Patents Assigned to Ginkgo BioWorks, Inc.
  • Publication number: 20240141308
    Abstract: Aspects of the disclosure relate to phosphotriesterase (PTE) enzymes and PTE-related (PTER) enzymes and their use in hydrolyzing OPNAs.
    Type: Application
    Filed: April 15, 2022
    Publication date: May 2, 2024
    Applicant: Ginkgo Bioworks, Inc.
    Inventors: David Borhani, Dylan Alexander Carlin, Alex Tucker
  • Publication number: 20240110206
    Abstract: Aspects of the disclosure relate to biosynthesis of cannabinoids and cannabinoid precursors in recombinant cells and in vitro. Specifically, the disclosure is directed to a prenyltransferase variant, a chimeric prenyltransferase comprising one or more portions of at least two different prenyltransferase proteins, and a fusion polypeptide comprising a CBG-type producing prenyltransferase and farnesyl pyrophosphate synthase.
    Type: Application
    Filed: October 12, 2021
    Publication date: April 4, 2024
    Applicant: Ginkgo Bioworks, Inc.
    Inventors: Dylan Alexander Carlin, Brian Carvalho, Nicholas Flores, Katrina Forrest, Gabriel Rodriguez, Nathan W. Schmidt, Michelle Spencer
  • Patent number: 11905523
    Abstract: Provided herein are gene therapy compositions and methods for treating, preventing, and/or curing NPC1. More specifically, the disclosure provides Adeno-associated virus (AAV) vectors for delivery of nucleic acids and nucleic acids (including AAV transfer cassettes) for treating, preventing, and/or curing NPC1.
    Type: Grant
    Filed: October 16, 2020
    Date of Patent: February 20, 2024
    Assignee: Ginkgo Bioworks, Inc.
    Inventors: Daniel McCoy, Garrett E. Berry, David Dismuke
  • Publication number: 20240026392
    Abstract: Aspects of the disclosure relate to biosynthesis of cannabinoids and cannabinoid precursors in recombinant cells and in vitro, and to variant terminal synthases having altered catalytic activity to synthesize THC-type, CBD-type and/or CBC-type cannabinoids.
    Type: Application
    Filed: July 8, 2021
    Publication date: January 25, 2024
    Applicant: Ginkgo Bioworks, Inc.
    Inventors: Kim Cecelia Anderson, Jeffrey Ian Boucher, Elena Brevnova, Brian Carvalho, Nicholas Flores, Katrina Forrest, Fiona Qu, Gabriel Rodrigues, Michelle Spencer
  • Publication number: 20240002847
    Abstract: This application describes synthetic promoters capable of facilitating the high-yield synthesis of proteins and molecules.
    Type: Application
    Filed: November 12, 2021
    Publication date: January 4, 2024
    Applicant: Ginkgo Bioworks, Inc.
    Inventors: Swaminath Srinivas, Justin Michael Gardin
  • Patent number: 11859189
    Abstract: The present disclosure provides host cells, e.g., bacterial cells, that comprise a methionine decarboxylase enzyme for the treatment of diseases and disorders associated with methionine metabolism in a subject. The disclosure further provides pharmaceutical compositions and methods of treating disorders associated with methionine metabolism, such as homocystinuria.
    Type: Grant
    Filed: August 11, 2022
    Date of Patent: January 2, 2024
    Assignees: Synlogic Operating Company, Inc., Ginkgo Bioworks, Inc.
    Inventors: Dylan Alexander Carlin, Vincent M. Isabella, Jonathan McMurry, Theodore Carlton Moore, III, Mylene Perreault, Nathan Schmidt, Mark Simon
  • Publication number: 20230383318
    Abstract: The present disclosure identifies pathways, mechanisms, systems and methods to confer chemoautotrophic production of carbon-based products of interest, such as sugars, alcohols, chemicals, amino acids, polymers, fatty acids and their derivatives, hydrocarbons, isoprenoids, and intermediates thereof, in organisms such that these organisms efficiently convert inorganic carbon to organic carbon-based products of interest using inorganic energy, such as formate, and in particular the use of organisms for the commercial production of various carbon-based products of interest.
    Type: Application
    Filed: May 31, 2023
    Publication date: November 30, 2023
    Applicant: Ginkgo Bioworks, Inc.
    Inventors: Curt R. Fischer, Austin J. Che, Reshma P. Shetty, Jason R. Kelly
  • Publication number: 20230357728
    Abstract: The current methods and compositions provide for nucleotide sequences of promoters from Yarrowia lipolytica which may be used to drive gene expression in a cell. In some aspects, the promoters are useful for modulating lipid production in oleaginous organisms such as yeast.
    Type: Application
    Filed: December 27, 2022
    Publication date: November 9, 2023
    Applicant: GINKGO BIOWORKS, INC.
    Inventors: Vasiliki TSAKRAKLIDES, Annapurna KAMINENI
  • Publication number: 20230340446
    Abstract: Aspects of the disclosure relate to biosynthesis of cannabinoids and cannabinoid precursors in recombinant cells and in vitro. In particular, the disclosure relates to variants of olivetolic acid cyclase.
    Type: Application
    Filed: June 17, 2021
    Publication date: October 26, 2023
    Applicant: Ginkgo Bioworks, Inc.
    Inventors: Kim Cecelia Anderson, Brian Carvalho, Nicholas Flores, Seth Ritter, Gabriel Rodriguez, Michelle Spencer, Emily E. Wrenbeck
  • Publication number: 20230257793
    Abstract: This application describes transcriptional units, synthetic expression systems, and host cells comprising transcriptional units and synthetic expression systems, wherein the synthetic expression system is capable of expressing a gene of interest. Also described are methods for the production of bioproducts (including, but not limited to, proteins or RNA expressed from the gene of interest). In some embodiments, bioproducts are produced from host cells under culture conditions without addition of methanol.
    Type: Application
    Filed: September 5, 2021
    Publication date: August 17, 2023
    Applicant: Ginkgo Bioworks, Inc.
    Inventors: Nikos Reppas, Swaminath Srinivas, Adam Meyer, Alex Tucker, Punita Manga, Sneha Srikrishnan
  • Patent number: 11702665
    Abstract: Signal sequences useful for targeting proteins and peptides to the surface of endospores produced by Paenibacillus family members and methods of using the same are provided. The display of heterologous molecules, such as peptides, polypeptides and other recombinant constructs, on the spore surface of Paenibacillus family members, using particular N-terminal targeting sequences and derivatives of the same, are also provided.
    Type: Grant
    Filed: March 30, 2021
    Date of Patent: July 18, 2023
    Assignee: Ginkgo Bioworks, Inc.
    Inventors: Damian Curtis, Benjamin L. Golomb, Dilara Ally, Florencia A. Ficarra, Rauf Salamzade, Bjorn A. Traag
  • Patent number: 11697829
    Abstract: The present disclosure identifies pathways, mechanisms, systems and methods to confer chemoautotrophic production of carbon-based products of interest, such as sugars, alcohols, chemicals, amino acids, polymers, fatty acids and their derivatives, hydrocarbons, isoprenoids, and intermediates thereof, in organisms such that these organisms efficiently convert inorganic carbon to organic carbon-based products of interest using inorganic energy, such as formate, and in particular the use of organisms for the commercial production of various carbon-based products of interest.
    Type: Grant
    Filed: July 30, 2020
    Date of Patent: July 11, 2023
    Assignee: Ginkgo Bioworks, Inc.
    Inventors: Curt R. Fischer, Austin J. Che, Reshma P. Shetty, Jason R. Kelly
  • Patent number: 11674162
    Abstract: Disclosed are transformed cells and related nucleotide and protein sequences, and fermentation compositions and methods, all of which are related to providing selective advantage in fermentation. For example, a selective advantage results from transformation of a cell with a nucleic acid that allows a transformed cell to metabolize one or more nitrogen-, phosphorous-, and/or sulfur-containing compounds that a native cell of the same species as the transformed cell cannot metabolize, and from fermentation of the transformed cell using one or more feedstocks, such as fractioned grain, which are depleted in or free of conventional nitrogen-, phosphorous-, and/or sulfur-containing compounds that a native cell of the same species as the transformed cell can metabolize. Also disclosed are methods for improved oxygen transfer in an aerobic or microaerobic fermentation.
    Type: Grant
    Filed: April 8, 2015
    Date of Patent: June 13, 2023
    Assignee: Ginkgo Bioworks, Inc.
    Inventors: Emily H. Greenhagen, Maureen Hamilton, William G. LaTouf, Andrew L. Consiglio, Kyle M. MacEwen, Arthur J. Shaw, IV
  • Publication number: 20230174993
    Abstract: Described in this application are UDP-glycosyltransferases (UGT) enzymes, host cells expressing the UGTs, and methods of producing mogrol precursors, mogrol, and/or mogrosides using such host cells.
    Type: Application
    Filed: May 13, 2021
    Publication date: June 8, 2023
    Applicant: Ginkgo Bioworks, Inc.
    Inventors: Jeffrey Ian Boucher, Justin Michael Gardin, Scott Marr, Matthew McMahon, Krishnaben S. Patel, Jie Zhu
  • Publication number: 20230137139
    Abstract: Aspects of the disclosure relate to biosynthesis of cannabinoids and cannabinoid precursors in recombinant cells and in vitro.
    Type: Application
    Filed: March 26, 2021
    Publication date: May 4, 2023
    Applicant: Ginkgo Bioworks, Inc.
    Inventors: Kim Cecelia Anderson, Jeffrey lan Boucher, Elena Brevnova, Dylan Alexander Carlin, Brian Carvalho, Nicholas Flores, Katrina Forrest, Gabriel Rodriguez, Michelle Spencer
  • Patent number: 11634737
    Abstract: Disclosed are transformed cells comprising one or more genetic modifications that affect the lipid content of the cell, e.g., by increasing the concentration of oleic acid in the cell relative to an unmodified cell of the same type. Also disclosed are methods for modifying the lipid content of a cell by increasing the activity of one or more proteins in the cell and/or by decreasing the activity of one or more proteins in the same cell.
    Type: Grant
    Filed: December 9, 2015
    Date of Patent: April 25, 2023
    Assignee: Ginkgo Bioworks, Inc.
    Inventors: Vasiliki Tsakraklides, Elena E. Brevnova, Jonathan Friedlander, Annapurna Kamineni, Arthur J. Shaw, IV
  • Publication number: 20230107986
    Abstract: The present disclosure identifies pathways, mechanisms, systems and methods to confer production of carbon-based products of interest, such as sugars, alcohols, chemicals, amino acids, polymers, fatty acids and their derivatives, hydrocarbons, isoprenoids, and intermediates thereof, in engineered and/or evolved methylotrophs such that these organisms efficiently convert C1 compounds, such as formate, formic acid, formaldehyde or methanol, to organic carbon-based products of interest, and in particular the use of organisms for the commercial production of various carbon-based products of interest.
    Type: Application
    Filed: September 30, 2022
    Publication date: April 6, 2023
    Applicant: Ginkgo Bioworks, Inc.
    Inventors: Reshma P. Shetty, Curt R. Fischer
  • Publication number: 20230065419
    Abstract: Aspects of the disclosure relate to biosynthesis of histidine in host cells. For example, host cells may comprise: a promoter; a ribosome binding site (RBS); and a nucleic acid comprising: hisG; hisD; hisC hisB; hisH; hisA; hisF; and/or hisI. Host cells may further comprise a nucleic acid encoding a ribose phosphate pyrophosphokinase (RPPK), optionally comprising one or more amino acid substitutions relative to the sequence of wildtype E. coli RPPK. Host cells of the disclosure may comprise a nucleic acid encoding a 5,10-methylene-tetrahydrofolate dehydrogenase/5,10-methylene-tetrahydrofolate cyclohydrolase (MTHFDC) enzyme. Further aspects of the disclosure relate to production of purine pathway metabolites and/or plasmid DNA in host cells.
    Type: Application
    Filed: December 16, 2020
    Publication date: March 2, 2023
    Applicant: Ginkgo Bioworks, Inc.
    Inventors: Alkiviadis Orfefs Chatzivasileiou, Jason King, Huey-Ming Mak, Gabriel Rodriguez, Emily E. Wrenbeck, David Young
  • Patent number: 11572546
    Abstract: The current methods and compositions provide for nucleotide sequences of promoters from Yarrowia lipolytica which may be used to drive gene expression in a cell. In some aspects, the promoters are useful for modulating lipid production in oleaginous organisms such as yeast.
    Type: Grant
    Filed: July 29, 2020
    Date of Patent: February 7, 2023
    Assignee: GINKGO BIOWORKS, INC.
    Inventors: Vasiliki Tsakraklides, Annapurna Kamineni
  • Patent number: 11535829
    Abstract: Disclosed are genetically engineered organisms, such as yeast and bacteria, that have the ability to metabolize atypical phosphorus or sulfur sources. Fermentation methods using the genetically engineered organisms are also described. The fermentation methods are robust processes for the industrial bioproduction of a variety of compounds, including commodities, fine chemicals, an pharmaceuticals.
    Type: Grant
    Filed: November 27, 2018
    Date of Patent: December 27, 2022
    Assignee: Ginkgo Bioworks, Inc.
    Inventors: Arthur J. Shaw, IV, Colin R. South, Johannes P. Van Dijken