- Bacteria (already in our earlier table)
- Archaea (Methanosarcina, Methanococcus, etc.)
- Codon reassignment (Selenocysteine or Pyrrolysine)
- Etymology of genus and species names
- Taxonomic notes
Natural Codon Reassignments: Etymology + Codon Mapping
| Organism | Domain | Codon Reassignment | Etymology (Genus + Species) | Taxonomy / Notes |
|---|---|---|---|---|
| Escherichia coli | Bacteria | UGA → Selenocysteine | Escherichia — Named after Theodor Escherich (1857–1911), German-Austrian pediatrician who first described it in 1885. coli — Latin colī, “of the colon,” habitat in the large intestine. | Gram-negative rod in Enterobacteriaceae; model organism. |
| Clostridium spp. | Bacteria | UGA → Selenocysteine | Clostridium — Greek kloster “spindle” + -idion (diminutive), referring to spindle-shaped endospores. Species epithets vary. | Gram-positive, anaerobic, spore-forming rods; includes pathogens (C. botulinum). |
| Treponema pallidum | Bacteria | UGA → Selenocysteine | Treponema — Greek trepo “to turn” + nema “thread,” spiral morphology. pallidum — Latin “pale,” for faint staining in light microscopy. | Gram-negative-like spirochete; syphilis agent. |
| Desulfitobacterium hafniense | Bacteria | UAG → Pyrrolysine | Desulfitobacterium — Latin de- “removal” + sulfitum “sulfite” + bacterium “rod-shaped microbe.” hafniense — From Hafnia, Latin for Copenhagen, Denmark (site of isolation). | Gram-positive anaerobe; dehalogenating methyltransferases use Pyl. |
| Methanosarcina barkeri | Archaea | UAG → Pyrrolysine | Methanosarcina — Greek methan (methane) + sarkinos “fleshy,” describing cell aggregates. barkeri — Named for Harold Barker, microbiologist who studied methanogens. | Methanogenic archaeon; uses Pyl in methyltransferases for methane metabolism. |
| Methanosarcina mazei | Archaea | UAG → Pyrrolysine | Methanosarcina as above. mazei — Honors microbiologist Jules Maze. | Methanogenic archaeon; Pyl system similar to M. barkeri. |
| Methanococcus jannaschii | Archaea | UGA → Selenocysteine | Methanococcus — Greek methan (methane) + kokkos “berry,” spherical methane-producing cells. jannaschii — Honors Holger Jannasch, deep-sea microbiologist. | First archaeon with fully sequenced genome; deep-sea hydrothermal vent methanogen. |
| Methanopyrus kandleri | Archaea | UGA → Selenocysteine | Methanopyrus — Greek methan (methane) + pyr “fire,” heat-loving methane producer. kandleri — Named after microbiologist Johannes Kandler. | Hyperthermophilic archaeon from deep-sea vents; high-temp selenoprotein use. |
Observations
- UGA → Selenocysteine: Widespread across Bacteria and Archaea, especially in anaerobes with redox enzymes that benefit from selenium.
- UAG → Pyrrolysine: So far restricted to methanogenic Archaea and a few bacteria; mostly enzymes involved in methyl group transfer in methane metabolism.
- Etymology patterns:
- Many methanogen names combine methan- (methane) with shape (-coccus, -sarcina) or habitat (-pyr, “fire”).
- Species epithets often honor scientists (jannaschii, barkeri) or describe origin location (hafniense).
Codon → Amino Acid → Organism(s) with Natural Reassignment → Etymology integrated chart.
This focuses on the two reassignable stop codons (UGA and UAG) plus the canonical stop UAA for completeness, showing the special cases in both Bacteria and Archaea.
Integrated Codon–Organism–Etymology Chart
| mRNA Codon | Standard Genetic Code Meaning | Natural Reassignment in Certain Organisms | Amino Acid Inserted (in reassignment) | Example Organism(s) | Etymology of Organism Name |
|---|---|---|---|---|---|
| UGA (opal) | Stop codon | Reassigned in various Bacteria & Archaea with SECIS element | Selenocysteine (Sec, U) | Escherichia coli | Escherichia — Named after Theodor Escherich (1857–1911), pediatrician who described it; coli — Latin “of the colon,” habitat. |
| Clostridium spp. | Clostridium — Greek kloster “spindle” + -idion “small,” for endospore shape. | ||||
| Treponema pallidum | Treponema — Greek trepo “to turn” + nema “thread,” spiral shape; pallidum — Latin “pale.” | ||||
| Methanococcus jannaschii | Methanococcus — Greek methan (methane) + kokkos “berry,” spherical methanogen; jannaschii — Honors Holger Jannasch. | ||||
| Methanopyrus kandleri | Methanopyrus — Greek methan (methane) + pyr “fire,” hyperthermophile; kandleri — Honors Johannes Kandler. | ||||
| UAG (amber) | Stop codon | Reassigned in some Bacteria & Archaea with pyl operon | Pyrrolysine (Pyl, O) | Desulfitobacterium hafniense | Desulfitobacterium — Latin de- “removal” + sulfitum “sulfite” + bacterium “rod bacterium”; hafniense — From Hafnia, Latin for Copenhagen. |
| Methanosarcina barkeri | Methanosarcina — Greek methan (methane) + sarkinos “fleshy” cell aggregates; barkeri — Honors Harold Barker. | ||||
| Methanosarcina mazei | Methanosarcina — as above; mazei — Honors Jules Maze. | ||||
| UAA (ochre) | Stop codon | No known natural reassignment | — | — | — |
Reading the Chart
- mRNA Codon: Triplet in the mRNA (remember in DNA T replaces U).
- Standard Genetic Code Meaning: What that codon means in the universal genetic code.
- Natural Reassignment: Special translation systems that change its meaning.
- Amino Acid Inserted: Which amino acid replaces the stop signal.
- Example Organism(s): Species where this reassignment is naturally found.
- Etymology: Origins of genus/species names — either descriptive (shape, habitat, property) or commemorative (named after people).
If you want, I can merge this back into the full codon dictionary we built earlier, so for every codon you get:
- Grapheme triplet
- Standard amino acid
- Chemical formula & ASCII structure
- Known natural reassignments + organisms
- Etymology of those organisms
Do you want me to create that full integrated codon–chemistry–organism–etymology master chart?