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ancient_metabolism — Biosphere-level and ancient phosphate-free metabolism (2017)

Description

Bipartite networks of metabolic reactions and metabolites from the KEGG database, assembled by J. E. Goldford, H. Hartman, T. F. Smith and D. Segrè as a model of the metabolism of the whole biosphere, and used to find a core metabolic network that could have functioned without phosphate in an early, prebiotic environment. Nodes represent reactions and metabolites, and an undirected edge connects a reaction to each metabolite that it consumes or produces, with the stoichiometric coefficient as edge property.

The reactions of KEGG were filtered to keep only those whose compounds all have a known structure (SMILES string) and no polymer subunits of undefined size, and which are elementally balanced (for every element except hydrogen; generic "R" groups are allowed if balanced). There are three networks:

  • kegg: the elementally balanced KEGG network (the "full KEGG network" of the paper), with 6,880 reactions and the 5,944 metabolites listed in the source data (146 of which take part in none of the reactions, and are isolated nodes).
  • anaerobic: the anaerobic (oxygen-independent) network, obtained by removing all reactions that involve molecular oxygen, and keeping only the largest connected component of the remaining bipartite graph, with 5,651 reactions and 5,252 metabolites.
  • core: the phosphate-free core network, with 315 reactions and 260 metabolites, obtained by "network expansion" from a seed set of eight simple compounds thought to be available in prebiotic environments (lacking phosphate), i.e. by iteratively adding all reactions of the KEGG network whose substrates are available (reactions considered reversible, except the ones that would produce oxygen), together with their products, until no new reactions can be added.

The networks have the following properties:

  • Nodes: is_reaction, whether the node is a reaction (otherwise it is a metabolite); kegg_id, the KEGG identifier (e.g. R00004 for reactions and C00001 for compounds); name, the name of the reaction or compound (empty for some reactions); formula, for reactions, the reaction equation with KEGG compound identifiers (reactions involving oxygen are written with "=>", the others with "<=>"), and for metabolites, the chemical formula; smiles, the SMILES string of metabolites; delta_g, the standard molar free energy of reactions in kJ/mol (at pH 7 and ionic strength 0.1 M; NaN if unavailable); anaerobic, whether the node belongs to the anaerobic network; core, whether the node belongs to the phosphate-free core network.
  • Edges: stoichiometry, the stoichiometric coefficient of the metabolite in the reaction, negative for metabolites on the left-hand side of the reaction equation (substrates in the direction written) and positive for those on the right-hand side (products).1

  1. Description obtained in part from the ICON project. ↩

Tags
Biological Metabolic Unweighted Metadata
Citation
Upstream URL OK
https://doi.org/10.1016/j.cell.2017.02.001
Upstream license
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0), https://creativecommons.org/licenses/by-nc-nd/4.0/
Networks
Tip: click on a column header to sort the list, or hover over it for a description.
Column legend
$\left<k\right>$
Mean degree
$\sigma_k$
Standard deviation of the degrees
$\lambda_h$
Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$
Random walk mixing time
$r$
Degree assortativity
$c$
Global clustering coefficient
$\oslash$
(Pseudo-) diameter
$S$
Relative size of the largest component
NPs
Node properties
EPs
Edge properties
Name Nodes Edges $\left<k\right>$ $\sigma_k$ $\lambda_h$ $\tau$ $r$ $c$ $\oslash$ $S$ Kind Mode NPs EPs gt GraphML GML csv
kegg 12,824 30,374 4.74 36.80 59.14 76.72 -0.19 0.00 16 0.98 Undirected Bipartite is_reaction kegg_id name formula smiles delta_g anaerobic core stoichiometry 288 KiB 409 KiB 398 KiB 445 KiB
anaerobic 10,903 23,013 4.22 26.35 41.11 79.29 -0.17 0.00 18 0.98 Undirected Bipartite is_reaction kegg_id name formula smiles delta_g anaerobic core stoichiometry 243 KiB 342 KiB 331 KiB 372 KiB
core 575 1,080 3.76 8.20 8.79 15.91 -0.16 0.00 11 1.00 Undirected Bipartite is_reaction kegg_id name formula smiles delta_g anaerobic core stoichiometry 15 KiB 19 KiB 18 KiB 17 KiB