Part of the cell · Transcription and RNA maturation
Reading genes into RNA
On the cell picture: Rna processing, Transcription
Transcribing DNA into the RNA messages that the protein factory reads, and trimming those messages into usable form.
Proteins in the model: 80
Part of the model's 1051 proteins. Each group below is a book group, counted in the working count after the repeats and non-first-cell groups were removed. The proteins are not yet matched gene by gene.
| Group | Proteins |
|---|---|
| RNA recycling | 5 |
| Transcription factors | 1 |
| RNA Polymerase | 1 |
| Sigma factors | 4 |
| Primary sigma factor σ70 | 1 |
| Transcription regulation | 1 |
| Transcription termination | 3 |
| Early transcription processing | 5 |
| Transcription fidelity | 5 |
| tRNA synthesis and modification | 6 |
| tRNA modification | 4 |
| tRNA recycling | 6 |
| rRNA synthesis QC | 15 |
| tRNA quality control | 17 |
| rRNA modification | 6 |
Its pathways
- Transcriptionatlas pathway8
- RNA processing and turnoveratlas pathway3
- DNA replicationKEGG map3
- Not yet placed in a pathwayto sort13
If it fails
Gene expression stops within minutes. Nothing new can be made.
Dies at once · within the current generation
What it depends on
- Copying and repairing the genomeMaintained DNA provides templates encoding mRNAs, functional RNAs, and the translation machinery.Book pp. 501–502
- Making DNA and RNA lettersRibonucleotides supply RNA synthesis; ATP and GTP also serve as substrates in translation-related reactions.Book pp. 499–502
- Making the twenty amino acidsAmino acids are the building blocks loaded onto tRNAs and joined into proteins.Book pp. 500–502
- Turning hydrogen into usable energyATP supports tRNA charging and GTP supports major translation steps; energy supply must replenish these currencies.Book pp. 499–502
- Quality control (not a separate group in the tree)RNA maturation, ribosome assembly, folding, and rescue help maintain productive translation.Book pp. 255–309, 503
- Mineral ions (not a separate group in the tree)Appropriate ions, especially magnesium, support RNA structure and ribosome activity.Book pp. 499, 502–503
- Holding the internal balanceCompatible pH, ionic strength, and redox conditions support RNA and protein function.Book pp. 183–225, 504
What it supplies
- Copying and repairing the genomeTranslation produces the proteins that carry out DNA replication, repair, and segregation.Book pp. 501–502
- Switching genes on and offRegulators, sensors, kinases, and phosphatases are protein products of translation.Book pp. 502
- Pulling nutrients in from outsideTranslation supplies channels, pumps, and other transport proteins.Book pp. 501–503
- Quality control (not a separate group in the tree)Translation produces chaperones, nucleases, assembly factors, and proteases.Book pp. 501–503
- Dividing into two cellsTranslation provides structural and division proteins.Book pp. 501–502, 504
- Surviving oxygen damageTranslation replaces damaged proteins and produces stress-response factors.Book pp. 501–502, 505
- Loading metals into enzymesTranslation supplies scaffolds, sulfur-mobilization enzymes, and maturation factors.Book pp. 501–502, 505
Dependencies are curated from the book at the level of the map’s systems and are not measured protein contacts. See all systems together.
How it is built and controlled
Counts from UniProt annotations of this group’s proteins.
Its place in the control layer
Information
- Copying the genome:
- Reading genes: , , , , , , ,
Signaling pathways
- What the minimal cell keeps:
Gene regulatory network
- The switches that are kept: , , ,
From the control-layer pages. Which genes a regulator controls is mostly inferred from related bacteria, because Aquifex has no genetic system for testing it directly.
Origins
What needs to be explained
How did templated copying, adaptors, amino-acid activation and peptide synthesis become a heritable coded translation system?
What needs explaining. Explain the coupling of message, adaptor charging, peptide synthesis and inherited maintenance, distinguishing prebiotic chemistry from a complete translation system.
Hurdles
- H-RNA-1Functional RNAsThe problem. Translation needs ribosomal RNAs of about 1,500 and 2,900 nucleotides, dozens of transfer RNAs and other structured RNAs.Why it is hard. Catalytic RNAs obtained in the laboratory are short, work only in selected conditions, and are far from the size and accuracy of these RNAs.Molecular machinesStage 2: One step shown on its ownShown: RNA chains form on clay surfaces, and catalytic RNAs can be selected in the laboratory.In the books: 144 open problems on rna processing and translation ↗
- H-RNA-2Code assignmentsThe problem. The genetic code assigns 64 codons to 20 amino acids and stop signals. In cells the assignments are made by about twenty enzymes (aminoacyl-tRNA synthetases), each recognising one amino acid and its tRNAs.Why it is hard. No chemical rule fixes which codon goes with which amino acid; the assignments exist only in the enzymes that implement them.Information and controlStage 0: Not yet addressed by experimentShown: not yet addressed by experiment.In the books: 144 open problems on rna processing and translation ↗
- H-RNA-3Adapters and chargingThe problem. Each tRNA must carry the right amino acid. Synthetases attach them with about one error in ten thousand, helped by editing sites.Why it is hard. Catalytic RNAs from the laboratory attach amino acids with low specificity, which would scramble every protein.Molecular machinesStage 2: One step shown on its ownShown: Laboratory-selected ribozymes can attach amino acids to RNA.In the books: 144 open problems on rna processing and translation ↗
- H-RNA-4Mutual dependenceThe problem. The ribosome contains over fifty proteins as well as its RNAs, and the synthetases are proteins too; all of them are made by translation.Why it is hard. The machinery that makes proteins is itself made of proteins, so it cannot be built until it already exists.The integrated cellStage 0: Not yet addressed by experimentShown: not yet addressed by experiment.In the books: 144 open problems on rna processing and translation ↗
- H-RNA-5Self-reproduction of translationThe problem. The whole translation apparatus must be rebuilt in every generation, using about four energy-rich bonds for every peptide bond.Why it is hard. Translation depends on monomer supply, energy and accurate copying of its own genes, all of which in turn depend on translation.The integrated cellStage 0: Not yet addressed by experimentShown: not yet addressed by experiment.In the books: 144 open problems on rna processing and translation ↗
Scope. The ribosome animation illustrates selected bacterial translation steps. It is not a reconstruction of the first translation apparatus or a complete account of all RNA processing.
Experimental progress. Time-resolved cryo-electron microscopy captured bacterial ribosome–EF-G intermediates during GTP-associated translocation, directly examining movement within the translation cycle.
What would strengthen a natural account. Steps shown to work together under plausible early-Earth conditions, without a chemist choosing the reagents, purifying the products or changing conditions between steps, would strengthen a natural account of origins in proportion to what they explain. Loss of a claimed dependency or discovery of functional alternatives would weaken the corresponding design argument. Gaps in the record do not supply a numerical likelihood for either explanation.
Observations. mRNA sequence becomes amino-acid sequence through adaptors, charging enzymes and ribosomes. Translation produces components required for further gene expression; closure belongs to the interacting system.
Hallmarks that apply.
- H07 Translation: mRNA sequence becomes amino-acid sequence through adaptors, charging enzymes and ribosomes.
- H11 Semiotic closure: Translation produces components required for further gene expression; closure belongs to the interacting system.
- H33 Multi-level error monitoring: Charging, decoding, maturation and rescue handle errors at different stages.
The author’s conclusion. Within the author’s framework, the convergence of coding, translation and inherited construction supports a provisional preference for design as an explanation of the integrated architecture. This is a qualitative abductive judgment, not an experimentally established origin or a calculated probability. Its force depends on whether the comparison with agency is causally informative and whether alternative pathways can explain the same organization.
From the book article RNA Processing and Translation, with its scientific references.
How it was discovered
- 1959An enzyme that makes RNA from a DNA template, RNA polymerase, is first described.Weiss & Gladstone, Journal of the American Chemical Society 81:4118–4119 (1959)
- 1961Brenner, Jacob and Meselson show that a short-lived messenger RNA carries genetic instructions to the ribosome.Brenner, Jacob & Meselson, Nature 190:576–581 (1961)
- 1969Burgess and colleagues discover the sigma factor, which tells RNA polymerase where genes start.Burgess et al., Nature 221:43–46 (1969)
- 1982Thomas Cech finds an RNA that cuts and rejoins itself without a protein: RNA can be a catalyst (Nobel Prize 1989).Kruger et al., Cell 31:147–157 (1982)
- 1983Sidney Altman’s group shows that the RNA part of RNase P does the cutting (Nobel Prize 1989).Guerrier-Takada et al., Cell 35:849–857 (1983)
- 1986Walter Gilbert names the “RNA world”: a proposed stage when RNA both stored information and catalysed reactions.Gilbert, Nature 319:618 (1986)
- 2001A ribozyme made by laboratory selection copies up to 14 nucleotides of another RNA.Johnston et al., Science 292:1319–1325 (2001)
Each hurdle above is sorted by kind and by how far experiments have got (see “How hurdles are sorted” at the top).
All parts of the cell side by side: origins hub. The book articles:
- RNA Processing and Translation: system page · full description · origins