Suppl. Figure 3. Bayesian phylogeny of the E-isoprenytransferases (IPPS). Tree is unrooted and
reconstructed using 208 sequences and 201 conserved sites. Multifurcations correspond to branches
with Bayesian posterior probabilities <0.5, whereas numbers at nodes indicate Bayesian posterior
probabilities higher than 0.5. The bootstrap values from the maximum likelihood analyses have been
reported on basal and major nodes. Colors on leaves represent the affiliation of sequences to their
respective domain of life: archaea (blue), bacteria (orange) and eukaryotes (purple).
IPPS are classified according to the size of their products into short-chain IPPS (up to ~5
isoprenoid units) and long-chain IPPS (>5 isoprenoid units). Short-chain and long-chain IPPS are
homologous to each other but the size of the molecules they produce is constrained by differences in
their substrate-binding pockets (Kellogg & Poulter, 1997). Point mutations may easily change the size
of these pockets (Ohnuma et al., 1996, 1998), so substrate specificity for particular genes cannot be
predicted from sequence analysis only and requires biochemical confirmation (Chen, Kroon & Poulter,
1994; Tachibana et al., 2000). Yet, previous phylogenetic analyses have shown that homologues of the
IPPS family actually split in two clades that roughly correspond to short-chain and long-chain IPPS
(Boucher, Kamekura & Doolittle, 2004; Lombard, López-García & Moreira, 2012). Both IPPS subfamilies were shown to be probably ancestral to archaea and bacteria and, therefore, it is likely that
they were present in the cenancestor (Lombard, López-García & Moreira, 2012). The evolution of the
short-chain IPPS–including the FPP synthase (FPPS) and the GGPP synthase (GGPPS)–was
reexamined here in order to also include the eukaryotes.
A preliminary phylogenetic tree was built to discriminate short- and long-chain IPPS (data not
shown). The subsequent phylogeny limited to the short-chain IPPS (this figure) has three parts: 1) a
large group containing most eukaryotic sequences (BPP = 0.68); 2) a mainly bacterial group at the
bottom of the figure (BPP = 0.53); and 3) several unresolved paraphyletic archaeal groups, also
containing a few bacterial sequences. Most bacterial and archaeal sequences group together according
to their taxonomic classification, but the lack of strong phylogenetic signal prevents from obtaining a
resolved phylogeny, especially among the archaeal section of the tree. A reason that may explain these
resolution issues is the noise introduced by the very divergent eukaryotic sequences, which was less
dominant in prokaryotic-only analyses published elsewhere (Lombard, López-García & Moreira,
2012).
Regarding the eukaryotic sequences, three groups are discernible: one group of plastid-bearing
eukaryotes related to cyanobacteria in the bacterial clade (BPP = 1)–and, therefore, probably acquired
from the cyanobacterial ancestor of plastids; and two divergent eukaryotic paralogues (BPP = 1 in both
cases). The eukaryotic paralogues can respectively be assigned to the FPPS and GGPPS functions.
Both paralogues are widespread and likely ancestral to eukaryotes. Both paralogues are also related to a
few prokaryotic basal sequences. The basal sequences related to the GGPPS are a small group of mixed
archaea, whereas the basal prokaryotic sequences related to FPPS are a mix of cyanobacteria and
Deinococcus-Thermus bacteria. The little number of basal prokaryotic sequences, their taxonomic
diversity and the strong divergence of the eukaryotic sequences with regard to the other prokaryotic
sequences suggest that the placement of these prokaryotic basal sequences could result from
reconstruction artifacts and can hardly be seen as significant. The fact that the two short-chain IPPS
paralogues are only widespread in eukaryotes argues in favor of the idea that short-IPPS were
duplicated in the eukaryotic lineage prior to LECA. This phylogeny does not allow to confidently
ascertain the origin of the eukaryotic short-chain IPPS, but it supports the monophyly of the eukaryotic
sequences. Since the presence of IPPS genes can be traced back to the last common ancestor of
eukaryotes (this work) and the respective common ancestors of bacteria and archaea (Lombard, LópezGarcía & Moreira, 2012), an IPPS gene is likely to have existed in the cenancestor.
Boucher Y, Kamekura M, Doolittle WF. 2004. Origins and evolution of isoprenoid lipid biosynthesis in
archaea. Molecular Microbiology. 52:515–27. DOI: 10.1111/j.1365-2958.2004.03992.x.
Chen A, Kroon PA, Poulter C. 1994. Isoprenyl diphosphate synthases: Protein sequences comparisons,
a phylogenetic tree and predictions of secondary structure. Protein Science. 3:600–607.
Kellogg BA, Poulter CD. 1997. Chain elongation in the isoprenoid biosynthetic pathway. Current
Opinion in Chemical Biology. 1:570–578.
Lombard J, López-García P, Moreira D. 2012. Phylogenomic investigation of phospholipid synthesis in
archaea. Archaea 2012:630910. DOI: 10.1155/2012/630910.
Ohnuma S, Hirooka K, Hemmi H, Ishida C, Ohto C, Nishino T. 1996. Conversion of product
specificity of archaebacterial geranylgeranyl-diphosphate synthase. Journal of Biological
Chemistry. 271:18831–18837.
Ohnuma S, Hirooka K, Tsuruoka N, Yano M, Ohto C, Nakane H, Nishino T. 1998. A pathway where
polyprenyl diphosphate elongates in prenyltransferase. Journal of Biological Chemistry.
273:26705–26713.
Tachibana A, Yano Y, Otani S, Nomura N, Sako Y, Taniguchi M. 2000. Novel prenyltransferase gene
encoding farnesylgeranyl diphosphate synthase from a hyperthermophilic archaeon, Aeropyrum
pernix. European Journal of Biochemistry. 267:321–328.
Suppl. Figure 3
Oxytricha trifallax [GenBank: EJY78820.1]
Paramecium tetraurelia [GenBank: XP_001441749.1]
Ciliates
Tetrahymena thermophila [GenBank: XP_001015938.2]
Ichthyophthirius multifiliis [GenBank: XP_004031247.1]
Candidatus Caldiarchaeum subterraneum [GenBank: WP_020863672.1]
Proteoarchaea
Candidatus
Korarchaeum
cryptofilum
[GenBank:
YP_001737508.1]
0.52
Natronomonas pharaonis [GenBank: YP_331006.1]
Euryarchaea
0.54
Bigelowiella natans [JGI: 80013]
Rhizaria
1
Dinophyceae
Symbiodinium munutum [OIST: 040765_t1s6885]
1
1/96
Angomonas
deanei
[GenBank:
EPY25208.1]
1
Euglenozoa
Leishmania major [GenBank: XP_001682599.1]
Saccharomyces cerevisiae [KEGG: BTS1]
Ustilago maydis [GenBank: XP_760606.1]
0.99
Cryptococcus neoformans [GenBank: XP_572774.1]
0.91
Fonticula alba [GenBank: KCV72083.1]
1
0 . 9 8 Rhizophagus
irregularis [GenBank: ERZ95163.1]
Capsaspora owczarzaki [GenBank: XP_004363786.1]
Opisthokonta
Trichoplax adhaerens [GenBank: XP_002112074.1]
0.99
Monosiga
brevicollis [GenBank: XP_001743144.1]
1
0.99
Salpingoeca rosetta [GenBank: XP_004997186.1]
Drosophila melanogaster [GenBank: AAF50574.1]
0.69
sapiens [KEGG: GGPPS]
1Homo
Mus musculus [KEGG: GGPPS]
0.88
0.68
Thecamonas trahens [Broad: AMSG_00206T0]
Apusozoa
0.67
Guillardia theta [GenBank: XP_005821197.1]
Cryptophyta
0.78
Dictyostelium discoideum [GenBank: XP_629028.1]
1
Polysphondylium pallidum [GenBank: EFA75498.1]
Amoebozoa
0.91
Acanthamoeba castellanii [GenBank: XP_004341343.1]
Emiliania
huxleyi
[GenBank:
XP_005763137.1]
Haptophyta
1
0.56
Aureococcus anophagefferens [GenBank: XP_009034905.1]
0.99
Stramenopiles
Phytophthora parasitica [GenBank: ETI46205.1]
0.58
Phaeodactylum tricornutum [GenBank: XP_002181666.1]
0.75
Schizochytrium aggregatum [JGI: 80815]
Acaryochloris sp. [GenBank:WP_010479213.1]
0.97
Cyanobacteria
Arthrospira platensis [GenBank: EKD09392.1]
Deinococcus radiodurans [GenBank: NP_295118.1]
0.96
0.76
Truepera radiovictrix [GenBank: YP_003704782.1]
1
Deinococcus-Thermus
Oceanithermus profundus [GenBank: YP_004058858.1]
1
Marinithermus hydrothermalis [GenBank: YP_004366928.1]
0.7
Ciliates
Plasmodium falciparum [GenBank: XP_001347966.2]
Parabasalia
Trichomonas vaginalis [GenBank: XP_001329081.1]
Toxoplasma gondii [GenBank: XP_002366124.1]
Apicomplexa
1/100
Giardia lamblia [GenBank: EFO63579.1]
Diplomonad
0.79
Perkinsus marinus [GenBank: XP_002769627.1]
Eimeria brunetti [GenBank: CDJ45916.1]
0.56
Alveolata
Babesia
equi
[GenBank:
XP_004833872.1]
1
Theileria annulata [GenBank: XP_955531.1]
0.79
Bigelowiella natans [JGI: 33405]
Rhizaria
Reticulomyxa filosa [GenBank: ETO12857.1]
Dictyostelium discoideum [GenBank: XP_641989.1]
Amoebozoa
Acanthamoeba castellanii [GenBank: XP_004345905.1]
Guillardia theta [GenBank: XP_005819303.1]
Cryptophyta
Fonticula alba [GenBank: KCV73224.1]
Naegleria gruberi [GenBank: XP_002682719.1]
0.9
Excavata
Trichoplax adhaerens [GenBank: XP_002116714.1]
Opisthokonta
Capsaspora owczarzaki [GenBank: XP_004345458.1]
sapiens [KEGG: FPPS]
1 Homo
Mus musculus [KEGG: FPPS]
Trypanosoma vivax [GenBank: CCC48988.1]
0.71
1
major [pdb: 4JZB]
Euglenozoa
1 Leishmania
Angomonas deanei [GenBank: EPY29838.1]
Monosiga brevicollis [GenBank: XP_001743857.1]
Choanoflagellate
0.89
[GenBank: XP_009038976.1]
Stramenopile
1 Aureococcus anophagefferens
Symbiodinium munutum [OIST: 018339_t1s1459]
Dinophyceae
Cyanophora paradoxa [rutgers: Cypara_22176]
0.69
Phytophthora parasitica [GenBank: ETI50130.1]
0 . 9 7 Phaeodactylum
Stramenopiles
tricornutum [GenBank: XP_002184024.1]
Galdieria sulphuraria [GenBank: XP_005706102.1]
1
Chondrus crispus [GenBank: XP_005713327.1]
0.69
Cyanidioschyzon merolae [GenBank: XP_005537135.1]
0.6
Pyropia yezoensis [NRIFS: contig_36715_g8702]
Rhizophagus irregularis [GenBank: ERZ99608.1]
0.99
Schizosaccharomyces pombe [GenBank: BAA13767.1]
0.97
Saccharomyces cerevisiae [KEGG: ERG20]
Archaeplastida
Fungi
0.99
Ustilago maydis [GenBank: XP_757593.1]
1
Cryptococcus neoformans [GenBank: XP_571137.1]
variabilis [GenBank: XP_005851791.1]
0 . 6 2 Chlorella
Chlamydomonas reinhardtii [GenBank: XP_001693168.1]
Haptophyta
Emiliania huxleyi [GenBank: XP_005771269.1]
0.67
Bathycoccus prasinos [GenBank: XP_007511050.1]
0.97
1 Ostreococcus
lucimarinus [GenBank: XP_001416643.1]
0.92
Physcomitrella patens [GenBank: XP_001768279.1]
1
Arabidopsis thaliana [GenBank: NP_199588.1]
1
Oryza sativa [GenBank: NP_001043959.1]
Actinobaculum massiliae [GenBank: EKU95967.1]
Acidimicrobium ferrooxidans [GenBank: YP_003109111.1]
1
Frankia alni [GenBank: YP_712389.1]
Actinobacteria
1
0.99
Nocardia
farcinica
[GenBank:
YP_120613.1]
0.98
Actinoplanes friuliensis [GenBank: YP_008731520.1]
Thermosipho
africanus
[GenBank:
YP_002335290.1]
1
Thermotogae
Fervidobacterium nodosum [GenBank: YP_001409838.1]
Thermoplasma volcanium [GenBank: NP_110781.1]
0.61
1
Euryarchaea
Ferroplasma acidarmanus [GenBank: YP_008142164.1]
0.99
Staphylothermus marinus [GenBank: YP_001040510.1]
1
Thermogladius cellulolyticus [GenBank: YP_006363303.1]
0.99
Crenarchaea
Desulfurococcus
kamchatkensis
[GenBank:
YP_002429148.1]
0 . 7 8Thermosphaera aggregans [GenBank: YP_003650291.1]
Proteoarchaea
archaeon Lokiarchaeota [GenBank: KKK43939.1]
Pyrococcus
abyssi
[GenBank:
NP_126597.1]
1
Thermococcus kodakarensis [GenBank: YP_183881.1]
Euryarchaea
fervens [GenBank: YP_003128430.1]
1 Methanocaldococcus
Methanococcus maripaludis [GenBank: YP_001098146.1]
Planctomyces limnophilus [GenBank: YP_003630936.1]
1
Rhodopirellula baltica [GenBank: NP_866974.1]
Planctomycetes
1
Blastopirellula marina [GenBank: EAQ78123.1]
0 . 9 5 Pirellula
staleyi [GenBank: YP_003368731.1]
Bacteroides fragilis [GenBank: EKA90356.1]
1
Cytophaga
hutchinsonii
[GenBank: YP_677090.1]
Bacteroidetes/
1
Chloroherpeton thalassium [GenBank: YP_001995322.1]
1
aestuarii [GenBank: YP_002015087.1]
Chlorobi
1 Prosthecochloris
Chlorobium luteolum [GenBank: YP_375662.1]
Methanopyrus kandleri [GenBank: WP_011019143.1]
0.6
Methanothermus fervidus [GenBank: YP_004004459.1]
1
Methanobacterium formicicum [GenBank: EKF85907.1]
0.81
Ferroglobus placidus [GenBank: YP_003435928.1]
1
Archaeoglobus fulgidus [GenBank: NP_071111.1]
Euryarchaea
0.99
Methanosarcina mazei [GenBank: YP_007490458.1]
1
Methanoculleus marisnigri [GenBank: YP_001047724.1]
0.64
Natronomonas pharaonis [GenBank: YP_327492.1]
1
0.56
Halogeometricum borinquense [GenBank: YP_004036227.1]
Candidatus Nitrososphaera gargensis [GenBank: YP_006862746.1]
1
maritimus [GenBank: YP_001581646.1]
Thaumarchaea
1 Nitrosopumilus
Cenarchaeum symbiosum [GenBank: YP_876540.1]
0.52
Kitasatospora sp. [GenBank: WP_030460407.1]
1
Actinobacteria
Frankia alni [GenBank: YP_711679.1]
1
Caldilinea
aerophila
[GenBank:
YP_005441531.1]
0.99
Anaerolinea thermophila [GenBank: YP_004174678.1]
0.59
Nitrolancea hollandica [GenBank: CCF82681.1]
Chloroflexi
0.74
Ktedonobacter racemifer [GenBank: EFH86374.1]
0.64
Chloroflexus aurantiacus [GenBank: YP_001635461.1]
Ignicoccus hospitalis [GenBank: YP_001434928.1]
Caldisphaera lagunensis [GenBank: YP_007175575.1]
1
Hyperthermus butylicus [GenBank: YP_001012240.1]
Pyrolobus fumarii [GenBank: YP_004781806.1]
0.93
Thermofilum pendens [GenBank: YP_920014.1]
Vulcanisaeta
distributa
[GenBank:
YP_003902192.1]
1
0.95
Caldivirga maquilingensis [GenBank: YP_001540467.1]
1
Thermoproteus tenax [GenBank: YP_004893742.1]
1
Pyrobaculum
islandicum
[GenBank:
YP_930716.1]
1 Pyrobaculum aerophilum [GenBank: NP_559016.1]
Crenarchaea
Ignicoccus hospitalis [GenBank: YP_001435752.1]
0.98
Ignisphaera aggregans [GenBank: YP_003858931.1]
0.87
Sulfolobus solfataricus [GenBank: NP_341633.1]
1
Metallosphaera sedula [GenBank: YP_001192198.1]
0 . 9 8Acidianus
hospitalis [GenBank: YP_004457836.1]
0.98
Fervidicoccus fontis [GenBank: YP_005841896.1]
Pyrolobus fumarii [GenBank: YP_004781038.1]
Prokaryotic
1
Hyperthermus butylicus [GenBank: YP_001012745.1]
0.88
short-chain
Aeropyrum pernix [GenBank: NP_148152.2]
1
Acidilobus
saccharovorans
[GenBank:
YP_003815770.1]
1
IPPS
Caldisphaera lagunensis [GenBank: YP_007174508.1]
Aquificae
Persephonella marina [GenBank: YP_002730153.1]
0.83
Alicyclobacillus acidocaldarius [GenBank: YP_003185175.1]
Enterococcus faecalis [GenBank: YP_005705393.1]
0.9
Firmicutes
Streptococcus agalactiae [GenBank: EAO71085.1]
0.52
Staphylococcus aureus [GenBank: EZT85259.1]
Hydrogenivirga sp. [GenBank: WP_008285790.1]
1
Aquifex aeolicus [GenBank: NP_213513.1]
Aquificae
0.67
Hydrogenobaculum sp. [GenBank: YP_007647645.1]
0.99
Hydrogenobacter thermophilus [GenBank: YP_003432858.1]
Opitutus terrae [GenBank: YP_001817460.1]
0.91
Chlamydiae/
Chlamydophila felis [GenBank: YP_514920.1]
0.95
Simkania negevensis [GenBank: YP_004670438.1]
Verrucomicrobia
1
Waddlia chondrophila [GenBank: YP_003708395.1]
Kosmotoga olearia [GenBank: YP_002941137.1]
1
Mesotoga
prima
[GenBank: YP_006345241.1]
1
Thermotoga maritima [pdb: 2FTZ]
Thermotogae
0.53/70
0.91
Petrotoga mobilis [GenBank: YP_001567257.1]
1
Marinitoga piezophila [GenBank: YP_005097551.1]
Simkania negevensis [GenBank: YP_004671311.1]
Chlamydiae
0.6
Nitratifractor salsuginis [GenBank: YP_004168945.1]
Epsilon
1
Campylobacter jejuni [GenBank: KDA21012.1]
0.76
profundicola [GenBank: YP_002608066.1]
proteobacteria
0 . 5 7 Nautilia
Sulfurimonas autotrophica [GenBank: YP_003891363.1]
Natranaerobius thermophilus [GenBank: YP_001917859.1]
0.97
Firmicutes
Halobacteroides halobius [GenBank: YP_007314628.1]
Bathycoccus prasinos [GenBank: XP_007511871.1]
Cyanidioschyzon merolae [GenBank: XP_005536487.1]
0.62
1
Haptophyta
Emiliania
huxleyi
[GenBank:
XP_005779411.1]
1
Nannochloropsis gaditana [GenBank: EWM28774.1]
Stramenopiles Archaeplastida
1/60 Physcomitrella
patens [GenBank: XP_001752313.1]
1
Arabidopsis thaliana [GenBank: NP_188069.1]
1 Prunus
persica [GenBank: XP_007204376.1]
Synechococcus sp. JA-3-3Ab [GenBank: WP_011429285.1]
Acaryochloris sp. [GenBank: WP_010470824.1]
0.98 1
Gloeobacter violaceus [GenBank: NP_923362.1]
Cyanobacteria
sp. [GenBank: YP_007081736.1]
1 Pleurocapsa
Nostoc punctiforme [GenBank: YP_001867098.1]
0 . 6 8 Lyngbya
aestuarii [GenBank: ERT07013.1]
Planctomyces limnophilus [GenBank: YP_003630466.1]
0.98
Blastopirellula marina [GenBank: EAQ81287.1]
1
Pirellula staleyi [GenBank: YP_003372485.1]
Planctomycetes
0.93
Singulisphaera acidiphila [GenBank: YP_007207185.1]
1
Isosphaera pallida [GenBank: YP_004178917.1]
0.71
Parvularcula bermudensis [GenBank: YP_003855792.1]
0.98
Rhodospirillum centenum [GenBank: YP_002296813.1]
1
Caulobacter crescentus [GenBank: ENZ82266.1]
0.57
0.53
Sphingobium chlorophenolicum [GenBank: YP_004553503.1]
Alcanivorax pacificus [GenBank: EKE36422.1]
0.87
Psychrobacter arcticus [GenBank: YP_265217.1]
0.58 1
Pasteurella multocida [GenBank: EPE75875.1]
Proteobacteria
Oceanimonas sp. [GenBank: WP_014291658.1]
0.87
Nitrosococcus halophilus [GenBank: YP_003528251.1]
0.91
Methylophilus methylotrophus [GenBank: WP_018986174.1]
0.91
Bordetella bronchiseptica [GenBank: KCV51409.1]
0.84
Azoarcus sp. [GenBank: WP_015434824.1]
0.94
0.2
eutropha [GenBank: YP_747710.1]
0 . 9 2 Nitrosomonas
Neisseria gonorrhoeae [GenBank: EEH62994.1]
dhca
0.68/31
1
GGPPS
Eukaryotes
0.8
0.99
0.53
FPPS