title: A classification scheme for alternative oxidases reveals the taxonomic distribution and evolutionary history of the enzyme in angiosperms.
abstract: A classification scheme based on protein phylogenies and sequence harmony method was used to clarify the taxonomic distribution and evolutionary history of the alternative oxidase (AOX) in angiosperms. A large data set analyses showed that AOX1 and AOX2 subfamilies were distributed into 4 phylogenetic clades: AOX1a-c/1e, AOX1d, AOX2a-c and AOX2d. High diversity in AOX family compositions was found. While the AOX2 subfamily was not detected in monocots, the AOX1 subfamily has expanded (AOX1a-e) in the large majority of these plants. In addition, Poales AOX1b and 1d were orthologous to eudicots AOX1d and then renamed as AOX1d1 and 1d2. AOX1 or AOX2 losses were detected in some eudicot plants. Several AOX2 duplications (AOX2a-c) were identified in eudicot species, mainly in the asterids. The AOX2b originally identified in eudicots in the Fabales order (soybean, cowpea) was divergent from AOX2a-c showing some specific amino acids with AOX1d and then it was renamed as AOX2d. AOX1d and AOX2d seem to be stress-responsive, facultative and mutually exclusive among species suggesting a complementary role with an AOX1(a) in stress conditions. Based on the data collected, we present a model for the evolutionary history of AOX in angiosperms and highlight specific areas where further research would be most beneficial.
authors.affiliation: Department of Biochemistry and Molecular Biology, Federal University of Ceara, 60455-760 Fortaleza, Ceará, Brazil. Electronic address: helio.costa@ufc.br.
authors.forename: José Hélio
authors.initials: JH
authors.lastname: Costa
authors.affiliation: Department of Biology, Wilfrid Laurier University, Science Building, 75 University Avenue West, Waterloo, Ontario N2L 3C5, Canada.
authors.forename: Allison E
authors.initials: AE
authors.lastname: McDonald
authors.affiliation: EU Marie Curie Chair, ICAAM, University of Évora, Apartado 94, 7002-554 Évora, Portugal.
authors.forename: Birgit
authors.initials: B
authors.lastname: Arnholdt-Schmitt
authors.affiliation: Department of Biochemistry and Molecular Biology, Federal University of Ceara, 60455-760 Fortaleza, Ceará, Brazil.
authors.forename: Dirce
authors.initials: D
authors.lastname: Fernandes de Melo
mesh_terms: D019295:Computational Biology; D019143:Evolution, Molecular; D014644:Genetic Variation; D019684:Magnoliopsida / Q000145:classification / Q000201:enzymology* / Q000235:genetics*; D024101:Mitochondrial Proteins / Q000145:classification* / Q000235:genetics*; D010088:Oxidoreductases / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification* / Q000235:genetics*; D000099188:Alternative Oxidase
chemical_list: D024101:Mitochondrial Proteins; D010088:Oxidoreductases; D010940:Plant Proteins; D000099188:Alternative Oxidase
keywords: Alternative oxidase; Classification; Evolution; Flowering plants; Taxonomic distribution