論文 - 日下部 岳広
-
Fuki Gyoja, Keita Sato, Takahiro Yamashita, Takehiro G Kusakabe
Genome Biology and Evolution 70 ( 3 ) evaf032 2025年3月
共著
担当区分：最終著者 出版者・発行元：Oxford University Press (OUP)
A group of nonvisual opsins specific to vertebrates is essential to understand evolution of lateral eyes, one of the most prominent innovations in this lineage. Nevertheless, our knowledge of their evolutionary history remains limited. To develop an integrated view of their evolution, we surveyed these non-visual opsins (VA opsin, pinopsin, parapinopsin, parietopsin, and parapinopsin-like) in 451 vertebrate genomes. Through extensive manual curation, we completed a high-quality catalog. We could not find them in 202 mammals, supporting previous reports of their loss. VA opsins are highly conserved among nonmammals. In contrast, other opsin subfamilies experienced more dynamic molecular evolution with many secondary losses. In addition, we found a previously unreported opsin subfamily that we named Q113-Bistable (QB) opsin. We found its orthologs only in several lizards and the tuatara. Nevertheless, QB opsin pseudogenes were discovered in diverse taxa, including ray-finned fishes, indicating its ancient origin. QB opsin, parapinopsin, and parietopsin are extremely prone to be lost in the course of evolution, and loss events involving these opsins seem to occur concomitantly. Furthermore, we demonstrated the spectral properties of QB opsin as a UV-sensitive, bistable photo-pigment. This study provides the first integrated view of the entire evolutionary history of this group of opsins.
DOI： 10.1093/gbe/evaf032
-
Xin Zeng, Fuki Gyoja, Yang Cui, Martin Loza, Takehiro G Kusakabe, Kenta Nakai
NAR Genomics and Bioinformatics 6 ( 4 ) lqae149 2024年11月
共著
出版者・発行元：Oxford University Press (OUP)
Abstract
Despite known single-cell expression profiles in vertebrate retinas, understanding of their developmental and evolutionary expression patterns among homologous cell classes remains limited. We examined and compared approximately 240 000 retinal cells from four species and found significant similarities among homologous cell classes, indicating inherent regulatory patterns. To understand these shared patterns, we constructed gene regulatory networks for each developmental stage for three of these species. We identified 690 regulons governed by 530 regulators across three species, along with 10 common cell class-specific regulators and 16 highly preserved regulons. RNA velocity analysis pinpointed conserved putative driver genes and regulators to retinal cell differentiation in both mouse and zebrafish. Investigation of the origins of retinal cells by examining conserved expression patterns between vertebrate retinal cells and invertebrate Ciona intestinalis photoreceptor-related cells implied functional similarities in light transduction mechanisms. Our findings offer insights into the evolutionarily conserved regulatory frameworks and differentiation drivers of vertebrate retinal cells. -
Neural crest lineage in the protovertebrate model Ciona 査読あり 国際共著 国際誌
Lauren G. Todorov, Kouhei Oonuma, Takehiro G. Kusakabe, Michael S. Levine, Laurence A. Lemaire
Nature 635 ( 8040 ) 912 - 916 2024年10月
-
Functional diversification process of opsin genes for teleost visual and pineal photoreceptions 査読あり 国際誌
Chihiro Fujiyabu, Fuki Gyoja, Keita Sato, Emi Kawano-Yamashita, Hideyo Ohuchi, Takehiro G. Kusakabe, and Takahiro Yamashita
Cellular and Molecular Life Sciences 81 ( 1 ) 428 2024年10月
共著
出版者・発行元：Springer
DOI： 10.1007/s00018-024-05461-3
DOI： 10.1007/s00018-024-05461-3
その他リンク： https://link.springer.com/article/10.1007/s00018-024-05461-3/fulltext.html
-
Characterization of trans-spliced chimeric RNAs: insights into the mechanism of trans-splicing 査読あり 国際誌
Rui Yokomori, Takehiro G. Kusakabe, and Kenta Nakai
NAR Genomics and Bioinformatics 6 ( 2 ) lqae067 2024年6月
-
Retinal Cone Mosaic in sws1-Mutant Medaka (Oryzias latipes), A Teleost 査読あり 国際誌
Megumi Matsuo, Makoto Matsuyama, Tomoe Kobayashi, Shinji Kanda, Satoshi Ansai, Taichi Kawakami, Erika Hosokawa, Yutaka Daido, Takehiro G. Kusakabe, Kiyoshi Naruse, and Shoji Fukamachi
Investigative Opthalmology & Visual Science 63 ( 11 ) 21 - 21 2022年10月
共著
出版者・発行元：Association for Research in Vision and Ophthalmology (ARVO)
PURPOSE: Ablation of short single cones (SSCs) expressing short-wavelength-sensitive opsin (SWS1) is well analyzed in the field of regenerative retinal cells. In contrast with ablation studies, the phenomena caused by the complete deletion of SWS1 are less well-understood. To assess the effects of SWS1 deficiency on retinal structure, we established and analyzed sws1-mutant medaka. METHODS: To visualize SWS1, a monoclonal anti-SWS1 antibody and transgenic reporter fish (Tg(sws1:mem-egfp)) were generated. We also developed a CRISPR/Cas-driven sws1-mutant line. Retinal structure of sws1 mutant was visualized using anti-SWS1, 1D4, and ZPR1 antibodies and coumarin derivatives and compared with wild type, Tg(sws1:mem-egfp), and another opsin (lws) mutant. RESULTS: Our rat monoclonal antibody specifically recognized medaka SWS1. Sws1 mutant retained regularly arranged cone mosaic as lws mutant and its SSCs had neither SWS1 nor long wavelength sensitive opsin. Depletion of sws1 did not affect the expression of long wavelength sensitive opsin, and vice versa. ZPR1 antibody recognized arrestin spread throughout double cones and long single cones in wild-type, transgenic, and sws1-mutant lines. CONCLUSIONS: Comparative observation of sws1-mutant and wild-type retinas revealed that ZPR1 negativity is not a marker for SSCs with SWS1, but SSCs themselves. Loss of functional sws1 did not cause retinal degeneration, indicating that sws1 is not essential for cone mosaic development in medaka. Our two fish lines, one with visualized SWS1 and the other lacking functional SWS1, offer an opportunity to study neural network synapsing with SSCs and to clarify the role of SWS1 in vision.
-
Neuronal identities derived by misexpression of the POU IV sensory determinant in a protovertebrate 査読あり 国際共著 国際誌
Prakriti Paul Chacha, Ryoko Horie, Takehiro G. Kusakabe, Yasunori Sasakura, Mona Singh, Takeo Horie, Michael Levine
Proceedings of the National Academy of Sciences 119 ( 4 ) e2118817119 - e2118817119 2022年1月
共著
出版者・発行元：Proceedings of the National Academy of Sciences
The protovertebrate <italic>Ciona intestinalis</italic> type A (sometimes called <italic>Ciona robusta</italic>) contains a series of sensory cell types distributed across the head–tail axis of swimming tadpoles. They arise from lateral regions of the neural plate that exhibit properties of vertebrate placodes and neural crest. The sensory determinant <italic>POU IV/Brn3</italic> is known to work in concert with regional determinants, such as <italic>Foxg</italic> and <italic>Neurogenin</italic>, to produce palp sensory cells (PSCs) and bipolar tail neurons (BTNs), in head and tail regions, respectively. A combination of single-cell RNA-sequencing (scRNA-seq) assays, computational analysis, and experimental manipulations suggests that misexpression of <italic>POU IV</italic> results in variable transformations of epidermal cells into hybrid sensory cell types, including those exhibiting properties of both PSCs and BTNs. Hybrid properties are due to coexpression of <italic>Foxg</italic> and <italic>Neurogenin</italic> that is triggered by an unexpected <italic>POU IV</italic> feedback loop. Hybrid cells were also found to express a synthetic gene battery that is not coexpressed in any known cell type. We discuss these results with respect to the opportunities and challenges of reprogramming cell types through the targeted misexpression of cellular determinants.
その他リンク： https://syndication.highwire.org/content/doi/10.1073/pnas.2118817119
-
A single motor neuron determines the rhythm of early motor behavior in Ciona 査読あり 国際誌
Taichi Akahoshi, Madoka K. Utsumi, Kouhei Oonuma, Makoto Murakami, Takeo Horie, Takehiro G. Kusakabe, Kotaro Oka, Kohji Hotta
Science Advances 7 ( 50 ) 2021年12月
共著
出版者・発行元：American Association for the Advancement of Science (AAAS)
Recent work in tunicate supports the similarity between the motor circuits of vertebrates and basal deuterostome lineages. To understand how the rhythmic activity in motor circuits is acquired during development of protochordate Ciona, we investigated the coordination of the motor response by identifying a single pair of oscillatory motor neurons (MN2/A10.64). The MN2 neurons had Ca2+ oscillation with an ~80-s interval that was cell autonomous even in a dissociated single cell. The Ca2+ oscillation of MN2 coincided with the early tail flick (ETF). The spikes of the membrane potential in MN2 gradually correlated with the rhythm of ipsilateral muscle contractions in ETFs. The optogenetic experiments indicated that MN2 is a necessary and sufficient component of ETFs. These results indicate that MN2 is indispensable for the early spontaneous rhythmic motor behavior of Ciona. Our findings shed light on the understanding of development and evolution of chordate rhythmical locomotion.
-
Kouhei Oonuma, Maho Yamamoto, Naho Moritsugu, Nanako Okawa, Megumi Mukai, Miku Sotani, Shuto Tsunemi, Haruka Sugimoto, Eri Nakagome, Yuichi Hasegawa, Kotaro Shimai, Takeo Horie, Takehiro G. Kusakabe
Frontiers in Cell and Developmental Biology 9 ( 704367 ) 704367 - 704367 2021年5月
共著
担当区分：最終著者, 責任著者
In vertebrate embryos, dorsal midline tissues, including the notochord, the prechordal plate, and the floor plate, play important roles in patterning of the central nervous system, somites, and endodermal tissues by producing extracellular signaling molecules, such as Sonic hedgehog (Shh). In Ciona, hedgehog.b, one of the two hedgehog genes, is expressed in the floor plate of the embryonic neural tube, while none of the hedgehog genes are expressed in the notochord. We have identified a cis-regulatory region of hedgehog.b that was sufficient to drive a reporter gene expression in the floor plate. The hedgehog.b cis-regulatory region also drove ectopic expression of the reporter gene in the endodermal strand, suggesting that the floor plate and the endodermal strand share a part of their gene regulatory programs. The endodermal strand occupies the same topographic position of the embryo as does the vertebrate hypochord, which consists of a row of single cells lined up immediately ventral to the notochord. The hypochord shares expression of several genes with the floor plate, including Shh and FoxA, and play a role in dorsal aorta development. Whole-embryo single-cell transcriptome analysis identified a number of genes specifically expressed in both the floor plate and the endodermal strand in Ciona tailbud embryos. A Ciona FoxA orthologue FoxA.a is shown to be a candidate transcriptional activator for the midline gene battery. The present findings suggest an ancient evolutionary origin of a common developmental program for the midline structures in Olfactores.
-
Kouhei Oonuma, Takehiro G. Kusakabe
Development dev.198754 ( 12 ) dev198754 2021年5月
共著
担当区分：最終著者
The Ciona larva has served as a unique model for understanding the development of dopaminergic cells at single-cell resolution due to the exceptionally small number of neurons in its brain and its fixed cell lineage during embryogenesis. A recent study suggested that the transcription factors Fer2 and Meis directly regulate the dopamine synthesis genes in Ciona, but the dopaminergic cell lineage and the gene regulatory networks that control the development of dopaminergic cells have not been fully elucidated. Here, we reveal that the dopaminergic cells in Ciona are derived from a bilateral pair of cells called a9.37 cells at the center of the neural plate. The a9.37 cells divide along the anterior-posterior axis, and all of the descendants of the posterior daughter cells differentiate into the dopaminergic cells. We show that the MAPK pathway and the transcription factor Otx are required for the expression of Fer2 in the dopaminergic cell lineage. Our findings establish the cellular and molecular framework for fully understanding the commitment to dopaminergic cells in the simple chordate brain.
DOI： 10.1242/dev.198754
その他リンク： http://journals.biologists.com/dev/article-pdf/doi/10.1242/dev.198754/2079868/dev198754.pdf
-
Nanako Okawa, Kotaro Shimai, Kohei Ohnishi, Masamichi Ohkura, Junichi Nakai, Takeo Horie, Atsushi Kuhara, Takehiro G Kusakabe
Scientific reports 10 ( 1 ) 18590 - 18590 2020年10月
共著
担当区分：最終著者, 責任著者
Tunicate larvae have a non-reproductive gonadotropin-releasing hormone (GnRH) system with multiple ligands and receptor heterodimerization enabling complex regulation. In Ciona intestinalis type A larvae, one of the gnrh genes, gnrh2, is conspicuously expressed in the motor ganglion and nerve cord, which are homologous structures to the hindbrain and spinal cord, respectively, of vertebrates. The gnrh2 gene is also expressed in the proto-placodal sensory neurons, which are the proposed homologue of vertebrate olfactory neurons. Tunicate larvae occupy a non-reproductive dispersal stage, yet the role of their GnRH system remains elusive. In this study, we investigated neuronal types of gnrh2-expressing cells in Ciona larvae and visualized the activity of these cells by fluorescence imaging using a calcium sensor protein. Some cholinergic neurons and dopaminergic cells express gnrh2, suggesting that GnRH plays a role in controlling swimming behavior. However, none of the gnrh2-expressing cells overlap with glycinergic or GABAergic neurons. A role in motor control is also suggested by a relationship between the activity of gnrh2-expressing cells and tail movements. Interestingly, gnrh2-positive ependymal cells in the nerve cord, known as a kind of glia cells, actively produced Ca2+ transients, suggesting that active intercellular signaling occurs in the glia cells of the nerve cord.
-
Oonuma, K., Kusakabe, T. G.
Developmental Biology 445 ( 2 ) 245 - 255 2019年1月
-
Horie, T., Horie, R., Chen, K., Cao, C., Nakagawa, M., Kusakabe, T. G., Satoh, N., Sasakura, Y., Levine, M.
Genes & Development 32 ( 19-20 ) 1297 - 1302 2018年10月
-
The Use of cis-Regulatory DNAs as Molecular Tools
Kotaro Shimai and Takehiro Kusakabe
Advances in Experimental Medicine and Biology 1029 49 - 68 2018年3月
-
Brozovic, M., Dantec, C., Dardaillon, J., Dauga, D., Faure, E., Gineste, M., Louis, A., Naville, M., Nitta, K.R., Piette, J., Reeves, W., Scornavacca, C., Simion, P., Vincentelli, R., Bellec, M., Aicha, S.B., Fagotto, M., Guéroult-Bellone, M., Haeussler, M., Jacox, E., Lowe, E.K., Mendez, M., Roberge, A., Stolfi, A., Yokomori, R., Brown, C.T., Cambillau, C., Christiaen, L., Delsuc, F., Douzery, E., Dumollard, R,, Kusakabe, T., Nakai, K., Nishida, H., Satou, Y., Swalla, B., Veeman, M., Volff, J.N., Lemaire, P.
Nucleic Acids Research 46 ( D1 ) D718 - D725 2018年1月
-
Constrained vertebrate evolution by pleiotropic genes 査読あり 国際共著 国際誌
Hu, H., Uesaka, M., Guo, S., Shimai, K., Lu, T.-M. Li, F., Fujimoto, S., Ishikawa, M., Liu, S., Sasagawa, Y., Zhang, G., Kuratani, S., Yu, J.-K. Kusakabe, T. G., Khaitovich, P., Irie, N., the EXPANDE Consortium
Nature Ecology and Evolution 1 ( 11 ) 1722 - 1730 2017年11月
-
Evolutionary steps involving counterion displacement in a tunicate opsin 査読あり 国際誌
Kojima, K., Yamashita, T., Imamoto, Y., Kusakabe, T. G., Tsuda, M., Shichida, Y.
Proceedings of the National Academy of Sciences of the United States of America 114 ( 23 ) 6028 - 6033 2017年6月
-
Identifying vertebrate brain prototypes in deuterostomes
Takehiro G. Kusakabe
Brain Evolution by Design: From Neural Origin to Cognitive Architecture 153 - 186 2017年2月
-
Oonuma, K., Tanaka, M., Nishitsuji, K., Kato, Y., Shimai, K., Kusakabe, T. G.
Developmental Biology 420 ( 1 ) 178 - 185 2016年12月
-
Yokomori, R., Shimai, K., Nishitsuji, K., Suzuki, Y., Kusakabe, T. G. and Nakai K.
Genome Research 26 ( 1 ) 140 - 150 2016年1月