according to Clinical Laboratory Standards Institute guidelines. The Modified Hodge Test (MHT) and inhibitor potentiated disk diffusion tests with ethylenediaminetetraacetic acid (EDTA) were used for screening of carbapenamases and MBL production respectively. Polymerase chain reaction (PCR) was performed for the detection of MBL (blaVIM and blaIMP) genes. Gene sequencing was performed for representative isolates.
RESULTS
MHT was positive in 94.4% (n = 169). MBL screening with EDTA was positive in 80.4% (n = 144). MBL genes bla VIM and bla IMP were detected in 92 (51.4%) isolates. Bla VIM alone was detected in 89 isolates while two isolates had bla IMP alone. One isolate had both bla VIM and bla IMP. Among the P. aeruginosa, 36 carried the MBL gene. In A. baumannii, 54 carried the MBL gene. Bla VIM was found in P. stutzeri and A. lwoffii isolates.
CONCLUSION
Carbapenem resistance in P. aeruginosa and A. baumannii is chiefly mediated by MBL production. The common MBL gene is the blaVIM.
Topics: Acinetobacter; Acinetobacter Infections; Amikacin; Anti-Bacterial Agents; Bacterial Proteins; Disk Diffusion Antimicrobial Tests; Drug Resistance, Bacterial; Genes, Bacterial; Humans; Imipenem; India; Intensive Care Units; Meropenem; Phenotype; Polymerase Chain Reaction; Pseudomonas; Pseudomonas Infections; Thienamycins; beta-Lactamases
PubMed: 23277500
DOI: 10.3855/jidc.2268