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Ashaolu TJ, Zarei M, Agrawal H, Kharazmi MS, Jafari SM. A critical review on immunomodulatory peptides from plant sources; action mechanisms and recent advances. Crit Rev Food Sci Nutr 2023; 64:7220-7236. [PMID: 36855310 DOI: 10.1080/10408398.2023.2183380] [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] [Indexed: 03/02/2023]
Abstract
Plant protein components contribute positively to human well-being as they modulate the immune status of a consumer, especially when the enzymatic method is employed in order to release their bioactive peptides. These peptides are derived from plant-based foods such as soy, wheat, barley, rye, oats, rice, corn, sorghum, and millet, the famous staple foods around the world. Since these peptides are crucial to functional food among other key industries, the present study endeavored to scout for relevant information within the past three decades, using the Web of Science, Scopus, and Google search engines. In this review, first, the core of immunomodulation and types of immunomodulatory agents will be discussed, followed by the production of plant-based immunomodulatory peptides and their immunomodulatory mechanisms in cells, animals, and humans are also studied. Finally, applications and challenges associated with plant-based immunomodulatory peptides are put forward.
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Affiliation(s)
| | - Mohammad Zarei
- Virginia Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University, Hampton, VA, USA
| | - Himani Agrawal
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | | | - Seid Mahdi Jafari
- Department of Food Materials and Process Design Engineering, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
- Faculty of Science, Department of Analytical Chemistry and Food Science, Universidade de Vigo, Nutrition and Bromatology Group, Ourense, Spain
- College of Food Science and Technology, Hebei Agricultural University, Baoding, China
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2
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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] [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. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01038-w.
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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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3
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Liberti A, Natarajan O, Atkinson CGF, Dishaw LJ. Secreted immunoglobulin domain effector molecules of invertebrates and management of gut microbial ecology. Immunogenetics 2022; 74:99-109. [PMID: 34988622 DOI: 10.1007/s00251-021-01237-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/18/2021] [Indexed: 02/01/2023]
Abstract
The origins of a "pass-through" gut in early bilaterians facilitated the exploration of new habitats, motivated the innovation of feeding styles and behaviors, and helped drive the evolution of more complex organisms. The gastrointestinal tract has evolved to consist of a series of interwoven exchanges between nutrients, host immunity, and an often microbe-rich environmental interface. Not surprisingly, animals have expanded their immune repertoires to include soluble effectors that can be secreted into luminal spaces, e.g., in the gut, facilitating interactions with microbes in ways that influence their settlement dynamics, virulence, and their interaction with other microbes. The immunoglobulin (Ig) domain, which is also found in some non-immune molecules, is recognized as one of the most versatile recognition domains lying at the interface of innate and adaptive immunity; among vertebrates, secreted Igs are known to play crucial roles in the management of gut microbial communities. In this mini-review, we will focus on secreted immune effectors possessing Ig-like domains in invertebrates, such as the fibrinogen-related effector proteins first described in the gastropod Biomphalaria glabrata, the Down syndrome cellular adhesion molecule first described in the arthropod, Drosophila melanogaster, and the variable region-containing chitin-binding proteins of the protochordates. We will highlight our current understanding of their function and their potential role, if not yet recognized, in the establishment and maintenance of host-microbial interfaces and argue that these Igs are likely also essential to microbiome management.
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Affiliation(s)
- Assunta Liberti
- Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Ojas Natarajan
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Division of Molecular Genetics, Children's Research Institute, St. Petersburg, FL, USA
| | - Celine Grace F Atkinson
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, USA.,Division of Molecular Genetics, Children's Research Institute, St. Petersburg, FL, USA
| | - Larry J Dishaw
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL, USA. .,Division of Molecular Genetics, Children's Research Institute, St. Petersburg, FL, USA.
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4
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Qu B, Zhang S, Ma Z, Gao Z. Hepatic cecum: a key integrator of immunity in amphioxus. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:279-292. [PMID: 37073295 PMCID: PMC10077268 DOI: 10.1007/s42995-020-00080-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/21/2020] [Indexed: 05/03/2023]
Abstract
The vertebrate liver is regarded as an organ essential to the regulation of immunity and inflammation as well as being central to the metabolism of nutrients. Here, we discuss the functions that the hepatic cecum of amphioxus plays in the regulation of immunity and inflammation, and the molecular basis of this. It is apparent that the hepatic cecum performs important roles in the immunity of amphioxus including immune surveillance, clearance of pathogens and acute phase response. Therefore, the hepatic cecum, like the vertebrate liver, is an organ functioning as a key integrator of immunity in amphioxus.
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Affiliation(s)
- Baozhen Qu
- Department of Marine Biology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Shicui Zhang
- Department of Marine Biology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237 China
| | - Zengyu Ma
- Department of Marine Biology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Zhan Gao
- Department of Marine Biology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
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Zhou J, Xiao Z, Zhan Y, Qu X, Mou S, Deng C, Zhang T, Lan X, Huang S, Li Y. Identification and Characterization of the Amphioxus Lck and Its Associated Tyrosine Phosphorylation-Dependent Inhibitory LRR Receptor. Front Immunol 2021; 12:656366. [PMID: 34149695 PMCID: PMC8211107 DOI: 10.3389/fimmu.2021.656366] [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: 01/20/2021] [Accepted: 05/17/2021] [Indexed: 11/13/2022] Open
Abstract
Amphioxus (e.g., Branchiostoma belcheri, Bb) has recently emerged as a new model for studying the origin and evolution of vertebrate immunity. Mammalian lymphocyte-specific tyrosine kinase (Lck) plays crucial roles in T cell activation, differentiation and homeostasis, and is reported to phosphorylate both the ITIM and ITSM of PD-1 to induce the recruitment of phosphatases and thus the inhibitory function of PD-1. Here, we identified and cloned the amphioxus homolog of human Lck. By generating and using an antibody against BbLck, we found that BbLck is expressed in the amphioxus gut and gill. Through overexpression of BbLck in Jurkat T cells, we found that upon TCR stimulation, BbLck was subjected to tyrosine phosphorylation and could partially rescue Lck-dependent tyrosine phosphorylation in Lck-knockdown T cells. Mass spectrometric analysis of BbLck immunoprecipitates from immunostimulants-treated amphioxus, revealed a BbLck-associated membrane-bound receptor LRR (BbLcLRR). By overexpressing BbLcLRR in Jurkat T cells, we demonstrated that BbLcLRR was tyrosine phosphorylated upon TCR stimulation, which was inhibited by Lck knockdown and was rescued by overexpression of BbLck. By mutating single tyrosine to phenylalanine (Y-F), we identified three tyrosine residues (Y539, Y655, and Y690) (3Y) of BbLcLRR as the major Lck phosphorylation sites. Reporter gene assays showed that overexpression of BbLcLRR but not the BbLcLRR-3YF mutant inhibited TCR-induced NF-κB activation. In Lck-knockdown T cells, the decline of TCR-induced IL-2 production was reversed by overexpression of BbLck, and this reversion was inhibited by co-expression of BbLcLRR but not the BbLcLRR-3YF mutant. Sequence analysis showed that the three tyrosine-containing sequences were conserved with the tyrosine-based inhibition motifs (ITIMs) or ITIM-like motifs. And TCR stimulation induced the association of BbLcLRR with tyrosine phosphatases SHIP1 and to a lesser extent with SHP1/2. Moreover, overexpression of wild-type BbLcLRR but not its 3YF mutant inhibited TCR-induced tyrosine phosphorylation of multiple signaling proteins probably via recruiting SHIP1. Thus, we identified a novel immunoreceptor BbLcLRR, which is phosphorylated by Lck and then exerts a phosphorylation-dependent inhibitory role in TCR-mediated T-cell activation, implying a mechanism for the maintenance of self-tolerance and homeostasis of amphioxus immune system and the evolutionary conservatism of Lck-regulated inhibitory receptor pathway.
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Affiliation(s)
- Jiatao Zhou
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhihui Xiao
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yanli Zhan
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xuemei Qu
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Sisi Mou
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chong Deng
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Tianxiang Zhang
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xin Lan
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 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
| | - Yingqiu Li
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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6
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Wang W, Wang C, Chen W, Ding S. Advances in immunological research of amphioxus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 118:103992. [PMID: 33387559 DOI: 10.1016/j.dci.2020.103992] [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: 10/12/2020] [Revised: 12/17/2020] [Accepted: 12/26/2020] [Indexed: 06/12/2023]
Abstract
Amphioxus, one of the most closely related invertebrates to vertebrates, is an important animal model for studying the origin and evolution of vertebrate immunity, especially the transition from innate immunity to adaptive immunity. The current research progresses of amphioxus in the field of immune organs, immune cells, complement system, cytokines, nuclear factor kappa B, immune-related lectins and enzymes are summarized, and some issues that remain to be understood or are in need of further clarification are highlighted. We hope to provide references for more in-depth study of the amphioxus immune system and lay a solid foundation for the construction of three-dimensional immune network in amphioxus from ontogeny to phylogeny.
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Affiliation(s)
- Wenjun Wang
- School of Life Sciences, Ludong University, Yantai, 264025, People's Republic of China
| | - Changliu Wang
- School of Life Sciences, Ludong University, Yantai, 264025, People's Republic of China.
| | - Wei Chen
- School of Life Sciences, Ludong University, Yantai, 264025, People's Republic of China; Yantai Productivity Promotion Center, Yantai, 264003, People's Republic of China
| | - Shuo Ding
- School of Life Sciences, Ludong University, Yantai, 264025, People's Republic of China
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7
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Bertrand S, Carvalho JE, Dauga D, Matentzoglu N, Daric V, Yu JK, Schubert M, Escrivá H. The Ontology of the Amphioxus Anatomy and Life Cycle (AMPHX). Front Cell Dev Biol 2021; 9:668025. [PMID: 33981708 PMCID: PMC8107275 DOI: 10.3389/fcell.2021.668025] [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: 02/15/2021] [Accepted: 03/31/2021] [Indexed: 11/13/2022] Open
Abstract
An ontology is a computable representation of the different parts of an organism and its different developmental stages as well as the relationships between them. The ontology of model organisms is therefore a fundamental tool for a multitude of bioinformatics and comparative analyses. The cephalochordate amphioxus is a marine animal representing the earliest diverging evolutionary lineage of chordates. Furthermore, its morphology, its anatomy and its genome can be considered as prototypes of the chordate phylum. For these reasons, amphioxus is a very important animal model for evolutionary developmental biology studies aimed at understanding the origin and diversification of vertebrates. Here, we have constructed an amphioxus ontology (AMPHX) which combines anatomical and developmental terms and includes the relationships between these terms. AMPHX will be used to annotate amphioxus gene expression patterns as well as phenotypes. We encourage the scientific community to adopt this amphioxus ontology and send recommendations for future updates and improvements.
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Affiliation(s)
- Stephanie Bertrand
- CNRS, Biologie Intégrative des Organismes Marins, Sorbonne Université, Paris, France
| | - João E. Carvalho
- CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche, Sorbonne Université, Paris, France
| | | | | | - Vladimir Daric
- CNRS, Biologie Intégrative des Organismes Marins, Sorbonne Université, Paris, France
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei City, Taiwan
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | - Michael Schubert
- CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche, Sorbonne Université, Paris, France
| | - Hector Escrivá
- CNRS, Biologie Intégrative des Organismes Marins, Sorbonne Université, Paris, France
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8
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Swann JB, Nusser A, Morimoto R, Nagakubo D, Boehm T. Retracing the evolutionary emergence of thymopoiesis. SCIENCE ADVANCES 2020; 6:6/48/eabd9585. [PMID: 33246964 PMCID: PMC7695478 DOI: 10.1126/sciadv.abd9585] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/08/2020] [Indexed: 05/09/2023]
Abstract
The onset of lymphocyte development in the vertebrate primordial thymus, about 500 million years ago, represents one of the foundational events of the emerging adaptive immune system. Here, we retrace the evolutionary trajectory of thymopoiesis, from early vertebrates to mammals, guided by members of the Foxn1/4 transcription factor gene family, which direct the differentiation of the thymic microenvironment. Molecular engineering in transgenic mice recapitulated a gene duplication event, exon replacements, and altered expression patterns. These changes predictably modified the lymphopoietic characteristics of the thymus, identifying molecular features contributing to conversion of a primordial bipotent lymphoid organ to a tissue specializing in T cell development. The phylogenetic reconstruction associates increasing efficiency of T cell generation with diminishing B cell-generating capacity of the thymus during jawed vertebrate evolution.
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Affiliation(s)
- Jeremy B Swann
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Anja Nusser
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Ryo Morimoto
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Daisuke Nagakubo
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany.
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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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10
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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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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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12
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Qu B, Ma Z, Zhang Y, Gao Z, Zhang S. Characterization of a novel protein identified by proteomics analysis as a modulator of inflammatory networks in amphioxus. FISH & SHELLFISH IMMUNOLOGY 2020; 96:97-106. [PMID: 31805412 DOI: 10.1016/j.fsi.2019.12.003] [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: 10/10/2019] [Revised: 11/29/2019] [Accepted: 12/01/2019] [Indexed: 06/10/2023]
Abstract
Inflammatory response is an innate host defense mechanism, and its regulation is essential for the host to get rid of harm by the excessive reactions. We first utilized proteomics approach to identify amphioxus humoral fluid proteins in response to LPS-induced inflammation. A total of 26 differentially expressed proteins, mainly involved in energy metabolism and cytoskeleton rearrangement processes, were identified between LPS-treated and control animals. Furthermore, we found a single uncharacterized protein (termed BjIM1) out of the most up-regulated ones, and examined its role in the regulation of immune and inflammatory responses. BjIM1 is predominantly expressed in the hepatic caecum, and its promoter sequence includes many binding sites for immune-relevant transcription factors. Importantly, recombinant BjIM1 (rBjIM1) is able to inhibit LPS-induced up-regulation of TLR pathway genes, such as MyD88, IKK, NF-κB1, Rel, p38, JNK and AP-1, indicating that BjIM1 may negatively regulate the TLR signaling pathway in amphioxus. Moreover, rBjIM1 also modulates the expression of genes involved in the interaction network of inflammation, energy metabolism and cytoskeleton rearrangement, including SIRT1, Rac1 and NOX2, in the LPS-induced inflammatory response in amphioxus. Collectively, our studies suggest that BjIM1 is an uncharacterized protein functioning as a modulator of inflammatory networks in amphioxus.
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Affiliation(s)
- Baozhen Qu
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao, 266003, China
| | - Zengyu Ma
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao, 266003, China
| | - Yu Zhang
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao, 266003, China
| | - Zhan Gao
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao, 266003, China.
| | - Shicui Zhang
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266003, China.
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13
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Wang W, Qu Q, Chen J. Identification, expression analysis, and antibacterial activity of Apolipoprotein A-I from amphioxus (Branchiostoma belcheri). Comp Biochem Physiol B Biochem Mol Biol 2019; 238:110329. [DOI: 10.1016/j.cbpb.2019.110329] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/25/2019] [Accepted: 08/22/2019] [Indexed: 12/29/2022]
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14
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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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15
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Flajnik MF. A Convergent Immunological Holy Trinity of Adaptive Immunity in Lampreys: Discovery of the Variable Lymphocyte Receptors. THE JOURNAL OF IMMUNOLOGY 2019; 201:1331-1335. [PMID: 30127062 DOI: 10.4049/jimmunol.1800965] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD 21201
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16
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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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17
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Chen ZL, Gong BN, Wang QL, Xiao ZH, Deng C, Wang WQ, Li Y. Characterisation of amphioxus protein kinase C-δ/θ reveals a unique proto-V3 domain suggesting an evolutionary mechanism for PKC-θ unique V3. FISH & SHELLFISH IMMUNOLOGY 2019; 84:1100-1107. [PMID: 30408601 DOI: 10.1016/j.fsi.2018.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/29/2018] [Accepted: 11/01/2018] [Indexed: 06/08/2023]
Abstract
A primitive adaptive immune system has recently been suggested to be present in a basal chordate amphioxus (Branchiostoma belcheri, Bb), making it an ideal model for studying the origin of adaptive immune. The novel protein kinase C isoform PKC-θ, but not its closest isoform PKC-δ, plays a critical role for mammalian T-cell activation via translocation to immunological synapse (IS) mediated by a unique PKC-θ V3 domain containing one PxxP motif. To understand the evolution of this unique PKC-θ V3 domain and the primitive adaptive immune system in amphioxus, we comparatively studied the orthologs of PKC-δ and -θ from amphioxus and other species. Phylogenetic analysis showed BbPKC-δ/θ to be the common ancestor of vertebrate PKC-δ and PKC-θ, with a V3 domain containing two PxxP motifs. One motif is conserved in both zebrafish and mammalian PKC-θ but is absent in PKC-δ V3 domain of these species, and has already emerged in drosophila PKC-δ. The other non-conserved motif emerged in BbPKC-δ/θ, and only retained in Danio rerio PKC-δ (DrPKC-δ) but lost in mammalian PKC-δ and -θ. Comparative analyses of the sequence and function of BbPKC-δ/θ, DrPKC-δ, DrPKC-θ and Homo sapiens PKC-θ (HsPKC-θ) in IS translocation and T-cell receptor (TCR)-induced NF-κB activation revealed that retention of the conserved PxxP motif and loss of the non-conserved PxxP motif in mammalian PKC-θ and loss of both PxxP motifs in mammalian PKC-δ accomplish the unique function of PKC-θ in T cells. Together, this study suggests an evolutionary mechanism for PKC-θ unique V3 and reveals BbPKC-δ/θ is the common ancestor of PKC-δ and -θ with a functional proto-V3 domain, supplying new evidence for the existence of primitive adaptive immune system in amphioxus.
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Affiliation(s)
- Zhi-Long Chen
- State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Bei-Ni Gong
- State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Qi-Long Wang
- State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Zhi-Hui Xiao
- State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Chong Deng
- State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Wen-Qian Wang
- State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Yingqiu Li
- State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, 510006, PR China.
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18
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Yang Z, Hu F. Investigation of gene evolution in vertebrate genome reveals novel insights into spine study. Gene 2018; 679:360-368. [PMID: 30218752 DOI: 10.1016/j.gene.2018.09.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 09/08/2018] [Accepted: 09/11/2018] [Indexed: 11/30/2022]
Abstract
Vertebrate genomes have been considered to have undergone a complicated evolution during their early period and to have generated a large number of genetic templates with novel functions, such as an extended spinal cord and a dorsal central nervous system. However, consistent gene evolution in vertebrate genomes has not been fully elucidated. In this study, we have systematically investigated the gene evolution in vertebrates utilizing a series of comparative genomics tools. We determined that three critical genes were consistently lost in vertebrate genomes, and 14 genes initially emerged in vertebrate formation. Furthermore, another 29 genes were identified with consistent amino acid variation between the vertebrates and invertebrates. A function analysis of five genes (TEP3, ABLIM2, ABLIM3, GAD1 and GAD2) was performed, and their evolution mechanisms in vertebrate genomes further investigated. These findings provide novel insights for studying the vertebrate evolution and spine development.
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Affiliation(s)
- Zhiyuan Yang
- College of Life Information Science & Instrument Engineering, Hangzhou Dianzi University, Hangzhou, PR China; School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR.
| | - Fuyan Hu
- Department of Statistics, Faculty of Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan, PR China
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19
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Zhang QL, Zhu QH, Liang MZ, Wang F, Guo J, Deng XY, Chen JY, Wang YJ, Lin LB. Comparative transcriptomic analysis provides insights into antibacterial mechanisms of Branchiostoma belcheri under Vibrio parahaemolyticus infection. FISH & SHELLFISH IMMUNOLOGY 2018; 76:196-205. [PMID: 29510259 DOI: 10.1016/j.fsi.2018.03.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 02/24/2018] [Accepted: 03/02/2018] [Indexed: 06/08/2023]
Abstract
UNLABELLED Amphioxus, a basal chordate, is widely considered to be an existing proxy of the invertebrate ancestor of vertebrates, and it exhibits susceptibility to various pathogen infections and pathogenic mimic challenges. Here, in order to understand more clearly its antibacterial mechanisms, we analyzed the ribosomal RNA (rRNA)-depleted transcriptome of Chinese amphioxus (Branchiostoma belcheri) infected with Vibrio parahaemolyticus (V. p.) via next-generation deep sequencing technology (RNA-seq). We identified a total of 3214 differentially expressed genes (DEGs) by comparing V. p.-infected and control transcriptome libraries, including 2219 significantly up-regulated and 995 significantly down-regulated DEGs in V. p.-infected amphioxus. The DEGs with the top 10 most dramatic expression fold changes after V. p. infection, as well as 53 immune-related DEGs (IRDs) belonging to four primary categories of innate immunity were analyzed further. Through gene ontology (GO) and pathway enrichment analysis, DEGs were found to be primarily related to immune processes, apoptosis, catabolic and metabolic processes, binding and enzyme activity, while pathways involving bacterial infection, immune signaling, immune response, cancer, and apoptosis were overrepresented. We validated the RNA-seq results by detecting the expression levels of 10 IRDs using qRT-PCR, and we surveyed the dynamic variation in gene expression for these IRDs at 0, 6, 12, 24, and 48 h after V. p. TREATMENT Subsequently, according to the RNA-seq results, the presence of a primitive Toll-like receptor (TLR)-mediated antibacterial immune signaling pathway was predicted in B. belcheri. This study provides valuable information regarding antibacterial immunity for further research into the evolution of immunity in vertebrates and broadens our understanding of the innate immune response against bacterial invasion 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; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, 210023, China
| | - Qian-Hua Zhu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Ming-Zhong Liang
- Department of Marine Science, Qinzhou University, Qinzhou, 535000, China
| | - Feng Wang
- 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
| | - Xian-Yu Deng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Jun-Yuan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, 210023, China
| | - Yu-Jun Wang
- Department of Marine Science, Qinzhou University, Qinzhou, 535000, China.
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
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20
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Identification of microRNA expression profiles in the gill, intestine and hepatic caecum of Branchiostoma belcheri. Protein Cell 2018; 8:302-307. [PMID: 28116671 PMCID: PMC5359183 DOI: 10.1007/s13238-016-0365-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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21
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The conserved ancient role of chordate PIAS as a multilevel repressor of the NF-κB pathway. Sci Rep 2017; 7:17063. [PMID: 29213053 PMCID: PMC5719053 DOI: 10.1038/s41598-017-16624-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 11/15/2017] [Indexed: 12/21/2022] Open
Abstract
In vertebrates, PIAS genes encode versatile cellular regulators, with functions extremely complex and redundant. Here we try to understand their functions from an evolutionary perspective. we evaluate the sequences, expression and molecular functions of amphioxus PIAS genes and compare them with their vertebrate counterparts. Phylogenetic analysis suggests a single PIAS gene in ancestral chordates, which has been duplicated into four families (PIAS1-4) in vertebrates by 2R-WGD but remained single in a basal chordate (amphioxus). Amphioxus PIAS encodes two variants with and without a Serine/Threonine-rich tail, which are retained in human PIAS1-3 but lost in PIAS4. We show that amphioxus PIAS binds C-terminus of NF-κB Rel and blocks the DNA binding activity. In humans, such function is retained in PIAS1, altered in PIAS4, and lost in PIAS2-3. Instead, PIAS3 has evolved new ability to inhibit Rel by binding RHD and promoting SUMOylation. We show that amphioxus PIAS also inhibits NF-κB by binding with upstream signalling adaptor TICAM-like and MyD88. Finally, we verify that human PIAS1, 3 and 4, but not 2, were capable of these newly-discovered functions. Our study offers insight into the sub- and neo-functionalization of PIAS genes and suggests a conserved ancient role for chordate PIAS in NF-κB signalling.
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22
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Udroiu I, Sgura A. The Phylogeny of the Spleen. THE QUARTERLY REVIEW OF BIOLOGY 2017. [DOI: 10.1086/695327] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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23
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Zhang QL, Xie ZQ, Liang MZ, Luo B, Wang XQ, Chen JY. Genome-wide gene expression analysis in the amphioxus, Branchiostoma belcheri after poly (I: C) challenge using strand-specific RNA-seq. Oncotarget 2017; 8:108392-108405. [PMID: 29312538 PMCID: PMC5752451 DOI: 10.18632/oncotarget.21553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 10/02/2017] [Indexed: 02/07/2023] Open
Abstract
The gene expression associated with immune response to bacteria/bacterial mimic has been extensively analyzed in amphioxus, but remains largely unknown about how gene are involved in the immune response to viral invasion at expression level. Here, we analyze the rRNA-depleted transcriptomes of Branchiostoma belcheri using strand-specific RNA-seq in response to the viral mimic, poly (I:C) (pIC). A total of 5,317 differentially expressed genes were detected at treatment group by comparing with control. The gene with the most significant expression changes (top 15) after pIC challenge and 7 immune-related categories involving 58 differently expressed genes were scrutinized. By functional enrichment analysis of differently expressed genes, gene ontology terms involving response to stress and stimulus, apoptosis, catabolic and metabolic processes and enzyme activity were overrepresented, and several pathways related to immune signaling, immune response, cancer, apoptosis, viral disease, metabolism were activated after pIC injection. A positive correlation between the qRT-PCR and strand-specific RNA-seq data confirmed the accuracy of the RNA-seq results. Additionally, the expression of genes encoding NLRC5, CASP1, CASP6, CYP450, CAT, and MDA5 were induced in B. belcheri under pIC challenge. Our experiments provide insight into the immune response of amphioxus to pIC and valuable gene expression information for studying the evolution of antiviral immunity in vertebrates.
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Affiliation(s)
- Qi-Lin Zhang
- LPS, Nanjing Institute of Geology and Paleontology, Chinese Academy of Science, Nanjing, China.,State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, China
| | - Zheng-Qing Xie
- LPS, Nanjing Institute of Geology and Paleontology, Chinese Academy of Science, Nanjing, China.,State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, China
| | - Ming-Zhong Liang
- Department of Marine Science, Qinzhou University, Qinzhou, China
| | - Bang Luo
- Guangxi Academy of Fishery Sciences, Nanning, China
| | - Xiu-Qiang Wang
- LPS, Nanjing Institute of Geology and Paleontology, Chinese Academy of Science, Nanjing, China
| | - Jun-Yuan Chen
- LPS, Nanjing Institute of Geology and Paleontology, Chinese Academy of Science, Nanjing, China
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24
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Tassia MG, Whelan NV, Halanych KM. Toll-like receptor pathway evolution in deuterostomes. Proc Natl Acad Sci U S A 2017; 114:7055-7060. [PMID: 28630328 PMCID: PMC5502590 DOI: 10.1073/pnas.1617722114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Animals have evolved an array of pattern-recognition receptor families essential for recognizing conserved molecular motifs characteristic of pathogenic microbes. One such family is the Toll-like receptors (TLRs). On pathogen binding, TLRs initiate specialized cytokine signaling catered to the class of invading pathogen. This signaling is pivotal for activating adaptive immunity in vertebrates, suggesting a close evolutionary relationship between innate and adaptive immune systems. Despite significant advances toward understanding TLR-facilitated immunity in vertebrates, knowledge of TLR pathway evolution in other deuterostomes is limited. By analyzing genomes and transcriptomes across 37 deuterostome taxa, we shed light on the evolution and diversity of TLR pathway signaling elements. Here, we show that the deuterostome ancestor possessed a molecular toolkit homologous to that which drives canonical MYD88-dependent TLR signaling in contemporary mammalian lineages. We also provide evidence that TLR3-facilitated antiviral signaling predates the origin of its TCAM1 dependence recognized in the vertebrates. SARM1, a negative regulator of TCAM1-dependent pathways in vertebrates, was also found to be present across all major deuterostome lineages despite the apparent absence of TCAM1 in invertebrate deuterostomes. Whether the presence of SARM1 is the result of its role in immunity regulation, neuron physiology, or a function of both is unclear. Additionally, Bayesian phylogenetic analyses corroborate several lineage-specific TLR gene expansions in urchins and cephalochordates. Importantly, our results underscore the need to sample across taxonomic groups to understand evolutionary patterns of the innate immunity foundation on which complex immunological novelties arose.
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Affiliation(s)
- Michael G Tassia
- Department of Biological Sciences, Auburn University, Auburn, AL 36849;
| | - Nathan V Whelan
- Department of Biological Sciences, Auburn University, Auburn, AL 36849
- Warm Springs Fish Technology Center, US Fish and Wildlife Service, Warm Springs, GA 31830
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Milutinović B, Kurtz J. Immune memory in invertebrates. Semin Immunol 2016; 28:328-42. [PMID: 27402055 DOI: 10.1016/j.smim.2016.05.004] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/11/2016] [Accepted: 05/17/2016] [Indexed: 12/21/2022]
Abstract
Evidence for innate immune memory (or 'priming') in invertebrates has been accumulating over the last years. We here provide an in-depth review of the current state of evidence for immune memory in invertebrates, and in particular take a phylogenetic viewpoint. Invertebrates are a very heterogeneous group of animals and accordingly, evidence for the phenomenon of immune memory as well as the hypothesized molecular underpinnings differ largely for the diverse invertebrate taxa. The majority of research currently focuses on Arthropods, while evidence from many other groups of invertebrates is fragmentary or even lacking. We here concentrate on immune memory that is induced by pathogenic challenges, but also extent our view to a non-pathogenic context, i.e. allograft rejection, which can also show forms of memory and can inform us about general principles of specific self-nonself recognition. We discuss definitions of immune memory and a number of relevant aspects such as the type of antigens used, the route of exposure, and the kinetics of reactions following priming.
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Affiliation(s)
- Barbara Milutinović
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria.
| | - Joachim Kurtz
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, 48149 Münster, Germany.
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Yuan S, Zheng T, Li P, Yang R, Ruan J, Huang S, Wu Z, Xu A. Characterization of Amphioxus IFN Regulatory Factor Family Reveals an Archaic Signaling Framework for Innate Immune Response. THE JOURNAL OF IMMUNOLOGY 2015; 195:5657-5666. [DOI: 10.4049/jimmunol.1501927] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Abstract
The IFN regulatory factor (IRF) family encodes transcription factors that play important roles in immune defense, stress response, reproduction, development, and carcinogenesis. Although the origin of the IRF family has been dated back to multicellular organisms, invertebrate IRFs differ from vertebrate IRFs in genomic structure and gene synteny, and little is known about their functions. Through comparison of multiple amphioxus genomes, in this study we suggested that amphioxus contains nine IRF members, whose orthologs are supposed to be shared among three amphioxus species. As the orthologs to the vertebrate IRF1 and IRF4 subgroups, Branchiostoma belcheri tsingtauense (bbt)IRF1 and bbtIRF8 bind the IFN-stimulated response element (ISRE) and were upregulated when amphioxus intestinal cells were stimulated with poly(I:C). As amphioxus-specific IRFs, both bbtIRF3 and bbtIRF7 bind ISRE. When activated, they can be phosphorylated by bbtTBK1 and then translocate into nucleus for target gene transcription. As transcriptional repressors, bbtIRF2 and bbtIRF4 can inhibit the transcriptional activities of bbtIRF1, 3, 7, and 8 by competing for the binding of ISRE. Interestingly, amphioxus IRF2, IRF8, and Rel were identified as target genes of bbtIRF1, bbtIRF7, and bbtIRF3, respectively, suggesting a dynamic feedback regulation among amphioxus IRF and NF-κB. Collectively, to our knowledge we present for the first time an archaic IRF signaling framework in a basal chordate, shedding new insights into the origin and evolution of vertebrate IFN-based antiviral networks.
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Affiliation(s)
- Shaochun Yuan
- *State Key Laboratory of Biocontrol, Department of Biochemistry, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, People’s Republic of China; and
| | - Tingting Zheng
- *State Key Laboratory of Biocontrol, Department of Biochemistry, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, People’s Republic of China; and
| | - Peiyi Li
- *State Key Laboratory of Biocontrol, Department of Biochemistry, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, People’s Republic of China; and
| | - Rirong Yang
- *State Key Laboratory of Biocontrol, Department of Biochemistry, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, People’s Republic of China; and
| | - Jie Ruan
- *State Key Laboratory of Biocontrol, Department of Biochemistry, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, People’s Republic of China; and
| | - Shengfeng Huang
- *State Key Laboratory of Biocontrol, Department of Biochemistry, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, People’s Republic of China; and
| | - Zhenxin Wu
- *State Key Laboratory of Biocontrol, Department of Biochemistry, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, People’s Republic of China; and
| | - Anlong Xu
- *State Key Laboratory of Biocontrol, Department of Biochemistry, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, People’s Republic of China; and
- †Beijing University of Chinese Medicine, Beijing 100029, People’s Republic of China
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Peng J, Tao X, Li R, Hu J, Ruan J, Wang R, Yang M, Yang R, Dong X, Chen S, Xu A, Yuan S. Novel Toll/IL-1 Receptor Homologous Region Adaptors Act as Negative Regulators in Amphioxus TLR Signaling. THE JOURNAL OF IMMUNOLOGY 2015; 195:3110-8. [PMID: 26324776 DOI: 10.4049/jimmunol.1403003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 08/03/2015] [Indexed: 12/13/2022]
Abstract
Studies have shown that the basal chordate amphioxus possesses an extraordinarily complex TLR system, including 39 TLRs and at least 40 Toll/IL-1R homologous region (TIR) adaptors. Besides homologs to MyD88 and TIR domain-containing adaptor molecule (TICAM), most amphioxus TIR adaptors exhibit domain architectures that are not observed in other species. To reveal how these novel TIR adaptors function in amphioxus Branchiostoma belcheri tsingtauense (bbt), four representatives, bbtTIRA, bbtTIRB, bbtTIRC, and bbtTIRD, were selected for functional analyses. We found bbtTIRA to show a unique inhibitory role in amphioxus TICAM-mediated pathway by interacting with bbtTICAM and bbt receptor interacting protein 1b, whereas bbtTIRC specifically inhibits the amphioxus MyD88-dependent pathway by interacting with bbtMyD88 and depressing the polyubiquitination of bbt TNFR-associated factor 6. Although both bbtTIRB and bbtTIRD are located on endosomes, the TIR domain of bbtTIRB can interact with bbtMyD88 in the cytosol, whereas the TIR domain of bbtTIRD is enclosed in endosome, suggesting that bbtTIRD may be a redundant gene in amphioxus. This study indicated that most expanded TIR adaptors play nonredundant regulatory roles in amphioxus TLR signaling, adding a new layer to understanding the diversity and complexity of innate immunity at basal chordate.
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Affiliation(s)
- Jian Peng
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China; and
| | - Xin Tao
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China; and
| | - Rui Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China; and
| | - Jingru Hu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China; and
| | - Jie Ruan
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China; and
| | - Ruihua Wang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China; and
| | - Manyi Yang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China; and
| | - Rirong Yang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China; and
| | - Xiangru Dong
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China; and
| | - Shangwu Chen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China; and
| | - Anlong Xu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China; and Beijing University of Chinese Medicine, Beijing 100029, People's Republic of China
| | - Shaochun Yuan
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China; and
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Corcos D. Food-Nonfood Discrimination in Ancestral Vertebrates: Gamete Cannibalism and the Origin of the Adaptive Immune System. Scand J Immunol 2015; 82:409-17. [PMID: 26286030 DOI: 10.1111/sji.12348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/29/2015] [Indexed: 01/21/2023]
Abstract
Adaptive immunity is a complex system that appeared twice in vertebrates (in gnathostomes and in jawless fish) although it is not required for invertebrate defence. The adaptive immune system is tightly associated with self-non-self discrimination, and it is now clear that this interplay is not limited to the prevention of autoreactivity. Micro-organisms are usually considered for their pathogenicity or symbiotic ability, but, for most small metazoans, they mainly constitute food. Vertebrates are characterized by feeding by predation on larger preys, when compared to their ancestors who were filter feeders and ate micro-organisms. Predation gives a strong selective advantage, not only due to the availability of new food resources but also by the ability to eliminate competitors for environmental resources (intraguild predation (IGP)). Unlike size-structured IGP, intraspecific predation of juveniles, zygotes or gametes can be detrimental for species fitness in some circumstances. The ability of individuals to recognize highly polymorphic molecules on the surface of gametes present in the plankton and so distinguish self versus non-self gametes might have constituted a strong selective advantage in intraspecific competition. Here, I propose the theory that the capacity to rearrange receptors has been selected in ancestral vertebrates as a consequence of this strong need for discriminating between hetero-cannibalism versus filial cannibalism. This evolutionary origin sheds light on presently unexplained features of the immune system, including the existence of regulatory T cells and of non-pathogenic natural autoimmunity.
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Affiliation(s)
- D Corcos
- U1021 INSERM, Institut Curie, Centre National de la Recherche Scientifique (CNRS) UMR3347, Institut National de la Santé et de Recherche Médicale (INSERM) U1021, Université Paris-Sud 11, Centre Universitaire, Orsay, France
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Yuan D, Pan M, Zou Q, Chen C, Chen S, Xu A. The effect of antibiotic exposure on eicosanoid generation from arachidonic acid and gene expression in a primitive chordate, Branchiostoma belcheri. FEBS Open Bio 2015; 5:615-24. [PMID: 26288743 PMCID: PMC4536258 DOI: 10.1016/j.fob.2015.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 07/24/2015] [Accepted: 07/24/2015] [Indexed: 11/24/2022] Open
Abstract
Chloramphenicol treatment induced immunosuppression and severe tissue damage in amphioxus. KEGG clustering showed that chloramphenicol and ampicillin treatment resulted in immunostimulation. Chloramphenicol treatment induced a ∼3-fold decrease of eicosanoid levels. Chloramphenicol and ampicillin treatment resulted in a 1.7-fold increase of eicosanoid levels. Eicosanoids derived from arachidonic acid provide insights into the effect of chloramphenicol treatment.
Chloramphenicol (Chl) is an effective antimicrobial agent widely used in veterinary medicine and commonly used in fish. Its use is restricted in the clinic because of adverse effects on the immune system and oxidative stress in mammals. However, the effects of Chl treatment on invertebrates remain unclear. Amphioxus, a basal chordate, is an ideal model to study the origin and evolution of the vertebrate immune system as it has a primary vertebrate-like arachidonic acid (AA) metabolic system. Here, we combined transcriptomic and lipidomic approaches to investigate the immune system and observe the oxygenated metabolites of AA to address the antibiotic effects on amphioxus. Tissue necrosis of the gill slits occurred in the Chl-treated amphioxus, but fewer epithelial cells were lost when treated with both Chl and ampicillin (Amp). The immune related pathways were dysregulated in both of the antibiotic treatment groups. The Chl alone treatment resulted in immunosuppression with down-regulation of the innate immune genes. In contrast, the Chl + Amp treatment resulted in immunostimulation to some extent, as shown by KEGG clustering. Furthermore, Chl induced a 3-fold reduction in the level of the eicosanoids, while the Chl + Amp treatment resulted in 1.7-fold increase of eicosanoid level. Thus in amphioxus, Amp might relieve the effects of the Chl-induced immune suppression and increase the level of eicosanoids from AA. Finally, the oxygenated metabolites from AA might be crucial to evaluate the effects of Chl treatment in animals.
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Affiliation(s)
- Dongjuan Yuan
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China ; Department of Biochemistry, College of Life Sciences, State Key Laboratory of Biocontrol, National Engineering Research Center of South China Sea Marine Biotechnology, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Minming Pan
- Department of Biochemistry, College of Life Sciences, State Key Laboratory of Biocontrol, National Engineering Research Center of South China Sea Marine Biotechnology, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Qiuqiong Zou
- Department of Biochemistry, College of Life Sciences, State Key Laboratory of Biocontrol, National Engineering Research Center of South China Sea Marine Biotechnology, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Chengyong Chen
- Department of Biochemistry, College of Life Sciences, State Key Laboratory of Biocontrol, National Engineering Research Center of South China Sea Marine Biotechnology, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Shangwu Chen
- Department of Biochemistry, College of Life Sciences, State Key Laboratory of Biocontrol, National Engineering Research Center of South China Sea Marine Biotechnology, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Anlong Xu
- Department of Biochemistry, College of Life Sciences, State Key Laboratory of Biocontrol, National Engineering Research Center of South China Sea Marine Biotechnology, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Sun Yat-sen University, Guangzhou 510275, PR China ; Beijing University of Chinese Medicine, 11 Bei San Huan Dong Road, Chao-yang District, Beijing 100029, PR China
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30
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Pan M, Yuan D, Chen S, Xu A. Diversity and composition of the bacterial community in Amphioxus feces. J Basic Microbiol 2015; 55:1336-42. [PMID: 26173442 DOI: 10.1002/jobm.201500124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 06/23/2015] [Indexed: 12/12/2022]
Abstract
Amphioxus is a typical filter feeder animal and is confronted with a complex bacterial community in the seawater of its habitat. It has evolved a strong innate immune system to cope with the external bacterial stimulation, however, the ecological system of the bacterial community in Amphioxus remains unknown. Through massive parallel 16S rRNA gene tag pyrosequencing, the investigation indicated that the composition of wild and lab-cultured Amphioxus fecal bacteria was complex with more than 85,000 sequence tags being assigned to 12/13 phyla. The bacterial diversity between the two fecal samples was similar according to OTU richness of V4 tag, Chao1 index, Shannon index and Rarefaction curves, however, the most prominent bacteria in wild feces were genera Pseudoalteromonas (gamma Proteobacteria) and Arcobacter (epsilon Proteobacteria); the highly abundant bacteria in lab-cultured feces were other groups, including Leisingera, Phaeobacter (alpha Proteobacteria), and Vibrio (gamma Proteobacteria). Such difference indicates the complex fecal bacteria with the potential for multi-stability. The bacteria of habitat with 28 assigned phyla had the higher bacterial diversity and species richness than both fecal bacteria. Shared bacteria between wild feces and its habitat reached to approximately 90% (153/169 genera) and 28% (153/548 genera), respectively. As speculative, the less diversity of both fecal bacteria compared to its habitat partly because Amphioxus lives buried and the feces will ultimately end up in the sediment. Therefore, our study comprehensively investigates the complex bacterial community of Amphioxus and provides evidence for understanding the relationship of this basal chordate with the environment.
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Affiliation(s)
- Minming Pan
- Department of Biochemistry, College of Life Sciences, State Key Laboratory of Biocontrol, National Engineering Research Center of South China Sea Marine Biotechnology, Sun Yat-sen University, Guangzhou, P. R. China
| | - Dongjuan Yuan
- Department of Biochemistry, College of Life Sciences, State Key Laboratory of Biocontrol, National Engineering Research Center of South China Sea Marine Biotechnology, Sun Yat-sen University, Guangzhou, P. R. China.,Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China
| | - Shangwu Chen
- Department of Biochemistry, College of Life Sciences, State Key Laboratory of Biocontrol, National Engineering Research Center of South China Sea Marine Biotechnology, Sun Yat-sen University, Guangzhou, P. R. China
| | - Anlong Xu
- Department of Biochemistry, College of Life Sciences, State Key Laboratory of Biocontrol, National Engineering Research Center of South China Sea Marine Biotechnology, Sun Yat-sen University, Guangzhou, P. R. China.,Beijing University of Chinese Medicine, 11 Bei San Huan Dong Road, Chao-yang District, Beijing 100029, P. R. China
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