Control layer
Signaling inside machines
How the parts of one molecular machine pass signals to each other.
The ribosome checks before it commits
When a transfer RNA’s anticodon pairs with the codon in the decoding centre, bases of the small-subunit RNA check the shape of the pair. A correct pair changes the shape of the ribosome, and the change reaches elongation factor EF-Tu at a distance, which then splits GTP and releases the transfer RNA into the ribosome. Wrong pairs rarely trigger this, so the check comes before the amino acid is added.
EF-G then uses GTP to move the messenger RNA and transfer RNAs on by one codon.
| Aquifex protein | Evidence (UniProt) | Home pathway |
|---|---|---|
| Elongation factor Tu | Inferred from related proteins | Translation cycle |
| Elongation factor Ts | Inferred from related proteins | Translation cycle |
| Elongation factor G | Inferred from related proteins | Translation cycle |
| Small ribosomal subunit protein uS12 | Inferred from related proteins | Ribosomal subunits |
| Large ribosomal subunit protein bL12 | Inferred from related proteins | Ribosomal subunits |
Source: Ogle et al., Science 292:897–902 (2001); Schmeing et al., Science 326:688–694 (2009)
ATP synthase turns flow into chemistry
Protons flowing through the membrane part turn a ring of c subunits and the central stalk. The turning stalk changes the shape of the three catalytic sites in turn, so that each binds, makes and releases ATP in sequence.
| Aquifex protein | Evidence (UniProt) | Home pathway |
|---|---|---|
| ATP synthase subunit alpha | Inferred from related proteins | ATP synthesis |
| ATP synthase subunit a | Inferred from related proteins | ATP synthesis |
| ATP synthase epsilon chain | Inferred from related proteins | ATP synthesis |
| ATP synthase subunit beta | Inferred from related proteins | ATP synthesis |
| ATP synthase subunit c | Inferred from related proteins | ATP synthesis |
| ATP synthase subunit b | Inferred from related proteins | ATP synthesis |
| ATP synthase subunit b | Inferred from related proteins | ATP synthesis |
| ATP synthase gamma chain | Inferred from related proteins | ATP synthesis |
| ATP synthase subunit delta | Inferred from related proteins | ATP synthesis |
Source: Abrahams et al., Nature 370:621–628 (1994); Noji et al., Nature 386:299–302 (1997)
Complex I passes energy along its arm
Electrons enter complex I at one end of its arm. The energy released is passed along the membrane arm to drive proton pumping at sites far from where the electrons travel.
| Aquifex protein | Evidence (UniProt) | Home pathway |
|---|---|---|
| NADH-quinone oxidoreductase subunit A | Inferred from related proteins | Quinone-linked electron transfer |
| NADH-quinone oxidoreductase subunit B | Seen as a protein | Quinone-linked electron transfer |
| NADH-quinone oxidoreductase subunit C/D 2 | Seen as a protein | Quinone-linked electron transfer |
| NADH-quinone oxidoreductase subunit E | Seen as a protein | Quinone-linked electron transfer |
| NADH-quinone oxidoreductase subunit F | Seen as a protein | Quinone-linked electron transfer |
| NADH dehydrogenase I chain G | Seen as a protein | Quinone-linked electron transfer |
| NADH-quinone oxidoreductase subunit H | Inferred from related proteins | Quinone-linked electron transfer |
| NADH-quinone oxidoreductase subunit I | Seen as a protein | Oxidative phosphorylation |
| NADH-quinone oxidoreductase subunit J | Inferred from related proteins | Quinone-linked electron transfer |
| NADH-quinone oxidoreductase subunit K 1 | Inferred from related proteins | Quinone-linked electron transfer |
| NADH dehydrogenase I chain L | Predicted from the genome | Quinone-linked electron transfer |
| NADH dehydrogenase I chain M | Inferred from related proteins | Oxidative phosphorylation |
| NADH-quinone oxidoreductase subunit N 1 | Inferred from related proteins | Quinone-linked electron transfer |
Source: Baradaran et al., Nature 494:443–448 (2013)
The origins question
How did the parts of a machine come to check work before committing to it?
Ribosomal RNA is thought to be the oldest part of the ribosome, with its core proposed to have grown outward by adding layers. ATP synthase is thought to combine older modules: a head related to other ATP-using enzymes and a membrane rotor.
Checking before commitment, rotary coupling and energy passed over a distance are the kind of coordinated, interdependent function the hallmarks describe. The design analysis asks whether module-by-module assembly keeps a working function at every step.
Hallmarks that apply.
Sources
- Petrov et al., PNAS 111:10251–10256 (2014)
- Mulkidjanian et al., Nature Reviews Microbiology 5:892–899 (2007)
- Protein lists and evidence levels: UniProt proteome UP000000798