Echinoderm - Sea Urchin genome

Key findings are the following:

• The sea urchin is estimated to have 23,300 genes with representatives of nearly all

vertebrate gene families, although often the families are not as large as in

vertebrates.

• Some genes thought to be vertebrate-specific were found in the sea urchin

(deuterostome-specific); others were identified in sea urchin but not the chordate

lineage, which suggests loss in the vertebrates.

• Expansion of some gene families occurred apparently independently in the sea

urchin and vertebrates.

• The sea urchin has a diverse and sophisticated immune system mediated by an

astonishingly large repertoire of innate pathogen recognition proteins.

• An extensive defensome was identified.

• The sea urchin has orthologs of genes associated with vision, hearing, balance, and

chemosensation in vertebrates, which suggests hitherto unknown sensory

capabilities.

• Distinct genes for biomineralization exist in the sea urchin and vertebrates.

• Orthologs of many human disease–associated genes were found in the sea urchin.

Details:

1) Genome features

A window on the genetic landscape is scaffold-centric in S. purpuratus, because linkage and

cytogenetic maps are not available. The 36.9% GC content of the genome is uniformly low

because assessment of the average GC content by domains is consistent (36.8%), and the

distribution is tight (see SOM). Genes from the OGS show no tendency to occupy regions of

higher- or lower-than-average GC content. In fact, nearly all genes lie in regions of 35 to

39% GC.

2) The Echinoderm Genome in the Context of Metazoan Evolution

Two of the

most abundant domains make up 3% of the total and mark genes that are involved in the

innate immune response. Others define proteins associated with apoptosis and cell death

regulation, as well as proteins that serve as downstream effectors in the Toll–interleukin 1

(IL-1) receptor (TIR) cascade. The quinoprotein amine dehydrogenase domain seen in the

sea urchin set is 10 times as abundant as in other representative genomes and may be used in

the systems of quinone-containing pigments known to occur in these marine animals. The

large number of nucleosomal histone domains found agrees with the long-established sea

urchin–specific expansion of histone genes. In summary, the distribution of proteins among

these conserved families shows the trend of expansion and shrinkage of the preexisting

protein families, rather than frequent gene innovation or loss. Gene family sizes in the sea

urchin are more closely correlated with what is seen in deuterostomes than what is seen in

the protostomes.

Of equal interest are the sorts of proteins not found in sea urchins. The sea urchin gene set

shares with other bilaterian gene models about 4000 domains, whereas 1375 domains from

other bilaterian genomes are not found in the sea urchin set. 

In agreement with the lack of

morphological evidence of gap junctions in sea urchins, there are no gap junction proteins

(connexins, pannexins, and innexins). 

Also missing are several protein domains unique to

insects, such as insect cuticle protein, chitin-binding protein, and several pheromone- or

odorant-binding proteins, as well as a vertebrate invention—the Krüppel-associated box or

KRAB domain, a repressor domain in zinc finger transcription factors (12). 

Finally, searches

for specific subfamilies of G protein–coupled receptors (GPCRs) that are known as

chemosensory and/or odorant receptors in distinct bilaterian phyla failed to detect clear

representatives in the sea urchin genome. 

However, this failure more likely reflects the

independent evolution of these receptors, rather than a lack of chemoreceptive molecules,

because the sea urchin genome encodes close to 900 GPCRs of the same superfamily

(rhodopsin-type GPCRs), several of which are expressed in sensory structures (13). 

A

conservative way to compare gene sets is to count the strict orthologs that give reciprocal

BLAST matches. Genes that are genuine orthologs are likely to yield each other as a best

hit. Comparison of sea urchin, fruit fly, nematode, ascidian, mouse, and human gene sets

(Fig. 2) indicates that the greatest number of reciprocal best matches is observed between

mouse and human, which reflects their close relation. The numbers of presumed orthologous

genes between the ascidian and the two mammals are about equal, but are less than the

number counted between these species and the sea urchin. The difference is consistent with

the lower gene number and reduced genome size in the urochordates (4).

The number of reciprocal pairs for sea urchin and mouse is about 1.5 times the matches

between proteins in sea urchin and fruit fly. The number of nematode proteins matching

either sea urchin or fruit fly is even lower. This is likely the result of the more rapid

sequence changes in the nematode compared with the other species used in this analysis.

More than 75% of the genes that are shared by sea urchin and fruit fly are also shared

between sea urchin and mouse. Thus, these genes constitute a set of genes common to the

bilaterians, whereas the additional sea urchin–mouse pairs are unique to the deuterostomes.

The sea urchin genome consequently provides evidence for the now extremely robust

concept of the deuterostome superclade. A 1908 concept that originated in the form of

embryos of dissimilar species (14) is demonstrated by genomic comparisons.

3) Developmental Genomics

In the 1980s, the sea urchin embryo became the focus of cis-regulatory analyses of

embryonic gene expression, and there was a great expansion of molecular explorations of

the developmental cell biology, signaling interactions, and regulatory control systems of the

embryo. Analysis of the entire genome facilitated the first large-scale correlation of the gene

regulatory network for development, which represents the genomic control circuitry for

specification of the endoderm and mesoderm of this embryo (15–17)with the encoded

potential of the sea urchin.

The embryo transcriptome and regulome

Because of indirect development in the sea urchin, embryogenesis is cleanly separated from

adult body plan formation, in developmental process and in time, and therefore, it is possible

to estimate the genetic repertoire specifically required for formation of a simple embryo

(10). Pooled mRNA preparations from four stages of development, up to the mid-late

gastrula stage (48 hours), were hybridized with a whole-genome tiling array. Expression of

about 12,000 to 13,000 genes, as conservatively assessed, was seen during this early period,

indicating that ~52% of the entire protein-coding capacity of the sea urchin genome is

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expressed during development to the mid-late gastrula stage. An additional set of microarray

experiments extended the interrogation of embryonic expression to the 3-day pluteus larva

stage (see SOM) (18).

The DNA binding domains of transcription factor families are conserved across the

Bilateria, and these protein domain motifs were used to extract the sea urchin homologs (see

SOM). For each identified gene, if data were not already available, probes were built from

the genome sequence and used to measure transcript concentration by quantitative

polymerase chain reaction with a time series of embryo mRNAs, as well as to determine

spatial expression by whole-mount in situ hybridization.

All bilaterian transcription factor families were represented in the sea urchin with a few rare

exceptions (see below), so the sea urchin data strongly substantiate the concept of a

panbilaterian regulatory tool kit (19) or “regulome.” We found that 80% of the whole sea

urchin regulome (except the zinc finger genes) was expressed by 48 hours of embryogenesis

(20), an even greater genetic investment than the 52% total gene use in the same embryo.

4) Signal transduction pathways

More than 1200 genes involved in signal transduction were identified. Comparative analysis

highlights include the protein kinases that mediate the majority of signaling and

coordination of complex pathways in eukaryotes. The S. purpuratus genome has 353 protein

kinases, intermediate between the core vertebrate set of 510 and the fruit fly and nematode

conserved sets of ~230. Fine-scale classification and comparison with annotated kinomes

(21, 22) reveals a remarkable parsimony. Indeed, with only 68% of the total number of

human kinases, the sea urchin has members of 97% of the human kinase subfamilies,

lacking just four of those subfamilies (Axl, FastK, H11, and NKF3),whereas Drosophila

lacks 20 and nematodes 32 (Fig. 3) (23). Most sea urchin kinase subfamilies have just a

single member, although many are expanded in vertebrates; thus, the sea urchin kinome is

largely nonredundant. The sea urchin therefore possesses a kinase diversity surprisingly

comparable to that of vertebrates without the complexity. A small number of kinases were

more similar to insect than to vertebrate homologs (including the Titin homolog Projection,

the Syk-like tyrosine kinase Shark, and several guanylate cyclases), which indicated for the

first time the loss of kinase classes in vertebrates (23). Expression profiling showed that

87% of the signaling kinases and 80% of the 91 phosphatases were expressed in the embryo

(23, 24), which emphasized the importance of signaling pathways in embryonic

development.

The small guanosine triphosphatases (GTPases) function as molecular switches in signal

transduction, nuclear import and export, lipid metabolism, and vesicle docking. Vertebrate

GTPase families were expanded after their divergence from echinoderms, in part by wholegenome

duplications (25–27). The sea urchin genome did not undergo a whole-genome

duplication, yet phylogenies for four Ras GTPase families (Ras, Rho, Rab, and Arf) revealed

that local gene duplications occurred (Fig. 4), which ultimately resulted in a comparable

number of monomeric GTPases in the human and sea urchin genomes (28). Thus, expansion

of each family in vertebrates and echinoderms was achieved by distinct mechanisms (genespecific

versus whole genome duplication). More than 90% of the small GTPases are

expressed during sea urchin embryogenesis, which suggests that the complexity of signaling

through GTPases is comparable between sea urchins and vertebrates.

The Wnt family of secreted signaling molecules plays a central role in specification and

patterning during embryonic development. Phylogenetic analyses from cnidarian to human

indicate that of the 13 known Wnt subfamilies, S. purpuratus has 11, missing Wnt2 and

Wnt11 homologs (Fig. 5). S. purpuratus has WntA, previously reported as being absent

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from deuterostomes (29). Of 126 genes described as components of the Wnt signal

transduction machinery, homologs of ~90% were present in the sea urchin genome, which

indicates a high level of conservation of all three Wnt pathways (30). However, of 94 Wnt

transcriptional target genes reported in the literature, mostly from vertebrates (31), only 53%

were found with high confidence in the sea urchin genome (Fig. 6). The absent Wnt targets

include vertebrate adhesion molecules, which were frequently missing from the sea urchin

genome (32), as well as signaling receptors, which are more divergent and thus more

difficult to identify. In contrast, most transcription factor targets of the Wnt pathway are

present in the genome, which reflects a higher degree of conservation of transcription factor

families (20). Taken together, the genomic analysis of signal transduction components

indicates that sea urchins have signaling machinery strikingly comparable to that of

vertebrates, often without the complexity that arises from genetic redundancy.

5) Defense Systems

The need to deal with physical, chemical, and biological challenges in the environment

underlies the evolution of an array of defense gene families and pathways. One set of

protective mechanisms involves the immune system, which responds to biotic stressors such

as pathogens. A second group of genes comprises a chemical “defensome,” anetworkof

stress-sensing transcription factors and defense proteins that transform and eliminate many

potentially toxic chemicals.

6) The sea urchin immune system

The sea urchin has a greatly expanded innate immunity repertoire compared with any other

animal studied to date (table S5). Three classes of innate receptor proteins are particularly

increased (Fig. 7). These make up a vast family of Toll-like receptors (TLRs), a similarly

large family of genes that encode NACHT and leucine-rich repeat (LRR)–containing

proteins (NLRs), and a set of genes encoding multiple scavenger receptor cysteine-rich

(SRCR) domain proteins of a class highly expressed in the sea urchin immune cells or

coelomocytes (33, 34). Receptors from each of these families participate in immunity by

recognizing nonself molecules that are conserved in pathogens or by responding to self

molecules that indicate the presence of infection (35). In contrast, homologs of signal

transduction proteins and nuclear factor kappa B (NFκB)/Rel domain transcription factors

that are known to function further downstream of these genes were present in numbers

similar to those in other invertebrate species. One of the more unexpected findings from our

analysis of sea urchin immune genes was the identification of a Rag1/2-like gene cluster

(36). The presence of this cluster, along with other recent findings (37), suggested the

possibility that these genes had been part of animal genomes for longer than previously

considered. Further analysis of the genomic insights into the innate immune system and the

underpinnings of vertebrate adaptive immunity can be found in a review in this issue (38).

The complement system

The complement system of vertebrates is a complex array of soluble serum proteins and

cellular receptors arranged into three activation pathways (classical, lectin, and alternative)

that converge and activate the terminal or lytic pathway. This system opsonizes pathogenic

cells for phagocytosis and sometimes activates the terminal pathway, which leads to

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pathogen destruction. An invertebrate complement system was first identified in the sea

urchin [for reviews, see (39, 40)], and the analysis of the genome sequence presented a more

complete picture of this important immune effector system. In chordates, collectins initiate

the lectin cascade through members of the mannose-binding protein (MBP)–associated

protease (MASP)/C1r/C1s family. Several genes encoding collectins, C1q and MBP, have

been predicted (39) and were present in the genome; however, members of the MASP/C1r/

C1s family were not identified. There was no evidence for the classical pathway, which

links the complement cascade with immunoglobulin recognition in jawed vertebrates. The

alternative pathway is initiated by members of the thioester protein family, which, in the sea

urchin, was somewhat expanded with four genes. Two of the thioester proteins, SpC3 and

SpC3-2, are known to be expressed, respectively, in coelomocytes and in embryos and

larvae. Furthermore, there were three homologs of factor B, the second member of the

alternative pathway (41).

The terminal complement pathway in vertebrates acts to destroy pathogens or pathogeninfected

cells with large pores called membrane attack complexes (MACs). Twenty-eight

gene models were identified that encode MAC-perforin domains, but none of these had the

additional domains expected for terminal complement factors (C6 through C9). Instead,

these are members of a novel and very interesting gene family with perforin-like structure.

In vertebrates, perforins carry out cell-killing functions by cytotoxic lymphocytes through

the formation of small pores in the cell membranes. If the complement system in the sea

urchin functions through multiple lectin and alternative pathways in the absence of the lytic

functions of the terminal pathway, the major activity of this system is expected to be

opsonization.

7) Homologs of immune regulatory proteins

Cytokines are key regulators of intercellular communication involving immune cells, acting

to coordinate vertebrate immune systems. Genes encoding cytokines and their receptors

often evolve at a rapid pace, and most families are known only from vertebrate systems.

Although members of many cytokine, chemokine, and receptor families were not identified

in the sea urchin genome, a number of important immune signaling homologs were present.

These included members of the tumor necrosis factor (TNF) ligand and receptor

superfamilies, an IL-1 receptor and accessory proteins, two IL-17 receptor–like genes and

30 IL-17 family ligands, and nine macrophage inhibitory factor (MIF)–like genes. Receptor

tyrosine kinases (RTKs) included those that bind important growth factors that regulate cell

proliferation in vertebrate hematopoietic systems. Of particular note, from the sea urchin

genome, were two vascular endothelial growth factor (VEGF) receptor–like genes and a

Tie1/2 receptor, all of which were expressed in adult coelomocytes. Many of these genes are

homologs of important inflammatory regulators and growth factors in higher vertebrates,

and these sea urchin homologs may have similar functions in regulating coelomocyte

differentiation and recruitment.

Representatives of nearly all subclasses of important vertebrate hematopoietic and immune

transcription factors were present in the sea urchin genome. Notably, the genome contained

homologs of immune transcription factors that had not been identified previously outside of

chordates, including PU.1/SpiB/SpiC, a member of the Ets subfamily, and a zinc finger gene

with similarity to the Ikaros subfamily. Transcript prevalence measurements showed that

PU.1, the Ikaros-like gene and homologs of Gata1/2/3, E2A/HEB/ITF2, and Stem Cell

Leukemia (SCL) were all expressed at substantial levels in coelomocytes (41). This was

consistent with the presence of conserved mechanisms of regulating gene expression among

sea urchin coelomocytes and vertebrate blood cells.

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8) ABC transporters

Many chemicals are removed from cells by efflux proteins known as ATP-binding cassette

(ABC) or multidrug efflux transporters. S. purpuratus has 65 ABC transporter genes in the

eight major subfamilies of these genes [ABC A to H; (42)]. The ABCC family of multidrug

transporters is about 25% larger than in other deuterostome genomes with at least 30 genes

in this family (nearly half of the sea urchin ABC transporters), and 25 of these 30 genes

showed substantial mRNA expression in eggs, embryos, or larvae. Much of the expansion is

in the Sp-ABCC5 and Sp-ABCC9 families, whereas orthologs of the vertebrate gene

ABCC2 (also called MRP2) are absent. Because the ABCC family is known to generally

transport more hydrophilic compounds than other transporter families, such as the ABCB

genes, sea urchins may have increased need for transport of these compounds. ABCC efflux

activity has been described in sea urchin embryos and, consistent with the genomic

expansion of the ABCC family, the major activity in early embryos ensues from an ABCClike

efflux mechanism.

9) Cytochrome P-450 monooxygenase (CYP)

Enzymes in the CYP1, CYP2, CYP3, and CYP4 families carry out oxidative

biotransformation of chemicals to more hydrophilic products. The sea urchin has 120 CYP

genes, and those related to CYP gene families 1 to 4 constitute 80% of the total, which

suggests that there has been selective pressure to expand functionality in these gene families

(42). Eleven CYP1-like genes are present in the sea urchin genome, more than twice the

number in chordates. CYP2-like and CYP3-like genes are also present at greater numbers

than in other deuterostomes. In addition to the CYPs in families 1 to 4, the sea urchin

genome contains homologs of proteins involved in developmental patterning (CYP26),

cholesterol synthesis (CYP51), and metabolism (CYP27, CYP46). Homologs of some CYPs

with endogenous functions in vertebrates were not found; however, (CYP19, androgen

aromatase; CYP8, prostacyclin synthase; CYP11, pregnenolone synthase; CYP7,

cholesterol-7α-hydroxylase). These CYP genes in concert with additional expanded

defensive gene families represent a large diversification of defense gene families by the sea

urchin relative to mammals (42).

10) Oxidative defense and metal-complexing proteins

The metal-complexing proteins include three metallothionein genes and three homologs of

phytochelatin synthase genes. Genes for antioxidant proteins include three superoxide

dismutase (SOD) genes and a gene encoding ovoperoxidase (an unusual peroxidase with

SOD-like activity), along with one catalase, four glutathione peroxidase, and at least three

thioredoxin peroxidase genes. Reactive oxygen detoxification genes may be important in

conferring the long life-span of sea urchins, because oxidative damage is thought to be a

major factor in aging.

11) Diversity and conservation in xenobiotic signaling

The diversity of genes encoding xenobiotic-sensing transcription factors that regulate

biotransformation enzymes and transporters was similar to other invertebrate genomes, but

in most cases lower than vertebrates. For example, the sea urchin genome encoded a single

predicted CNC-bZIP protein homologous to the four human CNC-bZIP proteins involved in

the response to oxidative stress. There were two sea urchin homologs of the aryl

hydrocarbon receptor (AHR), which in vertebrates mediates the transcriptional response to

polynuclear and halogenated aromatic hydrocarbons and, in both protostomes and

deuterostomes, also regulates specific developmental processes (43–45). One of the sea

urchin AHR homologs was more closely related to the vertebrate AHR; the other shared

greatest sequence identity with the Drosophila AHR homolog spineless. Sea urchins also

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had two genes encoding hypoxia-inducible factors (HIFα subunits), which regulate adaptive

responses to hypoxia, and a gene encoding ARNT, a PAS protein that is a dimerization

partner for both AHRs and HIFs.

Strongylocentrotus purpuratus has 32 nuclear receptor (NR) genes (20), two-thirds the

number in humans, including several with potential roles in chemical defense (42). The sea

urchin genome also contains two peroxisome proliferator–activated receptor (PPAR, NR1C)

homologs and an NR1H gene coorthologous to both liver X receptor (LXR) and farnesoid X

receptor (FXR) (42). Genes homologous to the vertebrate xenobiotic sensor NR1I genes

[pregnane X receptor, PXR; constitutive androstane receptor, CAR (46)] are absent,

although three NR1H-related genes were found, which possibly form a new subfamily of

genes involved in xenobiotic sensing.

Many of the defense genes are expressed during development (10, 42), which suggests that

they have dual roles in chemical defense and in developmental signaling. In several cases

(CYPs, AHR, NF-E2), the evolution of pathways for chemical defense may have involved

recruitment from developmental signaling pathways (42).

12) Nervous System

The echinoderm nervous system is the least well studied of all the major metazoan phyla.

For a number of technical reasons, the structure and function of echinoderm nerves have

been neglected. Analysis of the sea urchin genome has enabled an unprecedented glimpse

into the neural and sensory functions and has revealed several novel molecular approaches

to the study of echinoderm nervous systems (Table 3).

The nervous systems of echinoderm larvae and adults are dispersed, but they are not simple

nerve nets. This organization differs from both vertebrates, which do not have a dispersed

nervous system, and hemichordates, which do have nerve nets (47). Adult sea urchins have

thousands of appendages, each with sensory neurons, ganglia, and motor neurons arranged

in local reflex arcs. These peripheral appendages are connected to each other and to radial

nerves, which provide overall control and coordination (47, 48).

Nearly all of the genes encoding known neurogenic transcription factors are present in the

sea urchin genome, and several are expressed in neurogenic domains before gastrulation,

which indicates that they may operate near the top of a conserved neural gene regulatory

network (47). Axon guidance molecules known from other metazoans are also expressed in

the developing embryo. Unexpectedly, genes encoding the neurotrophin-Trk receptor system

that were thought to be vertebrate-specific because they were not found in Ciona, are present

in sea urchin, which suggests a deuterostome origin and a potential loss in urochordates.

The genes required to construct neurons and to transmit signals are present, but the

repertoire of neural genes and the initial characterization of expression of a number of them

led to unexpected and surprising conclusions. There appear to be no genes encoding gap

junction proteins, which suggests that communication among neurons depends on chemical

synapses without ionic coupling. The repertoire of sea urchin neurotransmitters is large, but

melatonin and adrenalin are lacking, as they are in ascidians (4, 47). Cannabinoid,

lysophospholipid, and melanocortin receptors are not present in urchins, but orthologs were

found in ascidians (4, 47). In contrast, some sets of genes thought to be chordate-specific

have sea urchin orthologs, for example, insulin and insulin-like growth factors (IGFs) that

are more similar to their chordate counterparts than those of other invertebrates (47).

Overall, the genome contains representatives of all five large superfamilies of GPCRs,

including those that mediate signals from neuropeptides and peptide hormones. Both the

secretin and rhodopsin superfamilies display marked lineage-specific expansions (13, 47).

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13) Sensory systems

There were 200 to 700 putative chemosensory genes that formed large clusters and lacked

introns, which are features of chemosensory genes in vertebrates, but not in Caenorhabditis

elegans and Drosophila melanogaster. Many of these genes encoded amino acid motifs that

were characteristic of vertebrate chemosensory and odorant receptors (13, 47). Sea urchins

had an elaborate collection of photoreceptor genes that quite surprisingly appeared to be

expressed in tube feet (13, 47). These included many genes encoding transcription factors

regulating retinal development and a photorhodopsin gene.

Human Usher syndromes are genetic diseases affecting hearing, balance, and retinitis

pigmentosa (retinal photoreceptor degeneration). Most of the genes involved have been

identified, and they encode a set of membrane and cytoskeletal proteins that form an

interacting network that controls the arrangement of mechanosensory stereocilia in hair cells

of the mammalian ear. Many or all of the proteins play some roles in photoreceptor

organization and/or maintenance. Orthologs of virtually the entire set of membrane and

cytoskeletal proteins of the Usher syndrome network were found in the sea urchin genome.

These include the very large membrane proteins, usherin and VLGR-1 and large cadherins

(Cadh23 and possibly Pcad15), all of which participate in forming links between stereocilia

in mammalian hair cells, as well as myosin 7 and 15, two PDZ proteins (harmonin and

whirlin) and another adaptor protein (SANS), which participate in linking these membrane

proteins to the cytoskeleton. In addition, two membrane transporters, NBC (a candidate

Usher syndrome target known to interact with harmonin) and TrpA1 (the mechanosensory

channel connected to the tip links containing cadherin 23), have orthologs in the sea urchin

genome. Sea urchins do not have ears or eyes, so they must deploy these proteins in other

sensory processes. Sea urchins respond to light, touch, and displacement and probably use

some of same sensory genes used by vertebrates.

14) The Echinoderm Adhesome

The S. purpuratus genome contained representatives of all the standard metazoan adhesion

receptors (table S7), but the emphasis on different classes of receptors differed substantially

from that used by vertebrates. The integrin family was intermediate in size between those of

protostomes and vertebrates—several chordate-specific expansions of the integrin repertoire

were absent, and there were some expansions unique (so far) to echinoderms. The cadherin

repertoire was also small relative to vertebrates (a dozen or so instead of over a hundred),

and many chordate-specific expansions were missing. Specialized large cadherins shared by

protostomes and vertebrates were present, as well as some specialized large cadherins

previously thought to be chordate-specific, but overall, the cadherin repertoire was more

invertebrate than vertebrate in character. Sea urchins lacked the integrins and cadherins that

link to intermediate filaments in vertebrates.

In contrast, sea urchins had large repertoires of adhesion molecules containing

immunoglobulin superfamily, fibronectin type 3 repeat (FN3), epidermal growth factor

(EGF), and LRR repeats. In addition to the expansion of TLRs and NLRs mentioned above,

there are large expansions of other LRR receptor families, including GPCRs (32). The key

neural adhesion systems involved in regulating axonal outgrowth were present (netrin/Unc5/

DCC; Slit/Robo; and semaphorins/plexins), as were adhesion molecules involved in

synaptogenesis (Agrin/MUSK; and neurexin/neuroligins). This was not surprising because

these molecules were known in both protostomes and vertebrates. However, structurally, the

synapses of echinoderms are unusual because there are no direct synaptic contacts (49).

Some of them were expressed in sea urchin embryos before there are any neurons,

suggesting that they may have other roles as well.

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The basic metazoan basement membrane extracellular matrix (ECM) tool kit was present—

two alpha-IV collagen genes, perlecan, laminin subunits, nidogen, and collagen XV/XVIII.

There did not appear to be much, if any, expansion of these gene families, as is found in

vertebrates, which suggests that there is less diversity among basement membranes. Quite a

few ECM proteins present in chordates, but not protostomes, were also missing in sea

urchins, including fibronectins, tenascins, von Willebrand factor, vitronectin, most

vertebrate-type matrix proteoglycans, and complex VWA/FN3 collagens among others (32).

Absence of these genes may be related to the absences of neural crest migration, a high

shear endothelial-lined vasculature and, of course, cartilage and bone.

In addition to the components of Usher syndromes mentioned above, it was surprising to

find a clear ortholog of reelin, a large ECM protein involved in establishing the layered

organization of neurons in the vertebrate cerebral cortex. Reelin is mutated in the reeler

mouse, and mutations in the reeler gene in humans have been associated with Norman-

Roberts-type lissencephaly syndrome. Reelin has a unique domain composition and

organization (Reeler, EGF, BNR) that has not been found outside chordates, but the sea

urchin genome included a very good homolog of reelin. Receptors for reelin are believed to

include low-density lipoprotein receptor–related proteins (LRPs), and there are a number of

these receptors in S. purpuratus although it is as yet unclear whether they are reelin

receptors, lipoprotein receptors, or something else. Similar receptors are also involved in

human disease (atherosclerosis).

15) Biomineralization Genes

Among the deuterostomes, only echinoderms and vertebrates produce extensive skeletons.

The possible evolutionary relations between biomineralization processes in these two groups

have been controversial. Analysis of the S. purpuratus genome revealed major differences in

the proteins that mediate biomineralization in echinoderms and vertebrates (50). First, there

were few sea urchin counterparts of extracellular proteins that mediate biomineral deposition

in vertebrates. For example, in vertebrates, an important class of proteins involved in

biomineralization is the family of secreted, calcium-binding phosphoproteins, or SCPPs. Sea

urchins did not have counterparts of SCPP genes, which supports the hypothesis that this

family arose via a series of gene duplications after the echinoderm-chordate divergence (51).

Second, almost all of the proteins that have been directly implicated in the control of

biomineralization in sea urchins were specific to that clade. The echinoderm skeleton

consists of magnesium calcite (as distinct from the calcium phosphate skeletons of

vertebrates) in which is occluded many secreted matrix proteins. The sea urchin spicule

matrix proteins were encoded by a family of 16 genes that are organized in small clusters

and likely proliferated by gene duplication. Counterparts of sea urchin spicule matrix genes

were not found in vertebrates, amphioxus, or ascidians. Likewise, other genes that have been

implicated in biomineralization in sea urchins, including genes that encode the

transmembrane protein P16 and MSP130, a glycosylphosphatidylinositol-linked

glycoprotein, were members of small clusters of closely related genes without apparent

homologs in other deuterostomes. The members of all three of these sea urchin–specific

gene families were expressed specifically by the biomineral-forming cells of the embryo, the

primary mesenchyme cells [see (50)]. As a whole, these findings highlighted substantial

differences in the primary sequences of the proteins that mediate biomineralization in

echinoderms and vertebrates.

16) Cytoskeletal genes

In addition to identifying genes for all previously known S. purpuratus actins and tubulins,

one δ- and two ε-tubulin genes were found (52). Newly identified motor protein genes

include members of four more classes of myosin, and eight more families of kinesins. The

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NIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author Manuscript

first dynein cloned and sequenced was from sea urchin, and although most S. purpuratus

dynein heavy chain genes mapped one-to-one to mammalian homologs, Sp-DNAH9 mapped

one-to-three, as it was equidistant between the closely similar mammalian genes DNAH9,

DNA11, and DNAH17 (52).

17) Conclusions

Our estimate of 23,300 genes is similar to estimates for vertebrates, despite the fact that two

whole-genome duplications are believed to have occurred in the chordate lineage after

divergence from the lineage leading to the echinoderms (25–27). 

From the analysis

presented here, it seems likely that many mechanisms shaped the final genetic content of

these genomes. On the one hand, there are cases of gene families that are expanded in

vertebrates compared with sea urchin, including examples of the expected 4:1 ratio from two

duplications (15). However other patterns are also found. 

The nuclear receptor family is only

slightly reduced in sea urchin compared with that of humans, which suggests gene loss

followed the vertebrate duplications. 

The unprecedented expansions of innate immune

system diversity contrast sharply with the much smaller sets of counterparts that are present

in the sequenced genomes of protostomes, Ciona, and vertebrates, an example of

independent expansion in the sea urchin, whereas the GTPases described here have

expanded in sea urchin to about the same numbers as in vertebrates. Thus, whereas the

duplications of the chordate lineage were a contributor to the increased complexity of

vertebrates, regional expansions clearly play a large role in the evolution of these animals.

The refinement of the inventory of vertebrate-specific or protostome-specific genes likewise

benefits from the sea urchin genome. Many more human genes have shared ancestry across

the deuterostomes, and in fact, bilaterian genes are more broadly shared than had been

inferred from comparison of the previously limited genome sequences. The new biological

niche sampled by the sea urchin genome provides not only a clearer view of the

deuterostome and bilaterian ancestor, but has also provided a number of surprises. 

The

finding of sea urchin homologs for sensory proteins related to vision and hearing in humans

may lead to interesting new concepts of perception, and the extraordinary organization of

the sea urchin immune system is different from any animal yet studied. 

From a practical

standpoint, the sea urchin may be a treasure trove. Because of the many pathways shared by

sea urchin and human, the sea urchin genome includes a large number of human disease

gene orthologs. Many of the genes described in the preceding sections fall into this category

(see tables S8 and S9) and cover a surprising diversity of systems such as nervous,

endocrine, and blood systems, as well as muscle and skeleton, as exemplified by the

Huntington and muscular dystrophy genes. 

Continued exploration of the sea urchin immune

system is expected to uncover additional variations for protection against pathogens. The

immense diversity of pathogen-binding motifs encoded in the sea urchin genome provides

an invaluable resource for antimicrobial applications and the identification of new

deuterostome immune functions with direct relevance to human health. These exciting

possibilities show that much biodiversity is yet to be uncovered by sampling additional

evolutionary branches of the tree of life.