Evolution of the eukaryotic ARP2/3 activators of the WASP family: WASP, WAVE, WASH, and WHAMM, and the proposed new family members WAWH and WAML
© Kollmar et al.; licensee BioMed Central Ltd. 2012
Received: 3 November 2011
Accepted: 8 February 2012
Published: 8 February 2012
WASP family proteins stimulate the actin-nucleating activity of the ARP2/3 complex. They include members of the well-known WASP and WAVE/Scar proteins, and the recently identified WASH and WHAMM proteins. WASP family proteins contain family specific N-terminal domains followed by proline-rich regions and C-terminal VCA domains that harbour the ARP2/3-activating regions.
To reveal the evolution of ARP2/3 activation by WASP family proteins we performed a "holistic" analysis by manually assembling and annotating all homologs in most of the eukaryotic genomes available. We have identified two new families: the WAML proteins (WASP and MIM like), which combine the membrane-deforming and actin bundling functions of the IMD domains with the ARP2/3-activating VCA regions, and the WAWH protein (WASP without WH1 domain) that have been identified in amoebae, Apusozoa, and the anole lizard. Surprisingly, with one exception we did not identify any alternative splice forms for WASP family proteins, which is in strong contrast to other actin-binding proteins like Ena/VASP, MIM, or NHS proteins that share domains with WASP proteins.
Our analysis showed that the last common ancestor of the eukaryotes must have contained a homolog of WASP, WAVE, and WASH. Specific families have subsequently been lost in many taxa like the WASPs in plants, algae, Stramenopiles, and Euglenozoa, and the WASH proteins in fungi. The WHAMM proteins are metazoa specific and have most probably been invented by the Eumetazoa. The diversity of WASP family proteins has strongly been increased by many species- and taxon-specific gene duplications and multimerisations. All data is freely accessible via http://www.cymobase.org.
KeywordsARP2/3 activation WASP family proteins WASP WAVE WASH WHAMM
Eukaryotes mediate many cellular processes, including phagocytosis, intracellular trafficking, cell division, and cell locomotion, by remodelling of the actin cytoskeleton [1–4]. In many cases, signals from Rho family G-proteins activate proteins of the WASP family (WASP, Wiskott-Aldrich syndrome protein), which stimulate the actin filament branching activity of the ARP2/3 complex  resulting in specialised networks of actin filaments [6, 7]. The ARP2/3 complex consists of two actin-related proteins, Arp2 and Arp3, and five additional subunits [5, 8]. The ARP2/3 complex alone is very inefficient in nucleating actin filaments but becomes activated when binding to the sites of existing actin filaments. In addition, it needs to bind to so-called nucleation promoting factors (NPFs). NPFs of the WASP family belong to class I NPFs and have characteristic VCA domains at their C-termini consisting of one or more WH2 domains (V; W ASP h omology 2 domain, also known as verprolin homology domain), a central domain (C; also known as cofilin homology or connector domain), and an acidic (A) C-terminal domain. While the WH2 domains bind G-actin the CA domains bind to and activate the ARP2/3 complex.
The founding member of the WASP family was the WASP protein, which is deficient in Wiskott-Aldrich syndrome. The Wiskott-Aldrich syndrome is an X-linked human genetic disorder that leads to a variety of defects in the immune system, including thrombocytopenia, compromised immune function, and susceptibility to leukemias and lymphomas [9–11]. In a genetic screen for second-site suppressors of a mutation in one of the cAMP receptors, another protein that showed significant homology to WASP, called Scar, was identified in Dictyostelium discoideum. At the same time the so-called WAVE-1 protein (WASP-family verprolin-homologous protein-1) was identified in a database search for proteins with sequence homology to the VCA region . The name Scar has subsequently been used for the Dictyostelium and the plant homologs, while WAVE has been used for all metazoan family members.
WASP proteins are multi-domain proteins consisting of an N-terminal WH1 domain, a basic domain containing many lysine and arginine residues, a GTPase binding domain (GBD) consisting of a CRIB motif (for Cdc42/Rac interactive binding) followed by an autoinhibitory domain, a poly-proline region, and the VCA domain. The WASP protein by itself is inactive through intramolecular binding of the C domain to the autoinhibitory domain . Binding of G-proteins to the GBD domain releasing the intramolecular link activates the WASP proteins. A comparison of proteins of the WASP and the WAVE family shows that WAVE shares many of the WASP domains, including the polyproline rich region and the VCA domain. Unlike WASP, WAVE family members do not contain a GBD domain and they have a novel protein region instead of the WH1 domain, termed WAVE homology domain (WHD). WASP forms a constitutive complex with WIP (WASP interacting protein), which binds to the WH1 domain and has been shown to stabilize WASP . Three WIP homologs have been identified in the human genome , and all seem to be able to bind to the two WASP homologs. In contrast, WAVE proteins form a 400 kDa heteropentameric assembly called the WAVE regulatory complex that consists of WAVE, a protein from the CYFIP family (e.g. SRA1), NAP1, ABI, and HSPC300 [17, 18]. The three mammalian WAVE homologs seem to participate in the same protein complex and thus differences between them are likely to be at the level of tissue distribution .
In the last years, several further proteins have been identified that also activate the ARP2/3 complex like WASH (Wiskott-Aldrich syndrome protein and Scar homolog) , WHAMM (WASP homolog associated with actin, membranes, and microtubules) , and JMY , which is a WHAMM homolog . Still, there is only limited knowledge about their structure, sequence homology, and phylogenetic distribution. Early analyses have revealed that WHAMM might be restricted to vertebrates , while WASH seems to be more widely distributed [19, 22]. Like WAVE, WASH functions in a heteropentameric complex containing Strumpelin, FAM21, SWIP, and CCDC53, which show some sequence homology to the corresponding proteins of the WAVE complex .
Very recently, the genomes of some representative eukaryotes have been analysed with respect to their WASP family protein content . However, the analysis of motor proteins in sequenced insects  has shown that it is essential not only to analyse the genomes of representative members of the main eukaryotic taxa but to also analyse the genomes of very closely related species, because not even those might contain the same set of homologs. In addition, it is essential to search directly in the respective genome sequences and to manually reconstruct potential homologs because datasets of predicted proteins are far from being complete. In those automatically generated datasets many proteins are missing at all, and most of the predicted proteins contain mispredicted intronic sequence and miss exons thus hindering the identification of all homologs. Especially in the case of the WASP family proteins, that contain many very short domains and sequence motifs, mispredicted exons easily result in missing domains and thus misleading hypotheses about potential physiological functions. Here we performed a search for WASP family proteins in the available genome assemblies of more than 400 eukaryotes. All sequences were identified at the genomic DNA level and the genes reconstructed manually.
Identification and assembly of WASP family proteins
The WASP family proteins contain many but very short sequence motifs and domains. These domains are not only characteristic for WASP proteins but are also part of proteins from other families like the WHD domain, that is shared by the Nance-Horan syndrome protein (NHS), the WH1 domain, that is shared by the Ena/VASP protein family, the WH2 domain, that is contained for example in Spire, Cobl, missing-in-metastasis (MIM), and WIP, and the CA domains, that are shared for example by certain coronins and class-1 myosins. Given such short sequence motifs a few missing residues could prevent their identification and lead to a wrong classification or even removal from the dataset. Vice versa, the identification of just one or two of the domains contained in one of the WASP family proteins and subsequent thorough analysis of the genomic region could lead to the identification of so far unrecognized or very divergent members of the WASP family. While this subfamily categorization is mainly based on domain organisation patterns, the classification of the duplicated WASP family genes into subgroups is based on the phylogenetic analysis of the corresponding protein sequences. Thus, it is of major importance to obtain the best sequence data possible and to create the most accurate sequence alignment. We had to manually assemble and annotate all WASP protein family sequences used in this study mainly for two reasons. A) Automatic gene predictions are error-prone and even those gene predictions are only available for a small subset of all sequenced eukaryotic genomes . B) Because all WASP family genes encode long unstructured and low-complexity regions (for example the poly-proline regions), and the acidic C-termini (the A domain, also of low complexity) are often encoded by a single exon, the automatic gene predictions contain many mispredicted exons/introns and unrecognised N-terminal/C-terminal parts. Most likely due to the long low-complexity regions, only a few full-length mRNA/cDNA sequences for WASP family proteins are available. If partial cDNA/EST clones were found then those encoded in most cases the N-terminal WH1, WHD, WAHD, or WMD domains. The eukaryotic genomes were analysed in an iterative search process, meaning that those genomes, for which the WASP family proteins could not unambiguously assembled in the first instance, were reanalysed as soon as further data was added to the multiple sequence alignments. In this way the completeness of the search for WASP family proteins and the accuracy of the gene assembly and annotation have continuously been re-evaluated and improved. In addition to manually assembling all sequences, the multiple sequence alignments of the WASP sequences have been created and were maintained and improved manually (Additional file 1).
Pseudogenes without sequence
WGS- and EST-projects
Classification and analysis of the WASP protein family
Several species encode multiple WASP homologs. To reveal subfamily relationships fragmented sequences and the unique regions were omitted from the multiple sequence alignment that was used to generate the phylogenetic tree (Supplementary Information). The tree shows that there have been many species-specific WASP duplications (e.g. in Trichomonas vaginalis, Dictyostelium fasciculatum, Trichoplax adhaerens, Saccoglossus kowalevski) and multiplications (e.g. in Naegleria gruberi, Acytostelium subglobosum, Acanthamoeba castellanii) but also two clade-specific duplications, one of which happened in the ancestor of the Mucoromycotina, and one at the onset of the vertebrates resulting in WASP and N-WASP. The duplication and subsequent subfunctionalization of the WASP homologs at the origin of the vertebrates is most probably the result of the two whole genome duplications (2R) that happened shortly after the emergence of the vertebrates . WASP (but not N-WASP) has been lost in birds, and duplicates of both WASP and N-WASP are found in fish genomes. The additional duplications in fish genomes are probably the result of another whole genome duplication that happened at the origin of the Actinopterygii branch . Some of the fish encode a further WASP homolog that is much shorter than the other WASP types and misses the basic, the central and the acidic domain (Figure 1, Orn S-WASP). Therefore, we suggest naming these WASP homologs S-WASP (short WASP). Similarly, some of the sequenced Basidiomycotes encode one or two further WASP homologs that do not encode a poly-proline rich region and a VCA domain. Although these short WASPs in fish and Basidiomycotes do not encode CA and VCA domains, respectively, that are the basis of ARP2/3-complex activation and therefore a requirement of WASP protein family membership, we would suggest to also group these proteins to the WASP family because of the strong sequence homology to the WH1 and CRIB/WAID domains of the long WASPs. Thus, they were most likely derived from WASP duplications followed by domain loss events. Trichomonas vaginalis encodes two special WASP homologs that have two (Tv WASP_B) and three (Tv WASP_A) tandem repeats of the poly-proline rich region and the VC domain but that miss the C-terminal acidic A domain (Figure 1). In comparison to a previous analysis  we were able to identify more WASP homologs even in species, which had been analysed before, and to complete sequences for which domains had been missing before. First, we also identified WASP homologs in Trichomonas vaginalis and the Haptophyte species Emiliania huxleyi. However, we found only one WASP homolog in Caenorhabditis elegans and all other nematode species. Second, there are invertebrate WASP homologs that do contain only one WH2 domain, like all Acoelomata WASPs sequenced so far, the tunicate Oikopleura dioica WASP, and one of the Trichoplax adhaerens homologs, Tia WASP_B. Our extensive analysis also allowed us to identify species outside the metazoa that do encode WASP homologs containing two WH2 domains like Sphaeroforma arctica, which belongs to the Fungi/Metazoa incertae sedis branch.
Classification and analysis of the WAVE protein family
Classification and analysis of the WASH protein family
Classification and analysis of the WHAMM protein family
We have also found a WHAMM homolog in the Hydrozoa species Clytia hemisphaerica, which is outside Bilaterians and thus extends a previously proposed origin of WHAMM homologs . The WHAMM homolog of Strongylocentrotus purpuratus has been proposed to contain a tandem N-terminal WMD and coiled-coil region , but this is most likely an artefact from the genome assembly. In fact, the duplicated part (WMD domain and coiled-coil region) is surrounded by stretches of 'N' bases and has most probably misleadingly been placed inside the supercontig containing the WHAMM gene during the genome assembly process. The Strongylocentrotus genome is one of the worst assemblies available because of the high polymorphism between the two alleles. Therefore, not even the well-conserved myosin family proteins could unambiguously be annotated .
It has been reported initially  and subsequently adopted in recent reviews [4, 30] that class-2 WHAMM homologs (JMY) contain three WH2 domains. The region comprising the supposed first WH2 domain is highly conserved in all vertebrates (Figure 7). However, this region does not show homology to the WH2 regions of the WASP family proteins (see also below) that are characterised by a highly conserved pattern ([VILM]-[LM]-[ASED]-[ASDEQ]-[IL]-[KRQ]-x10-[L]-[KR]-[KR]-[VTA]). The prediction of a third WH2 domain in class-2 WHAMM homologs is thus most likely an artefact, or the respective region would comprise an extremely unusual WH2 domain. There is no experimental data available supporting this motif being a true WH2 domain.
Identification and domain organisation of the WAWH and WAML families
Because all amoeba genomes contain at least one WASP gene we were searching for WASP homologs in Entamoebae for a long time. Low-scoring hits were only obtained for the WH2 domain, and because this domain is very short (Entamoebae genes rarely contain introns so that we would have expected longer hits if there would be homology to neighbouring regions, which we would expect for WASP homologs) and also present in many other proteins we did not analyse these hits further in the first instance. As soon as further amoebozoan genomes became available we always searched the Entamoeba genomes again for WASP homologs. As we started to inspect the short hits for the WH2 domains further, the corresponding assembled genes revealed a similar domain organisation as WASP proteins starting with the WAID domain (Figure 8). Surprisingly, five to seven proteins with a similar domain organisation have been found in the three sequenced Entamoeba genomes. In contrast to WASP proteins, these proteins each encode an IMD domain (IRSp53/MIM homology domain) at the N-terminus and lack the CRIB motif. IMD domains are found in proteins of the IRSp53 (insulin receptor tyrosine kinase substrate p53) and proteins of the MIM (missing-in-metastasis) family, for example. The MIM family proteins additionally contain proline-rich regions and a C-terminal WH2 domain (in one of the alternatively spliced transcripts). We therefore suggest calling these new types of WASP family proteins WAML (WASP and MIM like). One subclass of the WAML proteins comprises a short version that misses the PPR and VCA region.
Comparison of the WH2 and central domains
The acidic C-termini of the WASP family proteins are thought to mediate ARP2/3 binding. Most acidic domains contain a tryptophan residue as last coding residues or close to the terminus. While phenylalanines instead of the tryptophans have been reported to be unique to invertebrate WHAMM homologs  we have identified WASP homologs, which contain F's instead of W's (e.g. in Acoelomata), WASH homologs without any hydrophobic residues in the A domain (e.g. Leishmania WASH proteins), and many WASP and WAVE homologs that contain both a tryptophan and a phenylalanine/tyrosine, both separated by variable numbers of acidic residues. Thus, it remains an open question whether a tryptophan or just an aromatic residue is needed for proper function, and whether there is a difference in encoding only a tryptophan or an additional phenylalanine/tyrosine.
Alternative splice forms of WASP family proteins
Surprisingly, alternative splice forms of WASP family proteins have not been reported yet except for a neural-specific splicing of WASP through that a truncated WASP protein is generated lacking exon-2 . Exon-2 encodes the N-terminal five ß-strands of the seven ß-strands of the WH1 domain  and it seems impossible that a functional and folded WH1 domain could be formed without the exon-2 encoded residues. We have extensively searched all cDNA/EST databases available of all species for clones encoding the reported exon-2 deletion but have not found any. Interestingly, none of the four to nine isoforms of the three mammalian homer proteins, that also contain an N-terminal WH1 domain, encodes a sequence in which part of the WH1 domain is missing . The exon-2 deletion might thus be a very limited event, so that it has not yet been included in cDNA/EST libraries (although dozens of cDNA/EST clones from many species exist for the full-length WH1 domain), or it might be an experimental artefact. The available data argues for the latter.
This situation is in sharp contrast to other proteins sharing WASP domains like the NHS proteins or the homer proteins. The Nance-Horan syndrome protein has an N-terminal WHD domain like the WAVE proteins, is alternatively spliced, and encodes at least five isoforms . The three mammalian homer family proteins have N-terminal WH1 domains (EVH1 domain) like the Ena/VASP and the WASP proteins and encode four to nine different isoforms .
Initially, the WASP family of proteins consisted of the WASP proteins and the WAVE proteins [7, 38]. Both share the ability to catalyze actin filament branching via activation of the ARP2/3 complex but are localized and regulated differently. The shared function is encoded in a similar subsequent set of domains located at the C-termini. A poly-proline or proline-rich region is followed by a WH2 domain, a central domain, and a C-terminal acidic domain that together are called the VCA domain. This set of domains has very recently been identified in further proteins, WASH , WHAMM , and JMY  that have also been shown to activate the ARP2/3 complex. The common characteristic of all WASP family proteins is thus the VCA domain following a proline rich region. The aforementioned proteins are regarded as subfamilies, and newly identified proteins containing a VCA domain but different N-terminal domains should be regarded as new subfamilies. The N-terminal domains defining the subfamilies are also present in other proteins (for example the WH1 domain is present in Ena/VASP proteins, the WHD domain in NHS proteins, and the IMD domain in IRSp53 and missing-in-metastasis proteins) and therefore most WASP family proteins also belong to other protein families.
The analysis of most eukaryotic sequenced genomes available allowed us to reconstruct the evolution of the WASP family members in the different branches of the eukaryotic tree and to identify and characterise new subfamilies. It is very important to analyse as many genomes as possible because even closely related species might contain different sets of the WASP subfamilies and subfamily members. For example, the Entamoeba species Entamoeba histolytica and Entamoeba dispar both contain one WASH protein, and three WAWH and five WAML homologs, while the close relative Entamoeba invadens has lost WASH but instead encodes three WAWH and seven WAML homologs. Another example represents the green algae species sequenced by today. For the Ostreococcus species a WASH homolog could be identified, while WASP family homologs could not be identified in Volvox carteri and Chlamydomonas reinhardtii although both have ARP2/3, and the Micromonas and Chlorella species do not have the ARP2/3 complex anymore and thus do not encode any WASP family protein. Therefore, it is not sufficient to only analyse a few sample genomes of each of the main eukaryotic kingdoms as it has been done in previous analyses [22, 39]. Of course, sequencing of further genomes might also lead to a revision of the conclusions drawn below.
For species for which we were not able to identify any WASP family protein homolog we searched for all actin and actin-related protein genes. If these species also did not contain members of the ARP2 and ARP3 subfamilies the absence of ARP2/3-complex activating proteins was confirmed. However, we identified ARP2 and ARP3 in some species for which we were not able to find WASP family protein members yet. Based on the comparison of about 2,200 homologs of actin-related proteins the identification of ARP2 and ARP3 homologs is straightforward (data not shown). This is in contrast to the search for homologs of the other four members of the pentameric WAVE complex. Each of the other proteins of the WAVE complex is part of a protein family whose members are also incorporated into the WASH complex . In addition, the WAVE complex subunits also interact with the NHS (Nance-Horan syndrome) proteins . The Nance-Horan syndrome is, like the Wiskott-Aldrich syndrome, linked to the X-chromosome. The protein causing the syndrome, the NHS protein, contains an N-terminal WHD domain like the WAVE proteins [37, 40]. Three NHS family members exist in humans, NHS, NHSL1, and NHSL2, and it could be shown that NHS also regulates actin remodelling and cell morphology . Interestingly, the WHD domain of NHS interacts with all three members of the Abi protein family, Nap1, Sra1, and HSPC300 , as has been shown for the mammalian WAVE proteins [17, 18, 41]. Thus, if we had wanted to confirm the presence or absence of WAVE or WASH proteins in certain species by searching for the presence of the other members of the WAVE and WASH complexes we would have had to perform an exhaustive analysis of all members of the complexes as well as the NHS proteins. This is, however, out of the scope of this analysis, and we therefore rely on our experience in WASP protein family identification to approve their presence or absence.
Our analysis shows that the most ancient eukaryote must have contained a WASP, a WAVE, and a WASH homolog, because homologs of these subfamilies have been found in all major eukaryotic branches (Figure 12). Some species contain extended repertoires of WASP family proteins like Trichomonas vaginalis encoding eleven WAVE homologs. In contrast, the Euglenozoa contain only a WASH homolog, while the Stramenopiles encode either a single WASH or a single WAVE protein, and the Haptophyceae Emiliania huxleyi contains only a WASP homolog. The ARP2/3 complex, and thus WASP family proteins, is absent in Diplomonoda, Rhodophyta, Bacillariophyta, and Apicomplexa. The Stramenopiles Blastocystis hominis contains the ARP2/3 complex, but WASP family proteins could not be found in its genome. Here, proteins from class II NPFs might regulate the ARP2/3 complex.
We could show that most eukaryotes encode a rich repertoire of WASP family proteins to regulate the ARP2/3 dependent remodelling of the actin cytoskeleton. Surprisingly, alternative splice variants could be identified for only a single WASP homolog from the sea hare Aplysia californica. This is in strong contrast to other actin-binding proteins that have the same N-terminal domains like Ena/VASP (N-terminal WH1 domain), NHS (N-terminal WHD domain), and MIM (N-terminal IMD domain). Single transcripts are most probably a characteristic of the WASP family proteins because extensive cDNA data is already available. Given the recent identification of two new WASP protein subfamilies, WASH and WHAMM, and of the two new subfamilies described here, WAML and WAWH, and in the prospect of many upcoming genome sequences the WASP protein family is expected to grow further.
Identification and annotation of the WASP family genes
WASP family genes have been identified in TBLASTN searches of the completed or almost completed genomes of 529 organisms starting with the protein sequences of the human homologs. Species outside the metazoans that were expected to encode very divergent homologs were searched with many different homologs and every single hit showing homology to either the C-terminal domains (WH2, central, and acidic domains), the GBD domain, or the N-terminal domains was analysed in detail. During this search, the new WASP subfamilies WAWH and WAML were identified based on the homology of their GBD domains to those from WASP proteins. All hits were manually analysed at the genomic DNA level. The correct coding sequences were identified with the help of the multiple sequence alignment of the respective protein family. As the amount of sequences increased (especially the number of sequences of taxa with few representatives), many of the initially predicted sequences were reanalysed to correctly identify all exon borders. Where possible, EST data has been analysed to help in the annotation process. In addition to the analysis of these large-scale sequencing projects, all WASP family genes in the "nr" database at NCBI have been collected and reanalysed. All sequence related data (names, corresponding species, GenBank ID's, alternative names, corresponding reference publications, domain predictions, and sequences) and references to genome sequencing centers are available through the CyMoBase (http://www.cymobase.org, ).
Generating the multiple sequence alignment
The multiple sequence alignments of the WASP family proteins have been built and extended during the process of annotating and assembling new sequences. The initial alignments have been generated from the first 10 non-validated sequences obtained from NCBI using the ClustalW software with standard settings . During the following correction of the sequences (removing wrongly annotated sequences and filling gaps) the alignment has been adjusted manually. Subsequently, every newly predicted sequence has been preliminary aligned to its supposed closest relative using ClustalW, the aligned sequence added to the multiple sequence alignment of the respective WASP family, and the alignment adjusted manually during the subsequent sequence validation process. Still, many gaps in sequences derived from low-coverage genomes remained. In those cases, the integrity of the exons surrounding the gaps has been maintained (gaps in the genomic sequence are reflected as gaps in the multiple sequence alignment). The unique poly-proline regions are completely divergent in sequence and length and could therefore only be aligned manually. The VCA domains are interrupted by linkers of different lengths, especially in WASH proteins, and were therefore also aligned manually. The sequence alignments of the WASP family proteins can be obtained from CyMoBase, and are also included in Additional file 1.
Computing and visualizing the phylogenetic trees
The phylogenetic trees were built based on the manually constructed and maintained multiple sequence alignments of the concatenated WASP protein family characteristic N-terminal and VCA (without linker) domains using two different methods: 1. Maximum likelihood (ML) using the PROTMIXBLOSUM62 amino acid model and bootstrapping (1,000 replicates) using RAxML . 2. Posterior probabilities were generated using MrBayes v3.1.2 . Two independent runs with 4,000,000 generations, four chains, and a random starting tree were computed using the mixed amino-acid option. From the 1,000th generation MrBayes exclusively used the JTT model  in both runs. Trees were sampled every 1,000th generation and the first 100,000 of the trees were discarded as "burn-in" before generating a consensus tree. Phylogenetic trees were visualized with FigTree (http://tree.bio.ed.ac.uk/software/figtree).
Availability of supporting data
The data sets supporting the results of this article are included within the article (and its additional files).
Cdc42/Rac interactive binding
GTPase binding domain
ediating and regulatory protein
WASH homology domain
WASP autoinhibitory domain
WASP and MIM like
Wiskott-Aldrich syndrome protein and Scar homolog
Wiskott-Aldrich syndrome protein
WASP-family verprolin-homologous protein
WASP without WH1 domain
WASP homology domain 1
WASP homology domain 2
WASP homolog associated with actin, membranes, and microtubules
WAVE homology domain, WIP: WASP-interacting protein
WHAMM membrane interaction domain.
We thank the many sequencing centers and funding agencies for making unpublished sequence data available. Also, we want to thank Dr. Florian Odronitz and Björn Hammesfahr for their help with maintaining and developing CyMoBase.
- Le Clainche C, Carlier MF: Regulation of actin assembly associated with protrusion and adhesion in cell migration. Physiol Rev. 2008, 88 (2): 489-513. 10.1152/physrev.00021.2007.PubMedView ArticleGoogle Scholar
- Chhabra ES, Higgs HN: The many faces of actin: matching assembly factors with cellular structures. Nat Cell Biol. 2007, 9 (10): 1110-1121. 10.1038/ncb1007-1110.PubMedView ArticleGoogle Scholar
- Firat-Karalar EN, Welch MD: New mechanisms and functions of actin nucleation. Curr Opin Cell Biol. 2011, 23 (1): 4-13. 10.1016/j.ceb.2010.10.007.PubMedPubMed CentralView ArticleGoogle Scholar
- Campellone KG, Welch MD: A nucleator arms race: cellular control of actin assembly. Nat Rev Mol Cell Biol. 2010, 11 (4): 237-251.PubMedPubMed CentralView ArticleGoogle Scholar
- Pollard TD: Regulation of actin filament assembly by Arp2/3 complex and formins. Annu Rev Biophys Biomol Struct. 2007, 36: 451-477-PubMedView ArticleGoogle Scholar
- Chesarone MA, Goode BL: Actin nucleation and elongation factors: mechanisms and interplay. Curr Opin Cell Biol. 2009, 21 (1): 28-37. 10.1016/j.ceb.2008.12.001.PubMedPubMed CentralView ArticleGoogle Scholar
- Takenawa T, Suetsugu S: The WASP-WAVE protein network: connecting the membrane to the cytoskeleton. Nat Rev Mol Cell Biol. 2007, 8 (1): 37-48. 10.1038/nrm2069.PubMedView ArticleGoogle Scholar
- Goley ED, Welch MD: The ARP2/3 complex: an actin nucleator comes of age. Nat Rev Mol Cell Biol. 2006, 7 (10): 713-726. 10.1038/nrm2026.PubMedView ArticleGoogle Scholar
- Ochs HD, Filipovich AH, Veys P, Cowan MJ, Kapoor N: Wiskott-Aldrich syndrome: diagnosis, clinical and laboratory manifestations, and treatment. Biol Blood Marrow Transplant. 2008, 15 (1 Suppl): 84-90.Google Scholar
- Notarangelo LD, Miao CH, Ochs HD: Wiskott-Aldrich syndrome. Curr Opin Hematol. 2008, 15 (1): 30-36. 10.1097/MOH.0b013e3282f30448.PubMedView ArticleGoogle Scholar
- Kirchhausen T, Rosen FS: Disease mechanism: unravelling Wiskott-Aldrich syndrome. Curr Biol. 1996, 6 (6): 676-678. 10.1016/S0960-9822(09)00447-3.PubMedView ArticleGoogle Scholar
- Bear JE, Rawls JF, Saxe CL: SCAR, a WASP-related protein, isolated as a suppressor of receptor defects in late Dictyostelium development. J Cell Biol. 1998, 142 (5): 1325-1335. 10.1083/jcb.142.5.1325.PubMedPubMed CentralView ArticleGoogle Scholar
- Miki H, Suetsugu S, Takenawa T: WAVE, a novel WASP-family protein involved in actin reorganization induced by Rac. EMBO J. 1998, 17 (23): 6932-6941. 10.1093/emboj/17.23.6932.PubMedPubMed CentralView ArticleGoogle Scholar
- Kim AS, Kakalis LT, Abdul-Manan N, Liu GA, Rosen MK: Autoinhibition and activation mechanisms of the Wiskott-Aldrich syndrome protein. Nature. 2000, 404 (6774): 151-158. 10.1038/35004513.PubMedView ArticleGoogle Scholar
- de la Fuente MA, Sasahara Y, Calamito M, Anton IM, Elkhal A, Gallego MD, Suresh K, Siminovitch K, Ochs HD, Anderson KC, et al: WIP is a chaperone for Wiskott-Aldrich syndrome protein (WASP). Proc Natl Acad Sci USA. 2007, 104 (3): 926-931. 10.1073/pnas.0610275104.PubMedPubMed CentralView ArticleGoogle Scholar
- Ramesh N, Geha R: Recent advances in the biology of WASP and WIP. Immunol Res. 2009, 44 (1-3): 99-111. 10.1007/s12026-008-8086-1.PubMedView ArticleGoogle Scholar
- Stovold CF, Millard TH, Machesky LM: Inclusion of Scar/WAVE3 in a similar complex to Scar/WAVE1 and 2. BMC Cell Biol. 2005, 6 (1): 11-10.1186/1471-2121-6-11.PubMedPubMed CentralView ArticleGoogle Scholar
- Eden S, Rohatgi R, Podtelejnikov AV, Mann M, Kirschner MW: Mechanism of regulation of WAVE1-induced actin nucleation by Rac1 and Nck. Nature. 2002, 418 (6899): 790-793. 10.1038/nature00859.PubMedView ArticleGoogle Scholar
- Linardopoulou EV, Parghi SS, Friedman C, Osborn GE, Parkhurst SM, Trask BJ: Human subtelomeric WASH genes encode a new subclass of the WASP family. PLoS Genet. 2007, 3 (12): e237-10.1371/journal.pgen.0030237.PubMedPubMed CentralView ArticleGoogle Scholar
- Campellone KG, Webb NJ, Znameroski EA, Welch MD: WHAMM is an Arp2/3 complex activator that binds microtubules and functions in ER to Golgi transport. Cell. 2008, 134 (1): 148-161. 10.1016/j.cell.2008.05.032.PubMedPubMed CentralView ArticleGoogle Scholar
- Zuchero JB, Coutts AS, Quinlan ME, Thangue NB, Mullins RD: p53-cofactor JMY is a multifunctional actin nucleation factor. Nat Cell Biol. 2009, 11 (4): 451-459. 10.1038/ncb1852.PubMedPubMed CentralView ArticleGoogle Scholar
- Veltman DM, Insall RH: WASP family proteins: their evolution and its physiological implications. Mol Biol Cell. 2010, 21 (16): 2880-2893. 10.1091/mbc.E10-04-0372.PubMedPubMed CentralView ArticleGoogle Scholar
- Jia D, Gomez TS, Metlagel Z, Umetani J, Otwinowski Z, Rosen MK, Billadeau DD: WASH and WAVE actin regulators of the Wiskott-Aldrich syndrome protein (WASP) family are controlled by analogous structurally related complexes. Proc Natl Acad Sci USA. 2010, 107 (23): 10442-10447. 10.1073/pnas.0913293107.PubMedPubMed CentralView ArticleGoogle Scholar
- Odronitz F, Becker S, Kollmar M: Reconstructing the phylogeny of 21 completely sequenced arthropod species based on their motor proteins. BMC Genomics. 2009, 10: 173-10.1186/1471-2164-10-173.PubMedPubMed CentralView ArticleGoogle Scholar
- Odronitz F, Kollmar M: Drawing the tree of eukaryotic life based on the analysis of 2,269 manually annotated myosins from 328 species. Genome Biol. 2007, 8 (9): R196-10.1186/gb-2007-8-9-r196.PubMedPubMed CentralView ArticleGoogle Scholar
- Kurtzman CP: Phylogeny of the ascomycetous yeasts and the renaming of Pichia anomala to Wickerhamomyces anomalus. Antonie Van Leeuwenhoek. 2011, 99 (1): 13-23. 10.1007/s10482-010-9505-6.PubMedView ArticleGoogle Scholar
- Van de Peer Y, Maere S, Meyer A: 2R or not 2R is not the question anymore. Nat Rev Genet. 2010, 11 (2): 166-PubMedView ArticleGoogle Scholar
- Steinke D, Hoegg S, Brinkmann H, Meyer A: Three rounds (1R/2R/3R) of genome duplications and the evolution of the glycolytic pathway in vertebrates. BMC Biol. 2006, 4: 16-10.1186/1741-7007-4-16.PubMedPubMed CentralView ArticleGoogle Scholar
- Padrick SB, Rosen MK: Physical mechanisms of signal integration by WASP family proteins. Annu Rev Biochem. 2010, 79: 707-735. 10.1146/annurev.biochem.77.060407.135452.PubMedPubMed CentralView ArticleGoogle Scholar
- Rottner K, Hanisch J, Campellone KG: WASH, WHAMM and JMY: regulation of Arp2/3 complex and beyond. Trends Cell Biol. 2010, 20 (11): 650-661. 10.1016/j.tcb.2010.08.014.PubMedView ArticleGoogle Scholar
- Dominguez R: Actin filament nucleation and elongation factors-structure-function relationships. Crit Rev Biochem Mol Biol. 2009, 44 (6): 351-366. 10.3109/10409230903277340.PubMedPubMed CentralView ArticleGoogle Scholar
- Lee SH, Kerff F, Chereau D, Ferron F, Klug A, Dominguez R: Structural basis for the actin-binding function of missing-in-metastasis. Structure. 2007, 15 (2): 145-155. 10.1016/j.str.2006.12.005.PubMedPubMed CentralView ArticleGoogle Scholar
- Dominguez R: The beta-thymosin/WH2 fold: multifunctionality and structure. Ann N Y Acad Sci. 2007, 1112: 86-94. 10.1196/annals.1415.011.PubMedView ArticleGoogle Scholar
- Le Page Y, Demay F, Salbert G: A neural-specific splicing event generates an active form of the Wiskott-Aldrich syndrome protein. EMBO Rep. 2004, 5 (9): 895-900. 10.1038/sj.embor.7400239.PubMedPubMed CentralView ArticleGoogle Scholar
- Volkman BF, Prehoda KE, Scott JA, Peterson FC, Lim WA: Structure of the N-WASP EVH1 domain-WIP complex: insight into the molecular basis of Wiskott-Aldrich Syndrome. Cell. 2002, 111 (4): 565-576. 10.1016/S0092-8674(02)01076-0.PubMedView ArticleGoogle Scholar
- Shiraishi-Yamaguchi Y, Furuichi T: The Homer family proteins. Genome Biol. 2007, 8 (2): 206-10.1186/gb-2007-8-2-206.PubMedPubMed CentralView ArticleGoogle Scholar
- Brooks SP, Coccia M, Tang HR, Kanuga N, Machesky LM, Bailly M, Cheetham ME, Hardcastle AJ: The Nance-Horan syndrome protein encodes a functional WAVE homology domain (WHD) and is important for co-ordinating actin remodelling and maintaining cell morphology. Hum Mol Genet. 2010, 19 (12): 2421-2432. 10.1093/hmg/ddq125.PubMedPubMed CentralView ArticleGoogle Scholar
- Millard TH, Sharp SJ, Machesky LM: Signalling to actin assembly via the WASP (Wiskott-Aldrich syndrome protein)-family proteins and the Arp2/3 complex. Biochem J. 2004, 380 (Pt 1): 1-17.PubMedPubMed CentralView ArticleGoogle Scholar
- Kurisu S, Takenawa T: The WASP and WAVE family proteins. Genome Biol. 2009, 10 (6): 226-10.1186/gb-2009-10-6-226.PubMedPubMed CentralView ArticleGoogle Scholar
- Burdon KP, McKay JD, Sale MM, Russell-Eggitt IM, Mackey DA, Wirth MG, Elder JE, Nicoll A, Clarke MP, FitzGerald LM, et al: Mutations in a novel gene, NHS, cause the pleiotropic effects of Nance-Horan syndrome, including severe congenital cataract, dental anomalies, and mental retardation. Am J Hum Genet. 2003, 73 (5): 1120-1130. 10.1086/379381.PubMedPubMed CentralView ArticleGoogle Scholar
- Innocenti M, Zucconi A, Disanza A, Frittoli E, Areces LB, Steffen A, Stradal TE, Di Fiore PP, Carlier MF, Scita G: Abi1 is essential for the formation and activation of a WAVE2 signalling complex. Nat Cell Biol. 2004, 6 (4): 319-327. 10.1038/ncb1105.PubMedView ArticleGoogle Scholar
- Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Federhen S: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2011, D38-D51. 39 Database
- Parfrey LW, Grant J, Tekle YI, Lasek-Nesselquist E, Morrison HG, Sogin ML, Patterson DJ, Katz LA: Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life. Syst Biol. 2010, 59 (5): 518-533. 10.1093/sysbio/syq037.PubMedPubMed CentralView ArticleGoogle Scholar
- Burki F, Shalchian-Tabrizi K, Minge M, Skjaeveland A, Nikolaev SI, Jakobsen KS, Pawlowski J: Phylogenomics reshuffles the eukaryotic supergroups. PLoS One. 2007, 2 (8): e790-10.1371/journal.pone.0000790.PubMedPubMed CentralView ArticleGoogle Scholar
- Nozaki H, Maruyama S, Matsuzaki M, Nakada T, Kato S, Misawa K: Phylogenetic positions of Glaucophyta, green plants (Archaeplastida) and Haptophyta (Chromalveolata) as deduced from slowly evolving nuclear genes. Mol Phylogenet Evol. 2009, 53 (3): 872-880. 10.1016/j.ympev.2009.08.015.PubMedView ArticleGoogle Scholar
- Keeling PJ: Chromalveolates and the evolution of plastids by secondary endosymbiosis. J Eukaryot Microbiol. 2009, 56 (1): 1-8. 10.1111/j.1550-7408.2008.00371.x.PubMedView ArticleGoogle Scholar
- Hackett JD, Yoon HS, Li S, Reyes-Prieto A, Rummele SE, Bhattacharya D: Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates. Mol Biol Evol. 2007, 24 (8): 1702-1713. 10.1093/molbev/msm089.PubMedView ArticleGoogle Scholar
- Reeb VC, Peglar MT, Yoon HS, Bai JR, Wu M, Shiu P, Grafenberg JL, Reyes-Prieto A, Rummele SE, Gross J, et al: Interrelationships of chromalveolates within a broadly sampled tree of photosynthetic protists. Mol Phylogenet Evol. 2009, 53 (1): 202-211. 10.1016/j.ympev.2009.04.012.PubMedView ArticleGoogle Scholar
- Hampl V, Hug L, Leigh JW, Dacks JB, Lang BF, Simpson AG, Roger AJ: Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups". Proc Natl Acad Sci USA. 2009, 106 (10): 3859-3864. 10.1073/pnas.0807880106.PubMedPubMed CentralView ArticleGoogle Scholar
- Burki F, Shalchian-Tabrizi K, Pawlowski J: Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes. Biol Lett. 2008, 4 (4): 366-369. 10.1098/rsbl.2008.0224.PubMedPubMed CentralView ArticleGoogle Scholar
- Keeling PJ: The endosymbiotic origin, diversification and fate of plastids. Philos Trans R Soc Lond B Biol Sci. 2010, 365 (1541): 729-748. 10.1098/rstb.2009.0103.PubMedPubMed CentralView ArticleGoogle Scholar
- Paps J, Baguna J, Riutort M: Bilaterian phylogeny: a broad sampling of 13 nuclear genes provides a new Lophotrochozoa phylogeny and supports a paraphyletic basal acoelomorpha. Mol Biol Evol. 2009, 26 (10): 2397-2406. 10.1093/molbev/msp150.PubMedView ArticleGoogle Scholar
- Bourlat SJ, Nielsen C, Economou AD, Telford MJ: Testing the new animal phylogeny: a phylum level molecular analysis of the animal kingdom. Mol Phylogenet Evol. 2008, 49 (1): 23-31. 10.1016/j.ympev.2008.07.008.PubMedView ArticleGoogle Scholar
- Simpson AG, Inagaki Y, Roger AJ: Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of "primitive" eukaryotes. Mol Biol Evol. 2006, 23 (3): 615-625.PubMedView ArticleGoogle Scholar
- Deeks MJ, Kaloriti D, Davies B, Malho R, Hussey PJ: Arabidopsis NAP1 is essential for Arp2/3-dependent trichome morphogenesis. Curr Biol. 2004, 14 (15): 1410-1414. 10.1016/j.cub.2004.06.065.PubMedView ArticleGoogle Scholar
- Peter BJ, Kent HM, Mills IG, Vallis Y, Butler PJ, Evans PR, McMahon HT: BAR domains as sensors of membrane curvature: the amphiphysin BAR structure. Science. 2004, 303 (5657): 495-499. 10.1126/science.1092586.PubMedView ArticleGoogle Scholar
- Itoh T, De Camilli P: BAR, F-BAR (EFC) and ENTH/ANTH domains in the regulation of membrane-cytosol interfaces and membrane curvature. Biochim Biophys Acta. 2006, 1761 (8): 897-912.PubMedView ArticleGoogle Scholar
- Frost A, Unger VM, De Camilli P: The BAR domain superfamily: membrane-molding macromolecules. Cell. 2009, 137 (2): 191-196. 10.1016/j.cell.2009.04.010.PubMedView ArticleGoogle Scholar
- Millard TH, Bompard G, Heung MY, Dafforn TR, Scott DJ, Machesky LM, Futterer K: Structural basis of filopodia formation induced by the IRSp53/MIM homology domain of human IRSp53. EMBO J. 2005, 24 (2): 240-250. 10.1038/sj.emboj.7600535.PubMedPubMed CentralView ArticleGoogle Scholar
- Yamagishi A, Masuda M, Ohki T, Onishi H, Mochizuki N: A novel actin bundling/filopodium-forming domain conserved in insulin receptor tyrosine kinase substrate p53 and missing in metastasis protein. J Biol Chem. 2004, 279 (15): 14929-14936. 10.1074/jbc.M309408200.PubMedView ArticleGoogle Scholar
- Liu SL, Needham KM, May JR, Nolen BJ: Mechanism of a concentration-dependent switch between activation and inhibition of Arp2/3 complex by coronin. J Biol Chem. 2011, 286 (19): 17039-17046. 10.1074/jbc.M111.219964.PubMedPubMed CentralView ArticleGoogle Scholar
- Eckert C, Hammesfahr B, Kollmar M: A holistic phylogeny of the coronin gene family reveals an ancient origin of the tandem-coronin, defines a new subfamily, and predicts protein function. BMC Evol Biol. 2011, 11: 268-10.1186/1471-2148-11-268.PubMedPubMed CentralView ArticleGoogle Scholar
- Galletta BJ, Chuang DY, Cooper JA: Distinct roles for Arp2/3 regulators in actin assembly and endocytosis. PLoS Biol. 2008, 6: (1):e1-PubMedPubMed CentralView ArticleGoogle Scholar
- Sirotkin V, Beltzner CC, Marchand JB, Pollard TD: Interactions of WASp, myosin-I, and verprolin with Arp2/3 complex during actin patch assembly in fission yeast. J Cell Biol. 2005, 170 (4): 637-648. 10.1083/jcb.200502053.PubMedPubMed CentralView ArticleGoogle Scholar
- Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, et al: Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature. 2004, 431 (7011): 946-957. 10.1038/nature03025.PubMedView ArticleGoogle Scholar
- Odronitz F, Kollmar M: Pfarao: a web application for protein family analysis customized for cytoskeletal and motor proteins (CyMoBase). BMC Genomics. 2006, 7: 300-10.1186/1471-2164-7-300.PubMedPubMed CentralView ArticleGoogle Scholar
- Thompson JD, Gibson TJ, Higgins DG: Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics. 2002, Chapter 2: Unit 2.3Google Scholar
- Stamatakis A, Hoover P, Rougemont J: A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol. 2008, 57 (5): 758-771. 10.1080/10635150802429642.PubMedView ArticleGoogle Scholar
- Ronquist F, Huelsenbeck JP: MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003, 19 (12): 1572-1574. 10.1093/bioinformatics/btg180.PubMedView ArticleGoogle Scholar
- Jones DT, Taylor WR, Thornton JM: The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 1992, 8 (3): 275-282.PubMedGoogle Scholar
This article is published under license to 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.