A novel algorithm to calculate elementary modes: Analysis of Campylobacter jejuni metabolism.

Autor: Said Y; Cell Systems Modelling Group, Oxford Brookes University, Oxford, OX3 0BP, UK; Department of Mathematics, University of Malta, Msida, MSD 2080, Malta., Singh D; Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK., Sebu C; Department of Mathematics, University of Malta, Msida, MSD 2080, Malta., Poolman M; Cell Systems Modelling Group, Oxford Brookes University, Oxford, OX3 0BP, UK. Electronic address: mgpoolman@brookes.ac.uk.
Jazyk: angličtina
Zdroj: Bio Systems [Biosystems] 2023 Oct 27, pp. 105047. Date of Electronic Publication: 2023 Oct 27.
DOI: 10.1016/j.biosystems.2023.105047
Abstrakt: We describe a novel algorithm, 'LPEM', that given a steady-state flux vector from a (possibly genome-scale) metabolic model, decomposes that vector into a set of weighted elementary modes such that the sum of these elementary modes is equal to the original flux vector. We apply the algorithm to a genome scale metabolic model of the human pathogen Campylobacter jejuni. This organism is unusual in that it has an absolute growth requirement for oxygen, despite being able to operate the electron transport chain anaerobically. We conclude that (1) Microaerophilly in C. jejuni can be explained by the dependence of pyridoxine 5 ' -phosphate oxidase for the synthesis of pyridoxal 5 ' - phosphate (the biologically active form of vitamin B6), (2) The LPEM algorithm is capable of determining the elementary modes of a linear programming solution describing the simultaneous production of 51 biomass precursors, (3) Elementary modes for the production of individual biomass precursors are significantly more complex when all others are produced simultaneously than those for the same product in isolation and (4) The sum of elementary modes for the production of all precursors in isolation requires a greater number of reactions and overall total flux than the simultaneous production of all precursors.
Competing Interests: Declaration of competing interest All authors have participated in (a) conception and design, or analysis and interpretation of the data; (b) drafting the article or revising it critically for important intellectual content; and (c) approval of the final version. This manuscript has not been submitted to, nor is under review at, another journal or other publishing venue. The authors have no affiliation with any organization with a direct or indirect financial interest in the subject matter discussed in the manuscript. The authors declare no conflict of interest.
(Copyright © 2023. Published by Elsevier B.V.)
Databáze: MEDLINE
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