- Research article
- Open Access
Molecular evolution of NASP and conserved histone H3/H4 transport pathway
© Nabeel-Shah et al.; licensee BioMed Central Ltd. 2014
Received: 27 February 2014
Accepted: 12 June 2014
Published: 20 June 2014
NASP is an essential protein in mammals that functions in histone transport pathways and maintenance of a soluble reservoir of histones H3/H4. NASP has been studied exclusively in Opisthokonta lineages where some functional diversity has been reported. In humans, growing evidence implicates NASP miss-regulation in the development of a variety of cancers. Although a comprehensive phylogenetic analysis is lacking, NASP-family proteins that possess four TPR motifs are thought to be widely distributed across eukaryotes.
We characterize the molecular evolution of NASP by systematically identifying putative NASP orthologs across diverse eukaryotic lineages ranging from excavata to those of the crown group. We detect extensive silent divergence at the nucleotide level suggesting the presence of strong purifying selection acting at the protein level. We also observe a selection bias for high frequencies of acidic residues which we hypothesize is a consequence of their critical function(s), further indicating the role of functional constraints operating on NASP evolution. Our data indicate that TPR1 and TPR4 constitute the most rapidly evolving functional units of NASP and may account for the functional diversity observed among well characterized family members. We also show that NASP paralogs in ray-finned fish have different genomic environments with clear differences in their GC content and have undergone significant changes at the protein level suggesting functional diversification.
We draw four main conclusions from this study. First, wide distribution of NASP throughout eukaryotes suggests that it was likely present in the last eukaryotic common ancestor (LECA) possibly as an important innovation in the transport of H3/H4. Second, strong purifying selection operating at the protein level has influenced the nucleotide composition of NASP genes. Further, we show that selection has acted to maintain a high frequency of functionally relevant acidic amino acids in the region that interrupts TPR2. Third, functional diversity reported among several well characterized NASP family members can be explained in terms of quickly evolving TPR1 and TPR4 motifs. Fourth, NASP fish specific paralogs have significantly diverged at the protein level with NASP2 acquiring a NNR domain.
The fundamental repeating unit of eukaryotic chromatin is the nucleosome that wraps a 146 bp stretch of DNA around a histone octamer consisting of two of each of histone H2A, H2B, H3 and H4 . The transport of histones from the cytoplasm to the nucleus and their subsequent assembly into nucleosomes is mediated by a diverse set of proteins including histone chaperones  that are classified into several families based on their binding specificities and sequence and structural similarities . One group of histone H3/H4 chaperones is the nuclear autoantigenic sperm protein (NASP) family also known as the N1/N2 family.
The founding member of the NASP family is Xenopus laevis N1/N2, which is expressed in oocytes and specifically binds histones H3/H4, providing a mechanism for the storage of the soluble histones required for DNA replication in the early embryo [3, 4]. NASP is the mammalian homolog of N1/N2 and was first described in rabbit testes as a highly autoantigenic protein which shares greater than 50% similarity to N1/N2 [5, 6]. In mammals, NASP predominantly exists as two alternatively spliced isoforms; one is considerably longer than the other and is expressed in embryonic tissues and testis (tNASP) whereas the smaller version which lacks a region of 339 amino acids is called the somatic NASP (sNASP) and is highly expressed in all dividing cells . NASP expression is tightly cell cycle regulated and its over-expression causes delay in cell cycle progression at the G1/S border [7, 8]. NASP expression is essential in mammals as its gene disruption results in early embryonic lethality in mice . Previous studies have shown that human NASP co-purifies with replication dependent and independent histones H3.1 and H3.3 respectively [10, 11]. In human cells, newly synthesized histones H3.1/H4 are thought to successively pass through at least four distinct cytosolic complexes [10, 12]. In this context, NASP has been shown to be involved in accepting the histones from heat shock proteins, in the Hat1-dependent acetylation of H4, and subsequently handing over these histones to another histone chaperone, anti-silencing factor 1 (Asf1) through a physical interaction that has been shown to exist in humans and Saccharomyces cerevisiae[10, 12, 13].
NASP family proteins share conserved motifs, possessing four tetratricopeptide repeats (TPR) where the second TPR is typically interrupted by a large acidic domain . The NASP structural organisation is conserved from fungi to mice forming the SHNi-TPR protein family that was named for three initially characterized members, Silencing in the middle of the centromere protein 3 (Sim3– Schizosaccharomyces pombe), H at1p-interacting factor-1 (Hif1, S.cerevisiae), and N ASP-interrupted TPR repeats . The TPR motifs are 34 amino acid long amphipathic helices that form a helix-turn-helix arrangement and are thought to provide a structural scaffold for mediating protein-protein interactions . Different TPR motifs in human NASP show different binding affinities for either histone H3/H4 or H1. For example, the acidic patch present within TPR2 is critical for H1-binding whereas TPR4 mediates the interaction with core H3/H4 histones . These studies suggest that NASP might be involved in multiple functions involving histone dynamics (for review see ).
In addition to mammals, NASP homologs have been detected in several eukaryotic models such as S. cerevisiae (Hif1), S. pombe (Sim3) and Caenorhabditis elegans (NASP-1) [14, 18, 19]. In addition to their conserved motif arrangement, these proteins share functional similarity in that they generally demonstrate histone H3/H4 chaperone activity . Despite this, some functional diversity does exist among NASP family proteins. For example, Hif1 physically interacts with Hat1 and Hat2 as part of the Hat1 complex that functions in the acetylation of newly synthesized histone H4 [19, 20], whereas Sim3 appears to specifically function in deposition of the centromeric H3 variant , and does not appear to physically interact with Hat1 [21, 22]. In addition to this, a recent report suggests that Sim3 also has a general role in chromatin maintenance and acts as an H3/H4 chaperone with some overlapping functional characteristics with Asf1 . In C. elegans, NASP-1 has been implicated in female development through its interactions with histone deacetylase and TRA-4 proteins . Additionally, human NASP functions in the fine tuning of a soluble reservoir of histones H3/H4 by handing over excess histone H3 and H4 to heat shock proteins (HSP90/HSC70) for chaperone mediated autophagy .
In humans, NASP expression is significantly altered in a variety of cancers including those of the ovary and prostate [25–27]. Despite the demonstrated role of NASP in a wide range of cellular processes, questions remain about the underlying mechanistic details of NASP function. Recently, we found that a NASP family protein, NASP-related protein 1 (Nrp1) co-purifies with Asf1 in the ciliate protozoan Tetrahymena thermophila suggesting that the Asf1-NASP physical interaction is evolutionarily conserved in eukaryotes. Molecular evolutionary analysis has the potential to provide useful insights into protein function as well as providing information about changes in interacting partners [29, 30]. Molecular evolutionary analyses of the proteins involved in the transport of histones H3/H4 including HSP90, Asf1 and Importinβ have previously been reported and suggest that these proteins are highly conserved throughout the eukaryotes [31–33]. Although NASP has been suggested to be equally widely present among eukaryotes , a comprehensive phylogenetic analysis of NASP family proteins is lacking.
We present here a comprehensive phylogenetic analysis of NASP family proteins. Our analysis indicates that NASP is conserved across all of the major eukaryotic lineages ranging from the excavata to the crown group (animals, fungi, amoebozoans and plants) suggesting that the NASP histone chaperone was most likely present in the LECA. Furthermore, we show that in addition to the conserved arrangement of the four TPR motifs, an overall negatively charged nature is preserved in NASP family members suggesting that diversification of these proteins during eukaryotic evolution must have been determined by strong functional and structural constraints. High acidic amino acid composition in the TPR2 interruption region has been maintained by the presence of strong selection which in turn has biased the nucleotide composition in the corresponding NASP gene. Furthermore, we show that among ray-finned fish, NASP has undergone gene duplication and two paralogs exist under different genomic G + C environments which suggests functional diversification of the two proteins. The present work combined with previous evolutionary analyses on Asf1, HSP90 and Importinβ proteins, suggests that histones H3/H4 are transported via an evolutionarily conserved pathway that most likely was present in the last eukaryotic ancestor.
NASP is highly conserved in eukaryotes
We used PSI-BLAST searches with default parameters to identify putative NASP orthologs across a wide range of eukaryotic lineages including those of the crown group (animals, fungi, amoebozoans and plants), the Guillardia nucleomorph, chromalveolates (apicomplexans, ciliates, oomycetes, and diatoms), and excavatas (parabasalids and kinetoplastida). Searches were carried out using the non-redundant database available at the NCBI website (http://www.ncbi.nlm.nih.gov/) and identified sequences were recovered in the reciprocal searches (for accession numbers see Additional file 1: Table S1). The NASP family proteins contain a Pfam domain (PF10516) called SHNi-TPR which is an interrupted form of the TPR motif . In order to correctly identify putative NASP orthologs, all sequences we obtained were analysed using the Pfam database  to confirm the presence of SHNi-TPR (PF10516) (see Methods for details). We queried the eggNOG orthology database  using human NASP and T. thermophila Nrp1protein sequences as reference, and observed that NASP forms an orthology group (KOG4563) with 117 protein members from 90 different eukaryotic species including several that were identified through our PSI-BLAST searches. However, several previously unreported putative NASP orthologs not present in the eggNOG database were also identified in this study through PSI-BLAST searches.
The distinctive feature of NASP family proteins is the presence of a TPR motif which is interrupted by a large acidic tract , and also revealed by our comparative sequence alignments (see below). In order to gauge the broad distribution of NASP proteins among eukaryotes, we prepared a hidden Markov Model (HMM) profile of the alignment of this region of the sequences culled from PSI-BLAST searches and screened through UniProtKB using HMMsearch . This resulted in the recovery of significant hits (e ≤ 10-5) throughout eukaryotes with the notable exception of diplomonads (Additional file 2). Recovered sequences were analysed for the motif organisation and presence of SHNi-TPR/PF10516. Thus NASP appears widely distributed across the eukaryotes and may have emerged very early during the eukaryotic diversification. In fact the identification of putative NASP proteins through BLAST searches in excavata lineages (e.g., Parabasalids (Trichomonas vaginalis) and kinetoplastids (Trypanosoma)) which are thought to be highly divergent eukaryotic lineages [38–40] suggest that NASP was likely present in the LECA. Despite our repeated searches, we were unable to identify any putative NASP orthologs in diplomonads suggesting loss of this gene in these lineages.
Synteny, or gene neighbourhood analysis, often provides a good indication of correct identification of orthologs within closely related species . We analysed the synteny of NASP among sequenced tetrapods and some other vertebrates using Genomicus . We observed that gene pairs CCDC17, GPBP1L1 (coiled-coil domain containing 17 and GC-rich promoter binding protein 1-like 1, respectively) and AKR1A1, PRDX1 (aldo-ketoreductase family 1, member A1 and peroxiredoxin 1, respectively) are found on either side of the NASP gene. We were able to trace back this conserved gene neighbourhood to the coelacanth Latimeria chalumnae which is considered the closest living relative of tetrapods . These results suggest that the NASP genomic organisation is conserved among tetrapods.
Conserved TPR domain organisation
NASP proteins are defined by the presence of four TPR motifs where the second TPR is typically interrupted by large acidic patches. In addition, the TPR4 in S. pombe has also been predicted to contain a small insertion of 5 residues within the linker region that connects the two helices . Our multiple sequence alignment (MSA) analysis indicates that the TPR motif sequence and arrangement are well conserved with TPR1 and TPR3/4 flanking the interrupted TPR2 (Additional file 3: Figure S1A-E). The second residue of each TPR repeat often has a side chain that is either negatively charged or amidated . For kinetoplastid lineages, we observed that the region interrupting TPR2 is significantly smaller than the others including humans, fungi and ciliates, consisting of 16 amino acid residues that mostly are hydrophobic and not predominantly acidic (For TPR organisation see: Additional file 3: Figure S1E). These kinetoplastid NASP do however possess an overall net negative charge with several acidic residues located mostly at the N-terminus. Furthermore, our analysis also indicates that T. vaginalis putative NASP is highly divergent and the TPR2 interruption region consists of only 10 residues with at least half of them acidic. However, several acidic residues are also found dispersed throughout the protein, thus giving it an overall net negative charge (data not shown). Interestingly, MSA and Pfam domain analysis also revealed that among a few selected lineages NASP has gained additional domains. For example, in addition to the conserved four TPRs, the putative NASP in Trichoplax adhaerens (phylum: Placozoa) contains an N-terminal MADF domain (PF10545) whereas Phytophthora infestans and P. sojae (both oomycetes) have gained an N-terminal Longin domain (PF13774). Such isolated instances of domain gain likely represent lineage specific functional divergence.
MSA analysis of NASP family TPRs from a wide range of eukaryotic lineages permitted us to identify highly conserved residues that have been kept almost unchanged throughout evolution. For example, we noted that in addition to conserved hydrophobic residues found in all four TPRs, the amino acids at positions 7 and 8 are also highly conserved (Additional file 3: Figure S1 A-E). For TPR1, the amino acids at positions 12 (leucine) and 21 (valine) have also remained almost unchanged suggesting that these residues are functionally relevant. Similarly, residues at positions 12 (leucine), 15 (alanine), 21 (tryptophan) and 24 (leucine) in TPR2 as well as positions 9 (glutamic acid), 11 (serine), 28/30 (leucine/leucine or isoleucine) in TPR3 and positions 10 (alanine) and 31 (isoleucine or leucine) of TPR4 are highly conserved. In addition, selected positions contain amino acids with similar biochemical properties (see the MSA in Additional file 3). It is also worth noting that a previously reported small C-terminal basic patch that could function as a nuclear localization signal  is also conserved in all NASP family members studied here (data not shown). Nevertheless, we also observed some lineage specific variations at selected amino acid positions. For instance, among vertebrates, TPR1 amino acid positions 6 and 9 invariably are glycine and glutamine respectively, whereas among insects these residues have been substituted with serine and lysine, respectively. Similarly, amino acid positions 9 and 6 (both lysine) in TPR2 and TPR3, respectively, are highly conserved among vertebrates whereas they are more variable among other lineages (see the MSA in Additional file 3). The wide distribution of NASP in eukaryotic super-groups as well as the conserved pattern of TPR motifs strongly suggests that these amino acid variations represent a case of functional divergence among different orthologous proteins. In accordance with Dunleavy et al.  we also detected small insertions in the TPR4 of certain fungal lineages including S. pombe, S. japonicus, Cryptococcus gattii, Candida albicans, Coccidioides immitis and Neurospora crassa. Furthermore, Albugo laibachii (a genus of oomycetes) and Thalassiosira pseudonana (marine centric diatom) have each also experienced an insertion of 38 residues in the TPR4 (Additional file 3: Figure S1-D). The functional importance of these insertions is unknown. They may however represent convergent changes that arose independently among different lineages.
Phylogenetic analysis of NASP
The resulting phylogenetic tree recovered different taxonomic groups with well-defined topology as indicated by high statistical support for each internal node (Figure 1). This highly structured tree topology closely resembles the eukaryotic phylogeny inferred from rRNA sequences [46, 49]. Thus with a few notable exceptions (see below), the overall topology suggests that NASP evolution parallels eukaryotic evolution. Chromalveolates branched first forming a monophyletic group followed by the diversification of the crown group lineages. Significant diversification is observed among different chromalveolata lineages as evidenced from the average amino acid variations (p = 0.721 ± 0.019 substitutions per site) along with the varying branch lengths and grouping patterns on the tree (Figure 1). Ciliates form their own subgroup which is closely related to the apicomplexans with a monophyletic origin whereas oomycetes and diatoms are more closely related to each other than to the ciliates or apicomplexans. The crown group lineages with the exception of choanoflagellates and amoebozoans form a monophyletic group with a dichotomous topology such that fungi and plants fall within one monophyletic group whereas the remaining animals fall within another group.
The NASP differentiation within fungal and plant lineages occurred at the same time as evidenced from the monophyly of these groups with a moderate statistical support (ML bootstrap support of 35, Bayesian posterior probability of 65; Figure 1). This pattern of divergence deviates from accepted eukaryotic species phylogeny in which plants and fungi acquire distinct monophyletic groups [46–49]. Figure 1 demonstrates that plant lineages cluster together with relatively short branch lengths suggesting that NASP is highly conserved within plants. This observation is further supported by estimating average evolutionary divergence values (p = 0.251±0.027 substitutions per site) for plant lineages. Fungal species form their own monophyletic subgroup with significant diversity apparent within basidiomycota and most ascomycota lineages. Long branches and moderately high average of amino acid sequence variations (p = 0.696±0.019 substitutions per site) among nine fungal lineages provide further support for the presence of considerable differentiation among these proteins. Interestingly, S. cerevisiae and another related ascomycota fungus Tetrapisispora phaffii appear to be closely related to each other and quite divergent from the remaining ascomycotes as can be seen from their position in the phylogeny which is closer to basidiomycotes (Trichosporon asahii and C. gattii) than other ascomycota lineages. This suggests that Hif1 of S. cerevisiae and T. phaffii might have evolved faster in comparison to the other fungal lineages.
The chordate lineages form a monophyletic sub-group within which tunicates, which are thought to be the closest living relatives of vertebrates , group together and take the basal position followed by diversification among vertebrate lineages. Further analysis of the tree topology reveals that NASP lineages corresponding to fish cluster together whereas the differentiation of NASP in amphibians is followed by its diversification within mammals and aves. For NASP lineages corresponding to mammals and aves, we observed a minor disagreement between ML and Bayesian analyses. For the ML tree, aves lineages form a distinct subgroup as a sister clade to the mammals. Under Bayesian analysis however the differentiation of mammals and aves appears to have occurred concurrently. This discrepancy is consistent with the relatively low statistical support for the ML tree (Figure 1). As noted earlier, choanoflagellates and amoebozoans are the two exceptions to the general trend of NASP evolution seen for the crown group lineages. Both of these lineages take the basal position in the phylogeny before the differentiation of chromalveolates indicating that these proteins are highly diverged and may be subject to strict lineage-specific functional constraints. Consistent with this we observed a long stretch of serine/threonine tandem repeats at the N-terminus of amoebozoan lineages (data not shown). Human NASP proteins have previously been predicted to contain a large number of potential serine/threonine phosphorylation sites with a few found towards the protein’s N-terminus . However, the presence of serine/threonine tandem repeats at the N-terminus may represent a lineage-specific adaptation although the functional significance remains unclear. An examination of multiple sequence alignments (Additional file 3: Figure S1, A-D) indicates amino acid variations at certain highly conserved and structurally relevant positions in TPRs1-4 for choanoflagellates. For example, glycine is invariably found at position 8 of TPR1 (Additional file 3). However in choanoflagellates, it has been substituted to the basic residue lysine. Furthermore, position 17 of TPR1 and position 4 of TPR2 in choanoflagellates have been substituted by lysine and glutamine respectively in place of conserved hydrophobic residues (Additional file 3: Figure S1-A,B). Similarly, we observed that position 9 of TPR3 which almost invariably contains an acidic amino acid (glutamic acid/aspartic acid) has been replaced by a serine which is a polar neutral amino acid and only becomes acidic when phosphorylated, and highly conserved hydrophobic positions 21 and 13 have been substituted by glutamic acid and glutamine residues for TPR3 and TPR4, respectively (Additional file 3: Figure S1-C, D). Such variation at apparently key amino acid positions in the functional units (TPRs in this case) of a protein could possibly impact/alter its function and/or interactions with other proteins.
Average number of amino acid and nucleotide variations along with average synonymous ( p S ) and non-synonymous ( p N ) differences per site among NASP lineages from various taxonomic groups
Average number of amino acid and nucleotide variations among different TPR domains
Constraints on NASP evolution
We employed several complementary methods to estimate the selective forces operating on NASP evolution. We used the NASP nucleotide coding sequences from the representative lineages of all eukaryotic super groups (Additional file 6: figure S4-A). We carried out a codon-based Z-test of selection by comparing synonymous and non-synonymousvariations. Our results reveal extensive synonymous variation, considerably higher than non-synonymous variations (***P<0.001) in all comparisons (Table 1). In fact the level of silent substitutions was generally very high when compared across all the species (pS(SE)=0.73±0.006, pN(SE)=0.5± 0.01; ***P<0.001; Additional file 6: Figure S4-A). These results suggest the presence of strong purifying selection acting at the protein level, presumably to maintain appropriate structure required for NASP function. To ascertain the functional constraints operating on different regions of the protein, we extended our analysis by distinguishing between TPRs (combined), the acidic region and the remaining parts of the protein for different taxonomic groups (Additional file 1: Table S2), as well as among individual TPRs (Table 2). The results indicate that the amount of silent variation is always significantly higher than the non-silent variation in all Z-test comparisons (for P-values and test statistics refer to Table 2 and Additional file 1: Table S2). Table 2 also reveals that although the number of synonymous variations is always higher than the non-synonymous, the non-synonymous variations are significantly greater for TPR1/4 in comparison to TPR2/3. These results support our observation that TPR1/4 are diverging more quickly than the TPR2/3. In addition, overall nucleotide diversity for four TPRs calculated using a sliding window approach indicates that TPR1 and TPR4 exhibit higher amounts of divergence relative to TPR2/3 (Additional file 6: Figure S4-B).
Positive selection often affects only a few sites during a protein’s molecular evolution. We therefore conducted an ML-based analysis for detecting the nature of selective forces operating upon each individual codon in NASP coding sequences among different taxonomic groups. We used the program HyPhy to conduct the analysis (see Methods for details) . Our results do not indicate that any codons have been under positive selection at the statistical threshold of P<0.05 (codon data not shown). These studies suggest that the purifying selection has been the dominant factor during NASP evolution.
Codon usage bias referred to as the effective number of codons (ENC) estimated in NASP discriminating different taxonomic groups
Genomic GC correlation with GC-rich and GC-poor amino acids in NASP family proteins
Spearman rank correlation coefficient (r S )
Genomic GC vs. GAPW
Genomic GC vs. FYMINL
Genomic GC vs. Alanine
Genomic GC vs. Lysine
To further assess the role of natural selection, we compared the changes at the first codon position (non-synonymous) with those at the third codon position (synonymous) in the most abundant residues. The nucleotide frequencies at these two codon positions should not be significantly different from each other according to the expectations of the neutral model . Codons for the GC-rich residue alanine possess G at the first position whereas codons for the GC-poor residue lysine have A at the first position. Our analysis indicates that the mean G+A content at the first position (69.7±3.8) is significantly greater than the mean G+A content (46.54±15.8) at the four fold degenerate sites (t test = 8.98, p= 0.000). Furthermore, the mean G+A content at the first codon position and at four-fold degenerate sites do not significantly correlate (rS= 0.01, p-value= 0.945). These results suggest that selection has influenced the nucleotide composition to maintain a high frequency of alanine and lysine.
Glutamic acid and aspartic acid are also found from high to moderate frequencies as determined by the amino acid composition of NASP family proteins (data not shown; Additional file 1: Table S4). Codons for both of these residues have G at their first position as do alanine codons. It is therefore reasonable to assume that the elevated levels of G+A at the first codon position might be due to the selection for glutamic and aspartic acids in addition to alanine and lysine. This conclusion is further supported by the observation that nucleotide differences between the first and the third codon positions for alanine and lysine was most evident in the acidic domain that interrupts the TPR2 of the NASP proteins. The mean G+A content at the first position (81.0±7.6) is significantly greater than the mean G+A content (6.7±23.1) at the four fold degenerate sites (t test = 20.05, p= 0.000). Furthermore, Z-test of selection also indicates the presence of strong purifying selection on the acidic domain of NASP proteins (Additional file 1: Table S2).
Provided that the clustering pattern of negatively charged NASP proteins is well differentiated with respect to different taxonomic groups (Figure 1), we assessed the potential role in selection of electrostatic interaction properties of different NASP proteins from each eukaryotic representative group (Additional file 7: Figure S7). Given that the crystal structure is not at present available for any of the NASP proteins, we used the I-TASSER server for structural predictions . Subsequently, the predicted structures were used to estimate the electrostatic potentials and their similarity indices using the web-PIPSA pipeline . Our results indicate that differences in electrostatic potential is not the major evolutionary driving force as the representative NASP proteins from different taxonomic groups do not follow any particular clustering patterns (Additional file 7: Figure S7). These results suggest that selection has continuously acted in one direction to maintain high amounts of negatively charged amino acids particularly in the acidic domain, resulting in an overall net negative charge of NASP proteins presumably for their interaction with positively charged histones (also see Additional file 1: Table S4).
In addition to the NASP splice variants present in most vertebrate species which generate functional diversity in NASP (for review see ), we observed that selected lineages have undergone gene duplication events. Gorilla, Felis and Taeniopygia among chordates and Caenorhabditis among nematodes each contain two NASP paralogs. Furthermore, we observed that among chordates, the ray-finned fish lineages also have undergone the gene duplication in the ancestral genome of clupeocephala (~320 million years ago) , and Danio rerio has subsequently lost one copy of the gene. In most cases each of the two NASP paralogs has protein coding splice variants as assessed by ‘ensembl’ gene annotation . This may generate additional functional diversity although the significance remains obscure.
Different genomic contexts for NASP1 and NASP2
To gain insight into the genomic environment in which the two paralogs reside we analysed the synteny of duplicated genes. We observed that similar to other tetrapods, the ancestral NASP in the genome of clupeocephala has CCDC17 and AKR1A1 as its neighbours. Furthermore, among ray-finned fish lineages GPBP1L1 and PRDX1 genes which are also found in the NASP neighbourhood among other tetrapods are present as the immediate neighbours for at least one of the NASP paralogs (NASP1) whereas the direct neighbours of the NASP2 include GPC5 and LRRC7 genes. Along with NASP, the TMEM69 gene which is found in the NASP neighbourhood among most of the vertebrates has also been duplicated suggesting a large segmental duplication event. This duplication (~320MYA) may represent the signature of the whole genome duplication that took place in the ancestor of ray-finned fish . Among other vertebrate lineage specific paralogs, NASP1 has the conserved gene neighbourhood (see above) whereas NASP2 neighbours include CHD7 in Gorilla, BICD1 in Felis catus and a gene that encodes a putative Zinc Finger protein in Taeniopygia guttata. Our analysis also indicates that the NASP1 immediate neighbour in C. elegans is APC-17, whereas an uncharacterized gene lies next to the NASP2. From the analysis of gene structure and predicted protein sequences for T. guttata and F. catus paralogs, we observed that NASP2 are relatively smaller proteins (105 and 152 amino acids, respectively) and comprise only N- and C-termini respectively of the NASP1in these lineages. As these proteins lack TPR motifs or any other known functional units of NASP, we omitted them from further analyses.
The single NASP in the distantly related D. rerio clusters with NASP2 on the phylogenetic tree (Additional file 8: FigureS8A), and has a 42.5% GC3 (Additional file 7: Figure S5), suggesting that the lost copy of the gene is NASP1. However, the syntenic organisation of D. rerio NASP resembles that of NASP1 where it directly neighbours CCDC17 and AKR1A1 whereas GPBP1L1 is found next to CCDC17. Low %GC3 for D. rerio NASP correlates with the previous findings that the D. rerio genome has a lower GC content relative to the other fishes e.g., Oryzias latipes and Tetraodon.
The differences in the genomic environments may have a role in acquiring paralog-specific functions through distinct mutational biases  (for review, see ). High GC content has previously been correlated with elevated levels of gene transcription  as well as with the extent of codon usage bias . We assessed the extent of codon bias between the two paralogs and observed that among fish lineages, NASP1 demonstrates more biased trends in codon usage than the NASP2 (Figure 4B). Similar trends were also seen for their corresponding neighbouring genes (Additional file 8: Figure S8 B-C). Furthermore, it is also evident from Figure 4B that among Caenorhabditis, NASP2 exhibits slightly more biased codon usage than NASP1. Codon usage bias has previously been linked to selection for translational efficiency required for highly expressed genes and it has been shown that the preferred codons are often those which are recognised by the most frequent tRNAs . For ray-finned fish and Caenorhabditis specific NASP paralogs however, compositional bias (G+C content) appears to be an important factor in shaping the codon usage. The observed compositional and codon usage bias could be linked to differential gene expression which has been proposed to provide indirect evidence for sub-functionalization and/or neo-functionalization .
Functional differentiation of NASP Paralogs
We analysed the four TPR motifs and found that NASP paralogs in fish and Caenorhabditis have maintained the conserved arrangement of four TPRs whereas Gorilla NASP2 has lost the entire TPR1 and partially the TPR2 (see below). We focused on fish-specific NASP1/2 due to their clear pattern of evolutionary divergence as evident from Figure 3. We compared the two paralogous proteins with the reconstructed ancestral sequence and observed amino acid substitutions at key residues within each TPR suggesting that both lineages have diverged from the ancestral state (For MSA Additional file 8: Figure S8D-G). Our analysis indicates that TPR4 accumulated the greatest number of variations with 15 residues substituted followed by TPR1which has 6 residues changed. In order to assess the selective pressures operating on different regions of the two paralogs, we conducted a codon based Z-test of selection for each pair of sequences. While our analysis suggests the presence of purifying selection (data not shown and Additional file 1: Table S5), it should be noted that after a gene duplication, positive selection may affect only a few residues that might not be detected by pair-wise comparison methods . Nevertheless amino acid variations in the functional units along with the loss of N-terminal residues from NASP1 and the presence of an NNR domain in NASP2 provides indirect evidence for the functional differentiation between the two paralogs.
In contrast to the fish lineages, Gorilla NASP2 has lost the entire TPR1 and part of TPR2, as noted above. Furthermore, in the TPR2 interruption region it also lacks a stretch of 141 amino acid residues that are present in the NASP1. As a result NASP2 (582 amino acids in length) is much smaller than NASP1 (789 amino acids). Ensemble gene annotation indicates that unlike its other mammalian homologs (e.g. humans), Gorilla NASP1 does not have any splice variants equivalent in size to sNASP. These observations suggest that NASP2 might have assumed important functions regarding histone dynamics, e.g., similar to sNASP in other mammals. Our MSA analysis shows that the remaining regions of two paralogs including TPRs 3/4 are highly conserved with only a few amino acid substitutions (Additional file 8: Figure S8H-K). Low level of amino acid substitutions suggest that gene duplication probably occurred relatively recently. A Z-test of selection indicates that while most regions of the two proteins are evolving neutrally, the TPR2 interruption region demonstrates signs of positive selection (Additional file 1: Table S6). These results suggest that despite overall sequence conservation between Gorilla NASP1 and NASP2, the TPR2 interruption region has diverged significantly under the positive selection, possibly acquiring new function(s).
NASP interacting partners are conserved
NASP functions in the H3/H4 transport pathway and interacts with a histone chaperone Asf1 as well as an Impβ which is a karyopherin-β family protein [10, 12, 13]. To estimate the wide distribution of NASP interacting proteins, we used Asf1 and Impβ protein sequences from well characterized family members such as humans and S. cerevisiae and explored the non-redundant database with PSI-BLAST using default parameters. Reciprocally recovered sequences for both Asf1 and Impβ were used to prepare an HMMprofile for each of the proteins and Hmmsearch was conducted to scan the UniProKb. We recovered the putative Asf1 and Impβ orthologs throughout the major eukaryotes, consistent with previous reports [31, 33] (See Additional file 9 and Additional file 10 for accession numbers and species). The karyopherin-β family proteins contain a Pfam domain IBN_N (PF03810) whereas the Asf1 family has a PF04729 domain. The recovered sequences from Hmmsearch were analysed for the presence of these domains in each case. The presence of Asf1 and Impβ proteins throughout the major eukaryotic groups suggests that similar to NASP, these proteins are also highly conserved and likely were present in the LECA.
NASP is an essential protein in mammals and has a critical role in the trafficking of newly synthesized histones H3/H4 [10, 12]. However, until now there has been a lack of information regarding the molecular evolution of NASP. We carried out a detailed phylogenetic analysis and establish that NASP evolution parallels that of eukaryotes. We also shed light on the selective forces operating on the evolution of NASP.
Evolutionary conservation of NASP
Our ability to detect NASP in a wide range of eukaryotic lineages including highly divergent T. vaginalis and an organism with a reduced genome (G. theta), argues that the protein is widely distributed throughout eukaryotes, and is a key generalized histone chaperone that most likely was present in the LECA. The histone chaperone Asf1 which has been shown to physically interact with NASP in humans, budding yeast and the ciliate protozoan T. thermophila[10, 13, 28] is also highly conserved throughout the eukaryotes , and most likely was present in the LECA. We propose that that the NASP-Asf1-Importinβ interaction is equally ancient and has a critical role in histone H3/H4 metabolism.
Despite our extensive searches, we were unable to detect putative NASP homologs in diplomonads. This apparent loss is analogous to the absence of Histone Periodic Control 2 (Hpc2) in diplomonads . Hpc2 is a subunit of an evolutionarily conserved H3/H4 chaperone Histone Regulator (HIR) complex which physically interacts with Asf1 during replication independent chromatin assembly . The HUN domain of Hpc2 has been suggested to be a histone tail-binding subunit of the HIR complex which might be critical for the transfer of H3/H4 from Asf1  and has been shown to be crucial for the HIR complex stability and preferential deposition of H3.3 .
Protein families are often categorized by the presence or absence of a conserved motif. In the case of NASP, the possession of interrupted forms of TPR (SHNi-TPR) motifs defines this family . We have extended previous findings and shown that the structural arrangement of TPR motifs is conserved in NASP throughout the eukaryotic lineages. In this regard, NASP TPR analysis in kinetoplastids and parabasalids reveals that the TPR2 interruption is significantly smaller than the other family members and the acidic residues are either mostly N-terminal or dispersed throughout the protein, respectively. Phylogenies based on rRNA sequences have previously shown that excavata are one of the earliest diverging eukaryotes [46, 49]. It seems reasonable therefore to assume that the interruption of TPR2 with acidic patches occurred later during eukaryotic evolution, after the diversification of excavata lineages e.g., parabasalids and kinetoplastids.
A phylogeny based on the functional units of a protein may provide insights into a protein’s functional diversification. The phylogeny shown in Figure 1 was reconstructed using conserved blocks of NASP TPR1-4 amino acid sequences, and indicates that NASP evolution largely parallels eukaryotic evolution. Existing genetic and biochemical evidence available for several well characterized NASP proteins including Hif1, Sim3, and sNASP reveal that in addition to being H3/H4 chaperones, these proteins exhibit some level of functional diversity. For example, Hif1 has been shown to physically interact in a stoichiometric manner with Hat1 and Hat2 in S. cerevisiae and is involved with acetylation of newly synthesized histone H4, whereas Sim3 which is a fission yeast NASP homolog appears to function specifically in the deposition of centromere-specific histone H3 variant CENP-A [14, 20]. Different NASP proteins cluster together based on their taxonomic groups suggesting a lineage-specific functionalization pattern. Such clustering patterns along with varying branch lengths observed among different groups provide a good indication for the possible functional diversity. For example, our analysis suggests that S. cerevisiae and T. phaffii might be evolving faster in comparison to the other fungal lineages and may participate in lineage specific functions. A test of positive selection using branch site models may help reveal the identity of any residues that might have been positively selected in these lineages. Our phylogenetic (Figure 1) and sequence alignment (Additional file 3) analyses indicate that NASP is highly conserved among chordates consistent with a previous report which indicated that NASP antibody has high cross reactivity across different chordate species . The choanoflagellate and amoebozoan NASP proteins are however highly divergent in comparison to the other crown group lineages and several key residues in the TPR motifs that are conserved in other lineages have changed. These amino acid substitutions might be functionally significant although this hypothesis awaits biochemical and structural analysis.
Selective constraints operating on NASP
Estimation of amino acid p-distances suggests that TPR1 and TPR4 are evolving faster than TPR2 and TPR3 potentially accounting for the functional diversification observed among the NASP family members. This is further supported by our observation of more non-synonymous variations in TPR1/4 relative to TPR2/3 (Table 2). A deletion analysis of TPRs in a model system such as budding yeast [Fillingham et al. unpublished observations] that is amenable to a relatively straight forward biochemical analysis may provide further insights into specific TPR motif function. Comparison of synonymous and non-synonymous nucleotide substitutions indicated the presence of strong purifying selection that is operating at the protein level. This silent divergence indicates that NASP evolution has been subject to strong functional constraints maintaining essential structural features required for the protein’s proper functioning. Similar functional constraints have also been reported for other histone interacting proteins such as the nucleoplasmin (NPM) family of H2A/H2B histone chaperones . Although the number of synonymous variations was always significantly higher than non-synonymous variations, by comparing the number of non-silent variations between the acidic and TPR regions, it is possible to assign significantly lower levels of non-silent variations in the latter. This indicates the presence of the strongest functional constraints on these regions operating in the form of purifying selection. Slightly higher levels of non-silent variations in the acidic regions could be due to the fact that selection for either aspartic acid or glutamic acid serves to maintain an overall negative charge.
Negatively charged residues found in NASP are important for the stability and proper functioning of the protein . Selection has acted to maintain high frequency of these residues in the acidic region suggesting a deviation from neutrality. The neutral model of evolution predicts that the amino acid content of a protein is influenced by the nucleotide composition of its corresponding gene [93, 94]. For example, the protein encoded by a gene with high GC bias will primarily be composed of amino acids that are encoded by GC-rich codons as a result of mutational bias. However, in contrast to the neutral model, the presence of strong selection at the protein level could alter the nucleotide composition bias. For NASP proteins, a deviation from neutrality is revealed when genomic GC content is compared with GC-rich and GC-poor residues. In contrast to the neutral model which predicts that GC-rich and GC-poor residues should have a positive and negative correlation with the genomic GC content, respectively, we observe no significant correlation between GC-rich/GC-poor residues and the genomic GC content. Comparison of the nucleotide frequencies at the first and third codon positions of lysine and alanine which comprise the most abundant residues in NASP provide insight into the role of natural selection. According to the neutral model, if the mutations are random and have equal probability of being fixed, then accordingly the four bases A, T, G, and C should occur with equal frequencies in the DNA [62, 93]. Our results indicate that the frequency of G+A is significantly higher at the first codon position in comparison to the third codon position. This difference is particularly evident when frequencies are compared for the acidic domains. The nucleotide frequencies have therefore been influenced by strong selection for lysine, alanine, glutamic acid, and aspartic acid. Most studies at the genome level do not support selection as the major determinant of the amino acid composition [95–97]. However, it has been suggested that local scale deviations from neutrality are generally overlooked in studies that aim to focus on genome-wide patterns . Accordingly, a few studies have shown that natural selection is more important than mutational biases in shaping the nucleotide/amino acid composition [92, 98–100]. For example, in proteo-bacteria, high levels of alanine and lysine in the Tol A protein are maintained due to strong selective pressures . Similarly, for the NPM family of histone chaperones, high levels of adenine at the second codon position occur due to a selection for amino acids lysine and/or glutamic acid and aspartic acid . The present work, in addition to other studies, provides useful insights regarding the role of natural selection in determining the nucleotide/amino acid composition of a protein by demonstrating that elevated levels of G+A in NASP are maintained due to selection for alanine and/or glutamic acid/aspartic acid rather than the random mutational biases.
Several studies suggest that the unequal usage of synonymous codons exists because some codons are translated more efficiently and accurately and hence are the subject of selection (for review see ). We do not observe any significant codon bias among different NASP lineages (Table 3), although it has been shown that the sites that encode the most conserved and functionally important amino acids exhibit a greater bias in codon usage [60, 61] due either to selection or mutational bias. Further work will be required to investigate whether or not this is also the case for NASP proteins among different lineages. The determination of the most frequently used synonymous codons that encode the conserved residues in NASP TPRs may provide some insight. GC bias has previously been shown to positively correlate with the extent of codon usage bias . In the case of ray-finned fish-specific NASP paralogs, we observed that NASP1 has higher GC content than NASP2 and accordingly shows more biased trends in codon usage. These differences may represent the possible functional divergence between the two paralogs. Furthermore, GC content has been linked with elevated gene expression levels [84, 86]. The comparison of gene expression of the two paralogs should provide further insight into their functional differentiation. The amino acid substitutions in the TPRs as well as the absence of the N-terminal region in NASP1 and the presence of the NNR domain in NASP2 provide good indications that functional diversity exists between the two ray-finned fish specific paralogs. A test of positive selection using the branch-site method as well as determination of interacting partners and sub-cellular localization for each paralogous protein will further elucidate the existence of sub- or neo-functionalization.
Conserved pathway of H3/H4 transport
Transport of histones H3/H4 from the cytoplasm to the nucleus in yeast and human cells occurs in a stepwise fashion and is mediated by several proteins including heat-shock protein HSP90, NASP, Asf1 and Importinβ [10, 12]. HSP90 and Asf1 have been shown to be highly conserved throughout the eukaryotes and most likely were present in the LECA [31, 32, 101]. A recent report established that the Karyopherin-β family of proteins is also highly conserved throughout the eukaryotic lineages and was well established prior to the LECA . In this regard, the present work completes the evolutionary analyses of the major proteins involved in the transport of H3/H4 from the cytoplasm to the nucleus.
The physical interaction between HSP90-NASP, NASP-Asf1 and Asf1-Importinβ has been well described in humans and yeast [10, 13]. Our recent report established that Nrp1-Asf1–Importinβ physical interactions are well-conserved in a more divergent eukaryote T. thermophila. The evidence for the physical interaction between heat-shock protein and NASP is still restricted to Opisthokonta lineages. Our preliminary proteomic analysis of Nrp1 in T. thermophila indicates that this interaction is conserved [Nabeel-Shah and Fillingham, unpublished observations]. The predicted functional annotation of T. thermophila Nrp1 using the COFACTOR server suggests that TPR1 residues constitute the potential heat shock binding sites (Additional file 11). This prediction is of interest because human NASP TPR2 and TPR3/4 have been demonstrated to be critical for histones H1 and H3/H4-binding, respectively . Nevertheless, the validity and generality of this prediction requires experimental verification.
In order to re-capitulate and extend previous work on Asf1 and Karyopherin-β family proteins we performed extensive database searches and identified putative Asf1 and Impβ orthologs throughout the major eukaryotes. This, combined with previous studies [31, 33] suggests that these proteins were most likely present in the LECA. These studies indicate a conserved transport pathway of histones H3/H4 that most likely was present in the LECA and implicates HSP90, NASP, Asf1 and Importinβ proteins as the major components as their physical interactions have been described in divergent eukaryotic lineages including ciliates . Other protein factors such as Hat1 complex, Codanin-1(human) and AIP1/AIP2 (ciliates) also play a role in histone H3/H4 transport [10, 28, 102]. However the evolutionary origin of their role in the pathway is unclear at present and the available biochemical evidence is limited to either one or a small subset of taxonomic groups.
We have presented a detailed phylogenetic analysis of NASP family proteins. Several conclusions can be drawn from this study. First, NASP is widely distributed throughout the eukaryotes. It was most likely encoded in the genome of the last common ancestor of modern eukaryotes possibly representing an important innovation regarding the transport of H3/H4 from the cytoplasm to the nucleus. Second, natural selection has influenced the frequency of nucleotides encoding NASP in order to maintain high frequency of functionally important glutamic and aspartic acid amino acids. Third, TPRs1/4 are diverging more quickly relative to TPR2 and TPR4 possibly accounting for the functional diversity that has been reported among well characterized family members. Fourth, NASP paralogs found among ray finned fish potentially represent separate functional entities with NASP2 acquiring an NNR domain.
Sequence data retrieval and alignment
Amino acid sequences for well characterized NASP family members including X. laevis N1/N2 and human NASP were initially acquired from the NCBI protein database and were subsequently used as a query to search the non-redundant database with PSI-BLAST with default parameters. A phylogenomic approach was often used to increase the probability of identifying putative orthologs. For example, a putative NASP ortholog from the ciliate protozoan T. thermophila was used to detect further orthologs in other ciliate lineages. Sequences identified from each search were subsequently used as query for reciprocal recoveries. Protein sequences retrieved were analyzed at the Pfam database (http://pfam.sanger.ac.uk/) to examine the presence of SHNi-TPR (PF10516) . However, SHNi-TPR for highly divergent lineages such as ciliates was delineated through sequence alignments. HMMprofile was prepared using hmmbuild and the UniProtKB database was scanned using hmmsearch from the HMMER package . Nucleotide coding sequences were acquired from GenBank with the exception of sequences for fungal lineages which were extracted from the Broad Institute of genome database (http://www.broadinstitute.org). Nucleotide coding sequences for tNASP lineages and duplicated genes were obtained from sequenced genomes available at Ensemble v72 .
Protein multiple sequence alignments were built using MUSCLE with default parameters  and Jalview  was subsequently employed to inspect and edit the alignments. TPR 1–4 regions were predicted using well characterized human NASP TPR sequences as a template and were aligned against consensus TPR sequences. Secondary structure prediction and further domain analysis was carried out using the Protein homology/analogy recognition engine V 2.0 (PHYRE 2) . The alignment of nucleotide sequences was built on the basis of their translated amino acid sequences using MUSCLE as implemented in software MEGAv5.2.1 .
For Asf1 and Importinβ, sequences for well characterized yeast and human proteins were retrieved from the NCBI database and were subsequently used as queries for BLAST searches with default settings to explore the non-redundant database. Retrieved sequences were aligned using MUSCLE and an HMMprofile was prepared as above. The UniProtKB database was scanned using HMMsearch limiting the search to eukaryotes only. For the karyopherin-β family the retrieved sequences were analysed for the presence of IBN_N domain (PF03810) and sequences lacking the domain or smaller than 500 amino acids were eliminated from the final data set, in accordance with . Similarly Asf1 significant hits were checked for the presence of Pfam domain PF04729.
Synteny analysis and GC content calculation
The Genomicus database v72.01 was queried using the human genome to investigate the genomic organisation of NASP family proteins . DnaSP v5 was used to calculate GC content at the third codon positions .
Molecular evolutionary and phylogenetic analyses
Protein phylogenetic analyses were accomplished under maximum likelihood (ML) and Bayesian frameworks using NASP amino acid sequences for 52 different eukaryotic lineages. MEGA v5.2.1 (MEGA) was used for inferring an ML tree whereas Bayesian analysis was carried out using Mr. Bayes v3.2.0 . We carried out 6 different protein phylogenetic analyses using data sets consisting of: 1) combined amino acid sequences for all four predicted TPRs (excluding the acidic domain) in each protein; 2) entire protein sequences; 3) four analyses based on amino acid sequences for each of four individual TPRs. The analysis based on all four combined TPR sequences was conducted under rtREV+G+F as selected by MEGA and ProtTest v3.2 . For the remaining five analyses the model of protein evolution that best fits the data was selected using MEGA. For entire protein sequences, rtREV+G+F was used whereas for individual TPRs 1–4 model WAG+G was selected for TPR1/2/4 and rtREV+G for TPR 3. For individual TPR2 phylogenetic analysis we also included the acidic amino acid patches that interrupt the TPR2 acidic domain. For this, alignment positions with more than 50% gaps were eliminated using trimAL before conducting the analysis. For each data set, a total of 1000 bootstrap replicates were run to obtain statistical support for the resulting ML tree. For Bayesian inferences, for each data set, two runs of 2 million generations were conducted with 0.25 burn-in frequency and resulting posterior probabilities were taken as indicators of phylogenetic reliability. FigTree v1.4.0 (http://tree.bio.ed.ac.uk/software/figtree/) and MEGA were used to visualize the resulting phylogenies.
Phylogenetic trees based on nucleotide coding sequences were reconstructed using ML, Bayesian and MP methods. A total of 1000 bootstrap replicates were run to obtain statistical support for the resulting MP and ML trees. ML analysis was carried out under the model GTR+G+I as selected by MEGA whereas MP trees were reconstructed using tree bisection and reconnection search method with search level 1 and with 10 replications for the random addition trees method. The ML phylogeny reconstruction to investigate the NASP paralogous relationships was conducted under the Tamura-Nei model with gamma distributions as selected by MEGA and statistical support was obtained based on 1000 replications. Bayesian analysis was conducted with two runs of 1 million generations (0.25 burn-in frequency) and resulting posterior probabilities were taken as indicators of phylogenetic reliability. For fish specific NASP paralogs, ancestral sequences corresponding to the pre-duplication node of the tree were inferred using MEGA under the empirical Bayesian method.
MEGA was used to analyse the nucleotide and amino acid compositions. To estimate the degree of amino acid and nucleotide divergence we used uncorrected differences (p distance) unless mentioned. This method was used because it gives better results than more complicated methods in particular for distantly related taxa due to its smaller variance. The modified Nei and Gojobori method  was used to compute the number of synonymous (ps) and non-synonymous (p N ) nucleotide differences per site by providing transition/transversion ratios (R) in both cases. A complete deletion option was used to calculate the distances and the bootstrap method with 1000 replicates was employed for estimating the standard errors.
Several approaches were used to estimate the nature of selective forces operating on NASP evolution. A codon based Z-test of selection was carried out to study the presence and nature of selection. The alternative and null hypotheses were established as follows; H 1 : p N <p S and H o :p N= p S . Probability to reject the null hypothesis and Z-test statistics were obtained. We tested deviation from neutrality by determining if selection has influenced certain amino acids. The GC content at fourfold degenerate sites was assumed to represent the genomic GC content providing that the latter has previously been shown to be a good approximation of the former [79, 80]. In addition, GC content at four-fold degenerate sites was used as an approximation to the neutral expectation. Spearman rank correlation coefficient was used to compute the correlations and standard regression analysis was conducted for statistical significance. A comparison of nucleotide frequencies at the first codon position (always non-synonymous for the residues studied here) and at fourfold degenerate codon positions (always synonymous) was carried out in order to assess the influence of mutation and selection bias. Statistical significance of the results was also assessed by conducting student’s t test. In addition, estimation of the positive selection operating on individual codons was conducted using an ML-based method. We used the HyPhy program which is implemented in MEGA5. It involves the ML reconstructions of ancestral states under a Muse-Gaut model  of codon substitution. A nucleotide substitution model ‘GTR’ was also used as selected by MEGA and a user defined tree topology was provided. For detecting positively selected codons, the test statistic of dN –dS was used, where dS is the number of synonymous substitutions per site and dN is the number of nonsynonymous substitutions per site. Results were considered statistically significant for positive selection if the probability value was less than 0.05. Furthermore, the overall nucleotide variations (average number of synonymous and non-synonymous diversity per site) within TPRs 1–4 was estimated using a slide window approach with a window length of 50 bp and step size of 10 bp. The estimation of codon usage bias among NASP genes was conducted as the effective number of codons (ENC). Both analyses were carried out using the program DnaSP v5. In addition, relative synonymous codon usage (RSCU)  was estimated by MEGA using nucleotide coding sequences of the human NASP gene. To this end, an RSCU value greater than 1 indicates that a particular codon is used more frequently than expected whereas a value less than 1 indicates the reverse. Accordingly, an RSCU value of 1 indicates no codon bias .
Tertiary structures for different NASP proteins were predicted using the I TASSER server (http://zhanglab.ccmb.med.umich.edu/I-TASSER/)  and subsequently were submitted to the web-PIPSA pipeline for estimating the electrostatic potentials. See Additional file 12 for details.
Availability of supporting data
The data set supporting the results of this article is available in the TreeBase repository: http://purl.org/phylo/treebase/phylows/study/TB2:S15931. Supporting data are also included as additional files.
We thank Dr. Clifford Brunk (UCLA) and Dr. Brian Golding (McMaster University) for critically reading the manuscript and providing helpful feedback. We also thank Dr. Jyoti Garg (York University) for her helpful discussions. We thank two anonymous reviewers for their helpful feedback. This work was supported by: NSERC Discovery Grants to J.S.F (grant number: 386646–2010) and R.E.P (grant number: 539509), Ryerson University Health Sciences Fund (J.S.F), and an operating grant from CIHR to R.E.P (grant number: MOP13347).
- Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ: Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature. 1997, 389 (6648): 251-260. 10.1038/38444.PubMedGoogle Scholar
- De Koning L, Corpet A, Haber JE, Almouzni G: Histone chaperones: an escort network regulating histone traffic. Nat Struct Mol Biol. 2007, 14 (11): 997-1007. 10.1038/nsmb1318.PubMedGoogle Scholar
- Kleinschmidt JA, Fortkamp E, Krohne G, Zentgraf H, Franke WW: Co-existence of two different types of soluble histone complexes in nuclei of Xenopus laevis oocytes. J Biol Chem. 1985, 260 (2): 1166-1176.PubMedGoogle Scholar
- Dilworth SM, Black SJ, Laskey RA: Two complexes that contain histones are required for nucleosome assembly in vitro: role of nucleoplasmin and N1 in Xenopus egg extracts. Cell. 1987, 51 (6): 1009-1018. 10.1016/0092-8674(87)90587-3.PubMedGoogle Scholar
- Welch JE, Zimmerman LJ, Joseph DR, O’Rand MG: Characterization of a sperm-specific nuclear autoantigenic protein. I. Complete sequence and homology with the Xenopus protein, N1/N2. Biol Reprod. 1990, 43 (4): 559-568. 10.1095/biolreprod43.4.559.PubMedGoogle Scholar
- Batova I, O’Rand MG: Histone-binding domains in a human nuclear autoantigenic sperm protein. Biol Reprod. 1996, 54 (6): 1238-1244. 10.1095/biolreprod54.6.1238.PubMedGoogle Scholar
- Richardson RT, Batova IN, Widgren EE, Zheng LX, Whitfield M, Marzluff WF, O’Rand MG: Characterization of the histone H1-binding protein, NASP, as a cell cycle-regulated somatic protein. J Biol Chem. 2000, 275 (39): 30378-30386. 10.1074/jbc.M003781200.PubMedGoogle Scholar
- Alekseev OM, Bencic DC, Richardson RT, Widgren EE, O’Rand MG: Overexpression of the Linker histone-binding protein tNASP affects progression through the cell cycle. J Biol Chem. 2003, 278 (10): 8846-8852. 10.1074/jbc.M210352200.PubMedGoogle Scholar
- Richardson RT, Alekseev OM, Grossman G, Widgren EE, Thresher R, Wagner EJ, Sullivan KD, Marzluff WF, O’Rand MG: Nuclear autoantigenic sperm protein (NASP), a linker histone chaperone that is required for cell proliferation. J Biol Chem. 2006, 281 (30): 21526-21534. 10.1074/jbc.M603816200.PubMedGoogle Scholar
- Campos EI, Fillingham J, Li G, Zheng H, Voigt P, Kuo WH, Seepany H, Gao Z, Day LA, Greenblatt JF, et al: The program for processing newly synthesized histones H3.1 and H4. Nat Struct Mol Biol. 2010, 17 (11): 1343-1351. 10.1038/nsmb.1911.PubMedPubMed CentralGoogle Scholar
- Tagami H, Ray-Gallet D, Almouzni G, Nakatani Y: Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. Cell. 2004, 116 (1): 51-61. 10.1016/S0092-8674(03)01064-X.PubMedGoogle Scholar
- Alvarez F, Munoz F, Schilcher P, Imhof A, Almouzni G, Loyola A: Sequential establishment of marks on soluble histones H3 and H4. J Biol Chem. 2011, 286 (20): 17714-17721. 10.1074/jbc.M111.223453.PubMedPubMed CentralGoogle Scholar
- Fillingham J, Recht J, Silva AC, Suter B, Emili A, Stagljar I, Krogan NJ, Allis CD, Keogh MC, Greenblatt JF: Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109. Mol Cell Biol. 2008, 28 (13): 4342-4353. 10.1128/MCB.00182-08.PubMedPubMed CentralGoogle Scholar
- Dunleavy EM, Pidoux AL, Monet M, Bonilla C, Richardson W, Hamilton GL, Ekwall K, McLaughlin PJ, Allshire RC: A NASP (N1/N2)-related protein, Sim3, binds CENP-A and is required for its deposition at fission yeast centromeres. Mol Cell. 2007, 28 (6): 1029-1044. 10.1016/j.molcel.2007.10.010.PubMedPubMed CentralGoogle Scholar
- D’Andrea LD, Regan L: TPR proteins: the versatile helix. Trends Biochem Sci. 2003, 28 (12): 655-662. 10.1016/j.tibs.2003.10.007.PubMedGoogle Scholar
- Wang H, Ge Z, Walsh ST, Parthun MR: The human histone chaperone sNASP interacts with linker and core histones through distinct mechanisms. Nucleic Acids Res. 2012, 40 (2): 660-669. 10.1093/nar/gkr781.PubMedPubMed CentralGoogle Scholar
- Finn RM, Ellard K, Eirin-Lopez JM, Ausio J: Vertebrate nucleoplasmin and NASP: egg histone storage proteins with multiple chaperone activities. FASEB J. 2012, 26 (12): 4788-4804. 10.1096/fj.12-216663.PubMedGoogle Scholar
- Grote P, Conradt B: The PLZF-like protein TRA-4 cooperates with the Gli-like transcription factor TRA-1 to promote female development in C. elegans. Dev Cell. 2006, 11 (4): 561-573. 10.1016/j.devcel.2006.07.015.PubMedGoogle Scholar
- Poveda A, Pamblanco M, Tafrov S, Tordera V, Sternglanz R, Sendra R: Hif1 is a component of yeast histone acetyltransferase B, a complex mainly localized in the nucleus. J Biol Chem. 2004, 279 (16): 16033-16043. 10.1074/jbc.M314228200.PubMedGoogle Scholar
- Ai X, Parthun MR: The nuclear Hat1p/Hat2p complex: a molecular link between type B histone acetyltransferases and chromatin assembly. Mol Cell. 2004, 14 (2): 195-205. 10.1016/S1097-2765(04)00184-4.PubMedGoogle Scholar
- Tong K, Keller T, Hoffman CS, Annunziato AT: Schizosaccharomyces pombe Hat1 (Kat1) is associated with Mis16 and is required for telomeric silencing. Eukaryot Cell. 2012, 11 (9): 1095-1103. 10.1128/EC.00123-12.PubMedPubMed CentralGoogle Scholar
- Kim HS, Mukhopadhyay R, Rothbart SB, Silva AC, Vanoosthuyse V, Radovani E, Kislinger T, Roguev A, Ryan CJ, Xu J: Identification of a BET family bromodomain/casein kinase II/TAF-containing complex as a regulator of mitotic condensin function. Cell Rep. 2014, 6 (5): 892-905. 10.1016/j.celrep.2014.01.029.PubMedPubMed CentralGoogle Scholar
- Tanae K, Horiuchi T, Yamakawa T, Matsuo Y, Kawamukai M: Sim3 shares some common roles with the histone chaperone Asf1 in fission yeast. FEBS Lett. 2012, 586 (23): 4190-4196. 10.1016/j.febslet.2012.10.020.PubMedGoogle Scholar
- Cook AJ, Gurard-Levin ZA, Vassias I, Almouzni G: A specific function for the histone chaperone NASP to fine-tune a reservoir of soluble H3-H4 in the histone supply chain. Mol Cell. 2011, 44 (6): 918-927. 10.1016/j.molcel.2011.11.021.PubMedGoogle Scholar
- Ali-Fehmi R, Chatterjee M, Ionan A, Levin NK, Arabi H, Bandyopadhyay S, Shah JP, Bryant CS, Hewitt SM, O’Rand MG, Alekseev OM, Morris R, Munkarah A, Abrams J, Tainsky MA: Analysis of the expression of human tumor antigens in ovarian cancer tissues. Cancer Biomark. 2010, 6 (1): 33-48.PubMedPubMed CentralGoogle Scholar
- Alekseev OM, Richardson RT, Tsuruta JK, O’Rand MG: Depletion of the histone chaperone tNASP inhibits proliferation and induces apoptosis in prostate cancer PC-3 cells. Reprod Biol Endocrinol. 2011, 9: 50-10.1186/1477-7827-9-50.PubMedPubMed CentralGoogle Scholar
- Ma W, Xie S, Ni M, Huang X, Hu S, Liu Q, Liu A, Zhang J, Zhang Y: MicroRNA-29a inhibited epididymal epithelial cell proliferation by targeting nuclear autoantigenic sperm protein (NASP). J Biol Chem. 2012, 287 (13): 10189-10199. 10.1074/jbc.M111.303636.PubMedPubMed CentralGoogle Scholar
- Garg J, Lambert JP, Karsou A, Marquez S, Nabeel-Shah S, Bertucci V, Retnasothie DV, Radovani E, Pawson T, Gingras AC, Gingras AC, Pearlman RE, Fillingham JS: Conserved Asf1-importin beta physical interaction in growth and sexual development in the ciliate Tetrahymena thermophila. J Proteome. 2013, 94: 311-326.Google Scholar
- Eisen JA: Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res. 1998, 8 (3): 163-167. 10.1101/gr.8.3.163.PubMedGoogle Scholar
- Altenhoff AM, Dessimoz C: Inferring orthology and paralogy. Methods Mol Biol. 2012, 855: 259-279. 10.1007/978-1-61779-582-4_9.PubMedGoogle Scholar
- Daganzo SM, Erzberger JP, Lam WM, Skordalakes E, Zhang R, Franco AA, Brill SJ, Adams PD, Berger JM, Kaufman PD: Structure and function of the conserved core of histone deposition protein Asf1. Curr Biol. 2003, 13 (24): 2148-2158. 10.1016/j.cub.2003.11.027.PubMedGoogle Scholar
- Balaji S, Iyer LM, Aravind L: HPC2 and ubinuclein define a novel family of histone chaperones conserved throughout eukaryotes. Mol Biosyst. 2009, 5 (3): 269-275. 10.1039/b816424j.PubMedPubMed CentralGoogle Scholar
- O’Reilly AJ, Dacks JB, Field MC: Evolution of the karyopherin-beta family of nucleocytoplasmic transport factors; ancient origins and continued specialization. PLoS ONE. 2011, 6 (4): e19308-10.1371/journal.pone.0019308.PubMedPubMed CentralGoogle Scholar
- Finn RM, Browne K, Hodgson KC, Ausio J: sNASP, a histone H1-specific eukaryotic chaperone dimer that facilitates chromatin assembly. Biophys J. 2008, 95 (3): 1314-1325. 10.1529/biophysj.108.130021.PubMedPubMed CentralGoogle Scholar
- Coggill P, Finn RD, Bateman A: Identifying protein domains with the Pfam database. Curr Protoc Bioinformatics. 2008, Chapter 2: Unit 2 5-PubMedGoogle Scholar
- Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ, von Mering C, Bork P: eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res. 2012, 40 (Database issue): D284-D289.PubMedPubMed CentralGoogle Scholar
- Eddy SR: Profile hidden Markov models. Bioinformatics. 1998, 14 (9): 755-763. 10.1093/bioinformatics/14.9.755.PubMedGoogle 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 U S A. 2009, 106 (10): 3859-3864. 10.1073/pnas.0807880106.PubMedPubMed CentralGoogle Scholar
- Rodriguez-Ezpeleta N, Brinkmann H, Burey SC, Roure B, Burger G, Loffelhardt W, Bohnert HJ, Philippe H, Lang BF: Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes. Curr Biol. 2005, 15 (14): 1325-1330. 10.1016/j.cub.2005.06.040.PubMedGoogle 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 CentralGoogle Scholar
- Kuzniar A, van Ham RC, Pongor S, Leunissen JA: The quest for orthologs: finding the corresponding gene across genomes. Trends Genet. 2008, 24 (11): 539-551. 10.1016/j.tig.2008.08.009.PubMedGoogle Scholar
- Muffato M, Louis A, Poisnel CE, Roest Crollius H: Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes. Bioinformatics. 2010, 26 (8): 1119-1121. 10.1093/bioinformatics/btq079.PubMedPubMed CentralGoogle Scholar
- Amemiya CT, Alfoldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N, Organ C, Chalopin D, Smith JJ, Robinson M, Dorrington RA, Gerdol M, Aken B, Biscotti MA, Barucca M, Baurain D, Berlin AM, Blatch GL, Buonocore F, Burmester T, Campbell MS, Canapa A, Cannon JP, Christoffels A, De Moro G, Edkins AL: The African coelacanth genome provides insights into tetrapod evolution. Nature. 2013, 496 (7445): 311-316. 10.1038/nature12027.PubMedPubMed CentralGoogle Scholar
- Darriba D, Taboada GL, Doallo R, Posada D: ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics. 2011, 27 (8): 1164-1165. 10.1093/bioinformatics/btr088.PubMedGoogle Scholar
- Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011, 28 (10): 2731-2739. 10.1093/molbev/msr121.PubMedPubMed CentralGoogle Scholar
- Kumar S, Rzhetsky A: Evolutionary relationships of eukaryotic kingdoms. J Mol Evol. 1996, 42 (2): 183-193. 10.1007/BF02198844.PubMedGoogle Scholar
- Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF: A kingdom-level phylogeny of eukaryotes based on combined protein data. Science. 2000, 290 (5493): 972-977. 10.1126/science.290.5493.972.PubMedGoogle Scholar
- Marande W, Lopez-Garcia P, Moreira D: Eukaryotic diversity and phylogeny using small- and large-subunit ribosomal RNA genes from environmental samples. Environ Microbiol. 2009, 11 (12): 3179-3188. 10.1111/j.1462-2920.2009.02023.x.PubMedGoogle Scholar
- Bolivar I, Fahrni JF, Smirnov A, Pawlowski J: SSU rRNA-based phylogenetic position of the genera Amoeba and Chaos (Lobosea, Gymnamoebia): the origin of gymnamoebae revisited. Mol Biol Evol. 2001, 18 (12): 2306-2314. 10.1093/oxfordjournals.molbev.a003777.PubMedGoogle 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.PubMedGoogle Scholar
- Delsuc F, Brinkmann H, Chourrout D, Philippe H: Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature. 2006, 439 (7079): 965-968. 10.1038/nature04336.PubMedGoogle Scholar
- Pond SL, Frost SD, Muse SV: HyPhy: hypothesis testing using phylogenies. Bioinformatics. 2005, 21 (5): 676-679. 10.1093/bioinformatics/bti079.PubMedGoogle Scholar
- Bernardi G: The vertebrate genome: isochores and evolution. Mol Biol Evol. 1993, 10 (1): 186-204.PubMedGoogle Scholar
- Bulmer M: The selection-mutation-drift theory of synonymous codon usage. Genetics. 1991, 129 (3): 897-907.PubMedPubMed CentralGoogle Scholar
- Gouy M, Gautier C: Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 1982, 10 (22): 7055-7074. 10.1093/nar/10.22.7055.PubMedPubMed CentralGoogle Scholar
- Akashi H: Codon bias evolution in Drosophila. Population genetics of mutation-selection drift. Gene. 1997, 205 (1–2): 269-278.PubMedGoogle Scholar
- Wright F: The ‘effective number of codons’ used in a gene. Gene. 1990, 87 (1): 23-29. 10.1016/0378-1119(90)90491-9.PubMedGoogle Scholar
- Martindale DW: Codon usage in Tetrahymena and other ciliates. J Protozool. 1989, 36 (1): 29-34. 10.1111/j.1550-7408.1989.tb02679.x.PubMedGoogle Scholar
- Salim HM, Ring KL, Cavalcanti AR: Patterns of codon usage in two ciliates that reassign the genetic code: tetrahymena thermophila and Paramecium tetraurelia. Protist. 2008, 159 (2): 283-298. 10.1016/j.protis.2007.11.003.PubMedGoogle Scholar
- Akashi H: Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics. 1994, 136 (3): 927-935.PubMedPubMed CentralGoogle Scholar
- Stoletzki N, Eyre-Walker A: Synonymous codon usage in Escherichia coli: selection for translational accuracy. Mol Biol Evol. 2007, 24 (2): 374-381.PubMedGoogle Scholar
- Kimura M: Rare variant alleles in the light of the neutral theory. Mol Biol Evol. 1983, 1 (1): 84-93.PubMedGoogle Scholar
- Zhang Y: I-TASSER server for protein 3D structure prediction. BMC Bioinformatics. 2008, 9: 40-10.1186/1471-2105-9-40.PubMedPubMed CentralGoogle Scholar
- Richter S, Wenzel A, Stein M, Gabdoulline RR, Wade RC: webPIPSA: a web server for the comparison of protein interaction properties. Nucleic Acids Res. 2008, 36 (Web Server issue): W276-W280.PubMedPubMed CentralGoogle Scholar
- Broughton RE, Betancur RR, Li C, Arratia G, Orti G: Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution. PLoS Curr. 2013, 5: ecurrents.tol.2ca8041495ffafd0c92756e75247483e-PubMedPubMed CentralGoogle Scholar
- Koscielny G, Le Texier V, Gopalakrishnan C, Kumanduri V, Riethoven JJ, Nardone F, Stanley E, Fallsehr C, Hofmann O, Kull M, Harrington E, Boué S, Eyras E, Plass M, Lopez F, Ritchie W, Moucadel V, Ara T, Pospisil H, Herrmann A, G Reich J, Guigó R, Bork P, Doeberitz Mv, Vilo J, Hide W, Apweiler R, Thanaraj TA, Gautheret D: ASTD: the alternative splicing and transcript diversity database. Genomics. 2009, 93 (3): 213-220. 10.1016/j.ygeno.2008.11.003.PubMedGoogle Scholar
- Meyer A, Van de Peer Y: From 2R to 3R: evidence for a fish-specific genome duplication (FSGD). BioEssays. 2005, 27 (9): 937-945. 10.1002/bies.20293.PubMedGoogle Scholar
- Lynch M, Conery JS: The evolutionary fate and consequences of duplicate genes. Science. 2000, 290 (5494): 1151-1155. 10.1126/science.290.5494.1151.PubMedGoogle Scholar
- Wagner A: Selection and gene duplication: a view from the genome. Genome Biol. 2002, 3 (5): reviews1012-PubMedPubMed CentralGoogle Scholar
- Zhang J: Evolution by gene duplication: an update. Trends Ecol Evol. 2003, 18 (6): 292-298. 10.1016/S0169-5347(03)00033-8.Google Scholar
- Conant GC, Wolfe KH: Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet. 2008, 9 (12): 938-950. 10.1038/nrg2482.PubMedGoogle Scholar
- Innan H, Kondrashov F: The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet. 2010, 11 (2): 97-108.PubMedGoogle Scholar
- Rao YS, Chai XW, Wang ZF, Nie QH, Zhang XQ: Impact of GC content on gene expression pattern in chicken. Genet Sel Evol. 2013, 45: 9-10.1186/1297-9686-45-9.PubMedPubMed CentralGoogle Scholar
- Jabbari K, Bernardi G: CpG doublets, CpG islands and Alu repeats in long human DNA sequences from different isochore families. Gene. 1998, 224 (1–2): 123-127.PubMedGoogle Scholar
- Duret L, Mouchiroud D, Gautier C: Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores. J Mol Evol. 1995, 40 (3): 308-317. 10.1007/BF00163235.PubMedGoogle Scholar
- Eisenbarth I, Vogel G, Krone W, Vogel W, Assum G: An isochore transition in the NF1 gene region coincides with a switch in the extent of linkage disequilibrium. Am J Hum Genet. 2000, 67 (4): 873-880. 10.1086/303085.PubMedPubMed CentralGoogle Scholar
- Woodfine K, Fiegler H, Beare DM, Collins JE, McCann OT, Young BD, Debernardi S, Mott R, Dunham I, Carter NP: Replication timing of the human genome. Hum Mol Genet. 2004, 13 (2): 191-202.PubMedGoogle Scholar
- Kudla G, Lipinski L, Caffin F, Helwak A, Zylicz M: High guanine and cytosine content increases mRNA levels in mammalian cells. PLoS Biol. 2006, 4 (6): e180-10.1371/journal.pbio.0040180.PubMedPubMed CentralGoogle Scholar
- Aota S, Ikemura T: Diversity in G + C content at the third position of codons in vertebrate genes and its cause. Nucleic Acids Res. 1986, 14 (16): 6345-6355. 10.1093/nar/14.16.6345.PubMedPubMed CentralGoogle Scholar
- Bernardi G: Isochores and the evolutionary genomics of vertebrates. Gene. 2000, 241 (1): 3-17. 10.1016/S0378-1119(99)00485-0.PubMedGoogle Scholar
- Han L, Zhao Z: Comparative analysis of CpG islands in four fish genomes. Comp Funct Genom. 2008, 2008: 565631-565637.Google Scholar
- Abascal F, Corpet A, Gurard-Levin ZA, Juan D, Ochsenbein F, Rico D, Valencia A, Almouzni G: Subfunctionalization via adaptive evolution influenced by genomic context: the case of histone chaperones ASF1a and ASF1b. Mol Biol Evol. 2013, 30 (8): 1853-1866. 10.1093/molbev/mst086.PubMedGoogle Scholar
- Hershberg R, Petrov DA: Selection on codon bias. Annu Rev Genet. 2008, 42: 287-299. 10.1146/annurev.genet.42.110807.091442.PubMedGoogle Scholar
- Vinogradov AE: Dualism of gene GC content and CpG pattern in regard to expression in the human genome: magnitude versus breadth. Trends Genet. 2005, 21 (12): 639-643. 10.1016/j.tig.2005.09.002.PubMedGoogle Scholar
- Hershberg R, Petrov DA: General rules for optimal codon choice. PLoS Genet. 2009, 5 (7): e1000556-10.1371/journal.pgen.1000556.PubMedPubMed CentralGoogle Scholar
- Kanaya S, Yamada Y, Kinouchi M, Kudo Y, Ikemura T: Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis. J Mol Evol. 2001, 53 (4–5): 290-298.PubMedGoogle Scholar
- Li WH, Yang J, Gu X: Expression divergence between duplicate genes. Trends Genet. 2005, 21 (11): 602-607. 10.1016/j.tig.2005.08.006.PubMedGoogle Scholar
- Wong YH, Lee TY, Liang HK, Huang CM, Wang TY, Yang YH, Chu CH, Huang HD, Ko MT, Hwang JK: KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. Nucleic Acids Res. 2007, 35 (Web Server issue): W588-W594.PubMedPubMed CentralGoogle Scholar
- Zhai W, Nielsen R, Goldman N, Yang Z: Looking for Darwin in genomic sequences–validity and success of statistical methods. Mol Biol Evol. 2012, 29 (10): 2889-2893. 10.1093/molbev/mss104.PubMedGoogle Scholar
- Tang Y, Poustovoitov MV, Zhao K, Garfinkel M, Canutescu A, Dunbrack R, Adams PD, Marmorstein R: Structure of a human ASF1a-HIRA complex and insights into specificity of histone chaperone complex assembly. Nat Struct Mol Biol. 2006, 13 (10): 921-929. 10.1038/nsmb1147.PubMedPubMed CentralGoogle Scholar
- Song Y, Seol JH, Yang JH, Kim HJ, Han JW, Youn HD, Cho EJ: Dissecting the roles of the histone chaperones reveals the evolutionary conserved mechanism of transcription-coupled deposition of H3.3. Nucleic Acids Res. 2013, 41 (10): 5199-5209. 10.1093/nar/gkt220.PubMedPubMed CentralGoogle Scholar
- Eirin-Lopez JM, Frehlick LJ, Ausio J: Long-term evolution and functional diversification in the members of the nucleophosmin/nucleoplasmin family of nuclear chaperones. Genetics. 2006, 173 (4): 1835-1850. 10.1534/genetics.106.058990.PubMedPubMed CentralGoogle Scholar
- Sueoka N: Correlation between base composition of deoxyribonucleic acid and amino acid composition of protein. Proc Natl Acad Sci U S A. 1961, 47 (8): 1141-1149. 10.1073/pnas.47.8.1141.PubMedPubMed CentralGoogle Scholar
- Sueoka N: Directional mutation pressure and neutral molecular evolution. Proc Natl Acad Sci U S A. 1988, 85 (8): 2653-2657. 10.1073/pnas.85.8.2653.PubMedPubMed CentralGoogle Scholar
- Karlin S, Blaisdell BE, Bucher P: Quantile distributions of amino acid usage in protein classes. Protein Eng. 1992, 5 (8): 729-738. 10.1093/protein/5.8.729.PubMedGoogle Scholar
- Foster PG, Jermiin LS, Hickey DA: Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria. J Mol Evol. 1997, 44 (3): 282-288. 10.1007/PL00006145.PubMedGoogle Scholar
- Wang HC, Singer GA, Hickey DA: Mutational bias affects protein evolution in flowering plants. Mol Biol Evol. 2004, 21 (1): 90-96.PubMedGoogle Scholar
- Rooney AP: Selection for highly biased amino acid frequency in the TolA cell envelope protein of Proteobacteria. J Mol Evol. 2003, 57 (6): 731-736. 10.1007/s00239-003-2530-6.PubMedGoogle Scholar
- Rooney AP, Zhang J, Nei M: An unusual form of purifying selection in a sperm protein. Mol Biol Evol. 2000, 17 (2): 278-283. 10.1093/oxfordjournals.molbev.a026307.PubMedGoogle Scholar
- Akashi H, Gojobori T: Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc Natl Acad Sci U S A. 2002, 99 (6): 3695-3700. 10.1073/pnas.062526999.PubMedPubMed CentralGoogle Scholar
- Chen B, Zhong D, Monteiro A: Comparative genomics and evolution of the HSP90 family of genes across all kingdoms of organisms. BMC Genomics. 2006, 7: 156-10.1186/1471-2164-7-156.PubMedPubMed CentralGoogle Scholar
- Ask K, Jasencakova Z, Menard P, Feng Y, Almouzni G, Groth A: Codanin-1, mutated in the anaemic disease CDAI, regulates Asf1 function in S-phase histone supply. EMBO J. 2012, 31 (8): 2013-2023. 10.1038/emboj.2012.55.PubMedPubMed CentralGoogle Scholar
- Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Larsson P, Longden I, McLaren W, Overduin B, Pritchard B, Riat HS, Rios D, Ritchie GR, Ruffier M, Schuster M: Ensembl 2011. Nucleic Acids Res. 2011, 39 (Database issue): D800-D806.PubMedPubMed CentralGoogle Scholar
- Edgar RC: MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004, 5: 113-10.1186/1471-2105-5-113.PubMedPubMed CentralGoogle Scholar
- Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ: Jalview Version 2–a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009, 25 (9): 1189-1191. 10.1093/bioinformatics/btp033.PubMedPubMed CentralGoogle Scholar
- Kelley LA, Sternberg MJ: Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc. 2009, 4 (3): 363-371. 10.1038/nprot.2009.2.PubMedGoogle Scholar
- Louis A, Muffato M, Roest Crollius H: Genomicus: five genome browsers for comparative genomics in eukaryota. Nucleic Acids Res. 2013, 41 (Database issue): D700-D705.PubMedPubMed CentralGoogle Scholar
- Librado P, Rozas J: DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009, 25 (11): 1451-1452. 10.1093/bioinformatics/btp187.PubMedGoogle Scholar
- Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hohna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP: MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012, 61 (3): 539-542. 10.1093/sysbio/sys029.PubMedPubMed CentralGoogle Scholar
- Zhang J, Rosenberg HF, Nei M: Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc Natl Acad Sci U S A. 1998, 95 (7): 3708-3713. 10.1073/pnas.95.7.3708.PubMedPubMed CentralGoogle Scholar
- Muse SV, Gaut BS: A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol. 1994, 11 (5): 715-724.PubMedGoogle Scholar
- Sharp PM, Tuohy TM, Mosurski KR: Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 1986, 14 (13): 5125-5143. 10.1093/nar/14.13.5125.PubMedPubMed CentralGoogle Scholar
- Roy A, Kucukural A, Zhang Y: I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc. 2010, 5 (4): 725-738. 10.1038/nprot.2010.5.PubMedPubMed CentralGoogle Scholar
- Nabeel-shah S, Ashraf K, Pearlman RE, Fillingham JS: Molecular evolution of NASP and conserved histone H3/H4 transport pathway. TreeBASE. 2014, http://purl.org/phylo/treebase/phylows/study/TB2:S15931,Google Scholar
- Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG: Clustal W and Clustal X version 2.0. Bioinformatics. 2007, 23 (21): 2947-2948. 10.1093/bioinformatics/btm404.PubMedGoogle Scholar
- Wade RC, Gabdoulline RR, De Rienzo F: Protein interaction property similarity analysis. Intl J Quantum Chem. 2001, 83: 122-127. 10.1002/qua.1204.Google Scholar
- Cortajarena AL, Wang J, Regan L: Crystal structure of a designed tetratricopeptide repeat module in complex with its peptide ligand. FEBS J. 2010, 277 (4): 1058-1066. 10.1111/j.1742-4658.2009.07549.x.PubMedGoogle Scholar
- Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, Pupko T, Ben-Tal N: ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res. 2005, 33 (Web Server issue): W299-W302.PubMedPubMed CentralGoogle 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/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.