The Origins of Novel Protein Interactions during Animal Opsin Evolution
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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/944186"], "description"=>"<p>Previously described G protein binding states, together with amino acid sequences of the 4<sup>th</sup> cytoplasmic loop regions from our opsin dataset, were used to test the hypothesis that the two character sets co-vary across our opsin phylogeny. Co-variation was assessed using mutual information content (MIC). Shown here is a representation of these results. Predictive P-values (Bottom axis) based on MIC for co-variation between each residue in the 4<sup>th</sup> cytoplasimic loop and their respective G protein interactions (Right axis) are shown. These analyses were conducted using Bayesian mutational simulation mapping in SIMMAP <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001054#pone.0001054-Bollback1\" target=\"_blank\">[64]</a>. We also tested possibility that these residues had evolved under a selective regime using the criterion of site specific rate heterogeneity as implemented in DIVERGE2 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001054#pone.0001054-Zheng1\" target=\"_blank\">[29]</a>. The two highest scoring residues from co-variation analyses (310 and 312) also retain the signature of selection (asterisk). See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001054#pone.0001054.s001\" target=\"_blank\">table S1</a> for citations. <i>P</i> = predictive P-value, <i>M</i> = the M statistic given by MIC.</p>", "links"=>[], "tags"=>["co-variation"], "article_id"=>614587, "categories"=>["Evolutionary Biology", "Biochemistry"], "users"=>["David C. Plachetzki", "Bernard M. Degnan", "Todd H. Oakley"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001054.g007", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_co_variation_analyses_and_tests_for_selection_/614587", "title"=>"Summary of co-variation analyses and tests for selection.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-10-17 01:16:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/943661"], "description"=>"<p>Circles at nodes indicate Bayesian posterior probabilities (White = 1.0, Red>0.90, Blue>0.80, Green>0.70, Yellow>0.60, Black>0.50). cil = ciliary, rh = rhabdomeric.</p>", "links"=>[], "tags"=>["metazoan-wide", "phylogeny", "cnidarian", "genes", "branches", "proportional", "substitutions"], "article_id"=>614051, "categories"=>["Evolutionary Biology", "Biochemistry"], "users"=>["David C. Plachetzki", "Bernard M. Degnan", "Todd H. Oakley"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001054.g002", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Unrooted_metazoan_wide_phylogeny_of_opsins_new_cnidarian_genes_in_bold_branches_proportional_to_substitutions_per_site_/614051", "title"=>"Unrooted metazoan-wide phylogeny of opsins, new cnidarian genes in bold, branches proportional to substitutions per site.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-10-17 01:07:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/464561", "https://ndownloader.figshare.com/files/464575", "https://ndownloader.figshare.com/files/464592"], "description"=>"<div><h3>Background</h3><p>Biologists are gaining an increased understanding of the genetic bases of phenotypic change during evolution. Nevertheless, the origins of phenotypes mediated by novel protein-protein interactions remain largely undocumented.</p><h3>Methodology/Principle Findings</h3><p>Here we analyze the evolution of opsin visual pigment proteins from the genomes of early branching animals, including a new class of opsins from Cnidaria. We combine these data with existing knowledge of the molecular basis of opsin function in a rigorous phylogenetic framework. We identify adaptive amino acid substitutions in duplicated opsin genes that correlate with a diversification of physiological pathways mediated by different protein-protein interactions.</p><h3>Conclusions/Significance</h3><p>This study documents how gene duplication events early in the history of animals followed by adaptive structural mutations increased organismal complexity by adding novel protein-protein interactions that underlie different physiological pathways. These pathways are central to vision and other photo-reactive phenotypes in most extant animals. Similar evolutionary processes may have been at work in generating other metazoan sensory systems and other physiological processes mediated by signal transduction.</p></div>", "links"=>[], "tags"=>["origins", "interactions", "opsin"], "article_id"=>151569, "categories"=>["Evolutionary Biology", "Biochemistry"], "users"=>["David C. Plachetzki", "Bernard M. Degnan", "Todd H. Oakley"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0001054.s001", "https://dx.doi.org/10.1371/journal.pone.0001054.s002", "https://dx.doi.org/10.1371/journal.pone.0001054.s003"], "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Origins_of_Novel_Protein_Interactions_during_Animal_Opsin_Evolution/151569", "title"=>"The Origins of Novel Protein Interactions during Animal Opsin Evolution", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2007-10-17 00:26:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/943790"], "description"=>"<p>Illustrated is each possible unrooted and rooted hypothesis, assuming monophyly of four major opsin clades. Trees in (A) 1–3 correspond to possible unrooted topologyies and those in (B) 1–15 represent all possible rooted trees, see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001054#pone-0001054-t001\" target=\"_blank\">Table 1</a>. Orange X indicates that tree had significantly lower likelihood in opsin-only dataset. Red X indicates tree had significantly lower likelihood in opsin+outgroup dataset. Yellow X indicates that tree implies additional gene duplication/loss events compared to minimum (tree 1 is minimum with 2 duplications 0 losses implied). Grey X indicates tree with cnidops as earliest branching opsin group–a result inferred in parametric bootstrap analyses, which incorrectly grouped cnidops+outgroup opsins because of long branch-attraction (see supplementary <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001054#s4\" target=\"_blank\">methods</a>). Cil = ciliary; Rh = rhabdomeric; RG = Go/RGR.</p>", "links"=>[], "tags"=>["opsin"], "article_id"=>614193, "categories"=>["Evolutionary Biology", "Biochemistry"], "users"=>["David C. Plachetzki", "Bernard M. Degnan", "Todd H. Oakley"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001054.g003", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_analyses_to_determine_and_root_opsin_phylogeny_/614193", "title"=>"Summary of analyses to determine and root opsin phylogeny.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-10-17 01:09:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/943900"], "description"=>"<p>These are statistically indistinguishable when considering only the likelihood of observed amino acid sequences. (A) Our preferred phylogenetic hypothesis where ciliary opsins are an outgroup to other opsin clades and cnidops is the sister to the rhabdomeric+G<sub>o</sub> clade. This hypothesis minimizes the number of gene duplication and loss events required to explain the evolutionary history of metazoan opsins and is consistent with morphological data <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001054#pone.0001054-Eakin1\" target=\"_blank\">[33]</a>. (B and C) Phylogenetic hypotheses in which cnidops represents the outgroup to other opsins. Given our finding of a ciliary opsin in <i>Nematostella</i>, these hypotheses require the additional loss of ciliary opsin in the <i>Hydra</i> lineage and an additional loss of cnidops in bilaterian animals.</p>", "links"=>[], "tags"=>["hypotheses", "metazoan", "opsin"], "article_id"=>614301, "categories"=>["Evolutionary Biology", "Biochemistry"], "users"=>["David C. Plachetzki", "Bernard M. Degnan", "Todd H. Oakley"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001054.g004", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Three_hypotheses_for_metazoan_opsin_relationships_/614301", "title"=>"Three hypotheses for metazoan opsin relationships.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-10-17 01:11:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/944086"], "description"=>"<p>For each class of opsin, the P value of the reconstructed ancestral G α interactions is represented in pie graphs. Ancestral G protein interactions in phototransduction cascades mediated by ciliary, rhabdomeric and G<sub>o</sub> opsins can be significantly resolved (P>0.95) but the ancestral states of the rhabdomeric+G<sub>o</sub>, and cnidops clades are equivocal. ML state reconstructions shown for each node as colored branches. Red, G<sub>i/t</sub>; Blue, G<sub>q</sub>; Green, G<sub>o</sub>; Black, no G protein interaction (as is the case for RGR/Retinochrome opsins); Grey, equivocal reconstruction from ML. Reconstructed ancestral amino acid motifs of the 4th cytoplasmic loop region of opsin are shown along branches in logos. Maximum vertical height scales to P  = 1.0. We obtained clear reconstructed states for most of the residues in a conserved tripeptide motif (residues 310, 311 and 312, horizontal bar) for the ciliary, rhabdomeric and G<sub>o</sub> /RGR nodes. For the most part, the remainder of the residues in can be unequivocally reconstructed to the level of Dayhoff classes. B = HRK, X = LIVM, J = GATSP, Z = DENQ.</p>", "links"=>[], "tags"=>["reconstruction", "protein-binding", "interactions", "metazoan", "opsin-mediated", "phototransduction", "cascade", "simulated", "mutational"], "article_id"=>614475, "categories"=>["Evolutionary Biology", "Biochemistry"], "users"=>["David C. Plachetzki", "Bernard M. Degnan", "Todd H. Oakley"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001054.g006", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ancestral_state_reconstruction_of_G_protein_binding_interactions_for_each_metazoan_opsin_mediated_phototransduction_cascade_obtained_by_simulated_mutational_mapping_64_see_methods_/614475", "title"=>"Ancestral state reconstruction of G protein-binding interactions for each metazoan opsin-mediated phototransduction cascade obtained by simulated mutational mapping [64] (see methods).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-10-17 01:14:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/943972"], "description"=>"<p>Black circles indicate gene duplication events. Tan ovals indicate the opsin complement at key nodes in metazoan phylogeny. By this hypothesis, both ciliary and cnidops opsins were present in the eumetazoan ancestor of Cnidaria+Bilateria while rhabdomeric and G<sub>o</sub> opsins evolved by gene duplication prior to the evolution of bilaterian animals, but not before.</p>", "links"=>[], "tags"=>["preferred", "opsin", "phylogeny", "reconciled", "metazoan"], "article_id"=>614364, "categories"=>["Evolutionary Biology", "Biochemistry"], "users"=>["David C. Plachetzki", "Bernard M. Degnan", "Todd H. Oakley"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001054.g005", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Our_preferred_hypothesis_for_opsin_phylogeny_figure_4A_reconciled_to_a_conservative_view_of_metazoan_phylogeny_/614364", "title"=>"Our preferred hypothesis for opsin phylogeny (figure 4A) reconciled to a conservative view of metazoan phylogeny.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-10-17 01:12:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/943560"], "description"=>"<p>(A) Sequence alignment of 4<sup>th</sup> cytoplasmic loop region of animal opsins used in this study indicating the Lys 296 chromophore binding site (arrowhead) and the G protein-binding tripeptide (asterisks). (B) In situ hybridization with Hm2 cnidops probe. Asterisk denotes the hypostome. Opsin is expressed most strongly in a ring of sensory neurons that surround the mouth. Inset, oral view.</p>", "links"=>[], "tags"=>["motifs", "cnidarian", "opsin"], "article_id"=>613957, "categories"=>["Evolutionary Biology", "Biochemistry"], "users"=>["David C. Plachetzki", "Bernard M. Degnan", "Todd H. Oakley"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001054.g001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_motifs_and_expression_of_cnidarian_opsin_in_the_nerve_net_of_Hydra_magnipallata_/613957", "title"=>"Sequence motifs and expression of cnidarian opsin in the nerve net of <i>Hydra magnipallata</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-10-17 01:05:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/944267"], "description"=>"<p>Likelihood comparison tests for trees in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001054#pone-0001054-g003\" target=\"_blank\">figure 3</a>. Results were calculated under the WAG+I+G model. <i>L,</i> likelihood; AU, Approximately Unbiased Test <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001054#pone.0001054-Shimodaira2\" target=\"_blank\">[66]</a>; KH, Kishino-Hasegawa test <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001054#pone.0001054-Kishino1\" target=\"_blank\">[67]</a>; SH, Shimodaria-Hasegawa test <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001054#pone.0001054-Shimodaira1\" target=\"_blank\">[55]</a>; pRELL, resampled log-likelihood bootstrap percentage <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001054#pone.0001054-Yang2\" target=\"_blank\">[68]</a>.</p>1<p>Requires Cnidarians Lost RGR/Go Clade</p>2<p>Requires Cnidarians lost Rhabdomeric</p>3<p>Requires Bilaterians lost cnidops</p>", "links"=>[], "tags"=>["comparisons", "hypotheses", "opsin"], "article_id"=>614659, "categories"=>["Evolutionary Biology", "Biochemistry"], "users"=>["David C. Plachetzki", "Bernard M. Degnan", "Todd H. Oakley"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001054.t001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Likelihood_comparisons_for_alternative_hypotheses_of_opsin_evolution_/614659", "title"=>"Likelihood comparisons for alternative hypotheses of opsin evolution", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2007-10-17 01:17:39"}

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Relative Metric

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