the hedgehog gene family of the cnidarian, nematostella ...the hedgehog gene family of the...

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Developmental Biology 3

The Hedgehog gene family of the cnidarian, Nematostella vectensis, andimplications for understanding metazoan Hedgehog pathway evolution

David Q. Matus a, Craig R. Magie a, Kevin Pang a, Mark Q. Martindale a, Gerald H. Thomsen b,⁎

a Kewalo Marine Lab University of Hawaii Honolulu, HI 76813, USAb Department of Biochemistry and Cell Biology, Center for Developmental Genetics, Stony Brook University, Stony Brook, NY 11794-5215, USA

Received for publication 1 May 2007; revised 10 September 2007; accepted 10 September 2007Available online 26 September 2007

Abstract

Hedgehog signaling is an important component of cell–cell communication during bilaterian development, and abnormal Hedgehog signalingcontributes to disease and birth defects. Hedgehog genes are composed of a ligand (“hedge”) domain and an autocatalytic intein (“hog”) domain.Hedgehog (hh) ligands bind to a conserved set of receptors and activate downstream signal transduction pathways terminating with Gli/Citranscription factors. We have identified five intein-containing genes in the anthozoan cnidarian Nematostella vectensis, two of which (NvHh1 andNvHh2) contain definitive hedgehog ligand domains, suggesting that to date, cnidarians are the earliest branching metazoan phylum to possessdefinitive Hh orthologs. Expression analysis of NvHh1 and NvHh2, the receptor NvPatched, and a downstream transcription factor NvGli (a Gli3/Ci ortholog) indicate that these genes may have conserved roles in planar and trans-epithelial signaling during gut and germline development,while the three remaining intein-containing genes (NvHint1,2,3) are expressed in a cell-type-specific manner in putative neural precursors.Metazoan intein-containing genes that lack a hh ligand domain have previously only been identified within nematodes. However, we haveidentified intein-containing genes from both Nematostella and in two newly annotated lophotrochozoan genomes. Phylogenetic analyses suggestthat while nematode inteins may be derived from an ancestral true hedgehog gene, the newly identified cnidarian and lophotrochozoan inteins maybe orthologous, suggesting that both true hedgehog and hint genes may have been present in the cnidarian-bilaterian ancestor. Genomic surveys ofN. vectensis suggest that most of the components of both protostome and deuterostome Hh signaling pathways are present in anthozoans and thatsome appear to have been lost in ecdysozoan lineages. Cnidarians possess many bilaterian cell–cell signaling pathways (Wnt, TGFβ, FGF, andHh) that appear to act in concert to pattern tissues along the oral–aboral axis of the polyp. Cnidarians represent a diverse group of animals with apredominantly epithelial body plan, and perhaps selective pressures to pattern epithelia resulted in the ontogeny of the hedgehog pathway in thecommon ancestor of the Cnidaria and Bilateria.© 2007 Elsevier Inc. All rights reserved.

Keywords: Anthozoa; Cnidaria; Ectoderm; Endoderm; Evolution; Genomics; Gli; Hedgehog; Induction; Nematostella vectensis; Patched; Pattern formation; Signaltransduction

Introduction

Cell to cell signaling, or induction, governs cell fate andpattern formation during early development of essentially allmetazoan embryos. In general, the principal inductive signalsregulating animal embryogenesis are conveyed by members of asmall number of cell signaling pathways including the Wnt,TGF-beta/bone morphogenetic protein (BMP), fibroblast growthfactor (FGF), Notch, and Hedgehog gene families (Chen et al.,

⁎ Corresponding author.E-mail address: [email protected] (G.H. Thomsen).

0012-1606/$ - see front matter © 2007 Elsevier Inc. All rights reserved.doi:10.1016/j.ydbio.2007.09.032

2004; Cornell and Eisen, 2005; Ingham and McMahon, 2001;Kishigami and Mishina, 2005; Lai, 2004; Logan and Nusse,2004; Tabata and Takei, 2004; Thisse and Thisse, 2005). TheHedgehog pathway in particular mediates a variety of importantpatterning and cell fate determination events across the Metazoa.The original hedgehog gene (hh) was discovered in Drosophilaas a mutation affecting a variety of pattern formation events.Drosophila hh is first expressed in blastoderm-stage embryoswhere it regulates anteroposterior segment polarity by acting as amorphogen (Heemskerk and DiNardo, 1994; Mohler and Vani,1992). Drosophila hh also governs cell fate and patterning of theprimitive gut, wing disc, eye, and muscle, and in vertebrates hh

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paralogs display similar diverse functions in regulating cell fateand pattering of the spinal cord, somites, limb, brain, bone,smooth muscle, and gut, among others (see recent reviews byHooper and Scott, 2005; Ingham and Placzek, 2006; McGlinnand Tabin, 2006; McMahon et al., 2003).

Hedgehogs encode proteins characterized by the presence ofa soluble N-terminal ligand domain that gets released by self-proteolysis from a larger precursor through the action of a C-terminal intein domain. Mutations in genes encoding Hh-relatedligands and their downstream signal transduction componentscause developmental defects in Drosophila and vertebratemodel organisms, human birth defects, and various diseases(McMahon et al., 2003; Mullor et al., 2002; Nieuwenhuis andHui, 2005; Rubin and de Sauvage, 2006). Molecular aspects ofsignaling by hedgehog ligands, receptors, and downstreamcomponents are best understood in Drosophila and vertebrates,and their respective pathways share many features yet exhibitdistinct differences (Huangfu and Anderson, 2006; Ingham andPlaczek, 2006). At the ligand level, just a single hh gene hasbeen described in Drosophila, other protostomes, and mostdeuterostomes, but two to five hh ligands are encoded bychordate genomes, such as those of tunicates (two) andvertebrates (three–five) (Hino et al., 2003; Meyer and Schartl,1999; Pires-daSilva and Sommer, 2003). Receptors for hhligands in Drosophila and vertebrates are very similar and aretypified by two multi-transmembrane domain receptors namedPatched (Ptc) and Smoothened (Smo). One Ptc and two Smogenes have been identified in vertebrates, while one of each areknown in Drosophila. Ptc and Smo regulate cytoplasmic signaltransduction that ultimately affects the activity of transcriptionfactors at the terminus of the pathway named Cubitus interuptus(Ci) in Drosophila and Gli proteins in vertebrates (three in all:Gli1/2/3) (Huangfu and Anderson, 2006; Wang et al., 2007).In the absence of hh ligand, Ptc inhibits signaling by Ci/Gliproteins by directing their proteolysis by an intracellular proteincomplex that destroys Gli1/2 or cleaves and partially destroysCi/Gli3 to produce a stable N-terminal fragment that functionsas a transcriptional repressor and blocks the activity of Hh-responsive genes. Binding of a Hh ligand to Ptc derepressesSmo and inactivates its associated Ci/Gli cleavage complex,allowing full-length Ci/Gli1/2/3 to accumulate and function astranscriptional activators of Hh-responsive genes. In verte-brates, but apparently not Drosophila, the nuclear action of Gliproteins is further regulated by Iguana, a protein essential for hhsignaling (Vokes and McMahon, 2004). Another majordifference between vertebrate and Drosophila hh signaling isthat signaling downstream of Smo in vertebrates requires non-sensory cilia and specific intraflagellar transport proteins(Huangfu and Anderson, 2006), but in Drosophila theseproteins are not essential for hh signaling (Avidor-Reiss et al.,2004; Han et al., 2003; Ray et al., 1999).

Surveys of various metazoan genomes and expressed cDNAsequences demonstrate the presence of a variety of hh geneorthologs among both deuterostomes and protostomes, with theexception of the nematode Caenorhabditis elegans, which lacksa clear hh ortholog but possesses at least 10 intein-containinggenes (Aspock et al., 1999; Hao et al., 2006b). However, an EST

(Expressed Sequence Tag) survey of the plant ectoparasiticdagger nematode, Xiphinema index, has identified a single truehedgehog gene within this more slowly evolving nematode(M. Blaxter, personal communication). As already noted, proto-stomes appear to possess just a single hh gene, but deute-rostomes possess several hh-related genes (three in mammalsand five in zebrafish). In the genome of the choanoflagellate,Monosiga ovata, a single-celled protozoan believed to sharecommon ancestry with the Metazoa, recent work identified ahedgehog-related gene (Hoglet) (Snell et al., 2006), composedof a C-terminal intein domain that lacks an identifiable N-terminal Hh signaling domain. A hedgehog-related, intein-onlycontaining gene has also been identified in the mycorrhizalfungus, Glomus mosseae (Requena et al., 2002). The presenceof a hedgehog-related intein gene in an outgroup to the Metazoa,a single hh gene among protostomes, and the presence ofmultiple vertebrate hh homologs, and the notable lack of a hhortholog in C. elegans, raises important questions about howand when hh genes originated and diversified over the course ofmetazoan evolution, particularly in the Cnidaria or other non-bilaterian metazoan phyla.

To help understand the evolutionary relationships and originsof invertebrate and vertebrate Hedgehog signaling pathways, weexamined the Hh pathway outside of the Bilateria, in theanthozoan cnidarian, Nematostella vectensis, the starlet seaanemone. We report the existence and expression of fiveN. vectensis hh-related genes, two of which encode Hh signalingligands (NvHedgehog1 and 2), while the other three encodeproteins containing an intein but no recognizable ligand domains(NvHint1, 2, and 3). The embryonic expressions of both true hhgenes are involved with mesentery, pharynx, and gut formation,while the three intein-only hh-related genes (NvHint1–3) areexpressed in a cell-type-specific manner and are likely to beinvolved in neural patterning. Genomic data and mRNAexpression patterns suggest that downstream of the ligands, N.vectensis possesses a full suite of genes implicated in Hhsignaling, from extracellular ligand modulators, through recep-tors, signal transduction components and Gli transcriptionfactors, most of which appear to be orthologs of correspondingvertebrate and invertebrate signaling proteins. Furthermore, theembryonic expression of the receptor NvPatched (NvPtc) and thedownstream transcriptional regulator NvGli demonstrate that Hhlikely conveys both planar and trans-epithelial inductive signalswithin the mesendoderm. Our data suggest that the antecedentsof both vertebrate and invertebrate hh ligand and signal trans-duction proteins arose early in metazoan evolution, with geneloss and gene duplication over the course of evolution accountingfor the differences now observed between protostome anddeuterostome pathways. Interestingly, particular members of theHh signaling pathway in N. vectenis have been lost in theecdysozoan model systems but retained in vertebrate lineages.

Materials and methods

Isolation of genes from N. vectensis

The Joint Genome Institute (JGI) assembly of the N. vectensis genome(genome.jgi-psf.org/Nemve1/Nemve1.home.html) and available ESTs (NCBI)

http://genome.jgi%1Epsf.org/Nemve1/Nemve1.home.html

503D.Q. Matus et al. / Developmental Biology 313 (2008) 501–518

were searched using the C-terminal intein or HINT domain of bilaterian hed-gehogs utilizing TBLASTN parameters to isolate potential hedgehog genes. Gliand patched genes were identified by TBLASTN searches of the N. vectensisgenome, using vertebrate orthologs. Gene-specific primers were then designedfor both 5′ and 3′ RACE for each gene with annealing temperatures between 68°and 70 °C. RACE was performed using the Smart Race cDNA amplification kit(BD Biosciences Clontech). RACE products were cloned in a plasmid vector(P-Gem T easy, Promega) and sequenced at Macrogen, Inc. (South Korea). Fivehedgehog-related genes were identified in this manner. Overlapping 5′ and 3′RACE fragments were aligned and submitted to GenBank as compositetranscripts (in process—we will supply prior to publication).

Phylogenetic analyses of Hedgehog-related genes

Phylogenetic analysis of hedgehog-related genes were performed in orderto determine orthology. N. vectensis genes were analyzed via BlastX searchesof the GenBank database (http://www.ncbi.nlm.nih.gov/BLAST/) in order tobuild an alignment. Amino acid alignments of both the C-terminal signalingdomain and the N-terminal HINT domain were then made using Muscle 3.6(Edgar, 2004) and corrected by hand for obvious alignment errors. A Bayesianphylogenetic analysis was conducted using MrBayes 3.1.2 (Ronquist andHuelsenbeck, 2003) using either the mixed or “WAG+G” amino acid modeloption with four independent runs of 1,000,000 generations each, sampledevery 100 generations with four chains. A summary “consensus tree” wasproduced in MrBayes, from the last 9,500 trees of each run (38,000 total trees)representing 950,000 stationary generations. Posterior probabilities werecalculated from this “consensus”. Additionally, Maximum Likelihood (usingPHYML; Guindon and Gascuel, 2003) with the WAG+I+G model ofevolution (selected via ProtTest; Abascal et al., 2005) using 1000 bootstrapreplicates) and RAxML v 2.2.3 (Stamatakis, 2006) analyses were conducted.Nexus alignment files can be found in Figs. S2–S4. For analyses of the hint/hog domain, 800 searches were performed using RAxML v 2.2.3 (Stamatakis,2006) to find the most likely tree. Results of these analyses are available inFigs. S5–S7.

Phylogenetic analyses of downstream components

Alignments were made for both patched and Gli/Ci genes using metazoanorthologs and representative sequences from N. vectensis predicted proteins.Phylogenetic analyses were conducted as above, using MrBayes3.1.2 for1,000,000 with four independent runs generations and a mixed model of proteinevolution. For the patched phylogenetic analysis, the JTT model was selectedwith a 99.8% posterior probability, while for the Gli/Ci analysis JTT model wasselected with 100% posterior probability.

Nexus alignment files can be found in Figs. S8–S9. Identification of otherhh pathway genes in the N. vectensis genome, presented in Table 1, wasperformed using vertebrate or Drosophila protein sequences for TBLASTNsearches, and/or gene names to search annotated gene models on the N.vectensis genome, using search functions of the JGI Nematostella genomeWeb server (http://genome.jgi-psf.org/Nemve1/Nemve1.home.html). Candi-date Nematostella homologs were retested by BLASTP against the entirehuman non-redundant protein database using the NCBI server and defaultsettings to verify the degree of homology represented by the indicated e-valuesin Table 1.

In situ hybridization

In situ hybridizations using 1–3 kb digoxigenin-labeled antisenseribonucleotide probes were performed to follow transcript distribution aspreviously described (Martindale et al., 2004). Probe concentrations rangedfrom 1.0 to 2.0 ng/μl and hybridizations were performed at 60 °C for 24–48 h.Alkaline phosphatase reaction products were visualized with NBT-BCIP.Specimens were photographed on a Zeiss Axioplan and AxioImager with aNikon Coolpix 990 digital camera and a Zeiss HRC digital camera. Detailedprotocols are available upon request ([email protected]). Lithiumchloride treatments were performed as previously described (Matus et al.,2006b).

Results

Identification of Hedgehog-related genes in N. vectensis

Hedgehog genes have been identified in Metazoa throughoutthe Bilateria (protostomes and deuterostomes), and a fewhomologous sequences have been identified outside of theBilateria in both a recent Expressed Sequence Tag (EST) survey(Nichols et al., 2006) as well as in an analysis of a preliminaryannotation of the Nematostella genome (Walton et al., 2006).We performed RACE PCR on cDNA from mixed blastulathrough planula stage cDNA that yielded five independent hh-related cDNAs. All five clones encode predicted proteinsequences with significant homology to intein domains ofother metazoan Hh-related proteins (Fig. 1, Fig. S1). TheseHedgehog intein or Hint/Hog domains catalyze self-proteolyticcleavage to generate an active ligand from the N-terminus,which is typically modified by cholesterol and lipid acylationprior to secretion from the signaling cell (Guerrero and Chiang,2007; Ingham, 2001). Additionally, the N. vectensis genomepossesses one gene, NvHedgling, that has a hedge/signaldomain while missing a Hint domain and is instead tetheredto a large cadherin-related protein (Fig. 1; Adamska et al.,2007).

Hedgehogs convey signals from cell to cell by an N-terminalligand domain that gets cleaved from a precursor protein byintein-driven proteolysis. Only two of the clones we retrieved(NvHh1 and NvHh2) encode predicted ligand domains thatshow a high degree of amino acid identity to other metazoanHedgehogs (Fig. 1, Fig. S1). As with other Hedgehogs, thesignaling domains of NvHh1 and NvHh2 are located within theN-terminal half of the proteins, adjacent to an intein or Hint/Hogdomain. The other three clones we retrieved, lack predicted Hhligand domains and thus are designated NvHint1, NvHint2 andNvHint3 to reflect the presence of a Hint domain at their C-terminus. The sequences of the N-terminus of NvHint1 andNvHint3 are not homologous to other known proteins basedon both Interpro Scan and BLASTP searches against the PFAMdatabase and NCBI, while the N-terminal portion of NvHint2shows weak blast similarity to the C-terminal portion of Pod-EPPT, a hydrozoan cnidarian (Podocoryne carnea) gene. AnInterpro Scan of NvHint2 identifies a potential domain upstreamof the Hint domain: (IPR013994) a Carbohydrate-binding WSCsubgroup, based on conserved cysteines.

Comparisons of the cloned and sequenced RACE PCRproducts to the Nematostella genome assembly allowed us tocharacterize intron/exon sites in the five hh-related genes. Thetwo true hedgehog genes, NvHh1 and NvHh2, as well as thethree hint genes (NvHint1–3) possess conserved intron/exonsites in common with bilaterian hedgehog genes (Fig. 1, Fig.S1). The first conserved site is located at the beginning of thesecond exon in bilaterian hedgehog genes in the signal domainand is found in both true N. vectensis hedgehog genes (NvHh1and NvHh2). The second conserved intron/exon boundary isfound in a position ∼10–11 amino acids upstream of theautocatalytic cleavage site and is found in all N. vectensishedgehog-related genes (Fig. 1, Fig. S1).

http://www.ncbi.nlm.nih.gov/BLAST/http://genome.jgi%1Epsf.org/Nemve1/Nemve1.home.htmlhttp://mqmartin%40hawaii.edu

Table 1Identification of Nematostella vectensis counterparts of bilaterian Hedgehog signal transduction genes

N. vectensis pathwaycomponent

Function Nv JGI proteinmodel ID(or EST ID)

Human homologUniProt ID

Drosophilahomolog

e-value inBLASTp withhuman homolog

NvHint1 Unknown This study n/a n/a n/aNvHint2 Unknown This study n/a n/a n/aNvHint3 Unknown This study n/a n/a n/aNvHh1 Ligand This study Q15465 Sonic

Hh O43323Desert Hh Q14623Indian Hh

hedgehog 0

NvHh2 Ligand This study Q15465 SonicHh O43323 DesertHh Q14623 Indian Hh

hedgehog 0

NvSkinny Hh[rasp, sightless]

Palmitoylation of Hh ligand 217054 Q17N53 skinny Hh, sightless,central missing

2 e−40

NvDispatched Ligand transporter-sending cell 199988 Q96F81 Q9U477 1 e−88NvGlypican5 Hh movement, signaling range 218206 P35052 dally-like

UP:Q9GPL5 dallyUP:Q966V5

8 e−32

NvGlypican6 Hh movement and signaling range 218207, 247677 Q8N158 dally-likeUP:Q9GPL5

7 e−92

NvHIP Hh binding membrane protein 197846 Q96QV1 Unknown 1 e−40NvCdon/Boc Hh-binding type I receptor 185528, 105427 Q4KMG0 (Cdon)

Q9BWV1 (Boc)iHog Cdon 7 e−30

Boc 4 e−31NvGAS1 GDNF-receptor-like Hh binding protein

represses Hh activity/range104344 Unknown 6 e−13

NvExostosin-1 Glycosyl transferase for heparan biosynthesis;Hh movement and reception

173450 Q16394 tout-velut 0


168451 Q93063 tout-velut 0


235881 O43909 tout-velut 0

NvMegalin/gp330 Ligand binding and endocytosis 196768 Q7Z5C0 CG12139 0NvPatched (Ptch) 11 TM receptor binds Hh, represses Smo This study Q13635 patched 0NvSmoothened-1(Smo1)

7 TM receptor regulated by Ptch; interfaceswith costal and downstream pathway

208236 Q99835 smoothened 2 e−138

NvSmoothened-2(Smo2)

7 TM receptor regulated by Ptch; interfaceswith intracellular pathway

201646 Q99835 smoothened 1 e−91

Nvβarrestin1 Internalization of Smoothened 97737 kurtz 3 e−111Nvβarrestin2 Internalization of Smoothened 149831 kurtz 8 e−14NvGPRK2/βARK-1 G-protein coupled receptor kinase that targets

Smoothened246204 Q86YK6 Gprk2, CG17998 0

NvFKBP8 Peptidylprolyl isomerase, repressesSmoothened

91671 Q7K3D4 CG5482 7 e−34

Nvrab23 Small GTPase for endocytosis and traffickingof Hh-receptor complexes

25310 Q9VNG6 CG2108 2 e−64

NvTectonic Signal transduction downstream of Rab23 (JGI_CAGN8498) Q2MV58 Unknown 3 e−47NvKif3A Potential Costal 2 (Cos2) ortholog, Gli/fused

scaffold interface with ciliary microtubules160820 Q59EN1 costal? 0

NvKif4A Potential Costal 2 (Cos2) ortholog, Gli/fusedscaffold interface with ciliary microtubules

233887 O95239 costal? 3 e−131

NvKIF27A Costal 2 (Cos2) ortholog, Gli/fused scaffoldinterface with ciliary microtubules

196177 Q86VH2 costal 0

NvFantom/Rpgrip1L Ciliary basal body protein required for Hhsignal transduction

181095 Q68CZ1 Unknown 0

NvIft88/polaris/Tg737 Ciliary Hh signaling regulator 40068 Q13099 nompB 0NvIft172/wimple Ciliary Hh signaling regulator (JGI_CAGF7669) Q96HW4 osm-1 2 e−99NvIft52/Ngd5 Ciliary Hh signaling regulator 239245 Q9Y366 osm-6 2 e−158NvFused1 Protein kinase phosphorylates Cos2 219073 Q9NRP7 fused 1 e−68NvFused2 Protein kinase-Gli regulation 173313 XP_950751 a fused 0NvSuppressor ofFused, SuFu

Binds and represses Gli 246114 Q9UMX1 Su(Fu) 6 e−120Su(Fu)

NvIguana Regulates Gli downstream of Smo,interacts with Sufu

247454 Q86YF9 Unknown 2 e−23

NvPKA Gli phosphorylation/processing 120559 P22694 Pka-C1, CG4379 2 e−100


Table 1 (continued)

N. vectensis pathwaycomponent

Function Nv JGI proteinmodel ID(or EST ID)

Human homologUniProt ID

Drosophilahomolog

e-value inBLASTp withhuman homolog

NvGSK3β Gli phosphorylation/processing 11896 P49841 shaggy 0NvCK1 Smo and Gli phosphorylation/processing 159193 P48729 gilgamesh 4 e−152NvβTRCP1 Fbox Ub ligase for Gli-R processing 228088 Q9Y297 slimb 0NvβTRCP2 Fbox Ub ligase for Gli-R processing 648 Q9Y297 slimb 2 e−165NvSIL Signal transduction, function unclear 246782 Q15468 Unknown 2 e−65NvGli3 Transcriptional activator (Gli-full-length)

or repressor (Gli-R) when cleavedThis study P10071 Cubitus interruptus

(Ci)0

NvSap18 Gli partner: histone deacetylasesubunit:Sin3-associated polypeptide 18

226633 O00422 Bin1 5 e−41

NvSPOP Gli ubiquitylation and proteolysis 177584 O43791 roadkill 1 e−153NvTalpid3 Gli regulation (JGI_CAGG5027) Q1G7G8b Unknown 1 e−9b

a NCBI protein accession number.b Chick protein.


Evolutionary relationships of Nematostella hedgehog andhedgehog-related genes

To establish potential orthology and evolutionary correspon-dence between Nematostella and other metazoan hedgehog andHint-related genes, we subjected Hh-related predicted proteinsequences to Bayesian and maximum likelihood phylogeneticanalyses. Analyses were performed using both the N- and C-terminal domains, separately, and together. Using predicted full-length protein sequences, phylogenetic analyses support a sistergroup relationship between the two true Nematostella hedgehoggenes (NvHh1 and NvHh2; Fig. S6), suggesting that these genesmay have arisen by gene duplication within Nematostella orwithin the Cnidaria. The vertebrate Hedgehog proteins clustertogether in Bayesian and ML analyses (Fig. 2 and Figs. S5–S7)and suggest that sonic and indian hedgehog genes arosefollowing a gene duplication event from a desert hedgehog-likegene, in agreement with earlier analyses (Kumar et al., 1996;Shimeld, 1999). In analyses of just the hedge or signal domain,the two true Nematostella hedgehogs (NvHh1–2) show a gradedrelationship rather than forming a clade but branch to the

Fig. 1. Nematostella vectensis hedgehog-related proteins. The functional domainshedgehog genes in the N. vectensis genome (NvHh1 and NvHh2). NvHh1 and NvHhintein (black box) domains. Three other genes encode hint/intein domains but lack hedhint/intein domain, but instead the hedge domain is tethered to a von Willebrand facrelated domains (Ig and l-set), two EGF repeats, and a C-terminal SH2 domain (AdaNCBI database (http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi). The two conFig. S1 for additional information.

exclusion of the bilaterian hedgehog genes (Fig. S5). Inanalyses of just the hint or intein domain (Fig. 2 and Fig. S7),there is no support for a sister-group relationship between thetwo true Nematostella hedgehogs. Taken together, this suggeststhat either the cnidarian–bilaterian ancestor possessed twohedgehogs or that due to sequence divergence the weaklysupported sister-group relationship found in full-length proteinanalyses is masked in analyses of individual domains. Theabsence of a second hedgehog gene in most bilaterians surveyedsuggests that the cnidarian–bilaterian ancestor only possessedone hedgehog gene, and that the two Nematostella hedgehogsare the result of a cnidarian-specific duplication event. Analysesof just the intein domain (Fig. 2, Fig. S7) included the fivesponge hint/hog genes (Adamska et al., 2007), the two non-metazoan hint genes (G. mosseae and M. ovata), and the tenC. elegans intein-containing genes (groundhogs, warthogs, andquahog) (Aspock et al., 1999) as well as potential orthologsfrom related nematode ESTs identified via BlastP queries atNemBase (www.nematode.net), and three newly identified hintgenes from newly annotated lophotrochozoan genomes inaddition to bilaterian true hedgehog genes. In Hint-only

of predicted N. vectensis hedgehog-related proteins. There are two definitive2 encode proteins with both a “hedge” signal ligand (white box) and “hog” hint/gehog ligand domains. A sixth, hedgehog-related protein, NvHedgling, lacks thetor (vWA) domain, a series of 21 cadherin (cad) repeats, two immunoglobulin-mska et al., 2007). Domain structure was identified with PFAM searches of theserved intron sites with bilaterian hedgehog genes are marked with arrows. See

http://www.nematode.netmailto:[email protected]

Fig. 2. Phylogenetic analyses of hint/intein containing genes. Both Bayesian and maximum likelihood analyses were conducted utilizing MrBayes 3.1.2 (Ronquist,2003), Phyml (Guindon et al., 2003), and RAxML v.2.3.2 (Stamatakis, 2006) utilizing an amino acid alignment of hint/intein-containing genes from metazoan andnon-metazoan representatives. The three Nematostella hint-only containing genes (Hint1–3) (shown in red) form a monophyletic group in Bayesian analyses. The twotrue Nematostella (Nv) hedgehog genes (shown in red) do not show a sister group relationship as they do in analyses of the hedge and hint domains together (see Fig.S6). NvHh1 is weakly supported as the sister group to vertebrate hh genes (shown in green (sonic), pink (Indian), and blue (desert)). All nematode hint-only containinggenes (shown in light blue) from a monophyletic group including the true hedgehog gene from the nematode Xiphinema index (M. Blaxter, personal communication)as well as a hint-containing gene from the mollusc, Lottia gigantea. The two other lophotrochozoan hint-only genes (shown in dark green) form a sister group toNematostella hint genes in baytesian analyses. The five hint-only genes from the demosponge, Amphimedon queenslandica (shown in orange), form a monophyleticgroup as well. Numbers above branches indicate Bayesian posterior probabilities while numbers below indicate ML bootstrap support. Additional details ofphylogenetic analyses and nexus alignments are available in Figs. S2–S7.


phylogenetic analyses, all nematode Hints form a monophyleticclade with varying levels of support, including the true hedge-hog gene found in the slowly evolving nematode, X. index (M.Blaxter, personal communication) (Fig. 2 and Fig. S7) and ahint-only gene from the mollusc, Lottia gigantea. This suggests

a potential single origin for nematode Hint-containing genes.The three Nematostella genes that encode intein domains, butnot a conserved signaling domain (NvHint1–3), cluster togethersuggesting they arose from tandem duplications either withinNematostella or during cnidarian evolution (Fig. 2 and Fig.


S7). These cnidarian hint genes fail to cluster with thewarthog, groundhog, and quahog nematode genes (Fig. 2and Fig. S7), but do show a sister-group relationship inBayesian analyses with a hint gene from the polychaete, Ca-pitella sp. I and the mollusc, Lottia gigantea, suggesting apossible relationship between cnidarian and bilaterian hintgenes. Notably, the lophotrochozoan hint genes do not show arelationship to the true hedgehog genes from these same taxa(Fig. 2 and Fig. S7). While sequence diversity within metazoanhedgehog-related genes may mask relationships, leading topoorer statistical support, it is clear that Nematostella possessesfive hedgehog-related genes, of which two possess both ahedge and a hog/hint domain that show clear orthology to othermetazoan hedgehogs.

Developmental expression of hedgehog genes

To understand the potential role of Nematostella hedgehoggenes in embryonic development, we examined the spatial andtemporal expression dynamics of the hedgehog-related genesby whole mount in situ hybridization on N. vectensis embryosand early juvenile polyps. Fig. 3 shows the expression patternsof the two Nematostella hh genes that encode signaling ligands,NvHedgehog1 (NvHh1) and NvHedgehog2 (NvHh2). Neithergene is detected maternally. Zygotic expression for NvHh1begins at early gastrula stages (Fig. 3B) and in late planulastages for NvHh2 (Fig. 3I). NvHh1 expression begins at

Fig. 3. Embryonic expression of the N. vectensis Hh genes. Transcripts for NvHh1gastrulation in cells that will form the pharynx (pha). (B, C) Expression elevates signithe pharynx and extends to the ectoderm of the primary or directive mesenteries, at midof the pharynx and the two directive (primary) mesenteries (d.mes). NvHh2 expressiforming all eight body mesenteries (I, J) (mes). As the tentacles begin to emerge, expmesentery and tentacular endoderm persists into juvenile polyp stages (L, M). All embexcept panel A, which shows early cleavage and blastula stages, and panels B, D, G

gastrulation in presumptive pharyngeal ectodermal cells duringtheir invagination into the blastocoel (Fig. 3E). NvHh1 ex-pression persists in the pharyngeal ectoderm and spreads to theectodermal components of the first two mesenteries (thedirective mesenteries) throughout planula and polyp stages(Figs. 3F–H).

In contrast to NvHh1, transcripts for NvHh2 were notdetected until planula stages (Fig. 3I) where they are restrictedto tentacle bud endoderm (Figs. 3J, K) and in the endoderm ofthe eight thickened body wall mesenteries. At polyp stagesexpression is more diffuse but remains confined to endoderm, inthe mesenteries and tentacle endoderm, as well as in the bodywall endoderm (Figs. 3L, M).

Developmental expression of hint-only containing genes

All three hint-only genes are expressed in a cell-type-specific manner during Nematostella development. NvHint1expression commences in the early planula, peaks at lateplanula/early polyp, and persists into the juvenile polyp stagewhen tentacle buds are clearly visible (Figs. 4A–D). Through-out this timeframe, expression is punctate and primarily seen inthe ectoderm, although a few endodermal cells associated withthe pharynx of the polyp may also express NvHint1. Thereappears to be concentrated expression of NvHint1 in ectodermalcells located at the tentacle bud tips orally and at the aboral end(Figs. 4C, D), likely associated with the apical tuft of the

are not detectable until gastrulation (A). Expression begins after the onset officantly during pharynx formation (C–E). Expression persists in the ectoderm of-planula stages (F, G). In the polyp (H), expression is limited to the aboral regionon (I, J) begins during planula stages in the body wall endodermal componentsression is strong in the underlying tentacular endoderm (J, K). Expression in theryo views are lateral, with the asterisk denoting the blastopore and future mouth,, and K, which are oral views.

Fig. 4. Hint/intein containing genes in N. vectensis are likely involved in neural patterning. (A–D) Expression of NvHint1 is punctate in the ectoderm and initiates inthe early planula stage (A). Expression increases at mid-planula (B) and persists into the polyp (C, D). Expression is exclusively ectodermal, in scattered cells that arelikely to be neural in origin due to their basal position. Expression is relatively uniform across the oral–aboral axis of the planula but becomes more concentrated atboth the oral and aboral ends of the polyp. (E–H) Expression of NvHint2 is confined in a cell-type-specific manner to body wall endoderm and cells within thedirective mesenteries. Expression is detected in a few scattered endodermal cells in the planula (E, F). In the polyp expression can be detected in both body wallendodermal cells and within the directive mesenteries (G, H). (I–N) Expression of NvHint3 is also ectodermal and begins in a punctate fashion in the planula (I–K).Expression in the early polyp becomes elevated in tentacular ectoderm as well as a ring of cells surrounding the mouth, which are likely to be components of thecircumoral nerve ring (nr) (arrows, L, M). Expression persists mainly in the tentacular ectoderm with some scattered expression in the body wall ectoderm of the polyp(N). All embryo views are lateral, with the asterisk denoting the blastopore and future mouth, except panels A, E, M, which are oral views.


planula, a ciliated structure with sensory neural characteristics(Matus et al., 2007; Pang et al., 2004). Expression is seen in thecell bodies, which are located towards the basal surface of theepithelium, a position characteristic of ganglionic neurons(Marlow et al., in preparation).

NvHint2 is expressed in a few scattered cells during planula(Figs. 4E, F) and polyp stages (Figs. 4G–H) of development inbody wall endoderm and the directive mesenteries. Theexpression pattern of NvHint3 (Figs. 4I–N) is similar toNvHint1, with expression in a punctate pattern in the ectodermat planula through polyp stages. The asymmetric localization ofNvHint3-expressing cells shares a similar distribution towardsthe basal surface of the epithelium but differ in their distributionalong the body column (Figs. 4I–L). During tentacle-bud stagesof the late planula/early polyp, a greater number of cells at theoral end express NvHint3, and there is no expression in theapical sensory tuft or in the pharynx (Figs. 4L, M). The circularpattern of cells expressing NvHint3 around the blastopore/mouth corresponds to the position of the cnidarian circumoralnerve ring (Koizumi et al., 1992; Mackie, 2004; Miljkovic-

Licina et al., 2004). In the polyp (Fig. 4N), NvHint3 continuesto show expression throughout the ectoderm of the bodycolumn, as well as within specific ectodermal cells of thegrowing tentacles.

Developmental expression of patched and Gli genes

The 11 transmembrane receptor, Patched, is the ligand-binding component at the apex of the hedgehog signal receptionand relay system. At the terminus of the pathway, one or moreGli/Ci transcription factors regulate Hh-responsive genes.Because these receptor and transcription factor componentsare critical for Hh responses, these genes would be predicted tobe expressed in cells which receive hh signals, and thereforetheir expression patterns could be used to obtain clues aboutwhere hh signals might affectNematostella embryos. We clonedN. vectensis embryonic cDNAs for one patched (NvPtc) and oneGli gene (NvGli), which are the only representatives of thesetypes of genes in the N. vectensis genome (Table 1, discussedbelow; Figs. S10–S11). We examined their expression by in situ

Fig. 5. The hedgehog receptor, NvPatched, is expressed in endoderm during development. NvPtc transcripts are not detected at the onset of gastrulation (A) and arefirst detected in body wall and pharyngeal endoderm (p.end) at the oral pole in late gastrula (B, C). Expression is upregulated in the planula and polyp stages (D–F),where NvPtc is expressed in endoderm of the pharynx (p.end), body wall (b.end), and directive mesenteries (d.mes). Note the absence of NvPtc transcripts in theectodermal component of the pharynx (p.ect) and directive mesenteries (m.ect) (B–H). All embryo views are lateral, with the asterisk denoting the blastopore andfuture mouth, except panels C and E, which are oral views.


hybridization, and the results indicate that NvPtc and NvGli areexpressed in endoderm during development. NvPtc transcriptsare detected in oral body wall endoderm and pharyngealendoderm at mid to late gastrulation (Figs. 5B, C). NvPtcexpression is endodermal at late planula and polyp stages (Figs.5D–H), including tentacular endoderm (Fig. 5G), but itsexpression is noticeably higher in the endoderm of the twodirective mesenteries and in pharyngeal endoderm (Figs. 5F–H).The NvGli expression pattern (Fig. 6) is almost identical to thatof NvPtc, although NvGli transcripts are detected earlier thanthose of NvPtc. Expression commences at the onset ofgastrulation in invaginating presumptive endodermal cells(Fig. 6B) and persists in the endoderm through polyp stages.NvGli expression appears restricted to the endoderm, similar toNvPtc, with a significantly higher level of expression inendodermal cells of the directive mesenteries and the endoder-

Fig. 6. NvGli is expressed in the nearly the same endodermal pattern of NvPatched dfirst detected during the onset of gastrulation in invaginating endodermal cells (B). Abody wall endoderm (b. end) but not in the pharynx (pha). This expression patternexpressed in body wall endoderm, as well as the endodermal component of the direcendoderm (p. end). All views are lateral, with the asterisk denoting the blastopore anwhich is a dorsoventral view.

mal layer of the pharynx that faces the gastrocoel. Theseexpression patterns, together with those of the NvHh genes,prompt us to suggest that the embryonic endoderm, but perhapsnot the ectoderm, is the principal tissue that can receive and beaffected by NvHh1 and NvHh2 signals.

Additional Hedgehog signaling pathway components inNematostella

In addition to directly cloning and examining the expressionof Hh, Ptc, and Gli genes in N. vectensis, we surveyed the N.vectensis genome for the presence of sequences predicted tocorrespond to genes for other components of Hh signalingpathways known from studies of bilaterian animals. We usedprotein sequences and nomenclature for Drosophila andvertebrate hh signaling components to search the N. vectensis

uring development. Transcripts for NvGli are not present in the blastula (A) andt the end of gastrulation (C) and in the early planula (D), NvGli is expressed inpersists in tentacle bud stages (E). In the polyp (F–H), NvGli continues to betive mesenteries (d.mes), in tentacular endoderm (t.end), and in the pharyngeald future mouth, except panel A, which is a cleavage stage embryo, and panel H,


genome, EST sequences, and predicted protein using BLASTand name queries at the N. vectensis genome Web site, http://genome.jgi-psf.org/Nemve1/Nemve1.home.html. Table 1 sum-marizes N. vectensis gene sequences we identified that encodepredicted proteins with significant homology to knownbilaterian hh pathway components. Table 1 reveals that N.vectensis appears to contain a near full scope of hh pathwaycomponents identified in protostome and deuterostome modelsystems. Genomic sequence for a few of these (Ptc, Smo, Disp,and Gli) were also identified in a recent study (Walton et al.,2006). In bilaterians, Hh ligand activity can be affected by manyextracellular modifiers, and the N. vectensis genome containssequences predicted to encode many of these genes, includingskinny hedgehog/rasp/sightless, which encodes an acetyltrans-ferase that regulates hh activity by palmitoylation (Lee andTreisman, 2001); Dispatched, which encodes a membraneprotein for hh ligand transmission from the source cell; (Burkeet al., 1999); two glypicans, which govern extracellular hhligand movement (Desbordes and Sanson, 2003; Han et al.,2004); and orthologs of HIP and GAS1, which bindextracellular hh ligands and regulate their activity and rangeof movement (Cabrera et al., 2006; Chuang and McMahon,1999; Lee et al., 2001). We also found likely orthologs ofvertebrate exostosins and Drosophila tout-velut, which encodeglycosyl transferases that affect heparan biosynthesis, which inturn regulates hh intercellular movement and reception by targetcells (Bellaiche et al., 1998; Siekmann and Brand, 2005).

At the receptor level and downstream we identified twohomologs of Smoothened (NvSmo1, 2), the partner receptor thatis regulated by Patched, (Fig. 5). We also identified an N.vectensis ortholog of another type of Hh receptor, megalin,which encodes an LDL-related protein that binds and canendocytose extracellular Hh ligand (McCarthy et al., 2002;Morales et al., 2006). Predicted regulators of intracellular Hhreceptor trafficking (Eggenschwiler et al., 2006; Kalderon,2005; Meloni et al., 2006) are also present in the genome,including two forms of β-arrestin, GRK2/βARK-1 and the smallGTPase, Rab23. We further identified an N. vectensis homologof tectonic, which functions downstream of Smo by anunknown mechanism that can enhance or repress Hh signaltransduction (Reiter and Skarnes, 2006).

At the signal transduction level, in addition to a Gli3/Citranscription factor ortholog NvGli described above, N.vectensis possesses predicted genes encoding core componentsof the Gli cleavage complex (reviewed by Huangfu andAnderson, 2006; Osterlund and Kogerman, 2006), consistingof costal2, fused, suppressor of fused (SuFu), and βTRCP/slimb, as well as associated Gli kinases (PKA, GSK3β, CaseinKinase 1). We identified other Gli regulators as well, including ahomolog of Drosophila roadkill and its vertebrate orthologSPOP, which are substrate adaptors for cullin-type E3 ubiquitinligases that affect Ci/Gli proteasomal processing and degrada-tion (Kent et al., 2006; Zhang et al., 2006).

We also found a potential homolog of a vertebrate Gli1/2/3transcriptional partner protein sap18 (Cheng and Bishop, 2002)in the N. vectensis genome. Furthermore, Hh signal transductionin vertebrates (but not Drosophila) requires intact cilia and

associated intraflagellar transport proteins (Ifts), particularlyIft88/polaris, Ift172/wimple, and Ift52/Ngd5 (Huangfu et al.,2003; Liu et al., 2005), as well as Fantom, an apparentlyvertebrate-specific, ciliary basal body protein required for Hhsignal transduction (Vierkotten et al., 2007). Homologs of eachof these are represented in the N. vectensis genome (Table 1).Additionally, other genes implicated in vertebrate but notDrosophila hh signaling (with unknown mechanisms) arepresent in the N. vectensis genome: sil, a novel gene encodingan essential intracellular signaling regulator (Izraeli et al.,2001), iguana (Sekimizu et al., 2004), and talpid3 (Davey etal., 2006), the latter two being novel regulators of Gli activity.Perhaps orthologs of these genes were lost during the evolutionof Drosophila and other ecdysozoan lineages. Conversely, afew bilaterian Hh regulators appear to be absent in the N.vectensis genome, including homologs of Drosophila inter-ference Hedgehog (iHog) and its vertebrate ortholog Cdon,which bind Hh ligands (Okada et al., 2006; Yao et al., 2006),and WIF (wnt inhibitory factor), which can bind Hh as well asWnt ligands (Glise et al., 2005; Gorfinkiel et al., 2005). Thissuggests these genes evolved after the divergence of cnidariansand bilaterians. The sum of our cloning, expression and geno-mic survey results indicate that N. vectensis possessesessentially the full repertoire of Hh signaling pathway com-ponents found among bilaterian model organisms. Thus, the Hhsignaling pathway appears to have evolved its high degree ofcomplexity in an ancient, common ancestor of the Cnidaria andBilateria.

Discussion

The function of cell signaling pathways during embryogen-esis is well documented in representative protostome ecdy-sozoans (e.g., nematode and insect) and deuterostomes, but theextent to which such signaling systems function in theembryogenesis of non-bilaterians such as sponges, ctenophoresand cnidarians has only recently begun to be investigated (Adellet al., 2003; Nichols et al., 2006; Suga et al., 1999; Wiens et al.,in press). Recent exploration of some of these gene families incnidarian embryos have been particularly revealing and havedemonstrated the existence and embryonic deployment ofdiverse Wnt (Kusserow et al., 2005), TGF-beta and BMP(Finnerty et al., 2004; Hayward et al., 2002; Hobmayer et al.,2001; Matus et al., 2006a,b; Reber-Muller et al., 2006; Rentzschet al., 2006; Samuel et al., 2001), and FGF-related genes (Matuset al., 2007). Hedgehog signaling plays a critical role in patternformation and cell fate decisions in bilaterians (Fuccillo et al.,2006; Huangfu and Anderson, 2006; McMahon et al., 2003;Wang et al., 2007). Hedgehog-related genes have beendescribed in protostomes, within ecdysozoan lineages (Tashiroet al., 1993), as well as in several lophotrochozoans (Kang et al.,2003; Nederbragt et al., 2002; Seaver and Kaneshige, 2006),and in non-vertebrate deuterostomes including sea urchins(Walton et al., 2006), urochordates (Hino et al., 2003), andcephalochordates (Shimeld, 1999).

To understand the evolutionary origins of hedgehog signal-ing, we investigated whether hedgehog genes are present in the

http://genome.jgi%1Epsf.org/Nemve1/Nemve1.home.htmlhttp://genome.jgi%1Epsf.org/Nemve1/Nemve1.home.html


genome of N. vectensis, an anthozoan cnidarian. From genomicsearches using the Hint/Hog domain, we found that N. vectensispossesses five hedgehog-related genes, two of which are pre-dicted to encode ligands and are thus “true” hedgehog genes,while three others encode proteins missing the N-terminalsignaling domain, possessing only the C-terminal intein or Hint/Hog domain, a key feature of Hedgehogs, but also found out-side of the Metazoa in protists (e.g., choanoflagellates; Snell etal., 2006) and the fungus, Glomus messeae (Requena et al.,2002). We also identified an ortholog of the poriferan hedglinggene from A. queenslandica in N. vectensis (Adamska et al.,2007), that appears to have been lost in bilaterians.

Ancient origins and evolution of metazoan Hedgehog-relatedgenes

The presence of Hint genes outside of the Metazoa, such asthe hoglet gene (Snell et al., 2006) identified in the freshwaterchoanoflagellate, M. ovata, and GmGin1 (Requena et al., 2002)in the mycorrhizal fungi,G. mosseae, suggests that evolutionaryprecursors of hedgehog signaling existed prior to the metazoan

Fig. 7. A model for Hedgehog evolution. Data from the genomes of the anthqueenslandica, suggest that the origin of the Hedgehog signaling molecule arose in thovata, possesses a hint/intein “hog” containing gene (Snell et al., 2006), but no genqueenslandica, possesses both hint/intein genes as well as a gene possessing a “hedgthis gene has been found in the N. vectensis genome. However, N. vectensis also pocontaining genes have not been identified in most bilaterians surveyed, Caenorhabd2006a), possesses two families of Hint/intein containing genes, with novel N-terminidentified in the slowly evolving nematode, X. index (M. Blaxter, personal communigroundhog, warthog, and quahog genes are derived from an ancestral nematode true hthe Lophotrochozoa raises the possibility (dashed arrow) that the cnidarian-bilateriagenomic data will be necessary to determine if these bilaterian hints are derived from

radiation. Choanoflagellates are unicellular protozoa consideredto be the likely sister group to the Metazoa (King and Carroll,2001; Snell et al., 2001). M. ovata hoglet encodes an N-terminal, threonine-rich domain of unknown function linked toa C-terminal Hint domain (Snell et al., 2006), while GmGin1possesses a C-terminal Hedgehog-related intein domain linkedto an N-terminal domain that shares sequence similarity with anovel family of GTP binding proteins (Requena et al., 2002).Phylogenetic analysis of Hint/Hogs in N. vectensis and otherspecies suggest that the Hint/Hogs of Nematostella and those ofthe sponge, Amphimedon, likely arose from independent geneduplication events within each lineage (Fig. 2). The lack of truehedgehogs in the Amphimedon genome (Adamska et al., 2007)suggests that the origins of the metazoan hedgehog ligand mayhave occurred following the divergence of sponges withEumetazoa (Adamska et al., 2007). The identification of bothHint/Hog genes and hedgehog genes in Nematostella arguesthat the evolution of a hedgehog gene in the cnidarian–bilaterian ancestor occurred by a domain-capturing event of anN-terminal signaling (or “hedge”) domain and a Hint/Hogdomain-containing gene (“hog”) (Fig. 7).

ozoan cnidarian Nematostella vectensis and the demosponge, Amphimedone eumetazoan ancestor (Adamska et al., 2007). The choanoflagellate,Monosigae possessing a signal or “hedge” domain has been found. The demosponge, A.e” domain tethered to a fat-like cadherin (Adamska et al., 2007). An ortholog ofssesses two true hedgehogs as well as three hint/intein genes. While Hint/inteinitis elegans, which lacks true hedgehog genes (Aspock et al., 1999; Hao et al.,al domains (warthog and groundhog). However, a true hedgehog gene has beencation). Based on phylogenetic analyses (Fig. 2) it appears likely that nematodeedgehog gene (solid arrow). The identification of several hint-only genes withinn ancestor possessed both true hedgehogs and hint genes, however additionaltrue hedgehog genes. The hedgehog ligands diversified within the Vertebrata.


The recent annotation of two lophotrochozoan genomes (thepolychaete annelid, Capitella sp. I, and the gastropod mollusc,Lottia gigantea (Joint Genome Institute), allowed for theidentification of new bilaterian hint-only genes. Previously, theonly other bilaterians to definitively possess both hint-onlygenes and true hedgehogs appeared to be the nematodes. It hasbeen suggested that nematodes possess as many as ten differenthedgehog-related genes (e.g., warthogs, groundhogs, and qua-hog). We have identified orthologs of these genes withinpublicly available ESTs available at NemBase (www.nematode.net) along with a single EST cluster from the slowly evolvingnematode, X. index, that appears to be a definitive hedgehoggene possessing both a signaling or hedge domain as well as ahint/hog domain (M. Blaxter, personal communication, and Fig.2). The identification of a definitive nematode hedgehog genesupports earlier hypotheses that the C. elegans hh-related genesare derived from an ancestral hedgehog (Aspock et al., 1999;Hao et al., 2006a). The potential relationship between the hintgenes of lophotrochozoans and Nematostella suggests that ahint-only gene may have been present in the cnidarian-bilaterianancestor. Alternatively, it is possible that these lophotrochozoanhint-only genes are derived from true hedgehog genes in thesetaxa. Hopefully, additional taxonomic sampling will helpresolve this issue (Fig. 7). The conservation of intron/exonboundaries in all of the Nematostella hedgehog-related geneswith bilaterian hedgehogs also supports a monophyletic originof the hedgehog in the cnidarian–bilaterian ancestor. Hedgehoggenes later underwent gene duplication events (Fig. 7), likelycorrelated with the genome duplication events within thevertebrate lineages, to give rise to the hedgehog paralogs (sonic,indian, and desert) found in extant vertebrates.

Assigning the origin of the first true hedgehog gene withinthe Cnidaria is somewhat contentious due to conflicting databetween two sponges, Oscarella carmella (Nichols et al., 2006)and A. queenslandica (Adamska et al., 2007). A recentExpressed Sequence Tag (EST) survey in the demosponge, O.carmella. (Nichols et al., 2006) used blast searches of∼11,000 ESTs to identify both cell adhesion and signaltransduction genes that had previously never been identified insponges. Included in this survey were a putative hedgehogligand, three clones with Blast identity to the hh receptorpatched, and one membrane modifier, dispatched. While thissuggests that components of the hedgehog pathway pre-datedthe cnidarian–bilaterian ancestor, these data are preliminary.Their putative hedgehog sequence is missing a definitive Hintdomain, and the three non-overlapping patched sequencefragments are of insufficient length to establish definitiveorthology beyond that of simple Blast identity. Contrary to theOscarella data, the recently sequenced genome of the demos-ponge, A. queenslandica, lacks a true hedgehog ortholog butdoes possess several Hint-only containing genes, as well as onehedge containing gene, hedgling, that is tethered to a series ofcadherin domains (Adamska et al., 2007). Additionally, the A.queenslandica genome is missing a definitive Ptc ortholog (B.Degnan, personal communication). Together, this suggests thateither there are large differences in the genomic content betweenthese two sponge species, or that the identified ESTsequences in

O. carmella need to be verified by either genomic southerns or insitu hybridizations. However, given the lack of true hedghoggenes in the genome of the sponge, A. queenslandica, and thepresence of a hedge-only containing ortholog, hedgling, in bothA. queenslandica and N. vectensis, this would suggest that theorigin of the first hedgehog ligand occurred after the divergenceof sponges from the Eumetazoa (Adamska et al., 2007). With therecent sequencing of a placozoan genome, and more extensivesampling within the ctenophores, the exact timing of the originand diversification of the hedgehog pathway within the Metazoawill soon be determined.

Coordination between the Wnt, TGF-β, FGF, and hedgehogsignaling pathways

Signal transduction pathways are often functionally coordi-nated during ontogeny. Interactions between the Wnt, TGFβ,FGF, and Hh pathways in particular have been described in avariety of contexts, including Drosophila body segmentation(DiNardo et al., 1994; Sanson, 2001) and retinal development(Silver and Rebay, 2005), mammalian jaw and tooth develop-ment (Cobourne and Sharpe, 2003; Tompkins, 2006), insect andvertebrate limb patterning (Angelini and Kaufman, 2005;Stopper and Wagner, 2005), gut development (Fukuda andYasugi, 2002; Grapin-Botton, 2005; Tam et al., 2003),vertebrate somitogenesis (Aulehla and Herrmann, 2004; Bakeret al., 2006; Pourquie, 2003), and neural tube development(Cayuso and Marti, 2005; Roussa and Krieglstein, 2004; Wilsonand Maden, 2005). Recent evidence has suggested a role forWnt (Kusserow et al., 2005; Wikramanayake et al., 2003),TGFβ/BMP (Matus et al., 2006a; Matus et al., 2006b), and FGFsignaling (Matus et al., 2007) in gastrulation and endodermdevelopment in Nematostella. Various components of thesesignal transduction pathways along with the hh pathway aredeployed at the onset of and during gastrulation in invaginatingmesendoderm or later in mesendodermally associated structuressuch as the pharynx (Figs. 8A, B) or mesenteries (Fig. 8B).

Specifically, NvHh1 shows co-expression with FGF8A(Matus et al., 2007) and the transcription factor NvForkhead(Martindale et al., 2004) in the developing pharynx (Fig. 8A).The Wnt1 (Wg) ortholog, NvWnt1, is expressed along withseveral other Wnt ligands (Kusserow et al., 2005) and the T-boxtranscription factor NvBra (Scholz and Technau, 2003) in oralectoderm in a domain abutting NvHh1 and NvFGF8A ex-pression (Fig. 8A). During mesentery patterning, two TGFβligands (NvDpp and NvBMP5-8; Matus et al., 2006b) are co-expressed in the body wall endodermal components of the eightmesenteries along with NvHh2 (Fig. 8B). The close coordina-tion of the expression of these signal transduction pathwaysduring gastrulation and in structures such as the pharynx andmesenteries may represent a conserved developmental cassetteof cell–cell signaling components and may provide clues to theevolutionarily conserved roles of these signal transductionpathways during development. In support of this, treatment withlithium chloride, a known activator of the canonical Wntsignaling pathway via GSK3β inhibition and nuclear stabiliza-tion of β-catenin (Klein and Melton, 1996), appears to

http://www.nematode.nethttp://www.nematode.net

Fig. 8. Summary of Hedgehog, Wnt, TGFβ, and FGF signaling inNematostella vectensis. Signal transduction pathway ligands of the Wnt, TGFβ, FGF, and Hedgehogpathways appear to be involved in patterning the oral/aboral axis during N. vectensis development. (A) Wnt ligands (e.g., NvWnt1) (Kusserow et al., 2005) and theT-box transcription factor NvBra (Scholz and Technau, 2003)) are expressed in oral ectoderm. Ligands for both Hedgehog (NvHh1) and FGF (NvFGF8A) (Matus et al.,2007) are expressed along with the transcription factor, forkhead (Martindale et al., 2004), in the ectodermal component of the pharynx, indicating a conserved role ingut formation between cnidarians and bilaterians. TGFβ ligands NvDpp and NvBMP5-8 (Finnerty et al., 2004; Matus et al., 2006a,b) are expressed in body wallendoderm along with downstream components of the hedgehog pathway, including a receptor, NvPtc, and transcription factor, NvGli. (B) During polyp stages, thesesame signal transduction pathways appear to be coordinately involved in patterning the mesenteries. Both TGFβ (NvDpp andNvBMP5-8) (Finnerty et al., 2004; Matuset al., 2006a,b), Wnt ligands (e.g., NvWnt8) (Kusserow et al., 2005), along with an FGF ligand (NvFGF8A) (Matus et al., 2007) are all expressed in endodermallyderived structures. Hedgehog ligands are expressed in either the pharyngeal ectodermal component of the directive mesenteries (NvHh1) or the body wall endodermalcomponent of the eight mesenteries (NvHh2). (C) Downstream components of the hedgehog pathway, NvPtc and NvGli are expressed exclusively in body wallendoderm and in the endodermal components of the eight mesenteries, suggesting that the Hedeghog ligands may be acting in both a trans-epithelial (signaling fromNvHh1 positive cells in pharyngeal ectoderm to NvPtc/NvGli-positive cells in the body wall endoderm and mesenteries) and a planar fashion (NvHh2 in the sameendodermal cells as NvPtc/NvGli) within the endoderm.


downregulate the expression of hedgehog pathway componentsduring Nematostella development (Fig. S11). An ectopicincrease in Wnt signaling has also been shown to have arepressive affect on Hh signaling in chick Sonic hedgehogneural plate explants, both via exposure to Wnt1 and Wnt3 aswell as the addition of lithium chloride (Robertson et al., 2004),suggesting that the relationship between these pathways is anancient one.

A conserved role for Hh and TGFβ signaling in germ celldevelopment

TGFβ and Hh signaling have been implicated in germ celldevelopment in Drosophila, where TGFβ signaling via dpp andglass bottom boat (gbb) are essential for promoting the self-renewal and proliferation of germline stem cells (Kirilly et al.,2005; Chen and McKearin 2003), while the hedgehog pathwaymay be functioning in a cell-autonomous fashion for germ cellmigration (Deshpande et al., 2001). In vertebrates, the ligand,desert hedgehog regulates spermatogenesis in mice via Sertolicell signaling (Bitgood et al., 1996). Hedgehog signaling hasbeen suggested to play an ancient conserved role in mediatingsomatic and germ cell interactions (Bitgood et al., 1996). Datafrom N. vectensis support this claim, as both TGFβ ligands(NvDpp and NvBMP5-8, an ortholog of Drosophila gbb)(Finnerty et al., 2004; Matus et al., 2006a,b) and both of the Hhligands are expressed in the mesenteries during development,with NvHh1 expressed in the pharyngeal component of thedirective mesenteries and NvHh2 expressed in the endodermal

components of all eight mesenteries (Fig. 8B). Previous workhas shown that germ cells in Nematostella first appear late indevelopment, associated with compartments within the mesen-teries, and that a vasa gene, Nvvas1, and a nanos ortholog,Nvnos2, are expressed in putative germ cells within thedeveloping mesenteries (Extavour et al., 2005). While func-tional experiments are needed, based upon observed expressionpatterns and data from bilaterians, it is likely that the involve-ment of Hh and TGFβ signaling in germline development pre-dates the cnidarian–bilaterian divergence. If the two Nematos-tella hedgehogs share a common origin, based on both aminoacid identity and phylogenetic analyses (Fig. S6), it is likely thatthey split their ancestral function (duplication and subfunctio-nalization) in the Nematostella-specific or cnidarian-line ofdescent.

A conserved role for hedgehog signaling in gut development

Similar to most signal transduction pathways, Hedgehogsignaling is utilized in a variety of different contexts duringbilaterian development. A conserved role for the Hedgehogpathway in gut development has been suggested on the basis ofhedgehog gene expression in deuterostomes (e.g., sea urchin,Walton et al., 2006; zebrafish and medaka, Kobayashi et al.,2006; Strahle et al., 1996; frog, Ekker et al., 1995; chick,Roberts et al., 1995; Sukegawa et al., 2000; mouse, Bitgood andMcMahon, 1995) and in protostomes (e.g., the arthropodsDrosophila, Hoch and Pankratz, 1996; Gryllus, Inoue et al.,2002; Euscorpius and Aretemia, Simonnet et al., 2004; and


recently in the annelids Helobdella, Capitella, and Hydroides,Kang et al., 2003; Seaver and Kaneshige, 2006). Indeed, gainand loss-of-function studies in many of these animalsdemonstrates that abnormal hedgehog signaling causes gutmalformation and disease (Diiorio et al., 2007; Hatini et al.,2005; Inoue et al., 2002; Iwaki et al., 2001; Mullor et al., 2002;Takashima and Murakami, 2001; Wang et al., 2002; Warburtonet al., 2000; Zhang et al., 2001; with a recent review by Lees etal., 2005). The endodermal and pharyngeal expression of hed-gehog genes in N. vectensis (Figs. 3 and 8) suggests that the roleof hh in endoderm specification and gut development may alsohave pre-dated the origin of the Bilateria, and was likely presentin the cnidarian–bilaterian ancestor.

In bilaterians, hedgehog ligands are often found expressed inendodermal epithelia during gut and lung formation (Narita etal., 1998; Sukegawa et al., 2000) and have been shown to signalto downstream components, such as patched and gli/Ci, whichare found in neighboring mesenchyme (Ramalho-Santos et al.,2000; Rubin, 2007; Shannon and Hyatt, 2004; Zhang et al.,2001). This scenario has recently been described in the seaurchin, Lytechinus variegatus, where hedgehog is expressed atthe vegetal pole at the onset of gastrulation, in the invaginatingendodermal vegetal plate, and is expressed in the endodermthrough prism and larval pluteus stages, while patched andsmoothened are expressed in neighboring secondary mesench-yme cells (Walton et al., 2006). A similar situation in observedto Nematostella, as NvHh1 is expressed in neighboring tissue toPtc and gli positive cells (Fig. 8). It has been suggested that thecnidarian endoderm is either a remnant of the endomesoderm/mesendoderm of a triploblastic ancestor or the evolutionaryprecursor to triploblasty (Martindale et al., 2004). The Nema-tostella gastrodermis is a bi-functional (contractive andabsorptive) endoderm and has been previously been shown toexpress many of the same transcription factors and signalingmolecules associated with patterning endomesoderm in bilater-ians (Wikramanayake et al., 2003; Martindale et al., 2004;Finnerty et al., 2004; Matus et al., 2006a,b; Matus et al., 2007;Rentzsch et al., 2006; Scholz and Technau, 2003). Theexpression of hedgehog pathway components described hereprovides additional support for homology between the endo-derm of cnidarians and the endomesoderm of bilaterians.

Spatial dynamics of Hh signaling in Nematostella

The potential function of these hedgehog genes is difficult topredict, as the ligands produced by each of the genes wouldhave the potential to either signal within the plane of theendodermal (i.e., NvHh1 and NvHh2) and ectodermal(NvHint1–3) epithelia, or between these germ layers. Hedgehogsignaling typically occurs within the plane of an epithelialtissue, often through the formation of a gradient of Hh ligand(Vincent and Dubois, 2002), such as observed in Drosophila inthe cellular blastoderm of the early embryo, or the wing or legimaginal discs in the larvae. Hedgehog ligands are particularly“equipped” for planar signaling within epithelia, as Hh ligandscan either move from a source cell to receiving cells through theextracellular space (where cholesterol modification can affect

their diffusion) or through the epithelial cells via endocyticvesicles called argosomes (Cadigan, 2002). Based on theexpression data presented here, it appears likely that both trans-epithelial and planar signaling is occurring: NvHh1 expressed inpharyngeal and directive mesentery ectoderm signaling in transto adjacent endoderm, and NvHh2 in body wall and mesenteryendoderm signaling in a planar fashion within the endoderm.This prediction is supported by the expression of both NvPtcand NvGli in the same, endodermal epithelial layer as the Hhligands, overlapping with NvHh2 expression in the body wallendoderm and eight mesenteries, and adjacent to the NvHh1expressing cells of the pharyngeal ectoderm (Fig. 8C).

Unexpected complexity in the N. vectensis Hedgehog signalingpathway

In addition to directly cloning cDNAs for Hh-related ligands,receptors and Gli proteins, we further surveyed the N. vectensisgenome and EST databases for the presence of sequences thatencode additional components of Hh signaling regulation. Themost striking feature revealed by this survey is that homologsfor nearly every protein implicated in hedgehog signaling inBilateria can be found in N. vectensis (Table 1). These findingsindicate that a complex Hh signaling pathway had alreadyevolved in the cnidarian–bilaterian ancestor. From the diversityof ligand and signal transduction components we haveuncovered, the putative N. vectensis hedgehog pathway moreclosely resembles the vertebrate pathway than that of Droso-phila, although some gene duplication has occurred invertebrates (e.g., the Gli's). The Drosophila hh pathwayappears to be a somewhat simplified (derived) version of amore complex pathway likely present in the cnidarian–bilaterian ancestor. C. elegans presents an even more extremecase of apparent gene loss in an ecdysozoan lineage. Althoughnumerous Hint genes and patched homologs are present, C.elegans lacks virtually all other components of Hh signaling(Hao et al., 2006a), although more slowly evolving nematodes(e.g., X. index) appear to possess true hedgehog ligands (Fig. 2and M. Blaxter, personal communication). Such findingscorrelate with studies showing extensive gene loss within themodel ecdysozoans, Drosophila and C. elegans (Copley et al.,2004; Miller et al., 2005; Wolf et al., 2004; Kusserow et al.,2005; Putnam et al., 2007; Technau et al., 2005).

To fully understand the evolutionary picture of Hedgehogsignaling, we need to tap emerging genomes of non-modelbilaterians, particularly within the Lophotrochozoa and Ecdy-sozoa, as well as in non-bilaterians such as sponges, placozoans,and ctenophores, to obtain a complete picture of the evolution ofthis important signaling pathway.

Acknowledgments

We thank Bernie Degnan and members of the MartindaleLab for useful discussions and Mark Blaxter for alerting us toslow evolving nematode taxa. MQM is supported by grantsfrom NSF and NASA, and GHT and CM are supported bygrants from the NIH.


Appendix A. Supplementary data

Supplementary data associated with this article can be found,in the online version, at doi:10.1016/j.ydbio.2007.09.032.

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the hedgehog gene family of the cnidarian, nematostella ...the hedgehog gene family of the...

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