A Forward-Design Approach to Increase the Production of Poly-3-Hydroxybutyrate in Genetically Engineered Escherichia coli
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{"title"=>"A forward-design approach to increase the production of poly-3-hydroxybutyrate in genetically engineered escherichia coli", "type"=>"journal", "authors"=>[{"first_name"=>"Richard", "last_name"=>"Kelwick", "scopus_author_id"=>"37097322000"}, {"first_name"=>"Margarita", "last_name"=>"Kopniczky", "scopus_author_id"=>"56530759800"}, {"first_name"=>"Iain", "last_name"=>"Bower", "scopus_author_id"=>"56530749300"}, {"first_name"=>"Wenqiang", "last_name"=>"Chi", "scopus_author_id"=>"56530289500"}, {"first_name"=>"Matthew Ho Wai", "last_name"=>"Chin", "scopus_author_id"=>"56530203700"}, {"first_name"=>"Sisi", "last_name"=>"Fan", "scopus_author_id"=>"56529997500"}, {"first_name"=>"Jemma", "last_name"=>"Pilcher", "scopus_author_id"=>"56530370800"}, {"first_name"=>"James", "last_name"=>"Strutt", "scopus_author_id"=>"56509311800"}, {"first_name"=>"Alexander J.", "last_name"=>"Webb", "scopus_author_id"=>"15120178000"}, {"first_name"=>"Kirsten", "last_name"=>"Jensen", "scopus_author_id"=>"7401675453"}, {"first_name"=>"Guy Bart", "last_name"=>"Stan", "scopus_author_id"=>"16053936800"}, {"first_name"=>"Richard", "last_name"=>"Kitney", "scopus_author_id"=>"7005163862"}, {"first_name"=>"Paul", "last_name"=>"Freemont", "scopus_author_id"=>"35502381100"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84923667049", "pui"=>"602525012", "doi"=>"10.1371/journal.pone.0117202", "isbn"=>"10.1371/journal.pone.0117202", "sgr"=>"84923667049", "pmid"=>"25699671"}, "id"=>"b48012f5-7974-3338-a296-6cd8456059a7", "abstract"=>"Biopolymers, such as poly-3-hydroxybutyrate (P(3HB)) are produced as a carbon store in an array of organisms and exhibit characteristics which are similar to oil-derived plastics, yet have the added advantages of biodegradability and biocompatibility. Despite these advantages, P(3HB) production is currently more expensive than the production of oil-derived plastics, and therefore, more efficient P(3HB) production processes would be desirable. In this study, we describe the model-guided design and experimental validation of several engineered P(3HB) producing operons. In particular, we describe the characterization of a hybrid phaCAB operon that consists of a dual promoter (native and J23104) and RBS (native and B0034) design. P(3HB) production at 24 h was around six-fold higher in hybrid phaCAB engineered Escherichia coli in comparison to E. coli engineered with the native phaCAB operon from Ralstonia eutropha H16. Additionally, we describe the utilization of non-recyclable waste as a low-cost carbon source for the production of P(3HB).", "link"=>"http://www.mendeley.com/research/forwarddesign-approach-increase-production-poly3hydroxybutyrate-genetically-engineered-escherichia-c-1", "reader_count"=>30, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Researcher"=>5, "Student > Ph. D. Student"=>10, "Student > Master"=>5, "Student > Bachelor"=>8, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Researcher"=>5, "Student > Ph. D. Student"=>10, "Student > Master"=>5, "Student > Bachelor"=>8, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>5, "Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>16, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>5}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>16}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"United States"=>1, "China"=>1, "Egypt"=>1, "Mexico"=>1, "United Kingdom"=>1, "Spain"=>1, "India"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1914613"], "description"=>"<p><i>E</i>. <i>coli</i> MG1655 transformed with either empty vector [EV], native [N], constitutive [C] or hybrid [H] <i>phaCAB</i> constructs were cultured in 5 ml of waste-media for 36 h at 37°C. P(3HB) content was assessed via flow cytometry analysis of Nile Red staining. (<b>A</b>) Representative forward scatter (FSC) and side scatter (SSC) contour plots. (<b>B</b>) Representative histogram (FL-5). (<b>C</b>) Normalized fluorescence of Nile Red stained <i>phaCAB</i>-engineered <i>E</i>. <i>coli</i>, from three independent experiments. Error bars, +/- the standard deviation. Student t-test, *P<0.05 and ***P <0.001.</p>", "links"=>[], "tags"=>["Ralstonia eutropha H 16.", "phaCAB operon", "rbs", "Genetically Engineered Escherichia coli Biopolymers"], "article_id"=>1314001, "categories"=>["Biological Sciences"], "users"=>["Richard Kelwick", "Margarita Kopniczky", "Iain Bower", "Wenqiang Chi", "Matthew Ho Wai Chin", "Sisi Fan", "Jemma Pilcher", "James Strutt", "Alexander J. Webb", "Kirsten Jensen", "Guy-Bart Stan", "Richard Kitney", "Paul Freemont"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0117202.g004", "stats"=>{"downloads"=>0, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flow_cytometry_analysis_of_P_3HB_production_in_phaCAB_engineered_E_coli_from_waste_media_cultures_/1314001", "title"=>"Flow cytometry analysis of P(3HB) production in <i>phaCAB</i>-engineered <i>E</i>. <i>coli</i> from waste-media cultures.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-02-20 02:58:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1914624", "https://ndownloader.figshare.com/files/1914625", "https://ndownloader.figshare.com/files/1914626", "https://ndownloader.figshare.com/files/1914627", "https://ndownloader.figshare.com/files/1914628", "https://ndownloader.figshare.com/files/1914629"], "description"=>"<div><p>Biopolymers, such as poly-3-hydroxybutyrate (P(3HB)) are produced as a carbon store in an array of organisms and exhibit characteristics which are similar to oil-derived plastics, yet have the added advantages of biodegradability and biocompatibility. Despite these advantages, P(3HB) production is currently more expensive than the production of oil-derived plastics, and therefore, more efficient P(3HB) production processes would be desirable. In this study, we describe the model-guided design and experimental validation of several engineered P(3HB) producing operons. In particular, we describe the characterization of a hybrid <i>phaCAB</i> operon that consists of a dual promoter (native and J23104) and RBS (native and B0034) design. P(3HB) production at 24 h was around six-fold higher in hybrid <i>phaCAB</i> engineered <i>Escherichia coli</i> in comparison to <i>E. coli</i> engineered with the native <i>phaCAB</i> operon from <i>Ralstonia eutropha</i> H16. Additionally, we describe the utilization of non-recyclable waste as a low-cost carbon source for the production of P(3HB).</p></div>", "links"=>[], "tags"=>["Ralstonia eutropha H 16.", "phaCAB operon", "rbs", "Genetically Engineered Escherichia coli Biopolymers"], "article_id"=>1314006, "categories"=>["Biological Sciences"], "users"=>["Richard Kelwick", "Margarita Kopniczky", "Iain Bower", "Wenqiang Chi", "Matthew Ho Wai Chin", "Sisi Fan", "Jemma Pilcher", "James Strutt", "Alexander J. Webb", "Kirsten Jensen", "Guy-Bart Stan", "Richard Kitney", "Paul Freemont"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0117202.s001", "https://dx.doi.org/10.1371/journal.pone.0117202.s002", "https://dx.doi.org/10.1371/journal.pone.0117202.s003", "https://dx.doi.org/10.1371/journal.pone.0117202.s004", "https://dx.doi.org/10.1371/journal.pone.0117202.s005", "https://dx.doi.org/10.1371/journal.pone.0117202.s006"], "stats"=>{"downloads"=>21, "page_views"=>50, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Forward_Design_Approach_to_Increase_the_Production_of_Poly_3_Hydroxybutyrate_in_Genetically_Engineered_Escherichia_coli_/1314006", "title"=>"A Forward-Design Approach to Increase the Production of Poly-3-Hydroxybutyrate in Genetically Engineered <i>Escherichia coli</i>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-02-20 02:58:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1914602"], "description"=>"<p>(<b>A</b>) Schematic of poly-3-hydroxybutyrate (P(3HB)) production via the <i>phaCAB</i> operon pathway. (<b>B</b>) The constructs used in this study. Abbreviations: Pwt (wildtype promoter; green arrow), J23104 (Anderson constitutive promoter, BBa_J23104; red arrow), B0034 (ribosomal binding site, BBa_B0034; red half-circle), <i>phaC</i> (PHA synthase), <i>phaA</i> (3-ketothiolase) and <i>phaB</i> (acetoacetyl-CoA reductase). Green half-circles denote native ribosomal binding sites. Construct symbols are based on the Synthetic Biology Open Language Visual (SBOLv) v1.0.0 guidelines [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117202#pone.0117202.ref021\" target=\"_blank\">21</a>].</p>", "links"=>[], "tags"=>["Ralstonia eutropha H 16.", "phaCAB operon", "rbs", "Genetically Engineered Escherichia coli Biopolymers"], "article_id"=>1313993, "categories"=>["Biological Sciences"], "users"=>["Richard Kelwick", "Margarita Kopniczky", "Iain Bower", "Wenqiang Chi", "Matthew Ho Wai Chin", "Sisi Fan", "Jemma Pilcher", "James Strutt", "Alexander J. Webb", "Kirsten Jensen", "Guy-Bart Stan", "Richard Kitney", "Paul Freemont"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0117202.g001", "stats"=>{"downloads"=>3, "page_views"=>44, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_phaCAB_pathway_and_constructs_/1313993", "title"=>"<i>phaCAB</i> pathway and constructs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-02-20 02:58:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1914603"], "description"=>"<p>In order to simulate P(3HB) production in <i>phaCAB</i>-engineered <i>E</i>. <i>coli</i>, a P(3HB) synthesis model was constructed using the Simbiology toolbox of Matlab. Using this model the flux of several metabolites and species were simulated in order to identify aspects of the system that could be selectively tuned to increase the production of P(3HB). From these analyses, several novel <i>phaCAB</i> operons were designed. These data show the simulated P(3HB) production across several different <i>phaCAB</i> operon designs, where <i>phaCAB</i> expression is under the control of the indicated Anderson constitutive promoters.</p>", "links"=>[], "tags"=>["Ralstonia eutropha H 16.", "phaCAB operon", "rbs", "Genetically Engineered Escherichia coli Biopolymers"], "article_id"=>1313994, "categories"=>["Biological Sciences"], "users"=>["Richard Kelwick", "Margarita Kopniczky", "Iain Bower", "Wenqiang Chi", "Matthew Ho Wai Chin", "Sisi Fan", "Jemma Pilcher", "James Strutt", "Alexander J. Webb", "Kirsten Jensen", "Guy-Bart Stan", "Richard Kitney", "Paul Freemont"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0117202.g002", "stats"=>{"downloads"=>3, "page_views"=>46, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Simulated_P_3HB_production_in_phaCAB_engineered_E_coli_/1313994", "title"=>"Simulated P(3HB) production in <i>phaCAB</i>-engineered <i>E</i>. <i>coli</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-02-20 02:58:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1914609"], "description"=>"<p><i>E</i>. <i>coli</i> MG1655 transformed with empty vector, native, constitutive or hybrid <i>phaCAB</i> constructs were cultured in 1 liter LB media, supplemented with 3% glucose (w/v) for 24 hours or 48 hours. P(3HB) was purified from these cultures and measured as <b>(A)</b> P(3HB) production (g/L) and <b>(B)</b> P(3HB) content (weight [wt.] % of cell dry weight [CDW]). Data represent the mean +/- the standard deviation of three independent experiments. Student t-test, *P<0.05, **P <0.01, ***P <0.001 and ****P <0.0001.</p>", "links"=>[], "tags"=>["Ralstonia eutropha H 16.", "phaCAB operon", "rbs", "Genetically Engineered Escherichia coli Biopolymers"], "article_id"=>1313999, "categories"=>["Biological Sciences"], "users"=>["Richard Kelwick", "Margarita Kopniczky", "Iain Bower", "Wenqiang Chi", "Matthew Ho Wai Chin", "Sisi Fan", "Jemma Pilcher", "James Strutt", "Alexander J. Webb", "Kirsten Jensen", "Guy-Bart Stan", "Richard Kitney", "Paul Freemont"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0117202.g003", "stats"=>{"downloads"=>0, "page_views"=>33, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_P_3HB_production_in_phaCAB_engineered_E_coli_/1313999", "title"=>"P(3HB) production in <i>phaCAB</i>-engineered <i>E</i>. <i>coli</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-02-20 02:58:02"}

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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