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de Wiljes OO, van Elburg RAJ, Biehl M, Keijzer FA. Modeling spontaneous activity across an excitable epithelium: Support for a coordination scenario of early neural evolution. Front Comput Neurosci 2015; 9:110. [PMID: 26441620 PMCID: PMC4569742 DOI: 10.3389/fncom.2015.00110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 08/24/2015] [Indexed: 11/24/2022] Open
Abstract
Internal coordination models hold that early nervous systems evolved in the first place to coordinate internal activity at a multicellular level, most notably the use of multicellular contractility as an effector for motility. A recent example of such a model, the skin brain thesis, suggests that excitable epithelia using chemical signaling are a potential candidate as a nervous system precursor. We developed a computational model and a measure for whole body coordination to investigate the coordinative properties of such excitable epithelia. Using this measure we show that excitable epithelia can spontaneously exhibit body-scale patterns of activation. Relevant factors determining the extent of patterning are the noise level for exocytosis, relative body dimensions, and body size. In smaller bodies whole-body coordination emerges from cellular excitability and bidirectional excitatory transmission alone. Our results show that basic internal coordination as proposed by the skin brain thesis could have arisen in this potential nervous system precursor, supporting that this configuration may have played a role as a proto-neural system and requires further investigation.
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Affiliation(s)
- Oltman O. de Wiljes
- Department of Theoretical Philosophy, Faculty of Philosophy, University of GroningenGroningen, Netherlands
- Faculty of Mathematics and Natural Sciences, Institute of Artificial Intelligence, University of GroningenGroningen, Netherlands
| | - Ronald A. J. van Elburg
- Faculty of Mathematics and Natural Sciences, Institute of Artificial Intelligence, University of GroningenGroningen, Netherlands
| | - Michael Biehl
- Faculty of Mathematics and Natural Sciences, Johann Bernoulli Institute for Mathematics and Computer Science, University of GroningenGroningen, Netherlands
| | - Fred A. Keijzer
- Department of Theoretical Philosophy, Faculty of Philosophy, University of GroningenGroningen, Netherlands
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Fortunato SAV, Adamski M, Adamska M. Comparative analyses of developmental transcription factor repertoires in sponges reveal unexpected complexity of the earliest animals. Mar Genomics 2015; 24 Pt 2:121-9. [PMID: 26253310 DOI: 10.1016/j.margen.2015.07.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 07/27/2015] [Accepted: 07/27/2015] [Indexed: 12/18/2022]
Abstract
Developmental transcription factors (DTFs) control development of animals by affecting expression of target genes, some of which are transcription factors themselves. In bilaterians and cnidarians, conserved DTFs are involved in homologous processes such as gastrulation or specification of neurons. The genome of Amphimedon queenslandica, the first sponge to be sequenced, revealed that only a fraction of these conserved DTF families are present in demosponges. This finding was in line with the view that morphological complexity in the animal lineage correlates with developmental toolkit complexity. However, as the phylum Porifera is very diverse, Amphimedon's genome may not be representative of all sponges. The recently sequenced genomes of calcareous sponges Sycon ciliatum and Leucosolenia complicata allowed investigations of DTFs in a sponge lineage evolutionarily distant from demosponges. Surprisingly, the phylogenetic analyses of identified DTFs revealed striking differences between the calcareous sponges and Amphimedon. As these differences appear to be a result of independent gene loss events in the two sponge lineages, the last common ancestor of sponges had to possess a much more diverse repertoire of DTFs than extant sponges. Developmental expression of sponge homologs of genes involved in specification of the Bilaterian endomesoderm and the neurosensory cells suggests that roles of many DTFs date back to the last common ancestor of all animals. Strikingly, even DTFs displaying apparent pan-metazoan conservation of sequence and function are not immune to being lost from individual species genomes. The quest for a comprehensive picture of the developmental toolkit in the last common metazoan ancestor is thus greatly benefitting from the increasing accessibility of sequencing, allowing comparisons of multiple genomes within each phylum.
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Affiliation(s)
- Sofia A V Fortunato
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway; Department of Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway
| | - Marcin Adamski
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway
| | - Maja Adamska
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway.
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Role of Lynx1 and related Ly6 proteins as modulators of cholinergic signaling in normal and neoplastic bronchial epithelium. Int Immunopharmacol 2015; 29:93-8. [PMID: 26025503 DOI: 10.1016/j.intimp.2015.05.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 05/09/2015] [Accepted: 05/13/2015] [Indexed: 01/05/2023]
Abstract
The ly-6 proteins are a large family of proteins that resemble the snake three finger alpha toxins such as α-bungarotoxin and are defined by their multiple cysteine residues. Multiple members of the ly-6 protein family can modulate nicotinic signaling including lynx1, lynx2, slurp-1, slurp-2 and prostate stem cell antigen (PSCA). Consistent with the expression of multiple nicotinic receptors in bronchial epithelium, multiple members of the nicotinic-modulatory ly-6 proteins are expressed in lung including lynx1 and lynx2. We studied the role of lynx1 as an exemplar of the role of ly-6 proteins in lung. Our data demonstrates that lynx1 acts as a negative modulator of nicotinic signaling in normal and neoplastic lung. In normal lung lynx1 serves to limit the ability of chronic nicotine exposure to increase levels of nicotinic receptors and also serves to limit the ability of nicotine to upregulate levels of GABAA receptors in lung. In turn this allows lynx1 to limit the ability of nicotine to upregulate levels of mucin which is mediated by GABAergic signaling. This suggests that lynx1-mimetics may have potential for treatment of asthma and COPD. In that most lung cancer cells also express nicotinic receptor and lynx1 we examined the role of lynx-1 in lung cancer. Lynx1 levels are decreased in lung cancers compared to adjacent normal lung. Knockdown of lynx1 by siRNAs increased growth of lung cancer cells while expression of lynx1 in lung cancer cell decreased cell proliferation. This suggests that lynx1 is an endogenous regulator of lung cancer growth. Given that multiple small molecule negative and positive allosteric modulators of nicotinic receptors have already been developed, this suggests that lynx1 is a highly druggable target both for development of drugs that may limit lung cancer growth as well as for drugs that may be effective for asthma or COPD treatment.
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54
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Tang QY, Larry T, Hendra K, Yamamoto E, Bell J, Cui M, Logothetis DE, Boland LM. Mutations in Nature Conferred a High Affinity Phosphatidylinositol 4,5-Bisphosphate-binding Site in Vertebrate Inwardly Rectifying Potassium Channels. J Biol Chem 2015; 290:16517-29. [PMID: 25957411 DOI: 10.1074/jbc.m115.640409] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Indexed: 11/06/2022] Open
Abstract
All vertebrate inwardly rectifying potassium (Kir) channels are activated by phosphatidylinositol 4,5-bisphosphate (PIP2) (Logothetis, D. E., Petrou, V. I., Zhang, M., Mahajan, R., Meng, X. Y., Adney, S. K., Cui, M., and Baki, L. (2015) Annu. Rev. Physiol. 77, 81-104; Fürst, O., Mondou, B., and D'Avanzo, N. (2014) Front. Physiol. 4, 404-404). Structural components of a PIP2-binding site are conserved in vertebrate Kir channels but not in distantly related animals such as sponges and sea anemones. To expand our understanding of the structure-function relationships of PIP2 regulation of Kir channels, we studied AqKir, which was cloned from the marine sponge Amphimedon queenslandica, an animal that represents the phylogenetically oldest metazoans. A requirement for PIP2 in the maintenance of AqKir activity was examined in intact oocytes by activation of a co-expressed voltage-sensing phosphatase, application of wortmannin (at micromolar concentrations), and activation of a co-expressed muscarinic acetylcholine receptor. All three mechanisms to reduce the availability of PIP2 resulted in inhibition of AqKir current. However, time-dependent rundown of AqKir currents in inside-out patches could not be re-activated by direct application to the inside membrane surface of water-soluble dioctanoyl PIP2, and the current was incompletely re-activated by the more hydrophobic arachidonyl stearyl PIP2. When we introduced mutations to AqKir to restore two positive charges within the vertebrate PIP2-binding site, both forms of PIP2 strongly re-activated the mutant sponge channels in inside-out patches. Molecular dynamics simulations validate the additional hydrogen bonding potential of the sponge channel mutants. Thus, nature's mutations conferred a high affinity activation of vertebrate Kir channels by PIP2, and this is a more recent evolutionary development than the structures that explain ion channel selectivity and inward rectification.
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Affiliation(s)
- Qiong-Yao Tang
- From the Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298, the Jiangsu Province Key Laboratory of Anesthesiology and Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, XuZhou Medical College, Xuzhou, 221004 Jiangsu Province, China
| | - Trevor Larry
- the Department of Biology, University of Richmond, Richmond, Virginia 23173
| | - Kalen Hendra
- the Department of Biology, University of Richmond, Richmond, Virginia 23173
| | - Erica Yamamoto
- the Department of Biology, University of Richmond, Richmond, Virginia 23173
| | - Jessica Bell
- the Department of Chemistry and Biochemistry, University of San Diego, San Diego, California 92110, and
| | - Meng Cui
- From the Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298
| | - Diomedes E Logothetis
- From the Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298
| | - Linda M Boland
- the Department of Biology, University of Richmond, Richmond, Virginia 23173
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Nam HJ, Kim I, Bowie JU, Kim S. Metazoans evolved by taking domains from soluble proteins to expand intercellular communication network. Sci Rep 2015; 5:9576. [PMID: 25923201 PMCID: PMC4894438 DOI: 10.1038/srep09576] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 03/09/2015] [Indexed: 12/15/2022] Open
Abstract
A central question in animal evolution is how multicellular animals evolved from unicellular ancestors. We hypothesize that membrane proteins must be key players in the development of multicellularity because they are well positioned to form the cell-cell contacts and to provide the intercellular communication required for the creation of complex organisms. Here we find that a major mechanism for the necessary increase in membrane protein complexity in the transition from non-metazoan to metazoan life was the new incorporation of domains from soluble proteins. The membrane proteins that have incorporated soluble domains in metazoans are enriched in many of the functions unique to multicellular organisms such as cell-cell adhesion, signaling, immune defense and developmental processes. They also show enhanced protein-protein interaction (PPI) network complexity and centrality, suggesting an important role in the cellular diversification found in complex organisms. Our results expose an evolutionary mechanism that contributed to the development of higher life forms.
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Affiliation(s)
- Hyun-Jun Nam
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, 790-784, Korea
| | - Inhae Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, Korea
| | - James U Bowie
- Department of Chemistry and Biochemistry, UCLA-DOE Institute of Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095-1570, United States
| | - Sanguk Kim
- 1] School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, 790-784, Korea [2] Department of Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, Korea
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56
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Nakanishi N, Stoupin D, Degnan SM, Degnan BM. Sensory Flask Cells in Sponge Larvae Regulate Metamorphosis via Calcium Signaling. Integr Comp Biol 2015; 55:1018-27. [PMID: 25898842 DOI: 10.1093/icb/icv014] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Porifera (sponges) is one of the earliest phyletic lineages to branch off the metazoan tree. Although the body-plan of sponges is among the simplest in the animal kingdom and sponges lack nervous systems that communicate environmental signals to other cells, their larvae have sensory systems that generate coordinated responses to environmental cues. In eumetazoans (Cnidaria and Bilateria), the nervous systems of larvae often regulate metamorphosis through Ca(2+)-dependent signal transduction. In sponges, neither the identity of the receptor system that detects an inductive environmental cue (hereafter "metamorphic cues") nor the signaling system that mediates settlement and metamorphosis are known. Using a combination of behavioral assays and surgical manipulations, we show here that specialized epithelial cells-referred to as flask cells-enriched in the anterior third of the Amphimedon queenslandica larva are most likely to be the sensory cells that detect the metamorphic cues. Surgical removal of the region enriched in flask cells in a larva inhibits the initiation of metamorphosis. The flask cell has an apical sensory apparatus with a cilium surrounded by an apical F-actin-rich protrusion, and numerous vesicles, hallmarks of eumetazoan sensory-neurosecretory cells. We demonstrate that these flask cells respond to metamorphic cues by elevating intracellular Ca(2+) levels, and that this elevation is necessary for the initiation of metamorphosis. Taken together, these analyses suggest that sponge larvae have sensory-secretory epithelial cells capable of converting exogenous cues into internal signals via Ca(2+)-mediated signaling, which is necessary for the initiation of metamorphosis. Similarities in the morphology, physiology, and function of the sensory flask cells in sponge larvae with the sensory/neurosecretory cells in eumetazoan larvae suggest this sensory system predates the divergence of Porifera and Eumetazoa.
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Affiliation(s)
- Nagayasu Nakanishi
- School of Biological Sciences, University of Queensland, Brisbane QLD 4072, Australia
| | - Daniel Stoupin
- School of Biological Sciences, University of Queensland, Brisbane QLD 4072, Australia
| | - Sandie M Degnan
- School of Biological Sciences, University of Queensland, Brisbane QLD 4072, Australia
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane QLD 4072, Australia
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57
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Abstract
Recent sequencing of ctenophore genomes opens a new era in the study of this unique and phylogenetically distant group. The presence of neurodevelopmental genes, pre- and postsynaptic modules, and transmitter molecules is consistent with a single origin of neurons.
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Affiliation(s)
- Heather Marlow
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69012 Heidelberg, Germany.
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69012 Heidelberg, Germany.
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58
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Keijzer F. Moving and sensing without input and output: early nervous systems and the origins of the animal sensorimotor organization. BIOLOGY & PHILOSOPHY 2015; 30:311-331. [PMID: 26005236 PMCID: PMC4438119 DOI: 10.1007/s10539-015-9483-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 02/18/2015] [Indexed: 05/28/2023]
Abstract
It remains a standing problem how and why the first nervous systems evolved. Molecular and genomic information is now rapidly accumulating but the macroscopic organization and functioning of early nervous systems remains unclear. To explore potential evolutionary options, a coordination centered view is discussed that diverges from a standard input-output view on early nervous systems. The scenario involved, the skin brain thesis (SBT), stresses the need to coordinate muscle-based motility at a very early stage. This paper addresses how this scenario with its focus on coordination also deals with sensory aspects. It will be argued that the neural structure required to coordinate extensive sheets of contractile tissue for motility provides the starting point for a new multicellular organized form of sensing. Moving a body by muscle contraction provides the basis for a multicellular organization that is sensitive to external surface structure at the scale of the animal body. Instead of thinking about early nervous systems as being connected to the environment merely through input and output, the implication developed here is that early nervous systems provide the foundation for a highly specific animal sensorimotor organization in which neural activity directly reflects bodily and environmental spatiotemporal structure. While the SBT diverges from the input-output view, it is closely linked to and supported by ongoing work on embodied approaches to intelligence to which it adds a new interpretation of animal embodiment and sensorimotor organization.
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Affiliation(s)
- Fred Keijzer
- Department of Theoretical Philosophy, University of Groningen, Oude Boteringestraat 52, 9712 GL Groningen, The Netherlands
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59
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Abstract
The foundation of the diverse metazoan nervous systems is laid by embryonic patterning mechanisms, involving the generation and movement of neural progenitors and their progeny. Here we divide early neurogenesis into discrete elements, including origin, pattern, proliferation, and movement of neuronal progenitors, which are controlled by conserved gene cassettes. We review these neurogenetic mechanisms in representatives of the different metazoan clades, with the goal to build a conceptual framework in which one can ask specific questions, such as which of these mechanisms potentially formed part of the developmental "toolkit" of the bilaterian ancestor and which evolved later.
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Affiliation(s)
- Volker Hartenstein
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Angelika Stollewerk
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
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60
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Ecological constraints on the origin of neurones. J Math Biol 2015; 71:1299-324. [DOI: 10.1007/s00285-015-0862-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 01/14/2015] [Indexed: 12/20/2022]
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61
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Friedman LG, Benson DL, Huntley GW. Cadherin-based transsynaptic networks in establishing and modifying neural connectivity. Curr Top Dev Biol 2015; 112:415-65. [PMID: 25733148 DOI: 10.1016/bs.ctdb.2014.11.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
It is tacitly understood that cell adhesion molecules (CAMs) are critically important for the development of cells, circuits, and synapses in the brain. What is less clear is what CAMs continue to contribute to brain structure and function after the early period of development. Here, we focus on the cadherin family of CAMs to first briefly recap their multidimensional roles in neural development and then to highlight emerging data showing that with maturity, cadherins become largely dispensible for maintaining neuronal and synaptic structure, instead displaying new and narrower roles at mature synapses where they critically regulate dynamic aspects of synaptic signaling, structural plasticity, and cognitive function. At mature synapses, cadherins are an integral component of multiprotein networks, modifying synaptic signaling, morphology, and plasticity through collaborative interactions with other CAM family members as well as a variety of neurotransmitter receptors, scaffolding proteins, and other effector molecules. Such recognition of the ever-evolving functions of synaptic cadherins may yield insight into the pathophysiology of brain disorders in which cadherins have been implicated and that manifest at different times of life.
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Affiliation(s)
- Lauren G Friedman
- Fishberg Department of Neuroscience, Friedman Brain Institute and the Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Deanna L Benson
- Fishberg Department of Neuroscience, Friedman Brain Institute and the Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - George W Huntley
- Fishberg Department of Neuroscience, Friedman Brain Institute and the Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA.
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62
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Abstract
Multicellularity has evolved multiple times, but animals are the only multicellular lineage with nervous systems. This fact implies that the origin of nervous systems was an unlikely event, yet recent comparisons among extant taxa suggest that animal nervous systems may have evolved multiple times independently. Here, we use ancestral gene content reconstruction to track the timing of gene family expansions for the major families of ion-channel proteins that drive nervous system function. We find that animals with nervous systems have broadly similar complements of ion-channel types but that these complements likely evolved independently. We also find that ion-channel gene family evolution has included large loss events, two of which were immediately followed by rounds of duplication. Ctenophores, cnidarians, and bilaterians underwent independent bouts of gene expansion in channel families involved in synaptic transmission and action potential shaping. We suggest that expansions of these family types may represent a genomic signature of expanding nervous system complexity. Ancestral nodes in which nervous systems are currently hypothesized to have originated did not experience large expansions, making it difficult to distinguish among competing hypotheses of nervous system origins and suggesting that the origin of nerves was not attended by an immediate burst of complexity. Rather, the evolution of nervous system complexity appears to resemble a slow fuse in stem animals followed by many independent bouts of gene gain and loss.
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63
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Nikitin M. Bioinformatic prediction of Trichoplax adhaerens regulatory peptides. Gen Comp Endocrinol 2015; 212:145-55. [PMID: 24747483 DOI: 10.1016/j.ygcen.2014.03.049] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 03/29/2014] [Accepted: 03/31/2014] [Indexed: 01/29/2023]
Abstract
Trichoplax adhaerens (phylum Placozoa) is a very simple organism that lacks a nervous system. However, its genome contains many genes essential for neuronal function and development. I report the results of regulatory peptide predictions for this enigmatic animal. Extensive transcriptome, genome, and predicted proteome mining allowed us to predict four insulins, at least five short peptide precursors, one granulin, one paracrine regulator of cell growth, and one complex temptin-attractin pheromone signaling system. The expression of three insulins, four short peptide precursors, granulin, and one out of the six temptin genes was detected. Five predicted regulatory peptide precursors could potentially release over 60 different mature peptides. Some of the predicted peptides are somewhat similar to anthozoan RW amides, Aplysia pedal peptide 3, and PRQFV amide. Other predicted short peptides could not readily be classified into established families. These data provide the foundation for the molecular, biochemical, physiological, and behavioral studies of one the most primitive animal coordination systems, and give unique insight into the origins and early evolution of the nervous system.
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Affiliation(s)
- Mikhail Nikitin
- Lomonosov Moscow State University, A.N. Belozersky Institute of Physico-chemical Biology, Leninskie Gory 1, Bldg. 40, Moscow 119991, Russia.
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64
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Schlosser G. Vertebrate cranial placodes as evolutionary innovations--the ancestor's tale. Curr Top Dev Biol 2015; 111:235-300. [PMID: 25662263 DOI: 10.1016/bs.ctdb.2014.11.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Evolutionary innovations often arise by tinkering with preexisting components building new regulatory networks by the rewiring of old parts. The cranial placodes of vertebrates, ectodermal thickenings that give rise to many of the cranial sense organs (ear, nose, lateral line) and ganglia, originated as such novel structures, when vertebrate ancestors elaborated their head in support of a more active and exploratory life style. This review addresses the question of how cranial placodes evolved by tinkering with ectodermal patterning mechanisms and sensory and neurosecretory cell types that have their own evolutionary history. With phylogenetic relationships among the major branches of metazoans now relatively well established, a comparative approach is used to infer, which structures evolved in which lineages and allows us to trace the origin of placodes and their components back from ancestor to ancestor. Some of the core networks of ectodermal patterning and sensory and neurosecretory differentiation were already established in the common ancestor of cnidarians and bilaterians and were greatly elaborated in the bilaterian ancestor (with BMP- and Wnt-dependent patterning of dorsoventral and anteroposterior ectoderm and multiple neurosecretory and sensory cell types). Rostral and caudal protoplacodal domains, giving rise to some neurosecretory and sensory cells, were then established in the ectoderm of the chordate and tunicate-vertebrate ancestor, respectively. However, proper cranial placodes as clusters of proliferating progenitors producing high-density arrays of neurosecretory and sensory cells only evolved and diversified in the ancestors of vertebrates.
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Affiliation(s)
- Gerhard Schlosser
- School of Natural Sciences & Regenerative Medicine Institute (REMEDI), National University of Ireland, Galway, Ireland.
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65
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Krishnan A, Dnyansagar R, Almén MS, Williams MJ, Fredriksson R, Manoj N, Schiöth HB. The GPCR repertoire in the demosponge Amphimedon queenslandica: insights into the GPCR system at the early divergence of animals. BMC Evol Biol 2014; 14:270. [PMID: 25528161 PMCID: PMC4302439 DOI: 10.1186/s12862-014-0270-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 12/12/2014] [Indexed: 11/10/2022] Open
Abstract
Background G protein-coupled receptors (GPCRs) play a central role in eukaryotic signal transduction. However, the GPCR component of this signalling system, at the early origins of metazoans is not fully understood. Here we aim to identify and classify GPCRs in Amphimedon queenslandica (sponge), a member of an earliest diverging metazoan lineage (Porifera). Furthermore, phylogenetic comparisons of sponge GPCRs with eumetazoan and bilaterian GPCRs will be essential to our understanding of the GPCR system at the roots of metazoan evolution. Results We present a curated list of 220 GPCRs in the sponge genome after excluding incomplete sequences and false positives from our initial dataset of 282 predicted GPCR sequences obtained using Pfam search. Phylogenetic analysis reveals that the sponge genome contains members belonging to four of the five major GRAFS families including Glutamate (33), Rhodopsin (126), Adhesion (40) and Frizzled (3). Interestingly, the sponge Rhodopsin family sequences lack orthologous relationships with those found in eumetazoan and bilaterian lineages, since they clustered separately to form sponge specific groups in the phylogenetic analysis. This suggests that sponge Rhodopsins diverged considerably from that found in other basal metazoans. A few sponge Adhesions clustered basal to Adhesion subfamilies commonly found in most vertebrates, suggesting some Adhesion subfamilies may have diverged prior to the emergence of Bilateria. Furthermore, at least eight of the sponge Adhesion members have a hormone binding motif (HRM domain) in their N-termini, although hormones have yet to be identified in sponges. We also phylogenetically clarified that sponge has homologs of metabotropic glutamate (mGluRs) and GABA receptors. Conclusion Our phylogenetic comparisons of sponge GPCRs with other metazoan genomes suggest that sponge contains a significantly diversified set of GPCRs. This is evident at the family/subfamily level comparisons for most GPCR families, in particular for the Rhodopsin family of GPCRs. In summary, this study provides a framework to perform future experimental and comparative studies to further verify and understand the roles of GPCRs that predates the divergence of bilaterian and eumetazoan lineages. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0270-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Arunkumar Krishnan
- Department of Neuroscience, Functional Pharmacology, Uppsala University, Biomedical Center, Box 593, 75 124, Uppsala, Sweden.
| | - Rohit Dnyansagar
- Department of Neuroscience, Functional Pharmacology, Uppsala University, Biomedical Center, Box 593, 75 124, Uppsala, Sweden. .,Department of Biotechnology, Indian Institute of Technology Madras, Chennai, 600036, India.
| | - Markus Sällman Almén
- Department of Neuroscience, Functional Pharmacology, Uppsala University, Biomedical Center, Box 593, 75 124, Uppsala, Sweden.
| | - Michael J Williams
- Department of Neuroscience, Functional Pharmacology, Uppsala University, Biomedical Center, Box 593, 75 124, Uppsala, Sweden.
| | - Robert Fredriksson
- Department of Neuroscience, Functional Pharmacology, Uppsala University, Biomedical Center, Box 593, 75 124, Uppsala, Sweden.
| | - Narayanan Manoj
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, 600036, India.
| | - Helgi B Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University, Biomedical Center, Box 593, 75 124, Uppsala, Sweden.
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66
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Cai X, Wang X, Patel S, Clapham DE. Insights into the early evolution of animal calcium signaling machinery: a unicellular point of view. Cell Calcium 2014; 57:166-73. [PMID: 25498309 PMCID: PMC4355082 DOI: 10.1016/j.ceca.2014.11.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/18/2014] [Accepted: 11/24/2014] [Indexed: 11/15/2022]
Abstract
The basic principles of Ca(2+) regulation emerged early in prokaryotes. Ca(2+) signaling acquired more extensive and varied functions when life evolved into multicellular eukaryotes with intracellular organelles. Animals, fungi and plants display differences in the mechanisms that control cytosolic Ca(2+) concentrations. The aim of this review is to examine recent findings from comparative genomics of Ca(2+) signaling molecules in close unicellular relatives of animals and in common unicellular ancestors of animals and fungi. Also discussed are the evolution and origins of the sperm-specific CatSper channel complex, cation/Ca(2+) exchangers and four-domain voltage-gated Ca(2+) channels. Newly identified evolutionary evidence suggests that the distinct Ca(2+) signaling machineries in animals, plants and fungi likely originated from an ancient Ca(2+) signaling machinery prior to early eukaryotic radiation.
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Affiliation(s)
- Xinjiang Cai
- Division of Endocrinology, Metabolism and Nutrition, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA.
| | - Xiangbing Wang
- Division of Endocrinology, Metabolism and Nutrition, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
| | - Sandip Patel
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - David E Clapham
- Howard Hughes Medical Institute, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
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67
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Monk T, Paulin MG. Predation and the origin of neurones. BRAIN, BEHAVIOR AND EVOLUTION 2014; 84:246-61. [PMID: 25472692 DOI: 10.1159/000368177] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 04/24/2014] [Indexed: 11/19/2022]
Abstract
The core design of spiking neurones is remarkably similar throughout the animal kingdom. Their basic function as fast-signalling thresholding cells might have been established very early in their evolutionary history. Identifying the selection pressures that drove animals to evolve spiking neurones could help us interpret their design and function today. We review fossil, ecological and molecular evidence to investigate when and why animals evolved spiking neurones. Fossils suggest that animals evolved nervous systems soon after the advent of animal-on-animal predation, 550 million years ago (MYa). Between 550 and 525 MYa, we see the first fossil appearances of many animal innovations, including eyes. Animal behavioural complexity increased during this period as well, as evidenced by their traces, suggesting that nervous systems were an innovation of that time. Fossils further suggest that, before 550 MYa, animals were either filter feeders or microbial mat grazers. Extant sponges and Trichoplax perform these tasks using energetically cheaper alternatives than spiking neurones. Genetic evidence testifies that nervous systems evolved before the protostome-deuterostome split. It is less clear whether nervous systems evolved before the cnidarian-bilaterian split, so cnidarians and bilaterians might have evolved their nervous systems independently. The fossil record indicates that the advent of predation could fit into the window of time between those two splits, though molecular clock studies dispute this claim. Collectively, these lines of evidence indicate that animals evolved spiking neurones soon after they started eating each other. The first sensory neurones could have been threshold detectors that spiked in response to other animals in their proximity, alerting them to perform precisely timed actions, such as striking or fleeing.
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Affiliation(s)
- Travis Monk
- Department of Zoology, University of Otago, Dunedin, New Zealand
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68
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Šestak MS, Domazet-Lošo T. Phylostratigraphic profiles in zebrafish uncover chordate origins of the vertebrate brain. Mol Biol Evol 2014; 32:299-312. [PMID: 25415965 PMCID: PMC4298178 DOI: 10.1093/molbev/msu319] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
An elaborated tripartite brain is considered one of the important innovations of vertebrates. Other extant chordate groups have a more basic brain organization. For instance, cephalochordates possess a relatively simple brain possibly homologous to the vertebrate forebrain and hindbrain, whereas tunicates display the tripartite organization, but without the specialized brain centers. The difference in anatomical complexity is even more pronounced if one compares chordates with other deuterostomes that have only a diffuse nerve net or alternatively a rather simple central nervous system. To gain a new perspective on the evolutionary roots of the complex vertebrate brain, we made here a phylostratigraphic analysis of gene expression patterns in the developing zebrafish (Danio rerio). The recovered adaptive landscape revealed three important periods in the evolutionary history of the zebrafish brain. The oldest period corresponds to preadaptive events in the first metazoans and the emergence of the nervous system at the metazoan-eumetazoan transition. The origin of chordates marks the next phase, where we found the overall strongest adaptive imprint in almost all analyzed brain regions. This finding supports the idea that the vertebrate brain evolved independently of the brains within the protostome lineage. Finally, at the origin of vertebrates we detected a pronounced signal coming from the dorsal telencephalon, in agreement with classical theories that consider this part of the cerebrum a genuine vertebrate innovation. Taken together, these results reveal a stepwise adaptive history of the vertebrate brain where most of its extant organization was already present in the chordate ancestor.
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Affiliation(s)
- Martin Sebastijan Šestak
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Tomislav Domazet-Lošo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia Catholic University of Croatia, Zagreb, Croatia
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69
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Abstract
Vertebrate adherens junctions mediate cell–cell adhesion via a “classical” cadherin–catenin “core” complex, which is associated with and regulated by a functional network of proteins, collectively named the cadherin adhesome (“cadhesome”). The most basal metazoans have been shown to conserve the cadherin–catenin “core”, but little is known about the evolution of the cadhesome. Using a bioinformatics approach based on both sequence and structural analysis, we have traced the evolution of this larger network in 26 organisms, from the uni-cellular ancestors of metazoans, through basal metazoans, to vertebrates. Surprisingly, we show that approximately 70% of the cadhesome, including proteins with similarity to the catenins, predate metazoans. We found that the transition to multicellularity was accompanied by the appearance of a small number of adaptor proteins, and we show how these proteins may have helped to integrate pre-metazoan sub-networks via PDZ domain–peptide interactions. Finally, we found the increase in network complexity in higher metazoans to have been driven primarily by expansion of paralogs. In summary, our analysis helps to explain how the complex protein network associated with cadherin at adherens junctions first came together in the first metazoan and how it evolved into the even more complex mammalian cadhesome.
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Affiliation(s)
- Paul S Murray
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA Center of Computational Biology and Bioinformatics, Department of Systems Biology, Columbia University, Irving Cancer Research Center, New York, NY 10032, USA
| | - Ronen Zaidel-Bar
- Mechanobiology Institute Singapore, National University of Singapore, Singapore 117411 Department of Biomedical Engineering, National University of Singapore, Singapore 117575
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Ganot P, Zoccola D, Tambutté E, Voolstra CR, Aranda M, Allemand D, Tambutté S. Structural molecular components of septate junctions in cnidarians point to the origin of epithelial junctions in eukaryotes. Mol Biol Evol 2014; 32:44-62. [PMID: 25246700 DOI: 10.1093/molbev/msu265] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Septate junctions (SJs) insure barrier properties and control paracellular diffusion of solutes across epithelia in invertebrates. However, the origin and evolution of their molecular constituents in Metazoa have not been firmly established. Here, we investigated the genomes of early branching metazoan representatives to reconstruct the phylogeny of the molecular components of SJs. Although Claudins and SJ cytoplasmic adaptor components appeared successively throughout metazoan evolution, the structural components of SJs arose at the time of Placozoa/Cnidaria/Bilateria radiation. We also show that in the scleractinian coral Stylophora pistillata, the structural SJ component Neurexin IV colocalizes with the cortical actin network at the apical border of the cells, at the place of SJs. We propose a model for SJ components in Cnidaria. Moreover, our study reveals an unanticipated diversity of SJ structural component variants in cnidarians. This diversity correlates with gene-specific expression in calcifying and noncalcifying tissues, suggesting specific paracellular pathways across the cell layers of these diploblastic animals.
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Affiliation(s)
- Philippe Ganot
- Marine Biology Department, Centre Scientifique de Monaco, Quai Antoine Premier, Monaco
| | - Didier Zoccola
- Marine Biology Department, Centre Scientifique de Monaco, Quai Antoine Premier, Monaco
| | - Eric Tambutté
- Marine Biology Department, Centre Scientifique de Monaco, Quai Antoine Premier, Monaco
| | - Christian R Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Manuel Aranda
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Denis Allemand
- Marine Biology Department, Centre Scientifique de Monaco, Quai Antoine Premier, Monaco
| | - Sylvie Tambutté
- Marine Biology Department, Centre Scientifique de Monaco, Quai Antoine Premier, Monaco
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71
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Thacker RW, Díaz MC, Kerner A, Vignes-Lebbe R, Segerdell E, Haendel MA, Mungall CJ. The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology. J Biomed Semantics 2014; 5:39. [PMID: 25276334 PMCID: PMC4177528 DOI: 10.1186/2041-1480-5-39] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 07/22/2014] [Indexed: 12/31/2022] Open
Abstract
Background Porifera (sponges) are ancient basal metazoans that lack organs. They provide insight into key evolutionary transitions, such as the emergence of multicellularity and the nervous system. In addition, their ability to synthesize unusual compounds offers potential biotechnical applications. However, much of the knowledge of these organisms has not previously been codified in a machine-readable way using modern web standards. Results The Porifera Ontology is intended as a standardized coding system for sponge anatomical features currently used in systematics. The ontology is available from http://purl.obolibrary.org/obo/poro.owl, or from the project homepage http://porifera-ontology.googlecode.com/. The version referred to in this manuscript is permanently available from http://purl.obolibrary.org/obo/poro/releases/2014-03-06/. Conclusions By standardizing character representations, we hope to facilitate more rapid description and identification of sponge taxa, to allow integration with other evolutionary database systems, and to perform character mapping across the major clades of sponges to better understand the evolution of morphological features. Future applications of the ontology will focus on creating (1) ontology-based species descriptions; (2) taxonomic keys that use the nested terms of the ontology to more quickly facilitate species identifications; and (3) methods to map anatomical characters onto molecular phylogenies of sponges. In addition to modern taxa, the ontology is being extended to include features of fossil taxa.
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Affiliation(s)
- Robert W Thacker
- Department of Biology, University of Alabama at Birmingham, Birmingham, USA
| | | | - Adeline Kerner
- CR2P, UMR 7207 CNRS-MNHN-UPMC, Département Histoire de la Terre, Muséum National d'Histoire Naturelle, Bâtiment de Géologie, CP48, 57 rue Cuvier, 75005 Paris, France
| | - Régine Vignes-Lebbe
- CR2P, UMR 7207 CNRS-MNHN-UPMC, Département Histoire de la Terre, Muséum National d'Histoire Naturelle, Bâtiment de Géologie, CP48, 57 rue Cuvier, 75005 Paris, France
| | - Erik Segerdell
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, USA
| | - Melissa A Haendel
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, USA
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72
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Achim K, Arendt D. Structural evolution of cell types by step-wise assembly of cellular modules. Curr Opin Genet Dev 2014; 27:102-8. [PMID: 24998387 DOI: 10.1016/j.gde.2014.05.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 04/16/2014] [Accepted: 05/10/2014] [Indexed: 12/22/2022]
Abstract
Cell types are composed of cellular modules exerting specific subfunctions. The evolutionary emergence and diversification of these modules can be tracked through the comparative analysis of genomes. Here, we survey recent advances elucidating the origin of neurons, of smooth and striated muscle cells and of the T- and B-cells of the immune system in the diverging lineages of animal evolution. Gene presence and absence analyses in various metazoan genomes allow mapping the step-wise assembly of key modules - such as the postsynaptic density characteristic for neurons or the z-disk characteristic for striated muscle - on the animal evolutionary tree. Using this approach, first insight into the structural evolution of cell types can be gained.
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Affiliation(s)
- Kaia Achim
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69012 Heidelberg, Germany
| | - Detlev Arendt
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69012 Heidelberg, Germany.
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73
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Burkhardt P, Grønborg M, McDonald K, Sulur T, Wang Q, King N. Evolutionary insights into premetazoan functions of the neuronal protein homer. Mol Biol Evol 2014; 31:2342-55. [PMID: 24899667 PMCID: PMC4137706 DOI: 10.1093/molbev/msu178] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Reconstructing the evolution and ancestral functions of synaptic proteins promises to shed light on how neurons first evolved. The postsynaptic density (PSD) protein Homer scaffolds membrane receptors and regulates Ca2+ signaling in diverse metazoan cell types (including neurons and muscle cells), yet its ancestry and core functions are poorly understood. We find that the protein domain organization and essential biochemical properties of metazoan Homer proteins, including their ability to tetramerize, are conserved in the choanoflagellate Salpingoeca rosetta, one of the closest living relatives of metazoans. Unlike in neurons, Homer localizes to the nucleoplasm in S. rosetta and interacts directly with Flotillin, a protein more commonly associated with cell membranes. Surprisingly, we found that the Homer/Flotillin interaction and its localization to the nucleus are conserved in metazoan astrocytes. These findings suggest that Homer originally interacted with Flotillin in the nucleus of the last common ancestor of metazoans and choanoflagellates and was later co-opted to function as a membrane receptor scaffold in the PSD.
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Affiliation(s)
- Pawel Burkhardt
- Howard Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley
| | | | - Kent McDonald
- Electron Microscopy Laboratory, University of California, Berkeley
| | - Tara Sulur
- Howard Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley
| | - Qi Wang
- California Institute for Quantitative Biosciences, University of California, Berkeley
| | - Nicole King
- Howard Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley
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74
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Wenger Y, Galliot B. Punctuated emergences of genetic and phenotypic innovations in eumetazoan, bilaterian, euteleostome, and hominidae ancestors. Genome Biol Evol 2014; 5:1949-68. [PMID: 24065732 PMCID: PMC3814200 DOI: 10.1093/gbe/evt142] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Phenotypic traits derive from the selective recruitment of genetic materials over macroevolutionary times, and protein-coding genes constitute an essential component of these materials. We took advantage of the recent production of genomic scale data from sponges and cnidarians, sister groups from eumetazoans and bilaterians, respectively, to date the emergence of human proteins and to infer the timing of acquisition of novel traits through metazoan evolution. Comparing the proteomes of 23 eukaryotes, we find that 33% human proteins have an ortholog in nonmetazoan species. This premetazoan proteome associates with 43% of all annotated human biological processes. Subsequently, four major waves of innovations can be inferred in the last common ancestors of eumetazoans, bilaterians, euteleostomi (bony vertebrates), and hominidae, largely specific to each epoch, whereas early branching deuterostome and chordate phyla show very few innovations. Interestingly, groups of proteins that act together in their modern human functions often originated concomitantly, although the corresponding human phenotypes frequently emerged later. For example, the three cnidarians Acropora, Nematostella, and Hydra express a highly similar protein inventory, and their protein innovations can be affiliated either to traits shared by all eumetazoans (gut differentiation, neurogenesis); or to bilaterian traits present in only some cnidarians (eyes, striated muscle); or to traits not identified yet in this phylum (mesodermal layer, endocrine glands). The variable correspondence between phenotypes predicted from protein enrichments and observed phenotypes suggests that a parallel mechanism repeatedly produce similar phenotypes, thanks to novel regulatory events that independently tie preexisting conserved genetic modules.
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Affiliation(s)
- Yvan Wenger
- Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
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75
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Sensory fusion in Physarum polycephalum and implementing multi-sensory functional computation. Biosystems 2014; 119:45-52. [DOI: 10.1016/j.biosystems.2014.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 03/17/2014] [Accepted: 03/20/2014] [Indexed: 11/22/2022]
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76
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Abstract
The first animals arose more than six hundred million years ago, yet they left little impression in the fossil record. Nonetheless, the cell biology and genome composition of the first animal, the Urmetazoan, can be reconstructed through the study of phylogenetically relevant living organisms. Comparisons among animals and their unicellular and colonial relatives reveal that the Urmetazoan likely possessed a layer of epithelium-like collar cells, preyed on bacteria, reproduced by sperm and egg, and developed through cell division, cell differentiation, and invagination. Although many genes involved in development, body patterning, immunity, and cell-type specification evolved in the animal stem lineage or after animal origins, several gene families critical for cell adhesion, signaling, and gene regulation predate the origin of animals. The ancestral functions of these and other genes may eventually be revealed through studies of gene and genome function in early-branching animals and their closest non-animal relatives.
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Affiliation(s)
- Daniel J Richter
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3200; ,
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77
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Fast neurotransmission related genes are expressed in non nervous endoderm in the sea anemone Nematostella vectensis. PLoS One 2014; 9:e93832. [PMID: 24705400 PMCID: PMC3976352 DOI: 10.1371/journal.pone.0093832] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 03/07/2014] [Indexed: 11/25/2022] Open
Abstract
Cnidarian nervous systems utilize chemical transmission to transfer signals through synapses and neurons. To date, ample evidence has been accumulated for the participation of neuropeptides, primarily RFamides, in neurotransmission. Yet, it is still not clear if this is the case for the classical fast neurotransmitters such as GABA, Glutamate, Acetylcholine and Monoamines. A large repertoire of cnidarian Fast Neurotransmitter related Genes (FNGs) has been recently identified in the genome of the sea anemone, Nematostella vectensis. In order to test whether FNGs are localized in cnidarian neurons, we characterized the expression patterns of eight Nematostella genes that are closely or distantly related to human central and peripheral nervous systems genes, in adult Nematostella and compared them to the RFamide localization. Our results show common expression patterns for all tested genes, in a single endodermal cell layer. These expressions did not correspond with the RFamide expressing nerve cell network. Following these results we suggest that the tested Nematostella genes may not be directly involved in vertebrate-like fast neurotransmission.
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78
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Riesgo A, Farrar N, Windsor PJ, Giribet G, Leys SP. The analysis of eight transcriptomes from all poriferan classes reveals surprising genetic complexity in sponges. Mol Biol Evol 2014; 31:1102-20. [PMID: 24497032 DOI: 10.1093/molbev/msu057] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Sponges (Porifera) are among the earliest evolving metazoans. Their filter-feeding body plan based on choanocyte chambers organized into a complex aquiferous system is so unique among metazoans that it either reflects an early divergence from other animals prior to the evolution of features such as muscles and nerves, or that sponges lost these characters. Analyses of the Amphimedon and Oscarella genomes support this view of uniqueness-many key metazoan genes are absent in these sponges-but whether this is generally true of other sponges remains unknown. We studied the transcriptomes of eight sponge species in four classes (Hexactinellida, Demospongiae, Homoscleromorpha, and Calcarea) specifically seeking genes and pathways considered to be involved in animal complexity. For reference, we also sought these genes in transcriptomes and genomes of three unicellular opisthokonts, two sponges (A. queenslandica and O. carmela), and two bilaterian taxa. Our analyses showed that all sponge classes share an unexpectedly large complement of genes with other metazoans. Interestingly, hexactinellid, calcareous, and homoscleromorph sponges share more genes with bilaterians than with nonbilaterian metazoans. We were surprised to find representatives of most molecules involved in cell-cell communication, signaling, complex epithelia, immune recognition, and germ-lineage/sex, with only a few, but potentially key, absences. A noteworthy finding was that some important genes were absent from all demosponges (transcriptomes and the Amphimedon genome), which might reflect divergence from main-stem lineages including hexactinellids, calcareous sponges, and homoscleromorphs. Our results suggest that genetic complexity arose early in evolution as shown by the presence of these genes in most of the animal lineages, which suggests sponges either possess cryptic physiological and morphological complexity and/or have lost ancestral cell types or physiological processes.
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Affiliation(s)
- Ana Riesgo
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University
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79
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Ludeman DA, Farrar N, Riesgo A, Paps J, Leys SP. Evolutionary origins of sensation in metazoans: functional evidence for a new sensory organ in sponges. BMC Evol Biol 2014; 14:3. [PMID: 24410880 PMCID: PMC3890488 DOI: 10.1186/1471-2148-14-3] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 12/11/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND One of the hallmarks of multicellular organisms is the ability of their cells to trigger responses to the environment in a coordinated manner. In recent years primary cilia have been shown to be present as 'antennae' on almost all animal cells, and are involved in cell-to-cell signaling in development and tissue homeostasis; how this sophisticated sensory system arose has been little-studied and its evolution is key to understanding how sensation arose in the Animal Kingdom. Sponges (Porifera), one of the earliest evolving phyla, lack conventional muscles and nerves and yet sense and respond to changes in their fluid environment. Here we demonstrate the presence of non-motile cilia in sponges and studied their role as flow sensors. RESULTS Demosponges excrete wastes from their body with a stereotypic series of whole-body contractions using a structure called the osculum to regulate the water-flow through the body. In this study we show that short cilia line the inner epithelium of the sponge osculum. Ultrastructure of the cilia shows an absence of a central pair of microtubules and high speed imaging shows they are non-motile, suggesting they are not involved in generating flow. In other animals non-motile, 'primary', cilia are involved in sensation. Here we show that molecules known to block cationic ion channels in primary cilia and which inhibit sensory function in other organisms reduce or eliminate sponge contractions. Removal of the cilia using chloral hydrate, or removal of the whole osculum, also stops the contractions; in all instances the effect is reversible, suggesting that the cilia are involved in sensation. An analysis of sponge transcriptomes shows the presence of several transient receptor potential (TRP) channels including PKD channels known to be involved in sensing changes in flow in other animals. Together these data suggest that cilia in sponge oscula are involved in flow sensation and coordination of simple behaviour. CONCLUSIONS This is the first evidence of arrays of non-motile cilia in sponge oscula. Our findings provide support for the hypothesis that the cilia are sensory, and if true, the osculum may be considered a sensory organ that is used to coordinate whole animal responses in sponges. Arrays of primary cilia like these could represent the first step in the evolution of sensory and coordination systems in metazoans.
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Affiliation(s)
| | | | | | | | - Sally P Leys
- Department of Biological Sciences, University of Alberta, CW 405 Biological Sciences Building, Edmonton, Alberta T6G 2E9, Canada.
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80
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Ryan JF, Pang K, Schnitzler CE, Nguyen AD, Moreland RT, Simmons DK, Koch BJ, Francis WR, Havlak P, Smith SA, Putnam NH, Haddock SHD, Dunn CW, Wolfsberg TG, Mullikin JC, Martindale MQ, Baxevanis AD. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 2013; 342:1242592. [PMID: 24337300 DOI: 10.1126/science.1242592] [Citation(s) in RCA: 453] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
An understanding of ctenophore biology is critical for reconstructing events that occurred early in animal evolution. Toward this goal, we have sequenced, assembled, and annotated the genome of the ctenophore Mnemiopsis leidyi. Our phylogenomic analyses of both amino acid positions and gene content suggest that ctenophores rather than sponges are the sister lineage to all other animals. Mnemiopsis lacks many of the genes found in bilaterian mesodermal cell types, suggesting that these cell types evolved independently. The set of neural genes in Mnemiopsis is similar to that of sponges, indicating that sponges may have lost a nervous system. These results present a newly supported view of early animal evolution that accounts for major losses and/or gains of sophisticated cell types, including nerve and muscle cells.
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Affiliation(s)
- Joseph F Ryan
- Genome Technology Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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81
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Hartmann AM, Tesch D, Nothwang HG, Bininda-Emonds OR. Evolution of the Cation Chloride Cotransporter Family: Ancient Origins, Gene Losses, and Subfunctionalization through Duplication. Mol Biol Evol 2013; 31:434-47. [DOI: 10.1093/molbev/mst225] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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82
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Rivera A, Winters I, Rued A, Ding S, Posfai D, Cieniewicz B, Cameron K, Gentile L, Hill A. The evolution and function of the Pax/Six regulatory network in sponges. Evol Dev 2013; 15:186-96. [PMID: 23607302 DOI: 10.1111/ede.12032] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Examining the origins of highly conserved gene regulatory networks (GRNs) will inform our understanding of the evolution of animal body plans. Sponges are believed to be the most ancient extant metazoan lineage, and as such, hold clues about the evolution of genetic programs deployed in animal development. We used the emerging freshwater sponge model, Ephydatia muelleri, to study the evolutionary origins of the Pax/Six/Eya/Dac (PSED) GRN. Orthologs to Pax and Six family members are present in E. muelleri and are expressed in endothelial cells lining the canal system as well as cells in the choanoderm. Knockdown of EmPaxB and EmSix1/2 by RNAi resulted in defects to the canal systems. We further show that PaxB may be in a regulatory relationship with Six1/2 in E. muelleri, thus demonstrating that a component of the PSED network was present early in metazoan evolution.
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Affiliation(s)
- A Rivera
- University of Richmond, Richmond, VA 23173, USA
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83
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Ontogeny repeats the phylogenetic recruitment of the cargo exporter cornichon into AMPA receptor signaling complexes. Mol Cell Neurosci 2013; 56:10-7. [DOI: 10.1016/j.mcn.2013.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 02/01/2013] [Indexed: 12/26/2022] Open
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84
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Capra JA, Stolzer M, Durand D, Pollard KS. How old is my gene? Trends Genet 2013; 29:659-68. [PMID: 23915718 DOI: 10.1016/j.tig.2013.07.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 06/13/2013] [Accepted: 07/03/2013] [Indexed: 11/26/2022]
Abstract
Gene functions, interactions, disease associations, and ecological distributions are all correlated with gene age. However, it is challenging to estimate the intricate series of evolutionary events leading to a modern-day gene and then to reduce this history to a single age estimate. Focusing on eukaryotic gene families, we introduce a framework that can be used to compare current strategies for quantifying gene age, discuss key differences between these methods, and highlight several common problems. We argue that genes with complex evolutionary histories do not have a single well-defined age. As a result, care must be taken to articulate the goals and assumptions of any analysis that uses gene age estimates. Recent algorithmic advances offer the promise of gene age estimates that are fast, accurate, and consistent across gene families. This will enable a shift to integrated genome-wide analyses of all events in gene evolutionary histories in the near future.
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Affiliation(s)
- John A Capra
- Center for Human Genetics Research and Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, USA
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85
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Dunlap WC, Starcevic A, Baranasic D, Diminic J, Zucko J, Gacesa R, van Oppen MJH, Hranueli D, Cullum J, Long PF. KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome. BMC Genomics 2013; 14:509. [PMID: 23889801 PMCID: PMC3750612 DOI: 10.1186/1471-2164-14-509] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 07/15/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Contemporary coral reef research has firmly established that a genomic approach is urgently needed to better understand the effects of anthropogenic environmental stress and global climate change on coral holobiont interactions. Here we present KEGG orthology-based annotation of the complete genome sequence of the scleractinian coral Acropora digitifera and provide the first comprehensive view of the genome of a reef-building coral by applying advanced bioinformatics. DESCRIPTION Sequences from the KEGG database of protein function were used to construct hidden Markov models. These models were used to search the predicted proteome of A. digitifera to establish complete genomic annotation. The annotated dataset is published in ZoophyteBase, an open access format with different options for searching the data. A particularly useful feature is the ability to use a Google-like search engine that links query words to protein attributes. We present features of the annotation that underpin the molecular structure of key processes of coral physiology that include (1) regulatory proteins of symbiosis, (2) planula and early developmental proteins, (3) neural messengers, receptors and sensory proteins, (4) calcification and Ca2+-signalling proteins, (5) plant-derived proteins, (6) proteins of nitrogen metabolism, (7) DNA repair proteins, (8) stress response proteins, (9) antioxidant and redox-protective proteins, (10) proteins of cellular apoptosis, (11) microbial symbioses and pathogenicity proteins, (12) proteins of viral pathogenicity, (13) toxins and venom, (14) proteins of the chemical defensome and (15) coral epigenetics. CONCLUSIONS We advocate that providing annotation in an open-access searchable database available to the public domain will give an unprecedented foundation to interrogate the fundamental molecular structure and interactions of coral symbiosis and allow critical questions to be addressed at the genomic level based on combined aspects of evolutionary, developmental, metabolic, and environmental perspectives.
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Affiliation(s)
- Walter C Dunlap
- Centre for Marine Microbiology and Genetics, Australian Institute of Marine Science, PMB No. 3 Townsville MC, Townsville 4810, Queensland, Australia
- Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Antonio Starcevic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Damir Baranasic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Janko Diminic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Jurica Zucko
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Ranko Gacesa
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Madeleine JH van Oppen
- Centre for Marine Microbiology and Genetics, Australian Institute of Marine Science, PMB No. 3 Townsville MC, Townsville 4810, Queensland, Australia
| | - Daslav Hranueli
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - John Cullum
- Department of Genetics, University of Kaiserslautern, Postfach 3049, 67653 Kaiserslautern, Germany
| | - Paul F Long
- Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
- Department of Chemistry King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
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86
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Predicting protein-protein interactions in the post synaptic density. Mol Cell Neurosci 2013; 56:128-39. [PMID: 23628905 DOI: 10.1016/j.mcn.2013.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 04/09/2013] [Accepted: 04/19/2013] [Indexed: 12/27/2022] Open
Abstract
The post synaptic density (PSD) is a specialization of the cytoskeleton at the synaptic junction, composed of hundreds of different proteins. Characterizing the protein components of the PSD and their interactions can help elucidate the mechanism of long-term changes in synaptic plasticity, which underlie learning and memory. Unfortunately, our knowledge of the proteome and interactome of the PSD is still partial and noisy. In this study we describe a computational framework to improve the reconstruction of the PSD network. The approach is based on learning the characteristics of PSD protein interactions from a set of trusted interactions, expanding this set with data collected from large scale repositories, and then predicting novel interaction with proteins that are suspected to reside in the PSD. Using this method we obtained thirty predicted interactions, with more than half of which having supporting evidence in the literature. We discuss in details two of these new interactions, Lrrtm1 with PSD-95 and Src with Capg. The first may take part in a mechanism underlying glutamatergic dysfunction in schizophrenia. The second suggests an alternative mechanism to regulate dendritic spines maturation.
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87
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Abstract
Proteomic studies of the composition of mammalian synapses have revealed a high degree of complexity. The postsynaptic and presynaptic terminals are molecular systems with highly organized protein networks producing emergent physiological and behavioral properties. The major classes of synapse proteins and their respective functions in intercellular communication and adaptive responses evolved in prokaryotes and eukaryotes prior to the origins of neurons in metazoa. In eukaryotes, the organization of individual proteins into multiprotein complexes comprising scaffold proteins, receptors, and signaling enzymes formed the precursor to the core adaptive machinery of the metazoan postsynaptic terminal. Multiplicative increases in the complexity of this protosynapse machinery secondary to genome duplications drove synaptic, neuronal, and behavioral novelty in vertebrates. Natural selection has constrained diversification in mammalian postsynaptic mechanisms and the repertoire of adaptive and innate behaviors. The evolution and organization of synapse proteomes underlie the origins and complexity of nervous systems and behavior.
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Affiliation(s)
- Richard D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Leicestershire LE12 5RD, United Kingdom.
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88
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Richards GS, Degnan BM. The expression of Delta ligands in the sponge Amphimedon queenslandica suggests an ancient role for Notch signaling in metazoan development. EvoDevo 2012; 3:15. [PMID: 22824137 PMCID: PMC3482393 DOI: 10.1186/2041-9139-3-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 06/27/2012] [Indexed: 01/09/2023] Open
Abstract
Background Intercellular signaling via the Notch pathway regulates cell fate, patterning, differentiation and proliferation, and is essential for the proper development of bilaterians and cnidarians. To investigate the origins of the Notch pathway, we are studying its deployment in a representative of an early branching lineage, the poriferan Amphimedon queenslandica. The A. queenslandica genome encodes a single Notch receptor and five membrane-bound Delta ligands, as well as orthologs of many genes that enact and regulate canonical Notch signaling events in other animals. Methods In the present report we analyze the structure of the five A. queenslandica Deltas using bioinformatic methods, and characterize their developmental expression via whole mount in situ hybridization and histological staining. Results Sequence analysis of the A. queenslandica Delta ligands highlights the conservation of their extracellular domains. This contrasts with the divergence of their intracellular regions, each of which is predicted to bear a unique repertoire of protein interaction motifs. In keeping with this diversity, these ligands are expressed differentially and dynamically throughout A. queenslandica embryogenesis, both in cell type specific patterns and broader regional domains. Notably, this expression coincides with the development of the photosensitive larval pigment ring, the non-ciliated cuboidal cells located at the anterior pole of the larva, and the intraepithelial flask cells and globular cells that are presumed to have sensory and/or secretory roles. Conclusions Based on the dynamic and complex patterns of expression of these Delta ligands and the Notch receptor, we propose that the Notch signaling pathway is involved in regulating the development of diverse cell types in A. queenslandica. From these observations we infer that Notch signaling is a conserved feature of metazoan development, ancestrally contributing to cell determination, patterning and differentiation processes.
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Affiliation(s)
- Gemma S Richards
- School of Biological Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.
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89
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Irimia M, Tena JJ, Alexis MS, Fernandez-Miñan A, Maeso I, Bogdanovic O, de la Calle-Mustienes E, Roy SW, Gómez-Skarmeta JL, Fraser HB. Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints. Genome Res 2012; 22:2356-67. [PMID: 22722344 PMCID: PMC3514665 DOI: 10.1101/gr.139725.112] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The order of genes in eukaryotic genomes has generally been assumed to be neutral, since gene order is largely scrambled over evolutionary time. Only a handful of exceptional examples are known, typically involving deeply conserved clusters of tandemly duplicated genes (e.g., Hox genes and histones). Here we report the first systematic survey of microsynteny conservation across metazoans, utilizing 17 genome sequences. We identified nearly 600 pairs of unrelated genes that have remained tightly physically linked in diverse lineages across over 600 million years of evolution. Integrating sequence conservation, gene expression data, gene function, epigenetic marks, and other genomic features, we provide extensive evidence that many conserved ancient linkages involve (1) the coordinated transcription of neighboring genes, or (2) genomic regulatory blocks (GRBs) in which transcriptional enhancers controlling developmental genes are contained within nearby bystander genes. In addition, we generated ChIP-seq data for key histone modifications in zebrafish embryos, which provided further evidence of putative GRBs in embryonic development. Finally, using chromosome conformation capture (3C) assays and stable transgenic experiments, we demonstrate that enhancers within bystander genes drive the expression of genes such as Otx and Islet, critical regulators of central nervous system development across bilaterians. These results suggest that ancient genomic functional associations are far more common than previously thought—involving ∼12% of the ancestral bilaterian genome—and that cis-regulatory constraints are crucial in determining metazoan genome architecture.
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Affiliation(s)
- Manuel Irimia
- Department of Biology, Stanford University, Stanford, California 94305, USA
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90
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Functionalization of a protosynaptic gene expression network. Proc Natl Acad Sci U S A 2012; 109 Suppl 1:10612-8. [PMID: 22723359 DOI: 10.1073/pnas.1201890109] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Assembly of a functioning neuronal synapse requires the precisely coordinated synthesis of many proteins. To understand the evolution of this complex cellular machine, we tracked the developmental expression patterns of a core set of conserved synaptic genes across a representative sampling of the animal kingdom. Coregulation, as measured by correlation of gene expression over development, showed a marked increase as functional nervous systems emerged. In the earliest branching animal phyla (Porifera), in which a nearly complete set of synaptic genes exists in the absence of morphological synapses, these "protosynaptic" genes displayed a lack of global coregulation although small modules of coexpressed genes are readily detectable by using network analysis techniques. These findings suggest that functional synapses evolved by exapting preexisting cellular machines, likely through some modification of regulatory circuitry. Evolutionarily ancient modules continue to operate seamlessly within the synapses of modern animals. This work shows that the application of network techniques to emerging genomic and expression data can provide insights into the evolution of complex cellular machines such as the synapse.
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91
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Conaco C, Neveu P, Zhou H, Arcila ML, Degnan SM, Degnan BM, Kosik KS. Transcriptome profiling of the demosponge Amphimedon queenslandica reveals genome-wide events that accompany major life cycle transitions. BMC Genomics 2012; 13:209. [PMID: 22646746 PMCID: PMC3447736 DOI: 10.1186/1471-2164-13-209] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 04/02/2012] [Indexed: 11/22/2022] Open
Abstract
Background The biphasic life cycle with pelagic larva and benthic adult stages is widely observed in the animal kingdom, including the Porifera (sponges), which are the earliest branching metazoans. The demosponge, Amphimedon queenslandica, undergoes metamorphosis from a free-swimming larva into a sessile adult that bears no morphological resemblance to other animals. While the genome of A. queenslandica contains an extensive repertoire of genes very similar to that of complex bilaterians, it is as yet unclear how this is drawn upon to coordinate changing morphological features and ecological demands throughout the sponge life cycle. Results To identify genome-wide events that accompany the pelagobenthic transition in A. queenslandica, we compared global gene expression profiles at four key developmental stages by sequencing the poly(A) transcriptome using SOLiD technology. Large-scale changes in transcription were observed as sponge larvae settled on the benthos and began metamorphosis. Although previous systematics suggest that the only clear homology between Porifera and other animals is in the embryonic and larval stages, we observed extensive use of genes involved in metazoan-associated cellular processes throughout the sponge life cycle. Sponge-specific transcripts are not over-represented in the morphologically distinct adult; rather, many genes that encode typical metazoan features, such as cell adhesion and immunity, are upregulated. Our analysis further revealed gene families with candidate roles in competence, settlement, and metamorphosis in the sponge, including transcription factors, G-protein coupled receptors and other signaling molecules. Conclusions This first genome-wide study of the developmental transcriptome in an early branching metazoan highlights major transcriptional events that accompany the pelagobenthic transition and point to a network of regulatory mechanisms that coordinate changes in morphology with shifting environmental demands. Metazoan developmental and structural gene orthologs are well-integrated into the expression profiles at every stage of sponge development, including the adult. The utilization of genes involved in metazoan-associated processes throughout sponge development emphasizes the potential of the genome of the last common ancestor of animals to generate phenotypic complexity.
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Affiliation(s)
- Cecilia Conaco
- Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
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92
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93
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Cellular and molecular processes leading to embryo formation in sponges: evidences for high conservation of processes throughout animal evolution. Dev Genes Evol 2012; 223:5-22. [PMID: 22543423 DOI: 10.1007/s00427-012-0399-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 03/26/2012] [Indexed: 12/21/2022]
Abstract
The emergence of multicellularity is regarded as one of the major evolutionary events of life. This transition unicellularity/pluricellularity was acquired independently several times (King 2004). The acquisition of multicellularity implies the emergence of cellular cohesion and means of communication, as well as molecular mechanisms enabling the control of morphogenesis and body plan patterning. Some of these molecular tools seem to have predated the acquisition of multicellularity while others are regarded as the acquisition of specific lineages. Morphogenesis consists in the spatial migration of cells or cell layers during embryonic development, metamorphosis, asexual reproduction, growth, and regeneration, resulting in the formation and patterning of a body. In this paper, our aim is to review what is currently known concerning basal metazoans--sponges' morphogenesis from the tissular, cellular, and molecular points of view--and what remains to elucidate. Our review attempts to show that morphogenetic processes found in sponges are as diverse and complex as those found in other animals. In true epithelial sponges (Homoscleromorpha), as well as in others, we find similar cell/layer movements, cellular shape changes involved in major morphogenetic processes such as embryogenesis or larval metamorphosis. Thus, sponges can provide information enabling us to better understand early animal evolution at the molecular level but also at the cell/cell layer level. Indeed, comparison of molecular tools will only be of value if accompanied by functional data and expression studies during morphogenetic processes.
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94
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Attenborough RMF, Hayward DC, Kitahara MV, Miller DJ, Ball EE. A "neural" enzyme in nonbilaterian animals and algae: preneural origins for peptidylglycine α-amidating monooxygenase. Mol Biol Evol 2012; 29:3095-109. [PMID: 22496439 DOI: 10.1093/molbev/mss114] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Secreted peptides, produced by enzymatic processing of larger precursor molecules, are found throughout the animal kingdom and play important regulatory roles as neurotransmitters and hormones. Many require a carboxy-terminal modification, involving the conversion of a glycine residue into an α-amide, for their biological activity. Two sequential enzymatic activities catalyze this conversion: a monooxygenase (peptidylglycine α-hydroxylating monooxygenase or PHM) and an amidating lyase (peptidyl-α-hydroxyglycine α-amidating lyase or PAL). In vertebrates, these activities reside in a single polypeptide known as peptidylglycine α-amidating monooxygenase (PAM), which has been extensively studied in the context of neuropeptide modification. Bifunctional PAMs have been reported from some invertebrates, but the phylogenetic distribution of PAMs and their evolutionary relationship to PALs and PHMs is unclear. Here, we report sequence and expression data for two PAMs from the coral Acropora millepora (Anthozoa, Cnidaria), as well as providing a comprehensive survey of the available sequence data from other organisms. These analyses indicate that bifunctional PAMs predate the origins of the nervous and endocrine systems, consistent with the idea that within the Metazoa their ancestral function may have been to amidate epitheliopeptides. More surprisingly, the phylogenomic survey also revealed the presence of PAMs in green algae (but not in higher plants or fungi), implying that the bifunctional enzyme either predates the plant/animal divergence and has subsequently been lost in a number of lineages or perhaps that convergent evolution or lateral gene transfer has occurred. This finding is consistent with recent discoveries that other molecules once thought of as "neural" predate nervous systems.
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Affiliation(s)
- Rosalind M F Attenborough
- Evolution, Ecology and Genetics, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
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95
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Simmons DK, Pang K, Martindale MQ. Lim homeobox genes in the Ctenophore Mnemiopsis leidyi: the evolution of neural cell type specification. EvoDevo 2012; 3:2. [PMID: 22239757 PMCID: PMC3283466 DOI: 10.1186/2041-9139-3-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 01/13/2012] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Nervous systems are thought to be important to the evolutionary success and diversification of metazoans, yet little is known about the origin of simple nervous systems at the base of the animal tree. Recent data suggest that ctenophores, a group of macroscopic pelagic marine invertebrates, are the most ancient group of animals that possess a definitive nervous system consisting of a distributed nerve net and an apical statocyst. This study reports on details of the evolution of the neural cell type specifying transcription factor family of LIM homeobox containing genes (Lhx), which have highly conserved functions in neural specification in bilaterian animals. RESULTS Using next generation sequencing, the first draft of the genome of the ctenophore Mnemiopsis leidyi has been generated. The Lhx genes in all animals are represented by seven subfamilies (Lhx1/5, Lhx3/4, Lmx, Islet, Lhx2/9, Lhx6/8, and LMO) of which four were found to be represented in the ctenophore lineage (Lhx1/5, Lhx3/4, Lmx, and Islet). Interestingly, the ctenophore Lhx gene complement is more similar to the sponge complement (sponges do not possess neurons) than to either the cnidarian-bilaterian or placozoan Lhx complements. Using whole mount in situ hybridization, the Lhx gene expression patterns were examined and found to be expressed around the blastopore and in cells that give rise to the apical organ and putative neural sensory cells. CONCLUSION This research gives us a first look at neural cell type specification in the ctenophore M. leidyi. Within M. leidyi, Lhx genes are expressed in overlapping domains within proposed neural cellular and sensory cell territories. These data suggest that Lhx genes likely played a conserved role in the patterning of sensory cells in the ancestor of sponges and ctenophores, and may provide a link to the expression of Lhx orthologs in sponge larval photoreceptive cells. Lhx genes were later co-opted into patterning more diversified complements of neural and non-neural cell types in later evolving animals.
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Affiliation(s)
- David K Simmons
- Kewalo Marine Laboratory, Department of Zoology, University of Hawaii at Manoa, Honolulu, HI, USA, 96813
| | - Kevin Pang
- Sars, International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway
| | - Mark Q Martindale
- Kewalo Marine Laboratory, Department of Zoology, University of Hawaii at Manoa, Honolulu, HI, USA, 96813
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96
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Abstract
Cnidarians belong to the first phylum differentiating a nervous system, thus providing suitable model systems to trace the origins of neurogenesis. Indeed corals, sea anemones, jellyfish and hydra contract, swim and catch their food thanks to sophisticated nervous systems that share with bilaterians common neurophysiological mechanisms. However, cnidarian neuroanatomies are quite diverse, and reconstructing the urcnidarian nervous system is ambiguous. At least a series of characters recognized in all classes appear plesiomorphic: (1) the three cell types that build cnidarian nervous systems (sensory-motor cells, ganglionic neurons and mechanosensory cells called nematocytes or cnidocytes); (2) an organization of nerve nets and nerve rings [those working as annular central nervous system (CNS)]; (3) a neuronal conduction via neurotransmitters; (4) a larval anterior sensory organ required for metamorphosis; (5) a persisting neurogenesis in adulthood. By contrast, the origin of the larval and adult neural stem cells differs between hydrozoans and other cnidarians; the sensory organs (ocelli, lens-eyes, statocysts) are present in medusae but absent in anthozoans; the electrical neuroid conduction is restricted to hydrozoans. Evo-devo approaches might help reconstruct the neurogenic status of the last common cnidarian ancestor. In fact, recent genomic analyses show that if most components of the postsynaptic density predate metazoan origin, the bilaterian neurogenic gene families originated later, in basal metazoans or as eumetazoan novelties. Striking examples are the ParaHox Gsx, Pax, Six, COUP-TF and Twist-type regulators, which seemingly exert neurogenic functions in cnidarians, including eye differentiation, and support the view of a two-step process in the emergence of neurogenesis.
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Affiliation(s)
- Brigitte Galliot
- Department of Genetics and Evolution, Faculty of Science, University of Geneva, Sciences III, 30 quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland.
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97
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Abstract
Adherens junctions are the most common junction type found in animal epithelia. Their core components are classical cadherins and catenins, which form membrane-spanning complexes that mediate intercellular binding on the extracellular side and associate with the actin cytoskeleton on the intracellular side. Junctional cadherin-catenin complexes are key elements involved in driving animal morphogenesis. Despite their ubiquity and importance, comparative studies of classical cadherins, catenins and their related molecules suggest that the cadherin/catenin-based adherens junctions have undergone structural and compositional transitions during the diversification of animal lineages. This chapter describes the molecular diversities related to the cadherin-catenin complex, based on accumulated molecular and genomic information. Understanding when and how the junctional cadherin-catenin complex originated, and its subsequent diversification in animals, promotes a comprehensive understanding of the mechanisms of animal morphological diversification.
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Affiliation(s)
- Oda Hiroki
- JT Biohistory Research Hall, 1-1 Murasaki-cho, 569-1125, Takatsuki, Osaka, Japan,
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98
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Mahmood K, Webb GI, Song J, Whisstock JC, Konagurthu AS. Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs. Nucleic Acids Res 2011; 40:e44. [PMID: 22210858 PMCID: PMC3315314 DOI: 10.1093/nar/gkr1261] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Broadly, computational approaches for ortholog assignment is a three steps process: (i) identify all putative homologs between the genomes, (ii) identify gene anchors and (iii) link anchors to identify best gene matches given their order and context. In this article, we engineer two methods to improve two important aspects of this pipeline [specifically steps (ii) and (iii)]. First, computing sequence similarity data [step (i)] is a computationally intensive task for large sequence sets, creating a bottleneck in the ortholog assignment pipeline. We have designed a fast and highly scalable sort-join method (afree) based on k-mer counts to rapidly compare all pairs of sequences in a large protein sequence set to identify putative homologs. Second, availability of complex genomes containing large gene families with prevalence of complex evolutionary events, such as duplications, has made the task of assigning orthologs and co-orthologs difficult. Here, we have developed an iterative graph matching strategy where at each iteration the best gene assignments are identified resulting in a set of orthologs and co-orthologs. We find that the afree algorithm is faster than existing methods and maintains high accuracy in identifying similar genes. The iterative graph matching strategy also showed high accuracy in identifying complex gene relationships. Standalone afree available from http://vbc.med.monash.edu.au/∼kmahmood/afree. EGM2, complete ortholog assignment pipeline (including afree and the iterative graph matching method) available from http://vbc.med.monash.edu.au/∼kmahmood/EGM2.
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Affiliation(s)
- Khalid Mahmood
- Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia
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Leys SP, Riesgo A. Epithelia, an evolutionary novelty of metazoans. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2011; 318:438-47. [PMID: 22057924 DOI: 10.1002/jez.b.21442] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 08/06/2011] [Accepted: 08/24/2011] [Indexed: 12/12/2022]
Abstract
At the point in animal evolution when cells began to adhere to each other they presumably initially functioned as colonies. The formation of an epithelium that enclosed and controlled an internal milieu would have been the first event to distinguish an individual animal from a colony. To better understand when the first epithelium arose and what its characteristics were, we evaluate the morphological, functional, and molecular characters of epithelia in sponges, considered here the extant representatives of the first metazoans. In particular, we show new claudin-like sequences from sponges align most closely with sequences from Drosophila that have a barrier function in septate junctions. We also show that type IV collagen, the main component of the basement membrane (BM), is present in calcareous sponges, and we confirm the presence of type IV-like collagen (spongin short chain collagen) in other sponges. Though in sponges as in other metazoans the epithelium has grades of specialization with varying complexity of junctions and the BM, the main character of a functional epithelium, the ability to seal and control the ionic composition of the internal milieu, is a property of even the simplest sponge epithelium, and therefore the first metazoans likely also had epithelia with these characteristics, which we consider a "true" epithelium.
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Affiliation(s)
- Sally P Leys
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
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Liebeskind BJ. Evolution of sodium channels and the new view of early nervous system evolution. Commun Integr Biol 2011; 4:679-83. [PMID: 22446526 PMCID: PMC3306330 DOI: 10.4161/cib.17069] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Advances in genomics have revealed that many genes implicated in the nervous systems of bilaterians were already present in the last common ancestor (LCA) of animals, and some even before that.(1) (-) (5) This new information coincides with a growing reinterpretation of cnidarian nervous systems which holds that they are 'fundamentally conventional' with regards to bilaterian nervous systems,(6) and do not represent ancient forms. Since in general adult forms are expected to be the most derived features of organisms, the study of non-bilaterian larval forms may be a better way to investigate potential plesiomorphies. We recently showed that voltage-gated sodium channel (Na(v)) genes, which make action potentials in nerves and muscles, were present in the LCA of animals and choanoflagellates, the closest unicellular relatives to animals.(2) This addendum will attempt to put this finding within the context of the new views of nervous system evolution.
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