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Saito T, Sawada H. Fertilization of Ascidians: Gamete Interaction, Self/Nonself Recognition and Sperm Penetration of Egg Coat. Front Cell Dev Biol 2022; 9:827214. [PMID: 35186958 PMCID: PMC8849226 DOI: 10.3389/fcell.2021.827214] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/30/2021] [Indexed: 12/22/2022] Open
Abstract
Fertilization is one of the most important events in living organisms to generate a new life with a mixed genetic background. To achieve successful fertilization, sperm and eggs must undergo complex processes in a sequential order. Fertilization of marine invertebrate Ciona intestinalis type A (Ciona robusta) has been studied for more than a hundred years. Ascidian sperm are attracted by chemoattractants from eggs and bind to the vitelline coat. Subsequently, sperm penetrate through the vitelline coat proteolytically and finally fuse with the egg plasma membrane. Here, we summarize the fertilization mechanisms of ascidians, particularly from sperm-egg interactions to sperm penetration of the egg coat. Since ascidians are hermaphrodites, inbreeding depression is a serious problem. To avoid self-fertilization, ascidians possess a self-incompatibility system. In this review, we also describe the molecular mechanisms of the self-incompatibility system in C. intestinalis type A governed by three allelic gene pairs of s-Themis and v-Themis.
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Affiliation(s)
- Takako Saito
- Faculty of Agriculture Department of Applied Life Sciences, Shizuoka University, Shizuoka, Japan
| | - Hitoshi Sawada
- Depatment of Food and Nutritional Environment, College of Human Life and Environment, Kinjo Gakuin University, Nagoya, Japan
- Graduate School of Science, Nagoya University, Nagoya, Japan
- *Correspondence: Hitoshi Sawada,
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Kutomi O, Yamamoto R, Hirose K, Mizuno K, Nakagiri Y, Imai H, Noga A, Obbineni JM, Zimmermann N, Nakajima M, Shibata D, Shibata M, Shiba K, Kita M, Kigoshi H, Tanaka Y, Yamasaki Y, Asahina Y, Song C, Nomura M, Nomura M, Nakajima A, Nakachi M, Yamada L, Nakazawa S, Sawada H, Murata K, Mitsuoka K, Ishikawa T, Wakabayashi KI, Kon T, Inaba K. A dynein-associated photoreceptor protein prevents ciliary acclimation to blue light. SCIENCE ADVANCES 2021; 7:7/9/eabf3621. [PMID: 33637535 PMCID: PMC7909887 DOI: 10.1126/sciadv.abf3621] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/14/2021] [Indexed: 05/07/2023]
Abstract
Light-responsive regulation of ciliary motility is known to be conducted through modulation of dyneins, but the mechanism is not fully understood. Here, we report a novel subunit of the two-headed f/I1 inner arm dynein, named DYBLUP, in animal spermatozoa and a unicellular green alga. This subunit contains a BLUF (sensors of blue light using FAD) domain that appears to directly modulate dynein activity in response to light. DYBLUP (dynein-associated BLUF protein) mediates the connection between the f/I1 motor domain and the tether complex that links the motor to the doublet microtubule. Chlamydomonas lacking the DYBLUP ortholog shows both positive and negative phototaxis but becomes acclimated and attracted to high-intensity blue light. These results suggest a mechanism to avoid toxic strong light via direct photoregulation of dyneins.
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Affiliation(s)
- Osamu Kutomi
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka 415-0025, Japan
- Department of Anatomy and Cell Biology, Faculty of Medicine, University of Yamanashi, Chuo, Yamanashi 409-3898, Japan
| | - Ryosuke Yamamoto
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka 415-0025, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Keiko Hirose
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Katsutoshi Mizuno
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka 415-0025, Japan
- School of Medical Sciences, University of Fukui, Yoshida-gun, Fukui 910-1193, Japan
| | - Yuuhei Nakagiri
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Hiroshi Imai
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Akira Noga
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Jagan Mohan Obbineni
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
- School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, Vellore 632014, Tamil Nadu, India
| | - Noemi Zimmermann
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
- Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Masako Nakajima
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Daisuke Shibata
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka 415-0025, Japan
| | - Misa Shibata
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka 415-0025, Japan
| | - Kogiku Shiba
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka 415-0025, Japan
| | - Masaki Kita
- Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Hideo Kigoshi
- Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Yui Tanaka
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Yuya Yamasaki
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Yuma Asahina
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Chihong Song
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Mami Nomura
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka 415-0025, Japan
| | - Mamoru Nomura
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka 415-0025, Japan
| | - Ayako Nakajima
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka 415-0025, Japan
| | - Mia Nakachi
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka 415-0025, Japan
| | - Lixy Yamada
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, Mie 517-0004, Japan
| | - Shiori Nakazawa
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, Mie 517-0004, Japan
| | - Hitoshi Sawada
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, Mie 517-0004, Japan
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Kaoru Mitsuoka
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Takashi Ishikawa
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
- Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Ken-Ichi Wakabayashi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Takahide Kon
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Kazuo Inaba
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka 415-0025, Japan.
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Effect of Polycyclic Aromatic Hydrocarbons on Development of the Ascidian Ciona intestinalis Type A. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17041340. [PMID: 32093017 PMCID: PMC7068557 DOI: 10.3390/ijerph17041340] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/14/2020] [Accepted: 02/16/2020] [Indexed: 11/16/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are pollutants that exert harmful effects on marine invertebrates; however, the molecular mechanism underlying PAH action remains unclear. We investigated the effect of PAHs on the ascidian Ciona intestinalis type A (Ciona robusta). First, the influence of PAHs on early Ciona development was evaluated. PAHs such as dibenzothiophene, fluorene, and phenanthrene resulted in formation of abnormal larvae. PAH treatment of swimming larva induced malformation in the form of tail regression. Additionally, we observed the Cionaaryl hydrocarbon receptor (Ci-AhR) mRNA expression in swimming larva, mid body axis rotation, and early juvenile stages. The time correlation between PAH action and AhR mRNA expression suggested that Ci-AhR could be associated with PAH metabolism. Lastly, we analyzed Ci-AhR mRNA localization in Ciona juveniles. Ci-AhR mRNA was localized in the digestive tract, dorsal tubercle, ganglion, and papillae of the branchial sac, suggesting that Ci-AhR is a candidate for an environmental pollutant sensor and performs a neural function. Our results provide basic knowledge on the biological function of Ci-AhR and PAH activity in marine invertebrates.
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4
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Alternative NAD(P)H dehydrogenase and alternative oxidase: Proposed physiological roles in animals. Mitochondrion 2019; 45:7-17. [DOI: 10.1016/j.mito.2018.01.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 11/01/2017] [Accepted: 01/26/2018] [Indexed: 12/12/2022]
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Brozovic M, Dantec C, Dardaillon J, Dauga D, Faure E, Gineste M, Louis A, Naville M, Nitta KR, Piette J, Reeves W, Scornavacca C, Simion P, Vincentelli R, Bellec M, Aicha SB, Fagotto M, Guéroult-Bellone M, Haeussler M, Jacox E, Lowe EK, Mendez M, Roberge A, Stolfi A, Yokomori R, Brown C, Cambillau C, Christiaen L, Delsuc F, Douzery E, Dumollard R, Kusakabe T, Nakai K, Nishida H, Satou Y, Swalla B, Veeman M, Volff JN, Lemaire P. ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. Nucleic Acids Res 2018; 46:D718-D725. [PMID: 29149270 PMCID: PMC5753386 DOI: 10.1093/nar/gkx1108] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 10/22/2017] [Accepted: 11/09/2017] [Indexed: 12/14/2022] Open
Abstract
ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates.
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Affiliation(s)
| | | | | | - Delphine Dauga
- Bioself Communication; 28 rue de la Bibliothèque, F-13001 Marseille, France
| | - Emmanuel Faure
- Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France
- Team VORTEX, Institut de Recherche en Informatique de Toulouse, Universities Toulouse I and III, CNRS, INPT, ENSEEIHT; 2 rue Camichel, BP 7122, F-31071 Toulouse Cedex 7, France
| | | | - Alexandra Louis
- DYOGEN, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005, Paris, France
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS; 46 allée d’Italie, F-69364 Lyon, France
| | - Kazuhiro R Nitta
- IBDM, Aix-Marseille Université, CNRS, Campus de Luminy, Case 907; 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | - Jacques Piette
- CRBM, Université de Montpellier, CNRS, Montpellier, France
| | - Wendy Reeves
- Division of Biology, Kansas State University, Manhattan, Kansas
| | | | - Paul Simion
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Renaud Vincentelli
- AFMB, Aix-Marseille Université, CNRS, Campus de Luminy, Case 932, 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | | | - Sameh Ben Aicha
- Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Sorbonne Universités, Université Pierre-et-Marie-Curie, CNRS; Quai de la Darse, F-06234 Villefranche-sur-Mer Cedex, France
| | | | | | - Maximilian Haeussler
- Santa Cruz Genomics Institute, MS CBSE, University of California, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Edwin Jacox
- CRBM, Université de Montpellier, CNRS, Montpellier, France
| | - Elijah K Lowe
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI48824, USA
| | - Mickael Mendez
- IBDM, Aix-Marseille Université, CNRS, Campus de Luminy, Case 907; 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | | | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Rui Yokomori
- Human Genome Center, the Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato, Tokyo 108-8639, Japan
| | - C Titus Brown
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI48824, USA
- Population Health and Reproduction, UC Davis, Davis, CA 95616, USA
| | - Christian Cambillau
- AFMB, Aix-Marseille Université, CNRS, Campus de Luminy, Case 932, 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | - Lionel Christiaen
- New York University, Center for Developmental Genetics, Department of Biology, 1009 Silver Center, 100 Washington Square East, New York City, NY10003, USA
| | - Frédéric Delsuc
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Emmanuel Douzery
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Rémi Dumollard
- Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Sorbonne Universités, Université Pierre-et-Marie-Curie, CNRS; Quai de la Darse, F-06234 Villefranche-sur-Mer Cedex, France
| | - Takehiro Kusakabe
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe 658-8501, Japan
| | - Kenta Nakai
- Human Genome Center, the Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato, Tokyo 108-8639, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Billie Swalla
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI48824, USA
- Friday Harbor Laboratories, 620 University Road, Friday Harbor, WA 98250-9299, USA
| | - Michael Veeman
- Division of Biology, Kansas State University, Manhattan, Kansas
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS; 46 allée d’Italie, F-69364 Lyon, France
| | - Patrick Lemaire
- CRBM, Université de Montpellier, CNRS, Montpellier, France
- Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France
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Stanley EC, Azzinaro PA, Vierra DA, Howlett NG, Irvine SQ. The Simple Chordate Ciona intestinalis Has a Reduced Complement of Genes Associated with Fanconi Anemia. Evol Bioinform Online 2016; 12:133-48. [PMID: 27279728 PMCID: PMC4898443 DOI: 10.4137/ebo.s37920] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 02/10/2016] [Accepted: 02/16/2016] [Indexed: 12/26/2022] Open
Abstract
Fanconi anemia (FA) is a human genetic disease characterized by congenital defects, bone marrow failure, and increased cancer risk. FA is associated with mutation in one of 24 genes. The protein products of these genes function cooperatively in the FA pathway to orchestrate the repair of DNA interstrand cross-links. Few model organisms exist for the study of FA. Seeking a model organism with a simpler version of the FA pathway, we searched the genome of the simple chordate Ciona intestinalis for homologs of the human FA-associated proteins. BLAST searches, sequence alignments, hydropathy comparisons, maximum likelihood phylogenetic analysis, and structural modeling were used to infer the likelihood of homology between C. intestinalis and human FA proteins. Our analysis indicates that C. intestinalis indeed has a simpler and potentially functional FA pathway. The C. intestinalis genome was searched for candidates for homology to 24 human FA and FA-associated proteins. Support was found for the existence of homologs for 13 of these 24 human genes in C. intestinalis. Members of each of the three commonly recognized FA gene functional groups were found. In group I, we identified homologs of FANCE, FANCL, FANCM, and UBE2T/FANCT. Both members of group II, FANCD2 and FANCI, have homologs in C. intestinalis. In group III, we found evidence for homologs of FANCJ, FANCO, FANCQ/ERCC4, FANCR/RAD51, and FANCS/BRCA1, as well as the FA-associated proteins ERCC1 and FAN1. Evidence was very weak for the existence of homologs in C. intestinalis for any other recognized FA genes. This work supports the notion that C. intestinalis, as a close relative of vertebrates, but having a much reduced complement of FA genes, offers a means of studying the function of certain FA proteins in a simpler pathway than that of vertebrate cells.
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Affiliation(s)
- Edward C Stanley
- Integrative and Evolutionary Biology Graduate Specialization, University of Rhode Island, Kingston, RI, USA
| | - Paul A Azzinaro
- Cell and Molecular Biology Graduate Specialization, University of Rhode Island, Kingston, RI, USA
| | - David A Vierra
- Cell and Molecular Biology Graduate Specialization, University of Rhode Island, Kingston, RI, USA
| | - Niall G Howlett
- Cell and Molecular Biology Graduate Specialization, University of Rhode Island, Kingston, RI, USA.; Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI, USA
| | - Steven Q Irvine
- Integrative and Evolutionary Biology Graduate Specialization, University of Rhode Island, Kingston, RI, USA.; Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
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Dauga D. Biocuration: A New Challenge for the Tunicate Community. Genesis 2015; 53:132-42. [DOI: 10.1002/dvg.22842] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 11/10/2014] [Accepted: 11/12/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Delphine Dauga
- Bioself Communication; 28 rue de la Bibliothèque Marseille France
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Vassalli QA, Anishchenko E, Caputi L, Sordino P, D'Aniello S, Locascio A. Regulatory elements retained during chordate evolution: Coming across tunicates. Genesis 2014; 53:66-81. [DOI: 10.1002/dvg.22838] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 11/06/2014] [Accepted: 11/11/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Quirino Attilio Vassalli
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Evgeniya Anishchenko
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Luigi Caputi
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Paolo Sordino
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
- CNR ISAFOM, Institute for Agricultural and Forest Systems in the Mediterranean, Unitá organizzativa di supporto; Catania Italy
| | - Salvatore D'Aniello
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Annamaria Locascio
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
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9
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Horikawa Y, Matsumoto H, Yamaguchi F, Ishida S, Fujiwara S. Transcriptional regulation in the early ectodermal lineage of ascidian embryos. Dev Growth Differ 2013; 55:776-85. [PMID: 24192291 DOI: 10.1111/dgd.12100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 10/09/2013] [Accepted: 10/10/2013] [Indexed: 11/28/2022]
Abstract
In ascidian embryos, ectodermal tissues derive from blastomeres in the animal hemisphere. The animal hemisphere-specific gene expression is observed as early as the 16-cell stage. Here, we characterized animal hemisphere-specific enhancers of three genes, Ci-ephrin-Ad, Ci-TGFβ-NA1 and Ci-Fz4. Deletion analyses identified minimal essential elements. Although these elements contained multiple GATA sequences, electrophoretic mobility shift assays revealed that only some of them were strong binding sites for the transcription factor Ci-GATAa. On the other hand, the motif-searching software MEME identified an octamer, GA (T/G) AAGGG, shared by these enhancers. In Ci-ephrin-Ad and Ci-TGFβ-NA1, the octamer was GATAAGGG, which strongly bound Ci-GATAa. The 397-bp upstream region of Ci-ephrin-Ad contained two strong Ci-GATAa-binding sites, one of which was the octamer motif. Mutation in the octamer motif, but not the other Ci-GATAa-binding site, severely affected the enhancer activity. The 204-bp upstream region of Ci-TGFβ-NA1 contained four strong Ci-GATAa-binding sites, including the octamer motif. Mutation only in the octamer motif, leaving the other three Ci-GATAa-binding sites intact, abolished the enhancer activity. These results suggest a crucial role for the octamer motif.
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Affiliation(s)
- Yosuke Horikawa
- Department of Applied Science, Kochi University, 2-5-1 Akebono-cho, Kochi-shi, Kochi, 780-8520, Japan
| | - Haruka Matsumoto
- Department of Applied Science, Kochi University, 2-5-1 Akebono-cho, Kochi-shi, Kochi, 780-8520, Japan
| | - Fumika Yamaguchi
- Department of Applied Science, Kochi University, 2-5-1 Akebono-cho, Kochi-shi, Kochi, 780-8520, Japan
| | - Satomi Ishida
- Department of Applied Science, Kochi University, 2-5-1 Akebono-cho, Kochi-shi, Kochi, 780-8520, Japan
| | - Shigeki Fujiwara
- Department of Applied Science, Kochi University, 2-5-1 Akebono-cho, Kochi-shi, Kochi, 780-8520, Japan
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Irvine SQ. Study of Cis-regulatory Elements in the Ascidian Ciona intestinalis. Curr Genomics 2013; 14:56-67. [PMID: 23997651 PMCID: PMC3580780 DOI: 10.2174/138920213804999192] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Revised: 12/30/2012] [Accepted: 01/01/2013] [Indexed: 01/31/2023] Open
Abstract
The ascidian (sea squirt) C. intestinalis has become an important model organism for the study of cis-regulation. This is largely due to the technology that has been developed for assessing cis-regulatory activity through the use of transient reporter transgenes introduced into fertilized eggs. This technique allows the rapid and inexpensive testing of endogenous or altered DNA for regulatory activity in vivo. This review examines evidence that C. intestinaliscis-regulatory elements are located more closely to coding regions than in other model organisms. I go on to compare the organization of cis-regulatory elements and conserved non-coding sequences in Ciona, mammals, and other deuterostomes for three representative C.intestinalis genes, Pax6, FoxAa, and the DlxA-B cluster, along with homologs in the other species. These comparisons point out some of the similarities and differences between cis-regulatory elements and their study in the various model organisms. Finally, I provide illustrations of how C. intestinalis lends itself to detailed study of the structure of cis-regulatory elements, which have led, and promise to continue to lead, to important insights into the fundamentals of transcriptional regulation.
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Affiliation(s)
- Steven Q Irvine
- Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
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Armengaud J, Hartmann EM, Bland C. Proteogenomics for environmental microbiology. Proteomics 2013; 13:2731-42. [PMID: 23636904 DOI: 10.1002/pmic.201200576] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 03/06/2013] [Accepted: 04/09/2013] [Indexed: 11/09/2022]
Abstract
Proteogenomics sensu stricto refers to the use of proteomic data to refine the annotation of genomes from model organisms. Because of the limitations of automatic annotation pipelines, a relatively high number of errors occur during the structural annotation of genes coding for proteins. Whether putative orphan sequences or short genes encoding low-molecular-weight proteins really exist is still frequently a mystery. Whether start codons are well defined is also an open debate. These problems are exacerbated for genomes of microorganisms belonging to poorly documented genera, as related sequences are not always available for homology-guided annotation. The functional annotation of a significant proportion of genes is also another well-known issue when annotating environmental microorganisms. High-throughput shotgun proteomics has recently greatly evolved, allowing the exploration of the proteome from any microorganism at an unprecedented depth. The structural and functional annotation process may be usefully complemented with experimental data. Indeed, proteogenomic mapping has been successfully performed for a wide variety of organisms. Specific approaches devoted to systematically establishing the N-termini of a large set of proteins are being developed. N-terminomics is giving rise to datasets of experimentally proven translational start codons as well as validated peptide signals for secreted proteins. By extension, combining genomic and proteomic data is becoming routine in many research projects. The proteomic analysis of organisms with unfinished genome sequences, the so-called composite proteomics, and the search for microbial biomarkers by bottom-up and top-down combined approaches are some examples of proteogenomic-flavored studies. They illustrate the advent of a new era of environmental microbiology where proteomics and genomics are intimately integrated to answer key biological questions.
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Affiliation(s)
- Jean Armengaud
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, France
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Matsumae H, Hamada M, Fujie M, Niimura Y, Tanaka H, Kawashima T. A methodical microarray design enables surveying of expression of a broader range of genes in Ciona intestinalis. Gene 2013; 519:82-90. [PMID: 23388151 DOI: 10.1016/j.gene.2013.01.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 01/22/2013] [Accepted: 01/24/2013] [Indexed: 10/27/2022]
Abstract
We provide a new oligo-microarray for Ciona intestinalis, based on the NimbleGen 12-plex×135k format. The array represents 106,285 probes, which is more than double the probe number of the currently available 44k microarray. These probes cover 99.2% of the transcripts in the KyotoHoya (KH) models, published in 2008, and they contain 81.1% of the entries in the UniGene database that are not included in the KH models. In this paper, we show that gene expression levels measured by this new 135k microarray are highly correlated with those obtained by the existing 44k microarray for genes common to both arrays. We also investigated gene expression using samples obtained from the ovary and the neural complex of adult C. intestinalis, showing that the expression of tissue-specific genes is consistent with previous reports. Approximately half of the highly expressed genes identified in the 135k microarray are not included in the previous microarray. The high coverage of gene models by this microarray made it possible to identify splicing variants for a given transcript. The 135k microarray is useful in investigating the functions of genes that are not yet well characterized. Detailed information about this 135k microarray is accessible at no charge from supplemental materials, NCBI Gene Expression Omnibus (GEO), and http://marinegenomics.oist.jp.
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Affiliation(s)
- Hiromi Matsumae
- Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
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Franco C, Soares R, Pires E, Koci K, Almeida AM, Santos R, Coelho AV. Understanding regeneration through proteomics. Proteomics 2013; 13:686-709. [DOI: 10.1002/pmic.201200397] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 10/31/2012] [Accepted: 11/06/2012] [Indexed: 12/29/2022]
Affiliation(s)
- Catarina Franco
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
| | - Renata Soares
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
| | - Elisabete Pires
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
| | - Kamila Koci
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
| | - André M. Almeida
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
- Instituto de Investigação Científica Tropical; Lisboa Portugal
| | - Romana Santos
- Unidade de Investigação em Ciências Orais e Biomédicas, Faculdade de Medicina Dentária; Universidade de Lisboa; Portugal
| | - Ana Varela Coelho
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
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Chenevert J, Pruliere G, Ishii H, Sardet C, Nishikata T. Purification of mitochondrial proteins HSP60 and ATP synthase from ascidian eggs: implications for antibody specificity. PLoS One 2013; 8:e52996. [PMID: 23326373 PMCID: PMC3542361 DOI: 10.1371/journal.pone.0052996] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 11/20/2012] [Indexed: 01/25/2023] Open
Abstract
Use of antibodies is a cornerstone of biological studies and it is important to identify the recognized protein with certainty. Generally an antibody is considered specific if it labels a single band of the expected size in the tissue of interest, or has a strong affinity for the antigen produced in a heterologous system. The identity of the antibody target protein is rarely confirmed by purification and sequencing, however in many cases this may be necessary. In this study we sought to characterize the myoplasm, a mitochondria-rich domain present in eggs and segregated into tadpole muscle cells of ascidians (urochordates). The targeted proteins of two antibodies that label the myoplasm were purified using both classic immunoaffinity methods and a novel protein purification scheme based on sequential ion exchange chromatography followed by two-dimensional gel electrophoresis. Surprisingly, mass spectrometry sequencing revealed that in both cases the proteins recognized are unrelated to the original antigens. NN18, a monoclonal antibody which was raised against porcine spinal cord and recognizes the NF-M neurofilament subunit in vertebrates, in fact labels mitochondrial ATP synthase in the ascidian embryo. PMF-C13, an antibody we raised to and purified against PmMRF, which is the MyoD homolog of the ascidian Phallusia mammillata, in fact recognizes mitochondrial HSP60. High resolution immunolabeling on whole embryos and isolated cortices demonstrates localization to the inner mitochondrial membrane for both ATP synthase and HSP60. We discuss the general implications of our results for antibody specificity and the verification methods which can be used to determine unequivocally an antibody's target.
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Affiliation(s)
- Janet Chenevert
- Université Pierre et Marie Curie and CNRS, Developmental Biology Unit UMR7009, Villefranche-sur-mer, France.
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15
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Nakaya A, Katayama T, Itoh M, Hiranuka K, Kawashima S, Moriya Y, Okuda S, Tanaka M, Tokimatsu T, Yamanishi Y, Yoshizawa AC, Kanehisa M, Goto S. KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. Nucleic Acids Res 2012. [PMID: 23193276 PMCID: PMC3531156 DOI: 10.1093/nar/gks1239] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The identification of orthologous genes in an increasing number of fully sequenced genomes is a challenging issue in recent genome science. Here we present KEGG OC (http://www.genome.jp/tools/oc/), a novel database of ortholog clusters (OCs). The current version of KEGG OC contains 1 176 030 OCs, obtained by clustering 8 357 175 genes in 2112 complete genomes (153 eukaryotes, 1830 bacteria and 129 archaea). The OCs were constructed by applying the quasi-clique-based clustering method to all possible protein coding genes in all complete genomes, based on their amino acid sequence similarities. It is computationally efficient to calculate OCs, which enables to regularly update the contents. KEGG OC has the following two features: (i) It consists of all complete genomes of a wide variety of organisms from three domains of life, and the number of organisms is the largest among the existing databases; and (ii) It is compatible with the KEGG database by sharing the same sets of genes and identifiers, which leads to seamless integration of OCs with useful components in KEGG such as biological pathways, pathway modules, functional hierarchy, diseases and drugs. The KEGG OC resources are accessible via OC Viewer that provides an interactive visualization of OCs at different taxonomic levels.
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Affiliation(s)
- Akihiro Nakaya
- Center for Transdisciplinary Research, Niigata University, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8585, Japan
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Stolfi A, Christiaen L. Genetic and genomic toolbox of the chordate Ciona intestinalis. Genetics 2012; 192:55-66. [PMID: 22964837 PMCID: PMC3430545 DOI: 10.1534/genetics.112.140590] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Accepted: 04/30/2012] [Indexed: 02/01/2023] Open
Abstract
The experimental malleability and unique phylogenetic position of the sea squirt Ciona intestinalis as part of the sister group to the vertebrates have helped establish these marine chordates as model organisms for the study of developmental genetics and evolution. Here we summarize the tools, techniques, and resources available to the Ciona geneticist, citing examples of studies that employed such strategies in the elucidation of gene function in Ciona. Genetic screens, germline transgenesis, electroporation of plasmid DNA, and microinjection of morpholinos are all routinely employed, and in the near future we expect these to be complemented by targeted mutagenesis, homologous recombination, and RNAi. The genomic resources available will continue to support the design and interpretation of genetic experiments and allow for increasingly sophisticated approaches on a high-throughput, whole-genome scale.
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Affiliation(s)
- Alberto Stolfi
- Center for Developmental Genetics, Department of Biology, New York University, New York, New York 10003, USA.
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Fisch C, Dupuis-Williams P. [The rebirth of the ultrastructure of cilia and flagella]. Biol Aujourdhui 2012; 205:245-67. [PMID: 22251859 DOI: 10.1051/jbio/2011023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Indexed: 11/14/2022]
Abstract
The sensory and motility functions of eukaryotic cilia and flagella are essential for cell survival in protozoans and for cell differentiation and homoeostasis in metazoans. Ciliary biology has benefited early on from the input of electron microscopy. Over the last decade, the visualization of cellular structures has greatly progressed, thus it becomes timely to review the ultrastructure of cilia and flagella. Briefly touching upon the typical features of a 9+2 axoneme, we dwell extensively on the transition zone, the singlet zone, the ciliary necklace, cap and crown. The relation of the singlet zone to sensory and/or motile function, the link of the ciliary cap to microtubule dynamics and to ciliary beat, the involvement of the ciliary crown in ovocyte and mucosal propulsion, and the role of the transition zone/the ciliary necklace in axonemal stabilization, autotomy and as a diffusion barrier will all be discussed.
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Affiliation(s)
- Cathy Fisch
- ATIGE Centriole et Pathologies Associées, INSERM/UEVE U829, 91000 Évry, France.
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Cell-Cycle Control in Oocytes and During Early Embryonic Cleavage Cycles in Ascidians. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2012; 297:235-64. [DOI: 10.1016/b978-0-12-394308-8.00006-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Abstract
Eukaryotic cilia and flagella perform motility and sensory functions which are essential for cell survival in protozoans, and to organism development and homoeostasis in metazoans. Their ultrastructure has been studied from the early beginnings of electron microscopy, and these studies continue to contribute to much of our understanding about ciliary biology. In the light of the progress made in the visualization of cellular structures over the last decade, we revisit the ultrastructure of cilia and flagella. We briefly describe the typical features of a 9+2 axoneme before focusing extensively on the transition zone, the ciliary necklace, the singlet zone, the ciliary cap and the ciliary crown. We discuss how the singlet zone is linked to sensory and/or motile function, the contribution of the ciliary crown to ovocyte and mucosal propulsion, and the relationship between the ciliary cap and microtubule growth and shortening, and its relation to ciliary beat. We further examine the involvement of the transition zone/the ciliary necklace in axonemal stabilization, autotomy and as a diffusion barrier.
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Nakachi M, Nakajima A, Nomura M, Yonezawa K, Ueno K, Endo T, Inaba K. Proteomic profiling reveals compartment-specific, novel functions of ascidian sperm proteins. Mol Reprod Dev 2011; 78:529-49. [DOI: 10.1002/mrd.21341] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 05/18/2011] [Indexed: 11/11/2022]
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Abstract
The tunicates, or urochordates, constitute a large group of marine animals whose recent common ancestry with vertebrates is reflected in the tadpole-like larvae of most tunicates. Their diversity and key phylogenetic position are enhanced, from a research viewpoint, by anatomically simple and transparent embryos, compact rapidly evolving genomes, and the availability of powerful experimental and computational tools with which to study these organisms. Tunicates are thus a powerful system for exploring chordate evolution and how extreme variation in genome sequence and gene regulatory network architecture is compatible with the preservation of an ancestral chordate body plan.
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Affiliation(s)
- Patrick Lemaire
- Institut du Biologie de Développement de Marseille Luminy (IBDML, UMR 6216, CNRS, Université de la Méditerranée), Parc Scientifique de Luminy Case 907, F-13288, Marseille Cedex 9, France
- Centre de Recherches en Biochimie Macromoléculaire (CRBM, UMR5237, CNRS, Universités Montpellier 1 and 2), 1919 route de Mende, F-34293, Montpellier Cedex 05, France
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