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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Effect of FadR overexpression in an engineered fatty acid overproducer

ABSTRACT: 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.

ORGANISM(S): Escherichia coli

SUBMITTER: Mario Ouellet

PROVIDER: E-GEOD-35392 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Effect of FadR overexpression in an engineered fatty acid overproducer

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)

2012-01-28 | GSE35392 | GEO

Simultaneous in vivo enzyme and host engineering through laboratory evolution

Project description:Two genetic selection systems that couple metabolite hydroxylation or methylation of small molecules to growth of Escherichia coli are presented in this study. One system targets pterin-dependent hydroxylation (tBPt) while another focuses on S-adenosylmethionine-dependent methylation (SAM). Using adaptive laboratory evolution with growth selection, these two systems are demonstrated to not only achieve in vivo directed evolution of enzymes involved in human hormone biosynthesis but also reveal non-intuitive host factors that elude existing synthetic biology approaches. Raw sequencing data for the relevant strains generated in this study are presented here.

2019-01-30 | E-MTAB-6779 | biostudies-arrayexpress

Highly parallel identification of sequence preferences for eukaryotic C2H2 zinc finger domains using a bacterial 1-hybrid assay

Project description:The largest and most diverse class of eukaryotic transcription factors contain Cys2-His2 zinc fingers (C2H2-ZFs), each of which typically binds a DNA nucleotide triplet within a larger binding site. Frequent recombination and diversification of their DNA-contacting residues suggests that these zinc fingers play a prevalent role in adaptive evolution. Very little is known about the function and evolution of the vast majority of C2H2-ZFs, including whether they even bind DNA. Using the bacterial 1-hybrid (B1H) system, we determined DNA-binding motifs for thousands of individual natural C2H2-ZFs, and correlated them with the C2H2-ZF specificity residues. We generated 47,072 variants of the DNA-binding domain of the well-characterized three-C2H2-ZF protein Egr1, in which the third C2H2-ZF ('F3') was replaced with a natural C2H2-ZF. We screened this library using the bacterial 1-hybrid (B1H) system to assess the relative preference of each protein for 200 of the 256 possible NNN NGG GCG variants of the optimal Egr1 binding site, GCG TGG GCG, each in duplicate. Each sample might have been sequenced multiple times, in which case multiple raw and processed data files are indicated. This data represent bacterial 1-hybrid assays using three different "Original Library Samples", OLS-A, OLS-B, and OLS-C. The 'characteristics:OLS' indicates which OLS was used as the initial material for each of the assays. The processed data contains unique ID given to each sequence in the library and its abundance count. The 'OLS.info.xlsx' file contains the mapping of these IDs to different sequences.

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Comparative protein profiles of differentially temperature tolerant maize genotypes

Project description:Two maize genotypes exhibiting differential tolerance towards LT including the temperate grown Gurez local and its tropical counterpart GM6 were dissected for analysing and characterizing the functions of differentially regulated proteins (DRPs) in response to LT stress.

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Illumina sequencing analysis of mutagenicity of EvoluGene

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Proteome dynamics in persisting and resuscitating bacterial cells

Project description:Bacterial persister cells become transiently tolerant to antibiotics by restraining their growth and metabolic activity. Detailed molecular characterization of bacterial persistence is hindered by low count of persisting cells and the need for their isolation. Here we used sustained addition of stable isotope-labeled lysine to selectively label the proteome of hipA-induced persisting and hipB-induced resuscitating E. coli cells in minimal medium after antibiotic treatment. Time-resolved, 24-hour measurement of label incorporation allowed detection of more than 500 newly synthetized proteins in persister cells, demonstrating low but widespread protein synthesis during persistence. Many essential proteins were newly synthesized; several ribosome-associated proteins showed unusually high synthesis levels and are involved in maintenance of persistence. At the onset of resuscitation, cells synthesized ABC transporters, restored translation machinery and resumed metabolism by inducing glycolysis and biosynthesis of amino acids. This dataset provides an unprecedented insight into the processes governing persistence and resuscitation of bacterial cells.

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Myc-dependent transcriptome of Drosophila L3 larval wing imaginal discs, and its dependency on Max and/or the PAF1 complex component Atu/Leo1

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2017-10-02 | E-MTAB-5470 | biostudies-arrayexpress

Direct GR binding sites potentiate clusters of TF binding across the human genome [4]

Project description:The glucocorticoid receptor (GR) binds the human genome at >10,000 sites, but only regulates the expression of hundreds of genes. To determine the functional effect of each site, we measured the glucocorticoid (GC) responsive activity of nearly all GR binding sites (GBSs) captured using chromatin immunoprecipitation (ChIP) in A549 cells. 13% of GBSs assayed had GC-induced activity. The responsive sites were defined by direct GR binding via a GC response element (GRE) and exclusively increased reporter- gene expression. Meanwhile, most GBSs lacked GC-induced reporter activity. The non-responsive sites had epigenetic features of steady state enhancers and clustered around direct GBSs. Together, our data support a model in which clusters of GBSs observed with ChIP-seq reflect interactions between direct and tethered GBSs over tens of kilobases. We further show that those interactions can synergistically modulate the activity of direct GBSs, and may therefore play a major role in driving gene activation in response to GCs. Glucoroticoid receptor binding site chip-seq libraries were cloned into STARR-seq for massively parallel functional analysis. The results were confirmed by ChIP-Exo performed on the GR in A549 cells treated with 100 nM dexamethasone for one hour. This dataset [4] contains the sequences of GR ChIP-seq fragments that have been cloned into the STARR-seq backbone. [4] *.fragments files contain DNA fragments that were cloned into a massively parallel reporter assay. These fragments were generated via ChIP-seq for the glucororticoid receptor. The ChIP-seq library that was used for this source material was sequenced and the data from that sequencing was deposited in [8]. The [4] *.fragments file contains the abundance of each reporter plasmid produced by cloning the GR ChIP-seq library into the reporter vector.

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