Lombard and Moreira BMC Evolutionary Biology 2012, 12:117 http://www.biomedcentral.com/1471-2148/12/117

CORRECTION Open Access Correction: Early evolution of the biotin-dependent carboxylase family Jonathan Lombard and David Moreira*

Correction After publication of our work [1], we noticed several major mistakes in the figure images provided for final publication: although the main text and the legends are correct, Figure three (Figure 1) has been replaced by an image present in the Addition file 1 and Figure four (Figure 2), Figure five (Figure 3) and Figure six (Figure 4) are displaced with regard to their correct numbers and legends. Please, accept our apologies and refer to the correct corresponding Figure three (Figure 1), Figure four (Figure 2), Figure five (Figure 3) and Figure six (Figure 4) that we provide in this erratum. Legends are the same as in the original article.

* Correspondence: [email protected] Unité d’Ecologie, Systématique et Evolution, UMR CNRS 8079, Univ. Paris-Sud, Paris-Sud, Orsay Cedex 91405, France

© 2012 Lombard and Moreira; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Lombard and Moreira BMC Evolutionary Biology 2012, 12:117 Page 2 of 6 http://www.biomedcentral.com/1471-2148/12/117

72 Syntrophus aciditrophicus [YP_461620] Deltaproteobacteria 78 Wolinella succinogenes [NP_907467] Epsilonproteobacteria 100 Gamma- 98 Aquifex aeolicus [pdb_1ULZ] 88 100 Cenarchaeum symbiosum [YP_876583] Thaumarchaeota 63 Nitrosopumilus maritimus [YP_001581607] Crenarchaeota group I Hydrogenobaculum sp. [YP_002121444] Aquificae 100 Sulfurihydrogenibium sp. [YP_001931216] 72 99 Epsilon-proteobacteria Eucarya 100 100 100 Rhodococcus jostii [YP_704171] 86 72 Thermobifida fusca [YP_289589] Aquifex aeolicus [NP_214146] 76 99 Aquificae 100 Hydrogenobaculum sp. [YP_002122040] 81 Epsilon-proteobacteria Leuconostoc mesenteroides [YP_818462] 85 Dorea formicigenerans [ZP_02234910] 51 Leuconostoc citreum [YP_001727586] 86 99 99 Enterococcus faecalis [ZP_05425368] 96 Streptococcus thermophilus [AAV60109] Delta-proteobacteria 100 Alpha/Beta/Gamma-proteobacteria Verrucomicrobium spinosum [ZP_02925947] 71 ACC 100 Planctomyces maris [ZP_01857220] 75 Rhodopirellula baltica [NP_868429] 87 [YP_001999473] 100Chlorobaculum parvum 70 Chlorobium limicola [YP_001942276] Chlorobi 93 Prosthecochloris aestuarii [YP_002014994] Cytophaga hutchinsonii [YP_678231] 99 82 Dokdonia donghaensis [ZP_01050069] 85 Microscilla marina [ZP_01690743] Candidatus Protochlamydia [YP_007771] 89 [YP_001699154] 100 Lysinibacillus sphaericus 56 Geobacillus kaustophilus [YP_148252] Firmicutes Oceanobacillus iheyensis [NP_692806] 75 Chloroflexus aurantiacus [YP_001636995] 68 [YP_642829] Actinobacteria 66 100 Burkholderia cenocepacia [YP_002229818] Betaproteobacteria Pseudomonas aeruginosa [ZP_04936910] Gammaproteobacteria 63 Thermus thermophilus [YP_004731] 100 Deinococcus geothermalis [YP_603938] Deinococcus-Thermus 100 77 100 [NP_293843] Eucarya (Viridiplantae) 97 Gloeobacter violaceus [NP_924958] 72 Thermosynechococcus elongatus [NP_682598] 98 70 Nostoc punctiforme [YP_001869185] Synechocystis sp. [NP_442228] 99 Herpetosiphon aurantiacus [YP_001546967] Roseiflexus castenholzii [YP_001434335] Chloroflexi Haloquadratum walsbyi [YP_658614] 82 100 97 Natrialba magadii [YP_003481208] Euryarchaeota (Haloarchaea) 85 Natronomonas pharaonis [YP_330913] Kineococcus radiotolerans [YP_001360285] 100 Micrococcus luteus [YP_002957960] 90 100 Acinetobacter baumannii [YP_001845930] Gammaproteobacteria Beta-proteobacteria Actinobacteria 81 Rhodococcus jostii [YP_706217] 97 Frankia alni [YP_711464] 82 97 Micrococcus luteus [ZP_06501280] 88 Propionibacterium acnes [ZP_06426704] Bradyrhizobium japonicum [NP_773932] 100 Phenylobacterium zucineum [YP_002131389] Alphaproteobacteria 58 Ralstonia eutropha [YP_727732] 68 Deinococcus radiodurans [NP_285633] Deinococcus-Thermus 62 Betaproteobacteria 100 Delftia acidovorans [YP_001562103] Verminephrobacter eiseniae [YP_996455] 86 Bacillus subtilis [NP_389369] 100 Staphylococcus aureus [pdb_3HBL] 93 Carnobacterium sp. [ZP_02184755] 100 Lactococcus lactis [YP_001031977] Firmicutes 100 Delta-proteobacteria 82 57 99 Anaerostipes caccae [ZP_02421002] Syntrophomonas wolfei [YP_753224] 88 Dokdonia donghaensis [ZP_01049098] 100 100 Croceibacter atlanticus [YP_003716762] Bacteroidetes 78 Gramella forsetii [YP_862701] Gemmata obscuriglobus [ZP_02733533] 90 100 Planctomyces maris [ZP_01855225] Planctomycetes 91 50 100 Rhodopirellula baltica [NP_869506] 86 Alpha-proteobacteria Tropheryma whipplei [NP_787758] PYC 100 Corynebacterium diphtheriae [NP_939020] 92 Clavibacter michiganensis [YP_001710078] Actinobacteria 65 76 90 Mycobacterium avium [NP_959228] 79 Streptomyces coelicolor [NP_624860] Eucarya 100 Methanocaldococcus jannaschii [NP_248224] Methanococcus vannielii [YP_001323860] 100 Archaeoglobus fulgidus [NP_069058] 83 100 Methanoculleus marisnigri [YP_001047551] Methanospirillum hungatei [YP_504591] 62 100 Methanobrevibacter smithii [YP_001273338] Euryarchaeota Methanosphaera stadtmanae [YP_447945] 65 71 Dehalococcoides ethenogenes [YP_180870] Chloroflexi 54 Methanosaeta thermophila [YP_843223] 96 Methanococcoides burtonii [YP_567027] Methanosarcina acetivorans [NP_615635] 66 Bacteroides vulgatus [YP_001298772] Bacteroidetes Myxococcus xanthus [YP_629371] 96 Deltaproteobacteria 92 Desulfococcus oleovorans [YP_001530060] Solibacter usitatus [YP_823133] Salinibacter ruber [YP_003570417] 98 100 Microscilla marina [ZP_01689080] Bacteroidetes Robiginitalea biformata [YP_003196538] 100 74 Deltaproteobacteria 70 Roseiflexus castenholzii [YP_001433033] Chloroflexi 100 88 Chlorobium limicola [YP_001943414] Chlorobi 99 96 Chloroherpeton thalassium [YP_001997534] 99 Hyperthermus butylicus [YP_001013339] Staphylothermus marinus [YP_001040161] 77 Thermofilum pendens [YP_919532] ACC-PCC 77 Sulfolobus solfataricus [NP_343814] Crenarchaeota 100 100 Metallosphaera sedula [YP_001190248] Archaea Sulfolobus tokodaii [NP_376481] Bordetella bronchiseptica [NP_889226] Betaproteobacteria 81 75 Actinobacteria 57 Acidothermus cellulolyticus [YP_872307] Myxococcus xanthus [YP_633734] Deltaproteobacteria Alicyclobacillus acidocaldarius [ZP_03495356] 99 100 Anoxybacillus flavithermus [YP_002314550] Firmicutes 97 Bacillus subtilis [NP_389706] 100 Eucarya (Fungi) Arthrobacter aurescens [YP_946009] 100 100 Actinobacteria 91 Clavibacter michiganensis [YP_001711029] Novosphingobium aromaticivorans [YP_495887] Alphaproteobacteria 67 UCA 95 58 Alpha/Beta-proteobacteria 95 Gamma-proteobacteria 85 98 97 Eucarya (Fungi) Alpha-proteobacteria 100 88 Eucarya PCC Alpha-proteobacteria 92 67 Eucarya (Fungi) 62 82 100 Janibacter sp. [ZP_00994709] 100 87 Mycobacterium avium [ZP_05215485] Actinobacteria Rhodococcus jostii [YP_701899] 84 [YP_001636422] 100 Chloroflexus aurantiacus 55 Herpetosiphon aurantiacus [YP_001545394] Chloroflexi Roseiflexus castenholzii [YP_001431109] Nitrobacter hamburgensis [YP_577381] Alphaproteobacteria 61 67 Micrococcus luteus [YP_002956772] 100 Thermobifida fusca [YP_289008] 57 Actinobacteria 96 67 Mycobacterium avium [NP_961247] 54 Saccharopolyspora erythraea [YP_00110912] Alpha/Beta/Gamma-proteobacteria 65 Alpha-proteobacteria 97 72 MCC 94 Eucarya 0.2 Figure 1 Maximum likelihood tree of the biotin carboxylase (BC) . This tree is based on 284 representative sequences and 384 conserved sites and was arbitrarily roosted on the bacterial ACC-related sequences. Numbers at nodes indicate bootstrap values higher than 50. Triangles correspond to collapsed groups of eukaryotes and Proteobacteria. Colors on leaves represent the affiliation of the sequences to their respective domain of life: archaea (red), (blue) and eukaryotes (green). Bars on the right report the functional assignment of the sequences; sequences that are not in front of any bar are assumed to bear an acyl-CoA carboxylase activity. Lombard and Moreira BMC Evolutionary Biology 2012, 12:117 Page 3 of 6 http://www.biomedcentral.com/1471-2148/12/117

Herpetosiphon aurantiacus [YP_001546967] 98 Roseiflexus castenholzii [YP_001434335] Chloroflexi 91 Haloquadratum walsbyi [YP_658614] 100 Natrialba magadii [YP_003481208] 87 Natronomonas pharaonis [YP_330913] Euryarchaeota 65 Archaeoglobus fulgidus [NP_069058] 73 Sulfolobus solfataricus [NP_343814] 100 96 Metallosphaera sedula [YP_001190248] Crenarchaeota 91 Sulfolobus tokodaii [NP_376481] Dehalococcoides ethenogenes [YP_180870] Chloroflexi Methanoculleus marisnigri [YP_001047551] 69 100 Methanospirillum hungatei [YP_504591] 72 Methanocaldococcus jannaschii [NP_248224] 96 Methanococcus vannielii [YP_001323860] 59 Methanobrevibacter smithii [YP_001273338] Euryarchaeota 100 Methanosphaera stadtmanae [YP_447945] 64 Methanosaeta thermophila [YP_843223] 79 Methanococcoides burtonii [YP_567027] 95 Methanosarcina acetivorans [NP_615635] Syntrophus aciditrophicus [YP_461620] Deltaproteobacteria 67 Wolinella succinogenes [NP_907467] Legionella pneumophila [YP_125023] Epsilonproteobacteria 100 Thioalkalivibrio sp. [YP_002513983] 83 Chromohalobacter salexigens [YP_573607] Gammaproteobacteria 92 100 Pseudomonas aeruginosa [YP_001351535] 100 Cenarchaeum symbiosum [YP_876583] Thaumarchaeota 82 Nitrosopumilus maritimus [YP_001581607] Crenarchaeota group I Aquifex aeolicus [pdb_1ULZ] 56 Hydrogenobaculum sp. [YP_002121444] Aquificae 100 Sulfurihydrogenibium sp. [YP_001931216] 86 Arcobacter butzleri [YP_001489539] 61 100 Caminibacter mediatlanticus [ZP_01871657] Epsilonproteobacteria Roseiflexus castenholzii [YP_001433033] Chloroflexi 100 Chlorobium limicola [YP_001943414] 79 Chloroherpeton thalassium [YP_001997534] Chlorobi PYC Thermofilum pendens [YP_919532] 71 Hyperthermus butylicus [YP_001013339] Crenarchaeota 89 Staphylothermus marinus [YP_001040161] 90 Staphylococcus aureus [pdb_3HBL] 100 Bacillus subtilis [NP_389369] Carnobacterium sp. [ZP_02184755] Firmicutes 99 Lactococcus lactis [YP_001031977] 64 83 Desulfuromonas acetoxidans [ZP_01312174] 100 Anaeromyxobacter dehalogenans [YP_466222] Deltaproteobacteria 99 Geobacter metallireducens [ZP_383783] Anaerostipes caccae [ZP_02421002] 98 Syntrophomonas wolfei [YP_753224] Firmicutes 82 Dokdonia donghaensis [ZP_01049098] 100 Croceibacter atlanticus [YP_003716762] Bacteroidetes 100 100 Gramella forsetii [YP_862701] Magnetospirillum magneticum [YP_419602] Mesorhizobium loti [NP_104954] 100 100 86 Rhizobium leguminosarum [YP_770202] 60 Sinorhizobium meliloti [NP_387384] Alphaproteobacteria Sagittula stellata [ZP_01744770] 100 Octadecabacter antarcticus [ZP_05067787] 76 63 Ruegeria pomeroyi [YP_166418] Gemmata obscuriglobus [ZP_02733533] 99 61 Planctomyces maris [ZP_01855225] Planctomycetes 53 Rhodopirellula baltica [NP_869506] Tropheryma whipplei [NP_787758] 100 Corynebacterium diphtheriae [NP_939020] 97 Clavibacter michiganensis [YP_001710078] 59 Streptomyces coelicolor [NP_624860] Actinobacteria 92 Mycobacterium avium [NP_959228] 96 Mycobacterium tuberculosis [ZP_05765464] Desulfococcus oleovorans [YP_001530060] 95 Myxococcus xanthus [YP_629371] Deltaproteobacteria 62 Solibacter usitatus [YP_823133] Acidobacteria Salinibacter ruber [YP_003570417] 67 Microscilla marina [ZP_01689080] Bacteroidetes 100 Robiginitalea biformata [YP_003196538] Myxococcus xanthus [YP_633734] Deltaproteobacteria 73 Alicyclobacillus acidocaldarius [ZP_03495356] 91 Anoxybacillus flavithermus [YP_002314550] Firmicutes 100 Bacillus subtilis [NP_389706] 69 Novosphingobium aromaticivorans [YP_495887] Alphaproteobacteria 97 53 Arthrobacter aurescens [YP_946009] 77 Clavibacter michiganensis [YP_001711029] Actinobacteria 100 Cellvibrio japonicus [YP_001981735] 87 Pectobacterium atrosepticum [YP_050237] Gammaproteobacteria 88 Cellvibrio japonicus [YP_001983182] 61 Acidiphilium cryptum [YP_001235837] UCA 97 Methylocella silvestris [YP_002362891] 68 Methylobacterium extorquens [YP_00164116] 97 Rhizobium leguminosarum [YP_002978611] Alphaproteobacteria 92 Neorickettsia sennetsu [YP_506687] 95 Rickettsia prowazekii [NP_220985] 82 Acidovorax ebreus [YP_002553310] 100 Verminephrobacter eiseniae [YP_998142] 100 Aromatoleum aromaticum [YP_159134] Betaproteobacteria 50 Polynucleobacter necessarius [YP_0011556] 80 Ochrobactrum anthropi [YP_001370547] 97 Ruegeria pomeroyi [YP_166352] PCC 90 Brevundimonas sp. [ZP_05033591] Alphaproteobacteria 88 Aurantimonas manganoxydans [ZP_01227482] 74 55 Rhodopseudomonas palustris [ZP_06357965] Chloroflexus aurantiacus [YP_001636422] 100 Herpetosiphon aurantiacus [YP_001545394] Chloroflexi 53 Roseiflexus castenholzii [YP_001431109] Myxococcus xanthus [YP_628365] Deltaproteobacteria 100 Pseudomonas aeruginosa [YP_002439776] Janibacter sp. [ZP_00994709] Gammaproteobacteria 69 68 100 Mycobacterium avium [ZP_05215485] 55 Rhodococcus jostii [YP_701899] 75 Micrococcus luteus [YP_002956772] 87 Mycobacterium avium [NP_961247] Actinobacteria 98 72 Thermobifida fusca [YP_289008] 79 84 Saccharopolyspora erythraea [YP_00110912] 77 Streptomyces albus [ZP_04702091] Acidiphilium cryptum [YP_001234641] Azorhizobium caulinodans [YP_001527509] 97 72 Nitrobacter hamburgensis [YP_577381] Oceanicaulis alexandrii [ZP_00957838] Alphaproteobacteria 55 87 Aurantimonas manganoxydans [ZP_01225783] 98 Phaeobacter gallaeciensis [ZP_02148887] 58 Oceanobacter sp. [ZP_01308646] 92 Colwellia psychrerythraea [YP_268342] MCC Marinobacter algicola [ZP_01894929] Gammaproteobacteria 79 Acinetobacter baumannii [ZP_05827627] 91 Thauera sp. [YP_002354418] 72 Ralstonia eutropha [YP_724704] 93 Rhodoferax ferrireducens [YP_525060] Burkholderia cenocepacia [YP_002229818] Betaproteobacteria 100 Pseudomonas aeruginosa [ZP_04936910] Gammaproteobacteria Ralstonia eutropha [YP_727732] 100 Delftia acidovorans [YP_001562103] 97 100 Verminephrobacter eiseniae [YP_996455] 59 Deinococcus radiodurans [NP_285633] Deinococcus-Thermus 61 55 Bradyrhizobium japonicum [NP_773932] 63 Phenylobacterium zucineum [YP_002131389] Alphaproteobacteria Kineococcus radiotolerans [YP_001360285] Actinobacteria 100 Micrococcus luteus [YP_002957960] Acinetobacter baumannii [YP_001845930] Gammaproteobacteria 88 93 Acidovorax avenae [ZP_06212366] 99 Betaproteobacteria 93 Delftia acidovorans [YP_001566739] Frankia alni [YP_711464] 93 Micrococcus luteus [ZP_06501280] 82 Rhodococcus jostii [YP_706217] Propionibacterium acnes [ZP_06426704] Actinobacteria Streptomyces coelicolor [AAD28553] Rubrobacter xylanophilus [YP_642829] Gluconacetobacter diazotrophicus [YP_002276427] Maricaulis maris [YP_756495] 97 Sphingopyxis alaskensis [YP_616485] 55 Alphaproteobacteria 62 Azorhizobium caulinodans [YP_001525991] 50 Rhizobium leguminosarum [YP_002975555] 100 Loktanella vestfoldensis [ZP_01002783] 98 Roseovarius nubinhibens [ZP_00958417] 70 Neisseria gonorrhoeae [ZP_04718098] 94 Nitrosomonas europaea [NP_840734] 97 Thiobacillus denitrificans [YP_313939] Betaproteobacteria Acidovorax avenae [ZP_06211912] 100 99 Ralstonia eutropha [YP_727615] Francisella tularensis [YP_001892040] 73 Pseudomonas aeruginosa [pdb_2VQD] 100 Reinekea sp. [ZP_01115022] 69 Nitrosococcus oceani [YP_343089] Gammaproteobacteria 54 77 Haemophilus influenzae [ZP_01792937] 52 Escherichia coli [NP_312155] 52 Aliivibrio salmonicida [YP_002264170] 93 Glaciecola sp. [ZP_03559850] Aquifex aeolicus [NP_214146] 100 Hydrogenobaculum sp. [YP_002122040] Aquificae 94 Caminibacter mediatlanticus [ZP_01871862] 100 Campylobacter jejuni [ZP_01068220] Epsilonproteobacteria 90 Helicobacter pylori [YP_627763] Pelobacter propionicus [YP_901688] 96 Myxococcus xanthus [YP_633904] Deltaproteobacteria 95 Plesiocystis pacifica [ZP_01912345] Verrucomicrobium spinosum [ZP_02925947] Verrucomicrobia 66 Planctomyces maris [ZP_01857220] ACC 100 Rhodopirellula baltica [NP_868429] Planctomycetes 51 Chlorobaculum parvum [YP_001999473] 100 74 Chlorobium limicola [YP_001942276] Chlorobi 91 Prosthecochloris aestuarii [YP_002014994] Cytophaga hutchinsonii [YP_678231] 98 Dokdonia donghaensis [ZP_01050069] Bacteroidetes 86 Microscilla marina [ZP_01690743] 83 Chloroflexus aurantiacus [YP_001636995] Chloroflexi 68 Deinococcus radiodurans [NP_293843] 97 Thermus thermophilus [YP_004731] Deinococcus-Thermus 83 Gloeobacter violaceus [NP_924958] 100 Anabaena variabilis [YP_321035] 92 Nostoc punctiforme [YP_001869185] Cyanobacteria 96 Synechocystis sp. [NP_442228] 51 54 Thermosynechococcus elongatus [NP_682598] Dorea formicigenerans [ZP_02234910] 92 Leuconostoc citreum [YP_001727586] 82 99 Enterococcus faecalis [ZP_05425368] 95 Streptococcus thermophilus [AAV60109] Candidatus Protochlamydia [YP_007771] Firmicutes Geobacillus kaustophilus [YP_148252] 73 Oceanobacillus iheyensis [NP_692806] 0.2 99 Lysinibacillus sphaericus [YP_001699154] Staphylococcus aureus [CAQ50016] Figure 2 Maximum likelihood tree of archaeal and bacterial biotin carboxylase (BC) domain sequences. This tree is based on 196 representative sequences and 322 conserved sites and was arbitrarily rooted on the PYC-related sequences. Numbers at nodes indicate bootstrap robustness values higher than 50. Colors on leaves represent the affiliation of the sequences to their respective domain of life: archaea (red), bacteria (blue) and eukaryotes (green). Bars on the right report the functional assignment of the sequences; sequences that are not in front of any bar are assumed to bear an acyl-CoA carboxylase activity. Lombard and Moreira BMC Evolutionary Biology 2012, 12:117 Page 4 of 6 http://www.biomedcentral.com/1471-2148/12/117

Sorangium cellulosum [YP_001612425] Deltaproteobacteria Natronomonas pharaonis_[YP_327378] 100 Haloarcula marismortui [YP_138139] (Haloarchaea) 100 Euryarchaeota 100 Halobacterium sp. [NP_279647] Acidothermus cellulolyticus [YP_872163] Actinobacteria 90 Anaeromyxobacter dehalogenans [YP_464856] 95 Myxococcus xanthus [YP_631941] Deltaproteobacteria 98 Geobacillus kaustophilus [YP_147456] 99 82 Bacillus subtilis [BAI85510] Firmicutes Oceanobacillus iheyensis [NP_692620] Mycobacterium avium [YP_880842] Actinobacteria 98 Eucarya (Fungi) 100 Ruegeria pomeroyi [YP_167756] Alphaproteobacteria 98 68 Acidovorax ebreus [YP_002554846] 74 100 Verminephrobacter eiseniae [YP_995629] 99 Erythrobacter litoralis [YP_458870] Betaproteobacteria 51 96 Bradyrhizobium japonicum [NP_770580] 74 Rhodospirillum centenum [YP_002296488] Phenylobacterium zucineum [YP_002131389] Alphaproteobacteria 100 Delftia acidovorans [YP_001562103] 100 Ralstonia eutropha [YP_727390] Betaproteobacteria 86 Rhodococcus jostii [YP_702745] 93 Saccharopolyspora erythraea [YP_00110535] Actinobacteria 56 Phenylobacterium zucineum [YP_002131888] Alphaproteobacteria 66 60 Pseudomonas aeruginosa [ZP_04927823] Gammaproteobacteria 59 Bradyrhizobium japonicum [NP_773932] 68 Parvibaculum lavamentivorans [YP_0014139] Alphaproteobacteria Deinococcus radiodurans [NP_295265] 100 Thermus thermophilus [YP_144823] Deinococcus-Thermus 98 Salinibacter ruber [YP_445343] 96 Pedobacter sp. [ZP_01884157] 100 Capnocytophaga sputigena [ZP_03389935] Bacteroidetes 98 Flavobacterium johnsoniae [YP_001194892] Cupriavidus taiwanensis [YP_002006836] Betaproteobacteria Ustilago maydis [XP_761394] Fungi 100 59 96 Salinispora arenicola [YP_001539511] 97 Mycobacterium tuberculosis [NP_335437] 98 Actinobacteria 99 Saccharopolyspora erythraea [YP_00110544] Bradyrhizobium japonicum [NP_767626] Alphaproteobacteria 100 Verminephrobacter eiseniae [YP_997177] Betaproteobacteria 100 Myxococcus xanthus [YP_628364] Deltaproteobacteria 98 79 Oceanicaulis alexandrii [ZP_00952609] Alphaproteobacteria 55 Acinetobacter baumannii [YP_001712456] 100 Hahella chejuensis [YP_436825] Gammaproteobacteria 90 Pseudomonas aeruginosa [YP_002439779] Roseiflexus castenholzii [YP_001431105] Chloroflexi Stenotrophomonas maltophilia [YP_0020265] Gammaproteobacteria 100 Thermobifida fusca [YP_289009] 100 Arthrobacter aurescens [YP_947295] Actinobacteria 83 68 Rhodococcus jostii [YP_706030] Hyphomonas neptunium [YP_759995] 100 Caulobacter crescentus [NP_420973] Alphaproteobacteria 63 100 Methylocella silvestris [YP_002363690] Azoarcus sp. [YP_934573] 83 Acidovorax avenae [ZP_06212018] 65 100 Acidovorax ebreus [YP_002554477] Betaproteobacteria Chromobacterium violaceum [NP_901434] 82 Idiomarina baltica [ZP_01043053] Gammaproteobacteria 79 91 Pseudovibrio sp. [ZP_05087246] 100 Sinorhizobium meliloti [NP_437241] MCC 100 Roseobacter denitrificans [YP_683485] 100 Dinoroseobacter shibae [YP_001532643] Alphaproteobacteria 78 53 Phaeobacter gallaeciensis [ZP_02148888] Xanthobacter autotrophicus [YP_001416759] 71 Ralstonia eutropha [YP_726442] Betaproteobacteria 87 Rhodospirillum centenum [YP_002296643] Alphaproteobacteria Congregibacter litoralis [ZP_01102124] 97 79 Legionella pneumophila [YP_095853] Gammaproteobacteria 85 Oceanospirillum sp. [ZP_01165309] 86 Pseudomonas aeruginosa [NP_250704] 58 99 Eucarya Leptospira interrogans [YP_001476] 100 Anaeromyxobacter dehalogenans [YP_463676] 96 Sorangium cellulosum [YP_001613931] Deltaproteobacteria Sulfolobus tokodaii [NP_376479] 100 100 Metallosphaera sedula [YP_001191457] 76 Sulfolobus acidocaldarius [YP_254971] ACC-PCC Hyperthermus butylicus [YP_001013337] Crenarchaeota 99 88 Desulfurococcus kamchatkensis [YP_002428] Archaea 100 Staphylothermus marinus [YP_001041424] Roseiflexus castenholzii [YP_001431082] Chloroflexi 53 Thermobifida fusca [YP_289276] 100 Streptomyces albus [ZP_06593745] Actinobacteria 100 Streptomyces coelicolor [NP_629669] Bacteroides vulgatus [YP_001300358] Bacteroidetes 93 Cenarchaeum symbiosum [YP_876582] Thaumarchaeota 100 Nitrosopumilus maritimus [YP_001581606] Crenarchaeota Group I 63 Acidothermus cellulolyticus [YP_872633] 85 100 Mycobacterium tuberculosis [ZP_06799173] Actinobacteria 65 Eubacterium siraeum [CBK96845] 78 99 Bryantella formatexigens [ZP_05349002] Firmicutes 100 Ruminococcus gnavus [ZP_02039588] Tropheryma whipplei [NP_787151] 99 Renibacterium salmoninarum [YP_001626087] 92 57 Streptomyces coelicolor [NP_629079] 62 Corynebacterium diphtheriae [NP_940496] 100 64 Rhodococcus jostii [YP_704021] Actinobacteria Nocardioides sp. [YP_924682] 90 Rhodococcus jostii [YP_708121] 100 Corynebacterium diphtheriae [NP_939034] 84 Mycobacterium avium [ZP_05218201] Symbiobacterium thermophilum [YP_075018] Firmicutes 80 Desulfococcus oleovorans [YP_001527964] 98 56 Syntrophus aciditrophicus [YP_462007] Deltaproteobacteria Heliobacterium modesticaldum [YP_0016790] 85 87 Mitsuokella multacida [ZP_05404801] 93 Thermosinus carboxydivorans [ZP_01665943] Firmicutes Bacillus subtilis [ZP_03592158] 99 100 Geobacillus kaustophilus [YP_148202] Deinococcus radiodurans [NP_295040] 100 Thermus thermophilus [YP_004756] Deinococcus-Thermus Opitutus terrae [YP_001820186] Verrucomicrobia 98 100 Chloroflexus aurantiacus [YP_001636643] Chloroflexi 78 Solibacter usitatus [YP_823536] Acidobacteria 66 Corynebacterium diphtheriae [NP_939113] 97 67 Propionibacterium acnes [YP_056680] Actinobacteria Petrotoga mobilis [YP_001567610] 99 Fervidobacterium nodosum [YP_001410821] 71 63 Marinitoga piezophila [ZP_05097043] Thermofilum pendens [YP_919569] Crenarchaeota 61 86 Archaeoglobus fulgidus [NP_071042] 87 96 Pyrococcus abyssi [NP_126570] Pyrococcus furiosus [NP_578400] 100 Thermococcus barophilus [ZP_04878205] Euryarchaeota 95 Thermococcus kodakarensis [YP_184035] 98 Thermococcus onnurineus [YP_002306422] Roseiflexus castenholzii [YP_001434152] Chloroflexi 99 Rubrobacter xylanophilus [YP_645205] Actinobacteria 90 Natrialba magadii [YP_003481206] 100 Halobacterium sp. [NP_280337] Euryarchaeota(Haloarchaea) 96 Haloquadratum walsbyi [YP_658717] Anaeromyxobacter dehalogenans [YP_463463] 100 95 73 Myxococcus xanthus [YP_629373] Deltaproteobacteria Bdellovibrio bacteriovorus [NP_970561] 61 Solibacter usitatus [YP_822769] Acidobacteria Algoriphagus sp. [ZP_01721235] 100 Croceibacter atlanticus [ZP_00950919] 100 98 92 Gramella forsetii [YP_861017] Bacteroidetes Bacteroides fragilis [YP_212741] 100 Chlorobium limicola [YP_001942947] 100 Chloroherpeton thalassium [YP_001995096] Chlorobi 100 84 Eucarya Magnetospirillum magneticum [YP_423606] Alphaproteobacteria 98 Azoarcus sp. [YP_932191] 97 Delftia acidovorans [YP_001564772] 83 Betaproteobacteria 100 Polaromonas naphthalenivorans [YP_982609] 100 79 Verminephrobacter eiseniae [YP_998140] Anaplasma marginale [YP_153964] 100 Rickettsia prowazekii [NP_220986] PCC 64 Novosphingobium aromaticivorans [YP_496087] 98 Azorhizobium caulinodans [YP_001524691] 98 Brevundimonas sp. [ZP_05033122] Alphaproteobacteria 92 Hoeflea phototrophica [ZP_02168578] 0.3 98 Rhizobium leguminosarum [YP_002283914] 69 Paracoccus denitrificans [YP_917451] 85 Sulfitobacter sp. [ZP_00955314] Figure 3 Maximum likelihood tree of CoA-substrate related carboxyl tranferase (CCT) domain sequences. This tree is based on 179 representative sequences and 438 conserved sites and was midpoint rooted. Numbers at nodes indicate bootstrap robustness values higher than 50. Triangles correspond to collapsed groups of eukaryotes. Colors on leaves represent the affiliation of the sequences to their respective domain of life: archaea (red), bacteria (blue) and eukaryotes (green). Bars on the right report the functional assignment of the sequences; sequences that are not in front of any bar are assumed to bear an acyl-CoA carboxylase activity. Lombard and Moreira BMC Evolutionary Biology 2012, 12:117 Page 5 of 6 http://www.biomedcentral.com/1471-2148/12/117

Thermodesulfovibrio yellowstonii [YP_002249528] Heliobacterium modesticaldum [YP_0016790] Firmicutes Gloeobacter violaceus [NP_923825] Cyanobacteria 65 Desulfitobacterium hafniense [YP_518600] 100 55 Desulfotomaculum reducens [YP_001112424] 100 60 Heliobacterium modesticaldum [YP_0016789] Thermoanaerobacter tengcongensis [NP_622834] 93 97 Enterococcus faecalis [ZP_05475390] Fusobacterium nucleatum [NP_604273] Firmicutes 79 99 Anaerocellum thermophilum [YP_002573192] 73 Eubacterium siraeum [ZP_02423763] 95 100 Bryantella formatexigens [ZP_05349050] Coprococcus eutactus [ZP_02205537] 89 Hahella chejuensis [YP_437757] Oceanobacter sp. [ZP_01308611] Gammaproteobacteria 99 Legionella pneumophila [YP_094510] 91 Thioalkalivibrio sp. [YP_002513984] 52 100 Methylobacillus flagellatus [YP_545621] Betaproteobacteria 69 100 Thiobacillus denitrificans [YP_315314] Treponema pallidum [NP_218496] Spirochaetes 96 Chlorobium phaeobacteroides [YP_912039] Chlorobi Pelobacter propionicus [YP_899731] Deltaproteobacteria 99 100 Propionibacterium acnes [ZP_06264122] 73 Actinobacteria 74 Nocardioides sp. [YP_922448] Solibacter usitatus [YP_828159] Acidobacteria 59 Vibrio cholerae [pdb_2NX9] ODC 100 Salmonella enterica [ACY90440] 100 97 Haemophilus somnus [YP_718409] 100 Mannheimia haemolytica [ZP_04978707] Oceanobacter sp. [ZP_01307795] 91 Methylophaga thiooxidans [ZP_05105636] Gammaproteobacteria 68 53 Magnetococcus sp. [YP_867092] 87 Idiomarina baltica [ZP_01043500] 92 Pseudoalteromonas atlantica [YP_662574] Psychromonas ingrahamii [YP_944661] Methanocaldococcus jannaschii [NP_248226] 99 100 Methanococcus maripaludis [YP_001330555] Methanococcus voltae [YP_003708350] 97 Methanocorpusculum labreanum [YP_0010295] 100 85 Methanoculleus marisnigri [YP_001047552] Methanospirillum hungatei [YP_504590] Euryarchaeota 100 65 Methanobrevibacter smithii [YP_001273512] 55 Methanosphaera stadtmanae [YP_448197] 70 100 Methanococcoides burtonii [YP_567026] Methanosarcina acetivorans [NP_615634] 89 Coprothermobacter proteolyticus [YP_002246780] Firmicutes Dehalococcoides ethenogenes [YP_180869] Chloroflexi Petrotoga mobilis [YP_001568465] 58 100 93 Fervidobacterium nodosum [ABS61588] Thermotogae Thermotoga maritima [NP_227944] 93 Archaeoglobus fulgidus [NP_070080] Euryarchaeota 100 Aquifex aeolicus [NP_214049] 66 Hydrogenivirga sp. [ZP_02176910] 79 Sulfurihydrogenibium sp. [YP_001930339] Aquificae 100 100 Hydrogenivirga sp. [ZP_02177541] 71 Hydrogenobaculum sp. [YP_002121296] Desulfurococcus kamchatkensis [YP_002428] 100 Staphylothermus marinus [YP_001040361] Crenarchaeota 91 Pyrococcus horikoshii [NP_142769] 100 100Thermococcus kodakarensis [YP_183403] Euryarchaeota Thermococcus sp. [ZP_04879340] 100 Desulfuromonas acetoxidans [ZP_01312174] Geobacter metallireducens [YP_383783] Deltaproteobacteria Alkaliphilus metalliredigens [YP_0013184] 72 99 PYC 88 Anaerofustis stercorihominis [ZP_0286305] 70 Dorea formicigenerans [ZP_02236239] Staphylococcus aureus [pdb_3HBL] Firmicutes 100 70 Bacillus subtilis [NP_389369] 64 Exiguobacterium sibiricum [YP_001814461] 97 Enterococcus faecalis [ZP_04438096] Listeria innocua [NP_470397] Microscilla marina [ZP_01693297] 100 Dokdonia donghaensis [ZP_01049098] 100 Bacteroidetes 100 Gramella forsetii [YP_862701] Polaribacter irgensii [ZP_01119116] 100 89 Lentisphaera araneosa [ZP_01875204] Lestisphaerae 94 Gemmata obscuriglobus [ZP_02733533] 100 Planctomyces maris [ZP_01855225] Planctomycetes Rhodopirellula baltica [NP_869506] 95 Verrucomicrobium spinosum [ZP_02926810] 100 100 Chthoniobacter flavus [ZP_03130321] Verrucomicrobia Opitutus terrae [YP_001817860] 59 98 Bordetella bronchiseptica [NP_887160] Cupriavidus taiwanensis [YP_002005236] Betaproteobacteria 100 Maricaulis maris [YP_756373] Acidiphilium cryptum [YP_001235779] 90 94 Pseudovibrio sp. [ZP_05086383] 64 Mesorhizobium loti [NP_104954] 100 64 97 Ochrobactrum anthropi [YP_001373113] Rhizobium leguminosarum [YP_770202] Alphaproteobacteria Paracoccus denitrificans [YP_917904] 100 Ruegeria sp. [ZP_05089294] 89 Oceanibulbus indolifex [ZP_02153471] 62 86 Octadecabacter antarcticus [ZP_05067787] Sagittula stellata [ZP_01744770] Symbiobacterium thermophilum [YP_076011] Firmicutes Myxococcus xanthus [YP_632061] Deltaproteobacteria 66 Rubrobacter xylanophilus [YP_644798] Tropheryma whipplei [NP_787758] 91 100 91 86 Arthrobacter aurescens [YP_947447] 86 Kocuria rhizophila [YP_001855357] Streptomyces coelicolor [NP_624860] Actinobacteria 55 65 99 Mycobacterium tuberculosis [ZP_05765464] Nocardia farcinica [YP_120404] 100 Micromonas pusilla [EEH56848] Ostreococcus tauri [CAL54832] Viridiplantae Emiliania huxleyi [BAH22705] Haptophyceae 100 100 Phaeodactylum tricornutum [XP_002183906] 100 Thalassiosira pseudonana [XP_002294371] Stramenopiles Naegleria gruberi [XP_002669470] Heterolobosea 96 Trichoplax adhaerens [XP_002115759] 78 72 Schistosoma mansoni [XP_002582167] 99 100 Danio rerio [AAI62583] Homo sapiens [AAA82937] 87 73 Saccoglossus kowalevskii [XP_002735883] 53 100 Drosophila melanogaster [NP_610527] Nasonia vitripennis [XP_001600219] Monosiga brevicollis [XP_001748229] Fungi/Metazoa 62 100 Laccaria bicolor [XP_001883738] Ustilago maydis [XP_757201] 100 Schizosaccharomyces pombe [NP_595900] 97 100 Pichia guilliermondii [EDK39659] Saccharomyces cerevisiae [NP_011453] 0.3 94 Phaeosphaeria nodorum [XP_001794065] 93 97 Arthroderma benhamiae [EFE32191] Aspergillus niger [XP_001401577] Figure 4 Maximum likelihood tree of pyruvate carboxylase carboxyl tranferase (PCT) domain sequences. This tree is based on 126 representative sequences and 432 conserved sites and was midpoint rooted. Numbers at nodes indicate bootstrap robustness values higher than 50. Colors on leaves represent the affiliation of the sequences to their respective domain of life: archaea (red), bacteria (blue) and eukaryotes (green). Bars on the right report the functional assignment of the sequences; sequences that are not in front of any bar have unknown function. Lombard and Moreira BMC Evolutionary Biology 2012, 12:117 Page 6 of 6 http://www.biomedcentral.com/1471-2148/12/117

Competing interests The authors declare no competing interests.

Authors' contributions JL and DM designed research; JL carried out phylogenetic analyses, and JL and DM wrote the manuscript. Both authors read and approved the final version.

Received: 2 May 2012 Accepted: 11 May 2012 Published: 20 July 2012

References 1. Lombard J, Moreira D: Early evolution of the biotin-dependent carboxylase family. BMC Evol Biol 2011, 11:232.

doi: 10.1186/1471-2148-12-117 Cite this article as: Lombard and Moreira: Correction: Early evolution of the biotin-dependent carboxylase family. Correction: Early evolution of the biotin-dependent carboxylase family. BMC Evolutionary Biology 2012 12:117.

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