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MBE Advance Access originally published online on March 28, 2006
Molecular Biology and Evolution 2006 23(6):1180-1191; doi:10.1093/molbev/msk010
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

The Rieske Protein: A Case Study on the Pitfalls of Multiple Sequence Alignments and Phylogenetic Reconstruction

Evelyne Lebrun*, Joanne M. Santini{dagger}, Myriam Brugna*, Anne-Lise Ducluzeau*, Soufian Ouchane{ddagger}, Barbara Schoepp-Cothenet*, Frauke Baymann* and Wolfgang Nitschke*

* Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Biologie Structurale et Microbiologie (IFR), Marseille, France; {dagger} Department of Biology, University College, London WC1E 6BT, United Kingdom; and {ddagger} Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique (UPR 2167), Gif-sur-Yvette, France

E-mail: nitschke{at}ibsm.cnrs-mrs.fr.

Previously published phylogenetic trees reconstructed on "Rieske protein" sequences frequently are at odds with each other, with those of other subunits of the parent enzymes and with small-subunit rRNA trees. These differences are shown to be at least partially if not completely due to problems in the reconstruction procedures. A major source of erroneous Rieske protein trees lies in the presence of a large, poorly conserved domain prone to accommodate very long insertions in well-defined structural hot spots substantially hampering multiple alignments. The remaining smaller domain, in contrast, is too conserved to allow distant phylogenies to be deduced with sufficient confidence. Three-dimensional structures of representatives from this protein family are now available from phylogenetically distant species and from diverse enzymes. Multiple alignments can thus be refined on the basis of these structures. We show that structurally guided alignments of Rieske proteins from Rieske–cytochrome b complexes and arsenite oxidases strongly reduce conflicts between resulting trees and those obtained on their companion enzyme subunits. Further problems encountered during this work, mainly consisting in database errors such as wrong annotations and frameshifts, are described. The obtained results are discussed against the background of hypotheses stipulating pervasive lateral gene transfer in prokaryotes.

Key Words: Rieske protein • phylogeny • lateral gene transfer • indel • bioenergetics


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