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Journal of Inorganic Biochemistry Nov 2018A strategy for elucidating sequence determinants of function in the class of cytochrome P450 (CYP) enzymes that catalyze the first steps of terpene metabolism in wild...
A strategy for elucidating sequence determinants of function in the class of cytochrome P450 (CYP) enzymes that catalyze the first steps of terpene metabolism in wild microbiomes is described. Wild organisms that can use camphor, terpineol, pinene and limonene were isolated from soils rich in coniferous waste. Cell free extracts and growth beers were analyzed by gas chromatography/mass spectrometry to identify primary oxidative metabolites. For one organism, Pseudomonas nitroreducens TPJM, a cytochrome P450 (CYP108B1) isolated from cell free extracts was demonstrated to catalyze the oxidation of α-terpineol in assays combining the native ferredoxin and putidaredoxin reductase, and the resulting oxidation products identified by gas chromatography/mass spectrometry. Shotgun sequencing of PnTPJM identified four candidate P450 genes, including an apparently fragmentary gene with a high degree of homology with the known enzyme CYP108 (P450).
Topics: Bacterial Proteins; Cytochrome P-450 Enzyme System; Pseudomonas; Soil Microbiology; Terpenes
PubMed: 30170307
DOI: 10.1016/j.jinorgbio.2018.08.006 -
Scientific Reports May 2019Bacteria in the environment play a major role in the degradation of widely used man-made recalcitrant organic compounds. Pseudomonas nitroreducens TX1 is of special...
Bacteria in the environment play a major role in the degradation of widely used man-made recalcitrant organic compounds. Pseudomonas nitroreducens TX1 is of special interest because of its high efficiency to remove nonionic ethoxylated surfactants. In this study, a novel approach was demonstrated by a bacterial enzyme involved in the formation of radicals to attack ethoxylated surfactants. The dihydrolipoamide dehydrogenase was purified from the crude extract of strain TX1 by using octylphenol polyethoxylate (OPEO) as substrate. The extent of removal of OPEOs during the degradation process was conducted by purified recombinant enzyme from E. coli BL21 (DE3) in the presence of the excess of metal mixtures (Mn, Mg, Zn, and Cu). The metabolites and the degradation rates were analyzed and determined by liquid chromatography-mass spectrometry. The enzyme was demonstrated to form Fenton reagent in the presence of an excess of metals. Under this in vitro condition, it was shown to be able to shorten the ethoxylate chains of OPEO. After 2 hours of reaction, the products obtained from the degradation experiment revealed a prominent ion peak at m/z = 493.3, namely the ethoxylate chain unit is 6 (OPEO) compared to OPEO (m/z = 625.3), the main undegraded surfactant in the no enzyme control. It revealed that the concentration of OPEO and OPEO decreased by 90% and 40% after 4 hours, respectively. The disappearance rates for the OPEO homologs correlated to the length of the exothylate chains, suggesting it is not a specific enzymatic reaction which cleaves one unit by unit from the end of the ethoxylate chain. The results indicate the diverse and novel strategy by bacteria to catabolize organic compounds by using existing housekeeping enzyme(s).
Topics: Bacterial Proteins; Chromatography, Liquid; Copper; Dihydrolipoamide Dehydrogenase; Escherichia coli; Magnesium; Manganese; Mass Spectrometry; Phenols; Pseudomonas; Surface-Active Agents; Zinc
PubMed: 31048711
DOI: 10.1038/s41598-019-43266-8 -
Chinese Medicine Nov 2021Codonopsis pilosula, an important medicinal plant, can accumulate certain metabolites under moderate drought stress. Endophytes are involved in the metabolite...
BACKGROUND
Codonopsis pilosula, an important medicinal plant, can accumulate certain metabolites under moderate drought stress. Endophytes are involved in the metabolite accumulations within medicinal plants. It is still unknown that the endophytes of C. pilosula are associated with the accumulations of metabolites. This study aims to investigate the promoting effect of endophytes on the accumulations of active substances in C. pilosula under drought stress.
METHODS
High-performance liquid chromatography and high-throughput sequencing technology were performed to investigate changes in the contents of secondary metabolite and endophyte abundances of C. pilosula under drought stress, respectively. Spearman's correlation analysis was further conducted to identify the endophytic biomarkers related to accumulations of pharmacodynamic compounds. Culture-dependent experiments were performed to confirm the functions of endophytes in metabolite accumulations.
RESULTS
The distribution of pharmacological components and diversity and composition of endophytes showed tissue specificity within C. pilosula. The contents of lobetyolin, syringin, and atractylolide III in C. pilosula under drought stress were increased by 8.47%‒86.47%, 28.78%‒230.98%, and 32.17%‒177.86%, respectively, in comparison with those in untreated groups. The Chao 1 and Shannon indices in different parts of drought-stressed C. pilosula increased compared with those in untreated parts. The composition of endophytic communities in drought treatment parts of C. pilosula was different from that in control parts. A total of 226 microbial taxa were identified as potential biomarkers, of which the abundances of 42 taxa were significantly and positively correlated to the pharmacodynamic contents. Culture-dependent experiments confirmed that the contents of lobetyolin and atractylolide III were increased by the application of Epicoccum thailandicum, Filobasidium magnum, and Paraphoma rhaphiolepidis at the rates of 11.12%‒46.02%, and that the content of syringin was increased by Pseudomonas nitroreducens at the rates of 118.61%‒119.36%.
CONCLUSIONS
Certain endophytes participated in the accumulations of bioactive metabolites, which provided a scientific evidence for the development and application of microorganisms to improve the quality of traditional Chinese medicine.
PubMed: 34809641
DOI: 10.1186/s13020-021-00533-z -
Genomics Data Dec 2017. DF05 is a Gram negative, motile, aerobic, rod-shaped and psychrotrophic bacterium that was isolated from contaminated San Jacinto River sediment near River Terrace...
. DF05 is a Gram negative, motile, aerobic, rod-shaped and psychrotrophic bacterium that was isolated from contaminated San Jacinto River sediment near River Terrace Park in Channelview, Texas. The draft genome of strain DF05 consists of a total of 192 contigs assembled at the scaffold level totaling 6,487,527 bp and encoding for 5862 functional proteins, 1116 of which are annotated as hypothetical proteins. The bacterial chromosome has a GC content of 65.15% and contains 22 rRNA and 70 tRNA loci. In addition, approximately 142 proteins localized on the bacterial chromosome are associated with metabolism of aromatic compounds. A single plasmid approximately 95 kb in size was also detected carrying copies of RNA genes and multiple phage assembly proteins.
PubMed: 28856100
DOI: 10.1016/j.gdata.2017.07.011