1
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Zámocký M, Ferianc P. Discovering the deep evolutionary roots of serum amyloid A protein family. Int J Biol Macromol 2023; 252:126537. [PMID: 37634776 DOI: 10.1016/j.ijbiomac.2023.126537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 08/29/2023]
Abstract
Deep evolutionary origin of the conserved animal serum amyloid A (SAA) apolipoprotein family leading to yet unknown highly similar SAA-like sequences occurring in certain bacterial genomes is demonstrated in this contribution. Horizontal gene transfer event of corresponding genes between gut bacteria and non-vertebrate animals was discovered in the reconstructed phylogenetic tree obtained with maximum likelihood and neighbor-joining methods, respectively. This detailed phylogeny based on totally 128 complete sequences comprised diverse serum amyloid A isoforms from various animal vertebrate and non-vertebrate phyla and also corresponding genes coding for highly similar proteins from animal gut bacteria. Typical largely conserved sequence motifs and a peculiar structural fold consisting mainly of four α-helices in a bundle within all reconstructed clades of the SAA protein family are discussed with respect to their supposed biological functions in various organisms that contain corresponding genes.
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Affiliation(s)
- Marcel Zámocký
- Laboratory of Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia; Department of Inorganic Chemistry, Faculty of Natural Sciences, Comenius University Bratislava, Mlynská dolina, Ilkovičova 6, SK-84215 Bratislava, Slovakia.
| | - Peter Ferianc
- Laboratory of Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia
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2
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Lin Z, Qin Y, Chen H, Shi D, Zhong M, An T, Chen L, Wang Y, Lin F, Li G, Ji ZL. TransIntegrator: capture nearly full protein-coding transcript variants via integrating Illumina and PacBio transcriptomes. Brief Bioinform 2023; 24:bbad334. [PMID: 37779246 DOI: 10.1093/bib/bbad334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023] Open
Abstract
Genes have the ability to produce transcript variants that perform specific cellular functions. However, accurately detecting all transcript variants remains a long-standing challenge, especially when working with poorly annotated genomes or without a known genome. To address this issue, we have developed a new computational method, TransIntegrator, which enables transcriptome-wide detection of novel transcript variants. For this, we determined 10 Illumina sequencing transcriptomes and a PacBio full-length transcriptome for consecutive embryo development stages of amphioxus, a species of great evolutionary importance. Based on the transcriptomes, we employed TransIntegrator to create a comprehensive transcript variant library, namely iTranscriptome. The resulting iTrancriptome contained 91 915 distinct transcript variants, with an average of 2.4 variants per gene. This substantially improved current amphioxus genome annotation by expanding the number of genes from 21 954 to 38 777. Further analysis manifested that the gene expansion was largely ascribed to integration of multiple Illumina datasets instead of involving the PacBio data. Moreover, we demonstrated an example application of TransIntegrator, via generating iTrancriptome, in aiding accurate transcriptome assembly, which significantly outperformed other hybrid methods such as IDP-denovo and Trinity. For user convenience, we have deposited the source codes of TransIntegrator on GitHub as well as a conda package in Anaconda. In summary, this study proposes an affordable but efficient method for reliable transcriptomic research in most species.
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Affiliation(s)
- Zhe Lin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China
- National Institute for Data Science in Health and Medicine, Xiamen University, 361102, Xiamen, China
| | - Yangmei Qin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China
| | - Hao Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China
| | - Dan Shi
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China
| | - Mindong Zhong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China
| | - Te An
- School of Informatics, Xiamen University, 361005, Xiamen, China
| | - Linshan Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China
| | - Yiquan Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China
| | - Fan Lin
- National Institute for Data Science in Health and Medicine, Xiamen University, 361102, Xiamen, China
- School of Informatics, Xiamen University, 361005, Xiamen, China
| | - Guang Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China
| | - Zhi-Liang Ji
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China
- National Institute for Data Science in Health and Medicine, Xiamen University, 361102, Xiamen, China
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3
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Chowdhury R, Roure A, le Pétillon Y, Mayeur H, Daric V, Darras S. Highly distinct genetic programs for peripheral nervous system formation in chordates. BMC Biol 2022; 20:152. [PMID: 35761237 PMCID: PMC9238270 DOI: 10.1186/s12915-022-01355-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 06/20/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Vertebrates develop their peripheral nervous system (PNS) from transient unique embryonic structures, the neural crest, and the ectodermal placodes that are located at the border of the forming central nervous system. By contrast, in the invertebrate chordates, amphioxus and ascidians, a large part of the PNS originates at the opposite of the embryo, in the ventral ectoderm. In both groups, a biphasic mechanism regulates ventral PNS formation: high BMP levels specify a neurogenic territory within which glutamatergic epidermal sensory neuron formation is controlled by the Notch pathway. Given these similarities and the phylogenetic relationships within chordates, it is likely that ventral PNS is an ancestral feature in chordates and that it has been lost in vertebrates.
Results
In order to get insights into the molecular control of ventral PNS formation and to test the hypothesis of their homology and potential contribution to the emergence of vertebrate PNS, we undertook a close comparison of ventral PNS formation in the ascidian Phallusia mammillata and the amphioxus Branchiostoma lanceolatum. Using timed RNA-seq series, we identified novel markers of the ventral PNS during different phases of its development in both species. By extensively determining the expression of paralogous and orthologous genes, we observed that only a minority of genes have a shared expression in the ventral PNS. However, a large fraction of ventral PNS orthologous genes are expressed in the dorsally forming PNS of vertebrates.
Conclusions
Our work has significantly increased the molecular characterization of ventral PNS formation in invertebrate chordates. The low observed conservation of gene expression in the ventral PNS suggests that the amphioxus and ascidian ventral PNS are either not homologous, or alternatively extensive drift has occurred in their regulatory mechanisms following a long period (600 My) of separate evolution and accelerated evolution in the ascidian lineage. The homology to genes expressed in the dorsally forming PNS of vertebrates suggests that ancestral sensory neurons gene networks have been redeployed in vertebrates.
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4
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Caccavale F, Annona G, Subirana L, Escriva H, Bertrand S, D'Aniello S. Crosstalk between nitric oxide and retinoic acid pathways is essential for amphioxus pharynx development. eLife 2021; 10:e58295. [PMID: 34431784 PMCID: PMC8387019 DOI: 10.7554/elife.58295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 07/31/2021] [Indexed: 11/13/2022] Open
Abstract
During animal ontogenesis, body axis patterning is finely regulated by complex interactions among several signaling pathways. Nitric oxide (NO) and retinoic acid (RA) are potent morphogens that play a pivotal role in vertebrate development. Their involvement in axial patterning of the head and pharynx shows conserved features in the chordate phylum. Indeed, in the cephalochordate amphioxus, NO and RA are crucial for the correct development of pharyngeal structures. Here, we demonstrate the functional cooperation between NO and RA that occurs during amphioxus embryogenesis. During neurulation, NO modulates RA production through the transcriptional regulation of Aldh1a.2 that irreversibly converts retinaldehyde into RA. On the other hand, RA directly or indirectly regulates the transcription of Nos genes. This reciprocal regulation of NO and RA pathways is essential for the normal pharyngeal development in amphioxus and it could be conserved in vertebrates.
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Affiliation(s)
- Filomena Caccavale
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn NapoliNapoliItaly
| | - Giovanni Annona
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn NapoliNapoliItaly
| | - Lucie Subirana
- Sorbonne Université CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire OcéanologiqueBanyuls-sur-MerFrance
| | - Hector Escriva
- Sorbonne Université CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire OcéanologiqueBanyuls-sur-MerFrance
| | - Stephanie Bertrand
- Sorbonne Université CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire OcéanologiqueBanyuls-sur-MerFrance
| | - Salvatore D'Aniello
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn NapoliNapoliItaly
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5
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The Spindle Assembly Checkpoint Functions during Early Development in Non-Chordate Embryos. Cells 2020; 9:cells9051087. [PMID: 32354040 PMCID: PMC7290841 DOI: 10.3390/cells9051087] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/22/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022] Open
Abstract
In eukaryotic cells, a spindle assembly checkpoint (SAC) ensures accurate chromosome segregation, by monitoring proper attachment of chromosomes to spindle microtubules and delaying mitotic progression if connections are erroneous or absent. The SAC is thought to be relaxed during early embryonic development. Here, we evaluate the checkpoint response to lack of kinetochore-spindle microtubule interactions in early embryos of diverse animal species. Our analysis shows that there are two classes of embryos, either proficient or deficient for SAC activation during cleavage. Sea urchins, mussels, and jellyfish embryos show a prolonged delay in mitotic progression in the absence of spindle microtubules from the first cleavage division, while ascidian and amphioxus embryos, like those of Xenopus and zebrafish, continue mitotic cycling without delay. SAC competence during early development shows no correlation with cell size, chromosome number, or kinetochore to cell volume ratio. We show that SAC proteins Mad1, Mad2, and Mps1 lack the ability to recognize unattached kinetochores in ascidian embryos, indicating that SAC signaling is not diluted but rather actively silenced during early chordate development.
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Aldea D, Subirana L, Keime C, Meister L, Maeso I, Marcellini S, Gomez-Skarmeta JL, Bertrand S, Escriva H. Genetic regulation of amphioxus somitogenesis informs the evolution of the vertebrate head mesoderm. Nat Ecol Evol 2019; 3:1233-1240. [PMID: 31263232 DOI: 10.1038/s41559-019-0933-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/22/2019] [Indexed: 01/13/2023]
Abstract
The evolution of vertebrates from an ancestral chordate was accompanied by the acquisition of a predatory lifestyle closely associated to the origin of a novel anterior structure, the highly specialized head. While the vertebrate head mesoderm is unsegmented, the paraxial mesoderm of the earliest divergent chordate clade, the cephalochordates (amphioxus), is fully segmented in somites. We have previously shown that fibroblast growth factor signalling controls the formation of the most anterior somites in amphioxus; therefore, unravelling the fibroblast growth factor signalling downstream effectors is of crucial importance to shed light on the evolutionary origin of vertebrate head muscles. By using a comparative RNA sequencing approach and genetic functional analyses, we show that several transcription factors, such as Six1/2, Pax3/7 and Zic, act in combination to ensure the formation of three different somite populations. Interestingly, these proteins are orthologous to key regulators of trunk, and not head, muscle formation in vertebrates. Contrary to prevailing thinking, our results suggest that the vertebrate head mesoderm is of visceral and not paraxial origin and support a multistep evolutionary scenario for the appearance of the unsegmented mesoderm of the vertebrates new 'head'.
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Affiliation(s)
- Daniel Aldea
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Lucie Subirana
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Celine Keime
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM, U1258, CNRS, UMR7104, Université de Strasbourg, Illkirch-Graffenstaden, France
| | - Lydvina Meister
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Sylvain Marcellini
- Laboratory of Development and Evolution, Department of Cell Biology, Faculty of Biological Sciences, University of Concepción, Concepción, Chile
| | - Jose Luis Gomez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Stephanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls-sur-Mer, France.
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls-sur-Mer, France.
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7
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Mahajan S, Ramya TNC. Nature-inspired engineering of an F-type lectin for increased binding strength. Glycobiology 2019; 28:933-948. [PMID: 30202877 DOI: 10.1093/glycob/cwy082] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 09/07/2018] [Indexed: 11/13/2022] Open
Abstract
Individual lectin-carbohydrate interactions are usually of low affinity. However, high avidity is frequently attained by the multivalent presentation of glycans on biological surfaces coupled with the occurrence of high order lectin oligomers or tandem repeats of lectin domains in the polypeptide. F-type lectins are l-fucose binding lectins with a typical sequence motif, HX(26)RXDX(4)R/K, whose residues participate in l-fucose binding. We previously reported the presence of a few eukaryotic F-type lectin domains with partial sequence duplication that results in the presence of two l-fucose-binding sequence motifs. We hypothesized that such partial sequence duplication would result in greater avidity of lectin-ligand interactions. Inspired by this example from Nature, we attempted to engineer a bacterial F-type lectin domain from Streptosporangium roseum to attain avid binding by mimicking partial duplication. The engineered lectin demonstrated 12-fold greater binding strength than the wild-type lectin to multivalent fucosylated glycoconjugates. However, the affinity to the monosaccharide l-fucose in solution was similar and partial sequence duplication did not result in an additional functional l-fucose binding site. We also cloned, expressed and purified a Branchiostoma floridae F-type lectin domain with naturally occurring partial sequence duplication and confirmed that the duplicated region with the F-type lectin sequence motif did not participate in l-fucose binding. We found that the greater binding strength of the engineered lectin from S. roseum was instead due to increased oligomerization. We believe that this Nature-inspired strategy might be useful for engineering lectins to improve binding strength in various applications.
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Affiliation(s)
- Sonal Mahajan
- Institute of Microbial Technology, Sector 39-A, Chandigarh, India
| | - T N C Ramya
- Institute of Microbial Technology, Sector 39-A, Chandigarh, India
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8
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Zhang QL, Zhang GL, Yuan ML, Dong ZX, Li HW, Guo J, Wang F, Deng XY, Chen JY, Lin LB. A Phylogenomic Framework and Divergence History of Cephalochordata Amphioxus. Front Physiol 2018; 9:1833. [PMID: 30618839 PMCID: PMC6305399 DOI: 10.3389/fphys.2018.01833] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 12/06/2018] [Indexed: 11/21/2022] Open
Abstract
Amphioxus, or cephalochordates, are often used as the living invertebrate proxy of vertebrate ancestors and are widely used as evolutionary biology models of chordates. However, their phylogeny, divergence history, and speciation characteristics remain poorly understood, and phylogenomic studies to explore these problems lacking entirely from the literature. Here, we determined a new transcriptome of Branchiostoma japonicum. Combined with mass sequences of all other 18 species, a 19-way phylogeny was constructed via multiple methods (ML, BI, PhyloBayes, and ASTRAL), consistently supporting a phylogeny of [(B. belcheri + B. japonicum) + (B. lanceolatum + B. floridae) + Asymmetron lucayanum] in amphioxus. Congruent phylogenetic signals were found across mitochondrial genes, 12S RNA, and complete mitochondrial genomes according to previous reports, indicating that 12S RNA may have potential as a molecular marker for phylogenetic analysis in amphioxus. Molecular dating analysis indicated a radiation of the cephalochordates during the Cretaceous (∼104-61 million years ago), supporting an association between the diversification and speciation of cephalochordates with continental drift and associated changes in their respective habitats during this time. The identified functional enrichment analysis for species-specific domains indicated that their function mainly involves immune response, apoptosis, and lipid metabolism and utilization, signaling that pathogens and changes of energy requirements are an important driving force for amphioxus speciation. This study represents the first large-scale phylogenomic analysis of most major amphioxus genera based on phylogenomic data, providing a new perspective on both phylogeny and divergence speciation of cephalochordates.
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Affiliation(s)
- Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.,Evo-Devo Institute, School of Life Sciences, Nanjing University, Nanjing, China
| | - Guan-Ling Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Ming-Long Yuan
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhi-Xiang Dong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Hong-Wei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jun Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Feng Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xian-Yu Deng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jun-Yuan Chen
- Evo-Devo Institute, School of Life Sciences, Nanjing University, Nanjing, China.,State Key Laboratory of Palaeobiology and Stratigraphy (LPS), Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
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9
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Bányai L, Kerekes K, Trexler M, Patthy L. Morphological Stasis and Proteome Innovation in Cephalochordates. Genes (Basel) 2018; 9:genes9070353. [PMID: 30013013 PMCID: PMC6071037 DOI: 10.3390/genes9070353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/11/2018] [Accepted: 07/11/2018] [Indexed: 11/16/2022] Open
Abstract
Lancelets, extant representatives of basal chordates, are prototypic examples of evolutionary stasis; they preserved a morphology and body-plan most similar to the fossil chordates from the early Cambrian. Such a low level of morphological evolution is in harmony with a low rate of amino acid substitution; cephalochordate proteins were shown to evolve slower than those of the slowest evolving vertebrate, the elephant shark. Surprisingly, a study comparing the predicted proteomes of Chinese amphioxus, Branchiostoma belcheri and the Florida amphioxus, Branchiostoma floridae has led to the conclusion that the rate of creation of novel domain combinations is orders of magnitude greater in lancelets than in any other Metazoa, a finding that contradicts the notion that high rates of protein innovation are usually associated with major evolutionary innovations. Our earlier studies on a representative sample of proteins have provided evidence suggesting that the differences in the domain architectures of predicted proteins of these two lancelet species reflect annotation errors, rather than true innovations. In the present work, we have extended these studies to include a larger sample of genes and two additional lancelet species, Asymmetron lucayanum and Branchiostoma lanceolatum. These analyses have confirmed that the domain architecture differences of orthologous proteins of the four lancelet species are because of errors of gene prediction, the error rate in the given species being inversely related to the quality of the transcriptome dataset that was used to aid gene prediction.
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Affiliation(s)
- László Bányai
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary.
| | - Krisztina Kerekes
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary.
| | - Mária Trexler
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary.
| | - László Patthy
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary.
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10
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Zieger E, Garbarino G, Robert NSM, Yu JK, Croce JC, Candiani S, Schubert M. Retinoic acid signaling and neurogenic niche regulation in the developing peripheral nervous system of the cephalochordate amphioxus. Cell Mol Life Sci 2018; 75:2407-2429. [PMID: 29387904 PMCID: PMC11105557 DOI: 10.1007/s00018-017-2734-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 12/19/2017] [Indexed: 10/18/2022]
Abstract
The retinoic acid (RA) signaling pathway regulates axial patterning and neurogenesis in the developing central nervous system (CNS) of chordates, but little is known about its roles during peripheral nervous system (PNS) formation and about how these roles might have evolved. This study assesses the requirement of RA signaling for establishing a functional PNS in the cephalochordate amphioxus, the best available stand-in for the ancestral chordate condition. Pharmacological manipulation of RA signaling levels during embryogenesis reduces the ability of amphioxus larvae to respond to sensory stimulation and alters the number and distribution of ectodermal sensory neurons (ESNs) in a stage- and context-dependent manner. Using gene expression assays combined with immunohistochemistry, we show that this is because RA signaling specifically acts on a small population of soxb1c-expressing ESN progenitors, which form a neurogenic niche in the trunk ectoderm, to modulate ESN production during elongation of the larval body. Our findings reveal an important role for RA signaling in regulating neurogenic niche activity in the larval amphioxus PNS. Although only few studies have addressed this issue so far, comparable RA signaling functions have been reported for neurogenic niches in the CNS and in certain neurogenic placode derivatives of vertebrates. Accordingly, the here-described mechanism is likely a conserved feature of chordate embryonic and adult neural development.
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Affiliation(s)
- Elisabeth Zieger
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, Sorbonne Universités, UPMC Université Paris 06, CNRS, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France
| | - Greta Garbarino
- Department of Earth, Environment and Life Sciences (Dipartimento di Scienze della Terra dell'Ambiente e della Vita, DISTAV), University of Genoa, Viale Benedetto XV 5, 16132, Genoa, Italy
| | - Nicolas S M Robert
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, Sorbonne Universités, UPMC Université Paris 06, CNRS, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Jenifer C Croce
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, Sorbonne Universités, UPMC Université Paris 06, CNRS, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France
| | - Simona Candiani
- Department of Earth, Environment and Life Sciences (Dipartimento di Scienze della Terra dell'Ambiente e della Vita, DISTAV), University of Genoa, Viale Benedetto XV 5, 16132, Genoa, Italy
| | - Michael Schubert
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, Sorbonne Universités, UPMC Université Paris 06, CNRS, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France.
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11
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Barton-Owen TB, Ferrier DEK, Somorjai IML. Pax3/7 duplicated and diverged independently in amphioxus, the basal chordate lineage. Sci Rep 2018; 8:9414. [PMID: 29925900 PMCID: PMC6010424 DOI: 10.1038/s41598-018-27700-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/06/2018] [Indexed: 01/06/2023] Open
Abstract
The Pax3/7 transcription factor family is integral to developmental gene networks contributing to important innovations in vertebrate evolution, including the neural crest. The basal chordate lineage of amphioxus is ideally placed to understand the dynamics of the gene regulatory network evolution that produced these novelties. We report here the discovery that the cephalochordate lineage possesses two Pax3/7 genes, Pax3/7a and Pax3/7b. The tandem duplication is ancestral to all extant amphioxus, occurring in both Asymmetron and Branchiostoma, but originated after the split from the lineage leading to vertebrates. The two paralogues are differentially expressed during embryonic development, particularly in neural and somitic tissues, suggesting distinct regulation. Our results have implications for the study of amphioxus regeneration, neural plate and crest evolution, and differential tandem paralogue evolution.
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Affiliation(s)
- Thomas B Barton-Owen
- University of St Andrews, Gatty Marine Laboratory, Scottish Oceans Institute, East Sands, St Andrews, Fife, KY16 8LB, UK.,University of St Andrews, Biomedical Sciences Research Complex, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - David E K Ferrier
- University of St Andrews, Gatty Marine Laboratory, Scottish Oceans Institute, East Sands, St Andrews, Fife, KY16 8LB, UK
| | - Ildikó M L Somorjai
- University of St Andrews, Gatty Marine Laboratory, Scottish Oceans Institute, East Sands, St Andrews, Fife, KY16 8LB, UK. .,University of St Andrews, Biomedical Sciences Research Complex, North Haugh, St Andrews, Fife, KY16 9ST, UK.
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12
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Roles of Retinoic Acid Signaling in Shaping the Neuronal Architecture of the Developing Amphioxus Nervous System. Mol Neurobiol 2017; 55:5210-5229. [PMID: 28875454 DOI: 10.1007/s12035-017-0727-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/08/2017] [Indexed: 02/01/2023]
Abstract
The morphogen retinoic acid (RA) patterns vertebrate nervous systems and drives neurogenesis, but how these functions evolved remains elusive. Here, we show that RA signaling plays stage- and tissue-specific roles during the formation of neural cell populations with serotonin, dopamine, and GABA neurotransmitter phenotypes in amphioxus, a proxy for the ancestral chordate. Our data suggest that RA signaling restricts the specification of dopamine-containing cells in the ectoderm and of GABA neurons in the neural tube, probably by regulating Hox1 and Hox3 gene expression, respectively. The two Hox genes thus appear to serve distinct functions rather than to participate in a combinatorial Hox code. We were further able to correlate the RA signaling-dependent mispatterning of hindbrain GABA neurons with concomitant motor impairments. Taken together, these data provide new insights into how RA signaling and Hox genes contribute to nervous system as well as to motor control development in amphioxus and hence shed light on the evolution of these functions within vertebrates.
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Abstract
Neural induction is the process through which pluripotent cells are committed to a neural fate. This first step of Central Nervous System formation is triggered by the "Spemann organizer" in amphibians and by homologous embryonic regions in other vertebrates. Studies in classical vertebrate models have produced contrasting views about the molecular nature of neural inducers and no unifying scheme could be drawn. Moreover, how this process evolved in the chordate lineage remains an unresolved issue. In this work, by using graft and micromanipulation experiments, we definitively establish that the dorsal blastopore lip of the cephalochordate amphioxus is homologous to the vertebrate organizer and is able to trigger the formation of neural tissues in a host embryo. In addition, we demonstrate that Nodal/Activin is the main signal eliciting neural induction in amphioxus, and that it also functions as a bona fide neural inducer in the classical vertebrate model Xenopus. Altogether, our results allow us to propose that Nodal/Activin was a major player of neural induction in the ancestor of chordates. This study further reveals the diversity of neural inducers deployed during chordate evolution and advocates against a universally conserved molecular explanation for this process.
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Igawa T, Nozawa M, Suzuki DG, Reimer JD, Morov AR, Wang Y, Henmi Y, Yasui K. Evolutionary history of the extant amphioxus lineage with shallow-branching diversification. Sci Rep 2017; 7:1157. [PMID: 28442709 PMCID: PMC5430900 DOI: 10.1038/s41598-017-00786-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/13/2017] [Indexed: 01/20/2023] Open
Abstract
Amphioxus or lancelets have been regarded as a key animal in understanding the origin of vertebrates. However, the evolutionary history within this lineage remains unexplored. As the amphioxus lineage has likely been separated from other chordates for a very long time and displays a marked left-right asymmetry, its evolutionary history is potentially helpful in better understanding chordate and vertebrate origins. We studied the phylogenetic relationships within the extant amphioxus lineage based on mitochondrial genomes incorporating new Asymmetron and Epigonichthys populations, and based on previously reported nuclear transcriptomes. The resulting tree patterns are consistent, showing the Asymmetron clade diverging first, followed by the Epigonichthys and Branchiostoma clades splitting. Divergence time estimates based on nuclear transcriptomes with vertebrate calibrations support a shallow diversification of the extant amphioxus lineage in the Tertiary. These estimates fit well with the closure of seaways between oceans by continental drift, ocean currents, and present geographical distributions, and suggest a long cryptic history from the origin of amphioxus to its most recent diversification. Deduced character polarities based on phylogenetic analyses suggest that the common ancestor of the extant amphioxus existed in a tiny epibenthic state with larva-like appearance of extant amphioxus, likely with ciliate epidermis.
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Affiliation(s)
- Takeshi Igawa
- Amphibian Research Center, Hiroshima University, 1-3-1 Kagamiyama, Higashi-hiroshima, Hiroshima, 739-8529, Japan
| | - Masafumi Nozawa
- Department of Biological Sciences, School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo, 192-0397, Japan
| | - Daichi G Suzuki
- Department of Biological Sciences, Graduate School of Life and Environmental Sciences, Tsukuba University, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan.,Nobel Institute for Neurophysiology, Department of Neuroscience, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - James D Reimer
- Department of Biology, Chemistry & Marine Sciences, Faculty of Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| | - Arseniy R Morov
- Department of Biological Science, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-hiroshima, Hiroshima, 739-8526, Japan.,Depertment of Zoology and General Biology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 18 Kremlyovskaya St., Kazan, 420008, Republic of Tatarstan, Russian Federation
| | - Yiquan Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Yasuhisa Henmi
- Aitsu Marine Station, Center for Marine Environmental Studies, Kumamoto University, 6061 Aitsu, Kami-Amakusa, Kumamoto, 861-6102, Japan
| | - Kinya Yasui
- Department of Biological Science, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-hiroshima, Hiroshima, 739-8526, Japan.
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15
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Dailey SC, Kozmikova I, Somorjai IM. Amphioxus Sp5 is a member of a conserved Specificity Protein complement and is modulated by Wnt/β-catenin signalling. THE INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY 2017; 61:723-732. [PMID: 29319119 PMCID: PMC5777634 DOI: 10.1387/ijdb.170205is] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A cluster of three Specificity Protein (Sp) genes (Sp1-4, Sp5 and Sp6-9) is thought to be ancestral in both chordates and the wider Eumetazoa. Sp5 and Sp6-9 gene groups are associated with embryonic growth zones, such as tailbuds, and are both Wnt/β-catenin signalling pathway members and targets. Currently, there are conflicting reports as to the number and identity of Sp genes in the cephalochordates, the sister group to the vertebrates and urochordates. We confirm the SP complement of Branchiostoma belcheri and Branchiostoma lanceolatum, as well as their genomic arrangement, protein domain structure and residue frequency. We assay Sp5 expression in B. lanceolatum embryos, and determine its response to pharmacologically increased β-catenin signalling. Branchiostoma possesses three Sp genes, located on the same genomic scaffold. Phylogenetic and domain structure analyses are consistent with their identification as SP1-4, SP5 and SP6-9, although SP1-4 contains a novel glutamine-rich N-terminal region. SP5 is expressed in axial mesoderm and neurectoderm, and marks the cerebral vesicle and presumptive pharynx. Early exposure to increased β-catenin caused ubiquitous SP5 expression in late gastrula, while later treatment at gastrula stages reduced SP5 expression in the posterior growth zone during axis elongation. Amphioxus possess a typical invertebrate eumetazoan SP complement, and SP5 expression in embryos is well conserved with vertebrate homologues. Its expression in the tailbud, a posterior growth zone, is consistent with expression seen in other bilaterians. Branchiostoma SP5 shows a dynamic response to Wnt/β-catenin signalling.
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Affiliation(s)
- Simon C. Dailey
- University of St Andrews, Biomedical Sciences Research Complex, North Haugh, St Andrews, UK
- Scottish Oceans Institute, East Sands, St Andrews, UK
| | - Iryna Kozmikova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ildikó M.L. Somorjai
- University of St Andrews, Biomedical Sciences Research Complex, North Haugh, St Andrews, UK
- Scottish Oceans Institute, East Sands, St Andrews, UK
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16
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Yong LW, Yu JK. Tracing the evolutionary origin of vertebrate skeletal tissues: insights from cephalochordate amphioxus. Curr Opin Genet Dev 2016; 39:55-62. [DOI: 10.1016/j.gde.2016.05.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 04/01/2016] [Accepted: 05/30/2016] [Indexed: 12/20/2022]
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17
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Thélie A, Desiderio S, Hanotel J, Quigley I, Van Driessche B, Rodari A, Borromeo MD, Kricha S, Lahaye F, Croce J, Cerda-Moya G, Ordoño Fernandez J, Bolle B, Lewis KE, Sander M, Pierani A, Schubert M, Johnson JE, Kintner CR, Pieler T, Van Lint C, Henningfeld KA, Bellefroid EJ, Van Campenhout C. Prdm12 specifies V1 interneurons through cross-repressive interactions with Dbx1 and Nkx6 genes in Xenopus. Development 2016; 142:3416-28. [PMID: 26443638 DOI: 10.1242/dev.121871] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
V1 interneurons are inhibitory neurons that play an essential role in vertebrate locomotion. The molecular mechanisms underlying their genesis remain, however, largely undefined. Here, we show that the transcription factor Prdm12 is selectively expressed in p1 progenitors of the hindbrain and spinal cord in the frog embryo, and that a similar restricted expression profile is observed in the nerve cord of other vertebrates as well as of the cephalochordate amphioxus. Using frog, chick and mice, we analyzed the regulation of Prdm12 and found that its expression in the caudal neural tube is dependent on retinoic acid and Pax6, and that it is restricted to p1 progenitors, due to the repressive action of Dbx1 and Nkx6-1/2 expressed in the adjacent p0 and p2 domains. Functional studies in the frog, including genome-wide identification of its targets by RNA-seq and ChIP-Seq, reveal that vertebrate Prdm12 proteins act as a general determinant of V1 cell fate, at least in part, by directly repressing Dbx1 and Nkx6 genes. This probably occurs by recruiting the methyltransferase G9a, an activity that is not displayed by the amphioxus Prdm12 protein. Together, these findings indicate that Prdm12 promotes V1 interneurons through cross-repressive interactions with Dbx1 and Nkx6 genes, and suggest that this function might have only been acquired after the split of the vertebrate and cephalochordate lineages.
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Affiliation(s)
- Aurore Thélie
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
| | - Simon Desiderio
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
| | - Julie Hanotel
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
| | - Ian Quigley
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Anthony Rodari
- Laboratory of Molecular Virology, ULB, IBMM, Gosselies B-6041, Belgium
| | - Mark D Borromeo
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sadia Kricha
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
| | - François Lahaye
- Sorbonne Universités, UPMC Université Paris 06, CNRS UMR 7009, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (UMR 7009), Observatoire Océanologique de Villefranche-sur-Mer, Villefranche-sur-Mer 06230, France
| | - Jenifer Croce
- Sorbonne Universités, UPMC Université Paris 06, CNRS UMR 7009, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (UMR 7009), Observatoire Océanologique de Villefranche-sur-Mer, Villefranche-sur-Mer 06230, France
| | - Gustavo Cerda-Moya
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Jesús Ordoño Fernandez
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
| | - Barbara Bolle
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
| | - Katharine E Lewis
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244, USA
| | - Maike Sander
- Departments of Pediatrics and Cellular and Molecular Medicine, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92093-0695, USA
| | - Alessandra Pierani
- Génétique et développement du cortex cerebral, Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris Cedex 13 75205, France
| | - Michael Schubert
- Sorbonne Universités, UPMC Université Paris 06, CNRS UMR 7009, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (UMR 7009), Observatoire Océanologique de Villefranche-sur-Mer, Villefranche-sur-Mer 06230, France
| | - Jane E Johnson
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Christopher R Kintner
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Tomas Pieler
- Department of Developmental Biochemistry, Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), University of Göttingen, 37077 Göttingen, Germany
| | - Carine Van Lint
- Laboratory of Molecular Virology, ULB, IBMM, Gosselies B-6041, Belgium
| | - Kristine A Henningfeld
- Department of Developmental Biochemistry, Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), University of Göttingen, 37077 Göttingen, Germany
| | - Eric J Bellefroid
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
| | - Claude Van Campenhout
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
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18
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Dailey SC, Febrero Planas R, Rossell Espier A, Garcia-Fernàndez J, Somorjai IML. Asymmetric Distribution of pl10 and bruno2, New Members of a Conserved Core of Early Germline Determinants in Cephalochordates. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2015.00156] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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19
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Bürglin TR, Affolter M. Homeodomain proteins: an update. Chromosoma 2015; 125:497-521. [PMID: 26464018 PMCID: PMC4901127 DOI: 10.1007/s00412-015-0543-8] [Citation(s) in RCA: 256] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 09/20/2015] [Accepted: 09/21/2015] [Indexed: 12/17/2022]
Abstract
Here, we provide an update of our review on homeobox genes that we wrote together with Walter Gehring in 1994. Since then, comprehensive surveys of homeobox genes have become possible due to genome sequencing projects. Using the 103 Drosophila homeobox genes as example, we present an updated classification. In animals, there are 16 major classes, ANTP, PRD, PRD-LIKE, POU, HNF, CUT (with four subclasses: ONECUT, CUX, SATB, and CMP), LIM, ZF, CERS, PROS, SIX/SO, plus the TALE superclass with the classes IRO, MKX, TGIF, PBC, and MEIS. In plants, there are 11 major classes, i.e., HD-ZIP (with four subclasses: I to IV), WOX, NDX, PHD, PLINC, LD, DDT, SAWADEE, PINTOX, and the two TALE classes KNOX and BEL. Most of these classes encode additional domains apart from the homeodomain. Numerous insights have been obtained in the last two decades into how homeodomain proteins bind to DNA and increase their specificity by interacting with other proteins to regulate cell- and tissue-specific gene expression. Not only protein-DNA base pair contacts are important for proper target selection; recent experiments also reveal that the shape of the DNA plays a role in specificity. Using selected examples, we highlight different mechanisms of homeodomain protein-DNA interaction. The PRD class of homeobox genes was of special interest to Walter Gehring in the last two decades. The PRD class comprises six families in Bilateria, and tinkers with four different motifs, i.e., the PAIRED domain, the Groucho-interacting motif EH1 (aka Octapeptide or TN), the homeodomain, and the OAR motif. Homologs of the co-repressor protein Groucho are also present in plants (TOPLESS), where they have been shown to interact with small amphipathic motives (EAR), and in yeast (TUP1), where we find an EH1-like motif in MATα2.
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Affiliation(s)
- Thomas R. Bürglin
- />Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
- />Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Markus Affolter
- />Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
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20
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Aldea D, Leon A, Bertrand S, Escriva H. Expression of Fox genes in the cephalochordate Branchiostoma lanceolatum. Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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21
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Lecroisey C, Le Pétillon Y, Escriva H, Lammert E, Laudet V. Identification, evolution and expression of an insulin-like peptide in the cephalochordate Branchiostoma lanceolatum. PLoS One 2015; 10:e0119461. [PMID: 25774519 PMCID: PMC4361685 DOI: 10.1371/journal.pone.0119461] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/16/2015] [Indexed: 01/24/2023] Open
Abstract
Insulin is one of the most studied proteins since it is central to the regulation of carbohydrate and fat metabolism in vertebrates and its expression and release are disturbed in diabetes, the most frequent human metabolic disease worldwide. However, the evolution of the function of the insulin protein family is still unclear. In this study, we present a phylogenetic and developmental analysis of the Insulin Like Peptide (ILP) in the cephalochordate amphioxus. We identified an ILP in the European amphioxus Branchiostoma lanceolatum that displays structural characteristics of both vertebrate insulin and Insulin-like Growth Factors (IGFs). Our phylogenetic analysis revealed that amphioxus ILP represents the sister group of both vertebrate insulin and IGF proteins. We also characterized both temporal and spatial expression of ILP in amphioxus. We show that ilp is highly expressed in endoderm and paraxial mesoderm during development, and mainly expressed in the gut of both the developing embryo and adult. We hypothesize that ILP has critical implications in both developmental processes and metabolism and could display IGF- and insulin-like functions in amphioxus supporting the idea of a common ancestral protein.
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Affiliation(s)
- Claire Lecroisey
- Molecular Zoology Team, Institut de Génomique Fonctionnelle de Lyon, École Normale Supérieure de Lyon, CNRS, Université Lyon, Lyon, France
| | - Yann Le Pétillon
- CNRS, UMR 7232, BIOM, Observatoire Océanologique, F-66650 Banyuls/Mer, France
| | - Hector Escriva
- CNRS, UMR 7232, BIOM, Observatoire Océanologique, F-66650 Banyuls/Mer, France
| | - Eckhard Lammert
- Institute of Metabolic Physiology, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Vincent Laudet
- Molecular Zoology Team, Institut de Génomique Fonctionnelle de Lyon, École Normale Supérieure de Lyon, CNRS, Université Lyon, Lyon, France
- * E-mail:
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22
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Soukup V, Yong LW, Lu TM, Huang SW, Kozmik Z, Yu JK. The Nodal signaling pathway controls left-right asymmetric development in amphioxus. EvoDevo 2015; 6:5. [PMID: 25954501 PMCID: PMC4423147 DOI: 10.1186/2041-9139-6-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/27/2015] [Indexed: 11/24/2022] Open
Abstract
Background Nodal is an important determinant of the left-right (LR) body axis in bilaterians, specifying the right side in protostomes and non-chordate deuterostomes as opposed to the left side in chordates. Amphioxus represents an early-branching chordate group, rendering it especially useful for studying the character states that predate the origin of vertebrates. However, its anatomy, involving offset arrangement of axial structures, marked asymmetry of the oropharyngeal region, and, most notably, a mouth positioned on the left side, contrasts with the symmetric arrangement of the corresponding regions in other chordates. Results We show that the Nodal signaling pathway acts to specify the LR axis in the cephalochordate amphioxus in a similar way as in vertebrates. At early neurula stages, Nodal switches from initial bilateral to the left-sided expression and subsequently specifies the left embryonic side. Perturbation of Nodal signaling with small chemical inhibitors (SB505124 and SB431542) alters expression of other members of the pathway and of left/right-sided, organ-specific genes. Upon inhibition, larvae display loss of the innate alternation of both somites and axons of peripheral nerves and loss of left-sided pharyngeal structures, such as the mouth, the preoral pit, and the duct of the club-shaped gland. Concomitantly, the left side displays ectopic expression of otherwise right-sided genes, and the larvae exhibit bilaterally symmetrical morphology, with duplicated endostyle and club-shaped gland structures. Conclusions We demonstrate that Nodal signaling is necessary for establishing the LR embryonic axis and for developing profound asymmetry in amphioxus. Our data suggest that initial symmetry breaking in amphioxus and propagation of the pathway on the left side correspond with the situation in vertebrates. However, the organs that become targets of the pathway differ between amphioxus and vertebrates, which may explain the pronounced asymmetry of its oropharyngeal and axial structures and the left-sided position of the mouth. Electronic supplementary material The online version of this article (doi:10.1186/2041-9139-6-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vladimir Soukup
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague, 14220 Czech Republic
| | - Luok Wen Yong
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529 Taiwan
| | - Tsai-Ming Lu
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529 Taiwan
| | - Song-Wei Huang
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529 Taiwan
| | - Zbynek Kozmik
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague, 14220 Czech Republic
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529 Taiwan ; Institute of Oceanography, National Taiwan University, 1 Roosevelt Road, Section 4, Taipei, 10617 Taiwan
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23
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Genome-wide DNA methylation profiles and their relationships with mRNA and the microRNA transcriptome in bovine muscle tissue (Bos taurine). Sci Rep 2014; 4:6546. [PMID: 25306978 PMCID: PMC4194443 DOI: 10.1038/srep06546] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 09/15/2014] [Indexed: 12/21/2022] Open
Abstract
DNA methylation is a key epigenetic modification in mammals and plays important roles in muscle development. We sampled longissimus dorsi muscle (LDM) from a well-known elite native breed of Chinese Qinchuan cattle living within the same environment but displaying distinct skeletal muscle at the fetal and adult stages. We generated and provided a genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA for fetal and adult muscle studies. Integration analysis revealed a total of 77 and 1,054 negatively correlated genes with methylation in the promoter and gene body regions, respectively, in both the fetal and adult bovine libraries. Furthermore, we identified expression patterns of high-read genes that exhibit a negative correlation between methylation and expression from nine different tissues at multiple developmental stages of bovine muscle-related tissue or organs. In addition, we validated the MeDIP-Seq results by bisulfite sequencing PCR (BSP) in some of the differentially methylated promoters. Together, these results provide valuable data for future biomedical research and genomic and epigenomic studies of bovine skeletal muscle that may help uncover the molecular basis underlying economically valuable traits in cattle. This comprehensive map also provides a solid basis for exploring the epigenetic mechanisms of muscle growth and development.
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24
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Fischer AHL, Mozzherin D, Eren AM, Lans KD, Wilson N, Cosentino C, Smith J. SeaBase: a multispecies transcriptomic resource and platform for gene network inference. Integr Comp Biol 2014; 54:250-63. [PMID: 24907201 DOI: 10.1093/icb/icu065] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Marine and aquatic animals are extraordinarily useful as models for identifying mechanisms of development and evolution, regeneration, resistance to cancer, longevity and symbiosis, among many other areas of research. This is due to the great diversity of these organisms and their wide-ranging capabilities. Genomics tools are essential for taking advantage of these "free lessons" of nature. However, genomics and transcriptomics are challenging in emerging model systems. Here, we present SeaBase, a tool for helping to meet these needs. Specifically, SeaBase provides a platform for sharing and searching transcriptome data. More importantly, SeaBase will support a growing number of tools for inferring gene network mechanisms. The first dataset available on SeaBase is a developmental transcriptomic profile of the sea anemone Nematostella vectensis (Anthozoa, Cnidaria). Additional datasets are currently being prepared and we are aiming to expand SeaBase to include user-supplied data for any number of marine and aquatic organisms, thereby supporting many potentially new models for gene network studies. SeaBase can be accessed online at: http://seabase.core.cli.mbl.edu.
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Affiliation(s)
- Antje H L Fischer
- *Marine Biological Laboratory, Woods Hole, MA 02543, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Systems & Control Engineering, University of Magna Graecia, 88100 Catanzaro, Italy*Marine Biological Laboratory, Woods Hole, MA 02543, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Systems & Control Engineering, University of Magna Graecia, 88100 Catanzaro, Italy
| | - Dmitry Mozzherin
- *Marine Biological Laboratory, Woods Hole, MA 02543, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Systems & Control Engineering, University of Magna Graecia, 88100 Catanzaro, Italy
| | - A Murat Eren
- *Marine Biological Laboratory, Woods Hole, MA 02543, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Systems & Control Engineering, University of Magna Graecia, 88100 Catanzaro, Italy
| | - Kristen D Lans
- *Marine Biological Laboratory, Woods Hole, MA 02543, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Systems & Control Engineering, University of Magna Graecia, 88100 Catanzaro, Italy
| | - Nathan Wilson
- *Marine Biological Laboratory, Woods Hole, MA 02543, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Systems & Control Engineering, University of Magna Graecia, 88100 Catanzaro, Italy
| | - Carlo Cosentino
- *Marine Biological Laboratory, Woods Hole, MA 02543, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Systems & Control Engineering, University of Magna Graecia, 88100 Catanzaro, Italy
| | - Joel Smith
- *Marine Biological Laboratory, Woods Hole, MA 02543, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Systems & Control Engineering, University of Magna Graecia, 88100 Catanzaro, Italy
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Barboza CADM, Hadlich HL, Sandrini-Neto L, Martins CDC, Lana PDC. Is the distribution of the lancelet Branchiostoma caribaeum affected by sewage discharges? An analysis at multiple scales of variability. MARINE POLLUTION BULLETIN 2013; 69:178-188. [PMID: 23452624 DOI: 10.1016/j.marpolbul.2013.01.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 01/28/2013] [Accepted: 01/31/2013] [Indexed: 06/01/2023]
Abstract
Spatial variation in the density and biomass of Branchiostoma caribaeum was analyzed along a sewage contamination gradient identified by fecal steroids in a subtropical estuary, southern Brazil. Sampling, repeated in the austral winter and summer, followed a hierarchical design nested at four spatial scales (sector>1 km; area>100 m; site>10 m; replicate<1 m). Density and biomass were significantly lower at sites characterized by high concentrations of fecal steroids. The best combinations of variables that explained the biological similarities among sites involved contamination indicators. Most of the variation of biological data was found at the smallest scales and could be related with the sediment texture. Our study highlighted the usefulness of a multi-scale perspective to evaluate distribution patterns of benthic invertebrates as a biological indication of environmental pollution. Gradient analyses at larger spatial scales may be invalidated by the patchy distribution of benthic fauna if they do not account for such small scale variability.
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Affiliation(s)
- Carlos Alberto de Moura Barboza
- Universidade Federal do Paraná, Centro de Estudos do Mar, Av. Beira-mar, s/n, P.O. Box 50.002, CEP 83255-976, Pontal do Sul, Pontal do Paraná, Paraná, Brazil.
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Pascual-Anaya J, Adachi N, Alvarez S, Kuratani S, D'Aniello S, Garcia-Fernàndez J. Broken colinearity of the amphioxus Hox cluster. EvoDevo 2012. [PMID: 23198682 PMCID: PMC3534614 DOI: 10.1186/2041-9139-3-28] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Background In most eumetazoans studied so far, Hox genes determine the identity of structures along the main body axis. They are usually linked in genomic clusters and, in the case of the vertebrate embryo, are expressed with spatial and temporal colinearity. Outside vertebrates, temporal colinearity has been reported in the cephalochordate amphioxus (the least derived living relative of the chordate ancestor) but only for anterior and central genes, namely Hox1 to Hox4 and Hox6. However, most of the Hox gene expression patterns in amphioxus have not been reported. To gain global insights into the evolution of Hox clusters in chordates, we investigated a more extended expression profile of amphioxus Hox genes. Results Here we report an extended expression profile of the European amphioxus Branchiostoma lanceolatum Hox genes and describe that all Hox genes, except Hox13, are expressed during development. Interestingly, we report the breaking of both spatial and temporal colinearity for at least Hox6 and Hox14, which thus have escaped from the classical Hox code concept. We show a previously unidentified Hox6 expression pattern and a faint expression for posterior Hox genes in structures such as the posterior mesoderm, notochord, and hindgut. Unexpectedly, we found that amphioxus Hox14 had the most divergent expression pattern. This gene is expressed in the anterior cerebral vesicle and pharyngeal endoderm. Amphioxus Hox14 expression represents the first report of Hox gene expression in the most anterior part of the central nervous system. Nevertheless, despite these divergent expression patterns, amphioxus Hox6 and Hox14 seem to be still regulated by retinoic acid. Conclusions Escape from colinearity by Hox genes is not unusual in either vertebrates or amphioxus and we suggest that those genes escaping from it are probably associated with the patterning of lineage-specific morphological traits, requiring the loss of those developmental constraints that kept them colinear.
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Affiliation(s)
- Juan Pascual-Anaya
- Departament de Genètica and Institut de Biomedicina (IBUB), University of Barcelona, Av, Diagonal, 643, Barcelona, 08028, Spain.
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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.
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Affiliation(s)
- Maria Guirola
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.
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