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Takahashi H, Hisata K, Iguchi R, Kikuchi S, Ogasawara M, Satoh N. scRNA-seq analysis of cells comprising the amphioxus notochord. Dev Biol 2024; 508:24-37. [PMID: 38224933 DOI: 10.1016/j.ydbio.2024.01.003] [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: 09/25/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/17/2024]
Abstract
Cephalochordates occupy a key phylogenetic position for deciphering the origin and evolution of chordates, since they diverged earlier than urochordates and vertebrates. The notochord is the most prominent feature of chordates. The amphioxus notochord features coin-shaped cells bearing myofibrils. Notochord-derived hedgehog signaling contributes to patterning of the dorsal nerve cord, as in vertebrates. However, properties of constituent notochord cells remain unknown at the single-cell level. We examined these properties using Iso-seq analysis, single-cell RNA-seq analysis, and in situ hybridization (ISH). Gene expression profiles broadly categorize notochordal cells into myofibrillar cells and non-myofibrillar cells. Myofibrillar cells occupy most of the central portion of the notochord, and some cells extend the notochordal horn to both sides of the ventral nerve cord. Some notochord myofibrillar genes are not expressed in myotomes, suggesting an occurrence of myofibrillar genes that are preferentially expressed in notochord. On the other hand, non-myofibrillar cells contain dorsal, lateral, and ventral Müller cells, and all three express both hedgehog and Brachyury. This was confirmed by ISH, although expression of hedgehog in ventral Müller cells was minimal. In addition, dorsal Müller cells express neural transmission-related genes, suggesting an interaction with nerve cord. Lateral Müller cells express hedgehog and other signaling-related genes, suggesting an interaction with myotomes positioned lateral to the notochord. Ventral Müller cells also expressed genes for FGF- and EGF-related signaling, which may be associated with development of endoderm, ventral to the notochord. Lateral Müller cells were intermediate between dorsal/ventral Müller cells. Since vertebrate notochord contributes to patterning and differentiation of ectoderm (nerve cord), mesoderm (somite), and endoderm, this investigation provides evidence that an ancestral or original form of vertebrate notochord is present in extant cephalochordates.
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Affiliation(s)
- Hiroki Takahashi
- Interdisciplinary Research Unit, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan.
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Rin Iguchi
- Department of Biology, Graduate School of Science, Chiba University, Chiba, 262-8522, Japan
| | - Sakura Kikuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Michio Ogasawara
- Department of Biology, Graduate School of Science, Chiba University, Chiba, 262-8522, Japan.
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
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Sachslehner A, Zieger E, Calcino A, Wanninger A. HES and Mox genes are expressed during early mesoderm formation in a mollusk with putative ancestral features. Sci Rep 2021; 11:18030. [PMID: 34504115 PMCID: PMC8429573 DOI: 10.1038/s41598-021-96711-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/13/2021] [Indexed: 11/08/2022] Open
Abstract
The mesoderm is considered the youngest of the three germ layers. Although its morphogenesis has been studied in some metazoans, the molecular components underlying this process remain obscure for numerous phyla including the highly diverse Mollusca. Here, expression of Hairy and enhancer of split (HES), Mox, and myosin heavy chain (MHC) was investigated in Acanthochitona fascicularis, a representative of Polyplacophora with putative ancestral molluscan features. While AfaMHC is expressed throughout myogenesis, AfaMox1 is only expressed during early stages of mesodermal band formation and in the ventrolateral muscle, an autapomorphy of the polyplacophoran trochophore. Comparing our findings to previously published data across Metazoa reveals Mox expression in the mesoderm in numerous bilaterians including gastropods, polychaetes, and brachiopods. It is also involved in myogenesis in molluscs, annelids, tunicates, and craniates, suggesting a dual role of Mox in mesoderm and muscle formation in the last common bilaterian ancestor. AfaHESC2 is expressed in the ectoderm of the polyplacophoran gastrula and later in the mesodermal bands and in putative neural tissue, whereas AfaHESC7 is expressed in the trochoblasts of the gastrula and during foregut formation. This confirms the high developmental variability of HES gene expression and demonstrates that Mox and HES genes are pleiotropic.
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Affiliation(s)
- Attila Sachslehner
- Department of Evolutionary Biology, Unit for Integrative Zoology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Elisabeth Zieger
- Department of Evolutionary Biology, Unit for Integrative Zoology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Andrew Calcino
- Department of Evolutionary Biology, Unit for Integrative Zoology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Andreas Wanninger
- Department of Evolutionary Biology, Unit for Integrative Zoology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
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Satoh N, Tominaga H, Kiyomoto M, Hisata K, Inoue J, Nishitsuji K. A Preliminary Single-Cell RNA-Seq Analysis of Embryonic Cells That Express Brachyury in the Amphioxus, Branchiostoma japonicum. Front Cell Dev Biol 2021; 9:696875. [PMID: 34336847 PMCID: PMC8321703 DOI: 10.3389/fcell.2021.696875] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/08/2021] [Indexed: 11/13/2022] Open
Abstract
Among chordate taxa, the cephalochordates diverged earlier than urochordates and vertebrates; thus, they retain unique, primitive developmental features. In particular, the amphioxus notochord has muscle-like properties, a feature not seen in urochordates or vertebrates. Amphioxus contains two Brachyury genes, Bra1 and Bra2. Bra2 is reportedly expressed in the blastopore, notochord, somites, and tail bud, in contrast to a low level of Bra1 expression only in notochord. To distinguish the expression profiles of the two Brachyury genes at the single-cell level, we carried out single-cell RNA-seq (scRNA-seq) analysis using the amphioxus, Branchiostoma japonicum. This scRNA-seq analysis classified B. japonicum embryonic cells into 15 clusters at developmental stages from midgastrula to early swimming larva. Brachyury was expressed in cells of clusters 4, 5, 8, and 9. We first confirmed that cluster 8 comprises cells that form somites since this cluster specifically expresses four myogenic factor genes. Cluster 9 contains a larger number of cells with high levels of Bra2 expression and a smaller number of cells with Bra1 expression. Simultaneous expression in cluster 9 of tool-kit genes, including FoxA, Goosecoid, and hedgehog, showed that this cluster comprises cells that form the notochord. Expression of Bra2, but not Bra1, in cells of clusters 4 and 5 at the gastrula stage together with expression of Wnt1 and Caudal indicates that clusters 4 and 5 comprise cells of the blastopore, which contiguously form the tail bud. In addition, Hox1, Hox3, and Hox4 were highly expressed in Bra2-expressing clusters 4, 5, 8, and 9 in a temporally coordinated manner, suggesting roles of anterior Hox genes in specification of mesodermal organs, including somites, notochord, and tail bud. This scRNA-seq analysis therefore highlights differences between the two Brachyury genes in relation to embryonic regions in which they are expressed and their levels of expression. Bra2 is the ancestral Brachyury in amphioxus, since expression in the blastopore is shared with other deuterostomes. On the other hand, Bra1 is a duplicate copy and likely evolved a supplementary function in notochord and somite formation in the Branchiostoma lineage.
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Affiliation(s)
- Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Hitoshi Tominaga
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Masato Kiyomoto
- Tateyama Marine Laboratory, Marine and Coastal Research Center, Ochanomizu University, Chiba, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Jun Inoue
- Atmosphere and Ocean Research Institute, University of Tokyo, Chiba, Japan
| | - Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
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Aase-Remedios ME, Ferrier DEK. Improved Understanding of the Role of Gene and Genome Duplications in Chordate Evolution With New Genome and Transcriptome Sequences. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.703163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Comparative approaches to understanding chordate genomes have uncovered a significant role for gene duplications, including whole genome duplications (WGDs), giving rise to and expanding gene families. In developmental biology, gene families created and expanded by both tandem and WGDs are paramount. These genes, often involved in transcription and signalling, are candidates for underpinning major evolutionary transitions because they are particularly prone to retention and subfunctionalisation, neofunctionalisation, or specialisation following duplication. Under the subfunctionalisation model, duplication lays the foundation for the diversification of paralogues, especially in the context of gene regulation. Tandemly duplicated paralogues reside in the same regulatory environment, which may constrain them and result in a gene cluster with closely linked but subtly different expression patterns and functions. Ohnologues (WGD paralogues) often diversify by partitioning their expression domains between retained paralogues, amidst the many changes in the genome during rediploidisation, including chromosomal rearrangements and extensive gene losses. The patterns of these retentions and losses are still not fully understood, nor is the full extent of the impact of gene duplication on chordate evolution. The growing number of sequencing projects, genomic resources, transcriptomics, and improvements to genome assemblies for diverse chordates from non-model and under-sampled lineages like the coelacanth, as well as key lineages, such as amphioxus and lamprey, has allowed more informative comparisons within developmental gene families as well as revealing the extent of conserved synteny across whole genomes. This influx of data provides the tools necessary for phylogenetically informed comparative genomics, which will bring us closer to understanding the evolution of chordate body plan diversity and the changes underpinning the origin and diversification of vertebrates.
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Aase-Remedios ME, Coll-Lladó C, Ferrier DEK. More Than One-to-Four via 2R: Evidence of an Independent Amphioxus Expansion and Two-Gene Ancestral Vertebrate State for MyoD-Related Myogenic Regulatory Factors (MRFs). Mol Biol Evol 2021; 37:2966-2982. [PMID: 32520990 PMCID: PMC7530620 DOI: 10.1093/molbev/msaa147] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The evolutionary transition from invertebrates to vertebrates involved extensive gene duplication, but understanding precisely how such duplications contributed to this transition requires more detailed knowledge of specific cases of genes and gene families. Myogenic differentiation (MyoD) has long been recognized as a master developmental control gene and member of the MyoD family of bHLH transcription factors (myogenic regulatory factors [MRFs]) that drive myogenesis across the bilaterians. Phylogenetic reconstructions within this gene family are complicated by multiple instances of gene duplication and loss in several lineages. Following two rounds of whole-genome duplication (2R WGD) at the origin of the vertebrates, the ancestral function of MRFs is thought to have become partitioned among the daughter genes, so that MyoD and Myf5 act early in myogenic determination, whereas Myog and Myf6 are expressed later, in differentiating myoblasts. Comparing chordate MRFs, we find an independent expansion of MRFs in the invertebrate chordate amphioxus, with evidence for a parallel instance of subfunctionalization relative to that of vertebrates. Conserved synteny between chordate MRF loci supports the 2R WGD events as a major force in shaping the evolution of vertebrate MRFs. We also resolve vertebrate MRF complements and organization, finding a new type of vertebrate MRF gene in the process, which allowed us to infer an ancestral two-gene state in the vertebrates corresponding to the early- and late-acting types of MRFs. This necessitates a revision of previous conclusions about the simple one-to-four origin of vertebrate MRFs.
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Affiliation(s)
- Madeleine E Aase-Remedios
- Gatty Marine Laboratory, The Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, Fife, United Kingdom
| | - Clara Coll-Lladó
- Gatty Marine Laboratory, The Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, Fife, United Kingdom
| | - David E K Ferrier
- Gatty Marine Laboratory, The Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, Fife, United Kingdom
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6
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Di Gregorio A. The notochord gene regulatory network in chordate evolution: Conservation and divergence from Ciona to vertebrates. Curr Top Dev Biol 2020; 139:325-374. [PMID: 32450965 DOI: 10.1016/bs.ctdb.2020.01.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The notochord is a structure required for support and patterning of all chordate embryos, from sea squirts to humans. An increasing amount of information on notochord development and on the molecular strategies that ensure its proper morphogenesis has been gleaned through studies in the sea squirt Ciona. This invertebrate chordate offers a fortunate combination of experimental advantages, ranging from translucent, fast-developing embryos to a compact genome and impressive biomolecular resources. These assets have enabled the rapid identification of numerous notochord genes and cis-regulatory regions, and provide a rather unique opportunity to reconstruct the gene regulatory network that controls the formation of this developmental and evolutionary chordate landmark. This chapter summarizes the morphogenetic milestones that punctuate notochord formation in Ciona, their molecular effectors, and the current knowledge of the gene regulatory network that ensures the accurate spatial and temporal orchestration of these processes.
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Affiliation(s)
- Anna Di Gregorio
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York, NY, United States.
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7
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Almazán A, Ferrández-Roldán A, Albalat R, Cañestro C. Developmental atlas of appendicularian Oikopleura dioica actins provides new insights into the evolution of the notochord and the cardio-paraxial muscle in chordates. Dev Biol 2019; 448:260-270. [DOI: 10.1016/j.ydbio.2018.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/13/2018] [Accepted: 09/05/2018] [Indexed: 12/22/2022]
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8
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Inoue J, Satoh N. Deuterostome Genomics: Lineage-Specific Protein Expansions That Enabled Chordate Muscle Evolution. Mol Biol Evol 2019; 35:914-924. [PMID: 29319812 PMCID: PMC5888912 DOI: 10.1093/molbev/msy002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Fish-like larvae were foundational to the chordate body plan, given the basal placement of free-living lancelets. That body plan probably made it possible for chordate ancestors to swim by beating a tail formed of notochord and bilateral paraxial muscles. In order to investigate the molecular genetic basis of the origin and evolution of paraxial muscle, we deduced the evolutionary histories of 16 contractile protein genes from paraxial muscle, based on genomic data from all five deuterostome lineages, using a newly developed orthology identification pipeline and a species tree. As a result, we found that more than twice as many orthologs of paraxial muscle genes are present in chordates, as in nonchordate deuterostomes (ambulacrarians). Orthologs of paraxial-type actin and troponin C genes are absent in ambulacrarians and most paraxial muscle protein isoforms diversified via gene duplications that occurred in each chordate lineage. Analyses of genes with known expression sites indicated that some isoforms were reutilized in specific muscles of nonvertebrate chordates via gene duplications. As orthologs of most paraxial muscle genes were present in ambulacrarians, in addition to expression patterns of related genes and functions of the two protein isoforms, regulatory mechanisms of muscle genes should also be considered in future studies of the origin of paraxial muscle.
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Affiliation(s)
- Jun Inoue
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
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9
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Schubert FR, Singh AJ, Afoyalan O, Kioussi C, Dietrich S. To roll the eyes and snap a bite - function, development and evolution of craniofacial muscles. Semin Cell Dev Biol 2018; 91:31-44. [PMID: 29331210 DOI: 10.1016/j.semcdb.2017.12.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 12/15/2017] [Accepted: 12/18/2017] [Indexed: 02/06/2023]
Abstract
Craniofacial muscles, muscles that move the eyes, control facial expression and allow food uptake and speech, have long been regarded as a variation on the general body muscle scheme. However, evidence has accumulated that the function of head muscles, their developmental anatomy and the underlying regulatory cascades are distinct. This article reviews the key aspects of craniofacial muscle and muscle stem cell formation and discusses how this differs from the trunk programme of myogenesis; we show novel RNAseq data to support this notion. We also trace the origin of head muscle in the chordate ancestors of vertebrates and discuss links with smooth-type muscle in the primitive chordate pharynx. We look out as to how the special properties of head muscle precursor and stem cells, in particular their competence to contribute to the heart, could be exploited in regenerative medicine.
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Affiliation(s)
- Frank R Schubert
- Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK
| | - Arun J Singh
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, 97331, USA
| | - Oluwatomisin Afoyalan
- Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK
| | - Chrissa Kioussi
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, 97331, USA
| | - Susanne Dietrich
- Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK.
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11
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Tolkin T, Christiaen L. Rewiring of an ancestral Tbx1/10-Ebf-Mrf network for pharyngeal muscle specification in distinct embryonic lineages. Development 2017; 143:3852-3862. [PMID: 27802138 DOI: 10.1242/dev.136267] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 08/30/2016] [Indexed: 01/01/2023]
Abstract
Skeletal muscles arise from diverse embryonic origins in vertebrates, yet converge on extensively shared regulatory programs that require muscle regulatory factor (MRF)-family genes. Myogenesis in the tail of the simple chordate Ciona exhibits a similar reliance on its single MRF-family gene, and diverse mechanisms activate Ci-Mrf Here, we show that myogenesis in the atrial siphon muscles (ASMs) and oral siphon muscles (OSMs), which control the exhalant and inhalant siphons, respectively, also requires Mrf We characterize the ontogeny of OSM progenitors and compare the molecular basis of Mrf activation in OSM versus ASM. In both muscle types, Ebf and Tbx1/10 are expressed and function upstream of Mrf However, we demonstrate that regulatory relationships between Tbx1/10, Ebf and Mrf differ between the OSM and ASM lineages. We propose that Tbx1, Ebf and Mrf homologs form an ancient conserved regulatory state for pharyngeal muscle specification, whereas their regulatory relationships might be more evolutionarily variable.
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Affiliation(s)
- Theadora Tolkin
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA
| | - Lionel Christiaen
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA
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12
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Satoh N, Tagawa K, Lowe CJ, Yu JK, Kawashima T, Takahashi H, Ogasawara M, Kirschner M, Hisata K, Su YH, Gerhart J. On a possible evolutionary link of the stomochord of hemichordates to pharyngeal organs of chordates. Genesis 2014; 52:925-34. [PMID: 25303744 PMCID: PMC5673098 DOI: 10.1002/dvg.22831] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 10/02/2014] [Accepted: 10/07/2014] [Indexed: 01/24/2023]
Abstract
As a group closely related to chordates, hemichordate acorn worms are in a key phylogenic position for addressing hypotheses of chordate origins. The stomochord of acorn worms is an anterior outgrowth of the pharynx endoderm into the proboscis. In 1886 Bateson proposed homology of this organ to the chordate notochord, crowning this animal group "hemichordates." Although this proposal has been debated for over a century, the question still remains unresolved. Here we review recent progress related to this question. First, the developmental mode of the stomochord completely differs from that of the notochord. Second, comparison of expression profiles of genes including Brachyury, a key regulator of notochord formation in chordates, does not support the stomochord/notochord homology. Third, FoxE that is expressed in the stomochord-forming region in acorn worm juveniles is expressed in the club-shaped gland and in the endostyle of amphioxus, in the endostyle of ascidians, and in the thyroid gland of vertebrates. Based on these findings, together with the anterior endodermal location of the stomochord, we propose that the stomochord has evolutionary relatedness to chordate organs deriving from the anterior pharynx rather than to the notochord.
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Affiliation(s)
- Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Kunifumi Tagawa
- Marine Biological Laboratory, Graduate School of Science, Hiroshima University, Onomichi, Hiroshima, Japan
| | - Christopher J. Lowe
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Takeshi Kawashima
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Hiroki Takahashi
- Division of Developmental Biology, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Michio Ogasawara
- Department of Nanobiology, Graduate School of Advanced Integration Science, Chiba University, Chiba, Japan
| | - Marc Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - John Gerhart
- Department of Molecular and Cell Biology, University of California, Berkeley, California
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13
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Patterns of positive selection of the myogenic regulatory factor gene family in vertebrates. PLoS One 2014; 9:e92873. [PMID: 24651579 PMCID: PMC3961423 DOI: 10.1371/journal.pone.0092873] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 02/26/2014] [Indexed: 11/19/2022] Open
Abstract
The functional divergence of transcriptional factors is critical in the evolution of transcriptional regulation. However, the mechanism of functional divergence among these factors remains unclear. Here, we performed an evolutionary analysis for positive selection in members of the myogenic regulatory factor (MRF) gene family of vertebrates. We selected 153 complete vertebrate MRF nucleotide sequences from our analyses, which revealed substantial evidence of positive selection. Here, we show that sites under positive selection were more frequently detected and identified from the genes encoding the myogenic differentiation factors (MyoG and Myf6) than the genes encoding myogenic determination factors (Myf5 and MyoD). Additionally, the functional divergence within the myogenic determination factors or differentiation factors was also under positive selection pressure. The positive selection sites were more frequently detected from MyoG and MyoD than Myf6 and Myf5, respectively. Amino acid residues under positive selection were identified mainly in their transcription activation domains and on the surface of protein three-dimensional structures. These data suggest that the functional gain and divergence of myogenic regulatory factors were driven by distinct positive selection of their transcription activation domains, whereas the function of the DNA binding domains was conserved in evolution. Our study evaluated the mechanism of functional divergence of the transcriptional regulation factors within a family, whereby the functions of their transcription activation domains diverged under positive selection during evolution.
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14
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Affiliation(s)
- Nori Satoh
- Marine Genomics Unit; Okinawa Institute of Science and Technology; Onna Okinawa 904-0495 Japan
| | - Kuni Tagawa
- Marine Biological Laboratory; Graduate School of Science; Hiroshima University; Mukaishima Hiroshima 722-0073 Japan
| | - Hiroki Takahashi
- Division of Developmental Biology; National Institute of Basic Biology; Okagaki Aichi 445-8585 Japan
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15
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Nagano I, Wu Z, Asano K, Takahashi Y. Molecular cloning and characterization of transgelin-like proteins mainly transcribed in newborn larvae of Trichinella spp. Vet Parasitol 2011; 178:134-42. [DOI: 10.1016/j.vetpar.2010.12.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 12/06/2010] [Accepted: 12/17/2010] [Indexed: 11/24/2022]
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16
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Kugler JE, Kerner P, Bouquet JM, Jiang D, Di Gregorio A. Evolutionary changes in the notochord genetic toolkit: a comparative analysis of notochord genes in the ascidian Ciona and the larvacean Oikopleura. BMC Evol Biol 2011; 11:21. [PMID: 21251251 PMCID: PMC3034685 DOI: 10.1186/1471-2148-11-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Accepted: 01/20/2011] [Indexed: 11/12/2022] Open
Abstract
Background The notochord is a defining feature of the chordate clade, and invertebrate chordates, such as tunicates, are uniquely suited for studies of this structure. Here we used a well-characterized set of 50 notochord genes known to be targets of the notochord-specific Brachyury transcription factor in one tunicate, Ciona intestinalis (Class Ascidiacea), to begin determining whether the same genetic toolkit is employed to build the notochord in another tunicate, Oikopleura dioica (Class Larvacea). We identified Oikopleura orthologs of the Ciona notochord genes, as well as lineage-specific duplicates for which we determined the phylogenetic relationships with related genes from other chordates, and we analyzed their expression patterns in Oikopleura embryos. Results Of the 50 Ciona notochord genes that were used as a reference, only 26 had clearly identifiable orthologs in Oikopleura. Two of these conserved genes appeared to have undergone Oikopleura- and/or tunicate-specific duplications, and one was present in three copies in Oikopleura, thus bringing the number of genes to test to 30. We were able to clone and test 28 of these genes. Thirteen of the 28 Oikopleura orthologs of Ciona notochord genes showed clear expression in all or in part of the Oikopleura notochord, seven were diffusely expressed throughout the tail, six were expressed in tissues other than the notochord, while two probes did not provide a detectable signal at any of the stages analyzed. One of the notochord genes identified, Oikopleura netrin, was found to be unevenly expressed in notochord cells, in a pattern reminiscent of that previously observed for one of the Oikopleura Hox genes. Conclusions A surprisingly high number of Ciona notochord genes do not have apparent counterparts in Oikopleura, and only a fraction of the evolutionarily conserved genes show clear notochord expression. This suggests that Ciona and Oikopleura, despite the morphological similarities of their notochords, have developed rather divergent sets of notochord genes after their split from a common tunicate ancestor. This study demonstrates that comparisons between divergent tunicates can lead to insights into the basic complement of genes sufficient for notochord development, and elucidate the constraints that control its composition.
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Affiliation(s)
- Jamie E Kugler
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY 10065, USA
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Bočina I, Ljubešić N, Saraga-Babić M. Cilia-like structures anchor the amphioxus notochord to its sheath. Acta Histochem 2011; 113:49-52. [PMID: 19740530 DOI: 10.1016/j.acthis.2009.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Revised: 08/04/2009] [Accepted: 08/12/2009] [Indexed: 11/18/2022]
Abstract
Body stiffness is important during undulatory locomotion in fish. In amphioxus, the myosepta play an important role in transmission of muscular forces to the notochord. In order to define the specific supporting role of the notochord in amphioxus during locomotion, the ultrastructure of 10 adult amphioxus specimens was analyzed using transmission electron microscopy. Numerous cilia-like structures were found on the surface of each notochordal cell at the sites of their attachment to the notochordal sheath. Ultrastructurally, these structures consisted of the characteristic arrangement of peripheral and central microtubular doublets and were anchored to the inner layer of the notochordal sheath. Immunohistochemically, a positive reaction to applied dynein and β-tubulin antibodies characterized the area of the cilia-like structures. We propose that reduced back-and-forth movements of the cilia-like structures might contribute to the flow of the fluid content inside the notochord, thus modulating the stiffness of the amphioxus body during its undulatory locomotion.
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Affiliation(s)
- Ivana Bočina
- Department of Biology, University of Split, Teslina, Croatia.
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Expression, immunolocalization and serodiagnostic value of a myophilin-like protein from Schistosoma japonicum. Exp Parasitol 2008; 119:117-24. [PMID: 18329020 PMCID: PMC2756502 DOI: 10.1016/j.exppara.2008.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2007] [Revised: 12/24/2007] [Accepted: 01/03/2008] [Indexed: 11/23/2022]
Abstract
The cDNA of a Schistosoma japonicum myophilin-like protein was cloned, sequenced, and expressed in Escherichia coli as a recombined protein (rSj myophilin-like protein), and the protein was purified by affinity chromatography. The deduced amino acid sequences of the Sj myophilin-like protein showed significant homology to myophilin, calponin, Np22 and Mp20. Northern blot and RT-PCR analyzes revealed expression of the Sj myophilin-like protein mRNA in eggs, sporocysts, cercariae, hepatic schistosomula and adult worms. Confocal fluorescence microscopy localized the native protein to the muscle of the adult worm. In schistosome-infected rabbits, the rSj myophilin-like protein antibody level, assessed by ELISA, was elevated after infection but was reduced after praziquantel treatment. In humans, the myophilin-like protein antibody level was evaluated by ELISA in sera from 33 non-infected humans and 61 schistosomiasis patients; the results showed a highly significant difference between the two groups with a sensitivity of 57.4%. Taken together, the myophilin-like protein may prove useful for monitoring the therapeutic effect of praziquantel rather than in serodiagnosis of schistosomiasis.
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Zhang Y, Wang L, Shao M, Zhang H. Characterization and developmental expression of AmphiMef2 gene in amphioxus. ACTA ACUST UNITED AC 2008; 50:637-41. [PMID: 17879062 DOI: 10.1007/s11427-007-0082-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2007] [Accepted: 06/09/2007] [Indexed: 12/18/2022]
Abstract
Myocyte enhancer factor 2 proteins are members of MADS family of transcription factors, which can control the expression of muscle-specific genes in vertebrates. However, not all Mef2 genes are essential for muscle development in invertebrates. Here we have isolated a full-length cDNA from amphioxus, designated AmphiMef2. The predicted amino acid sequence has highly conserved MADS and MEF2 domains, showing higher identity with the corresponding regions of its homologues in vertebrates than those in invertebrates. Results from whole-mount in situ hybridization show that the expression of AmphiMef2 initially appears in the presomitic mesoderm at early neurula stage, then the transcripts are detected in both the somites and the unsegmented presomitic mesoderm. At 36 h larval stage, the expression is only detected in the posterior somites. By 48 h larval stage, the expression is shifted to the preoral pit (a homologous organ to the vertebrate adenohypophysis) and persists until at least 72 h larval stage. The results suggest that AmphiMef2 may be not only involved in the myogenesis but also the development or function of the preoral pit in amphioxus.
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Affiliation(s)
- Ying Zhang
- Institute of Developmental Biology, Life Science College, Key Lab of Experimental Teratology of Ministry of Education, Shandong University, Jinan 250100, China
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Beaster-Jones L, Schubert M, Holland LZ. Cis-regulation of the amphioxus engrailed gene: Insights into evolution of a muscle-specific enhancer. Mech Dev 2007; 124:532-42. [PMID: 17624741 DOI: 10.1016/j.mod.2007.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Revised: 06/04/2007] [Accepted: 06/05/2007] [Indexed: 11/24/2022]
Abstract
To gain insights into the relation between evolution of cis-regulatory DNA and evolution of gene function, we identified tissue-specific enhancers of the engrailed gene of the basal chordate amphioxus (Branchiostoma floridae) and compared their ability to direct expression in both amphioxus and its nearest chordate relative, the tunicate Ciona intestinalis. In amphioxus embryos, the native engrailed gene is expressed in three domains - the eight most anterior somites, a few cells in the central nervous system (CNS) and a few ectodermal cells. In contrast, in C. intestinalis, in which muscle development is highly divergent, engrailed expression is limited to the CNS. To characterize the tissue-specific enhancers of amphioxus engrailed, we first showed that 7.8kb of upstream DNA of amphioxus engrailed directs expression to all three domains in amphioxus that express the native gene. We then identified the amphioxus engrailed muscle-specific enhancer as the 1.2kb region of upstream DNA with the highest sequence identity to the mouse en-2 jaw muscle enhancer. This amphioxus enhancer directed expression to both the somites in amphioxus and to the larval muscles in C. intestinalis. These results show that even though expression of the native engrailed has apparently been lost in developing C. intestinalis muscles, they express the transcription factors necessary to activate transcription from the amphioxus engrailed enhancer, suggesting that gene networks may not be completely disrupted if an individual component is lost.
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Affiliation(s)
- Laura Beaster-Jones
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0202, USA
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Bocina I, Saraga-Babić M. Immunohistochemical study of cytoskeletal and extracellular matrix components in the notochord and notochordal sheath of amphioxus. Int J Biol Sci 2006; 2:73-8. [PMID: 16733537 PMCID: PMC1458430 DOI: 10.7150/ijbs.2.73] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2006] [Accepted: 03/10/2006] [Indexed: 11/05/2022] Open
Abstract
A major cytoskeletal and extracellular matrix proteins of the amphioxus notochordal cells and sheath were detected by immunohistochemical techniques. The three-layered amphioxus notochordal sheath strongly expressed fish collagen type I in its outer and middle layers, while in the innermost layer expression did not occur. The amphioxus notochordal sheath was reactive to applied anti-human antibodies for intermediate filament proteins such as cytokeratins, desmin and vimentin, as well as to microtubule components (beta-tubulin), particularly in the area close to the epipharyngeal groove. Alpha-smooth muscle actin was expressed in some notochordal cells and in the area of the notochordal attachment to the sheath. Thus muscular nature of notochordal cells was shown by immunohistochemistry in tissue section. Our results confirm that genes encoding intermediate filament proteins, microtubules and microfilaments are highly conserved during evolution. Collagen type I was proven to be the key extracellular matrix protein that forms the amphioxus notochordal sheath.
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Affiliation(s)
- Ivana Bocina
- Department of Biology, Faculty of Natural Scieneces, University of Split, Teslina 12, 21000 Split, Croatia.
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Satoh G. A trajectory of increasing activity and the elaboration of chemosensory modality: a new perspective on vertebrate origins. Zoolog Sci 2005; 22:613-26. [PMID: 15988155 DOI: 10.2108/zsj.22.613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This article reviews recent advances in comparative biological studies of vertebrate origins, with the aim of revisiting the long-standing controversy concerning these origins. Since early vertebrate evolution is paralleled by an evolutionary trend towards increasing activity, I focus on the evolution of respiratory and circulatory systems and discuss their potential roles in early vertebrate evolution. I give particular attention to the nasohypophyseal duct, an orifice characteristically found in agnathan vertebrates, and hypothesize that this duct originally functioned to convey oxygen dissolved in seawater to the respiratory gills. The chemosensory cell population that originated from the wall of the duct became the incipient olfactory organ and played a role in the organization of feeding behavior. An increase in chemosensory receptor genes via large-scale genomic evolution in the vertebrate lineage caused the repertoire of chemosensory cells to diversify and led to the appearance of the integrative center, including telencephalic structures typically lacking in protochordates.
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Affiliation(s)
- Gouki Satoh
- Seto Marine Biological Laboratory, Field Science Education and Research Center, Kyoto University, Wakayama, Japan.
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Lin Y, Zhang X, Liang K, Yang H, Zhang H. Phylogenetic analysis and developmental expression of brp-like genes in amphioxus and zebrafish. Comp Biochem Physiol B Biochem Mol Biol 2005; 141:71-6. [PMID: 15820136 DOI: 10.1016/j.cbpc.2005.01.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2004] [Revised: 01/20/2005] [Accepted: 01/22/2005] [Indexed: 11/27/2022]
Abstract
The brp-like genes in amphioxus (Branchiostoma belcheri tsingtauense) and in zebrafish (Danio rerio) are reported. The putative brp-like proteins are orthologous to the ancestor of the human brain protein 239FB and 239AB. Previous studies showed that human brain protein 239 might play a role in central nervous system development and function. In this study, the transcripts of zebrafish brp-like gene are mainly located in the developing central neural system in embryo and larva similar to its orthologous genes in human. In contrast, the developmental expression pattern of amphioxus brp-like gene suggests that the gene might be involved in the development of the notochord, pharynx, gills and gut in amphioxus embryos and larvae. Phylogenetic analysis shows that the amphioxus brp-like gene is closer to the orthologous genes in vertebrates than those in invertebrates. The results suggest that the function of the brain protein 239 family genes may change in evolution.
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Affiliation(s)
- Yushuang Lin
- Institute of Developmental Biology, Life Science College, Shandong University, Jinan 250100, PR China
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Lin Y, Liang K, Zhang Y, Chen Z, Zhang H. The expression of AmphiMdp during amphioxus early development. Gene Expr Patterns 2004; 5:253-5. [PMID: 15567722 DOI: 10.1016/j.modgep.2004.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2003] [Revised: 07/20/2004] [Accepted: 07/20/2004] [Indexed: 11/25/2022]
Abstract
We report here the expression of AmphiMdp in embryos and larvae. Faint AmphiMdp transcripts were first detected in the mesendoderm at the mid-gastrula stage and later in the somites of the early neurula. Expression remained in somites throughout the neurula and early larval stages and then disappeared from the somites starting with the most anterior somite and progressing posteriorly. At the 48-h larval stage, transcripts were detected in the developing tail bud. No transcripts were detectable in the somites of the 72-h larva. The result suggests that AmphiMdp is involved in myogenesis in amphioxus.
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Affiliation(s)
- Yushuang Lin
- Life Science College, Institute of Developmental Biology, Shanda Nan Lu No. 27, Shandong University, Jinan 250100, China
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Oda H, Akiyama-Oda Y, Zhang S. Two classic cadherin-related molecules with no cadherin extracellular repeats in the cephalochordate amphioxus: distinct adhesive specificities and possible involvement in the development of multicell-layered structures. J Cell Sci 2004; 117:2757-67. [PMID: 15150317 DOI: 10.1242/jcs.01045] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We previously reported the existence of Bb-cadherin, a molecule related to classic cadherin, in the cephalochordate amphioxus (Branchiostoma belcheri). The structure of Bb-cadherin is unique in that it lacks the cadherin extracellular repeats, although its cytoplasmic domain shows close similarities to those of typical classic cadherins. The extracellular region of Bb-cadherin consists of laminin globular domains and a cysteine-rich EGF-like domain that are similar to domains in nonchordate classic cadherins. In this study, we identified a second amphioxus cadherin. It was designated Bb2-cadherin (Bb2C) while the previously reported cadherin has been renamed Bb1-cadherin (Bb1C). Bb2C is very similar to Bb1C in its overall structure and amino acid sequence. Genomic BLAST searches and phylogenetic analyses suggested that these two amphioxus genes have been generated through a gene duplication that occurred after separation of the cephalochordates from the other animals. They also bear distinct adhesive specificities. Immunohistochemical analyses showed that Bb1C and Bb2C, together with β-catenin, appear to function as adherens junction constituents in the epithelia of different germ layers of the amphioxus embryo. Differential expression of the two cadherins was also observed in the developing, multicell-layered notochord. These observations suggest that, despite their unique structures, the functions and developmental roles of Bb1C and Bb2C are comparable to those of the classic cadherins characterized to date in other animal groups, such as the vertebrate E- and N-cadherins and the Drosophila DE- and DN-cadherins. The possible involvement of Bb1C and Bb2C in the development of multicell-layered structures characteristic of the cephalochordate body plan is presented.
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Affiliation(s)
- Hiroki Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan.
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