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Ascidian Early Development
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Ascidian Early Development

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (29 February 2024) | Viewed by 10508

Special Issue Editors

Prof. Dr. Takahito Nishikata

E-Mail Website
Guest Editor
Frontiers of Innovative Research in Science and Technology (FIRST), Konan University Research Institute for Human Health Science (RIH2S), Konan University, Kobe 658-8501, Japan
Interests: developmental biology; molecular biology; immunology; regenerative medicine; dermatology
Prof. Dr. Takeo Horie

E-Mail Website
Guest Editor
Osaka University Graduate School of Frontier Biosciences, Suita, Osaka 565-0871, Japan
Interests: developmental biology; animal physiochemistry; physiology; behavior; genome biology

Special Issue Information

Dear Colleagues,

Ascidians are a well-established model animal for understanding human beings as a member of the superphylum Chordata. After the draft genome of Ciona intestinalis was reported in 2002, molecular understandings of early development have been expanded. Moreover, new methods, such as single-cell RNA sequencing, optogenetics, and innovative microscopic technology have started to reveal novel biological mechanisms. This Special Issue aims to summarize the current status of lower chordate biology and prospects for this new era, in which outcomes from ascidian biology have a great impact on medicine and human health.

Potential topics include, but are not limited to, the following:

  • Maternal information, including localized factors, transcriptional and translational regulation, and cytoskeletal rearrangement;
  • Morphogenesis, tissue and organ development, cell-fate determination, and metamorphosis;
  • Neuronal and hormonal signals, the development of the central and peripheral nervous systems, photoreception, memory, and behavior;
  • Oogenesis and spermatogenesis, fertilization, self–nonself recognition, and the immune system;
  • Molecular evolution, molecular phylogeny, and the origin of vertebrates.

Original research and review articles are welcome in this Special Issue.

Prof. Dr. Takahito Nishikata
Prof. Dr. Takeo Horie
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • tunicates (Ascidiacea, Thaliacea, and Appendicularia)
  • amphioxus (Cephalochordata)
  • acorn worms (Hemichordata)
  • gametogenesis
  • cleavages and gastrulation
  • horizontal gene transfer
  • cell–cell interaction
  • transcription factors
  • omics
  • bioimaging

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Published Papers (5 papers)

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Research

28 pages, 8919 KiB  
Article
Fine-Tuned Expression of Evolutionarily Conserved Signaling Molecules in the Ciona Notochord
by Lenny J. Negrón-Piñeiro, Yushi Wu, Ravij Mehta, Julie E. Maguire, Cindy Chou, Joyce Lee, Chitra L. Dahia and Anna Di Gregorio
Int. J. Mol. Sci. 2024, 25(24), 13631; https://doi.org/10.3390/ijms252413631 - 20 Dec 2024
Viewed by 933
Abstract
The notochord is an axial structure required for the development of all chordate embryos, from sea squirts to humans. Over the course of more than half a billion years of chordate evolution, in addition to its structural function, the notochord has acquired increasingly [...] Read more.
The notochord is an axial structure required for the development of all chordate embryos, from sea squirts to humans. Over the course of more than half a billion years of chordate evolution, in addition to its structural function, the notochord has acquired increasingly relevant patterning roles for its surrounding tissues. This process has involved the co-option of signaling pathways and the acquisition of novel molecular mechanisms responsible for the precise timing and modalities of their deployment. To reconstruct this evolutionary route, we surveyed the expression of signaling molecules in the notochord of the tunicate Ciona, an experimentally amenable and informative chordate. We found that several genes encoding for candidate components of diverse signaling pathways are expressed during notochord development, and in some instances, display distinctive regionalized and/or lineage-specific patterns. We identified and deconstructed notochord enhancers associated with TGF-β and Ctgf, two evolutionarily conserved signaling genes that are expressed dishomogeneously in the Ciona notochord, and shed light on the cis-regulatory origins of their peculiar expression patterns. Full article
(This article belongs to the Special Issue Ascidian Early Development)
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17 pages, 3710 KiB  
Article
A Novel Hemocyte-Derived Peptide and Its Possible Roles in Immune Response of Ciona intestinalis Type A
by Shin Matsubara, Rin Iguchi, Michio Ogasawara, Hiroya Nakamura, Tatsuki R. Kataoka, Akira Shiraishi, Tomohiro Osugi, Tsuyoshi Kawada and Honoo Satake
Int. J. Mol. Sci. 2024, 25(4), 1979; https://doi.org/10.3390/ijms25041979 - 6 Feb 2024
Viewed by 2175
Abstract
A wide variety of bioactive peptides have been identified in the central nervous system and several peripheral tissues in the ascidian Ciona intestinalis type A (Ciona robusta). However, hemocyte endocrine peptides have yet to be explored. Here, we report a novel [...] Read more.
A wide variety of bioactive peptides have been identified in the central nervous system and several peripheral tissues in the ascidian Ciona intestinalis type A (Ciona robusta). However, hemocyte endocrine peptides have yet to be explored. Here, we report a novel 14-amino-acid peptide, CiEMa, that is predominant in the granular hemocytes and unilocular refractile granulocytes of Ciona. RNA-seq and qRT-PCR revealed the high CiEma expression in the adult pharynx and stomach. Immunohistochemistry further revealed the highly concentrated CiEMa in the hemolymph of the pharynx and epithelial cells of the stomach, suggesting biological roles in the immune response. Notably, bacterial lipopolysaccharide stimulation of isolated hemocytes for 1–4 h resulted in 1.9- to 2.4-fold increased CiEMa secretion. Furthermore, CiEMa-stimulated pharynx exhibited mRNA upregulation of the growth factor (Fgf3/7/10/22), vanadium binding proteins (CiVanabin1 and CiVanabin3), and forkhead and homeobox transcription factors (Foxl2, Hox3, and Dbx) but not antimicrobial peptides (CrPap-a and CrMam-a) or immune-related genes (Tgfbtun3, Tnfa, and Il17-2). Collectively, these results suggest that CiEMa plays roles in signal transduction involving tissue development or repair in the immune response, rather than in the direct regulation of immune response genes. The present study identified a novel Ciona hemocyte peptide, CiEMa, which paves the way for research on the biological roles of hemocyte peptides in chordates. Full article
(This article belongs to the Special Issue Ascidian Early Development)
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12 pages, 1394 KiB  
Article
Comparison of Evolutionary Relationships between Branchiostoma floridae, Ciona intestinalis, and Homo sapiens Globins Provide Evidence of Gene Co-Option and Convergent Evolution
by Nanako Yano, Toshifumi Minamoto, Hirosi Yamaguchi, Toshiyuki Goto and Takahito Nishikata
Int. J. Mol. Sci. 2023, 24(21), 16009; https://doi.org/10.3390/ijms242116009 - 6 Nov 2023
Viewed by 2114
Abstract
Globins have been studied as model proteins to elucidate the principles of protein evolution. This was achieved by understanding the relationship between amino acid sequence, three-dimensional structure, physicochemical properties, and physiological function. Previous molecular phylogenies of chordate globin genes revealed the monophyletic evolution [...] Read more.
Globins have been studied as model proteins to elucidate the principles of protein evolution. This was achieved by understanding the relationship between amino acid sequence, three-dimensional structure, physicochemical properties, and physiological function. Previous molecular phylogenies of chordate globin genes revealed the monophyletic evolution of urochordate globins and suggested convergent evolution. However, to provide evidence of convergent evolution, it is necessary to determine the physicochemical and functional similarities between vertebrates and urochordate globins. In this study, we determined the expression patterns of Ciona globin genes using real-time RT-PCR. Two genes (Gb-1 and Gb-2) were predominantly expressed in the branchial sac, heart, and hemocytes and were induced under hypoxia. Combined with the sequence analysis, our findings suggest that Gb-1/-2 correspond to vertebrate hemoglobin-α/-β. However, we did not find a robust similarity between Gb-3, Gb-4, and vertebrate globins. These results suggested that, even though Ciona globins obtained their unique functions differently from vertebrate globins, the two of them shared some physicochemical features and physiological functions. Our findings offer a good example for understanding the molecular mechanisms underlying gene co-option and convergence, which could lead to evolutionary innovations. Full article
(This article belongs to the Special Issue Ascidian Early Development)
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13 pages, 1583 KiB  
Article
Ring Finger 149-Related Is an FGF/MAPK-Independent Regulator of Pharyngeal Muscle Fate Specification
by Burcu Vitrinel, Christine Vogel and Lionel Christiaen
Int. J. Mol. Sci. 2023, 24(10), 8865; https://doi.org/10.3390/ijms24108865 - 16 May 2023
Cited by 2 | Viewed by 1976
Abstract
During embryonic development, cell-fate specification gives rise to dedicated lineages that underlie tissue formation. In olfactores, which comprise tunicates and vertebrates, the cardiopharyngeal field is formed by multipotent progenitors of both cardiac and branchiomeric muscles. The ascidian Ciona is a powerful model to [...] Read more.
During embryonic development, cell-fate specification gives rise to dedicated lineages that underlie tissue formation. In olfactores, which comprise tunicates and vertebrates, the cardiopharyngeal field is formed by multipotent progenitors of both cardiac and branchiomeric muscles. The ascidian Ciona is a powerful model to study cardiopharyngeal fate specification with cellular resolution, as only two bilateral pairs of multipotent cardiopharyngeal progenitors give rise to the heart and to the pharyngeal muscles (also known as atrial siphon muscles, ASM). These progenitors are multilineage primed, in as much as they express a combination of early ASM- and heart-specific transcripts that become restricted to their corresponding precursors, following oriented and asymmetric divisions. Here, we identify the primed gene ring finger 149 related (Rnf149-r), which later becomes restricted to the heart progenitors, but appears to regulate pharyngeal muscle fate specification in the cardiopharyngeal lineage. CRISPR/Cas9-mediated loss of Rnf149-r function impairs atrial siphon muscle morphogenesis, and downregulates Tbx1/10 and Ebf, two key determinants of pharyngeal muscle fate, while upregulating heart-specific gene expression. These phenotypes are reminiscent of the loss of FGF/MAPK signaling in the cardiopharyngeal lineage, and an integrated analysis of lineage-specific bulk RNA-seq profiling of loss-of-function perturbations has identified a significant overlap between candidate FGF/MAPK and Rnf149-r target genes. However, functional interaction assays suggest that Rnf149-r does not directly modulate the activity of the FGF/MAPK/Ets1/2 pathway. Instead, we propose that Rnf149-r acts both in parallel to the FGF/MAPK signaling on shared targets, as well as on FGF/MAPK-independent targets through (a) separate pathway(s). Full article
(This article belongs to the Special Issue Ascidian Early Development)
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17 pages, 2561 KiB  
Article
Comparative Transcriptomic Analysis Reveals the Functionally Segmented Intestine in Tunicate Ascidian
by Wei Zhang, An Jiang, Haiyan Yu and Bo Dong
Int. J. Mol. Sci. 2023, 24(7), 6270; https://doi.org/10.3390/ijms24076270 - 27 Mar 2023
Cited by 3 | Viewed by 2340
Abstract
The vertebrate intestinal system consists of separate segments that remarkably differ in morphology and function. However, the origin of intestinal segmentation remains unclear. In this study, we investigated the segmentation of the intestine in a tunicate ascidian species, Ciona savignyi, by performing RNA [...] Read more.
The vertebrate intestinal system consists of separate segments that remarkably differ in morphology and function. However, the origin of intestinal segmentation remains unclear. In this study, we investigated the segmentation of the intestine in a tunicate ascidian species, Ciona savignyi, by performing RNA sequencing. The gene expression profiles showed that the whole intestine was separated into three segments. Digestion, ion transport and signal transduction, and immune-related pathway genes were enriched in the proximal, middle, and distal parts of the intestine, respectively, implying that digestion, absorption, and immune function appear to be regional specializations in the ascidian intestine. We further performed a multi−species comparison analysis and found that the Ciona intestine showed a similar gene expression pattern to vertebrates, indicating tunicates and vertebrates might share the conserved intestinal functions. Intriguingly, vertebrate pancreatic homologous genes were expressed in the digestive segment of the Ciona intestine, suggesting that the proximal intestine might play the part of pancreatic functions in C. savignyi. Our results demonstrate that the tunicate intestine can be functionally separated into three distinct segments, which are comparable to the corresponding regions of the vertebrate intestinal system, offering insights into the functional evolution of the digestive system in chordates. Full article
(This article belongs to the Special Issue Ascidian Early Development)
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