title: Distribution in microbial genomes of genes similar to lodA and goxA which encode a novel family of quinoproteins with amino acid oxidase activity.
abstract: BACKGROUND
  L-Amino acid oxidases (LAOs) have been generally described as flavoproteins that oxidize amino acids releasing the corresponding ketoacid, ammonium and hydrogen peroxide. The generation of hydrogen peroxide gives to these enzymes antimicrobial characteristics. They are involved in processes such as biofilm development and microbial competition. LAOs are of great biotechnological interest in different applications such as the design of biosensors, biotransformations and biomedicine. The marine bacterium Marinomonas mediterranea synthesizes LodA, the first known LAO that contains a quinone cofactor. LodA is encoded in an operon that contains a second gene coding for LodB, a protein required for the post-translational modification generating the cofactor. Recently, GoxA, a quinoprotein with sequence similarity to LodA but with a different enzymatic activity (glycine oxidase instead of lysine-ε-oxidase) has been described. The aim of this work has been to study the distribution of genes similar to lodA and/or goxA in sequenced microbial genomes and to get insight into the evolution of this novel family of proteins through phylogenetic analysis.
  
  
  RESULTS
  Genes encoding LodA-like proteins have been detected in several bacterial classes. However, they are absent in Archaea and detected only in a small group of fungi of the class Agaromycetes. The vast majority of the genes detected are in a genome region with a nearby lodB-like gene suggesting a specific interaction between both partner proteins. Sequence alignment of the LodA-like proteins allowed the detection of several conserved residues. All of them showed a Cys and a Trp that aligned with the residues that are forming part of the cysteine tryptophilquinone (CTQ) cofactor in LodA. Phylogenetic analysis revealed that LodA-like proteins can be clustered in different groups. Interestingly, LodA and GoxA are in different groups, indicating that those groups are related to the enzymatic activity of the proteins detected.
  
  
  CONCLUSIONS
  Genome mining has revealed for the first time the broad distribution of LodA-like proteins containing a CTQ cofactor in many different microbial groups. This study provides a platform to explore the potentially novel enzymatic activities of the proteins detected, the mechanisms of post-translational modifications involved in their synthesis, as well as their biological relevance.
authors.affiliation: Department of Genetics and Microbiology, University of Murcia, Campus de Espinardo, Murcia, 30100, Spain. jonatancristian.campillo@um.es.
authors.forename: Jonatan C
authors.initials: JC
authors.lastname: Campillo-Brocal
authors.affiliation: Department of Genetics and Microbiology, University of Murcia, Campus de Espinardo, Murcia, 30100, Spain. mcv17747@um.es.
authors.forename: María Dolores
authors.initials: MD
authors.lastname: Chacón-Verdú
authors.affiliation: Department of Genetics and Microbiology, University of Murcia, Campus de Espinardo, Murcia, 30100, Spain. patlucel@um.es.
authors.forename: Patricia
authors.initials: P
authors.lastname: Lucas-Elío
authors.affiliation: Department of Genetics and Microbiology, University of Murcia, Campus de Espinardo, Murcia, 30100, Spain. antonio@um.es.
authors.forename: Antonio
authors.initials: A
authors.lastname: Sánchez-Amat
mesh_terms: D000594:Amino Acid Oxidoreductases / Q000145:classification / Q000235:genetics*; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D019295:Computational Biology; D016680:Genome, Bacterial; D053544:Marinomonas / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment
chemical_list: D001426:Bacterial Proteins; D000594:Amino Acid Oxidoreductases; C115925:glycine oxidase