ABSTRACT: Unusual gram negative bacterium that has glycosphingolipid instead of lipopolysaccharide and can degrade a wide variety of aromatic hydrocarbons
Project description:Aromatic diketones are a major product of formic acid lignin depolymerization. Novosphingobium aromaticivorans can degrade these diketones, but the enzymes used in this process were unknown. We used RNA-Seq to identify aromatic dimer dehydrogenases as potential candidates for the initial reduction of the aromatic G-diketone, then verified this using in vitro enzyme assays.
Project description:Cytochrome P450 enzymes catalyze a variety of reactions and are widely distributed in living organisms. In recent studies, the first members of five new families of cytochrome P450 enzymes have been identified, including cytochrome P450 219A1 (CYP219A1) from Novosphingobium aromaticivorans DSM 12444. It has also been reported that isolongifolen-9-one (C(15)H(22)O), a sesquiterpenoid ketone derivative, is a potential substrate for CYP219A1, inducing a >or=95% shift of the haem spin state to high spin upon binding. The CYP219A1 protein has been crystallized and single crystals have been studied by X-ray crystallography. Diffraction data were collected to 2.4 A resolution. The crystals belonged to space group P6, with unit-cell parameters a = 93.1, b = 93.1, c = 98.0 A. Preliminary X-ray diffraction data analysis revealed that the asymmetric unit contained one protein molecule.
Project description:Aromatic compounds are an important renewable source of commodity chemicals traditionally produced from fossil fuels. Aromatics derived from plant lignin can potentially be converted into commodity chemicals through depolymerization followed by microbial funneling of monomers and low molecular weight oligomers. This study investigates the catabolism of the b-5 linked aromatic dimer dehydrodiconiferyl alcohol (DC-A) by the bacterium Novosphingobium aromaticivorans. We used genome wide screens to identify candidate genes involved in DC-A catabolism. Subsequent in vivo and in vitro analyses of these candidates elucidated a catabolic pathway composed of four required gene products and several partially redundant dehydrogenases that convert DC-A to aromatic monomers that can be funneled into the central aromatic metabolic pathway of N. aromaticivorans. Specifically, a newly identified γ-formaldehyde lyase, PcfL, opens the phenylcoumaran ring to form a stilbene and formaldehyde. A lignostilbene dioxygenase, LsdD, then cleaves the stilbene to generate the aromatic monomers, vanillin and 5-formylferulate (5-FF). We also show that an aldehyde dehydrogenase FerD oxidizes 5-FF before it is decarboxylated by LigW, yielding ferulic acid. We found that some enzymes involved in b-5 catabolism pathway can act on multiple substrates and that some steps in the pathway can be mediated by multiple enzymes, providing new insights into the robust flexibility of aromatic catabolism in N. aromaticivorans. We performed a comparative genomic analysis to predict that key enzymes in the newly discovered b-5 aromatic catabolic pathway are common among Sphingomonads.
Project description:Here, we report the genome-wide identification of transcription start sites (TSSs) from two Alphaproteobacteria grown under conditions that result in significant changes in gene expression. TSSs that were identified as present in one condition or both will be an important resource for future studies of these, and possibly other, Alphaproteobacteria.
Project description:Coal tar pitch (CTP) is a byproduct of cooking process which is used in making coatings, corrosion protection materials, and electrode. and it has been verified that Coal tar pitch extract (CTPE) constitutes polycyclic aromatic hydrocarbons (PAHs) (87.91%) and monocyclic aromatic hydrocarbons, heterocyclic compounds and alkenes (the remaining total is 12.09%) using gas chromatography/mass spectrometry (GC/MS). In this study, we determine the lncRNA expression profile in CTPE group and control group. The key lncRNAs were screen out by using microarray analysis in defferent group.
Project description:This microarray experiment aimed at studying the response of Aedes aegypti 4th stage-larvae to various xenobiotics, including insecticides, polycyclic aromatic hydrocarbons, herbicides and heavy metals.
Project description:Patients with inflammatory lung diseases are often additionally exposed to polycyclic aromatic hydrocarbons like B[a]P and B[a]P-induced alterations in gene expression in these patients may contribute to the development of lung cancer. Mice were intra-nasally treated with lipopolysaccharide (LPS, 20 μg/mouse) to induce pulmonary inflammation and subsequently exposed to B[a]P (0.5 mg/mouse) by intratracheal instillation We used RNA microarrays to detail the global gene expression change after each treatment. Meanwhile, compared the up- and down-regulated gene between the LPS&BaP and BaP in order to identify the role of inflammation on BaP induced carcinogenesis
Project description:In this study, we compare genomic signature safter treatment ofprimary human bronchial epithelial cells (HBEC) cultured in 3D with polycyclic aromatic hydrocarbons (PAHs) and identify genesets predictive of cancer risk.
