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Genome-wide targets identification by CRISPRi-Omics for high-titer production of free fatty acids in Escherichia coli

ABSTRACT: We employ omics analyses to identify potential targets in multiple cellular processes, enabling systematical discovery of beneficial chromosomal gene targets that can be engineered to optimize free fatty acids (FFAs) production in Escherichia coli. As a result, we identify 56 beneficial genes , including 46 novel targets functioning in cell structure and division, and signaling transduction that efficiently facilitate FFAs production.

ORGANISM(S): Escherichia coli BL21(DE3)

PROVIDER: GSE146162 | GEO | 2020/03/03

REPOSITORIES: GEO

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Genome-wide targets identification for high-titer production of free fatty acids in Escherichia coli

Project description:We employed omics analyses to identify potential targets in multiple cellular processes, enabling systematical discovery of beneficial chromosomal gene targets that can be engineered to optimize free fatty acids (FFAs) production in Escherichia coli.

2020-06-03 | PXD017890 | iProX

the Effect of Fatty Acids in Hepatic Insulin resistance-part2

Project description:Monounsaturated fatty acid (MUFA) oleic acid (OA) has been reported to reverse saturated fatty acid palmitic acid (PA)-induced hepatic insulin resistance (IR). However, the detailed molecular mechanism remains elusive. In addition, previous research also showed that -3 polyunsaturated fatty acid (PUFA) eicosapentaenoic acid (EPA), exerted opposite effects to PA in muscle IR, but whether it plays the same role in hepatic IR and the possible mechanism involved needs to be further explored. Here, we confirmed that EPA reversed PA-induced IR in HepG2 cells and compared the proteome change after different free fatty acids (FFAs) treatments. For MUFA, 234 proteins were identified as differentially expressed proteins, and their functions were mainly related to response to stress and endogenous stimuli, lipid metabolic process and protein binding. For PUFA, the PA-induced expression change of 1326 proteins could be reversed by EPA and 415 of them were mitochondrial proteins, which covered most of the functional proteins in oxidative phosphorylation (OXPHOS) and tricarboxylic acid cycle (TCA). Mechanism study revealed that c-Jun and ROS played a role in OA- and EPA-reversed PA-induced IR, respectively. EPA or OA alleviated PA-induced abnormal ATP production, ROS generation, and calcium content. Importantly, H2O2-activated production of ROS increased the expression of c-Jun, further resulting in IR of HepG2 cells. Besides, we provided more feasible candidates as potential c-Jun-targeted “responders” for FFAs treatments. Taken together, we demonstrated that ROS/c-Jun is a common pathway to different FFAs-regulated IR in HepG2 cells.

2019-07-11 | PXD012066 | Pride

RNA-Seq analysis and targeted mutagenesis for improved free fatty acid production in an engineered cyanobacterium

Project description:Background: High-energy-density biofuels are typically derived from the fatty acid biosynthesis pathway, thus establishing free fatty acids (FFAs) as important fuel precursors. FFA production using photosynthetic microorganisms like cyanobacteria allows for direct conversion of carbon dioxide into fuel precursors. Recent studies investigating cyanobacterial FFA production have demonstrated the potential of this process, yet FFA production was also shown to have negative physiological effects on the cyanobacterial host, ultimately limiting high yields of FFAs. Results: Cyanobacterial FFA production was shown to generate reactive oxygen species (ROS) and lead to increased cell membrane permeability. To identify genetic targets that may mitigate these toxic effects, RNA-seq analysis was used to investigate the host response of Synechococcus elongatus PCC 7942. Stress response, nitrogen metabolism, photosynthesis, and protein folding genes were up-regulated during FFA production while genes involved in carbon and hydrogen metabolisms were down-regulated. Select genes were targeted for mutagenesis to confirm their role in mitigating FFA toxicity. Gene knockout of two porins and the overexpression of ROS-degrading proteins and hypothetical proteins reduced the toxic effects of FFA production, allowing for improved growth, physiology, and FFA production. Comparative transcriptomics, analyzing gene expression changes associated with FFA production and other stress conditions, identified additional key genes involved in cyanobacterial stress response. Conclusions: A total of 15 gene targets were identified to reduce the toxic effects of FFA production. While single-gene targeted mutagenesis led to minor increases in FFA production, the combination of these targeted mutations may yield additional improvement, advancing the development of high-energy-density fuels derived from cyanobacteria.

2013-08-22 | GSE45762 | GEO

Free fatty acids and TNF-alpha in HepG2 cell culture

Project description:The regulation of complex cellular activities in palmitate treated HepG2 cells, and the ensuing cytotoxic phenotype, involves cooperative interactions between genes. While previous approaches have largely focused on identifying individual target genes, elucidating interacting genes has thus far remained elusive. We applied the concept of information synergy to reconstruct a ?gene-cooperativity? network for palmititate-induced cytotoxicity in liver cells. Our approach integrated gene expression data with metabolic profiles to select a subset of genes for network reconstruction. Subsequent analysis of the network revealed insulin signaling as the most significantly enriched pathway, and desmoplakin (DSP) as its top neighbor. We determined that palmitate significantly reduces DSP expression, and treatment with insulin restores the lost expression of DSP. Insulin resistance is a common pathological feature of fatty liver and related ailments, whereas loss of DSP has been noted in liver carcinoma. Reduced DSP expression can lead to loss of cell-cell adhesion via desmosomes, and disrupt the keratin intermediate filament network. Our findings suggest that DSP expression may be perturbed by palmitate and, along with insulin resistance, may play a role in palmitate induced cytotoxicity, and serve as potential targets for further studies on non-alcoholic fatty liver disease (NAFLD). free fatty acids(palmitate, oleate, linoleate) 0.7mM and tnf-alpha (0 20,100 ng/ml) were subjected to HepG2 cell line to study the cytotoxicity induced by these two factors. control(Hepg2 medium and BSA medium) treatment(combinations of TNFa+FFAs) two biological replicates for each condition, color swap for each sample

2012-05-01 | E-GEOD-26885 | biostudies-arrayexpress

Genome-wide targets identification by CRISPRi-Omics for high-titer production of free fatty acids in Escherichia coli

Project description:Genome-wide targets identification by CRISPRi-Omics for high-titer production of free fatty acids in Escherichia coli

| PRJNA609633 | ENA

Plant roots employ cell-layer specific programs to respond to pathogenic and beneficial microbes

Project description:Plant roots employ cell-layer specific programs to respond to pathogenic and beneficial microbes

| PRJNA665689 | ENA

Effect of overexpression of ZBED3 on gene expression in HHL-5 hepatocytes

Project description:To investigate the regulatory function of ZBED3 in NAFLD, we established a ZBED3-overexpressing HHL-5 cell line treated with FFAs. We then performed gene expression profiling using RNA-seq data from 2 different cells treated with the same concentration of FFAs.

2023-05-12 | GSE231875 | GEO

Protein production by Aspergillus oryzae

Project description:The filamentous fungus Aspergillus oryzae is an important microbial cell factory for industrial production of useful enzymes, such as α-amylase. In order to optimize the industrial enzyme production process, there is a need to understand fundamental processes underlying protein production, here under how protein production links to metabolism through global regulatory structures. In this study, two α-amylase-producing strains of A. oryzae, a wild type strain and a transformant strain containing additional copies of the α-amylase gene, were characterized at a systematic level. Based on integrated analysis of ome-data together with genome-scale metabolic network and flux calculation, we identified key genes, key enzymes, key proteins, and key metabolites involved in the processes of protein synthesis and secretion, nucleotide metabolism, and amino acid metabolism that can be the potential targets for improving industrial protein production. Keywords: Two Aspergillus oryzae strains and two different carbon sources Two carbon sources (glucose, maltose) with three biological replicates for A. oryzae strain A1560 and strain CF1.1

2012-02-12 | E-GEOD-22566 | biostudies-arrayexpress

Time-course transcriptome analysis-guided identification of a four-component system, SbrH1-R that regulates milbemycin biosynthesis by influencing gene cluster expression, precursor supply, and antibiotic efflux

Project description:Streptomyces bingchenggensis is a soil bacterium that produces milbemycins, which have been applied widely as insecticides and anthelmintics in agricultural and veterinary field. To gain further insights into the regulatory mechanisms in Streptomyces bingchenggensis and mine useful targets for future metabolic engineering to improve milbemycin production, we have compared two strains（the parental strain and high-yielding strain）by comparative transcriptome analysis.This work provides beneficial targets and corresponding engineering methods to facilitate high-production of milbemycins and other polyketide pesticides.

2022-03-02 | GSE186852 | GEO

Palmitate-induced gene expression in human gingival fibroblasts (HGF)

Project description:DNA microarray analysis was performed to investigate the expression of genes in HGF stimulated with palmitate Type 2 diabetes (T2D) is characterized by decreased insulin sensitivity and higher concentrations of free fatty acids (FFAs) in plasma. Among FFAs, saturated fatty acids (SFAs), such as palmitate, have been proposed to promote inflammatory responses. Although many epidemiological studies have shown a link between periodontitis and T2D, little is known about the clinical significance of SFAs in periodontitis. The goal of this study is to demonstrate a potential link between the pathogenesis of periodontitis and SFAs in plasma. HGF were treated with either with 0 (1% Bovine serum albumin) or 100 ÂµM Palmitate for 36 hours (n=2 each).

2015-12-31 | E-GEOD-62761 | biostudies-arrayexpress

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