Sharma2022 - Temperature-dependent NAD biosynthesis model

  public model
Model Identifier
MODEL2103290001
Short description

A computational mathematical model of NAD biosynthesis via PncA and Nampt pathway in thermophiles. It includes the temperature dependence of the reaction rates.

Format
SBML (L2V4)
Related Publication
  • Early Evolutionary Selection of NAD Biosynthesis Pathway in Bacteria
  • Suraj Sharma, Yin-Chen Hsieh, Jörn Dietze, Mathias Bockwoldt, \Oyvind Str\omland, Mathias Ziegler, Ines Heiland
  • Metabolites , 6/ 2022 , Volume 12 , Issue 7 , pages: 569 , DOI: 10.3390/metabo12070569
  • Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, 9037 Tromsø, Norway
  • Bacteria use two alternative pathways to synthesize nicotinamide adenine dinucleotide (NAD) from nicotinamide (Nam). A short, two-step route proceeds through nicotinamide mononucleotide (NMN) formation, whereas the other pathway, a four-step route, includes the deamidation of Nam and the reamidation of nicotinic acid adenine dinucleotide (NAAD) to NAD. In addition to having twice as many enzymatic steps, the four-step route appears energetically unfavourable, because the amidation of NAAD includes the cleavage of ATP to AMP. Therefore, it is surprising that this pathway is prevalent not only in bacteria but also in yeast and plants. Here, we demonstrate that the considerably higher chemical stability of the deamidated intermediates, compared with their amidated counterparts, might compensate for the additional energy expenditure, at least at elevated temperatures. Moreover, comprehensive bioinformatics analyses of the available >6000 bacterial genomes indicate that an early selection of one or the other pathway occurred. The mathematical modelling of the NAD pathway dynamics supports this hypothesis, as there appear to be no advantages in having both pathways.
Contributors
Submitter of the first revision: Suraj Sharma
Submitter of this revision: Suraj Sharma
Modellers: Suraj Sharma

Metadata information

hasProperty
Mathematical Modelling Ontology Mathematical model
Mathematical Modelling Ontology Ordinary differential equation model

Curation status
Non-curated


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Sharma2022_NAD_biosynthesis.xml A temperature-dependent model of NAD biosynthesis via PncA and Nampt pathway in bacteria 260.83 KB Preview | Download

  • Model originally submitted by : Suraj Sharma
  • Submitted: May 18, 2022 9:59:52 AM
  • Last Modified: Jul 19, 2022 12:36:25 PM
Revisions
  • Version: 5 public model Download this version
    • Submitted on: Jul 19, 2022 12:36:25 PM
    • Submitted by: Suraj Sharma
    • With comment: Model revised without commit message
  • Version: 4 public model Download this version
    • Submitted on: May 18, 2022 9:59:52 AM
    • Submitted by: Suraj Sharma
    • With comment: Model revised without commit message

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