From: Evolution of gene fusions: horizontal transfer versus independent events
COG A | Protein function | COG B | Protein function | Kingdom pattern* | Principal mode of evolution†| Fusion | Gene juxtaposition‡ | Evolutionary scenario |
---|---|---|---|---|---|---|---|---|
COG0046 | Phospho-ribosyl-formylglycinamidine (FGAM) synthase, synthetase domain | COG0047 | Phospho-ribosyl-formyl-glycinamidine (FGAM) synthase glutamine Amidotransferase domain | -be | HGT | Ecol, Paer, Vcho, Hinf, Xfas, Nmen | Pyro, Paby, Tmar, Drad, Bsub, Bhal | One fusion event, fused gene transfer between eukaryotes and proteobacteria |
COG0067 | Glutamate synthase domain 1 | COG0069 | Glutamate synthase domain 2 | -be | HGT | Most bacteria | Aful, Mjan, Tmar | One fusion event, fused gene transfer between eukaryotes and bacteria |
COG0067 | Glutamate synthase domain 1 | COG0070 | Glutamate synthase domain 3 | -be | HGT | Most bacteria | - | One fusion event, fused gene transfer between eukaryotes and bacteria |
COG0069 | Glutamate synthase domain 2 | COG0070 | Glutamate synthase domain 3 | -be | HGT | Most bacteria | Aful, Mjan, Mthe | One fusion event, fused gene transfer between eukaryotes and bacteria |
COG0139 | Phospho-ribosyl-AMP cyclohydrolase (histidine biosynthesis) | COG0140 | Phospho-ribosyl-ATP pyrophospho-hydrolase (histidine biosynthesis) | -be | Â | Most bacteria | - | Uncertain |
COG0145 | N-methylhydaintoinase A | COG0146 | N-methylhydaintoinase B | -be | HGT | Mtub, Syne, Scer | Mjan, Aero, Hpyl | One fusion event, fused gene transfer between eukaryotes and (the ancestor of) Cyanobacteria and Actinomycetes |
COG0147 | Anthranilate/para-aminobenzoate synthase component I | COG0512 | Anthranilate/para-aminobenzoate synthase component II | -be | IFE | Nmen, Cjej, Paer, Scer | Aful, Mthe, Taci, Aero, Tmar, Drad, Bsub, Bhal, Ecol, Vcho, Xfas | Independent fusion events in eukaryotes and bacteria |
COG0169 | Shikimate 5-dehydrogenase | COG0710 | 3-dehydro-quinate dehydratase | -be | IFE | Ctra, Cpne, Scer | Paby¶Ecol | Independent fusion events in eukaryotes and bacteria |
COG0294 | Dihydropteroate synthase | COG0801 | 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase | -be | IFE | Ctra, Cpne, Scer | Llac¶, Tmar, Drad, Bsub, Bhal | Independent fusion events in eukaryotes and bacteria |
COG0304 | 3-oxoacyl-(acyl-carrier-protein) synthase | COG0331 | (acyl-carrier-protein) S-malonyl-transferase | -be | HGT | Mtub, Scer | Drad, Ecol, Vcho | One fusion event, fused gene transfer between eukaryotes and bacteria |
COG0331 | 3-oxoacyl-(acyl-carrier-protein) synthase | COG2030 | Acyl dehydratase | -be | HGT | Mtub, Bsub, Scer | - | Fused gene transfer between eukaryotes and Actinomycetes; additional, independent fusions in bacteria |
COG0337 | 3-dehydroquinate synthetase | COG0703 | Shikimate kinase | -be | IFE | Tmar, Scer | Drad, Mtub, Proteo-bacteria, Ctra, Cpne | Independent fusion events in eukaryotes and bacteria (with different domain organizations) |
COG0403 | Glycine cleavage system protein P (pyridoxal-binding), amino-terminal domain | COG1003 | Glycine cleavage system protein P (pyridoxal-binding), carboxy-terminal domain | -be | HGT | Drad, Mtub, Syne, Ecol, Paer, Xfas, Nmen | Hbsp, Pyro, Taci, Aero, Tmar, Bsub, Bhal | One fusion event, fused gene transfer between eukaryotes and proteobacteria |
COG0439 | Biotin carboxylase | COG0511 | Biotin carboxyl carrier protein | -be | HGT | Hbsp, Mtub, Rpxx, Scer | Bhal, Ecol, Paer Vcho, Hinf, Xfas, Nmen, Hpyl, Ctra, Cpne | One fusion event, fused gene transfer between eukaryotes and bacteria; additional, independent fusions in bacteria |
COG0439 | Biotin carboxylase | COG1038 | Pyruvate carboxylase, carboxy-terminal domain/subunit | -be | HGT | Bsub, Scer | Mjan | One fusion event, fused gene transfer between eukaryotes and bacteria; subsequent domain accretion in eukaryotes |
COG0439 | Biotin carboxylase | COG0825 | Acetyl-CoA carboxylase α-subunit | -be | HGT | Mtub, Scer | Hbsp, Rpxx | One fusion event, fused gene transfer between eukaryotes and bacteria; subsequent domain accretion in eukaryotes |
COG0476 | Dinucleotide-utilizing enzyme involved in molybdopterin and thiamine biosynthesis | COG0607 | Rhodanese-related sulfurtransferase | -be | IFE | Mtub, Syne, Paer, Scer | - | Independent fusion events in x sulfurtransferase |
COG0511 | Biotin carboxyl carrier protein | COG0825 | Acetyl-CoA carboxylase α-subunit | -be | IFE | Drad, Paer, Scer | Pyro, Tmar, Hbsp¥ | Independent fusion events in eukaryotes and bacteria |
COG0664 | cAMP-binding domain | COG1752 | Esterase | -be | HGT | Mtub, Ccre||, Scer | - | One fusion event, fused gene transfer between eukaryotes and actinomycetes; an additional, independent fusion event in bacteria |
COG1984 | Allophanate hydrolase subunit 2 | COG2049 | Allophanate hydrolase subunit 1 | -be | IFE | Bsub, Scer | Most bacteria | Independent fusion events in eukaryotes and bacteria |
COG1155 | Archaeal/vacuolar-type H+-ATPase subunit A | COG1372 | Intein | a-e | IFE | Taci, Pyro, Scer | - | Independent fusion events in eukaryotes and archaea |
COG0025 | Na+/H+ and K+/H+ antiporters | COG0569 | K+ transport systems, NAD-binding component | ab- | Â | Hbsp, Bhal, Syne | - | Uncertain |
COG0062 | Uncharacterized, conserved protein | COG0063 | Predicted sugar kinase | ab- | AF | All archaea; all bacteria that have COG0062 | NA | One ancestral fusion; fission in eukaryotes |
COG0069 | Glutamate synthase domain 2 | COG1037 | Ferredoxin-like domain | ab- | HGT | Aful, Mjan, Mthe, Tmar; (all that have COG1037) | NA | One ancestral fusion; fused gene transfer from archaea to bacteria (Thermotoga) |
COG0077 | Prephenate dehydratase | COG1605 | Chorismate mutase | ab- | HGT | Aful, Aqua, Tmar, Ecol, Vcho, Paer, Hinf, Xfas, Nmen, Cjej | - | Fused gene transfer between bacteria and archaea (Archaeoglobus and Thermotoga lineages); additional, independent fusions in bacteria |
COG0108 | 3,4-dihydroxy-2-butanone 4-phosphate synthase | COG0807 | GTP cyclohydrolase II | ab- | Â | Aful, Aqua, Tmar, Drad, Mtub, Bsub, Bhal, Syne, Paer, Vcho, Xfas, Nmen, Hpyl, Cjej, Ctra, Cpne | - | Uncertain |
COG0280 | Phosphotransacetylase | COG0281 | Malic enzyme | ab- | HGT | Hbsp, Ecol, Hinf, Xfas, Rpxx | - | One fusion event, fused gene transfer from bacteria to archaea (Halobacterium) |
COG0287 | Prephenate dehydrogenase | COG1605 | Chorismate mutase | ab- | IFE | Aful, Ecol, Vcho, Hinf | Taci, Aero, Ccre | Independent fusion events in archaea and bacteria |
COG0301 | ATP pyrophosphatase (thiamine biosynthesis) | COG0607 | Rhodanese-related sulfurtransferase | ab- | IFE | Taci, Ecol, Vcho, Paer, Hinf | - | Independent fusion events in archaea and bacteria |
COG0340 | Biotin-(acetyl-CoA carboxylase) ligase | COG1654 | Biotin operon repressor | ab- | HGT | Aful, Paby, Drad, Bsub, Bhal, Ecol, Paer, Vcho, Xfas; (all that have COG1654) | NA | One fusion event, fused gene transfer from bacteria to archaea (Archaeoglobus) |
COG0351 | Hydroxymethyl-pyrimidine/phospho-methylpyrimidine kinase | COG1992 | Uncharacterized conserved protein | ab- | HGT | Hbsp, Mjan, Pyro, Aero, Tmar | - | One fusion event, fused gene transfer from archaea to bacteria (Thermotoga) |
COG0468 | RecA/RadA recombinase | COG1372 | Intein | ab- | IFE | Hbsp, Pyro, Mtub | NA | Independent fusion events in archaea and bacteria |
COG0475 | Kef-type K+ transport systems, membrane component | COG1226 | Kef-type K+ transport systems, NAD-binding component | ab- | HGT | Mthe, Ecol, Paer, Hinf, Xfas, Nmen, Cjej, Rpxx | - | One fusion event, fused gene transfer from bacteria to archaea (Methanobacterium) |
COG0550 | Topoisomerase IA | COG0551 | Zn-finger domain associated with topoisomerase type IA | ab- | AF | Most bacteria and archaea | - | One ancestral fusion with subsequent fission in Aper, Aqua |
COG0558 | Phosphatidyl-glycerophosphate synthase | COG1213 | Predicted sugar nucleotidyltransferase | ab- | HGT | Aful, Pyro, Aqua | Aero | One fusion event, fused gene transfer from archaea to bacteria (AquIFEx) |
COG0560 | Phosphoserine phosphatase | COG2716 | ACT-domain-containing protein | ab- | Â | Aful, Mtub, Paer | - | Uncertain |
COG0649 | NADH:ubiquinone oxidoreductase subunit 7 | COG0852 | NADH:ubiquinone oxidoreductase 27 kD subunit | ab- | HGT | Hbsp, Aqua, Ecol, Paer | Most archaea and bacteria | One fusion event, fused gene transfer from bacteria to archaea (Halobacterium) |
COG0662 | Mannose-6-phosphate isomerase | COG0836 | Mannose-1-phosphate guanylyltransferase | ab- | HGT | Aful, Pyro, Aqua, Ecol, Paer, Vcho, Xfas, Hpyl, Cjej | - | Fused gene transfer from bacteria to archaea; a second, independent fusion event in bacteria |
COG0674 | Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, alpha subunit | COG1014 | Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit | ab- | HGT | Aful, Hbsp, Taci, Aero, Mtub, Bhal, Syne, Ecol, Vcho, Tpal | Mjan, Mthe, Aqua, Tmar, Hpyl, Cjej | Fused gene transfer from archaea to bacteria; a second, independent fusion event in bacteria |
COG0777 | Acetyl-CoA carboxylase β subunit | COG0825 | Acetyl-CoA carboxylase α subunit | ab- | HGT | Aful, Hbsp, Pyro, Tmar, Drad, Mtub, Bsub, Bhal, Paer, Rpxx | - | Fused gene transfer from bacteria to archaea; a second, independent fusion event in bacteria |
COG1013 | Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, beta subunit | COG1014 | Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit | ab- | IFE | Mthe, Syne, Ecol, Vcho, Tpal | Aful, Taci, Aero, Mtub, Bhal | Independent fusion events in archaea and bacteria |
COG1112 | Superfamily I DNA and RNA helicases and helicase subunits | COG2251 | Predicted metal-binding domain | ab- | IFE | Pyro, Mtub | - | Independent fusion events in archaea and bacteria |
COG1239 | Mg-chelatase subunit ChlI | COG1240 | Mg-chelatase subunit ChlD | ab- | HGT | Hbsp, Mthe, Taci, Mtub, Syne | Mjan, Paer | Fused gene transfer between bacteria and archaea, with subsequent fissions |
COG1361 | S-layer domain | COG1470 | Predicted membrane protein | ab- | HGT | Aful, Pyro, Bhal | - | One fusion event, fused gene transfer from archaea to bacteria |
COG1387 | Histidinol phosphatase and related hydrolases of the PHP family | COG1796 | DNA polymerase IV (family X) | ab- | HGT | Mthe, Taci, Drad, Bsub, Bhal; (all prokaryotes that have COG1796) | NA | One fusion event, fused gene transfer between archaea to bacteria |
COG1683 | Uncharacterized conserved protein | COG3272 | Uncharacterized conserved protein | ab- | HGT | Mthe, Paer, Vcho | - | One fusion event, fused gene transfer between archaea and bacteria (Methanobacterium and Vibrio/Pseudomonas, respectively) |
COG1788 | Acyl-CoA:acetate CoA transferase alpha subunit | COG2057 | Acyl-CoA:acetate CoA transferase beta subunit | ab- | HGT | Hbsp, Taci, Aero, Drad, Bhal, Ecol | Mtub, Bsub, Paer, Hinf, Hpyl | Fused gene transfer between bacteria and archaea; a second, independent fusion event in bacteria |
COG3261 | Ni, Fe-hydrogenase III large subunit | COG3262 | Ni, Fe-hydrogenase III component G | ab- | HGT | Paby, Mtub, Ecol | Pyro | One fusion event, fused gene transfer from bacteria to archaea |
COG0518 | GMP synthase - Glutamine amidotransferase domain | COG0519 | GMP synthase-PP-ATPase domain | abe | HGT | Aero, Scer, most bacteria | Mthe, Pyro, Paby | Fused gene transfer among bacteria, archaea, and eukaryotes |
COG0674 | Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, alpha subunit | COG1013 | Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, beta subunit | abe | HGT | Aful, Mthe, Taci, Pyro, Paby, Scer, Syne, Ecol, Vcho, Cjej, Tpal | Hbsp, Mjan, Aero, Aqua, Tmar, Mtub, Hpyl | Fused gene transfer from archaea to bacteria (α-proteobacteria) |