1
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Jimenez-Guri E, Paganos P, La Vecchia C, Annona G, Caccavale F, Molina MD, Ferrández-Roldán A, Donnellan RD, Salatiello F, Johnstone A, Eliso MC, Spagnuolo A, Cañestro C, Albalat R, Martín-Durán JM, Williams EA, D'Aniello E, Arnone MI. Developmental toxicity of pre-production plastic pellets affects a large swathe of invertebrate taxa. Chemosphere 2024; 356:141887. [PMID: 38583530 DOI: 10.1016/j.chemosphere.2024.141887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/14/2024] [Accepted: 04/01/2024] [Indexed: 04/09/2024]
Abstract
Microplastics pose risks to marine organisms through ingestion, entanglement, and as carriers of toxic additives and environmental pollutants. Plastic pre-production pellet leachates have been shown to affect the development of sea urchins and, to some extent, mussels. The extent of those developmental effects on other animal phyla remains unknown. Here, we test the toxicity of environmental mixed nurdle samples and new PVC pellets for the embryonic development or asexual reproduction by regeneration of animals from all the major animal superphyla (Lophotrochozoa, Ecdysozoa, Deuterostomia and Cnidaria). Our results show diverse, concentration-dependent impacts in all the species sampled for new pellets, and for molluscs and deuterostomes for environmental samples. Embryo axial formation, cell specification and, specially, morphogenesis seem to be the main processes affected by plastic leachate exposure. Our study serves as a proof of principle for the potentially catastrophic effects that increasing plastic concentrations in the oceans and other ecosystems can have across animal populations from all major animal superphyla.
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Affiliation(s)
- Eva Jimenez-Guri
- Stazione Zoologica Anton Dohrn, Department of Biology and Evolution of Marine Organisms, Naples, Italy; Center for Ecology and Conservation, University of Exeter, Cornwall Campus, Penryn, UK.
| | - Periklis Paganos
- Stazione Zoologica Anton Dohrn, Department of Biology and Evolution of Marine Organisms, Naples, Italy
| | - Claudia La Vecchia
- Stazione Zoologica Anton Dohrn, Department of Biology and Evolution of Marine Organisms, Naples, Italy
| | - Giovanni Annona
- Stazione Zoologica Anton Dohrn, Department of Research Infrastructures for Marine Biological Resources, Naples, Italy
| | - Filomena Caccavale
- Stazione Zoologica Anton Dohrn, Department of Biology and Evolution of Marine Organisms, Naples, Italy
| | - Maria Dolores Molina
- Department of Genetica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Catalunya, Spain; Institute of Biomedicine of the University of Barcelona (IBUB), Catalunya, Spain
| | - Alfonso Ferrández-Roldán
- Department of Genetica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Catalunya, Spain; Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Catalunya, Spain
| | - Rory Daniel Donnellan
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Federica Salatiello
- Stazione Zoologica Anton Dohrn, Department of Biology and Evolution of Marine Organisms, Naples, Italy
| | - Adam Johnstone
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Maria Concetta Eliso
- Stazione Zoologica Anton Dohrn, Department of Biology and Evolution of Marine Organisms, Naples, Italy
| | - Antonietta Spagnuolo
- Stazione Zoologica Anton Dohrn, Department of Biology and Evolution of Marine Organisms, Naples, Italy
| | - Cristian Cañestro
- Department of Genetica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Catalunya, Spain; Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Catalunya, Spain
| | - Ricard Albalat
- Department of Genetica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Catalunya, Spain; Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Catalunya, Spain
| | - José María Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Elizabeth A Williams
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Enrico D'Aniello
- Stazione Zoologica Anton Dohrn, Department of Biology and Evolution of Marine Organisms, Naples, Italy
| | - Maria Ina Arnone
- Stazione Zoologica Anton Dohrn, Department of Biology and Evolution of Marine Organisms, Naples, Italy
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2
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García-Risco M, Calatayud S, Pedrini-Martha V, Albalat R, Palacios Ò, Capdevila M, Dallinger R. A de novo evolved domain improves the cadmium detoxification capacity of limpet metallothioneins. Sci Rep 2023; 13:8895. [PMID: 37264073 DOI: 10.1038/s41598-023-35786-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/23/2023] [Indexed: 06/03/2023] Open
Abstract
Metallothioneins (MTs) constitute an important family of metal binding proteins. Mollusk MTs, in particular, have been used as model systems to better understand the evolution of their metal binding features and functional adaptation. In the present study two recombinantly produced MTs, LgiMT1 and LgiMT2, and their de novo evolved γ domain, of the marine limpet Lottia gigantea, were analyzed by electronic spectroscopy and mass spectrometry. Both MT proteins, as well as their γ domains, exhibit a strong binding specificity for Cd(II), but not for Zn(II) or Cu(I). The LgiMTs' γ domain renders an MII4(SCys)10 cluster with an increased Cd stoichiometry (binding 4 instead of 3 Cd2+ ions), representing a novel structural element in the world of MTs, probably featuring an adamantane 3D structure. This cluster significantly improves the Cd(II)-binding performance of the full length proteins and thus contributes to the particularly high Cd coping capacity observed in free-living limpets.
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Affiliation(s)
- Mario García-Risco
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain
| | - Sara Calatayud
- Departament de Genètica, Facultat de Biologia, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Diagonal 643, 08028, Barcelona, Spain
| | - Veronika Pedrini-Martha
- Institute of Zoology, Center of Molecular Biosciences, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria
| | - Ricard Albalat
- Departament de Genètica, Facultat de Biologia, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Diagonal 643, 08028, Barcelona, Spain
| | - Òscar Palacios
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain
| | - Mercè Capdevila
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain.
| | - Reinhard Dallinger
- Institute of Zoology, Center of Molecular Biosciences, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria.
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3
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García-Risco M, González A, Calatayud S, Lopez-Jaramillo FJ, Pedrini-Martha V, Albalat R, Dallinger R, Dominguez-Vera JM, Palacios Ò, Capdevila M. Metal-dependent glycosylation in recombinant metallothioneins. Chem Commun (Camb) 2022; 58:13755-13758. [PMID: 36416731 DOI: 10.1039/d2cc05589a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We show for the first time glycosylation of recombinant metallothioneins (MTs) produced in E. coli. Interestingly, our results show that the glycosylation level of the recombinant MTs is inversely proportional to the degree of protein structuration, and reflects their different metal preferences.
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Affiliation(s)
- Mario García-Risco
- Department of Chemistry, Universitat Autònoma de Barcelona, Cerdanyola del Vallès (E-08193), Spain.
| | - Ana González
- Department of Inorganic Chemistry and Biotechnology Institute, University of Granada, Granada (E-18071), Spain.
| | - Sara Calatayud
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona (E-08028), Spain
| | - Francisco J Lopez-Jaramillo
- Department of Organic Chemistry and Biotechnology Institute, University of Granada, Granada (E-18071), Spain
| | - Veronika Pedrini-Martha
- Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck, Innsbruck (A-60210), Austria
| | - Ricard Albalat
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona (E-08028), Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona (E-08028), Spain
| | - Reinhard Dallinger
- Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck, Innsbruck (A-60210), Austria
| | - José M Dominguez-Vera
- Department of Inorganic Chemistry and Biotechnology Institute, University of Granada, Granada (E-18071), Spain.
| | - Òscar Palacios
- Department of Chemistry, Universitat Autònoma de Barcelona, Cerdanyola del Vallès (E-08193), Spain.
| | - Mercè Capdevila
- Department of Chemistry, Universitat Autònoma de Barcelona, Cerdanyola del Vallès (E-08193), Spain.
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4
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García-Risco M, Calatayud S, Pedrini-Martha V, Albalat R, Dallinger R, Palacios Ò, Capdevila M. Metal-Specificity Divergence between Metallothioneins of Nerita peloronta (Neritimorpha, Gastropoda) Sets the Starting Point for a Novel Chemical MT Classification Proposal. Int J Mol Sci 2021; 22:13114. [PMID: 34884919 PMCID: PMC8658704 DOI: 10.3390/ijms222313114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/27/2021] [Accepted: 12/02/2021] [Indexed: 11/29/2022] Open
Abstract
Metallothioneins' (MTs) biological function has been a matter of debate since their discovery. The importance to categorize these cysteine-rich proteins with high coordinating capacity into a specific group led to numerous classification proposals. We proposed a classification based on their metal-binding abilities, gradually sorting them from those with high selectivity towards Zn/Cd to those that are Cu-specific. However, the study of the NpeMT1 and NpeMT2isoforms of Nerita peloronta, has put a new perspective on this classification. N. peloronta has been chosen as a representative mollusk to elucidate the metal-binding abilities of Neritimorpha MTs, an order without any MTs characterized recently. Both isoforms have been recombinantly synthesized in cultures supplemented with ZnII, CdII, or CuII, and the purified metal-MT complexes have been thoroughly characterized by spectroscopic and spectrometric methods, leading to results that confirmed that Neritimorpha share Cd-selective MTs with Caenogastropoda and Heterobranchia, solving a so far unresolved question. NpeMTs show high coordinating preferences towards divalent metal ions, although one of them (NpeMT1) shares features with the so-called genuine Zn-thioneins, while the other (NpeMT2) exhibits a higher preference for Cd. The dissimilarities between the two isoforms let a window open to a new proposal of chemical MT classification.
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Affiliation(s)
- Mario García-Risco
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, E-08193 Cerdanyola del Vallès, Spain; (M.G.-R.); (Ò.P.)
| | - Sara Calatayud
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 643, E-08028 Barcelona, Spain; (S.C.); (R.A.)
| | - Veronika Pedrini-Martha
- Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria;
| | - Ricard Albalat
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 643, E-08028 Barcelona, Spain; (S.C.); (R.A.)
| | - Reinhard Dallinger
- Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria;
| | - Òscar Palacios
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, E-08193 Cerdanyola del Vallès, Spain; (M.G.-R.); (Ò.P.)
| | - Mercè Capdevila
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, E-08193 Cerdanyola del Vallès, Spain; (M.G.-R.); (Ò.P.)
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5
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Ferrández-Roldán A, Fabregà-Torrus M, Sánchez-Serna G, Duran-Bello E, Joaquín-Lluís M, Bujosa P, Plana-Carmona M, Garcia-Fernàndez J, Albalat R, Cañestro C. Cardiopharyngeal deconstruction and ancestral tunicate sessility. Nature 2021; 599:431-435. [PMID: 34789899 DOI: 10.1038/s41586-021-04041-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 09/17/2021] [Indexed: 12/26/2022]
Abstract
A central question in chordate evolution is the origin of sessility in adult ascidians, and whether the appendicularian complete free-living style represents a primitive or derived condition among tunicates1. According to the 'a new heart for a new head' hypothesis, the evolution of the cardiopharyngeal gene regulatory network appears as a pivotal aspect to understand the evolution of the lifestyles of chordates2-4. Here we show that appendicularians experienced massive ancestral losses of cardiopharyngeal genes and subfunctions, leading to the 'deconstruction' of two ancestral modules of the tunicate cardiopharyngeal gene regulatory network. In ascidians, these modules are related to early and late multipotency, which is involved in lineage cell-fate determination towards the first and second heart fields and siphon muscles. Our work shows that the deconstruction of the cardiopharyngeal gene regulatory network involved the regressive loss of the siphon muscle, supporting an evolutionary scenario in which ancestral tunicates had a sessile ascidian-like adult lifestyle. In agreement with this scenario, our findings also suggest that this deconstruction contributed to the acceleration of cardiogenesis and the redesign of the heart into an open-wide laminar structure in appendicularians as evolutionary adaptations during their transition to a complete pelagic free-living style upon the innovation of the food-filtering house5.
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Affiliation(s)
- Alfonso Ferrández-Roldán
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Marc Fabregà-Torrus
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Gaspar Sánchez-Serna
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Enya Duran-Bello
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Martí Joaquín-Lluís
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Paula Bujosa
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Marcos Plana-Carmona
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Jordi Garcia-Fernàndez
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.,Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Ricard Albalat
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Cristian Cañestro
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain. .,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
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6
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Calatayud S, Garcia-Risco M, Palacios Ò, Capdevila M, Cañestro C, Albalat R. Tunicates Illuminate the Enigmatic Evolution of Chordate Metallothioneins by Gene Gains and Losses, Independent Modular Expansions, and Functional Convergences. Mol Biol Evol 2021; 38:4435-4448. [PMID: 34146103 PMCID: PMC8476144 DOI: 10.1093/molbev/msab184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
To investigate novel patterns and processes of protein evolution, we have focused in the metallothioneins (MTs), a singular group of metal-binding, cysteine-rich proteins that, due to their high degree of sequence diversity, still represents a "black hole" in Evolutionary Biology. We have identified and analyzed more than 160 new MTs in nonvertebrate chordates (especially in 37 species of ascidians, 4 thaliaceans, and 3 appendicularians) showing that prototypic tunicate MTs are mono-modular proteins with a pervasive preference for cadmium ions, whereas vertebrate and cephalochordate MTs are bimodular proteins with diverse metal preferences. These structural and functional differences imply a complex evolutionary history of chordate MTs-including de novo emergence of genes and domains, processes of convergent evolution, events of gene gains and losses, and recurrent amplifications of functional domains-that would stand for an unprecedented case in the field of protein evolution.
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Affiliation(s)
- Sara Calatayud
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Mario Garcia-Risco
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Òscar Palacios
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Mercè Capdevila
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Cristian Cañestro
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Ricard Albalat
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
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7
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Calatayud S, Garcia-Risco M, Capdevila M, Cañestro C, Palacios Ò, Albalat R. Modular Evolution and Population Variability of Oikopleura dioica Metallothioneins. Front Cell Dev Biol 2021; 9:702688. [PMID: 34277643 PMCID: PMC8283569 DOI: 10.3389/fcell.2021.702688] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/09/2021] [Indexed: 01/29/2023] Open
Abstract
Chordate Oikopleura dioica probably is the fastest evolving metazoan reported so far, and thereby, a suitable system in which to explore the limits of evolutionary processes. For this reason, and in order to gain new insights on the evolution of protein modularity, we have investigated the organization, function and evolution of multi-modular metallothionein (MT) proteins in O. dioica. MTs are a heterogeneous group of modular proteins defined by their cysteine (C)-rich domains, which confer the capacity of coordinating different transition metal ions. O. dioica has two MTs, a bi-modular OdiMT1 consisting of two domains (t-12C and 12C), and a multi-modular OdiMT2 with six t-12C/12C repeats. By means of mass spectrometry and spectroscopy of metal-protein complexes, we have shown that the 12C domain is able to autonomously bind four divalent metal ions, although the t-12C/12C pair –as it is found in OdiMT1– is the optimized unit for divalent metal binding. We have also shown a direct relationship between the number of the t-12C/12C repeats and the metal-binding capacity of the MTs, which means a stepwise mode of functional and structural evolution for OdiMT2. Finally, after analyzing four different O. dioica populations worldwide distributed, we have detected several OdiMT2 variants with changes in their number of t-12C/12C domain repeats. This finding reveals that the number of repeats fluctuates between current O. dioica populations, which provides a new perspective on the evolution of domain repeat proteins.
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Affiliation(s)
- Sara Calatayud
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Mario Garcia-Risco
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Mercè Capdevila
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Cristian Cañestro
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Òscar Palacios
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ricard Albalat
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
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8
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Calatayud S, Garcia-Risco M, Pedrini-Martha V, Eernisse DJ, Dallinger R, Palacios Ò, Capdevila M, Albalat R. Modularity in Protein Evolution: Modular Organization and De Novo Domain Evolution in Mollusk Metallothioneins. Mol Biol Evol 2021; 38:424-436. [PMID: 32915992 PMCID: PMC7826182 DOI: 10.1093/molbev/msaa230] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Metallothioneins (MTs) are proteins devoted to the control of metal homeostasis and detoxification, and therefore, MTs have been crucial for the adaptation of the living beings to variable situations of metal bioavailability. The evolution of MTs is, however, not yet fully understood, and to provide new insights into it, we have investigated the MTs in the diverse classes of Mollusks. We have shown that most molluskan MTs are bimodular proteins that combine six domains—α, β1, β2, β3, γ, and δ—in a lineage-specific manner. We have functionally characterized the Neritimorpha β3β1 and the Patellogastropoda γβ1 MTs, demonstrating the metal-binding capacity of the new γ domain. Our results have revealed a modular organization of mollusk MT, whose evolution has been impacted by duplication, loss, and de novo emergence of domains. MTs represent a paradigmatic example of modular evolution probably driven by the structural and functional requirements of metal binding.
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Affiliation(s)
- Sara Calatayud
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Mario Garcia-Risco
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Veronika Pedrini-Martha
- Department of Zoology and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Douglas J Eernisse
- Department of Biological Science, California State University Fullerton, Fullerton, CA
| | - Reinhard Dallinger
- Department of Zoology and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Òscar Palacios
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Mercè Capdevila
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ricard Albalat
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
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9
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Martí-Solans J, Godoy-Marín H, Diaz-Gracia M, Onuma TA, Nishida H, Albalat R, Cañestro C. Massive Gene Loss and Function Shuffling in Appendicularians Stretch the Boundaries of Chordate Wnt Family Evolution. Front Cell Dev Biol 2021; 9:700827. [PMID: 34179025 PMCID: PMC8220140 DOI: 10.3389/fcell.2021.700827] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 05/19/2021] [Indexed: 01/17/2023] Open
Abstract
Gene loss is a pervasive source of genetic variation that influences species evolvability, biodiversity and the innovation of evolutionary adaptations. To better understand the evolutionary patterns and impact of gene loss, here we investigate as a case study the evolution of the wingless (Wnt) family in the appendicularian tunicate Oikopleura dioica, an emergent EvoDevo model characterized by its proneness to lose genes among chordates. Genome survey and phylogenetic analyses reveal that only four of the thirteen Wnt subfamilies have survived in O. dioica—Wnt5, Wnt10, Wnt11, and Wnt16,—representing the minimal Wnt repertoire described in chordates. While the loss of Wnt4 and Wnt8 likely occurred in the last common ancestor of tunicates, representing therefore a synapomorphy of this subphylum, the rest of losses occurred during the evolution of appendicularians. This work provides the first complete Wnt developmental expression atlas in a tunicate and the first insights into the evolution of Wnt developmental functions in appendicularians. Our work highlights three main evolutionary patterns of gene loss: (1) conservation of ancestral Wnt expression domains not affected by gene losses; (2) function shuffling among Wnt paralogs accompanied by gene losses; and (3) extinction of Wnt expression in certain embryonic directly correlated with gene losses. Overall our work reveals that in contrast to “conservative” pattern of evolution of cephalochordates and vertebrates, O. dioica shows an even more radical “liberal” evolutionary pattern than that described ascidian tunicates, stretching the boundaries of the malleability of Wnt family evolution in chordates.
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Affiliation(s)
- Josep Martí-Solans
- Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Hector Godoy-Marín
- Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Miriam Diaz-Gracia
- Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Takeshi A Onuma
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Ricard Albalat
- Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Cristian Cañestro
- Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
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10
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García-Risco M, Calatayud S, Niederwanger M, Albalat R, Palacios Ò, Capdevila M, Dallinger R. Two Unconventional Metallothioneins in the Apple Snail Pomacea bridgesii Have Lost Their Metal Specificity during Adaptation to Freshwater Habitats. Int J Mol Sci 2020; 22:ijms22010095. [PMID: 33374169 PMCID: PMC7796288 DOI: 10.3390/ijms22010095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 01/08/2023] Open
Abstract
Metallothioneins (MTs) are a diverse group of proteins responsible for the control of metal homeostasis and detoxification. To investigate the impact that environmental conditions might have had on the metal-binding abilities of these proteins, we have characterized the MTs from the apple snail Pomacea bridgesii, a gastropod species belonging to the class of Caenogastropoda with an amphibious lifestyle facing diverse situations of metal bioavailability. P. bridgesii has two structurally divergent MTs, named PbrMT1 and PbrMT2, that are longer than other gastropod MTs due to the presence of extra sequence motifs and metal-binding domains. We have characterized the Zn(II), Cd(II), and Cu(I) binding abilities of these two MTs after their heterologous expression in E. coli. Our results have revealed that despite their structural differences, both MTs share an unspecific metal-binding character, and a great ability to cope with elevated amounts of different metal ions. Our analyses have also revealed slight divergences in their metal-binding features: PbrMT1 shows a more pronounced Zn(II)-thionein character than PbrMT2, while the latter has a stronger Cu(I)-thionein character. The characterization of these two unconventional PbrMTs supports the loss of the metal-binding specificity during the evolution of the MTs of the Ampullariid family, and further suggests an evolutionary link of this loss with the adaptation of these gastropod lineages to metal-poor freshwater habitats.
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Affiliation(s)
- Mario García-Risco
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, E-08193 Cerdanyola del Vallès, Spain; (M.G.-R.); (Ò.P.); (M.C.)
| | - Sara Calatayud
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 643, E-08028 Barcelona, Spain; (S.C.); (R.A.)
| | - Michael Niederwanger
- Institute of Zoology, Center of Molecular Biosciences, University of Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria;
| | - Ricard Albalat
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 643, E-08028 Barcelona, Spain; (S.C.); (R.A.)
| | - Òscar Palacios
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, E-08193 Cerdanyola del Vallès, Spain; (M.G.-R.); (Ò.P.); (M.C.)
| | - Mercè Capdevila
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, E-08193 Cerdanyola del Vallès, Spain; (M.G.-R.); (Ò.P.); (M.C.)
| | - Reinhard Dallinger
- Institute of Zoology, Center of Molecular Biosciences, University of Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria;
- Correspondence:
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11
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Dallinger R, Zerbe O, Baumann C, Egger B, Capdevila M, Palacios Ò, Albalat R, Calatayud S, Ladurner P, Schlick-Steiner BC, Steiner FM, Pedrini-Martha V, Lackner R, Lindner H, Dvorak M, Niederwanger M, Schnegg R, Atrian S. Metallomics reveals a persisting impact of cadmium on the evolution of metal-selective snail metallothioneins. Metallomics 2020; 12:702-720. [DOI: 10.1039/c9mt00259f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The tiny contribution of cadmium (Cd) to the composition of the earth's crust contrasts with its high biological significance. We suggest that in gastropod clades, the protein family of metallothioneins (MTs) has evolved to specifically detoxify Cd.
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Affiliation(s)
- Reinhard Dallinger
- Department of Zoology
- University of Innsbruck
- Austria
- Center for Molecular Biosciences Innsbruck
- Austria
| | - Oliver Zerbe
- Department of Chemistry
- University of Zürich
- Switzerland
| | | | | | - Mercé Capdevila
- Departament de Química
- Universitat Autònoma de Barcelona
- Spain
| | - Òscar Palacios
- Departament de Química
- Universitat Autònoma de Barcelona
- Spain
| | | | | | - Peter Ladurner
- Department of Zoology
- University of Innsbruck
- Austria
- Center for Molecular Biosciences Innsbruck
- Austria
| | | | | | | | | | - Herbert Lindner
- Division of Clinical Biochemistry
- Innsbruck Medical University
- Austria
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12
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Almazán A, Ferrández-Roldán A, Albalat R, Cañestro C. Developmental atlas of appendicularian Oikopleura dioica actins provides new insights into the evolution of the notochord and the cardio-paraxial muscle in chordates. Dev Biol 2019; 448:260-270. [DOI: 10.1016/j.ydbio.2018.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/13/2018] [Accepted: 09/05/2018] [Indexed: 12/22/2022]
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13
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Ferrández-Roldán A, Martí-Solans J, Cañestro C, Albalat R. Oikopleura dioica: An Emergent Chordate Model to Study the Impact of Gene Loss on the Evolution of the Mechanisms of Development. Results Probl Cell Differ 2019; 68:63-105. [PMID: 31598853 DOI: 10.1007/978-3-030-23459-1_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The urochordate Oikopleura dioica is emerging as a nonclassical animal model in the field of evolutionary developmental biology (a.k.a. evo-devo) especially attractive for investigating the impact of gene loss on the evolution of mechanisms of development. This is because this organism fulfills the requirements of an animal model (i.e., has a simple and accessible morphology, a short generation time and life span, and affordable culture in the laboratory and amenable experimental manipulation), but also because O. dioica occupies a key phylogenetic position to understand the diversification and origin of our own phylum, the chordates. During its evolution, O. dioica genome has suffered a drastic process of compaction, becoming the smallest known chordate genome, a process that has been accompanied by exacerbating amount of gene losses. Interestingly, however, despite the extensive gene losses, including entire regulatory pathways essential for the embryonic development of other chordates, O. dioica retains the typical chordate body plan. This unexpected situation led to the formulation of the so-called inverse paradox of evo-devo, that is, when a genetic diversity is able to maintain a phenotypic unity. This chapter reviews the biological features of O. dioica as a model animal, along with the current data on the evolution of its genes and genome. We pay special attention to the numerous examples of gene losses that have taken place during the evolution of this unique animal model, which is helping us to understand to which the limits of evo-devo can be pushed off.
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Affiliation(s)
- Alfonso Ferrández-Roldán
- Facultat de Biologia, Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Josep Martí-Solans
- Facultat de Biologia, Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Cristian Cañestro
- Facultat de Biologia, Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Ricard Albalat
- Facultat de Biologia, Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain.
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14
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Torres-Águila NP, Martí-Solans J, Ferrández-Roldán A, Almazán A, Roncalli V, D'Aniello S, Romano G, Palumbo A, Albalat R, Cañestro C. Diatom bloom-derived biotoxins cause aberrant development and gene expression in the appendicularian chordate Oikopleura dioica. Commun Biol 2018; 1:121. [PMID: 30272001 PMCID: PMC6123688 DOI: 10.1038/s42003-018-0127-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/31/2018] [Indexed: 12/18/2022] Open
Abstract
Investigating environmental hazards than could affect appendicularians is of prime ecological interest because they are among the most abundant components of the mesozooplankton. This work shows that embryo development of the appendicularian Oikopleura dioica is compromised by diatom bloom-derived biotoxins, even at concentrations in the same range as those measured after blooms. Developmental gene expression analysis of biotoxin-treated embryos uncovers an aberrant golf ball-like phenotype affecting morphogenesis, midline convergence, and tail elongation. Biotoxins induce a rapid upregulation of defensome genes, and considerable delay and silencing of zygotic transcription of developmental genes. Upon a possible future intensification of blooms associated with ocean warming and acidification, our work puts an alert on the potential impact that an increase of biotoxins may have on marine food webs, and points to defensome genes as molecular biosensors that marine ecologists could use to monitor the genetic stress of natural populations exposed to microalgal blooms.
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Affiliation(s)
- Nuria P Torres-Águila
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona. Av. Diagonal 643, 08028, Barcelona, Catalonia, Spain
| | - Josep Martí-Solans
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona. Av. Diagonal 643, 08028, Barcelona, Catalonia, Spain
| | - Alfonso Ferrández-Roldán
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona. Av. Diagonal 643, 08028, Barcelona, Catalonia, Spain
| | - Alba Almazán
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona. Av. Diagonal 643, 08028, Barcelona, Catalonia, Spain
| | - Vittoria Roncalli
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona. Av. Diagonal 643, 08028, Barcelona, Catalonia, Spain
| | - Salvatore D'Aniello
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale 80121, Napoli, Italy
| | - Giovanna Romano
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Anna Palumbo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale 80121, Napoli, Italy
| | - Ricard Albalat
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona. Av. Diagonal 643, 08028, Barcelona, Catalonia, Spain.
| | - Cristian Cañestro
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona. Av. Diagonal 643, 08028, Barcelona, Catalonia, Spain.
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15
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Somorjai IML, Martí-Solans J, Diaz-Gracia M, Nishida H, Imai KS, Escrivà H, Cañestro C, Albalat R. Wnt evolution and function shuffling in liberal and conservative chordate genomes. Genome Biol 2018; 19:98. [PMID: 30045756 PMCID: PMC6060547 DOI: 10.1186/s13059-018-1468-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/22/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND What impact gene loss has on the evolution of developmental processes, and how function shuffling has affected retained genes driving essential biological processes, remain open questions in the fields of genome evolution and EvoDevo. To investigate these problems, we have analyzed the evolution of the Wnt ligand repertoire in the chordate phylum as a case study. RESULTS We conduct an exhaustive survey of Wnt genes in genomic databases, identifying 156 Wnt genes in 13 non-vertebrate chordates. This represents the most complete Wnt gene catalog of the chordate subphyla and has allowed us to resolve previous ambiguities about the orthology of many Wnt genes, including the identification of WntA for the first time in chordates. Moreover, we create the first complete expression atlas for the Wnt family during amphioxus development, providing a useful resource to investigate the evolution of Wnt expression throughout the radiation of chordates. CONCLUSIONS Our data underscore extraordinary genomic stasis in cephalochordates, which contrasts with the liberal and dynamic evolutionary patterns of gene loss and duplication in urochordate genomes. Our analysis has allowed us to infer ancestral Wnt functions shared among all chordates, several cases of function shuffling among Wnt paralogs, as well as unique expression domains for Wnt genes that likely reflect functional innovations in each chordate lineage. Finally, we propose a potential relationship between the evolution of WntA and the evolution of the mouth in chordates.
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Affiliation(s)
- Ildikó M L Somorjai
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, KY16 9ST, Scotland, UK.
- Scottish Oceans Institute, School of Biology, University of St Andrews, East Sands, St Andrews, KY16 8LB, Scotland, UK.
| | - Josep Martí-Solans
- Departament de Genètica, , Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Miriam Diaz-Gracia
- Departament de Genètica, , Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Kaoru S Imai
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Hector Escrivà
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650, Banyuls/Mer, France
| | - Cristian Cañestro
- Departament de Genètica, , Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
| | - Ricard Albalat
- Departament de Genètica, , Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
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16
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Handberg-Thorsager M, Gutierrez-Mazariegos J, Arold ST, Kumar Nadendla E, Bertucci PY, Germain P, Tomançak P, Pierzchalski K, Jones JW, Albalat R, Kane MA, Bourguet W, Laudet V, Arendt D, Schubert M. The ancestral retinoic acid receptor was a low-affinity sensor triggering neuronal differentiation. Sci Adv 2018; 4:eaao1261. [PMID: 29492455 PMCID: PMC5821490 DOI: 10.1126/sciadv.aao1261] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 01/10/2018] [Indexed: 06/02/2023]
Abstract
Retinoic acid (RA) is an important intercellular signaling molecule in vertebrate development, with a well-established role in the regulation of hox genes during hindbrain patterning and in neurogenesis. However, the evolutionary origin of the RA signaling pathway remains elusive. To elucidate the evolution of the RA signaling system, we characterized RA metabolism and signaling in the marine annelid Platynereis dumerilii, a powerful model for evolution, development, and neurobiology. Binding assays and crystal structure analyses show that the annelid retinoic acid receptor (RAR) binds RA and activates transcription just as vertebrate RARs, yet with a different ligand-binding pocket and lower binding affinity, suggesting a permissive rather than instructive role of RA signaling. RAR knockdown and RA treatment of swimming annelid larvae further reveal that the RA signal is locally received in the medial neuroectoderm, where it controls neurogenesis and axon outgrowth, whereas the spatial colinear hox gene expression in the neuroectoderm remains unaffected. These findings suggest that one early role of the new RAR in bilaterian evolution was to control the spatially restricted onset of motor and interneuron differentiation in the developing ventral nerve cord and to indicate that the regulation of hox-controlled anterior-posterior patterning arose only at the base of the chordates, concomitant with a high-affinity RAR needed for the interpretation of a complex RA gradient.
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Affiliation(s)
- Mette Handberg-Thorsager
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
| | - Juliana Gutierrez-Mazariegos
- Molecular Zoology Team, Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, Institut National de la Recherche Agronomique, Ecole Normale Supérieure de Lyon, 46 Allée d’Italie, 69364 Lyon Cedex 07, France
| | - Stefan T. Arold
- King Abdullah University of Science and Technology, Center for Computational Bioscience Research, Division of Biological and Environmental Sciences and Engineering, Thuwal 23955-6900, Saudi Arabia
| | - Eswar Kumar Nadendla
- Centre de Biochimie Structurale, Inserm, CNRS, Université de Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Paola Y. Bertucci
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
| | - Pierre Germain
- Centre de Biochimie Structurale, Inserm, CNRS, Université de Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Pavel Tomançak
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Keely Pierzchalski
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 North Pine Street, Baltimore, MD 21201, USA
| | - Jace W. Jones
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 North Pine Street, Baltimore, MD 21201, USA
| | - Ricard Albalat
- Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain
| | - Maureen A. Kane
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 North Pine Street, Baltimore, MD 21201, USA
| | - William Bourguet
- Centre de Biochimie Structurale, Inserm, CNRS, Université de Montpellier, 29 Rue de Navacelles, 34090 Montpellier, France
| | - Vincent Laudet
- Molecular Zoology Team, Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, Institut National de la Recherche Agronomique, Ecole Normale Supérieure de Lyon, 46 Allée d’Italie, 69364 Lyon Cedex 07, France
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Michael Schubert
- Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Université Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, 181 Chemin du Lazaret, 06230 Villefranche-sur-Mer, France
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17
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Dvorak M, Lackner R, Niederwanger M, Rotondo C, Schnegg R, Ladurner P, Pedrini-Martha V, Salvenmoser W, Kremser L, Lindner H, García-Risco M, Calatayud S, Albalat R, Palacios Ò, Capdevila M, Dallinger R. Metal binding functions of metallothioneins in the slugArion vulgarisdiffer from metal-specific isoforms of terrestrial snails. Metallomics 2018; 10:1638-1654. [DOI: 10.1039/c8mt00215k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Arion vulgarisis a European slug with a huge potential for accumulating and detoxifying heavy metals.
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Affiliation(s)
- Martin Dvorak
- Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck
- A-6020 Innsbruck
- Austria
| | - Reinhard Lackner
- Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck
- A-6020 Innsbruck
- Austria
| | - Michael Niederwanger
- Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck
- A-6020 Innsbruck
- Austria
| | - Claire Rotondo
- Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck
- A-6020 Innsbruck
- Austria
| | - Raimund Schnegg
- Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck
- A-6020 Innsbruck
- Austria
| | - Peter Ladurner
- Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck
- A-6020 Innsbruck
- Austria
| | - Veronika Pedrini-Martha
- Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck
- A-6020 Innsbruck
- Austria
| | - Willi Salvenmoser
- Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck
- A-6020 Innsbruck
- Austria
| | - Leopold Kremser
- Innsbruck Medical University, Biocenter, Division of Clinical Biochemistry
- A-6020 Innsbruck
- Austria
| | - Herbert Lindner
- Innsbruck Medical University, Biocenter, Division of Clinical Biochemistry
- A-6020 Innsbruck
- Austria
| | - Mario García-Risco
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona
- Barcelona
- Spain
| | - Sara Calatayud
- Departament de Genètica, Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona
- E-08028 Barcelona
- Spain
| | - Ricard Albalat
- Departament de Genètica, Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona
- E-08028 Barcelona
- Spain
| | - Òscar Palacios
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona
- Barcelona
- Spain
| | - Mercè Capdevila
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona
- Barcelona
- Spain
| | - Reinhard Dallinger
- Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck
- A-6020 Innsbruck
- Austria
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Calatayud S, Garcia-Risco M, Rojas NS, Espinosa-Sánchez L, Artime S, Palacios Ò, Cañestro C, Albalat R. Metallothioneins of the urochordate Oikopleura dioica have Cys-rich tandem repeats, large size and cadmium-binding preference. Metallomics 2018; 10:1585-1594. [DOI: 10.1039/c8mt00177d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Oikopleura dioica has the longest metallothionein described so far, made of repeats generated by a modular and step-wise evolution.
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Affiliation(s)
- Sara Calatayud
- Departament de Genètica
- Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio)
- Facultat de Biologia
- Universitat de Barcelona
- Barcelona
| | - Mario Garcia-Risco
- Departament de Química
- Facultat de Ciències
- Universitat Autònoma de Barcelona
- E-08193 Cerdanyola del Vallès
- Spain
| | - Natalia S. Rojas
- Departament de Genètica
- Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio)
- Facultat de Biologia
- Universitat de Barcelona
- Barcelona
| | - Lizethe Espinosa-Sánchez
- Departament de Genètica
- Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio)
- Facultat de Biologia
- Universitat de Barcelona
- Barcelona
| | - Sebastián Artime
- Departament de Genètica
- Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio)
- Facultat de Biologia
- Universitat de Barcelona
- Barcelona
| | - Òscar Palacios
- Departament de Química
- Facultat de Ciències
- Universitat Autònoma de Barcelona
- E-08193 Cerdanyola del Vallès
- Spain
| | - Cristian Cañestro
- Departament de Genètica
- Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio)
- Facultat de Biologia
- Universitat de Barcelona
- Barcelona
| | - Ricard Albalat
- Departament de Genètica
- Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio)
- Facultat de Biologia
- Universitat de Barcelona
- Barcelona
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Martí-Solans J, Belyaeva OV, Torres-Aguila NP, Kedishvili NY, Albalat R, Cañestro C. Coelimination and Survival in Gene Network Evolution: Dismantling the RA-Signaling in a Chordate. Mol Biol Evol 2016; 33:2401-16. [PMID: 27406791 DOI: 10.1093/molbev/msw118] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The bloom of genomics is revealing gene loss as a pervasive evolutionary force generating genetic diversity that shapes the evolution of species. Outside bacteria and yeast, however, the understanding of the process of gene loss remains elusive, especially in the evolution of animal species. Here, using the dismantling of the retinoic acid metabolic gene network (RA-MGN) in the chordate Oikopleura dioica as a case study, we combine approaches of comparative genomics, phylogenetics, biochemistry, and developmental biology to investigate the mutational robustness associated to biased patterns of gene loss. We demonstrate the absence of alternative pathways for RA-synthesis in O. dioica, which suggests that gene losses of RA-MGN were not compensated by mutational robustness, but occurred in a scenario of regressive evolution. In addition, the lack of drastic phenotypic changes associated to the loss of RA-signaling provides an example of the inverse paradox of Evo-Devo. This work illustrates how the identification of patterns of gene coelimination-in our case five losses (Rdh10, Rdh16, Bco1, Aldh1a, and Cyp26)-is a useful strategy to recognize gene network modules associated to distinct functions. Our work also illustrates how the identification of survival genes helps to recognize neofunctionalization events and ancestral functions. Thus, the survival and extensive duplication of Cco and RdhE2 in O. dioica correlated with the acquisition of complex compartmentalization of expression domains in the digestive system and a process of enzymatic neofunctionalization of the Cco, while the surviving Aldh8 could be related to its ancestral housekeeping role against toxic aldehydes.
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Affiliation(s)
- Josep Martí-Solans
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Olga V Belyaeva
- Department of Biochemistry and Molecular Genetics, University of Alabama-Birmingham
| | - Nuria P Torres-Aguila
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Natalia Y Kedishvili
- Department of Biochemistry and Molecular Genetics, University of Alabama-Birmingham
| | - Ricard Albalat
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Cristian Cañestro
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
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Martí-Solans J, Ferrández-Roldán A, Godoy-Marín H, Badia-Ramentol J, Torres-Aguila NP, Rodríguez-Marí A, Bouquet JM, Chourrout D, Thompson EM, Albalat R, Cañestro C. Oikopleura dioicaculturing made easy: A Low-Cost facility for an emerging animal model in EvoDevo. Genesis 2014; 53:183-93. [DOI: 10.1002/dvg.22800] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/04/2014] [Accepted: 07/07/2014] [Indexed: 12/11/2022]
Affiliation(s)
- Josep Martí-Solans
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio); Universitat de Barcelona; Barcelona 08028 Spain
| | - Alfonso Ferrández-Roldán
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio); Universitat de Barcelona; Barcelona 08028 Spain
| | - Hector Godoy-Marín
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio); Universitat de Barcelona; Barcelona 08028 Spain
| | - Jordi Badia-Ramentol
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio); Universitat de Barcelona; Barcelona 08028 Spain
| | - Nuria P. Torres-Aguila
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio); Universitat de Barcelona; Barcelona 08028 Spain
| | - Adriana Rodríguez-Marí
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio); Universitat de Barcelona; Barcelona 08028 Spain
| | - Jean Marie Bouquet
- Sars International Centre for Marine Molecular Biology; University of Bergen; N-5008 Bergen Bergen Norway
- Department of Biology; University of Bergen; Postbox 7803 N-5020 Bergen Norway
| | - Daniel Chourrout
- Sars International Centre for Marine Molecular Biology; University of Bergen; N-5008 Bergen Bergen Norway
| | - Eric M. Thompson
- Sars International Centre for Marine Molecular Biology; University of Bergen; N-5008 Bergen Bergen Norway
- Department of Biology; University of Bergen; Postbox 7803 N-5020 Bergen Norway
| | - Ricard Albalat
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio); Universitat de Barcelona; Barcelona 08028 Spain
| | - Cristian Cañestro
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio); Universitat de Barcelona; Barcelona 08028 Spain
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Borràs E, Albalat R, Duester G, Parés X, Farrés J. The Xenopus alcohol dehydrogenase gene family: characterization and comparative analysis incorporating amphibian and reptilian genomes. BMC Genomics 2014; 15:216. [PMID: 24649825 PMCID: PMC4028059 DOI: 10.1186/1471-2164-15-216] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 03/11/2014] [Indexed: 11/12/2022] Open
Abstract
Background The alcohol dehydrogenase (ADH) gene family uniquely illustrates the concept of enzymogenesis. In vertebrates, tandem duplications gave rise to a multiplicity of forms that have been classified in eight enzyme classes, according to primary structure and function. Some of these classes appear to be exclusive of particular organisms, such as the frog ADH8, a unique NADP+-dependent ADH enzyme. This work describes the ADH system of Xenopus, as a model organism, and explores the first amphibian and reptilian genomes released in order to contribute towards a better knowledge of the vertebrate ADH gene family. Results Xenopus cDNA and genomic sequences along with expressed sequence tags (ESTs) were used in phylogenetic analyses and structure-function correlations of amphibian ADHs. Novel ADH sequences identified in the genomes of Anolis carolinensis (anole lizard) and Pelodiscus sinensis (turtle) were also included in these studies. Tissue and stage-specific libraries provided expression data, which has been supported by mRNA detection in Xenopus laevis tissues and regulatory elements in promoter regions. Exon-intron boundaries, position and orientation of ADH genes were deduced from the amphibian and reptilian genome assemblies, thus revealing syntenic regions and gene rearrangements with respect to the human genome. Our results reveal the high complexity of the ADH system in amphibians, with eleven genes, coding for seven enzyme classes in Xenopus tropicalis. Frogs possess the amphibian-specific ADH8 and the novel ADH1-derived forms ADH9 and ADH10. In addition, they exhibit ADH1, ADH2, ADH3 and ADH7, also present in reptiles and birds. Class-specific signatures have been assigned to ADH7, and ancestral ADH2 is predicted to be a mixed-class as the ostrich enzyme, structurally close to mammalian ADH2 but with class-I kinetic properties. Remarkably, many ADH1 and ADH7 forms are observed in the lizard, probably due to lineage-specific duplications. ADH4 is not present in amphibians and reptiles. Conclusions The study of the ancient forms of ADH2 and ADH7 sheds new light on the evolution of the vertebrate ADH system, whereas the special features showed by the novel forms point to the acquisition of new functions following the ADH gene family expansion which occurred in amphibians.
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Affiliation(s)
| | | | | | | | - Jaume Farrés
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193, Bellaterra, Barcelona, Spain.
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Cañestro C, Albalat R, Irimia M, Garcia-Fernàndez J. Impact of gene gains, losses and duplication modes on the origin and diversification of vertebrates. Semin Cell Dev Biol 2013; 24:83-94. [DOI: 10.1016/j.semcdb.2012.12.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 12/25/2012] [Indexed: 02/06/2023]
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Canestro C, Albalat R. Transposon diversity is higher in amphioxus than in vertebrates: functional and evolutionary inferences. Brief Funct Genomics 2012; 11:131-41. [DOI: 10.1093/bfgp/els010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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Albalat R, Martí-Solans J, Cañestro C. DNA methylation in amphioxus: from ancestral functions to new roles in vertebrates. Brief Funct Genomics 2012; 11:142-55. [PMID: 22389042 DOI: 10.1093/bfgp/els009] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
In vertebrates, DNA methylation is an epigenetic mechanism that modulates gene transcription, and plays crucial roles during development, cell fate maintenance, germ cell pluripotency and inheritable genome imprinting. DNA methylation might also play a role as a genome defense mechanism against the mutational activity derived from transposon mobility. In contrast to the heavily methylated genomes in vertebrates, most genomes in invertebrates are poorly or just moderately methylated, and the function of DNA methylation remains unclear. Here, we review the DNA methylation system in the cephalochordate amphioxus, which belongs to the most basally divergent group of our own phylum, the chordates. First, surveys of the amphioxus genome database reveal the presence of the DNA methylation machinery, DNA methyltransferases and methyl-CpG-binding domain proteins. Second, comparative genomics and analyses of conserved synteny between amphioxus and vertebrates provide robust evidence that the DNA methylation machinery of amphioxus represents the ancestral toolkit of chordates, and that its expansion in vertebrates was originated by the two rounds of whole-genome duplication that occurred in stem vertebrates. Third, in silico analysis of CpGo/e ratios throughout the amphioxus genome suggests a bimodal distribution of DNA methylation, consistent with a mosaic pattern comprising domains of methylated DNA interspersed with domains of unmethylated DNA, similar to the situation described in ascidians, but radically different to the globally methylated vertebrate genomes. Finally, we discuss potential roles of the DNA methylation system in amphioxus in the context of chordate genome evolution and the origin of vertebrates.
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Abstract
The discovery in invertebrates of ciliary photoreceptor cells and ciliary (c)-opsins established that at least two of the three elements that characterize the vertebrate photoreceptor system were already present before vertebrate evolution. However, the origin of the third element, a series of biochemical reactions known as the "retinoid cycle," remained uncertain. To understand the evolution of the retinoid cycle, I have searched for the genetic machinery of the cycle in invertebrate genomes, with special emphasis on the cephalochordate amphioxus. Amphioxus is closely related to vertebrates, has a fairly prototypical genome, and possesses ciliary photoreceptor cells and c-opsins. Phylogenetic and structural analyses of the amphioxus sequences related with the vertebrate machinery do not support a function of amphioxus proteins in chromophore regeneration but suggest that the genetic machinery of the retinoid cycle arose in vertebrates due to duplications of ancestral nonvisual genes. These results favor the hypothesis that the retinoid cycle machinery was a functional innovation of the primitive vertebrate eye.
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Affiliation(s)
- Ricard Albalat
- Departament de Genètica, Universitat de Barcelona, Barcelona, Spain.
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Albalat R, Brunet F, Laudet V, Schubert M. Evolution of retinoid and steroid signaling: vertebrate diversification from an amphioxus perspective. Genome Biol Evol 2011; 3:985-1005. [PMID: 21856648 PMCID: PMC3184775 DOI: 10.1093/gbe/evr084] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although the physiological relevance of retinoids and steroids in vertebrates is very well established, the origin and evolution of the genetic machineries implicated in their metabolic pathways is still very poorly understood. We investigated the evolution of these genetic networks by conducting an exhaustive survey of components of the retinoid and steroid pathways in the genome of the invertebrate chordate amphioxus (Branchiostoma floridae). Due to its phylogenetic position at the base of chordates, amphioxus is a very useful model to identify and study chordate versus vertebrate innovations, both on a morphological and a genomic level. We have characterized more than 220 amphioxus genes evolutionarily related to vertebrate components of the retinoid and steroid pathways and found that, globally, amphioxus has orthologs of most of the vertebrate components of these two pathways, with some very important exceptions. For example, we failed to identify a vertebrate-like machinery for retinoid storage, transport, and delivery in amphioxus and were also unable to characterize components of the adrenal steroid pathway in this invertebrate chordate. The absence of these genes from the amphioxus genome suggests that both an elaboration and a refinement of the retinoid and steroid pathways took place at the base of the vertebrate lineage. In stark contrast, we also identified massive amplifications in some amphioxus gene families, most extensively in the short-chain dehydrogenase/reductase superfamily, which, based on phylogenetic and genomic linkage analyses, were likely the result of duplications specific to the amphioxus lineage. In sum, this detailed characterization of genes implicated in retinoid and steroid signaling in amphioxus allows us not only to reconstruct an outline of these pathways in the ancestral chordate but also to discuss functional innovations in retinoid homeostasis and steroid-dependent regulation in both cephalochordate and vertebrate evolution.
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Affiliation(s)
- Ricard Albalat
- Departament de Genètica, Facultat de Biologia and Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Spain.
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27
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Andreakis N, D'Aniello S, Albalat R, Patti FP, Garcia-Fernàndez J, Procaccini G, Sordino P, Palumbo A. Evolution of the nitric oxide synthase family in metazoans. Mol Biol Evol 2010; 28:163-79. [PMID: 20639231 DOI: 10.1093/molbev/msq179] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nitric oxide (NO) is essential to many physiological functions and operates in several signaling pathways. It is not understood how and when the different isoforms of nitric oxide synthase (NOS), the enzyme responsible for NO production, evolved in metazoans. This study investigates the number and structure of metazoan NOS enzymes by genome data mining and direct cloning of Nos genes from the lamprey. In total, 181 NOS proteins are analyzed from 33 invertebrate and 63 vertebrate species. Comparisons among protein and gene structures, combined with phylogenetic and syntenic studies, provide novel insights into how NOS isoforms arose and diverged. Protein domains and gene organization--that is, intron positions and phases--of animal NOS are remarkably conserved across all lineages, even in fast-evolving species. Phylogenetic and syntenic analyses support the view that a proto-NOS isoform was recurrently duplicated in different lineages, acquiring new structural configurations through gains and losses of protein motifs. We propose that in vertebrates a first duplication took place after the agnathan-gnathostome split followed by a paralog loss. A second duplication occurred during early tetrapod evolution, giving rise to the three isoforms--I, II, and III--in current mammals. Overall, NOS family evolution was the result of multiple gene and genome duplication events together with changes in protein architecture.
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Affiliation(s)
- Nikos Andreakis
- Australian Institute of Marine Science, Townsville, Queensland, Australia
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Cañestro C, Albalat R, Postlethwait JH. Oikopleura dioica alcohol dehydrogenase class 3 provides new insights into the evolution of retinoic acid synthesis in chordates. Zoolog Sci 2010; 27:128-33. [PMID: 20141418 DOI: 10.2108/zsj.27.128] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Enzymes that synthesize retinoic acid (RA) constitute the first level of regulation of RA action. In vertebrates, enzymes of the medium-chain alcohol dehydrogenase (MDR-Adh) family catalyze the first step of the RA synthetic pathway by oxidizing retinol. Among MDR-Adh enzymes, Adh3 is the only member present in non-vertebrates, and whether Adh3 is actually involved in RA biosynthesis remains uncertain. Here, we investigate the MDR-Adh family in Oikopleura dioica, a urochordate representing the sister group to vertebrates. Oikopleura is of special interest because it has lost the classical RA role in development, which relaxed evolutionary constraints to preserve the RA-genetic machinery, leading to the loss of RA-system components. The hypothesis that Adh3 plays a role in RA synthesis predicts that the relaxation of selection in Oikopleura should have led to the loss of Adh3, or changes in residues related to retinol oxidation. The hypothesis also predicts changes in the expression pattern of Oikopleura Adh3 compared to other chordates that preserved RA-signaling. Our results, however, revealed the presence of a highly conserved Adh3 gene in Oikopleura, with no significant changes in functional residues. Our results also revealed that the Oikopleura Adh3 expression remains unchanged in comparison to other non-vertebrate chordates, restricted to specific compartments of the digestive system. Because Adh3 has been highly conserved in an animal that has dismantled the RA system, we conclude that Adh3 preservation is not due to a conserved role in RA synthesis. Thereby, if Adh3 plays a role in RA synthesis in vertebrates, it might be a lineage-specific neofunctionalization.
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Affiliation(s)
- Cristian Cañestro
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
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Albalat R. The retinoic acid machinery in invertebrates: ancestral elements and vertebrate innovations. Mol Cell Endocrinol 2009; 313:23-35. [PMID: 19737598 DOI: 10.1016/j.mce.2009.08.029] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Revised: 07/21/2009] [Accepted: 08/31/2009] [Indexed: 10/20/2022]
Abstract
Recent discoveries have changed our view of the evolutionary history of retinoic acid (RA) machinery. It is no longer considered a vertebrate or chordate invention but rather a common genetic toolkit of diverse lineages of metazoans. In particular, the basic machinery of RA-metabolizing enzymes, retinoid-binding proteins and RA-binding nuclear receptors has been identified in protostome and deuterostome lineages. Moreover, the retinoid content and the effects of RA treatment have been described in a number of invertebrates, although the physiological role of RA signaling outside vertebrates is still not fully understood. This review summarizes the evidence gathered over many years on the invertebrate RA system, highlighting the ancient origin of the RA genetic machinery and a basic role in neuronal differentiation. Comparison of invertebrate and vertebrate RA toolkits suggests some innovations in the RA machinery of vertebrates that might have contributed to improving the physiological control of retinoid homeostasis, compensating for vitamin A fluctuations in this lineage. Analysis of the RA machinery in invertebrates also reveals independent losses of RA components during evolution, which might be related to changes in embryonic developmental modes and the absence of the temporal collinearity of hox clusters. Additional studies analyzing the biochemical and functional characteristics of the invertebrate RA genetic machinery are warranted to lend experimental support to the hypotheses sketched in this review. These hypotheses open, however, new perspectives toward understanding how the RA genetic machinery evolved to suit the physiological and developmental requirements of metazoans.
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Affiliation(s)
- Ricard Albalat
- Departament de Genètica, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IrBio), Universitat de Barcelona, Av. Diagonal, 645, E-08028 Barcelona, Spain.
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Albalat R, Baquero M, Minguillón C. Identification and characterisation of the developmental expression pattern of tbx5b, a novel tbx5 gene in zebrafish. Gene Expr Patterns 2009; 10:24-30. [PMID: 19925885 DOI: 10.1016/j.gep.2009.11.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 11/09/2009] [Accepted: 11/10/2009] [Indexed: 10/20/2022]
Abstract
Tbx5 is a T-box transcription factor that has been characterised in most vertebrate lineages and is widely expressed during the development of various embryonic structures, including the heart, the eyes and the anterior set of paired appendages (tetrapod forelimbs and fish pectoral fins). Mutations in TBX5 cause Holt-Oram syndrome, an autosomal dominant human "heart-hand" condition characterised by upper limb and heart malformations. In zebrafish, embryos with compromised tbx5 function show a complete absence of pectoral fins, whereas heart and eye development are not so highly disturbed. Here, we identify a new tbx5 gene in zebrafish that we have called tbx5b. This duplicate gene is present in all teleost genomes whose sequence is available, suggesting it resulted from the teleost-specific genome duplication event that took place during fish evolution. We show that tbx5b has lost the characteristic forelimb/pectoral fin expression of Tbx5 genes but has retained the eye and heart expression, partially overlapping with that of its paralogue, now referred to as tbx5a. Functional redundancy of tbx5a and tbx5b in the eye and heart would therefore explain the mild phenotypes observed during development of these organs in fish embryos with compromised tbx5a function.
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Affiliation(s)
- Ricard Albalat
- Departament de Genètica, Universitat de Barcelona, Barcelona, Spain
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Schubert M, Simões-Costa M, Marlétaz F, P. Sobreira TJ, L. de Oliveira PS, Schechtman D, Brunet F, Albalat R, Bronner-Fraser M, Laudet V, Xavier-Neto J. 15-P010 Evolutionary shifts in ALDH structure suggest transitions between pleiotropic and patterning functions. Mech Dev 2009. [DOI: 10.1016/j.mod.2009.06.654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Albalat R. Evolution of DNA-methylation machinery: DNA methyltransferases and methyl-DNA binding proteins in the amphioxus Branchiostoma floridae. Dev Genes Evol 2008; 218:691-701. [DOI: 10.1007/s00427-008-0247-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Accepted: 08/29/2008] [Indexed: 11/30/2022]
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Albalat R, Cañestro C. Identification of Aldh1a, Cyp26 and RAR orthologs in protostomes pushes back the retinoic acid genetic machinery in evolutionary time to the bilaterian ancestor. Chem Biol Interact 2008; 178:188-96. [PMID: 18926806 DOI: 10.1016/j.cbi.2008.09.017] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Revised: 09/05/2008] [Accepted: 09/09/2008] [Indexed: 12/22/2022]
Abstract
In vertebrates, retinoic acid (RA) is an important morphogenetic signal that controls embryonic development, as well as organ homeostasis in adults. RA action depends on the function of the RA-genetic machinery, which includes a metabolic module and a signaling module. The metabolic module regulates the spatiotemporal distribution of RA by the combined action of the RA-synthesizing Aldh1a enzymes, and the RA-degrading Cyp26 enzymes. The signaling module includes members of the nuclear hormone receptors family RAR and RXR, and controls the transcriptional state of RA-target genes. RA-signaling has been described primarily in chordates, but the recent finding of elements of the RA-genetic machinery in non-chordate deuterostomes has changed our perspective on the evolutionary origin of this morphogenetic signal, challenging previous assumptions that related the invention of the RA-genetic machinery with the origin of the chordate body plan. To illuminate the evolutionary origin of the RA machinery we have conducted an extensive survey of Aldh1a, Cyp26 and RAR orthologs in genomic databases of 13 non-deuterostome metazoans. Our results show for the first time the presence of Aldh1a, Cyp26 and RAR in protostomes, which implies that the components of the RA machinery may be ancient elements of animal genomes, already present in the last common ancestor of bilaterians. Interestingly, our data also reveal that independent losses of the RA toolkit have occurred multiple times during animal evolution, which may have been relevant for the evolution and developmental diversity of the current metazoan lineages.
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Affiliation(s)
- Ricard Albalat
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.
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Holland LZ, Albalat R, Azumi K, Benito-Gutiérrez E, Blow MJ, Bronner-Fraser M, Brunet F, Butts T, Candiani S, Dishaw LJ, Ferrier DEK, Garcia-Fernàndez J, Gibson-Brown JJ, Gissi C, Godzik A, Hallböök F, Hirose D, Hosomichi K, Ikuta T, Inoko H, Kasahara M, Kasamatsu J, Kawashima T, Kimura A, Kobayashi M, Kozmik Z, Kubokawa K, Laudet V, Litman GW, McHardy AC, Meulemans D, Nonaka M, Olinski RP, Pancer Z, Pennacchio LA, Pestarino M, Rast JP, Rigoutsos I, Robinson-Rechavi M, Roch G, Saiga H, Sasakura Y, Satake M, Satou Y, Schubert M, Sherwood N, Shiina T, Takatori N, Tello J, Vopalensky P, Wada S, Xu A, Ye Y, Yoshida K, Yoshizaki F, Yu JK, Zhang Q, Zmasek CM, de Jong PJ, Osoegawa K, Putnam NH, Rokhsar DS, Satoh N, Holland PWH. The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res 2008; 18:1100-11. [PMID: 18562680 DOI: 10.1101/gr.073676.107] [Citation(s) in RCA: 368] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we intensively searched for particular genes, gene families, and conserved noncoding elements in the sequenced genome of the cephalochordate Branchiostoma floridae, commonly called amphioxus or lancelets. Special attention was given to homeobox genes, opsin genes, genes involved in neural crest development, nuclear receptor genes, genes encoding components of the endocrine and immune systems, and conserved cis-regulatory enhancers. The amphioxus genome contains a basic set of chordate genes involved in development and cell signaling, including a fifteenth Hox gene. This set includes many genes that were co-opted in vertebrates for new roles in neural crest development and adaptive immunity. However, where amphioxus has a single gene, vertebrates often have two, three, or four paralogs derived from two whole-genome duplication events. In addition, several transcriptional enhancers are conserved between amphioxus and vertebrates--a very wide phylogenetic distance. In contrast, urochordate genomes have lost many genes, including a diversity of homeobox families and genes involved in steroid hormone function. The amphioxus genome also exhibits derived features, including duplications of opsins and genes proposed to function in innate immunity and endocrine systems. Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates.
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Affiliation(s)
- Linda Z Holland
- Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, California 92093-0202, USA.
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Dalfó D, Marqués N, Albalat R. Analysis of the NADH-dependent retinaldehyde reductase activity of amphioxus retinol dehydrogenase enzymes enhances our understanding of the evolution of the retinol dehydrogenase family. FEBS J 2007; 274:3739-3752. [PMID: 17608724 DOI: 10.1111/j.1742-4658.2007.05904.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In vertebrates, multiple microsomal retinol dehydrogenases are involved in reversible retinol/retinal interconversion, thereby controlling retinoid metabolism and retinoic acid availability. The physiologic functions of these enzymes are not, however, fully understood, as each vertebrate form has several, usually overlapping, biochemical roles. Within this context, amphioxus, a group of chordates that are simpler, at both the functional and genomic levels, than vertebrates, provides a suitable evolutionary model for comparative studies of retinol dehydrogenase enzymes. In a previous study, we identified two amphioxus enzymes, Branchiostoma floridae retinol dehydrogenase 1 and retinol dehydrogenase 2, both candidates to be the cephalochordate orthologs of the vertebrate retinol dehydrogenase enzymes. We have now proceeded to characterize these amphioxus enzymes. Kinetic studies have revealed that retinol dehydrogenase 1 and retinol dehydrogenase 2 are microsomal proteins that catalyze the reduction of all-trans-retinaldehyde using NADH as cofactor, a remarkable combination of substrate and cofactor preferences. Moreover, evolutionary analysis, including the amphioxus sequences, indicates that Rdh genes were extensively duplicated after cephalochordate divergence, leading to the gene cluster organization found in several mammalian species. Overall, our data provide an evolutionary reference with which to better understand the origin, activity and evolution of retinol dehydrogenase enzymes.
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Affiliation(s)
- Diana Dalfó
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Spain
| | - Neus Marqués
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Spain
| | - Ricard Albalat
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Spain
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Fuentes M, Benito E, Bertrand S, Paris M, Mignardot A, Godoy L, Jimenez-Delgado S, Oliveri D, Candiani S, Hirsinger E, D'Aniello S, Pascual-Anaya J, Maeso I, Pestarino M, Vernier P, Nicolas JF, Schubert M, Laudet V, Geneviere AM, Albalat R, Garcia Fernandez J, Holland ND, Escriva H. Insights into spawning behavior and development of the european amphioxus (Branchiostoma lanceolatum). J Exp Zool 2007; 308:484-93. [PMID: 17520703 DOI: 10.1002/jez.b.21179] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The cephalochordate amphioxus (Branchiostoma sp.) is an important animal model for studying the evolution of chordate developmental mechanisms. Obtaining amphioxus embryos is a key step for these studies. It has been shown that an increase of 3-4 degrees C in water temperature triggers spawning of the European amphioxus (Branchiostoma lanceolatum) in captivity, however, very little is known about the natural spawning behavior of this species in the field. In this work, we have followed the spawning behavior of the European amphioxus during two spawning seasons (2004 and 2005), both in the field and in captivity. We show that animals in the field spawn approximately from mid-May through early July, but depending on the year, they show different patterns of spawning. Thus, even if temperature has a critical role in the induction of the spawning in captivity, it is not the major factor in the field. Moreover, we report some improvements on the methodology for inducing spawning in captivity (e.g. in maintenance, light cycle control and induction of spawning in a laboratory without running sea water system). These studies have important implications for amphioxus animal husbandry and for improving laboratory techniques to develop amphioxus as an experimental animal model.
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Affiliation(s)
- Michael Fuentes
- Laboratoire Arago, UMR7628 CNRS, University Pierre and Marie Curie-Paris6 Banyuls sur Mer, F-66650, France
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Godoy L, Gonzàlez-Duarte R, Albalat R. Analysis of planarian Adh3 supports an intron-rich architecture and tissue-specific expression for the urbilaterian ancestral form. Comp Biochem Physiol B Biochem Mol Biol 2006; 146:489-95. [PMID: 17270479 DOI: 10.1016/j.cbpb.2006.11.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Revised: 11/20/2006] [Accepted: 11/20/2006] [Indexed: 10/23/2022]
Abstract
The alcohol dehydrogenase class 3 enzyme (ADH3) is the presumed ancestral form of the medium-chain dehydrogenase-reductase ADH family. This enzyme has been involved in formaldehyde and nitric oxide metabolism of a variety of deuterostomes and ecdysozoan protostomes. We have now characterized the structure and expression of the Adh3 gene in the lophotrochozoan Schmidtea mediterranea, a freshwater planarian. The planarian gene expands over 8.7 kb and is organized into 7 exons. The 1340 bp long Adh3cDNA contains a 1137 bp open reading frame corresponding to a deduced protein of 379 amino acids. The protein sequence is consistent with that expected for a typical class III enzyme. Twenty out of the twenty-two amino acid positions associated with enzymatic roles are strictly preserved, which suggests that the enzymatic capabilities have been conserved. In situ hybridization experiments show that Adh3 is expressed along the intestine of S. mediterranea specimens. This is consistent with the pattern observed in invertebrates and in contrast with the widespread expression of vertebrate Adh3. The comparative study across bilateria, which now includes a lophotrochozoan representative, further supports the idea that the urbilaterian Adh3 ancestor showed an intron-rich architecture and tissue-specific expression, and strengthens the view that widespread expression of Adh3 was a vertebrate innovation.
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Affiliation(s)
- Laura Godoy
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona. Av. Diagonal, 645, E-08028 Barcelona, Spain
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Abstract
Development of many chordate features depends on retinoic acid (RA). Because the action of RA during development seems to be restricted to chordates, it had been previously proposed that the "invention" of RA genetic machinery, including RA-binding nuclear hormone receptors (Rars), and the RA-synthesizing and RA-degrading enzymes Aldh1a (Raldh) and Cyp26, respectively, was an important step for the origin of developmental mechanisms leading to the chordate body plan. We tested this hypothesis by conducting an exhaustive survey of the RA machinery in genomic databases for twelve deuterostomes. We reconstructed the evolution of these genes in deuterostomes and showed for the first time that RA genetic machinery--that is Aldh1a, Cyp26, and Rar orthologs--is present in nonchordate deuterostomes. This finding implies that RA genetic machinery was already present during early deuterostome evolution, and therefore, is not a chordate innovation. This new evolutionary viewpoint argues against the hypothesis that the acquisition of gene families underlying RA metabolism and signaling was a key event for the origin of chordates. We propose a new hypothesis in which lineage-specific duplication and loss of RA machinery genes could be related to the morphological radiation of deuterostomes.
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Affiliation(s)
- Cristian Cañestro
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
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Claret J, Crusats J, Albalat R, Ignés-Mullol J, Martínez-Seara H, Reigada R, Sagués F. Travelling waves in two-dimensional smectic-C domains. Eur Phys J E Soft Matter 2006; 21:111-6. [PMID: 17180641 DOI: 10.1140/epje/i2006-10049-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2006] [Accepted: 10/16/2006] [Indexed: 05/13/2023]
Abstract
Continued irradiation of smectic-C-like domains of photosensitive Langmuir monolayers from azobenzene derivatives induces the nucleation and propagation of orientational travelling waves as observed with Brewster angle microscopy (BAM). BAM image analysis has allowed to identify different dynamical behaviors involving the generation and propagation of such waves. A model based on the coupling between an orientational and a composition field proposes a scenario for dynamic self-assembly that accounts for most of the observed phenomena, and allows to pinpoint the relevance of boundary defects in wave-emitting structures.-1.
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Affiliation(s)
- J Claret
- Departament de Química Física, Universitat de Barcelona, Martí i Franqués 1, 08028, Barcelona, Catalonia, Spain
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Godoy L, Gonzàlez-Duarte R, Albalat R. S-Nitrosogluthathione reductase activity of amphioxus ADH3: insights into the nitric oxide metabolism. Int J Biol Sci 2006; 2:117-24. [PMID: 16763671 PMCID: PMC1458435 DOI: 10.7150/ijbs.2.117] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2006] [Accepted: 04/09/2006] [Indexed: 11/07/2022] Open
Abstract
Nitric oxide (NO) is a signalling molecule involved in many physiological functions. An important via of NO action is through the S-nitrosylation of proteins, a post-translational modification that regulates the activity of enzymes, protein-protein interactions and signal transduction pathways. Alcohol dehydrogenase class III (ADH3) recognises S-nitrosoglutathione (GSNO), the main reservoir of non-protein S-nitrosothiol, and functions as an effective GSNO reductase (GSNOR) and as a safeguard against nitrosative stress. To investigate the evolutionary conservation of this metabolic role, we have produced recombinant Branchiostoma floridae ADH3. Pure preparations of ADH3 showed 2-fold higher activity as GSNOR than as formaldehyde dehydrogenase, the previously assumed main role for ADH3. To correlate ADH3 expression in the gut with areas of NO production, we analysed the tissue distribution of the nitric oxide synthase (NOS) enzyme in amphioxus larvae. Immunostaining of the NOS enzyme revealed expression in the gut and in the dorsal region of the club-shaped gland. Co-localization in the gut supports the ADH3 and NOS joint contribution to the NO/SNO homeostasis.
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Affiliation(s)
- Laura Godoy
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Spain
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Permanyer J, Albalat R, Gonzàlez-Duarte R. Getting closer to a pre-vertebrate genome: the non-LTR retrotransposons of Branchiostoma floridae. Int J Biol Sci 2006; 2:48-53. [PMID: 16733533 PMCID: PMC1458424 DOI: 10.7150/ijbs.2.48] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2006] [Accepted: 03/10/2006] [Indexed: 11/28/2022] Open
Abstract
Non-LTR retrotransposons are common in vertebrate genomes and although present in invertebrates they appear at a much lower frequency. The cephalochordate amphioxus is the closest living relative to vertebrates and has been considered a good model for comparative analyses of genome expansions during vertebrate evolution. With the aim to assess the involvement of transposable elements in these events, we have analysed the non-LTR retrotransposons of Branchiostoma floridae. In silico searches have allowed to reconstruct non-LTR elements of six different clades (CR1, I, L1, L2, NeSL and RTE) and assess their structural features. According to the estimated copy number of these elements they account for less than 1% of the haploid genome, which reminds of the low abundance also encountered in the urochordate Ciona intestinalis. Amphioxus (B. floridae) and Ciona share a pre-vertebrate-like organization for the non-LTR retrotransposons (<150 copies, < 1% of the genome) versus the complexity associated to higher vertebrates (Homo sapiens >1.3·106 copies, > 20% of the genome).
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Affiliation(s)
- Jon Permanyer
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain
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Abstract
Multiple members of the MDR-ADH (MDR: Medium-chain dehydrogenases/reductases; ADH: alcohol dehydrogenase) family are found in vertebrates, although the enzymes that belong to this family have also been isolated from bacteria, yeast, plant and animal sources. Initial understanding of the physiological roles and evolution of the family relied on biochemical studies, protein alignments and protein structure comparisons. Subsequently, studies at the genetic level yielded new information: the expression pattern, exon-intron distribution, in silico-derived protein sequences and murine knockout phenotypes. More recently, genomic and EST databases have revealed new family members and the chromosomal location and position in the cluster of both the first and new forms. The data now available provide a comprehensive scenario, from which a reliable picture of the evolutionary history of this family can be made.
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Affiliation(s)
- R Gonzàlez-Duarte
- Departament de Genètica, Universitat de Barcelona, Avda. Diagonal 645, Barcelona 08028, Spain.
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Abstract
We report the first class II transposon in cephalochordates, which we have named Amphioxus Transposable Element 1 (ATE-1). ATE-1 members have been identified in the genome of Branchiostoma lanceolatum (BlATE-1) and B. floridae (BfATE-1). Structural analysis revealed that ATE-1 elements consist of a central region (CR) with no homology with any coding sequence, nor any detectable open reading frame (ORF), flanked by internal direct repeats (DR) of about 100 nt, each adjacent to a terminal inverted repeat (TIR) of 16 nt. Although the estimated copy number in the amphioxus genome is low, there is evidence of mobility. Sequence and hybridization analyses pointed to TIR and DR inter-species conservation, whereas no structural similarities among the CR were detected. Moreover, this element is found in two amphioxus species that diverged long ago, which argues in favor of its ancient origin. However, the structural hallmarks needed for transposition are still preserved.
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Affiliation(s)
- Cristian Cañestro
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal, 645, E-08028 Barcelona, Spain
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Fuentes M, Schubert M, Dalfo D, Candiani S, Benito E, Gardenyes J, Godoy L, Moret F, Illas M, Patten I, Permanyer J, Oliveri D, Boeuf G, Falcon J, Pestarino M, Fernandez JG, Albalat R, Laudet V, Vernier P, Escriva H. Preliminary observations on the spawning conditions of the European amphioxus (Branchiostoma lanceolatum) in captivity. ACTA ACUST UNITED AC 2004; 302:384-91. [PMID: 15287102 DOI: 10.1002/jez.b.20025] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Members of the subphylum Cephalochordata, which include the genus Branchiostoma (i.e. amphioxus), represent the closest living invertebrate relatives of the vertebrates. To date, developmental studies have been carried out on three amphioxus species (the European Branchiostoma lanceolatum, the East Asian B. belcheri, and Floridian-Caribbean B. floridae). In most instances, adult animals have been collected from the field during their ripe season and allowed (or stimulated) to spawn in the laboratory. In any given year, dates of laboratory pawning have been limited by two factors. First, natural populations of these three most studied species of amphioxus are ripe, at most, for only a couple of months each year and, second, even when apparently ripe, animals spawn only at unpredictable intervals of every several days. This limited supply of living material hinders the development of amphioxus as a model system because this limitation makes it more difficult to work out protocols for new laboratory techniques. Therefore we are developing laboratory methods for increasing the number of amphioxus spawning dates per year. The present study found that a Mediterranean population of B. lanceolatum living near the Franco-Spanish border spawned naturally at the end of May and again at the end of June in 2003. Re-feeding experiments in the laboratory demonstrated that the gonads emptied at the end of May refilled with gametes by the end of June. We also found that animals with large gonads (both, obtained from the field and kept and fed at the laboratory during several weeks) could be induced to spawn in the laboratory out of phase with the field population if they were temperature shocked (spawning occurred 36 hours after a sustained increase in water temperature from 19 degrees C to 25 degrees C).
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Affiliation(s)
- Michael Fuentes
- Laboratoire Arago, UMR 7628, CNRS and Université Pierre et Marie Curie, BP 44, F-66651 Banyuls sur Mer, France
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Permanyer J, Gonzàlez-Duarte R, Albalat R. The non-LTR retrotransposons in Ciona intestinalis: new insights into the evolution of chordate genomes. Genome Biol 2003; 4:R73. [PMID: 14611659 PMCID: PMC329123 DOI: 10.1186/gb-2003-4-11-r73] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2003] [Revised: 09/17/2003] [Accepted: 09/25/2003] [Indexed: 11/10/2022] Open
Abstract
In silico and experimental approaches have been used to identify the non-long terminal repeat retrotransposons of the urochordate Ciona intestinalis providing valuable data for understanding the evolution of early chordate genomes. Background Non-long terminal repeat (non-LTR) retrotransposons have contributed to shaping the structure and function of genomes. In silico and experimental approaches have been used to identify the non-LTR elements of the urochordate Ciona intestinalis. Knowledge of the types and abundance of non-LTR elements in urochordates is a key step in understanding their contribution to the structure and function of vertebrate genomes. Results Consensus elements phylogenetically related to the I, LINE1, LINE2, LOA and R2 elements of the 14 eukaryotic non-LTR clades are described from C. intestinalis. The ascidian elements showed conservation of both the reverse transcriptase coding sequence and the overall structural organization seen in each clade. The apurinic/apyrimidinic endonuclease and nucleic-acid-binding domains encoded upstream of the reverse transcriptase, and the RNase H and the restriction enzyme-like endonuclease motifs encoded downstream of the reverse transcriptase were identified in the corresponding Ciona families. Conclusions The genome of C. intestinalis harbors representatives of at least five clades of non-LTR retrotransposons. The copy number per haploid genome of each element is low, less than 100, far below the values reported for vertebrate counterparts but within the range for protostomes. Genomic and sequence analysis shows that the ascidian non-LTR elements are unmethylated and flanked by genomic segments with a gene density lower than average for the genome. The analysis provides valuable data for understanding the evolution of early chordate genomes and enlarges the view on the distribution of the non-LTR retrotransposons in eukaryotes.
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Affiliation(s)
- Jon Permanyer
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 645, E-08028 Barcelona, Spain
| | - Roser Gonzàlez-Duarte
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 645, E-08028 Barcelona, Spain
| | - Ricard Albalat
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 645, E-08028 Barcelona, Spain
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Albalat R, Permanyer J, Cañestro C, Martínez-Mir A, Gonzàlez-Angulo O, Gonzàlez-Duarte R. The first non-LTR retrotransposon characterised in the cephalochordate amphioxus, BfCR1, shows similarities to CR1-like elements. Cell Mol Life Sci 2003; 60:803-9. [PMID: 12785727 DOI: 10.1007/s00018-003-2329-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BfCR1 is the first non-long terminal repeat retrotransposon to be characterised in the amphioxus genome. Sequence alignment of the predicted translation product reveals that BfCR1 belongs to the CR1-like retroposon class, a family widely distributed in vertebrate and invertebrate lineages. Structural analysis shows conservation of the specific motifs of the ORF2-CR1 elements: the N-terminal endonuclease, the reverse transcriptase and the C-terminal domains. The BfCR1 element possesses an atypical 3' terminus consisting of the tandem repeat (AAG)6. We gathered evidence supporting the mobility of this element and report an estimated 15 copies of BfCR1, mostly truncated, per haploid genome, a remarkably low number when compared to that of vertebrates. Phylogenetic analysis, including the amphioxus element, seems to indicate that (i) CR1-like retroposons cluster in a monophyletic group and (ii) the CR1-like family was already present in the chordate ancestor. Our data provide further support for the horizontal transmission of CR1-like elements during early vertebrate evolution.
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Affiliation(s)
- R Albalat
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal, 645, 08028 Barcelona, Spain
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Cañestro C, Godoy L, Gonzàlez-Duarte R, Albalat R. Comparative expression analysis of Adh3 during arthropod, urochordate, cephalochordate, and vertebrate development challenges its predicted housekeeping role. Evol Dev 2003; 5:157-62. [PMID: 12622732 DOI: 10.1046/j.1525-142x.2003.03022.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Gene and genome duplications in the vertebrate lineage explain the complexity of extant gene families. Among these, the medium-chain alcohol dehydrogenase (ADH), which expanded by tandem duplications after the cephalochordate-vertebrate split, is a good model with which to analyze the evolution of gene function. Although the ancestral member of this family, ADH3, has been strictly conserved throughout animal evolution, its physiological role is still controversial. Previous evidence indicates that it contributes to formaldehyde cytoprotection, retinoic acid metabolism, and nitric oxide homeostasis. We performed in situ hybridization during Drosophila, ascidian (Ciona intestinalis), and zebrafish (Danio rerio) development. We showed that Adh3 expression was restricted to the fat body in Drosophila embryos at stage 17 and to the anterior endoderm in C. intestinalis tail bud, whereas in the zebrafish 2.5-day larvae the signal appeared widespread. A more comprehensive expression analysis including amphioxus and mice revealed that ancestral Adh3 was tissue specific, whereas a widespread expression was later attained in vertebrates. These variations occurred concomitantly with the expansion of the ADH family and the acquisition of new functions but were unlinked to the genomic changes that led to the transition from fractional to global methylation in vertebrates. Our data challenge the housekeeping role of ADH3 and question its involvement in the prevertebrate retinoic acid pathway.
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Affiliation(s)
- Cristian Cañestro
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal, 645, E-08028 Barcelona, Spain
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Dalfó D, Albalat R, Molotkov A, Duester G, Gonzàlez-Duarte R. Retinoic acid synthesis in the prevertebrate amphioxus involves retinol oxidation. Dev Genes Evol 2002; 212:388-93. [PMID: 12203095 DOI: 10.1007/s00427-002-0254-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2002] [Accepted: 05/23/2002] [Indexed: 10/27/2022]
Abstract
All- trans-retinoic acid (RA) contributes to the establishment of the anterior-posterior (AP) axis in chordates. In vertebrates, all- trans-retinol is oxidized to RA by two oxidative steps. However, the controversy about the enzymes responsible for retinol oxidation (ADH vs RDH) and the fact that some candidates are absent in cephalochordates questioned retinol oxidation in this lineage. Retinoid quantitation has revealed that Branchiostoma floridae adults contain both retinol and retinoic acid as well as retinal, the intermediate in the metabolic pathway. Furthermore, our data show that the developmental effects of retinol treatment are comparable to those reported for RA. SEM analysis revealed mouth and gill slit aberrations due to a posteriorization effect, also visualized by changes in the beta-galactosidase pattern. Overall, these findings support the idea that amphioxus metabolizes endogenous retinol to retinoic acid and suggest a common oxidative pathway for RA in the chordate phylum.
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Affiliation(s)
- Diana Dalfó
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 645, 08028 Barcelona, Spain
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Abstract
Amphioxus (subphylum Cephalochordata) is the closest living relative to vertebrates and widely used for phylogenetic analyses of vertebrate gene evolution. Amphioxus genes are highly polymorphic, but the origin and nature of this variability is unknown. We have analyzed the alcohol dehydrogenase locus (Adh3) in two amphioxus species (Branchiostoma lanceolatum and Branchiostoma floridae) and found that genetic variation is related to repetitive DNA sequences, mainly minisatellites. Small pool-PCR assays indicated that allelic variants are generated by minisatellite instability. We conclude that the generation of new forms was not preferentially linked to germline processes but rather to somatic events leading to mosaic adult animals. Furthermore, most Adh minisatellites belong to a novel class, which we have named mirages. Their distinctive feature is that the repeat subunit spans the exon-intron boundaries and generates potential duplications of the splice sites. However, splicing may not be compromised as no aberrant mRNA variants were detected.
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Affiliation(s)
- Cristian Cañestro
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal, 645, E-08028 Barcelona, Spain
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Cañestro C, Albalat R, Hjelmqvist L, Godoy L, Jörnvall H, Gonzàlez-Duarte R. Ascidian and amphioxus Adh genes correlate functional and molecular features of the ADH family expansion during vertebrate evolution. J Mol Evol 2002; 54:81-9. [PMID: 11734901 DOI: 10.1007/s00239-001-0020-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2001] [Accepted: 05/23/2001] [Indexed: 10/24/2022]
Abstract
The alcohol dehydrogenase (ADH) family has evolved into at least eight ADH classes during vertebrate evolution. We have characterized three prevertebrate forms of the parent enzyme of this family, including one from an urochordate (Ciona intestinalis) and two from cephalochordates (Branchiostoma floridae and Branchiostoma lanceolatum). An evolutionary analysis of the family was performed gathering data from protein and gene structures, exon-intron distribution, and functional features through chordate lines. Our data strongly support that the ADH family expansion occurred 500 million years ago, after the cephalochordate/vertebrate split, probably in the gnathostome subphylum line of the vertebrates. Evolutionary rates differ between the ancestral, ADH3 (glutathione-dependent formaldehyde dehydrogenase), and the emerging forms, including the classical alcohol dehydrogenase, ADH1, which has an evolutionary rate 3.6-fold that of the ADH3 form. Phylogenetic analysis and chromosomal mapping of the vertebrate Adh gene cluster suggest that family expansion took place by tandem duplications, probably concurrent with the extensive isoform burst observed before the fish/tetrapode split, rather than through the large-scale genome duplications also postulated in early vertebrate evolution. The absence of multifunctionality in lower chordate ADHs and the structures compared argue in favor of the acquisition of new functions in vertebrate ADH classes. Finally, comparison between B. floridae and B. lanceolatum Adhs provides the first estimate for a cephalochordate speciation, 190 million years ago, probably concomitant with the beginning of the drifting of major land masses from the Pangea.
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Affiliation(s)
- Cristian Cañestro
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 645, E-08028 Barcelona, Spain
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