Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcriptome reorganization of gene-rewired Escherichia coli cells in response to histidine depletion

ABSTRACT: An assortment of genetically engineered Escherichia coli strains of the rewired gene regulation were used to study whether the cells could adapt to the environmental changes without the evolved gene regulatory machinaries. These E. coli strains had a synthetic gene circuit comprising a rewried gene that natively located within the His opeon. The cells growing under histidine supplied or depleted conditions were subjected to the macrioarray analysis. Multilevel analyses were performed to evaluate the global reorganization of gene expression in response to histidine depletion. A common pattern in transcriptome was observed in the adpative cells, indicating a survival strategy of "stochastic adaptation with regular transcriptome reorganization". The genetically engineered strains of rewired genes and the control strain of the native gene regulation were grown in the presence and absence of histidine, and the cells within the exponetially growing phase were collected for the microarray analysis. Temproal changes in response to histidine depletion were also investigated. Every 3 biological replications for each condition were performed. Total 90 array assays were reported here.

ORGANISM(S): Escherichia coli

SUBMITTER: Bei-Wen Ying

PROVIDER: E-GEOD-55719 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Global coordination in adaptation to gene rewiring.

Murakami Yoshie Y Matsumoto Yuki Y Tsuru Saburo S Ying Bei-Wen BW Yomo Tetsuya T

Nucleic acids research 20150106 2

Gene rewiring is a common evolutionary phenomenon in nature that may lead to extinction for living organisms. Recent studies on synthetic biology demonstrate that cells can survive genetic rewiring. This survival (adaptation) is often linked to the stochastic expression of rewired genes with random transcriptional changes. However, the probability of adaptation and the underlying common principles are not clear. We performed a systematic survey of an assortment of gene-rewired Escherichia coli s ...[more]

PMID: 25564530

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Project description:This dataset contains transcription profiles of TOP10 E.coli transformed with 85 rewired network plasmids first described in: Evolvability and hierarchy in rewired bacterial gene networks. Nature 452:840-5 (2008). The data are described and analysed in an accompanying paper Baumstark et al.,The propagation of perturbations in shuffled bacterial gene networks (Submitted, 2015). 260 raw data microarrays are provided in total, representing biological triplicates (a,b and c; independent colonies grown from the same transformation, under standard growth conditions; LB, 16h). This is done for each of 255 promoter-ORF constructs (e.g. appY-crp, etc.) and 5 control construct microarrays (empty plasmid; Co). Co controls are provided for comparison, to show the relative effect of the rewiring genetic perturbation. The final processed data compares the number of perturbed genes, comparing between the average expression values of each rewired construct and Co. Methods: The 85 rewiring plasmids (Isalan et al, 2008) were transformed into E. coli TOP10 cells and grown under standardised conditions: bacteria were freshly plated onto LB Agar plates (with 100 μg/ml Ampicillin and 50 μg/ml Streptomycin) and incubated overnight at 37oC to form colonies. Single colonies (<3 days old) were used to inoculate 2 ml of LB in 14 ml culture tubes, containing 100 μg/ml Ampicillin and 50 μg/ml Streptomycin. Constructs were grown for 16h at 37oC, at 220 rpm in an orbital shaker. 10 μg of extracted total bacterial RNA (integrity number > 7.0) was used with Affymetrix GeneChip E. coli Genome 2.0 Arrays. Key to names: RAW DATA samples 1-260 _Co_1a.CEL = Control Co, colony a _Co_1b.CEL = Control Co, colony b etc. appY_O_30a.CEL = appY-promoter only, colony a appY_O_30b.CEL = appY-promoter only, colony b etc. appY_crp_34a.CEL = rewired construct, appY-promoter expressing crp ORF, colony a appY_crp_34b.CEL = rewired construct, appY-promoter expressing crp ORF, colony b appY_crp_34b.CEL = rewired construct, appY-promoter expressing crp ORF, colony c etc. PROCESSED DATA sample 261: probe_set_expression_value_norm_all - normalised data for all samples, for all E. coli K12 genes sample 262: probe_set_expression_value_norm_MG1655 - normalised data for all samples, for E. coli MG1655 subset of genes

Dataset Information

Transcriptome reorganization of gene-rewired Escherichia coli cells in response to histidine depletion

Publications

Global coordination in adaptation to gene rewiring.

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