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Title: Identifying apparent local stable isotope equilibrium in a complex non-equilibrium system

Abstract

Rationale Although being out of equilibrium, biomolecules in organisms have the potential to approach isotope equilibrium locally because enzymatic reactions are intrinsically reversible. A rigorous approach that can describe isotope distribution among biomolecules and their apparent deviation from equilibrium state is lacking, however. Methods Applying the concept of distance matrix in graph theory, we propose that apparent local isotope equilibrium among a subset of biomolecules can be assessed using an apparent fractionation difference (|Δα|) matrix, in which the differences between the observed isotope composition (δ') and the calculated equilibrium fractionation factor (1000lnβ) can be more rigorously evaluated than by using a previous approach for multiple biomolecules. We tested our |Δα| matrix approach by re‐analyzing published data of different amino acids (AAs) in potato and in green alga. Results Our re‐analysis shows that biosynthesis pathways could be the reason for an apparently close‐to‐equilibrium relationship inside AA families in potato leaves. Different biosynthesis/degradation pathways in tubers may have led to the observed isotope distribution difference between potato leaves and tubers. The analysis of data from green algae does not support the conclusion that AAs are further from equilibrium in glucose‐cultured green algae than in the autotrophic ones. Conclusions Application of the |Δα|more » matrix can help us to locate potential reversible reactions or reaction networks in a complex system such as a metabolic system. The same approach can be broadly applied to all complex systems that have multiple components, e.g. geochemical or atmospheric systems of early Earth or other planets.« less

Authors:
ORCiD logo [1];  [1];  [1];  [1]
  1. Department of Geology and Geophysics, Louisiana State University, E235 Howe Russell Kniffen Baton Rouge LA 70803 USA
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory-National Energy Research Scientific Computing Center (NERSC)
Sponsoring Org.:
USDOE
OSTI Identifier:
1543484
Resource Type:
Journal Article
Journal Name:
Rapid Communications in Mass Spectrometry
Additional Journal Information:
Journal Volume: 32; Journal Issue: 4; Journal ID: ISSN 0951-4198
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
Biochemistry & Molecular Biology; Chemistry; Spectroscopy

Citation Formats

He, Yuyang, Cao, Xiaobin, Wang, Jianwei, and Bao, Huiming. Identifying apparent local stable isotope equilibrium in a complex non-equilibrium system. United States: N. p., 2018. Web. doi:10.1002/rcm.8040.
He, Yuyang, Cao, Xiaobin, Wang, Jianwei, & Bao, Huiming. Identifying apparent local stable isotope equilibrium in a complex non-equilibrium system. United States. doi:10.1002/rcm.8040.
He, Yuyang, Cao, Xiaobin, Wang, Jianwei, and Bao, Huiming. Tue . "Identifying apparent local stable isotope equilibrium in a complex non-equilibrium system". United States. doi:10.1002/rcm.8040.
@article{osti_1543484,
title = {Identifying apparent local stable isotope equilibrium in a complex non-equilibrium system},
author = {He, Yuyang and Cao, Xiaobin and Wang, Jianwei and Bao, Huiming},
abstractNote = {Rationale Although being out of equilibrium, biomolecules in organisms have the potential to approach isotope equilibrium locally because enzymatic reactions are intrinsically reversible. A rigorous approach that can describe isotope distribution among biomolecules and their apparent deviation from equilibrium state is lacking, however. Methods Applying the concept of distance matrix in graph theory, we propose that apparent local isotope equilibrium among a subset of biomolecules can be assessed using an apparent fractionation difference (|Δα|) matrix, in which the differences between the observed isotope composition (δ') and the calculated equilibrium fractionation factor (1000lnβ) can be more rigorously evaluated than by using a previous approach for multiple biomolecules. We tested our |Δα| matrix approach by re‐analyzing published data of different amino acids (AAs) in potato and in green alga. Results Our re‐analysis shows that biosynthesis pathways could be the reason for an apparently close‐to‐equilibrium relationship inside AA families in potato leaves. Different biosynthesis/degradation pathways in tubers may have led to the observed isotope distribution difference between potato leaves and tubers. The analysis of data from green algae does not support the conclusion that AAs are further from equilibrium in glucose‐cultured green algae than in the autotrophic ones. Conclusions Application of the |Δα| matrix can help us to locate potential reversible reactions or reaction networks in a complex system such as a metabolic system. The same approach can be broadly applied to all complex systems that have multiple components, e.g. geochemical or atmospheric systems of early Earth or other planets.},
doi = {10.1002/rcm.8040},
journal = {Rapid Communications in Mass Spectrometry},
issn = {0951-4198},
number = 4,
volume = 32,
place = {United States},
year = {2018},
month = {1}
}

Works referenced in this record:

Fractionation of Carbon and Hydrogen Isotopes in Biosynthetic Processes
journal, January 2001

  • Hayes, J. M.
  • Reviews in Mineralogy and Geochemistry, Vol. 43, Issue 1, p. 225-277
  • DOI: 10.2138/gsrmg.43.1.225

Carbon Isotope Fractionation In Formation Of Amino Acids By Photosynthetic Organisms
journal, May 1961

  • Abelson, P. H.; Hoering, T. C.
  • Proceedings of the National Academy of Sciences, Vol. 47, Issue 5, p. 623-632
  • DOI: 10.1073/pnas.47.5.623