Comparative Transcriptomics between Synechococcus PCC 7942 and Synechocystis PCC 6803 Provide Insights into Mechanisms of Stress Acclimation
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{"title"=>"Comparative transcriptomics between Synechococcus PCC 7942 and Synechocystis PCC 6803 provide insights into mechanisms of stress acclimation", "type"=>"journal", "authors"=>[{"first_name"=>"Konstantinos", "last_name"=>"Billis", "scopus_author_id"=>"55990338800"}, {"first_name"=>"Maria", "last_name"=>"Billini", "scopus_author_id"=>"24066529800"}, {"first_name"=>"H. James", "last_name"=>"Tripp", "scopus_author_id"=>"9248942700"}, {"first_name"=>"Nikos C.", "last_name"=>"Kyrpides", "scopus_author_id"=>"34570925900"}, {"first_name"=>"Konstantinos", "last_name"=>"Mavromatis", "scopus_author_id"=>"16039719300"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"isbn"=>"1408353490", "scopus"=>"2-s2.0-84908432965", "pui"=>"600279936", "doi"=>"10.1371/journal.pone.0109738", "issn"=>"19326203", "pmid"=>"25340743", "sgr"=>"84908432965"}, "id"=>"5a195d38-9a8a-3ac1-acc5-5c8b777ee0d1", "abstract"=>"Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803 are model cyanobacteria from which the metabolism and adaptive responses of other cyanobacteria are inferred. Using stranded and 5' enriched libraries, we measured the gene expression response of cells transferred from reference conditions to stress conditions of decreased inorganic carbon, increased salinity, increased pH, and decreased illumination at 1-h and 24-h after transfer. We found that the specific responses of the two strains were by no means identical. Transcriptome profiles allowed us to improve the structural annotation of the genome i.e. identify possible missed genes (including anti-sense), alter gene coordinates and determine transcriptional units (operons). Finally, we predicted associations between proteins of unknown function and biochemical pathways by revealing proteins of known functions that are co-regulated with the unknowns. Future studies of these model organisms will benefit from the cataloging of their responses to environmentally relevant stresses, and improvements in their genome annotations found here.", "link"=>"http://www.mendeley.com/research/comparative-transcriptomics-between-synechococcus-pcc-7942-synechocystis-pcc-6803-provide-insights-m-2", "reader_count"=>56, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>16, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>1, "Student > Master"=>8, "Other"=>2, "Student > Bachelor"=>9}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>16, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>1, "Student > Master"=>8, "Other"=>2, "Student > Bachelor"=>9}, "reader_count_by_subject_area"=>{"Engineering"=>4, "Unspecified"=>2, "Environmental Science"=>4, "Biochemistry, Genetics and Molecular Biology"=>11, "Agricultural and Biological Sciences"=>32, "Medicine and Dentistry"=>2, "Chemistry"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>4}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>32}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>11}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>4}}, "reader_count_by_country"=>{"United States"=>2, "South Africa"=>1}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1762672"], "description"=>"<p>The colored lines represent the expression coverage of this region in each condition. Green arrows represent the existing annotation. 5′ peaks are indicated with a vertical red line, blue arrows that follow 5′ peaks denote the potential Transcriptional unit and follows the expression of this region. a. Example of a CDS of <i>Synechococcus</i> (Synpcc7942_0114) with one clear 5′ enriched indication, RNA-seq coverage and proper annotation. b. Example of a TU inside non-coding region with one clear 5′ peak. c. Example of an annotated CDS (Synpcc7942_0174) without 5′ peak and ambiguous RNA-seq coverage. d. Example of a CDS (Synpcc7942_0801) with evidence of structural misannotation since the 5′ peak is located 60 bps after the annotated start site. e. Two annotated genes with contiguous expression and a peak at the 5′ of the first gene suggesting that both CDSs are expressed together as one transcript forming an operon.</p>", "links"=>[], "tags"=>["function", "gene coordinates", "genome i.e", "protein", "genome annotations", "reference conditions", "Synechocystis PCC 6803", "adaptive responses", "Stress Acclimation Synechococcus sp", "model cyanobacteria", "Model organisms", "future studies", "PCC 6803", "Synechococcus PCC 7942", "Comparative Transcriptomics", "transcriptional units", "PCC 7942", "gene expression response", "transcriptome profiles", "Synechocystis sp", "stress conditions"], "article_id"=>1220158, "categories"=>["Biological Sciences"], "users"=>["Konstantinos Billis", "Maria Billini", "H. James Tripp", "Nikos C. Kyrpides", "Konstantinos Mavromatis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0109738.g001", "stats"=>{"downloads"=>2, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Regions_of_the_genome_combined_with_annotation_RNA_seq_expression_and_5_8242_peaks_information_/1220158", "title"=>"Regions of the genome combined with annotation, RNA-seq expression and 5′ peaks information.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-23 17:05:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1762701"], "description"=>"<p>Summary of structural annotation for <i>Synechococcus</i> sp. PCC7942.</p>", "links"=>[], "tags"=>["function", "gene coordinates", "genome i.e", "protein", "genome annotations", "reference conditions", "Synechocystis PCC 6803", "adaptive responses", "Stress Acclimation Synechococcus sp", "model cyanobacteria", "Model organisms", "future studies", "PCC 6803", "Synechococcus PCC 7942", "Comparative Transcriptomics", "transcriptional units", "PCC 7942", "gene expression response", "transcriptome profiles", "Synechocystis sp", "stress conditions"], "article_id"=>1220166, "categories"=>["Biological Sciences"], "users"=>["Konstantinos Billis", "Maria Billini", "H. James Tripp", "Nikos C. Kyrpides", "Konstantinos Mavromatis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0109738.t002", "stats"=>{"downloads"=>3, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_structural_annotation_for_Synechococcus_sp_PCC7942_/1220166", "title"=>"Summary of structural annotation for <i>Synechococcus</i> sp. PCC7942.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-10-23 17:05:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1762760", "https://ndownloader.figshare.com/files/1762761", "https://ndownloader.figshare.com/files/1762762", "https://ndownloader.figshare.com/files/1762764", "https://ndownloader.figshare.com/files/1762766", "https://ndownloader.figshare.com/files/1762767"], "description"=>"<div><p><i>Synechococcus</i> sp. PCC 7942 and <i>Synechocystis</i> sp. PCC 6803 are model cyanobacteria from which the metabolism and adaptive responses of other cyanobacteria are inferred. Using stranded and 5′ enriched libraries, we measured the gene expression response of cells transferred from reference conditions to stress conditions of decreased inorganic carbon, increased salinity, increased pH, and decreased illumination at 1-h and 24-h after transfer. We found that the specific responses of the two strains were by no means identical. Transcriptome profiles allowed us to improve the structural annotation of the genome i.e. identify possible missed genes (including anti-sense), alter gene coordinates and determine transcriptional units (operons). Finally, we predicted associations between proteins of unknown function and biochemical pathways by revealing proteins of known functions that are co-regulated with the unknowns. Future studies of these model organisms will benefit from the cataloging of their responses to environmentally relevant stresses, and improvements in their genome annotations found here.</p></div>", "links"=>[], "tags"=>["function", "gene coordinates", "genome i.e", "protein", "genome annotations", "reference conditions", "Synechocystis PCC 6803", "adaptive responses", "Stress Acclimation Synechococcus sp", "model cyanobacteria", "Model organisms", "future studies", "PCC 6803", "Synechococcus PCC 7942", "Comparative Transcriptomics", "transcriptional units", "PCC 7942", "gene expression response", "transcriptome profiles", "Synechocystis sp", "stress conditions"], "article_id"=>1220176, "categories"=>["Biological Sciences"], "users"=>["Konstantinos Billis", "Maria Billini", "H. James Tripp", "Nikos C. Kyrpides", "Konstantinos Mavromatis"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0109738.s001", "https://dx.doi.org/10.1371/journal.pone.0109738.s002", "https://dx.doi.org/10.1371/journal.pone.0109738.s003", "https://dx.doi.org/10.1371/journal.pone.0109738.s004", "https://dx.doi.org/10.1371/journal.pone.0109738.s005", "https://dx.doi.org/10.1371/journal.pone.0109738.s006"], "stats"=>{"downloads"=>14, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Comparative_Transcriptomics_between_Synechococcus_PCC_7942_and_Synechocystis_PCC_6803_Provide_Insights_into_Mechanisms_of_Stress_Acclimation/1220176", "title"=>"Comparative Transcriptomics between <i>Synechococcus</i> PCC 7942 and <i>Synechocystis</i> PCC 6803 Provide Insights into Mechanisms of Stress Acclimation", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-10-23 17:05:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1762699"], "description"=>"<p>Growth Conditions applied on the two organisms and their run ids from NCBI SRA.</p>", "links"=>[], "tags"=>["function", "gene coordinates", "genome i.e", "protein", "genome annotations", "reference conditions", "Synechocystis PCC 6803", "adaptive responses", "Stress Acclimation Synechococcus sp", "model cyanobacteria", "Model organisms", "future studies", "PCC 6803", "Synechococcus PCC 7942", "Comparative Transcriptomics", "transcriptional units", "PCC 7942", "gene expression response", "transcriptome profiles", "Synechocystis sp", "stress conditions"], "article_id"=>1220165, "categories"=>["Biological Sciences"], "users"=>["Konstantinos Billis", "Maria Billini", "H. James Tripp", "Nikos C. Kyrpides", "Konstantinos Mavromatis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0109738.t001", "stats"=>{"downloads"=>4, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Growth_Conditions_applied_on_the_two_organisms_and_their_run_ids_from_NCBI_SRA_/1220165", "title"=>"Growth Conditions applied on the two organisms and their run ids from NCBI SRA.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-10-23 17:05:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1762698"], "description"=>"<p>The thickness of the respective arrows represents the suggested intensity of the energy flow. The conditions that apply to the panel are shown in the upper right of the panel. Panel A. Reference conditions, in the presence of light the photosynthetic electron transport chain has a higher capacity of electron flow than the respiratory chain. Panel B. Conditions where photosynthetic genes are upregulated and respiratory ones are downregulated (<i>Synechoccus</i>: alkaline pH (1-h & 24-h), low light (1-h & 24-h), low temperature (24-h), and <i>Synechocystis</i>: low temperature (24-h)). Panel C. Conditions where respiratory genes are upregulated (<i>Synechococcu</i>s: low temperature (24-h) and carbon limitation (1-h)). Panel D. Conditions where photosynthetic and respiratory genes are both downregulated (<i>Synechocystis</i>: low light (1-h & 24-h), elevated salinity (1-h)). Panel E. Conditions where photosynthetic genes are downregulated (<i>Synechocystis</i>: low temperature (1-h), and carbon limitation (24-h)). For simplicity, the two electron transport chains are represented in two different membrane sections, even though respiration is met in the cytoplasmic and both respiration and photosynthesis are intertwined in the thylakoid membrane. The intersection of the two pathways in the thylakoids is more apparent in <i>Synechocystis</i> than <i>Synechococcus</i>, where those two processes are more separated between the cytoplasmic and the thylakoid membrane. This representation only serves the portrayal of the transcriptional changes and their putative affect on energy flow and not the actual distribution of the two chains between the thylakoid and the cytoplasmic membrane. Abbreviations: Temperature (Tm).</p>", "links"=>[], "tags"=>["function", "gene coordinates", "genome i.e", "protein", "genome annotations", "reference conditions", "Synechocystis PCC 6803", "adaptive responses", "Stress Acclimation Synechococcus sp", "model cyanobacteria", "Model organisms", "future studies", "PCC 6803", "Synechococcus PCC 7942", "Comparative Transcriptomics", "transcriptional units", "PCC 7942", "gene expression response", "transcriptome profiles", "Synechocystis sp", "stress conditions"], "article_id"=>1220164, "categories"=>["Biological Sciences"], "users"=>["Konstantinos Billis", "Maria Billini", "H. James Tripp", "Nikos C. Kyrpides", "Konstantinos Mavromatis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0109738.g003", "stats"=>{"downloads"=>1, "page_views"=>36, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Model_How_the_relative_expression_of_components_of_the_electron_transport_chains_of_photosynthesis_and_respiration_may_affect_the_energy_flow_at_specified_time_points_of_stress_acclimation_/1220164", "title"=>"Model: How the relative expression of components of the electron transport chains of photosynthesis and respiration may affect the energy flow at specified time points of stress acclimation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-23 17:05:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1762676"], "description"=>"<p>Hierarchical clustering of stress conditions for <i>Synechococcus</i> sp. PCC 7942 and <i>Synechocystis</i> sp. PCC 6803.</p>", "links"=>[], "tags"=>["function", "gene coordinates", "genome i.e", "protein", "genome annotations", "reference conditions", "Synechocystis PCC 6803", "adaptive responses", "Stress Acclimation Synechococcus sp", "model cyanobacteria", "Model organisms", "future studies", "PCC 6803", "Synechococcus PCC 7942", "Comparative Transcriptomics", "transcriptional units", "PCC 7942", "gene expression response", "transcriptome profiles", "Synechocystis sp", "stress conditions"], "article_id"=>1220159, "categories"=>["Biological Sciences"], "users"=>["Konstantinos Billis", "Maria Billini", "H. James Tripp", "Nikos C. Kyrpides", "Konstantinos Mavromatis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0109738.g002", "stats"=>{"downloads"=>2, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hierarchical_clustering_of_stress_conditions_for_Synechococcus_sp_PCC_7942_and_Synechocystis_sp_PCC_6803_/1220159", "title"=>"Hierarchical clustering of stress conditions for <i>Synechococcus</i> sp. PCC 7942 and <i>Synechocystis</i> sp. PCC 6803.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-23 17:05:33"}

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Relative Metric

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