BACKGROUND
the emergence of multicellularity, considered to be one of the major evolutionary events concerning life on earth, occurred several times independently during the evolution of eukaryota in the proterozoic geological period  <cit> .
multicellular organisms are not only a superimposition of the fundamental unit of life, namely the cell; the emergence of multicellularity further implies that cells must communicate, coordinate and organise.
in embryophyta and metazoa, higher levels of differentiation and organization of cells resulted in the emergence of organs and their organisation into complex body plans.
reaching this critical step required the elaboration of sophisticated intercellular communication mechanisms  <cit> .
cell-cell interactions through signal transduction pathways are therefore crucial for the development and the evolution of multicellular organisms.
the modifications of these signal transduction pathways explain the macroevolution process observed.
in metazoans, fewer than  <dig> different signal transduction pathways are required to generate the observed high diversity of cell types, patterns and tissues  <cit> .
among them, only seven control most of the cell communications that occur during animal development: wnt; transforming growth factor β ; hedgehog; receptor tyrosine kinase ; jak/stat; nuclear hormone receptor; and notch  <cit> .
these pathways are used throughout development in many and various metazoans to establish polarity and body axes, coordinate pattern formation and choreograph morphogenesis  <cit> .
the common outcome to all of these pathways is that they act, at least in part, through the regulation of the transcription of specific target genes by signal-dependent transcription factors  <cit> .
the notch signalling pathway is a major direct paracrine signalling system and is involved in the control of cell identity, proliferation, differentiation and apoptosis in various animals .
notch signalling is used iteratively in many developmental events and its diverse functions can be categorized into two main modalities "lateral inhibition" and "boundaries/inductive mechanisms"  <cit> .
during lateral inhibition, notch signalling has mainly a permissive function and contributes to binary cell fate choices in populations of developmentally equivalent cells, by inhibiting one of the fates in some cells and therefore allowing them to later adopt an alternative one.
lateral inhibition is a key patterning process that often results in the regular spacing of different cell types within a field.
the notch pathway may also have more instructive roles, whereby signalling between neighbouring populations of different cells and induces the adoption of a third cell fate at their border, establishing a developmental boundary  <cit> .
a large number of studies, mainly conducted on drosophila, caenorhabditis and vertebrates, have characterized the molecular properties and functions of the main components and auxiliary factors of the notch pathway.
these are strongly conserved in bilaterians .
both the notch receptor and its ligands  are type i transmembrane proteins with a modular architecture.
in eumetazoans, the notch protein is classically considered to be composed of an extracellular domain  that comprises several egf and lnr motifs, an intracellular domain  that includes ank domains and a pest region  <cit> .
the notch protein is synthesized as an inactive precursor that has to be cleaved three times and to undergo various post-translational modifications to become active  <cit> .
in the golgi apparatus, the first cleavage  is done by the furin protease resulting in two fragments  that subsequently undergo o-fucosylation  and glycosylation .
upon ligand binding, the second cleavage  occurs by the metalloproteases adam  <dig> and  <dig>  <cit> .
the final cleavage  is performed by the γ-secretase complex .
these cleavages result in the release, upon ligand binding, of nicd into the cytoplasm and its subsequent translocation to the nucleus.
there, nicd interacts with the csl , lag-1)/ncor/smrt/histone deacetylase  transcriptional complex and recruits the coactivator mastermind and a histone acetylase , thus activating the transcription of target genes in particular the hes/e genes   <cit> .
in addition to these core components of the notch pathway, several other proteins are used to regulate notch signalling in some cellular contexts, and act either on the receptor notch or on the ligand dsl .
some of these regulators modulate the amount of receptor available for signalling  <cit> .
numb, the nedd4/su e <dig> ubiquitin ligases, and notchless are important negative regulators, while deltex is considered to antagonize nedd4/su and therefore to be an activator of notch signalling  <cit> .
strawberry notch , another modulator of the pathway whose role is still unclear, seems to be active downstream and disrupts the cslrepression complex  <cit> .
regulation may also occur at the level of ligand activity via the e <dig> ubiquitin ligases neuralized and mindbomb  <cit> .
most of what we know about the notch signalling pathway comes from studies conducted on a few bilaterian species.
recently, studies have shown the existence of a notch signalling pathway in non-bilaterian species, such as the cnidarian hydra and the sponge amphimedon, and its putative functions in the former species  <cit> .
however, the ancestral structure, functionality and emergence of this complex multi-component signalling system are still open questions.
few studies have been initiated to understand how signalling pathways appeared and evolved beyond the bilateria  <cit>  but the recent sequencing of the first sponge genome, amphimedon queenslandica has opened new perspectives for studying the origin and evolution of signalling pathways in the metazoa  <cit> .
with the goal of illuminating the early evolution of the notch pathway, we have therefore undertaken a comparative genomic study of the components of this pathway across the eukaryota.
our study encompasses  <dig> species  covering the  <dig> major clades of eukaryotes  <cit>  , and includes the  <dig> main components of the notch pathway .
we have also paid special attention to the evolution of domain composition  of the multidomain proteins notch, delta, mindbomb, su and furin, to investigate whether domain shuffling has occurred during their evolution, as in other signalling pathways  <cit> .
this wide genomic comparison reveals that most of the notch components are present in all the metazoan species studied, including putative basal metazoans such as sponges and placozoan, suggesting that a functional notch pathway was already present in the last common ancestor of present-day metazoans and was subsequently strongly conserved during metazoan evolution.
while many of the notch pathway components are also shared with non-metazoan eukaryote lineages, thus suggesting a more ancient origin, nine of the components are metazoan-specific, including the notch receptor and the dsl ligands.
this indicates that while the notch pathway is a metazoan synapomorphy, it has been assembled through the co-option of pre-metazoan proteins, and their integration with novel metazoan-specific molecules acquired by various evolutionary mechanisms.
RESULTS
genome-wide identification of the main notch signalling pathway components in eukaryotes
to understand more precisely the evolution of the notch pathway at the scale of the eukaryotes, we systematically searched for all the main notch pathway elements in completely sequenced genomes and expressed sequence tag  data of  <dig> different eukaryote species .
table  <dig> lists the  <dig> genes that we analysed and summarizes their functions in the notch pathway .
we included in this list both genes that encode core components of the notch pathways  and genes that encode modulators of the pathway not used in all cases of notch signalling   <cit> .
we selected  <dig> species representative of the major clades of eukaryotes  <cit> :  <dig> metazoans,  <dig> fungi ,  <dig> choanoflagellate,  <dig> amoebozoans,  <dig> species of plants ,  <dig> alveolates,  <dig> heterokonts,  <dig> species of discicristates,  <dig> species of excavates and  <dig> rhizaria.
figure  <dig> provides the full list of the chosen species with their assumed phylogenetic position and internet links to the genomic databases.
we performed blast searches  <cit>  to assess the presence or absence of notch pathway genes in the sampled species, as described in the methods section.
in most cases, the notch pathway elements are multidomain proteins and share some of their domains with other proteins.
for each target protein, only the combined occurrence of all requisite domains was considered diagnostic for identification.
we systematically defined a diagnostic domain organization for each target protein  and identified genes as detailed in the methods section.
we also constructed multiple alignments for each protein and performed phylogenetic analyses to confirm the orthology relationships .
figure  <dig> summarizes the output of our analyses: genes were scored as "present" when all the domains were identified, "incomplete" when some domains were missing, or "absent" when blast searches gave no significant result.
for est libraries, as the absence and the incomplete status of genes cannot be definitive due to the partial nature of this type of data, we chose to indicate "present" only when all domains were retrieved.
detailed domain composition for each gene in each species is presented in the additional file  <dig>
our data confirm the strong evolutionary conservation of the notch pathway in bilaterians as all components are present in almost all the analysed bilaterian species .
there are two exceptions to this rule, fringe which is absent from the genome of two protostomes, caenorhabditis and helobdella, and mastermind is not found in  <dig> of the studied bilaterian species across both protostomes and deuterostomes.
the latter case is puzzling given the documented importance of mastermind in both vertebrates and drosophila  <cit>  and its presence in the non-bilaterian species nematostella .
this suggests that mastermind has been repeatedly lost in various bilaterian species.
alternatively, as the sequence similarity between the mastermind genes in drosophila and vertebrates is quite weak  <cit> , these genes may be difficult to track by sequence similarity searches.
our data also indicate that the overall notch pathway conservation extends to non-bilaterian species.
indeed, most pathway components can be identified in the cnidarians nematostella and hydra, in the placozoan trichoplax and the sponge amphimedon .
we can therefore conclude that most notch pathway components were already present in the last common ancestor of all metazoans, the urmetazoa.
four genes were not found complete outside bilaterians, smrt, furin, numb and neuralized, suggesting that these genes are specific to bilaterians .
genes encoding proteins with a sant domain  are found in non-bilaterians, but the sequence similarity is too weak to establish that some are bona fide smrt genes.
the case of the furin protein is puzzling.
this protein pertains to the proprotein convertase subtilisin/kexin family   <cit> .
in the demosponge amphimedon and the choanoflagellate, there are some proteins of the pcsk family and some of them possess the diagnostic domains of the furin proteins .
nevertheless, the phylogenetic analysis revealed that these proteins do not group with bilaterian furins, however the latter are paraphyletic in the phylogenetic tree .
in the case of neuralized, while neuz domains are found in non-bilaterians, they are only found in association with a ring binding domain in the bilateria.
in the same way, ph-like domains of numb are only found in association with a numbf domain in bilaterians.
the gene mastermind is only found in eumetazoans and two others, fringe and mindbomb, are found in amphimedon but not in trichoplax .
the absence of some components in some non-bilaterian species may represent a progressive elaboration of the pathway during early metazoan evolution, or else may correspond to secondary losses in some lineages.
however, these data can be difficult to interpret in terms of the evolution of the notch pathway, as the phylogenetic relationships of the aforementioned non-bilaterian species are still controversial  <cit> .
nevertheless, we decided to base our discussion on the metazoan relationships hypothesised in the most recent phylogenomic study  <cit>  as we believe it to be the most robust and complete analysis to date.
our data so far indicate that most of the notch pathway components were already present in urmetazoa.
interestingly, among the  <dig> targeted genes, only nine are specific to metazoans .
strikingly, among these, nine are the genes encoding the ligand and the receptor, suggesting that the canonical notch pathway only exists in metazoans.
indeed, in the genome of the choanoflagellate monosiga, no notch gene has been found, only cassettes of some protein domains encoded on separate genes have been reported  <cit> .
of note, we also found another gene in this species that possesses the domain arrangement of a notch gene .
while this gene contains the minimum set of diagnostic notch domains, it has very weak sequence similarity to notch genes, and in the absence of further evidence we choose here to name it "notch-like".
nevertheless, we can not exclude that a "protonotch" receptor might have been already present in holozoa.
<dig> components are found in various other eukaryote taxa; some are likely to have appeared during early eukaryote evolution and may even have been present in the last common ancestor of present-day eukaryotes .
others seem to have specifically appeared in the opisthokont lineage.
figure  <dig> represents the possible scenarios of emergence and loss of the various notch components, inferred from the most recent and robust phylogenetic hypotheses  <cit>  and on the basis of the parsimony principle.
four genes of this pathway seem to have appeared early in evolution and are inferred to have been present in the leca.
these include notchless  and three of the four genes coding for proteins implicated in the so-called "γ-secretase complex".
indeed, the presenilin gene is shared by all eukaryotes  whereas nicastrin and aph <dig> are found in the holozoa, the amoebozoa, the plantae and the heterokonta.
interestingly, none of these genes are found in species of fungi + microsporidia and alveolata, suggesting a secondary loss.
for other genes  that are shared by fewer taxa, it is difficult to state whether they were present in the leca and lost various times, or acquired independently: this is the case for pen <dig>  strawberry notch , the role of which in the notch pathway is not yet clear, and fringe .
all other genes originated more recently, in the last common ancestor of opisthokonts ) <cit> ; suppressor of deltex ).
this might also be the case for the two adam genes.
we cannot confidently assign the adam genes we found in fungi and microsporidia to a particular adam group; however these genes are most closely related to metazoan adam  <dig> and  <dig> families  as already reported by another study on aspergillus fumigatus  <cit> .
other genes are specific to holozoans .
for the ctenophore species  as well as the homoscleromorph sponge oscarella, only a few target genes were identified in the available non exhaustive est databases and we were unable to conclude whether or not the remaining genes are present in those taxa.
focus on notch and dsl proteins evolution in metazoan: phylogenetic analyses and domain composition arrangement
we chose to focus our further analyses on the two main molecules of the pathway, notch and dsl, and study their evolution in metazoans.
we first performed phylogenetic analyses using both maximum likelihood  and bayesian inference  approaches and then investigated the domain organizations of each.
topologies obtained in our phylogenetic analyses are not fully resolved, as previously noticed for the notch ligands  <cit> .
long branch attraction bias  may be suspected in some cases and, as previously reported by different authors  <cit> , ml appears more sensitive to lba than bi.
concerning domain composition and organization, generally all the diagnostic domains in delta or notch genes are present in bilaterian sequences, but some domains seem to be lacking in a few species.
in these cases, we can not state whether this is due to prediction errors, sequencing gaps in the available genome sequences or secondary losses.
when the available software prediction is equivocal, important conserved residues can often be identified in the regions where domains would be expected, suggesting functional conservation.
despite these technical limits, our analysis presents several features of interest.
first, a single notch gene is found in most species , except in vertebrates  and in the annelid helobdella .
in the former case, this is most probably due to the well documented occurrence of two whole genome duplication events in this lineage  <cit> .
in the latter case, it may correspond to a recent duplication, limited to an annelid lineage.
indeed, the two helobdella genes form a monophyletic group in our trees  and only a single notch gene has been found in the genome of another annelid species, capitella sp.
i  <cit> .
in the bayesian analysis, we note that the sequences from bilaterians form a monophyletic group and the cnidarian sequence clearly appears more related to bilaterian sequences than to other non-bilaterian sequences .
the receptor notch is considered to be made of several domains: egf repeats , three lnr  or notch domains, two enigmatic domains nod and nodp , a ram  <dig> domain, a pest domain and several ankyrin repeats .
the number of egfs is variable and spans from  <dig> in caenorhabditis to  <dig> in humans.
the nod and the nodp are absent in sponges and in some bilaterian species.
the absence of a signal peptide is observed in  <dig> of the  <dig> sequences, and the pest domain is absent at the c-terminus of three sequences .
second, in the dsl family  jagged is absent from placozoans and sponges and present  in all other studied metazoans.
delta is present in all metazoan species of our study, and in contrast to jagged, is also found in non-eumetazoans.
the number of copies of delta is also variable but is notably high  in the gastropod snail lottia.
we also note that  <dig> copies are present in the sponge genome, which is remarkably high in comparison to the other non-bilaterians such as trichoplax and nematostella.
in spite of the differences between the ml and bi topologies and the weak statistical support of deep nodes in both analyses, we are able to draw some conclusions about the evolution of the dsl family.
in the bayesian tree , a strongly supported clade  contains all eumetazoan jagged sequences plus one sequence from branchiostoma and one from the sponge oscarella .
this suggests the existence of a subfamily of serrate/jagged proteins that is found in all the major animal lineages and therefore is of ancient origin.
most of the other studied proteins  form another large monophyletic group  likely corresponding to what may be called a delta clade  since it includes the known deltas from vertebrates as well as from the main metazoan lineages, including the sponge amphimedon and the placozoan trichoplax.
nevertheless, the internal branching of the delta sequences makes no sense in the light of species phylogenies.
our phylogenetic analysis rather suggests that the last common ancestor of all eumetazoans already possessed at least one delta and one jagged/serrate gene and that the urmetazoa possessed at least one sequence of delta.
the position of the of d/j-oscarella carmela in the bayesian tree is puzzling, the blast analysis revealed a higher similarity between this sponge  sequence and delta sequences but we cannot definitively rule out the possibility that it might be an incomplete jagged protein.
to support our phylogenetic analyses, we also systematically investigated the domain arrangements of the dsl family proteins .
dsl proteins are usually considered to be composed of several domains, namely a signal peptide , a mnll domain , a dsl domain , a variable number of egf repeats and a transmembrane region.
in addition to these domains, the serrate/jagged proteins also contain a supplementary domain, the von willebrand factor c domain   <cit> .
interestingly, all but two proteins included in the jagged group in our phylogenetic trees contain the vwc domain, confirming that they are bona fide jagged proteins .
the exceptions are the two branchiostoma genes; phylogenetic analyses highly support their belonging to the jagged clade, suggesting that the absence of the vwc domain may be due to incorrect protein predictions, incomplete genome assemblage or secondary loss.
third, in our ligand domain analyses , we found that the mnll, the signal peptide and the transmembrane domains are not present  across all metazoan delta ligands but we could find them in the majority of jaggeds.
most deuterostome delta sequences possess the mnll domain, in contrast to the protostome sequences.
among the sponge species a mnll is only predicted in one copy of the amphimedon deltas.
the number of egf repeats ranges from  <dig>  to  <dig> in delta and from  <dig> to  <dig> in jagged.
an average of 7- <dig> egf motifs are present in deuterostome delta sequences; it is much more variable in protostomes.
we note that motifs expected at the n or c terminus are more often lacking.
as this absence of a signal peptide or a transmembrane region appears incongruous and hardly compatible with the conservation of functionality, the assembly and annotation of the concerned genomes may require a re-examination  <cit> .
surprisingly, in cnidarian genomes, in addition to the delta and jagged sequences, we found genes composed only of dsl domains  and one gene composed of a mnll domain associated to  <dig> dsl domains .
it remains to be seen either these are true genes with unique functionalities, or represent misassembled regions of the genome.
origin and evolution of protein domains involved in the pathway
we focused on five genes that encode multidomain proteins in the pathway: dsl, notch, mindbomb, su, furin.
we mapped the possible acquisition and loss events of the different domains during eukaryote evolution according to the phylogenetic hypothesis of baldauf   <cit>  .
on one hand, it appears that various domains have an ancient origin; they are shared by several eukaryote lineages, so we can hypothesize their presence in the leca .
this is the case for: egf repeats of notch and dsl , ank repeats of mindbomb and notch ; the lnr domain of notch; both zz and ring type zn finger domains of mindbomb; the ipt rbp-jkappa domain of su; the subtilisin domain and the furin domain.
in all of these cases, a hypothesis of ancestrality followed by one or more secondary losses is most parsimonious.
on the other hand, several domains appear to have originated more recently since they are specific to opisthokonts or even to metazoans: the mnll, dsl and vwc domains involved in dsl composition; the nod and nodp domains of notch; the mib/herc <dig> domain of mindbomb; the lag <dig> and beta-trefoil domains of su.
thus, a total of six domains may represent synapomorphies of the metazoa.
in the case of the p-proprotein of furin, the more parsimonious inference is that it may have appeared convergently three times in excavata, heterokonta and in opistokonta .
discussion
a functional notch pathway seems to have been present in the urmetazoa and comprised at least  <dig> components  <cit> .
the later addition of five other components  can thus be considered as facultative and responsible for additional regulation properties of the pathway.
our study indicates that the presence of the notch pathway is a synapomorphy of metazoans as this is the only kingdom to possess all the key components of the pathway, most importantly the receptor and ligands.
our analysis also sheds light on the molecular mechanisms that may have been invoked in the formation of this pathway.
indeed, as we discuss hereafter, our study shows that notch signalling has originated by cooption of pan-eukaryotic ancestral genes; modification of ancestral functions by new protein-protein interactions ; lateral gene transfer; formation of new proteins by both exon shuffling and duplications + divergence.
cooption of pre-existing genes and ancestral functions
this study, at the scale of the eukaryota super-kingdom, reveals the presence of notch components in diverse eukaryotic organisms, and thus their ancient origin.
certain highly conserved genes, despite their ancestrality, seem to be absent in fungi and microsporidia.
this is consistent with previous genomic analyses that have documented massive gene losses in the lca of fungi + microsporidia, and a further round of losses in microsporidies in relation to their parasitic life style  <cit> .
the origin of presenilin and of the γ-secretase complex
one of the most striking features uncovered by our study is the evolutionary conservation of the γ-secretase complex  <cit> : the four proteins composing this large transmembrane complex  are present in both plants and unikonts .
while the entire γ-secretase complex does not seem to be pan-eukaryotic, our analysis nonetheless supports an altered evolutionary scenario than that formerly proposed for its main player, presenilin.
previously, authors have hypothesized  a convergent acquisition of this gene in the metazoan and the plant lineages  <cit> .
our study reveals instead that presenilin was present in the leca, and then lost independently twice .
the aph <dig> and nicastrin proteins may also be ancestral to eukaryota, but our data is inconclusive for pen <dig> on this point .
until now, functional analyses of this complex are available only in embryophyta  <cit>  and metazoa, where it is known to be involved in the cleavage of notch and other proteins such as erbb <dig>  <cit>  and app .
but the lack of evidence for a complete γ-secretase complex in the leca  parallels recent functional data indicating that in both mammals  <cit>  and a bryophyte , presenilin is also involved in various γ-secretase-independent functions such as protein degradation and trafficking.
the association of pen <dig>  is considered to be necessary to acquire the proteolytic activity of presenilin via conformational changes  <cit> .
these changes may result in the accessibility of the two catalytic motifs y/wd and gxgd, which are conserved at the eukaryotic scale  <cit> .
this suggests that proteolysis might not have been the ancestral function of presenilin , but might have been acquired secondarily by its co-option into the four protein γ-secretase complex .
this challenging evolutionary scenario requires further investigations to be tested.
the origin of the notchless inhibitor
notchless encodes a protein containing a nle domain and wd40-repeats  <cit> .
in eumetazoa, this member of the wd-repeat  protein superfamily  <cit>  modulates the notch pathway by binding the nicd  <cit>  but also by interacting with deltex and su  <cit> .
our analysis shows that notchless was probably present in leca.
nevertheless, in some of the studied species, the nle domain is missing, and we cannot define whether this is due to secondary loss or to a high level of sequence divergence obscuring domain prediction.
the high conservation of nle sequences seems to be compatible with functional conservation as shown by transgenic experiments between a plant, solanum chacoense and an animal, drosophila  <cit> .
however, while both plant and yeast notchless proteins share an involvement in ribosome biogenesis, until now no such role has been reported in animals  <cit> .
these observations have led authors to propose that either notchless was primarily involved in ribosome biogenesis in eukaryotes and was secondarily recruited in the metazoans for a new function , or that this role may still exist in animals despite the lack of experimental evidence  <cit> .
ancestrality or lateral gene transfer?
two other members of the notch pathway show an ambiguous history, in which the eventuality of lateral gene transfer  cannot be excluded.
this is the case for both fringe  <cit>  and strawberry notch .
our analyses reveal that fringe is present in metazoa, but also in plants and parabasalia .
a fringe domain alone was also identified in the studied ascomyceta species; however no complete fringe or fringe-like gene seems to be present in this taxon .
we could hypothesize that the fringe gene was present in the leca and then lost several times; nevertheless, the most parsimonious scenario suggests three independent acquisitions.
we can speculate that lgt might have occurred, favoured by either the tight association existing between parabasalia and metazoa lineages or via bacterial transfers  <cit> .
however, we failed to find any specific relationships or signatures  between the fringe genes of homo and its parasite trichomonas as well as we failed to detect fringe outside eukaryota to strongly argue for a lgt hypothesis.
in our analysis, sno is shown to be present in holozoa and plantae.
unexpectedly, sno has been reported recently in a nuclear and cytoplasmic large dna virus  of the haptophyte  emiliania huxleyi  <cit> .
as our analysis on the genomes of the two chosen heterokonts  failed to reveal the presence of sno, we chose to extend our research to other heterokonta related species.
interestingly, sno is not only present in the genome of the haptophyte emiliania, suggesting a lgt between this species and its virus ehv , but also in two other heterokonta, aureococcus anophaegefferens and thalassiosina pseudonana .
another interesting feature is that sno has been shown to be derived from the snf2/swi <dig> atpases encoding gene of α-proteobacteria  <cit> .
the presence of sno or sno-related genes in both ncldv and α-proteobacteria may suggest lgt events in the history of these genes because i) α-proteobacteria are often found in tight associations with various eukaryote taxa  and ii) ncldvs have been reported from amoebozoa, haptophyta, discicristata and viridiplantae however their ecological distribution and importance is still largely unknown and newly described virophage of ncldvs may also be involved in lgt  <cit> .
in the two cases , further analyses  are needed to shed light on the origin and history of these genes and to state whether they were acquired by lgt or not.
the notch pathway is specific to metazoa
the cooption or acquisition  of "old" genes is not sufficient to explain the formation of the canonical notch pathway.
one of the pivotal steps in the evolutionary history of the notch pathway seems to be the transition between the choanoflagellates and the animals  <cit> .
indeed, this study reveals that the majority of notch components appeared in the lca of the holozoa.
nevertheless, several molecular components critical for signal transduction are lacking in choanoflagellates, in particular, the ligand delta and the receptor notch , thus we consider the notch pathway as a synapomorphy of the metazoa .
an increase in the complexity of this pathway has also occurred after the divergence between sponges and other metazoans.
several notch components are absent from the demosponge amphimedon , yet the pathway may still be functional in this species  <cit> .
this suggests that these components were not critical for the function of the pathway and may constitute additional regulatory elements that were subsequently added to the pathway in eumetazoans.
nevertheless, the possible pan-metazoan ancestry of these genes  cannot be excluded; data from other sponges may help to resolve this issue.
the absence of furin in amphimedon is not really unexpected; although furin has a critical role for the maturation of the receptor notch in vertebrates, it has been shown in drosophila that furin is not essential for notch signalling.
indeed, the notch receptor can still be trafficked to the membrane without this initial cleavage  <cit> .
furin belongs to the pcsk superfamily which contains diverse families of proteases.
several pcsk proteins are present in amphimedon although none seem to be bona fide furins .
nevertheless, we cannot exclude the possibility that one of these pcsks may perform the s <dig> cleavage in the amphimedon notch pathway instead of furin.
indeed, all pcsks share the same canonical cleavage site r-x-r/k-r and  available functional data suggest that some of them may play similar roles in different cellular lineages  <cit> .
the absence of a complete neuralized in non-bilaterians is not incompatible with a functional pathway, due to the functional redundancy of neuralized and mindbomb  <cit> : the latter being present in non-bilaterians.
indeed, these two components are both e <dig> ubiquitin ligases involved in ligand endocytosis and regulation  <cit> via ubiquitylation  <cit> , and were shown to be able to rescue each other in drosophila  <cit> .
a functional study of the notch pathway in placozoa, which lacks both a complete neuralized and mindbomb, would allow a better understanding of the effects of the absence of e <dig> ubiquitin ligase regulation.
regarding the inhibitor numb, it inhibits notch via endocytosis and regulates cell fate acquisition by asymmetric cell division or by lineage decision processes  <cit> .
functional studies in sponges would be necessary to state whether another protein replaces numb function.
nonetheless, it appears that the mechanism of numb-mediated asymmetric cell fate acquisition is a synapomorphy of notch pathway activity in bilateria.
the co-activator mastermind  is classically considered an integral part of the co-activation complex.
its non critical nature is highly unexpected and its absence from the demosponge species, as well as several bilaterian species, is puzzling.
the high sequence divergence of the mam proteins in bilaterians  and nicd  <cit> ) could make searching for them by sequence similarity alone inconclusive.
alternatively, these proteins may have been secondarily lost in several species, indicating that mam proteins may be facultative for pathway function or replaceable by other proteins.
in the absence of functional data on species that apparently lack mam, we cannot distinguish between these two hypotheses.
recent acquisition of new functions: intervention of domain shuffling
it is clear from our data that novelty arose either in the lca of holozoa or in the metazoan stem lineage, which resulted in the assembly of disparate components into the functional notch signal transduction pathway in animals.
our study further enables us to partly understand the molecular evolutionary mechanisms that may have facilitated these events.
hereafter, we focus on the origin of the two main players, the receptor notch and the ligands delta-jagged, all of which are metazoan specific multidomain proteins.
the origin and evolution of notch
in the light of the recent data concerning sponges  <cit>  and the present study, we can infer that notch is a synapomorphy of metazoa and consists of  <dig> core protein domains: egf, ank and lnr.
interestingly, these  <dig> domains exist in all eukaryotes.
proteins composed of egf domains, lnr domains or ank domains have been reported on separate chromosomes in m. brevicollis  <cit> .
it has been proposed that the presence of these domains in separate monosiga proteins suggests that notch is the result of a new recombination of existing domains, known as exon or domain shuffling  <cit> .
data concerning the role of the lnr domains also found in the pregnancy associated plasma protein a  are too scarce to infer the ancestral function of this domain  <cit> .
the only common feature that we can note between the lnr domains of notch and papp-a is a calcium binding capability  <cit> .
in contrast, egf and ank are modular protein subunits, that are very common in eukaryote proteins and that are known to be involved in protein-protein interactions  <cit> .
the ank repeat is one of the most common protein-protein interaction motifs in living beings  <cit> .
it has been primarily reported in eukaryotes, although examples from prokaryotes and viruses are also known and may be the result of lateral gene transfer  <cit> .
ank domains are not only part of the composition of notch  but also of mindbomb .
the ank repeat is a relatively well conserved motif with strongly conserved residues  and  <dig> α-helices  <cit> .
we note that the mindbomb ank motifs are less well conserved than the notch anks, suggesting that the structural integrity of the ank motifs of mindbomb are less constrained than in notch.
ank motifs in notch have a crucial role; they are involved in the assembly and stability of the complex with su and mastermind  <cit> .
when anks are deleted, the notch signalling pathway is not functional in mice  <cit> .
mindbomb ank repeats are important for the delta internalization process but are not necessary for delta ubiquitination  <cit> .
as already mentioned, mindbomb can be functionally replaced by neuralized; this flexibility may have led to weaker evolutionary constraints on the mindbomb ank repeats than on those of notch.
the two enigmatic domains nod and nodp, the roles of which are still unknown, seem to be an innovation of eumetazoa.
our analysis does not allow us to infer the process by which they appeared.
the origin of dsl proteins: delta and jagged
notch has two possible ligands encoded by the two paralogous genes delta and jagged.
our analyses show that delta was ancestrally present in metazoa, while a complete jagged is absent from placozoa and porifera.
phylogenetic analyses of the ligands do not provide conclusive results.
as already mentioned, we can envisage that the ligands are evolving in a rapid and divergent way in each lineage, and this could cause the loss of ancient phylogenetic signals.
experimental data suggest that delta and jagged may be complementary, functionally interchangeable or antagonistic  <cit> .
they share two protein domains, mnll and dsl, associated with the egf repeats that they have in common with notch, and are directly involved in receptor/ligands interactions.
while egf repeats represent an ancient domain, as previously discussed, mnll and dsl domains are absent outside metazoa.
their origin cannot be clarified by our study.
nevertheless, we may speculate that the dsl domain shares ancestry with the lnr domains of the notch receptor.
indeed, comparison of cysteine patterns from these two domains revealed that, for  <dig> of the  <dig> cysteines, positions and spacing are conserved.
despite the common characteristics of delta and jagged, they differ by two main features: i) a vwc domain present in jagged and absent in delta, the function of which is not clear but it may be involved in protein complex formation; ii) the number and spacing of egf repeats differ between delta and jagged .
nevertheless, no correlation between the number of egf repeats in the ligand and the affinity to the notch receptor has been reported.
instead, notch ligand choice is modulated by other proteins such as fringe and o-fucosyltransferase that modify notch egf residues  <cit> .
it is worth noting that the sponges and the placozoan possess complete delta genes  but jagged genes seem to be absent.
nevertheless, in the case of the sponges  and of trichoplax, the vwc domain,  is indeed present in the genomes, but it is never found in association with a dsl domain .
intriguingly though, in trichoplax, the vwc domain is found in association with egf domains .
these observations lead us to propose two possible evolutionary scenarios for the notch ligands :
- an ancestral delta gene duplicated before the radiation of the eumetazoa, followed by an association of the vwc domain to one of these delta copies.
the number of egfs increased either by tandem duplications within a gene , exon shuffling  or dna slippage   <cit> .
- an ancestral delta gene duplicated before the radiation of the eumetazoa, at which time egf repeats were already independently associated with a vwc domain .
one copy of the ancestral delta joined the egf+vwc motif to create jagged.
this second hypothesis could explain the higher number of egfs in jagged compared to delta .
the fact that egf motifs from jagged seems to be physically separated into two groups, as shown in figure  <dig>  may support this hypothesis.
this second scenario is also convincing because the shared possession of motif repeats  between independent genes was previously reported to favour domain shuffling  with likely consequences the creation of new exon combinations and thus new proteins  <cit> .
as we failed to find any specific signature in egf repeats that could allow us to favour one of these two scenarios, the sequencing of additional non-bilaterian genomes may help to resolve this question.
nevertheless we have to keep mind that currently the placozoan phylogenetic position is still controversial  <cit> .
CONCLUSIONS
this study focusing on the notch signalling pathway provides for the first time a complete description of notch components and auxiliary factors across the eukaryota.
these investigations have enabled us to re-assess the ancient origin of some components such as the γ-secretase complex and notchless.
fringe and sno are probably old genes that were convergently acquired by lateral gene transfer.
several new functions of the notch pathway likely originated in the last common ancestor of holozoa, which already possessed  <dig> genes of the pathway.
nevertheless, the core genes needed for a functional pathway are only present in metazoans and it apparent that the two main players, notch and delta, emerged via both the shuffling of old domains , and the invention of new ones .
at present, functional data on non-bilaterian models are scarce, but such efforts need to be realized in order to understand the emergence of functionality in the notch pathway.
more largely this will pertain to an understanding of the emergence of signal transduction pathways during the acquisition of multicellularity in the metazoa.

 the emergence of multicellularity, considered to be one of the major evolutionary events concerning life on earth, occurred several times independently during the evolution of eukaryota in the proterozoic geological period. multicellular organisms are not only a superimposition of the fundamental unit of life, namely the cell; the emergence of multicellularity further implies that cells must communicate, coordinate and organise. in embryophyta and metazoa, higher levels of differentiation and organization of cells resulted in the emergence of organs and their organisation into complex body plans. reaching this critical step required the elaboration of sophisticated intercellular communication mechanisms. cell-cell interactions through signal transduction pathways are therefore crucial for the development and the evolution of multicellular organisms. the modifications of these signal transduction pathways explain the macroevolution process observed. in metazoans, fewer than different signal transduction pathways are required to generate the observed high diversity of cell types, patterns and tissues. among them, only seven control most of the cell communications that occur during animal development: wnt; transforming growth factor β; hedgehog; receptor tyrosine kinase; jak/stat; nuclear hormone receptor; and notch. these pathways are used throughout development in many and various metazoans to establish polarity and body axes, coordinate pattern formation and choreograph morphogenesis. the common outcome to all of these pathways is that they act, at least in part, through the regulation of the transcription of specific target genes by signal-dependent transcription factors. the notch signalling pathway is a major direct paracrine signalling system and is involved in the control of cell identity, proliferation, differentiation and apoptosis in various animals. notch signalling is used iteratively in many developmental events and its diverse functions can be categorized into two main modalities "lateral inhibition" and "boundaries/inductive mechanisms". during lateral inhibition, notch signalling has mainly a permissive function and contributes to binary cell fate choices in populations of developmentally equivalent cells, by inhibiting one of the fates in some cells and therefore allowing them to later adopt an alternative one. lateral inhibition is a key patterning process that often results in the regular spacing of different cell types within a field. the notch pathway may also have more instructive roles, whereby signalling between neighbouring populations of different cells and induces the adoption of a third cell fate at their border, establishing a developmental boundary. a large number of studies, mainly conducted on drosophila, caenorhabditis and vertebrates, have characterized the molecular properties and functions of the main components and auxiliary factors of the notch pathway. these are strongly conserved in bilaterians. both the notch receptor and its ligands are type i transmembrane proteins with a modular architecture. in eumetazoans, the notch protein is classically considered to be composed of an extracellular domain that comprises several egf and lnr motifs, an intracellular domain that includes ank domains and a pest region. the notch protein is synthesized as an inactive precursor that has to be cleaved three times and to undergo various post-translational modifications to become active. in the golgi apparatus, the first cleavage is done by the furin protease resulting in two fragments that subsequently undergo o-fucosylation and glycosylation. upon ligand binding, the second cleavage occurs by the metalloproteases adam and. the final cleavage is performed by the γ-secretase complex. these cleavages result in the release, upon ligand binding, of nicd into the cytoplasm and its subsequent translocation to the nucleus. there, nicd interacts with the csl, lag-1)/ncor/smrt/histone deacetylase transcriptional complex and recruits the coactivator mastermind and a histone acetylase, thus activating the transcription of target genes in particular the hes/e genes. in addition to these core components of the notch pathway, several other proteins are used to regulate notch signalling in some cellular contexts, and act either on the receptor notch or on the ligand dsl. some of these regulators modulate the amount of receptor available for signalling. numb, the nedd4/su e ubiquitin ligases, and notchless are important negative regulators, while deltex is considered to antagonize nedd4/su and therefore to be an activator of notch signalling. strawberry notch, another modulator of the pathway whose role is still unclear, seems to be active downstream and disrupts the cslrepression complex. regulation may also occur at the level of ligand activity via the e ubiquitin ligases neuralized and mindbomb. most of what we know about the notch signalling pathway comes from studies conducted on a few bilaterian species. recently, studies have shown the existence of a notch signalling pathway in non-bilaterian species, such as the cnidarian hydra and the sponge amphimedon, and its putative functions in the former species. however, the ancestral structure, functionality and emergence of this complex multi-component signalling system are still open questions. few studies have been initiated to understand how signalling pathways appeared and evolved beyond the bilateria but the recent sequencing of the first sponge genome, amphimedon queenslandica has opened new perspectives for studying the origin and evolution of signalling pathways in the metazoa. with the goal of illuminating the early evolution of the notch pathway, we have therefore undertaken a comparative genomic study of the components of this pathway across the eukaryota. our study encompasses species covering the major clades of eukaryotes, and includes the main components of the notch pathway. we have also paid special attention to the evolution of domain composition of the multidomain proteins notch, delta, mindbomb, su and furin, to investigate whether domain shuffling has occurred during their evolution, as in other signalling pathways. this wide genomic comparison reveals that most of the notch components are present in all the metazoan species studied, including putative basal metazoans such as sponges and placozoan, suggesting that a functional notch pathway was already present in the last common ancestor of present-day metazoans and was subsequently strongly conserved during metazoan evolution. while many of the notch pathway components are also shared with non-metazoan eukaryote lineages, thus suggesting a more ancient origin, nine of the components are metazoan-specific, including the notch receptor and the dsl ligands. this indicates that while the notch pathway is a metazoan synapomorphy, it has been assembled through the co-option of pre-metazoan proteins, and their integration with novel metazoan-specific molecules acquired by various evolutionary mechanisms.  genome-wide identification of the main notch signalling pathway components in eukaryotes to understand more precisely the evolution of the notch pathway at the scale of the eukaryotes, we systematically searched for all the main notch pathway elements in completely sequenced genomes and expressed sequence tag data of different eukaryote species. table lists the genes that we analysed and summarizes their functions in the notch pathway. we included in this list both genes that encode core components of the notch pathways and genes that encode modulators of the pathway not used in all cases of notch signalling. we selected species representative of the major clades of eukaryotes: metazoans, fungi, choanoflagellate, amoebozoans, species of plants, alveolates, heterokonts, species of discicristates, species of excavates and rhizaria. figure provides the full list of the chosen species with their assumed phylogenetic position and internet links to the genomic databases. we performed blast searches to assess the presence or absence of notch pathway genes in the sampled species, as described in the methods section. in most cases, the notch pathway elements are multidomain proteins and share some of their domains with other proteins. for each target protein, only the combined occurrence of all requisite domains was considered diagnostic for identification. we systematically defined a diagnostic domain organization for each target protein and identified genes as detailed in the methods section. we also constructed multiple alignments for each protein and performed phylogenetic analyses to confirm the orthology relationships. figure summarizes the output of our analyses: genes were scored as "present" when all the domains were identified, "incomplete" when some domains were missing, or "absent" when blast searches gave no significant result. for est libraries, as the absence and the incomplete status of genes cannot be definitive due to the partial nature of this type of data, we chose to indicate "present" only when all domains were retrieved. detailed domain composition for each gene in each species is presented in the additional file our data confirm the strong evolutionary conservation of the notch pathway in bilaterians as all components are present in almost all the analysed bilaterian species. there are two exceptions to this rule, fringe which is absent from the genome of two protostomes, caenorhabditis and helobdella, and mastermind is not found in of the studied bilaterian species across both protostomes and deuterostomes. the latter case is puzzling given the documented importance of mastermind in both vertebrates and drosophila and its presence in the non-bilaterian species nematostella. this suggests that mastermind has been repeatedly lost in various bilaterian species. alternatively, as the sequence similarity between the mastermind genes in drosophila and vertebrates is quite weak, these genes may be difficult to track by sequence similarity searches. our data also indicate that the overall notch pathway conservation extends to non-bilaterian species. indeed, most pathway components can be identified in the cnidarians nematostella and hydra, in the placozoan trichoplax and the sponge amphimedon. we can therefore conclude that most notch pathway components were already present in the last common ancestor of all metazoans, the urmetazoa. four genes were not found complete outside bilaterians, smrt, furin, numb and neuralized, suggesting that these genes are specific to bilaterians. genes encoding proteins with a sant domain are found in non-bilaterians, but the sequence similarity is too weak to establish that some are bona fide smrt genes. the case of the furin protein is puzzling. this protein pertains to the proprotein convertase subtilisin/kexin family. in the demosponge amphimedon and the choanoflagellate, there are some proteins of the pcsk family and some of them possess the diagnostic domains of the furin proteins. nevertheless, the phylogenetic analysis revealed that these proteins do not group with bilaterian furins, however the latter are paraphyletic in the phylogenetic tree. in the case of neuralized, while neuz domains are found in non-bilaterians, they are only found in association with a ring binding domain in the bilateria. in the same way, ph-like domains of numb are only found in association with a numbf domain in bilaterians. the gene mastermind is only found in eumetazoans and two others, fringe and mindbomb, are found in amphimedon but not in trichoplax. the absence of some components in some non-bilaterian species may represent a progressive elaboration of the pathway during early metazoan evolution, or else may correspond to secondary losses in some lineages. however, these data can be difficult to interpret in terms of the evolution of the notch pathway, as the phylogenetic relationships of the aforementioned non-bilaterian species are still controversial. nevertheless, we decided to base our discussion on the metazoan relationships hypothesised in the most recent phylogenomic study as we believe it to be the most robust and complete analysis to date. our data so far indicate that most of the notch pathway components were already present in urmetazoa. interestingly, among the targeted genes, only nine are specific to metazoans. strikingly, among these, nine are the genes encoding the ligand and the receptor, suggesting that the canonical notch pathway only exists in metazoans. indeed, in the genome of the choanoflagellate monosiga, no notch gene has been found, only cassettes of some protein domains encoded on separate genes have been reported. of note, we also found another gene in this species that possesses the domain arrangement of a notch gene. while this gene contains the minimum set of diagnostic notch domains, it has very weak sequence similarity to notch genes, and in the absence of further evidence we choose here to name it "notch-like". nevertheless, we can not exclude that a "protonotch" receptor might have been already present in holozoa. components are found in various other eukaryote taxa; some are likely to have appeared during early eukaryote evolution and may even have been present in the last common ancestor of present-day eukaryotes. others seem to have specifically appeared in the opisthokont lineage. figure represents the possible scenarios of emergence and loss of the various notch components, inferred from the most recent and robust phylogenetic hypotheses and on the basis of the parsimony principle. four genes of this pathway seem to have appeared early in evolution and are inferred to have been present in the leca. these include notchless and three of the four genes coding for proteins implicated in the so-called "γ-secretase complex". indeed, the presenilin gene is shared by all eukaryotes whereas nicastrin and aph are found in the holozoa, the amoebozoa, the plantae and the heterokonta. interestingly, none of these genes are found in species of fungi + microsporidia and alveolata, suggesting a secondary loss. for other genes that are shared by fewer taxa, it is difficult to state whether they were present in the leca and lost various times, or acquired independently: this is the case for pen strawberry notch, the role of which in the notch pathway is not yet clear, and fringe. all other genes originated more recently, in the last common ancestor of opisthokonts ); suppressor of deltex ). this might also be the case for the two adam genes. we cannot confidently assign the adam genes we found in fungi and microsporidia to a particular adam group; however these genes are most closely related to metazoan adam and families as already reported by another study on aspergillus fumigatus. other genes are specific to holozoans. for the ctenophore species as well as the homoscleromorph sponge oscarella, only a few target genes were identified in the available non exhaustive est databases and we were unable to conclude whether or not the remaining genes are present in those taxa. focus on notch and dsl proteins evolution in metazoan: phylogenetic analyses and domain composition arrangement we chose to focus our further analyses on the two main molecules of the pathway, notch and dsl, and study their evolution in metazoans. we first performed phylogenetic analyses using both maximum likelihood and bayesian inference approaches and then investigated the domain organizations of each. topologies obtained in our phylogenetic analyses are not fully resolved, as previously noticed for the notch ligands. long branch attraction bias may be suspected in some cases and, as previously reported by different authors, ml appears more sensitive to lba than bi. concerning domain composition and organization, generally all the diagnostic domains in delta or notch genes are present in bilaterian sequences, but some domains seem to be lacking in a few species. in these cases, we can not state whether this is due to prediction errors, sequencing gaps in the available genome sequences or secondary losses. when the available software prediction is equivocal, important conserved residues can often be identified in the regions where domains would be expected, suggesting functional conservation. despite these technical limits, our analysis presents several features of interest. first, a single notch gene is found in most species, except in vertebrates and in the annelid helobdella. in the former case, this is most probably due to the well documented occurrence of two whole genome duplication events in this lineage. in the latter case, it may correspond to a recent duplication, limited to an annelid lineage. indeed, the two helobdella genes form a monophyletic group in our trees and only a single notch gene has been found in the genome of another annelid species, capitella sp. i. in the bayesian analysis, we note that the sequences from bilaterians form a monophyletic group and the cnidarian sequence clearly appears more related to bilaterian sequences than to other non-bilaterian sequences. the receptor notch is considered to be made of several domains: egf repeats, three lnr or notch domains, two enigmatic domains nod and nodp, a ram domain, a pest domain and several ankyrin repeats. the number of egfs is variable and spans from in caenorhabditis to in humans. the nod and the nodp are absent in sponges and in some bilaterian species. the absence of a signal peptide is observed in of the sequences, and the pest domain is absent at the c-terminus of three sequences. second, in the dsl family jagged is absent from placozoans and sponges and present in all other studied metazoans. delta is present in all metazoan species of our study, and in contrast to jagged, is also found in non-eumetazoans. the number of copies of delta is also variable but is notably high in the gastropod snail lottia. we also note that copies are present in the sponge genome, which is remarkably high in comparison to the other non-bilaterians such as trichoplax and nematostella. in spite of the differences between the ml and bi topologies and the weak statistical support of deep nodes in both analyses, we are able to draw some conclusions about the evolution of the dsl family. in the bayesian tree, a strongly supported clade contains all eumetazoan jagged sequences plus one sequence from branchiostoma and one from the sponge oscarella. this suggests the existence of a subfamily of serrate/jagged proteins that is found in all the major animal lineages and therefore is of ancient origin. most of the other studied proteins form another large monophyletic group likely corresponding to what may be called a delta clade since it includes the known deltas from vertebrates as well as from the main metazoan lineages, including the sponge amphimedon and the placozoan trichoplax. nevertheless, the internal branching of the delta sequences makes no sense in the light of species phylogenies. our phylogenetic analysis rather suggests that the last common ancestor of all eumetazoans already possessed at least one delta and one jagged/serrate gene and that the urmetazoa possessed at least one sequence of delta. the position of the of d/j-oscarella carmela in the bayesian tree is puzzling, the blast analysis revealed a higher similarity between this sponge sequence and delta sequences but we cannot definitively rule out the possibility that it might be an incomplete jagged protein. to support our phylogenetic analyses, we also systematically investigated the domain arrangements of the dsl family proteins. dsl proteins are usually considered to be composed of several domains, namely a signal peptide, a mnll domain, a dsl domain, a variable number of egf repeats and a transmembrane region. in addition to these domains, the serrate/jagged proteins also contain a supplementary domain, the von willebrand factor c domain. interestingly, all but two proteins included in the jagged group in our phylogenetic trees contain the vwc domain, confirming that they are bona fide jagged proteins. the exceptions are the two branchiostoma genes; phylogenetic analyses highly support their belonging to the jagged clade, suggesting that the absence of the vwc domain may be due to incorrect protein predictions, incomplete genome assemblage or secondary loss. third, in our ligand domain analyses, we found that the mnll, the signal peptide and the transmembrane domains are not present across all metazoan delta ligands but we could find them in the majority of jaggeds. most deuterostome delta sequences possess the mnll domain, in contrast to the protostome sequences. among the sponge species a mnll is only predicted in one copy of the amphimedon deltas. the number of egf repeats ranges from to in delta and from to in jagged. an average of 7- egf motifs are present in deuterostome delta sequences; it is much more variable in protostomes. we note that motifs expected at the n or c terminus are more often lacking. as this absence of a signal peptide or a transmembrane region appears incongruous and hardly compatible with the conservation of functionality, the assembly and annotation of the concerned genomes may require a re-examination. surprisingly, in cnidarian genomes, in addition to the delta and jagged sequences, we found genes composed only of dsl domains and one gene composed of a mnll domain associated to dsl domains. it remains to be seen either these are true genes with unique functionalities, or represent misassembled regions of the genome. origin and evolution of protein domains involved in the pathway we focused on five genes that encode multidomain proteins in the pathway: dsl, notch, mindbomb, su, furin. we mapped the possible acquisition and loss events of the different domains during eukaryote evolution according to the phylogenetic hypothesis of baldauf. on one hand, it appears that various domains have an ancient origin; they are shared by several eukaryote lineages, so we can hypothesize their presence in the leca. this is the case for: egf repeats of notch and dsl, ank repeats of mindbomb and notch; the lnr domain of notch; both zz and ring type zn finger domains of mindbomb; the ipt rbp-jkappa domain of su; the subtilisin domain and the furin domain. in all of these cases, a hypothesis of ancestrality followed by one or more secondary losses is most parsimonious. on the other hand, several domains appear to have originated more recently since they are specific to opisthokonts or even to metazoans: the mnll, dsl and vwc domains involved in dsl composition; the nod and nodp domains of notch; the mib/herc domain of mindbomb; the lag and beta-trefoil domains of su. thus, a total of six domains may represent synapomorphies of the metazoa. in the case of the p-proprotein of furin, the more parsimonious inference is that it may have appeared convergently three times in excavata, heterokonta and in opistokonta. discussion a functional notch pathway seems to have been present in the urmetazoa and comprised at least components. the later addition of five other components can thus be considered as facultative and responsible for additional regulation properties of the pathway. our study indicates that the presence of the notch pathway is a synapomorphy of metazoans as this is the only kingdom to possess all the key components of the pathway, most importantly the receptor and ligands. our analysis also sheds light on the molecular mechanisms that may have been invoked in the formation of this pathway. indeed, as we discuss hereafter, our study shows that notch signalling has originated by cooption of pan-eukaryotic ancestral genes; modification of ancestral functions by new protein-protein interactions; lateral gene transfer; formation of new proteins by both exon shuffling and duplications + divergence. cooption of pre-existing genes and ancestral functions this study, at the scale of the eukaryota super-kingdom, reveals the presence of notch components in diverse eukaryotic organisms, and thus their ancient origin. certain highly conserved genes, despite their ancestrality, seem to be absent in fungi and microsporidia. this is consistent with previous genomic analyses that have documented massive gene losses in the lca of fungi + microsporidia, and a further round of losses in microsporidies in relation to their parasitic life style. the origin of presenilin and of the γ-secretase complex one of the most striking features uncovered by our study is the evolutionary conservation of the γ-secretase complex: the four proteins composing this large transmembrane complex are present in both plants and unikonts. while the entire γ-secretase complex does not seem to be pan-eukaryotic, our analysis nonetheless supports an altered evolutionary scenario than that formerly proposed for its main player, presenilin. previously, authors have hypothesized a convergent acquisition of this gene in the metazoan and the plant lineages. our study reveals instead that presenilin was present in the leca, and then lost independently twice. the aph and nicastrin proteins may also be ancestral to eukaryota, but our data is inconclusive for pen on this point. until now, functional analyses of this complex are available only in embryophyta and metazoa, where it is known to be involved in the cleavage of notch and other proteins such as erbb and app. but the lack of evidence for a complete γ-secretase complex in the leca parallels recent functional data indicating that in both mammals and a bryophyte, presenilin is also involved in various γ-secretase-independent functions such as protein degradation and trafficking. the association of pen is considered to be necessary to acquire the proteolytic activity of presenilin via conformational changes. these changes may result in the accessibility of the two catalytic motifs y/wd and gxgd, which are conserved at the eukaryotic scale. this suggests that proteolysis might not have been the ancestral function of presenilin, but might have been acquired secondarily by its co-option into the four protein γ-secretase complex. this challenging evolutionary scenario requires further investigations to be tested. the origin of the notchless inhibitor notchless encodes a protein containing a nle domain and wd40-repeats. in eumetazoa, this member of the wd-repeat protein superfamily modulates the notch pathway by binding the nicd but also by interacting with deltex and su. our analysis shows that notchless was probably present in leca. nevertheless, in some of the studied species, the nle domain is missing, and we cannot define whether this is due to secondary loss or to a high level of sequence divergence obscuring domain prediction. the high conservation of nle sequences seems to be compatible with functional conservation as shown by transgenic experiments between a plant, solanum chacoense and an animal, drosophila. however, while both plant and yeast notchless proteins share an involvement in ribosome biogenesis, until now no such role has been reported in animals. these observations have led authors to propose that either notchless was primarily involved in ribosome biogenesis in eukaryotes and was secondarily recruited in the metazoans for a new function, or that this role may still exist in animals despite the lack of experimental evidence. ancestrality or lateral gene transfer? two other members of the notch pathway show an ambiguous history, in which the eventuality of lateral gene transfer cannot be excluded. this is the case for both fringe and strawberry notch. our analyses reveal that fringe is present in metazoa, but also in plants and parabasalia. a fringe domain alone was also identified in the studied ascomyceta species; however no complete fringe or fringe-like gene seems to be present in this taxon. we could hypothesize that the fringe gene was present in the leca and then lost several times; nevertheless, the most parsimonious scenario suggests three independent acquisitions. we can speculate that lgt might have occurred, favoured by either the tight association existing between parabasalia and metazoa lineages or via bacterial transfers. however, we failed to find any specific relationships or signatures between the fringe genes of homo and its parasite trichomonas as well as we failed to detect fringe outside eukaryota to strongly argue for a lgt hypothesis. in our analysis, sno is shown to be present in holozoa and plantae. unexpectedly, sno has been reported recently in a nuclear and cytoplasmic large dna virus of the haptophyte emiliania huxleyi. as our analysis on the genomes of the two chosen heterokonts failed to reveal the presence of sno, we chose to extend our research to other heterokonta related species. interestingly, sno is not only present in the genome of the haptophyte emiliania, suggesting a lgt between this species and its virus ehv, but also in two other heterokonta, aureococcus anophaegefferens and thalassiosina pseudonana. another interesting feature is that sno has been shown to be derived from the snf2/swi atpases encoding gene of α-proteobacteria. the presence of sno or sno-related genes in both ncldv and α-proteobacteria may suggest lgt events in the history of these genes because i) α-proteobacteria are often found in tight associations with various eukaryote taxa and ii) ncldvs have been reported from amoebozoa, haptophyta, discicristata and viridiplantae however their ecological distribution and importance is still largely unknown and newly described virophage of ncldvs may also be involved in lgt. in the two cases, further analyses are needed to shed light on the origin and history of these genes and to state whether they were acquired by lgt or not. the notch pathway is specific to metazoa the cooption or acquisition of "old" genes is not sufficient to explain the formation of the canonical notch pathway. one of the pivotal steps in the evolutionary history of the notch pathway seems to be the transition between the choanoflagellates and the animals. indeed, this study reveals that the majority of notch components appeared in the lca of the holozoa. nevertheless, several molecular components critical for signal transduction are lacking in choanoflagellates, in particular, the ligand delta and the receptor notch, thus we consider the notch pathway as a synapomorphy of the metazoa. an increase in the complexity of this pathway has also occurred after the divergence between sponges and other metazoans. several notch components are absent from the demosponge amphimedon, yet the pathway may still be functional in this species. this suggests that these components were not critical for the function of the pathway and may constitute additional regulatory elements that were subsequently added to the pathway in eumetazoans. nevertheless, the possible pan-metazoan ancestry of these genes cannot be excluded; data from other sponges may help to resolve this issue. the absence of furin in amphimedon is not really unexpected; although furin has a critical role for the maturation of the receptor notch in vertebrates, it has been shown in drosophila that furin is not essential for notch signalling. indeed, the notch receptor can still be trafficked to the membrane without this initial cleavage. furin belongs to the pcsk superfamily which contains diverse families of proteases. several pcsk proteins are present in amphimedon although none seem to be bona fide furins. nevertheless, we cannot exclude the possibility that one of these pcsks may perform the s cleavage in the amphimedon notch pathway instead of furin. indeed, all pcsks share the same canonical cleavage site r-x-r/k-r and available functional data suggest that some of them may play similar roles in different cellular lineages. the absence of a complete neuralized in non-bilaterians is not incompatible with a functional pathway, due to the functional redundancy of neuralized and mindbomb: the latter being present in non-bilaterians. indeed, these two components are both e ubiquitin ligases involved in ligand endocytosis and regulation via ubiquitylation, and were shown to be able to rescue each other in drosophila. a functional study of the notch pathway in placozoa, which lacks both a complete neuralized and mindbomb, would allow a better understanding of the effects of the absence of e ubiquitin ligase regulation. regarding the inhibitor numb, it inhibits notch via endocytosis and regulates cell fate acquisition by asymmetric cell division or by lineage decision processes. functional studies in sponges would be necessary to state whether another protein replaces numb function. nonetheless, it appears that the mechanism of numb-mediated asymmetric cell fate acquisition is a synapomorphy of notch pathway activity in bilateria. the co-activator mastermind is classically considered an integral part of the co-activation complex. its non critical nature is highly unexpected and its absence from the demosponge species, as well as several bilaterian species, is puzzling. the high sequence divergence of the mam proteins in bilaterians and nicd ) could make searching for them by sequence similarity alone inconclusive. alternatively, these proteins may have been secondarily lost in several species, indicating that mam proteins may be facultative for pathway function or replaceable by other proteins. in the absence of functional data on species that apparently lack mam, we cannot distinguish between these two hypotheses. recent acquisition of new functions: intervention of domain shuffling it is clear from our data that novelty arose either in the lca of holozoa or in the metazoan stem lineage, which resulted in the assembly of disparate components into the functional notch signal transduction pathway in animals. our study further enables us to partly understand the molecular evolutionary mechanisms that may have facilitated these events. hereafter, we focus on the origin of the two main players, the receptor notch and the ligands delta-jagged, all of which are metazoan specific multidomain proteins. the origin and evolution of notch in the light of the recent data concerning sponges and the present study, we can infer that notch is a synapomorphy of metazoa and consists of core protein domains: egf, ank and lnr. interestingly, these domains exist in all eukaryotes. proteins composed of egf domains, lnr domains or ank domains have been reported on separate chromosomes in m. brevicollis. it has been proposed that the presence of these domains in separate monosiga proteins suggests that notch is the result of a new recombination of existing domains, known as exon or domain shuffling. data concerning the role of the lnr domains also found in the pregnancy associated plasma protein a are too scarce to infer the ancestral function of this domain. the only common feature that we can note between the lnr domains of notch and papp-a is a calcium binding capability. in contrast, egf and ank are modular protein subunits, that are very common in eukaryote proteins and that are known to be involved in protein-protein interactions. the ank repeat is one of the most common protein-protein interaction motifs in living beings. it has been primarily reported in eukaryotes, although examples from prokaryotes and viruses are also known and may be the result of lateral gene transfer. ank domains are not only part of the composition of notch but also of mindbomb. the ank repeat is a relatively well conserved motif with strongly conserved residues and α-helices. we note that the mindbomb ank motifs are less well conserved than the notch anks, suggesting that the structural integrity of the ank motifs of mindbomb are less constrained than in notch. ank motifs in notch have a crucial role; they are involved in the assembly and stability of the complex with su and mastermind. when anks are deleted, the notch signalling pathway is not functional in mice. mindbomb ank repeats are important for the delta internalization process but are not necessary for delta ubiquitination. as already mentioned, mindbomb can be functionally replaced by neuralized; this flexibility may have led to weaker evolutionary constraints on the mindbomb ank repeats than on those of notch. the two enigmatic domains nod and nodp, the roles of which are still unknown, seem to be an innovation of eumetazoa. our analysis does not allow us to infer the process by which they appeared. the origin of dsl proteins: delta and jagged notch has two possible ligands encoded by the two paralogous genes delta and jagged. our analyses show that delta was ancestrally present in metazoa, while a complete jagged is absent from placozoa and porifera. phylogenetic analyses of the ligands do not provide conclusive results. as already mentioned, we can envisage that the ligands are evolving in a rapid and divergent way in each lineage, and this could cause the loss of ancient phylogenetic signals. experimental data suggest that delta and jagged may be complementary, functionally interchangeable or antagonistic. they share two protein domains, mnll and dsl, associated with the egf repeats that they have in common with notch, and are directly involved in receptor/ligands interactions. while egf repeats represent an ancient domain, as previously discussed, mnll and dsl domains are absent outside metazoa. their origin cannot be clarified by our study. nevertheless, we may speculate that the dsl domain shares ancestry with the lnr domains of the notch receptor. indeed, comparison of cysteine patterns from these two domains revealed that, for of the cysteines, positions and spacing are conserved. despite the common characteristics of delta and jagged, they differ by two main features: i) a vwc domain present in jagged and absent in delta, the function of which is not clear but it may be involved in protein complex formation; ii) the number and spacing of egf repeats differ between delta and jagged. nevertheless, no correlation between the number of egf repeats in the ligand and the affinity to the notch receptor has been reported. instead, notch ligand choice is modulated by other proteins such as fringe and o-fucosyltransferase that modify notch egf residues. it is worth noting that the sponges and the placozoan possess complete delta genes but jagged genes seem to be absent. nevertheless, in the case of the sponges and of trichoplax, the vwc domain, is indeed present in the genomes, but it is never found in association with a dsl domain. intriguingly though, in trichoplax, the vwc domain is found in association with egf domains. these observations lead us to propose two possible evolutionary scenarios for the notch ligands: - an ancestral delta gene duplicated before the radiation of the eumetazoa, followed by an association of the vwc domain to one of these delta copies. the number of egfs increased either by tandem duplications within a gene, exon shuffling or dna slippage. - an ancestral delta gene duplicated before the radiation of the eumetazoa, at which time egf repeats were already independently associated with a vwc domain. one copy of the ancestral delta joined the egf+vwc motif to create jagged. this second hypothesis could explain the higher number of egfs in jagged compared to delta. the fact that egf motifs from jagged seems to be physically separated into two groups, as shown in figure may support this hypothesis. this second scenario is also convincing because the shared possession of motif repeats between independent genes was previously reported to favour domain shuffling with likely consequences the creation of new exon combinations and thus new proteins. as we failed to find any specific signature in egf repeats that could allow us to favour one of these two scenarios, the sequencing of additional non-bilaterian genomes may help to resolve this question. nevertheless we have to keep mind that currently the placozoan phylogenetic position is still controversial.  this study focusing on the notch signalling pathway provides for the first time a complete description of notch components and auxiliary factors across the eukaryota. these investigations have enabled us to re-assess the ancient origin of some components such as the γ-secretase complex and notchless. fringe and sno are probably old genes that were convergently acquired by lateral gene transfer. several new functions of the notch pathway likely originated in the last common ancestor of holozoa, which already possessed genes of the pathway. nevertheless, the core genes needed for a functional pathway are only present in metazoans and it apparent that the two main players, notch and delta, emerged via both the shuffling of old domains, and the invention of new ones. at present, functional data on non-bilaterian models are scarce, but such efforts need to be realized in order to understand the emergence of functionality in the notch pathway. more largely this will pertain to an understanding of the emergence of signal transduction pathways during the acquisition of multicellularity in the metazoa. 
the notch signalling pathway emerged in metazoa via a diversity of molecular mechanisms, incorporating both novel and ancient protein domains during eukaryote evolution. we searched for components of the notch pathway in different species that represent major clades of eukaryotes, performed phylogenetic analyses and compared the domain compositions of the two fundamental molecules: the receptor notch and its ligands delta/jagged. the origin of several components can be accounted for by the shuffling of pre-existing protein domains, or via lateral gene transfer. we confirm that a notch pathway, with true receptors and ligands is specific to the metazoa. in light of this essential role played in metazoan development, we surveyed a wide range of eukaryotic genomes to determine the origin and evolution of the components and auxiliary factors that compose and modulate this pathway. of the or so signal transduction pathways that orchestrate cell-cell interactions in metazoans, seven are involved during development. this study also sheds light on the deep ancestry of a number of genes involved in this pathway, while other members are revealed to have a more recent origin. one of these is the notch signalling pathway which regulates cellular identity, proliferation, differentiation and apoptosis via the developmental processes of lateral inhibition and boundary induction.
 of the or so signal transduction pathways that orchestrate cell-cell interactions in metazoans, seven are involved during development. one of these is the notch signalling pathway which regulates cellular identity, proliferation, differentiation and apoptosis via the developmental processes of lateral inhibition and boundary induction. in light of this essential role played in metazoan development, we surveyed a wide range of eukaryotic genomes to determine the origin and evolution of the components and auxiliary factors that compose and modulate this pathway.  we searched for components of the notch pathway in different species that represent major clades of eukaryotes, performed phylogenetic analyses and compared the domain compositions of the two fundamental molecules: the receptor notch and its ligands delta/jagged. we confirm that a notch pathway, with true receptors and ligands is specific to the metazoa. this study also sheds light on the deep ancestry of a number of genes involved in this pathway, while other members are revealed to have a more recent origin. the origin of several components can be accounted for by the shuffling of pre-existing protein domains, or via lateral gene transfer. in addition, certain domains have appeared de novo more recently, and can be considered metazoan synapomorphies.  the notch signalling pathway emerged in metazoa via a diversity of molecular mechanisms, incorporating both novel and ancient protein domains during eukaryote evolution. thus, a functional notch signalling pathway was probably present in urmetazoa. 