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Cited by 170Receptor Mechanisms and SignalingOlfactory and Sensory Function StudiesMarine Invertebrate Physiology and Ecology

Opsins and clusters of sensory G-protein-coupled receptors in the sea urchin genome

Open access
Raible, Florian, Tessmar-Raible, Kristin, Arboleda, Enrique, Kaller, Tobias, Bork, Peer, Arendt, Detlev, Arnone, Maria I.·2006·Developmental Biology
DOI 10.1016/j.ydbio.2006.08.070
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Abstract

Rhodopsin-type G-protein-coupled receptors (GPCRs) contribute the majority of sensory receptors in vertebrates. With 979 members, they form the largest GPCR family in the sequenced sea urchin genome, constituting more than 3% of all predicted genes. The sea urchin genome encodes at least six Opsin proteins. Of these, one rhabdomeric, one ciliary and two G(o)-type Opsins can be assigned to ancient bilaterian Opsin subfamilies. Moreover, we identified four greatly expanded subfamilies of rhodopsin-type GPCRs that we call sea urchin specific rapidly expanded lineages of GPCRs (surreal-GPCRs). Our analysis of two of these groups revealed genomic clustering and single-exon gene structures similar to the most expanded group of vertebrate rhodopsin-type GPCRs, the olfactory receptors. We hypothesize that these genes arose by rapid duplication in the echinoid lineage and act as chemosensory receptors of the animal. In support of this, group B surreal-GPCRs are most prominently expressed in distinct classes of pedicellariae and tube feet of the adult sea urchin, structures that have previously been shown to react to chemical stimuli and to harbor sensory neurons in echinoderms. Notably, these structures also express different opsins, indicating that sea urchins possess an intricate molecular set-up to sense their environment.

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Crossref · 10.1016/j.ydbio.2006.08.070

Cites

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Statistics

Nothing to recompute.

Claims the paper makes

0 of 52 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    Sp-Opsin4 is a member of the rhabdomeric Opsin family.

    “Sp-Opsin4 is a clear member of the r-Opsin family”
    Quote in the paperSubstantial claim
  • Findingown data

    The sea urchin genome contains 979 rhodopsin-type GPCRs.

    “With 979 members, they form the largest GPCR family in the sequenced sea urchin genome, constituting more than 3% of all predicted genes.”
    • Also stated in: § Rhodopsin-type GPCRs constitute the largest GPCR superfamily in the sea urchin genome · hedged
      “we could identify 979 rhodopsin-type GPCRs in the S. purpuratus proteome predicted from the first genome assembly.”
    Quote in the paperSubstantial claim
  • Findingown data

    Many predicted sea urchin GPCRs show only distant similarity to known bilaterian GPCRs.

    “However, we noted that many of the predicted molecules showed only distant similarity to known bilaterian GPCRs.”
    Quote in the paperSubstantial claim
  • Findingown data

    Sp-Opsin2 and Sp-Opsin5 show no clear affiliation to any larger Opsin subfamily in phylogenetic and sequence analyses.

    “The two remaining sea urchin opsins, Sp-Opsin2 and Sp-Opsin5, show no clear affiliation to any of the larger Opsin subfamilies in phylogenetic and sequence analyses (Figs.1A, B).”
    Quote in the paperSubstantial claim
  • Findingown data

    Pedicellariae and tube feet also express different opsins.

    “Notably, these structures also express different opsins”
    Quote in the paperSubstantial claim
  • May combine two claims. 32
  • The quote only partly states this claim. 2
  • Classified as probably not a substantial claim. 18

  • May combine two claims.

    Findingown data

    The six predicted sea urchin Opsins are bona fide Opsins because they contain the key lysine residue for Schiff base formation, share Opsin-specific amino acids, and cluster in phylogenetic trees.

    “These rhodopsin-type GPCRs are Opsins based on three characteristics: (1) the presence of the key lysine residue necessary for the Schiff base formation with retinal (Fig. 1B); (2) amino acids specifically shared among Opsin (Fig. 1B and data not shown); and (3) their well-supported clustering in phylogenetic trees (Fig. 1A and data not shown).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Representatives of both opsins and presumed chemosensory receptors are specifically and differentially expressed in tube feet and pedicellariae, but not in other tissues such as testes, ovaries, axial gland, coelomocytes or gut.

    “In agreement with their presumed function, we find representatives of both opsins and the presumed chemosensory receptors specifically and differentially expressed in prominent sensory structures of the adult sea urchin, the tube feet and pedicellariae, but not in other tissues, such as testes, ovaries, axial gland, coelomocytes or gut.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Sp-Opsin3.1 and Sp-Opsin3.2 are closely similar and their genes are adjacent in the sea urchin genome.

    “This is suggested by the close similarity of the Sp-Opsin3.1 and Sp-Opsin3.2sequences and is further supported by the adjacent position of these genes in the sea urchin genome.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In group B surreal-GPCRs, additional strong variability is seen in the N- and C-terminal regions and in the third intracellular loop between TM V and VI, all of which also carry length polymorphisms.

    “Additional strong variability was seen in the Nand C-terminal regions as well as in the third intracellular loop between TM V and VI, all of which also carried length polymorphisms.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The number of rhodopsin-type GPCRs in Strongylocentrotus is similar to that found in mammals and exceeds that of many other invertebrates.

    “From this perspective, it is remarkable to note that the number of rhodopsin-type GPCRs in Strongylocentrotus is similar to that found in mammals and exceeds that of many other invertebrates.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Group A surreal-GPCRs display a lower proportion of single-exon genes, whereas group D has many genes with a high number of exons.

    “Group A surreal-GPCRs display a lower proportion of single-exon genes, whereas group D has many genes with a high number of exons.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    In both minor groups e and f, genomic clustering was detected, in one case including a total of twelve closely related sequences.

    “In both groups, we also detected genomic clustering, in one case (e) including a total of twelve closely related sequences.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingcitation

    The fraction of rhodopsin-type GPCRs in the sea urchin genome (3.4%) is comparable to that reported for mouse and human (3.4% and 2.8%, respectively) and exceeds that observed in pufferfish (1.6%), nematode (2%), or fruit fly (0.6%).

    “The latter fraction is well comparable to the abundance of rhodopsin-type GPCRs reported for the mouse and human genomes (3.4% and 2.8%, respectively) and exceeds that observed in the pufferfish (1.6%), nematode (2%) or fruit fly genomes (0.6%) (Waterston et al., 2002).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Waterston et al., 2002

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    The model derived from group D surreal-GPCRs showed highest similarity to a pond snail protein assigned as glycoprotein hormone receptor (GR101_LYMST), and lower significance to various vertebrate receptors of the relaxin receptor group (IPR008112).

    “The model derived from group D surreal-GPCRs showed highest similarity to a pond snail protein assigned as glycoprotein hormone receptor (GR101_LYMST), and, although with lower significance, to various vertebrate receptors of the relaxin receptor group (IPR008112).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Six opsins are present in the sea urchin, and two of them are opsin3 paralogs.

    “The magnified insert shows the six sea urchin opsins, with the two opsin3 paralogs visible as bright quadruplet in the right lower corner.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The presence of Go-Opsin orthologs in sea urchin helped confirm Go-Opsins as an ancestral group, improving bootstrap support for the monophyletic origin of Go-Opsins prior to bilaterian radiation.

    “The presence of G o -Opsin orthologs is particularly revealing because the sea urchin sequences have helped to confirm G o -Opsins as an ancestral group, improving bootstrap support for the monophyletic origin of G o -Opsins prior to bilaterian radiation.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    More than 60% of all sea urchin rhodopsin-type GPCRs are single-exon genes, many of which are only remotely related to receptors of other animals.

    “A survey among all rhodopsin-type GPCRs revealed that more than 60% of all sea urchin rhodopsin-GPCRs are single-exon genes, many of which are only remotely related to receptors of other animals (Table S3).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Rhodopsin-type GPCRs are the largest GPCR superfamily encoded by the sequenced sea urchin genome, constituting 3.4% of all currently predicted genes.

    “Despite these changes, it is clear that rhodopsin-type GPCRs are the largest GPCR superfamily encoded by the sequenced sea urchin genome, constituting 3.4% of all the currently predicted genes.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    QPCR analysis revealed that within adult urchins the clearly strongest level of expression of group B surreal-GPCRs is present in pedicellariae and tube feet, which express different sets of surreal-GPCRs at different levels.

    “QPCR analysis revealed that within adult urchins the clearly strongest level of the expression is present in pedicellariae and tube feet, whichsimilar to the opsinsexpress different sets of surreal-GPCRs at different levels (Fig. 5A).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Opsin expression occurs in one-week-old larvae and in adult tissues.

    “Expression of opsins in one-week-old larvae and adult tissues as detected by QPCR.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Among sea urchin GPCRs, there are four major expanded lineages (groups A-D) and two smaller lineages (e and f).

    “Four major expanded lineages (group A-D surreal-GPCRs) are indicated with colored bars, and two smaller ones (e, f) are marked with small letters.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Group B and group C surreal-GPCRs show length polymorphisms.

    “Length polymorphisms are also indicated: Hatched lines mark positions at which other members of the group differ by the insertion of 5 or more amino acids”
    Quote in the paperNot a substantial claim

  • The quote only partly states this claim.

    Findingown data

    The group B surreal-GPCR genes on Scaffold_v2_21524 are arranged in tandem orientation.

    “Note that all genes are oriented in tandem orientation.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    Many sea urchin GPCRs display remote similarity to their cognates in other animals, and it appeared likely that they have also lost or modified important characteristics of these groups.

    “However, regarding the remote similarity that many sea urchin GPCRs display to their cognates in other animals, it appeared likely that they have also lost or modified important characteristics of these groups.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Study design and conductcitation

    Ubiquitin and 18S ribosomal RNA are expressed at constant levels during development and were used as internal controls, with 18S used to normalize all data.

    “Ubiquitin and 18S ribosomal RNA, which are known to be expressed at constant levels during development (Nemer et al., 1991;Ransick et al., 2002), were used as internal controls, and 18S Ribosomal RNA was used to normalize all data.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Nemer et al., 1991

      Not checked in the free run.

    • cites Ransick et al., 2002 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Rhodopsin-type GPCRs make up the majority of sensory receptors in vertebrates.

    “Rhodopsin-type G-protein-coupled receptors (GPCRs) contribute the majority of sensory receptors in vertebrates.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Ache and Young, 2005

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Pedicellariae and tube feet have previously been shown to react to chemical stimuli and to harbor sensory neurons in echinoderms.

    “structures that have previously been shown to react to chemical stimuli and to harbor sensory neurons in echinoderms.”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites Campbell, 1973

      Not checked in the free run.

    • cites Snyder and Snyder, 1970

      Not checked in the free run.

    • cites Peters and Campbell, 1987

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Vertebrate olfactory receptors arose by multiple gene duplication events.

    “Olfactory receptors of vertebrates arose by multiple gene duplication events (reviewed, e.g., in Ache and Young, 2005).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Ache and Young, 2005

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    The secretin-type GPCR superfamily is the second largest GPCR superfamily in the sea urchin genome, with about one sixth the number of rhodopsin-type GPCRs.

    “followed second by the secretintype GPCR superfamily with only one sixth of the number (Cameron et al., 2006).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Cameron et al., 2006

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Gene duplications have long been implied as a major mechanism generating evolutionary innovations.

    “Gene duplications have long been implied as a major mechanism generating evolutionary innovations (Kimura, 1983;Ohno, 1970).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Kimura, 1983

      Not checked in the free run.

    • cites Ohno, 1970

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Four of the sea urchin Opsins are also reported in Burke et al. (2006).

    “Four of these are also reported in the independent publication by Burke et al. (2006).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Burke et al. (2006)

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Premisecitation

    Among the five main GPCR superfamilies in the GRAFS classification, two encode photosensory and chemosensory functions of vertebrates: the glutamate-receptor superfamily (pheromone and taste) and the rhodopsin-type superfamily (light, olfaction and possibly pheromones).

    “Among the five main superfamilies of GPCRs distinguished by the GRAFS classification scheme (Schiöth and Fredriksson, 2005), two encode photosensory and chemosensory functions of vertebrates, namely the glutamate-receptor superfamily (pheromone and taste) and the rhodopsin-type superfamily (light, olfaction and possibly pheromones) (Bjarnadóttir et al., 2005;Liberles and Buck, 2006).”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites Schiöth and Fredriksson, 2005

      Not checked in the free run.

    • cites Bjarnadóttir et al., 2005

      Not checked in the free run.

    • cites Liberles and Buck, 2006

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Increasing organismal complexity has been correlated with higher rates of duplicate retention.

    “Moreover, increasing organismal complexity has been correlated with higher rates of duplicate retention (Yang et al., 2003).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Yang et al., 2003

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S1 (asserted).

    Interpretationreasoning

    Surreal-GPCRs arose by rapid duplication in the echinoid lineage.

    “We hypothesize that these genes arose by rapid duplication in the echinoid lineage”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    Primer efficiencies were found to exceed 1.9.

    “Primer efficiencies (i.e., the amplification factor for each cycle) were found to exceed 1.9.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Premisecitation

    Chemoreception and light reception are mediated by GPCR superfamilies in vertebrates and invertebrates, with the main exceptions of Trp channels and cryptochrome molecules.

    “Chemoreception and light reception arewith the main exception of the Trp channels and cryptochrome moleculesmediated by members of the G-protein-coupled receptor superfamilies in vertebrates and invertebrates (Ache and Young, 2005).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Ache and Young, 2005

      Not checked in the free run.

  • Classified as probably not a substantial claim. The quote only partly states this claim.

    Study design and conductown data

    Only proteins containing full, non-overlapping rhodopsin-type GPCR domains with an e-value cut-off of 0.001 were included in the final list of 979 peptides.

    “Candidates were compared against the full PFAM database (Finn et al., 2006), and only proteins containing full, non-overlapping domains (e-value cut-off: 0.001) were included in the final list of 979 peptides.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Finn et al., 2006

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Several distinct Opsin families were present at the base of Bilateria: rhabdomeric and ciliary Opsins, as well as RGR Opsins, with only one clear protostome member so far.

    “In contrast to the uncertain evolutionary origin of the olfactory receptors, it is clear that several distinct Opsin families were present at the base of Bilateria, namely the rhabdomeric and the ciliary Opsins (Arendt et al., 2004), as well as the RGR Opsins, with only one clear protostome member so far (Hara-Nishimura et al., 1990;Terakita, 2005).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Arendt et al., 2004

      Not checked in the free run.

    • cites Hara-Nishimura et al., 1990

      Not checked in the free run.

    • cites Terakita, 2005

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Photosensitivity is a common phenomenon in sea urchins.

    “These reports suggest that photosensitivity is a common phenomenon in sea urchins.”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Millott, 1975

      Not checked in the free run.

    • cites Smith, 1965

      Not checked in the free run.

    • cites Barnes and Cook, 2001

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    These data suggest that the four main surreal-GPCR groups have arisen independently and from different members of the ancestral bilaterian GPCR repertoire.

    “These data suggest that the four main surreal-GPCR groups have arisen independently and from different members of the ancestral bilaterian GPCR repertoire.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Cryptochromes originate from photolyases and typically respond to UV light.

    “Cryptochromes are molecules derived from photolyases, and usually light sensitive in the UV range (Gehring and Rosbash, 2003).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Gehring and Rosbash, 2003 source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    The ancestral molecules from which the different surreal-GPCRs arose are difficult to determine, resulting in distinct GPCR variants with little similarity to any existing classification scheme.

    “However, similar to the olfactory receptors of vertebrates, the ancestral molecules from which the different surreal-GPCRs arose are difficult to determine, resulting in distinct GPCR variants with little similarity to any existing classification scheme.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Interpretationreasoning

    The abundance of rhodopsin-type GPCRs in a given genome might be a good indicator of the overall versatility of cell types and functions within a species.

    “Due to this versatility, the abundance of rhodopsin-type GPCRs in a given genome might be a good indicator of the overall versatility of cell types and functions within a species.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Premisecitation

    The rhodopsin-type GPCR superfamily is a highly versatile substrate for evolution, adapted to functions as diverse as light reception, cell-cell signaling, and chemoreception.

    “The rhodopsin-type GPCR superfamily appears to be a highly versatile substrate for evolution, as it has been adapted to functions as diverse as light reception, cell-cell signaling and chemoreception (Bockaert and Pin, 1999).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Bockaert and Pin, 1999

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning

    The absolute number of rhodopsin-type GPCRs in the sea urchin genome reported in this study (979) might still change upon completion of the genome.

    “The absolute number of rhodopsin-type GPCRs in the sea urchin genome reported in this study (979) might still change upon completion of the genome”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Tube feet and different pedicellariae classes have long been proposed or, in the case of globiferous pedicellariae, demonstrated to contain chemosensory neurons.

    “that have long been proposed or, in the case of globiferous pedicellariae, even demonstrated to contain chemosensory neurons.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Campbell, 1976

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Retinochrome (RGR Opsins) is a group of Opsins found in vertebrates and squid, and possibly (with low branch point support) in the tunicate Ciona intestinalis.

    “a group of Opsins that has been found in vertebrates and squid, and possibly (with low branch point support) in the tunicate Ciona intestinalis (Hara-Nishimura et al., 1990;Nakashima et al., 2003;Terakita, 2005).”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites Hara-Nishimura et al., 1990

      Not checked in the free run.

    • cites Nakashima et al., 2003

      Not checked in the free run.

    • cites Terakita, 2005

      Not checked in the free run.

  • May combine two claims.

    Interpretationcitation

    The limited expression in the transcriptome map probably reflects that these genes are expressed only at late larval stages, whereas the tiling expression data were generated from four embryonic stages (egg to prism, 65 hpf).

    “This probably reflects the fact that these genes are expressed only at late larval stages, whereas the tiling expression data were generated based on poly-A RNA purified from four embryonic stages (from egg to prism, 65 hpf) (Samanta et al., 2006).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Samanta et al., 2006

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    In mouse olfactory GPCRs, transmembrane domains 3-5 contain most of the variable residues, with TM IV and TMV being most divergent.

    “In mouse, the transmembrane domains 3-5 contain most of the variable residues, with TM IV and TMV being most divergent (Buck and Axel, 1991;Pilpel and Lancet, 1999)”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Buck and Axel, 1991

      Not checked in the free run.

    • cites Pilpel and Lancet, 1999

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    The finding of no retinochrome in sea urchin, together with the observed loss of Go-type Opsins in all sequenced vertebrates, insects, and nematodes, emphasizes that at least the molecular set-up of the ancient bilaterian light sensory system was highly complex and that gene loss has frequently occurred during the evolution of these systems in Bilateria.

    “This finding, together with the observed loss of G o -type Opsins in all sequenced vertebrates, insects and nematodes emphasizes that at least the molecular set-up of the ancient bilaterian light sensory system was highly complex and that gene loss has frequently occurred during the evolution of the these systems in Bilateria.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Globiferous pedicellariae have been described to bear chemoreceptor cells on their sensory hillock.

    “given the fact that these pedicellariae have been described to bear chemoreceptor cells on their sensory hillock (Campbell, 1976).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Campbell, 1976

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Vertebrate olfactory receptors are characteristically single-exon genes that locate to large genomic clusters.

    “Notably, the vertebrate olfactory receptors are also characteristically single-exon genes that locate to large genomic clusters (reviewed in Dryer, 2000).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Dryer, 2000

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S2 (checkable).

    Interpretationreasoning

    Targeting specific sensory cells through their molecular repertoire should aid dissection of sensory output circuits in the animal.

    “the possibility to address specific sensory cells by virtue of their molecular repertoire will help to dissect sensoryoutput circuits in the animal.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    Despite apparently lacking central sensory organs, the sea urchin has a diverse set of sensory molecules and structures.

    “In summary, it appears as if the sea urchin, despite its apparent lack of central sensory organs, possesses a rich repertoire of sensory molecules and sensory structures”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The sea urchin lacks central sensory organs.
49 of 49

  • The paper relies on this without support.

    The molecular basis of chemoreception and photosensation in sea urchins is not yet understood.

    “Despite the rich amount of stimuli-dependent behaviors that have been described, and some basic knowledge of putative sensory structures in sea urchins that has been gathered, neither chemo-nor photosensation of the animal are understood at the molecular level.”

  • The paper relies on this without support.

    The sea urchin pluteus larva is a primary ciliated larva.

    “Because the sea urchin pluteus larva represents such a primary ciliated larva”

  • The paper relies on this without support.

    The sea urchin pluteus larva has not been described to possess eyes.

    “but has not been described to possess eyes”

  • The paper relies on this without support.

    Dedicated complex photosensory organs have not yet been described in the sea urchin.

    “As mentioned, dedicated complex photosensory organs have not yet been described in the sea urchin.”

  • The paper relies on this without support.

    Specific rapid and large expansions of transmembrane domain genes are common to molecules that animals use to detect a large variety of divergent molecules, as in the immune system and chemoreception.

    “Specific rapid and large expansions of transmembrane domain genes are common to molecules that are utilized by the animal to detect a large variety of divergent molecules, as it is the case in the immune system and in chemoreception.”

  • The paper relies on this without support.

    The sea urchin lacks central sensory organs.

    “despite its apparent lack of central sensory organs”

  • The paper relies on this without support.

    Understanding of the molecular machinery behind sea urchin sensory responses remains very limited.

    “but our understanding of the underlying molecular machineries is still very limited.”
7 of 7

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • These GPCRs originated by lineage-specific expansion, and many are single-exon genes forming clusters in the genome, reminiscent of lineage-specific putative chemosensory GPCRs in other animal groups.

    “These GPCRs originated by lineage-specific expansion, and many are single-exon genes forming clusters in the genome [1], reminiscent of lineage-specific putative chemosensory GPCRs in other animal groups [43].”

    From Origin and early evolution of neural circuits for the control of ciliary locomotion (2011) · cites this paper as [43]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • QPCR results are assigned to a sequence-variability figure

    Minor

    The methods identify Fig. 4A as showing QPCR results, but the Fig. 4 caption identifies panel A as an analysis of amino-acid variability. The QPCR expression results are identified in the Fig. 5 caption.

  • Claim of G o-Opsin absence conflicts with Amphioxus sequences

    Minor

    The discussion says G o-Opsins appear absent from other deuterostome groups, but the results place two Amphioxus opsins in the G o-Opsin group. Amphioxus is a cephalochordate and therefore another deuterostome.

2 of 2

Cites

Flagged first, then by citations

4 of the 87 references couldn’t be matched to a known paper.

Research works printed but not linked: 3

  1. Döderlein, 1898, Ueber “Krystallkörper” bei Seesternen, Denkschr. Med. Nat. Ges. Jena, 8, 491
  2. 2006, The sequence of the sea urchin genome, Science
  3. Smith, 1965, Echinodermata, vol. 2, 1519

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Authors
Raible, F., Tessmar-Raible, K., Arboleda, E., Kaller, T., Bork, P., Arendt, D., & Arnone, M. I.
Affiliations
  • European Molecular Biology Laboratory (DE)
  • Stazione Zoologica Anton Dohrn (IT)
Corresponding author
  • Raible, Florian
  • Arnone, Maria I.
ORCID
Venue
Developmental Biology
Publisher
Elsevier BV
Published
2006-12
Volume
300
Issue
1
Pages
461-475
ISSN
0012-1606 (ISSN-L)
DOI
10.1016/j.ydbio.2006.08.070
OpenAlex
W2015311975
Semantic Scholar
43763491a203173b16bacd905876f685c3259875
Cited by
170
References
87
Citations by year
2026: 2 · 2025: 3 · 2024: 4 · 2023: 10 · 2022: 5 · 2021: 12 · 2020: 8 · 2019: 6 · 2018: 8 · 2017: 9 · 2016: 8 · 2015: 6 · 2014: 11 · 2013: 8 · 2012: 4
FWCI
6.79
Type
journal article
Language
en
Open access
Licence
Locations
  • Developmental Biology (publishedVersion)
  • PubMed (publishedVersion)
Funders
Deutsche Forschungsgemeinschaft
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
  • Life Sciences › Neuroscience › Sensory Systems › Olfactory and Sensory Function Studies
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Marine Invertebrate Physiology and Ecology
Keywords
sea urchin genome, opsin, genome clustering, olfactory receptors, chemosensory receptors, pedicellariae, tube feet, sensory neurons, echinoderm evolution, gene duplication
MeSH terms
Amino Acid Sequence, Animals, Models, Molecular, Molecular Sequence Data, Protein Conformation, Receptors, Cell Surface, RNA, Sea Urchins, Polymerase Chain Reaction, Consensus Sequence, Sequence Alignment, Genome, Rod Opsins, Sequence Homology, Amino Acid, In Situ Hybridization, Receptors, G-Protein-Coupled

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