title: The complement of enzymatic sets in different species.
abstract: We present here a comprehensive analysis of the complement of enzymes in a large variety of species. As enzymes are a relatively conserved group there are several classification systems available that are common to all species and link a protein sequence to an enzymatic function. Enzymes are therefore an ideal functional group to study the relationship between sequence expansion, functional divergence and phenotypic changes. By using information retrieved from the well annotated SWISS-PROT database together with sequence information from a variety of fully sequenced genomes and information from the EC functional scheme we have aimed here to estimate the fraction of enzymes in genomes, to determine the extent of their functional redundancy in different domains of life and to identify functional innovations and lineage specific expansions in the metazoa lineage. We found that prokaryote and eukaryote species differ both in the fraction of enzymes in their genomes and in the pattern of expansion of their enzymatic sets. We observe an increase in functional redundancy accompanying an increase in species complexity. A quantitative assessment was performed in order to determine the degree of functional redundancy in different species. Finally, we report a massive expansion in the number of mammalian enzymes involved in signalling and degradation.
authors.affiliation: EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. shirigo@ebi.ac.uk
authors.forename: Shiri
authors.initials: S
authors.lastname: Freilich
authors.forename: Ruth V
authors.initials: RV
authors.lastname: Spriggs
authors.forename: Richard A
authors.initials: RA
authors.lastname: George
authors.forename: Bissan
authors.initials: B
authors.lastname: Al-Lazikani
authors.forename: Mark
authors.initials: M
authors.lastname: Swindells
authors.forename: Janet M
authors.initials: JM
authors.lastname: Thornton
mesh_terms: D000818:Animals; D019295:Computational Biology; D030562:Databases, Protein; D004798:Enzymes / Q000235:genetics / Q000378:metabolism*; D005057:Eukaryotic Cells / Q000378:metabolism; D016678:Genome; D006801:Humans; D008322:Mammals / Q000145:classification / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D011387:Prokaryotic Cells / Q000378:metabolism; D020543:Proteome / Q000235:genetics / Q000378:metabolism*; D040901:Proteomics; D013045:Species Specificity
chemical_list: D004798:Enzymes; D020543:Proteome