Skip to main content

Table 2 Evolutionary history of trans-kingdom gene fusions

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

 

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-

 

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-

 

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-

 

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)

  1. *Abbreviations: a, archaea, b, bacteria, e, eukaryotes; a dash indicates that the given kingdom is not represented in at least one of the fusion-linked COGs. †AF, ancestral fusion, HGT, horizontal gene transfer, IFE, independent fusion events. ‡ In several cases, the indicated genes are separated by one to three genes or their order is switched compared to that of the fusion components. §Paby, Pyrococcus abyssi, an archaeal genome not included in the master set of genomes analyzed in this study. ¶Llac, Lactococcus lactis, a bacterial genome not included in the master set of genomes analyzed in this study. ||Ccre, Caulobacter crescentus, a bacterial genome not included in the master set of genomes analyzed in this study. ¥Hbsp, Halobacterium sp., an archaeal genome not included in the master set of genomes analyzed in this study.