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Open Access Research article

Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergence

Marina Marcet-Houben1, Giuseppe Marceddu12 and Toni Gabaldón1*

Author Affiliations

1 Comparative Genomics, Centre for Genomics Regulation, Dr. Aiguader, 88, 08003 Barcelona, Spain

2 Dipartamento di Biologia Vegetale, Università Degli Studi di Torino, Viale P.A. Mattioly, 25, 10125 Torino, Italy

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BMC Evolutionary Biology 2009, 9:295  doi:10.1186/1471-2148-9-295

Published: 21 December 2009

Abstract

Background

Oxidative phosphorylation is central to the energy metabolism of the cell. Due to adaptation to different life-styles and environments, fungal species have shaped their respiratory pathways in the course of evolution. To identify the main mechanisms behind the evolution of respiratory pathways, we conducted a phylogenomics survey of oxidative phosphorylation components in the genomes of sixty fungal species.

Results

Besides clarifying orthology and paralogy relationships among respiratory proteins, our results reveal three parallel losses of the entire complex I, two of which are coupled to duplications in alternative dehydrogenases. Duplications in respiratory proteins have been common, affecting 76% of the protein families surveyed. We detect several instances of paralogs of genes coding for subunits of respiratory complexes that have been recruited to other multi-protein complexes inside and outside the mitochondrion, emphasizing the role of evolutionary tinkering.

Conclusions

Processes of gene loss and gene duplication followed by functional divergence have been rampant in the evolution of fungal respiration. Overall, the core proteins of the respiratory pathways are conserved in most lineages, with major changes affecting the lineages of microsporidia, Schizosaccaromyces and Saccharomyces/Kluyveromyces due to adaptation to anaerobic life-styles. We did not observe specific adaptations of the respiratory metabolism common to all pathogenic species.