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A 5-formyltetrahydrofolate cycloligase paralog from all domains of life: comparative genomic and experimental evidence for a cryptic role in thiamin metabolism.

Bibliographic reference Pribat, Anne ; Blaby, Ian K ; Lara-Núñez, Aurora ; Jeanguenin, Linda ; Fouquet, Romain ; et. al. A 5-formyltetrahydrofolate cycloligase paralog from all domains of life: comparative genomic and experimental evidence for a cryptic role in thiamin metabolism.. In: Functional & integrative genomics, Vol. 11, no. 3, p. 467-478 (2011)
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  1. Ajjawi Imad, Tsegaye Yoseph, Shintani David, Determination of the genetic, molecular, and biochemical basis of the Arabidopsis thaliana thiamin auxotroph th1, 10.1016/
  2. Allers T., Ngo H.-P., Mevarech M., Lloyd R. G., Development of Additional Selectable Markers for the Halophilic Archaeon Haloferax volcanii Based on the leuB and trpA Genes, 10.1128/aem.70.2.943-953.2004
  3. Altschul S., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, 10.1093/nar/25.17.3389
  4. Boroujerdi Arezue F. B., Young John K., NMR-derived folate-bound structure of dihydrofolate reductase 1 from the halophileHaloferax volcanii, 10.1002/bip.21096
  5. Buchenau B�rbel, Thauer Rudolf K., Tetrahydrofolate-specific enzymes in Methanosarcina barkeri and growth dependence of this methanogenic archaeon on folic acid or p-aminobenzoic acid, 10.1007/s00203-004-0714-0
  6. Chen Shengfeng, Shin Dong-Hae, Pufan Ramona, Kim Rosalind, Kim Sung-Hou, Crystal structure of methenyltetrahydrofolate synthetase from Mycoplasma pneumoniae (GI: 13508087) at 2.2 Å resolution, 10.1002/prot.20214
  7. Chen Shengfeng, Yakunin Alexander F., Proudfoot Michael, Kim Rosalind, Kim Sung-Hou, Structural and functional characterization of a 5,10-methenyltetrahydrofolate synthetase from Mycoplasma pneumoniae (GI: 13508087), 10.1002/prot.20591
  8. Date Shailesh V, Marcotte Edward M, Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages, 10.1038/nbt861
  9. de Crécy-Lagard Valérie, El Yacoubi Basma, de la Garza Rocío, Noiriel Alexandre, Hanson Andrew D, Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations, 10.1186/1471-2164-8-245
  10. Durot Maxime, Bourguignon Pierre-Yves, Schachter Vincent, Genome-scale models of bacterial metabolism: reconstruction and applications, 10.1111/j.1574-6976.2008.00146.x
  11. Dyal-Smith M (2008) The halohandbook: protocols for halobacterial genetics, Version 7.
  12. Edwards K., Johnstone C., Thompson C., A simple and rapid method for the preparation of plant genomic DNA for PCR analysis, 10.1093/nar/19.6.1349
  13. Yacoubi Basma El, Phillips Gabriela, Blaby Ian K., Haas Crysten E., Cruz Yulien, Greenberg Jamie, de Crécy-Lagard Valérie, A Gateway platform for functional genomics inHaloferax volcanii: deletion of three tRNA modification genes, 10.1155/2009/428489
  14. Falb Michaela, Müller Kerstin, Königsmaier Lisa, Oberwinkler Tanja, Horn Patrick, von Gronau Susanne, Gonzalez Orland, Pfeiffer Friedhelm, Bornberg-Bauer Erich, Oesterhelt Dieter, Metabolism of halophilic archaea, 10.1007/s00792-008-0138-x
  15. Field Martha S., Szebenyi Doletha M.E., Perry Cheryll A., Stover Patrick J., Inhibition of 5,10-methenyltetrahydrofolate synthetase, 10.1016/
  16. Frishman Dmitrij, Protein Annotation at Genomic Scale:  The Current Status, 10.1021/cr068303k
  17. Galperin Michael Y., Koonin Eugene V., Who's your neighbor? New computational approaches for functional genomics, 10.1038/76443
  18. Galperin Michael Y., Koonin Eugene V., From complete genome sequence to ‘complete’ understanding?, 10.1016/j.tibtech.2010.05.006
  19. Galperin Michael Y., Moroz Olga V., Wilson Keith S., Murzin Alexey G., House cleaning, a part of good housekeeping, 10.1111/j.1365-2958.2005.04950.x
  20. Gorris LG, van der Drift C (1994) Cofactor contents of methanogenic bacteria reviewed. Biofactors 4:139–145
  21. Goyer Aymeric, Thiamine in plants: Aspects of its metabolism and functions, 10.1016/j.phytochem.2010.06.022
  22. Goyer Aymeric, Collakova Eva, de la Garza Rocío Díaz, Quinlivan Eoin P., Williamson Jerry, Gregory Jesse F., Shachar-Hill Yair, Hanson Andrew D., 5-Formyltetrahydrofolate Is an Inhibitory but Well Tolerated Metabolite inArabidopsisLeaves, 10.1074/jbc.m503106200
  23. Grochowski Laura L., Xu Huimin, Leung Kapo, White Robert H., Characterization of an Fe2+-Dependent Archaeal-Specific GTP Cyclohydrolase, MptA, fromMethanocaldococcus jannaschii†, 10.1021/bi700052a
  24. Guzman L M, Belin D, Carson M J, Beckwith J, Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter., 10.1128/jb.177.14.4121-4130.1995
  25. Hanson Andrew D., Pribat Anne, Waller Jeffrey C., Crécy-Lagard  Valérie de, ‘Unknown’ proteins and ‘orphan’ enzymes: the missing half of the engineering parts list – and how to find it, 10.1042/bj20091328
  26. Holmes William B., Appling Dean R., Cloning and Characterization of Methenyltetrahydrofolate Synthetase fromSaccharomyces cerevisiae, 10.1074/jbc.m201242200
  27. Ishii Kazuhiko, Sarai Keisuke, Sanemori Hiroshi, Kawasaki Takashi, Analysis of thiamine and its phosphate esters by high-performamze liquid chromatography, 10.1016/0003-2697(79)90345-2
  28. Janga S.C., Díaz-Mejía J. Javier, Moreno-Hagelsieb G., Network-based function prediction and interactomics: The case for metabolic enzymes, 10.1016/j.ymben.2010.07.001
  29. Jeanguenin Linda, Lara-Núñez Aurora, Pribat Anne, Mageroy Melissa Hamner, Gregory Jesse F., Rice Kelly C., de Crécy-Lagard Valérie, Hanson Andrew D., Moonlighting Glutamate Formiminotransferases Can Functionally Replace 5-Formyltetrahydrofolate Cycloligase, 10.1074/jbc.m110.190504
  30. Jenkins Amy Haas, Schyns Ghislain, Potot Sébastien, Sun Guangxing, Begley Tadhg P, A new thiamin salvage pathway, 10.1038/nchembio.2007.13
  31. Jensen L. J., Kuhn M., Stark M., Chaffron S., Creevey C., Muller J., Doerks T., Julien P., Roth A., Simonovic M., Bork P., von Mering C., STRING 8--a global view on proteins and their functional interactions in 630 organisms, 10.1093/nar/gkn760
  32. Jurgenson Christopher T., Begley Tadhg P., Ealick Steven E., The Structural and Biochemical Foundations of Thiamin Biosynthesis, 10.1146/annurev.biochem.78.072407.102340
  33. Levin I., Mevarech M., Palfey B. A., Characterization of a Novel Bifunctional Dihydropteroate Synthase/Dihydropteroate Reductase Enzyme from Helicobacter pylori, 10.1128/jb.01878-06
  34. Lin Zhaosheng, Sparling Richard, Investigation of serine hydroxymethyltransferase in methanogens, 10.1139/w98-050
  35. Lin Xinli, White Robert H., Distribution of charged pterins in nonmethanogenic archaebacteria, 10.1007/bf00408246
  36. Liolios Konstantinos, Chen I-Min A., Mavromatis Konstantinos, Tavernarakis Nektarios, Hugenholtz Philip, Markowitz Victor M., Kyrpides Nikos C., The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata, 10.1093/nar/gkp848
  37. MADEN B. Edward H., Tetrahydrofolate and tetrahydromethanopterin compared: functionally distinct carriers in C1 metabolism, 10.1042/0264-6021:3500609
  38. Maris Christophe, Dominguez Cyril, Allain Frédéric H.-T., The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression : The RRM domain, a plastic RNA-binding platform, 10.1111/j.1742-4658.2005.04653.x
  39. Mukherjee Tathagata, McCulloch Kathryn M., Ealick Steven E., Begley Tadhg P., Cofactor Catabolism, Comprehensive Natural Products II (2010) ISBN:9780080453828 p.649-674, 10.1016/b978-008045382-8.00153-2
  40. NIWA Yasuo, A Synthetic Green Fluorescent Protein Gene for Plant Biotechnology., 10.5511/plantbiotechnology.20.1
  41. Obayashi Takeshi, Kinoshita Kengo, Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways, 10.1007/s10265-010-0333-6
  42. Overbeek R., Fonstein M., D'Souza M., Pusch G. D., Maltsev N., The use of gene clusters to infer functional coupling, 10.1073/pnas.96.6.2896
  43. Overbeek R., The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes, 10.1093/nar/gki866
  44. Pribat Anne, Noiriel Alexandre, Morse Alison M., Davis John M., Fouquet Romain, Loizeau Karen, Ravanel Stéphane, Frank Wolfgang, Haas Richard, Reski Ralf, Bedair Mohamed, Sumner Lloyd W., Hanson Andrew D., Nonflowering Plants Possess a Unique Folate-Dependent Phenylalanine Hydroxylase That Is Localized in Chloroplasts, 10.1105/tpc.110.078824
  45. Reddick Jason J., Nicewonger Robb, Begley Tadhg P., Mechanistic Studies on Thiamin Phosphate Synthase:  Evidence for a Dissociative Mechanism†, 10.1021/bi010267q
  46. Rodionov Dmitry A., Vitreschak Alexey G., Mironov Andrey A., Gelfand Mikhail S., Comparative Genomics of Thiamin Biosynthesis in Procaryotes : NEW GENES AND REGULATORY MECHANISMS, 10.1074/jbc.m208965200
  47. Rodionov D. A., Hebbeln P., Eudes A., ter Beek J., Rodionova I. A., Erkens G. B., Slotboom D. J., Gelfand M. S., Osterman A. L., Hanson A. D., Eitinger T., A Novel Class of Modular Transporters for Vitamins in Prokaryotes, 10.1128/jb.01208-08
  48. Roje Sanja, Janave Machhindra T., Ziemak Michael J., Hanson Andrew D., Cloning and Characterization of Mitochondrial 5-Formyltetrahydrofolate Cycloligase from Higher Plants, 10.1074/jbc.m205632200
  49. Rudhe Charlotta, Chew Orinda, Whelan James, Glaser Elzbieta, A novelin vitrosystem for simultaneous import of precursor proteins into mitochondria and chloroplasts, 10.1046/j.1365-313x.2002.01280.x
  50. Schnoes Alexandra M., Brown Shoshana D., Dodevski Igor, Babbitt Patricia C., Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies, 10.1371/journal.pcbi.1000605
  51. Spang Anja, Hatzenpichler Roland, Brochier-Armanet Céline, Rattei Thomas, Tischler Patrick, Spieck Eva, Streit Wolfgang, Stahl David A., Wagner Michael, Schleper Christa, Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota, 10.1016/j.tim.2010.06.003
  52. Stover Patrick, Schirch Verne, The metabolic role of leucovorin, 10.1016/0968-0004(93)90162-g
  53. Tamura K., Dudley J., Nei M., Kumar S., MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0, 10.1093/molbev/msm092
  54. Tatusov Roman L, Fedorova Natalie D, Jackson John D, Jacobs Aviva R, Kiryutin Boris, Koonin Eugene V, Krylov Dmitri M, Mazumder Raja, Mekhedov Sergei L, Nikolskaya Anastasia N, Rao B Sridhar, Smirnov Sergei, Sverdlov Alexander V, Vasudevan Sona, Wolf Yuri I, Yin Jodie J, Natale Darren A, 10.1186/1471-2105-4-41
  55. Temple CT, Montgomery JA (1984) Chemical and physical properties of folic acid and reduced derivatives. In: Blakley RL, Benkovic SJ (eds) Folates and pterins, vol 1, 2nd edn. Wiley, New York, pp 61–120
  56. Thomas Allen A., De Meese J., Le Huerou Y., Boyd Steven A., Romoff Todd T., Gonzales Steven S., Gunawardana Indrani, Kaplan Tomas, Sullivan Francis, Condroski Kevin, Lyssikatos Joseph P., Aicher Thomas D., Ballard Josh, Bernat Bryan, DeWolf Walter, Han May, Lemieux Christine, Smith Darin, Weiler Solly, Wright S. Kirk, Vigers Guy, Brandhuber Barb, Non-charged thiamine analogs as inhibitors of enzyme transketolase, 10.1016/j.bmcl.2007.11.098
  57. van de Wijngaard WM, Creemers J, Vogels GD, van der Drift C (1991) Methanogenic pathways in Methanosphaera stadtmanae. FEMS Microbiol Lett 64:207–211
  58. White R H, Analysis and characterization of the folates in the nonmethanogenic archaebacteria., 10.1128/jb.170.10.4608-4612.1988
  59. White R H, Distribution of folates and modified folates in extremely thermophilic bacteria., 10.1128/jb.173.6.1987-1991.1991
  60. White R H, Structures of the modified folates in the extremely thermophilic archaebacterium Thermococcus litoralis., 10.1128/jb.175.11.3661-3663.1993
  61. Worrell V E, Nagle D P, Folic acid and pteroylpolyglutamate contents of archaebacteria., 10.1128/jb.170.9.4420-4423.1988
  62. Wu D., Li Y., Song G., Cheng C., Zhang R., Joachimiak A., Shaw N., Liu Z.-J., Structural Basis for the Inhibition of Human 5,10-Methenyltetrahydrofolate Synthetase by N10-Substituted Folate Analogues, 10.1158/0008-5472.can-09-1927
  63. Zybailov Boris, Rutschow Heidi, Friso Giulia, Rudella Andrea, Emanuelsson Olof, Sun Qi, van Wijk Klaas J., Sorting Signals, N-Terminal Modifications and Abundance of the Chloroplast Proteome, 10.1371/journal.pone.0001994