Attractor Concepts to Evaluate the Transcriptome-wide Dynamics Guiding Anaerobic to Aerobic State Transition in Escherichia coli.

Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE

Original Publication: London : Nature Publishing Group, copyright 2011-

Transcriptome*/genetics; Aerobiosis/*genetics ; Escherichia coli/*metabolism; Aerobiosis/physiology ; Anaerobiosis/genetics ; Anaerobiosis/physiology ; Escherichia coli/genetics ; Escherichia coli/physiology ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial/genetics ; Gene Expression Regulation, Bacterial/physiology ; Genes, Bacterial/physiology

For any dynamical system, like living organisms, an attractor state is a set of variables or mechanisms that converge towards a stable system behavior despite a wide variety of initial conditions. Here, using multi-dimensional statistics, we investigate the global gene expression attractor mechanisms shaping anaerobic to aerobic state transition (AAT) of Escherichia coli in a bioreactor at early times. Out of 3,389 RNA-Seq expression changes over time, we identified 100 sharply changing genes that are key for guiding 1700 genes into the AAT attractor basin. Collectively, these genes were named as attractor genes constituting of 6 dynamic clusters. Apart from the expected anaerobic (glycolysis), aerobic (TCA cycle) and fermentation (succinate pathways) processes, sulphur metabolism, ribosome assembly and amino acid transport mechanisms together with 332 uncharacterised genes are also key for AAT. Overall, our work highlights the importance of multi-dimensional statistical analyses for revealing novel processes shaping AAT.

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Date Created: 20200405 Date Completed: 20201125 Latest Revision: 20210403

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