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Open Access Commentary

A new standard nomenclature for proteins related to Apx and Shroom

Olivier Hagens1, Andrea Ballabio2, Vera Kalscheuer1, Jean-Pierre Kraehenbuhl3, M Vittoria Schiaffino4, Peter Smith5, Olivier Staub6, Jeff Hildebrand7 and John B Wallingford8*

Author affiliations

1 Dept. of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany

2 Telethon Institute of Genetics and Medicine, Naples, Italy

3 Swiss Institute for Experimental Cancer Research and the Institute of Biochemistry, University of Lausanne, Lausanne, Switzerland

4 Dept. of Biotechnology, San Raffaele Scientific Institute, Milan, Italy

5 Dept. of Physiology and Biophysics, University of Alabama at Birmingham, Birmingham, AL, USA

6 Dept. of Pharmacology & Toxicology, University of Lausanne, Lausanne, Switzerland

7 Dept. of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA

8 Dept. of Molecular Cell and Developmental Biology & Institute for Cellular and Molecular Biology, University of Texas, Austin, TX, USA

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Citation and License

BMC Cell Biology 2006, 7:18  doi:10.1186/1471-2121-7-18


The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2121/7/18


Received:29 March 2006
Accepted:14 April 2006
Published:14 April 2006

© 2006 Hagens et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Shroom is a recently-described regulator of cell shape changes in the developing nervous system. This protein is a member of a small family of related proteins that are defined by sequence similarity and in most cases by some link to the actin cytoskeleton. At present these proteins are named Shroom, APX, APXL, and KIAA1202. In light of the growing interest in this family of proteins, we propose here a new standard nomenclature.

Commentary

In 1992, the primary structure of an

    a
pical protein in
    X
enopus
(Apx) was described [1]. Since then, three related proteins have been characterized, namely the human proteins APXL (
    a
pical
    p
rotein
    X
enopus
-like) [2] and KIAA1202 [3] and mouse Shroom [4], named after the mouse mutant phenotype. We now know that the Apx protein of Xenopus is not in fact the orthologue of human APXL. Instead, the protein previously called human APXL2 is the likely homologue of frog Apx, while human APXL is the likely homologue of a Xenopus APXL. In this letter, we report a new standardized nomenclature to eliminate the confusing present naming situation for these proteins (Table 1).

Table 1. New nomenclature for Shroom-related proteins

From global multiple alignments of genomic sequences, it is clear that these proteins are not simply encoded by homologous genes. There are in fact four different proteins in this family, showing similarity in their domains (Table 2), which include a PDZ and two

    A
px/
    S
hrm
    d
omains (ASD1 and ASD2) and putative EVH1 and PDZ binding sites [4]. It should be noted however that Apx lacks the PDZ domain and the EVH1 binding site, APXL lacks a PDZ binding site and KIAA1202 does not contain an obvious ASD1 domain. Therefore, the ASD2 domain seems to be the common denominator among family members.

Table 2. Sequence identity matrix for the four different Shroom proteins which have been characterised experimentally.

Bioinformatics-based searches identified Shroom-related proteins in all chordates examined. In addition, insect genomes, including Drosophila melanogaster, Anopheles gambiae and Apis mellifera, encode a partially related protein containing an ASD2 domain (Table 1). Finally, BLAST searches of the deposited sequences from invertebrate genome projects identify what may be considered Shroom orthologues in both Ciona intestinalis (data not shown) and Strongylocentrotus purpuratus (Table 1). Based on the putative open reading frames and genomic organization, these predicted proteins contain, at least, the N-terminal PDZ domain and the C-terminally positioned ASD2 motif.

To clarify future studies, we propose a unifying nomenclature, emphasizing the relatedness of those proteins (Table 1). We feel that while the founding member is Apx, this name is undesirable as a root for naming this family because it requires that 'Xenopus' would appear in protein names from all species. Instead, we propose that the new nomenclature be based upon the name 'Shroom' as this is now the most thoroughly studied member of the family [4-6]. An Arabic number following 'Shroom' would distinguish between the different proteins. A lower-case letter would distinguish between different protein products encoded by the same locus generated by alternative mRNA processing. According to these rules, we suggest the re-naming presented in Table 1.

Several papers suggest that these related proteins play diverse and important roles in the development of the nervous system and other tissues [2-8]. Future studies will be required to show if sequence similarity among Shroom protein family members is mirrored by conservation of their cellular and molecular function.

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