ArticleBMC genomics2013
Multilevel comparative analysis of the contributions of genome reduction and heat shock to the Escherichia coli transcriptome.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Data-driven analysis reveals distinct genomic and environmental contributions to bacterial growth curves.Scientific reports · 2025Article
- Article
- Response and adaptation of the transcriptional heat shock response to pressure.Frontiers in microbiology · 2024Article
- Engineering resource allocation in artificially minimized cells: Is genome reduction the best strategy?Microbial biotechnology · 2023Article
- Machine learning-assisted medium optimization revealed the discriminated strategies for improved production of the foreign and native metabolites.Computational and structural biotechnology journal · 2023Article
- Growth rate-associated transcriptome reorganization in response to genomic, environmental, and evolutionary interruptions.Frontiers in microbiology · 2023Article
- Article
- Correlated chromosomal periodicities according to the growth rate and gene expression.Scientific reports · 2020Article
- The highly conserved chromosomal periodicity of transcriptomes and the correlation of its amplitude with the growth rate in Escherichia coli.DNA research : an international journal for rapid publication of reports on genes and genomes · 2020Article
- Experimental Challenges for Reduced Genomes: The Cell ModelMicroorganisms · 2019Review
- Gene Expression Order Attributed to Genome Reduction and the Steady Cellular State inFrontiers in microbiology · 2018Article
- Article
- Correlation between genome reduction and bacterial growth.DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
- The Escherichia coli transcriptome linked to growth fitness.Genomics data · 2016Article
- Bacterial transcriptome reorganization in thermal adaptive evolution.BMC genomics · 2015Article
- Global relationships in fluctuation and response in adaptive evolution.Journal of the Royal Society, Interface · 2015Article
- Global coordination in adaptation to gene rewiring.Nucleic acids research · 2015Article
- A reduced genome decreases the host carrying capacity for foreign DNA.Microbial cell factories · 2014Article
- Growth rate-coordinated transcriptome reorganization in bacteria.BMC genomics · 2013Article
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5 authors.
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Abstract
backgroundBoth large deletions in genome and heat shock stress would lead to alterations in the gene expression profile; however, whether there is any potential linkage between these disturbances to the transcriptome have not been discovered. Here, the relationship between the genomic and environmental contributions to the transcriptome was analyzed by comparing the transcriptomes of the bacterium Escherichia coli (strain MG1655 and its extensive genomic deletion derivative, MDS42) grown in regular and transient heat shock conditions.
resultsThe transcriptome analysis showed the following: (i) there was a reorganization of the transcriptome in accordance with preferred chromosomal periodicity upon genomic or heat shock perturbation; (ii) there was a considerable overlap between the perturbed regulatory networks and the categories enriched for differentially expressed genes (DEGs) following genome reduction and heat shock; (iii) the genes sensitive to genome reduction tended to be located close to genomic scars, and some were also highly responsive to heat shock; and (iv) the genomic and environmental contributions to the transcriptome displayed not only a positive correlation but also a negatively compensated relationship (i.e., antagonistic epistasis).
conclusionThe contributions of genome reduction and heat shock to the Escherichia coli transcriptome were evaluated at multiple levels. The observations of overlapping perturbed networks, directional similarity in transcriptional changes, positive correlation and epistatic nature linked the two contributions and suggest somehow a crosstalk guiding transcriptional reorganization in response to both genetic and environmental disturbances in bacterium E. coli.
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