Responses of the Emiliania huxleyi Proteome to Ocean Acidification
Publication Date
April 12, 2013
Journal
PLOS ONE
Authors
Bethan M. Jones, M. Debora Iglesias Rodriguez, Paul J. Skipp, Richard J. Edwards, et al
Volume
8
Issue
4
Pages
e61868
DOI
https://dx.plos.org/10.1371/journal.pone.0061868
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0061868
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/23593500
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3625171
Europe PMC
http://europepmc.org/abstract/MED/23593500
Web of Science
000317385300086
Scopus
84876094752
Mendeley
http://www.mendeley.com/research/responses-emiliania-huxleyi-proteome-ocean-acidification
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Mendeley | Further Information

{"title"=>"Responses of the Emiliania huxleyi Proteome to Ocean Acidification", "type"=>"journal", "authors"=>[{"first_name"=>"Bethan M.", "last_name"=>"Jones", "scopus_author_id"=>"56325280600"}, {"first_name"=>"M. Debora", "last_name"=>"Iglesias-Rodriguez", "scopus_author_id"=>"6602446022"}, {"first_name"=>"Paul J.", "last_name"=>"Skipp", "scopus_author_id"=>"6506507806"}, {"first_name"=>"Richard J.", "last_name"=>"Edwards", "scopus_author_id"=>"56929686400"}, {"first_name"=>"Mervyn J.", "last_name"=>"Greaves", "scopus_author_id"=>"7402534554"}, {"first_name"=>"Jeremy R.", "last_name"=>"Young", "scopus_author_id"=>"7408525261"}, {"first_name"=>"Henry", "last_name"=>"Elderfield", "scopus_author_id"=>"7006113002"}, {"first_name"=>"C. David", "last_name"=>"O'Connor", "scopus_author_id"=>"6701553544"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84876094752", "sgr"=>"84876094752", "pui"=>"368721466", "isbn"=>"1932-6203", "pmid"=>"23593500", "doi"=>"10.1371/journal.pone.0061868"}, "id"=>"c6e60304-6fba-3903-ad44-5a427764a8d9", "abstract"=>"Ocean acidification due to rising atmospheric CO2 is expected to affect the physiology of important calcifying marine organisms, but the nature and magnitude of change is yet to be established. In coccolithophores, different species and strains display varying calcification responses to ocean acidification, but the underlying biochemical properties remain unknown. We employed an approach combining tandem mass-spectrometry with isobaric tagging (iTRAQ) and multiple database searching to identify proteins that were differentially expressed in cells of the marine coccolithophore species Emiliania huxleyi (strain NZEH) between two CO2 conditions: 395 (current day) and 1340 p.p.m.v. CO2. Cells exposed to the higher CO2 condition contained more cellular particulate inorganic carbon (CaCO3) and particulate organic nitrogen and carbon than those maintained in present-day conditions. These results are linked with the observation that cells grew slower under elevated CO2, indicating cell cycle disruption. Under high CO2 conditions, coccospheres were larger and cells possessed bigger coccoliths that did not show any signs of malformation compared to those from cells grown under present-day CO2 levels. No differences in calcification rate, particulate organic carbon production or cellular organic carbon: nitrogen ratios were observed. Results were not related to nutrient limitation or acclimation status of cells. At least 46 homologous protein groups from a variety of functional processes were quantified in these experiments, of which four (histones H2A, H3, H4 and a chloroplastic 30S ribosomal protein S7) showed down-regulation in all replicates exposed to high CO2, perhaps reflecting the decrease in growth rate. We present evidence of cellular stress responses but proteins associated with many key metabolic processes remained unaltered. Our results therefore suggest that this E. huxleyi strain possesses some acclimation mechanisms to tolerate future CO2 scenarios, although the observed decline in growth rate may be an overriding factor affecting the success of this ecotype in future oceans.", "link"=>"http://www.mendeley.com/research/responses-emiliania-huxleyi-proteome-ocean-acidification", "reader_count"=>56, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Researcher"=>16, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>1, "Other"=>5, "Student > Master"=>4, "Student > Bachelor"=>5, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Researcher"=>16, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>1, "Other"=>5, "Student > Master"=>4, "Student > Bachelor"=>5, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Environmental Science"=>8, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>35, "Chemistry"=>1, "Earth and Planetary Sciences"=>11}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>11}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>35}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Environmental Science"=>{"Environmental Science"=>8}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>3, "Poland"=>1, "United Kingdom"=>3, "Australia"=>1, "Portugal"=>1, "Germany"=>1}, "group_count"=>2}

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1023132"], "description"=>"<p>* p≤0.05; ** p≤0.01; *** p≤0.001. A point with no star indicates differences were non-significant. Arrows indicate inoculations into media with different <i>p</i>CO<sub>2</sub> conditions, as outlined in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061868#s2\" target=\"_blank\">Materials and Methods</a>. Open circles represent cells grown under under 395 p.p.m.v. CO<sub>2</sub> that were harvested after 12–13 generations (<i>t2</i> = day 8). Solid circles indicate cells grown under 1340 p.p.m.v. CO<sub>2</sub>. In order to ensure suitable biomass for proteomics, these were harvested after 9–12 generations (<i>t2</i> = day 9 or 10) because of their lower growth rates.</p>", "links"=>[], "tags"=>["ecology", "Global change ecology", "Marine ecology", "microbial ecology", "Marine biology", "Phycology", "Plant science", "plants", "algae", "proteomics", "Protein abundance", "marine and aquatic sciences", "oceanography", "Biological oceanography", "nzeh", "coccosphere", "sizes", "395", "1340"], "article_id"=>681395, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Bethan M. Jones", "M. Debora Iglesias-Rodriguez", "Paul J. Skipp", "Richard J. Edwards", "Mervyn J. Greaves", "Jeremy R. Young", "Henry Elderfield", "C. David O'Connor"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0061868.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_Emiliania_huxleyi_NZEH_coccosphere_sizes_at_395_and_1340_p_p_m_v_CO_2_/681395", "title"=>"Comparison of <i>Emiliania huxleyi</i> NZEH coccosphere sizes at 395 and 1340 p.p.m.v. CO<sub>2</sub>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-12 00:23:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/1023133"], "description"=>"<p>Morphometric analysis of detached coccoliths obtained at the end of the experiment (<i>t2</i>) from monoclonal cultures of <i>Emiliania huxleyi</i> NZEH bubbled with 395 and 1340 p.p.m.v. CO<sub>2.</sub></p>", "links"=>[], "tags"=>["ecology", "Global change ecology", "Marine ecology", "microbial ecology", "Marine biology", "Phycology", "Plant science", "plants", "algae", "proteomics", "Protein abundance", "marine and aquatic sciences", "oceanography", "Biological oceanography", "detached", "coccoliths", "monoclonal", "cultures", "nzeh", "bubbled", "395", "1340"], "article_id"=>681396, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Bethan M. Jones", "M. Debora Iglesias-Rodriguez", "Paul J. Skipp", "Richard J. Edwards", "Mervyn J. Greaves", "Jeremy R. Young", "Henry Elderfield", "C. David O'Connor"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0061868.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Morphometric_analysis_of_detached_coccoliths_obtained_at_the_end_of_the_experiment_t2_from_monoclonal_cultures_of_Emiliania_huxleyi_NZEH_bubbled_with_395_and_1340_p_p_m_v_CO_2_/681396", "title"=>"Morphometric analysis of detached coccoliths obtained at the end of the experiment (<i>t2</i>) from monoclonal cultures of <i>Emiliania huxleyi</i> NZEH bubbled with 395 and 1340 p.p.m.v. CO<sub>2.</sub>", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-12 00:23:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1023134"], "description"=>"<p>Panel A: typical coccoliths from 395 p.p.m.v. CO<sub>2</sub> treatment; B: coccoliths from the lower pH (∼7.6) and 1340 p.p.m.v. CO<sub>2</sub> treatment which are typically larger and are slighly less calcified but possess no signs of dissolution or malformation.</p>", "links"=>[], "tags"=>["ecology", "Global change ecology", "Marine ecology", "microbial ecology", "Marine biology", "Phycology", "Plant science", "plants", "algae", "proteomics", "Protein abundance", "marine and aquatic sciences", "oceanography", "Biological oceanography", "coccoliths", "derived"], "article_id"=>681397, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Bethan M. Jones", "M. Debora Iglesias-Rodriguez", "Paul J. Skipp", "Richard J. Edwards", "Mervyn J. Greaves", "Jeremy R. Young", "Henry Elderfield", "C. David O'Connor"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0061868.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Example_of_coccoliths_derived_at_the_end_of_the_experiment_t2_/681397", "title"=>"Example of coccoliths derived at the end of the experiment (<i>t2</i>).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-12 00:23:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/1023135"], "description"=>"a<p>Average values at the beginning of the experiment before the inoculation of cells.</p>b<p>Figures in parentheses represent blank seawater medium bubbled with the appropriate <i>p</i>CO<sub>2</sub> mixture.</p>c<p>There was only one sample available for the initial pre-inoculation blank of the ambient/current day CO<sub>2</sub> condition. For this instance alone, values in parentheses are from the second 395 p.p.m.v. CO<sub>2</sub> treatment.</p>d<p>Average values at the end of the experiment (<i>t2</i>).</p>", "links"=>[], "tags"=>["ecology", "Global change ecology", "Marine ecology", "microbial ecology", "Marine biology", "Phycology", "Plant science", "plants", "algae", "proteomics", "Protein abundance", "marine and aquatic sciences", "oceanography", "Biological oceanography", "carbonate", "cultures"], "article_id"=>681398, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Bethan M. Jones", "M. Debora Iglesias-Rodriguez", "Paul J. Skipp", "Richard J. Edwards", "Mervyn J. Greaves", "Jeremy R. Young", "Henry Elderfield", "C. David O'Connor"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0061868.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mean_carbonate_chemistry_values_associated_with_experimental_cultures_t2_/681398", "title"=>"Mean carbonate chemistry values associated with experimental cultures (<i>t2</i>).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-04-12 00:23:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1023136"], "description"=>"a<p>Identifications are associated with either UniProtKB accession, <i>Emiliania huxleyi</i> genome protein ID or BUDAPEST consensus sequence. Further information can be found in <b><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061868#pone.0061868.s002\" target=\"_blank\">Data S2</a>;</b> BUDAPEST sequence files can be found in <b><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061868#pone.0061868.s001\" target=\"_blank\">Data S1</a></b>.</p>b<p>Ratio of protein identified between the two CO<sub>2</sub> treatments for each replicate incubation, whereby 114∶113 is the first replicate, 116∶115 is the second and 118∶117 the third. Reporter ions 114, 116 and 118 were applied to peptides extracted from the high CO<sub>2</sub> treatments and 113, 115, 117 to the current day treatment.</p>c<p>“Range” (<i>G</i>−<i>CI</i>)–(<i>G</i>+<i>CI</i>) as defined in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061868#s2\" target=\"_blank\">Materials and Methods</a>.</p>", "links"=>[], "tags"=>["ecology", "Global change ecology", "Marine ecology", "microbial ecology", "Marine biology", "Phycology", "Plant science", "plants", "algae", "proteomics", "Protein abundance", "marine and aquatic sciences", "oceanography", "Biological oceanography", "down-regulated", "nzeh"], "article_id"=>681399, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Bethan M. Jones", "M. Debora Iglesias-Rodriguez", "Paul J. Skipp", "Richard J. Edwards", "Mervyn J. Greaves", "Jeremy R. Young", "Henry Elderfield", "C. David O'Connor"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0061868.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proteins_Homolgous_Protein_Groups_down_regulated_in_Emilania_huxleyi_NZEH_under_high_CO_2_/681399", "title"=>"Proteins (Homolgous Protein Groups) down-regulated in <i>Emilania huxleyi</i> NZEH under high CO<sub>2</sub>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-04-12 00:23:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/1023137"], "description"=>"*, **, ***<p>Significant results from t-tests comparing results from different <i>p</i>CO<sub>2</sub> treatments at the same time point (i.e. 395 v 1340 p.p.m.v. CO<sub>2</sub> at <i>t1</i>; 395 v. 1340 p.p.m.v. CO<sub>2</sub> at <i>t2</i>) are designated as follows: <sup>*</sup> p≤0.05; <sup>**</sup> p≤0.01; <sup>***</sup> p≤0.001.</p>a, b,<p>Significant results from t-tests comparing results from the same <i>p</i>CO<sub>2</sub> treatment at different time points (e.g. 395 <i>t1</i> v 395 p.p.m.v. CO<sub>2</sub><i>t2</i>) are defined according to: <sup>a</sup> p≤0.05; <sup>b</sup> p≤0.01.</p>", "links"=>[], "tags"=>["ecology", "Global change ecology", "Marine ecology", "microbial ecology", "Marine biology", "Phycology", "Plant science", "plants", "algae", "proteomics", "Protein abundance", "marine and aquatic sciences", "oceanography", "Biological oceanography", "nzeh", "grown", "395", "1340"], "article_id"=>681400, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Bethan M. Jones", "M. Debora Iglesias-Rodriguez", "Paul J. Skipp", "Richard J. Edwards", "Mervyn J. Greaves", "Jeremy R. Young", "Henry Elderfield", "C. David O'Connor"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0061868.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Physiological_parameters_of_Emiliania_huxleyi_NZEH_grown_under_395_and_1340_p_p_m_v_CO_2_at_t1_and_2_/681400", "title"=>"Physiological parameters of <i>Emiliania huxleyi</i> NZEH grown under 395 and 1340 p.p.m.v. CO<sub>2</sub> at <i>t1</i> and <i>2</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-04-12 00:23:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/1023138"], "description"=>"a, b, c<p>As defined for <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061868#pone-0061868-t003\" target=\"_blank\">table 3</a>.</p>d<p>If an identification was made from numerous ESTs with valid iTRAQ quantification, an geometric average has been made (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061868#s2\" target=\"_blank\">Materials and Methods</a>). Please refer to <b><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061868#pone.0061868.s002\" target=\"_blank\">Data S2</a></b> for individual EST quantification.</p>", "links"=>[], "tags"=>["ecology", "Global change ecology", "Marine ecology", "microbial ecology", "Marine biology", "Phycology", "Plant science", "plants", "algae", "proteomics", "Protein abundance", "marine and aquatic sciences", "oceanography", "Biological oceanography", "exhibiting", "non-significant", "expressional", "nzeh"], "article_id"=>681401, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Bethan M. Jones", "M. Debora Iglesias-Rodriguez", "Paul J. Skipp", "Richard J. Edwards", "Mervyn J. Greaves", "Jeremy R. Young", "Henry Elderfield", "C. David O'Connor"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0061868.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proteins_Homologous_Protein_Groups_exhibiting_non_significant_expressional_change_in_Emilania_huxleyi_NZEH_under_high_CO_2_/681401", "title"=>"Proteins (Homologous Protein Groups) exhibiting non-significant expressional change in <i>Emilania huxleyi</i> NZEH under high CO<sub>2</sub>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-04-12 00:23:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/1023140", "https://ndownloader.figshare.com/files/1023141", "https://ndownloader.figshare.com/files/1023142", "https://ndownloader.figshare.com/files/1023143", "https://ndownloader.figshare.com/files/1023144", "https://ndownloader.figshare.com/files/1023145", "https://ndownloader.figshare.com/files/1023146", "https://ndownloader.figshare.com/files/1023147"], "description"=>"<div><p>Ocean acidification due to rising atmospheric CO<sub>2</sub> is expected to affect the physiology of important calcifying marine organisms, but the nature and magnitude of change is yet to be established. In coccolithophores, different species and strains display varying calcification responses to ocean acidification, but the underlying biochemical properties remain unknown. We employed an approach combining tandem mass-spectrometry with isobaric tagging (iTRAQ) and multiple database searching to identify proteins that were differentially expressed in cells of the marine coccolithophore species <i>Emiliania huxleyi</i> (strain NZEH) between two CO<sub>2</sub> conditions: 395 (∼current day) and ∼1340 p.p.m.v. CO<sub>2</sub>. Cells exposed to the higher CO<sub>2</sub> condition contained more cellular particulate inorganic carbon (CaCO<sub>3</sub>) and particulate organic nitrogen and carbon than those maintained in present-day conditions. These results are linked with the observation that cells grew slower under elevated CO<sub>2</sub>, indicating cell cycle disruption. Under high CO<sub>2</sub> conditions, coccospheres were larger and cells possessed bigger coccoliths that did not show any signs of malformation compared to those from cells grown under present-day CO<sub>2</sub> levels. No differences in calcification rate, particulate organic carbon production or cellular organic carbon: nitrogen ratios were observed. Results were not related to nutrient limitation or acclimation status of cells. At least 46 homologous protein groups from a variety of functional processes were quantified in these experiments, of which four (histones H2A, H3, H4 and a chloroplastic 30S ribosomal protein S7) showed down-regulation in all replicates exposed to high CO<sub>2</sub>, perhaps reflecting the decrease in growth rate. We present evidence of cellular stress responses but proteins associated with many key metabolic processes remained unaltered. Our results therefore suggest that this <i>E. huxleyi</i> strain possesses some acclimation mechanisms to tolerate future CO<sub>2</sub> scenarios, although the observed decline in growth rate may be an overriding factor affecting the success of this ecotype in future oceans.</p></div>", "links"=>[], "tags"=>["ecology", "Global change ecology", "Marine ecology", "microbial ecology", "Marine biology", "Phycology", "Plant science", "plants", "algae", "proteomics", "Protein abundance", "marine and aquatic sciences", "oceanography", "Biological oceanography", "responses", "proteome", "acidification"], "article_id"=>681402, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Bethan M. Jones", "M. Debora Iglesias-Rodriguez", "Paul J. Skipp", "Richard J. Edwards", "Mervyn J. Greaves", "Jeremy R. Young", "Henry Elderfield", "C. David O'Connor"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0061868.s001", "https://dx.doi.org/10.1371/journal.pone.0061868.s002", "https://dx.doi.org/10.1371/journal.pone.0061868.s003", "https://dx.doi.org/10.1371/journal.pone.0061868.s004", "https://dx.doi.org/10.1371/journal.pone.0061868.s005", "https://dx.doi.org/10.1371/journal.pone.0061868.s006", "https://dx.doi.org/10.1371/journal.pone.0061868.s007", "https://dx.doi.org/10.1371/journal.pone.0061868.s008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Responses_of_the_Emiliania_huxleyi_Proteome_to_Ocean_Acidification/681402", "title"=>"Responses of the <i>Emiliania huxleyi</i> Proteome to Ocean Acidification", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-04-12 00:23:22"}

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Relative Metric

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