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Ashey J, McKelvie H, Freeman J, Shpilker P, Zane LH, Becker DM, Cowen L, Richmond RH, Paul VJ, Seneca FO, Putnam HM. Characterizing transcriptomic responses to sediment stress across location and morphology in reef-building corals. PeerJ 2024; 12:e16654. [PMID: 38313033 PMCID: PMC10836209 DOI: 10.7717/peerj.16654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 11/20/2023] [Indexed: 02/06/2024] Open
Abstract
Anthropogenic activities increase sediment suspended in the water column and deposition on reefs can be largely dependent on colony morphology. Massive and plating corals have a high capacity to trap sediments, and active removal mechanisms can be energetically costly. Branching corals trap less sediment but are more susceptible to light limitation caused by suspended sediment. Despite deleterious effects of sediments on corals, few studies have examined the molecular response of corals with different morphological characteristics to sediment stress. To address this knowledge gap, this study assessed the transcriptomic responses of branching and massive corals in Florida and Hawai'i to varying levels of sediment exposure. Gene expression analysis revealed a molecular responsiveness to sediments across species and sites. Differential Gene Expression followed by Gene Ontology (GO) enrichment analysis identified that branching corals had the largest transcriptomic response to sediments, in developmental processes and metabolism, while significantly enriched GO terms were highly variable between massive corals, despite similar morphologies. Comparison of DEGs within orthogroups revealed that while all corals had DEGs in response to sediment, there was not a concerted gene set response by morphology or location. These findings illuminate the species specificity and genetic basis underlying coral susceptibility to sediments.
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Affiliation(s)
- Jill Ashey
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, United States
| | - Hailey McKelvie
- Department of Computer Science, Tufts University, Medford, Massachusetts, United States
| | - John Freeman
- Department of Computer Science, Tufts University, Medford, Massachusetts, United States
| | - Polina Shpilker
- Department of Computer Science, Tufts University, Medford, Massachusetts, United States
| | - Lauren H. Zane
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, United States
| | - Danielle M. Becker
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, United States
| | - Lenore Cowen
- Department of Computer Science, Tufts University, Medford, Massachusetts, United States
| | - Robert H. Richmond
- Kewalo Marine Lab, University of Hawaii at Manoa, Honolulu, Hawaii, United States
| | - Valerie J. Paul
- Smithsonian Marine Station, Smithsonian, Fort Pierce, Florida, United States
| | | | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, United States
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2
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Chiu HY, Lin LY, Chen Y, Liu ER, Li HH. A New Method for Collecting Large Amounts of Symbiotic Gastrodermal Cells from Octocorals. Int J Mol Sci 2020; 21:ijms21113911. [PMID: 32486176 PMCID: PMC7313047 DOI: 10.3390/ijms21113911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/12/2020] [Accepted: 05/28/2020] [Indexed: 11/27/2022] Open
Abstract
The study of cnidarian-dinoflagellate endosymbiosis in octocorals is becoming increasingly important. As symbiotic gastrodermal cells (SGCs) are the key cells in a symbiotic relationship, obtaining SGCs and studying their functions represent an urgent need. The majority of the cells dissociated from octocoral tissues consist of host cells and algal cells, and very few intact SGCs can be observed. To solve this problem, we developed a new method to collect large amounts of SGCs from octocorals. We incubated the tissue of Sinularia flexibilis in high-salinity (60‰) filtered seawater for 6 h and were able to collect more than 18 times the number of SGCs from the control group. To test the quality of the dissociated cells, we performed three assays to evaluate their cell viability. All three assays demonstrated that cell viability was good after incubating in a high-salinity solution. We also used two other octocorals, Paralemnalia thyrsoides and Sinularia compressa, to perform the same experiment, and the results were similar to those for Sinularia flexibilis. Therefore, a high-salinity-induced increase in the SGC ratio is a common phenomenon among octocorals. This method allows researchers to collect large amounts of SGCs from octocorals and helps us to better understand the complex molecular interactions in cnidarian-dinoflagellate endosymbiosis.
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Affiliation(s)
- Hsiang-Yi Chiu
- Taiwan Coral Research Center, National Museum of Marine Biology and Aquarium, Pingtung 94450, Taiwan; (H.-Y.C.); (L.-Y.L.)
| | - Li-Yi Lin
- Taiwan Coral Research Center, National Museum of Marine Biology and Aquarium, Pingtung 94450, Taiwan; (H.-Y.C.); (L.-Y.L.)
| | - Ying Chen
- Department of Oceanography, National Sun Yat-Sen University, Kaohsiung City 80424, Taiwan;
| | - En-Ru Liu
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Kaohsiung 81143, Taiwan;
| | - Hsing-Hui Li
- Taiwan Coral Research Center, National Museum of Marine Biology and Aquarium, Pingtung 94450, Taiwan; (H.-Y.C.); (L.-Y.L.)
- Graduate Institute of Marine Biotechnology, National Dong Hwa University, Pingtung 94450, Taiwan
- Correspondence: ; Tel.: +886-8-8824632
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Huang KJ, Huang ZY, Lin CY, Wang LH, Chou PH, Chen CS, Li HH. Generation of clade- and symbiont-specific antibodies to characterize marker molecules during Cnidaria-Symbiodinium endosymbiosis. Sci Rep 2017; 7:5488. [PMID: 28710419 PMCID: PMC5511166 DOI: 10.1038/s41598-017-05945-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 06/06/2017] [Indexed: 01/24/2023] Open
Abstract
The endosymbiosis between cnidarians and dinoflagellates is responsible for the formation of coral reefs. Changes in molecules have been identified during the process of cnidaria-Symbiodinium endosymbiosis. However, the complexity of the molecular interaction has prevented the establishment of a mechanistic explanation of cellular regulation in this mutualistic symbiosis. To date, no marker molecules have been identified to specifically represent the symbiotic status. Because the endosymbiotic association occurs in the symbiotic gastrodermal cells (SGCs), whole cells of isolated SGCs were used as an antigen to generate monoclonal antibodies (mAb) to screen possible molecular candidates of symbiotic markers. The results showed that one of the generated monoclonal antibodies, 2–6F, specifically recognized clade C symbiotic Symbiodinium but not its free-living counterpart or other Symbiodinium clades. The expression levels of 2–6F mAb-recognized proteins are highly correlated with the symbiotic status, and these proteins were characterized as N-linked glycoproteins via treatment with peptide N-glycosidase F. Furthermore, their glycan moieties were markedly different from those of free-living Symbiodinium, potentially suggesting host regulation of post-translational modification. Consequently, the 2–6F mAb can be used to detect the symbiotic state of corals and investigate the complex molecular interactions in cnidaria-Symbiodinium endosymbiosis.
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Affiliation(s)
- Kao-Jean Huang
- Institute of Biologics, Development Center for Biotechnology, New Taipei City, 22180, Taiwan
| | - Zi-Yu Huang
- Graduate Institute of Marine Biology, National Dong-Hwa University, Pingtung, 94450, Taiwan
| | - Ching-Yen Lin
- Department of Life Science, National Dong Hwa University, Hualien, 97401, Taiwan
| | - Li-Hsueh Wang
- Graduate Institute of Marine Biology, National Dong-Hwa University, Pingtung, 94450, Taiwan.,Taiwan Coral Research Center, National Museum of Marine Biology and Aquarium, Pingtung, 94450, Taiwan
| | - Pin-Hsiang Chou
- Taiwan Coral Research Center, National Museum of Marine Biology and Aquarium, Pingtung, 94450, Taiwan
| | - Chii-Shiarng Chen
- Graduate Institute of Marine Biology, National Dong-Hwa University, Pingtung, 94450, Taiwan. .,Taiwan Coral Research Center, National Museum of Marine Biology and Aquarium, Pingtung, 94450, Taiwan. .,Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan.
| | - Hsing-Hui Li
- Graduate Institute of Marine Biology, National Dong-Hwa University, Pingtung, 94450, Taiwan. .,Taiwan Coral Research Center, National Museum of Marine Biology and Aquarium, Pingtung, 94450, Taiwan.
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4
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Garcia GD, Santos EDO, Sousa GV, Zingali RB, Thompson CC, Thompson FL. Metaproteomics reveals metabolic transitions between healthy and diseased stony coral Mussismilia braziliensis. Mol Ecol 2016; 25:4632-44. [PMID: 27492757 DOI: 10.1111/mec.13775] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 06/28/2016] [Accepted: 07/05/2016] [Indexed: 12/21/2022]
Abstract
Infectious diseases such as white plague syndrome (WPS) and black band disease (BBD) have caused massive coral loss worldwide. We performed a metaproteomic study on the Abrolhos coral Mussismilia braziliensis to define the types of proteins expressed in healthy corals compared to WPS- and BBD-affected corals. A total of 6363 MS/MS spectra were identified as 361 different proteins. Healthy corals had a set of proteins that may be considered markers of holobiont homoeostasis, including tubulin, histone, Rab family, ribosomal, peridinin-chlorophyll a-binding protein, F0F1-type ATP synthase, alpha-iG protein, calmodulin and ADP-ribosylation factor. Cnidaria proteins found in healthy M. braziliensis were associated with Cnidaria-Symbiodinium endosymbiosis and included chaperones (hsp70, hsp90 and calreticulin), structural and membrane modelling proteins (actin) and proteins with functions related to intracellular vesicular traffic (Rab7 and ADP-ribosylation factor 1) and signal transduction (14-3-3 protein and calmodulin). WPS resulted in a clear shift in the predominance of proteins, from those related to aerobic nitrogen-fixing bacteria (i.e. Rhizobiales, Sphingomonadales and Actinomycetales) in healthy corals to those produced by facultative/anaerobic sulphate-reducing bacteria (i.e. Enterobacteriales, Alteromonadales, Clostridiales and Bacteroidetes) in WPS corals. BBD corals developed a diverse community dominated by cyanobacteria and sulphur cycle bacteria. Hsp60, hsp90 and adenosylhomocysteinase proteins were produced mainly by cyanobacteria in BBD corals, which is consistent with elevated oxidative stress in hydrogen sulphide- and cyanotoxin-rich environments. This study demonstrates the usefulness of metaproteomics for gaining better comprehension of coral metabolic status in health and disease, especially in reef systems such as the Abrolhos that are suffering from the increase in global and local threatening events.
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Affiliation(s)
- Gizele D Garcia
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Fo. SN., Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-902, Brasil
| | - Eidy de O Santos
- Divisão de Metrologia Aplicada às Ciências da Vida (DIMAV), Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMETRO), Av. Nossa Senhora das Graças, 50, Xerém Duque de Caxias, Rio de Janeiro, RJ, CEP 25250-020, Brasil.,Unidade de Biologia, Centro Universitário Estadual da Zona Oeste (UEZO), Av. Manoel Caldeira de Alvarenga, 1203, Campo Grande, Rio de Janeiro, RJ, CEP 23070200, Brasil
| | - Gabriele V Sousa
- Divisão de Metrologia Aplicada às Ciências da Vida (DIMAV), Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMETRO), Av. Nossa Senhora das Graças, 50, Xerém Duque de Caxias, Rio de Janeiro, RJ, CEP 25250-020, Brasil
| | - Russolina B Zingali
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Fo. SN, Ilha do Fundão, Rio de Janeiro, RJ, CEP21941-902, Brasil
| | - Cristiane C Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Fo. SN., Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-902, Brasil
| | - Fabiano L Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Fo. SN., Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-902, Brasil. .,Laboratório de Sistemas Avançados de Gestão da Produção (SAGE), COPPE, Universidade Federal do Rio de Janeiro (UFRJ), Rua Moniz de Aragão, no.360 - Bloco 2, Ilha do Fundão - Cidade Universitária, Rio de Janeiro, RJ, 21.941-972, Brasil.
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Schiapparelli LM, McClatchy DB, Liu HH, Sharma P, Yates JR, Cline HT. Direct detection of biotinylated proteins by mass spectrometry. J Proteome Res 2014; 13:3966-78. [PMID: 25117199 PMCID: PMC4156236 DOI: 10.1021/pr5002862] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mass spectrometric strategies to identify protein subpopulations involved in specific biological functions rely on covalently tagging biotin to proteins using various chemical modification methods. The biotin tag is primarily used for enrichment of the targeted subpopulation for subsequent mass spectrometry (MS) analysis. A limitation of these strategies is that MS analysis does not easily discriminate unlabeled contaminants from the labeled protein subpopulation under study. To solve this problem, we developed a flexible method that only relies on direct MS detection of biotin-tagged proteins called "Direct Detection of Biotin-containing Tags" (DiDBiT). Compared with conventional targeted proteomic strategies, DiDBiT improves direct detection of biotinylated proteins ∼200 fold. We show that DiDBiT is applicable to several protein labeling protocols in cell culture and in vivo using cell permeable NHS-biotin and incorporation of the noncanonical amino acid, azidohomoalanine (AHA), into newly synthesized proteins, followed by click chemistry tagging with biotin. We demonstrate that DiDBiT improves the direct detection of biotin-tagged newly synthesized peptides more than 20-fold compared to conventional methods. With the increased sensitivity afforded by DiDBiT, we demonstrate the MS detection of newly synthesized proteins labeled in vivo in the rodent nervous system with unprecedented temporal resolution as short as 3 h.
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Affiliation(s)
- Lucio Matias Schiapparelli
- The Dorris Neuroscience Center, Department of Molecular and Cellular Neuroscience, ‡Department of Chemical Physiology, and §Kellogg School of Science and Technology, The Scripps Research Institute , La Jolla, California 92037, United States
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