Genes Related to Ion-Transport and Energy Production Are Upregulated in Response to CO2-Driven pH Decrease in Corals: New Insights from Transcriptome Analysis
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{"title"=>"Genes Related to Ion-Transport and Energy Production Are Upregulated in Response to CO2-Driven pH Decrease in Corals: New Insights from Transcriptome Analysis", "type"=>"journal", "authors"=>[{"first_name"=>"Jeremie", "last_name"=>"Vidal-Dupiol", "scopus_author_id"=>"26640004200"}, {"first_name"=>"Didier", "last_name"=>"Zoccola", "scopus_author_id"=>"6603258913"}, {"first_name"=>"Eric", "last_name"=>"Tambutté", "scopus_author_id"=>"6602773089"}, {"first_name"=>"Christoph", "last_name"=>"Grunau", "scopus_author_id"=>"6602853341"}, {"first_name"=>"Céline", "last_name"=>"Cosseau", "scopus_author_id"=>"6507548063"}, {"first_name"=>"Kristina M.", "last_name"=>"Smith", "scopus_author_id"=>"7410186493"}, {"first_name"=>"Michael", "last_name"=>"Freitag", "scopus_author_id"=>"7005690560"}, {"first_name"=>"Nolwenn M.", "last_name"=>"Dheilly", "scopus_author_id"=>"26040598500"}, {"first_name"=>"Denis", "last_name"=>"Allemand", "scopus_author_id"=>"7003604806"}, {"first_name"=>"Sylvie", "last_name"=>"Tambutté", "scopus_author_id"=>"6507063305"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"23544045", "doi"=>"10.1371/journal.pone.0058652", "sgr"=>"84875438796", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "scopus"=>"2-s2.0-84875438796", "issn"=>"19326203", "pui"=>"368602333"}, "id"=>"57d823e5-219f-3754-9db8-66db956c92d5", "abstract"=>"Since the preindustrial era, the average surface ocean pH has declined by 0.1 pH units and is predicted to decline by an additional 0.3 units by the year 2100. Although subtle, this decreasing pH has profound effects on the seawater saturation state of carbonate minerals and is thus predicted to impact on calcifying organisms. Among these are the scleractinian corals, which are the main builders of tropical coral reefs. Several recent studies have evaluated the physiological impact of low pH, particularly in relation to coral growth and calcification. However, very few studies have focused on the impact of low pH at the global molecular level. In this context we investigated global transcriptomic modifications in a scleractinian coral (Pocillopora damicornis) exposed to pH 7.4 compared to pH 8.1during a 3-week period. The RNAseq approach shows that 16% of our transcriptome was affected by the treatment with 6% of upregulations and 10% of downregulations. A more detailed analysis suggests that the downregulations are less coordinated than the upregulations and allowed the identification of several biological functions of interest. In order to better understand the links between these functions and the pH, transcript abundance of 48 candidate genes was quantified by q-RT-PCR (corals exposed at pH 7.2 and 7.8 for 3 weeks). The combined results of these two approaches suggest that pH≥7.4 induces an upregulation of genes coding for proteins involved in calcium and carbonate transport, conversion of CO2 into HCO3− and organic matrix that may sustain calcification. Concomitantly, genes coding for heterotrophic and autotrophic related proteins are upregulated. This can reflect that low pH may increase the coral energy requirements, leading to an increase of energetic metabolism with the mobilization of energy reserves. In addition, the uncoordinated downregulations measured can reflect a general trade-off mechanism that may enable energy reallocation.", "link"=>"http://www.mendeley.com/research/genes-related-iontransport-energy-production-upregulated-response-co2driven-ph-decrease-corals-new-i", "reader_count"=>142, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>6, "Librarian"=>1, "Researcher"=>33, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>43, "Student > Postgraduate"=>6, "Student > Master"=>25, "Other"=>5, "Student > Bachelor"=>12, "Professor"=>5}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>6, "Librarian"=>1, "Researcher"=>33, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>43, "Student > Postgraduate"=>6, "Student > Master"=>25, "Other"=>5, "Student > Bachelor"=>12, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Engineering"=>1, "Environmental Science"=>13, "Biochemistry, Genetics and Molecular Biology"=>10, "Materials Science"=>2, "Agricultural and Biological Sciences"=>99, "Medicine and Dentistry"=>1, "Neuroscience"=>1, "Arts and Humanities"=>1, "Social Sciences"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>7}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Materials Science"=>{"Materials Science"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Neuroscience"=>{"Neuroscience"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>7}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>99}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>10}, "Unspecified"=>{"Unspecified"=>5}, "Environmental Science"=>{"Environmental Science"=>13}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "Belgium"=>3, "United States"=>1, "Japan"=>1, "Brazil"=>1, "United Kingdom"=>1, "France"=>1, "Australia"=>1, "Germany"=>4}, "group_count"=>7}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/999294"], "description"=>"<p>The detection of genes differentially expressed in the two conditions was performed using the DEGseq R package and plotted as a MA plot. The M axis is the log2 fold change for the pH-treated sample compared with the control sample (log2 fold change  =  log2 [RPKM acid stress/RPKM control]), and the A axis is the average log2 normalized counts in both samples. Each point represents a single contig of the reference transcriptome. The red points correspond to contigs significantly differentially represented between the two conditions (<i>p</i><0.0001). Among the 57,259 contigs analyzed, 5758 were significantly downregulated (10%) and 3204 (6%) were upregulated.</p>", "links"=>[], "tags"=>["samples", "exposed", "ph"], "article_id"=>661284, "categories"=>["Physiology", "Inorganic Chemistry", "Biological Sciences", "Genetics"], "users"=>["Jeremie Vidal-Dupiol", "Didier Zoccola", "Eric Tambutté", "Christoph Grunau", "Céline Cosseau", "Kristina M. Smith", "Michael Freitag", "Nolwenn M. Dheilly", "Denis Allemand", "Sylvie Tambutté"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0058652.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differential_gene_expression_between_control_samples_and_samples_exposed_to_pH_7_4_for_three_weeks_/661284", "title"=>"Differential gene expression between control samples and samples exposed to pH 7.4 for three weeks.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-28 08:52:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/999295"], "description"=>"<p>Twenty-five genes that whose expression was significantly different in the control and treatment conditions were arbitrary selected from highly upregulated to highly downregulated contig. Their levels of expression were quantified by q-RT-PCR, and the results were compared with those obtained using the RNAseq approach. The log2 change in expression of q-RT-PCR and RNAseq was closely correlated (<i>r</i><sup>2</sup> = 0.86; <i>p</i><0.0001), indicating the accuracy of the RNAseq approach for quantification.</p>", "links"=>[], "tags"=>["rnaseq"], "article_id"=>661285, "categories"=>["Physiology", "Inorganic Chemistry", "Biological Sciences", "Genetics"], "users"=>["Jeremie Vidal-Dupiol", "Didier Zoccola", "Eric Tambutté", "Christoph Grunau", "Céline Cosseau", "Kristina M. Smith", "Michael Freitag", "Nolwenn M. Dheilly", "Denis Allemand", "Sylvie Tambutté"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0058652.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Validation_of_the_RNAseq_approach_using_q_RT_PCR_/661285", "title"=>"Validation of the RNAseq approach using q-RT-PCR.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-28 08:52:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/999296"], "description"=>"<p>The enrichment analysis (x axis) is expressed as the percentage of sequences at both, test (black bars) and reference (grey bars) set, for GO terms having a <i>p</i>value A) Enrichment analysis performed with the set of induced genes (“test set”, state condition, black bars) compared with genes detected in the RNAseq experiment (“reference set”, grey bars). B) Enrichment analysis performed with the set of repressed genes (“test set”, black bars) compared with all genes detected in the RNAseq experiment (reference set, grey bars). Black bars represent the percentage of induced gene (A) or repressed gene (B) in the test set, for a given GO terms. The grey bars represent the percentage of gene for a given GO terms in the reference set. The statistical test was considered significant at the 1% error level.</p>", "links"=>[], "tags"=>["functions", "ph", "enrichment"], "article_id"=>661286, "categories"=>["Physiology", "Inorganic Chemistry", "Biological Sciences", "Genetics"], "users"=>["Jeremie Vidal-Dupiol", "Didier Zoccola", "Eric Tambutté", "Christoph Grunau", "Céline Cosseau", "Kristina M. Smith", "Michael Freitag", "Nolwenn M. Dheilly", "Denis Allemand", "Sylvie Tambutté"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0058652.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Biological_functions_involved_in_the_response_to_pH_7_4_treatment_GO_term_enrichment_analysis_/661286", "title"=>"Biological functions involved in the response to pH 7.4 treatment, GO term enrichment analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-28 08:52:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/999299"], "description"=>"<p>The data included q-RT-PCR results for samples exposed to pH 7.8 and 7.2, and RNAseq results for samples exposed to pH 7.4. Quantification was normalized by comparison with results for exposure to pH 8.1 (present seawater pH); the results are presented as a log2 fold change in expression.</p>", "links"=>[], "tags"=>["functions", "ph"], "article_id"=>661289, "categories"=>["Physiology", "Inorganic Chemistry", "Biological Sciences", "Genetics"], "users"=>["Jeremie Vidal-Dupiol", "Didier Zoccola", "Eric Tambutté", "Christoph Grunau", "Céline Cosseau", "Kristina M. Smith", "Michael Freitag", "Nolwenn M. Dheilly", "Denis Allemand", "Sylvie Tambutté"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0058652.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_expression_for_key_biological_functions_following_exposure_to_various_pH_levels_for_three_weeks_/661289", "title"=>"Gene expression for key biological functions following exposure to various pH levels for three weeks.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-28 08:53:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/999301"], "description"=>"<p>A) Anatomy of two polyps of a coral colony. B) Representation of the coenosarc composed of the oral and aboral tissues. C) Magnification of the calicoblastic ectoderm showing the calicoblastic cells with the up and downregulation of the key biological processes at different pH. At pH 7.8 or 7.4, Ca<sup>2+</sup> and HCO<sub>3</sub><sup>−</sup> transport to the extracellular calcifying medium (ECM) increase through an increasing number of Ca<sup>2+</sup> and HCO<sub>3</sub><sup>−</sup> transporters. The rate of CO<sub>2</sub> conversion to HCO<sub>3</sub><sup>−</sup> increases through an upregulation of carbonic anhydrase (CA). Production and secretion of organic matrix protein (OMP round green shape) also increase. This process may help to maintain a sufficient aragonite saturation state (Ω<sub>arag</sub>) despite a decrease in pH, enabling to maintain the same calcification in less favorable pH conditions. This process is energetically costly and need an increase in energy production (ATP) through an increasing metabolic activity and a general trade off mechanism. Finally, at a pH 7.2, the coral cannot cope anymore with such a low pH and there could be a physiological collapse of the colony. Values of omega aragonite (Ω) and pH in the ECM at pH 8.1 are from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058652#pone.0058652-Venn2\" target=\"_blank\">[97]</a>.</p>", "links"=>[], "tags"=>["processes", "regulated"], "article_id"=>661291, "categories"=>["Physiology", "Inorganic Chemistry", "Biological Sciences", "Genetics"], "users"=>["Jeremie Vidal-Dupiol", "Didier Zoccola", "Eric Tambutté", "Christoph Grunau", "Céline Cosseau", "Kristina M. Smith", "Michael Freitag", "Nolwenn M. Dheilly", "Denis Allemand", "Sylvie Tambutté"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0058652.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_representation_of_key_biological_processes_regulated_under_different_levels_of_low_pH_/661291", "title"=>"Schematic representation of key biological processes regulated under different levels of low pH.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-28 08:53:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/999304", "https://ndownloader.figshare.com/files/999308", "https://ndownloader.figshare.com/files/999310"], "description"=>"<div><p>Since the preindustrial era, the average surface ocean pH has declined by 0.1 pH units and is predicted to decline by an additional 0.3 units by the year 2100. Although subtle, this decreasing pH has profound effects on the seawater saturation state of carbonate minerals and is thus predicted to impact on calcifying organisms. Among these are the scleractinian corals, which are the main builders of tropical coral reefs. Several recent studies have evaluated the physiological impact of low pH, particularly in relation to coral growth and calcification. However, very few studies have focused on the impact of low pH at the global molecular level. In this context we investigated global transcriptomic modifications in a scleractinian coral (<i>Pocillopora damicornis</i>) exposed to pH 7.4 compared to pH 8.1during a 3-week period. The RNAseq approach shows that 16% of our transcriptome was affected by the treatment with 6% of upregulations and 10% of downregulations. A more detailed analysis suggests that the downregulations are less coordinated than the upregulations and allowed the identification of several biological functions of interest. In order to better understand the links between these functions and the pH, transcript abundance of 48 candidate genes was quantified by q-RT-PCR (corals exposed at pH 7.2 and 7.8 for 3 weeks). The combined results of these two approaches suggest that pH≥7.4 induces an upregulation of genes coding for proteins involved in calcium and carbonate transport, conversion of CO<sub>2</sub> into HCO<sub>3</sub><sup>−</sup> and organic matrix that may sustain calcification. Concomitantly, genes coding for heterotrophic and autotrophic related proteins are upregulated. This can reflect that low pH may increase the coral energy requirements, leading to an increase of energetic metabolism with the mobilization of energy reserves. In addition, the uncoordinated downregulations measured can reflect a general trade-off mechanism that may enable energy reallocation.</p> </div>", "links"=>[], "tags"=>["ion-transport", "upregulated", "ph", "insights", "transcriptome"], "article_id"=>661294, "categories"=>["Physiology", "Inorganic Chemistry", "Biological Sciences", "Genetics"], "users"=>["Jeremie Vidal-Dupiol", "Didier Zoccola", "Eric Tambutté", "Christoph Grunau", "Céline Cosseau", "Kristina M. Smith", "Michael Freitag", "Nolwenn M. Dheilly", "Denis Allemand", "Sylvie Tambutté"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0058652.s001", "https://dx.doi.org/10.1371/journal.pone.0058652.s002", "https://dx.doi.org/10.1371/journal.pone.0058652.s003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_Related_to_Ion_Transport_and_Energy_Production_Are_Upregulated_in_Response_to_CO_2_Driven_pH_Decrease_in_Corals_New_Insights_from_Transcriptome_Analysis_/661294", "title"=>"Genes Related to Ion-Transport and Energy Production Are Upregulated in Response to CO<sub>2</sub>-Driven pH Decrease in Corals: New Insights from Transcriptome Analysis", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-03-28 08:53:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1008419"], "description"=>"<p>Seawater chemistry (CO<sub>2</sub>, HCO<sub>3</sub><sup>−</sup>, CO<sub>3</sub><sup>−</sup>, Ω Ca<sup>2−</sup> and Ω Aragonite) obtained from continuously monitored pH.</p>", "links"=>[], "tags"=>["continuously", "monitored"], "article_id"=>669040, "categories"=>["Physiology", "Inorganic Chemistry", "Biological Sciences", "Genetics"], "users"=>["Jeremie Vidal-Dupiol", "Didier Zoccola", "Eric Tambutté", "Christoph Grunau", "Céline Cosseau", "Kristina M. Smith", "Michael Freitag", "Nolwenn M. Dheilly", "Denis Allemand", "Sylvie Tambutté"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0058652.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Seawater_chemistry_CO_2_HCO_3_8722_CO_3_8722_937_Ca_2_8722_and_937_Aragonite_obtained_from_continuously_monitored_pH_/669040", "title"=>"Seawater chemistry (CO<sub>2</sub>, HCO<sub>3</sub><sup>−</sup>, CO<sub>3</sub><sup>−</sup>, Ω Ca<sup>2−</sup> and Ω Aragonite) obtained from continuously monitored pH.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-27 02:30:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1008440"], "description"=>"<p>Seawater chemistry (Total alkalinity, pH, TC and <i>p</i>CO<sub>2</sub>) obtained from continuously monitored pH.</p>", "links"=>[], "tags"=>["tc", "continuously", "monitored"], "article_id"=>669062, "categories"=>["Physiology", "Inorganic Chemistry", "Biological Sciences", "Genetics"], "users"=>["Jeremie Vidal-Dupiol", "Didier Zoccola", "Eric Tambutté", "Christoph Grunau", "Céline Cosseau", "Kristina M. Smith", "Michael Freitag", "Nolwenn M. Dheilly", "Denis Allemand", "Sylvie Tambutté"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0058652.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Seawater_chemistry_Total_alkalinity_pH_TC_and_p_CO_2_obtained_from_continuously_monitored_pH_/669062", "title"=>"Seawater chemistry (Total alkalinity, pH, TC and <i>p</i>CO<sub>2</sub>) obtained from continuously monitored pH.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-27 02:31:02"}

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Relative Metric

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