Reconstructing phylogeny from metabolic substrate-product relationships

BMC Bioinformatics

Volumn 12, Issue SUPPL. 1, 2011, Pages

  Chang, Che Wei ^a   Lyu, Ping Chiang ^a   Arita, Masanori ^b,c,d  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^b UNIVERSITY OF TOKYO   (Japan)

^c NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^d KEIO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME REACTION; HIERARCHICAL METHOD; METABOLIC INFORMATION; METABOLIC NETWORK; METABOLIC PATHWAYS; NETWORK PROPERTIES; STRUCTURAL RELATIONSHIP; PHYLOGENETIC RECONSTRUCTION;

ENZYMES; FORESTRY; GENES; METABOLISM;

METABOLISM; BIOINFORMATICS;

SPIROCHAETA; SPIROCHAETALES;

ALGORITHM; ARCHAEBACTERIUM; ARTICLE; BACTERIUM; BIOLOGY; CLUSTER ANALYSIS; COMPUTER PROGRAM; EUKARYOTE; GENETICS; METABOLISM; METHODOLOGY; PHYLOGENY;

ALGORITHMS; ARCHAEA; BACTERIA; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; EUKARYOTA; METABOLIC NETWORKS AND PATHWAYS; PHYLOGENY; SOFTWARE;

EID: 79951527898     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-S1-S27     Document Type: Article

References (24)

1. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A 1990, 87:4576-4579. 10.1073/pnas.87.12.4576, 54159, 2112744.
2. Ma HW, Zeng AP. Phylogenetic comparison of metabolic capacities of organisms at genome level. Mol Phylogenet Evol 2004, 31:204-213. 10.1016/j.ympev.2003.08.011, 15019620.
3. Lin J, Gerstein M. Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. Genome Res 2000, 10:808-818. 10.1101/gr.10.6.808, 310900, 10854412.
4. Aguilar D, Aviles FX, Querol E, Sternberg MJ. Analysis of phenetic trees based on metabolic capabilites across the three domains of life. J Mol Biol 2004, 340:491-512. 10.1016/j.jmb.2004.04.059, 15210350.
5. Almaas E, Kovacs B, Vicsek T, Oltvai ZN, Barabasi AL. Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature 2004, 427:839-843. 10.1038/nature02289, 14985762.
6. Varma A, Palsson BO. Stoichiometric flux balance models quantitatively predict growth and metabolic byproduct secretion in wild-type Escherichia coli W3110. Appl Environ Microbiol 1994, 60:3724-3731. 201879, 7986045.
7. Oh SJ, Joung JG, Chang JH, Zhang BT. Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks. BMC Bioinformatics 2006, 7:284. 10.1186/1471-2105-7-284, 1534063, 16753070.
8. Zhang Y, Li S, Skogerbo G, Zhang Z, Zhu X, Sun S, Lu H, Shi B, Chen R. Phylophenetic properties of metabolic pathway topologies as revealed by global analysis. BMC Bioinformatics 2006, 7:252. 10.1186/1471-2105-7-252, 1483838, 16684350.
9. Clemente JC, Satou K, Valiente G. Phylogenetic reconstruction from non-genomic data. Bioinformatics 2007, 23:e110-115. 10.1093/bioinformatics/btl307, 17237077.
10. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 1999, 27:29-34. 10.1093/nar/27.1.29, 148090, 9847135.
11. Arita M. The metabolic world of Escherichia coli is not small. Proc Natl Acad Sci U S A 2004, 101:1543-1547. 10.1073/pnas.0306458101, 341771, 14757824.
12. Borenstein E, Kupiec M, Feldman MW, Ruppin E. Large-scale reconstruction and phylogenetic analysis of metabolic environments. Proc Natl Acad Sci U S A 2008, 105:14482-14487. 10.1073/pnas.0806162105, 2567166, 18787117.
13. Arita M. In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism. Genome Res 2003, 13:2455-2466. 10.1101/gr.1212003, 403765, 14559781.
14. Kotera M, Hattori M, Oh M-A, Yamamoto R, Komeno T, Yabuzaki J, Tonomura K, Goto S, Kanehisa M. RPAIR: a reactant-pair database representing chemical changes in enzymatic reactions. Genome Informatics 2004, 15:P062. (poster abstract).
15. Faust K, Croes D, van Helden J. Metabolic pathfinding using RPAIR annotation. J Mol Biol 2009, 388:390-414. 10.1016/j.jmb.2009.03.006, 19281817.
16. Pitkänen E, Jouhten P, Rousu J. Inferring branching pathways in genome-scale metabolic networks. BMC Syst Biol 2009, 3:103. 2791103, 19874610.
17. Tohsato Y, Nishimura Y. Reaction Similarities Focusing Substructure Changes of Chemical Compounds and Metabolic Pathway Alignments. Inform Media Technol 2009, 4:390-399.
18. de Hoon MJ, Imoto S, Nolan J, Miyano S. Open source clustering software. Bioinformatics 2004, 20:1453-1454. 10.1093/bioinformatics/bth078, 14871861.
19. Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, Rupp R. Dendroscope: An interactive viewer for large phylogenetic trees. BMC Bioinformatics 2007, 8:460. 10.1186/1471-2105-8-460, 2216043, 18034891.
20. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. Toward automatic reconstruction of a highly resolved tree of life. Science 2006, 311:1283-1287. 10.1126/science.1123061, 16513982.
21. Gamulin V, Muller IM, Muller WEG. Sponge proteins are more similar to those of Homo sapiens than to Caenorhabditis elegans. Biol J Linnean Soc 2000, 71:821-828.
22. Caetano-Anollés G, Kim HS, Mittenthal JE. The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture. Proc Natl Acad Sci U S A 2007, 104:9358-9963. 1890499, 17517598.
23. Mano A, Tuller T, Béjà O, Pinter RY. Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways. BMC Bioinformatics 2010, 11(Suppl 1):S38. 10.1186/1471-2105-11-S1-S38, 3009510, 20122211.
24. Pitkänen E, Rantanen A, Rousu J, Ukkonen E. Finding Feasible Pathways in Metabolic Networks. Lecture Notes in Comput Sci 2005, 3746:123-133.