Insights into the Regulation of DMSP Synthesis in the Diatom Thalassiosira pseudonana through APR Activity, Proteomics and Gene Expression Analyses on Cells Acclimating to Changes in Salinity, Light and Nitrogen
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{"title"=>"Insights into the regulation of DMSP synthesis in the diatom Thalassiosira pseudonana through APR activity, proteomics and gene expression analyses on cells acclimating to changes in salinity, light and nitrogen", "type"=>"journal", "authors"=>[{"first_name"=>"Nicola Louise", "last_name"=>"Kettles", "scopus_author_id"=>"56142704800"}, {"first_name"=>"Stanislav", "last_name"=>"Kopriva", "scopus_author_id"=>"7003739536"}, {"first_name"=>"Gill", "last_name"=>"Malin", "scopus_author_id"=>"7003767310"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84899624784", "sgr"=>"84899624784", "pui"=>"372981613", "isbn"=>"1932-6203", "pmid"=>"24733415", "doi"=>"10.1371/journal.pone.0094795"}, "id"=>"3ca0ec14-6e53-3449-a00f-165ef29e7273", "abstract"=>"Despite the importance of dimethylsulphoniopropionate (DMSP) in the global sulphur cycle and climate regulation, the biological pathways underpinning its synthesis in marine phytoplankton remain poorly understood. The intracellular concentration of DMSP increases with increased salinity, increased light intensity and nitrogen starvation in the diatom Thalassiosira pseudonana. We used these conditions to investigate DMSP synthesis at the cellular level via analysis of enzyme activity, gene expression and proteome comparison. The activity of the key sulphur assimilatory enzyme, adenosine 5'-phosphosulphate reductase was not coordinated with increasing intracellular DMSP concentration. Under all three treatments coordination in the expression of sulphur assimilation genes was limited to increases in sulphite reductase transcripts. Similarly, proteomic 2D gel analysis only revealed an increase in phosphoenolpyruvate carboxylase following increases in DMSP concentration. Our findings suggest that increased sulphur assimilation might not be required for increased DMSP synthesis, instead the availability of carbon and nitrogen substrates may be important in the regulation of this pathway. This contrasts with the regulation of sulphur metabolism in higher plants, which generally involves up-regulation of several sulphur assimilatory enzymes. In T. pseudonana changes relating to sulphur metabolism were specific to the individual treatments and, given that little coordination was seen in transcript and protein responses across the three growth conditions, different patterns of regulation might be responsible for the increase in DMSP concentration seen under each treatment.", "link"=>"http://www.mendeley.com/research/insights-regulation-dmsp-synthesis-diatom-thalassiosira-pseudonana-through-apr-activity-proteomics-g", "reader_count"=>47, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>1, "Researcher"=>10, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>18, "Student > Postgraduate"=>1, "Student > Master"=>3, "Other"=>1, "Student > Bachelor"=>4, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>1, "Researcher"=>10, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>18, "Student > Postgraduate"=>1, "Student > Master"=>3, "Other"=>1, "Student > Bachelor"=>4, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>6, "Engineering"=>1, "Environmental Science"=>4, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>27, "Chemistry"=>1, "Earth and Planetary Sciences"=>6}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>6}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>27}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>6}, "Environmental Science"=>{"Environmental Science"=>4}}, "reader_count_by_country"=>{"United States"=>1, "Egypt"=>1, "France"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1463669"], "description"=>"<p>The effect of increased salinity (A,B,C; solid line indicates cultures maintained at 10 psu and dashed line indicates cultures transferred to 35 psu), increased light intensity (D,E,F,; solid line indicates cultures maintained at 50 µmols m<sup>−2</sup> s<sup>−1</sup> and dashed line indicates cultures transferred to 1000 µmols m<sup>−2</sup> s<sup>−1</sup>) and nitrogen starvation (G,H,I; solid line indicates nitrogen replete cultures and dashed line indicates nitrogen starved cultures) on cell number (A,D,G), the DMSP concentration (B,E,H) and Fv/Fm (C,F,I) of <i>Thalassiosira pseudonana</i>. Results are shown as means ± standard deviation from 3 independent cultures. The vertical line indicates the point at which the salinity/light intensity of the cultures was adjusted. Asterisks show t-test, P<0.05. Arrows indicate the point at which cultures were sampled for proteomics and gene expression analysis.</p>", "links"=>[], "tags"=>["Biochemistry", "biosynthesis", "metabolism", "Plant biochemistry", "proteomics", "cell biology", "Cell processes", "Cellular stress responses", "Cell physiology", "Molecular cell biology", "ecology", "Plant ecology", "Plant-environment interactions", "genetics", "gene expression", "Marine biology", "Phycology", "organisms", "plants", "algae", "Plant science", "Plant physiology", "dmsp"], "article_id"=>998624, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Nicola Louise Kettles", "Stanislav Kopriva", "Gill Malin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0094795.g002", "stats"=>{"downloads"=>2, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Regulation_of_DMSP_concentration_/998624", "title"=>"Regulation of DMSP concentration.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-14 03:39:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/1463681", "https://ndownloader.figshare.com/files/1463682", "https://ndownloader.figshare.com/files/1463683", "https://ndownloader.figshare.com/files/1463684", "https://ndownloader.figshare.com/files/1463685"], "description"=>"<div><p>Despite the importance of dimethylsulphoniopropionate (DMSP) in the global sulphur cycle and climate regulation, the biological pathways underpinning its synthesis in marine phytoplankton remain poorly understood. The intracellular concentration of DMSP increases with increased salinity, increased light intensity and nitrogen starvation in the diatom <i>Thalassiosira pseudonana</i>. We used these conditions to investigate DMSP synthesis at the cellular level via analysis of enzyme activity, gene expression and proteome comparison. The activity of the key sulphur assimilatory enzyme, adenosine 5′-phosphosulphate reductase was not coordinated with increasing intracellular DMSP concentration. Under all three treatments coordination in the expression of sulphur assimilation genes was limited to increases in sulphite reductase transcripts. Similarly, proteomic 2D gel analysis only revealed an increase in phosphoenolpyruvate carboxylase following increases in DMSP concentration. Our findings suggest that increased sulphur assimilation might not be required for increased DMSP synthesis, instead the availability of carbon and nitrogen substrates may be important in the regulation of this pathway. This contrasts with the regulation of sulphur metabolism in higher plants, which generally involves up-regulation of several sulphur assimilatory enzymes. In <i>T. pseudonana</i> changes relating to sulphur metabolism were specific to the individual treatments and, given that little coordination was seen in transcript and protein responses across the three growth conditions, different patterns of regulation might be responsible for the increase in DMSP concentration seen under each treatment.</p></div>", "links"=>[], "tags"=>["Biochemistry", "biosynthesis", "metabolism", "Plant biochemistry", "proteomics", "cell biology", "Cell processes", "Cellular stress responses", "Cell physiology", "Molecular cell biology", "ecology", "Plant ecology", "Plant-environment interactions", "genetics", "gene expression", "Marine biology", "Phycology", "organisms", "plants", "algae", "Plant science", "Plant physiology", "insights", "dmsp", "synthesis", "diatom", "apr", "cells", "acclimating", "nitrogen"], "article_id"=>998633, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Nicola Louise Kettles", "Stanislav Kopriva", "Gill Malin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0094795.s001", "https://dx.doi.org/10.1371/journal.pone.0094795.s002", "https://dx.doi.org/10.1371/journal.pone.0094795.s003", "https://dx.doi.org/10.1371/journal.pone.0094795.s004", "https://dx.doi.org/10.1371/journal.pone.0094795.s005"], "stats"=>{"downloads"=>3, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Insights_into_the_Regulation_of_DMSP_Synthesis_in_the_Diatom_Thalassiosira_pseudonana_through_APR_Activity_Proteomics_and_Gene_Expression_Analyses_on_Cells_Acclimating_to_Changes_in_Salinity_Light_and_Nitrogen/998633", "title"=>"Insights into the Regulation of DMSP Synthesis in the Diatom <i>Thalassiosira pseudonana</i> through APR Activity, Proteomics and Gene Expression Analyses on Cells Acclimating to Changes in Salinity, Light and Nitrogen", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-04-14 03:39:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/1463678"], "description"=>"m<p>Manual Annotation.</p>b<p>Supported by BlastP (E<3×10<sup>−32</sup>).</p>c<p>Supported by conserved domains identified through Pfam.</p>z<p>Combined with another protein making fold change imprecise.</p><p>Protein names are based on UniProtKB unless otherwise stated and Protein IDs are from the Joint Genome Institute <i>T. pseudonana</i> genome version 3 (<a href=\"http://genome.jgi-psf.org/Thaps3/Thaps3.home.html\" target=\"_blank\">http://genome.jgi-psf.org/Thaps3/Thaps3.home.html</a>).</p>", "links"=>[], "tags"=>["Biochemistry", "biosynthesis", "metabolism", "Plant biochemistry", "proteomics", "cell biology", "Cell processes", "Cellular stress responses", "Cell physiology", "Molecular cell biology", "ecology", "Plant ecology", "Plant-environment interactions", "genetics", "gene expression", "Marine biology", "Phycology", "organisms", "plants", "algae", "Plant science", "Plant physiology", "sulphur", "methionine", "photosynthesis", "abundance", "nitrogen", "starvation", "salinity"], "article_id"=>998630, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Nicola Louise Kettles", "Stanislav Kopriva", "Gill Malin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0094795.t001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proteins_related_to_sulphur_assimilation_methionine_metabolism_and_photosynthesis_changing_in_abundance_under_nitrogen_starvation_N_increased_salinity_S_or_increased_light_intensity_L_/998630", "title"=>"Proteins related to sulphur assimilation, methionine metabolism, and photosynthesis changing in abundance under nitrogen starvation (N), increased salinity (S) or increased light intensity (L).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-14 03:39:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/1463672"], "description"=>"<p>Venn diagram showing the number of protein spots identified by 2-dimensional gel electrophoresis, changing in relative abundance by more than 1.5-fold (t-test, FDR, q<0.05) in <i>Thalassiosira pseudonana</i> under nitrogen starvation, increased salinity and increased light intensity.</p>", "links"=>[], "tags"=>["Biochemistry", "biosynthesis", "metabolism", "Plant biochemistry", "proteomics", "cell biology", "Cell processes", "Cellular stress responses", "Cell physiology", "Molecular cell biology", "ecology", "Plant ecology", "Plant-environment interactions", "genetics", "gene expression", "Marine biology", "Phycology", "organisms", "plants", "algae", "Plant science", "Plant physiology", "proteome"], "article_id"=>998627, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Nicola Louise Kettles", "Stanislav Kopriva", "Gill Malin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0094795.g005", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Global_proteome_changes_/998627", "title"=>"Global proteome changes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-14 03:39:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/1463671"], "description"=>"<p>The relative fold change in the transcript levels of genes involved in sulphur assimilation in <i>Thalassiosira pseudonana</i> exposed to nitrogen starvation, increased salinity and increased light intensity quantified by qRT-PCR. Gene abbreviations are as follows: Sulphate transporter (Trans), ATP sulphurylase (ATPS), APS reductase (APR), OAS thiollyase (OASTL), Serine acetyltransferase (SAT), Sulphite reductase (SiR). Numbers denote different isoforms of the enzymes (for gene IDs see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094795#pone.0094795.s004\" target=\"_blank\">Table S1</a>). Results are shown as means ± standard deviation from 3 independent cultures. Asterisks mark values significantly different between treatments and control at P<0.05 (T-test).</p>", "links"=>[], "tags"=>["Biochemistry", "biosynthesis", "metabolism", "Plant biochemistry", "proteomics", "cell biology", "Cell processes", "Cellular stress responses", "Cell physiology", "Molecular cell biology", "ecology", "Plant ecology", "Plant-environment interactions", "genetics", "gene expression", "Marine biology", "Phycology", "organisms", "plants", "algae", "Plant science", "Plant physiology"], "article_id"=>998626, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Nicola Louise Kettles", "Stanislav Kopriva", "Gill Malin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0094795.g004", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Regulation_of_gene_expression_/998626", "title"=>"Regulation of gene expression.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-14 03:39:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/1463677"], "description"=>"<p>Enzymes that increased in abundance with increased salinity in <i>T. pseudonana</i> are marked with bold arrows.</p>", "links"=>[], "tags"=>["Biochemistry", "biosynthesis", "metabolism", "Plant biochemistry", "proteomics", "cell biology", "Cell processes", "Cellular stress responses", "Cell physiology", "Molecular cell biology", "ecology", "Plant ecology", "Plant-environment interactions", "genetics", "gene expression", "Marine biology", "Phycology", "organisms", "plants", "algae", "Plant science", "Plant physiology", "methyl"], "article_id"=>998629, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Nicola Louise Kettles", "Stanislav Kopriva", "Gill Malin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0094795.g006", "stats"=>{"downloads"=>2, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_scheme_of_the_active_methyl_cycle_/998629", "title"=>"A scheme of the active methyl cycle.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-14 03:39:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/1463670"], "description"=>"<p>The effect of increased salinity (A; solid line, cultures maintained at 10 psu; dashed line, cultures transferred to 35 psu), increased light intensity (B; solid line, cultures maintained at 50 µmol m<sup>−2</sup> s<sup>−1</sup>; dashed line, cultures transferred to 1000 µmol m<sup>−2</sup> s<sup>−1</sup>) and nitrogen starvation (C; solid line, nitrogen replete cultures; dashed line, nitrogen starved cultures) on APR activity in <i>Thalassiosira pseudonana</i>. Results are shown as means ± standard deviation from 3 independent cultures. The vertical line indicates the point at which the salinity/light intensity of the cultures was adjusted. Asterisks mark significantly different values (P<0.05, T-test).</p>", "links"=>[], "tags"=>["Biochemistry", "biosynthesis", "metabolism", "Plant biochemistry", "proteomics", "cell biology", "Cell processes", "Cellular stress responses", "Cell physiology", "Molecular cell biology", "ecology", "Plant ecology", "Plant-environment interactions", "genetics", "gene expression", "Marine biology", "Phycology", "organisms", "plants", "algae", "Plant science", "Plant physiology", "apr"], "article_id"=>998625, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Nicola Louise Kettles", "Stanislav Kopriva", "Gill Malin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0094795.g003", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Regulation_of_APR_activity_/998625", "title"=>"Regulation of APR activity.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-14 03:39:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/1463668"], "description"=>"<p>Enzymes between the methionine and DMSP have not yet been identified. The putative reactions proposed by <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094795#pone.0094795-Greene1\" target=\"_blank\">[13]</a> are shown in capitals.</p>", "links"=>[], "tags"=>["Biochemistry", "biosynthesis", "metabolism", "Plant biochemistry", "proteomics", "cell biology", "Cell processes", "Cellular stress responses", "Cell physiology", "Molecular cell biology", "ecology", "Plant ecology", "Plant-environment interactions", "genetics", "gene expression", "Marine biology", "Phycology", "organisms", "plants", "algae", "Plant science", "Plant physiology", "pathway", "sulphate", "assimilation", "dmsp"], "article_id"=>998623, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Nicola Louise Kettles", "Stanislav Kopriva", "Gill Malin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0094795.g001", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_proposed_pathway_of_sulphate_assimilation_and_DMSP_biosynthesis_in_algae_/998623", "title"=>"A proposed pathway of sulphate assimilation and DMSP biosynthesis in algae.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-14 03:39:54"}

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