The Influence of pCO2 and Temperature on Gene Expression of Carbon and Nitrogen Pathways in Trichodesmium IMS101
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{"title"=>"The influence of pCO2 and temperature on gene expression of carbon and nitrogen pathways in Trichodesmium IMS101", "type"=>"journal", "authors"=>[{"first_name"=>"Orly", "last_name"=>"Levitan", "scopus_author_id"=>"15843399700"}, {"first_name"=>"Stefanie", "last_name"=>"Sudhaus", "scopus_author_id"=>"36631118200"}, {"first_name"=>"Julie", "last_name"=>"LaRoche", "scopus_author_id"=>"7007063232"}, {"first_name"=>"Ilana", "last_name"=>"Berman-Frank", "scopus_author_id"=>"6602853012"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pui"=>"360158267", "doi"=>"10.1371/journal.pone.0015104", "sgr"=>"78650125612", "scopus"=>"2-s2.0-78650125612", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"21151907"}, "id"=>"5aaf53bb-04d8-367a-8fb8-7b8c6b0ca679", "abstract"=>"Growth, protein amount, and activity levels of metabolic pathways in Trichodesmium are influenced by environmental changes such as elevated pCO(2) and temperature. This study examines changes in the expression of essential metabolic genes in Trichodesmium grown under a matrix of pCO(2) (400 and 900 µatm) and temperature (25 and 31°C). Using RT-qPCR, we studied 21 genes related to four metabolic functional groups: CO(2) concentrating mechanism (bicA1, bicA2, ccmM, ccmK2, ccmK3, ndhF4, ndhD4, ndhL, chpX), energy metabolism (atpB, sod, prx, glcD), nitrogen metabolism (glnA, hetR, nifH), and inorganic carbon fixation and photosynthesis (rbcL, rca, psaB, psaC, psbA). nifH and most photosynthetic genes exhibited relatively high abundance and their expression was influenced by both environmental parameters. A two to three orders of magnitude increase was observed for glnA and hetR only when both pCO(2) and temperature were elevated. CO(2) concentrating mechanism genes were not affected by pCO(2) and temperature and their expression levels were markedly lower than that of the nitrogen metabolism and photosynthetic genes. Many of the CO(2) concentrating mechanism genes were co-expressed throughout the day. Our results demonstrate that in Trichodesmium, CO(2) concentrating mechanism genes are constitutively expressed. Co-expression of genes from different functional groups were frequently observed during the first half of the photoperiod when oxygenic photosynthesis and N(2) fixation take place, pointing at the tight and complex regulation of gene expression in Trichodesmium. Here we provide new data linking environmental changes of pCO(2) and temperature to gene expression in Trichodesmium. Although gene expression indicates an active metabolic pathway, there is often an uncoupling between transcription and enzyme activity, such that transcript level cannot usually be directly extrapolated to metabolic activity.", "link"=>"http://www.mendeley.com/research/influence-pco2-temperature-gene-expression-carbon-nitrogen-pathways-trichodesmium-ims101", "reader_count"=>44, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>10, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>1, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>10, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>1, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>4, "Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>23, "Chemistry"=>1, "Earth and Planetary Sciences"=>8}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>8}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>23}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>4}}, "reader_count_by_country"=>{"United States"=>2, "Australia"=>1, "Spain"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/814084"], "description"=>"<p>Significant influence of pCO<sub>2</sub> (400 and 900 µatm) temperature (25 and 31°C) and their interaction on the GOI expression was determined according to a 3-Way ANOVA (p<0.05, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015104#pone-0015104-t002\" target=\"_blank\">Table 2</a>). All genes were also influenced by time. The upper panel presents genes related to nitrogen metabolism (<i>nifH, glnA</i> and <i>hetR</i>), the middle panel represents genes related with Ci fixation (<i>rbcL</i>) and photosynthesis (<i>psaB, psba</i>) and the lower panel represents genes related to CCM (<i>ccmK2</i>) and energy generation (<i>glcD</i> and <i>prx</i>). Circles and triangles represent <i>Trichodesmium</i> acclimated to 25°C and 31°C, respectively. Black and open symbols represent <i>Trichodesmium</i> acclimated to 400 and 900 µatm pCO<sub>2</sub>, respectively. Relative abundance estimated according to the 2<sup>−ΔΔCt</sup> method, with 16S rRNA as the endogenous reference gene, and average ΔCt values of the <i>nifH</i> from the 400 µatm/25°C acclimation (control) as a calibrator. White and black bars on top of the graphs represent light and dark hours, respectively. n = 3 for each gene at each time point per treatment. Errors are ±1 standard deviation, following Bustin et al. (2009). Note: 1. the different y-axes scales; 2. the results and standard deviations are presented using logarithmic scale y axes.</p>", "links"=>[], "tags"=>["mrna", "transcript", "enrichment", "influenced"], "article_id"=>484448, "categories"=>["Inorganic Chemistry", "Ecology", "Genetics", "Microbiology"], "users"=>["Orly Levitan", "Stefanie Sudhaus", "Julie LaRoche", "Ilana Berman-Frank"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015104.g002", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Daily_mRNA_transcript_enrichment_of_the_nine_GOIs_significantly_influenced_by_the_changing_environmental_factors_/484448", "title"=>"Daily mRNA transcript enrichment of the nine GOIs, significantly influenced by the changing environmental factors.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-12-06 01:14:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/406104", "https://ndownloader.figshare.com/files/406125"], "description"=>"<div><p>Growth, protein amount, and activity levels of metabolic pathways in <em>Trichodesmium</em> are influenced by environmental changes such as elevated pCO<sub>2</sub> and temperature. This study examines changes in the expression of essential metabolic genes in <em>Trichodesmium</em> grown under a matrix of pCO<sub>2</sub> (400 and 900 µatm) and temperature (25 and 31°C). Using RT-qPCR, we studied 21 genes related to four metabolic functional groups: CO<sub>2</sub> concentrating mechanism (<em>bicA1, bicA2, ccmM, ccmK2, ccmK3, ndhF4, ndhD4, ndhL, chpX</em>), energy metabolism (<em>atpB</em>, <em>sod</em>, <em>prx</em>, <em>glcD</em>), nitrogen metabolism (<em>glnA</em>, <em>hetR, nifH</em>), and inorganic carbon fixation and photosynthesis (<em>rbcL, rca, psaB, psaC, psbA</em>). <em>nifH</em> and most photosynthetic genes exhibited relatively high abundance and their expression was influenced by both environmental parameters. A two to three orders of magnitude increase was observed for <em>glnA</em> and <em>hetR</em> only when both pCO<sub>2</sub> and temperature were elevated. CO<sub>2</sub> concentrating mechanism genes were not affected by pCO<sub>2</sub> and temperature and their expression levels were markedly lower than that of the nitrogen metabolism and photosynthetic genes. Many of the CO<sub>2</sub> concentrating mechanism genes were co-expressed throughout the day. Our results demonstrate that in <em>Trichodesmium</em>, CO<sub>2</sub> concentrating mechanism genes are constitutively expressed. Co-expression of genes from different functional groups were frequently observed during the first half of the photoperiod when oxygenic photosynthesis and N<sub>2</sub> fixation take place, pointing at the tight and complex regulation of gene expression in <em>Trichodesmium</em>. Here we provide new data linking environmental changes of pCO<sub>2</sub> and temperature to gene expression in <em>Trichodesmium</em>. Although gene expression indicates an active metabolic pathway, there is often an uncoupling between transcription and enzyme activity, such that transcript level cannot usually be directly extrapolated to metabolic activity.</p> </div>", "links"=>[], "tags"=>["carbon", "nitrogen", "pathways", "ims101"], "article_id"=>140234, "categories"=>["Inorganic Chemistry", "Ecology", "Genetics", "Microbiology"], "users"=>["Orly Levitan", "Stefanie Sudhaus", "Julie LaRoche", "Ilana Berman-Frank"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0015104.s001", "https://dx.doi.org/10.1371/journal.pone.0015104.s002"], "stats"=>{"downloads"=>7, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Influence_of_pCO_2_and_Temperature_on_Gene_Expression_of_Carbon_and_Nitrogen_Pathways_in_Trichodesmium_IMS101/140234", "title"=>"The Influence of pCO<sub>2</sub> and Temperature on Gene Expression of Carbon and Nitrogen Pathways in <em>Trichodesmium</em> IMS101", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-12-06 00:03:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/814388"], "description"=>"a<p>- n = 3–4</p>b<p>- n = 12–13</p><p>Acclimation pCO<sub>2</sub> levels were 400 and 900 µatm and temperatures were 25 and 31°C. The extended data set and discussion of the physiological responses were previously reported (Levitan et al., 2010a) and are summarized here to emphasize physiological changes associated with the gene abundance presented from the same cultures.</p>", "links"=>[], "tags"=>["characteristics", "ims101", "cultures", "acclimated", "matrix"], "article_id"=>484750, "categories"=>["Inorganic Chemistry", "Ecology", "Genetics", "Microbiology"], "users"=>["Orly Levitan", "Stefanie Sudhaus", "Julie LaRoche", "Ilana Berman-Frank"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015104.t003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Physiological_characteristics_of_Trichodesmium_IMS101_cultures_acclimated_to_a_matrix_of_pCO_2_and_temperature_/484750", "title"=>"Physiological characteristics of <i>Trichodesmium</i> IMS101 cultures acclimated to a matrix of pCO<sub>2</sub> and temperature.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-12-06 01:19:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/814322"], "description"=>"<p>Presented values are the Pearson correlation coefficient and the significance is in the parentheses. Sampling points were 1, 5, 9, 13 hours after the onset of light.</p>", "links"=>[], "tags"=>["goi", "pairs", "co-expressed"], "article_id"=>484689, "categories"=>["Inorganic Chemistry", "Ecology", "Genetics", "Microbiology"], "users"=>["Orly Levitan", "Stefanie Sudhaus", "Julie LaRoche", "Ilana Berman-Frank"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015104.t004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlations_between_four_GOI_pairs_that_were_co_expressed_at_all_measured_time_points_/484689", "title"=>"Correlations between four GOI pairs that were co-expressed at all measured time points.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-12-06 01:18:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/814420"], "description"=>"<p>The environmental conditions are pCO<sub>2</sub>, temperature, and time. Gene expression was determined using 2<sup>−ΔΔct</sup> method. Statistical analysis was made using 3-Way ANOVA (p<0.05). n = 24–25 for both temperatures, n = 23–25 for both pCO<sub>2</sub>, and n = 11–13 for each measuring time point.</p>", "links"=>[], "tags"=>["conditions", "enrichment"], "article_id"=>484786, "categories"=>["Inorganic Chemistry", "Ecology", "Genetics", "Microbiology"], "users"=>["Orly Levitan", "Stefanie Sudhaus", "Julie LaRoche", "Ilana Berman-Frank"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015104.t002", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_influence_of_changing_environmental_conditions_on_the_enrichment_of_all_our_GOIs_/484786", "title"=>"The influence of changing environmental conditions on the enrichment of all our GOIs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-12-06 01:19:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/814354"], "description"=>"<p>Description and sequences of forward and reverse primers for our target genes.</p>", "links"=>[], "tags"=>["sequences", "primers"], "article_id"=>484723, "categories"=>["Inorganic Chemistry", "Ecology", "Genetics", "Microbiology"], "users"=>["Orly Levitan", "Stefanie Sudhaus", "Julie LaRoche", "Ilana Berman-Frank"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015104.t001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Description_and_sequences_of_forward_and_reverse_primers_for_our_target_genes_/484723", "title"=>"Description and sequences of forward and reverse primers for our target genes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-12-06 01:18:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/814231"], "description"=>"<p>Sampling times were 1, 5, 9, 13 hours after the onset of light, presented from top-left to bottom-right. Colored cells represent a Pearson correlation coefficient r>0.75. Correlations are presented regardless to the different acclimations. Genes are divided to 4 groups: CCM (pink), energy metabolism (yellow), nitrogen metabolism (blue), and photosynthesis and Ci fixation (green). When correlations were between genes from the same group, the cells were colored in the groups' color. When correlations were between genes from two different groups, the cells were colored using a gradient from one groups' color to the other. All the correlation coefficients and significances according to the Pearson correlation are supplied in the supplemental data (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015104#pone.0015104.s002\" target=\"_blank\">Table S1</a> i-iv). Relative abundance estimated according to the 2<sup>−ΔΔCt</sup> method, with 16S rRNA as the endogenous reference gene, and average ΔCt values of the <i>nifH</i> from the 400 µatm/25°C acclimation (control) as a calibrator. n = 11–13 for each gene at a given sampling time.</p>", "links"=>[], "tags"=>["abundance", "21", "gois"], "article_id"=>484597, "categories"=>["Inorganic Chemistry", "Ecology", "Genetics", "Microbiology"], "users"=>["Orly Levitan", "Stefanie Sudhaus", "Julie LaRoche", "Ilana Berman-Frank"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015104.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlations_between_the_abundance_of_the_21_GOIs_during_the_daily_cycle_/484597", "title"=>"Correlations between the abundance of the 21 GOIs during the daily cycle.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-12-06 01:16:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/813980"], "description"=>"<p>Culture were grown under an acclimation matrix of pCO<sub>2</sub> (400 and 900 µatm) and temperature (25 and 31°C). The curves are an average of the gene expression levels under all four acclimations. The genes are arranged on the same y-axis scale from left to right, according to their functions: CCM (circles), Energy generation (rectangles), nitrogen metabolism (starts) and photosynthetic and Ci fixation (triangles). Relative abundance estimated according to the 2<sup>−ΔΔCt</sup> method, with 16S rRNA as the endogenous reference gene, and average ΔCt values of the <i>nifH</i> from the 400 µatm/25°C treatments (control) as a calibrator. White and black bars on top of the graphs represent light and dark hours, respectively. n = 11–13 for each time point. Errors are ±1 standard deviation, following Bustin et al. (2009). Note that the results and standard deviations are presented using logarithmic scale y axes.</p>", "links"=>[], "tags"=>["transcript", "enrichment", "21", "gois"], "article_id"=>484345, "categories"=>["Inorganic Chemistry", "Ecology", "Genetics", "Microbiology"], "users"=>["Orly Levitan", "Stefanie Sudhaus", "Julie LaRoche", "Ilana Berman-Frank"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015104.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_mRNA_transcript_enrichment_of_21_GOIS_from_Trichodesmium_IMS101_/484345", "title"=>"mRNA transcript enrichment of 21 GOIS from <i>Trichodesmium</i> IMS101.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-12-06 01:12:25"}

PMC Usage Stats | Further Information

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