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MBE Advance Access published online on March 28, 2006
Molecular Biology and Evolution, 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
Accepted March 9, 2006

Research Article

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

Evelyne Lebrun 1, Joanne M. Santini 2, Myriam Brugna 1, Anne-Lise Ducluzeau 1, Soufian Ouchane 3, Barbara Schoepp-Cothenet 1, Frauke Baymann 1, and Wolfgang Nitschke 1 *

1 Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Biologie Structurale et Microbiologie (IFR..), 31 chemin Joseph-Aiguier, 13402 Marseille Cedex 20, France
2 Department of Biology, University College, Room 524 Darwin Building, Gower Street, London WC1E 6BT, UK
3 Centre de Génétique Moléculaire CNRS (UPR 2167), Bât. 24, avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France

* To whom correspondence should be addressed.
Wolfgang Nitschke, E-mail: nitschke{at}ibsm.cnrs-mrs.fr


  Abstract

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 hotspots substantially hampering multiple alignments. The remaining smaller domain, in contrast, is too conserved to allow distant phylogenies to be deduced with sufficient confidence. 3D 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/cytb 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.

Keywords: Rieske protein; phylogeny; lateral gene transfer; indel; bioenergetics.
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