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Genes Aug 2020The sewage sludge isolate HBP-1 was the first bacterium known to completely degrade the fungicide 2-hydroxybiphenyl. PacBio and Illumina whole-genome sequencing...
The sewage sludge isolate HBP-1 was the first bacterium known to completely degrade the fungicide 2-hydroxybiphenyl. PacBio and Illumina whole-genome sequencing revealed three circular DNA replicons: a chromosome and two plasmids. Plasmids were shown to code for putative adaptive functions such as heavy metal resistance, but with unclarified ability for self-transfer. About one-tenth of strain HBP-1's chromosomal genes are likely of recent horizontal influx, being part of genomic islands, prophages and integrative and conjugative elements (ICEs). carries two large ICEs with different functional specialization, but with homologous core structures to the well-known ICE of B13. The variable regions of ICE1 (96 kb) code for, among others, heavy metal resistances and formaldehyde detoxification, whereas those of ICE2 (171 kb) encodes complete -cleavage pathways for catabolism of 2-hydroxybiphenyl and salicylate, a protocatechuate pathway and peripheral enzymes for 4-hydroxybenzoate, ferulate, vanillin and vanillate transformation. Both ICEs transferred at frequencies of 10-10 per HBP-1 donor into , where they integrated site specifically into -gene targets, as expected. Our study highlights the underlying determinants and mechanisms driving dissemination of adaptive properties allowing bacterial strains to cope with polluted environments.
Topics: Computational Biology; Conjugation, Genetic; DNA Transposable Elements; DNA, Bacterial; Disinfectants; Fatty Acids; Gene Order; Gene Transfer, Horizontal; Genome, Bacterial; Genomic Islands; Genomics; High-Throughput Nucleotide Sequencing; Molecular Sequence Annotation; Plasmids; Prophages; Pseudomonas
PubMed: 32806781
DOI: 10.3390/genes11080930 -
Molecular Plant-microbe Interactions :... Apr 2022
Topics: Acyl-Butyrolactones; Pseudomonas; Quorum Sensing
PubMed: 35285671
DOI: 10.1094/MPMI-12-21-0310-A -
BMJ Case Reports May 2021A man in his 50s with neutropenic fever and multifocal lung opacities was diagnosed with a viral pneumonia. A small number of bacteria grown from bronchoalveolar lavage...
A man in his 50s with neutropenic fever and multifocal lung opacities was diagnosed with a viral pneumonia. A small number of bacteria grown from bronchoalveolar lavage fluid collected during a repeat bronchoscopy were initially identified as by VITEK-2 and mass spectrometry platforms. Whole-genome sequencing, however, subsequently demonstrated that the bacteria were , representing the first known case of cultured from human lungs.
Topics: Bronchoalveolar Lavage Fluid; Humans; Lung; Male; Pneumonia; Pseudomonas; Pseudomonas Infections; Pseudomonas aeruginosa
PubMed: 34031078
DOI: 10.1136/bcr-2020-241327 -
Microbiology (Reading, England) Jan 2020Azelaic acid is a dicarboxylic acid that has recently been shown to play a role in plant-bacteria signalling and also occurs naturally in several cereals. Several...
Azelaic acid is a dicarboxylic acid that has recently been shown to play a role in plant-bacteria signalling and also occurs naturally in several cereals. Several bacteria have been reported to be able to utilize azelaic acid as a unique source of carbon and energy, including . In this study, we utilize as a model organism to study bacterial degradation of and response to azelaic acid. We report genetic evidence of azelaic acid degradation and the identification of a transcriptional regulator that responds to azelaic acid in DSM 9128. Three mutants possessing transposons in genes of an acyl-CoA ligase, an acyl-CoA dehydrogenase and an isocitrate lyase display a deficient ability in growing in azelaic acid. Studies on transcriptional regulation of these genes resulted in the identification of an IclR family repressor that we designated as AzeR, which specifically responds to azelaic acid. A bioinformatics survey reveals that AzeR is confined to a few proteobacterial genera that are likely to be able to degrade and utilize azelaic acid as the sole source of carbon and energy.
Topics: Bacteria; Bacterial Proteins; Dicarboxylic Acids; Gene Expression Regulation, Bacterial; Molecular Structure; Mutation; Phylogeny; Promoter Regions, Genetic; Pseudomonas; Repressor Proteins; Transcription Factors
PubMed: 31621557
DOI: 10.1099/mic.0.000865 -
Pyrimidine nucleotide synthesis in Pseudomonas nitroreducens and the regulatory role of pyrimidines.Microbiological Research Dec 2014Control of pyrimidine biosynthesis in the commercially important, hydrocarbon-utilizing bacterium Pseudomonas nitroreducens ATCC 33634 was investigated. When...
Control of pyrimidine biosynthesis in the commercially important, hydrocarbon-utilizing bacterium Pseudomonas nitroreducens ATCC 33634 was investigated. When glucose-grown wild-type cells were supplemented with uracil or orotic acid, the pyrimidine biosynthetic activities were depressed. Pyrimidine limitation of glucose-grown cells of an orotate phosphoribosyltransferase mutant caused aspartate transcarbamoylase and dihydroorotase activities to increase by about 4-fold while the other enzyme activities about doubled. In succinate-grown phosphoribosyltransferase mutant cells subjected to pyrimidine limitation, transcarbamoylase and dehydrogenase activities rose by about 5-fold while dihydroorotase activity more than tripled. In an OMP decarboxylase mutant, pyrimidine limitation of glucose-grown cells increased transcarbamoylase, dihydroorotase, dehydrogenase and phosphoribosyltransferase activities by 4-, 10-, 6- and 3.8-fold, respectively. Pyrimidine limitation of the succinate-grown decarboxylase mutant cells increased aspartate transcarbamoylase or dihydroorotase by more than 4-fold and the other activities by about 2-fold. Pyrimidine biosynthetic enzyme synthesis appeared to be regulated by pyrimidines with the regulation being influenced by the carbon source present. Aspartate transcarbamoylase activity in Ps. nitroreducens was regulated at the level of enzyme activity since the enzyme was strongly inhibited by UDP, pyrophosphate, ATP and ADP. Overall, the regulation of pyrimidine biosynthesis in Ps. nitroreducens can be used to differentiate it from other taxonomically related species of Pseudomonas.
Topics: Aspartate Carbamoyltransferase; Pseudomonas; Pyrimidine Nucleotides; Pyrimidines
PubMed: 24867376
DOI: 10.1016/j.micres.2014.04.003 -
Journal of the Science of Food and... Mar 2021L-Glutaminase is considered to be an important industrial enzyme in both the pharmaceutical and food industries, especially for producing functional glutamyl compounds,...
BACKGROUND
L-Glutaminase is considered to be an important industrial enzyme in both the pharmaceutical and food industries, especially for producing functional glutamyl compounds, such as l-theanine. Pseudomonas nitroreducens SP.001 with intracellular l-glutaminase activity has been screened previously. In the present study, three physical permeabilization methods were used to improve l-glutaminase activity. Then, the whole-cell immobilization conditions of permeabilized cells using sodium alginate as an embedding agent were optimized to enhance the enzyme's stability and reusability. The characteristics of the immobilized cells were investigated in comparison with those of permeabilized cells.
RESULTS
The results obtained showed that cell permeabilization using osmotic shock with 155 g L sucrose markedly improved enzyme activity. Then, an effective procedure for immobilization of permeabilized P. nitroreducens cells was established. The optimum conditions for cell immobilization were: sodium alginate 40 g L , calcium chloride 30 g L , cell mass 100 g L and a curing time of 3 h. After successful immobilization, characterization studies revealed that the thermostability and pH resistance of l-glutaminase from immobilized cells were enhanced compared to those from permeabilized cells. Moreover, the immobilized biocatalyst could be reused up to 10 times and retained 80% of its activity.
CONCLUSION
The stability and reusability of the permeabilized cells were improved through the immobilization. These findings indicated that immobilized whole-cell l-glutaminase from P. nitroreducens SP.001 possesses more potential for various industrial biotechnological applications than free cells. © 2020 Society of Chemical Industry.
Topics: Alginates; Bacterial Proteins; Biocatalysis; Cells, Immobilized; Glutamates; Glutaminase; Pseudomonas
PubMed: 32790072
DOI: 10.1002/jsfa.10736 -
Journal of Hazardous Materials Sep 2023The presence of the sulfonic acid group in sulfonated anthraquinones (SAs) resulted in the difficulty in the mineralization of anthraquinone ring. Little information is...
The presence of the sulfonic acid group in sulfonated anthraquinones (SAs) resulted in the difficulty in the mineralization of anthraquinone ring. Little information is available on the removal pathway of the sulfonic acid group of SAs under aerobic/anaerobic conditions. Herein, sodium 1-aminoanthraquinone-2-sulfonate (ASA-2) was used as an important intermediate of SAs. A novel Pseudomonas nitroreducens WA capable of ASA-2 desulfonation was isolated from the Reactive Blue 19-degrading consortium WRB. Anaerobic desulfonation efficiency of 0.165 mM ASA-2 by strain WA reached 99% in 36 h at pH 7.5 and 35 ℃ using glucose as an electron donor. Further analysis showed that ASA-2 as an electron acceptor could be anaerobically transformed into 1-aminoanthraquinone and sulfite via the cleavage of C-S bond. Strain WA could also desulfonate sodium 1-amino-4-bromoanthraquinone-2-sulfonate and sodium anthraquinone-2-sulfonate. Under denitrification conditions, the formed sulfite could be oxidized to sulfate by nitrite via a chemical reaction, which was beneficial for nitrite removal. This phenomenon was observed in consortium WRB-amended system. Moreover, the consortium WRB could reduce the formed sulfite to sulfide due to the presence of Desulfovibrio. These results provide a theoretical basis for the anaerobic biodesulfonation of SAs along with nitrate removal and support for the development of sulfite-based biotechnology.
Topics: Nitrates; Sulfonic Acids; Nitrites; Anaerobiosis; Anthraquinones; Alkanesulfonates; Biotransformation; Sulfites; Denitrification
PubMed: 37348367
DOI: 10.1016/j.jhazmat.2023.131887 -
Biochemical and Biophysical Research... Jan 2021γ-Glutamyltranspeptidase (GGT) is a ubiquitous enzyme that catalyzes the hydrolysis of the γ-glutamyl linkage of γ-glutamyl compounds and the transfer of their...
γ-Glutamyltranspeptidase (GGT) is a ubiquitous enzyme that catalyzes the hydrolysis of the γ-glutamyl linkage of γ-glutamyl compounds and the transfer of their γ-glutamyl moiety to acceptor substrates. Pseudomonas nitroreducens GGT (PnGGT) is used for the industrial synthesis of theanine, thus it is important to determine the structural basis of hydrolysis and transfer reactions and identify the acceptor site of PnGGT to improve the efficient of theanine synthesis. Our previous structural studies of PnGGT have revealed that crucial interactions between three amino acid residues, Trp385, Phe417, and Trp525, distinguish PnGGT from other GGTs. Here we report the role of Trp525 in PnGGT based on site-directed mutagenesis and structural analyses. Seven mutant variants of Trp525 were produced (W525F, W525V, W525A, W525G, W525S, W525D, and W525K), with substitution of Trp525 by nonaromatic residues resulting in dramatically reduced hydrolysis activity. All Trp525 mutants exhibited significantly increased transfer activity toward hydroxylamine with hardly any effect on acceptor substrate preference. The crystal structure of PnGGT in complex with the glutamine antagonist, 6-diazo-5-oxo-l-norleucine, revealed that Trp525 is a key residue limiting the movement of water molecules within the PnGGT active site.
Topics: Bacterial Proteins; Catalytic Domain; Crystallography, X-Ray; Models, Molecular; Mutagenesis, Site-Directed; Mutant Proteins; Pseudomonas; Static Electricity; Substrate Specificity; Tryptophan; gamma-Glutamyltransferase
PubMed: 33288198
DOI: 10.1016/j.bbrc.2020.11.093 -
International Journal of Systematic and... Apr 2007Polyphasic characterization of strain DSM 9128, described as 'Pseudomonas azelaica' by Janota-Bassalik et al. [Acta Microbiol Pol B 3, 143-153 (1971)], and four...
Characterization of 'Pseudomonas azelaica' DSM 9128, leading to emended descriptions of Pseudomonas citronellolis Seubert 1960 (Approved Lists 1980) and Pseudomonas nitroreducens Iizuka and Komagata 1964 (Approved Lists 1980), including Pseudomonas multiresinivorans as its later heterotypic synonym.
Polyphasic characterization of strain DSM 9128, described as 'Pseudomonas azelaica' by Janota-Bassalik et al. [Acta Microbiol Pol B 3, 143-153 (1971)], and four biochemically similar isolates was performed with the aim of validly publishing the name 'Pseudomonas azelaica'. Based on 16S rRNA gene sequence analysis, DNA-DNA hybridization, fatty acid patterns and extensive biochemical testing, it was concluded that DSM 9128, two further strains and the type strains of Pseudomonas nitroreducens and Pseudomonas multiresinivorans form a highly related cluster. However, DNA-DNA binding did not conclusively resolve whether these strains should be regarded as members of one species. Based on results gained with the above-mentioned methods, two other isolates were assigned to the species Pseudomonas citronellolis, a species very close to P. nitroreducens. Based on genetic and biochemical similarities, it is suggested that Pseudomonas multiresinivorans should be considered as a later heterotypic synonym of Pseudomonas nitroreducens. The species descriptions of P. nitroreducens and P. citronellolis are emended.
Topics: DNA, Bacterial; DNA, Ribosomal; Molecular Sequence Data; Pseudomonas; RNA, Ribosomal, 16S
PubMed: 17392224
DOI: 10.1099/ijs.0.64849-0 -
Applied Biochemistry and Biotechnology Apr 2021Currently, the biotechnological preparation of fragrances using natural materials attracted growing attention. Enzymatic synthesis of vanillin from isoeugenol by...
Currently, the biotechnological preparation of fragrances using natural materials attracted growing attention. Enzymatic synthesis of vanillin from isoeugenol by recombinant isoeugenol monooxygenase from Pseudomonas nitroreducens Jin1 was systematically investigated herein. With series of work on the construction of recombinant E. coli over-expressing isoeugenol monooxygenase, optimization of the culture conditions for enzyme production and reaction process for converting isoeugenol into vanillin, an increase of 22-fold in the enzyme activity (2050 U/L) was obtained, and the conversion was significantly increased at high substrate concentration with the aid of magnetic chitosan membrane for product isolation in situ. Under optimal conditions, the product concentration and space-time yield reached 252 mM and 115 g/L/d, respectively, and vanillin was obtained in 82.3% yield and > 99% purity in the gram preparative scale. The developed bioprocess showed application potential for efficient preparation of vanillin from inexpensive natural resources.
Topics: Bacterial Proteins; Benzaldehydes; Eugenol; Mixed Function Oxygenases; Pseudomonas; Recombinant Proteins
PubMed: 33411131
DOI: 10.1007/s12010-020-03478-5