Effect of FadR overexpression in an engineered fatty acid overproducer
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ABSTRACT:
ORGANISM(S): Escherichia coli K-12 Escherichia coli
PROVIDER: GSE35392 | GEO | 2012/01/28
SECONDARY ACCESSION(S): PRJNA152695
REPOSITORIES: GEO
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Project description:Transcriptome analysis of strains LT-ΔfadE (control) and FRT-ΔfadE (FadR overexpressor) after 12h of fatty acid production. The strains used are described in detail in Zhang F, M Ouellet, TS Batth, CJ Petzold, A Mukhopadhyay and JD Keasling. Enhancing fatty acid production by the expression of the regulatory transcription factor FadR. (In preparation) Three independent cultures of control strain LT-ΔfadE and four independent cultures of FadR overexpressor strain FRT-ΔfadE were induced. One sample derived from each culture was hybridized.
2012-01-28 | E-GEOD-35392 | biostudies-arrayexpress
Project description:Purpose: The goals of this study are to find out the differential expression genes in the fadR mutant strain(ΔfadR) compared with wild-type (WT) and to further explore the regulation mechanisms of fadR. Methods: Shewanella oneidensis MR-1 WT and ΔfadR were collected in log phage(OD~0.6). RNA extraction was performed using the RNeasy minikit (Qiagen) and the RNA was quantified by using a NanoVue spectrophotometer (GE Healthcare). RNA seq was performed using Illumina NextSeq 500, 2×150 bp. Results: Our study represents that the expression of 146 genes were decreased and 94 genes were increased inΔfadR compared with WT. Branched-chain keto acid dehydrogenase (BKD) produces corresponding branched-chain acyl coenzyme A which further participating branchend-chain fatty acids synthesis. The expression of bkdA2 was also promoted in △fadR compared with WT. Conclusions: Combined with our expression results, it declared that FadR can suppress bkd operon in some degree,which further increase the synthesis of branched-chain fatty acids in ΔfadR.
2020-01-01 | GSE133375 | GEO
Project description:Nutrient starvation is an important survival challenge for bacteria during industrial production of functional foods. Lactobacilli are increasingly being used as probiotics in functional foods. As next-generation sequencing technology has greatly advanced, we performed integrative proteomic and genomic analysis to investigate the response of Lactobacillus casei Zhang to a glucose-restricted environment. L. casei Zhang strains were permitted to evolve in glucose-limited or normal medium from a common ancestor over a 3-year period, and they were sampled after 1000, 2000, 3000, 4000, 5000, 6000, 7000, and 8000 generations and subjected to proteomic and genomic analyses. Genomic resequencing data revealed different point mutations and other mutational events in each generation of L. casei Zhang under glucose limitation stress. The proteins expressed differentially under glucose limitation were found to be significantly related to fructose and mannose metabolism, carbohydrate metabolic processes, lyase activity, and amino acid-transporting ATPase activity. The integrative proteomic and genomic analysis revealed that the mutations protected L. casei Zhang against glucose starvation by regulating other cellular carbohydrate, fatty acid, and amino acid catabolism; phosphoenolpyruvate system pathway activation; glycogen synthesis; ATP consumption; pyruvate metabolism; and general stress response protein expression. The results help reveal the mechanisms of adapting to glucose starvation and provide new strategies for enhancing the industrial utility of L. casei Zhang.
2018-02-08 | PXD006643 | Pride
Project description:Effect of FadR overexpression in an engineered fatty acid overproducer
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Project description:Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of Johne’s disease (JD), which is also known as paratuberculosis, in ruminants. The mechanisms of JD pathogenesis are still unclear, but it is known that MAP subverts the host immune system for years by using macrophages as its primary reservoir. The effect of MAP infection on macrophages is often studied in healthy or experimentally infected cows, but reports on primary macrophages from naturally infected cows are lacking. In our study, the transcriptome of primary monocyte-derived macrophages challenged with live MAP was analyzed using next-generation sequencing (RNA‑seq). The gene expression signatures of macrophages from cows diagnosed as negative or positive for JD [JD(–) or JD(+), respectively] revealed differential host–pathogen interplay, highlighting long-term mechanisms established during mycobacterial disease. In JD(–) cows, a considerable number of genes (1,436) were differentially expressed at 8 h post-infection (hpi). Interestingly, while expected inflammatory immune response pathways were among the significant pathways, others related to Hepatic fibrosis/hepatic stellate cell activation, lipid homeostasis, such as the LXR/RXR [liver X receptor/retinoid X receptor] activation, and autoimmune diseases such as atherosclerosis and rheumatoid arthritis were consistently among the top significant pathways. Unexpectedly, the macrophages from JD(+) cows did not present a clear response pattern to ex vivo MAP infection, neither during the early period nor at 24 hpi. Analyzing of the transcriptomic profile of the uninfected macrophages, revealed 868 genes that were differentially expressed in JD(+) versus JD(–) cows. The down-regulated genes particularly modified the general cell metabolism by down-regulating amino acid synthesis, cholesterol biosynthesis, and other energy production pathways while introducing a pro-fibrotic pattern associated with foam cells. These modifications show the apparent importance of the metabolic pathways hijacked by MAP to subvert the immune cells. Our findings support the hypothesis that MAP could induce a tolerant-like state in circulating peripheral blood monocytes when they are differentiating into macrophages, which could further promote the persistence. Similar to other mycobacteria and pathogen-associated molecular patterns, MAP could influence macrophage behavior in the long term. This report contributes to a better understanding of MAP control of immune cells and its mechanisms of survival.
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Project description:Adult male goldfish, exposed to estrogen (E2) implant, 1 day exposure See the following for further details; Marlatt VL, Martyniuk, CJ, Zhang, D, Xiong, H, Xia, X, Trudeau, VL, Moon, T. Tissue-specific auto-regulation of estrogen receptor subtypes and transcript profiling of estrogen-responsive genes in the neuroendocrine brain of male goldfish (Carassius auratus) exposed to 17beta-estradiol. J. Mol. Endocrinol. (accepted). Keywords: Estrogen effect on male goldfish hypothalamus, microarray
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Project description:Enhancing volatile fatty acid production in pig manure
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Project description:Lactobacillus casei Zhang is a probiotic bacterium isolated from koumiss in Inner Mongolia of China that has been commercially used as a starter in the manufacture of dairy products. To study the gene expression profiles of L. casei Zhang during growth in milk, a whole-genome microarray was used. Compared to L. casei Zhang grown to late logarithmic phase in milk, 61 genes were significantly up-regulated (>5 fold) in stationary phase, whereas 26 genes were down-regulated. Collectively, these data showed that the majority of the identified genes was involved in carbohydrate metabolism and energy production, followed by genes involved in nucleotide metabolism, inorganic ion transport, amino acid transport and metabolism, chaperone, etc. This study demonstrates the fundamental effects of cultural conditions on the transcriptome of L. casei Zhang. Moreover, it improves the understanding of the growth and survival mechanism of the bacterium during the late stage of milk fermentation.
2011-12-31 | GSE24597 | GEO
Project description:Transcriptomics analysis of biopolymer (medium chain length polyhydroxyalkanoate) producing strain P.putida LS46 cultured with biodiesel derived waste carbon sources: studies of cellular adaptation to the industrial waste streams and metabolic profiling under the polymer producing conditions. We are reporting RNAseq analysis data here as part of our multi-level Omics study of medium chain length polyhydroxyalkanoate (mcl-PHA) producing strain P.putida LS46 culture with biodiesel derived waste glycerol and waste fatty acids. The data presented here will be used in two separate manuscripts. The objectives of this study are a): to evaluate cellular responses of P.putida LS46 under industrial waste stream. b): to study gene expression profile under two selected mcl-PHA producing conditions of P.putida LS46. Comparative multi-level Omics study: for objective a): Exponential P.putida LS46 cell from waste glycerol culture compared against reagent grade pure glycerol culture. For objective b): Two mcl-PHA producing conditions, namely stationary phase waste glycerol culture and exponential phase waste fatty acid culture of P.putida LS46, were compared against exponential phase waste glycerol culture of P.putida LS46. Major results from objective a): The waste glycerol substrate induced expression of a large number of genes putatively involved in heavy metal tolerance, including three gene clusters: a putative cusABC transcript unit and two copies of copAB, which are usually involved in copper resistance and tolerance to other monovalent heavy metals. A local gene relocation was observed in cluster 1 consisting cusABC and copAB relative to the KT2440 type strain according to the phylogenetic and gene neighbourhood analyses on various P. putida strains. P. putida LS46 also contains 11 putative MerR family regulators, which sense various environmental stimuli including heavy metals. MerR-1 is an ortholog of the copper response regulator of other gram-negative bacteria, and was highly up-regulated in waste glycerol cultures. Finally, a number of genes involved in cell responses to high extra-cellular Na+ concentrations, and genes of the fatty acid beta-oxidation pathway were up-regulated in waste glycerol cultures Major results from objective b): Regardless to the type of substrates, up-regulation of two mcl-PHA synthase (PhaC1 and PhaC2), and two phasin proteins (PhaF and PhaI) are the most common genotype under mcl-PHA production conditions. PhaG and possible PhaJ4 connect fatty acid de novo synthesis to mcl-PHA in waste glycerol culture. Interestingly, expression of gene, fabZ, in production of unsaturated fatty acid from fatty acid de novo synthesis was only observed in waste glycerol culture. On the other hand, PhaJ1 and PhaJ4 derived mcl-PHA production via fatty acid beta-oxidation was observed under waste fatty acid culture. These results would help to explain observed different production kinetics and monomer distribution of the polymer. Although under active mcl-PHA production condition, depression on the expression of glpF genes in glycerol transportation system prevent further channelling extra-cellular glycerol into the cell. Waste glycerol culture also triggers trahalose synthesis pathway, a potential competing pathway during mcl-PHA synthesizing. In waste fatty acid culture, the intermediates (acyl-CoA and 3-hydroxyacyl-CoA) of fatty acid beta-oxidation were used for mcl-PHA production and were also likely hydrolysed to their free acid forms via an up-regulated thioesteras coding gene, tesA. Acetyl-CoA cleaved from the pathway was clearly channeled into glyoxylate shut for C2 carbon assimilation over spillage as CO2 through TCA cycle or used in fatty acid biosynthesis pathway. In total 4 sampling points, namely exponential phase of pure glycerol, waste glycerol and waste free fatty acids cultures, and stationary phase of waste glycerol culture. For each sampling point, 2 biological replicates were taken. (Thus 8 samples in total)
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