Novosphingobium aromaticivorans
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA35127 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| CCBH01.dat.gz | Other | |||
| CCBH01.fasta.gz | Fasta.gz | |||
| CCBH01.master.dat | Other | |||
| SRR10150637_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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.
2024-02-29 | GSE259365 | GEO
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.
2021-05-22 | GSE174697 | GEO
Project description:Aromatic hydrocarbon-degrading bacterium
| PRJNA35451 | ENA
Project description:Polycyclic aromatic hydrocarbon-degrading bacterium
| PRJNA35791 | ENA
Project description:Unusual gram negative bacterium that has glycosphingolipid instead of lipopolysaccharide and can degrade a wide variety of aromatic hydrocarbons
| PRJNA204 | ENA
Project description:Novosphingobium resinovorum strain SA1 is one of few strains capable of degrading sulfanilic acid which is a widely used representative of sulfonated aromatic compounds. In order to identify the elements involved in the biodegradation process and to understand the metabolic responces of the cells exposed to this aromatic compound, we performed a whole transcriptome analysis of cells grown on sulfanilic acid and glucose. Additionally, for distinguish the potential stress/starvation effects of the xenobiotic we compared the transcript profiles of samples taken from both the exponential and stationary growth phases.
2017-08-15 | GSE102626 | GEO
Project description:The bacterium Novosphingobium sp. THN1 (THN1) is capable of degrading microcystin-LR (MCLR). To get an insight into genes expression during MCLR degradation and the regulation of different carbon concentrations on MCLR degradation, we performed RNA-seq of THN1 during MCLR degradation under different carbon concentrations.
2019-01-30 | GSE125827 | GEO
Project description:Aromatic dimer dehydrogenases from Novosphingobium aromaticivorans reduce aromatic diketones
| PRJNA731907 | ENA
Project description:Lignin is a potential source of valuable chemicals, but its chemical depolymerization results in a heterogeneous mixture of aromatics and other products. Microbes could valorize depolymerized lignin by converting multiple substrates into one or a small number of products. In this study, we describe the ability of Novosphingobium aromaticivorans to metabolize 1-(4-hydroxy-3-methoxyphenyl)propane-1,2-dione (G-diketone), an aromatic Hibbert diketone that is produced during formic acid-catalyzed lignin depolymerization. By assaying genome-wide transcript levels from N. aromaticivorans during growth on G-diketone and other chemically-related aromatics, we hypothesized that the Lig dehydrogenases, previously characterized as oxidizing β-O-4 linkages in aromatic dimers, were involved in G-diketone metabolism by N. aromaticivorans. Using purified N. aromaticivorans Lig dehydrogenases, we found that LigL, LigN, and LigD each reduced the Cα ketone of G-diketone in vitro but with different substrate specificities and rates. Furthermore, LigL, but not LigN or LigD, also reduced the Cα ketone of 2-hydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-1-one (GP-1) in vitro, a derivative of G-diketone with the Cβ ketone reduced, when GP-1 was provided as a substrate. The newly identified activity of these Lig dehydrogenases expands the potential range of substrates utilized by N. aromaticivorans beyond what has been previously recognized. This is beneficial both for metabolizing a wide range of natural and non-native depolymerized lignin substrates and for engineering microbes and enzymes that are active with a broader range of aromatic compounds. IMPORTANCE Lignin is a major plant polymer composed of aromatic units that have value as chemicals. However, the structure and composition of lignin have made it difficult to use this polymer as a renewable source of industrial chemicals. Bacteria like Novosphingobium aromaticivorans have the potential to make chemicals from lignin not only because of their natural ability to metabolize a variety of aromatics but also because there are established protocols to engineer N. aromaticivorans strains to funnel lignin-derived aromatics into valuable products. In this work, we report a newly discovered activity of previously characterized dehydrogenase enzymes with a chemically modified by-product of lignin depolymerization. We propose that the activity of N. aromaticivorans enzymes with both native lignin aromatics and those produced by chemical depolymerization will expand opportunities for producing industrial chemicals from the heterogenous components of this abundant plant polymer.
| S-EPMC8612281 | biostudies-literature