메뉴 건너뛰기




Volumn 28, Issue 7, 2011, Pages 2087-2099

Eukaryotic pyruvate formate lyase and its activating enzyme were acquired laterally from a firmicute

Author keywords

eukaryotic phylogeny; lateral gene transfer; origin; pyruvate formate lyase

Indexed keywords

COMPLEMENTARY DNA; FORMATE ACETYLTRANSFERASE; FORMATE ACETYLTRANSFERASE ACTIVATING ENZYME; LYASE; UNCLASSIFIED DRUG;

EID: 79959401340     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msr032     Document Type: Article
Times cited : (56)

References (49)
  • 1
    • 18744382506 scopus 로고    scopus 로고
    • ProtTest: Selection of best-fit models of protein evolution
    • DOI 10.1093/bioinformatics/bti263
    • Abascal F, Zardoya R, Posada D. 2005. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21: 2104-2105. (Pubitemid 40668057)
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 2104-2105
    • Abascal, F.1    Zardoya, R.2    Posada, D.3
  • 3
    • 70049087749 scopus 로고    scopus 로고
    • Gene transfer and diversification of microbial eukaryotes
    • Andersson JO. 2009. Gene transfer and diversification of microbial eukaryotes. Annu Rev Microbiol. 63:177-193.
    • (2009) Annu Rev Microbiol , vol.63 , pp. 177-193
    • Andersson, J.O.1
  • 4
    • 0036550477 scopus 로고    scopus 로고
    • Evolutionary analyses of the small subunit of glutamate synthase: Gene order conservation, gene fusions, and prokaryote-to-eukaryote lateral gene transfers
    • DOI 10.1128/EC.1.2.304-310.2002
    • Andersson JO, Roger AJ. 2002. Evolutionary analyses of the small subunit of glutamate synthase: gene order conservation, gene fusions, and prokaryote-to-eukaryote lateral gene transfers. Eukaryot Cell. 1:304-310. (Pubitemid 36562406)
    • (2002) Eukaryotic Cell , vol.1 , Issue.2 , pp. 304-310
    • Andersson, J.O.1    Roger, A.J.2
  • 5
    • 2942620629 scopus 로고    scopus 로고
    • Evolution of glutamate dehydroge-nase genes: Evidence for lateral gene transfer within and between prokaryotes and eukaryotes
    • Andersson JO, Roger AJ. 2003. Evolution of glutamate dehydroge-nase genes: evidence for lateral gene transfer within and between prokaryotes and eukaryotes. BMC Evol Biol. 3:14.
    • (2003) BMC Evol Biol , vol.3 , pp. 14
    • Andersson, J.O.1    Roger, A.J.2
  • 9
    • 0029915525 scopus 로고    scopus 로고
    • Computational method to predict mitochondrially imported proteins and their targeting sequences
    • Claros MG, Vincens P. 1996. Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur J Biochem. 241:779-786. (Pubitemid 26379380)
    • (1996) European Journal of Biochemistry , vol.241 , Issue.3 , pp. 779-786
    • Claros, M.G.1    Vincens, P.2
  • 10
    • 0028809514 scopus 로고
    • Sulfite reductase structure at 1.6 A: Evolution and catalysis for reduction of inorganic anions
    • Crane BR, Siegel LM, Getzoff ED. 1995. Sulfite reductase structure at 1.6 A: evolution and catalysis for reduction of inorganic anions. Science 270:59-67.
    • (1995) Science , vol.270 , pp. 59-67
    • Crane, B.R.1    Siegel, L.M.2    Getzoff, E.D.3
  • 11
    • 13244255415 scopus 로고    scopus 로고
    • MUSCLE: A multiple sequence alignment method with reduced time and space complexity
    • Edgar RC. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 5:113.
    • (2004) BMC Bioinformatics , vol.5 , pp. 113
    • Edgar, R.C.1
  • 12
    • 0034697980 scopus 로고    scopus 로고
    • Predicting subcellular localization of proteins based on their N-terminal amino acid sequence
    • Emanuelsson O, Nielsen H, Brunak S, von Heijne G. 2000. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol. 300:1005-1016.
    • (2000) J Mol Biol , vol.300 , pp. 1005-1016
    • Emanuelsson, O.1    Nielsen, H.2    Brunak, S.3    Von Heijne, G.4
  • 13
    • 33645456207 scopus 로고    scopus 로고
    • Eukaryotic evolution, changes and challenges
    • Embley TM, Martin W. 2006. Eukaryotic evolution, changes and challenges. Nature 440:623-630.
    • (2006) Nature , vol.440 , pp. 623-630
    • Embley, T.M.1    Martin, W.2
  • 14
    • 0003437299 scopus 로고    scopus 로고
    • Seattle (WA): Distributed by the author. Department of Genome Sciences, University of Washington
    • Felsenstein J. 2005. PHYLIP (Phylogeny Inference Package) version 3.6. Seattle (WA): Distributed by the author. Department of Genome Sciences, University of Washington.
    • (2005) PHYLIP (Phylogeny Inference Package) Version 3.6.
    • Felsenstein, J.1
  • 15
    • 0028275314 scopus 로고
    • Adenosylmethio-nine-dependent synthesis of the glycyl radical in pyruvate formate-lyase by abstraction of the glycine C-2 pro-S hydrogen atom. Studies of [2H]glycine-substituted enzyme and peptides homologous to the glycine 734 site
    • Frey M, Rothe M, Wagner AF, Knappe J. 1994. Adenosylmethio-nine-dependent synthesis of the glycyl radical in pyruvate formate-lyase by abstraction of the glycine C-2 pro-S hydrogen atom. Studies of [2H]glycine-substituted enzyme and peptides homologous to the glycine 734 site. J Biol Chem. 269: 12432-12437.
    • (1994) J Biol Chem , vol.269 , pp. 12432-12437
    • Frey, M.1    Rothe, M.2    Wagner, A.F.3    Knappe, J.4
  • 16
    • 3242879186 scopus 로고    scopus 로고
    • Pyruvate Formate Lyase (PFL) and PFL activating enzyme in the chytrid fungus Neocallimastix frontalis: A free-radical enzyme system conserved across divergent eukaryotic lineages
    • DOI 10.1111/j.1550-7408.2004.tb00394.x
    • Gelius-Dietrich G, Henze K. 2004. Pyruvate formate lyase (PFL) and PFL activating enzyme in the chytrid fungus Neocallimastix frontalis: a free-radical enzyme system conserved across divergent eukaryotic lineages. J Eukaryot Microbiol. 51:456-463. (Pubitemid 38995244)
    • (2004) Journal of Eukaryotic Microbiology , vol.51 , Issue.4 , pp. 456-463
    • Gelius-Dietrich, G.1    Henze, K.2
  • 17
    • 77951778552 scopus 로고    scopus 로고
    • A role for host-parasite interactions in the horizontal transfer of transposons across phyla
    • Gilbert C, Schaack S, Pace JK 2nd, Brindley PJ, Feschotte C. 2010. A role for host-parasite interactions in the horizontal transfer of transposons across phyla. Nature 464:1347-1350.
    • (2010) Nature , vol.464 , pp. 1347-1350
    • Gilbert, C.1    Schaack, S.2    Brindley, P.J.3    Feschotte, C.4
  • 18
    • 62649113993 scopus 로고    scopus 로고
    • Phylogenomic analyses support the monophyly of excavata and resolve relationships among eukaryotic "supergroups"
    • Hampl V, Hug L, Leigh JW, Dacks JB, Lang BF, Simpson AG, Roger AJ. 2009. Phylogenomic analyses support the monophyly of excavata and resolve relationships among eukaryotic "supergroups". Proc Natl Acad Sci USA. 106:3859-3864.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 3859-3864
    • Hampl, V.1    Hug, L.2    Leigh, J.W.3    Dacks, J.B.4    Lang, B.F.5    Simpson, A.G.6    Roger, A.J.7
  • 19
    • 40949115388 scopus 로고    scopus 로고
    • Biochemical and physiological characterization of the pyruvate formate-lyase pfl1 of chlamydomonas reinhardtii, a typically bacterial enzyme in a eukaryotic alga
    • DOI 10.1128/EC.00368-07
    • Hemschemeier A, Jacobs J, Happe T. 2008. Biochemical and physiological characterization of the pyruvate formate-lyase Pfl1 of chlamydomonas reinhardtii, a typically bacterial enzyme in a eukaryotic alga. Eukaryot Cell. 7:518-526. (Pubitemid 351959679)
    • (2008) Eukaryotic Cell , vol.7 , Issue.3 , pp. 518-526
    • Hemschemeier, A.1    Jacobs, J.2    Happe, T.3
  • 20
    • 0028874227 scopus 로고
    • Primary structure and eubacterial relationships of the pyruvate:ferredoxin oxidoreductase of the amitochondriate eukaryote Trichomonas vaginalis
    • Hrdy I, Muller M. 1995. Primary structure and eubacterial relationships of the pyruvate:ferredoxin oxidoreductase of the amitochondriate eukaryote Trichomonas vaginalis. J Mol Evol. 41:388-396.
    • (1995) J Mol Evol , vol.41 , pp. 388-396
    • Hrdy, I.1    Muller, M.2
  • 21
    • 74549210085 scopus 로고    scopus 로고
    • Phylogenetic distributions and histories of proteins involved in anaerobic pyruvate metabolism in eukaryotes
    • Hug LA, Stechmann A, Roger AJ. 2010. Phylogenetic distributions and histories of proteins involved in anaerobic pyruvate metabolism in eukaryotes. Mol Biol Evol. 27:311-324.
    • (2010) Mol Biol Evol. , vol.27 , pp. 311-324
    • Hug, L.A.1    Stechmann, A.2    Roger, A.J.3
  • 22
    • 69049116087 scopus 로고    scopus 로고
    • Expanded phylogenies of canonical and non-canonical types of methionine adenosyltransferase reveal a complex history of these gene families in eukaryotes
    • Kamikawa R, Sanchez-Perez GF, Sako Y, Roger AJ, Inagaki Y. 2009. Expanded phylogenies of canonical and non-canonical types of methionine adenosyltransferase reveal a complex history of these gene families in eukaryotes. Mol Phylogenet Evol. 53:565-570.
    • (2009) Mol Phylogenet Evol , vol.53 , pp. 565-570
    • Kamikawa, R.1    Sanchez-Perez, G.F.2    Sako, Y.3    Roger, A.J.4    Inagaki, Y.5
  • 25
    • 43049085945 scopus 로고    scopus 로고
    • The eukaryotic tree of life: endosymbiosis takes its TOL
    • DOI 10.1016/j.tree.2008.02.004, PII S0169534708001055
    • Lane CE, Archibald JM. 2008. The eukaryotic tree of life: endosymbiosis takes its TOL. Trends Ecol Evol. 23:268-275. (Pubitemid 351626208)
    • (2008) Trends in Ecology and Evolution , vol.23 , Issue.5 , pp. 268-275
    • Lane, C.E.1    Archibald, J.M.2
  • 26
    • 69949126557 scopus 로고    scopus 로고
    • PhyloBayes 3: A Bayesian software package for phylogenetic reconstruction and molecular dating
    • Lartillot N, Lepage T, Blanquart S. 2009. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics. 25:2286-2288.
    • (2009) Bioinformatics , vol.25 , pp. 2286-2288
    • Lartillot, N.1    Lepage, T.2    Blanquart, S.3
  • 27
    • 45849154166 scopus 로고    scopus 로고
    • An improved general amino acid replacement matrix
    • DOI 10.1093/molbev/msn067
    • Le SQ, Gascuel O. 2008. An improved general amino acid replacement matrix. Mol Biol Evol. 25:1307-1320. (Pubitemid 351882003)
    • (2008) Molecular Biology and Evolution , vol.25 , Issue.7 , pp. 1307-1320
    • Le, S.Q.1    Gascuel, O.2
  • 29
    • 8444226694 scopus 로고    scopus 로고
    • The pyruvate formate lyase family: Sequences, structures and activation
    • DOI 10.1093/protein/gzh059
    • Lehtio L, Goldman A. 2004. The pyruvate formate lyase family: sequences, structures and activation. Protein Eng Des Sel. 17:545-552. (Pubitemid 39487534)
    • (2004) Protein Engineering, Design and Selection , vol.17 , Issue.6 , pp. 545-552
    • Lehtio, L.1    Goldman, A.2
  • 31
    • 2642689666 scopus 로고    scopus 로고
    • The hydrogen hypothesis for the first eukaryote
    • DOI 10.1038/32096
    • Martin W, Müller M. 1998. The hydrogen hypothesis for the first eukaryote. Nature 392:37-41. (Pubitemid 28150580)
    • (1998) Nature , vol.392 , Issue.6671 , pp. 37-41
    • Martin, W.1    Muller, M.2
  • 33
    • 77955332146 scopus 로고    scopus 로고
    • Diversity in mitochondrial metabolic pathways in parasitic protists plasmodium and cryptosporidium
    • Mogi T, Kita K. 2010. Diversity in mitochondrial metabolic pathways in parasitic protists plasmodium and cryptosporidium. Parasitol Int. 59:305-312.
    • (2010) Parasitol Int. , vol.59 , pp. 305-312
    • Mogi, T.1    Kita, K.2
  • 34
    • 73149111994 scopus 로고    scopus 로고
    • Phylogenetic positions of Glaucophyta, green plants (Archaeplastida) and Haptophyta (Chromalveolata) as deduced from slowly evolving nuclear genes
    • Nozaki H, Maruyama S, Matsuzaki M, Nakada T, Kato S, Misawa K. 2009. Phylogenetic positions of Glaucophyta, green plants (Archaeplastida) and Haptophyta (Chromalveolata) as deduced from slowly evolving nuclear genes. Mol Phylogenet Evol. 53: 872-880.
    • (2009) Mol Phylogenet Evol , vol.53 , pp. 872-880
    • Nozaki, H.1    Maruyama, S.2    Matsuzaki, M.3    Nakada, T.4    Kato, S.5    Misawa, K.6
  • 35
    • 58149197596 scopus 로고    scopus 로고
    • OperonDB: A comprehensive database of predicted operons in microbial genomes
    • Pertea M, Ayanbule K, Smedinghoff M, Salzberg SL. 2009. OperonDB: a comprehensive database of predicted operons in microbial genomes. Nucleic Acids Res. 37:D479-D482.
    • (2009) Nucleic Acids Res , vol.37
    • Pertea, M.1    Ayanbule, K.2    Smedinghoff, M.3    Salzberg, S.L.4
  • 36
    • 34547751897 scopus 로고    scopus 로고
    • Supertrees disentangle the chimerical origin of eukaryotic genomes
    • DOI 10.1093/molbev/msm095
    • Pisani D, Cotton JA, McInerney JO. 2007. Supertrees disentangle the chimerical origin of eukaryotic genomes. Mol Biol Evol. 24:1752-1760. (Pubitemid 47236695)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.8 , pp. 1752-1760
    • Pisani, D.1    Cotton, J.A.2    McInerney, J.O.3
  • 38
    • 0035029530 scopus 로고    scopus 로고
    • + oxidoreductase from the mitochondrion of Euglena gracilis and from the apicomplexan Cryptosporidium parvum: A biochemical relic linking pyruvate metabolism in mitochondriate and amitochondriate protists
    • Rotte C, Stejskal F, Zhu G, Keithly JS, Martin W. 2001. Pyruvate: NADP\+ oxidoreductase from the mitochondrion of Euglena gracilis and from the apicomplexan cryptosporidium parvum: a biochemical relic linking pyruvate metabolism in mito-chondriate and amitochondriate protists. Mol Biol Evol. 18: 710-720. (Pubitemid 32372942)
    • (2001) Molecular Biology and Evolution , vol.18 , Issue.5 , pp. 710-720
    • Rotte, C.1    Stejskal, F.2    Zhu, G.3    Keithly, J.S.4    Martin, W.5
  • 39
    • 0036205377 scopus 로고    scopus 로고
    • TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
    • Schmidt HA, Strimmer K, Vingron M, von Haeseler A. 2002. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504. (Pubitemid 34284960)
    • (2002) Bioinformatics , vol.18 , Issue.3 , pp. 502-504
    • Schmidt, H.A.1    Strimmer, K.2    Vingron, M.3    Von Haeseler, A.4
  • 40
    • 26444466173 scopus 로고    scopus 로고
    • The comparison of the confidence regions in phylogeny
    • DOI 10.1093/molbev/msi226
    • Shi X, Gu H, Susko E, Field C. 2005. The comparison of the confidence regions in phylogeny. Mol Biol Evol. 22:2285-2296. (Pubitemid 41437809)
    • (2005) Molecular Biology and Evolution , vol.22 , Issue.11 , pp. 2285-2296
    • Shi, X.1    Gu, H.2    Susko, E.3    Field, C.4
  • 41
    • 0036139287 scopus 로고    scopus 로고
    • CONSEL: For assessing the confidence of phylogenetic tree selection
    • Shimodaira H, Hasegawa M. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17: 1246-1247. (Pubitemid 33735360)
    • (2001) Bioinformatics , vol.17 , Issue.12 , pp. 1246-1247
    • Shimodaira, H.1    Hasegawa, M.2
  • 42
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • DOI 10.1093/bioinformatics/btl446
    • Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690. (Pubitemid 44642609)
    • (2006) Bioinformatics , vol.22 , Issue.21 , pp. 2688-2690
    • Stamatakis, A.1
  • 43
    • 0022744840 scopus 로고
    • Anaerobic pyruvate metabolism of Tritrichomonas foetus and Trichomonas vaginalis hydrogeno-somes
    • Steinbuchel A, Müller M. 1986. Anaerobic pyruvate metabolism of Tritrichomonas foetus and Trichomonas vaginalis hydrogeno-somes. Mol Biochem Parasitol. 20:57-65.
    • (1986) Mol Biochem Parasitol , vol.20 , pp. 57-65
    • Steinbuchel, A.1    Müller, M.2
  • 44
    • 67749122255 scopus 로고    scopus 로고
    • Bootstrap support is not first-order correct
    • Susko E. 2009. Bootstrap support is not first-order correct. Syst Biol. 58:211-223.
    • (2009) Syst Biol , vol.58 , pp. 211-223
    • Susko, E.1
  • 45
    • 77953738812 scopus 로고    scopus 로고
    • First-order correct bootstrap support adjustments for splits that allow hypothesis testing when using maximum likelihood estimation
    • Susko E. 2010. First-order correct bootstrap support adjustments for splits that allow hypothesis testing when using maximum likelihood estimation. Mol Biol Evol. 27:1621-1629.
    • (2010) Mol Biol Evol. , vol.27 , pp. 1621-1629
    • Susko, E.1
  • 46
    • 0015520637 scopus 로고
    • Properties and function of the pyruvate-formate-lyase reaction in clostridiae
    • Thauer RK, Kirchniawy FH, Jungermann KA. 1972. Properties and function of the pyruvate-formate-lyase reaction in clostridiae. Eur J Biochem. 27:282-290.
    • (1972) Eur J Biochem , vol.27 , pp. 282-290
    • Thauer, R.K.1    Kirchniawy, F.H.2    Jungermann, K.A.3
  • 47
    • 0032321582 scopus 로고    scopus 로고
    • The electron transport chain in anaerobically functioning eukaryotes
    • DOI 10.1016/S0005-2728(98)00045-0, PII S0005272898000450
    • Tielens AG, Van Hellemond JJ. 1998. The electron transport chain in anaerobically functioning eukaryotes. Biochim Biophys Acta. 1365:71-78. (Pubitemid 29359241)
    • (1998) Biochimica et Biophysica Acta - Bioenergetics , vol.1365 , Issue.1-2 , pp. 71-78
    • Tielens, A.G.M.1    Van Hellemond, J.J.2
  • 49
    • 0032577240 scopus 로고    scopus 로고
    • The flavoprotein component of the Escherichia coli sulfite reductase can act as a cytochrome P450c17 reductase
    • DOI 10.1006/bbrc.1998.8671
    • Zeghouf M, Defaye G, Fontecave M, Coves J. 1998. The flavoprotein component of the Escherichia coli sulfite reductase can act as a cytochrome P450c17 reductase. Biochem Biophys Res Commun. 246:602-605. (Pubitemid 28420903)
    • (1998) Biochemical and Biophysical Research Communications , vol.246 , Issue.3 , pp. 602-605
    • Zeghouf, M.1    Defaye, G.2    Fontecave, M.3    Coves, J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.