Received June 8, 2005; Revised September 16, 2005; Accepted September 21, 2005.
MATERIALS AND METHODS Sequence Searches and Alignment To cover the maximum diversity of ARPs, sequence searches were performed using as sequence queries: three actin sequences, representative sequences from each ARP subfamily selected from three distantly related organisms ( S. cerevisiae, Drosophila melanogaster, and Homo sapiens when available), and five orphan sequences. The sequences were retrieved from Uniprot using SRS (Sequence Retrieval System; Etzold et al., 1996 ) with their identification (ID) or accession (AC) numbers. This resulted in an initial set of 37 reference proteins shown in Supplementary Data 2. For each reference protein, a BlastP (Altschul et al., 1990 , 1997 ) search of the Uniprot database ( Bairoch et al., 2005 ; July 2004) was performed and the sequences detected with E < 10 -2 were multiply aligned using the PipeAlign program without the clustering step ( Plewniak et al., 2003 ). The PipeAlign web server is available at http://bips.u-strasbg.fr/PipeAlign. These 37 MACS were then merged into a single multiple alignment. Unrelated sequences were removed from the final alignment with LEON (multiple a lignment evaluation of neighbors; Thompson et al., 2004 ). This composite alignment was then refined using RASCAL ( rapid scanning and correction of multiple sequence alignment; Thompson et al., 2003 ) to automatically correct local alignment errors. Finally, manual verification and correction, paying attention to secondary structures, was performed using the seqlab alignment viewer and editor ( GCG, 2001 ). The quality of the final alignment was objectively evaluated using NorMD ( normalized mean distance; Thompson et al., 2001 ). Subfamilies were defined automatically using DPC ( density of point clustering; Wicker et al., 2002 ) and validated by human expertise. Furthermore, a phylogenetic tree based on the final alignment was built with the neighbor joining method (see Supplementary Figure 1). The analysis of this tree confirmed the defined subfamilies. Overall, the BlastP similarity searches yielded 73,340 proteins, representing 4200 nonredundant and “nonfragment” proteins. Sequences with <15% amino acid identity, notably some bacterial actinlike proteins, were not included in the final alignment. To obtain an objective evaluation of the true number of ARP sequences in Uniprot, we removed database redundancy by counting only nonidentical sequences for each different organism. The final version of the complete multiple alignment of ARPs (ARP-MACS) contains more than 700 proteins (sequence list included in Supplementary Data 3) clustered into one actin subfamily, 11 ARP subfamilies, and orphans. ARPMACS is available at http://bips.u-strasbg.fr/ARPAnno/ARPMACS.html. Sequence Analysis Two statistics were used to characterize each ARP subfamily, RefID and FamID. First, the RefID is defined to compare the current subfamily classification with the one used in 1997 ( Poch and Winsor, 1997 ; called IniID here). It is computed for each ARP subfamily as the mean pairwise percent identity of each sequence in the subset against a reference sequence. Positions in the alignment of these sequences corresponding to gaps were excluded from the calculation. The reference actin sequence used is the human actin gene annotated as “Actin, alpha skeletal muscle (Alpha-actin 1)” Uniprot ID ACTS_HUMAN and AC P02568, that is strictly identical to the actins from Bos taurus, Gallus gallus, Mus musculus, Sus scrofa, Oryctolagus cuniculus, Rattus norvegicus. All indications of amino acid positions used in the following analyses refer to this reference sequence (Supplementary Data 4). where: n is total number of sequence tested, S i and S REF are, respectively, the ith and reference actin sequence, and ID Si,SREF is the pairwise percent identity between the ith and the reference actin sequence, excluding gap regions. Second, the FamID describes the conservation within each subfamily. The FamID of each ARP subfamily was calculated as the mean pairwise percent identity of each sequence against each other sequence in a given subset. As above, positions in the alignment corresponding to gaps within the subset were excluded from the calculation. where: n is the total number of sequence tested, S i and S j are the ith and jth sequence, and ID Si,Sj are pairwise percent identity between the ith and jth sequence, excluding gap regions. Limitations of the RefID and FamID calculations are the absence of certain subfamilies in different organisms and the incomplete representation of ARPs in protein databases. Taking this into account, the two statistics were calculated on a subset of sequences encompassing at least one sequence from mammals, insects, worms, fungi, and plants for each subfamily, except ARP7, ARP9, and ARP10, restricted to yeasts (Accession numbers of sequences used are available upon request). Discriminating Residues and Insertions/Deletions The discriminating residues were identified as amino acids strictly present within a particular ARP subfamily and strictly absent in all other sequences. We also identified motifs (2-7 residues) that could distinguish an ARP subfamily (see Figure 2 legend). Insertion and deletions in ARPs were defined as a minimum of 10 residues added to or deleted from the reference actin sequence (Supplementary Data 5). To characterize the INDELs, the entry point was defined as a single position where at least one ARP has an INDEL and the “hot spot” as a short sequence stretch in which many different ARPs have INDELs. The discriminating residues, motifs, and INDELs constitute a knowledge filter used to characterize the ARP subfamilies. | Figure 2.Schema representing residues, motifs, insertions, and deletions in ARP subfamilies. The reference human α-actin sequence (377 aa) is represented as green rectangles and positions are given according to this reference. The upper arrows illustrate (more ...) |
ARPAnno Web Server To make our results easily available to the scientific community, a web server ARPAnno (actin-related proteins annotation server) has been developed to allow reliable classification and annotation of newly sequenced potential actinlike proteins. ARPAnno is written in Tcl/Tk script or in ANSI C for some functions. ARPAnno also requires the Blast and ClustalW programs. The strategy of ARPAnno is based on a three-step process: - First ARPAnno aligns the query sequence with BlastP against dedicated databases of each subfamily contained in ARP-MACS (actin, 11 ARP subfamilies and orphans). Eligible subfamilies which are the most suitable for further investigation are then determined by the calculation of two cutoffs. First, a global percent identity (GID) is defined as the ratio of the number of identical residues to the total number of residues in all HSPs (high scoring pairs) of the query. Second, a percent coverage (pCover) is defined as the ratio of the number of identical residues to the number of residues that could be aligned between the two sequences.
- The query is then aligned against the eligible subfamilies in the ARPMACS using the ClustalW global multiple alignment program (Thompson et al., 1994 ) in profile mode and filtered according to the knowledge-based criteria (residues and INDELs signatures) defined above. For each eligible subfamily, two scores are calculated: the number of discriminating insertions (pDI) detected as a percentage of the total number of discriminating insertions characterized for the considered subfamily, and the number of discriminating residues (pDR) detected as a percentage of the total number of residues described for the subfamily.
- A final score on a scale of 0-100 is computed for each subfamily based on the local and global alignment and the knowledge-based filter.
where S ARPi is the final score, pDR ARPi is the percentage of detected residues, and pDI ARPi is the percentage of detected insertions for the ith ARP subfamily. The relative weights of each score were determined experimentally to best separate the subfamilies previously established by ARP-MACS. The alignments of the query with each eligible subfamily are displayed with Family features highlighted in different colors and are available for download in XML or MSF format. ARPAnno is available at http://bips.u-strasbg.fr/ARPAnno and mirrored at www.bioinfomatics.lu. ATP Binding To explore the potentiality of ARPs for ATP binding, we calculated the conservation of the 17 key reference actin amino acids for nucleotide binding (D13, S16, G17, L18, K20, Q139, D156, D159, G160, V161, K215, E216, G304, T305, M307, Y308, K338) for all ARP subfamilies as described previously ( Kabsch et al., 1990 ; Lees-Miller et al., 1992a ). The mean percent of conserved identical residues and similar residues were computed for each ARP subfamily. Structural Studies The actin molecule is represented by the 3D structure of yeast actin (Uniprot ID ACT_YEAST, PDB 1YAG; Vorobiev et al., 2003 ) and secondary structures are named according to the PDB data (see Figure 4). The actin fold is mainly defined by subdomains 1 and 3 excluding helices H15, H19, and H20, as well as helix H11 and the bottom part of helices H8 and H9 in subdomain 4, with no contribution from subdomain 2 ( Kabsch and Holmes, 1995 ). One major actin-binding interface of actin, known as the “hydrophobic cleft” is defined essentially by residues in three helices (H18, H19, and H20) in subdomain 1 ( Dominguez, 2004 ). The mean percent identity to the reference actin in ARPMACS was calculated using a sliding-window corresponding to each secondary structure. This statistic was used to replace the temperature factor field in the PDB file. Figure 4A represents the mean percent identity of all ARP subfamilies and Figure 4B that of each ARP subfamily individually. The sequence conservations are mapped onto the structure with colors ranging from dark blue to red, corresponding to 0-65% identity (Id.; loops excluded) in Figure 4A and to 0-100% Id. in Figure 4B. | Figure 4Actin amino acid conservation in secondary structure throughout ARP subfamilies. Actin 3D structure is drawn from the yeast PDB data 1YAG in standard orientation with secondary structures labeled H for helices and S for strands, numbered in order of appearance (more ...) |
Phylogenetic Distribution of ARPs in Complete Genomes The ARP distribution was examined in 20 eukaryotic organisms for which the complete genome sequences are available. The presence/absence of each ARP was cross-validated at both the proteomic and genomic levels. Inspection of recently reported genomic sequences identified potential new ARP genes missed during the gene prediction process. A table summarizing proteomic and genomic searches is included in Supplementary Data 6. Where available, the nucleotide sequence was retrieved from the NCBI nucleotide sequence database known as GenBank ( Benson et al., 2005 ) and RefSeq ( Pruitt et al., 2005 ) and queried with the 37 reference sequences using the TBlastN program. The 20 complete eukaryotic genomes used are: Oryza sativa ( Goff et al., 2002 ), Arabidopsis thaliana ( Arabidopsis Genome Initiative, 2000 ), Plasmodium falciparum ( Gardner et al., 2002 ), Encephalitozoon cuniculi ( Katinka et al., 2001 ), Neurospora crassa ( Galagan et al., 2003 ), S. cerevisiae ( Goffeau et al., 1996 ), Candida glabrata, Yarrowia lipolytica ( Dujon et al., 2004 ), S. pombe ( Wood et al., 2002 ), Anopheles gambiae ( Holt et al., 2002 ), D. melanogaster ( Adams et al., 2000 ), Caenorhabditis elegans ( Chervitz et al., 1998 ; C. elegans Sequencing Consortium, 1998 ), Ciona intestinalis ( Dehal et al., 2002 ), Tetraodon nigroviridis ( Jaillon et al., 2004 ), M. musculus ( Waterston et al., 2002 ), H. sapiens ( Lander et al., 2001 ; Venter et al., 2001 ). We also used dedicated websites in order to retrieve the latest sequence version for Thalassiosira pseudonana ( http://genome.jgipsf.org/thaps1; Armbrust et al., 2004 ), Dictyostelium discoideum ( http://dictybase.org; Kreppel et al., 2004 ; Eichinger et al., 2005 ), and other sites for additional Blast searches for Cryptosporidium parvum ( http://cryptodb.org/CryptoDB.shtml; Abrahamsen et al., 2004 ; Puiu et al., 2004 ), and Cyanidioschyzon merolae ( http://merolae.biol.s.u-tokyo.ac.jp; Matsuzaki et al., 2004 ). An extended exploration of all complete and incomplete Fungi proteomes and genomes reported and existing at the NCBI Blast server was made. We used 31 Fungi, divided into Ascomycota Saccharomycotina (C. albicans, C. glabrata, D. hansenii, E. gossypii, K. lactis, K waltii, N. castellii, S. bayanus 623-6C, S. bayanus MCYC 623, S. cerevisiae, S. kluyveri, S. kudriavzevii, S. mikatae, S. paradoxus and Y. lipolytica), Ascomycota Pezizomycotina (A. fumigatus, A. nidulans, A. terreus, C. immitis, C. posadasii, G. zeae, M. grisea, N. crassa), Ascomycota Schizosaccharomycetes (S. pombe), Basidiomycota (C. cinerea okayama, C. neoformans var. grubii H99, C. neoformans var. neoformans B-3501A, C. neoformans var. neoformans JEC21, P. chrysosporium, U. maydis) and Microsporidia (E. cuniculi). |
RESULTS Sequence Analysis and Subfamily Definition We built ARP-MACS, a new high quality multiple alignment of complete sequences of all ARPs and actins available in Uniprot (July 2004) as the basis for an extended characterization of ARP subfamilies. In our earlier study, the previously defined ARP1-ARP3 subfamilies ( Schroer et al., 1994 ) were confirmed on the basis of 5-8 sequences, and the remaining ARP subfamilies were proposed essentially on the basis of S. cerevisiae sequences ( Poch and Winsor, 1997 ). Later these subfamilies were established by phylogenetic analyses ( Eckley et al., 1999 ; Harata et al., 2001 ; Goodson and Hawse, 2002 ). Since 1997, including this analysis, the only new major ARP that was identified is ARP11 ( Eckley et al., 1999 ). The growing number of ARP proteins available in protein databases and classified in ARP-MACS ( Table 1) consolidates the ARP4-ARP11 subfamilies classification. In agreement with previous studies, the major ARP subfamilies are ARP1-6, ARP8, and ARP11, whereas fewer sequences are available for subfamilies ARP7, ARP9, and ARP10. As illustrated below, these subfamilies are restricted to certain phyla. Twenty-seven orphan protein sequences were found in Metazoa ( H. sapiens, M. fascicularis, M. musculus, and C. elegans), plants ( O. sativa and A. thaliana) and in the parasites E. cuniculi, P. falciparum, and P. yoelii. These sequences range in size from 328 to 1207 amino acids, and share from 21 to 49% Id. with the reference actin. They have been included in the overall alignment but are not considered as a subfamily because they lack common defining characteristics. | Table 1. Evolution of the number of actin and ARP sequences since 1997 |
To validate the reliability of the ARP classification based on the mean percent identity between ARP sequences and the reference actin (RefID), we compared the ranking obtained here with the ARP ranking based on initial percent identities (IniID) deduced from the data available in 1997 ( Poch and Winsor, 1997 ). IniID and RefID are highly correlated ( Figure 1); ARP1 is the closest to actin and ARP10 and ARP11 are the most distant in both cases, reinforcing the universal classification. Nevertheless, with our recent refinements and definitions, the relative order of some subfamilies could have been exchanged, e.g., ARP5 with ARP6. In spite of these small variations, to avoid confusion in naming genes and proteins, we do not recommend changing the existing nomenclature. The growing number of sequences per ARP subfamily allows an evaluation of the intrasubfamily conservation (FamID). Three groups of proteins were distinguished ( Figure 1). As expected, the conventional actins (546 sequences) are the most conserved subfamily (FamID > 80%). The second group is composed of cytoplasmic ARPs (ARP1-ARP3), and shares significantly more intrasubfamily conservation (50% < FamID < 80%) than the last group including all nuclear ARPs and ARP10 and ARP11 (FamID < 40%). | Figure 1.Actin and ARP conservation. The initial percent identity (IniID) used in 1997 (Poch and Winsor, 1997 ) to classify the ARPs is represented as open bars. A new percent identity (RefID) is shown as hatched bars. The closed bars are the mean percent identity (more ...) |
ARP Subfamily Characterization Because of high sequence identity and similarity between ARPs and actin sequences, it is frequently difficult to unambiguously detect and classify an ARP sequence from BlastP database searches. Indeed the Blast score and ranking of ARP homologous sequences is perturbed by the presence of insertions and deletions and the existence of a very limited number of discriminating residues (see Materials and Methods). As an example, the search of homologues (BlastP) for the human ARP1 in Uniprot leads to 1653 protein “hits” exhibiting a significant E-value (E ≥ 10 -2). Among these, ARP1 sequences are dispersed among conventional actin and other ARPs. The last ARP1 detected was the yeast ARP1 at rank 769, lower than many non-ARP1 sequences. This prompted us to define discriminating criteria, i.e., sequence features conserved in a given subfamily and strictly absent in any other, for each ARP subfamily using specific residues, motifs or INDELs as shown in Figure 2 and Supplementary Data 5. The analysis of the regions aligned in all ARP and actin sequences, revealed single discriminating residues and motifs for 8 ARP subfamilies, that is, 6 single residues and 23 motifs covering 76 residues. ARP2 and ARP3 subfamilies have the highest number of motifs (6 and 7, respectively), whereas no specific residues or motifs were found for the ARP4, ARP10, and ARP11 subfamilies. We next built a map of INDELs relative to the reference actin for each subfamily sequence ( Figure 2). Strikingly, ARPs show a high number of different insertions (41) of different sizes at various positions along the total 377 amino acid length of actin, but only four deletions. Excluding the N- and C-terminal extensions, a total of 16 entry points was observed. Four hot spots (named A, B, C, and D in Figure 2) are found at positions 42-63, 239-247, 271-288, and 323-334. INDELS have a maximum size of ~330 amino acids and occur mainly in loops. No large insertions were identified in the core structure of the actin fold. In terms of domain distribution, the discontinuous subdomain 1 is the least susceptible to INDELs with only ARP4, ARP6, and ARP10 having intrasubdomain insertions. In contrast, the smallest subdomain 2 is the most sensitive to adaptation, with the main hot spot (A) comprising 11 INDELs distributed in ARP3-ARP6 and ARP8-ARP11. Hot spot (A) includes one deletion from each of ARP6, ARP10, and ARP11 but none of these are characteristic of all subfamily members. The largest deletion is observed in subdomain 4 of S. cerevisiae ARP10 and results in the complete loss of almost all the subdomain. Another remarkable feature, if we consider the ARPs cellular localization, is the paucity of insertions larger than 10 residues in cytoplasmic ARP1, ARP2, and ARP3, in contrast to the nuclear ARPs, which contain from 1 to 5 insertions. Although many entry points are common to different ARP subfamilies, it is noteworthy that no sequence similarity was found between the insertions from different ARP subfamilies. Thus, ARP characterization can be completed by describing the presence of an insertion common to all members of a given ARP subfamily (Family Insertion, highlighted in yellow in Figure 2). However, ARP1 has no insertion ≥10 aa, and ARP10 and ARP11 have many different INDELs but none are conserved in all members of the subfamily. We also found that the N-terminal motif MS[G/A][G/A][V/L]YGG in ARP4 ( Choi et al., 2001 ), previously described as characteristic, is absent from 6 ARP4 sequences from different organisms (plasmodia and yeast). Two other Family Insertions are of particular interest. The largest insertion in ARP5 (position 246) is rich in charged residues, and the ARP9 Family Insertion at position 333 contains a pattern rich in rare aromatic amino acids [P/S][D/E]YF[P/S][E/S]WK. Taken together, the specific residues, motifs, and Family Insertions constitute a knowledge filter that defines at least one discriminative feature for each ARP subfamily except for ARP10 and ARP11, which are defined only by sequence similarity. ARPAnno Web Server Our approach, based on ARP-MACS, combines three complementary strategies with local and global sequence information and a knowledge filter (see Materials and Methods). Based on this, we implemented a web server to annotate ARP sequences. The web server, called ARPAnno, is available at http://bips.u-strasbg.fr/ARPAnno and allows the user to submit a sequence in FASTA format. The analysis of actin and ARP conservation ( Figure 1) shows that a query is identified as an actin if it has a GID >80% and a pCover >80% compared with any conventional actin sequence (see Materials and Methods). To estimate the accuracy and reliability of the ARPAnno annotations, we submitted each of the ~700 previously identified actin and ARP proteins in ARPMACS for automatic classification. In this large-scale test, all proteins were assigned to the correct subfamilies. To evaluate the predictive strength of our server, we performed a second test involving the newly detected proteins from a later version of Uniprot (January 2005). The second set was composed of 68 sequences that were classified by the program with best S ARPi ranging from 36.9 to 99.0 as follows: 36 conventional actins, 3 Orphans, 6 ARP1, 7 ARP2, 6 ARP3, 8 ARP4, 1 ARP9, and 1 ARP10 from diverse organisms such as Y. lipolytica, D. hansenii, Caenorhabditis briggsae, Paramecium tetraurelia, Xenopus tropicalis or Gallus gallus. For complete sequences, an S ARPi > 55 was highly reliable to assign a subfamily. Further validation by visual inspection suggested that the only 2 sequences with S ARPi < 55 corresponds to 2 proteins from P. tetraurelia, classified by ARPAnno as an actin and annotated as putative actin in Uniprot. ATP Binding In addition to actin, ARP1, ARP2, and ARP3 bind an ATP molecule, for which the hydrolysis is proposed to induce a conformational change required for their biological function ( Otterbein et al., 2001 ; Nolen et al., 2004 ; Martin et al., 2005 ). The mean conservation of 17 key reference residues involved in nucleotide binding was computed for each ARP subfamily and is illustrated in Figure 3. The same analysis was carried out using a slightly different set of nucleotide binding residues ( Beltzner and Pollard, 2004 ) and gave similar results (our unpublished results). We observed two groups. The first group, composed of conventional actin and cytoplasmic ARPs (ARP1-ARP3), has >60% identical and >90% similar residues, whereas the second group (ARP4-ARP11) has <35% identical and <46% similar residues. Thus, this predicts that the first group is able to bind ATP (K d ≤ μM), which has been shown to be the case ( Belmont et al., 1999 ; Bingham and Schroer, 1999 ; Sablin et al., 2002 ). In contrast, this analysis of key binding residues predicts that, the second group, mainly composed of nuclear ARPs, might not bind ATP or might bind with significantly less affinity and/or through other residues. | Figure 3.Conservation pattern of the 17 residues (D13, S16, G17, L18, K20, Q139, D156, D159, G160, V161, K215, E216, G304, T305, M307, Y308, and K338) known to participate in nucleotide binding to actin. For the 11 ARP subfamilies and actin, percent identity is (more ...) |
From Sequence to Structure To visualize the sequence to structure conservation of ARP subfamilies, we mapped the degree of amino acid conservation relative to the actin reference sequence onto the secondary structures using yeast actin as a model structure. The mean conservation for all ARP sequences in ARP-MACS is represented in Figure 4A, whereas the detail for individual ARP subfamilies is represented in Figure 4B. The secondary structures defining the actin fold are widely conserved in all ARP subfamilies as seen by the abundant green color corresponding to 25-35% Id. ( Figure 4A). Some specific regions are highly conserved (> 45% Id. from orange to red) corresponding to secondary structures in three subdomains: in subdomain 1 a complete beta sheet composed of 4 strands (S1, S2, S3, and S6) and two alpha-helices (H18 and H20), in subdomain 3, two beta strands (S8 and S13), and one helix (H6), and in subdomain 4, the two helices (H11 and H12). All these secondary structures, with the exception of H20, are part of the previously defined actin fold ( Kabsch and Holmes, 1995 ). The observed conservation points are localized in the bottom half of the actin fold and more precisely, in the hydrophobic cleft ( Dominguez, 2004 ), a key region for actin dimerization and for interaction with ABPs. The analyses of individual ARP subfamily conservation highlight specific patterns. As expected in view of the FamID, the main cytoplasmic ARP1-ARP3 share more conserved elements than nuclear ARPs. Surprisingly, ARP2 is less conserved in the helix H18 and H19 involved in the hydrophobic cleft than in either ARP1 or ARP3. Additional features can be observed in subdomains 2 and 4 for ARP1 and ARP2. We noticed that ARP1 and ARP2 reveal better sequence conservation in helix H9 and in strand S4 and S10 than ARP3. Within the nuclear ARPs, ARP4 unexpectedly maintains high conservation in the lower part of subdomain 1 (H18, H19, and H20). This observation underlines functional perspectives for ARP4 through its hydrophobic cleft. Finally, with regard to other secondary structures that are part of subdomain 1, S1 is highly conserved in ARP5, ARP6, and ARP11; S6 in ARP5; and S2 in ARP7 and ARP11. Phylogenetic Distribution The growing number of completely sequenced genomes available allows us to define the edges of the distribution of eukaryotic ARPs by in depth analysis of the proteomes and genomes of 20 organisms ranging across eukaryotic phyla. As observed in many organisms ( T. pseudonana, D. discoideum...; Supplementary Data 6), the genomic validation is essential to assess the presence of a given ARP, considering that a certain number of genes present have not been annotated as proteins. The phylogenetic distribution of ARP subfamilies and conventional actin is represented in Figure 5. According to defined ARP signatures, we detected 132 ARP proteins in 11 subfamilies from algae to mammals, and at least 1 actin and 1 ARP in each organism analyzed. It is noteworthy that the organisms with limited numbers of ARP ( E. cuniculi, C. merolae) have no detectable cytoplasmic ARPs but include at least one nuclear ARP. In all other organisms, both nuclear and cytoplasmic ARPs are present. Remarkably, the examination of the presence/absence profiles led to the definition of pairs of copresent/coabsent ARPs such as ARP2 with ARP3, ARP4 with ARP6, ARP5 with ARP8, ARP7, with ARP9, and to lesser extent ARP1 with ARP10 or ARP11. Surprisingly, the most widely distributed ARPs in evolution, copresent in all organisms studied with the exception of the small obligate parasite E. cuniculi, are the nuclear ARPs, ARP4, and ARP6. This result was unexpected and leads to the conclusion that ARP4 and ARP6 represent the most universal ARPs conserved throughout the eukaryotic phyla. The second most widely distributed pair of proteins is ARP2 and ARP3, well studied components of the actin nucleation complex. They are copresent in plants, fungi, and Metazoa but are coabsent in algae and in Apicomplexa. | Figure 5.Schematic representation of ARP distribution among the eukaryotic phyla. The columns represent different organisms with a completely sequenced genome: T. pseudonana (TP), C. merolae (CM), O. sativa (OS), A. thaliana (AT), P. falciparum (PF), C. parvum (more ...) |
ARP1, the closest ARP to conventional actin, is individually more widely distributed than ARP2 and ARP3. However, when one considers the functional complex dynactin where the ARP1 filament is capped by ARP11 ( Eckley et al., 1999 ), the pattern of presence/absence appears more complex than other pairs. In fact, although ARP11 is not present without ARP1, it is not found in every organism bearing ARP1. It is interesting to notice that ARP10, restricted to fungi, only partially complements the ARP11 pattern. Furthermore, our extended exploration of fungi (see Materials and Methods) confirms the presence of ARP1 in 30 out of 31 organisms (except E. cuniculi) and restricts ARP10 to only 5 Ascomycota Saccharomycotina ( D hansenii, E. gossypii, K lactis, S. cerevisiae, and Y. lipolytica) and 1 Ascomycota Schizosaccharomycetes ( S. pombe). One ARP11 was found in Ascomycota Pezizomycotina ( N. crassa). The coabsence profile of ARP5 and ARP8 is puzzling since they are missing in a number of different phyla such as the algae, the Apicomplexa, and two Metazoan phyla, C. elegans and C. intestinalis. Our results also confirm that the functionally obligate heterodimeric partners, ARP7 and ARP9 ( Szerlong et al., 2003 ), were restricted to fungi as previously suggested ( Goodson and Hawse, 2002 ; Blessing et al., 2004 ). The presence of ARP7 and ARP9 has been assessed in the 31 fungi genomes available at NCBI and we could clearly restrict ARP7 and ARP9 to Ascomycota Saccharomycotina and Ascomycota Schizosaccharomycetes. Neither ARP7 nor ARP9 were found in the Ascomycota Pezizomycotina, Basidiomycota, or Microsporidia. Surprisingly, the copresence of ARP7 and ARP9 is not observed in two completely sequenced organisms of Ascomycota, Y. lipolytica, and S. pombe, where ARP9 is present but ARP7 is absent. In this context it is noteworthy that these two organisms are the only fungi that encode an additional and distinct ARP4 (red box in Figure 5, Uniprot accession numbers Q6C0A9 and Q09849; annotated here as ARP4 *). This strongly suggests that ARP4 * may complement the lack of ARP7 in these yeasts. |
References - Abrahamsen, M. S. et al. (2004). Complete genome sequence of the apicomplexan, Cryptosporidium parvum. Science 304:, 441-445. [PubMed].
- Adams, M. D. et al. (2000). The genome sequence of Drosophila melanogaster. Science 287:, 2185-2195. [PubMed].
- Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215:, 403-410. [PubMed].
- Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:, 3389-3402. [PubMed].
- Amos, L. A., van den Ent, F., and Lowe, J. (2004). Structural/functional homology between the bacterial and eukaryotic cytoskeletons. Curr. Opin. Cell Biol. 16:, 24-31. [PubMed].
- Arabidospis Genome Initiative. (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:, 796-815. [PubMed].
- Archer, S. K., Behm, C. A., Claudianos, C., and Campbell, H. D. (2004). The flightless I protein and the gelsolin family in nuclear hormone receptor-mediated signalling. Biochem. Soc. Trans. 32:, 940-942. [PubMed].
- Armbrust, E. V. et al. (2004). The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science 306:, 79-86. [PubMed].
- Bairoch, A. et al. (2005). The Universal Protein Resource (UniProt). Nucleic Acids Res. 33: Database Issue, D154-D159. [PubMed].
- Bakshi, R., Prakash, T., Dash, D., and Brahmachari, V. (2004). In silico characterization of the INO80 subfamily of SWI2/SNF2 chromatin remodeling proteins. Biochem. Biophys. Res. Commun. 320:, 197-204. [PubMed].
- Belmont, L. D., Orlova, A., Drubin, D. G., and Egelman, E. H. (1999). A change in actin conformation associated with filament instability after Pi release. Proc. Natl. Acad. Sci. USA 96:, 29-34. [PubMed].
- Beltzner, C. C., and Pollard, T. D. (2004). Identification of functionally important residues of Arp2/3 complex by analysis of homology models from diverse species. J. Mol. Biol. 336:, 551-565. [PubMed].
- Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., and Wheeler, D. L. (2005). GenBank. Nucleic Acids Res. 33: Database Issue, D34-D38. [PubMed].
- Bingham, J. B., and Schroer, T. A. (1999). Self-regulated polymerization of the actin-related protein Arp1. Curr. Biol. 9:, 223-226. [PubMed].
- Blessing, C. A., Ugrinova, G. T., and Goodson, H. V. (2004). Actin and ARPs: action in the nucleus. Trends Cell Biol. 14:, 435-442. [PubMed].
- Bork, P., Sander, C., and Valencia, A. (1992). An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins. Proc. Natl. Acad. Sci. USA 89:, 7290-7294. [PubMed].
- Borkovich, K. A. et al. (2004). Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiol. Mol. Biol. Rev. 68:, 1-108, table of contents. [PubMed].
- Cairns, B. R., Erdjument-Bromage, H., Tempst, P., Winston, F., and Kornberg, R. D. (1998). Two actin-related proteins are shared functional components of the chromatin-remodeling complexes RSC and SWI/SNF. Mol. Cell 2:, 639-651. [PubMed].
- Chervitz, S. A. et al. (1998). Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science 282:, 2022-2028. [PubMed].
- Choi, E. Y., Park, J. A., Sung, Y. H., and Kwon, H. (2001). Generation of the dominant-negative mutant of hArpNbeta: a component of human SWI/SNF chromatin remodeling complex. Exp. Cell Res. 271:, 180-188. [PubMed].
- C. elegans Sequencing Consortium. (1998). Genome sequence of the nematode C. elegans: a platform for investigating biology. The C. elegans Sequencing Consortium. Science 282:, 2012-2018. [PubMed].
- Dayel, M. J., Holleran, E. A., and Mullins, R. D. (2001). Arp2/3 complex requires hydrolyzable ATP for nucleation of new actin filaments. Proc. Natl. Acad Sci. USA 98:, 14871-14876. [PubMed].
- Dehal, P. et al. (2002). The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 298:, 2157-2167. [PubMed].
- Delano, W. L. (2002). The PyMOL User's Manual.
- Dominguez, R. (2004). Actin-binding proteins—a unifying hypothesis. Trends Biochem. Sci. 29:, 572-578. [PubMed].
- Doyon, Y., Selleck, W., Lane, W. S., Tan, S., and Cote, J. (2004). Structural and functional conservation of the NuA4 histone acetyltransferase complex from yeast to humans. Mol. Cell Biol. 24:, 1884-1896. [PubMed].
- Dujon, B. et al. (2004). Genome evolution in yeasts. Nature 430:, 35-44. [PubMed].
- Eckley, D. M., Gill, S. R., Melkonian, K. A., Bingham, J. B., Goodson, H. V., Heuser, J. E., and Schroer, T. A. (1999). Analysis of dynactin subcomplexes reveals a novel actin-related protein associated with the arp1 minifilament pointed end. J. Cell Biol. 147:, 307-320. [PubMed].
- Eckley, D. M., and Schroer, T. A. (2003). Interactions between the evolutionarily conserved, actin-related protein, Arp11, actin, and Arp1. Mol. Biol. Cell 14:, 2645-2654. [PubMed].
- Eichinger, L. et al. (2005). The genome of the social amoeba Dictyostelium discoideum. Nature 435:, 43-57. [PubMed].
- Etzold, T., Ulyanov, A., and Argos, P. (1996). SRS: information retrieval system for molecular biology data banks. Methods Enzymol. 266:, 114-128. [PubMed].
- Galagan, J. E. et al. (2003). The genome sequence of the filamentous fungus Neurospora crassa. Nature 422:, 859-868. [PubMed].
- Galarneau, L., Nourani, A., Boudreault, A. A., Zhang, Y., Heliot, L., Allard, S., Savard, J., Lane, W. S., Stillman, D. J., and Cote, J. (2000). Multiple links between the NuA4 histone acetyltransferase complex and epigenetic control of transcription. Cell 5:, 927-937.
- Gardner, M. J. et al. (2002). Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419:, 498-511. [PubMed].
- GCG. (2001). Wisconsin Package Version 10.2, Genetics Computer Group (GCG), Madison, WI.
- Goff, S. A. et al. (2002). A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:, 92-100. [PubMed].
- Goffeau, A. et al. (1996). Life with 6000 genes. Science 274:, 546, 563-567. [PubMed].
- Gomez-Garcia, M. R., and Kornberg, A. (2004). Formation of an actin-like filament concurrent with the enzymatic synthesis of inorganic polyphosphate. Proc. Natl. Acad. Sci. USA 101:, 15876-15880. [PubMed].
- Goodson, H. V., and Hawse, W. F. (2002). Molecular evolution of the actin family. J. Cell Sci. 115:, 2619-2622. [PubMed].
- Gorzer, I., Schuller, C., Heidenreich, E., Krupanska, L., Kuchler, K., and Wintersberger, U. (2003). The nuclear actin-related protein Act3p/Arp4p of Saccharomyces cerevisiae is involved in transcription regulation of stress genes. Mol. Microbiol. 50:, 1155-1171. [PubMed].
- Grava, S., Dumoulin, P., Madania, A., Tarassov, I., and Winsor, B. (2000). Functional analysis of six genes from chromosomes XIV and XV of Saccharomyces cerevisiae reveals YOR145c as an essential gene and YNL059c/ARP5 as a strain-dependent essential gene encoding nuclear proteins. Yeast 16:, 1025-1033. [PubMed].
- Harata, M., Nishimori, K., and Hatta, S. (2001). Identification of two cDNAs for human actin-related proteins (Arps) that have remarkable similarity to conventional actin. Biochim. Biophys. Acta 1522:, 130-133. [PubMed].
- Harata, M., Oma, Y., Mizuno, S., Jiang, Y. W., Stillman, D. J., and Wintersberger, U. (1999). The nuclear actin-related protein of Saccharomyces cerevisiae, Act3p/Arp4, interacts with core histones. Mol. Biol. Cell 10:, 2595-2605. [PubMed].
- Harata, M., Oma, Y., Tabuchi, T., Zhang, Y., Stillman, D. J., and Mizuno, S. (2000). Multiple actin-related proteins of Saccharomyces cerevisiae are present in the nucleus. J. Biochem. (Tokyo) 128:, 665-671. [PubMed].
- Harata, M., Zhang, Y., Stillman, D. J., Matsui, D., Oma, Y., Nishimori, K., and Mochizuki, R. (2002). Correlation between chromatin association and transcriptional regulation for the Act3p/Arp4 nuclear actin-related protein of Saccharomyces cerevisiae. Nucleic Acids Res. 30:, 1743-1750. [PubMed].
- Higgs, H. N., and Peterson, K. J. (2005). Phylogenetic analysis of the formin homology 2 domain. Mol. Biol. Cell 16:, 1-13. [PubMed].
- Holmes, K. C., Sander, C., and Valencia, A. (1993). A new ATP-binding fold in actin, hexokinase and Hsc70. Trends Cell Biol. 3:, 53-59. [PubMed].
- Holt, R. A. et al. (2002). The genome sequence of the malaria mosquito Anopheles gambiae. Science 298:, 129-149. [PubMed].
- Ikura, T., Ogryzko, V. V., Grigoriev, M., Groisman, R., Wang, J., Horikoshi, M., Scully, R., Qin, J., and Nakatani, Y. (2000). Involvement of the TIP60 histone acetylase complex in DNA repair and apoptosis. Cell 102:, 463-473. [PubMed].
- Jaillon, O. et al. (2004). Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431:, 946-957. [PubMed].
- Kabsch, W., and Holmes, K. C. (1995). The actin fold. FASEB J. 9:, 167-174. [PubMed].
- Kabsch, W., Mannherz, H. G., Suck, D., Pai, E. F., and Holmes, K. C. (1990). Atomic structure of the actin:DNase I complex. Nature 347:, 37-44. [PubMed].
- Kandasamy, M. K., Deal, R. B., McKinney, E. C., and Meagher, R. B. (2004). Plant actin-related proteins. Trends Plant Sci. 9:, 196-202. [PubMed].
- Kandasamy, M. K., McKinney, E. C., and Meagher, R. B. (2003). Cell cycle-dependent association of Arabidopsis actin-related proteins AtARP4 and AtARP7 with the nucleus. Plant J. 33:, 939-948. [PubMed].
- Katinka, M. D. et al. (2001). Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 414:, 450-453 [PubMed].
- Kreppel, L., Fey, P., Gaudet, P., Just, E., Kibbe, W. A., Chisholm, R. L., and Kimmel, A. R. (2004). dictyBase: a new Dictyostelium discoideum genome database. Nucleic Acids Res. 32: Database issue, D332-D333. [PubMed].
- Lander, E. S. et al. (2001). Initial sequencing and analysis of the human genome. Nature 409:, 860-921. [PubMed].
- Le Clainche, C., Didry, D., Carlier, M. F., and Pantaloni, D. (2001). Activation of Arp2/3 complex by Wiskott-Aldrich Syndrome protein is linked to enhanced binding of ATP to Arp2. J. Biol. Chem. 276:, 46689-46692. [PubMed].
- Lecompte, O., Thompson, J. D., Plewniak, F., Thierry, J., and Poch, O. (2001). Multiple alignment of complete sequences (MACS) in the post-genomic era. Gene 270:, 17-30. [PubMed].
- Lee, I. H., Kumar, S., and Plamann, M. (2001). Null mutants of the neurospora actin-related protein 1 pointed-end complex show distinct phenotypes. Mol. Biol. Cell 12:, 2195-2206. [PubMed].
- Lee, Y. H., Campbell, H. D., and Stallcup, M. R. (2004). Developmentally essential protein flightless I is a nuclear receptor coactivator with actin binding activity. Mol. Cell. Biol. 24:, 2103-2117. [PubMed].
- Lees-Miller, J. P., Helfman, D. M., and Schroer, T. A. (1992a). A vertebrate actin-related protein is a component of a multisubunit complex involved in microtubule-based vesicle motility. Nature 359:, 244-246. [PubMed].
- Lees-Miller, J. P., Henry, G., and Helfman, D. M. (1992b). Identification of act2, an essential gene in the fission yeast Schizosaccharomyces pombe that encodes a protein related to actin. Proc. Natl. Acad. Sci. USA 89:, 80-83. [PubMed].
- Machesky, L. M., and May, R. C. (2001). Arps: actin-related proteins. Results Probl. Cell Differ. 32:, 213-229. [PubMed].
- Martin, A. C., Xu, X. P., Rouiller, I., Kaksonen, M., Sun, Y., Belmont, L., Volkmann, N., Hanein, D., Welch, M., and Drubin, D. G. (2005). Effects of Arp2 and Arp3 nucleotide-binding pocket mutations on Arp2/3 complex function. J. Cell Biol. 168:, 315-328. [PubMed].
- Matsuzaki, M. et al. (2004). Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 428:, 653-657. [PubMed].
- McKinney, E. C., Kandasamy, M. K., and Meagher, R. B. (2002). Arabidopsis contains ancient classes of differentially expressed actin-related protein genes. Plant Physiol. 128:, 997-1007. [PubMed].
- Medjkane, S., Novikov, E., Versteege, I., and Delattre, O. (2004). The tumor suppressor hSNF5/INI1 modulates cell growth and actin cytoskeleton organization. Cancer Res. 64:, 3406-3413. [PubMed].
- Minoda, A., Saitoh, S., Takahashi, K., and Toda, T. (2005). BAF53/Arp4 homolog Alp5 in fission yeast is required for histone H4 acetylation, kinetochore-spindle attachment, and gene silencing at centromere. Mol. Biol. Cell 16:, 316-327. [PubMed].
- Mohrmann, L., Langenberg, K., Krijgsveld, J., Kal, A. J., Heck, A. J., and Verrijzer, C. P. (2004). Differential targeting of two distinct SWI/SNF-related Drosophila chromatin-remodeling complexes. Mol. Cell. Biol. 24:, 3077-3088. [PubMed].
- Moseley, J. B., Sagot, I., Manning, A. L., Xu, Y., Eck, M. J., Pellman, D., and Goode, B. L. (2004). A conserved mechanism for Bni1- and mDia1-induced actin assembly and dual regulation of Bni1 by Bud6 and profilin. Mol. Biol. Cell 15:, 896-907. [PubMed].
- Nolen, B. J., Littlefield, R. S., and Pollard, T. D. (2004). Crystal structures of actin-related protein 2/3 complex with bound ATP or ADP. Proc. Natl. Acad. Sci. USA 101:, 15627-15632. [PubMed].
- Olave, I. A., Reck-Peterson, S. L., and Crabtree, G. R. (2002). Nuclear actin and actin-related proteins in chromatin remodeling. Annu. Rev. Biochem. 71:, 755-781. [PubMed].
- Otterbein, L. R., Graceffa, P., and Dominguez, R. (2001). The crystal structure of uncomplexed actin in the ADP state. Science 293:, 708-711. [PubMed].
- Papoulas, O., Beek, S. J., Moseley, S. L., McCallum, C. M., Sarte, M., Shearn, A., and Tamkun, J. W. (1998). The Drosophila trithorax group proteins BRM, ASH1 and ASH2 are subunits of distinct protein complexes. Development 125:, 3955-3966. [PubMed].
- Percipalle, P., Fomproix, N., Kylberg, K., Miralles, F., Bjorkroth, B., Daneholt, B., and Visa, N. (2003). An actin-ribonucleoprotein interaction is involved in transcription by RNA polymerase II. Proc. Natl. Acad. Sci. USA 100:, 6475-6480. [PubMed].
- Peterson, C. L., Zhao, Y., and Chait, B. T. (1998). Subunits of the yeast SWI/SNF complex are members of the actin-related protein (ARP) family. J. Biol. Chem. 273:, 23641-23644. [PubMed].
- Plewniak, F. et al. (2003). PipeAlign: A new toolkit for protein family analysis. Nucleic Acids Res. 31:, 3829-3832. [PubMed].
- Poch, O., and Winsor, B. (1997). Who's who among the Saccharomyces cerevisiae actin-related proteins? A classification and nomenclature proposal for a large family. Yeast 13:, 1053-1058. [PubMed].
- Pollard, T. D., Blanchoin, L., and Mullins, R. D. (2000). Molecular mechanisms controlling actin filament dynamics in nonmuscle cells. Annu. Rev. Biophys. Biomol. Struct 29:, 545-576. [PubMed].
- Pruitt, K. D., Tatusova, T., and Maglott, D. R. (2005). NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 33: Database Issue, D501-D504. [PubMed].
- Pruyne, D., Evangelista, M., Yang, C., Bi, E., Zigmond, S., Bretscher, A., and Boone, C. (2002). Role of formins in actin assembly: nucleation and barbedend association. Science 297:, 612-615. [PubMed].
- Puiu, D., Enomoto, S., Buck, G. A., Abrahamsen, M. S., and Kissinger, J. C. (2004). CryptoDB: the Cryptosporidium genome resource. Nucleic Acids Res. 32: Database issue, D329-D331. [PubMed].
- Robinson, R. C., Turbedsky, K., Kaiser, D. A., Marchand, J. B., Higgs, H. N., Choe, S., and Pollard, T. D. (2001). Crystal structure of Arp2/3 complex. Science 294:, 1679-1684. [PubMed].
- Rodal, A. A., Sokolova, O., Robins, D. B., Daugherty, K. M., Hippenmeyer, S., Riezman, H., Grigorieff, N., and Goode, B. L. (2005). Conformational changes in the Arp2/3 complex leading to actin nucleation. Nat. Struct. Mol. Biol. 12:, 26-31. [PubMed].
- Sablin, E. P., Dawson, J. F., VanLoock, M. S., Spudich, J. A., Egelman, E. H., and Fletterick, R. J. (2002). How does ATP hydrolysis control actin's associations? Proc. Natl. Acad. Sci. USA 99:, 10945-10947. [PubMed].
- Sagot, I., Rodal, A. A., Moseley, J., Goode, B. L., and Pellman, D. (2002). An actin nucleation mechanism mediated by Bni1 and profilin. Nat. Cell Biol. 4:, 626-631. [PubMed].
- Schafer, D. A., and Schroer, T. A. (1999). Actin-related proteins. Annu. Rev. Cell Dev. Biol. 15:, 341-363. [PubMed].
- Schroer, T. A., Fyrberg, E., Cooper, J. A., Waterston, R. H., Helfman, D., Pollard, T. D., and Meyer, D. I. (1994). Actin-related protein nomenclature and classification. J. Cell Biol. 127:, 1777-1778. [PubMed].
- Schwob, E., and Martin, R. P. (1992). New yeast actin-like gene required late in the cell cycle. Nature 355:, 179-182. [PubMed].
- Shen, X., Ranallo, R., Choi, E., and Wu, C. (2003). Involvement of actin-related proteins in ATP-dependent chromatin remodeling. Mol. Cell 12:, 147-155. [PubMed].
- Sunada, R., Görzer, I., Oma, Y., Yoshida, T., Suka, N., Wintersberger, U., and Harata, M. (2005). The nuclear actin-related protein Act3p/Arp4p is involved in the dynamics of chromatin-modulating complexes. Yeast 22:, 753-768. [PubMed].
- Szerlong, H., Saha, A., and Cairns, B. R. (2003). The nuclear actin-related proteins Arp7 and Arp9, a dimeric module that cooperates with architectural proteins for chromatin remodeling. EMBO J. 22:, 3175-3187. [PubMed].
- Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:, 4673-4680. [PubMed].
- Thompson, J. D., Plewniak, F., Ripp, R., Thierry, J. C., and Poch, O. (2001). Towards a reliable objective function for multiple sequence alignments. J. Mol. Biol. 314:, 937-951. [PubMed].
- Thompson, J. D., Prigent, V., and Poch, O. (2004). LEON: multiple alignment evaluation of neighbours. Nucleic Acids Res. 32:, 1298-1307. [PubMed].
- Thompson, J. D., Thierry, J. C., and Poch, O. (2003). RASCAL: rapid scanning and correction of multiple sequence alignments. Bioinformatics 19:, 1155-1161. [PubMed].
- van Attikum, H., Fritsch, O., Hohn, B., and Gasser, S. M. (2004). Recruitment of the INO80 complex by H2A phosphorylation links ATP-dependent chromatin remodeling with DNA double-strand break repair. Cell 119:, 777-788. [PubMed].
- Venter, J. C. et al. (2001). The sequence of the human genome. Science 291:, 1304-1351. [PubMed].
- Volkmann, N., Amann, K. J., Stoilova-McPhie, S., Egile, C., Winter, D. C., Hazelwood, L., Heuser, J. E., Li, R., Pollard, T. D., and Hanein, D. (2001). Structure of Arp2/3 complex in its activated state and in actin filament branch junctions. Science 293:, 2456-2459. [PubMed].
- Vorobiev, S., Strokopytov, B., Drubin, D. G., Frieden, C., Ono, S., Condeelis, J., Rubenstein, P. A., and Almo, S. C. (2003). The structure of nonvertebrate actin: implications for the ATP hydrolytic mechanism. Proc. Natl. Acad. Sci. USA 100:, 5760-5765. [PubMed].
- Waterston, R. H. et al. (2002). Initial sequencing and comparative analysis of the mouse genome. Nature 420:, 520-562. [PubMed].
- Weber, V., Harata, M., Hauser, H., and Wintersberger, U. (1995). The actin-related protein Act3p of Saccharomyces cerevisiae is located in the nucleus. Mol. Biol. Cell 6:, 1263-1270. [PubMed].
- Wicker, N., Dembele, D., Raffelsberger, W., and Poch, O. (2002). Density of points clustering, application to transcriptomic data analysis. Nucleic Acids Res. 30:, 3992-4000. [PubMed].
- Wood, V. et al. (2002). The genome sequence of Schizosaccharomyces pombe. Nature 415:, 871-880. [PubMed].
- Zhao, K., Wang, W., Rando, O. J., Xue, Y., Swiderek, K., Kuo, A., and Crabtree, G. R. (1998). Rapid and phosphoinositol-dependent binding of the SWI/SNF-like BAF complex to chromatin after T lymphocyte receptor signaling. Cell 95:, 625-636. [PubMed].
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