A Man-Made ATP-Binding Protein Evolved Independent of Nature Causes Abnormal Growth in Bacterial Cells
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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/436603", "https://ndownloader.figshare.com/files/436647", "https://ndownloader.figshare.com/files/436688", "https://ndownloader.figshare.com/files/436714", "https://ndownloader.figshare.com/files/436829", "https://ndownloader.figshare.com/files/436932", "https://ndownloader.figshare.com/files/437006", "https://ndownloader.figshare.com/files/437063", "https://ndownloader.figshare.com/files/437145", "https://ndownloader.figshare.com/files/437195", "https://ndownloader.figshare.com/files/437255"], "description"=>"<div><p>Recent advances in <em>de novo</em> protein evolution have made it possible to create synthetic proteins from unbiased libraries that fold into stable tertiary structures with predefined functions. However, it is not known whether such proteins will be functional when expressed inside living cells or how a host organism would respond to an encounter with a non-biological protein. Here, we examine the physiology and morphology of <em>Escherichia coli</em> cells engineered to express a synthetic ATP-binding protein evolved entirely from non-biological origins. We show that this man-made protein disrupts the normal energetic balance of the cell by altering the levels of intracellular ATP. This disruption cascades into a series of events that ultimately limit reproductive competency by inhibiting cell division. We now describe a detailed investigation into the synthetic biology of this man-made protein in a living bacterial organism, and the effect that this protein has on normal cell physiology.</p></div>", "links"=>[], "tags"=>["man-made", "atp-binding", "evolved", "causes", "abnormal", "bacterial", "cells"], "article_id"=>146092, "categories"=>["Cell Biology", "Biochemistry", "Molecular Biology"], "users"=>["Joshua M. Stomel", "James W. Wilson", "Megan A. León", "Phillip Stafford", "John C. Chaput"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0007385.s001", "https://dx.doi.org/10.1371/journal.pone.0007385.s002", "https://dx.doi.org/10.1371/journal.pone.0007385.s003", "https://dx.doi.org/10.1371/journal.pone.0007385.s004", "https://dx.doi.org/10.1371/journal.pone.0007385.s005", "https://dx.doi.org/10.1371/journal.pone.0007385.s006", "https://dx.doi.org/10.1371/journal.pone.0007385.s007", "https://dx.doi.org/10.1371/journal.pone.0007385.s008", "https://dx.doi.org/10.1371/journal.pone.0007385.s009", "https://dx.doi.org/10.1371/journal.pone.0007385.s010", "https://dx.doi.org/10.1371/journal.pone.0007385.s011"], "stats"=>{"downloads"=>4, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Man_Made_ATP_Binding_Protein_Evolved_Independent_of_Nature_Causes_Abnormal_Growth_in_Bacterial_Cells/146092", "title"=>"A Man-Made ATP-Binding Protein Evolved Independent of Nature Causes Abnormal Growth in Bacterial Cells", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-10-08 01:41:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/880465"], "description"=>"<p>(a) Western blot showing expression of DX and ubiquitin. The blots are normalized to a DX standard of 120 µg. Lanes 1–10 corresponds to 1–10 hours of induced growth. (b) Immunoprecipitation of protein DX. Lane 1, protein standards; lanes 2–4, crude lysate; lanes 5–7, wash fractions; lanes 8–10, immuno-precipitate. In each case, samples are given in order of DX, ubiquitin, and empty vector, respectively. Lane 11 is a bead only control. (c) Quantitative chemiluminescence analysis of ATP levels in cells expressing DX (•), ubiquitin (▴), and empty vector (▪).</p>", "links"=>[], "tags"=>["properties", "cells"], "article_id"=>550918, "categories"=>["Cell Biology", "Biochemistry", "Molecular Biology"], "users"=>["Joshua M. Stomel", "James W. Wilson", "Megan A. León", "Phillip Stafford", "John C. Chaput"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007385.g003", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Biochemical_properties_of_E_coli_cells_that_express_DX_/550918", "title"=>"Biochemical properties of <i>E. coli</i> cells that express DX.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-10-08 00:15:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/880929"], "description"=>"<p>The cells were cultured for 3 hours in liquid media in the absence (a) or presence (b–d) of inducer. (a) An uninduced cell displaying a forming septum and three membranous spheres marked by arrows. (b) An example of a filamentous cell expressing DX. Areas marked by arrows indicate regions of chromosomal segregation. (c) Increased magnification of the boxed area in (b). A selection of membranous structures associated with the surface of the cell is marked with arrows. The arrow marked with a * indicates structures which have become detached from the cell. Images examined both above and below the plan reveal that this portion of the cell is not forming a division septum. (d) High magnification image of several spherical structures.</p>", "links"=>[], "tags"=>["micrographs", "sections", "embedded", "expressing"], "article_id"=>551380, "categories"=>["Cell Biology", "Biochemistry", "Molecular Biology"], "users"=>["Joshua M. Stomel", "James W. Wilson", "Megan A. León", "Phillip Stafford", "John C. Chaput"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007385.g007", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Electron_micrographs_of_thin_sections_through_embedded_E_coli_expressing_DX_/551380", "title"=>"Electron micrographs of thin sections through embedded <i>E. coli</i> expressing DX.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-10-08 00:23:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/880279"], "description"=>"<p>Protein DX adopts a novel zinc-nucleated α/β-fold with a topology not yet been observed in nature. The zinc and ATP ligands are colored according to atom type (PDB: 2P09).</p>", "links"=>[], "tags"=>["dx", "translucent"], "article_id"=>550735, "categories"=>["Cell Biology", "Biochemistry", "Molecular Biology"], "users"=>["Joshua M. Stomel", "James W. Wilson", "Megan A. León", "Phillip Stafford", "John C. Chaput"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007385.g001", "stats"=>{"downloads"=>3, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_X_ray_crystal_structure_of_protein_DX_with_translucent_surface_rendering_/550735", "title"=>"X-ray crystal structure of protein DX with translucent surface rendering.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-10-08 00:12:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/880802"], "description"=>"<p>Phase-contrast micrograph images of <i>E. coli</i> TOP10, <i>E. coli</i> K12 MG1655, and <i>S. typhimurium</i> LT-2 taken at 9 hours post-induction of the DX protein. Control cells of each strain containing the empty vector are included to provide a basis of comparison. Images were acquired at 40× magnification.</p>", "links"=>[], "tags"=>["specificity", "dx", "filamentous"], "article_id"=>551255, "categories"=>["Cell Biology", "Biochemistry", "Molecular Biology"], "users"=>["Joshua M. Stomel", "James W. Wilson", "Megan A. León", "Phillip Stafford", "John C. Chaput"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007385.g006", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Species_and_strain_specificity_of_DX_filamentous_phenotype_/551255", "title"=>"Species and strain specificity of DX filamentous phenotype.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-10-08 00:20:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/880552"], "description"=>"<p>(a) <i>E. coli</i> cells cultured in the presence of inducer for 10 hours were allowed to recover in the absence of inducer for a variable amount of time (0–8 hours). Cells expressing protein DX were compared to control cells containing the empty vector exposed to a bacteriostat (tetracycline), bactericide (kanamycin), or no additional antibiotic. (b) <i>E. coli</i> cells were cultured in the presence of inducer for varying amounts of time (4–14 hours) and allowed to recover for 4 hours in LB media free of inducer.</p>", "links"=>[], "tags"=>["dx"], "article_id"=>551013, "categories"=>["Cell Biology", "Biochemistry", "Molecular Biology"], "users"=>["Joshua M. Stomel", "James W. Wilson", "Megan A. León", "Phillip Stafford", "John C. Chaput"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007385.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reversibility_of_DX_growth_suppression_/551013", "title"=>"Reversibility of DX growth suppression.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-10-08 00:16:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/880346"], "description"=>"<p><i>E. coli</i> cells containing the DX, ubiquitin, or empty vector were induced in liquid media with arabinose and spotted in 10-fold dilutions onto solid agar plates that either contained (column 2) or were devoid (column 1) of the arabinose inducer. A series of control experiments were performed in parallel in which uninduced cells were plated onto solid media that contained (column 4) or were devoid (column 3) of arabinose.</p>", "links"=>[], "tags"=>["characteristics", "cells", "expressing"], "article_id"=>550803, "categories"=>["Cell Biology", "Biochemistry", "Molecular Biology"], "users"=>["Joshua M. Stomel", "James W. Wilson", "Megan A. León", "Phillip Stafford", "John C. Chaput"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007385.g002", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_characteristics_of_E_coli_cells_expressing_protein_DX_/550803", "title"=>"Expression characteristics of <i>E. coli</i> cells expressing protein DX.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-10-08 00:13:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/880680"], "description"=>"<p>Phase-contrast micrograph images taken between 2 and 9 hours post-induction show the filamentous phenotype in cells expressing protein DX. The unbiquitin and empty control strains appear normal at all times of induced growth. Images were acquired at 40× magnification.</p>", "links"=>[], "tags"=>["dx"], "article_id"=>551140, "categories"=>["Cell Biology", "Biochemistry", "Molecular Biology"], "users"=>["Joshua M. Stomel", "James W. Wilson", "Megan A. León", "Phillip Stafford", "John C. Chaput"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0007385.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analyzing_the_effect_of_DX_expression_on_cell_morphology_/551140", "title"=>"Analyzing the effect of DX expression on cell morphology.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-10-08 00:19:00"}

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