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Microbial Genomics Mar 2021is one of the main microbial species colonizing the lungs of cystic fibrosis patients and is responsible for the decline in respiratory function. Despite the hostile... (Review)
Review
is one of the main microbial species colonizing the lungs of cystic fibrosis patients and is responsible for the decline in respiratory function. Despite the hostile pulmonary environment, is able to establish chronic infections thanks to its strong adaptive capacity. Various longitudinal studies have attempted to compare the strains of early infection with the adapted strains of chronic infection. Thanks to new '-omics' techniques, convergent genetic mutations, as well as transcriptomic and proteomic dysregulations have been identified. As a consequence of this evolution, the adapted strains of have particular phenotypes that promote persistent infection.
Topics: Adaptation, Physiological; Animals; Cystic Fibrosis; Genotype; Humans; Phenotype; Pseudomonas Infections; Pseudomonas aeruginosa
PubMed: 33529147
DOI: 10.1099/mgen.0.000513 -
Journal of Applied Microbiology Jan 2023The study systematically compared the N2O-reducing functional performances and the genomic features of two N2O-reducing isolates, aimed to screen out effective...
AIM
The study systematically compared the N2O-reducing functional performances and the genomic features of two N2O-reducing isolates, aimed to screen out effective N2O-reducing bacteria with strong environmental adaption, and explore the possible regulation.
METHODS AND RESULTS
Two N2O reducers, namely, Pseudomonas veronii DM15 (DM15) and Pseudomonas frederiksbergensis DM22 (DM22), isolated from paddy soil were selected. Their N2O-reducing abilities, and nosZ gene transcript abundance were determined under different temperatures (20°C, 30°C, 40°C) and oxygen concentrations (0%, 10%, 21%), and the whole genomes were sequenced by Illumina sequencing. The results showed that both DM15 and DM22 exhibited the strongest N2O reducing activity at 30°C and under anaerobic conditions. In comparison, DM15 generally exhibited significantly higher N2O reducing abilities and nosZ gene expression than DM22 under all tested conditions. In addition, DM15 possessed obviously higher expression potentials (codon adaptation index (CAI) value) of nos genes than DM22, and the nos cluster of the former contained a transcriptional regulator gene of dnr, while the latter did not.
CONCLUSIONS
The results indicate that DM15 showed obviously stronger N2O-reducing abilities than DM22 under various conditions, which might be closely associated with its dnr transcriptional regulator, and thus promoting the higher transcriptional activities of nos genes. Although anaerobic conditions were the optimal conditions for N2O reduction in both strains, DM15 still reduced a certain amount of N2O even under aerobic conditions.
Topics: Bacteria; Pseudomonas; Denitrification; Soil Microbiology
PubMed: 36626739
DOI: 10.1093/jambio/lxac011 -
Applied and Environmental Microbiology Oct 2023Coumarin (COU) is both a naturally derived phytotoxin and a synthetic pollutant which causes hepatotoxicity in susceptible humans. Microbes have potentials in COU...
Coumarin (COU) is both a naturally derived phytotoxin and a synthetic pollutant which causes hepatotoxicity in susceptible humans. Microbes have potentials in COU biodegradation; however, its underlying genetic determinants remain unknown. sp. strain NyZ480, a robust COU degrader, has been isolated and proven to grow on COU as its sole carbon source. In this study, five homologs of xenobiotic reductase A scattered throughout the chromosome of strain NyZ480 were identified, which catalyzed the conversion of COU to dihydrocoumarin (DHC) . Phylogenetic analysis indicated that these COU reductases belong to different subgroups of the old yellow enzyme family. Moreover, two hydrolases (CouB1 and CouB2) homologous to the 3,4-dihydrocoumarin hydrolase in the fluorene degradation were found to accelerate the generation of melilotic acid (MA) from DHC. CouC, a new member from the group A flavin monooxygenase, was heterologously expressed and purified, catalyzing the hydroxylation of MA to produce 3-(2,3-dihydroxyphenyl)propionate (DHPP). Gene deletion and complementation of indicated that played an essential role in the COU catabolism in strain NyZ480, considering that the genes involved in the downstream catabolism of DHPP have been characterized (Y. Xu and N. Y. Zhou, Appl Environ Microbiol 86:e02385-19, 2020) and homologous catabolic cluster exists in strain NyZ480. This study elucidated the genetic determinants for complete degradation of COU by sp. strain NyZ480.IMPORTANCECoumarin (COU) is a phytochemical widely distributed in the plant kingdom and also artificially produced as an ingredient for personal care products. Hence, the environmental occurrence of COU has been reported in different places. Toxicologically, COU was proven hepatotoxic to individuals with mutations in the CYP2A6 gene and listed as a group 3 carcinogen by the International Agency for Research on Cancer and thus has raised increasing concerns. Until now, different physicochemical methods have been developed for the removal of COU, whereas their practical applications were hampered due to high cost and the risk of secondary contamination. In this study, genetic evidence and biochemical characterization of the COU degradation by sp. strain NyZ480 are presented. With the gene and strain resources provided here, better managements of the hazards that humans face from COU could be achieved, and the possible microbiota-plant interaction mediated by the COU-utilizing rhizobacteria could also be investigated.
Topics: Humans; Pseudomonas; Phylogeny; Mixed Function Oxygenases; Biodegradation, Environmental; Coumarins
PubMed: 37815346
DOI: 10.1128/aem.01109-23 -
Nucleic Acids Research Oct 2021H-NS family proteins, bacterial xenogeneic silencers, play central roles in genome organization and in the regulation of foreign genes. It is thought that gene...
H-NS family proteins, bacterial xenogeneic silencers, play central roles in genome organization and in the regulation of foreign genes. It is thought that gene repression is directly dependent on the DNA binding modes of H-NS family proteins. These proteins form lateral protofilaments along DNA. Under specific environmental conditions they switch to bridging two DNA duplexes. This switching is a direct effect of environmental conditions on electrostatic interactions between the oppositely charged DNA binding and N-terminal domains of H-NS proteins. The Pseudomonas lytic phage LUZ24 encodes the protein gp4, which modulates the DNA binding and function of the H-NS family protein MvaT of Pseudomonas aeruginosa. However, the mechanism by which gp4 affects MvaT activity remains elusive. In this study, we show that gp4 specifically interferes with the formation and stability of the bridged MvaT-DNA complex. Structural investigations suggest that gp4 acts as an 'electrostatic zipper' between the oppositely charged domains of MvaT protomers, and stabilizes a structure resembling their 'half-open' conformation, resulting in relief of gene silencing and adverse effects on P. aeruginosa growth. The ability to control H-NS conformation and thereby its impact on global gene regulation and growth might open new avenues to fight Pseudomonas multidrug resistance.
Topics: Bacterial Proteins; DNA; DNA-Binding Proteins; Gene Expression Regulation, Bacterial; Gene Silencing; Models, Molecular; Protein Binding; Pseudomonas; Pseudomonas Phages; Trans-Activators; Viral Proteins
PubMed: 34520554
DOI: 10.1093/nar/gkab793 -
International Journal of Systematic and... Jun 2020Strains of a Gram-negative, aerobic, rod-shaped, non-spore-forming bacterium, designated MY50, MY63 and MY101, were isolated from wound samples of three hospitalized...
Strains of a Gram-negative, aerobic, rod-shaped, non-spore-forming bacterium, designated MY50, MY63 and MY101, were isolated from wound samples of three hospitalized patients in Yangon, Myanmar. Strains MY50, MY63 and MY101 grew at temperatures of 4-44 °C, in media containing 1.0-7.0 % (w/v) NaCl and at pH 6.0-9.5. Phylogenetic analysis based on 16S rRNA gene and whole genome sequences showed that these strains belonged to the genus and were part of the group and located close to and . Whole-genome comparisons, using average nucleotide identity and digital DNA-DNA hybridization analyses, confirmed that strains MY50, MY63 and MY101 were the same strain and they were a distinct species in the group. Results of phenotypic characterization tests demonstrated that utilization of p-hydroxy-phenylacetic acid, glycerol, l-pyroglutamic acid and quinic acid could distinguish these strains from other species of the group. These genetic and phenotypic characteristics suggest that they should be classified as representing a novel species, under the proposed name sp. nov. The type strain is MY50 (=LMG 31602,=JCM 33396), with a DNA G+C content of 62.82 mol%.
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Hospitals; Humans; Myanmar; Nucleic Acid Hybridization; Phylogeny; Pseudomonas; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Wounds and Injuries
PubMed: 32501786
DOI: 10.1099/ijsem.0.004181 -
Applied and Environmental Microbiology Mar 2020Microbial degradation of lignin and its related aromatic compounds has great potential for the sustainable production of chemicals and bioremediation of contaminated...
Microbial degradation of lignin and its related aromatic compounds has great potential for the sustainable production of chemicals and bioremediation of contaminated soils. We previously isolated sp. strain 9.1 from historical waste deposits (forming so-called fiber banks) released from pulp and paper mills along the Baltic Sea coast. The strain accumulated vanillyl alcohol during growth on vanillin, and while reported in other microbes, this phenotype is less common in wild-type pseudomonads. As the reduction of vanillin to vanillyl alcohol is an undesired trait in strains engineered to accumulate vanillin, connecting the strain 9.1 phenotype with a genotype would increase the fundamental understanding and genetic engineering potential of microbial vanillin metabolism. The genome of sp. 9.1 was sequenced and assembled. Annotation identified oxidoreductases with homology to alcohol dehydrogenase ADH6p, known to reduce vanillin to vanillyl alcohol, in both the 9.1 genome and the model strain KT2440. Recombinant expression of the sp. 9.1 FEZ21_09870 and KT2440 PP_2426 () genes in revealed that these open reading frames encode aldehyde reductases that convert vanillin to vanillyl alcohol, and that KT2440 PP_3839 encodes a coniferyl alcohol dehydrogenase that oxidizes coniferyl alcohol to coniferyl aldehyde (i.e., the function previously assigned to ). The deletion of PP_2426 in GN442 engineered to accumulate vanillin resulted in a decrease in by-product (vanillyl alcohol) yield from 17% to ∼1%. Based on these results, we propose the reannotation of PP_2426 and FEZ21_09870 as and PP_3839 as Valorization of lignocellulose (nonedible plant matter) is of key interest for the sustainable production of chemicals from renewable resources. Lignin, one of the main constituents of lignocellulose, is a heterogeneous aromatic biopolymer that can be chemically depolymerized into a heterogeneous mixture of aromatic building blocks; those can be further converted by certain microbes into value-added aromatic chemicals, e.g., the flavoring agent vanillin. We previously isolated a sp. strain with the (for the genus) unusual trait of vanillyl alcohol production during growth on vanillin. Whole-genome sequencing of the isolate led to the identification of a vanillin reductase candidate gene whose deletion in a recombinant vanillin-accumulating strain almost completely alleviated the undesired vanillyl alcohol by-product yield. These results represent an important step toward biotechnological production of vanillin from lignin using bacterial cell factories.
Topics: Bacterial Proteins; Benzaldehydes; Molecular Sequence Annotation; Oxidoreductases; Pseudomonas; Pseudomonas putida; Whole Genome Sequencing
PubMed: 31924622
DOI: 10.1128/AEM.02442-19 -
International Journal of Environmental... Dec 2021The aim of this study was to characterize 59 strains isolated from soil samples in terms of Inducible Beta-Lactamase (IBL), fluorescence production, antibiotic...
The aim of this study was to characterize 59 strains isolated from soil samples in terms of Inducible Beta-Lactamase (IBL), fluorescence production, antibiotic resistance, presence of plasmids and genetic diversity, as well as denitrification functional genes. Fourteen out of fifty-nine (23.7%) isolates were identified as multidrug-resistant. To evaluate the contribution of denitrification functional genes to genetic diversity, PCR products were screened by RFLP. It was determined that the 18, 6 and 22 out of 59 isolate harbored and genes, respectively. It was found that the 37 isolates were -negative. Thus, these results suggest that gene-missing pseudomonad denitrifiers are partly contribute to NO emission. Moreover, and genes were found to be positive with IBL and negatively correlated with fluorescence production. These results suggest that species have important roles in soil and even in biosphere due to their diversity and genetic factors.
Topics: Anti-Bacterial Agents; Denitrification; Drug Resistance, Multiple, Bacterial; Fluorescent Dyes; Genes, Bacterial; Genetic Variation; Plasmids; Pseudomonas; Soil Microbiology; beta-Lactamases
PubMed: 31994901
DOI: 10.1080/09603123.2020.1720619 -
MBio Feb 2021Plants form commensal associations with soil microorganisms, creating a root microbiome that provides benefits, including protection against pathogens. While bacteria...
Plants form commensal associations with soil microorganisms, creating a root microbiome that provides benefits, including protection against pathogens. While bacteria can inhibit pathogens through the production of antimicrobial compounds , it is largely unknown how microbiota contribute to pathogen protection . We developed a gnotobiotic model consisting of Arabidopsis thaliana and the opportunistic pathogen Pseudomonas sp. N2C3, to identify mechanisms that determine the outcome of plant-pathogen-microbiome interactions in the rhizosphere. We screened 25 phylogenetically diverse Pseudomonas strains for their ability to protect against N2C3 and found that commensal strains closely related to N2C3, including Pseudomonas sp. WCS365, were more likely to protect against pathogenesis. We used comparative genomics to identify genes unique to the protective strains and found no genes that correlate with protection, suggesting that variable regulation of components of the core Pseudomonas genome may contribute to pathogen protection. We found that commensal colonization level was highly predictive of protection, so we tested deletions in genes required for rhizosphere colonization. We identified a response regulator , and two ColR-dependent genes with predicted roles in membrane modifications ( and ), that are required for Pseudomonas-mediated protection from N2C3. We found that WCS365 also protects against the agricultural pathogen Pseudomonas fuscovaginae SE-1, the causal agent of bacterial sheath brown rot of rice, in a ColR-dependent manner. This work establishes a gnotobiotic model to uncover mechanisms by which members of the microbiome can protect hosts from pathogens and informs our understanding of the use of beneficial strains for microbiome engineering in dysbiotic soil systems. Microbiota can protect diverse hosts from pathogens, and microbiome dysbiosis can result in increased vulnerability to opportunistic pathogens. Here, we developed a rhizosphere commensal-pathogen model to identify bacterial strains and mechanisms that can protect plants from an opportunistic Pseudomonas pathogen. Our finding that protective strains are closely related to the pathogen suggests that the presence of specific microbial taxa may help protect plants from disease. We found that commensal colonization level was highly correlated with protection, suggesting that competition with pathogens may play a role in protection. As we found that commensal Pseudomonas were also able to protect against an agricultural pathogen, this system may be broadly relevant for identifying strains and mechanisms to control agriculturally important pathogens. This work also suggests that beneficial plant-associated microbes may be useful for engineering soils where microbial complexity is low, such as hydroponic, or disturbed agricultural soils.
Topics: Arabidopsis; Pseudomonas fluorescens; Pseudomonas; Soil; Plant Roots; Transcription Factors
PubMed: 35100865
DOI: 10.1128/mbio.02892-21 -
Journal of Hazardous Materials Apr 2023Biogenic manganese oxides (BMO) are widely distributed in groundwater and provides promise for adsorbing and oxidizing a wide range of micropollutants, however, the...
Biogenic manganese oxides (BMO) are widely distributed in groundwater and provides promise for adsorbing and oxidizing a wide range of micropollutants, however, the continuous biodegradation and bioavailability of micropollutants via cycle biogenic Mn(II) oxidation remains to be elucidated. In this study, glyphosate was degraded and to serve as the nutrient source by a Pseudomonas sp. QJX-1. The addition of glyphosate will not affect the Mn(II) oxidation function of the strain but will affect its Mn(II) oxidation process and effect. The glyphosate degradation products could further be used as the C, N and P sources for bacterium growth. Analysis of the RNA-seq data suggested that Mn(II) oxidation driven by oxidoreductases for glyphosate degradation. The long-term column experiments using biological Mn(II) cycling to realize continuous detoxification and metabolism of glyphosate, and thus revealed the synergism effects of biological and chemical conversion on toxic micropollutants and continuous metabolism in an aquatic ecosystem.
Topics: Manganese; Pseudomonas; Ecosystem; Oxidation-Reduction; Oxides; Manganese Compounds; Glyphosate
PubMed: 36731313
DOI: 10.1016/j.jhazmat.2023.130902 -
Applied Microbiology and Biotechnology Feb 2021The heat-stable peptidase AprX, secreted by psychrotolerant Pseudomonas species in raw milk, is a major cause of destabilization and premature spoilage of ultra-high...
The heat-stable peptidase AprX, secreted by psychrotolerant Pseudomonas species in raw milk, is a major cause of destabilization and premature spoilage of ultra-high temperature (UHT) milk and milk products. To enable rapid detection and quantification of seven frequent and proteolytic Pseudomonas species (P. proteolytica, P. gessardii, P. lactis, P. fluorescens, P. protegens, P. lundensis, and P. fragi) in raw milk, we developed two triplex qPCR assays taking into account species-dependent differences in AprX activity. Besides five species-specific hydrolysis probes, targeting the aprX gene, a universal rpoB probe was included in the assay to determine the total Pseudomonas counts. For all six probes, linear regression lines between C value and target DNA concentration were obtained in singleplex as well as in multiplex approaches, yielding R values of > 0.975 and amplification efficiencies of 85-97%. Moreover, high specificity was determined using genomic DNA of 75 Pseudomonas strains, assigned to 57 species, and 40 other bacterial species as templates in the qPCR. Quantification of the target species and total Pseudomonas counts resulted in linear detection ranges of approx. 10-10 cfu/ml, which correspond well to common Pseudomonas counts in raw milk. Application of the assay using 60 raw milk samples from different dairies showed good agreement of total Pseudomonas counts calculated by qPCR with cell counts derived from cultivation. Furthermore, a remarkably high variability regarding the species composition was observed for each milk sample, whereby P. lundensis and P. proteolytica/P. gessardii were the predominant species detected. KEY POINTS: • Multiplex qPCR for quantification of seven proteolytic Pseudomonas species and total Pseudomonas counts in raw milk • High specificity and sensitivity via hydrolysis probes against aprX and rpoB • Rapid method to determine Pseudomonas contamination in raw milk and predict spoilage potential.
Topics: Animals; Hot Temperature; Milk; Peptide Hydrolases; Proteolysis; Pseudomonas
PubMed: 33527148
DOI: 10.1007/s00253-021-11109-0