Patents Assigned to BIOWORKS, INC.
  • 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
  • Patent number: 11530406
    Abstract: A system for producing a therapeutic oligomer includes a computing device configured to design a proposed therapeutic oligomer sequence, wherein designing further comprises generating a genomic library for an organism from a gene target, initiating a sequence identification function, identifying a genomic locus that the proposed therapeutic oligomer sequence is predicted to bond to as a function of an off-target sequence function, selecting the proposed therapeutic oligomer sequence as a function of the sequence identification function, the genomic locus, and a criterion element, and synthesize a therapeutic oligomer as a function of the proposed therapeutic oligomer sequence.
    Type: Grant
    Filed: August 30, 2021
    Date of Patent: December 20, 2022
    Assignee: Sachi Bioworks Inc.
    Inventor: Prashant Nagpal
  • Publication number: 20220378072
    Abstract: The disclosure relates to enzymes, such as cucurbitadienol synthase (CDS), UDP-glycosyltransferase (UGT), C11 hydroxylase, epoxide hydrolase (EPH), squalene epoxidase (SQE), and/or cytochrome P450 reductase enzymes, recombinant host cells expressing the enzymes, and methods of producing mogrol precursors, mogrol, and/or mogrosides using such recombinant cells.
    Type: Application
    Filed: October 23, 2020
    Publication date: December 1, 2022
    Applicant: Ginkgo Bioworks, Inc.
    Inventors: Jeffrey Ian Boucher, Matthew McMahon, Scott Marr, Jie Zhu
  • Publication number: 20220380746
    Abstract: The present invention relates generally to the field of immune binding proteins and method for obtaining immune binding proteins from genomic or other sources. The present invention also relates to nucleic acids encoding the immune binding proteins in which the natural multimeric association of chains is maintained in the nucleic acids and the immune binding proteins made therefrom. For example, nucleic acids encoding antibodies that are amplified from a B-cell using the methods of the invention maintain the natural pairing of heavy and light chains from the B-cell. This maintenance of pairing (or multimerization) produces libraries and/or repertoires of immune binding proteins that are enriched for useful binding molecules.
    Type: Application
    Filed: August 10, 2022
    Publication date: December 1, 2022
    Applicant: Augmenta Bioworks, Inc.
    Inventors: Marco Antonio Mena, Christopher J. Emig, John Haliburton, Payam Shahi
  • Publication number: 20220372501
    Abstract: The disclosure relates to methods and compositions for the production of fructans using sucrose:sucrose 1-fructosyl-transferase (1-SST), fructan:fructan 1-fructosyltransferase (1-FFT), and/or sucrose fructan-6-fructosyltransferase (6-SFT) enzymes.
    Type: Application
    Filed: September 24, 2020
    Publication date: November 24, 2022
    Applicant: Ginkgo Bioworks, Inc.
    Inventors: Sudeep Agarwala, Michael G. Napolitano
  • Patent number: 11492647
    Abstract: Disclosed are methods and compositions for increasing the triacylglycerol content of a cell by increasing the activity of a type 1 diacylglycerol acyltransferase (i.e., DGA2) and increasing the activity of a type 2 diacylglycerol acyltransferase (i.e., DGA1). In some embodiments, the triacylglycerol content of a cell is also modified my decreasing the activity of a triacylglycerol lipase in the same cell. Also disclosed are methods and compositions for increasing the triacylglycerol content of a cell by increasing the activity of a type 1 diacylglycerol acyltransferase (i.e., DGA2), or by increasing the activity of a type 3 diacylglycerol acyltransferase (i.e., DGA3).
    Type: Grant
    Filed: April 5, 2019
    Date of Patent: November 8, 2022
    Assignee: Ginkgo Bioworks, Inc.
    Inventors: Vasiliki Tsakraklides, Elena E. Brevnova
  • Publication number: 20220348933
    Abstract: Provided in this disclosure, in some embodiments, are methods and compositions for treating maple syrup urine disease (MSUD) and other conditions characterized by excessive branched-chain amino acids.
    Type: Application
    Filed: June 19, 2020
    Publication date: November 3, 2022
    Applicants: Ginkgo Bioworks, Inc., Synlogic Operating Company, Inc.
    Inventors: Patrick Boyle, Dylan Alexander Carlin, Rishi Jain, Ryan Putman, Laura Stone, Alex C. Tucker, Kolea Zimmerman
  • Publication number: 20220348889
    Abstract: The present invention relates to methods and compositions that include enzymes and/or binding polypeptides useful for protecting polymers from damage caused by fatty acids from secreted biological fluids such as sebum or sweat.
    Type: Application
    Filed: May 13, 2022
    Publication date: November 3, 2022
    Applicant: Ginkgo Bioworks, Inc.
    Inventors: Patrick Magannig Boyle, Jeffery Ian Boucher, Michael Gregory Napolitano
  • Publication number: 20220348619
    Abstract: Described in this disclosure are rare earth element (REE)-binding proteins (e.g., lanthanide-binding proteins), host cells expressing the REE-binding proteins, and methods of recovering REEs.
    Type: Application
    Filed: June 19, 2020
    Publication date: November 3, 2022
    Applicant: Ginkgo Bioworks, Inc.
    Inventors: Patrick Boyle, Ramya L. Prathuri, Nathan W. Schmidt, Emily E. Wrenbeck, Mark David Simon
  • Publication number: 20220340939
    Abstract: Disclosed herein are cells, nucleic acids, and proteins that can be used to produce branched (methyl)lipids, such as 10-methylstearic acids, and compositions that include such lipids. Cells disclosed herein comprise methyltransferase and/or reductase genes from bacteria of the class Gammaproteobacteria, which encode enzymes capable of catalyzing the production of branched (methyl)lipids from unbranched, unsaturated lipids. Saturated branched (methyl)lipids produced using embodiments of the present invention have favorable low-temperature fluidity and favorable oxidative stability, which are desirable properties for lubricants and specialty fluids.
    Type: Application
    Filed: January 30, 2022
    Publication date: October 27, 2022
    Applicant: Ginkgo Bioworks, Inc.
    Inventors: Arthur J. Shaw, Hannah Blitzblau, Donald V. Crabtree
  • Patent number: 11479797
    Abstract: The present disclosure provides proteins, nucleic acids, vectors, and host molecules useful for the production of compounds of interest, and methods for their use.
    Type: Grant
    Filed: October 27, 2017
    Date of Patent: October 25, 2022
    Assignee: Ginkgo Bioworks, Inc.
    Inventors: Daniel C. Gray, Brian R. Bowman, Gregory L. Verdine, Mathew Edward Sowa
  • Patent number: 11479777
    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: Grant
    Filed: March 27, 2018
    Date of Patent: October 25, 2022
    Assignee: Ginkgo Bioworks, Inc.
    Inventors: Reshma P. Shetty, Curt R. Fischer
  • Patent number: 11470845
    Abstract: The present application is directed to antimicrobial compositions comprising chitosan polymers of at least two different average molecular weights (Mws), wherein the Mw of each different chitosan polymer is selected to target a different microorganism as well as method of making and using the compositions and product comprising the compositions.
    Type: Grant
    Filed: September 7, 2018
    Date of Patent: October 18, 2022
    Assignee: CHINOVA BIOWORKS INC.
    Inventors: David Brown, Tanzina Huq, Natasha Dhayagude
  • Publication number: 20220307060
    Abstract: Aspects of the disclosure relate to biosynthesis of cannabinoids and cannabinoid precursors in recombinant cells and in vitro.
    Type: Application
    Filed: March 9, 2022
    Publication date: September 29, 2022
    Applicant: Ginkgo Bioworks, Inc.
    Inventors: Kim Cecelia Anderson, Elena Brevnova, Dylan Alexander Carlin, Brian Carvalho, Nicholas Flores, Katrina Forrest, Matthew McMahon, Massimo Merighi, Gabriel Rodriguez, Emily E. Wrenbeck
  • Publication number: 20220306999
    Abstract: The disclosure relates to biosynthesis of cannabinoids and cannabinoid precursors in recombinant cells and in vitro comprising the use of disclosed prenyltransferase variants.
    Type: Application
    Filed: August 18, 2020
    Publication date: September 29, 2022
    Applicant: Ginkgo Bioworks, Inc.
    Inventors: Kim Cecelia Anderson, Dylan Alexander Carlin, Nicholas Flores, Katrina Forrest, Ramya L. Prathuri, Gabriel Rodriguez, Michelle Spencer
  • Patent number: 11447810
    Abstract: The present disclosure provides nucleic acids encoding a Large ATP-binding regulator of the LuxR family (LAL) of transcription factors, vectors and host cells including such nucleic acids, and methods for producing compounds (e.g., polyketides or ?-lactam compounds) with such nucleic acids, vectors, and/or host cells.
    Type: Grant
    Filed: January 29, 2021
    Date of Patent: September 20, 2022
    Assignee: Ginkgo Bioworks, Inc.
    Inventors: Brian R. Bowman, Joshua A. V. Blodgett, Gregory L. Verdine, Daniel C. Gray, Jay P. Morgenstern, Lucy Foulston, Keith Robison
  • Publication number: 20220213492
    Abstract: Described herein are enzymes, such as for example, methanol dehydrogenase (MDH), 3-hexulose-6-phosphate isomerase (PHI), 3-hexulose-6-phosphate synthase (HPS), ribose-5-phosphate isomerase (RPI), ribulose 5-phosphate 3-epimerase (RPE), transketolase (TKT), transaldolase (TAL) enzymes, phosphofructokinase (PFK), Sedoheptulose 1,7-Bisphosphatase (GLPX), fructose-bisphosphate aldolase (FBA), 6-phosphogluconate dehydrogenase (GND), and glucose-6-phosphate dehydrogenase (ZWF); recombinant host cells expressing the enzymes; methods of producing methylotrophic cells; and methods of producing amino acids (e.g., lysine).
    Type: Application
    Filed: April 17, 2020
    Publication date: July 7, 2022
    Applicant: Ginkgo Bioworks, Inc.
    Inventors: Hui Zhou, Massimo Merighi, Micjael G. Napolitano, Kennji Abe, Yoshihiro Ito, Takayuki Asahara, Thomas Perli, Sergio L. Florez, Ryan J. Putman, Ryo Takeshita, Yuri Uehara, Akito Chinen, Kazuteru Yamada
  • Publication number: 20220195472
    Abstract: Aspects of the disclosure relate to biosynthesis of cannabinoids and cannabinoid precursors in recombinant cells and in vitro.
    Type: Application
    Filed: February 4, 2022
    Publication date: June 23, 2022
    Applicant: Ginkgo Bioworks, Inc.
    Inventors: Kim Cecelia Anderson, Elena Brevnova, Dylan Alexander Carlin, Brian Carvalho, Nicholas Flores, Katrina Forrest, Massimo Merighi, Gabriel Rodriguez, Emily E. Wrenbeck