How the working minimum was reached

Every claim about the origin of life depends on what the first cell had to contain. This atlas works with one figure: 1,051 proteins. Here is where it comes from, what it replaced, and why each step was taken, so the reasoning can be checked instead of taken on trust.

1. The starting point: the published catalogue

Chapter 14 catalogues the minimal free-living cell as sixteen functional categories: carbon fixation, amino-acid and nucleotide synthesis, cofactors, energy, membranes, replication, transcription, translation, division, transport, homeostasis, metal-cluster assembly and others. The sixteen subtotals add up to a base count of 1,134 proteins. The chapter then adds 81 "additional complex subunits" (ribosomal proteins, RNA polymerase, Complex I, ATP synthase and respiratory complexes) for a total of 1,215 proteins and 702,700 amino acids (PDF p. 506). The book attaches a condition to that total: it "assumes that complex subunits are not double-counted in their respective categories" (p. 506, note 1).

2. Carried forward: the second book

The Cell: An Unsolved Mystery takes the same catalogue forward (Table E13.1, PDF p. 315; Image 1.3, p. 28) as the proteome of "a fully autotrophic cell", one that makes everything it needs from carbon dioxide and minerals. It sets this against JCVI-syn3.0, the laboratory minimal cell with 473 genes, and notes that the gap "reflects the difference between laboratory-supported minimal viability and a fully biosynthetic free-living" cell. That contrast is the heart of the question: a cell fed by its surroundings needs far less than a cell that must fend for itself.

3. Testing the catalogue against a real cell

A catalogue of functions needs checking against a living organism that actually does all of it. Aquifex aeolicus VF5 lives in volcanic hot springs on hydrogen, oxygen, carbon dioxide and minerals, builds every one of its molecules itself, and has a fully sequenced set of 1,553 proteins. The check led to three corrections.

• The 81 subunits are counted twice. The categories already list the subunits of the ribosome, polymerase and respiratory complexes. Adding them again breaks the book's own condition, so the catalogue supports 1,134, not 1,215.
• The catalogue counts functions, not proteins. No entry names a gene or a protein: a category says "9 enzymes", not which nine. A protein count needs every member named and checked.
• Some categories describe a different cell. Nitrogen fixation, siderophores, carbon-monoxide-based carbon fixation and quorum sensing do not exist in a hydrogen-living hot-spring cell. Other systems such a cell does need are not listed.

The group-by-group check is on Book catalogue checked against Aquifex.

4. Why a laboratory minimum cannot be the answer

Stripping every protein that a laboratory culture can do without gives a cell of about 440 to 470 proteins, the size of JCVI-syn3.0 or Mycoplasma genitalium. Such cells are not free-living. They survive only where a host or a rich medium hands them what they cannot make and keeps temperature, salt and food constant. The first cell had no host and no laboratory. It had to live with temperature that rises and falls, oxygen and hydrogen that come and go, changing salts, metals and acidity, surfaces to hold on to, and viruses. Sensing, regulation, repair, stress protection, transport and defence are the price of being free-living. A minimum defined by laboratory survival describes a host-dependent cell, not the first cell.

5. Measuring what a free-living cell needs

What a free-living cell must contain can be answered by evidence: look at what independent free-living cells with the same way of life all keep. Two other free-living hot-spring bacteria live as A. aeolicus does: Hydrogenobacter thermophilus and Thermocrinis albus. Every one of the 1,553 A. aeolicus proteins was aligned, amino acid by amino acid, against the complete protein sets of both. A protein was kept only when both carry a one-to-one counterpart. A protein that one of them lives without is not part of the minimum, because that organism is living proof it can be done without. Where A. aeolicus carries two copies and the others one, only one is counted. The result is 1,053 proteins. Another 81 have a clear relative in both organisms but no one-to-one match; if all of them were needed too, the ceiling would be 1,134, the same as the base count of X-ray of Life.

6. Why the minimum includes defence against viruses

Viruses are found wherever cells are found, hot springs included, and they outnumber cells. A cell with no defence is wiped out by the first virus that can enter it, so this atlas counts defence as a requirement of a free-living cell. To keep the count minimal, only the smallest complete defence system in the genome is included: a CRISPR-Cas system of 9 proteins. Two store pieces of invading DNA as a memory, one cuts that memory into guide RNAs, and six form the complex that finds and destroys matching viral RNA. Other defence proteins are left out, because one complete system is the minimum.

7. From 1,053 to 1,051

The figure of 1,051 is already used across this atlas. To keep one consistent number, the two least certain proteins of the 1,053 were removed: both have no known function and the weakest match in the two relatives (aq_1894 and aq_2140). Every other protein has stronger evidence than these two.

8. The numbers side by side

The figure has moved from a count of functions to a count of named, checkable proteins. The range 1,051 to 1,134 brackets the book's own base count.

9. What this number does and does not show

• Every one of the 1,051 proteins is listed below, under The 1,051 proteins, with its gene, its database entry and its evidence. Readers can check any of them.
• No protein in this set has been removed from a living Aquifex cell to test what happens; the organism cannot be genetically modified. The set rests on what free-living cells keep, which is strong evidence of need but not proof for each protein.
• 207 of the proteins sit in the category "Conserved, but we cannot say what they do"; 76 of these have no annotated function at all. They are counted because every free-living cell of this kind retains them, not because their role is understood.
• The true minimum could lie anywhere between 1,051 and 1,134.

Sources. X-ray of Life, Vol. III, Ch. 14, PDF p. 506. The Cell: An Unsolved Mystery, Table E13.1, PDF p. 315, and Image 1.3, p. 28. Hutchison CA et al. (2016), Science, JCVI-syn3.0. Deckert G et al. (1998), Nature 392:353–358, Aquifex aeolicus genome. UniProt proteomes UP000000798 (A. aeolicus), UP000002574 (H. thermophilus), UP000002043 (T. albus).