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ABSTRACT: Tnseq to identify catabolism of b-5 linked aromatics by Novosphingobium aromaticivorans

PROVIDER: PRJNA1082384 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28196350_1.fastq.gz	Fastqsanger.gz
	SRR28196350_2.fastq.gz	Fastqsanger.gz
	SRR28196351_1.fastq.gz	Fastqsanger.gz
	SRR28196351_2.fastq.gz	Fastqsanger.gz
	SRR28196352_1.fastq.gz	Fastqsanger.gz

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Catabolism of b-5 linked aromatics by Novosphingobium aromaticivorans

Project description:Catabolism of b-5 linked aromatics by Novosphingobium aromaticivorans

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Catabolism of b-5 linked aromatics by Novosphingobium aromaticivorans

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

Study of the effect of the trancription factor SARO_RS14285 in aromatics degradation in Novosphingobium aromaticivorans

Project description:Novosphingobium aromaticivorans DSM12444 is a bacterium capable of catabolizing several lignin aromatics. A main degradation pathway for these compounds is the protocatechuate (PCA) meta-cleavage. Nevertheless, the transcriptional regulation of this pathway is still unknown. Immediately upstream of the genes encoding the enzymes for this pathway, the LysR-type transcription factor (LTTF) SARO_RS14285 was identified. To evaluate the functionality of this LTTF, a deletion mutant was constructed. A transcriptomic analysis of the mutant strain cultured in several aromatic compounds is included in this report.

2025-02-20 | GSE290086 | GEO

Aromatic dimer dehydrogenases from Novosphingobium aromaticivorans reduce aromatic diketones

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

Using DNA Affinity Purification sequencing (DAP-seq) to identify in vitro binding sites of transcription factors potentially involved in aromatic degradation

Project description:The genome-wide binding sites of 44 transcription factors from the aromatic metabolizing Alphaproteobacterium Novosphingobium aromaticivorans were identified using DNA Affinity Purification sequencing (DAP-seq). We report 32 of these transcription factors have at least one area of enrichment. These data will be valuable for better understanding of aromatic metabolism.

2025-03-12 | GSE291618 | GEO

Study of the effect of the trancription factor SARO_RS14285 in aromatics degradation in Novosphingobium aromaticivorans

Project description:Study of the effect of the trancription factor SARO_RS14285 in aromatics degradation in Novosphingobium aromaticivorans

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Laboratory evolution in Novosphingobium aromaticivorans enables rapid catabolism of a model lignin-derived aromatic dimer

Project description:Lignin contains a variety of interunit linkages, which leads to a range of potential decomposition products that can be used as carbon and energy sources by microbes. B-O-4 linkages are the most common in native lignin and associated catabolic pathways have been well characterized. However, the fate of the mono-aromatic intermediates that result from B-O-4 dimer cleavage has not been fully elucidated. Here, we used experimental evolution to identify mutant strains of Novosphingobium aromaticivorans with improved catabolism of a model aromatic dimer containing a B-O-4 linkage, guaiacylglycerol-b-guaiacyl ether (GGE). We identified several parallel causal mutations, including a single nucleotide polymorphism in the promoter of an uncharacterized gene that roughly doubled the growth yield with GGE. We characterized the associated enzyme and demonstrated that it oxidizes an intermediate in GGE catabolism, B-hydroxypropiovanillone, to vanilloyl acetaldehyde. Identification of this enzyme and its key role in GGE catabolism furthers our understanding of catabolic pathways for lignin-derived aromatic compounds.

2024-08-29 | MSV000095729 | MassIVE

Novosphingobium aromaticivorans strain:B0695 | isolate:SMCC B0695

Project description:Novosphingobium aromaticivorans B0695 DAP-Seq epigenomics

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Novosphingobium aromaticivorans strain:P6D9

Project description:Novosphingobium aromaticivorans strain:P6D9 Genome sequencing

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Novosphingobium aromaticivorans strain:DSM 12444 JMN2

Project description:Novosphingobium aromaticivorans DSM 12444 JMN2 Resequencing

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