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Molecular Evolution of Alternative Oxidase Proteins: A Phylogenetic and Structure Modeling Approach

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Abstract

Alternative oxidases (AOXs) are mitochondrial cyanide-resistant membrane-bound metallo-proteins catalyzing the oxidation of ubiquinol and the reduction of oxygen to water bypassing two sites of proton pumping, thus dissipating a major part of redox energy into heat. Here, the structure of Arabidopsis thaliana AOX 1A has been modeled using the crystal structure of Trypanosoma brucei AOX as a template. Analysis of this model and multiple sequence alignment of members of the AOX family from all kingdoms of Life indicate that AOXs display a high degree of conservation of the catalytic core, which is formed by a four-α-helix bundle, hosting the di-iron catalytic site, and is flanked by two additional α-helices anchoring the protein to the membrane. Plant AOXs display a peculiar covalent dimerization mode due to the conservation in the N-terminal region of a Cys residue forming the inter-monomer disulfide bond. The multiple sequence alignment has also been used to infer a phylogenetic tree of AOXs whose analysis shows a polyphyletic origin for the AOXs found in Fungi and a monophyletic origin of the AOXs of Eubacteria, Mycetozoa, Euglenozoa, Metazoa, and Land Plants. This suggests that AOXs evolved from a common ancestral protein in each of these kingdoms. Within the Plant AOX clade, the AOXs of monocotyledon plants form two distinct clades which have unresolved relationships relative to the monophyletic clade of the AOXs of dicotyledonous plants. This reflects the sequence divergence of the N-terminal region, probably due to a low selective pressure for sequence conservation linked to the covalent homo-dimerization mode.

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Abbreviations

Δ9:

Desaturase

Stearoyl:

Acyl carrier desaturase

AOX:

Alternative oxidase

ML:

Maximum Likelihood

MMO:

Methane–monooxygenase

RNR:

R2 subunit from ribonucleotide reductase

ROS:

Reactive oxygen species

TAO:

Trypanosomal alternative oxidase

AtAOX:

Arabidopsis thaliana AOX 1A

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Acknowledgments

D.S. is supported by FCT post-doctoral fellowship SFRH/BPD/105274/2014 from the European Social Fund and Portuguese Ministério da Educação e Ciência, and by the project “Genomics and Evolutionary Biology” cofinanced by North Portugal Regional Operational Programme 2007/2013 (ON.2-O Novo Norte), under the National Strategic Reference Framework (NSRF), through the European Regional Development Fund (ERDF).

Author Contributions

RP collected the AOXs sequences, carried out the molecular modeling studies and drafted the manuscript. DS carried out the phylogenetic analysis and helped to draft the manuscript. VB carried out ab initio molecular modeling studies and electrostatic potential calculations. RA participated in the interpretation of the results and helped to draft the manuscript. PA and FP conceived the study, participated in its design and coordination and helped to draft the manuscript. All authors read and approved the final manuscript.

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    Authors and Affiliations

    1. Department of Sciences, Roma Tre University, Viale Guglielmo Marconi 446, 00146, Rome, Italy

      Rosa Pennisi, Valentina Brandi, Riccardo Angelini, Paolo Ascenzi & Fabio Polticelli

    2. CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485–661, Vairão, Portugal

      Daniele Salvi

    3. National Institute of Nuclear Physics, Roma Tre Section, 00146, Rome, Italy

      Fabio Polticelli

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    1. Rosa Pennisi
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    2. Daniele Salvi
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    Correspondence to Fabio Polticelli.

    Additional information

    Rosa Pennisi and Daniele Salvi contributed equally to this work.

    Database: AtAOX model data are available in the PMDB database under the accession number PM0080189.

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    Pennisi, R., Salvi, D., Brandi, V. et al. Molecular Evolution of Alternative Oxidase Proteins: A Phylogenetic and Structure Modeling Approach. J Mol Evol 82, 207–218 (2016). https://doi.org/10.1007/s00239-016-9738-8

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