1
|
Falcon F, Tanaka EM, Rodriguez-Terrones D. Transposon waves at the water-to-land transition. Curr Opin Genet Dev 2023; 81:102059. [PMID: 37343338 DOI: 10.1016/j.gde.2023.102059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/02/2023] [Accepted: 05/15/2023] [Indexed: 06/23/2023]
Abstract
The major transitions in vertebrate evolution are associated with significant genomic reorganizations. In contrast to the evolutionary processes that occurred at the origin of vertebrates or prior to the radiation of teleost fishes, no whole-genome duplication events occurred during the water-to-land transition, and it remains an open question how did genome dynamics contribute to this prominent evolutionary event. Indeed, the recent sequencing of sarcopterygian and amphibian genomes has revealed that the extant lineages immediately preceding and succeeding this transition harbor an exceptional number of transposable elements and it is tempting to speculate that these sequences might have catalyzed the adaptations that enabled vertebrates to venture into land. Here, we review the genome dynamics associated with the major transitions in vertebrate evolution and discuss how the highly repetitive genomic landscapes revealed by recent efforts to characterize the genomes of amphibians and sarcopterygians argue for turbulent genome dynamics occurring before the water-to-land transition and possibly enabling it.
Collapse
Affiliation(s)
- Francisco Falcon
- Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter, 1030, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria. https://twitter.com/@FcoJFalcon
| | - Elly M Tanaka
- Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter, 1030, Vienna, Austria.
| | - Diego Rodriguez-Terrones
- Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter, 1030, Vienna, Austria.
| |
Collapse
|
2
|
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] [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.
Collapse
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
| |
Collapse
|
3
|
Coppola U, Ristoratore F, Albalat R, D'Aniello S. The evolutionary landscape of the Rab family in chordates. Cell Mol Life Sci 2019; 76:4117-4130. [PMID: 31028425 PMCID: PMC11105323 DOI: 10.1007/s00018-019-03103-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/29/2019] [Accepted: 04/10/2019] [Indexed: 12/30/2022]
Abstract
Intracellular traffic amongst organelles represents a key feature for eukaryotes and is orchestrated principally by members of Rab family, the largest within Ras superfamily. Given that variations in Rab repertoire have been fundamental in animal diversification, we provided the most exhaustive survey regarding the Rab toolkit of chordates. Our findings reveal the existence of 42 metazoan conserved subfamilies exhibiting a univocal intron/exon structure preserved from cnidarians to vertebrates. Since the current view does not capture the Rab complexity, we propose a new Rab family classification in three distinct monophyletic clades. The Rab complement of chordates shows a dramatic diversification due to genome duplications and independent gene duplications and losses with sharp differences amongst cephalochordates, tunicates and gnathostome vertebrates. Strikingly, the analysis of the domain architecture of this family highlighted the existence of chimeric calcium-binding Rabs, which are animal novelties characterized by a complex evolutionary history in gnathostomes and whose role in cellular metabolism is obscure. This work provides novel insights in the knowledge of Rab family: our hypothesis is that chordates represent a hotspot of Rab variability, with many events of gene gains and losses impacting intracellular traffic capabilities. Our results help to elucidate the role of Rab members in the transport amongst endomembranes and shed light on intracellular traffic routes in vertebrates. Then, since the predominant role of Rabs in the molecular communication between different cellular districts, this study paves to way to comprehend inherited or acquired human disorders provoked by dysfunctions in Rab genes.
Collapse
Affiliation(s)
- Ugo Coppola
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Villa Comunale 1, 80121, Naples, Italy
- Molecular Cardiovascular Biology Division, Cincinnati Children's Hospital Medical Center, Cincinnati, USA
| | - Filomena Ristoratore
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Villa Comunale 1, 80121, Naples, Italy
| | - Ricard Albalat
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Diagonal 643, 08028, Barcelona, Spain.
| | - Salvatore D'Aniello
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Villa Comunale 1, 80121, Naples, Italy.
| |
Collapse
|
4
|
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] [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.
Collapse
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.
| |
Collapse
|
5
|
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] [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.
Collapse
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.
| |
Collapse
|
6
|
Pantzartzi CN, Pergner J, Kozmik Z. The role of transposable elements in functional evolution of amphioxus genome: the case of opsin gene family. Sci Rep 2018; 8:2506. [PMID: 29410521 PMCID: PMC5802833 DOI: 10.1038/s41598-018-20683-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/22/2018] [Indexed: 11/30/2022] Open
Abstract
Transposable elements (TEs) are able to jump to new locations (transposition) in the genome, usually after replication. They constitute the so-called selfish or junk DNA and take over large proportions of some genomes. Due to their ability to move around they can change the DNA landscape of genomes and are therefore a rich source of innovation in genes and gene regulation. Surge of sequence data in the past years has significantly facilitated large scale comparative studies. Cephalochordates have been regarded as a useful proxy to ancestral chordate condition partially due to the comparatively slow evolutionary rate at morphological and genomic level. In this study, we used opsin gene family from three Branchiostoma species as a window into cephalochordate genome evolution. We compared opsin complements in terms of family size, gene structure and sequence allowing us to identify gene duplication and gene loss events. Furthermore, analysis of the opsin containing genomic loci showed that they are populated by TEs. In summary, we provide evidence of the way transposable elements may have contributed to the evolution of opsin gene family and to the shaping of cephalochordate genomes in general.
Collapse
Affiliation(s)
- Chrysoula N Pantzartzi
- Laboratory of Eye Biology, Institute of Molecular Genetics of the ASCR, v.v.i., Division BIOCEV, Prumyslová 595, 252 50, Vestec, Czech Republic
| | - Jiri Pergner
- Department of Transcriptional Regulation, Institute of Molecular Genetics of the ASCR, v.v.i., Videnska 1083, 14220, Prague 4, Czech Republic
| | - Zbynek Kozmik
- Laboratory of Eye Biology, Institute of Molecular Genetics of the ASCR, v.v.i., Division BIOCEV, Prumyslová 595, 252 50, Vestec, Czech Republic. .,Department of Transcriptional Regulation, Institute of Molecular Genetics of the ASCR, v.v.i., Videnska 1083, 14220, Prague 4, Czech Republic.
| |
Collapse
|
7
|
Xu N, Pan J, Liu S, Xue Q, Zhang S. Three in one: Identification, expression and enzymatic activity of lysozymes in amphioxus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 46:508-517. [PMID: 24968076 DOI: 10.1016/j.dci.2014.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 06/16/2014] [Accepted: 06/17/2014] [Indexed: 06/03/2023]
Abstract
The lysozymes identified so far in animals belong to the g-type, c-type, and i-type. Vertebrate animals possess only the former two types, i.e., g- and c-types, while all the three types have been reported in invertebrates. Here we demonstrate that (1) three cDNAs that encode g-, c-, and i-type lysozymes, respectively, were identified in a single species of the amphioxus Branchiostoma japonicum; (2) all the 3-type genes displayed distinct tissue-specific expression pattern; (3) recombinant g-, c-, and i-type lysozymes all exhibited enzymatic activities; and (4) native g-, c-, and i-type lysozymes were identified in the different tissues of amphioxus. Collectively, these results suggest the presence of all the 3-type lysozymes in a single animal species, first such data ever reported. The presence of biologically active i-type lysozyme in amphioxus also suggests that i-type lysozyme gene is retained at least in Protochordata, contrasting to the previous proposal that i-type lysozyme gene has been lost in a common ancestor of all chordates.
Collapse
Affiliation(s)
- Na Xu
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; Laboratory for Evolution & Development, Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao 266003, China
| | - Junli Pan
- Laboratory for Evolution & Development, Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao 266003, China
| | - Shousheng Liu
- Laboratory for Evolution & Development, Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao 266003, China
| | - Qinggang Xue
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70830, USA.
| | - Shicui Zhang
- Laboratory for Evolution & Development, Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao 266003, China.
| |
Collapse
|
8
|
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] [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
| |
Collapse
|
9
|
Holland LZ. Genomics, evolution and development of amphioxus and tunicates: The Goldilocks principle. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 324:342-52. [DOI: 10.1002/jez.b.22569] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 01/29/2014] [Accepted: 02/27/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Linda Z. Holland
- Marine Biology Research Division; Scripps Institution of Oceanography; University of California San Diego; La Jolla California 92093-0202 USA
| |
Collapse
|
10
|
Chalopin D, Fan S, Simakov O, Meyer A, Schartl M, Volff JN. Evolutionary active transposable elements in the genome of the coelacanth. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 322:322-33. [DOI: 10.1002/jez.b.22521] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 05/22/2013] [Accepted: 06/17/2013] [Indexed: 12/30/2022]
Affiliation(s)
- Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon; Ecole Normale Supérieure de Lyon; CNRS UMR 5242; Université Lyon 1; Lyon France
| | - Shaohua Fan
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology; University of Konstanz; Konstanz Germany
- Konstanz Research School Chemical Biology; University of Konstanz; Konstanz Germany
| | - Oleg Simakov
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology; University of Konstanz; Konstanz Germany
- European Molecular Biology Laboratory; Heidelberg Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology; University of Konstanz; Konstanz Germany
- Konstanz Research School Chemical Biology; University of Konstanz; Konstanz Germany
| | - Manfred Schartl
- Department Physiological Chemistry, Biocenter; University of Wuerzburg; Wuerzburg Germany
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon; Ecole Normale Supérieure de Lyon; CNRS UMR 5242; Université Lyon 1; Lyon France
| |
Collapse
|
11
|
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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 12/25/2012] [Indexed: 02/06/2023]
|
12
|
Guirola M, Pérez-Rafael S, Capdevila M, Palacios O, Atrian S. Metal dealing at the origin of the Chordata phylum: the metallothionein system and metal overload response in amphioxus. PLoS One 2012; 7:e43299. [PMID: 22905252 PMCID: PMC3419175 DOI: 10.1371/journal.pone.0043299] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 07/19/2012] [Indexed: 11/18/2022] Open
Abstract
Non-vertebrate chordates, specifically amphioxus, are considered of the utmost interest for gaining insight into the evolutionary trends, i.e. differentiation and specialization, of gene/protein systems. In this work, MTs (metallothioneins), the most important metal binding proteins, are characterized for the first time in the cephalochordate subphylum at both gene and protein level, together with the main features defining the amphioxus response to cadmium and copper overload. Two MT genes (BfMT1 and BfMT2) have been identified in a contiguous region of the genome, as well as several ARE (antioxidant response element) and MRE (metal response element) located upstream the transcribed region. Their corresponding cDNAs exhibit identical sequence in the two lancelet species (B. floridae and B. lanceolatum), BfMT2 cDNA resulting from an alternative splicing event. BfMT1 is a polyvalent metal binding peptide that coordinates any of the studied metal ions (Zn, Cd or Cu) rendering complexes stable enough to last in physiological environments, which is fully concordant with the constitutive expression of its gene, and therefore, with a metal homeostasis housekeeping role. On the contrary, BfMT2 exhibits a clear ability to coordinate Cd(II) ions, while it is absolutely unable to fold into stable Cu (I) complexes, even as mixed species. This identifies it as an essential detoxification agent, which is consequently only induced in emergency situations. The cephalochordate MTs are not directly related to vertebrate MTs, neither by gene structure, protein similarity nor metal-binding behavior of the encoded peptides. The closest relative is the echinoderm MT, which confirm proposed phylogenetic relationships between these two groups. The current findings support the existence in most organisms of two types of MTs as for their metal binding preferences, devoted to different biological functions: multivalent MTs for housekeeping roles, and specialized MTs that evolve either as Cd-thioneins or Cu-thioneins, according to the ecophysiological needs of each kind of organisms.
Collapse
Affiliation(s)
- Maria Guirola
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.
| | | | | | | | | |
Collapse
|
13
|
Piskurek O, Jackson DJ. Transposable elements: from DNA parasites to architects of metazoan evolution. Genes (Basel) 2012; 3:409-22. [PMID: 24704977 PMCID: PMC3899998 DOI: 10.3390/genes3030409] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2012] [Revised: 06/19/2012] [Accepted: 06/25/2012] [Indexed: 01/22/2023] Open
Abstract
One of the most unexpected insights that followed from the completion of the human genome a decade ago was that more than half of our DNA is derived from transposable elements (TEs). Due to advances in high throughput sequencing technologies it is now clear that TEs comprise the largest molecular class within most metazoan genomes. TEs, once categorised as "junk DNA", are now known to influence genomic structure and function by increasing the coding and non-coding genetic repertoire of the host. In this way TEs are key elements that stimulate the evolution of metazoan genomes. This review highlights several lines of TE research including the horizontal transfer of TEs through host-parasite interactions, the vertical maintenance of TEs over long periods of evolutionary time, and the direct role that TEs have played in generating morphological novelty.
Collapse
Affiliation(s)
- Oliver Piskurek
- Courant Research Centre Geobiology, Georg-August-University of Göttingen, Goldschmidtstr. 3, Göttingen 37077, Germany.
| | - Daniel J Jackson
- Courant Research Centre Geobiology, Georg-August-University of Göttingen, Goldschmidtstr. 3, Göttingen 37077, Germany.
| |
Collapse
|