EMUlator: An Elementary Metabolite Unit (EMU) Based Isotope Simulator Enabled by Adjacency Matrix

Chao Wu, Jonathan Lo, William Michener, Pin-Ching Maness, Wei Xiong, Xhia-hsin Chen

Research output: Contribution to journalArticlepeer-review

4 Scopus Citations

Abstract

Stable isotope based metabolic flux analysis is currently the unique methodology that allows the experimental study of the integrated responses of metabolic networks. This method primarily relies on isotope labeling and modeling, which could be a challenge in both experimental and computational biology. In particular, the algorithm implementation for isotope simulation is a critical step, limiting extensive usage of this powerful approach. Here, we introduce EMUlator a Python-based isotope simulator which is developed on Elementary Metabolite Unit (EMU) algorithm, an efficient and powerful algorithm for isotope modeling. We propose a novel adjacency matrix method to implement EMU modeling and exemplify it stepwise. This method is intuitively straightforward and can be conveniently mastered for various customized purposes. We apply this arithmetic pipeline to understand the phosphoketolase flux in the metabolic network of an industrial microbe Clostridium acetobutylicum. The resulting design enables a high-throughput and non-invasive approach for estimating phosphoketolase flux in vivo. Our computational insights allow the systematic design and prediction of isotope-based metabolic models and yield a comprehensive understanding of their limitations and potentials.

Original languageAmerican English
Article number922
Number of pages12
JournalFrontiers in Microbiology
Volume10
Issue numberAPR
DOIs
StatePublished - 2019

Bibliographical note

Publisher Copyright:
© 2019 Wu, Chen, Lo, Michener, Maness and Xiong. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

NREL Publication Number

  • NREL/JA-2700-73924

Keywords

  • Adjacency matrix
  • Clostridium acetobutylicum
  • Elementary metabolite unit (EMU)
  • Fractional labeling (FL)
  • Phosphoketolase

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