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Vol. 16, Issue 12, 5736-5748, December 2005

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Sequence and Comparative Genomic Analysis of Actin-related Proteins

Jean Muller ^* , Yukako Oma  , Laurent Vallar , Evelyne Friederich , Olivier Poch ^*, and Barbara Winsor 

^* Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP 163, 67404 Illkirch Cedex, France; Laboratoire de Biologie Moléculaire, d'Analyse Génique et de Modélisation, Centre de Recherche Public-Santé, L-1911, Luxembourg, Luxembourg; and UMR 7156 "Génétique Moléculaire, Génomique et Microbiologie," Institut de Physiologie et de Chimie Biologique, 67084 Strasbourg Cedex, France

Submitted June 8, 2005; Revised September 16, 2005; Accepted September 21, 2005
Monitoring Editor: Thomas Pollard

Actin-related proteins (ARPs) are key players in cytoskeleton activities and nuclear functions. Two complexes, ARP2/3 and ARP1/11, also known as dynactin, are implicated in actin dynamics and in microtubule-based trafficking, respectively. ARP4 to ARP9 are components of many chromatin-modulating complexes. Conventional actins and ARPs codefine a large family of homologous proteins, the actin superfamily, with a tertiary structure known as the actin fold. Because ARPs and actin share high sequence conservation, clear family definition requires distinct features to easily and systematically identify each subfamily. In this study we performed an in depth sequence and comparative genomic analysis of ARP subfamilies. A high-quality multiple alignment of 700 complete protein sequences homologous to actin, including 148 ARP sequences, allowed us to extend the ARP classification to new organisms. Sequence alignments revealed conserved residues, motifs, and inserted sequence signatures to define each ARP subfamily. These discriminative characteristics allowed us to develop ARPAnno (http://bips.u-strasbg.fr/ARPAnno), a new web server dedicated to the annotation of ARP sequences. Analyses of sequence conservation among actins and ARPs highlight part of the actin fold and suggest interactions between ARPs and actin-binding proteins. Finally, analysis of ARP distribution across eukaryotic phyla emphasizes the central importance of nuclear ARPs, particularly the multifunctional ARP4.

The online version of this article contains supplemental material at MBC Online (http://www.molbiolcell.org).

Present address: Department of Biology, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan.

Address correspondence to: Jean Muller (jean.muller{at}igbmc.u-strasbg.fr).

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