Analyses of extracellular protein production in Bacillus subtilis - II: Responses of reaction network to oxygen transfer at transcriptional level

Kocabas P. , Calik G., ÇALIK P., Ozdamar T. H.

BIOCHEMICAL ENGINEERING JOURNAL, vol.127, pp.242-261, 2017 (Journal Indexed in SCI) identifier identifier

  • Publication Type: Article / Article
  • Volume: 127
  • Publication Date: 2017
  • Doi Number: 10.1016/j.bej.2017.07.004
  • Page Numbers: pp.242-261


Oxygen transfer influences intracellular fluxes which are orchestrated by genome and its transcription in Bacillus subtilis throughout fermentation in recombinant human growth hormone (rhGH) production. Responses of B. subtilis reaction network to oxygen transfer were analysed at transcriptional level with determined transcriptome and calculated intracellular fluxes by the reconstructed genome scale model iBsu1144(rhGH) based on updated gene-enzyme-reaction data. iBsu1144(rhGH) employing 1067 reactions linked to 719 genes was solved using time-profiles of rhGH fermentation data at three oxygen transfer conditions from low- to high-to create perturbations on the intracellular reaction-network. Insights obtained from transcriptional and metabolic responses were used to determine metabolic engineering sites. Flux variability analyses results reveal that 305 reactions are active, linked to 346 genes so called substantial genes; and, 730 reactions linked to 536 genes blocked in rhGH synthesis were determined with their enzymes, genes, and reaction fluxes to create a platform for guided gene deletions. Effects of oxygen transfer on the transcriptome of r-B. subtilis carrying hGH gene were investigated further with one-way analysis of variance with the confidence greater than 99.5% and the expression ratios greater than 3. Fifty probe sets were found to be significantly affected from oxygen transfer where eight genes performed different transcriptional and metabolic responses to oxygen transfer and determined as metabolic engineering sites besides scoC and degU. (C) 2017 Elsevier B.V. All rights reserved.