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Jiang L, Zhang P, Huang LT, Yu XL, Liu CY, Yuan XC, Liu S, Huang H. Life-stage specificity and temporal variations in transcriptomes and DNA methylomes of the reef coral Pocillopora damicornis in response to thermal acclimation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 921:171098. [PMID: 38387572 DOI: 10.1016/j.scitotenv.2024.171098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 02/03/2024] [Accepted: 02/17/2024] [Indexed: 02/24/2024]
Abstract
Understanding the acclimation capacity of reef corals across generations to thermal stress and its underlying molecular underpinnings could provide insights into their resilience and adaptive responses to future climate change. Here, we acclimated adult brooding coral Pocillopora damicornis to high temperature (32 °C vs. 29 °C) for three weeks and analyzed the changes in phenotypes, transcriptomes and DNA methylomes of adult corals and their brooded larvae. Results showed that although adult corals did not show noticeable bleaching after thermal exposure, they released fewer but larger larvae. Interestingly, larval cohorts from two consecutive lunar days exhibited contrasting physiological resistance to thermal stress, as evidenced by the divergent responses of area-normalized symbiont densities and photochemical efficiency to thermal stress. RNA-seq and whole-genome bisulfite sequencing revealed that adult and larval corals mounted distinct transcriptional and DNA methylation changes in response to thermal stress. Remarkably, larval transcriptomes and DNA methylomes also varied greatly among lunar days and thermal treatments, aligning well with their physiological metrics. Overall, our study shows that changes in transcriptomes and DNA methylomes in response to thermal acclimation can be highly life stage-specific. More importantly, thermally-acclimated adult corals could produce larval offspring with temporally contrasting photochemical performance and thermal resilience, and such variations in larval phenotypes are associated with differential transcriptomes and DNA methylomes, and are likely to increase the likelihood of reproductive success and plasticity of larval propagules under thermal stress.
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Affiliation(s)
- Lei Jiang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou 510301, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, SCSIO, Sanya 572000, China; Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China
| | - Pan Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou 510301, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, SCSIO, Sanya 572000, China; Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin-Tao Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou 510301, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, SCSIO, Sanya 572000, China; Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Lei Yu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou 510301, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, SCSIO, Sanya 572000, China; Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China
| | - Cheng-Yue Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou 510301, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, SCSIO, Sanya 572000, China; Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China
| | - Xiang-Cheng Yuan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou 510301, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, SCSIO, Sanya 572000, China; Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China
| | - Sheng Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou 510301, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, SCSIO, Sanya 572000, China; Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China
| | - Hui Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou 510301, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, SCSIO, Sanya 572000, China; Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China.
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Ayers TN, Nicotra ML, Lee MT. Parallels and contrasts between the cnidarian and bilaterian maternal-to-zygotic transition are revealed in Hydractinia embryos. PLoS Genet 2023; 19:e1010845. [PMID: 37440598 PMCID: PMC10368294 DOI: 10.1371/journal.pgen.1010845] [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: 05/11/2023] [Revised: 07/25/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Embryogenesis requires coordinated gene regulatory activities early on that establish the trajectory of subsequent development, during a period called the maternal-to-zygotic transition (MZT). The MZT comprises transcriptional activation of the embryonic genome and post-transcriptional regulation of egg-inherited maternal mRNA. Investigation into the MZT in animals has focused almost exclusively on bilaterians, which include all classical models such as flies, worms, sea urchin, and vertebrates, thus limiting our capacity to understand the gene regulatory paradigms uniting the MZT across all animals. Here, we elucidate the MZT of a non-bilaterian, the cnidarian Hydractinia symbiolongicarpus. Using parallel poly(A)-selected and non poly(A)-dependent RNA-seq approaches, we find that the Hydractinia MZT is composed of regulatory activities similar to many bilaterians, including cytoplasmic readenylation of maternally contributed mRNA, delayed genome activation, and separate phases of maternal mRNA deadenylation and degradation that likely depend on both maternally and zygotically encoded clearance factors, including microRNAs. But we also observe massive upregulation of histone genes and an expanded repertoire of predicted H4K20 methyltransferases, aspects thus far particular to the Hydractinia MZT and potentially underlying a novel mode of early embryonic chromatin regulation. Thus, similar regulatory strategies with taxon-specific elaboration underlie the MZT in both bilaterian and non-bilaterian embryos, providing insight into how an essential developmental transition may have arisen in ancestral animals.
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Affiliation(s)
- Taylor N. Ayers
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh Pennsylvania, United States of America
| | - Matthew L. Nicotra
- Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Miler T. Lee
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh Pennsylvania, United States of America
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3
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Ayers TN, Nicotra ML, Lee MT. Parallels and contrasts between the cnidarian and bilaterian maternal-to-zygotic transition are revealed in Hydractinia embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540083. [PMID: 37214839 PMCID: PMC10197650 DOI: 10.1101/2023.05.09.540083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Embryogenesis requires coordinated gene regulatory activities early on that establish the trajectory of subsequent development, during a period called the maternal-to-zygotic transition (MZT). The MZT comprises transcriptional activation of the embryonic genome and post-transcriptional regulation of egg-inherited maternal mRNA. Investigation into the MZT in animals has focused almost exclusively on bilaterians, which include all classical models such as flies, worms, sea urchin, and vertebrates, thus limiting our capacity to understand the gene regulatory paradigms uniting the MZT across all animals. Here, we elucidate the MZT of a non-bilaterian, the cnidarian Hydractinia symbiolongicarpus . Using parallel poly(A)-selected and non poly(A)-dependent RNA-seq approaches, we find that the Hydractinia MZT is composed of regulatory activities analogous to many bilaterians, including cytoplasmic readenylation of maternally contributed mRNA, delayed genome activation, and separate phases of maternal mRNA deadenylation and degradation that likely depend on both maternally and zygotically encoded clearance factors, including microRNAs. But we also observe massive upregulation of histone genes and an expanded repertoire of predicted H4K20 methyltransferases, aspects thus far unique to the Hydractinia MZT and potentially underlying a novel mode of early embryonic chromatin regulation. Thus, similar regulatory strategies with taxon-specific elaboration underlie the MZT in both bilaterian and non-bilaterian embryos, providing insight into how an essential developmental transition may have arisen in ancestral animals.
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Affiliation(s)
- Taylor N. Ayers
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15213 U.S.A
| | - Matthew L. Nicotra
- Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA 15261 U.S.A
| | - Miler T. Lee
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15213 U.S.A
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Reich HG, Camp EF, Roger LM, Putnam HM. The trace metal economy of the coral holobiont: supplies, demands and exchanges. Biol Rev Camb Philos Soc 2023; 98:623-642. [PMID: 36897260 DOI: 10.1111/brv.12922] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022]
Abstract
The juxtaposition of highly productive coral reef ecosystems in oligotrophic waters has spurred substantial interest and progress in our understanding of macronutrient uptake, exchange, and recycling among coral holobiont partners (host coral, dinoflagellate endosymbiont, endolithic algae, fungi, viruses, bacterial communities). By contrast, the contribution of trace metals to the physiological performance of the coral holobiont and, in turn, the functional ecology of reef-building corals remains unclear. The coral holobiont's trace metal economy is a network of supply, demand, and exchanges upheld by cross-kingdom symbiotic partnerships. Each partner has unique trace metal requirements that are central to their biochemical functions and the metabolic stability of the holobiont. Organismal homeostasis and the exchanges among partners determine the ability of the coral holobiont to adjust to fluctuating trace metal supplies in heterogeneous reef environments. This review details the requirements for trace metals in core biological processes and describes how metal exchanges among holobiont partners are key to sustaining complex nutritional symbioses in oligotrophic environments. Specifically, we discuss how trace metals contribute to partner compatibility, ability to cope with stress, and thereby to organismal fitness and distribution. Beyond holobiont trace metal cycling, we outline how the dynamic nature of the availability of environmental trace metal supplies can be influenced by a variability of abiotic factors (e.g. temperature, light, pH, etc.). Climate change will have profound consequences on the availability of trace metals and further intensify the myriad stressors that influence coral survival. Lastly, we suggest future research directions necessary for understanding the impacts of trace metals on the coral holobiont symbioses spanning subcellular to organismal levels, which will inform nutrient cycling in coral ecosystems more broadly. Collectively, this cross-scale elucidation of the role of trace metals for the coral holobiont will allow us to improve forecasts of future coral reef function.
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Affiliation(s)
- Hannah G Reich
- Department of Biological Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI, 02881, USA
| | - Emma F Camp
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Liza M Roger
- Chemical & Life Science Engineering, Virginia Commonwealth University, 601 W. Main Street, Richmond, VA, 23284, USA
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI, 02881, USA
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Jiang K, Nie H, Yin Z, Yan X, Li Q. Apextrin from Ruditapes philippinarum functions as pattern recognition receptor and modulates NF-κB pathway. Int J Biol Macromol 2022; 214:33-44. [PMID: 35697169 DOI: 10.1016/j.ijbiomac.2022.06.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 12/28/2022]
Abstract
Apextrin belongs to ApeC-containing proteins (ACPs) and features a signal-peptide, an N-terminal membrane attack complex component/perforin (MACPF) domain, and a C-terminal ApeC domain. Recently, apextrin-like proteins were identified as pattern recognition receptor (PRR), which recognize the bacterial cell wall component and participate in innate immunity. Here, an apextrin (Rpape) was identified and characterized in Ruditapes philippinarum. Our results showed that Rpape mRNA was significantly induced under bacterial challenges. The Rpape recombinant protein exhibited a significant inhibitory effect on gram-positive bacteria (Bacillus subtilis and Staphylococcus aureus) and bound with Vibrio anguillarum, S. aureus and B. subtilis. We found Rpape protein positively activated the NF-κB signaling cascade and increased the activity of Nitric oxide (NO). This study revealed the immunity role of apextrin in R. philippinarum and provided a reference for further study on the role of apextrin in bivalves.
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Affiliation(s)
- Kunyin Jiang
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China; Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Hongtao Nie
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China.
| | - Zhihui Yin
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China
| | - Xiwu Yan
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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6
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Ishii Y, Hatta M, Deguchi R, Kawata M, Maruyama S. Gene expression alterations from reversible to irreversible stages during coral metamorphosis. ZOOLOGICAL LETTERS 2022; 8:4. [PMID: 35078542 PMCID: PMC8787945 DOI: 10.1186/s40851-022-00187-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
For corals, metamorphosis from planktonic larvae to sedentary polyps is an important life event, as it determines the environment in which they live for a lifetime. Although previous studies on the reef-building coral Acropora have clarified a critical time point during metamorphosis when cells are committed to their fates, as defined by an inability to revert back to their previous states as swimming larvae (here referred to as the "point of no return"), the molecular mechanisms of this commitment to a fate remain unclear. To address this issue, we analyzed the transcriptomic changes before and after the point of no return by inducing metamorphosis of Acropora tenuis with Hym-248, a metamorphosis-inducing neuropeptide. Gene Ontology and pathway enrichment analysis of the 5893 differentially expressed genes revealed that G protein-coupled receptors (GPCRs) were enriched, including GABA receptor and Frizzled gene subfamilies, which showed characteristic temporal expression patterns. The GPCRs were then classified by comparison with those of Homo sapiens, Nematostella vectensis and Platynereis dumerilii. Classification of the differentially expressed genes into modules based on expression patterns showed that some modules with large fluctuations after the point of no return were biased toward functions such as protein metabolism and transport. This result suggests that in precommitted larvae, different types of GPCR genes function to ensure a proper environment, whereas in committed larvae, intracellular protein transport and proteolysis may cause a loss of the reversibility of metamorphosis as a result of cell differentiation.
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Affiliation(s)
- Yuu Ishii
- Department of Biology, Miyagi University of Education, Aoba-ku, Sendai, Sendai, Miyagi 980-0845 Japan
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8578 Japan
| | - Masayuki Hatta
- Graduate School of Humanities and Sciences, Ochanomizu University, Bunkyo-ku, Tokyo, 112-8610 Japan
| | - Ryusaku Deguchi
- Department of Biology, Miyagi University of Education, Aoba-ku, Sendai, Sendai, Miyagi 980-0845 Japan
| | - Masakado Kawata
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8578 Japan
| | - Shinichiro Maruyama
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8578 Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, Bunkyo-ku, Tokyo, 112-8610 Japan
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Chuang PS, Mitarai S. Genetic changes involving the coral gastrovascular system support the transition between colonies and bailed-out polyps: evidence from a Pocillopora acuta transcriptome. BMC Genomics 2021; 22:694. [PMID: 34563133 PMCID: PMC8466926 DOI: 10.1186/s12864-021-08026-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 09/13/2021] [Indexed: 11/21/2022] Open
Abstract
Background A coral colony is composed of physiologically integrated polyps. In stony corals, coloniality adopts a wide diversity of forms and involves complex ontogenetic dynamics. However, molecular mechanisms underlying coloniality have been little studied. To understand the genetic basis of coloniality and its contribution to coral ecology, we induced polyp bail-out in a colonial coral, Pocillopora acuta, and compared transcription profiles of bailed-out polyps and polyps in normal colonies, and their responses to heat shock and hyposalinity. Results Consistent with morphological formation of a gastrovascular system and its neural transmission and molecular transport functions, we found genetic activation of neurogenesis and development of tube-like structures in normal colonies that is absent in bailed-out polyps. Moreover, relative to bailed-out polyps, colonies showed significant overexpression of genes for angiotensin-converting enzymes and endothelin-converting enzymes. In response to hyperthermal and hyposaline treatments, a high proportion of genetic regulation proved specific to either bailed-out polyps or colonies. Elevated temperatures even activated NF-κB signaling in colonies. On the other hand, colonies showed no discernible advantage over bailed-out polyps in regard to hyposalinity. Conclusions The present study provides a first look at the genetic basis of coloniality and documents different responses to environmental stimuli in P. acuta colonies versus those in bailed-out polyps. Overexpression of angiotensin-converting enzymes and endothelin-converting enzymes in colonies suggests possible involvement of these genes in development of the gastrovascular system in P. acuta. Functional characterization of these coral genes and further investigation of other forms of the transition to coloniality in stony corals should be fruitful areas for future research. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08026-x.
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Affiliation(s)
- Po-Shun Chuang
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Kunigami-gun , 904-0495, Okinawa, Japan.
| | - Satoshi Mitarai
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Kunigami-gun , 904-0495, Okinawa, Japan
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Li J, Li Y, Fan Z, Chen S, Yan X, Yue Z, Huang G, Liu S, Zhang H, Chen S, Dong M, Xu A, Huang S. Two Amphioxus ApeC-Containing Proteins Bind to Microbes and Inhibit the TRAF6 Pathway. Front Immunol 2021; 12:715245. [PMID: 34394119 PMCID: PMC8361754 DOI: 10.3389/fimmu.2021.715245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
The apextrin C-terminal (ApeC) domain is a class of newly discovered protein domains with an origin dating back to prokaryotes. ApeC-containing proteins (ACPs) have been found in various marine and aquatic invertebrates, but their functions and the underlying mechanisms are largely unknown. Early studies suggested that amphioxus ACP1 and ACP2 bind to bacterial cell walls and have a role in immunity. Here we identified another two amphioxus ACPs (ACP3 and ACP5), which belong to the same phylogenetic clade with ACP1/2, but show distinct expression patterns and sequence divergence (40-50% sequence identities). Both ACP3 and ACP5 were mainly expressed in the intestine and hepatic cecum, and could be up-regulated after bacterial challenge. Both prokaryotic-expressed recombinant ACP3 and ACP5 could bind with several species of bacteria and yeasts, showing agglutinating activity but no microbicidal activity. ELISA assays suggested that their ApeC domains could interact with peptidoglycan (PGN), but not with lipoteichoic acid (LTA), lipopolysaccharides (LPS) and zymosan A. Furthermore, they can only bind to Lys-type PGN from Staphylococcus aureus, but not to DAP-type PGN from Bacillus subtilis and not to moieties of PGN such as MDPs, NAMs and NAGs. This recognition spectrum is different from that of ACP1/2. We also found that when expressed in mammalian cells, ACP3 could interact with TRAF6 via a conserved non-ApeC region, which inhibited the ubiquitination of TRAF6 and hence suppressed downstream NF-κB activation. This work helped define a novel subfamily of ACPs, which have conserved structures, and have related yet diversified molecular functions. Its members have dual roles, with ApeC as a lectin and a conserved unknown region as a signal transduction regulator. These findings expand our understanding of the ACP functions and may guide future research on the role of ACPs in different animal clades.
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Affiliation(s)
- Jin Li
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yuhui Li
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhaoyu Fan
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shenghui Chen
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xinyu Yan
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zirui Yue
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Guangrui Huang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Shumin Liu
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hao Zhang
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shangwu Chen
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Meiling Dong
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Anlong Xu
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Shengfeng Huang
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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9
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Li Y, Li J, Yan X, Chen S, Wu C, Huang H, Shi Y, Huang G, Dong M, Xu A, Huang S. Broad distribution, high diversity and ancient origin of the ApeC-containing proteins. Mol Phylogenet Evol 2020; 155:107009. [PMID: 33186688 DOI: 10.1016/j.ympev.2020.107009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 11/17/2022]
Abstract
Apextrin C-terminal (ApeC) is a novel protein domain with unknown functions, although early studies suggest that some ApeC-containing proteins (ACPs) bind to carbohydrates and have a role in development and immunity. Here we investigated the taxonomic distribution, sequence diversification and origin of ACPs in Metazoa. Most ACPs are present in invertebrates from aquatic or moist environments, including cnidarians, mollusks, echinoderms, cephalochordates, flatworms, water bears, nematodes and annelids. However, ACPs are absent in vertebrates and in most arthropod lineages (e.g. insects and crustaceans) except arachnids. ACPs apparently undergo rapid turnover and diversification, hence no orthologs could be found between (sub)phyla. ApeC can function either as a standalone domain or as a partner domain. It has been found to pair up with over ten different domain types in different ACPs. The partner domains are related to immunity, extracellular matrix, protein-protein and protein-carbohydrate interactions. Notably, the domain pair with the widest taxonomic distribution is MACPF/perforin-ApeC, which represent a classic group of ACPs called apextrins. ApeC also frequently pairs up with itself to form dual-ApeC modules in different phyla. Notably, in parasite flatworms, dual-ApeCs are present in 70% of ACPs and all inherited from a common ancestor. The broad distribution of MACPF-ApeC and dual-ApeC suggest their conserved yet unknown functions. We also discovered distant ApeC homologs in bacteria, hence tracing the origin of ApeC back to prokaryotes. Our findings show that ApeC has an ancient origin and is able to function alone or in complex domain architectures, though it is less prevalent than other versatile domains such as immunoglobulin domains and C-type lectin domains. This work provides a foundation for further functional study of this novel domain type.
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Affiliation(s)
- Yuhui Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519000, 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
| | - Jin Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519000, People's Republic of China
| | - Xinyu Yan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Shenghui Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Chengyi Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Huiqing Huang
- Guangdong Food and Drug Vocational College, Guangzhou, People's Republic of China
| | - Yi Shi
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China; CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
| | - Guangrui Huang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, People's Republic of China
| | - Meiling Dong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Anlong Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China; School of Life Sciences, Beijing University of Chinese Medicine, Beijing, People's Republic of China.
| | - Shengfeng Huang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519000, 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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Proteome of larval metamorphosis induced by epinephrine in the Fujian oyster Crassostrea angulata. BMC Genomics 2020; 21:675. [PMID: 32993483 PMCID: PMC7525975 DOI: 10.1186/s12864-020-07066-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 09/10/2020] [Indexed: 01/10/2023] Open
Abstract
Background The Fujian oyster Crassostrea angulata is an economically important species that has typical settlement and metamorphosis stages. The development of the oyster involves complex morphological and physiological changes, the molecular mechanisms of which are as yet unclear. Results In this study, changes in proteins were investigated during larval settlement and metamorphosis of Crassostrea angulata using epinephrine induction. Protein abundance and identity were characterized using label-free quantitative proteomics, tandem mass spectrometry (MS/ MS), and Mascot methods. The results showed that more than 50% (764 out of 1471) of the quantified proteins were characterized as differentially expressed. Notably, more than two-thirds of the differentially expressed proteins were down-regulated in epinephrine-induced larvae. The results showed that “metabolic process” was closely related to the development of settlement and metamorphosis; 5 × 10− 4 M epinephrine induced direct metamorphosis of larvae and was non-toxic. Calmodulin and MAPK pathways were involved in the regulation of settlement of the oyster. Expression levels of immune-related proteins increased during metamorphosis. Hepatic lectin-like proteins, cadherins, calmodulin, calreticulin, and cytoskeletal proteins were involved in metamorphosis. The nervous system may be remodeled in larval metamorphosis induced by epinephrine. Expression levels of proteins that were enriched in the epinephrine signaling pathway may reflect the developmental stage of the larvae, that may reflect whether or not larvae were directly involved in metamorphosis when the larvae were treated with epinephrine. Conclusion The study provides insight into proteins that function in energy metabolism, immune responses, settlement and metamorphosis, and shell formation in C. angulata. The results contribute valuable information for further research on larval settlement and metamorphosis. Graphical abstract ![]()
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11
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Siddik A, Satheesh S. Characterization and assessment of barnacle larval settlement-inducing activity of extracellular polymeric substances isolated from marine biofilm bacteria. Sci Rep 2019; 9:17849. [PMID: 31780773 PMCID: PMC6882797 DOI: 10.1038/s41598-019-54294-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/09/2019] [Indexed: 11/15/2022] Open
Abstract
Extracellular polymeric substances (EPSs) are the hydrated gelatinous matrix produced by microorganisms for attachment in a biofilm environment. In this study, the compositional variation between EPSs of three marine biofilm bacteria (Pseudoalteromonas shioyasakiensis, Vibrio harveyi and Planomicrobium sp.) were analysed by GC-MS, 1H NMR, FT-IR and XRD and SEM. The ecological significance of exopolymers was assessed in vivo using marine model organism barnacle larvae for their settlement-inducing activity. Chemical analysis revealed the presence of glycan fucosylated oligosaccharides, tetraose, trisaccharides, iso-B-Pentasaccharides, sialyllactose, oligomannose, galacto-N-biose, difucosyl-para-lacto-N-neohexaose, 3′-sialyl N-acetyllactosamine and isoglobotriaose-β-N(Acetyl)-Propargyl in all extracted EPSs. Bioassay results indicated that treatment of the barnacle larvae with EPSs from three bacterial strains enhanced settlement on substrates. In conclusion, this study highlighted the role of water-soluble EPSs in the invertebrate larval settlement on artificial materials.
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Affiliation(s)
- Aboobucker Siddik
- Department of Marine Biology, Faculty of Marine Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sathianeson Satheesh
- Department of Marine Biology, Faculty of Marine Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
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12
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Hartmann AC, Marhaver KL, Klueter A, Lovci MT, Closek CJ, Diaz E, Chamberland VF, Archer FI, Deheyn DD, Vermeij MJA, Medina M. Acquisition of obligate mutualist symbionts during the larval stage is not beneficial for a coral host. Mol Ecol 2019; 28:141-155. [PMID: 30506836 DOI: 10.1111/mec.14967] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 09/13/2018] [Accepted: 10/19/2018] [Indexed: 12/31/2022]
Abstract
Theory suggests that the direct transmission of beneficial endosymbionts (mutualists) from parents to offspring (vertical transmission) in animal hosts is advantageous and evolutionarily stable, yet many host species instead acquire their symbionts from the environment (horizontal acquisition). An outstanding question in marine biology is why some scleractinian corals do not provision their eggs and larvae with the endosymbiotic dinoflagellates that are necessary for a juvenile's ultimate survival. We tested whether the acquisition of photosynthetic endosymbionts (family Symbiodiniaceae) during the planktonic larval stage was advantageous, as is widely assumed, in the ecologically important and threatened Caribbean reef-building coral Orbicella faveolata. Following larval acquisition, similar changes occurred in host energetic lipid use and gene expression regardless of whether their symbionts were photosynthesizing, suggesting the symbionts did not provide the energetic benefit characteristic of the mutualism in adults. Larvae that acquired photosymbionts isolated from conspecific adults on their natal reef exhibited a reduction in swimming, which may interfere with their ability to find suitable settlement substrate, and also a decrease in survival. Larvae exposed to two cultured algal species did not exhibit differences in survival, but decreased their swimming activity in response to one species. We conclude that acquiring photosymbionts during the larval stage confers no advantages and can in fact be disadvantageous to this coral host. The timing of symbiont acquisition appears to be a critical component of a host's life history strategy and overall reproductive fitness, and this timing itself appears to be under selective pressure.
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Affiliation(s)
- Aaron C Hartmann
- Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California
| | | | | | - Michael T Lovci
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
| | - Collin J Closek
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania
| | - Erika Diaz
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania
| | - Valérie F Chamberland
- CARMABI Foundation, Willemstad, Curaçao.,Aquatic Microbiology/Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.,SECORE International, Hilliard, Ohio
| | | | - Dimitri D Deheyn
- Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California
| | - Mark J A Vermeij
- CARMABI Foundation, Willemstad, Curaçao.,Aquatic Microbiology/Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania
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13
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Walker NS, Fernández R, Sneed JM, Paul VJ, Giribet G, Combosch DJ. Differential gene expression during substrate probing in larvae of the Caribbean coral Porites astreoides. Mol Ecol 2019; 28:4899-4913. [PMID: 31596993 PMCID: PMC6900098 DOI: 10.1111/mec.15265] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 12/20/2022]
Abstract
The transition from larva to adult is a critical step in the life history strategy of most marine animals. However, the genetic basis of this life history change remains poorly understood in many taxa, including most coral species. Recent evidence suggests that coral planula larvae undergo significant changes at the physiological and molecular levels throughout the development. To investigate this, we characterized differential gene expression (DGE) during the transition from planula to adult polyp in the abundant Caribbean reef-building coral Porites astreoides, that is from nonprobing to actively substrate-probing larva, a stage required for colony initiation. This period is crucial for the coral, because it demonstrates preparedness to locate appropriate substrata for settlement based on vital environmental cues. Through RNA-Seq, we identified 860 differentially expressed holobiont genes between probing and nonprobing larvae (p ≤ .01), the majority of which were upregulated in probing larvae. Surprisingly, differentially expressed genes of endosymbiotic dinoflagellate origin greatly outnumbered coral genes, compared with a nearly 1:1 ratio of coral-to-dinoflagellate gene representation in the holobiont transcriptome. This unanticipated result suggests that dinoflagellate endosymbionts may play a significant role in the transition from nonprobing to probing behaviour in dinoflagellate-rich larvae. Putative holobiont genes were largely involved in protein and nucleotide binding, metabolism and transport. Genes were also linked to environmental sensing and response and integral signalling pathways. Our results thus provide detailed insight into molecular changes prior to larval settlement and highlight the complex physiological and biochemical changes that occur in early transition stages from pelagic to benthic stages in corals, and perhaps more importantly, in their endosymbionts.
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Affiliation(s)
- Nia S Walker
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA.,Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
| | - Rosa Fernández
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | | | | | - Gonzalo Giribet
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - David J Combosch
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA.,Marine Laboratory, University of Guam, Mangilao, GU, USA
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14
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Maiorova MA, Satoh N, Khalturin K, Odintsova NA. Transcriptomic profiling of the mussel Mytilus trossulus with a special emphasis on integrin-like genes during development. INVERTEBR REPROD DEV 2019. [DOI: 10.1080/07924259.2019.1626774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Mariia A. Maiorova
- Laboratory of Cytotechnology, National Scientific Center of Marine Biology, The Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Noriyuki Satoh
- Marine Genomcs Unit, Okinawa Institute Science & Technology, Okinawa, Japan
| | | | - Nelly A. Odintsova
- Laboratory of Cytotechnology, National Scientific Center of Marine Biology, The Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
- Marine Invertebrate Biology Interfaculty Laboratory, Far Eastern Federal University, Vladivostok, Russia
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15
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Ying H, Hayward DC, Cooke I, Wang W, Moya A, Siemering KR, Sprungala S, Ball EE, Forêt S, Miller DJ. The Whole-Genome Sequence of the Coral Acropora millepora. Genome Biol Evol 2019; 11:1374-1379. [PMID: 31059562 PMCID: PMC6501875 DOI: 10.1093/gbe/evz077] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2019] [Indexed: 12/17/2022] Open
Affiliation(s)
- Hua Ying
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia
| | - David C Hayward
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia
| | - Ira Cooke
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
| | - Weiwen Wang
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia
| | - Aurelie Moya
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Kirby R Siemering
- Australian Genome Research Facility Ltd, Level 13, Victorian Comprehensive Cancer Centre, Melbourne, Victoria, Australia
| | - Susanne Sprungala
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Eldon E Ball
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Sylvain Forêt
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - David J Miller
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
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16
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Del Prete S, Bua S, Alasmary FAS, AlOthman Z, Tambutté S, Zoccola D, Supuran CT, Capasso C. Comparison of the Sulfonamide Inhibition Profiles of the α-Carbonic Anhydrase Isoforms (SpiCA1, SpiCA2 and SpiCA3) Encoded by the Genome of the Scleractinian Coral Stylophora pistillata. Mar Drugs 2019; 17:E146. [PMID: 30832211 PMCID: PMC6471618 DOI: 10.3390/md17030146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 12/15/2022] Open
Abstract
The ubiquitous metalloenzymes carbonic anhydrases (CAs, EC 4.2.1.1) are responsible for the reversible hydration of CO₂ to bicarbonate (HCO₃-) and protons (H⁺). Bicarbonate may subsequently generate carbonate used in many functional activities by marine organisms. CAs play a crucial role in several physiological processes, e.g., respiration, inorganic carbon transport, intra and extra-cellular pH regulation, and bio-mineralization. Multiple transcript variants and protein isoforms exist in the organisms. Recently, 16 α-CA isoforms have been identified in the coral Stylophora pistillata. Here, we focalized the interest on three coral isoforms: SpiCA1 and SpiCA2, localized in the coral-calcifying cells; and SpiCA3, expressed in the cytoplasm of the coral cell layers. The three recombinant enzymes were heterologously expressed and investigated for their inhibition profiles with sulfonamides and sulfamates. The three coral CA isoforms differ significantly in their susceptibility to inhibition with sulfonamides. This study provides new insights into the coral physiology and the comprehension of molecular mechanisms involved in the bio-mineralization processes, since CAs interact with bicarbonate transporters, accelerating the trans-membrane bicarbonate movement and modulating the pH at both sides of the plasma membranes.
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Affiliation(s)
- Sonia Del Prete
- Istituto di Bioscienze e Biorisorse, National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy.
| | - Silvia Bua
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.
| | - Fatmah A S Alasmary
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455 Riyadh 11451, Saudi Arabia.
| | - Zeid AlOthman
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455 Riyadh 11451, Saudi Arabia.
| | - Sylvie Tambutté
- Department of Marine Biology, Centre Scientifique de Monaco, 8 Quai Antoine 1, 98000 Monaco, Monaco.
| | - Didier Zoccola
- Department of Marine Biology, Centre Scientifique de Monaco, 8 Quai Antoine 1, 98000 Monaco, Monaco.
| | - Claudiu T Supuran
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455 Riyadh 11451, Saudi Arabia.
| | - Clemente Capasso
- Istituto di Bioscienze e Biorisorse, National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy.
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17
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Attenborough RM, Hayward DC, Wiedemann U, Forêt S, Miller DJ, Ball EE. Expression of the neuropeptides RFamide and LWamide during development of the coral Acropora millepora in relation to settlement and metamorphosis. Dev Biol 2019; 446:56-67. [DOI: 10.1016/j.ydbio.2018.11.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/22/2018] [Accepted: 11/30/2018] [Indexed: 10/27/2022]
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18
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Traylor-Knowles N. In Situ Hybridization Techniques for Paraffin-Embedded Adult Coral Samples. J Vis Exp 2018. [PMID: 30222153 DOI: 10.3791/57853] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Corals are important ocean invertebrates that are critical for overall ocean health as well as human health. However, due to human impacts such as rising ocean temperatures and ocean acidification, corals are increasingly under threat. To tackle these challenges, advances in cell and molecular biology have proven to be crucial for diagnosing the health of corals. Modifying some of the techniques commonly used in human medicine could greatly improve researchers' ability to treat and save corals. To address this, a protocol for in situ hybridization used primarily in human medicine and evolutionary developmental biology has been adapted for use in adult corals under stress. The purpose of this method is to visualize the spatial expression of an RNA probe in adult coral tissue that has been embedded in paraffin and sectioned onto glass slides. This method focuses on removal of the paraffin and rehydration of the sample, pretreatment of the sample to ensure permeability of the sample, pre-hybridization incubation, hybridization of the RNA probe, and visualization of the RNA probe. This is a powerful method when using non-model organisms to discover where specific genes are expressed, and the protocol can be easily adapted for other non-model organisms. However, the method is limited in that it is primarily qualitative, because expression intensity can vary depending on the amount of time used during the visualization step and the concentration of the probe. Furthermore, patience is required, as this protocol can take up to 5 days (and in many cases, longer) depending on the probe being used. Finally, non-specific background staining is common, but this limitation can be overcome.
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Affiliation(s)
- Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, University of Miami, Rosenstiel School of Marine and Atmospheric Sciences;
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19
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Hamada M, Schröder K, Bathia J, Kürn U, Fraune S, Khalturina M, Khalturin K, Shinzato C, Satoh N, Bosch TC. Metabolic co-dependence drives the evolutionarily ancient Hydra-Chlorella symbiosis. eLife 2018; 7:35122. [PMID: 29848439 PMCID: PMC6019070 DOI: 10.7554/elife.35122] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/26/2018] [Indexed: 11/13/2022] Open
Abstract
Many multicellular organisms rely on symbiotic associations for support of metabolic activity, protection, or energy. Understanding the mechanisms involved in controlling such interactions remains a major challenge. In an unbiased approach we identified key players that control the symbiosis between Hydra viridissima and its photosynthetic symbiont Chlorella sp. A99. We discovered significant up-regulation of Hydra genes encoding a phosphate transporter and glutamine synthetase suggesting regulated nutrition supply between host and symbionts. Interestingly, supplementing the medium with glutamine temporarily supports in vitro growth of the otherwise obligate symbiotic Chlorella, indicating loss of autonomy and dependence on the host. Genome sequencing of Chlorella sp. A99 revealed a large number of amino acid transporters and a degenerated nitrate assimilation pathway, presumably as consequence of the adaptation to the host environment. Our observations portray ancient symbiotic interactions as a codependent partnership in which exchange of nutrients appears to be the primary driving force.
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Affiliation(s)
- Mayuko Hamada
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.,Ushimado Marine Institute, Okayama University, Okayama, Japan
| | - Katja Schröder
- Interdisciplinary Research Center, Kiel Life Science, Kiel University, Kiel, Germany.,Zoological Institute, Kiel Life Science, Kiel University, Kiel, Germany
| | - Jay Bathia
- Interdisciplinary Research Center, Kiel Life Science, Kiel University, Kiel, Germany.,Zoological Institute, Kiel Life Science, Kiel University, Kiel, Germany
| | - Ulrich Kürn
- Interdisciplinary Research Center, Kiel Life Science, Kiel University, Kiel, Germany.,Zoological Institute, Kiel Life Science, Kiel University, Kiel, Germany
| | - Sebastian Fraune
- Interdisciplinary Research Center, Kiel Life Science, Kiel University, Kiel, Germany.,Zoological Institute, Kiel Life Science, Kiel University, Kiel, Germany
| | - Mariia Khalturina
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Konstantin Khalturin
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.,Atmosphere and Ocean Research Institute, The University of Tokyo, Tokyo, Japan
| | - Nori Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Thomas Cg Bosch
- Interdisciplinary Research Center, Kiel Life Science, Kiel University, Kiel, Germany.,Zoological Institute, Kiel Life Science, Kiel University, Kiel, Germany
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20
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Shen M, Di G, Li M, Fu J, Dai Q, Miao X, Huang M, You W, Ke C. Proteomics Studies on the three Larval Stages of Development and Metamorphosis of Babylonia areolata. Sci Rep 2018; 8:6269. [PMID: 29674673 PMCID: PMC5908917 DOI: 10.1038/s41598-018-24645-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 04/06/2018] [Indexed: 11/20/2022] Open
Abstract
The ivory shell, Babylonia areolata, is a commercially important aquaculture species in the southeast coast of mainland China. The middle veliger stage, later veliger stage, and juvenile stage are distinct larval stages in B. areolata development. In this study, we used label-free quantification proteomics analysis of the three developmental stages of B. areolata. We identified a total of 5,583 proteins, of which 1,419 proteins expression level showed significant differential expression. The results of gene ontology enrichment analysis showed that the number of proteins involved in metabolic and cellular processes were the most abundant. Those proteins mostly had functions such as binding, catalytic activity and transporter activity. The results of Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that the number of proteins involved in the ribosome, carbon metabolism, and lysosome pathways were the most abundant, indicating that protein synthesis and the immune response were active during the three stages of development. This is the first study to use proteomics and real-time PCR to study the early developmental stages of B. areolata, which could provide relevant data on gastropod development. Our results provide insights into the novel aspects of protein function in shell formation, body torsion, changes in feeding habits, attachment and metamorphosis, immune-related activities in B. areolata larvae.
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Affiliation(s)
- Minghui Shen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.,Hainan Academy of Ocean and Fisheries Sciences, Haikou, 570206, China
| | - Guilan Di
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China. .,College of Fisheries, Henan Normal University, Xinxiang, 453007, China.
| | - Min Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Jingqiang Fu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Qi Dai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Xiulian Miao
- College of Life Sciences, Liaocheng University, Liaocheng, 252059, China
| | - Miaoqin Huang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Weiwei You
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.
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21
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Yuan X, Yuan T, Huang H, Jiang L, Zhou W, Liu S. Elevated CO 2 delays the early development of scleractinian coral Acropora gemmifera. Sci Rep 2018; 8:2787. [PMID: 29434364 PMCID: PMC5809585 DOI: 10.1038/s41598-018-21267-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 02/01/2018] [Indexed: 11/09/2022] Open
Abstract
The effects of elevated CO2 on the early life stages of coral were investigated by culturing the pelagic larvae and new recruits of Acropora gemmifera at three concentrations of CO2 (corresponding to pH = 8.1, 7.8 and 7.5, respectively). Acidified seawater resulted in fewer A. gemmifera larvae settling, and led to the production of smaller new recruits by slowing the development of the skeleton. The delayed development of new recruits due to elevated CO2 was consistent with the downregulation of calcification related genes. Several genes related to HCO3- and Ca2+ transporters were downregulated by elevated CO2, with solute carriers (SLC) (membrane transport proteins) possibly playing an important role. The downregulation of these membrane transport proteins might suppress the transport of calcium, bicarbonate and organic matter, resulting in the delayed development of A. gemmifera.
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Affiliation(s)
- Xiangcheng Yuan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China.,Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China
| | - Tao Yuan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China. .,Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China.
| | - Hui Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China. .,Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China. .,Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, China.
| | - Lei Jiang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China.,Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China
| | - Weihua Zhou
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China.,Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China.,Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, China
| | - Sheng Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China.,Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China
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22
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Strader ME, Aglyamova GV, Matz MV. Molecular characterization of larval development from fertilization to metamorphosis in a reef-building coral. BMC Genomics 2018; 19:17. [PMID: 29301490 PMCID: PMC5755313 DOI: 10.1186/s12864-017-4392-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/15/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Molecular mechanisms underlying coral larval competence, the ability of larvae to respond to settlement cues, determine their dispersal potential and are potential targets of natural selection. Here, we profiled competence, fluorescence and genome-wide gene expression in embryos and larvae of the reef-building coral Acropora millepora daily throughout 12 days post-fertilization. RESULTS Gene expression associated with competence was positively correlated with transcriptomic response to the natural settlement cue, confirming that mature coral larvae are "primed" for settlement. Rise of competence through development was accompanied by up-regulation of sensory and signal transduction genes such as ion channels, genes involved in neuropeptide signaling, and G-protein coupled receptor (GPCRs). A drug screen targeting components of GPCR signaling pathways confirmed a role in larval settlement behavior and metamorphosis. CONCLUSIONS These results gives insight into the molecular complexity underlying these transitions and reveals receptors and pathways that, if altered by changing environments, could affect dispersal capabilities of reef-building corals. In addition, this dataset provides a toolkit for asking broad questions about sensory capacity in multicellular animals and the evolution of development.
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Affiliation(s)
- Marie E Strader
- Department of Integrative Biology, The University of Texas at Austin, 1 University Station C0990, Austin, TX, 78712, USA.
| | - Galina V Aglyamova
- Department of Integrative Biology, The University of Texas at Austin, 1 University Station C0990, Austin, TX, 78712, USA
| | - Mikhail V Matz
- Department of Integrative Biology, The University of Texas at Austin, 1 University Station C0990, Austin, TX, 78712, USA
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23
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Lin MF, Moya A, Ying H, Chen CA, Cooke I, Ball EE, Forêt S, Miller DJ. Analyses of Corallimorpharian Transcriptomes Provide New Perspectives on the Evolution of Calcification in the Scleractinia (Corals). Genome Biol Evol 2017; 9:150-160. [PMID: 28158437 PMCID: PMC5604590 DOI: 10.1093/gbe/evw297] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2016] [Indexed: 12/12/2022] Open
Abstract
Corallimorpharians (coral-like anemones) have a close phylogenetic relationship with scleractinians (hard corals) and can potentially provide novel perspectives on the evolution of biomineralization within the anthozoan subclass Hexacorallia. A survey of the transcriptomes of three representative corallimorpharians led to the identification of homologs of some skeletal organic matrix proteins (SOMPs) previously considered to be restricted to corals. Carbonic anhydrases (CAs), which are ubiquitous proteins involved in CO2 trafficking, are involved in both coral calcification and photosynthesis by endosymbiotic Symbiodinium (zooxanthellae). These multiple roles are assumed to place increased demands on the CA repertoire and have presumably driven the elaboration of the complex CA repertoires typical of corals (note that “corals” are defined here as reef-building Scleractinia). Comparison of the CA inventories of corallimorpharians with those of corals reveals that corals have specifically expanded the secreted and membrane-associated type CAs, whereas similar complexity is observed in the two groups with respect to other CA types. Comparison of the CA complement of the nonsymbiotic corallimorph Corynactis australis with that of Ricordea yuma, a corallimorph which normally hosts Symbiodinium, reveals similar numbers and distribution of CA types and suggests that an expansion of the CA repertoire has been necessary to enable calcification but may not be a requirement to enable symbiosis. Consistent with this idea, preliminary analysis suggests that the CA complexity of zooxanthellate and nonzooxanthellate sea anemones is similar. The comparisons above suggest that although there are relatively few new genes in the skeletal organic matrix of corals (which controls the skeleton deposition process), the evolution of calcification required an expanded repertoire of secreted and membrane-associated CAs.
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Affiliation(s)
- Mei-Fang Lin
- Comparative Genomics Centre, Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, Australia.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Aurelie Moya
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Hua Ying
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Chaolun Allen Chen
- Biodiversity Research Centre, Academia Sinica, Nangang, Taipei, Taiwan.,Taiwan International Graduate Program (TIGP)-Biodiversity, Academia Sinica, Nangang, Taipei, Taiwan
| | - Ira Cooke
- Comparative Genomics Centre, Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, Australia
| | - Eldon E Ball
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.,Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Sylvain Forêt
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.,Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - David J Miller
- Comparative Genomics Centre, Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, Australia.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
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24
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Morgan MB, Edge SE, Venn AA, Jones RJ. Developing transcriptional profiles in Orbicella franksi exposed to copper: Characterizing responses associated with a spectrum of laboratory-controlled environmental conditions. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2017; 189:60-76. [PMID: 28599170 DOI: 10.1016/j.aquatox.2017.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/23/2017] [Accepted: 05/09/2017] [Indexed: 06/07/2023]
Affiliation(s)
- Michael B Morgan
- Department of Biology, Berry College, School of Mathematics and Natural Sciences, 2277 Martha Berry Hwy, Mount Berry, GA, 30149, USA.
| | - Sara E Edge
- Hawaii Pacific University, 45-045 Kamehameha Hwy, Kaneohe, HI, 96744, USA
| | - Alexander A Venn
- Marine Biology Department et Laboratoire International Associé 647 "BIOSENSIB", Centre Scientifique de Monaco, 8 Quai Antoine 1er, MC98000, Monaco
| | - Ross J Jones
- Australian Institute of Marine Science (AIMS), Perth, 6009, Australia
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25
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Dani V, Priouzeau F, Mertz M, Mondin M, Pagnotta S, Lacas-Gervais S, Davy SK, Sabourault C. Expression patterns of sterol transporters NPC1 and NPC2 in the cnidarian-dinoflagellate symbiosis. Cell Microbiol 2017; 19. [DOI: 10.1111/cmi.12753] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 05/16/2017] [Accepted: 05/18/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Vincent Dani
- Institut de Biologie Valrose (iBV); Université Côte d'Azur; Nice France
- UMR7138, Equipe Symbiose Marine; Université Côte d'Azur; Nice France
| | - Fabrice Priouzeau
- Institut de Biologie Valrose (iBV); Université Côte d'Azur; Nice France
- UMR7138, Equipe Symbiose Marine; Université Côte d'Azur; Nice France
| | - Marjolijn Mertz
- Institut de Biologie Valrose (iBV); Université Côte d'Azur; Nice France
| | - Magali Mondin
- Institut de Biologie Valrose (iBV); Université Côte d'Azur; Nice France
| | - Sophie Pagnotta
- Centre Commun de Microscopie Appliquée; Université Côte d'Azur; Nice France
| | | | - Simon K. Davy
- School of Biological Sciences; Victoria University of Wellington; Wellington New Zealand
| | - Cécile Sabourault
- Institut de Biologie Valrose (iBV); Université Côte d'Azur; Nice France
- UMR7138, Equipe Symbiose Marine; Université Côte d'Azur; Nice France
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26
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Mass T, Putnam HM, Drake JL, Zelzion E, Gates RD, Bhattacharya D, Falkowski PG. Temporal and spatial expression patterns of biomineralization proteins during early development in the stony coral Pocillopora damicornis. Proc Biol Sci 2017; 283:rspb.2016.0322. [PMID: 27122561 DOI: 10.1098/rspb.2016.0322] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/01/2016] [Indexed: 11/12/2022] Open
Abstract
Reef-building corals begin as non-calcifying larvae that, upon settling, rapidly begin to accrete skeleton and a protein-rich skeletal organic matrix that attach them to the reef. Here, we characterized the temporal and spatial expression pattern of a suite of biomineralization genes during three stages of larval development in the reef-building coral Pocillopora damicornis: stage I, newly released; stage II, oral-aborally compressed and stage III, settled and calcifying spat. Transcriptome analysis revealed 3882 differentially expressed genes that clustered into four distinctly different patterns of expression change across the three developmental stages. Immunolocalization analysis further reveals the spatial arrangement of coral acid-rich proteins (CARPs) in the overall architecture of the emerging skeleton. These results provide the first analysis of the timing of the biomineralization 'toolkit' in the early life history of a stony coral.
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Affiliation(s)
- Tali Mass
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Kaneohe, HI 96744, USA
| | | | - Jeana L Drake
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Kaneohe, HI 96744, USA
| | - Ehud Zelzion
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA
| | - Ruth D Gates
- Hawaii Institute of Marine Biology, Kaneohe, HI 96744, USA
| | - Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Paul G Falkowski
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Kaneohe, HI 96744, USA Department of Earth and Planetary Sciences, Rutgers University, Piscataway, NJ 08854, USA
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27
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Le Goff C, Ganot P, Zoccola D, Caminiti-Segonds N, Allemand D, Tambutté S. Carbonic Anhydrases in Cnidarians: Novel Perspectives from the Octocorallian Corallium rubrum. PLoS One 2016; 11:e0160368. [PMID: 27513959 PMCID: PMC4981384 DOI: 10.1371/journal.pone.0160368] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 07/18/2016] [Indexed: 11/19/2022] Open
Abstract
Although the ability to elaborate calcium carbonate biominerals was apparently gained independently during animal evolution, members of the alpha carbonic anhydrases (α-CAs) family, which catalyze the interconversion of CO2 into HCO3-, are involved in the biomineralization process across metazoans. In the Mediterranean red coral Corallium rubrum, inhibition studies suggest an essential role of CAs in the synthesis of two biominerals produced in this octocoral, the axial skeleton and the sclerites. Hitherto no molecular characterization of these enzymes was available. In the present study we determined the complete set of α-CAs in C. rubrum by data mining the genome and transcriptome, and measured their differential gene expression between calcifying and non-calcifying tissues. We identified six isozymes (CruCA1-6), one cytosolic and five secreted/membrane-bound among which one lacked two of the three zinc-binding histidines and was so referred to as a carbonic anhydrase related protein (CARP). One secreted isozyme (CruCA4) showed specific expression both by qPCR and western-blot in the calcifying tissues, suggesting its involvement in biomineralization. Moreover, phylogenetic analyses of α-CAs, identified in six representative cnidarians with complete genome, support an independent recruitment of α-CAs for biomineralization within anthozoans. Finally, characterization of cnidarian CARPs highlighted two families: the monophyletic cytosolic CARPs, and the polyphyletic secreted CARPs harboring a cnidarian specific cysteine disulfide bridge. Alignment of the cytosolic CARPs revealed an evolutionary conserved R-H-Q motif in place of the characteristic zinc-binding H-H-H necessary for the catalytic function of α-CAs.
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28
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Mohamed AR, Cumbo V, Harii S, Shinzato C, Chan CX, Ragan MA, Bourne DG, Willis BL, Ball EE, Satoh N, Miller DJ. The transcriptomic response of the coral
Acropora digitifera
to a competent
Symbiodinium
strain: the symbiosome as an arrested early phagosome. Mol Ecol 2016; 25:3127-41. [DOI: 10.1111/mec.13659] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 04/04/2016] [Accepted: 04/14/2016] [Indexed: 12/15/2022]
Affiliation(s)
- A. R. Mohamed
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Qld 4811 Australia
- Comparative Genomics Centre and Department of Molecular and Cell Biology James Cook University Townsville Qld 4811 Australia
- Zoology Department Faculty of Science Benha University Benha 13518 Egypt
- AIMS@JCU Department of Molecular and Cell Biology Australian Institute of Marine Science James Cook University Townsville Qld 4811 Australia
| | - V. Cumbo
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Qld 4811 Australia
- Department of Biological Sciences Macquarie University Sydney NSW 2109 Australia
| | - S. Harii
- Sesoko Station Tropical Biosphere Research Center University of the Ryukyus 3422 Sesoko Motobu Okinawa 905‐0227 Japan
| | - C. Shinzato
- Marine Genomics Unit Okinawa Institute of Science and Technology Promotion Corporation Onna Okinawa 904‐0412 Japan
| | - C. X. Chan
- ARC Centre of Excellence in Bioinformatics and Institute for Molecular Bioscience The University of Queensland Brisbane Qld 4072 Australia
| | - M. A. Ragan
- ARC Centre of Excellence in Bioinformatics and Institute for Molecular Bioscience The University of Queensland Brisbane Qld 4072 Australia
| | - D. G. Bourne
- Australian Institute for Marine Science PMB 3 Townsville Qld 4811 Australia
| | - B. L. Willis
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Qld 4811 Australia
- Department of Marine Ecosystems and Impacts James Cook University Townsville Qld 4811 Australia
| | - E. E. Ball
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Qld 4811 Australia
- Evolution, Ecology and Genetics Research School of Biology Australian National University Canberra ACT 0200 Australia
| | - N. Satoh
- Marine Genomics Unit Okinawa Institute of Science and Technology Promotion Corporation Onna Okinawa 904‐0412 Japan
| | - D. J. Miller
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Qld 4811 Australia
- Comparative Genomics Centre and Department of Molecular and Cell Biology James Cook University Townsville Qld 4811 Australia
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29
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Reyes-Bermudez A, Villar-Briones A, Ramirez-Portilla C, Hidaka M, Mikheyev AS. Developmental Progression in the Coral Acropora digitifera Is Controlled by Differential Expression of Distinct Regulatory Gene Networks. Genome Biol Evol 2016; 8:851-70. [PMID: 26941230 PMCID: PMC4824149 DOI: 10.1093/gbe/evw042] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2016] [Indexed: 12/20/2022] Open
Abstract
Corals belong to the most basal class of the Phylum Cnidaria, which is considered the sister group of bilaterian animals, and thus have become an emerging model to study the evolution of developmental mechanisms. Although cell renewal, differentiation, and maintenance of pluripotency are cellular events shared by multicellular animals, the cellular basis of these fundamental biological processes are still poorly understood. To understand how changes in gene expression regulate morphogenetic transitions at the base of the eumetazoa, we performed quantitative RNA-seq analysis duringAcropora digitifera's development. We collected embryonic, larval, and adult samples to characterize stage-specific transcription profiles, as well as broad expression patterns. Transcription profiles reconstructed development revealing two main expression clusters. The first cluster grouped blastula and gastrula and the second grouped subsequent developmental time points. Consistently, we observed clear differences in gene expression between early and late developmental transitions, with higher numbers of differentially expressed genes and fold changes around gastrulation. Furthermore, we identified three coexpression clusters that represented discrete gene expression patterns. During early transitions, transcriptional networks seemed to regulate cellular fate and morphogenesis of the larval body. In late transitions, these networks seemed to play important roles preparing planulae for switch in lifestyle and regulation of adult processes. Although developmental progression inA. digitiferais regulated to some extent by differential coexpression of well-defined gene networks, stage-specific transcription profiles appear to be independent entities. While negative regulation of transcription is predominant in early development, cell differentiation was upregulated in larval and adult stages.
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Affiliation(s)
- Alejandro Reyes-Bermudez
- Okinawa Institute of Science and Technology, Okinawa, Japan School of Natural Sciences, Ryukyus University, Okinawa, Japan
| | | | | | - Michio Hidaka
- School of Natural Sciences, Ryukyus University, Okinawa, Japan
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30
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Redefining metamorphosis in spiny lobsters: molecular analysis of the phyllosoma to puerulus transition in Sagmariasus verreauxi. Sci Rep 2015; 5:13537. [PMID: 26311524 PMCID: PMC4550925 DOI: 10.1038/srep13537] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 07/29/2015] [Indexed: 12/20/2022] Open
Abstract
The molecular understanding of crustacean metamorphosis is hindered by small sized individuals and inability to accurately define molt stages. We used the spiny lobster Sagmariasus verreauxi where the large, transparent larvae enable accurate tracing of the transition from a leaf-shaped phyllosoma to an intermediate larval-juvenile phase (puerulus). Transcriptomic analysis of larvae at well-defined stages prior to, during, and following this transition show that the phyllosoma-puerulus metamorphic transition is accompanied by vast transcriptomic changes exceeding 25% of the transcriptome. Notably, genes previously identified as regulating metamorphosis in other crustaceans do not fluctuate during this transition but in the later, morphologically-subtle puerulus-juvenile transition, indicating that the dramatic phyllosoma-puerulus morphological shift relies on a different, yet to be identified metamorphic mechanism. We examined the change in expression of domains and gene families, with focus on several key genes. Our research implies that the separation in molecular triggering systems between the phyllosoma-puerulus and puerulus-juvenile transitions might have enabled the extension of the oceanic phase in spiny lobsters. Study of similar transitions, where metamorphosis is uncoupled from the transition into the benthic juvenile form, in other commercially important crustacean groups might show common features to point on the evolutionary advantage of this two staged regulation.
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31
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Bertucci A, Forêt S, Ball EE, Miller DJ. Transcriptomic differences between day and night in Acropora millepora provide new insights into metabolite exchange and light-enhanced calcification in corals. Mol Ecol 2015. [PMID: 26198296 DOI: 10.1111/mec.13328] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The evolutionary success of reef-building corals is often attributed to their symbiotic relationship with photosynthetic dinoflagellates of the genus Symbiodinium, but metabolic interactions between the partners and the molecular bases of light-enhanced calcification (LEC) are not well understood. Here, the metabolic bases of the interaction between the coral Acropora millepora and its dinoflagellate symbiont were investigated by comparing gene expression levels under light and dark conditions at the whole transcriptome level. Among the 497 differentially expressed genes identified, a suite of genes involved in cholesterol transport was found to be upregulated under light conditions, confirming the significance of this compound in the coral symbiosis. Although ion transporters likely to have roles in calcification were not differentially expressed in this study, expression levels of many genes associated with skeletal organic matrix composition and organization were higher in light conditions. This implies that the rate of organic matrix synthesis is one factor limiting calcification at night. Thus, LEC during the day is likely to be a consequence of increases in both matrix synthesis and the supply of precursor molecules as a result of photosynthetic activity.
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Affiliation(s)
- A Bertucci
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, 4811, Australia
| | - S Forêt
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, 4811, Australia.,Evolution, Ecology and Genetics, Research School of Biology, Australian National University, Bldg. 46, Canberra, ACT, 0200, Australia
| | - E E Ball
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, 4811, Australia.,Evolution, Ecology and Genetics, Research School of Biology, Australian National University, Bldg. 46, Canberra, ACT, 0200, Australia
| | - D J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, 4811, Australia.,Comparative Genomics Centre and Department of Molecular and Cell Biology, James Cook University, Townsville, Qld, 4811, Australia
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32
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van de Water JAJM, Ainsworth TD, Leggat W, Bourne DG, Willis BL, van Oppen MJH. The coral immune response facilitates protection against microbes during tissue regeneration. Mol Ecol 2015; 24:3390-404. [PMID: 26095670 DOI: 10.1111/mec.13257] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 05/20/2015] [Accepted: 05/26/2015] [Indexed: 12/11/2022]
Abstract
Increasing physical damage on coral reefs from predation, storms and anthropogenic disturbances highlights the need to understand the impact of injury on the coral immune system. In this study, we examined the regulation of the coral immune response over 10 days following physical trauma artificially inflicted on in situ colonies of the coral Acropora aspera, simultaneously with bacterial colonization of the lesions. Corals responded to injury by increasing the expression of immune system-related genes involved in the Toll-like and NOD-like receptor signalling pathways and the lectin-complement system in three phases (<2, 4 and 10 days post-injury). Phenoloxidase activity was also significantly upregulated in two phases (<3 and 10 days post-injury), as were levels of non-fluorescent chromoprotein. In addition, green fluorescent protein expression was upregulated in response to injury from 4 days post-injury, while cyan fluorescent protein expression was reduced. No shifts in the composition of coral-associated bacterial communities were evident following injury based on 16S rRNA gene amplicon pyrosequencing. Bacteria-specific fluorescence in situ hybridization also showed no evidence of bacterial colonization of the wound or regenerating tissues. Coral tissues showed near-complete regeneration of lesions within 10 days. This study demonstrates that corals exhibit immune responses that support rapid recovery following physical injury, maintain coral microbial homeostasis and prevent bacterial infestation that may compromise coral fitness.
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Affiliation(s)
- Jeroen A J M van de Water
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld 4811, Australia.,College of Marine and Environmental Sciences, James Cook University, Townsville, Qld 4811, Australia.,AIMS@JCU, James Cook University, Townsville, Qld 4811, Australia.,Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, Qld 4810, Australia
| | - Tracy D Ainsworth
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld 4811, Australia
| | - William Leggat
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld 4811, Australia.,College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Qld 4811, Australia
| | - David G Bourne
- AIMS@JCU, James Cook University, Townsville, Qld 4811, Australia.,Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, Qld 4810, Australia
| | - Bette L Willis
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld 4811, Australia.,College of Marine and Environmental Sciences, James Cook University, Townsville, Qld 4811, Australia.,Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, Qld 4810, Australia
| | - Madeleine J H van Oppen
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld 4811, Australia.,AIMS@JCU, James Cook University, Townsville, Qld 4811, Australia.,Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, Qld 4810, Australia
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33
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Hopkinson BM, Tansik AL, Fitt WK. Internal carbonic anhydrase activity in the tissue of scleractinian corals is sufficient to support proposed roles in photosynthesis and calcification. ACTA ACUST UNITED AC 2015; 218:2039-48. [PMID: 25908060 DOI: 10.1242/jeb.118182] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 04/20/2015] [Indexed: 11/20/2022]
Abstract
Reef-building corals import inorganic carbon (Ci) to build their calcium carbonate skeletons and to support photosynthesis by the symbiotic algae that reside in their tissue. The internal pathways that deliver Ci for both photosynthesis and calcification are known to involve the enzyme carbonic anhydrase (CA), which interconverts CO2 and HCO3 (-). We have developed a method for absolute quantification of internal CA (iCA) activity in coral tissue based on the rate of (18)O-removal from labeled Ci. The method was applied to three Caribbean corals (Orbicella faveolata, Porites astreoides and Siderastrea radians) and showed that these species have similar iCA activities per unit surface area, but that S. radians has ∼10-fold higher iCA activity per unit tissue volume. A model of coral Ci processing shows that the measured iCA activity is sufficient to support the proposed roles for iCA in Ci transport for photosynthesis and calcification. This is the case even when iCA activity is homogeneously distributed throughout the coral, but the model indicates that it would be advantageous to concentrate iCA in the spaces where calcification (the calcifying fluid) and photosynthesis (the oral endoderm) take place. We argue that because the rates of photosynthesis and calcification per unit surface area are similar among the corals studied here, the areal iCA activity used to deliver Ci for these reactions should also be similar. The elevated iCA activity per unit volume of S. radians compared with that of the other species is probably due to the thinner effective tissue thickness in this species.
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Affiliation(s)
- Brian M Hopkinson
- Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA
| | - Anna L Tansik
- Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA
| | - William K Fitt
- School of Ecology, University of Georgia, Athens, GA 30602, USA
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Stillman JH, Armstrong E. Genomics Are Transforming Our Understanding of Responses to Climate Change. Bioscience 2015. [DOI: 10.1093/biosci/biu219] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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Moya A, Huisman L, Forêt S, Gattuso JP, Hayward DC, Ball EE, Miller DJ. Rapid acclimation of juvenile corals to CO2-mediated acidification by upregulation of heat shock protein and Bcl-2 genes. Mol Ecol 2015; 24:438-52. [DOI: 10.1111/mec.13021] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 11/17/2014] [Accepted: 11/20/2014] [Indexed: 01/08/2023]
Affiliation(s)
- A. Moya
- ARC Centre of Excellence for Coral Reef Studies; James Cook University; Townsville Qld 4811 Australia
- Laboratoire d'Océanographie de Villefranche; INSU-CNRS; 181 Chemin du Lazaret 06230 Villefranche-sur-mer France
- Sorbonne Universités; UPMC Univ. Paris 06; Observatoire Océanologique 06230 Villefranche-sur-mer France
| | - L. Huisman
- ARC Centre of Excellence for Coral Reef Studies; James Cook University; Townsville Qld 4811 Australia
- Section of Computational Science; Universiteit van Amsterdam; Science Park 904 1098 XH Amsterdam The Netherlands
| | - S. Forêt
- ARC Centre of Excellence for Coral Reef Studies; James Cook University; Townsville Qld 4811 Australia
- Evolution, Ecology and Genetics; Research School of Biology; Australian National University; Bldg. 46 Canberra ACT 0200 Australia
| | - J.-P. Gattuso
- Laboratoire d'Océanographie de Villefranche; INSU-CNRS; 181 Chemin du Lazaret 06230 Villefranche-sur-mer France
- Sorbonne Universités; UPMC Univ. Paris 06; Observatoire Océanologique 06230 Villefranche-sur-mer France
| | - D. C. Hayward
- Evolution, Ecology and Genetics; Research School of Biology; Australian National University; Bldg. 46 Canberra ACT 0200 Australia
| | - E. E. Ball
- ARC Centre of Excellence for Coral Reef Studies; James Cook University; Townsville Qld 4811 Australia
- Evolution, Ecology and Genetics; Research School of Biology; Australian National University; Bldg. 46 Canberra ACT 0200 Australia
| | - D. J. Miller
- ARC Centre of Excellence for Coral Reef Studies; James Cook University; Townsville Qld 4811 Australia
- School of Pharmacy and Molecular Sciences; James Cook University; Townsville Qld 4811 Australia
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Hemond EM, Kaluziak ST, Vollmer SV. The genetics of colony form and function in Caribbean Acropora corals. BMC Genomics 2014; 15:1133. [PMID: 25519925 PMCID: PMC4320547 DOI: 10.1186/1471-2164-15-1133] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 12/11/2014] [Indexed: 12/22/2022] Open
Abstract
Background Colonial reef-building corals have evolved a broad spectrum of colony morphologies based on coordinated asexual reproduction of polyps on a secreted calcium carbonate skeleton. Though cnidarians have been shown to possess and use similar developmental genes to bilaterians during larval development and polyp formation, little is known about genetic regulation of colony morphology in hard corals. We used RNA-seq to evaluate transcriptomic differences between functionally distinct regions of the coral (apical branch tips and branch bases) in two species of Caribbean Acropora, the staghorn coral, A. cervicornis, and the elkhorn coral, A. palmata. Results Transcriptome-wide gene profiles differed significantly between different parts of the coral colony as well as between species. Genes showing differential expression between branch tips and bases were involved in developmental signaling pathways, such as Wnt, Notch, and BMP, as well as pH regulation, ion transport, extracellular matrix production and other processes. Differences both within colonies and between species identify a relatively small number of genes that may contribute to the distinct “staghorn” versus “elkhorn” morphologies of these two sister species. Conclusions The large number of differentially expressed genes supports a strong division of labor between coral branch tips and branch bases. Genes involved in growth of mature Acropora colonies include the classical signaling pathways associated with development of cnidarian larvae and polyps as well as morphological determination in higher metazoans. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1133) contains supplementary material, which is available to authorized users.
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Kim JW, Kim SH, Jung MM, Kim HS, Han SJ, Moon TS, Kim BS, Nam BH, Park CI. Gene discovery in the finger leather coral Sinularia notanda by construction and sequencing of a normalized cDNA library. Mar Genomics 2014; 19:1-4. [PMID: 25450166 DOI: 10.1016/j.margen.2014.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 10/03/2014] [Accepted: 10/21/2014] [Indexed: 10/24/2022]
Abstract
The transplantation of coral fragments is one of methods that restore coral communities. To form coral colonies, the fragmented corals initiated skeletal extension from the cut-edge of fragment then success the settlement. In order to understand the molecular events underlying fragment adhesion and settlement, we constructed a normalized cDNA library and generated and annotated expressed sequence tags (ESTs) from the fragmented adult polyps of soft coral Sinularia notanda. We generated 3251 high-quality ESTs with an average length of 580 bp and the EST cluster and assembly analyses produced 2796 unigenes, including 2487 singletons and 309 contigs. Of the known genes, 55 genes were sel ected to be involved in polyp fragment adhesion and settlement based on Gene Ontology (GO) classification. Notably, two EST clones were identified to show homology with galaxin gene which was demonstrated as coral specific calcifying protein of organic matrix. These EST sequences can provide utility as molecular markers in molecular and genetic studies of S. notanda and other soft coral.
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Affiliation(s)
- Jae-Woo Kim
- Future Aquaculture Research Center, National Fisheries Research & Development Institute, 1928, Oedo2-dong, Jeju-si, Jeju-do 690-192, Republic of Korea
| | - Seong Ho Kim
- Future Aquaculture Research Center, National Fisheries Research & Development Institute, 1928, Oedo2-dong, Jeju-si, Jeju-do 690-192, Republic of Korea
| | - Min-Min Jung
- Future Aquaculture Research Center, National Fisheries Research & Development Institute, 1928, Oedo2-dong, Jeju-si, Jeju-do 690-192, Republic of Korea
| | - Heung Soo Kim
- Future Aquaculture Research Center, National Fisheries Research & Development Institute, 1928, Oedo2-dong, Jeju-si, Jeju-do 690-192, Republic of Korea
| | - Seock-Jung Han
- Future Aquaculture Research Center, National Fisheries Research & Development Institute, 1928, Oedo2-dong, Jeju-si, Jeju-do 690-192, Republic of Korea
| | - Tae Seok Moon
- Future Aquaculture Research Center, National Fisheries Research & Development Institute, 1928, Oedo2-dong, Jeju-si, Jeju-do 690-192, Republic of Korea
| | - Bong-Seok Kim
- Future Aquaculture Research Center, National Fisheries Research & Development Institute, 1928, Oedo2-dong, Jeju-si, Jeju-do 690-192, Republic of Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Fisheries Research & Development Institute, 152-1, Haean-ro, Gijang-eup, Gijang-gun, Busan 619-705, Republic of Korea.
| | - Chan-Il Park
- Institute of Marine Industry, Department of Marine Biology and Aquaculture, College of Marine Science, Gyeongsang National University, 455, Tongyeong 650-160, Republic of Korea.
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Le Roy N, Jackson DJ, Marie B, Ramos-Silva P, Marin F. The evolution of metazoan α-carbonic anhydrases and their roles in calcium carbonate biomineralization. Front Zool 2014. [DOI: 10.1186/s12983-014-0075-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Dani V, Ganot P, Priouzeau F, Furla P, Sabourault C. Are Niemann-Pick type C proteins key players in cnidarian-dinoflagellate endosymbioses? Mol Ecol 2014; 23:4527-40. [DOI: 10.1111/mec.12876] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 07/24/2014] [Accepted: 07/25/2014] [Indexed: 01/20/2023]
Affiliation(s)
- Vincent Dani
- UMR7138; Université de Nice-Sophia-Antipolis; Faculty of Science; 28 Avenue Valrose Nice 06108 France
- Institut de Biologie Paris-Seine; UMR7138; Sorbonne Universités Paris VI; 7 quai Saint Bernard Paris 75005 France
- Institut de Biologie Paris-Seine; UMR7138; Centre National de la Recherche Scientifique; Paris 75016 France
| | - Philippe Ganot
- UMR7138; Université de Nice-Sophia-Antipolis; Faculty of Science; 28 Avenue Valrose Nice 06108 France
- Institut de Biologie Paris-Seine; UMR7138; Sorbonne Universités Paris VI; 7 quai Saint Bernard Paris 75005 France
- Institut de Biologie Paris-Seine; UMR7138; Centre National de la Recherche Scientifique; Paris 75016 France
| | - Fabrice Priouzeau
- UMR7138; Université de Nice-Sophia-Antipolis; Faculty of Science; 28 Avenue Valrose Nice 06108 France
- Institut de Biologie Paris-Seine; UMR7138; Sorbonne Universités Paris VI; 7 quai Saint Bernard Paris 75005 France
- Institut de Biologie Paris-Seine; UMR7138; Centre National de la Recherche Scientifique; Paris 75016 France
| | - Paola Furla
- UMR7138; Université de Nice-Sophia-Antipolis; Faculty of Science; 28 Avenue Valrose Nice 06108 France
- Institut de Biologie Paris-Seine; UMR7138; Sorbonne Universités Paris VI; 7 quai Saint Bernard Paris 75005 France
- Institut de Biologie Paris-Seine; UMR7138; Centre National de la Recherche Scientifique; Paris 75016 France
| | - Cecile Sabourault
- UMR7138; Université de Nice-Sophia-Antipolis; Faculty of Science; 28 Avenue Valrose Nice 06108 France
- Institut de Biologie Paris-Seine; UMR7138; Sorbonne Universités Paris VI; 7 quai Saint Bernard Paris 75005 France
- Institut de Biologie Paris-Seine; UMR7138; Centre National de la Recherche Scientifique; Paris 75016 France
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Two apextrin-like proteins mediate extracellular and intracellular bacterial recognition in amphioxus. Proc Natl Acad Sci U S A 2014; 111:13469-74. [PMID: 25187559 DOI: 10.1073/pnas.1405414111] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Animals exploit different germ-line-encoded proteins with various domain structures to detect the signature molecules of pathogenic microbes. These molecules are known as pathogen-associated molecular patterns (PAMPs), and the host proteins that react with PAMPs are called pattern recognition proteins (PRPs). Here, we present a novel type of protein domain structure capable of binding to bacterial peptidoglycan (PGN) and the minimal PGN motif muramyl dipeptide (MDP). This domain is designated as apextrin C-terminal domain (ApeC), and its presence was confirmed in several invertebrate phyla and subphyla. Two apextrin-like proteins (ALP1 and ALP2) were identified in a basal chordate, the Japanese amphioxus Branchiostoma japonicum (bj). bjALP1 is a mucosal effector secreted into the gut lumen to agglutinate the Gram-positive bacterium Staphylococcus aureus via PGN binding. Neutralization of secreted bjALP1 by anti-bjALP1 monoclonal antibodies caused serious damage to the gut epithelium and rapid death of the animals after bacterial infection. bjALP2 is an intracellular PGN sensor that binds to TNF receptor-associated factor 6 (TRAF6) and prevents TRAF6 from self-ubiquitination and hence from NF-κB activation. MDP was found to compete with TRAF6 for bjALP2, which released TRAF6 to activate the NF-κB pathway. BjALP1 and bjALP2 therefore play distinct and complementary functions in amphioxus gut mucosal immunity. In conclusion, discovery of the ApeC domain and the functional analyses of amphioxus ALP1 and ALP2 allowed us to define a previously undocumented type of PRP that is represented across different animal phyla.
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Molecular evolution of calcification genes in morphologically similar but phylogenetically unrelated scleractinian corals. Mol Phylogenet Evol 2014; 77:281-95. [PMID: 24780747 DOI: 10.1016/j.ympev.2014.04.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 03/31/2014] [Accepted: 04/15/2014] [Indexed: 02/03/2023]
Abstract
Molecular phylogenies of scleractinian corals often fail to agree with traditional phylogenies derived from morphological characters. These discrepancies are generally attributed to non-homologous or morphologically plastic characters used in taxonomic descriptions. Consequently, morphological convergence of coral skeletons among phylogenetically unrelated groups is considered to be the major evolutionary process confounding molecular and morphological hypotheses. A strategy that may help identify cases of convergence and/or diversification in coral morphology is to compare phylogenies of existing "neutral" genetic markers used to estimate genealogic phylogenetic history with phylogenies generated from non-neutral genes involved in calcification (biomineralization). We tested the hypothesis that differences among calcification gene phylogenies with respect to the "neutral" trees may represent convergent or divergent functional strategies among calcification gene proteins that may correlate to aspects of coral skeletal morphology. Partial sequences of two nuclear genes previously determined to be involved in the calcification process in corals, "Cnidaria-III" membrane-bound/secreted α-carbonic anhydrase (CIII-MBSα-CA) and bone morphogenic protein (BMP) 2/4, were PCR-amplified, cloned and sequenced from 31 scleractinian coral species in 26 genera and 9 families. For comparison, "neutral" gene phylogenies were generated from sequences from two protein-coding "non-calcification" genes, one nuclear (β-tubulin) and one mitochondrial (cytochrome b), from the same individuals. Cloned CIII-MBSα-CA sequences were found to be non-neutral, and phylogenetic analyses revealed CIII-MBSα-CAs to exhibit a complex evolutionary history with clones distributed between at least 2 putative gene copies. However, for several coral taxa only one gene copy was recovered. With CIII-MBSα-CA, several recovered clades grouped taxa that differed from the "non-calcification" loci. In some cases, these taxa shared aspects of their skeletal morphology (i.e., convergence or diversification relative to the "non-calcification" loci), but in other cases they did not. For example, the "non-calcification" loci recovered Atlantic and Pacific mussids as separate evolutionary lineages, whereas with CIII-MBSα-CA, clones of two species of Atlantic mussids (Isophyllia sinuosa and Mycetophyllia sp.) and two species of Pacific mussids (Acanthastrea echinata and Lobophyllia hemprichii) were united in a distinct clade (except for one individual of Mycetophyllia). However, this clade also contained other taxa which were not unambiguously correlated with morphological features. BMP2/4 also contained clones that likely represent different gene copies. However, many of the sequences showed no significant deviation from neutrality, and reconstructed phylogenies were similar to the "non-calcification" tree topologies with a few exceptions. Although individual calcification genes are unlikely to precisely explain the diverse morphological features exhibited by scleractinian corals, this study demonstrates an approach for identifying cases where morphological taxonomy may have been misled by convergent and/or divergent molecular evolutionary processes in corals. Studies such as this may help illuminate our understanding of the likely complex evolution of genes involved in the calcification process, and enhance our knowledge of the natural history and biodiversity within this central ecological group.
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Liu L, Qu J, Zhou X, Liu X, Zhang Z, Wang X, Liu T, Liu G. Discovery of a strongly-interrelated gene network in corals under constant darkness by correlation analysis after wavelet transform on complex network model. PLoS One 2014; 9:e92434. [PMID: 24651851 PMCID: PMC3961355 DOI: 10.1371/journal.pone.0092434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 02/22/2014] [Indexed: 11/18/2022] Open
Abstract
Coral reefs occupy a relatively small portion of sea area, yet serve as a crucial source of biodiversity by establishing harmonious ecosystems with marine plants and animals. Previous researches mainly focused on screening several key genes induced by stress. Here we proposed a novel method--correlation analysis after wavelet transform of complex network model, to explore the effect of light on gene expression in the coral Acropora millepora based on microarray data. In this method, wavelet transform and the conception of complex network were adopted, and 50 key genes with large differences were finally captured, including both annotated genes and novel genes without accurate annotation. These results shed light on our understanding of coral's response toward light changes and the genome-wide interaction among genes under the control of biorhythm, and hence help us to better protect the coral reef ecosystems. Further studies are needed to explore how functional connections are related to structural connections, and how connectivity arises from the interactions within and between different systems. The method introduced in this study for analyzing microarray data will allow researchers to explore genome-wide interaction network with their own dataset and understand the relevant biological processes.
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Affiliation(s)
- Longlong Liu
- Ocean University of China, Qingdao, Shandong, People's Republic of China
| | - Jieqiong Qu
- Ocean University of China, Qingdao, Shandong, People's Republic of China
| | - Xilong Zhou
- Ocean University of China, Qingdao, Shandong, People's Republic of China
| | - Xuefeng Liu
- Ocean University of China, Qingdao, Shandong, People's Republic of China
| | - Zhaobao Zhang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, People's Republic of China
| | - Xumin Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Tao Liu
- Ocean University of China, Qingdao, Shandong, People's Republic of China
| | - Guiming Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
- * E-mail:
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Siboni N, Abrego D, Motti CA, Tebben J, Harder T. Gene expression patterns during the early stages of chemically induced larval metamorphosis and settlement of the coral Acropora millepora. PLoS One 2014; 9:e91082. [PMID: 24632854 PMCID: PMC3954620 DOI: 10.1371/journal.pone.0091082] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 02/06/2014] [Indexed: 11/19/2022] Open
Abstract
The morphogenetic transition of motile coral larvae into sessile primary polyps is triggered and genetically programmed upon exposure to environmental biomaterials, such as crustose coralline algae (CCA) and bacterial biofilms. Although the specific chemical cues that trigger coral larval morphogenesis are poorly understood there is much more information available on the genes that play a role in this early life phase. Putative chemical cues from natural biomaterials yielded defined chemical samples that triggered different morphogenetic outcomes: an extract derived from a CCA-associated Pseudoalteromonas bacterium that induced metamorphosis, characterized by non-attached metamorphosed juveniles; and two fractions of the CCA Hydrolithon onkodes (Heydrich) that induced settlement, characterized by attached metamorphosed juveniles. In an effort to distinguish the genes involved in these two morphogenetic transitions, competent larvae of the coral Acropora millepora were exposed to these predictable cues and the expression profiles of 47 coral genes of interest (GOI) were investigated after only 1 hour of exposure using multiplex RT-qPCR. Thirty-two GOI were differentially expressed, indicating a putative role during the early regulation of morphogenesis. The most striking differences were observed for immunity-related genes, hypothesized to be involved in cell recognition and adhesion, and for fluorescent protein genes. Principal component analysis of gene expression profiles resulted in separation between the different morphogenetic cues and exposure times, and not only identified those genes involved in the early response but also those which influenced downstream biological changes leading to larval metamorphosis or settlement.
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Affiliation(s)
- Nachshon Siboni
- Australian Institute of Marine Science, Townsville, Australia
- * E-mail:
| | - David Abrego
- Australian Institute of Marine Science, Townsville, Australia
| | - Cherie A. Motti
- Australian Institute of Marine Science, Townsville, Australia
| | - Jan Tebben
- School of Biological, Earth and Environmental Sciences, Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, Australia
| | - Tilmann Harder
- Australian Institute of Marine Science, Townsville, Australia
- School of Biological, Earth and Environmental Sciences, Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, Australia
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Karako-Lampert S, Zoccola D, Salmon-Divon M, Katzenellenbogen M, Tambutté S, Bertucci A, Hoegh-Guldberg O, Deleury E, Allemand D, Levy O. Transcriptome analysis of the scleractinian coral Stylophora pistillata. PLoS One 2014; 9:e88615. [PMID: 24551124 PMCID: PMC3923803 DOI: 10.1371/journal.pone.0088615] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 01/11/2014] [Indexed: 11/18/2022] Open
Abstract
The principal architects of coral reefs are the scleractinian corals; these species are divided in two major clades referred to as “robust” and “complex” corals. Although the molecular diversity of the “complex” clade has received considerable attention, with several expressed sequence tag (EST) libraries and a complete genome sequence having been constructed, the “robust” corals have received far less attention, despite the fact that robust corals have been prominent focal points for ecological and physiological studies. Filling this gap affords important opportunities to extend these studies and to improve our understanding of the differences between the two major clades. Here, we present an EST library from Stylophora pistillata (Esper 1797) and systematically analyze the assembled transcripts compared to putative homologs from the complete proteomes of six well-characterized metazoans: Nematostella vectensis, Hydra magnipapillata, Caenorhabditis elegans, Drosophila melanogaster, Strongylocentrotus purpuratus, Ciona intestinalis and Homo sapiens. Furthermore, comparative analyses of the Stylophora pistillata ESTs were performed against several Cnidaria from the Scleractinia, Actiniaria and Hydrozoa, as well as against other stony corals separately. Functional characterization of S. pistillata transcripts into KOG/COG categories and further description of Wnt and bone morphogenetic protein (BMP) signaling pathways showed that the assembled EST library provides sufficient data and coverage. These features of this new library suggest considerable opportunities for extending our understanding of the molecular and physiological behavior of “robust” corals.
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Affiliation(s)
- Sarit Karako-Lampert
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Didier Zoccola
- Centre Scientifique de Monaco, Monaco, Monaco
- * E-mail: (OL); (DZ)
| | | | - Mark Katzenellenbogen
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | | | - Anthony Bertucci
- Centre Scientifique de Monaco, Monaco, Monaco
- Université de Nice-Sophia-Antipolis, UFR Sciences, Nice, France
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Ove Hoegh-Guldberg
- Global Change Institute, The University of Queensland, St Lucia, Queensland, Australia
| | - Emeline Deleury
- Université de Nice-Sophia-Antipolis, UFR Sciences, Nice, France
- Institut Sophia Agrobiotech INRA 1355, CNRS 7254, Sophia-Antipolis, France
| | | | - Oren Levy
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- * E-mail: (OL); (DZ)
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Comparative embryology of eleven species of stony corals (Scleractinia). PLoS One 2013; 8:e84115. [PMID: 24367633 PMCID: PMC3867500 DOI: 10.1371/journal.pone.0084115] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 11/12/2013] [Indexed: 11/19/2022] Open
Abstract
A comprehensive understanding of coral reproduction and development is needed because corals are threatened in many ways by human activity. Major threats include the loss of their photosynthetic symbionts (Symbiodinium) caused by rising temperatures (bleaching), reduced ability to calcify caused by ocean acidification, increased storm severity associated with global climate change and an increase in predators caused by runoff from human agricultural activity. In spite of these threats, detailed descriptions of embryonic development are not available for many coral species. The current consensus is that there are two major groups of stony corals, the "complex" and the "robust". In this paper we describe the embryonic development of four "complex" species, Pseudosiderastrea tayamai, Galaxea fascicularis, Montipora hispida, and Pavona Decussata, and seven "robust" species, Oulastrea crispata, Platygyra contorta, Favites abdita, Echinophyllia aspera, Goniastrea favulus, Dipsastraea speciosa (previously Favia speciosa), and Phymastrea valenciennesi (previously Montastrea valenciennesi). Data from both histologically sectioned embryos and whole mounts are presented. One apparent difference between these two major groups is that before gastrulation the cells of the complex corals thus far described (mainly Acropora species) spread and flatten to produce the so-called prawn chip, which lacks a blastocoel. Our present broad survey of robust and complex corals reveals that prawn chip formation is not a synapomorphy of complex corals, as Pavona Decussata does not form a prawn chip and has a well-developed blastocoel. Although prawn chip formation cannot be used to separate the two clades, none of the robust corals which we surveyed has such a stage. Many robust coral embryos pass through two periods of invagination, separated by a return to a spherical shape. However, only the second of these periods is associated with endoderm formation. We have therefore termed the first invagination a pseudo-blastopore.
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Dunlap WC, Starcevic A, Baranasic D, Diminic J, Zucko J, Gacesa R, van Oppen MJH, Hranueli D, Cullum J, Long PF. KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome. BMC Genomics 2013; 14:509. [PMID: 23889801 PMCID: PMC3750612 DOI: 10.1186/1471-2164-14-509] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 07/15/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Contemporary coral reef research has firmly established that a genomic approach is urgently needed to better understand the effects of anthropogenic environmental stress and global climate change on coral holobiont interactions. Here we present KEGG orthology-based annotation of the complete genome sequence of the scleractinian coral Acropora digitifera and provide the first comprehensive view of the genome of a reef-building coral by applying advanced bioinformatics. DESCRIPTION Sequences from the KEGG database of protein function were used to construct hidden Markov models. These models were used to search the predicted proteome of A. digitifera to establish complete genomic annotation. The annotated dataset is published in ZoophyteBase, an open access format with different options for searching the data. A particularly useful feature is the ability to use a Google-like search engine that links query words to protein attributes. We present features of the annotation that underpin the molecular structure of key processes of coral physiology that include (1) regulatory proteins of symbiosis, (2) planula and early developmental proteins, (3) neural messengers, receptors and sensory proteins, (4) calcification and Ca2+-signalling proteins, (5) plant-derived proteins, (6) proteins of nitrogen metabolism, (7) DNA repair proteins, (8) stress response proteins, (9) antioxidant and redox-protective proteins, (10) proteins of cellular apoptosis, (11) microbial symbioses and pathogenicity proteins, (12) proteins of viral pathogenicity, (13) toxins and venom, (14) proteins of the chemical defensome and (15) coral epigenetics. CONCLUSIONS We advocate that providing annotation in an open-access searchable database available to the public domain will give an unprecedented foundation to interrogate the fundamental molecular structure and interactions of coral symbiosis and allow critical questions to be addressed at the genomic level based on combined aspects of evolutionary, developmental, metabolic, and environmental perspectives.
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Affiliation(s)
- Walter C Dunlap
- Centre for Marine Microbiology and Genetics, Australian Institute of Marine Science, PMB No. 3 Townsville MC, Townsville 4810, Queensland, Australia
- Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Antonio Starcevic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Damir Baranasic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Janko Diminic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Jurica Zucko
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Ranko Gacesa
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Madeleine JH van Oppen
- Centre for Marine Microbiology and Genetics, Australian Institute of Marine Science, PMB No. 3 Townsville MC, Townsville 4810, Queensland, Australia
| | - Daslav Hranueli
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - John Cullum
- Department of Genetics, University of Kaiserslautern, Postfach 3049, 67653 Kaiserslautern, Germany
| | - Paul F Long
- Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
- Department of Chemistry King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
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Bay LK, Guérécheau A, Andreakis N, Ulstrup KE, Matz MV. Gene expression signatures of energetic acclimatisation in the reef building coral Acropora millepora. PLoS One 2013; 8:e61736. [PMID: 23671571 PMCID: PMC3650039 DOI: 10.1371/journal.pone.0061736] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 03/13/2013] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Understanding the mechanisms by which natural populations cope with environmental stress is paramount to predict their persistence in the face of escalating anthropogenic impacts. Reef-building corals are increasingly exposed to local and global stressors that alter nutritional status causing reduced fitness and mortality, however, these responses can vary considerably across species and populations. METHODOLOGY/PRINCIPAL FINDINGS We compare the expression of 22 coral host genes in individuals from an inshore and an offshore reef location using quantitative Reverse Transcription-PCR (qRT-PCR) over the course of 26 days following translocation into a shaded, filtered seawater environment. Declines in lipid content and PSII activity of the algal endosymbionts (Symbiodinium ITS-1 type C2) over the course of the experiment indicated that heterotrophic uptake and photosynthesis were limited, creating nutritional deprivation conditions. Regulation of coral host genes involved in metabolism, CO2 transport and oxidative stress could be detected already after five days, whereas PSII activity took twice as long to respond. Opposing expression trajectories of Tgl, which releases fatty acids from the triacylglycerol storage, and Dgat1, which catalyses the formation of triglycerides, indicate that the decline in lipid content can be attributed, at least in part, by mobilisation of triacylglycerol stores. Corals from the inshore location had initially higher lipid content and showed consistently elevated expression levels of two genes involved in metabolism (aldehyde dehydrogenase) and calcification (carbonic anhydrase). CONCLUSIONS/SIGNIFICANCE Coral host gene expression adjusts rapidly upon change in nutritional conditions, and therefore can serve as an early signature of imminent coral stress. Consistent gene expression differences between populations indicate that corals acclimatize and/or adapt to local environments. Our results set the stage for analysis of these processes in natural coral populations, to better understand the responses of coral communities to global climate change and to develop more efficient management strategies.
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Affiliation(s)
- Line K Bay
- Climate Change and Ocean Acidification Team, Australian Institute of Marine Science, Townsville, Queensland, Australia.
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Granados-Cifuentes C, Bellantuono AJ, Ridgway T, Hoegh-Guldberg O, Rodriguez-Lanetty M. High natural gene expression variation in the reef-building coral Acropora millepora: potential for acclimative and adaptive plasticity. BMC Genomics 2013; 14:228. [PMID: 23565725 PMCID: PMC3630057 DOI: 10.1186/1471-2164-14-228] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 02/27/2013] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Ecosystems worldwide are suffering the consequences of anthropogenic impact. The diverse ecosystem of coral reefs, for example, are globally threatened by increases in sea surface temperatures due to global warming. Studies to date have focused on determining genetic diversity, the sequence variability of genes in a species, as a proxy to estimate and predict the potential adaptive response of coral populations to environmental changes linked to climate changes. However, the examination of natural gene expression variation has received less attention. This variation has been implicated as an important factor in evolutionary processes, upon which natural selection can act. RESULTS We acclimatized coral nubbins from six colonies of the reef-building coral Acropora millepora to a common garden in Heron Island (Great Barrier Reef, GBR) for a period of four weeks to remove any site-specific environmental effects on the physiology of the coral nubbins. By using a cDNA microarray platform, we detected a high level of gene expression variation, with 17% (488) of the unigenes differentially expressed across coral nubbins of the six colonies (jsFDR-corrected, p < 0.01). Among the main categories of biological processes found differentially expressed were transport, translation, response to stimulus, oxidation-reduction processes, and apoptosis. We found that the transcriptional profiles did not correspond to the genotype of the colony characterized using either an intron of the carbonic anhydrase gene or microsatellite loci markers. CONCLUSION Our results provide evidence of the high inter-colony variation in A. millepora at the transcriptomic level grown under a common garden and without a correspondence with genotypic identity. This finding brings to our attention the importance of taking into account natural variation between reef corals when assessing experimental gene expression differences. The high transcriptional variation detected in this study is interpreted and discussed within the context of adaptive potential and phenotypic plasticity of reef corals. Whether this variation will allow coral reefs to survive to current challenges remains unknown.
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Affiliation(s)
- Camila Granados-Cifuentes
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, 70504, USA
- Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA
| | - Anthony J Bellantuono
- Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA
| | - Tyrone Ridgway
- Oceanica Consulting Pty Ltd, PO Box 462, Wembley, WA, 6913, Australia
- The Oceans Institute, University of Western Australia, Crawley, WA, 6009, Australia
| | - Ove Hoegh-Guldberg
- ARC Centre of Excellence for Coral Reef Studies and Coral Genomics Group, School of Pharmacy and Molecular Sciences, James Cook University, Townsville, QLD, Australia
- Global Change Institute, The University of Queensland, St Lucia, QLD, Australia
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Sun J, Chen Q, Lun JCY, Xu J, Qiu JW. PcarnBase: development of a transcriptomic database for the brain coral Platygyra carnosus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2013; 15:244-251. [PMID: 22875536 DOI: 10.1007/s10126-012-9482-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 07/20/2012] [Indexed: 06/01/2023]
Abstract
The aims of this study were to sequence the transcriptome and organize the sequence data into a searchable database for the brain coral Platygyra carnosus, a structure-forming dominant species along the coast of southern China. We collected healthy and tumorous coral tissues from two locations, extracted RNA from each tissue sample, pooled the RNA from all tissue samples, generated a cDNA library from the pooled samples, and conducted paired-end sequencing of the cDNA library using the Illumina platform to produce 59.6 M clean sequences with a read length of 90 bp. De novo assembly of the sequence data resulted in 162,468 unigenes with an average length of 606 bp (range, 201 to 23,923 bp). This is the largest transcriptome dataset for a species of coral whose genome has not been sequenced. A BLASTx search against the NCBI protein database showed that 55,355 of the unigenes matched at least a sequence with an E-value of < 0.00001; 59 % of the matched sequences are from Metazoa, 13 % are from Alveolata to which the symbiont Symbiodinium belongs, and 7 % are from bacteria. A database (PcarnBase) was constructed to provide easy access to the unigenes with attributes such as NCBI protein annotation, GO annotation, and KEGG pathway. It will facilitate functional genomic studies of P. carnosus, such as biomarker discovery for bleaching, tumor formation, and disease development at the gene or protein level, involvement of coral symbiotic algae in the host coral's stress responses, and genetic basis of stress resistance.
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Affiliation(s)
- Jin Sun
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
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Tait K, Havenhand J. Investigating a possible role for the bacterial signal molecules N-acylhomoserine lactones in Balanus improvisus cyprid settlement. Mol Ecol 2013; 22:2588-602. [PMID: 23506419 DOI: 10.1111/mec.12273] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 01/18/2013] [Accepted: 01/25/2013] [Indexed: 01/29/2023]
Abstract
Increased settlement on bacterial biofilms has been demonstrated for a number of marine invertebrate larvae, but the nature of the cue(s) responsible is not well understood. We tested the hypothesis that the bay barnacle Balanus improvisus utilizes the bacterial signal molecules N-acylhomoserine lactones (AHLs) as a cue for the selection of sites for permanent attachment. Single species biofilms of the AHL-producing bacteria Vibrio anguillarum, Aeromonas hydrophila and Sulfitobacter sp. BR1 were attractive to settling cypris larvae of B. improvisus. However, when AHL production was inactivated, either by mutation of the AHL synthetic genes or by expression of an AHL-degrading gene (aiiA), the ability of the bacteria to attract cyprids was abolished. In addition, cyprids actively explored biofilms of E. coli expressing the recombinant AHL synthase genes luxI from Vibrio fischeri (3-oxo-C6-HSL), rhlI from Pseudomonas aeruginosa (C4-HSL/C6-HSL), vanI from V. anguillarum (3-oxo-C10-HSL) and sulI from Sulfitobacter sp. BR1 (C4-HSL, 3-hydroxy-C6-HSL, C8-HSL and 3-hydroxy-C10-HSL), but not E. coli that did not produce AHLs. Finally, synthetic AHLs (C8-HSL, 3-oxo-C10-HSL and C12-HSL) at concentrations similar to those found within natural biofilms (5 μm) resulted in increased cyprid settlement. Thus, B. improvisus cypris exploration of and settlement on biofilms appears to be mediated by AHL-signalling bacteria in the laboratory. This adds to our understanding of how quorum sensing inhibition may be used as for biofouling control. Nonetheless, the significance of our results for larvae settling naturally in the field, and the mechanisms that underlay the observed responses to AHLs, is as yet unknown.
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Affiliation(s)
- Karen Tait
- Plymouth Marine Laboratory, Plymouth, UK.
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