title: Metazoan remaining genes for essential amino acid biosynthesis: sequence conservation and evolutionary analyses.
abstract: Essential amino acids (EAA) consist of a group of nine amino acids that animals are unable to synthesize via de novo pathways. Recently, it has been found that most metazoans lack the same set of enzymes responsible for the de novo EAA biosynthesis. Here we investigate the sequence conservation and evolution of all the metazoan remaining genes for EAA pathways. Initially, the set of all 49 enzymes responsible for the EAA de novo biosynthesis in yeast was retrieved. These enzymes were used as BLAST queries to search for similar sequences in a database containing 10 complete metazoan genomes. Eight enzymes typically attributed to EAA pathways were found to be ubiquitous in metazoan genomes, suggesting a conserved functional role. In this study, we address the question of how these genes evolved after losing their pathway partners. To do this, we compared metazoan genes with their fungal and plant orthologs. Using phylogenetic analysis with maximum likelihood, we found that acetolactate synthase (ALS) and betaine-homocysteine S-methyltransferase (BHMT) diverged from the expected Tree of Life (ToL) relationships. High sequence conservation in the paraphyletic group Plant-Fungi was identified for these two genes using a newly developed Python algorithm. Selective pressure analysis of ALS and BHMT protein sequences showed higher non-synonymous mutation ratios in comparisons between metazoans/fungi and metazoans/plants, supporting the hypothesis that these two genes have undergone non-ToL evolution in animals.
authors.affiliation: Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil. igorc@ufrj.br.
authors.forename: Igor R
authors.initials: IR
authors.lastname: Costa
authors.affiliation: Department of Computer Science Research, ICube Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie, CNRS/Université de Strasbourg, 11 rue Humann, Strasbourg F-67000, France. thompson@unistra.fr.
authors.forename: Julie D
authors.initials: JD
authors.lastname: Thompson
authors.affiliation: Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil. miguel@icb.ufmg.br.
authors.forename: José Miguel
authors.initials: JM
authors.lastname: Ortega
authors.affiliation: Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil. prosdocimi@bioqmed.ufrj.br.
authors.forename: Francisco
authors.initials: F
authors.lastname: Prosdocimi
mesh_terms: D000095:Acetolactate Synthase / Q000235:genetics / Q000378:metabolism; D000595:Amino Acid Sequence; D000601:Amino Acids, Essential / Q000096:biosynthesis*; D000818:Animals; D050940:Betaine-Homocysteine S-Methyltransferase / Q000235:genetics / Q000378:metabolism; D005075:Biological Evolution; D017124:Conserved Sequence / Q000235:genetics*; D005658:Fungi / Q000201:enzymology / Q000235:genetics; D006801:Humans; D010802:Phylogeny; D010944:Plants / Q000201:enzymology / Q000235:genetics; D012443:Saccharopine Dehydrogenases / Q000235:genetics / Q000378:metabolism
chemical_list: D000601:Amino Acids, Essential; D012443:Saccharopine Dehydrogenases; D050940:Betaine-Homocysteine S-Methyltransferase; D000095:Acetolactate Synthase