-
Journal of Bacteriology Jan 2007Mycobacterium vanbaalenii PYR-1 was the first bacterium isolated by virtue of its ability to metabolize the high-molecular-weight polycyclic aromatic hydrocarbon (PAH)...
Mycobacterium vanbaalenii PYR-1 was the first bacterium isolated by virtue of its ability to metabolize the high-molecular-weight polycyclic aromatic hydrocarbon (PAH) pyrene. We used metabolic, genomic, and proteomic approaches in this investigation to construct a complete and integrated pyrene degradation pathway for M. vanbaalenii PYR-1. Genome sequence analyses identified genes involved in the pyrene degradation pathway that we have proposed for this bacterium. To identify proteins involved in the degradation, we conducted a proteome analysis of cells exposed to pyrene using one-dimensional gel electrophoresis in combination with liquid chromatography-tandem mass spectrometry. Database searching performed with the M. vanbaalenii PYR-1 genome resulted in identification of 1,028 proteins with a protein false discovery rate of <1%. Based on both genomic and proteomic data, we identified 27 enzymes necessary for constructing a complete pathway for pyrene degradation. Our analyses indicate that this bacterium degrades pyrene to central intermediates through o-phthalate and the beta-ketoadipate pathway. Proteomic analysis also revealed that 18 enzymes in the pathway were upregulated more than twofold, as indicated by peptide counting when the organism was grown with pyrene; three copies of the terminal subunits of ring-hydroxylating oxygenase (NidAB2, MvanDraft_0817/0818, and PhtAaAb), dihydrodiol dehydrogenase (MvanDraft_0815), and ring cleavage dioxygenase (MvanDraft_3242) were detected only in pyrene-grown cells. The results presented here provide a comprehensive picture of pyrene metabolism in M. vanbaalenii PYR-1 and a useful framework for understanding cellular processes involved in PAH degradation.
Topics: Bacterial Proteins; Gas Chromatography-Mass Spectrometry; Gene Order; Genes, Bacterial; Genomics; Metabolic Networks and Pathways; Molecular Structure; Multigene Family; Mycobacterium; Proteomics; Pyrenes; Systems Biology
PubMed: 17085566
DOI: 10.1128/JB.01310-06 -
Xenobiotica; the Fate of Foreign... 20161. The polycyclic hydrocarbons (PAHs), pyrene, 1-hydroxypyrene, 1-nitropyrene and 1-acetylpyrene, were found to induce Type I binding spectra with human cytochrome P450...
1. The polycyclic hydrocarbons (PAHs), pyrene, 1-hydroxypyrene, 1-nitropyrene and 1-acetylpyrene, were found to induce Type I binding spectra with human cytochrome P450 (P450) 2A13 and were converted to various mono- and di-oxygenated products by this enzyme. 2. Pyrene was first oxidized by P450 2A13 to 1-hydroxypyrene which was further oxidized to di-oxygenated products, i.e. 1,8- and 1,6-dihydroxypyrene. Of five other human P450s examined, P450 1B1 catalyzed pyrene oxidation to 1-hydroxypyrene at a similar rate to P450 2A13 but was less efficient in forming dihydroxypyrenes. P450 2A6, a related human P450 enzyme, which did not show any spectral changes with these four PAHs, showed lower activities in oxidation of these compounds than P450 2A13. 3. 1-Nitropyrene and 1-acetylpyrene were also found to be efficiently oxidized by P450 2A13 to several oxygenated products, based on mass spectrometry analysis. 4. Molecular docking analysis supported preferred orientations of pyrene and its derivatives in the active site of P450 2A13, with lower interaction energies (U values) than observed for P450 2A6 and that several amino acid residues (including Ala-301, Asn-297 and Ala-117) play important roles in directing the orientation of these PAHs in the P450 2A13 active site. In addition, Phe-231 and Gly-329 were found to interact with pyrene to orient this compound in the active site of P450 1B1. 5. These results suggest that P450 2A13 is one of the important enzymes that oxidizes these PAH compounds and may determine how these chemicals are detoxicated and bioactivated in humans.
Topics: Animals; Aryl Hydrocarbon Hydroxylases; Cytochrome P-450 CYP1A1; Cytochrome P-450 CYP2A6; Humans; Lepidoptera; Models, Biological; Molecular Docking Simulation; Oxidation-Reduction; Polycyclic Compounds; Pyrenes
PubMed: 26247835
DOI: 10.3109/00498254.2015.1069419 -
Applied and Environmental Microbiology Oct 1997The degradation of phenanthrene and pyrene was investigated by using five different wood-decaying fungi. After 63 days of incubation in liquid culture, 13.8 and 4.3% of... (Comparative Study)
Comparative Study
The degradation of phenanthrene and pyrene was investigated by using five different wood-decaying fungi. After 63 days of incubation in liquid culture, 13.8 and 4.3% of the [ring U-14C]phenantherene and 2.4 and 1.4% of the [4,5,9,10-14C]pyrene were mineralized by Trametes versicolor and Kuehneromyces mutabilis, respectively. No 14CO2 evolution was detected in either [14C]phenanthrene or [14C]pyrene liquid cultures of Flammulina velutipes, Laetiporus sulphureus, and Agrocybe aegerita. Cultivation in straw cultures demonstrated that, in addition to T. versicolor (15.5%) and K. mutabilis (5.0%), L. sulphureus (10.7%) and A. aegerita (3.7%) were also capable of mineralizing phenanthrene in a period of 63 days. Additionally, K. mutabilis (6.7%), L. sulphureus (4.3%), and A. aegerita (3.3%) mineralized [14C]pyrene in straw cultures. The highest mineralization of [14C] pyrene was detected in straw cultures of T. versicolor (34.1%), which suggested that mineralization of both compounds by fungi may be independent of the number of aromatic rings. Phenanthrene and pyrene metabolites were purified by high-performance liquid chromatography and identified by UV absorption, mass, and 1H nuclear magnetic resonance spectrometry. Fungi capable of mineralizing phenanthrene and pyrene in liquid culture produced enriched metabolites substituted in the K region (C-9,10 position of phenanthrene and C-4,5 position of pyrene), whereas all other fungi investigated produced metabolites substituted in the C-1,2, C-3,4, and C-9,10 positions of phenanthrene and the C-1 position of pyrene.
Topics: Agaricales; Biodegradation, Environmental; Carbon Radioisotopes; Chromatography, High Pressure Liquid; Fungi; Kinetics; Magnetic Resonance Spectroscopy; Mass Spectrometry; Minerals; Phenanthrenes; Polyporaceae; Pyrenes; Wood
PubMed: 9327556
DOI: 10.1128/aem.63.10.3919-3925.1997 -
Ecotoxicology and Environmental Safety Jan 2024Microplastics (MP) are harmful, causing stress in aquatic species and acting as carriers of hydrophobicity. In aquatic environments, benzo[α]pyrene (BaP) is an...
Microplastics (MP) are harmful, causing stress in aquatic species and acting as carriers of hydrophobicity. In aquatic environments, benzo[α]pyrene (BaP) is an endocrine-disrupting chemical that accumulates in the body and causes toxic reactions in living organisms. We investigated the effects of single and combined microbead (MB) and BaP environments on goldfish antioxidant response and apoptosis. For 120 h, goldfish were exposed to single (MB10, MB100, and BaP5) and combined (MB10+BaP5 and MB100+BaP5) environments of 10 and 100 beads/L of 0.2 µm polystyrene MB and 5 µg/L BaP. We measured MB and BaP bioaccumulation as well as plasma parameters including ALT, AST, and glucose. The level of oxidative stress was determined by evaluating lipid peroxidation (LPO) and total antioxidant capacity (TAC) in plasma, as well as antioxidant-related genes for superoxide dismutase and catalase (SOD and CAT) and caspase-3 (Casp3) mRNA expression in liver tissue. The TUNEL assay was used to examine SOD in situ hybridization and apoptosis in goldfish livers. Except for the control group, plasma LPO levels increased at the end of the exposure period in all experimental groups. TAC increased up to 24 h of exposure and then maintained a similar level until the trial ended. SOD, CAT, and Casp3 mRNA expression increased substantially up to 120 h as the exposure concentration and time increased. The TUNEL assay revealed more signals and apoptotic signals in the combined exposure environments as a consequence of SOD in situ hybridization than in single exposure environments. These results suggest that combined exposure to toxic substances causes oxidative stress in organisms, which leads to apoptosis.
Topics: Animals; Antioxidants; Goldfish; Benzo(a)pyrene; Caspase 3; Polystyrenes; Bioaccumulation; Microspheres; Plastics; Catalase; Oxidative Stress; Liver; Superoxide Dismutase; RNA, Messenger; Pyrenes
PubMed: 38101975
DOI: 10.1016/j.ecoenv.2023.115825 -
Nucleic Acids Research Apr 2020Guanine-rich regions of the human genome can adopt non-canonical secondary structures. Their role in regulating gene expression has turned them into promising targets...
Guanine-rich regions of the human genome can adopt non-canonical secondary structures. Their role in regulating gene expression has turned them into promising targets for therapeutic intervention. Ligands based on polyaromatic moieties are especially suitable for targeting G-quadruplexes utilizing their size complementarity to interact with the large exposed surface area of four guanine bases. A predictable way of (de)stabilizing specific G-quadruplex structures through efficient base stacking of polyaromatic functional groups could become a valuable tool in our therapeutic arsenal. We have investigated the effect of pyrene-modified uridine nucleotides incorporated at several positions of the thrombin binding aptamer (TBA) as a model system. Characterization using spectroscopic and biophysical methods provided important insights into modes of interaction between pyrene groups and the G-quadruplex core as well as (de)stabilization by enthalpic and entropic contributions. NMR data demonstrated that incorporation of pyrene group into G-rich oligonucleotide such as TBA may result in significant changes in 3D structure such as formation of novel dimeric topology. Site specific structural changes induced by stacking of the pyrene moiety on nearby nucleobases corelate with distinct thrombin binding affinities and increased resistance against nuclease degradation.
Topics: Aptamers, Nucleotide; Deoxyribonucleases; Dimerization; Entropy; G-Quadruplexes; Humans; Pyrenes; Thermodynamics; Thrombin; Uracil Nucleotides
PubMed: 32095808
DOI: 10.1093/nar/gkaa118 -
Environmental Pollution (Barking, Essex... Feb 2020Coal mining activities may increase residential exposure to polycyclic aromatic hydrocarbons (PAHs), but personal PAH exposures have not been studied in mining areas. We...
Coal mining activities may increase residential exposure to polycyclic aromatic hydrocarbons (PAHs), but personal PAH exposures have not been studied in mining areas. We used silicone wristbands as passive personal samplers to estimate PAH exposures in coal mining communities in Central Appalachia in the United States. Adults (N = 101) wore wristbands for one week; 51 resided in communities within approximately three miles of surface mining sites, and 50 resided 10 or more miles from mining sites. Passive indoor polyurethane foam (PUF) sampling was conducted in residents' homes, and a sample of 16 outdoor PUF samples were also collected. Nine PAH congeners were commonly detected in wristbands (mean ± standard deviation), including phenanthrene (50.2 ± 68.7 ng/g), benz[a]anthracene (20.2 ± 58.2 ng/g), fluoranthene (19.4 ± 24.1 ng/g) and pyrene (15.2 ± 18.2 ng/g). Controlling for participant characteristics and season, participants living closer to mining sites had significantly higher levels of phenanthrene, fluorene, fluoranthene, pyrene and ∑PAHs in wristbands compared to participants living farther from mining. Indoor air showed no significant group differences except for pyrene, but outdoor air showed significant or marginally significant differences for phenanthrene, fluorene, pyrene and ∑PAHs. The results suggest that mining community residents face exposure to outdoor mining-related pollutants, and demonstrate that personal silicone wristbands can be deployed as effective passive sampling devices.
Topics: Adult; Air Pollutants; Appalachian Region; Environmental Exposure; Environmental Monitoring; Environmental Pollutants; Fluorenes; Humans; Mining; Phenanthrenes; Polycyclic Aromatic Hydrocarbons; Pyrenes; Seasons
PubMed: 31706774
DOI: 10.1016/j.envpol.2019.113501 -
Environmental Toxicology and Chemistry Apr 2011The effects of loading and aging pyrene in soils in the presence of four environmentally common nonaqueous-phase liquids (NAPLs) (hexadecane,...
Effects of aging and mixed nonaqueous-phase liquid sources in soil systems on earthworm bioaccumulation, microbial degradation, sequestration, and aqueous desorption of pyrene.
The effects of loading and aging pyrene in soils in the presence of four environmentally common nonaqueous-phase liquids (NAPLs) (hexadecane, 2,2,4,4,6,8,8-heptamethylnonane [HMN], toluene, and dimethyl phthalate [DMP]) on its subsequent desorption from those soils, earthworm accumulation, biodegradation, and extractability were tested by using two dissimilar soils. The presence of each of the four NAPLs increased fractions and rates of pyrene desorption, and hexadecane slowed the effects of aging on these same parameters. Loading with hexadecane and HMN caused earthworm accumulation of pyrene to decrease. These results contrast with generally observed faster desorption rates resulting from NAPL addition, suggesting that additional factors (e.g., association of pyrene with NAPL phases and NAPL toxicities to earthworms) may impact bioaccumulation. The presence of HMN and toluene increased pyrene biodegradation, whereas hexadecane and DMP had the opposite effects. These results correlate with changes in the extractability of pyrene from the soils. After aging and biodegradation, hexadecane and DMP substantially increased pyrene residues extractable by methanol and decreased nonextractable fractions, whereas HMN and toluene had the opposite effects.
Topics: Adsorption; Alkanes; Animals; Biodegradation, Environmental; Hydrocarbons; Oligochaeta; Phthalic Acids; Pyrenes; Soil Microbiology; Soil Pollutants; Toluene
PubMed: 21309023
DOI: 10.1002/etc.470 -
Chemistry (Weinheim An Der Bergstrasse,... Dec 2022Purine-2,6-diamine and 8-aza-7-deaza-7-bromopurine-2,6-diamine 2'-deoxyribonucleosides (1 and 2) were implemented in isothermal DNA strand displacement reactions....
DNA Strand Displacement with Base Pair Stabilizers: Purine-2,6-Diamine and 8-Aza-7-Bromo-7-Deazapurine-2,6-Diamine Oligonucleotides Invade Canonical DNA and New Fluorescent Pyrene Click Sensors Monitor the Reaction.
Purine-2,6-diamine and 8-aza-7-deaza-7-bromopurine-2,6-diamine 2'-deoxyribonucleosides (1 and 2) were implemented in isothermal DNA strand displacement reactions. Nucleoside 1 is a weak stabilizer of dA-dT base pairs, nucleoside 2 evokes strong stabilization. Strand displacement reactions used single-stranded invaders with single and multiple incorporations of stabilizers. Displacement is driven by negative enthalpy changes between target and displaced duplex. Toeholds are not required. Two new environmental sensitive fluorescent pyrene sensors were developed to monitor the progress of displacement reactions. Pyrene was connected to the nucleobase in the invader or to a dendritic linker in the output strand. Both new sensors were constructed by click chemistry; phosphoramidites and oligonucleotides were prepared. Sensors show monomer or excimer emission. Fluorescence intensity changes when the displacement reaction progresses. Our work demonstrates that strand displacement with base pair stabilizers is applicable to DNA, RNA and to related biopolymers with applications in chemical biology, nanotechnology and medicinal diagnostics.
Topics: Oligonucleotides; Base Pairing; Nucleosides; DNA; Purines; Coloring Agents; Pyrenes
PubMed: 36178316
DOI: 10.1002/chem.202202412 -
Scientific Reports Aug 2022Biodegradation of high-molecular-weight petroleum hydrocarbons in saline conditions appears to be complicated and requires further investigation. This study used heavy...
Biodegradation of high-molecular-weight petroleum hydrocarbons in saline conditions appears to be complicated and requires further investigation. This study used heavy crude oil to enrich petroleum-degrading bacteria from oil-contaminated saline soils. Strain HG 01, with 100% sequence similarity to Bacillus subtilis, grew at a wide range of salinities and degraded 55.5 and 77.2% of 500 mg/l pyrene and 500 mg/l tetracosane, respectively, at 5% w/v NaCl. Additionally, a mixed-culture of HG 01 with Pseudomonas putida and Pseudomonas aeruginosa, named TMC, increased the yield of pyrene, and tetracosane degradation by about 20%. Replacing minimal medium with treated seawater (C/N/P adjusted to 100/10/1) enabled TMC to degrade more than 99% of pyrene and tetracosane, but TMC had lesser degradation in untreated seawater than in minimal medium. Also, the degradation kinetics of pyrene and tetracosane were fitted to a first-order model. Compared to B. subtilis, TMC increased pyrene and tetracosane's removal rate constant (K) from 0.063 and 0.110 per day to 0.123 and 0.246 per day. TMC also increased the maximum specific growth rate of B. subtilis, P. putida, and P. aeruginosa, respectively, 45% higher in pyrene, 24.5% in tetracosane, and 123.4% and 95.4% higher in pyrene and tetracosane.
Topics: Bacillus subtilis; Biodegradation, Environmental; Hydrocarbons; Molecular Weight; Petroleum; Pseudomonas; Pseudomonas aeruginosa; Pyrenes
PubMed: 35918482
DOI: 10.1038/s41598-022-17001-9 -
Biophysical Journal Feb 2004Here we have studied how the length of the pyrene-labeled acyl chain (n) of a phosphatidylcholine, sphingomyelin, or galactosylceramide affects the partitioning of these...
Here we have studied how the length of the pyrene-labeled acyl chain (n) of a phosphatidylcholine, sphingomyelin, or galactosylceramide affects the partitioning of these lipids between 1), gel and fluid domains coexisting in bovine brain sphingomyelin (BB-SM) or BB-SM/spin-labeled phosphatidylcholine (PC) bilayers or 2), between liquid-disordered and liquid-ordered domains in BB-SM/spin-labeled PC/cholesterol bilayers. The partitioning behavior was deduced either from modeling of pyrene excimer/monomer ratio versus temperature plots, or from quenching of the pyrene monomer fluorescence by spin-labeled PC. New methods were developed to model excimer formation and pyrene lipid quenching in segregated bilayers. The main result is that partition to either gel or liquid-ordered domains increased significantly with increasing length of the labeled acyl chain, probably because the pyrene moiety attached to a long chain perturbs these ordered domains less. Differences in partitioning were also observed between phosphatidylcholine, sphingomyelin, and galactosylceramide, thus indicating that the lipid backbone and headgroup-specific properties are not severely masked by the pyrene moiety. We conclude that pyrene-labeled lipids could be valuable tools when monitoring domain formation in model and biological membranes as well as when assessing the role of membrane domains in lipid trafficking and sorting.
Topics: Fluorometry; Lipid Bilayers; Liposomes; Macromolecular Substances; Membrane Fluidity; Membrane Microdomains; Models, Chemical; Molecular Conformation; Phase Transition; Phospholipids; Pyrenes; Sphingolipids; Staining and Labeling; Temperature
PubMed: 14747328
DOI: 10.1016/S0006-3495(04)74168-5