A Bioinformatics Classifier and Database for Heme-Copper Oxygen Reductases

Filipa L Sousa,Miguel Teixeira,Manuela M Pereira,Renato J Alves,José B Pereira-Leal,Annalisa Pastore

doi:10.1371/journal.pone.0019117

Filipa L Sousa, Miguel Teixeira + Show 4 more

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https://doi.org/10.1371/journal.pone.0019117

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Abstract

BackgroundHeme-copper oxygen reductases (HCOs) are the last enzymatic complexes of most aerobic respiratory chains, reducing dioxygen to water and translocating up to four protons across the inner mitochondrial membrane (eukaryotes) or cytoplasmatic membrane (prokaryotes). The number of completely sequenced genomes is expanding exponentially, and concomitantly, the number and taxonomic distribution of HCO sequences. These enzymes were initially classified into three different types being this classification recently challenged.MethodologyWe reanalyzed the classification scheme and developed a new bioinformatics classifier for the HCO and Nitric oxide reductases (NOR), which we benchmark against a manually derived gold standard sequence set. It is able to classify any given sequence of subunit I from HCO and NOR with a global recall and precision both of 99.8%. We use this tool to classify this protein family in 552 completely sequenced genomes.ConclusionsWe concluded that the new and broader data set supports three functional and evolutionary groups of HCOs. Homology between NORs and HCOs is shown and NORs closest relationship with C Type HCOs demonstrated. We established and made available a classification web tool and an integrated Heme-Copper Oxygen reductase and NOR protein database (www.evocell.org/hco).

Highlights

Heme-copper Oxygen reductases (HCOs) are the main enzymes responsible for reduction of oxygen to water in respiratory chains
Compilation of data sets The first step in our work was to manually compile a gold standard data set of sequences that we were certain to belong to the Heme-copper oxygen reductases (HCOs) superfamily
We further included Nitric oxide reductases (NOR), as they have been proposed to be evolutionarily related to HCOs [16,40,41]

Summary

Introduction

Heme-copper Oxygen reductases (HCOs) are the main enzymes responsible for reduction of oxygen to water in respiratory chains. HCOs are composed of 3–4 (prokaryotes) and up to 13 subunits (eukaryotes) of which only the catalytic subunit I is common to all HCOs. Subunit I contains at least 12 transmembrane helices and has as cofactors, a low-spin heme, a binuclear centre (high-spin heme and CuB ion) where the reduction of O2 occurs, and a tyrosine residue covalently bound to a histidine residue ligand of the CuB ion (for review see [1,2,3,4]). Subunit I contains at least 12 transmembrane helices and has as cofactors, a low-spin heme, a binuclear centre (high-spin heme and CuB ion) where the reduction of O2 occurs, and a tyrosine residue covalently bound to a histidine residue ligand of the CuB ion (for review see [1,2,3,4]) This tyrosine is proposed to be the source of the fourth electron needed for O2 reduction in HCOs [5,6]. These enzymes were initially classified into three different types being this classification recently challenged

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