Dataset Information

Gene Expression Order Attributed to Genome Reduction and the Steady Cellular State in Escherichia coli.

ABSTRACT: Transcriptomes not only reflect the growth status but also link to the genome in bacteria. To investigate if and how genome or cellular state changes contribute to the gene expression order, the growth profile-associated transcriptomes of an assortment of genetically differentiated Escherichia coli either exponentially growing under varied conditions or in response to environmental disturbance were analyzed. A total of 168 microarray data sets representing 56 transcriptome variations, were categorized by genome size (full length or reduced) and cellular state (steady or unsteady). At the genome-wide level, the power-law distribution of gene expression was found to be significantly disturbed by the genome size but not the cellular state. At the regulatory network level, more networks with improved coordination of growth rates were observed in genome reduction than at the steady state. At the single-gene level, both genome reduction and steady state increased the correlation of gene expression to growth rate, but the enriched gene categories with improved correlations were different. These findings not only illustrate the order of gene expression attributed to genome reduction and steady cellular state but also indicate that the accessory sequences acquired during genome evolution largely participated in the coordination of transcriptomes to growth fitness.

SUBMITTER: Ying BW

PROVIDER: S-EPMC6158460 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Gene Expression Order Attributed to Genome Reduction and the Steady Cellular State in <i>Escherichia coli</i>.

Ying Bei-Wen BW Yama Kazuma K

Frontiers in microbiology 20180920

Transcriptomes not only reflect the growth status but also link to the genome in bacteria. To investigate if and how genome or cellular state changes contribute to the gene expression order, the growth profile-associated transcriptomes of an assortment of genetically differentiated <i>Escherichia coli</i> either exponentially growing under varied conditions or in response to environmental disturbance were analyzed. A total of 168 microarray data sets representing 56 transcriptome variations, wer ...[more]

PMID: 30294319

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Project description:BACKGROUND:The genome-integrated T7 expression system offers significant advantages, in terms of productivity and product quality, even when expressing the gene of interest (GOI) from a single copy. Compared to plasmid-based expression systems, this system does not incur a plasmid-mediated metabolic load, and it does not vary the dosage of the GOI during the production process. However, long-term production with T7 expression system leads to a rapidly growing non-producing population, because the T7 RNA polymerase (RNAP) is prone to mutations. The present study aimed to investigate whether two ?70 promoters, which were recognized by the Escherichia coli host RNAP, might be suitable in genome-integrated expression systems. We applied a promoter engineering strategy that allowed control of expressing the model protein, GFP, by introducing lac operators (lacO) into the constitutive T5 and A1 promoter sequences. RESULTS:We showed that, in genome-integrated E. coli expression systems that used ?70 promoters, the number of lacO sites must be well balanced. Promoters containing three and two lacO sites exhibited low basal expression, but resulted in a complete stop in recombinant protein production in partially induced cultures. In contrast, expression systems regulated by a single lacO site and the lac repressor element, lacIQ, on the same chromosome caused very low basal expression, were highly efficient in recombinant protein production, and enables fine-tuning of gene expression levels on a cellular level. CONCLUSIONS:Based on our results, we hypothesized that this phenomenon was associated with the autoregulation of the lac repressor protein, LacI. We reasoned that the affinity of LacI for the lacO sites of the GOI must be lower than the affinity of LacI to the lacO sites of the endogenous lac operon; otherwise, LacI autoregulation could not take place, and the lack of LacI autoregulation would lead to a disturbance in lac repressor-mediated regulation of transcription. By exploiting the mechanism of LacI autoregulation, we created a novel E. coli expression system for use in recombinant protein production, synthetic biology, and metabolic engineering applications.

Dataset Information

Gene Expression Order Attributed to Genome Reduction and the Steady Cellular State in Escherichia coli.

Publications

Gene Expression Order Attributed to Genome Reduction and the Steady Cellular State in <i>Escherichia coli</i>.

Similar Datasets

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