Dataset Information

Transcriptional profiling of thymidine-producing strain recombineered from Escherichia coli BL21.

ABSTRACT: DNA microarrays were used to compare the expression profiles of a thymidine overproducing strain (BLT013) and its isogenic parent, Escherichia coli BL21(DE3), when each was grown under well-defined thymidine production conditions with glycerol as carbon source. Here we describe the experimental procedures and methods in detail to reproduce the results and provide resource to be applied to similar engineering approach (available at Gene Expression Omnibus database under GSE69963). Taken together, the microarray data provide a basis for new testable hypotheses regarding enhancement of thymidine productivity and attaining a more complete understanding of nucleotide metabolism in bacteria.

SUBMITTER: Kim JS

PROVIDER: S-EPMC4664681 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature

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Transcriptional profiling of thymidine-producing strain recombineered from Escherichia coli BL21.

Kim Jin-Sook JS Koo Bong-Seong BS Lee Hyeon-Cheol HC

Genomics data 20150814

DNA microarrays were used to compare the expression profiles of a thymidine overproducing strain (BLT013) and its isogenic parent, Escherichia coli BL21(DE3), when each was grown under well-defined thymidine production conditions with glycerol as carbon source. Here we describe the experimental procedures and methods in detail to reproduce the results and provide resource to be applied to similar engineering approach (available at Gene Expression Omnibus database under GSE69963). Taken together, ...[more]

PMID: 26697335

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Project description:BackgroundThe proteome reflects the available cellular machinery to deal with nutrients and environmental challenges. The most common E. coli strain BL21 growing in different, commonly employed media was evaluated using a detailed quantitative proteome analysis.ResultsThe presence of preformed biomass precursor molecules in rich media such as Luria Bertani supported rapid growth concomitant to acetate formation and apparently unbalanced abundances of central metabolic pathway enzymes, e.g. high levels of lower glycolytic pathway enzymes as well as pyruvate dehydrogenase, and low levels of TCA cycle and high levels of the acetate forming enzymes Pta and AckA. The proteome of cells growing exponentially in glucose-supplemented mineral salt medium was dominated by enzymes of amino acid synthesis pathways, contained more balanced abundances of central metabolic pathway enzymes, and a lower portion of ribosomal and other translational proteins. Entry into stationary phase led to a reconstruction of the bacterial proteome by increasing e.g. the portion of proteins required for scavenging rare nutrients and general cell protection. This proteomic reconstruction during entry into stationary phase was more noticeable in cells growing in rich medium as they have a greater reservoir of recyclable proteins from the translational machinery.ConclusionsThe proteomic comparison of cells growing exponentially in different media reflected the antagonistic and competitive regulation of central metabolic pathways through the global transcriptional regulators Cra, Crp, and ArcA. For example, the proteome of cells growing exponentially in rich medium was consistent with a dominating role of phosphorylated ArcA most likely a result from limitations in reoxidizing reduced quinones in the respiratory chain under these growth conditions. The proteomic alterations of exponentially growing cells into stationary phase cells were consistent with stringent-like and stationary phase responses and a dominating control through DksA-ppGpp and RpoS.

Dataset Information

Transcriptional profiling of thymidine-producing strain recombineered from Escherichia coli BL21.

Publications

Transcriptional profiling of thymidine-producing strain recombineered from Escherichia coli BL21.

Similar Datasets

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