The atlas as one tree
The cell, part by part
The cell of this atlas is the minimal free-living cell described in X-ray of Life. Its systems are shown here with proteins of a real free-living organism, Aquifex aeolicus VF5, as supporting evidence, sorted into 16 groups, their pathways and their proteins.
Supporting evidence only. The minimal cell of this atlas is the one described in X-ray of Life (Vol. III, Ch. 14). Proteins of Aquifex aeolicus VF5 are real-organism evidence for it.
How pathways are formed: curated atlas pathways first, then KEGG pathway maps for Aquifex, then a “not yet placed” list in each group. Every listed protein has exactly one home here.
Building carbon into molecules
The cell is given carbon dioxide gas and nothing else to build with. These proteins run the cycle that pulls CO₂ out of the water and turns it into the first carbon skeletons every other pathway starts from.
46 proteins · 9 pathways
Making the twenty amino acids
Proteins are chains of amino acids, and the medium supplies none of them. The cell has to manufacture all twenty from scratch.
92 proteins · 13 pathways
Pathways
- Aromatic amino acids11
- Branched-chain amino acids8
- Aspartate-family branches5
- Nitrogen assimilation4
- RNA maturation4
- Folate-linked carbon transfer2
- Arginine biosynthesis6
- Cysteine and methionine metabolism6
- Histidine metabolism6
- Lysine biosynthesis3
- Arginine and proline metabolism3
- Phenylalanine, tyrosine and tryptophan biosynthesis3
- Not yet placed in a pathway31
Making DNA and RNA letters
The four letters of DNA and RNA are built here from simpler pieces. None are supplied in the medium and there is nothing to recycle.
47 proteins · 9 pathways
Manufacturing cofactors and vitamins
Many enzymes only work while holding a small helper molecule — a vitamin or cofactor. The cell makes all of them itself.
138 proteins · 23 pathways
Pathways
- Heme and quinones12
- Biotin and lipoate7
- NAD and flavins6
- Thiamine and pyridoxal6
- Folate and pterin chemistry6
- Lipid and cofactor connections5
- Coenzyme A4
- Aspartate-family branches3
- Amino-acid connections2
- Folate-linked carbon transfer1
- Serine, glycine and sulfur1
- Folate biosynthesis9
- Oxidative phosphorylation5
- Thiamine metabolism5
- Pantothenate and CoA biosynthesis5
- Glycine, serine and threonine metabolism4
- Riboflavin metabolism4
- Nicotinate and nicotinamide metabolism4
- Biotin metabolism4
- Cysteine and methionine metabolism3
- Porphyrin metabolism3
- Pyruvate metabolism2
- Not yet placed in a pathway37
Turning hydrogen into usable energy
The cell lives on hydrogen gas and oxygen. These proteins capture the energy of that reaction and store it as ATP, the cell's energy currency.
31 proteins · 6 pathways
Building and maintaining the membrane
The oily envelope that holds the cell together, keeps the inside in, and holds the voltage that energy production depends on.
52 proteins · 9 pathways
Copying and repairing the genome
Copying DNA accurately, separating the two copies, and continuously repairing chemical damage — which at 95 °C is relentless.
55 proteins · 11 pathways
Reading genes into RNA
Transcribing DNA into the RNA messages that the protein factory reads, and trimming those messages into usable form.
27 proteins · 4 pathways
Building proteins and folding them
The ribosome and its supporting cast: assembling amino acids into proteins in the right order, then folding each one into shape. At 95 °C folding does not happen by itself, so the folding machinery is part of manufacturing, not a stress response.
178 proteins · 13 pathways
Dividing into two cells
Holding the cell's shape and pinching it into two viable daughters at the right place and the right moment.
44 proteins · 7 pathways
Pulling nutrients in from outside
The medium is rich in phosphate, nitrogen, sulfur and metals, but none of it crosses the membrane by itself. Each element has one dedicated doorway.
62 proteins · 6 pathways
Holding the internal balance
Keeping acidity, water pressure and chemical reactivity inside the cell within the narrow band where its machinery works.
5 proteins · 2 pathways
Surviving oxygen damage
Oxygen is this cell's fuel partner and also its poison. These proteins mop up the reactive by-products. Notably, this genome has no catalase at all, so a single route carries the whole load.
7 proteins · 3 pathways
Loading metals into enzymes
Many enzymes only work with an iron, nickel or copper centre built into them. This machinery assembles and inserts those metal centres.
15 proteins · 3 pathways
Switching genes on and off
The small amount of regulation the cell cannot do without — starting its housekeeping genes and keeping iron from running loose.
4 proteins · 2 pathways
Conserved, but we cannot say what they do
These proteins are kept because closely related organisms, including ones that have thrown away everything they could, still keep them. Their function is not known.
109 proteins · 13 pathways
Pathways
- tRNA charging3
- Nutrient and metabolic state2
- Biosynthesis of various nucleotide sugars7
- Purine metabolism6
- Bacterial secretion system5
- Glyoxylate and dicarboxylate metabolism4
- Starch and sucrose metabolism3
- Homologous recombination3
- Fructose and mannose metabolism2
- Streptomycin biosynthesis2
- Other carbon fixation pathways2
- Nicotinate and nicotinamide metabolism2
- Not yet placed in a pathway68
The 12 featured machines
Twelve of the cell’s molecular machines have their own illustrated articles: how each works, its parts in Aquifex, and its origins question.
The cell picture and the tree
The labels on the cell picture link to these groups. Two things differ. The picture labels cell motility, which has no group of its own here: see Cell motility for the six type IV pilus proteins in the minimal cell, and why the flagellum is not among them. These groups have no label on the picture: manufacturing cofactors and vitamins, holding the internal balance, surviving oxygen damage, loading metals into enzymes, conserved, but we cannot say what they do.