Evolutionary Scenarios for aaRSs
| Specificity | Inferred evolutionary events (standard model is assumed unless indicated otherwise) | Support for root placement (see Fig. 1 for likely synapomorphies manifest in distinct domain architectures)[i] |
| Class I | ||
| Tyrosine | horizontal transfer with displacement from Gram-positive bacteria to E. coli | synapomorphies in the carboxy-terminal region (ACB, S4 domain in bacteria); clustering; MMPR; compatible with rooting by paralogy (Brown et al. 1997). |
| Tryptophan | horizontal transfer from eukaryotes to the archaeal lineage including P. horikoshii | clustering; MMPR; compatible with rooting by paralogy (Brown et al. 1997). |
| Leucine | pure standard model, no interdivision horizontal transfer | synapomorphies in the large insert (A1–A5) typical of aliphatic aaRS (Zn-ribbon, module shuffling) and in the carboxy-terminal domain (see text); clustering; MMPR; compatible with rooting by paralogy (Brown and Doolittle 1995; Hashimoto et al. 1998). |
| Valine | displacement of ancestral eukaryotic enzyme by a bacterial, probably mitochondrial one (a single enzyme for the cytosol and the organelles in eukaryotes) | clustering; MMPR; rooting by paralogy; compatible with rooting by paralogy (Brown and Doolittle 1995; Hashimoto et al. 1998). |
| Isoleucine | horizontal transfer from eukaryotes to spirochaetes, Chlamydia, and Mycobacteria | multiple synapomorphies in the domain architecture (see text), clustering; MMPR; compatible with rooting by paralogy (Brown and Doolittle 1995; Hashimoto et al. 1998). |
| Methionine | (1) horizontal transfer from eukaryotes to spirochaetes andChlamydia; (2) horizontal transfer from archaea(?) to Proteobacteria; (3) horizontal transfer from eukaryotes or bacteria (e.g., spirochaetes) to the archaeal lineage leading to P. horikoshii. | apparent synapomorphies in the large insert (A1–A5) typical of aliphatic aaRS (Zn-ribbon in archaea, eukaryotes and a subset of bacteria), clustering; MMPR. |
| Arginine | independent horizontal transfer from eukaryotes to (1) spirochaetes; (2) Proteobacteria, Cyanobacteria, Chlamydia | apparent synapomorphy—the small inserted domain between the core and DALR domains in archaea, eukaryotes, and a subset of bacteria; MMPR; clustering suggested a different root position, on the branch between yeast and the spirochaetes |
| Glutamate/glutamine | duplication of GluRS in eukaryotes, followed by switch of specificity to glutamine in one of the copies; horizontal transfer of GlnRS from eukaryotes to Proteobacteria; horizontal transfer of mitochondrial GluRS from eukaryotes to spirochaetes and Chlamydiae | apparent synapomorphies—unrelated ACB domains in (1) archaeal and eukaryotic GluRS and in all GlnRS in the core insertion domain (bulging α-helices); and (2) bacterial GluRS; clustering, MMPR. |
| Cysteine | uncertain; the standard model does not directly apply; possible ancient gene loss in archaea, followed by horizontal transfer from bacteria to some of the archaeal species | clustering; MMPR suggests several possible rootings; the root position remains uncertain. |
| Lysine-I | no eukaryotic representatives; independent horizontal transfer from archaea to (1) spirochaetes; (2) Rickettsia (from the Cenarchaeum lineage) | clustering, MMPR |
| Class II | ||
| Alanine | displacement of ancestral eukaryotic enzyme by a bacterial, probably mitochondrial one (a single enzyme for the cytosol and the organelles in eukaryotes) | apparent synapomorphy—extra aminoterminal domain in archaeal AlaRs; clustering, MMPR |
| Threonine | duplication of mitochondrial ThrRS in eukaryotes, with displacement of the ancestral eukaryotic form | clustering, MMPR |
| Proline | horizontal transfer from eukaryotes to Borrelia (a spirochaete) and mycoplasmas | apparent synapomorphies—YbaK domain inserted within the core in bacterial ProRS and an extra carboxy-terminal domain in eukaryotes and bacteria; clustering, MMPR |
| Histidine | (1) horizontal transfer from eukaryotes to spirochaetes andHelicobacter; (2) horizontal transfer from archaea toAquifex, Synechocystis, Bacillus without displacement of the ancestral bacterial form | root position not defined |
| Aspartate/asparagine | duplication of AspRS in eukaryotes, followed by switch of specificity to asparagine in one of the copies; ancient horizontal transfer of AsnRS from eukaryotes to bacteria | synapomorphy—insertion of GAD domain in the core of bacterial AspRS; clustering, paralogous routing using LysRS. MMPR suggest a root position between AspRS and AsnRS |
| Serine | complex picture. Anomalous rapid evolution in one of the archaeal lineages; horizontal transfer from eukaryotes or archaea to Mycobacteria; possible displacement of mitochondrial genes by ancestral ones in eukaryotes; horizontal transfer, apparently of eukaryotic mitochondrial genes, to spirochaetes | root position not defined |
| Phenylalanine α | horizontal transfer to spirochaetes, probably from archaea | apparent synapomorphies in the amino-terminal region—HTH domain and an additional conserved domain in archaea, eukaryotes, and spirochaetes, a distinct amino-terminal domain in bacteria; clustering, MMPR |
| Phenylalanine α–β | horizontal transfer to spirochaetes, probably from archaea | apparent synapomorphies in domain architecture—EMAP domain and FDX–ACB domain in bacteria; clustering, MMPR |
| Lysine-II | no archaeal representatives; horizontal exchange of type X LysRS gene between Proteobacteria, Aquifex, Treponema | root position not defined |
| Glycine-1 | Early horizontal transfer from eukaryotes, archaea or a common ancestor thereof to spirochetes, Mycobacteria, Mycoplasmas; alternatively, an ancestral form displaced in most bacteria (see text) | apparent synapomorphy—insert in the core domain in archaea and eukaryotes; clustering, MMPR |
| Glycine-2 α–β | bacterial-only; phylogeny uncertain | root position not defined |
[i] (ACB) Anticodon-binding domain; (FDX–ACB) ferredoxin-fold ACB; (MMPR) modified midpoint rooting.