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Computational exploration of the chemical structure space of possible reverse tricarboxylic acid cycle constituents

Meringer, Markus and Cleaves, H. James (2017) Computational exploration of the chemical structure space of possible reverse tricarboxylic acid cycle constituents. Scientific Reports, 7, pp. 1-11. Nature Publishing Group. DOI: 10.1038/s41598-017-17345-7 ISBN 2045-2322 ISSN 2045-2322

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Official URL: http://www.nature.com/articles/s41598-017-17345-7

Abstract

The reverse tricarboxylic acid (rTCA) cycle has been explored from various standpoints as an idealized primordial metabolic cycle. Its simplicity and apparent ubiquity in diverse organisms across the tree of life have been used to argue for its antiquity and its optimality. In 2000 it was proposed that chemoinformatics approaches support some of these views. Specifically, defined queries of the Beilstein database showed that the molecules of the rTCA are heavily represented in such compound databases. We explore here the chemical structure space, e.g. the set of organic compounds which possesses some minimal set of defining characteristics, of the rTCA cycle's intermediates using an exhaustive structure generation method. The rTCA's chemical space as defined by the original criteria and explored by our method is some six to seven times larger than originally considered. Acknowledging that each assumption in what is a defining criterion making the rTCA cycle special limits possible generative outcomes, there are many unrealized compounds which fulfill these criteria. That these compounds are unrealized could be due to evolutionary frozen accidents or optimization, though this optimization may also be for systems-level reasons, e.g., the way the pathway and its elements interface with other aspects of metabolism.

Item URL in elib:https://elib.dlr.de/117402/
Document Type:Article
Title:Computational exploration of the chemical structure space of possible reverse tricarboxylic acid cycle constituents
Authors:
AuthorsInstitution or Email of AuthorsAuthors ORCID iD
Meringer, MarkusMarkus.Meringer (at) dlr.dehttps://orcid.org/0000-0001-8526-2429
Cleaves, H. JamesEarth-Life Science Institute, Tokyo Institute of TechnologyUNSPECIFIED
Date:13 December 2017
Journal or Publication Title:Scientific Reports
Refereed publication:Yes
Open Access:Yes
Gold Open Access:Yes
In SCOPUS:Yes
In ISI Web of Science:Yes
Volume:7
DOI :10.1038/s41598-017-17345-7
Page Range:pp. 1-11
Publisher:Nature Publishing Group
ISSN:2045-2322
ISBN:2045-2322
Status:Published
Keywords:astrobiology, chemical origin of life, metabolomics
HGF - Research field:Aeronautics, Space and Transport
HGF - Program:Space
HGF - Program Themes:Space Science and Exploration
DLR - Research area:Raumfahrt
DLR - Program:R EW - Erforschung des Weltraums
DLR - Research theme (Project):R - Vorhaben Planetary Evolution and Life
Location: Oberpfaffenhofen
Institutes and Institutions:Remote Sensing Technology Institute > Atmospheric Processors
Deposited By: Meringer, Dr.rer.nat. Markus
Deposited On:15 Dec 2017 10:08
Last Modified:15 Dec 2017 10:08

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