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Aromatic acid metabolism in Methylobacterium extorquens reveals interplay between methylotrophic and heterotrophic pathways

ABSTRACT: Aromatic acid metabolism in Methylobacterium extorquens reveals interplay between methylotrophic and heterotrophic pathways

PROVIDER: PRJNA1247397 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR33010605_1.fastq.gz	Fastqsanger.gz
	SRR33010605_2.fastq.gz	Fastqsanger.gz
	SRR33010606_1.fastq.gz	Fastqsanger.gz
	SRR33010606_2.fastq.gz	Fastqsanger.gz
	SRR33010607_1.fastq.gz	Fastqsanger.gz

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Aromatic acid metabolism in Methylobacterium extorquens reveals interplay between methylotrophic and heterotrophic pathways

Project description:Efforts towards microbial conversion of lignin to value-added products face many challenges because lignin’s methoxylated aromatic monomers release toxic C1 byproducts such as formaldehyde. The ability to grow on methoxylated aromatic acids (e.g., vanillic acid) has recently been identified in certain clades of methylotrophs, bacteria characterized by their unique ability to tolerate and metabolize high concentrations of formaldehyde. Here, we use a phyllosphere methylotroph isolate, Methylobacterium extorquens SLI 505, as a model to identify the fate of formaldehyde during methylotrophic growth on vanillic acids. M. extorquens SLI 505 displays concentration-dependent growth phenotypes on vanillic acid without concomitant formaldehyde accumulation. We conclude that M. extorquens SLI 505 overcomes potential metabolic bottlenecks from simultaneous assimilation of multicarbon and C1 intermediates by allocating formaldehyde towards dissimilation and assimilating the ring carbons of vanillic acid heterotrophically. We correlate this strategy with maximization of bioenergetic yields and demonstrate that formaldehyde dissimilation for energy generation rather than formaldehyde detoxification is advantageous for growth on aromatic acids. M. extorquens SLI 505 also exhibits catabolite repression during growth on methanol and low concentrations of vanillic acid, but no diauxie during growth on methanol and high concentrations of vanillic acid. Results from this study outline metabolic strategies employed by M. extorquens SLI 505 for growth on a complex single substrate that generates both C1 and multicarbon intermediates and emphasizes the robustness of M. extorquens for biotechnological applications for lignin valorization.

2025-04-09 | GSE293907 | GEO

Methylobacterium extorquens AM1 on acetate

Project description:Methylobacterium extorquens AM1 on acetate

2012-02-28 | PRD000445 | Pride

Methylobacterium extorquens AM1 on methanol

Project description:Methylobacterium extorquens AM1 on methanol

2012-02-28 | PRD000446 | Pride

Proteogenomic analysis of Mehtylobacterium extorquens DM4

Project description:Proteogenomic analysis of Methylobacterium extorquens DM4 using the dN-TOP strategy with heavy and light TMPP labelling

2018-04-25 | PXD006836 | Pride

Formaldehyde stress response in Methylobacterium extorquens AM1

2015-01-01 | GSE15631 | GEO

Transition from succinate to methanol growth in Methylobacterium Extorquens AM1

Project description:In order to provide information about the gene expression response that occurs when cells experience a change in carbon source, succinate limited chemostat cultures of Methylobacterium extorquens AM1 were grown to and maintained at an OD of ~0.63, transferred to flasks and methanol was added. Cells were harvested for RNA extraction at time: 0 min, 10 min, 30 min, 1 hr, 2 hr, 4 hr and 6 hr post transition. At 30 min, a no methanol addition sample was extracted as a carbon starvation control. These data were used in conjunction with flux, enzymatic and metabolite measurements to assess the changes in central metabolism during this transition. Abstract from manuscript: When organisms experience environmental change, how does their metabolic network reset and adapt to the new condition? This study focused on the mechanisms of metabolic adaptation occurring during the transition from succinate to methanol growth by the methylotrophic bacterium Methylobacterium extorquens, analyzing changes in carbon flux, gene expression, metabolites and enzymatic activities over time. Initially, cells experienced metabolic imbalance with excretion of metabolites, changes in nucleotide levels and cessation of cell growth. Though assimilatory pathways were induced rapidly, a transient block in carbon flow to biomass synthesis occurred, and enzymatic assays suggested methylenetetrahydrofolate dehydrogenase as one control point. This “downstream priming” mechanism ensures that significant carbon flux through these pathways does not occur until they are fully induced, precluding the buildup of toxic intermediates. Most metabolites that are required for growth on both carbon sources did not change significantly, even though transcripts and enzymatic activities required for their production changed radically, underscoring the concept of metabolic setpoints.

2011-08-01 | GSE22031 | GEO

Differential analysis of Methylobacterium extorquens DM4 in methanol versus dichloromethane condition

Project description:Differential analysis of Methylobacterium extorquens DM4 in methanol versus dichloromethane condition using shotgun label free MS1 quantification approach

2018-04-25 | PXD006838 | Pride

Ethylmalonyl-CoA mutase Operates as a Metabolic Control Point in Methylobacterium extorquens AM1

Project description:We report RNA-seq datasets profiling the transcriptional response to a sudden change in growth substrate, from succinate to ethylamine. This detailed combined dataset provides a dynamic assessment of the transcriptional response to a metabolic perturbation. These datasets are the first reported RNA-seq datasets for gene expression in Methylobacterium extorquens AM1

2014-11-08 | GSE63115 | GEO

Methylorubrum extorquens AM1

Project description:Methylobacterium extorquens AM1 genome sequencing

| PRJNA37299 | ENA

Formaldehyde stress response in Methylobacterium extorquens AM1

Project description:The goal of this study was to use microarrays to identify genes differentially regulated under conditions of formaldehyde stress relative to two other stress conditions (oxidative, osmotic) in an effort to identify genes that might be involved in a formaldehyde-specific stress response, rather than a general stress response, in the model methylotroph Methylobacterium extorquens AM1. Two color experiment, three treatments, three biological replicates per treatment, and two technical (dye swap) replicates per biological replicate: formaldehyde-stressed vs. unstressed cells; oxidative-stressed vs. unstressed cells; and osmotic-stressed vs. unstressed cells.

2015-01-01 | E-GEOD-15631 | biostudies-arrayexpress

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