Analyses of extracellular protein production in Bacillus subtilis - I: Genome-scale metabolic model reconstruction based on updated gene-enzyme-reaction data

Date

2017-11-15

Author

KOCABAŞ, PINAR
Çalık, Pınar
ÇALIK GARCİA, GÜZİDE
Ozdamar, Tuncer H.

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

24
views

0
downloads

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 third-generation GEM iBsu1 144 employing 1083 reactions linked to 719 genes was completed. The stoichiometric flux-balance based model was solved using time-profiles of serine alkaline protease fermentation-data at three different oxygen-transfer conditions creating perturbations on the intracellular reaction-network. Testing iBsu1 144 dignity with three different objective functions indicated superior robustness of the GEM. Comparison of iBsu1 144 results with a second-generation GEM was demonstrated. Insights obtained from flux distributions were used to determine metabolic engineering sites. Asparagine, isoleucine, threonine, and aspartic acid were determined as the primary rate-limiting amino acids to be considered as corresponding metabolic engineering sites in SAP synthesis in B. subtilis. Flux variability analysis carried out for the optimum condition reveals that 288 reactions are active and linked to 317 genes, so called substantial genes. The blocked 735 reactions linked to 533 genes, formed a platform for guided, gene deletions in B. subtilis to generate simplified host strains.

Subject Keywords

Biotechnology, Environmental Engineering, Bioengineering, Biomedical Engineering

URI

https://hdl.handle.net/11511/43929

Journal

BIOCHEMICAL ENGINEERING JOURNAL

DOI

https://doi.org/10.1016/j.bej.2017.07.005

Collections

Department of Chemical Engineering, Article

Suggestions

OpenMETU
Core

Analyses of extracellular protein production in Bacillus subtilis - II: Responses of reaction network to oxygen transfer at transcriptional level KOCABAŞ, PINAR; ÇALIK GARCİA, GÜZİDE; Çalık, Pınar; Ozdamar, Tuncer H. (Elsevier BV, 2017-11-15) 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 link...
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 ...
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...
Biodegradation of 4-CP and 2,4-DCP mixture in a rotating biological contactor (RBC) şahinkaya, Erkan; Dilek, Filiz Bengü (Elsevier BV, 2006-09-01) In this study, the performance of a two stage rotating biological contactor (RBC) was evaluated for the treatment of synthetic wastewater containing peptone, 4-chlorophenol (4-CP) and 2,4-dichlorophenol (2,4-DCP) at 5 rpm. Also, the effect of biogenic substrate (peptone) concentration on the reactor performance was investigated. High chlorophenols (> 98%) and COD (> 94%) removals were achieved throughout the reactor operation in the first stage and the second stage behaved as a polishing step. The observed ...
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...

Citation Formats

P. KOCABAŞ, P. Çalık, G. ÇALIK GARCİA, and T. H. Ozdamar, “Analyses of extracellular protein production in Bacillus subtilis - I: Genome-scale metabolic model reconstruction based on updated gene-enzyme-reaction data,” BIOCHEMICAL ENGINEERING JOURNAL, pp. 229–241, 2017, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/43929.