Transcriptomics

Dataset Information

43

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: Yoshie Murakami  Tetsuya Yomo   Bei-Wen Ying    

PROVIDER: E-GEOD-55719 | ArrayExpress | 2015-01-17

SECONDARY ACCESSION(S): GSE55719PRJNA240778

REPOSITORIES: GEO, 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]

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