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Ming J, Zhou R, Wu X, Gao Y, Yin Y, Fan W, Tan J, Song X. Characterization of Myxovirus resistance (Mx) gene from Chinese seabass Lateolabrax maculatus: Insights into the evolution and function of Mx genes. FISH & SHELLFISH IMMUNOLOGY 2024; 152:109749. [PMID: 39002557 DOI: 10.1016/j.fsi.2024.109749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/24/2024] [Accepted: 07/03/2024] [Indexed: 07/15/2024]
Abstract
Chinese seabass (Lateolabrax maculatus) stands out as one of the most sought-after and economically significant species in aquaculture within China. Diseases of L. maculatus occur frequently due to the degradation of the germplasm, the aggravation of environmental pollution of water, and the reproduction of pathogenic microorganisms, inflicting considerable economic losses on the Chinese seabass industry. The Myxovirus resistance (Mx) gene plays pivotal roles in the antiviral immune response ranging from mammals to fish. However, the function of the Mx gene in L. maculatus is still unknown. Firstly, the origin and evolutionary history of Mx proteins was elucidated in this study. Subsequently, an Mx gene from L. maculatus (designed as LmMxA gene) was identified, and its functions in combating antiviral and antibacterial threats were investigated. Remarkably, our findings suggested that while Mx group genes were present in chordates, DYN group genes were present in everything from single-celled animals to humans. Furthermore, our investigation revealed that the LmMxA mRNA level increased in the kidney, spleen and liver subsequent to Vibrio anguillarum and poly(I:C) challenged. Immunofluorescence analysis indicated that LmMxA is predominantly localization in the nucleus and the cytoplasm. Notably, the expression of MAVS, IFN1 and Mx1 increased when LmMxA was overexpression within the EPC cells. Moreover, through assessment via cytopathic effect (CPE), virus titer, and antibacterial activity, it becomes evident that LmMxA exerts a dual role in bolstering both antiviral and antibacterial immune responses. These compelling findings laid the foundation for further exploring the mechanism of LmMxA in response to innate immunity of L. maculatus.
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Affiliation(s)
- Jiagen Ming
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Rong Zhou
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Xiangyang Wu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yanlun Gao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yanze Yin
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Wenyu Fan
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jiabo Tan
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiaojun Song
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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2
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Shao F, Zeng M, Xu X, Zhang H, Peng Z. FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research. Database (Oxford) 2024; 2024:baae044. [PMID: 38829853 PMCID: PMC11146639 DOI: 10.1093/database/baae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 04/04/2024] [Accepted: 05/15/2024] [Indexed: 06/05/2024]
Abstract
We launched the initial version of FishTEDB in 2018, which aimed to establish an open-source, user-friendly, data-rich transposable element (TE) database. Over the past 5 years, FishTEDB 1.0 has gained approximately 10 000 users, accumulating more than 450 000 interactions. With the unveiling of extensive fish genome data and the increasing emphasis on TE research, FishTEDB needs to extend the richness of data and functions. To achieve the above goals, we introduced 33 new fish species to FishTEDB 2.0, encompassing a wide array of fish belonging to 48 orders. To make the updated database more functional, we added a genome browser to visualize the positional relationship between TEs and genes and the estimated TE insertion time in different species. In conclusion, we released a new version of the fish TE database, FishTEDB 2.0, designed to assist researchers in the future study of TE functions and promote the progress of biological theories related to TEs. Database URL: https://www.fishtedb.com/.
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Affiliation(s)
- Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, 2 Tiansheng Road, Chongqing 400715, China
| | - Minzhi Zeng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, 2 Tiansheng Road, Chongqing 400715, China
| | - Xiaofei Xu
- School of Computing Technologies, RMIT University, 124 La Trobe Street, Victoria 3000, Australia
| | - Huahao Zhang
- College of Pharmacy and Life Science, Jiujiang University, 551 Qianjin East Road, Jiujiang 332005, China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, 2 Tiansheng Road, Chongqing 400715, China
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3
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Chen S, Fan H, Ran C, Hong Y, Feng H, Yue Z, Zhang H, Pontarotti P, Xu A, Huang S. The IL-17 pathway intertwines with neurotrophin and TLR/IL-1R pathways since its domain shuffling origin. Proc Natl Acad Sci U S A 2024; 121:e2400903121. [PMID: 38683992 PMCID: PMC11087794 DOI: 10.1073/pnas.2400903121] [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: 02/02/2024] [Accepted: 03/11/2024] [Indexed: 05/02/2024] Open
Abstract
The IL-17 pathway displays remarkably diverse functional modes between different subphyla, classes, and even orders, yet its driving factors remains elusive. Here, we demonstrate that the IL-17 pathway originated through domain shuffling between a Toll-like receptor (TLR)/IL-1R pathway and a neurotrophin-RTK (receptor-tyrosine-kinase) pathway (a Trunk-Torso pathway). Unlike other new pathways that evolve independently, the IL-17 pathway remains intertwined with its donor pathways throughout later evolution. This intertwining not only influenced the gains and losses of domains and components in the pathway but also drove the diversification of the pathway's functional modes among animal lineages. For instance, we reveal that the crustacean female sex hormone, a neurotrophin inducing sex differentiation, could interact with IL-17Rs and thus be classified as true IL-17s. Additionally, the insect prothoracicotropic hormone, a neurotrophin initiating ecdysis in Drosophila by binding to Torso, could bind to IL-17Rs in other insects. Furthermore, IL-17R and TLR/IL-1R pathways maintain crosstalk in amphioxus and zebrafish. Moreover, the loss of the Death domain in the pathway adaptor connection to IκB kinase and stress-activated protein kinase (CIKSs) dramatically reduced their abilities to activate nuclear factor-kappaB (NF-κB) and activator protein 1 (AP-1) in amphioxus and zebrafish. Reinstating this Death domain not only enhanced NF-κB/AP-1 activation but also strengthened anti-bacterial immunity in zebrafish larvae. This could explain why the mammalian IL-17 pathway, whose CIKS also lacks Death, is considered a weak signaling activator, relying on synergies with other pathways. Our findings provide insights into the functional diversity of the IL-17 pathway and unveil evolutionary principles that could govern the pathway and be used to redesign and manipulate it.
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Affiliation(s)
- Shenghui Chen
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou510275, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao266237, China
| | - Huiping Fan
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou510275, China
| | - Chenrui Ran
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou510275, China
| | - Yun Hong
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou510275, China
| | - Huixiong Feng
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou510275, China
| | - Zirui Yue
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou510275, China
| | - Hao Zhang
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou510275, China
| | - Pierre Pontarotti
- MEPHI (Microbes, Evolution, Phylogénie et Infection), Aix Marseille Université, Marseille, France
| | - Anlong Xu
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou510275, China
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing100029, China
| | - Shengfeng Huang
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou510275, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao266237, China
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4
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Yu D, Ren Y, Uesaka M, Beavan AJS, Muffato M, Shen J, Li Y, Sato I, Wan W, Clark JW, Keating JN, Carlisle EM, Dearden RP, Giles S, Randle E, Sansom RS, Feuda R, Fleming JF, Sugahara F, Cummins C, Patricio M, Akanni W, D'Aniello S, Bertolucci C, Irie N, Alev C, Sheng G, de Mendoza A, Maeso I, Irimia M, Fromm B, Peterson KJ, Das S, Hirano M, Rast JP, Cooper MD, Paps J, Pisani D, Kuratani S, Martin FJ, Wang W, Donoghue PCJ, Zhang YE, Pascual-Anaya J. Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences. Nat Ecol Evol 2024; 8:519-535. [PMID: 38216617 DOI: 10.1038/s41559-023-02299-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 12/04/2023] [Indexed: 01/14/2024]
Abstract
Polyploidy or whole-genome duplication (WGD) is a major event that drastically reshapes genome architecture and is often assumed to be causally associated with organismal innovations and radiations. The 2R hypothesis suggests that two WGD events (1R and 2R) occurred during early vertebrate evolution. However, the timing of the 2R event relative to the divergence of gnathostomes (jawed vertebrates) and cyclostomes (jawless hagfishes and lampreys) is unresolved and whether these WGD events underlie vertebrate phenotypic diversification remains elusive. Here we present the genome of the inshore hagfish, Eptatretus burgeri. Through comparative analysis with lamprey and gnathostome genomes, we reconstruct the early events in cyclostome genome evolution, leveraging insights into the ancestral vertebrate genome. Genome-wide synteny and phylogenetic analyses support a scenario in which 1R occurred in the vertebrate stem-lineage during the early Cambrian, and 2R occurred in the gnathostome stem-lineage, maximally in the late Cambrian-earliest Ordovician, after its divergence from cyclostomes. We find that the genome of stem-cyclostomes experienced an additional independent genome triplication. Functional genomic and morphospace analyses demonstrate that WGD events generally contribute to developmental evolution with similar changes in the regulatory genome of both vertebrate groups. However, appreciable morphological diversification occurred only in the gnathostome but not in the cyclostome lineage, calling into question the general expectation that WGDs lead to leaps of bodyplan complexity.
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Affiliation(s)
- Daqi Yu
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yandong Ren
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Masahiro Uesaka
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Alan J S Beavan
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Bristol, UK
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
| | - Jieyu Shen
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yongxin Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Iori Sato
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
- iPS Cell Advanced Characterization and Development Team, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Wenting Wan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - James W Clark
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Bristol, UK
- Milner Centre for Evolution, University of Bath, Claverton Down, Bath, UK
| | - Joseph N Keating
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | - Emily M Carlisle
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | - Richard P Dearden
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
- Naturalis Biodiversity Center, Leiden, the Netherlands
| | - Sam Giles
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Emma Randle
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, UK
| | - Robert S Sansom
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, UK
| | - Roberto Feuda
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - James F Fleming
- Keio University Institute for Advanced Biosciences, Tsuruoka, Japan
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Fumiaki Sugahara
- Division of Biology, Hyogo Medical University, Nishinomiya, Japan
- Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR), Kobe, Japan
| | - Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Wasiu Akanni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Salvatore D'Aniello
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Villa Comunale, Napoli, Italy
| | - Cristiano Bertolucci
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Villa Comunale, Napoli, Italy
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Naoki Irie
- Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies, SOKENDAI, Hayama, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Cantas Alev
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
| | - Guojun Sheng
- International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Alex de Mendoza
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ignacio Maeso
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona (UB), Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Bastian Fromm
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Sabyasachi Das
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Masayuki Hirano
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Jonathan P Rast
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Max D Cooper
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Jordi Paps
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
- Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR), Kobe, Japan
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China.
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
| | - Juan Pascual-Anaya
- Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR), Kobe, Japan.
- Department of Animal Biology, Faculty of Science, University of Málaga (UMA), Málaga, Spain.
- Edificio de Bioinnovación, Universidad de Málaga, Málaga, Spain.
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5
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Peng Z, Zhang W, Fu H, Li Y, Zhang C, Li J, Chan J, Zhang L. Genome-Wide Comparative Analysis of SRCR Gene Superfamily in Invertebrates Reveals Massive and Independent Gene Expansions in the Sponge and Sea Urchin. Int J Mol Sci 2024; 25:1515. [PMID: 38338794 PMCID: PMC10855680 DOI: 10.3390/ijms25031515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/12/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Without general adaptative immunity, invertebrates evolved a vast number of heterogeneous non-self recognition strategies. One of those well-known adaptations is the expansion of the immune receptor gene superfamily coding for scavenger receptor cysteine-rich domain containing proteins (SRCR) in a few invertebrates. Here, we investigated the evolutionary history of the SRCR gene superfamily (SRCR-SF) across 29 metazoan species with an emphasis on invertebrates. We analyzed their domain architectures, genome locations and phylogenetic distribution. Our analysis shows extensive genome-wide duplications of the SRCR-SFs in Amphimedon queenslandica and Strongylocentrotus purpuratus. Further molecular evolution study reveals various patterns of conserved cysteines in the sponge and sea urchin SRCR-SFs, indicating independent and convergent evolution of SRCR-SF expansion during invertebrate evolution. In the case of the sponge SRCR-SFs, a novel motif with seven conserved cysteines was identified. Exon-intron structure analysis suggests the rapid evolution of SRCR-SFs during gene duplications in both the sponge and the sea urchin. Our findings across nine representative metazoans also underscore a heightened expression of SRCR-SFs in immune-related tissues, notably the digestive glands. This observation indicates the potential role of SRCR-SFs in reinforcing distinct immune functions in these invertebrates. Collectively, our results reveal that gene duplication, motif structure variation, and exon-intron divergence might lead to the convergent evolution of SRCR-SF expansions in the genomes of the sponge and sea urchin. Our study also suggests that the utilization of SRCR-SF receptor duplication may be a general and basal strategy to increase immune diversity and tissue specificity for the invertebrates.
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Affiliation(s)
- Zhangjie Peng
- College of Life Sciences, School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; (Z.P.); (H.F.); (Y.L.); (C.Z.)
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Wei Zhang
- College of Life Sciences, School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; (Z.P.); (H.F.); (Y.L.); (C.Z.)
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Hailun Fu
- College of Life Sciences, School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; (Z.P.); (H.F.); (Y.L.); (C.Z.)
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yuzhu Li
- College of Life Sciences, School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; (Z.P.); (H.F.); (Y.L.); (C.Z.)
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Chunyu Zhang
- College of Life Sciences, School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; (Z.P.); (H.F.); (Y.L.); (C.Z.)
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jie Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jiulin Chan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao 266071, China
| | - Linlin Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Qingdao 266071, China
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6
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Martínez-Burguete T, Peña-Marín ES, Llera-Herrera RA, Jiménez-Martínez LD, Martínez-García R, Alvarez-Villagomez CS, Alvarez-González CA. Identification and expression analysis of transcripts involved in taurine biosynthesis during early ontogeny of tropical gar Atractosteus tropicus. Comp Biochem Physiol A Mol Integr Physiol 2023; 285:111501. [PMID: 37562582 DOI: 10.1016/j.cbpa.2023.111501] [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: 06/20/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023]
Abstract
In fishes, the availability of taurine is regulated during ontogenetic development, where its endogenous synthesis capacity is species dependent. Thus, different pathways and involved enzymes have been described: pathway I (cysteine sulfinate-dependent pathway), cysteine dioxygenase type 1 (cdo1) and cysteine sulfinic acid decarboxylase (csad); pathway II (cysteic acid pathway), cdo1 and glutamic acid decarboxylase (gad); and pathway III (cysteamine pathway), 2-aminoethanethiol dioxygenase (ado); whereas taurine transporter (taut) is responsible for taurine entry into cells on the cell membrane and the mitochondria. This study determined if the tropical gar (Atractosteus tropicus), an ancient holostean fish model, has the molecular mechanism to synthesize taurine through the identification and analysis expression of transcripts coding for proteins involved in its biosynthesis and transportation, at different embryo-larvae stages and in different organs of juveniles (31 dah). We observed a fluctuating expression of all transcripts involved in the three pathways at all analyzed stages. All transcripts are expressed during the beginning of larval development; however, ado and taut show a peak expression at 9 dah, and all transcripts but csad decreased at 23 dah, when the organism ended the larval period. Furthermore, at 31 dah, we observed taut expression in all examined organs. The transcripts involved in pathways I and III are expressed differently across all organs, whereas pathway II was only observed in the brain, eye, and skin. The results suggested that taurine biosynthesis in tropical gar is regulated during its early development before first feeding, and the pathway might also be organ-type dependent.
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Affiliation(s)
- Talhia Martínez-Burguete
- Laboratorio de Fisiología en Recursos Acuáticos, División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Carretera Villahermosa-Cárdenas Km. 0.5, CP.86139 Villahermosa, Tabasco, Mexico.
| | - Emyr Saúl Peña-Marín
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California (UABC), Ensenada 21100, Baja California, Mexico.
| | - Raúl Antonio Llera-Herrera
- Instituto de Ciencias del Mar y Limnología - Unidad Académica Mazatlán, Universidad Nacional Autónoma de México, Joel Montes Camarena S/N, PO Box 811, Mazatlán, Sinaloa, Mexico.
| | - Luis Daniel Jiménez-Martínez
- División Académica Multidisciplinaria de Jalpa de Méndez, Universidad Juárez Autónoma de Tabasco, Carretera Nacajuca-Jalpa de Méndez R7a Rivera Alta, C.P. 86200 Jalpa de Méndez, Tabasco, Mexico.
| | - Rafael Martínez-García
- Laboratorio de Fisiología en Recursos Acuáticos, División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Carretera Villahermosa-Cárdenas Km. 0.5, CP.86139 Villahermosa, Tabasco, Mexico.
| | - Carina Shianya Alvarez-Villagomez
- Laboratorio de Fisiología en Recursos Acuáticos, División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Carretera Villahermosa-Cárdenas Km. 0.5, CP.86139 Villahermosa, Tabasco, Mexico.
| | - Carlos Alfonso Alvarez-González
- Laboratorio de Fisiología en Recursos Acuáticos, División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Carretera Villahermosa-Cárdenas Km. 0.5, CP.86139 Villahermosa, Tabasco, Mexico.
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7
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Carlson KB, Nguyen C, Wcisel DJ, Yoder JA, Dornburg A. Ancient fish lineages illuminate toll-like receptor diversification in early vertebrate evolution. Immunogenetics 2023; 75:465-478. [PMID: 37555888 DOI: 10.1007/s00251-023-01315-7] [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: 04/06/2023] [Accepted: 06/28/2023] [Indexed: 08/10/2023]
Abstract
Since its initial discovery over 50 years ago, understanding the evolution of the vertebrate RAG- mediated adaptive immune response has been a major area of research focus for comparative geneticists. However, how the evolutionary novelty of an adaptive immune response impacted the diversity of receptors associated with the innate immune response has received considerably less attention until recently. Here, we investigate the diversification of vertebrate toll-like receptors (TLRs), one of the most ancient and well conserved innate immune receptor families found across the Tree of Life, integrating genomic data that represent all major vertebrate lineages with new transcriptomic data from Polypteriformes, the earliest diverging ray-finned fish lineage. Our analyses reveal TLR sequences that reflect the 6 major TLR subfamilies, TLR1, TLR3, TLR4, TLR5, TLR7, and TLR11, and also currently unnamed, yet phylogenetically distinct TLR clades. We additionally recover evidence for a pulse of gene gain coincident with the rise of the RAG-mediated adaptive immune response in jawed vertebrates, followed by a period of rapid gene loss during the Cretaceous. These gene losses are primarily concentrated in marine teleost fish and synchronous with the mid Cretaceous anoxic event, a period of rapid extinction for marine species. Finally, we reveal a mismatch between phylogenetic placement and gene nomenclature for up to 50% of TLRs found in clades such as ray-finned fishes, cyclostomes, amphibians, and elasmobranchs. Collectively, these results provide an unparalleled perspective of TLR diversity and offer a ready framework for testing gene annotations in non-model species.
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Affiliation(s)
- Kara B Carlson
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
- Genetics and Genomics Academy, North Carolina State University, Raleigh, NC, USA
| | - Cameron Nguyen
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Dustin J Wcisel
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
- Genetics and Genomics Academy, North Carolina State University, Raleigh, NC, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA.
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8
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D'Aniello S, Bertrand S, Escriva H. Amphioxus as a model to study the evolution of development in chordates. eLife 2023; 12:e87028. [PMID: 37721204 PMCID: PMC10506793 DOI: 10.7554/elife.87028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 08/10/2023] [Indexed: 09/19/2023] Open
Abstract
Cephalochordates and tunicates represent the only two groups of invertebrate chordates, and extant cephalochordates - commonly known as amphioxus or lancelets - are considered the best proxy for the chordate ancestor, from which they split around 520 million years ago. Amphioxus has been an important organism in the fields of zoology and embryology since the 18th century, and the morphological and genomic simplicity of cephalochordates (compared to vertebrates) makes amphioxus an attractive model for studying chordate biology at the cellular and molecular levels. Here we describe the life cycle of amphioxus, and discuss the natural histories and habitats of the different species of amphioxus. We also describe their use as laboratory animal models, and discuss the techniques that have been developed to study different aspects of amphioxus.
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Affiliation(s)
- Salvatore D'Aniello
- Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton DohrnNapoliItaly
| | - Stephanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire OcéanologiqueBanyuls-sur-MerFrance
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire OcéanologiqueBanyuls-sur-MerFrance
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9
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Gao Z, Jiang W, Zhang Y, Zhang L, Yi M, Wang H, Ma Z, Qu B, Ji X, Long H, Zhang S. Amphioxus adenosine-to-inosine tRNA-editing enzyme that can perform C-to-U and A-to-I deamination of DNA. Commun Biol 2023; 6:744. [PMID: 37464027 PMCID: PMC10354150 DOI: 10.1038/s42003-023-05134-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
Adenosine-to-inosine tRNA-editing enzyme has been identified for more than two decades, but the study on its DNA editing activity is rather scarce. We show that amphioxus (Branchiostoma japonicum) ADAT2 (BjADAT2) contains the active site 'HxE-PCxxC' and the key residues for target-base-binding, and amphioxus ADAT3 (BjADAT3) harbors both the N-terminal positively charged region and the C-terminal pseudo-catalytic domain important for recognition of substrates. The sequencing of BjADAT2-transformed Escherichia coli genome suggests that BjADAT2 has the potential to target E. coli DNA and can deaminate at TCG and GAA sites in the E. coli genome. Biochemical analyses further demonstrate that BjADAT2, in complex with BjADAT3, can perform A-to-I editing of tRNA and convert C-to-U and A-to-I deamination of DNA. We also show that BjADAT2 preferentially deaminates adenosines and cytidines in the loop of DNA hairpin structures of substrates, and BjADAT3 also affects the type of DNA substrate targeted by BjADAT2. Finally, we find that C89, N113, C148 and Y156 play critical roles in the DNA editing activity of BjADAT2. Collectively, our study indicates that BjADAT2/3 is the sole naturally occurring deaminase with both tRNA and DNA editing capacity identified so far in Metazoa.
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Affiliation(s)
- Zhan Gao
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, 266003, Qingdao, China.
| | - Wanyue Jiang
- Institute of Evolution & Marine Biodiversity, KLMME, Ocean University of China, 266003, Qingdao, China
| | - Yu Zhang
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, 266003, Qingdao, China
| | - Liping Zhang
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, 266003, Qingdao, China
| | - Mengmeng Yi
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, 266003, Qingdao, China
| | - Haitao Wang
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, 266003, Qingdao, China
| | - Zengyu Ma
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, 266003, Qingdao, China
| | - Baozhen Qu
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, 266003, Qingdao, China
| | - Xiaohan Ji
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, 266003, Qingdao, China
| | - Hongan Long
- Institute of Evolution & Marine Biodiversity, KLMME, Ocean University of China, 266003, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, 266237, Qingdao, China
| | - Shicui Zhang
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, 266003, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, 266237, Qingdao, China.
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10
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Chen S, Fu X, Wang R, Li M, Yan X, Yue Z, Chen SW, Dong M, Xu A, Huang S. SUMO and PIAS repress NF-κB activation in a basal chordate. FISH & SHELLFISH IMMUNOLOGY 2023; 137:108754. [PMID: 37088348 DOI: 10.1016/j.fsi.2023.108754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/09/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023]
Abstract
Small ubiquitin-like modifier (SUMO) regulates various biological processes, including the MyD88/TICAMs-IRAKs-TRAF6-NF-κB pathway, one of the core immune pathways. However, its functions are inconsistent between invertebrates and vertebrates and have rarely been investigated in lower chordates, including amphioxus and fishes. Here, we investigated the SUMOylation gene system in the amphioxus, a living basal chordate. We found that amphioxus has a SUMOylation system that has a complete set of genes and preserves several ancestral traits. We proceeded to study their molecular functions using the mammal cell lines. Both amphioxus SUMO1 and SUMO2 were shown to be able to attach to NF-κB Rel and to inhibit NF-κB activation by 50-75% in a dose-dependent fashion. The inhibition by SUMO2 could be further enhanced by the addition of the SUMO E2 ligase UBC9. In comparison, while human SUMO2 inhibited RelA, human SUMO1 slightly activated RelA. We also showed that, similar to human PIAS1-4, amphioxus PIAS could serve as a SUMO E3 ligase and promote its self-SUMOylation. This suggests that amphioxus PIAS is functionally compatible in human cells. Moreover, we showed that amphioxus PIAS is not only able to inhibit NF-κB activation induced by MyD88, TICAM-like, TRAF6 and IRAK4 but also able to suppress NF-κB Rel completely in the presence of SUMO1/2 in a dose-insensitive manner. This suggests that PIAS could effectively block Rel by promoting Rel SUMOylation. In comparison, in humans, only PIAS3, but not PIAS1/2/4, has been reported to promote NF-κB SUMOylation. Taken together, the findings from amphioxus, together with those from mammals and other species, not only offer insights into the functional volatility of the animal SUMO system, but also shed light on its evolutionary transitions from amphioxus to fish, and ultimately to humans.
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Affiliation(s)
- Shenghui Chen
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangdong, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xianan Fu
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangdong, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Ruihua Wang
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangdong, China; Center for Regenerative and Translational Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510632, China
| | - Mingshi Li
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangdong, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xinyu Yan
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangdong, China
| | - Zirui Yue
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangdong, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shang-Wu Chen
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangdong, China
| | - Meiling Dong
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangdong, China
| | - Anlong Xu
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangdong, China; Beijing University of Chinese Medicine, Dong San Huang Road, Chao-yang District, Beijing, 100029, China
| | - Shengfeng Huang
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangdong, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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11
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Zhan Y, Zhao CS, Qu X, Xiao Z, Deng C, Li Y. Identification of a novel amphioxus leucine-rich repeat receptor involved in phagocytosis reveals a role for Slit2-N-type LRR in bacterial elimination. J Biol Chem 2023; 299:104689. [PMID: 37044216 DOI: 10.1016/j.jbc.2023.104689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 03/25/2023] [Accepted: 03/31/2023] [Indexed: 04/14/2023] Open
Abstract
The basal chordate amphioxus is a model for tracing the origin and evolution of vertebrate immunity. To explore the evolution of immunoreceptor signaling pathways, we searched the associated receptors of the amphioxus B. belcheri (Bb) homolog of immunoreceptor signaling adaptor protein Grb2. Mass-spectrum analysis of BbGrb2 immunoprecipitates from B. belcheri intestine lysates revealed a folate receptor (FR) domain- and leucine-rich repeat (LRR)-containing protein (FrLRR). Sequence and structural analysis showed that FrLRR is a membrane protein with a predicted curved solenoid structure. The N-terminal Fr domain contains very few folate-binding sites; the following LRR region is a Slit2-type LRR, and a GPI-anchored site was predicted at the C-terminus. RT-PCR analysis showed FrLRR is a transcription-mediated fusion gene of BbFR-like and BbSlit2-N-like genes. Genomic DNA structure analysis implied the B. belcheri FrLRR gene locus and the corresponding locus in B. floridae might be generated by exon shuffling of a Slit2-N-like gene into an FR gene. RT-qPCR, immunostaining and immunoblot results showed that FrLRR was primarily distributed in B. belcheri intestinal tissue. We further demonstrated that FrLRR localized to the cell membrane and lysosomes. Functionally, FrLRR mediated and promoted bacteria-binding and phagocytosis, and FrLRR antibody blocking or Grb2 knockdown inhibited FrLRR-mediated phagocytosis. Interestingly, we found that human Slit2-N (hSlit2-N) also mediated direct bacteria-binding and phagocytosis which was inhibited by Slit2-N antibody blocking or Grb2 knockdown. Together, these results indicate FrLRR and hSlit2-N may function as phagocytotic-receptors to promote phagocytosis through Grb2, implying the Slit2-N-type-LRR-containing proteins play a role in bacterial binding and elimination.
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Affiliation(s)
- Yanli Zhan
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Chen-Si Zhao
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xuemei Qu
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhihui Xiao
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Chong Deng
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yingqiu Li
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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12
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Huang Z, Xu L, Cai C, Zhou Y, Liu J, Xu Z, Zhu Z, Kang W, Cen W, Pei S, Chen D, Shi C, Wu X, Huang Y, Xu C, Yan Y, Yang Y, Xue T, He W, Hu X, Zhang Y, Chen Y, Bi C, He C, Xue L, Xiao S, Yue Z, Jiang Y, Yu JK, Jarvis E, Li G, Lin G, Zhang Q, Zhou Q. Three amphioxus reference genomes reveal gene and chromosome evolution of chordates. Proc Natl Acad Sci U S A 2023; 120:e2201504120. [PMID: 36867684 PMCID: PMC10013865 DOI: 10.1073/pnas.2201504120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 01/18/2023] [Indexed: 03/05/2023] Open
Abstract
The slow-evolving invertebrate amphioxus has an irreplaceable role in advancing our understanding of the vertebrate origin and innovations. Here we resolve the nearly complete chromosomal genomes of three amphioxus species, one of which best recapitulates the 17 chordate ancestor linkage groups. We reconstruct the fusions, retention, or rearrangements between descendants of whole-genome duplications, which gave rise to the extant microchromosomes likely existed in the vertebrate ancestor. Similar to vertebrates, the amphioxus genome gradually establishes its three-dimensional chromatin architecture at the onset of zygotic activation and forms two topologically associated domains at the Hox gene cluster. We find that all three amphioxus species have ZW sex chromosomes with little sequence differentiation, and their putative sex-determining regions are nonhomologous to each other. Our results illuminate the unappreciated interspecific diversity and developmental dynamics of amphioxus genomes and provide high-quality references for understanding the mechanisms of chordate functional genome evolution.
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Affiliation(s)
- Zhen Huang
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
- Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian350108, China
| | - Luohao Xu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing400715, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Chongqing400715, China
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna1090, Austria
| | - Cheng Cai
- The Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang310058, China
| | - Yitao Zhou
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Jing Liu
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna1090, Austria
| | - Zaoxu Xu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing400715, China
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Chongqing400715, China
| | - Zexian Zhu
- The Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang310058, China
| | - Wen Kang
- The Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang310058, China
| | - Wan Cen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Surui Pei
- Annoroad Gene Technology Co., Ltd, Beijing100180, China
| | - Duo Chen
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
- Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Chenggang Shi
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian361102, China
| | - Xiaotong Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian361102, China
| | - Yongji Huang
- Institute of Oceanography, Minjiang University, Fuzhou, Fujian350108, China
| | - Chaohua Xu
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Yanan Yan
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Ying Yang
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Ting Xue
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
- Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Wenjin He
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Xuefeng Hu
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Yanding Zhang
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Youqiang Chen
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
- Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Changwei Bi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu210096, China
| | - Chunpeng He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu210096, China
| | - Lingzhan Xue
- Aquaculture and Genetic breeding laboratory, Freshwater Fisheries Research Institute of Fujian, Fuzhou, Fujian350002, China
| | - Shijun Xiao
- College of Plant Protection, Jilin Agricultural University, Changchun, Jilin130118, China
| | - Zhicao Yue
- Department of Cell Biology and Medical Genetics, Carson International Cancer Center, and Guangdong Key Laboratory for Genome Stability and Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong518060, China
| | - Yu Jiang
- Annoroad Gene Technology Co., Ltd, Beijing100180, China
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei11529, Taiwan
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan26242, Taiwan
| | - Erich D. Jarvis
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY10065
- HHMI, Chevy Chase, MD20815
| | - Guang Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian361102, China
| | - Gang Lin
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
- Annoroad Gene Technology Co., Ltd, Beijing100180, China
- Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Qiujin Zhang
- Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization & Fujian Key Laboratory of Developmental and Neurobiology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian350117, China
- Annoroad Gene Technology Co., Ltd, Beijing100180, China
- Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, Fujian350117, China
| | - Qi Zhou
- The Ministry of Education Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang310058, China
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Hangzhou, Zhejiang310052, China
- Evolutionary and Organismal Biology Research Center, School of Medicine, Zhejiang University, Hangzhou, Zhejiang310058, China
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13
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Devaux CA, Pontarotti P, Nehari S, Raoult D. 'Cannibalism' of exogenous DNA sequences: The ancestral form of adaptive immunity which entails recognition of danger. Front Immunol 2022; 13:989707. [PMID: 36618387 PMCID: PMC9816338 DOI: 10.3389/fimmu.2022.989707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Adaptive immunity is a sophisticated form of immune response capable of retaining the molecular memory of a very great diversity of target antigens (epitopes) as non-self. It is capable of reactivating itself upon a second encounter with an immunoglobulin or T-cell receptor antigen-binding site with a known epitope that had previously primed the host immune system. It has long been considered that adaptive immunity is a highly evolved form of non-self recognition that appeared quite late in speciation and complemented a more generalist response called innate immunity. Innate immunity offers a relatively non-specific defense (although mediated by sensors that could specifically recognize virus or bacteria compounds) and which does not retain a memory of the danger. But this notion of recent acquisition of adaptive immunity is challenged by the fact that another form of specific recognition mechanisms already existed in prokaryotes that may be able to specifically auto-protect against external danger. This recognition mechanism can be considered a primitive form of specific (adaptive) non-self recognition. It is based on the fact that many archaea and bacteria use a genome editing system that confers the ability to appropriate viral DNA sequences allowing prokaryotes to prevent host damage through a mechanism very similar to adaptive immunity. This is indistinctly called, 'endogenization of foreign DNA' or 'viral DNA predation' or, more pictorially 'DNA cannibalism'. For several years evidence has been accumulating, highlighting the crucial role of endogenization of foreign DNA in the fundamental processes related to adaptive immunity and leading to a change in the dogma that adaptive immunity appeared late in speciation.
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Affiliation(s)
- Christian A. Devaux
- Aix-Marseille University, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-universitaire (IHU)-Méditerranée Infection, Marseille, France,Department of Biological Sciences, Centre National de la Recherche Scientifique, Centre National de la Recherche Scientifique (CNRS)-SNC5039, Marseille, France,*Correspondence: Christian A. Devaux,
| | - Pierre Pontarotti
- Aix-Marseille University, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-universitaire (IHU)-Méditerranée Infection, Marseille, France,Department of Biological Sciences, Centre National de la Recherche Scientifique, Centre National de la Recherche Scientifique (CNRS)-SNC5039, Marseille, France
| | - Sephora Nehari
- Aix-Marseille University, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille University, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-universitaire (IHU)-Méditerranée Infection, Marseille, France
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14
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Stäubert C, Wozniak M, Dupuis N, Laschet C, Pillaiyar T, Hanson J. Superconserved receptors expressed in the brain: Expression, function, motifs and evolution of an orphan receptor family. Pharmacol Ther 2022; 240:108217. [PMID: 35644261 DOI: 10.1016/j.pharmthera.2022.108217] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 12/14/2022]
Abstract
GPR27, GPR85 and GPR173 constitute a small family of G protein-coupled receptors (GPCR) that share the distinctive characteristics of being highly conserved throughout vertebrate evolution and predominantly expressed in the brain. Accordingly, they have been coined as "Superconserved Receptors Expressed in the Brain" (SREB), although their expression profile is more complex than what was originally thought. SREBs have no known validated endogenous ligands and are thus labeled as "orphan" receptors. The investigation of this particular category of uncharacterized receptors holds great promise both in terms of physiology and drug development. In the largest GPCR family, the Rhodopsin-like or Class A, around 100 receptors are considered orphans. Because GPCRs are the most successful source of drug targets, the discovery of a novel function or ligand most likely will lead to significant breakthroughs for the discovery of innovative therapies. The high level of conservation is one of the characteristic features of the SREBs. We propose herein a detailed analysis of the putative evolutionary origin of this family. We highlight the properties that distinguish SREBs from other rhodopsin-like GPCRs. We present the current evidence for these receptors downstream signaling pathways and functions. We discuss the pharmacological challenge for the identification of natural or synthetic ligands of orphan receptors like SREBs. The different SREB-related scientific questions are presented with a highlight on what should be addressed in the near future, including the confirmation of published evidence and their validation as drug targets. In particular, we discuss in which pathological conditions these receptors may be of great relevance to solve unmet medical needs.
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Affiliation(s)
- Claudia Stäubert
- Rudolf Schönheimer Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany.
| | - Monika Wozniak
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, Liège, Belgium
| | - Nadine Dupuis
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, Liège, Belgium
| | - Céline Laschet
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, Liège, Belgium
| | - Thanigaimalai Pillaiyar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tuebingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Julien Hanson
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, Liège, Belgium; Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines, University of Liège, Liège, Belgium.
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15
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Brasó-Vives M, Marlétaz F, Echchiki A, Mantica F, Acemel RD, Gómez-Skarmeta JL, Hartasánchez DA, Le Targa L, Pontarotti P, Tena JJ, Maeso I, Escriva H, Irimia M, Robinson-Rechavi M. Parallel evolution of amphioxus and vertebrate small-scale gene duplications. Genome Biol 2022; 23:243. [PMID: 36401278 PMCID: PMC9673378 DOI: 10.1186/s13059-022-02808-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 10/31/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Amphioxus are non-vertebrate chordates characterized by a slow morphological and molecular evolution. They share the basic chordate body-plan and genome organization with vertebrates but lack their 2R whole-genome duplications and their developmental complexity. For these reasons, amphioxus are frequently used as an outgroup to study vertebrate genome evolution and Evo-Devo. Aside from whole-genome duplications, genes continuously duplicate on a smaller scale. Small-scale duplicated genes can be found in both amphioxus and vertebrate genomes, while only the vertebrate genomes have duplicated genes product of their 2R whole-genome duplications. Here, we explore the history of small-scale gene duplications in the amphioxus lineage and compare it to small- and large-scale gene duplication history in vertebrates. RESULTS We present a study of the European amphioxus (Branchiostoma lanceolatum) gene duplications thanks to a new, high-quality genome reference. We find that, despite its overall slow molecular evolution, the amphioxus lineage has had a history of small-scale duplications similar to the one observed in vertebrates. We find parallel gene duplication profiles between amphioxus and vertebrates and conserved functional constraints in gene duplication. Moreover, amphioxus gene duplicates show levels of expression and patterns of functional specialization similar to the ones observed in vertebrate duplicated genes. We also find strong conservation of gene synteny between two distant amphioxus species, B. lanceolatum and B. floridae, with two major chromosomal rearrangements. CONCLUSIONS In contrast to their slower molecular and morphological evolution, amphioxus' small-scale gene duplication history resembles that of the vertebrate lineage both in quantitative and in functional terms.
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Affiliation(s)
- Marina Brasó-Vives
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
| | - Ferdinand Marlétaz
- Department of Genetics, Evolution and Environment (GEE), University College London, London, UK
| | - Amina Echchiki
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Federica Mantica
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rafael D Acemel
- Andalusian Centre for Developmental Biology (CABD), CSIC-Pablo Olavide University, Sevilla, Spain
| | - José L Gómez-Skarmeta
- Andalusian Centre for Developmental Biology (CABD), CSIC-Pablo Olavide University, Sevilla, Spain
| | - Diego A Hartasánchez
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Lorlane Le Targa
- IRD, APHM, MEPHI, Aix Marseille Université, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Pierre Pontarotti
- IRD, APHM, MEPHI, Aix Marseille Université, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
- CNRS, Paris, France
| | - Juan J Tena
- Andalusian Centre for Developmental Biology (CABD), CSIC-Pablo Olavide University, Sevilla, Spain
| | - Ignacio Maeso
- Andalusian Centre for Developmental Biology (CABD), CSIC-Pablo Olavide University, Sevilla, Spain
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Hector Escriva
- Biologie Intégrative des Organismes Marins, BIOM, CNRS-Sorbonne University, Banyuls-sur-Mer, France
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Pompeu Fabra University (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
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16
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Li J, Liu S, Zhang Y, Huang Q, Zhang H, OuYang J, Mao F, Fan H, Yi W, Dong M, Xu A, Huang S. Two novel mollusk short-form ApeC-containing proteins act as pattern recognition proteins for peptidoglycan. Front Immunol 2022; 13:971883. [PMID: 36275759 PMCID: PMC9585378 DOI: 10.3389/fimmu.2022.971883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/08/2022] [Indexed: 11/18/2022] Open
Abstract
The Apextrin C-terminal (ApeC) domain is a new protein domain largely specific to aquatic invertebrates. In amphioxus, a short-form ApeC-containing protein (ACP) family is capable of binding peptidoglycan (PGN) and agglutinating bacteria via its ApeC domain. However, the functions of ApeC in other phyla remain unknown. Here we examined 130 ACPs from gastropods and bivalves, the first and second biggest mollusk classes. They were classified into nine groups based on their phylogenetics and architectures, including three groups of short-form ACPs, one group of apextrins and two groups of ACPs of complex architectures. No groups have orthologs in other phyla and only four groups have members in both gastropods and bivalves, suggesting that mollusk ACPs are highly diversified. We selected one bivalve ACP (CgACP1; from the oyster Crossostrea gigas) and one gastropod ACP (BgACP1; from the snail Biomphalaria glabrata) for functional experiments. Both are highly-expressed, secreted short-form ACPs and hence comparable to the amphioxus ACPs previously reported. We found that recombinant CgACP1 and BgACP1 bound with yeasts and several bacteria with different affinities. They also agglutinated these microbes, but showed no inhibiting or killing effects. Further analyses show that both ACPs had high affinities to the Lys-type PGN from S. aureus but weak or no affinities to the DAP-type PGN from Bacillus subtilis. Both recombinant ACPs displayed weak or no affinities to other microbial cell wall components, including lipopolysaccharide (LPS), lipoteichoic acid (LTA), zymosan A, chitin, chitosan and cellulose, as well as to several PGN moieties, including muramyl dipeptide (MDP), N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc). Besides, CgACP1 had the highest expression in the gill and could be greatly up-regulated quickly after bacterial challenge. This is reminiscent of the amphioxus ACP1/2 which serve as essential mucus lectins in the gill. Taken together, the current findings from mollusk and amphioxus ACPs suggest several basic common traits for the ApeC domains, including the high affinity to Lys-type PGN, the bacterial binding and agglutinating capacity, and the role as mucus proteins to protect the mucosal surface.
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Affiliation(s)
- Jin Li
- Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shumin Liu
- Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yang Zhang
- Chinese Academy of Sciences Key Laboratory of Tropical Marine Bio-Resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Qiuyun Huang
- Chinese Academy of Sciences Key Laboratory of Tropical Marine Bio-Resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Hao Zhang
- Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jihua OuYang
- Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Fan Mao
- Chinese Academy of Sciences Key Laboratory of Tropical Marine Bio-Resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Huiping Fan
- Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Wenjie Yi
- Chinese Academy of Sciences Key Laboratory of Tropical Marine Bio-Resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Meiling Dong
- Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Anlong Xu
- Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
- *Correspondence: Anlong Xu, ; Shengfeng Huang,
| | - Shengfeng Huang
- Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- *Correspondence: Anlong Xu, ; Shengfeng Huang,
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17
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Sarkies P. Encyclopaedia of eukaryotic DNA methylation: from patterns to mechanisms and functions. Biochem Soc Trans 2022; 50:1179-1190. [PMID: 35521905 PMCID: PMC9246332 DOI: 10.1042/bst20210725] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 12/14/2022]
Abstract
DNA methylation is an epigenetic modification with a very long evolutionary history. However, DNA methylation evolves surprisingly rapidly across eukaryotes. The genome-wide distribution of methylation diversifies rapidly in different lineages, and DNA methylation is lost altogether surprisingly frequently. The growing availability of genomic and epigenomic sequencing across organisms highlights this diversity but also illuminates potential factors that could explain why both the DNA methylation machinery and its genome-wide distribution evolve so rapidly. Key to this are new discoveries about the fitness costs associated with DNA methylation, and new theories about how the fundamental biochemical mechanisms of DNA methylation introduction and maintenance could explain how new genome-wide patterns of methylation evolve.
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Affiliation(s)
- Peter Sarkies
- Department of Biochemistry, University of Oxford, Oxford, U.K
- MRC London Institute of Molecular Biology, London, U.K
- Institute of Clinical Sciences, Imperial College London, London, U.K
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18
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Zhu Y, Lu N, Chen JY, He C, Huang Z, Lu Z. Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs. BMC Genom Data 2022; 23:26. [PMID: 35395709 PMCID: PMC8994340 DOI: 10.1186/s12863-022-01038-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/13/2022] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND Amphioxus is a model organism for vertebrate evolutionary research. The significant contrast between morphological phenotypic similarity and high-level genetic polymorphism among amphioxus populations has aroused scientists' attention. Here we resequenced 21 amphioxus genomes to over 100X depth and mapped them to a haploid reference. RESULTS More than 11.5 million common SNPs were detected in the amphioxus population, which mainly affect genes enriched in ion transport, signal transduction and cell adhesion, while protein structure analysis via AlphaFold2 revealed that these SNPs fail to bring effective structural variants. CONCLUSIONS Our work provides explanation for "amphioxus polymorphism paradox" in a micro view, and generates an enhanced genomic dataset for amphioxus research.
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Affiliation(s)
- Yunchi Zhu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu, China
| | - Na Lu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu, China
| | - J-Y Chen
- Nanjing Institute of Paleontology and Geology, Nanjing, China
| | - Chunpeng He
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu, China.
| | - Zhen Huang
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China.
- Key Laboratory of Special Marine Bio-Resources Sustainable Utilization of Fujian Province, Fuzhou, Fujian, China.
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu, China.
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19
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Valencia JE, Feuda R, Mellott DO, Burke RD, Peter IS. Ciliary photoreceptors in sea urchin larvae indicate pan-deuterostome cell type conservation. BMC Biol 2021; 19:257. [PMID: 34863182 PMCID: PMC8642985 DOI: 10.1186/s12915-021-01194-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 11/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The evolutionary history of cell types provides insights into how morphological and functional complexity arose during animal evolution. Photoreceptor cell types are particularly broadly distributed throughout Bilateria; however, their evolutionary relationship is so far unresolved. Previous studies indicate that ciliary photoreceptors are homologous at least within chordates, and here, we present evidence that a related form of this cell type is also present in echinoderm larvae. RESULTS Larvae of the purple sea urchin Strongylocentrotus purpuratus have photoreceptors that are positioned bilaterally in the oral/anterior apical neurogenic ectoderm. Here, we show that these photoreceptors express the transcription factor Rx, which is commonly expressed in ciliary photoreceptors, together with an atypical opsin of the GO family, opsin3.2, which localizes in particular to the cilia on the cell surface of photoreceptors. We show that these ciliary photoreceptors express the neuronal marker synaptotagmin and are located in proximity to pigment cells. Furthermore, we systematically identified additional transcription factors expressed in these larval photoreceptors and found that a majority are orthologous to transcription factors expressed in vertebrate ciliary photoreceptors, including Otx, Six3, Tbx2/3, and Rx. Based on the developmental expression of rx, these photoreceptors derive from the anterior apical neurogenic ectoderm. However, genes typically involved in eye development in bilateria, including pax6, six1/2, eya, and dac, are not expressed in sea urchin larval photoreceptors but are instead co-expressed in the hydropore canal. CONCLUSIONS Based on transcription factor expression, location, and developmental origin, we conclude that the sea urchin larval photoreceptors constitute a cell type that is likely homologous to the ciliary photoreceptors present in chordates.
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Affiliation(s)
- Jonathan E Valencia
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Roberto Feuda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.,Present address: Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Dan O Mellott
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Robert D Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.
| | - Isabelle S Peter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
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20
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Zou J, Wu X, Shi C, Zhong Y, Zhang L, Yan Q, Su L, Li G. A Potential Method for Rapid Screening of Amphioxus Founder Harboring Germline Mutation and Transgene. Front Cell Dev Biol 2021; 9:702290. [PMID: 34458263 PMCID: PMC8387717 DOI: 10.3389/fcell.2021.702290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/22/2021] [Indexed: 11/13/2022] Open
Abstract
Amphioxus is a promising model organism for understanding the origin and evolution of vertebrates due to its basal phylogenetic position among chordates. We here compared the mutation efficacy and mutation type of tail tips and gametes of amphioxus founders injected with Cas9 protein and six different sgRNAs targeting five distinct genes, and revealed a strong correlation for mutation efficacy and a mild correlation for mutation type among the two tissues. In addition, we also observed a positive relationship between gene insertions observed in tail tips and gametes of amphioxus founders injected with Tol2 transposase and two different transgenic constructs. Finally, we showed that amphioxus larvae which had their tail tips cut at the 3-4 gill-slit stage were able to recover within 6 days and developed a normal number of gonads at the adult stage, and that F0 larvae carry similar mutation efficacy and type in the posterior end to that in the tail tips after their metamorphosis. Together, these findings suggest a great potential for obtaining valid amphioxus founders with desired mutations and transgenes at as early as the early larval stage, which will certainly speed up the generation of amphioxus mutants and transgenes and make it more cost- and labor-effective.
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Affiliation(s)
- Jiaqi Zou
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiaotong Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Chenggang Shi
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yanhong Zhong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Lei Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Qiuning Yan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Liuru Su
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Guang Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
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21
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Li J, Li Y, Fan Z, Chen S, Yan X, Yue Z, Huang G, Liu S, Zhang H, Chen S, Dong M, Xu A, Huang S. Two Amphioxus ApeC-Containing Proteins Bind to Microbes and Inhibit the TRAF6 Pathway. Front Immunol 2021; 12:715245. [PMID: 34394119 PMCID: PMC8361754 DOI: 10.3389/fimmu.2021.715245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
The apextrin C-terminal (ApeC) domain is a class of newly discovered protein domains with an origin dating back to prokaryotes. ApeC-containing proteins (ACPs) have been found in various marine and aquatic invertebrates, but their functions and the underlying mechanisms are largely unknown. Early studies suggested that amphioxus ACP1 and ACP2 bind to bacterial cell walls and have a role in immunity. Here we identified another two amphioxus ACPs (ACP3 and ACP5), which belong to the same phylogenetic clade with ACP1/2, but show distinct expression patterns and sequence divergence (40-50% sequence identities). Both ACP3 and ACP5 were mainly expressed in the intestine and hepatic cecum, and could be up-regulated after bacterial challenge. Both prokaryotic-expressed recombinant ACP3 and ACP5 could bind with several species of bacteria and yeasts, showing agglutinating activity but no microbicidal activity. ELISA assays suggested that their ApeC domains could interact with peptidoglycan (PGN), but not with lipoteichoic acid (LTA), lipopolysaccharides (LPS) and zymosan A. Furthermore, they can only bind to Lys-type PGN from Staphylococcus aureus, but not to DAP-type PGN from Bacillus subtilis and not to moieties of PGN such as MDPs, NAMs and NAGs. This recognition spectrum is different from that of ACP1/2. We also found that when expressed in mammalian cells, ACP3 could interact with TRAF6 via a conserved non-ApeC region, which inhibited the ubiquitination of TRAF6 and hence suppressed downstream NF-κB activation. This work helped define a novel subfamily of ACPs, which have conserved structures, and have related yet diversified molecular functions. Its members have dual roles, with ApeC as a lectin and a conserved unknown region as a signal transduction regulator. These findings expand our understanding of the ACP functions and may guide future research on the role of ACPs in different animal clades.
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Affiliation(s)
- Jin Li
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yuhui Li
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhaoyu Fan
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shenghui Chen
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xinyu Yan
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zirui Yue
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Guangrui Huang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Shumin Liu
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hao Zhang
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shangwu Chen
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Meiling Dong
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Anlong Xu
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Shengfeng Huang
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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22
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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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23
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Pappalardo AM, Ferrito V, Biscotti MA, Canapa A, Capriglione T. Transposable Elements and Stress in Vertebrates: An Overview. Int J Mol Sci 2021; 22:1970. [PMID: 33671215 PMCID: PMC7922186 DOI: 10.3390/ijms22041970] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/13/2021] [Accepted: 02/14/2021] [Indexed: 12/17/2022] Open
Abstract
Since their identification as genomic regulatory elements, Transposable Elements (TEs) were considered, at first, molecular parasites and later as an important source of genetic diversity and regulatory innovations. In vertebrates in particular, TEs have been recognized as playing an important role in major evolutionary transitions and biodiversity. Moreover, in the last decade, a significant number of papers has been published highlighting a correlation between TE activity and exposition to environmental stresses and dietary factors. In this review we present an overview of the impact of TEs in vertebrate genomes, report the silencing mechanisms adopted by host genomes to regulate TE activity, and finally we explore the effects of environmental and dietary factor exposures on TE activity in mammals, which is the most studied group among vertebrates. The studies here reported evidence that several factors can induce changes in the epigenetic status of TEs and silencing mechanisms leading to their activation with consequent effects on the host genome. The study of TE can represent a future challenge for research for developing effective markers able to detect precocious epigenetic changes and prevent human diseases.
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Affiliation(s)
- Anna Maria Pappalardo
- Department of Biological, Geological and Environmental Sciences-Section of Animal Biology "M. La Greca", University of Catania, Via Androne 81, 95124 Catania, Italy
| | - Venera Ferrito
- Department of Biological, Geological and Environmental Sciences-Section of Animal Biology "M. La Greca", University of Catania, Via Androne 81, 95124 Catania, Italy
| | - Maria Assunta Biscotti
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Adriana Canapa
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Teresa Capriglione
- Department of Biology, University of Naples "Federico II", Via Cinthia 21-Ed7, 80126 Naples, Italy
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24
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Conservative route to genome compaction in a miniature annelid. Nat Ecol Evol 2020; 5:231-242. [PMID: 33199869 PMCID: PMC7854359 DOI: 10.1038/s41559-020-01327-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 09/15/2020] [Indexed: 12/14/2022]
Abstract
The causes and consequences of genome reduction in animals are unclear because our understanding of this process mostly relies on lineages with often exceptionally high rates of evolution. Here, we decode the compact 73.8-megabase genome of Dimorphilus gyrociliatus, a meiobenthic segmented worm. The D. gyrociliatus genome retains traits classically associated with larger and slower-evolving genomes, such as an ordered, intact Hox cluster, a generally conserved developmental toolkit and traces of ancestral bilaterian linkage. Unlike some other animals with small genomes, the analysis of the D. gyrociliatus epigenome revealed canonical features of genome regulation, excluding the presence of operons and trans-splicing. Instead, the gene-dense D. gyrociliatus genome presents a divergent Myc pathway, a key physiological regulator of growth, proliferation and genome stability in animals. Altogether, our results uncover a conservative route to genome compaction in annelids, reminiscent of that observed in the vertebrate Takifugu rubripes. This study reports the genome of the miniature segmented annelid Dimorphilus gyrociliatus and reveals no drastic changes in genome architecture and regulation, unlike other cases of genome miniaturization.
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25
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Blommaert J. Genome size evolution: towards new model systems for old questions. Proc Biol Sci 2020; 287:20201441. [PMID: 32842932 PMCID: PMC7482279 DOI: 10.1098/rspb.2020.1441] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022] Open
Abstract
Genome size (GS) variation is a fundamental biological characteristic; however, its evolutionary causes and consequences are the topic of ongoing debate. Whether GS is a neutral trait or one subject to selective pressures, and how strong these selective pressures are, may remain open questions. Fundamentally, the genomic sequences responsible for this variation directly impact the potential evolutionary outcomes and, equally, are the targets of different evolutionary pressures. For example, duplications and deletions of genic regions (large or small) can have immediate and drastic phenotypic effects, while an expansion or contraction of non-coding DNA is less likely to cause catastrophic phenotypic effects. However, in the long term, the accumulation or deletion of ncDNA is likely to have larger effects. Modern sequencing technologies are allowing for the dissection of these proximate causes, but a combination of these new technologies with more traditional evolutionary experiments and approaches could revolutionize this debate and potentially resolve many of these arguments. Here, I discuss an ambitious way forward for GS research, putting it in context of historical debates, theories and sometimes contradictory evidence, and highlighting the promise of combining new sequencing technologies and analytical developments with more traditional experimental evolution approaches.
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Affiliation(s)
- Julie Blommaert
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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26
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Pergner J, Vavrova A, Kozmikova I, Kozmik Z. Molecular Fingerprint of Amphioxus Frontal Eye Illuminates the Evolution of Homologous Cell Types in the Chordate Retina. Front Cell Dev Biol 2020; 8:705. [PMID: 32850825 PMCID: PMC7417673 DOI: 10.3389/fcell.2020.00705] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 07/10/2020] [Indexed: 12/15/2022] Open
Abstract
The evolution of the vertebrate eye remains so far unresolved. Amphioxus frontal eye pigment cells and photoreceptors were proposed to be homologous to vertebrate photoreceptors and retinal pigmented epithelium, based on ultrastructural morphology and gene expression analysis in B. floridae. Here, we present comparative molecular data using two additional amphioxus species, a closely related B. lanceolatum, and the most divergent A. lucayanum. Taking advantage of a unique set of specific antibodies we characterized photoreceptors and putative interneurons of the frontal eye and investigated its neuronal circuitry. Our results corroborate generally conserved molecular fingerprint among cephalochordate species. Furthermore, we performed pharmacological perturbations and found that the Notch signaling pathway, a key regulator of retina development in vertebrates, is required for correct ratios among frontal eye cell types. In summary, our study provides a valuable insight into cell-type relationships in chordate visual organs and strengthens the previously proposed homology between amphioxus frontal eye and vertebrate eyes.
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Affiliation(s)
- Jiri Pergner
- Department of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Anna Vavrova
- Department of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Iryna Kozmikova
- Department of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Zbynek Kozmik
- Department of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
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27
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Bi C, Lu N, Huang Z, Chen J, He C, Lu Z. Whole-genome resequencing reveals the pleistocene temporal dynamics of Branchiostoma belcheri and Branchiostoma floridae populations. Ecol Evol 2020; 10:8210-8224. [PMID: 32788973 PMCID: PMC7417228 DOI: 10.1002/ece3.6527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 12/30/2022] Open
Abstract
Global climatic fluctuations governed the ancestral demographic histories of species and contributed to place the current population status into a more extensive ecological and evolutionary context. Genetic variations will leave unambiguous signatures in the patterns of intraspecific genetic variation in extant species since the genome of each individual is an imperfect mosaic of the ancestral genomes. Here, we report the genome sequences of 20 Branchiostoma individuals by whole-genome resequencing strategy. We detected over 140 million genomic variations for each Branchiostoma individual. In particular, we applied the pairwise sequentially Markovian coalescent (PSMC) method to estimate the trajectories of changes in the effective population size (N e) of Branchiostoma population during the Pleistocene. We evaluated the threshold of sequencing depth for proper inference of demographic histories using PSMC was ≥25×. The PSMC results highlight the role of historical global climatic fluctuations in the long-term population dynamics of Branchiostoma. The inferred ancestral N e of the Branchiostoma belcheri populations from Zhanjiang and Xiamen (China) seawaters was different in amplitude before the first (mutation rate = 3 × 10-9) or third glaciation (mutation rate = 9 × 10-9) of the Pleistocene, indicating that the two populations most probably started to evolve in isolation in their respective seas after the first or third glaciation of the Pleistocene. A pronounced population bottleneck coinciding with the last glacial maximum was observed in all Branchiostoma individuals, followed by a population expansion occurred during the late Pleistocene. Species that have experienced long-term declines may be especially vulnerable to recent anthropogenic activities. Recently, the industrial pollution and the exploitation of sea sand have destroyed the harmonious living environment of amphioxus species. In the future, we need to protect the habitat of Branchiostoma and make full use of these detected genetic variations to facilitate the functional study of Branchiostoma for adaptation to local environments.
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Affiliation(s)
- Changwei Bi
- State Key Laboratory of BioelectronicsSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjingChina
| | - Na Lu
- State Key Laboratory of BioelectronicsSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjingChina
| | - Zhen Huang
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic AdministrationCollege of Life SciencesFujian Normal UniversityFuzhouChina
- Key Laboratory of Special Marine Bio‐resources Sustainable Utilization of Fujian ProvinceFuzhouChina
| | - Junyuan Chen
- Nanjing Institute of Paleontology and GeologyChinese Academy of SciencesNanjingChina
| | - Chunpeng He
- State Key Laboratory of BioelectronicsSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjingChina
| | - Zuhong Lu
- State Key Laboratory of BioelectronicsSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjingChina
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28
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Yasuoka Y. Enhancer evolution in chordates: Lessons from functional analyses of cephalochordate cis‐regulatory modules. Dev Growth Differ 2020; 62:279-300. [DOI: 10.1111/dgd.12684] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Yuuri Yasuoka
- Laboratory for Comprehensive Genomic Analysis RIKEN Center for Integrative Medical Sciences Tsurumi‐ku Japan
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29
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Simakov O, Marlétaz F, Yue JX, O'Connell B, Jenkins J, Brandt A, Calef R, Tung CH, Huang TK, Schmutz J, Satoh N, Yu JK, Putnam NH, Green RE, Rokhsar DS. Deeply conserved synteny resolves early events in vertebrate evolution. Nat Ecol Evol 2020; 4:820-830. [PMID: 32313176 PMCID: PMC7269912 DOI: 10.1038/s41559-020-1156-z] [Citation(s) in RCA: 185] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/19/2020] [Indexed: 01/24/2023]
Abstract
Although it is widely believed that early vertebrate evolution was shaped by ancient whole-genome duplications, the number, timing and mechanism of these events remain elusive. Here, we infer the history of vertebrates through genomic comparisons with a new chromosome-scale sequence of the invertebrate chordate amphioxus. We show how the karyotypes of amphioxus and diverse vertebrates are derived from 17 ancestral chordate linkage groups (and 19 ancestral bilaterian groups) by fusion, rearrangement and duplication. We resolve two distinct ancient duplications based on patterns of chromosomal conserved synteny. All extant vertebrates share the first duplication, which occurred in the mid/late Cambrian by autotetraploidization (that is, direct genome doubling). In contrast, the second duplication is found only in jawed vertebrates and occurred in the mid-late Ordovician by allotetraploidization (that is, genome duplication following interspecific hybridization) from two now-extinct progenitors. This complex genomic history parallels the diversification of vertebrate lineages in the fossil record.
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Affiliation(s)
- Oleg Simakov
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria.
| | - Ferdinand Marlétaz
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Jia-Xing Yue
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Brendan O'Connell
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Alexander Brandt
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Che-Huang Tung
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Tzu-Kai Huang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Nori Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | | | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Daniel S Rokhsar
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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30
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Martin EC, Vicari C, Tsakou-Ngouafo L, Pontarotti P, Petrescu AJ, Schatz DG. Identification of RAG-like transposons in protostomes suggests their ancient bilaterian origin. Mob DNA 2020; 11:17. [PMID: 32399063 PMCID: PMC7204232 DOI: 10.1186/s13100-020-00214-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/14/2020] [Indexed: 12/27/2022] Open
Abstract
Background V(D) J recombination is essential for adaptive immunity in jawed vertebrates and is initiated by the RAG1-RAG2 endonuclease. The RAG1 and RAG2 genes are thought to have evolved from a RAGL (RAG-like) transposon containing convergently-oriented RAG1-like (RAG1L) and RAG2-like (RAG2L) genes. Elements resembling this presumptive evolutionary precursor have thus far only been detected convincingly in deuterostomes, leading to the model that the RAGL transposon first appeared in an early deuterostome. Results We have identified numerous RAGL transposons in the genomes of protostomes, including oysters and mussels (phylum Mollusca) and a ribbon worm (phylum Nemertea), and in the genomes of several cnidarians. Phylogenetic analyses are consistent with vertical evolution of RAGL transposons within the Bilateria clade and with its presence in the bilaterian ancestor. Many of the RAGL transposons identified in protostomes are intact elements containing convergently oriented RAG1L and RAG2L genes flanked by terminal inverted repeats (TIRs) and target site duplications with striking similarities with the corresponding elements in deuterostomes. In addition, protostome genomes contain numerous intact RAG1L-RAG2L adjacent gene pairs that lack detectable flanking TIRs. Domains and critical active site and structural amino acids needed for endonuclease and transposase activity are present and conserved in many of the predicted RAG1L and RAG2L proteins encoded in protostome genomes. Conclusions Active RAGL transposons were present in multiple protostome lineages and many were likely transmitted vertically during protostome evolution. It appears that RAGL transposons were broadly active during bilaterian evolution, undergoing multiple duplication and loss/fossilization events, with the RAGL genes that persist in present day protostomes perhaps constituting both active RAGL transposons and domesticated RAGL genes. Our findings raise the possibility that the RAGL transposon arose earlier in evolution than previously thought, either in an early bilaterian or prior to the divergence of bilaterians and non-bilaterians, and alter our understanding of the evolutionary history of this important group of transposons.
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Affiliation(s)
- Eliza C Martin
- 1Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031 Bucharest, Romania
| | - Célia Vicari
- 2Evolutionary biology team, Aix Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Louis Tsakou-Ngouafo
- 2Evolutionary biology team, Aix Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Pierre Pontarotti
- 2Evolutionary biology team, Aix Marseille Université IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France.,SNC5039 CNRS, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Andrei J Petrescu
- 1Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031 Bucharest, Romania
| | - David G Schatz
- 4Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011 USA
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31
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Trancoso I, Morimoto R, Boehm T. Co-evolution of mutagenic genome editors and vertebrate adaptive immunity. Curr Opin Immunol 2020; 65:32-41. [PMID: 32353821 PMCID: PMC7768089 DOI: 10.1016/j.coi.2020.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/18/2020] [Accepted: 03/02/2020] [Indexed: 12/28/2022]
Abstract
The adaptive immune systems of all vertebrates rely on self-DNA mutating enzymes to assemble their antigen receptors in lymphocytes of their two principal lineages. In jawed vertebrates, the RAG1/2 recombinase directs V(D)J recombination of B cell and T cell receptor genes, whereas the activation-induced cytidine deaminase AID engages in their secondary modification. The recombination activating genes (RAG) 1 and 2 evolved from an ancient transposon-encoded genome modifier into a self-DNA mutator serving adaptive immunity; this was possible as a result of domestication, involving several changes in RAG1 and RAG2 proteins suppressing transposition and instead facilitating-coupled cleavage and recombination. By contrast, recent evidence supports the notion that the antigen receptors of T-like and B-like cells of jawless vertebrates, designated variable lymphocyte receptors (VLRs), are somatically assembled through a process akin to gene conversion that is believed to be dependent on the activities of distant relatives of AID, the cytidine deaminases CDA1 and CDA2, respectively. It appears, therefore, that the precursors of AID and CDAs underwent a domestication process that changed their target range from foreign nucleic acids to self-DNA; this multi-step evolutionary process ensured that the threat to host genome integrity was minimized. Here, we review recent findings illuminating the evolutionary steps associated with the domestication of the two groups of genome editors, RAG1/2 and cytidine deaminases, indicating how they became the driving forces underlying the emergence of vertebrate adaptive immune systems.
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Affiliation(s)
- Inês Trancoso
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Ryo Morimoto
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
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32
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Fu X, Wang R, Li M, Yan X, Huang H, Li J, Chen S, Yue Z, Chen S, Li Y, Dong M, Xu A, Huang S. Chordate PIAS proteins act as conserved repressors of the TRAF6 self-polyubiquitination. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 104:103554. [PMID: 31758961 DOI: 10.1016/j.dci.2019.103554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 06/10/2023]
Abstract
In mammals, PIAS proteins are important SUMO E3 ligases and act as versatile regulators of over sixty different proteins, including components from the NF-κB pathways. But the PIAS functions are not well-understood due to complicated molecular mechanisms and multiple gene paralogs with overlapping roles, which is especially true in lower vertebrates where dedicated studies are scarce. As a basal chordate with a single PIAS gene, amphioxus is a convenient model to study PIAS from the evolutionary perspective. TRAF6 is a critical adaptor of the NF-κB pathways but it is not known whether TRAF6 is regulated by PIAS. Here we discover that in mammalian cells, amphioxus PIAS inhibited NF-κB activation by co-localizing and binding with TRAF6. The interaction relied on the N-terminal SAP and PINIT domains of PIAS. TRAF6 is an E3 ubiquitin ligase, which initiates downstream NF-κB signaling by promoting its self-ubiquitination. Both amphioxus SUMO1 and Ubc9 (SUMO E2 ligase) could suppress TRAF6 self-ubiquitination and NF-κB activation, suggesting that the SUMOylation activity competed away the ubiquitination activity of TRAF6. However, we show that the wild-type PIAS and the mutant PIAS without SUMO E3 ligase activity both could inhibit TRAF6-mediated NF-κB activation by reducing TRAF6 self-ubiquitination. This implies that SUMO ligase activity is not the only mechanism for PIAS to negatively regulate TRAF6. Finally, we tested the interactions between human PIAS1-4 and TRAF6. It reveals that human PIAS1, 3 and 4, but not 2, were able to repress NF-κB activation by reducing TRAF6 self-ubiquitination. Taken together, our study discovers a conserved regulatory interaction between chordate PIAS and TRAF6. It therefore sheds light on the complicated role of PIAS in immune regulation, and may help to understand the PIAS functions in other lower chordate taxa, such as jawless and jawed fishes.
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Affiliation(s)
- Xianan Fu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Ruihua Wang
- Center for Regenerative and Translational Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510632, People's Republic of China
| | - Mingshi Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Xinyu Yan
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Huiqing Huang
- Guangdong Food and Drug Vocational College, Guangzhou, People's Republic of China
| | - Jin Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Shenghui Chen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Zirui Yue
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Shangwu Chen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Yingqiu Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Meiling Dong
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Anlong Xu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China; Beijing University of Chinese Medicine, Dong San Huang Road, Chao-yang District, Beijing, 100029, People's Republic of China.
| | - Shengfeng Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), China.
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Capela R, Garric J, Castro LFC, Santos MM. Embryo bioassays with aquatic animals for toxicity testing and hazard assessment of emerging pollutants: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:135740. [PMID: 31838430 DOI: 10.1016/j.scitotenv.2019.135740] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/22/2019] [Accepted: 11/23/2019] [Indexed: 06/10/2023]
Abstract
This review article gathers the available information on the use of embryo-tests as high-throughput tools for toxicity screening, hazard assessment and prioritization of new and existing chemical compounds. The approach is contextualized considering the new legal trends for animal experimentation, fostering the 3R policy, with reduction of experimental animals, addressing the potential of embryo-tests as high-throughput toxicity screening and prioritizing tools. Further, the current test guidelines, such as the ones provided by OECD and EPA, focus mainly in a limited number of animal lineages, particularly vertebrates and arthropods. To extrapolate hazard assessment to the ecosystem scale, a larger diversity of taxa should be tested. The use of new experimental animal models in toxicity testing, from a representative set of taxa, was thoroughly revised and discussed in this review. Here, we critically review current tools and the main advantages and drawbacks of different animal models and set researcher priorities.
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Affiliation(s)
- Ricardo Capela
- CIMAR/CIIMAR - Interdisciplinary Centre for Marine and Environmental Research, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; FCUP - Faculty of Sciences of the University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; IRSTEA - National Research Institute of Science and Technology for Environment and Agriculture - Centre de Lyon-Villeurbanne, 5 rue de la Doua, CS20244, 69625 Villeurbanne Cedex, Lyon-Villeurbanne, France
| | - Jeanne Garric
- IRSTEA - National Research Institute of Science and Technology for Environment and Agriculture - Centre de Lyon-Villeurbanne, 5 rue de la Doua, CS20244, 69625 Villeurbanne Cedex, Lyon-Villeurbanne, France.
| | - Luís Filipe Costa Castro
- CIMAR/CIIMAR - Interdisciplinary Centre for Marine and Environmental Research, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; FCUP - Faculty of Sciences of the University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal.
| | - Miguel Machado Santos
- CIMAR/CIIMAR - Interdisciplinary Centre for Marine and Environmental Research, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; FCUP - Faculty of Sciences of the University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal.
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Whole-Genome Resequencing of Twenty Branchiostoma belcheri Individuals Provides a Brand-New Variant Dataset for Branchiostoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3697342. [PMID: 32090082 PMCID: PMC7008246 DOI: 10.1155/2020/3697342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/26/2019] [Accepted: 08/02/2019] [Indexed: 01/01/2023]
Abstract
As the extant representatives of the basal chordate lineage, amphioxi (including the genera Branchiostoma, Asymmetron and Epigonichthys) play important roles in tracing the state of chordate ancestry. Previous studies have reported that members of the Branchiostoma species have similar morphological phenotypic characteristics, but in contrast, there are high levels of genetic polymorphisms in the populations. Here, we resequenced 20 Branchiostomabelcheri genomes to an average depth of approximately 12.5X using the Illumina HiSeq 2000 platform. In this study, over 52 million variations (~12% of the total genome) were detected in the B. belcheri population, and an average of 12.8 million variations (~3% of the total genome) were detected in each individual, confirming that Branchiostoma is one of the most genetically diverse species sequenced to date. Demographic inference analysis highlighted the role of historical global temperature in the long-term population dynamics of Branchiostoma, and revealed a population expansion at the Greenlandian stage of the current geological epoch. We detected 594 Single nucleotide polymorphism and 148 Indels in the Branchiostoma mitochondrial genome, and further analyzed their genetic mutations. A recent study found that the epithelial cells of the digestive tract in Branchiostoma can directly phagocytize food particles and convert them into absorbable nontoxic nutrients using powerful digestive and immune gene groups. In this study, we predicted all potential mutations in intracellular digestion-associated genes. The results showed that most “probably damaging” mutations were related to rare variants (MAF<0.05) involved in strengthening or weakening the intracellular digestive capacity of Branchiostoma. Due to the extremely high number of polymorphisms in the Branchiostoma genome, our analysis with a depth of approximately 12.5X can only be considered a preliminary analysis. However, the novel variant dataset provided here is a valuable resource for further investigation of phagocytic intracellular digestion in Branchiostoma and determination of the phenotypic and genotypic features of Branchiostoma.
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You L, Chi J, Huang S, Yu T, Huang G, Feng Y, Sang X, Gao X, Li T, Yue Z, Liu A, Chen S, Xu A. LanceletDB: an integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5491331. [PMID: 31106360 PMCID: PMC6526094 DOI: 10.1093/database/baz056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 03/19/2019] [Accepted: 04/08/2019] [Indexed: 12/24/2022]
Abstract
Lancelet (amphioxus) represents the most basally divergent extant chordate (cephalochordates) that diverged from the other two chordate lineages (urochordates and vertebrates) more than half a billion years ago. As it occupies a key position in evolution, it is considered as one of the best proxies for understanding the chordate ancestral state. Thus, the construction of a database with multiple lancelet genomes and gene annotation data, including protein domains, is urgently needed to investigate the loss and gain of domains in orthologues among species, especially ancient domain types (non-vertebrate-specific domains) and novel domain combination, which is helpful for providing new insight into the chordate ancestral state and vertebrate evolution. Here, we present an integrated genome database for lancelet, LanceletDB, which provides reference haploid genome sequence and annotation data for lancelet (Branchiostoma belcheri), including gene models and annotation, protein domain types, gene expression pattern in embryogenesis, different expression sequence tag sets and alternative polyadenylation (APA) sites profiled by the sequencing APA sites method. Especially, LanceletDB allows comparison of domain types and combination in orthologues among type species so as to decode the ancient domain types and novel domain combination during evolution. We also integrated the released diploid lancelet genome annotation data (Branchiostoma floridae) to expand LanceletDB and extend its usefulness. These data are available through the search and analysis page, basic local alignment search tool page and genome browser to provide an integrated display.
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Affiliation(s)
- Leiming You
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China.,State Key Laboratory of Bio-control, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, China
| | - Jiaqi Chi
- Department of Oncology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Shengfeng Huang
- State Key Laboratory of Bio-control, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, China
| | - Ting Yu
- State Key Laboratory of Bio-control, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, China
| | - Guangrui Huang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Yuchao Feng
- State Key Laboratory of Bio-control, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, China
| | - Xiaopu Sang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Xinhui Gao
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Ting'an Li
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Zirui Yue
- State Key Laboratory of Bio-control, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, China
| | - Aijie Liu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Shangwu Chen
- State Key Laboratory of Bio-control, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, China
| | - Anlong Xu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China.,State Key Laboratory of Bio-control, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, China
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Yan X, Chen S, Huang H, Peng T, Lan M, Yang X, Dong M, Chen S, Xu A, Huang S. Functional Variation of IL-1R-Associated Kinases in the Conserved MyD88-TRAF6 Pathway during Evolution. THE JOURNAL OF IMMUNOLOGY 2020; 204:832-843. [PMID: 31915260 DOI: 10.4049/jimmunol.1900222] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 12/12/2019] [Indexed: 12/14/2022]
Abstract
IL-1R-associated kinases (IRAK) are important regulators in the TLR/IL-1R pathways, but their function appears inconsistent between Drosophila, bony fishes, and vertebrates. This causes a difficulty to understand the IRAK functions. As a step to reveal the evolution of IRAKs, in this study, we performed comparative and functional analysis of IRAKs by exploiting the amphioxus, a pivotal taxon connecting invertebrates and vertebrates. Sequence and phylogenetic analysis indicated three major IRAK lineages: IRAK1/2/3 is a vertebrate-specific lineage, IRAK4 is an ancient lineage conserved between invertebrate and vertebrates, and Pelle is another ancient lineage that is preserved in protostomes and invertebrate deuterostomes but lost in vertebrate deuterostomes. Pelle is closer neither to IRAK4 nor to IRAK1/2/3, hence suggesting no clear functional analogs to IRAK1/2/3 in nonvertebrates. Functional analysis showed that both amphioxus IRAK4 and Pelle could suppress NF-κB activation induced by MyD88 and TRAF6, which are unlike mammalian and Drosophila IRAKs, but, surprisingly, similar to bony fish IRAK4. Also unlike Drosophila IRAKs, no interaction was detected between amphioxus IRAK4 and Pelle, although both of them were shown capable of binding MyD88. These findings, together with previous reports, show that unlike other signal transducers in the TLR/IL-1R pathways, such as MyD88 and TRAF6, the functions of IRAKs are highly variable during evolution and very specialized in different major animal taxa. Indeed, we suggest that the functional variability of IRAKs might confer plasticity to the signal transduction of the TLR/IL-1R pathways, which in return helps the species to evolve against the pathogens.
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Affiliation(s)
- Xinyu Yan
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, China
| | - Shenghui Chen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, China
| | - Huiqing Huang
- Guangdong Food and Drug Vocational College, 510520 Guangzhou, China
| | - Ting Peng
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, China
| | - Mengjiao Lan
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, China
| | - Xia Yang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, China
| | - Meiling Dong
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, China
| | - Shangwu Chen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, China
| | - Anlong Xu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, China; .,School of Life Science, Beijing University of Chinese Medicine, 100029 Beijing, China; and
| | - Shengfeng Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, China; .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266003 Qingdao, China
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Shi Y, Fan Z, Li G, Zhang L, Yue Z, Yan X, Xu A, Huang S. The family of amphioxus chitin synthases offers insight into the evolution of chitin formation in chordates. Mol Phylogenet Evol 2019; 143:106691. [PMID: 31759175 DOI: 10.1016/j.ympev.2019.106691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/19/2019] [Accepted: 11/18/2019] [Indexed: 10/25/2022]
Abstract
Chitin is a very important and widely-used biopolymer in fungi and lower metazoans, but mysteriously disappears in mammals. Recent studies reveal that at least lower vertebrates have chitin synthases (CS) and use them to synthesize endogenous chitin. Amphioxus, a basal chordate, therefore becomes critical to understand the evolution of CS, as it occupies the transitional position from invertebrates to vertebrates, and is considered as a good proxy to the chordate ancestor. Here, by exploiting multiple genome assemblies, high-depth RNA-seq data and synteny relations, we identify 11-12 CS genes for each amphioxus species. It represents the largest CS gene pool ever found in eukaryotes so far. As comparison, most metazoans have one or two CSs. Amphioxus is the only chordate that has both the very ancient type-I CS family and the more broadly distributed type-II CS family. Specifically, amphioxus has only one type-II CS but 10-11 type-I CSs, which means that amphioxus is the only metazoan with a greatly expanded type-I CS family. Further analysis suggests that the chordate ancestor have at least one type-II CS and an expanded of type-I CS family. We hypothesize that: these ancient CSs are mostly retained in amphioxus; but the whole type-I CS family was lost in urochordates and vertebrates; the type-II CS was later duplicated into two lineages in vertebrates and followed by stochastic losses, till all type-II CSs were eventually lost in birds and mammals. Finally, our expression profiling and preliminary gene knockout analysis suggest that amphioxus CSs could have highly diverse but mildly overlapping functions in various tissues and organs. Taken together, these findings not only provide insights into the evolution of chordate CSs, lay a foundation for further functional study of the chordate CSs. After all, it is mysterious that our chordate ancestor needed so many isoenzymes for chitin formation.
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Affiliation(s)
- Yi Shi
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China; CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhaoyu Fan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Guang Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Lei Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Zirui Yue
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xinyu Yan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Anlong Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shengfeng Huang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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Zhang QL, Wang H, Zhu QH, Wang XX, Li YM, Chen JY, Morikawa H, Yang LF, Wang YJ. Genome-Wide Identification and Transcriptomic Analysis of MicroRNAs Across Various Amphioxus Organs Using Deep Sequencing. Front Genet 2019; 10:877. [PMID: 31616471 PMCID: PMC6775235 DOI: 10.3389/fgene.2019.00877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 08/21/2019] [Indexed: 01/28/2023] Open
Abstract
Amphioxus is the closest living invertebrate proxy of the vertebrate ancestor. Systematic gene identification and expression profile analysis of amphioxus organs are thus important for clarifying the molecular mechanisms of organ function formation and further understanding the evolutionary origin of organs and genes in vertebrates. The precise regulation of microRNAs (miRNAs) is crucial for the functional specification and differentiation of organs. In particular, those miRNAs that are expressed specifically in organs (OSMs) play key roles in organ identity, differentiation, and function. In this study, the genome-wide miRNA transcriptome was analyzed in eight organs of adult amphioxus Branchiostoma belcheri using deep sequencing. A total of 167 known miRNAs and 23 novel miRNAs (named novel_mir), including 139 conserved miRNAs, were discovered, and 79 of these were identified as OSMs. Additionally, analyses of the expression patterns of eight randomly selected known miRNAs demonstrated the accuracy of the miRNA deep sequencing that was used in this study. Furthermore, potentially OSM-regulated genes were predicted for each organ type. Functional enrichment of these predicted targets, as well as further functional analyses of known OSMs, was conducted. We found that the OSMs were potentially to be involved in organ-specific functions, such as epidermis development, gonad development, muscle cell development, proteolysis, lipid metabolism, and generation of neurons. Moreover, OSMs with non-organ-specific functions were detected and primarily include those related to innate immunity and response to stimuli. These findings provide insights into the regulatory roles of OSMs in various amphioxus organs.
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Affiliation(s)
- Qi-Lin Zhang
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Ocean College, Beibu Gulf University, Qinzhou, China.,Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Hong Wang
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Ocean College, Beibu Gulf University, Qinzhou, China
| | | | - Xiao-Xue Wang
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Ocean College, Beibu Gulf University, Qinzhou, China
| | - Yi-Min Li
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Ocean College, Beibu Gulf University, Qinzhou, China
| | - Jun-Yuan Chen
- Evo-devo Institute, School of Life Sciences, Nanjing University, Nanjing, China
| | - Hideaki Morikawa
- Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano, Japan
| | | | - Yu-Jun Wang
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Ocean College, Beibu Gulf University, Qinzhou, China
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Ruan J, Cao Y, Ling T, Li P, Wu S, Peng D, Wang Y, Jia X, Chen S, Xu A, Yuan S. DDX23, an Evolutionary Conserved dsRNA Sensor, Participates in Innate Antiviral Responses by Pairing With TRIF or MAVS. Front Immunol 2019; 10:2202. [PMID: 31620127 PMCID: PMC6759578 DOI: 10.3389/fimmu.2019.02202] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 08/30/2019] [Indexed: 12/24/2022] Open
Abstract
DExD/H-box helicases play essential roles in RNA metabolism, and emerging data suggests that they have additional functions in antiviral immunity across species. However, little is known about this evolutionarily conserved family in antiviral responses in lower species. Here, through isolation of poly(I:C)-binding proteins in amphioxus, an extant basal chordate, we found that DExD/H-box helicases DHX9, DHX15, and DDX23 are responsible for cytoplasmic dsRNA detection in amphioxus. Since the antiviral roles of DDX23 have not been characterized in mammals, we performed further poly(I:C) pull-down assays and found that human DDX23 binds to LMW poly(I:C) through its N-terminal region, suggesting that DDX23 is an evolutionarily conserved dsRNA sensor. Knockdown of human DDX23 enhanced the replication of VSV and reduced the activation of the NF-κB and IRF3. Moreover, when stimulated with poly(I:C) or VSV, human DDX23 translocated from the nucleus to the cytoplasm and formed complexes with TRIF or MAVS to initiate downstream signaling. Collectively, this comparative immunological study not only defined DDX23 as an emerging nuclear pattern recognition receptor (PRR) for the innate sensing of an RNA virus, but also extended the essential role of the DExD/H helicase family in viral RNA sensing from mammals to basal chordates.
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Affiliation(s)
- Jie Ruan
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yange Cao
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Tao Ling
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Peiyi Li
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shengpeng Wu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Dezhi Peng
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yao Wang
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xin Jia
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shangwu Chen
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Anlong Xu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou, China.,School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Shaochun Yuan
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Abstract
The BMP signaling pathway has been shown to be involved in different aspects of embryonic development across diverse metazoan phyla. Comparative studies on the roles of the BMP signaling pathway provide crucial insights into the evolution of the animal body plans. In this chapter, we present the general workflow on how to investigate the roles of BMP signaling pathway during amphioxus embryonic development. As amphioxus are basal invertebrate chordates, studies on the BMP signaling pathway in amphioxus could elucidate the functional evolution of BMP pathway in the chordate group. Here, we describe methods for animal husbandry, spawning induction, and manipulation of the BMP signaling pathway during embryonic development through drug inhibitors and recombinant proteins. We also introduce an efficient method of using mesh baskets to handle amphioxus embryos for fluorescence immunostaining and multicolor fluorescence in situ hybridization and to assay the effects of manipulating BMP signaling pathway during amphioxus embryogenesis.
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Nakayama S, Sekiguchi T, Ogasawara M. Molecular and evolutionary aspects of the protochordate digestive system. Cell Tissue Res 2019; 377:309-320. [PMID: 31049686 DOI: 10.1007/s00441-019-03035-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/12/2019] [Indexed: 02/03/2023]
Abstract
The digestive system is a functional unit consisting of an endodermal tubular structure (alimentary canal) and accessory organs that function in nutrition processing in most triploblastic animals. Various morphologies and apparatuses are formed depending on the phylogenetical relationship and food habits of the specific species. Nutrition processing and morphogenesis of the alimentary canal and accessory organs have both been investigated in vertebrates, mainly humans and mammals. When attempting to understand the evolutionary processes that led to the vertebrate digestive system, however, it is useful to examine other chordates, specifically protochordates, which share fundamental functional and morphogenetic molecules with vertebrates, which also possess non-duplicated genomes. In protochordates, basic anatomical and physiological studies have mainly described the characteristic traits of suspension feeders. Recent progress in genome sequencing has allowed researchers to comprehensively detail protochordate genes and has compared the genetic backgrounds among chordate nutrition processing and alimentary canal/accessory organ systems based on genomic information. Gene expression analyses have revealed spatiotemporal gene expression profiles in protochordate alimentary canals. Additionally, to investigate the basis of morphological diversity in the chordate alimentary canal and accessory organs, evolutionary developmental research has examined developmental transcription factors related to morphogenesis and anterior-posterior pattering of the alimentary canal and accessory organs. In this review, we summarize the current knowledge of molecules involved in nutrition processing and the development of the alimentary canal and accessory organs with innate immune and endocrine roles in protochordates and we explore the molecular basis for understanding the evolution of the chordate digestive system.
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Affiliation(s)
- Satoshi Nakayama
- The Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Toshio Sekiguchi
- The Noto Marine Laboratory, Division of Marine Environmental Studies, Institute of Nature and Environmental Technology, Kanazawa University, Hosu-gun, Ishikawa, 927-0553, Japan
| | - Michio Ogasawara
- The Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan.
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He C, Han T, Liao X, Zhou Y, Wang X, Guan R, Tian T, Li Y, Bi C, Lu N, He Z, Hu B, Zhou Q, Hu Y, Lu Z, Chen JY. Phagocytic intracellular digestion in amphioxus ( Branchiostoma). Proc Biol Sci 2019; 285:rspb.2018.0438. [PMID: 29875301 PMCID: PMC6015868 DOI: 10.1098/rspb.2018.0438] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 05/11/2018] [Indexed: 01/10/2023] Open
Abstract
The digestive methods employed by amphioxus (Branchiostoma)—both intracellular phagocytic digestion and extracellular digestion—have been discussed since 1937. Recent studies also show that epithelial cells lining the Branchiostoma digestive tract can express many immune genes. Here, in Branchiostoma belcheri, using a special tissue fixation method, we show that some epithelial cells, especially those lining the large diverticulum protruding from the gut tube, phagocytize food particles directly, and Branchiostoma can rely on this kind of phagocytic intracellular digestion to obtain energy throughout all stages of its life. Gene expression profiles suggest that diverticulum epithelial cells have functional features of both digestive cells and phagocytes. In starved Branchiostoma, these cells accumulate endogenous digestive and hydrolytic enzymes, whereas, when sated, they express many kinds of immune genes in response to stimulation by phagocytized food particles. We also found that the distal hindgut epithelium can phagocytize food particles, but not as many. These results illustrate phagocytic intercellular digestion in Branchiostoma, explain why Branchiostoma digestive tract epithelial cells express typical immune genes and suggest that the main physiological function of the Branchiostoma diverticulum is different from that of the vertebrate liver.
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Affiliation(s)
- Chunpeng He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Tingyu Han
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Xin Liao
- Nanjing Institute of Paleontology and Geology, Nanjing, People's Republic of China.,Guangxi Mangrove Research Center, Beihai, Guangxi, People's Republic of China
| | - Yuxin Zhou
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Xiuqiang Wang
- Beihai Marine Science and Economy Park, Beihai, Guangxi, People's Republic of China
| | - Rui Guan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Tian Tian
- Department of Neurobiology, Nanjing Medical University, Nanjing, People's Republic of China
| | - Yixin Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Changwei Bi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Na Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Ziyi He
- Electron Microscopy Research Center, School of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Bing Hu
- Electron Microscopy Research Center, School of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Qiang Zhou
- Department of Pathology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Yue Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
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Platanus-allee is a de novo haplotype assembler enabling a comprehensive access to divergent heterozygous regions. Nat Commun 2019; 10:1702. [PMID: 30979905 PMCID: PMC6461651 DOI: 10.1038/s41467-019-09575-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 03/19/2019] [Indexed: 12/14/2022] Open
Abstract
The ultimate goal for diploid genome determination is to completely decode homologous chromosomes independently, and several phasing programs from consensus sequences have been developed. These methods work well for lowly heterozygous genomes, but the manifold species have high heterozygosity. Additionally, there are highly divergent regions (HDRs), where the haplotype sequences differ considerably. Because HDRs are likely to direct various interesting biological phenomena, many genomic analysis targets fall within these regions. However, they cannot be accessed by existing phasing methods, and we have to adopt costly traditional methods. Here, we develop a de novo haplotype assembler, Platanus-allee ( http://platanus.bio.titech.ac.jp/platanus2 ), which initially constructs each haplotype sequence and then untangles the assembly graphs utilizing sequence links and synteny information. A comprehensive benchmark analysis reveals that Platanus-allee exhibits high recall and precision, particularly for HDRs. Using this approach, previously unknown HDRs are detected in the human genome, which may uncover novel aspects of genome variability.
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Zhang QL, Zhang GL, Xiong Y, Li HW, Guo J, Wang F, Deng XY, Chen JY, Wang YJ, Lin LB. Genome-wide gene expression analysis reveals novel insights into the response to nitrite stress in gills of Branchiostoma belcheri. CHEMOSPHERE 2019; 218:609-615. [PMID: 30502699 DOI: 10.1016/j.chemosphere.2018.11.156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 11/23/2018] [Accepted: 11/24/2018] [Indexed: 06/09/2023]
Abstract
Amphioxus has been widely used as a model for the comparative immunology of vertebrates. Studies have reported that gene expression changes in the amphioxus gill in response to biotic stress, such as microbial and their mimic challenge, but little is known about how gene expression is affected by abiotic stress in the marine environment, such as nitrite. A lack of information regarding gene expression response to abiotic stress hinders a comprehensive understanding of gill defense response in amphioxus. Here, RNA sequencing was used to carry out gene expression profiling analyses of Branchiostoma belcheri gills under nitrite stress. Six libraries were created for the control and treatment groups, including three biological replicates. In total, 2416 differently expressed genes (DEGs) were detected in response to nitrite stress, of which 1522 DEGs were up-regulated in the treatment group in comparison to the control, while the remaining 894 DEGs were down-regulated genes. Functional enrichment revealed that these DEGs are primarily involved in disease, innate immunity, xenobiotic biodegradation and metabolism, and biomolecular processes and apoptosis. We screened 11 key nitrite-responsive DEGs to detect their expression responses to nitrite stress at different time points, and validate the sequencing data using real time quantitative PCR. The results indicated that the expression of gene encoding CYP3A, POD, CASPR1, GST, MAO, DDH, and XDH/XO were induced, while those encoding MRC, GT, DNASE1L, and RIPK5 were reduced, to participate in the anti-nitrite response. This study provides a useful resource for research of molecular toxicology in amphioxus under environmental stress.
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Affiliation(s)
- Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500 China.
| | - Guan-Ling Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500 China
| | - Yan Xiong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500 China
| | - Hong-Wei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500 China
| | - Jun Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500 China
| | - Feng Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500 China
| | - Xian-Yu Deng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500 China
| | - Jun-Yuan Chen
- LPS, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing 210008 China; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, 210023 China
| | - Yu-Jun Wang
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Ocean College, Qinzhou University, Qinzhou 535011 China.
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500 China.
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Zhang QL, Ji XY, Li HW, Guo J, Wang F, Deng XY, Chen JY, Lin LB. Identification of circular RNAs and their altered expression under poly(I:C) challenge in key antiviral immune pathways in amphioxus. FISH & SHELLFISH IMMUNOLOGY 2019; 86:1053-1057. [PMID: 30590167 DOI: 10.1016/j.fsi.2018.12.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/11/2018] [Accepted: 12/24/2018] [Indexed: 06/09/2023]
Abstract
Amphioxus is a key model for studying comparative immunity of vertebrates. Circular RNA (circRNA), as RNAs with a circular structure, has received little attention until recently, where several studies have reported that circRNA expression changes are involved in the immune response in animals. However, circRNA and its immune role in amphioxus have not been previously studied. Here, circRNAs in Chinese amphioxus (Branchiostoma belcheri) were sequenced, and 1859 circRNAs were identified using two algorithms (find_circ and CIRI). The analysis of miRNA target sites on circRNAs showed that 332 circRNAs may function as miRNA sponges. Furthermore, we identified circRNAs that were conserved between B. belcheri and vertebrates, tracing the origin of these circRNAs within chordates. Additionally, in combination with several key antiviral immune (poly(I:C), pIC) pathways identified in our previous B. belcheri studies, nine circRNAs potentially involved in these pathways were identified using bioinformatic predictions. Among these nine circRNAs, eight were selected to examine their expression response in B. belcheri challenged by pIC in comparison to control using real-time quantitative PCR. The results showed that four circRNAs were induced as part of the antiviral response against pIC, while expression of two circRNAs was decreased, and the expression levels of the remaining two were not significantly altered after pIC challenge. This work is the first to identify circRNAs and reveal their antiviral role in amphioxus. Therefore, it opens a new window to explore the comparative immunology of circRNAs in chordates and the regulatory roles of circRNAs in antiviral immunity in amphioxus.
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Affiliation(s)
- Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Xin-Yu Ji
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Hong-Wei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Jun Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Feng Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Xian-Yu Deng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Jun-Yuan Chen
- LPS, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, 210008, China; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, 210023, China
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
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Junqueira Alves C, Yotoko K, Zou H, Friedel RH. Origin and evolution of plexins, semaphorins, and Met receptor tyrosine kinases. Sci Rep 2019; 9:1970. [PMID: 30760850 PMCID: PMC6374515 DOI: 10.1038/s41598-019-38512-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 12/28/2018] [Indexed: 12/20/2022] Open
Abstract
The transition from unicellular to multicellular organisms poses the question as to when genes that regulate cell-cell interactions emerged during evolution. The receptor and ligand pairing of plexins and semaphorins regulates cellular interactions in a wide range of developmental and physiological contexts. We surveyed here genomes of unicellular eukaryotes and of non-bilaterian and bilaterian Metazoa and performed phylogenetic analyses to gain insight into the evolution of plexin and semaphorin families. Remarkably, we detected plexins and semaphorins in unicellular choanoflagellates, indicating their evolutionary origin in a common ancestor of Choanoflagellida and Metazoa. The plexin domain structure is conserved throughout all clades; in contrast, semaphorins are structurally diverse. Choanoflagellate semaphorins are transmembrane proteins with multiple fibronectin type III domains following the N-terminal Sema domain (termed Sema-FN). Other previously not yet described semaphorin classes include semaphorins of Ctenophora with tandem immunoglobulin domains (Sema-IG) and secreted semaphorins of Echinoderamata (Sema-SP, Sema-SI). Our study also identified Met receptor tyrosine kinases (RTKs), which carry a truncated plexin extracellular domain, in several bilaterian clades, indicating evolutionary origin in a common ancestor of Bilateria. In addition, a novel type of Met-like RTK with a complete plexin extracellular domain was detected in Lophotrochozoa and Echinodermata (termed Met-LP RTK). Our findings are consistent with an ancient function of plexins and semaphorins in regulating cytoskeletal dynamics and cell adhesion that predates their role as axon guidance molecules.
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Affiliation(s)
- Chrystian Junqueira Alves
- Fishberg Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Karla Yotoko
- Biology Department, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Hongyan Zou
- Fishberg Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA.,Department of Neurosurgery, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Roland H Friedel
- Fishberg Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA. .,Department of Neurosurgery, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA.
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Maier D. The evolution of transcriptional repressors in the Notch signaling pathway: a computational analysis. Hereditas 2019; 156:5. [PMID: 30679936 PMCID: PMC6337844 DOI: 10.1186/s41065-019-0081-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/09/2019] [Indexed: 11/18/2022] Open
Abstract
Background The Notch signaling pathway governs the specification of different cell types in flies, nematodes and vertebrates alike. Principal components of the pathway that activate Notch target genes are highly conserved throughout the animal kingdom. Despite the impact on development and disease, repression mechanisms are less well studied. Repressors are known from arthropods and vertebrates that differ strikingly by mode of action: whereas Drosophila Hairless assembles repressor complexes with CSL transcription factors, competition between activator and repressors occurs in vertebrates (for example SHARP/MINT and KyoT2). This divergence raises questions on the evolution: Are there common ancestors throughout the animal kingdom? Results Available genome databases representing all animal clades were searched for homologues of Hairless, SHARP and KyoT2. The most distant species with convincing Hairless orthologs belong to Myriapoda, indicating its emergence after the Mandibulata-Chelicarata radiation about 500 million years ago. SHARP shares motifs with SPEN and SPENITO proteins, present throughout the animal kingdom. The CSL interacting domain of SHARP, however, is specific to vertebrates separated by roughly 600 million years of evolution. KyoT2 bears a C-terminal CSL interaction domain (CID), present only in placental mammals but highly diverged already in marsupials, suggesting introduction roughly 100 million years ago. Based on the LIM-domains that characterize KyoT2, homologues can be found in Drosophila melanogaster (Limpet) and Hydra vulgaris (Prickle 3 like). These lack the CID of KyoT2, however, contain a PET and additional LIM domains. Conservation of intron/exon boundaries underscores the phylogenetic relationship between KyoT2, Limpet and Prickle. Most strikingly, Limpet and Prickle proteins carry a tetra-peptide motif resembling that of several CSL interactors. Overall, KyoT2 may have evolved from prickle and Limpet to a Notch repressor in mammals. Conclusions Notch repressors appear to be specific to either chordates or arthropods. Orthologues of experimentally validated repressors were not found outside the phylogenetic group they have been originally identified. However, the data provide a hypothesis on the evolution of mammalian KyoT2 from Prickle like ancestors. The finding of a potential CSL interacting domain in Prickle homologues points to a novel, very ancestral CSL interactor present in the entire animal kingdom. Electronic supplementary material The online version of this article (10.1186/s41065-019-0081-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dieter Maier
- Institute of Genetics (240), University of Hohenheim, Garbenstr. 30, 70599 Stuttgart, Germany
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Abstract
Echinoderms are important research models for a wide range of biological questions. In particular, echinoderm embryos are exemplary models for dissecting the molecular and cellular processes that drive development and testing how these processes can be modified through evolution to produce the extensive morphological diversity observed in the phylum. Modern attempts to characterize these processes depend on some level of genomic analysis; from querying annotated gene sets to functional genomics experiments to identify candidate cis-regulatory sequences. Given how essential these data have become, it is important that researchers using available datasets or performing their own genome-scale experiments understand the nature and limitations of echinoderm genomic analyses. In this chapter we highlight the current state of echinoderm genomic data and provide methodological considerations for common approaches, including analysis of transcriptome and functional genomics datasets.
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Evolutionary distribution of deoxynucleoside 5-monophosphate N-glycosidase, DNPH1. Gene 2019; 683:1-11. [DOI: 10.1016/j.gene.2018.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 09/10/2018] [Accepted: 10/03/2018] [Indexed: 01/01/2023]
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Yasuoka Y, Tando Y, Kubokawa K, Taira M. Evolution of cis-regulatory modules for the head organizer gene goosecoid in chordates: comparisons between Branchiostoma and Xenopus. ZOOLOGICAL LETTERS 2019; 5:27. [PMID: 31388442 PMCID: PMC6679436 DOI: 10.1186/s40851-019-0143-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 07/12/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND In cephalochordates (amphioxus), the notochord runs along the dorsal to the anterior tip of the body. In contrast, the vertebrate head is formed anterior to the notochord, as a result of head organizer formation in anterior mesoderm during early development. A key gene for the vertebrate head organizer, goosecoid (gsc), is broadly expressed in the dorsal mesoderm of amphioxus gastrula. Amphioxus gsc expression subsequently becomes restricted to the posterior notochord from the early neurula. This has prompted the hypothesis that a change in expression patterns of gsc led to development of the vertebrate head during chordate evolution. However, molecular mechanisms of head organizer evolution involving gsc have never been elucidated. RESULTS To address this question, we compared cis-regulatory modules of vertebrate organizer genes between amphioxus, Branchiostoma japonicum, and frogs, Xenopus laevis and Xenopus tropicalis. Here we show conservation and diversification of gene regulatory mechanisms through cis-regulatory modules for gsc, lim1/lhx1, and chordin in Branchiostoma and Xenopus. Reporter analysis using Xenopus embryos demonstrates that activation of gsc by Nodal/FoxH1 signal through the 5' upstream region, that of lim1 by Nodal/FoxH1 signal through the first intron, and that of chordin by Lim1 through the second intron, are conserved between amphioxus and Xenopus. However, activation of gsc by Lim1 and Otx through the 5' upstream region in Xenopus are not conserved in amphioxus. Furthermore, the 5' region of amphioxus gsc recapitulated the amphioxus-like posterior mesoderm expression of the reporter gene in transgenic Xenopus embryos. CONCLUSIONS On the basis of this study, we propose a model, in which the gsc gene acquired the cis-regulatory module bound with Lim1 and Otx at its 5' upstream region to be activated persistently in anterior mesoderm, in the vertebrate lineage. Because Gsc globally represses trunk (notochord) genes in the vertebrate head organizer, this cooption of gsc in vertebrates appears to have resulted in inhibition of trunk genes and acquisition of the head organizer and its derivative prechordal plate.
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Affiliation(s)
- Yuuri Yasuoka
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495 Japan
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
| | - Yukiko Tando
- Center for Advance Marine Research, Ocean Research Institute, The University of Tokyo, 1-15-1, Minamidai, Nakano-ku, Tokyo, 164-8639 Japan
- Present address: Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Kaoru Kubokawa
- Center for Advance Marine Research, Ocean Research Institute, The University of Tokyo, 1-15-1, Minamidai, Nakano-ku, Tokyo, 164-8639 Japan
- Present address: SIRC, Teikyo University, 2-11-1, Itabashi-ku, Tokyo, 173-8605 Japan
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
- Present address: Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551 Japan
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