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Volumn 75, Issue 1, 2014, Pages 154-164

Genome-wide identification, domain architectures and phylogenetic analysis provide new insights into the early evolution of shikimate pathway in prokaryotes

Author keywords

Domain architectures; Horizontal gene transfer; Pathway evolution; Phylogenetic analysis; Shikimate pathway

Indexed keywords

3 PHOSPHOSHIKIMATE 1 CARBOXYVINYLTRANSFERASE; CHORISMATE SYNTHASE; LYASE; PHOSPHOTRANSFERASE; PROTEOME; SHIKIMATE KINASE; SHIKIMIC ACID; TRANSFERASE;

EID: 84896320787     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2014.02.015     Document Type: Article
Times cited : (7)

References (55)
  • 2
    • 0025581736 scopus 로고
    • The shikimate pathway-a metabolic tree with many branches
    • Bentley R. The shikimate pathway-a metabolic tree with many branches. Crit. Rev. Biochem. Mol. Biol. 1990, 25:307-384.
    • (1990) Crit. Rev. Biochem. Mol. Biol. , vol.25 , pp. 307-384
    • Bentley, R.1
  • 3
    • 34250896106 scopus 로고    scopus 로고
    • Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers
    • Brochier-Armanet C., Forterre P. Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers. Archaea 2007, 2:83-93.
    • (2007) Archaea , vol.2 , pp. 83-93
    • Brochier-Armanet, C.1    Forterre, P.2
  • 7
    • 79954529507 scopus 로고    scopus 로고
    • ProtTest 3: fast selection of best-fit models of protein evolution
    • Darriba D., Taboada G.L., Doallo R., Posada D. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 2011, 27:1164-1165.
    • (2011) Bioinformatics , vol.27 , pp. 1164-1165
    • Darriba, D.1    Taboada, G.L.2    Doallo, R.3    Posada, D.4
  • 8
    • 0035180870 scopus 로고    scopus 로고
    • Archaeal shikimate kinase, a new member of the GHMP-kinase family
    • Daugherty M., Vonstein V., Overbeek R., Osterman A. Archaeal shikimate kinase, a new member of the GHMP-kinase family. J. Bacteriol. 2001, 183:292-300.
    • (2001) J. Bacteriol. , vol.183 , pp. 292-300
    • Daugherty, M.1    Vonstein, V.2    Overbeek, R.3    Osterman, A.4
  • 9
    • 0029556907 scopus 로고
    • The biosynthesis of shikimate metabolites
    • Dewick P.M. The biosynthesis of shikimate metabolites. Nat. Prod. Rep. 1995, 12:579-607.
    • (1995) Nat. Prod. Rep. , vol.12 , pp. 579-607
    • Dewick, P.M.1
  • 12
    • 38649110663 scopus 로고    scopus 로고
    • BEAST: Bayesian evolutionary analysis by sampling trees
    • Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
    • (2007) BMC Evol. Biol. , vol.7 , pp. 214
    • Drummond, A.J.1    Rambaut, A.2
  • 13
    • 0028355575 scopus 로고
    • The evolution of the histidine biosynthetic genes in prokaryotes: a common ancestor for the hisA and hisF genes
    • Fani R., Chiarelli I., Liò P., Bazzicalupo M. The evolution of the histidine biosynthetic genes in prokaryotes: a common ancestor for the hisA and hisF genes. J. Mol. Evol. 1994, 38:489-495.
    • (1994) J. Mol. Evol. , vol.38 , pp. 489-495
    • Fani, R.1    Chiarelli, I.2    Liò, P.3    Bazzicalupo, M.4
  • 14
    • 4544272017 scopus 로고    scopus 로고
    • Modified pathway to synthesize ribulose 1,5-bisphosphate in methanogenic archaea
    • Finn M.W., Tabita F.R. Modified pathway to synthesize ribulose 1,5-bisphosphate in methanogenic archaea. J. Bacteriol. 2004, 186:6360-6366.
    • (2004) J. Bacteriol. , vol.186 , pp. 6360-6366
    • Finn, M.W.1    Tabita, F.R.2
  • 15
    • 33846266906 scopus 로고    scopus 로고
    • Modeling the evolution of protein domain architectures using maximum parsimony
    • Fong J.H., Geer L.Y., Panchenko A.R., Bryant S.H. Modeling the evolution of protein domain architectures using maximum parsimony. J. Mol. Biol. 2007, 366:307-315.
    • (2007) J. Mol. Biol. , vol.366 , pp. 307-315
    • Fong, J.H.1    Geer, L.Y.2    Panchenko, A.R.3    Bryant, S.H.4
  • 16
    • 0036574857 scopus 로고    scopus 로고
    • A hot story from comparative genomics: reverse gyrase is the only hyperthermophile-specific protein
    • Forterre P. A hot story from comparative genomics: reverse gyrase is the only hyperthermophile-specific protein. Trends Genet. 2002, 18:236-237.
    • (2002) Trends Genet. , vol.18 , pp. 236-237
    • Forterre, P.1
  • 17
    • 0034175943 scopus 로고    scopus 로고
    • Reverse gyrase from hyperthermophiles: probable transfer of a thermoadaptation trait from archaea to bacteria
    • Forterre P., Bouthier de la tour C., Philippe H., Duguet M. Reverse gyrase from hyperthermophiles: probable transfer of a thermoadaptation trait from archaea to bacteria. Trends Genet. 2000, 16:152-154.
    • (2000) Trends Genet. , vol.16 , pp. 152-154
    • Forterre, P.1    Bouthier De La Tour, C.2    Philippe, H.3    Duguet, M.4
  • 18
    • 74549125386 scopus 로고    scopus 로고
    • SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building
    • Gouy M., Guindon S., Gascuel O. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol. 2010, 27:221-224.
    • (2010) Mol. Biol. Evol. , vol.27 , pp. 221-224
    • Gouy, M.1    Guindon, S.2    Gascuel, O.3
  • 19
    • 41349108509 scopus 로고    scopus 로고
    • Promiscuous anaerobes: new and unconventional metabolism in methanogenic archaea
    • Grochowski L.L., White R.H. Promiscuous anaerobes: new and unconventional metabolism in methanogenic archaea. Ann. N. Y. Acad. Sci. 2008, 1125:190-214.
    • (2008) Ann. N. Y. Acad. Sci. , vol.1125 , pp. 190-214
    • Grochowski, L.L.1    White, R.H.2
  • 22
    • 0036857358 scopus 로고    scopus 로고
    • QuickTree: building huge Neighbour-Joining trees of protein sequences
    • Howe K., Bateman A., Durbin R. QuickTree: building huge Neighbour-Joining trees of protein sequences. Bioinformatics 2002, 18:1546-1547.
    • (2002) Bioinformatics , vol.18 , pp. 1546-1547
    • Howe, K.1    Bateman, A.2    Durbin, R.3
  • 23
    • 0017272554 scopus 로고
    • Enzyme recruitment in evolution of new function
    • Jensen R.A. Enzyme recruitment in evolution of new function. Annu. Rev. Microbiol. 1976, 30:409-425.
    • (1976) Annu. Rev. Microbiol. , vol.30 , pp. 409-425
    • Jensen, R.A.1
  • 24
    • 0036175457 scopus 로고    scopus 로고
    • The correct phylogenetic relationship of KdsA (3-deoxy-D-manno-octulosonate 8-phosphate synthase) with one of two independently evolved classes of AroA (3-deoxy-D-arabino-heptulosonate 7-phosphate synthase)
    • Jensen R.A., Xie G., Calhoun D.H., Bonner C.A. The correct phylogenetic relationship of KdsA (3-deoxy-D-manno-octulosonate 8-phosphate synthase) with one of two independently evolved classes of AroA (3-deoxy-D-arabino-heptulosonate 7-phosphate synthase). J. Mol. Evol. 2002, 54:416-423.
    • (2002) J. Mol. Evol. , vol.54 , pp. 416-423
    • Jensen, R.A.1    Xie, G.2    Calhoun, D.H.3    Bonner, C.A.4
  • 25
    • 31444453261 scopus 로고    scopus 로고
    • The physiological role of the ribulose monophosphate pathway in bacteria and archaea
    • Kato N., Yurimoto H., Thauer R.K. The physiological role of the ribulose monophosphate pathway in bacteria and archaea. Biosci. Biotechnol. Biochem. 2006, 70:10-21.
    • (2006) Biosci. Biotechnol. Biochem. , vol.70 , pp. 10-21
    • Kato, N.1    Yurimoto, H.2    Thauer, R.K.3
  • 26
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Katoh K., Misawa K., Kuma K., Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002, 30:3059-3066.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.3    Miyata, T.4
  • 27
    • 0034780910 scopus 로고    scopus 로고
    • Horizontal gene transfer in prokaryotes: quantification and classification
    • Koonin E.V., Makarova K.S., Aravind L. Horizontal gene transfer in prokaryotes: quantification and classification. Annu. Rev. Microbiol. 2001, 55:709-742.
    • (2001) Annu. Rev. Microbiol. , vol.55 , pp. 709-742
    • Koonin, E.V.1    Makarova, K.S.2    Aravind, L.3
  • 28
    • 13144259695 scopus 로고    scopus 로고
    • Relative rates of gene fusion and fission in multi-domain proteins
    • Kummerfeld S.K., Teichmann S.A. Relative rates of gene fusion and fission in multi-domain proteins. Trends Genet. 2005, 21:25-30.
    • (2005) Trends Genet. , vol.21 , pp. 25-30
    • Kummerfeld, S.K.1    Teichmann, S.A.2
  • 29
    • 0029847554 scopus 로고    scopus 로고
    • Selfish operons: horizontal transfer may drive the evolution of gene clusters
    • Lawrence J.G., Roth J.R. Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 1996, 143:1843-1860.
    • (1996) Genetics , vol.143 , pp. 1843-1860
    • Lawrence, J.G.1    Roth, J.R.2
  • 30
    • 0029905462 scopus 로고    scopus 로고
    • The origin and early evolution of life: prebiotic chemistry, the pre-RNA world, and time
    • Lazcano A., Miller S.L. The origin and early evolution of life: prebiotic chemistry, the pre-RNA world, and time. Cell 1996, 85:793-798.
    • (1996) Cell , vol.85 , pp. 793-798
    • Lazcano, A.1    Miller, S.L.2
  • 31
    • 45849154166 scopus 로고    scopus 로고
    • An improved general amino acid replacement matrix
    • Le S.Q., Gascuel O. An improved general amino acid replacement matrix. Mol. Biol. Evol. 2008, 25:1307-1320.
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 1307-1320
    • Le, S.Q.1    Gascuel, O.2
  • 32
    • 0041386069 scopus 로고    scopus 로고
    • ClustalW-MPI: ClustalW analysis using distributed and parallel computing
    • Li K.B. ClustalW-MPI: ClustalW analysis using distributed and parallel computing. Bioinformatics 2003, 19:1585-1586.
    • (2003) Bioinformatics , vol.19 , pp. 1585-1586
    • Li, K.B.1
  • 33
    • 0033609333 scopus 로고    scopus 로고
    • Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima
    • Nelson K.E., Clayton R.A., Gill S.R., et al. Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima. Nature 1999, 399:323-329.
    • (1999) Nature , vol.399 , pp. 323-329
    • Nelson, K.E.1    Clayton, R.A.2    Gill, S.R.3
  • 34
    • 64049094506 scopus 로고    scopus 로고
    • Aphids acquired symbiotic genes via lateral gene transfer
    • Nikoh N., Nakabachi A. Aphids acquired symbiotic genes via lateral gene transfer. BMC Biol. 2009, 7:12.
    • (2009) BMC Biol. , vol.7 , pp. 12
    • Nikoh, N.1    Nakabachi, A.2
  • 35
    • 33745444345 scopus 로고    scopus 로고
    • The ribulose monophosphate pathway substitutes for the missing pentose phosphate pathway in the archaeon Thermococcus kodakaraensis
    • Orita I., Sato T., Yurimoto H., Kato N., Atomi H., Imanaka T., Sakai Y. The ribulose monophosphate pathway substitutes for the missing pentose phosphate pathway in the archaeon Thermococcus kodakaraensis. J. Bacteriol. 2006, 188:4698-4704.
    • (2006) J. Bacteriol. , vol.188 , pp. 4698-4704
    • Orita, I.1    Sato, T.2    Yurimoto, H.3    Kato, N.4    Atomi, H.5    Imanaka, T.6    Sakai, Y.7
  • 36
    • 33750458027 scopus 로고    scopus 로고
    • Biochemical and genetic characterization of an early step in a novel pathway for the biosynthesis of aromatic amino acids and p-aminobenzoic acid in the archaeon Methanococcus maripaludis
    • Porat I., Sieprawska-Lupa M., Teng Q., Bohanon F.J., White R.H., Whitman W.B. Biochemical and genetic characterization of an early step in a novel pathway for the biosynthesis of aromatic amino acids and p-aminobenzoic acid in the archaeon Methanococcus maripaludis. Mol. Microbiol. 2006, 62:1117-1131.
    • (2006) Mol. Microbiol. , vol.62 , pp. 1117-1131
    • Porat, I.1    Sieprawska-Lupa, M.2    Teng, Q.3    Bohanon, F.J.4    White, R.H.5    Whitman, W.B.6
  • 37
    • 22444441190 scopus 로고    scopus 로고
    • Operon formation is driven by co-regulation and not by horizontal gene transfer
    • Price M.N., Huang K.H., Arkin A.P., Alm E.J. Operon formation is driven by co-regulation and not by horizontal gene transfer. Genome Res. 2005, 15:809-819.
    • (2005) Genome Res. , vol.15 , pp. 809-819
    • Price, M.N.1    Huang, K.H.2    Arkin, A.P.3    Alm, E.J.4
  • 38
    • 3042777950 scopus 로고    scopus 로고
    • Creation of a shikimate pathway variant
    • Ran N., Draths K.M., Frost J.W. Creation of a shikimate pathway variant. J. Am. Chem. Soc. 2004, 126:6856-6857.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 6856-6857
    • Ran, N.1    Draths, K.M.2    Frost, J.W.3
  • 39
    • 34249012749 scopus 로고    scopus 로고
    • Directed evolution of 2-keto-3-deoxy-6-phosphogalactonate aldolase to replace 3-deoxy-D-arabino-heptulosonic acid 7-phosphate synthase
    • Ran N., Frost J.W. Directed evolution of 2-keto-3-deoxy-6-phosphogalactonate aldolase to replace 3-deoxy-D-arabino-heptulosonic acid 7-phosphate synthase. J. Am. Chem. Soc. 2007, 129:6130-6139.
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 6130-6139
    • Ran, N.1    Frost, J.W.2
  • 40
    • 0032565968 scopus 로고    scopus 로고
    • Evidence for the shikimate pathway in apicomplexan parasites
    • Roberts F., Roberts C.W., Johnson J.J., et al. Evidence for the shikimate pathway in apicomplexan parasites. Nature 1998, 393:801-805.
    • (1998) Nature , vol.393 , pp. 801-805
    • Roberts, F.1    Roberts, C.W.2    Johnson, J.J.3
  • 41
    • 33748857142 scopus 로고    scopus 로고
    • Evolutionary origins of the eukaryotic shikimate pathway: gene fusions, horizontal gene transfer, and endosymbiotic replacements
    • Richards T.A., Dacks J.B., Campbell S.A., Blanchard J.L., Foster P.G., McLeod R., Roberts C.W. Evolutionary origins of the eukaryotic shikimate pathway: gene fusions, horizontal gene transfer, and endosymbiotic replacements. Eukaryot. Cell 2006, 5:1517-1531.
    • (2006) Eukaryot. Cell , vol.5 , pp. 1517-1531
    • Richards, T.A.1    Dacks, J.B.2    Campbell, S.A.3    Blanchard, J.L.4    Foster, P.G.5    McLeod, R.6    Roberts, C.W.7
  • 42
    • 0036205377 scopus 로고    scopus 로고
    • Tree-Puzzle: maximum likelihood phylogenetic analysis using quartets and parallel computing
    • Schmidt H.A., Strimmer K., Vingron M., von Haeseler A. Tree-Puzzle: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 2002, 18:502-504.
    • (2002) Bioinformatics , vol.18 , pp. 502-504
    • Schmidt, H.A.1    Strimmer, K.2    Vingron, M.3    von Haeseler, A.4
  • 43
    • 33751427438 scopus 로고    scopus 로고
    • Evolution of the syntrophic interaction between Desulfovibrio vulgaris and Methanosarcina barkeri: involvement of an ancient horizontal gene transfer
    • Scholten J.C., Culley D.E., Brockman F.J., Wu G., Zhang W. Evolution of the syntrophic interaction between Desulfovibrio vulgaris and Methanosarcina barkeri: involvement of an ancient horizontal gene transfer. Biochem. Biophys. Res. Commun. 2007, 352:48-54.
    • (2007) Biochem. Biophys. Res. Commun. , vol.352 , pp. 48-54
    • Scholten, J.C.1    Culley, D.E.2    Brockman, F.J.3    Wu, G.4    Zhang, W.5
  • 44
    • 0032766857 scopus 로고    scopus 로고
    • Multiple comparisons of log-likelihoods with applications to phylogenetic inference
    • Shimodaira H., Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 1999, 16:1114-1116.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1114-1116
    • Shimodaira, H.1    Hasegawa, M.2
  • 45
    • 20144364025 scopus 로고    scopus 로고
    • Biosynthesis of ribose-5-phosphate and erythrose-4-phosphate in archaea: a phylogenetic analysis of archaeal genomes
    • Soderberg T. Biosynthesis of ribose-5-phosphate and erythrose-4-phosphate in archaea: a phylogenetic analysis of archaeal genomes. Archaea 2005, 1:347-352.
    • (2005) Archaea , vol.1 , pp. 347-352
    • Soderberg, T.1
  • 46
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 47
    • 40649111872 scopus 로고    scopus 로고
    • Enzymes of the shikimate pathway encoded in the genome of a basal metazoan, Nematostella vectensis, have microbial origins
    • Starcevic A., Akthar S., Dunlap W.C., Shick J.M., Hranueli D., Cullum J., Long P.F. Enzymes of the shikimate pathway encoded in the genome of a basal metazoan, Nematostella vectensis, have microbial origins. Proc. Natl. Acad. Sci. USA 2008, 105:2533-2537.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 2533-2537
    • Starcevic, A.1    Akthar, S.2    Dunlap, W.C.3    Shick, J.M.4    Hranueli, D.5    Cullum, J.6    Long, P.F.7
  • 48
    • 0031963257 scopus 로고    scopus 로고
    • Substrate ambiguity of 3-deoxy-D-manno-octulosonate 8-phosphate synthase from Neisseria gonorrhoeae in the context of its membership in a protein family containing a subset of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthases
    • Subramaniam P.S., Xie G., Xia T., Jensen R.A. Substrate ambiguity of 3-deoxy-D-manno-octulosonate 8-phosphate synthase from Neisseria gonorrhoeae in the context of its membership in a protein family containing a subset of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthases. J. Bacteriol. 1998, 180:119-127.
    • (1998) J. Bacteriol. , vol.180 , pp. 119-127
    • Subramaniam, P.S.1    Xie, G.2    Xia, T.3    Jensen, R.A.4
  • 51
    • 0029846030 scopus 로고    scopus 로고
    • Evidence for a novel class of microbial 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase in Streptomyces coelicolor A3(2), Streptomyces rimosus and Neurosporacrassa
    • Walker G.E., Dunbar B., Hunter I.S., Nimmo H.G., Coggins J.R. Evidence for a novel class of microbial 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase in Streptomyces coelicolor A3(2), Streptomyces rimosus and Neurosporacrassa. Microbiology 1996, 142:1973-1982.
    • (1996) Microbiology , vol.142 , pp. 1973-1982
    • Walker, G.E.1    Dunbar, B.2    Hunter, I.S.3    Nimmo, H.G.4    Coggins, J.R.5
  • 52
    • 28444468809 scopus 로고    scopus 로고
    • The structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis reveals a common catalytic scaffold and ancestry for type I and type II enzymes
    • Webby C.J., Baker H.M., Lott J.S., Baker E.N., Parker E.J. The structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis reveals a common catalytic scaffold and ancestry for type I and type II enzymes. J. Mol. Biol. 2005, 354:927-939.
    • (2005) J. Mol. Biol. , vol.354 , pp. 927-939
    • Webby, C.J.1    Baker, H.M.2    Lott, J.S.3    Baker, E.N.4    Parker, E.J.5
  • 53
    • 2942563977 scopus 로고    scopus 로고
    • L-Aspartate semialdehyde and a 6-deoxy-5-ketohexose 1-phosphate are the precursors to the aromatic amino acids in Methanocaldococcus jannaschii
    • White R.H. L-Aspartate semialdehyde and a 6-deoxy-5-ketohexose 1-phosphate are the precursors to the aromatic amino acids in Methanocaldococcus jannaschii. Biochemistry 2004, 43:7618-7627.
    • (2004) Biochemistry , vol.43 , pp. 7618-7627
    • White, R.H.1
  • 54
    • 77949513721 scopus 로고    scopus 로고
    • The evolutionary history of protein domains viewed by species phylogeny
    • Yang S., Bourne P.E. The evolutionary history of protein domains viewed by species phylogeny. PLoS One 2009, 4:e8378.
    • (2009) PLoS One , vol.4
    • Yang, S.1    Bourne, P.E.2


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