Control layer
Information
What the cell needs to know, where that knowledge is stored, and how it is read.
The genome
Aquifex aeolicus VF5 carries its genes on one chromosome of about 1.55 million base pairs and a small extra DNA element. UniProt lists 1,553 proteins encoded there. Aquifex is only the reference organism; the minimal cell has 1,051 proteins.
Source: Deckert et al., Nature 392:353–358 (1998)
Copying the genome
These proteins open, copy, join and untwist the DNA.
| Aquifex protein | Evidence (UniProt) | Home pathway |
|---|---|---|
| Chromosomal replication initiator protein DnaA | Seen as a protein | Chromosome preparation |
| Replicative DNA helicase | Seen as a protein | Initiation and opening |
| DNA polymerase III subunit alpha | Inferred from related proteins | DNA synthesis |
| Beta sliding clamp | Inferred from related proteins | DNA synthesis |
| DNA polymerase III subunit gamma/tau | Inferred from related proteins | DNA synthesis |
| Probable DNA polymerase III subunit delta | Inferred from related proteins | DNA synthesis |
| DNA polymerase I | Inferred from related proteins | Joining and end processing |
| DNA ligase | Inferred from related proteins | Joining and end processing |
| Type 2 topoisomerase subunit A | Seen as a protein | Topology management |
| Type 2 topoisomerase subunit B | Seen as a protein | Topology management |
| DNA topoisomerase 1 | Inferred from related proteins | Topology management |
| Single-stranded DNA-binding protein | Inferred from related proteins | Homologous recombination |
| DNA primase | Seen as a protein | DNA replication |
Reading genes
RNA polymerase copies genes into RNA. Only one sigma factor, which tells it where genes start, is kept.
| Aquifex protein | Evidence (UniProt) | Home pathway |
|---|---|---|
| DNA-directed RNA polymerase subunit alpha | Inferred from related proteins | Transcription |
| DNA-directed RNA polymerase subunit beta | Inferred from related proteins | Transcription |
| DNA-directed RNA polymerase subunit beta' | Inferred from related proteins | Transcription |
| DNA-directed RNA polymerase subunit omega | Inferred from related proteins | Not yet placed in a pathway |
| RNA polymerase sigma factor SigA | Inferred from related proteins | Transcription |
| Transcription termination/antitermination protein NusA | Inferred from related proteins | Transcription |
| Transcription antitermination protein NusB | Seen as a protein | Transcription |
| Transcription termination/antitermination protein NusG | Seen as a protein | Transcription |
The code and its key
The genetic code links three-letter codons to amino acids. The key is a set of enzymes, the aminoacyl-tRNA synthetases, each of which attaches the right amino acid to its transfer RNAs. The kept set keeps 22 synthetase proteins (some enzymes are made of two different chains).
| Aquifex protein | Evidence (UniProt) | Home pathway |
|---|---|---|
| Alanine--tRNA ligase | Seen as a protein | Translation interface |
| Arginine--tRNA ligase | Inferred from related proteins | Translation interface |
| Aspartate--tRNA(Asp/Asn) ligase | Inferred from related proteins | Translation interface |
| Cysteine--tRNA ligase | Inferred from related proteins | Translation interface |
| Glutamate--tRNA ligase | Inferred from related proteins | Translation interface |
| Glycine--tRNA ligase alpha subunit | Seen as a protein | Translation interface |
| Glycine--tRNA ligase beta subunit | Inferred from related proteins | Translation interface |
| Histidine--tRNA ligase | Inferred from related proteins | Translation interface |
| Isoleucine--tRNA ligase | Inferred from related proteins | Translation interface |
| Leucine--tRNA ligase subunit alpha | Seen as a protein | Translation interface |
| Leucine--tRNA ligase subunit beta | Inferred from related proteins | Translation interface |
| Lysine--tRNA ligase | Inferred from related proteins | Translation interface |
| Methionine--tRNA ligase | Seen as a protein | Translation interface |
| Methionyl-tRNA synthetase beta subunit | Seen as a protein | Translation interface |
| Phenylalanine--tRNA ligase alpha subunit | Inferred from related proteins | Translation interface |
| Phenylalanine--tRNA ligase beta subunit | Inferred from related proteins | Translation interface |
| Proline--tRNA ligase | Seen as a protein | Translation interface |
| Serine--tRNA ligase | Seen as a protein | Translation interface |
| Threonine--tRNA ligase | Inferred from related proteins | Translation interface |
| Tryptophan--tRNA ligase | Inferred from related proteins | Translation interface |
| Tyrosine--tRNA ligase | Inferred from related proteins | Translation interface |
| Valine--tRNA ligase | Inferred from related proteins | Translation interface |
Epigenetic information
In bacteria, the main epigenetic marks are methyl groups added to DNA, often by restriction–modification systems. The Aquifex genome encodes 2 such DNA methylation or restriction enzymes, and none of them is among the kept proteins. In this scenario, then, the cell carries no DNA-methylation layer. It does keep enzymes that add methyl groups to its RNAs.
| Aquifex protein | Evidence (UniProt) | Home pathway |
|---|---|---|
| Uncharacterized RNA methyltransferase aq_257 | Inferred from related proteins | Not yet placed in a pathway |
| tRNA (adenine(58)-N(1))-methyltransferase TrmI | Seen as a protein | RNA maturation |
| Probable dual-specificity RNA methyltransferase RlmN | Inferred from related proteins | Not yet placed in a pathway |
| Ribosomal RNA small subunit methyltransferase A | Seen as a protein | RNA maturation |
| Ribosomal RNA small subunit methyltransferase E | Seen as a protein | RNA maturation |
| Ribosomal RNA small subunit methyltransferase G | Inferred from related proteins | RNA maturation |
| Ribosomal RNA small subunit methyltransferase H | Inferred from related proteins | RNA maturation |
| Ribosomal RNA small subunit methyltransferase I | Inferred from related proteins | RNA maturation |
| tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase | Seen as a protein | RNA maturation |
| tRNA (guanine-N(7)-)-methyltransferase | Seen as a protein | RNA maturation |
| tRNA (guanine-N(1)-)-methyltransferase | Seen as a protein | RNA maturation |
| Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | Inferred from related proteins | RNA maturation |
| tRNA (guanosine(18)-2'-O)-methyltransferase | Seen as a protein | RNA maturation |
Information not written in the genes
Some of what a cell needs is inherited as structure rather than as sequence. A membrane grows only from an existing membrane, and a ribosome is made with the help of existing ribosomes. A daughter cell therefore starts with working copies of these parts from its parent.
Source: Cavalier-Smith, Trends in Plant Science 5:174–182 (2000)
The origins question
Which came first: the genetic code, or the machinery that reads it?
Most proposals begin with an RNA stage, in which one kind of molecule both stored information and catalysed reactions. The genetic code is thought to have started with fewer amino acids and codons and to have grown through chemical affinities, selection against costly errors, and later additions.
Experiments have produced ribozymes that copy short RNAs and that attach amino acids to RNA. A system that reads its own code and builds its own readers has not been shown.
The design analysis treats the code as a central case: an arbitrary but consistent mapping between codons and amino acids, enforced by the 22 synthetase proteins kept in the working set.
Every part of the reading machinery is itself written in the code it reads, so the system has to be working in order to produce itself. The design analysis counts this circular dependence as positive evidence for planning. A stepwise, experimentally supported route from chemistry to a coded system would weaken that case.
Hallmarks that apply.
Sources
- Gilbert, Nature 319:618 (1986)
- Johnston et al., Science 292:1319–1325 (2001)
- Protein lists and evidence levels: UniProt proteome UP000000798