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Multiomics Study of Bacterial Growth Arrest in a Synthetic Biology Application

  • Delphine Ropers
    Delphine Ropers
    Université Grenoble Alpes, Inria, 38000 Grenoble, France
  • Yohann Couté
    Yohann Couté
    Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
  • Laëtitia Faure
    Laëtitia Faure
    Metabolic Explorer SA, 63360 Saint-Bauzire, France
  • Sabrina Ferré
    Sabrina Ferré
    Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
  • Delphine Labourdette
    Delphine Labourdette
    GeT-Biopuces, TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
  • Arieta Shabani
    Arieta Shabani
    Université Grenoble Alpes, Inria, 38000 Grenoble, France
  • Lidwine Trouilh
    Lidwine Trouilh
    GeT-Biopuces, TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
  • Perrine Vasseur
    Perrine Vasseur
    Metabolic Explorer SA, 63360 Saint-Bauzire, France
  • Gwénaëlle Corre
    Gwénaëlle Corre
    Metabolic Explorer SA, 63360 Saint-Bauzire, France
  • Myriam Ferro
    Myriam Ferro
    Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
    More by Myriam Ferro
  • Marie-Ange Teste
    Marie-Ange Teste
    GeT-Biopuces, TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
  • Johannes Geiselmann
    Johannes Geiselmann
    Université Grenoble Alpes, Inria, 38000 Grenoble, France
    Université Grenoble Alpes, CNRS, LIPhy, 38000 Grenoble, France
  • , and 
  • Hidde de Jong*
    Hidde de Jong
    Université Grenoble Alpes, Inria, 38000 Grenoble, France
    *Email: [email protected]. Phone: +33 4 76 61 53 35.
Cite this: ACS Synth. Biol. 2021, 10, 11, 2910–2926
Publication Date (Web):November 5, 2021
https://doi.org/10.1021/acssynbio.1c00115
Copyright © 2021 American Chemical Society

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    Supporting Info (10)»

    Abstract

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    We investigated the scalability of a previously developed growth switch based on external control of RNA polymerase expression. Our results indicate that, in liter-scale bioreactors operating in fed-batch mode, growth-arrested Escherichia coli cells are able to convert glucose to glycerol at an increased yield. A multiomics quantification of the physiology of the cells shows that, apart from acetate production, few metabolic side effects occur. However, a number of specific responses to growth slow-down and growth arrest are launched at the transcriptional level. These notably include the downregulation of genes involved in growth-associated processes, such as amino acid and nucleotide metabolism and translation. Interestingly, the transcriptional responses are buffered at the proteome level, probably due to the strong decrease of the total mRNA concentration after the diminution of transcriptional activity and the absence of growth dilution of proteins. Growth arrest thus reduces the opportunities for dynamically adjusting the proteome composition, which poses constraints on the design of biotechnological production processes but may also avoid the initiation of deleterious stress responses.

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    Supporting Information

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    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acssynbio.1c00115.

    • Transcription factors and sigma factors associated with over- or underexpressed genes and proteins between pairs of conditions, time–series profiles of metabolite concentrations, mRNA read counts, and protein abundances, additional analyses and results of the transcriptomic and proteomic data, including their correlation with computed promoter strengths, details on data integration software, primary data of the physiological, metabolomics, proteomics, and transcriptomics experiments, results of the differential expression and enrichment analyses, and the MATLAB code of data integration software (PDF)

    • Measured total protein concentrations, total RNA concentrations, and total mRNA concentrations of W-gly and R-gly strains (XLSX)

    • OD600 measurements and quantification of external metabolites and yield (XLS)

    • Transcriptomic analysis of mRNA contents of W-gly and R-gly strains (XLSX)

    • Differential expression of mRNAs between growth conditions (XLSX)

    • Quantitative proteomic analysis of total protein contents of W-gly and R-gly strains in the production phase (XLSX)

    • Results of enrichment analysis of GO categories (XLS)

    • Results of enrichment analysis of transcription factors (XLS)

    • Results of enrichment analysis of sigma factors (XLS)

    • MATLAB code of data integration software (ZIP)

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