title: Large-scale reconstruction and phylogenetic analysis of metabolic environments.
abstract: The topology of metabolic networks may provide important insights not only into the metabolic capacity of species, but also into the habitats in which they evolved. Here we introduce the concept of a metabolic network's "seed set"--the set of compounds that, based on the network topology, are exogenously acquired--and provide a methodological framework to computationally infer the seed set of a given network. Such seed sets form ecological "interfaces" between metabolic networks and their surroundings, approximating the effective biochemical environment of each species. Analyzing the metabolic networks of 478 species and identifying the seed set of each species, we present a comprehensive large-scale reconstruction of such predicted metabolic environments. The seed sets' composition significantly correlates with several basic properties characterizing the species' environments and agrees with biological observations concerning major adaptations. Species whose environments are highly predictable (e.g., obligate parasites) tend to have smaller seed sets than species living in variable environments. Phylogenetic analysis of the seed sets reveals the complex dynamics governing gain and loss of seeds across the phylogenetic tree and the process of transition between seed and non-seed compounds. Our findings suggest that the seed state is transient and that seeds tend either to be dropped completely from the network or to become non-seed compounds relatively fast. The seed sets also permit a successful reconstruction of a phylogenetic tree of life. The "reverse ecology" approach presented lays the foundations for studying the evolutionary interplay between organisms and their habitats on a large scale.
authors.affiliation: Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA. ebo@stanford.edu
authors.forename: Elhanan
authors.initials: E
authors.lastname: Borenstein
authors.forename: Martin
authors.initials: M
authors.lastname: Kupiec
authors.forename: Marcus W
authors.initials: MW
authors.lastname: Feldman
authors.forename: Eytan
authors.initials: E
authors.lastname: Ruppin
mesh_terms: D000818:Animals; D001105:Archaea / Q000145:classification / Q000378:metabolism; D001419:Bacteria / Q000145:classification / Q000378:metabolism; D004777:Environment; D056890:Eukaryota / Q000145:classification / Q000378:metabolism; D005658:Fungi / Q000145:classification / Q000378:metabolism; D008660:Metabolism; D010802:Phylogeny; D010944:Plants / Q000145:classification / Q000378:metabolism
references.citation: Mol Ecol. 2006 Apr;15(5):1251-61
references.pmid: 16626452
references.citation: Proc Natl Acad Sci U S A. 2004 Sep 7;101(36):13168-73
references.pmid: 15340153
references.citation: Nature. 2002 Nov 14;420(6912):186-9
references.pmid: 12432395
references.citation: Nat Genet. 2006 Sep;38(9):993-8
references.pmid: 16941010
references.citation: J Theor Biol. 2007 May 21;246(2):278-89
references.pmid: 17291537
references.citation: Genome Res. 2003 Oct;13(10):2229-35
references.pmid: 14525925
references.citation: J Mol Evol. 2005 Oct;61(4):498-512
references.pmid: 16155745
references.citation: Science. 1998 Oct 23;282(5389):754-9
references.pmid: 9784136
references.citation: Science. 2003 Sep 26;301(5641):1866-7
references.pmid: 14512615
references.citation: Nature. 2000 Oct 5;407(6804):651-4
references.pmid: 11034217
references.citation: Proc Natl Acad Sci U S A. 1945 Jun;31(6):153-7
references.pmid: 16578152
references.citation: PLoS Genet. 2006 Feb;2(2):e21
references.pmid: 16482227
references.citation: Mol Biol Evol. 1993 May;10(3):512-26
references.pmid: 8336541
references.citation: Genome Inform. 2005;16(1):203-13
references.pmid: 16362923
references.citation: Nature. 2004 Feb 26;427(6977):839-43
references.pmid: 14985762
references.citation: Science. 2006 Mar 24;311(5768):1764-7
references.pmid: 16556842
references.citation: FEBS Lett. 2005 Aug 29;579(21):4642-6
references.pmid: 16095595
references.citation: Nucleic Acids Res. 2007;35(1):e7
references.pmid: 17158152
references.citation: Nat Genet. 2005 Dec;37(12):1372-5
references.pmid: 16311593
references.citation: Genome Biol. 2001;2(12):RESEARCH0054
references.pmid: 11790257
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D354-7
references.pmid: 16381885
references.citation: Nature. 2004 Jun 10;429(6992):661-4
references.pmid: 15190353
references.citation: Proc Natl Acad Sci U S A. 2007 Feb 20;104(8):2909-14
references.pmid: 17301237
references.citation: Mol Biol Evol. 2007 Aug;24(8):1586-91
references.pmid: 17483113
references.citation: Nature. 2002 Nov 14;420(6912):190-3
references.pmid: 12432396
references.citation: BMC Evol Biol. 2007 Sep 23;7:169
references.pmid: 17888177
references.citation: PLoS Comput Biol. 2006 Dec 8;2(12):e167
references.pmid: 17154715
references.citation: Nucleic Acids Res. 2006 Aug 07;34(13):3687-97
references.pmid: 16893953
references.citation: J Mol Biol. 2006 Apr 28;358(2):614-33
references.pmid: 16530225
references.citation: J Bacteriol. 1993 Dec;175(23):7702-4
references.pmid: 8244941
references.citation: Curr Opin Struct Biol. 2002 Jun;12(3):374-82
references.pmid: 12127458
references.citation: Cell. 1996 Jun 14;85(6):793-8
references.pmid: 8681375
references.citation: Science. 2006 Mar 3;311(5765):1283-7
references.pmid: 16513982
references.citation: Syst Biol (Stevenage). 2006 Sep;153(5):354-8
references.pmid: 16986316
references.citation: Nature. 2000 Sep 7;407(6800):81-6
references.pmid: 10993077
references.citation: Bioinformatics. 2007 Aug 15;23(16):2139-46
references.pmid: 17586548
references.citation: Proc Natl Acad Sci U S A. 2008 May 13;105(19):6976-81
references.pmid: 18460604
references.citation: BMC Bioinformatics. 2006 Mar 13;7:130
references.pmid: 16533389