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Modeling Framework for Isotopic Labeling of Heteronuclear Moieties Mark I

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Modeling Framework for Isotopic Labeling of Heteronuclear Moieties Mark I Borkum et al. J Cheminform (2017) 9:14 DOI 10.1186/s13321-017-0201-7 RESEARCH ARTICLE Open Access Modeling framework for isotopic labeling of heteronuclear moieties Mark I. Borkum1*, Patrick N. Reardon1, Ronald C. Taylor2 and Nancy G. Isern1 Abstract Background: Isotopic labeling is an analytic technique that is used to track the movement of isotopes through reac- tion networks. In general, the applicability of isotopic labeling techniques is limited to the investigation of reaction networks that consider homonuclear moieties, whose atoms are of one tracer element with two isotopes, distin- guished by the presence of one additional neutron. Results: This article presents a reformulation of the modeling framework for isotopic labeling, generalized to arbitrar- ily large, heteronuclear moieties, arbitrary numbers of isotopic tracer elements, and arbitrary numbers of isotopes per element, distinguished by arbitrary numbers of additional neutrons. Conclusions: With this work, it is now possible to simulate the isotopic labeling states of metabolites in completely arbitrary biochemical reaction networks. Keywords: Isotopic labeling, Isotopomers, Cumomers, Elementary metabolite units, Metabolic engineering Introduction isotopes per element, distinguished by arbitrary numbers Isotopic labeling is an analytic technique that is used to of additional neutrons. track the movement of isotopes through reaction net- works. First, specific atoms of the reagent moieties are Background replaced with detectable, “labeled” isotopic variants. The first group to give a partial solution to the problem of Then, after the reactions have been allowed to proceed, the representation of isotopic labeling states of arbitrary the position and relative abundance of labeled isotopic moieties was Malloy et al. [1]. atoms are determined by experiment. Subsequent analy- Representing isotopic labeling states of carbon atoms sis of the measured quantities elucidates the characteris- in backbones of metabolites as vectors of Boolean truth tics of the reaction network, e.g., the rate constants of the values, which they referred to as “isotopomers” (a con- reactions. traction of the term “isotopic isomers”), using 0 and 1 12C 13C In general, the applicability of isotopic labeling tech- to denote, respectively, -unlabeled and -labeled niques is limited to the investigation of reaction networks atoms, they showed that relative abundances of metabo- that consider homonuclear moieties, whose atoms are lites in biological systems could be calculated using non- of one isotopic tracer element with two isotopes, distin- linear functions of relative abundances of isotopomers, guished by the presence of one additional neutron. which they referred to as “isotopomer fractions.” The contribution of this article is a reformulation of the For example, a metabolite of two carbon atoms has 2 modeling framework for isotopic labeling, generalized to 2 = 4 isotopomers, 00, 01, 10 and 11; and hence, the iso- arbitrarily large, heteronuclear moieties, arbitrary num- topic labeling state of the metabolite is given by 4 isoto- bers of isotopic tracer elements, and arbitrary numbers of pomer fractions. Aside from being nonlinear, Malloy et al.’s construction suffers from the fact that an exponential number of iso- *Correspondence: [email protected] 1 Environmental Molecular Sciences Laboratory, Pacific Northwest topomer fractions are required in order to determine the National Laboratory, 3335 Innovation Boulevard, Richland, WA 99354, USA isotopic labeling state of any given metabolite. Full list of author information is available at the end of the article © The Author(s) 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Borkum et al. J Cheminform (2017) 9:14 Page 2 of 11 Wiechert et al. [2] noted that, by the nature of the that preceded it. Is this issue intrinsic to the problem, problem, isotopic labeling states of biochemical reac- i.e., unavoidable, or simply, difficult to mitigate? Third, tion network substrates are wholly determined by spe- Antoniewicz et al. give neither a rigorous proof of the cific subsets of carbon atoms; and therefore, that isotopic correctness of the EMU method, nor a derivation of its labeling states of the complement of each subset can be construction from prior research. Why does the EMU omitted, incurring no loss of information. method appear to work? Is it the most effective decom- Representing isotopic labeling states of carbon atoms position that can be “done” to a model of a given biologi- in backbones of metabolites as vectors of placeholder cal system? Fourth, and finally, the EMU method has thus variables, which they referred to as “cumomers” (a con- far been demonstrated for homonuclear systems only; traction of the term “cumulative isotopomers”), using 1 specifically, those containing carbon atoms, where unla- and x to denote, respectively, determinate (13C-labeled) beled and labeled variants of isotopic tracer elements are 12C 13 and indeterminate ( -unlabeled or C-labeled) iso- distinguished by the presence of one additional neutron. topic labeling states, with a total ordering given by x < 1 , Can the EMU method be generalized to arbitrary, heter- they showed that Malloy et al.’s construction could be onuclear systems? reformulated as a cascade system of linear functions of At the conclusion of their essay, Antoniewicz et al. relative abundances of cumomers, which they referred promise to return to these cases later; but, thus far, this to as “cumomer fractions,” with the original construction promise has gone unfulfilled. Nor do the works of Srour being recovered via a “suitable variable transformation” et al. [11] fill this gap. Their essays, which are contempo- [2, Eq. 7] in the form of an invertible square matrix. raneous with those of Antoniewicz et al., develop a coun- For example, a metabolite of two carbon atoms has terpart to the EMU method, where system variables are 2 2 = 4 cumomers, xx, x1, 1x and 11; and hence, the combinations of flux variables and cumomer fractions, isotopic labeling state of the metabolite is given by 4 which they refer to as “fluxomers.” cumomer fractions. While the fluxomer method does enable a reformula- Antoniewicz et al. [3] shed new light on this subject. tion of the flux balance equation that, it is claimed, has Manipulating isotopic labeling states of specific sub- greater numerical precision and does not require matrix sets of carbon atoms as aggregations, rather than as inversion for its solution, it is, in actuality, a method for singletons, they showed that, under certain conditions, constructing a specific matrix in a single pass, which, Wiechert et al.’s cascade system could be optimized using with some algebraic manipulation, can be shown to be graph-theoretic methods, e.g., vertex reachability analy- equivalent to the EMU method for certain biochemi- sis, edge smoothing and Dulmage–Mendelsohn decom- cal reaction networks. Specifically, the fluxomer method position, thereby significantly reducing the total number involves the construction of the directed line graph for of system variables. each EMU reaction network (the new graph that repre- Representing isotopic labeling states of carbon atoms sents the adjacencies between the edges of the original in backbones of metabolites as mass distributions, which graph). Furthermore, the software implementation of they referred to as “Elementary Metabolite Units (EMU),” the fluxomer method is, in general, far more complex they showed that every EMU has a unique factorization, than that of the EMU method, limiting its widespread and that the mass distribution of a given EMU is equal adoption. to the vector convolution of the mass distributions of its The most recent work in this area, by Nillson and Jain proper factors. Moreover, they showed that, in a given [12], gives a construction for the representation and mass distribution, the mass fraction corresponding to the manipulation of “multivariate mass isotopomer distri- greatest number of mass shifts is equivalent to a specific butions” of heteronuclear moieties, which they demon- cumomer fraction. strate for moieties of carbon and nitrogen atoms. The Antoniewicz et al.’s work provided the foundation key advantage of their approach is that the probabilities for a whole host of important biological investigations associated with each combination of the contribution of [4–6], and inspired many software implementations [7– each isotopic tracer element are uniquely identifiable. 10]. Even so, the cases not solved by Antoniewicz et al. The disadvantage of their approach, however, is that it merit attention for four reasons. First, the subject is very requires the use of k-dimensional vectors, where k is the closely tied to the concept of isotopic labeling, and can number of isotopic tracer elements, increasing the com- thus serve to bring greater clarity and determinacy to plexity of the software implementation. In the discus- its mathematical formulation. In this respect, treatment
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