◉Cell atlasMinimal free-living cell ContentsTreeOriginsFinal analysisSearch
Where am I in the cell?

Control layer · interdependence

How the systems depend on each other

53 curated dependencies between the 16 systems of the cell map. A dot means the row supplies something the column needs. Hover a dot to read why.

Carbon metabolismCofactorsEnergy productionMineral ionsNucleotidesAmino acidsLipids & membraneDNA processingRNA & translationSignaling & regulationTransportQuality controlDivision & structureHomeostasisStress responseMetal clusterssupplies
Carbon metabolism·●●●●4
Cofactors●·●●●●5
Energy production●●·●●●●●●●●●●12
Mineral ions·●●2
Nucleotides·●●2
Amino acids●●·●●4
Lipids & membrane●·●●●4
DNA processing·●●2
RNA & translation●·●●●●●●7
Signaling & regulation·0
Transport●●●·●4
Quality control●·●2
Division & structure·0
Homeostasis●●·2
Stress response·0
Metal clusters●●●·3

Filled ring: the dependency runs both ways. Source: curated from X-ray of Life, Volume III (page references on each system page). Not exhaustive and not measured protein contacts.

Two-way dependencies

7 pairs of systems each need the other. Neither can be fully working first.

  • Carbon metabolism ⇄ CofactorsCarbon intermediates supply the molecular skeletons used to synthesize cofactors.CoA and one-carbon cofactors enable carbon transfer and acetyl-CoA metabolism in the proposed network.
  • Cofactors ⇄ Energy productionFlavin, NAD, and other cofactors participate in electron-transfer reactions.ATP and reducing power drive cofactor synthesis and regeneration.
  • Cofactors ⇄ Amino acidsCofactors support amino-group transfer, reduction, and other amino acid biosynthetic reactions.Amino-acid-derived precursors contribute to pathways such as SAM and other cofactor biosynthesis.
  • Energy production ⇄ Lipids & membraneATP and reducing power support membrane-component synthesis.A sufficiently ion-tight membrane supports electrochemical gradients and houses respiratory and ATP-synthase complexes.
  • Mineral ions ⇄ Metal clustersAvailable iron, sulfur-related substrates, nickel, and other metals support the chosen cofactor assembly pathways.Metal binding and cofactor incorporation help allocate available metals into functional enzymes.
  • DNA processing ⇄ RNA & translationMaintained DNA provides templates encoding mRNAs, functional RNAs, and the translation machinery.Translation produces the proteins that carry out DNA replication, repair, and segregation.
  • RNA & translation ⇄ Quality controlTranslation produces chaperones, nucleases, assembly factors, and proteases.RNA maturation, ribosome assembly, folding, and rescue help maintain productive translation.

If one system fails

What each system supplies directly, and how many others sit downstream of it in the curated network.

  • Carbon metabolismdirectly: Cofactors, Nucleotides, Amino acids, Lipids & membrane15 of 15 other systems are downstream of it.
  • Cofactorsdirectly: Carbon metabolism, Energy production, Nucleotides, Amino acids, Lipids & membrane15 of 15 other systems are downstream of it.
  • Energy productiondirectly: Carbon metabolism, Cofactors, Nucleotides, Amino acids, Lipids & membrane, DNA processing, RNA & translation, Signaling & regulation, Transport, Quality control, Homeostasis, Stress response15 of 15 other systems are downstream of it.
  • Mineral ionsdirectly: RNA & translation, Metal clusters15 of 15 other systems are downstream of it.
  • Nucleotidesdirectly: DNA processing, RNA & translation15 of 15 other systems are downstream of it.
  • Amino acidsdirectly: Cofactors, Nucleotides, RNA & translation, Metal clusters15 of 15 other systems are downstream of it.
  • Lipids & membranedirectly: Energy production, Transport, Division & structure, Homeostasis15 of 15 other systems are downstream of it.
  • DNA processingdirectly: RNA & translation, Division & structure15 of 15 other systems are downstream of it.
  • RNA & translationdirectly: DNA processing, Signaling & regulation, Transport, Quality control, Division & structure, Stress response, Metal clusters15 of 15 other systems are downstream of it.
  • Signaling & regulationdirectly: none listed0 of 15 other systems are downstream of it.
  • Transportdirectly: Mineral ions, Amino acids, Signaling & regulation, Homeostasis15 of 15 other systems are downstream of it.
  • Quality controldirectly: RNA & translation, Stress response15 of 15 other systems are downstream of it.
  • Division & structuredirectly: none listed0 of 15 other systems are downstream of it.
  • Homeostasisdirectly: Mineral ions, RNA & translation15 of 15 other systems are downstream of it.
  • Stress responsedirectly: none listed0 of 15 other systems are downstream of it.
  • Metal clustersdirectly: Carbon metabolism, Energy production, Mineral ions15 of 15 other systems are downstream of it.

Map systems and tree groups

The map uses the book’s 16 systems; the tree uses the inventory’s 16 groups.