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Takahashi H, Hisata K, Iguchi R, Kikuchi S, Ogasawara M, Satoh N. scRNA-seq analysis of cells comprising the amphioxus notochord. Dev Biol 2024; 508:24-37. [PMID: 38224933 DOI: 10.1016/j.ydbio.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/17/2024]
Abstract
Cephalochordates occupy a key phylogenetic position for deciphering the origin and evolution of chordates, since they diverged earlier than urochordates and vertebrates. The notochord is the most prominent feature of chordates. The amphioxus notochord features coin-shaped cells bearing myofibrils. Notochord-derived hedgehog signaling contributes to patterning of the dorsal nerve cord, as in vertebrates. However, properties of constituent notochord cells remain unknown at the single-cell level. We examined these properties using Iso-seq analysis, single-cell RNA-seq analysis, and in situ hybridization (ISH). Gene expression profiles broadly categorize notochordal cells into myofibrillar cells and non-myofibrillar cells. Myofibrillar cells occupy most of the central portion of the notochord, and some cells extend the notochordal horn to both sides of the ventral nerve cord. Some notochord myofibrillar genes are not expressed in myotomes, suggesting an occurrence of myofibrillar genes that are preferentially expressed in notochord. On the other hand, non-myofibrillar cells contain dorsal, lateral, and ventral Müller cells, and all three express both hedgehog and Brachyury. This was confirmed by ISH, although expression of hedgehog in ventral Müller cells was minimal. In addition, dorsal Müller cells express neural transmission-related genes, suggesting an interaction with nerve cord. Lateral Müller cells express hedgehog and other signaling-related genes, suggesting an interaction with myotomes positioned lateral to the notochord. Ventral Müller cells also expressed genes for FGF- and EGF-related signaling, which may be associated with development of endoderm, ventral to the notochord. Lateral Müller cells were intermediate between dorsal/ventral Müller cells. Since vertebrate notochord contributes to patterning and differentiation of ectoderm (nerve cord), mesoderm (somite), and endoderm, this investigation provides evidence that an ancestral or original form of vertebrate notochord is present in extant cephalochordates.
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Affiliation(s)
- Hiroki Takahashi
- Interdisciplinary Research Unit, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan.
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Rin Iguchi
- Department of Biology, Graduate School of Science, Chiba University, Chiba, 262-8522, Japan
| | - Sakura Kikuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Michio Ogasawara
- Department of Biology, Graduate School of Science, Chiba University, Chiba, 262-8522, Japan.
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
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Yang LY, Zhu QH, Chen JY, Lin LB, Liang MZ, Zhang QL. Genome-wide transcriptomics and microRNAomics analyses uncover multi-faceted mechanisms to cope with copper stress in ancient macrobenthos amphioxus. J Hazard Mater 2023; 458:131594. [PMID: 37330373 DOI: 10.1016/j.jhazmat.2023.131594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/20/2023] [Accepted: 05/05/2023] [Indexed: 06/19/2023]
Abstract
The mechanisms underlying the toxicity of environmental stress are unclear for marine macrobenthos. Copper/Cu has posed the most serious threats to amphioxus, an ancient and model benthic cephalochordate. Herein, a dynamic change in the physiological parameters (GR, SOD, ATP, and MDA) was detected with ROS accumulation in Branchiostoma belcheri exposed to 0.3 mg·L-1 Cu. Transcriptomes and microRNAomes of B. belcheri were generated to investigate the molecular mechanisms by which this amphioxus copes with Cu exposure. Time-specific genes identified at different time points after exposure were involved in the stimulus and immune response, detoxification and ionic homeostasis, aging and the nervous system, sequentially, with prolongation of exposure time, forming a dynamic process of molecular response to Cu stress. In total, 57 differentially expressed miRNAs were identified under Cu stress. Transcriptomics-miRNAomics analyses indicate that these miRNAs targeted genes associated with many key biological processes such as xenobiotics degradation, oxidative stress, and energy metabolism. The constructed miRNA-mRNA-pathway network uncovered a broad post-transcriptional regulatory mechanism in B. belcheri to cope with Cu stress. Overall, this integrated analyses show that enhanced defense response, accelerated ROS elimination, and repressed ATP production constitute a comprehensive strategy to cope with Cu toxicity in the ancient macrobenthos.
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Affiliation(s)
- Lin-Yu Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China; Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou 535011, China
| | - Qian-Hua Zhu
- 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
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Ming-Zhong Liang
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou 535011, China.
| | - Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China.
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Holland ND, Holland LZ. Cephalochordate Hemocytes: First Demonstration for Asymmetron lucayanum (Bahamas Lancelet) Plus Augmented Description for Branchiostoma floridae (Florida Amphioxus). Biol Bull 2023; 244:71-81. [PMID: 37725696 DOI: 10.1086/726774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
AbstractWithin phylum Chordata, the subphylum Cephalochordata (amphioxus and lancelets) has figured large in considerations of the evolutionary origin of the vertebrates. To date, these discussions have been predominantly based on knowledge of a single cephalochordate genus (Branchiostoma), almost to the exclusion of the other two genera (Asymmetron and Epigonichthys). This uneven pattern is illustrated by cephalochordate hematology, until now known entirely from work done on Branchiostoma. The main part of the present study is to describe hemocytes in the dorsal aorta of a species of Asymmetron by serial block-face scanning electron microscopy. This technique, which demonstrates three-dimensional fine structure, showed that the hemocytes have a relatively uniform morphology characterized by an oval shape and scanty cytoplasm. Ancillary information is also included for Branchiostoma hemocytes, known from previous studies to have relatively abundant cytoplasm; our serial block-face scanning electron microscopy provides more comprehensive views of the highly variable shapes of these cells, which typically extend one or several pseudopodium-like protrusions. The marked difference in hemocyte morphology found between Asymmetron and Branchiostoma was unexpected and directs attention to investigating comparable cells in the genus Epigonichthys. A broader knowledge of the hemocytes in all three cephalochordate genera would provide more balanced insights into the evolution of vertebrate hematopoiesis.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Cheng J, Meistertzheim AL, Leistenschneider D, Philip L, Jacquin J, Escande ML, Barbe V, Ter Halle A, Chapron L, Lartaud F, Bertrand S, Escriva H, Ghiglione JF. Impacts of microplastics and the associated plastisphere on physiological, biochemical, genetic expression and gut microbiota of the filter-feeder amphioxus. Environ Int 2023; 172:107750. [PMID: 36669287 DOI: 10.1016/j.envint.2023.107750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/11/2023] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
Oceanic plastic pollution is of major concern to marine organisms, especially filter feeders. However, limited is known about the toxic effects of the weathered microplastics instead of the pristine ones. This study evaluates the effects of weathered polystyrene microplastic on a filter-feeder amphioxus under starvation conditions via its exposure to the microplastics previously deployed in the natural seawater allowing for the development of a mature biofilm (so-called plastisphere). The study focused on the integration of physiological, histological, biochemical, molecular, and microbiota impacts on amphioxus. Overall, specific alterations in gene expression of marker genes were observed to be associated with oxidative stresses and immune systems. Negligible impacts were observed on antioxidant biochemical activities and gut microbiota of amphioxus, while we highlighted the potential transfer of 12 bacterial taxa from the plastisphere to the amphioxus gut microbiota. Moreover, the classical perturbation of body shape detected in control animals under starvation conditions (a slim and curved body) but not for amphioxus exposed to microplastic, indicates that the microorganisms colonizing plastics could serve as a nutrient source for this filter-feeder, commitment with the elevated proportions of goblet cell-like structures after the microplastic exposure. The multidisciplinary approach developed in this study underlined the trait of microplastics that acted as vectors for transporting microorganisms from the plastisphere to amphioxus.
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Affiliation(s)
- Jingguang Cheng
- Sorbonne Université, CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, F-66650 Banyuls-sur-Mer, France
| | | | - David Leistenschneider
- Sorbonne Université, CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, F-66650 Banyuls-sur-Mer, France; SAS Plastic@Sea, Observatoire Océanologique de Banyuls, F-66650, France
| | - Lena Philip
- Sorbonne Université, CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, F-66650 Banyuls-sur-Mer, France; SAS Plastic@Sea, Observatoire Océanologique de Banyuls, F-66650, France
| | - Justine Jacquin
- Sorbonne Université, CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, F-66650 Banyuls-sur-Mer, France
| | - Marie-Line Escande
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, F-91057 Evry, France
| | - Alexandra Ter Halle
- Université de Toulouse, CNRS, UMR 5623, Laboratoire des Interactions Moléculaires et Réactivité Chimique et Photochimique (IMRCP), F-31000 Toulouse, France
| | - Leila Chapron
- SAS Plastic@Sea, Observatoire Océanologique de Banyuls, F-66650, France; Sorbonne Université, CNRS, UMR 8222, Laboratoire d'Ecogéochimie des Environnements Benthiques, Observatoire Océanologique de Banyuls, F-66650 Banyuls-sur-Mer, France
| | - Franck Lartaud
- Sorbonne Université, CNRS, UMR 8222, Laboratoire d'Ecogéochimie des Environnements Benthiques, Observatoire Océanologique de Banyuls, F-66650 Banyuls-sur-Mer, France
| | - Stéphanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Jean-François Ghiglione
- Sorbonne Université, CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, F-66650 Banyuls-sur-Mer, France.
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Cao Y, Li R, Du Y, Jin N, Fang T, Ma F, Jin P. miR-92b-5p negatively regulates IKK through targeting its ORF region in the innate immune responses of amphioxus (Branchiostoma belcheri). Dev Comp Immunol 2023; 138:104556. [PMID: 36167145 DOI: 10.1016/j.dci.2022.104556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Cephalochordate (Amphioxus), situated at a key phylogenetic position in the phylum Chordata, serves as a model organism for studying the origin and evolution of the vertebrate innate immune. In this study, five members of precursor miR-92 family (miR-92a-1, miR-92a-2, miR-92b, miR-92c and miR-92d) are identified in Branchiostoma belcheri, and their evolutionary conservation and potential molecular functions in innate immunity are analyzed. Among them, miR-92b-5p was validated in HEK293 cells to target the coding region but not classic 3'UTR of IKK (inhibitor of nuclear factor kappa-B kinase) mRNA, one integral component of MAPK and TLR4 immune signaling. Furthermore, the spatiotemporal expression patterns of miR-92b-5p and IKK were examined in different tissues or different time points (2 h, 4 h, 8 h, 12 h, 24 h and 48 h) post LPS stimulation at RNA and protein level in vivo. The seemingly inverse expression pattern between miR-92b-5p and IKK supports the involvement of miR-92b-5p in Branchiostoma belcheri innate immune response. In conclusion, our work not only illustrates the evolutionary pattern of Branchiostoma belcheri miR-92 family across chordates, but also reveals that miR-92b-5p could target IKK expression to regulate innate immune response.
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Affiliation(s)
- Yunpeng Cao
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
| | - Ranting Li
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
| | - Yongxin Du
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
| | - Na Jin
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
| | - Tao Fang
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
| | - Fei Ma
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
| | - Ping Jin
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
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7
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Cao Y, Fang T, Du Y, Li R, Fan M, Ma F, Jin P. miR-2013 negatively regulates phylogenetically conserved PIP5K involved in TLR4 mediated immune responses of amphioxus (Branchiostoma belcheri Tsingtaunese). Dev Comp Immunol 2022; 133:104430. [PMID: 35500869 DOI: 10.1016/j.dci.2022.104430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 06/14/2023]
Abstract
Phosphatidylinositol 4-phosphate 5-kinase (PIP5K) is a catalytic kinase that performs multiple functions in organisms. Recent studies have shown that PIP5Kα in mammals can directly participate in the TLR-mediated innate immune regulation by controlling the production of PIP2. However, the PIP5K homologous gene has not been identified in Cephalochordata to date. In this study, we firstly identify and characterize a new PIP5K family member (designed as AmphiPIP5K) from Cephalochordata amphioxus (Branchiostoma belcheri tsingtaunese), particularly AmphiPIP5K is orthologous with vertebrate PIP5Kα and paralogous with PIP5Kβ and PIP5Kγ. Secondly, we find that the AmphiPIP5K is involved in amphioxus innate immune response to LPS stimulation. Thirdly, our results demonstrate that miR-2013 can inhibit AmphiPIP5K expression by binding to the CDS and 3' UTR regions of AmphiPIP5K. Collectively, our work not only demonstrates the evolutionary pattern of amphioxus PIP5K, but also reveals that miR-2013 negatively regulate PIP5K expression to involve in amphioxus innate immune response.
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Affiliation(s)
- Yunpeng Cao
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
| | - Tao Fang
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
| | - Yongxin Du
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
| | - Ranting Li
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
| | - Mingli Fan
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
| | - Fei Ma
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
| | - Ping Jin
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
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8
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Li Z, Shen F, Song L, Zhang S. Antifungal Activity of NP20 Derived from Amphioxus Midkine/Pleiotrophin Homolog Against Aspergillus niger and Aspergillus fumigatus. Mar Biotechnol (NY) 2022; 24:614-625. [PMID: 35610324 DOI: 10.1007/s10126-022-10131-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
With the emergence of antifungal resistance, systematic infections with Aspergillus are becoming the major cause of the clinical morbidity. The development of novel antifungal agents with high efficacy, low drug tolerance, and few side effects is urgent. In response to that need, we have identified NP20. Here we demonstrate clearly that NP20 has antifungal activity, capable of killing the spores of Aspergillus niger and Aspergillus fumigatus as well as causing direct damage to the surface, membrane, cytoplasm, organelle, and nucleus of the fungal spores. Interestingly, NP20 is active under temperature stress and a wide range of pH. Subsequently, MTT assay, assay for binding of NP20 to fungal cell wall components, membrane depolarization assay, confocal microscopy, ROS assay, DNA replication, and protein synthesis assay are performed to clarify the mechanisms underlying NP20 against Aspergillus. The results show that NP20 can bind with and pass through the fungal cell wall, and then interfere with the lipid membrane. Moreover, NP20 can induce intracellular ROS production, DNA fragmentation, and protein synthesis inhibition of the fungal cells. These together indicate that NP20 is a novel antifungal peptide, which has considerable potential for future development as novel peptide antibiotics against Aspergillus.
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Affiliation(s)
- Zhi Li
- Laboratory for Evolution & Development, Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Room 320, 5 Yushan Road, Darwin Building, Qingdao, 266003, China
| | - Fangwang Shen
- Laboratory for Evolution & Development, Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Room 320, 5 Yushan Road, Darwin Building, Qingdao, 266003, China
| | - Lili Song
- Laboratory for Evolution & Development, Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Room 320, 5 Yushan Road, Darwin Building, Qingdao, 266003, China
| | - Shicui Zhang
- Laboratory for Evolution & Development, Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Room 320, 5 Yushan Road, Darwin Building, 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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9
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Luo L, Lu J, Wang Q, Chen S, Xu A, Yuan S. Autophagy participates in innate immune defense in lamprey. Fish Shellfish Immunol 2018; 83:416-424. [PMID: 30195918 DOI: 10.1016/j.fsi.2018.09.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 08/29/2018] [Accepted: 09/05/2018] [Indexed: 06/08/2023]
Abstract
Autophagy is a homeostatic process which degrades cytoplasmic constituents to maintain the balance of organs when they were challenged with nutrient stress. It also participates in cancer, neurodegenerative disorders, aging and innate immune defense. In order to reveal how autophagy participates in innate immune response when invertebrates evolved into vertebrates. Firstly, we performed a systematic analysis of Atg genes and found that they are highly conserved among lancelet, lamprey and zebrafish. Then, we observed autophagosomes upon starvation by TEM in lancelet, lamprey and zebrafish and found that the morphology of autophagosome is similar to that was observed in yeast and mammals. In addition, rapamycin can induce autophagy in lamprey leukocytes and the deficiency of human Beclin1 protein can be rescued by lancelet and lamprey Beclin1 proteins. When lamprey leukocytes were treated with polyI:C and LPS, autophagy was induced. Moreover, when lamprey leukocytes were challenged with live E. coli, phagocytosis along with autophagy was triggered to degrade pathogenic bacteria. In all, our study here indicated that autophagy is highly conserved during evolution and plays a key role in innate defense when invertebrates evolved into vertebrates.
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Affiliation(s)
- Lingjie Luo
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Juan Lu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Qin Wang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, 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, 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, People's Republic of China; School of Life Science, 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, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, People's Republic of China.
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10
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Baker ME, Lathe R. The promiscuous estrogen receptor: Evolution of physiological estrogens and response to phytochemicals and endocrine disruptors. J Steroid Biochem Mol Biol 2018; 184:29-37. [PMID: 30009950 DOI: 10.1016/j.jsbmb.2018.07.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 06/25/2018] [Accepted: 07/03/2018] [Indexed: 01/03/2023]
Abstract
Many actions of estradiol (E2), the principal physiological estrogen in vertebrates, are mediated by estrogen receptor-α (ERα) and ERβ. An important physiological feature of vertebrate ERs is their promiscuous response to several physiological steroids, including estradiol (E2), Δ5-androstenediol, 5α-androstanediol, and 27-hydroxycholesterol. A novel structural characteristic of Δ5-androstenediol, 5α-androstanediol, and 27-hydroxycholesterol is the presence of a C19 methyl group, which precludes the presence of an aromatic A ring with a C3 phenolic group that is a defining property of E2. The structural diversity of these estrogens can explain the response of the ER to synthetic chemicals such as bisphenol A and DDT, which disrupt estrogen physiology in vertebrates, and the estrogenic activity of a variety of plant-derived chemicals such as genistein, coumestrol, and resveratrol. Diversity in the A ring of physiological estrogens also expands potential structures of industrial chemicals that can act as endocrine disruptors. Compared to E2, synthesis of 27-hydroxycholesterol and Δ5-androstenediol is simpler, leading us, based on parsimony, to propose that one or both of these steroids or a related metabolite was a physiological estrogen early in the evolution of the ER, with E2 assuming this role later as the canonical estrogen. In addition to the well-studied role of the ER in reproductive physiology, the ER also is an important transcription factor in non-reproductive tissues such as the cardiovascular system, kidney, bone, and brain. Some of these ER actions in non-reproductive tissues appeared early in vertebrate evolution, long before the emergence of mammals.
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Affiliation(s)
- Michael E Baker
- Division of Nephrology-Hypertension, Department of Medicine, 0693, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0693, USA.
| | - Richard Lathe
- Division of Infection and Pathway Medicine, University of Edinburgh, Little France, Edinburgh, UK.
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11
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Renzi M, Blašković A, Fastelli P, Marcelli M, Guerranti C, Cannas S, Barone L, Massara F. Is the microplastic selective according to the habitat? Records in amphioxus sands, Mäerl bed habitats and Cymodocea nodosa habitats. Mar Pollut Bull 2018; 130:179-183. [PMID: 29866544 DOI: 10.1016/j.marpolbul.2018.03.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/10/2018] [Accepted: 03/12/2018] [Indexed: 05/23/2023]
Abstract
This study estimated for the first time the total loads of plastic litter (macro- meso- and micro-plastics) in sediments of different habitat types from the Northern Adriatic Sea. Samples were collected in March 2016. The sampling sites were settled in shoreline, on the C. nodosa bottoms, Amphioxus sands, and Mäerl bed habitats. Microplastics items were present in all sampling site and ranging within 137-703 items/kg d.w. from Mäerl bed habitat to the shoreline. In C. nodosa bottoms 170 items/kg d.w. were found, while in Amphioxus sands were recorded on average 194 items/kg d.w. Due to the absence of statistical associations among litter levels and abundance of B. lanceolatum in the study area, this research present the needs to develop a new method and more research to for the evaluation of how much the interrelation between sensible habitats and microplastic exist.
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Affiliation(s)
- Monia Renzi
- Bioscience Research Center, Via Aurelia Vecchia, 32, 58015 Orbetello, GR, Italy.
| | - Andrea Blašković
- Bioscience Research Center, Via Aurelia Vecchia, 32, 58015 Orbetello, GR, Italy
| | - Paolo Fastelli
- Bioscience Research Center, Via Aurelia Vecchia, 32, 58015 Orbetello, GR, Italy
| | | | - Cristiana Guerranti
- Bioscience Research Center, Via Aurelia Vecchia, 32, 58015 Orbetello, GR, Italy
| | - Susanna Cannas
- Bioscience Research Center, Via Aurelia Vecchia, 32, 58015 Orbetello, GR, Italy
| | - Lorenzo Barone
- Poliservizi srl, Via di S. Andrea delle Fratte, 24, 00187 Roma, Italy
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12
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Muruganandam G, Raasakka A, Myllykoski M, Kursula I, Kursula P. Structural similarities and functional differences clarify evolutionary relationships between tRNA healing enzymes and the myelin enzyme CNPase. BMC Biochem 2017; 18:7. [PMID: 28511668 PMCID: PMC5434554 DOI: 10.1186/s12858-017-0084-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 05/10/2017] [Indexed: 11/10/2022]
Abstract
BACKGROUND Eukaryotic tRNA splicing is an essential process in the transformation of a primary tRNA transcript into a mature functional tRNA molecule. 5'-phosphate ligation involves two steps: a healing reaction catalyzed by polynucleotide kinase (PNK) in association with cyclic phosphodiesterase (CPDase), and a sealing reaction catalyzed by an RNA ligase. The enzymes that catalyze tRNA healing in yeast and higher eukaryotes are homologous to the members of the 2H phosphoesterase superfamily, in particular to the vertebrate myelin enzyme 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase). RESULTS We employed different biophysical and biochemical methods to elucidate the overall structural and functional features of the tRNA healing enzymes yeast Trl1 PNK/CPDase and lancelet PNK/CPDase and compared them with vertebrate CNPase. The yeast and the lancelet enzymes have cyclic phosphodiesterase and polynucleotide kinase activity, while vertebrate CNPase lacks PNK activity. In addition, we also show that the healing enzymes are structurally similar to the vertebrate CNPase by applying synchrotron radiation circular dichroism spectroscopy and small-angle X-ray scattering. CONCLUSIONS We provide a structural analysis of the tRNA healing enzyme PNK and CPDase domains together. Our results support evolution of vertebrate CNPase from tRNA healing enzymes with a loss of function at its N-terminal PNK-like domain.
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Affiliation(s)
- Gopinath Muruganandam
- Centre for Structural Systems Biology - Helmholtz Centre for Infection Research, German Electron Synchrotron (DESY), Hamburg, Germany
| | - Arne Raasakka
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Matti Myllykoski
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Inari Kursula
- Centre for Structural Systems Biology - Helmholtz Centre for Infection Research, German Electron Synchrotron (DESY), Hamburg, Germany
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Petri Kursula
- Centre for Structural Systems Biology - Helmholtz Centre for Infection Research, German Electron Synchrotron (DESY), Hamburg, Germany
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Biomedicine, University of Bergen, Bergen, Norway
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13
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Lei M, Liu H, Liu S, Zhang Y, Zhang S. Identification and functional characterization of viperin of amphioxus Branchiostoma japonicum: Implications for ancient origin of viperin-mediated antiviral response. Dev Comp Immunol 2015; 53:293-302. [PMID: 26190498 DOI: 10.1016/j.dci.2015.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Revised: 07/09/2015] [Accepted: 07/11/2015] [Indexed: 06/04/2023]
Abstract
Viperin, an antiviral protein, has been shown to be active against a wide range of DNA and RNA viruses, but no information is available regarding functional characterization of viperin in invertebrate species. In this study, we clearly demonstrate that amphioxus (Branchiostoma japonicum) viperin, BjVip, has features in common with those of vertebrate viperin, including the presence of the SAM superfamily domain with the characteristic CNYKCGFC motif, syntenic conservation, and predicted 3D structure. Bjvip exhibits a tissue-specific expression with abundant levels in the hepatic cecum, hind-gut, gill and muscle, and following challenge with the viral mimic poly I:C, its expression is significantly up-regulated, suggesting an involvement of BjVip in immune response of amphioxus against viral infection. Importantly, we show that the cells transfected with Bjvip is able to kill LCDV or inhibiting its propagation, and co-incubation of rBjVip with WSSV markedly attenuates its infectivity. Thus, we provide the first evidences that amphioxus viperin, like that of vertebrates, is capable of promoting resistance against viral infection in vitro and in vivo, indicating that viperin-mediated antiviral response already emerged in the primitive chordate. We also prove that amphioxus viperin has evolved under positive selection.
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Affiliation(s)
- Miaomiao Lei
- Laboratory for Evolution & Development, Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao 266003, PR China
| | - Haohan Liu
- Laboratory for Evolution & Development, Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao 266003, PR China
| | - Shousheng Liu
- Laboratory for Evolution & Development, Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao 266003, PR China
| | - Yu Zhang
- Laboratory for Evolution & Development, Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao 266003, PR China.
| | - Shicui Zhang
- Laboratory for Evolution & Development, Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao 266003, PR China.
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14
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Wang WJ, Cheng W, Luo M, Yan Q, Yu HM, Li Q, Cao DD, Huang S, Xu A, Mariuzza RA, Chen Y, Zhou CZ. Activity Augmentation of Amphioxus Peptidoglycan Recognition Protein BbtPGRP3 via Fusion with a Chitin Binding Domain. PLoS One 2015; 10:e0140953. [PMID: 26479246 PMCID: PMC4610682 DOI: 10.1371/journal.pone.0140953] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 10/02/2015] [Indexed: 11/19/2022] Open
Abstract
Peptidoglycan recognition proteins (PGRPs), which have been identified in most animals, are pattern recognition molecules that involve antimicrobial defense. Resulting from extraordinary expansion of innate immune genes, the amphioxus encodes many PGRPs of diverse functions. For instance, three isoforms of PGRP encoded by Branchiostoma belcheri tsingtauense, termed BbtPGRP1~3, are fused with a chitin binding domain (CBD) at the N-terminus. Here we report the 2.7 Å crystal structure of BbtPGRP3, revealing an overall structure of an N-terminal hevein-like CBD followed by a catalytic PGRP domain. Activity assays combined with site-directed mutagenesis indicated that the individual PGRP domain exhibits amidase activity towards both DAP-type and Lys-type peptidoglycans (PGNs), the former of which is favored. The N-terminal CBD not only has the chitin-binding activity, but also enables BbtPGRP3 to gain a five-fold increase of amidase activity towards the Lys-type PGNs, leading to a significantly broadened substrate spectrum. Together, we propose that modular evolution via domain shuffling combined with gene horizontal transfer makes BbtPGRP1~3 novel PGRPs of augmented catalytic activity and broad recognition spectrum.
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Affiliation(s)
- Wen-Jie Wang
- Hefei National Laboratory for Physical Sciences at Microscale and the Innovation Center for Cell Signaling Network, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Wang Cheng
- Hefei National Laboratory for Physical Sciences at Microscale and the Innovation Center for Cell Signaling Network, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Ming Luo
- Hefei National Laboratory for Physical Sciences at Microscale and the Innovation Center for Cell Signaling Network, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Qingyu Yan
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hong-Mei Yu
- Hefei National Laboratory for Physical Sciences at Microscale and the Innovation Center for Cell Signaling Network, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Qiong Li
- Hefei National Laboratory for Physical Sciences at Microscale and the Innovation Center for Cell Signaling Network, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Dong-Dong Cao
- Hefei National Laboratory for Physical Sciences at Microscale and the Innovation Center for Cell Signaling Network, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Shengfeng Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Anlong Xu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Roy A. Mariuzza
- University of Maryland Institute for Bioscience and Biotechnology Research, W. M. Keck Laboratory for Structural Biology, Rockville, Maryland, United States of America
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Yuxing Chen
- Hefei National Laboratory for Physical Sciences at Microscale and the Innovation Center for Cell Signaling Network, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
- * E-mail: (YC); (CZZ)
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at Microscale and the Innovation Center for Cell Signaling Network, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
- * E-mail: (YC); (CZZ)
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15
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Hopwood N. The cult of amphioxus in German Darwinism; or, our gelatinous ancestors in Naples' blue and balmy bay. Hist Philos Life Sci 2015; 36:371-93. [PMID: 26013195 PMCID: PMC4286652 DOI: 10.1007/s40656-014-0034-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 09/09/2014] [Indexed: 06/04/2023]
Abstract
Biologists having rediscovered amphioxus, also known as the lancelet or Branchiostoma, it is time to reassess its place in early Darwinist debates over vertebrate origins. While the advent of the ascidian-amphioxus theory and challenges from various competitors have been, documented, this article offers a richer account of the public appeal of amphioxus as a primitive ancestor. The focus is on how the 'German Darwin' Ernst Haeckel persuaded general magazine and newspaper readers to revere this "flesh of our flesh and blood of our blood", and especially on Das neue Laienbrevier des Haeckelismus (The new lay breviary of Haeckelism) by Moritz Reymond with cartoons by Fritz Steub. From the late 1870s these successful little books of verse introduced the Neapolitan discoveries that made the animal's name and satirized Haeckel's rise as high priest of its cult. One song is reproduced and translated here, with a contemporary "imitation" by the Canadian palaeontologist Edward John Chapman, and extracts from others. Predating the American "It's a long way from amphioxus" by decades, these rhymes dramatize neglected 'species politics' of Darwinism and highlight the roles of humour in negotiating evolution.
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Affiliation(s)
- Nick Hopwood
- Department of History and Philosophy of Science, University of Cambridge, Free School Lane, Cambridge, CB2 3RH UK
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16
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Jiang B, Liu Y, Chen R, Wang Z, Tariq M, Xia C. Crystallization and preliminary X-ray diffraction analysis of a single variable domain of the immunoglobulin superfamily in amphioxus, Amphi-IgSF-V. Acta Crystallogr F Struct Biol Commun 2014; 70:1072-5. [PMID: 25084385 PMCID: PMC4118807 DOI: 10.1107/s2053230x14012746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 06/01/2014] [Indexed: 11/10/2022] Open
Abstract
Amphioxus is regarded as an essential animal model for the study of immune evolution. Discovery of new molecules with the immunoglobulin superfamily (IgSF) variable (V) domain in amphioxus would help in studying the evolution of IgSF V molecules in the immune system. A protein was found which just contains only one IgSF V domain in amphioxus, termed Amphi-IgSF-V; it has over 30% sequence identity to the V domains of human immunoglobulins and mammalian T-cell receptors. In order to clarify the three-dimensional structure of this new molecule in amphioxus, Amphi-IgSF-V was expressed, purified and crystallized, and diffraction data were collected to a resolution of 1.95 Å. The crystal belonged to space group P3221, with unit-cell parameters a = b = 53.9, c = 135.5 Å. The Matthews coefficient and solvent content were calculated to be 2.58 Å(3) Da(-1) and 52.38%, respectively. The results will provide structural information to study the evolution of IgSF V molecules in the immune system.
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Affiliation(s)
- Bo Jiang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, People’s Republic of China
| | - Yanjie Liu
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, People’s Republic of China
| | - Rong Chen
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, People’s Republic of China
| | - Zhenbao Wang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, People’s Republic of China
| | - Mansoor Tariq
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, People’s Republic of China
| | - Chun Xia
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, People’s Republic of China
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, Beijing, People’s Republic of China
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17
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Pletnev VZ, Pletneva NV, Lukyanov KA, Souslova EA, Fradkov AF, Chudakov DM, Chepurnykh T, Yampolsky IV, Wlodawer A, Dauter Z, Pletnev S. Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine. Acta Crystallogr D Biol Crystallogr 2013; 69:1850-60. [PMID: 23999308 PMCID: PMC3760133 DOI: 10.1107/s0907444913015424] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 06/03/2013] [Indexed: 11/10/2022]
Abstract
A key property of proteins of the green fluorescent protein (GFP) family is their ability to form a chromophore group by post-translational modifications of internal amino acids, e.g. Ser65-Tyr66-Gly67 in GFP from the jellyfish Aequorea victoria (Cnidaria). Numerous structural studies have demonstrated that the green GFP-like chromophore represents the `core' structure, which can be extended in red-shifted proteins owing to modifications of the protein backbone at the first chromophore-forming position. Here, the three-dimensional structures of green laGFP (λex/λem = 502/511 nm) and red laRFP (λex/λem ≃ 521/592 nm), which are fluorescent proteins (FPs) from the lancelet Branchiostoma lanceolatum (Chordata), were determined together with the structure of a red variant laRFP-ΔS83 (deletion of Ser83) with improved folding. Lancelet FPs are evolutionarily distant and share only ∼20% sequence identity with cnidarian FPs, which have been extensively characterized and widely used as genetically encoded probes. The structure of red-emitting laRFP revealed three exceptional features that have not been observed in wild-type fluorescent proteins from Cnidaria reported to date: (i) an unusual chromophore-forming sequence Gly58-Tyr59-Gly60, (ii) the presence of Gln211 at the position of the conserved catalytic Glu (Glu222 in Aequorea GFP), which proved to be crucial for chromophore formation, and (iii) the absence of modifications typical of known red chromophores and the presence of an extremely unusual covalent bond between the Tyr59 C(β) atom and the hydroxyl of the proximal Tyr62. The impact of this covalent bond on the red emission and the large Stokes shift (∼70 nm) of laRFP was verified by extensive structure-based site-directed mutagenesis.
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Affiliation(s)
- Vladimir Z. Pletnev
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Nadya V. Pletneva
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Konstantin A. Lukyanov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Ekaterina A. Souslova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Arkady F. Fradkov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Dmitry M. Chudakov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Tatyana Chepurnykh
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Ilia V. Yampolsky
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL 60439, USA
| | - Sergei Pletnev
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL 60439, USA
- Basic Research Program, SAIC-Frederick, Argonne, IL 60439, USA
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Abstract
The structure of the longitudinal body muscles of Branchiostoma caribaeum has been studied by light and electron microscopy. These muscles are shown to be composed of fibers in the form of flat lamellae about 0.8µ in thickness, more than 100 µ wide, and reaching in length from one intermuscular septum to the next, a distance of about 0.6 mm. Each flat fiber is covered by a plasma membrane and contains a single myofibril consisting of myofilaments packed in the interdigitating hexagonal array characteristic of vertebrate striated muscle. Little or no sarcoplasmic reticulum is present. Mitochondria are found infrequently and have a tubular internal structure. These morphological observations are discussed in relation to a proposed hypothesis of excitation-contraction coupling. It is pointed out that the maximum distance from surface to myofilament in these muscles is about 0.5 µ and that diffusion of an "activating" substance over this distance would essentially be complete in less than 0.5 msec. after its release from the plasma membrane. It is concluded that the flat form of amphioxus muscle substitutes for the specialized mechanisms of excitation-contraction coupling thought possibly to involve the sarcoplasmic reticulum in higher vertebrate muscles.
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TUNG TC, TUNG YY, TU M. [NEURAL INDUCTION IN AMPHIOXUS STUDIED BY EXCHANGE OF BLASTOMERES AT THE 16-CELL STAGE]. Shi Yan Sheng Wu Xue Bao 1964:211-6. [PMID: 14234441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
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WU SC, CAI NE. [FURTHER STUDIES ON THE INTERACTIONS OF VARIOUS PARTS OF THE DEVELOPING AMPHIOXUS EGG]. Shi Yan Sheng Wu Xue Bao 1964:119-29. [PMID: 14200602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
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SERGEEV BF. REACTIONS OF AMPHIOXUS LANCEOLATUS TO EXTERNAL STIMULI. Fed Proc Transl Suppl 1964; 23:218-21. [PMID: 14145639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
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SERGEEV BF. [Reaction of the lancelet (Amphioxus lanceolatus) to external stimuli]. Fiziol Zh SSSR Im I M Sechenova 1963; 49:60-5. [PMID: 13992748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
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TUNG TC, WU SC, TUNG YY. [THE INTERCHANGEABILITY OF ECTODERMAL AND MESODERMAL CELLS IN AMPHIOXUS]. Shi Yan Sheng Wu Xue Bao 1963:408-14. [PMID: 14110601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
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TUNG TC, U SC, YEH YF. [Differentiation of the prospective ectodermal and entodermal cells after transplantation to new surroundings in Amphioxus]. Shi Yan Sheng Wu Xue Bao 1961; 7:253-62. [PMID: 13923089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/24/2023]
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TUNG TC, U SC, YEH YF. [Experimental studies on neural induction in Amphioxus]. Shi Yan Sheng Wu Xue Bao 1961; 7:263-70. [PMID: 13923090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/24/2023]
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STOLK A. Chromaffinoma in Amphioxus. Proc K Ned Akad Wet C 1961; 64:478-488. [PMID: 24547001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
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COVELLI I, SALVATORE G, SENA L, ROCHE J. [On the formation of thyroid hormones and of their precursors by Branchiostoma lanceolatum Pallas (Amphioxus)]. C R Seances Soc Biol Fil 1960; 154:1165-1169. [PMID: 24545560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
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TUNG TC, WU SC, TUNG YY. The developmental potencies of the blastomere layers in Amphioxus egg at the 32-cell stage. Sci Sin 1960; 9:119-41. [PMID: 13839832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/24/2023]
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ZAPF K, MOHAMED AAA. [Fine structure and function of striated muscular apparatus of the trunk of Branchiostoma lanceolatum (Amphioxus)]. Acta Biol Med Ger 1959; 2:331-4. [PMID: 13660658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/23/2023]
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ZAPF K, MOHAMED AA. [On submicroscopic morphology and function of the striated musculature of Branchiostoma lanceolatum (Amphioxus)]. Acta Biol Med Ger 1959; 2:508-19. [PMID: 13847013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/24/2023]
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TUNG TC, WU SC, TUNG YF. The development of isolated blastomeres of Amphioxus. Sci Sin 1958; 7:1280-320. [PMID: 13624735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/23/2023]
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ADAM H. [The third ventricle and the microscopic structure of its walls in Lampetra (Petromyzon) fluviatilis L. and Myxine glutinosa L., with some remarks on the infundibular organ of Branchiostoma (Amphioxus) lanceolatum Pall]. Prog Neurobiol 1956:146-58. [PMID: 13441790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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TENBAUM E. [Polarizing - microscopic study of tissues of the Branchiostoma lanceolatum (P)]. Z Zellforsch Mikrosk Anat 1955; 42:149-92. [PMID: 13257611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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EARLY development of amphioxus. Med Biol Illus 1951; 1:172-5. [PMID: 14890099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
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