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Chen J, Yu X, Yu K, Chen B, Qin Z, Liao Z, Ma Y, Xu L, Wang Y. Potential adaptation of scleractinian coral Pocillopora damicornis during hypo-salinity stress caused by extreme pre-flood rainfall over south China. ENVIRONMENTAL RESEARCH 2024; 262:119848. [PMID: 39216737 DOI: 10.1016/j.envres.2024.119848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 08/23/2024] [Accepted: 08/25/2024] [Indexed: 09/04/2024]
Abstract
Global warming intensifies the water cycle, resulting in significant increases in precipitation and river runoff, which brings severe hypo-salinity stress to nearshore coral reefs. Ecological investigations have found that some corals exhibit remarkable adaptability to hypo-salinity stress during mass-bleaching events. However, the exact cause of this phenomenon remains unclear. To elucidate the potential molecular mechanism leading to high tolerance to hypo-salinity stress, Pocillopora damicornis was used as a research object in this study. We compared the differences in transcriptional responses and symbiotic microbiomes between bleaching and unbleaching P. damicornis during hypo-salinity stress caused by extreme pre-flood rainfall over South China in 2022. The results showed that: (1) Under hypo-salinity stress, the coral genes related to immune defense and cellular stress were significantly upregulated in bleaching corals, indicating more severe immune damage and stress, and the Symbiodiniaceae had no significant gene enrichment. Conversely, metabolic genes related to glycolysis/gluconeogenesis were significantly downregulated in unbleaching corals, whereas Symbiodiniaceae genes related to oxidative phosphorylation were significantly upregulated to meet the energy requirements of coral holobiont; (2) C1d was the dominant Symbiodiniaceae subclade in all samples, with no significant difference between the two groups; (3) The symbiotic bacterial community structure was reorganized under hypo-salinity stress. The abundance of opportunistic bacteria increased significantly in bleaching coral, whereas the relative abundance of probiotics was higher in unbleaching coral. This may be due to severe immune damage, making the coral more susceptible to opportunistic infection and bleaching. These results suggest that long-term hypo-salinity acclimation in the Pearl River Estuary enhances the tolerance of some corals to hypo-salinity stress. Corals with higher tolerance may reduce energy consumption by slowing down their metabolism, improve the energy metabolism of Symbiodiniaceae to meet the energy requirements of the coral holobiont, and alter the structure of symbiotic bacterial communities to avoid bleaching.
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Affiliation(s)
- Junling Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Xiaopeng Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China.
| | - Biao Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhenjun Qin
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhiheng Liao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China; Nanning Normal University, Nanning, China
| | - Yuling Ma
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Lijia Xu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, China.
| | - Yongzhi Wang
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, China
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2
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Lin CY, Marlétaz F, Pérez-Posada A, Martínez-García PM, Schloissnig S, Peluso P, Conception GT, Bump P, Chen YC, Chou C, Lin CY, Fan TP, Tsai CT, Gómez Skarmeta JL, Tena JJ, Lowe CJ, Rank DR, Rokhsar DS, Yu JK, Su YH. Chromosome-level genome assemblies of 2 hemichordates provide new insights into deuterostome origin and chromosome evolution. PLoS Biol 2024; 22:e3002661. [PMID: 38829909 PMCID: PMC11175523 DOI: 10.1371/journal.pbio.3002661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/13/2024] [Accepted: 05/03/2024] [Indexed: 06/05/2024] Open
Abstract
Deuterostomes are a monophyletic group of animals that includes Hemichordata, Echinodermata (together called Ambulacraria), and Chordata. The diversity of deuterostome body plans has made it challenging to reconstruct their ancestral condition and to decipher the genetic changes that drove the diversification of deuterostome lineages. Here, we generate chromosome-level genome assemblies of 2 hemichordate species, Ptychodera flava and Schizocardium californicum, and use comparative genomic approaches to infer the chromosomal architecture of the deuterostome common ancestor and delineate lineage-specific chromosomal modifications. We show that hemichordate chromosomes (1N = 23) exhibit remarkable chromosome-scale macrosynteny when compared to other deuterostomes and can be derived from 24 deuterostome ancestral linkage groups (ALGs). These deuterostome ALGs in turn match previously inferred bilaterian ALGs, consistent with a relatively short transition from the last common bilaterian ancestor to the origin of deuterostomes. Based on this deuterostome ALG complement, we deduced chromosomal rearrangement events that occurred in different lineages. For example, a fusion-with-mixing event produced an Ambulacraria-specific ALG that subsequently split into 2 chromosomes in extant hemichordates, while this homologous ALG further fused with another chromosome in sea urchins. Orthologous genes distributed in these rearranged chromosomes are enriched for functions in various developmental processes. We found that the deeply conserved Hox clusters are located in highly rearranged chromosomes and that maintenance of the clusters are likely due to lower densities of transposable elements within the clusters. We also provide evidence that the deuterostome-specific pharyngeal gene cluster was established via the combination of 3 pre-assembled microsyntenic blocks. We suggest that since chromosomal rearrangement events and formation of new gene clusters may change the regulatory controls of developmental genes, these events may have contributed to the evolution of diverse body plans among deuterostomes.
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Affiliation(s)
- Che-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Ferdinand Marlétaz
- Center for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Alberto Pérez-Posada
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Pedro Manuel Martínez-García
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | | | - Paul Peluso
- Pacific Biosciences, Menlo Park, California, United States of America
| | | | - Paul Bump
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, California, United States of America
| | - Yi-Chih Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Cindy Chou
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Ching-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Tzu-Pei Fan
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Chang-Tai Tsai
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - José Luis Gómez Skarmeta
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Juan J. Tena
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Christopher J. Lowe
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, California, United States of America
- Chan-Zuckerberg Biohub, San Francisco, California, United States of America
| | - David R. Rank
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Daniel S. Rokhsar
- Chan-Zuckerberg Biohub, San Francisco, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
- Molecular Genetics Unit, Okinawa Institute for Science and Technology, Onna, Japan
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
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3
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He LS, Qi Y, Allard CAH, Valencia-Montoya WA, Krueger SP, Weir K, Seminara A, Bellono NW. Molecular tuning of sea anemone stinging. eLife 2023; 12:RP88900. [PMID: 37906220 PMCID: PMC10617991 DOI: 10.7554/elife.88900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023] Open
Abstract
Jellyfish and sea anemones fire single-use, venom-covered barbs to immobilize prey or predators. We previously showed that the anemone Nematostella vectensis uses a specialized voltage-gated calcium (CaV) channel to trigger stinging in response to synergistic prey-derived chemicals and touch (Weir et al., 2020). Here, we use experiments and theory to find that stinging behavior is suited to distinct ecological niches. We find that the burrowing anemone Nematostella uses uniquely strong CaV inactivation for precise control of predatory stinging. In contrast, the related anemone Exaiptasia diaphana inhabits exposed environments to support photosynthetic endosymbionts. Consistent with its niche, Exaiptasia indiscriminately stings for defense and expresses a CaV splice variant that confers weak inactivation. Chimeric analyses reveal that CaVβ subunit adaptations regulate inactivation, suggesting an evolutionary tuning mechanism for stinging behavior. These findings demonstrate how functional specialization of ion channel structure contributes to distinct organismal behavior.
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Affiliation(s)
- Lily S He
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - Yujia Qi
- Machine Learning Center Genoa (MalGa), Department of Civil, Chemical and Environmental Engineering (DICCA), University of GenoaGenoaItaly
| | - Corey AH Allard
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - Wendy A Valencia-Montoya
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard UniversityCambridgeUnited States
| | - Stephanie P Krueger
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - Keiko Weir
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - Agnese Seminara
- Machine Learning Center Genoa (MalGa), Department of Civil, Chemical and Environmental Engineering (DICCA), University of GenoaGenoaItaly
| | - Nicholas W Bellono
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
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4
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He LS, Qi Y, Allard CAH, Valencia-Montoya WA, Krueger SP, Weir K, Seminara A, Bellono NW. Molecular tuning of sea anemone stinging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.15.545144. [PMID: 37577638 PMCID: PMC10418081 DOI: 10.1101/2023.06.15.545144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Jellyfish and sea anemones fire single-use, venom-covered barbs to immobilize prey or predators. We previously showed that the anemone Nematostella vectensis uses a specialized voltage-gated calcium (CaV) channel to trigger stinging in response to synergistic prey-derived chemicals and touch (Weir et al., 2020). Here we use experiments and theory to find that stinging behavior is suited to distinct ecological niches. We find that the burrowing anemone Nematostella uses uniquely strong CaV inactivation for precise control of predatory stinging. In contrast, the related anemone Exaiptasia diaphana inhabits exposed environments to support photosynthetic endosymbionts. Consistent with its niche, Exaiptasia indiscriminately stings for defense and expresses a CaV splice variant that confers weak inactivation. Chimeric analyses reveal that CaVβ subunit adaptations regulate inactivation, suggesting an evolutionary tuning mechanism for stinging behavior. These findings demonstrate how functional specialization of ion channel structure contributes to distinct organismal behavior.
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Affiliation(s)
- Lily S He
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138 USA
| | - Yujia Qi
- Machine Learning Center Genoa (MalGa), Department of Civil, Chemical and Environmental Engineering (DICCA), University of Genoa, Via Montallegro 1, 16145 Genoa, Italy
| | - Corey AH Allard
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138 USA
| | - Wendy A Valencia-Montoya
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138 USA
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge MA 02138 USA
| | - Stephanie P Krueger
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138 USA
| | - Keiko Weir
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138 USA
| | - Agnese Seminara
- Machine Learning Center Genoa (MalGa), Department of Civil, Chemical and Environmental Engineering (DICCA), University of Genoa, Via Montallegro 1, 16145 Genoa, Italy
| | - Nicholas W Bellono
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138 USA
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5
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Fu JR, Zhou J, Zhang YP, Liu L. Effects of Caulerpa taxifolia on Physiological Processes and Gene Expression of Acropora hyacinthus during Thermal Stress. BIOLOGY 2022; 11:biology11121792. [PMID: 36552301 PMCID: PMC9775474 DOI: 10.3390/biology11121792] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
An increasing ecological phase shift from coral-dominated reefs to macroalgae-dominated reefs as a result of anthropogenic impacts, such as eutrophication, sedimentation, and overfishing, has been observed in many reef systems around the world. Ocean warming is a universal threat to both corals and macroalgae, which may alter the outcome of competition between them. Therefore, in order to explore the effects of indirect and direct exposure to macroalgae on the physiological, biochemical, and genetic expression of corals at elevated temperature, the coral Acropora hyacinthus and highly invasive green algae Caulerpa taxifolia were chosen. Physiologically, the results exhibited that, between the control and direct contact treatments, the density and chlorophyll a content of zooxanthella decreased by 53.1% and 71.2%, respectively, when the coral indirectly contacted with the algae at an ambient temperature (27 °C). Moreover, the enzyme activities of superoxide dismutase (SOD) and catalase (CAT) in coral tissue were enhanced by interacting with algae. After an increase of 3 °C, the density and chlorophyll a content of the zooxanthella reduced by 84.4% and 93.8%, respectively, whereas the enzyme activities of SOD and CAT increased 2.3- and 3.1-fold. However, only the zooxanthellae density and pigment content decreased when Caulerpa taxifolia was co-cultured with Acropora hyacinthus at 30 °C. Molecularly, different from the control group, the differentially expressed genes (DEGs) such as Rab family, ATG family, and Casp7 genes were significantly enriched in the endocytosis, autophagy, and apoptosis pathways, regardless of whether Acropora hyacinthus was directly or indirectly exposed to Caulerpa taxifolia at 27 °C. Under thermal stress without algae interaction, the DEGs were significantly enriched in the microbial immune signal transduction pathways, such as the Toll-like receptor signaling pathway and TNF signaling pathway, while multiple cellular immunity (IFI47, TRAF family) and oxidative stress (CAT, SODC, HSP70) genes were upregulated. Inversely, compared with corals without interaction with algae at 30 °C, the DEGs of the corals that interacted with Caulerpa taxifolia at 30 °C were remarkably enriched in apoptosis and the NOD-like receptor signaling pathway, including the transcription factors such as the Casp family and TRAF family. In conclusion, the density and chlorophyll a content of zooxanthella maintained a fading tendency induced by the macroalgae at ambient temperatures. The oxidative stress and immune response levels of the coral was elevated at 30 °C, but the macroalgae alleviated the negative effects triggered by thermal stress.
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Affiliation(s)
- Jian-Rong Fu
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Jie Zhou
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yan-Ping Zhang
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Li Liu
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
- Guangdong Laboratory of Southern Ocean Science and Engineering, Zhanjiang 524025, China
- Correspondence:
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6
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Sarper SE, Hirai T, Matsuyama T, Kuratani S, Fujimoto K. Polymorphism in the symmetries of gastric pouch arrangements in the sea anemone D. lineata. ZOOLOGICAL LETTERS 2021; 7:12. [PMID: 34488893 PMCID: PMC8419960 DOI: 10.1186/s40851-021-00180-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Symmetry in the arrangement of body parts is a distinctive phylogenetic feature of animals. Cnidarians show both bilateral and radial symmetries in their internal organs, such as gastric pouches and muscles. However, how different symmetries appear during the developmental process remains unknown. Here, we report intraspecific variations in the symmetric arrangement of gastric pouches, muscles, and siphonoglyphs, the Anthozoan-specific organ that drives water into the organism, in D. lineata (Diadumenidae, Actiniaria). We found that the positional arrangement of the internal organs was apparently constrained to either biradial or bilateral symmetries depending on the number of siphonoglyphs. Based on the morphological observations, a mathematical model of internal organ positioning was employed to predict the developmental backgrounds responsible for the biradial and bilateral symmetries. In the model, we assumed that the specification of gastric pouches is orchestrated by lateral inhibition and activation, which results in different symmetries depending on the number of siphonoglyphs. Thus, we propose that a common developmental program can generate either bilateral or biradial symmetries depending on the number of siphonoglyphs formed in the early developmental stages.
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Affiliation(s)
- Safiye E Sarper
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, Japan
| | - Tamami Hirai
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, Japan
| | - Take Matsuyama
- Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, Kobe, 650-0047, Japan
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, Japan
- Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR), Kobe, 650-0047, Japan
| | - Koichi Fujimoto
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan.
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Weir K, Dupre C, van Giesen L, Lee ASY, Bellono NW. A molecular filter for the cnidarian stinging response. eLife 2020; 9:57578. [PMID: 32452384 PMCID: PMC7250568 DOI: 10.7554/elife.57578] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 05/09/2020] [Indexed: 01/06/2023] Open
Abstract
All animals detect and integrate diverse environmental signals to mediate behavior. Cnidarians, including jellyfish and sea anemones, both detect and capture prey using stinging cells called nematocytes which fire a venom-covered barb via an unknown triggering mechanism. Here, we show that nematocytes from Nematostella vectensis use a specialized voltage-gated calcium channel (nCaV) to distinguish salient sensory cues and control the explosive discharge response. Adaptations in nCaV confer unusually sensitive, voltage-dependent inactivation to inhibit responses to non-prey signals, such as mechanical water turbulence. Prey-derived chemosensory signals are synaptically transmitted to acutely relieve nCaV inactivation, enabling mechanosensitive-triggered predatory attack. These findings reveal a molecular basis for the cnidarian stinging response and highlight general principles by which single proteins integrate diverse signals to elicit discrete animal behaviors.
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Affiliation(s)
- Keiko Weir
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Christophe Dupre
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Lena van Giesen
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Amy S-Y Lee
- Department of Biology, Brandeis University, Waltham, United States
| | - Nicholas W Bellono
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
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8
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Bouchard C, Michaels J, Brown-Harding H. RNA isolation from corals and other cnidarian species using urea-LiCl as a denaturant. Anal Biochem 2020; 588:113472. [PMID: 31605694 DOI: 10.1016/j.ab.2019.113472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/08/2019] [Indexed: 11/28/2022]
Abstract
A method of RNA isolation using a solution of urea-LiCl as a denaturing agent was tested on stony coral. As the method does not require homogenization of tissues prior to their incubation in the denaturant, specimen collected in the field can be immediately transferred to the urea-LiCl solution. The method was also tested on tissues of other cnidarian species. RNA was isolated from fresh tissues of jellyfish and sea anemones using two protocols - that is, incubations in the urea-LiCl solution were either performed on homogenized tissues or on intact tissues or specimen. RNA quality was evaluated on a bioanalyser.
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Affiliation(s)
- Christelle Bouchard
- College of Science and Mathematics, University of South Florida, 8350 N Tamiami Trail, Sarasota, FL, 34243, USA.
| | - Jay Michaels
- College of Science and Mathematics, University of South Florida, 8350 N Tamiami Trail, Sarasota, FL, 34243, USA
| | - Heather Brown-Harding
- Department of Biology and Center for Molecular Signaling, Wake Forest University, 455 Vine Street, Winston Salem, NC, 27101, USA
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Surm JM, Stewart ZK, Papanicolaou A, Pavasovic A, Prentis PJ. The draft genome of Actinia tenebrosa reveals insights into toxin evolution. Ecol Evol 2019; 9:11314-11328. [PMID: 31641475 PMCID: PMC6802032 DOI: 10.1002/ece3.5633] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 08/06/2019] [Accepted: 08/12/2019] [Indexed: 12/17/2022] Open
Abstract
Sea anemones have a wide array of toxic compounds (peptide toxins found in their venom) which have potential uses as therapeutics. To date, the majority of studies characterizing toxins in sea anemones have been restricted to species from the superfamily, Actinioidea. No highly complete draft genomes are currently available for this superfamily, however, highlighting our limited understanding of the genes encoding toxins in this important group. Here we have sequenced, assembled, and annotated a draft genome for Actinia tenebrosa. The genome is estimated to be approximately 255 megabases, with 31,556 protein-coding genes. Quality metrics revealed that this draft genome matches the quality and completeness of other model cnidarian genomes, including Nematostella, Hydra, and Acropora. Phylogenomic analyses revealed strong conservation of the Cnidaria and Hexacorallia core-gene set. However, we found that lineage-specific gene families have undergone significant expansion events compared with shared gene families. Enrichment analysis performed for both gene ontologies, and protein domains revealed that genes encoding toxins contribute to a significant proportion of the lineage-specific genes and gene families. The results make clear that the draft genome of A. tenebrosa will provide insight into the evolution of toxins and lineage-specific genes, and provide an important resource for the discovery of novel biological compounds.
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Affiliation(s)
- Joachim M. Surm
- Faculty of HealthSchool of Biomedical SciencesQueensland University of TechnologyKelvin GroveQldAustralia
- Institute of Health and Biomedical InnovationQueensland University of TechnologyKelvin GroveQldAustralia
| | - Zachary K. Stewart
- Science and Engineering FacultySchool of Earth, Environmental and Biological SciencesQueensland University of TechnologyBrisbaneQldAustralia
- Institute for Future EnvironmentsQueensland University of TechnologyBrisbaneQldAustralia
| | | | - Ana Pavasovic
- Faculty of HealthSchool of Biomedical SciencesQueensland University of TechnologyKelvin GroveQldAustralia
| | - Peter J. Prentis
- Science and Engineering FacultySchool of Earth, Environmental and Biological SciencesQueensland University of TechnologyBrisbaneQldAustralia
- Institute for Future EnvironmentsQueensland University of TechnologyBrisbaneQldAustralia
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10
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Wu Y, Zhou Z, Wang J, Luo J, Wang L, Zhang Y. Temperature regulates the recognition activities of a galectin to pathogen and symbiont in the scleractinian coral Pocillopora damicornis. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 96:103-110. [PMID: 30857983 DOI: 10.1016/j.dci.2019.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 06/09/2023]
Abstract
Lectins serve as essential pattern recognition receptors, and play important roles in the recognition of non-self and mediation of innate immune response in metazoans. Scleractinian corals are vulnerable to pathogen infection and endosymbiosis disruption under heat stress that can finally lead to coral bleaching. In this study, a cDNA sequence encoding one galectin was cloned in scleractinian coral Pocillopora damicornis (PdGLT-1). The deduced PdGLT-1 protein shared highest amino acid sequence similarity (99%) with galectin from Stylophora pistillata (XP_022806650.1), and was composed of one signal peptide, one Collagen domain and one Gal-Lectin domain. PdGLT-1 recombinant protein (rPdGLT-1) was expressed and purified in vitro. Binding activities of rPdGLT-1 to bacteria and symbiont were determined using western blotting method. Results showed that rPdGLT-1 was able to bind to gram-positive bacterium Streptococcus mutans, gram-negative bacteria Vibrio coralliilyticus and Escherichia coli, with the highest activity for V. coralliilyticus, and further agglutinated them. The bound rPdGLT-1 to Symbiodinium (10-104 cells mL-1) was detectable, and its binding ability was concentration-dependent. Furthermore, dual binding activities were determined under different temperatures (20, 25, 30 and 35 °C), and the optimal temperatures were found to be 25 and 30 °C for V. coralliilyticus and Symbiodinium, respectively. Results suggested that PdGLT-1 could recognize pathogenic bacteria and symbiotic dinoflagellates Symbiodinium. However, their recognition activities were repressed under high temperature (>30 °C). This study provided insights into the underlying mechanism of lectin modulation to heat bleaching through its pathogen and Symbiodinium recognition in the scleractinian coral P. damicornis.
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Affiliation(s)
- Yibo Wu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, 570228, China
| | - Zhi Zhou
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, 570228, China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Science, Hainan University, Haikou, 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China.
| | - Jun Wang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, 570228, China
| | - Jian Luo
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, 570228, China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Science, Hainan University, Haikou, 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Lingui Wang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, 570228, China
| | - Yidan Zhang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, 570228, China
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Zhou Z, Zhao S, Tang J, Liu Z, Wu Y, Wang Y, Lin S. Altered Immune Landscape and Disrupted Coral- Symbiodinium Symbiosis in the Scleractinian Coral Pocillopora damicornis by Vibrio coralliilyticus Challenge. Front Physiol 2019; 10:366. [PMID: 31001143 PMCID: PMC6454040 DOI: 10.3389/fphys.2019.00366] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/15/2019] [Indexed: 01/07/2023] Open
Abstract
Vibrio coralliilyticus is known to cause coral diseases, especially under environmental perturbation, but its impact on coral physiology and underpinning mechanism is poorly understood. In the present study, we investigated cytological, immunological, and metatranscriptomic responses of the scleractinian coral Pocillopora damicornis to V. coralliilyticus infection. The density and chlorophyll content of symbiotic zooxanthellae decreased significantly at 12 and 24 h after Vibrio challenge. The activities of antioxidant enzymes such as superoxide dismutase and catalase, nitric oxide synthase, phenoloxidase (PO), and the activation level of caspase3 all rose significantly in P. damicornis after Vibrio challenge. In the metatranscriptomic analysis, we found 10 significantly upregulated genes in the symbionts at 24 h after the challenge, which were mostly involved in the metabolism of nucleic acid and polysaccharide, and 133 significantly down-regulated symbiont genes, which were mainly related to amino acid catabolism and transport. Meanwhile, 1432 significantly upregulated coral genes were revealed, highly overrepresented in GO terms that are mostly related to the regulation of immune response, the regulation of cytokine production, and innate immune response. Furthermore, at 24 h after Vibrio challenge, 890 coral genes were significantly downregulated, highly overrepresented in four GO terms implicated in defense response. These results in concert suggest that V. coralliilyticus infection triggered the innate immune response including the redox, PO, and apoptosis systems, but repressed the response of the complement system in the scleractinian coral P. damicornis, accompanied by symbiont density decrease and symbiosis collapse through disordering the metabolism of the symbionts. These findings shed light on the molecular regulatory processes underlying bleaching and degradation of P. damicornis resulting from the infection of V. coralliilyticus.
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Affiliation(s)
- Zhi Zhou
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, China.,Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China
| | - Shuimiao Zhao
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, China
| | - Jia Tang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, China
| | - Zhaoqun Liu
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, China
| | - Yibo Wu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, China
| | - Yan Wang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, China
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, CT, United States
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Karabulut A, He S, Chen CY, McKinney SA, Gibson MC. Electroporation of short hairpin RNAs for rapid and efficient gene knockdown in the starlet sea anemone, Nematostella vectensis. Dev Biol 2019; 448:7-15. [PMID: 30641041 DOI: 10.1016/j.ydbio.2019.01.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/18/2018] [Accepted: 01/04/2019] [Indexed: 10/27/2022]
Abstract
A mechanistic understanding of evolutionary developmental biology requires the development of novel techniques for the manipulation of gene function in phylogenetically diverse organismal systems. Recently, gene-specific knockdown by microinjection of short hairpin RNA (shRNA) was applied in the sea anemone Nematostella vectensis, demonstrating that the shRNA approach can be used for efficient and robust sequence-specific knockdown of a gene of interest. However, the time- and labor-intensive process of microinjection limits access to this technique and its application in large scale experiments. To address this issue, here we present an electroporation protocol for shRNA delivery into Nematostella eggs. This method leverages the speed and simplicity of electroporation, enabling users to manipulate gene expression in hundreds of eggs or embryos within minutes. We provide a detailed description of the experimental procedure, including reagents, electroporation conditions, preparation of Nematostella eggs, and follow-up care of experimental animals. Finally, we demonstrate the knockdown of several endogenous and exogenous genes with known phenotypes and discuss the potential applications of this method.
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Affiliation(s)
- Ahmet Karabulut
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Shuonan He
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Cheng-Yi Chen
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Sean A McKinney
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Matthew C Gibson
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA; Dept. Anatomy and Cell Biology, University of Kansas School of Medicine, Kansas City, KS 66160 USA.
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Tang J, Ni X, Zhou Z, Wang L, Lin S. Acute microplastic exposure raises stress response and suppresses detoxification and immune capacities in the scleractinian coral Pocillopora damicornis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 243:66-74. [PMID: 30172125 DOI: 10.1016/j.envpol.2018.08.045] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/13/2018] [Accepted: 08/14/2018] [Indexed: 05/20/2023]
Abstract
Microplastics are widespread emerging contaminants that have been found globally in the marine and freshwater ecosystem, but there is limited knowledge regarding its impact on coral reef ecosystem and underpinning mechanism. In the present study, using Pocillopora damicornis as a model, we investigated cytological, physiological, and molecular responses of a scleractinian coral to acute microplastic exposure. No significant changes were observed in the density of symbiotic zooxanthellae during the entire period of microplastic exposure, while its chlorophyll content increased significantly at 12 h of microplastic exposure. We observed significant increases in the activities of antioxidant enzymes such as superoxide dismutase and catalase, significant decrease in the detoxifying enzyme glutathione S-transferase and the immune enzyme alkaline phosphatase, but no change in the other immune enzyme phenoloxidase during the whole experiment period. Transcriptomic analysis revealed 134 significantly up-regulated coral genes at 12 h after the exposure, enriched in 11 GO terms mostly related to stress response, zymogen granule, and JNK signal pathway. Meanwhile, 215 coral genes were significantly down-regulated at 12 h after exposure, enriched in 25 GO terms involved in sterol transport and EGF-ERK1/2 signal pathway. In contrast, only 12 zooxanthella genes exhibited significant up-regulation and 95 genes down-regulation at 12 h after the microplastic exposure; genes regulating synthesis and export of glucose and amino acids were not impacted. These results suggest that acute exposure of microplastics can activate the stress response of the scleractinian coral P. damicornis, and repress its detoxification and immune system through the JNK and ERK signal pathways. These demonstrate that microplastic exposure can compromise the anti-stress capacity and immune system of the scleractinian coral P. damicornis, despite the minimal impact on the abundance and major photosynthate translocation transporters of the symbiont in the short term.
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Affiliation(s)
- Jia Tang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, Hainan, China
| | - Xingzhen Ni
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, Hainan, China
| | - Zhi Zhou
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, Hainan, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, China; Department of Marine Sciences, University of Connecticut, Groton, CT, USA.
| | - Lingui Wang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, Hainan, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, China
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
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Possible roles of glutamine synthetase in responding to environmental changes in a scleractinian coral. Mol Biol Rep 2018; 45:2115-2124. [PMID: 30203242 DOI: 10.1007/s11033-018-4369-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/06/2018] [Indexed: 10/28/2022]
Abstract
Glutamine synthetase is an enzyme that plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine. In this study, the activity and responses of glutamine synthetase towards environmental changes were investigated in the scleractinian coral Pocillopora damicornis. The identified glutamine synthetase (PdGS) was comprised of 362 amino acids and predicted to contain one Gln-synt_N and one Gln-synt_C domain. Expression of PdGS mRNA increased significantly after 12 h (1.28-fold, p < 0.05) of exposure to elevated ammonium, while glutamine synthetase activity increased significantly from 12 to 24 h, peaking at 12 h (54.80 U mg-1, p < 0.05). The recombinant protein of the mature PdGS (rPdGS) was expressed in E. coli BL21, and its activities were detected under different temperature, pH and glufosinate levels. The highest levels of rPdGS activity were observed at 25 °C and pH 8 respectively, but decreased significantly at lower temperature, and higher or lower pH. Furthermore, the level of rPdGS activities was negatively correlated with the concentration of glufosinate, specifically decreasing at 10-5 mol L-1 glufosinate to be less than 50% (p < 0.05) of that in the blank. These results collectively suggest that PdGS, as a homologue of glutamine synthetase, was involved in the nitrogen assimilation in the scleractinian coral. Further, its physiological functions could be suppressed by high temperature, ocean acidification and residual glufosinate, which might further regulate the coral-zooxanthella symbiosis via the nitrogen metabolism in the scleractinian coral P. damicornis.
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Zhou Z, Zhao S, Ni J, Su Y, Wang L, Xu Y. Effects of environmental factors on C-type lectin recognition to zooxanthellae in the stony coral Pocillopora damicornis. FISH & SHELLFISH IMMUNOLOGY 2018; 79:228-233. [PMID: 29775739 DOI: 10.1016/j.fsi.2018.05.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 05/14/2018] [Accepted: 05/14/2018] [Indexed: 06/08/2023]
Abstract
C-type lectin is a superfamily of Ca2+-dependent carbohydrate-recognition proteins that play significant roles in nonself-recognition and pathogen clearance. In the present study, a C-type lectin (PdC-Lectin) was chosen from stony coral Pocillopora damicornis to understand its recognition characteristics to zooxanthellae. PdC-Lectin protein contained a signal peptide and a carbohydrate-recognition domain with EPN motif in Ca2+-binding site 2. The PdC-Lectin recombinant protein was expressed and purified in vitro. The binding of PdC-Lectin protein to zooxanthellae was determined with western blotting method, and the bound protein to 10-105 cell mL-1 zooxanthellae was detectable in a concentration-dependent manner. Less PdC-Lectin protein binding to zooxanthellae was observed for the incubation at 36 °C than that at 26 °C. Furthermore, the PAMP recognition spectrum of PdC-Lectin protein was tested through surface plasmon resonance method, and it bound to LPS and Lipid A, but not to LTA, β-glucan, mannose or Poly (I:C). When PdC-Lectin protein was preincubated with LPS, there was less protein binding to zooxanthellae compared with that in non-preincubation group. These results collectively suggest that PdC-Lectin could recognize zooxanthellae, and the recognition could be repressed by high temperature and pathogenic bacteria, which would help to further understand the molecular mechanism of coral bleaching and the establishment of coral-zooxanthella symbiosis in the stony coral P. damicornis.
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Affiliation(s)
- Zhi Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou 570228, China.
| | - Shuimiao Zhao
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou 570228, China
| | - Junyi Ni
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou 570228, China
| | - Yilu Su
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou 570228, China
| | - Lingui Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China; Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou 570228, China
| | - Yanlai Xu
- Department of Traditional Chinese Medicine, The Qingdao First Sanitarium of Navy, Qingdao 266071, China
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Zhang Y, Zhou Z, Wang L, Huang B. Transcriptome, expression, and activity analyses reveal a vital heat shock protein 70 in the stress response of stony coral Pocillopora damicornis. Cell Stress Chaperones 2018; 23:711-721. [PMID: 29435724 PMCID: PMC6045544 DOI: 10.1007/s12192-018-0883-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 01/25/2018] [Accepted: 01/30/2018] [Indexed: 12/29/2022] Open
Abstract
Coral bleaching occurs worldwide with increasing frequencies and intensities, which is caused by the stress response of stony coral to environmental change, especially increased sea surface temperature. In the present study, transcriptome, expression, and activity analyses were employed to illustrate the underlying molecular mechanisms of heat shock protein 70 (HSP70) in the stress response of coral to environmental changes. The domain analyses of assembled transcripts revealed 30 HSP70 gene contigs in stony coral Pocillopora damicornis. One crucial HSP70 (PdHSP70) was observed, whose expressions were induced by both elevated temperature and ammonium after expression difference analysis. The complete complementary DNA (cDNA) sequence of PdHSP70 was identified, which encoded a polypeptide of 650 amino acids with a molecular weight of 71.93 kDa. The deduced amino acid sequence of PdHSP70 contained a HSP70 domain (from Pro8 to Gly616), and it shared the highest similarity (95%) with HSP70 from Stylophora pistillata. The expression level of PdHSP70 gene increased significantly at 12 h, and returned to the initial level at 24 h after the stress of high temperature (32 °C). The cDNA fragment encoding the mature peptide of PdHSP70 was recombined and expressed in the prokaryotic expression system. The ATPase activity of recombinant PdHSP70 protein was determined, and it did not change significantly in a wide range of temperature from 25 to 40 °C. These results collectively suggested that PdHSP70 was a vital heat shock protein 70 in the stony coral P. damicornis, whose mRNA expression could be induced by diverse environmental stress and whose activity could remain stable under heat stress. PdHSP70 might be involved in the regulation of the bleaching owing to heat stress in the stony coral P. damicornis.
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Affiliation(s)
- Yidan Zhang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, Hainan, 570228, China
| | - Zhi Zhou
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, Hainan, 570228, China.
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, China.
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Science, Hainan University, Haikou, Hainan, 570228, China.
| | - Lingui Wang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, Hainan, 570228, China
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, China
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Science, Hainan University, Haikou, Hainan, 570228, China
| | - Bo Huang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, Hainan, 570228, China
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, China
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Science, Hainan University, Haikou, Hainan, 570228, China
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Intraspecific variation in oxidative stress tolerance in a model cnidarian: Differences in peroxide sensitivity between and within populations of Nematostella vectensis. PLoS One 2018; 13:e0188265. [PMID: 29373572 PMCID: PMC5786289 DOI: 10.1371/journal.pone.0188265] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/05/2017] [Indexed: 12/27/2022] Open
Abstract
Nematostella vectensis is a member of the phylum Cnidaria, a lineage that includes anemones, corals, hydras, and jellyfishes. This estuarine anemone is an excellent model system for investigating the evolution of stress tolerance because it is easy to collect in its natural habitat and to culture in the laboratory, and it has a sequenced genome. Additionally, there is evidence of local adaptation to environmental stress in different N. vectensis populations, and abundant protein-coding polymorphisms have been identified, including polymorphisms in proteins that are implicated in stress responses. N. vectensis can tolerate a wide range of environmental parameters, and has recently been shown to have substantial intraspecific variation in temperature preference. We investigated whether different clonal lines of anemones also exhibit differential tolerance to oxidative stress. N. vectensis populations are continually exposed to reactive oxygen species (ROS) generated during cellular metabolism and by other environmental factors. Fifteen clonal lines of N. vectensis collected from four different estuaries were exposed to hydrogen peroxide. Pronounced differences in survival and regeneration were apparent between clonal lines collected from Meadowlands, NJ, Baruch, SC, and Kingsport, NS, as well as among 12 clonal lines collected from a single Cape Cod marsh. To our knowledge, this is the first example of intraspecific variability in oxidative stress resistance in cnidarians or in any marine animal. As oxidative stress often accompanies heat stress in marine organisms, resistance to oxidative stress could strongly influence survival in warming oceans. For example, while elevated temperatures trigger bleaching in corals, oxidative stress is thought to be the proximal trigger of bleaching at the cellular level.
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Yu X, Huang B, Zhou Z, Tang J, Yu Y. Involvement of caspase3 in the acute stress response to high temperature and elevated ammonium in stony coral Pocillopora damicornis. Gene 2017; 637:108-114. [DOI: 10.1016/j.gene.2017.09.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 09/14/2017] [Accepted: 09/19/2017] [Indexed: 12/29/2022]
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Zhou Z, Wu Y, Zhang C, Li C, Chen G, Yu X, Shi X, Xu Y, Wang L, Huang B. Suppression of NF-κB signal pathway by NLRC3-like protein in stony coral Acropora aculeus under heat stress. FISH & SHELLFISH IMMUNOLOGY 2017; 67:322-330. [PMID: 28606864 DOI: 10.1016/j.fsi.2017.06.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 06/06/2017] [Accepted: 06/08/2017] [Indexed: 06/07/2023]
Abstract
Heat stress is the most common factor for coral bleaching, which has increased both in frequency and severity due to global warming. In the present study, the stony coral Acropora aculeus was subjected to acute heat stress and entire transcriptomes were sequenced via the next generation sequencing platform. Four paired-end libraries were constructed and sequenced in two groups, including a control and a heat stress group. A total of 120,319,751 paired-end reads with lengths of 2 × 100 bp were assembled and 55,021 coral-derived genes were obtained. After read mapping and abundance estimation, 9110 differentially expressed genes were obtained in the comparison between the control and heat stress group, including 4465 significantly upregulated and 4645 significantly downregulated genes. Twenty-three GO terms in the Biological Process category were overrepresented for significantly upregulated genes, and divided into six groups according to their relationship. These three groups were related to the NF-κB signal pathway, and the remaining three groups were relevant for pathogen response, immunocyte activation and protein ubiquitination. Forty-three common genes were found in four GO terms, which were directly related to the NF-κB signal pathway. These included 2 NACHT, LRR, PYD domains-containing protein, 5 nucleotide-binding oligomerization domain-containing protein, 29 NLRC3-like protein, 4 NLRC5-like protein, and 3 uncharacterized protein. For significantly downregulated genes, 27 overrepresented GO terms were found in the Biological Process category, which were relevant to protein ubiquitination and ATP metabolism. Our results indicate that heat stress suppressed the immune response level via the NLRC3-like protein, the fine-tuning of protein turnover activity, and ATP metabolism. This might disrupt the balance of coral-zooxanthellae symbiosis and result in the bleaching of the coral A. aculeus.
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Affiliation(s)
- Zhi Zhou
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou 570228, China.
| | - Yibo Wu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou 570228, China
| | - Chengkai Zhang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou 570228, China
| | - Can Li
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou 570228, China
| | - Guangmei Chen
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou 570228, China
| | - Xiaopeng Yu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou 570228, China
| | | | - Yanlai Xu
- Qingdao First Sanitarium of Jinan Military Region, Qingdao 266071, China
| | - Lingui Wang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou 570228, China
| | - Bo Huang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou 570228, China
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A transcriptional time-course analysis of oral vs. aboral whole-body regeneration in the Sea anemone Nematostella vectensis. BMC Genomics 2016; 17:718. [PMID: 27605362 PMCID: PMC5015328 DOI: 10.1186/s12864-016-3027-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/20/2016] [Indexed: 02/07/2023] Open
Abstract
Background The ability of regeneration is essential for the homeostasis of all animals as it allows the repair and renewal of tissues and body parts upon normal turnover or injury. The extent of this ability varies greatly in different animals with the sea anemone Nematostella vectensis, a basal cnidarian model animal, displaying remarkable whole-body regeneration competence. Results In order to study this process in Nematostella we performed an RNA-Seq screen wherein we analyzed and compared the transcriptional response to bisection in the wound-proximal body parts undergoing oral (head) or aboral (tail) regeneration at several time points up to the initial restoration of the basic body shape. The transcriptional profiles of regeneration responsive genes were analyzed so as to define the temporal pattern of differential gene expression associated with the tissue-specific oral and aboral regeneration. The identified genes were characterized according to their GO (gene ontology) assignations revealing groups that were enriched in the regeneration process with particular attention to their affiliation to the major developmental signaling pathways. While some of the genes and gene groups thus analyzed were previously known to be active in regeneration, we have also revealed novel and surprising candidate genes such as cilia-associated genes that likely participate in this important developmental program. Conclusions This work highlighted the main groups of genes which showed polarization upon regeneration, notably the proteinases, multiple transcription factors and the Wnt pathway genes that were highly represented, all displaying an intricate temporal balance between the two sides. In addition, the evolutionary comparison performed between regeneration in different animal model systems may reveal the basic mechanisms playing a role in this fascinating process. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3027-1) contains supplementary material, which is available to authorized users.
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Harishankar A, Chandy M, Bhattacharya S. How to develop an in-house real-time quantitative cytomegalovirus polymerase chain reaction: Insights from a cancer centre in Eastern India. Indian J Med Microbiol 2015; 33:482-90. [PMID: 26470952 DOI: 10.4103/0255-0857.167351] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Development of a reliable, cost-effective cytomegalovirus quantitative polymerase chain reaction (QPCR) is a priority for developing countries. Manufactured kits are expensive, and availability can be inconsistent. Development of an in-house QPCR kit that is reliable and quality assured requires significant effort and initial investment. However, the rewards of such an enterprise are manifold and include an in-depth understanding of molecular reactions, and expertise in the development of further low-cost molecular kits. The experience of an oncology centre in Eastern India has been shared. Hopefully, this would provide a brief roadmap for such an initiative. Staff with adequate understanding of molecular processes are essential along with vital infrastructure for molecular research and development.
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Affiliation(s)
| | | | - Sanjay Bhattacharya
- Departments of Microbiology and Clinical Hematology, Tata Medical Center, Rajarhat, Kolkata, India
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Warren CR, Kassir E, Spurlin J, Martinez J, Putnam NH, Farach-Carson MC. Evolution of the perlecan/HSPG2 gene and its activation in regenerating Nematostella vectensis. PLoS One 2015; 10:e0124578. [PMID: 25876075 PMCID: PMC4398486 DOI: 10.1371/journal.pone.0124578] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 02/24/2015] [Indexed: 01/08/2023] Open
Abstract
The heparan sulfate proteoglycan 2 (HSPG2)/perlecan gene is ancient and conserved in all triploblastic species. Its presence maintains critical cell boundaries in tissue and its large (up to ~900 kDa) modular structure has prompted speculation about the evolutionary origin of the gene. The gene's conservation amongst basal metazoans is unclear. After the recent sequencing of their genomes, the cnidarian Nematostella vectensis and the placozoan Trichoplax adhaerens have become favorite models for studying tissue regeneration and the evolution of multicellularity. More ancient basal metazoan phyla include the poriferan and ctenophore, whose evolutionary relationship has been clarified recently. Our in silico and PCR-based methods indicate that the HSPG2 gene is conserved in both the placozoan and cnidarian genomes, but not in those of the ctenophores and only partly in poriferan genomes. HSPG2 also is absent from published ctenophore and Capsaspora owczarzaki genomes. The gene in T. adhaerens is encoded as two separate but genetically juxtaposed genes that house all of the constituent pieces of the mammalian HSPG2 gene in tandem. These genetic constituents are found in isolated genes of various poriferan species, indicating a possible intronic recombinatory mechanism for assembly of the HSPG2 gene. Perlecan's expression during wound healing and boundary formation is conserved, as expression of the gene was activated during tissue regeneration and reformation of the basement membrane of N. vectensis. These data indicate that the complex HSPG2 gene evolved concurrently in a common ancestor of placozoans, cnidarians and bilaterians, likely along with the development of differentiated cell types separated by acellular matrices, and is activated to reestablish these tissue borders during wound healing.
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Affiliation(s)
- Curtis R. Warren
- Department of BioSciences, Rice University, Houston, Texas, United States
| | - Elias Kassir
- Department of BioSciences, Rice University, Houston, Texas, United States
| | - James Spurlin
- Department of BioSciences, Rice University, Houston, Texas, United States
| | - Jerahme Martinez
- Department of BioSciences, Rice University, Houston, Texas, United States
| | - Nicholas H. Putnam
- Department of BioSciences, Rice University, Houston, Texas, United States
| | - Mary C. Farach-Carson
- Department of BioSciences, Rice University, Houston, Texas, United States
- Department of Bioengineering, Rice University, Houston, Texas, United States
- * E-mail:
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Stefanik DJ, Lubinski TJ, Granger BR, Byrd AL, Reitzel AM, DeFilippo L, Lorenc A, Finnerty JR. Production of a reference transcriptome and transcriptomic database (EdwardsiellaBase) for the lined sea anemone, Edwardsiella lineata, a parasitic cnidarian. BMC Genomics 2014; 15:71. [PMID: 24467778 PMCID: PMC3909931 DOI: 10.1186/1471-2164-15-71] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 12/11/2013] [Indexed: 12/20/2022] Open
Abstract
Background The lined sea anemone Edwardsiella lineata is an informative model system for evolutionary-developmental studies of parasitism. In this species, it is possible to compare alternate developmental pathways leading from a larva to either a free-living polyp or a vermiform parasite that inhabits the mesoglea of a ctenophore host. Additionally, E. lineata is confamilial with the model cnidarian Nematostella vectensis, providing an opportunity for comparative genomic, molecular and organismal studies. Description We generated a reference transcriptome for E. lineata via high-throughput sequencing of RNA isolated from five developmental stages (parasite; parasite-to-larva transition; larva; larva-to-adult transition; adult). The transcriptome comprises 90,440 contigs assembled from >15 billion nucleotides of DNA sequence. Using a molecular clock approach, we estimated the divergence between E. lineata and N. vectensis at 215–364 million years ago. Based on gene ontology and metabolic pathway analyses and gene family surveys (bHLH-PAS, deiodinases, Fox genes, LIM homeodomains, minicollagens, nuclear receptors, Sox genes, and Wnts), the transcriptome of E. lineata is comparable in depth and completeness to N. vectensis. Analyses of protein motifs and revealed extensive conservation between the proteins of these two edwardsiid anemones, although we show the NF-κB protein of E. lineata reflects the ancestral structure, while the NF-κB protein of N. vectensis has undergone a split that separates the DNA-binding domain from the inhibitory domain. All contigs have been deposited in a public database (EdwardsiellaBase), where they may be searched according to contig ID, gene ontology, protein family motif (Pfam), enzyme commission number, and BLAST. The alignment of the raw reads to the contigs can also be visualized via JBrowse. Conclusions The transcriptomic data and database described here provide a platform for studying the evolutionary developmental genomics of a derived parasitic life cycle. In addition, these data from E. lineata will aid in the interpretation of evolutionary novelties in gene sequence or structure that have been reported for the model cnidarian N. vectensis (e.g., the split NF-κB locus). Finally, we include custom computational tools to facilitate the annotation of a transcriptome based on high-throughput sequencing data obtained from a “non-model system.”
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Affiliation(s)
| | | | | | | | | | | | | | - John R Finnerty
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA.
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24
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Fischer AHL, Tulin S, Fredman D, Smith J. Employing BAC-reporter constructs in the sea anemone Nematostella vectensis. Integr Comp Biol 2013; 53:832-46. [PMID: 23956207 DOI: 10.1093/icb/ict091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Changes in the expression and function of genes drive evolutionary change. Comparing how genes are regulated in different species is therefore becoming an important part of evo-devo studies. A key tool for investigating the regulation of genes is represented by bacterial artificial chromosomes (BAC)-reporter constructs. BACs are large insert libraries, often >100 kb, which thus capture the genomic sequences surrounding a gene of interest, including all, or nearly all, of the elements underpinning regulation. Recombinant BACs, containing a reporter gene in place of the endogenous coding sequence of genes, can be utilized to drive the expression of reporter genes under the regulatory control of the gene of interest while still embedded within its genomic context. Systematic deletions within the BAC-reporter construct can be used to identify the minimal reporter in an unbiased way, avoiding the risk of overlooking regulatory elements that may be many kilobases away from the transcription start-site. Nematostella vectensis (Edwardsiidae, Anthozoa, Cnidaria) has become an important model in regenerative biology, ecology, and especially in studies of evo-devo and gene-regulatory networks due to its interesting phylogenetic position and amenability to molecular techniques. The increasing interest in this rising model system also led to a demand for methods that can be used to study the regulation of genes in Nematostella. Here, we present our progress in employing BAC-reporter constructs to visualize gene-expression in Nematostella. Using a new Nematostella-specific recombination cassette, we made nine different BAC-reporter constructs. Although five BAC recombinants gave variable effects, three constructs, namely Nv-bra:eGFP::L10 BAC, Nv-dpp:eGFP::L10 BAC, and Nv-grm:eGFP::L10 BAC delivered promising results. We show that these three constructs express the reporter gene eGFP in 10.4-17.2% of all analyzed larvae, out of which 26.2-41.9% express GFP in a mosaic fashion within the expected domain. In addition to the expression within the known domains, we also observed cases of misexpression of eGFP and examples that could represent actual expression outside the described domain. Furthermore, we deep-sequenced and assembled five different BACs containing Nv-chordin, Nv-foxa, Nv-dpp, Nv-wnta, and Nv-wnt1, to improve assembly around these genes. The use of BAC-reporter constructs will foster cis-regulatory analyses in Nematostella and thus help to improve our understanding of the regulatory network in this cnidarian system. Ultimately, this will advance the comparison of gene-regulation across species and lead to a much better understanding of evolutionary changes and novelties.
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Affiliation(s)
- Antje H L Fischer
- *Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA; Department of Molecular Evolution and Development, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
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