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Ecogenomic assessment of soil toxicity associated with the production chain of 2,5-furandicarboxylic acid (FDCA), a candidate bio-based green chemical building block

ABSTRACT: 2,5-furan dicarboxylic acid (FDCA) is the top-12 value-added chemicals derived from biomass that may serve as a 'green' substitute for terephthalate acid (TPA) in polyesters. FDCA can be synthesized chemically from 5-(hydroxymethyl) furfural (HMF), which is produced from fructose or glucose. To investigate impact of the production chain of FDCA on terrestrial ecosystem and unravel molecular pathways invoked and the biological process affected in the animal, a microarray analysis was applied to measure the transcriptome-wide response in soil invertebrates Folsomia candida. Microarrays examined transcriptional changes at EC50 concentrations of FDCA, HMF and TPA spiked in sterilized LUFA 2.2 soils. The results indicated FDCA and TPA caused no significant change in gene expression, which may due to the low chemical water solubility leading to slow uptake by the animal from the pore water after. A substantial number of genes were significantly regulated in F. candida after exposure to HMF. Gene Ontology analysis showed many biological process were significantly affected, such as nucleic acid metabolism, transcriptional metabolic process, cell developmental process and oxidation-reduction process. Transcriptional profile also indicated HMF can be biotransformed by F. candida into SMF which is genotoxic and mutagenic. The current research shows that environmental risk of the FDCA production chain from biomass is not due to the final product but to the intermediate HMF.

ORGANISM(S): Folsomia candida

PROVIDER: GSE74640 | GEO | 2016/06/01

SECONDARY ACCESSION(S): PRJNA301049

REPOSITORIES: GEO

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Ecogenomic assessment of soil toxicity associated with the production chain of 2,5-furandicarboxylic acid (FDCA), a candidate bio-based green chemical building block

Project description:2,5-furan dicarboxylic acid (FDCA) is the top-12 value-added chemicals derived from biomass that may serve as a 'green' substitute for terephthalate acid (TPA) in polyesters. FDCA can be synthesized chemically from 5-(hydroxymethyl) furfural (HMF), which is produced from fructose or glucose. To investigate impact of the production chain of FDCA on terrestrial ecosystem and unravel molecular pathways invoked and the biological process affected in the animal, a microarray analysis was applied to measure the transcriptome-wide response in soil invertebrates Folsomia candida. Microarrays examined transcriptional changes at EC50 concentrations of FDCA, HMF and TPA spiked in sterilized LUFA 2.2 soils. The results indicated FDCA and TPA caused no significant change in gene expression, which may due to the low chemical water solubility leading to slow uptake by the animal from the pore water after. A substantial number of genes were significantly regulated in F. candida after exposure to HMF. Gene Ontology analysis showed many biological process were significantly affected, such as nucleic acid metabolism, transcriptional metabolic process, cell developmental process and oxidation-reduction process. Transcriptional profile also indicated HMF can be biotransformed by F. candida into SMF which is genotoxic and mutagenic. The current research shows that environmental risk of the FDCA production chain from biomass is not due to the final product but to the intermediate HMF. We used a one-color microarray design where each sample was hybridized to a single array

2016-06-01 | E-GEOD-74640 | biostudies-arrayexpress

The gene transcription of the efficient biodetoxification filamentous fungus Amorphotheca resinae ZN1 against the model lignocellulosic inhibitors

Project description:Furans (furfural and 5-hydroxymethylfurfural (HMF)), phenolic aldehydes (4-hydroxybenzaldehyde, syringaldehyde, and vanillin), and weak acids (acetic acid and formic acid) are the main degradation products of lignocellulose pretreatment process and seriously inhibit the cellullas enzyme activity and the fermentation process.

2022-07-21 | GSE208427 | GEO

RNA-seq of Ideonella sakaiensis 201-F6 when grown on PET, TPA·2Na, and EG

Project description:Poly(ethylene terephthalate) (PET)-degrading bacterium Ideonella sakaiensis produces hydrolytic enzymes that convert PET, via mono(2-hydroxyethyl) terephthalate (MHET), into the monomeric compounds, terephthalic acid (TPA) and ethylene glycol (EG). Understanding PET metabolism is critical if this bacterium is to be engineered for bioremediation and biorecycling. TPA uptake and catabolism in I. sakaiensis have previously been studied, but EG metabolism remains largely unexplored despite its importance. First, we identified two alcohol dehydrogenases (IsPedE and IsPedH) and one aldehyde dehydrogenase (IsPedI) in I. sakaiensis as the homologs of EG metabolic enzymes in Pseudomonas putida KT2440. IsPedE and IsPedH exhibited EG dehydrogenase activities with Ca2+ and a rare earth element (REE) Pr3+, respectively. We further found an upregulated dehydrogenase gene when the bacterium was grown on EG, whose gene product (IsXoxF) displays a minor EG dehydrogenase activity with Pr3+. IsPedE displayed a similar level of activity toward various alcohols. In contrast, IsPedH was more active toward small alcohols, whereas IsXoxF was the opposite. Structural analysis with homology models revealed that IsXoxF had a larger catalytic pocket than IsPedE and IsPedH, which could accommodate relatively bulkier substrates. Pr3+ regulated the protein expression of IsPedE negatively; IsPedH and IsXoxF were positively regulated. Taken together, these results indicated that the combination of IsPedH and IsXoxF complements the function of IsPedE in the presence of REEs. IsPedI exhibited dehydrogenase activity toward various aldehydes with the highest activity toward glycolaldehyde (GAD). This study demonstrated a unique alcohol oxidation pathway of I. sakaiensis, which could be efficient in EG utilization.

2022-10-17 | GSE205843 | GEO

Integrative Analysis of Sorghum Bicolor Green Prop Roots Under Elevated CO2 and Water Deficit Conditions

Project description:Elevated CO2 (E[CO2]) improves the biomass and yield when combined with water-stress in C4 plants. Although several studies described the molecular response of the C4 plant Sorghum bicolor during drought exposure, none reported its combinatorial effect with E[CO2] in the roots. We decided to perform a molecular analysis using green prop roots, the portion of the radicular system photosynthetically active and more sensible to drought. Whole-transcriptome analysis identified 394 up- and 1,471 down-regulated genes. Among the E[CO2] induced pathways, photosynthesis stood out. Carbon fixation, phenylpropanoid, phenolic compounds, and fatty acid biosynthesis-related pathways were repressed. Protein family analysis showed induction of chlorophyll a-b binding protein family, and repression of glutathione-related enzymes. Protein-protein interaction networks exhibited well-defined clusters, including genes related to cell organization and biogenesis, oxireduction process, and photosynthesis being induced. The findings suggest that the E[CO2] mitigates the water deficit by antioxidant and osmoregulation activity, as well as by accumulation of sugaralcohols in the green prop roots, which may be responsible by the increase in biomass together with the cell proliferation. The higher carbon uptake explains the increase in photosynthetic and primary metabolism activities. Our data revealed that green prop roots present an intriguing metabolism under water deficit and E[CO2], showing its crucial role in the drought tolerance acquisition in a predicted future global atmosphere.

2021-06-30 | GSE179109 | GEO

Transcriptomic differences between E. coli BL21 and K-12 MG1655 during n-heptanoic acid stress

Project description:Biosynthesis of carboxylic acids and fatty acids from renewable biomass is a key issue in biorefinery. However, their productivities are often limited due to various toxic effects of the products on the host organisms. Here, we have investigated the factors that influence tolerance of Escherichia coli to long chain carboxylic acid (e.g., n-heptanoic acid)-induced stress by using transcriptome analysis. The metabolic and genomic responses of E. coli BL21 and MG1655 strains with n-heptanoic acid indicated that acid stress is one of the major stresses, which might be generated by n-heptanoic acid in addition to the presumed solvent-like stress.

2016-10-11 | GSE73640 | GEO

Amplicon based single molecule footprinting on ES cells and derivatives

Project description:Single Molecule Footprinting (SMF) data from Sonmezer et al., 2020. SMF data is obtained by treating isolated nuclei with methyltransferases, where binding of proteins on DNA, e.g. nucleosomes and TFs, leave behind unmethylated cytosines as footprints. Data in this experiment comprises SMF data obtained from ES cells and various derivatives of ES cells, such DNMT-null, REST-knockout ES cells, neural progenitors and ES cells treated with NRF1 sirNA.

2020-12-26 | E-MTAB-9033 | biostudies-arrayexpress

Effects of terephthalate on Rhodococcus sp. RHA1

Project description:two cultures one grown on terephthalate and other on pyruvate Keywords: growth type

2007-01-19 | GSE6684 | GEO

miRNA genes in HMEC and HMF

Project description:This SuperSeries is composed of the following subset Series: GSE28374: DNA methylation of miRNA genes in HMEC and HMF GSE28375: Histone H3 acetylation of miRNA genes in HMEC and HMF GSE28376: Histone H3 lysine 27 trimethylation of miRNA genes in HMEC and HMF GSE28377: Histone H3 lysine 4 trimethylation of miRNA genes in HMEC and HMF GSE28378: Histone H3 lysine 9 dimethylation of miRNA genes in HMEC and HMF Refer to individual Series

2011-04-05 | E-GEOD-28380 | biostudies-arrayexpress

Bait-capture based single molecule footprinting of different mouse cell lines

Project description:Bait-capture based Single Molecule Footprinting (SMF) data from Kreibich et al., 2022. SMF data is obtained by treating extracted nuclei with a GpC methyltransferase, where binding of proteins on DNA, e.g. nucleosomes and transcription factors (TFs), leave behind unmethylated GpCs as footprints. Data in this experiment comprises SMF data obtained from WT embryonic stem cells (ES), DNMT TKO ES, TET TKO ES, F1 hybrid ES (129/CAST), neural progenitor (NP),�myoblast (C2C12) and�murine erythroleukemia (MEL)�cells. These data were generated by employing Agilent Sure-Select Mouse Methyl-Seq kit, enriching the sample for cis-regulatory regions of the mouse genome prior to library preparation. Thus, these data contain high coverage accessibility information at regulatory loci in different cell types. The SMF procedure maintains the endogenous DNA methtylation in CpG context, allowing the simultaneous detection of chromatin accessibility, TF binding and endogenous DNA methylation.

2023-02-06 | E-MTAB-11700 | biostudies-arrayexpress

Bait-capture based single molecule footprinting on ES cells and derivatives

Project description:Bait-capture based Single Molecule Footprinting (SMF) data from Sonmezer et al., 2020. SMF data is obtained by treating isolated nuclei with methyltransferases, where binding of proteins on DNA, e.g. nucleosomes and TFs, leave behind unmethylated cytosines as footprints. Data in this experiment comprises SMF data obtained from ES, DNMT-TKO, and neural progenitor (NP) cells. These data were generated by employing Agilent Sure-Select Mouse Methyl-Seq kit, enriching the sample for regulatory regions of mouse genome prior to library preparation. Thus, these data contain high coverage accessibility information at regulatory loci in different cell types.

2021-05-04 | E-MTAB-9123 | biostudies-arrayexpress

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