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Article

Revealing the Metabolic Alterations during Biofilm Development of Burkholderia cenocepacia Based on Genome-Scale Metabolic Modeling

1
Science for Life Laboratory, KTH–Royal Institute of Technology, 171 65 Solna, Sweden
2
Department of Clinical Microbiology, Sami Ulus Training and Research Hospital, University of Health Sciences, Ankara 06080, Turkey
3
School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
4
Department of Medical Biology, Faculty of Medicine, Atatürk University, Erzurum 25 240, Turkey
5
Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
6
Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London SE1 9RT, UK
*
Author to whom correspondence should be addressed.
Academic Editors: Dario Pescini and Marzia Di Filippo
Metabolites 2021, 11(4), 221; https://doi.org/10.3390/metabo11040221
Received: 1 February 2021 / Revised: 26 March 2021 / Accepted: 2 April 2021 / Published: 5 April 2021
(This article belongs to the Special Issue Computational Biology for Metabolic Modelling)
Burkholderia cenocepacia is among the important pathogens isolated from cystic fibrosis (CF) patients. It has attracted considerable attention because of its capacity to evade host immune defenses during chronic infection. Advances in systems biology methodologies have led to the emergence of methods that integrate experimental transcriptomics data and genome-scale metabolic models (GEMs). Here, we integrated transcriptomics data of bacterial cells grown on exponential and biofilm conditions into a manually curated GEM of B. cenocepacia. We observed substantial differences in pathway response to different growth conditions and alternative pathway susceptibility to extracellular nutrient availability. For instance, we found that blockage of the reactions was vital through the lipid biosynthesis pathways in the exponential phase and the absence of microenvironmental lysine and tryptophan are essential for survival. During biofilm development, bacteria mostly had conserved lipid metabolism but altered pathway activities associated with several amino acids and pentose phosphate pathways. Furthermore, conversion of serine to pyruvate and 2,5-dioxopentanoate synthesis are also identified as potential targets for metabolic remodeling during biofilm development. Altogether, our integrative systems biology analysis revealed the interactions between the bacteria and its microenvironment and enabled the discovery of antimicrobial targets for biofilm-related diseases. View Full-Text
Keywords: Burkholderia cenocepacia; biofilm; genome-scale metabolic models; synthetic lethality; transcriptomics; omics integration Burkholderia cenocepacia; biofilm; genome-scale metabolic models; synthetic lethality; transcriptomics; omics integration
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MDPI and ACS Style

Altay, O.; Zhang, C.; Turkez, H.; Nielsen, J.; Uhlén, M.; Mardinoglu, A. Revealing the Metabolic Alterations during Biofilm Development of Burkholderia cenocepacia Based on Genome-Scale Metabolic Modeling. Metabolites 2021, 11, 221. https://doi.org/10.3390/metabo11040221

AMA Style

Altay O, Zhang C, Turkez H, Nielsen J, Uhlén M, Mardinoglu A. Revealing the Metabolic Alterations during Biofilm Development of Burkholderia cenocepacia Based on Genome-Scale Metabolic Modeling. Metabolites. 2021; 11(4):221. https://doi.org/10.3390/metabo11040221

Chicago/Turabian Style

Altay, Ozlem, Cheng Zhang, Hasan Turkez, Jens Nielsen, Mathias Uhlén, and Adil Mardinoglu. 2021. "Revealing the Metabolic Alterations during Biofilm Development of Burkholderia cenocepacia Based on Genome-Scale Metabolic Modeling" Metabolites 11, no. 4: 221. https://doi.org/10.3390/metabo11040221

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