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

Çalık, Pınar
Ozdamar, Tuncer H.
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.


Analyses of extracellular protein production in Bacillus subtilis - I: Genome-scale metabolic model reconstruction based on updated gene-enzyme-reaction data
KOCABAŞ, PINAR; Çalık, Pınar; ÇALIK GARCİA, GÜZİDE; Ozdamar, Tuncer H. (Elsevier BV, 2017-11-15)
Bacillus subtilis genome-scale model (GEM) reconstruction was stimulated by the recent sequencing and consequent re-annotations. The updated gene-enzyme-reaction data were collected from databases to reconstruct B. subtilis reaction network BsRN-2016 containing 1144 genes linked to 1955 reactions and 1103 metabolites. Thermodynamic analysis was conducted to identify reversibility and directionality of the reactions. By elimination of unconnected-reactions from BsRN-2016, reconstruction process of the first ...
Covalent immobilization of chloroperoxidase onto magnetic beads: Catalytic properties and stability
Bayramoglu, Guelay; Kiralp, Senem; Yilmaz, Meltem; Toppare, Levent Kamil; Arica, M. Yakup (Elsevier BV, 2008-02-15)
Amino groups containing magnetic beads were used in covalent immobilization of the enzyme "chloroperoxidase (CPO)" which is one of a few enzymes that can catalyse the peroxide dependent oxidation of a wide spectrum of organic and inorganic compounds. The magnetic poly(glycidylmethacrylate-methylmethacrylate-etbyleneglycol dimethacrylate), magnetic p(GMA-MMA-EGDMA) beads were prepared via suspension polymerization in the presence of ferric ions. The magnetic beads were characterized with scanning electron mi...
In planta determination of GaMyb transcription factor as a target of pathogen induced microRNA, mir159
Akkaya, Mahinur; Dagdas, Gulay Gok; Dagdas, Yasin F. (2011-09-01)
One of the molecular mechanisms underlying the plant–pathogen interactions is the regulation of gene expressions in plant responses by microRNAs which are either stimulated or silenced against pathogen attacks. Among the plant miRNAs, we found that mir159 is one of which that differentially expressed upon Blumeria graminis f. sp. hordei (Bgh) infected resistant and susceptible barley lines. The study aims to confirm its role in regulating one of its putative target genes, GaMyb transcription factor, in vivo...
Carbon sources affect metabolic capacities of Bacillus species for the production of industrial enzymes: theoretical analyses for serine and neutral proteases and alpha-amylase
Çalık, Pınar (Elsevier BV, 2001-07-01)
The metabolic fluxes through the central carbon pathways were calculated for the genus Bacillus separately for the enzymes serine alkaline protease (SAP), neutral protease (NP) and alpha -amylase (AMY) on five carbon sources that have different reduction degrees (gamma), to determine the theoretical ultimate limits of the production capacities of Bacillus species and to predict the selective substrate for the media design. Glucose (gamma = 4.0), acetate (gamma = 4.0), and the TCA cycle organic-acids succina...
QCM-based DNA biosensor for detection of genetically modified organisms (GMOs)
Karamollaoglu, Irem; Oektem, Hueseyin Avni; Mutlu, Mehmet Kayhan (Elsevier BV, 2009-05-15)
Development of a mass sensitive quartz crystal microbalance (QCM)-based DNA biosensor for the detection of the hybridization of CaMV 35S promoter sequence (P35S) was investigated for the screening of genetically modified organisms (GMOs). Attention was focused on the choice of the coating chemistry that could be used for the immobilization of probe sequences on the gold surface of the quartz crystal. Two immobilization procedures were tested and compared considering the amount of the immobilized P35S probe ...
Citation Formats
P. KOCABAŞ, G. ÇALIK GARCİA, P. Çalık, and T. H. Ozdamar, “Analyses of extracellular protein production in Bacillus subtilis - II: Responses of reaction network to oxygen transfer at transcriptional level,” BIOCHEMICAL ENGINEERING JOURNAL, pp. 242–261, 2017, Accessed: 00, 2020. [Online]. Available: