Distribution in microbial genomes of genes similar to lodA and goxA which encode a novel family of quinoproteins with amino acid oxidase activity

Abstract

BackgroundL-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.ResultsGenes 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.ConclusionsGenome 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1455-y) contains supplementary material, which is available to authorized users.

Roles of active site residues in LodA, a cysteine tryptophylquinone dependent ε-lysine oxidase

“…Analysis of the Integrated Microbial Genomes database of genome sequences identified 168 genes from 144 different bacterial genomes that encoded LodA-like proteins [14]. LodA from M. mediterranea was classified as a member of Group IA LodA-like proteins.…”

“…The results of this study demonstrate that these residues in the active site of LodA play multiple roles in binding of lysine and O 2 , catalysis and CTQ biosynthesis. Analysis of the Integrated Microbial Genomes database of genome sequences identified 168 genes from 144 different bacterial sequences that encoded LodA-like proteins [14]. LodA from M. mediterranea was classified as a member of Group IA LodA-like proteins.…”

Insight into the resilience and susceptibility of marine bacteria to T6SS attack by Vibrio cholerae and Vibrio coralliilyticus

“…This species is also known to produce L-amino acid (lysine or glycine) oxidases that are capable of hydrolyzing amino acids present within cells or in the growth media to produce hydrogen peroxide [57]. These enzymes are bactericidal to a wide range of isolates and can be autotoxic [58][59][60]. Although P. flavipulchra achieved a CFU recovery of~1.5 x 10 7 mL -1 after 4 h monoculture incubation (S1 Fig), it is possible that production of these toxic compounds could be triggered by the presence of V. cholerae when grown in co-culture.…”

Roles of Copper and a Conserved Aspartic Acid in the Autocatalytic Hydroxylation of a Specific Tryptophan Residue during Cysteine Tryptophylquinone Biogenesis

“…LodA and GoxA from Marinomonas mediterranea are members of a newly discovered family of enzymes which are oxidases containing CTQ 22 . The gene clusters in which lodA and goxA reside each contain only one other gene, lodB and goxB , each of which is predicted to encode a flavoprotein that is required for expression of active LodA and GoxA, respectively 23, 24 .…”