CA3064612A1 - A htp genomic engineering platform for improving escherichia coli - Google Patents

A htp genomic engineering platform for improving escherichia coli Download PDF

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Publication number
CA3064612A1
CA3064612A1 CA3064612A CA3064612A CA3064612A1 CA 3064612 A1 CA3064612 A1 CA 3064612A1 CA 3064612 A CA3064612 A CA 3064612A CA 3064612 A CA3064612 A CA 3064612A CA 3064612 A1 CA3064612 A1 CA 3064612A1
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CA
Canada
Prior art keywords
coli strain
library
gene
coli
swap
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Abandoned
Application number
CA3064612A
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English (en)
French (fr)
Inventor
Matthew Davis
Christy WISNEWSKI
Patrick WESTFALL
Zach Serber
Erik Jedediah Dean
Shawn Manchester
Katherine GORA
Erin Shellman
Aaron Kimball
Shawn Szyjka
Barbara Frewen
Thomas Treynor
Michael Flashman
Robert Haushalter
Stacy-Anne MORGAN
Michael BLAISSE
Prabha RAMAKRISHNAN
Kyle ROTHSCHILD-MANCINELLI
Youngnyun Kim
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Zymergen Inc
Original Assignee
Zymergen Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Zymergen Inc filed Critical Zymergen Inc
Publication of CA3064612A1 publication Critical patent/CA3064612A1/en
Abandoned legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1058—Directional evolution of libraries, e.g. evolution of libraries is achieved by mutagenesis and screening or selection of mixed population of organisms
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1079—Screening libraries by altering the phenotype or phenotypic trait of the host
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/70—Vectors or expression systems specially adapted for E. coli
    • C12N15/73—Expression systems using phage (lambda) regulatory sequences

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  • Life Sciences & Earth Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Wood Science & Technology (AREA)
  • Organic Chemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biomedical Technology (AREA)
  • Zoology (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Biochemistry (AREA)
  • Plant Pathology (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Virology (AREA)
  • Ecology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Preparation Of Compounds By Using Micro-Organisms (AREA)
CA3064612A 2017-06-06 2018-06-06 A htp genomic engineering platform for improving escherichia coli Abandoned CA3064612A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201762515870P 2017-06-06 2017-06-06
US62/515,870 2017-06-06
PCT/US2018/036333 WO2018226880A1 (en) 2017-06-06 2018-06-06 A htp genomic engineering platform for improving escherichia coli

Publications (1)

Publication Number Publication Date
CA3064612A1 true CA3064612A1 (en) 2018-12-13

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Family Applications (1)

Application Number Title Priority Date Filing Date
CA3064612A Abandoned CA3064612A1 (en) 2017-06-06 2018-06-06 A htp genomic engineering platform for improving escherichia coli

Country Status (8)

Country Link
US (1) US20200370058A1 (enExample)
EP (2) EP3485013B1 (enExample)
JP (1) JP2020524490A (enExample)
KR (1) KR20200026874A (enExample)
CN (1) CN110945125A (enExample)
CA (1) CA3064612A1 (enExample)
ES (1) ES2875579T3 (enExample)
WO (1) WO2018226880A1 (enExample)

Families Citing this family (28)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3715454A4 (en) * 2017-11-22 2021-08-18 National University Corporation Kobe University COMPLEX FOR GENOME EDITING WITH STABILITY AND FEW SIDE EFFECTS AND NUCLEIC ACID TO ENCODE IT
EP3874037A4 (en) 2018-10-31 2021-12-15 Zymergen, Inc. DETERMINIST MULTIPLEXED SET OF DNA LIBRARIES
WO2020185584A1 (en) 2019-03-08 2020-09-17 Zymergen Inc. Pooled genome editing in microbes
WO2020185590A1 (en) * 2019-03-08 2020-09-17 Zymergen Inc. Iterative genome editing in microbes
US11526705B2 (en) * 2019-04-01 2022-12-13 Lg Electronics Inc. Method of classificating outlier in object recognition and device and robot of classifying thereof
US20220267782A1 (en) * 2019-06-21 2022-08-25 Glycom A/S Nucleic acid construct comprising 5' utr stem-loop for in vitro and in vivo gene expression
CN110272907B (zh) * 2019-08-12 2021-04-23 华中农业大学 一种调控番茄茎杆发育的基因sd1及其应用
GB202001211D0 (en) * 2020-01-29 2020-03-11 Imperial College Innovations Ltd Methods
CN111612133B (zh) * 2020-05-20 2021-10-19 广州华见智能科技有限公司 基于人脸图像多阶段关系学习的内脏器官特征编码方法
CN111700075B (zh) * 2020-06-05 2021-08-17 茂名市瑜丰沉香创意产业有限公司 人工结香沉香、沉香精油富集液、沉香香皂及其生产方法
WO2022124302A1 (ja) * 2020-12-08 2022-06-16 国立大学法人神戸大学 有用化合物を高生産する代謝改変微生物株の構築方法及び代謝改変大腸菌株
CN112941058B (zh) * 2021-04-02 2023-12-05 重庆科润生物医药研发有限公司 一种重组溶组织梭菌ii型胶原酶及其制备方法和应用
CN113265412A (zh) * 2021-05-20 2021-08-17 北京化工大学 多酶偶联定位体系及其构建方法和应用
CN113393900B (zh) * 2021-06-09 2022-08-02 吉林大学 基于改进Transformer模型的RNA状态推断研究方法
US11530406B1 (en) 2021-08-30 2022-12-20 Sachi Bioworks Inc. System and method for producing a therapeutic oligomer
US12636303B2 (en) 2021-08-30 2026-05-26 Sachi Bioworks Inc. Composition of a therapeutic oligomer
US12037621B2 (en) * 2021-09-15 2024-07-16 Archer-Daniels-Midland Company Threonine production strain having attenuated expression of the yafV gene
CN114672505A (zh) * 2022-03-15 2022-06-28 江苏省中国科学院植物研究所 一种功能性表达细胞色素p450酶的方法及其应用
CN114921463B (zh) * 2022-04-11 2023-12-01 中国农业科学院生物技术研究所 一种调控萜类化合物合成产量的人工非编码RNA分子CsiY及其应用
CN115074410B (zh) * 2022-06-30 2025-08-19 武汉合生科技有限公司 一种生物合成虾青素的方法及载体
CN115992160A (zh) * 2022-09-30 2023-04-21 倍生生物科技(深圳)有限公司 一种穿梭载体及其构建方法和应用
CN115820703B (zh) * 2022-12-20 2026-07-10 山东乾肽生物科技有限公司 利用rna环化技术制备寡肽的方法及寡肽的表达dna
CN116013407B (zh) * 2022-12-26 2025-06-27 杭州智科慧创科技有限公司 一种基于语言模型的性质解耦蛋白质生成方法
CN116504313A (zh) * 2023-05-08 2023-07-28 暨南大学 基因终止子查询方法、装置、设备及可读存储介质
CN117230135A (zh) * 2023-07-07 2023-12-15 南京工业大学 双酶偶联结合dna支架提高nmn合成效率的方法
CN117275590B (zh) * 2023-11-10 2024-03-26 华东师范大学 有机固废体系中大分子的降解功能基因数据库与分析平台
WO2025101028A1 (ko) * 2023-11-10 2025-05-15 한국과학기술원 TdT(Terminal deoxynucleotidyl transferase) 및 dNTP를 이용한 비번역영 역 (untranslated region) 라이브러리 합성 방법
CN117238380A (zh) * 2023-11-15 2023-12-15 中国医学科学院北京协和医院 宏基因组病原识别的ai推荐方法、装置、设备及介质

Family Cites Families (64)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US72197A (en) 1867-12-17 Jesse h
US824A (en) 1838-07-09 Construction of steam-engines
US4435504A (en) 1982-07-15 1984-03-06 Syva Company Immunochromatographic assay with support having bound "MIP" and second enzyme
GB8406752D0 (en) 1984-03-15 1984-04-18 Unilever Plc Chemical and clinical tests
CA1303983C (en) 1987-03-27 1992-06-23 Robert W. Rosenstein Solid phase assay
US4855240A (en) 1987-05-13 1989-08-08 Becton Dickinson And Company Solid phase assay employing capillary flow
US6060296A (en) 1991-07-03 2000-05-09 The Salk Institute For Biological Studies Protein kinases
US5605793A (en) 1994-02-17 1997-02-25 Affymax Technologies N.V. Methods for in vitro recombination
US5837458A (en) 1994-02-17 1998-11-17 Maxygen, Inc. Methods and compositions for cellular and metabolic engineering
US6117679A (en) * 1994-02-17 2000-09-12 Maxygen, Inc. Methods for generating polynucleotides having desired characteristics by iterative selection and recombination
US6090592A (en) 1994-08-03 2000-07-18 Mosaic Technologies, Inc. Method for performing amplification of nucleic acid on supports
US5789538A (en) 1995-02-03 1998-08-04 Massachusetts Institute Of Technology Zinc finger proteins with high affinity new DNA binding specificities
EP1717322B1 (en) * 1997-01-17 2012-07-18 Codexis Mayflower Holdings, LLC Evolution of whole cells and organisms by recursive sequence recombination
US6326204B1 (en) * 1997-01-17 2001-12-04 Maxygen, Inc. Evolution of whole cells and organisms by recursive sequence recombination
EP2327797B1 (en) 1997-04-01 2015-11-25 Illumina Cambridge Limited Method of nucleic acid sequencing
JPH1180185A (ja) 1997-09-05 1999-03-26 Res Dev Corp Of Japan オリゴヌクレオチドの化学合成法
US6410248B1 (en) 1998-01-30 2002-06-25 Massachusetts Institute Of Technology General strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites
AU758728B2 (en) 1998-02-20 2003-03-27 Genome Dynamics, Inc. Method for designing DNA-binding proteins of the zinc-finger class
AR021833A1 (es) 1998-09-30 2002-08-07 Applied Research Systems Metodos de amplificacion y secuenciacion de acido nucleico
US6140081A (en) 1998-10-16 2000-10-31 The Scripps Research Institute Zinc finger binding domains for GNN
US6300070B1 (en) 1999-06-04 2001-10-09 Mosaic Technologies, Inc. Solid phase methods for amplifying multiple nucleic acids
US6927046B1 (en) * 1999-12-30 2005-08-09 Archer-Daniels-Midland Company Increased lysine production by gene amplification using coryneform bacteria
US7785832B2 (en) * 2000-05-09 2010-08-31 HALLA Patent & Law Firm Method of protein synthesis
WO2002029032A2 (en) * 2000-09-30 2002-04-11 Diversa Corporation Whole cell engineering by mutagenizing a substantial portion of a starting genome, combining mutations, and optionally repeating
WO2002046412A2 (en) 2000-12-07 2002-06-13 Sangamo Biosciences, Inc. Regulation of angiogenesis with zinc finger proteins
US7067617B2 (en) 2001-02-21 2006-06-27 The Scripps Research Institute Zinc finger binding domains for nucleotide sequence ANN
US20070178454A1 (en) 2002-10-21 2007-08-02 Joung J K Context sensitive paralell optimization of zinc finger dna binding domains
WO2005021772A1 (en) 2003-08-29 2005-03-10 Degussa Ag Process for the preparation of l-lysine
KR20090018799A (ko) 2006-05-30 2009-02-23 다우 글로벌 테크놀로지스 인크. 코돈 최적화 방법
CN101177454B (zh) * 2007-05-09 2010-09-22 郑骏年 Il-18突变体多肽及制备及用途
EP2255005A4 (en) 2008-02-28 2012-01-25 Univ California USE OF SYNTHETIC EQUIPMENT FOR THE PRODUCTION OF BIOSYNTHESIS PATH PRODUCTS
EP2313507A2 (en) * 2008-07-03 2011-04-27 Pfenex Inc High throughput screening method and use thereof to identify a production platform for a multifunctional binding protein
WO2010025310A2 (en) 2008-08-27 2010-03-04 Westend Asset Clearinghouse Company, Llc Methods and devices for high fidelity polynucleotide synthesis
US20100137143A1 (en) 2008-10-22 2010-06-03 Ion Torrent Systems Incorporated Methods and apparatus for measuring analytes
US8783382B2 (en) 2009-01-15 2014-07-22 Schlumberger Technology Corporation Directional drilling control devices and methods
EP2398915B1 (en) 2009-02-20 2016-08-24 Synthetic Genomics, Inc. Synthesis of sequence-verified nucleic acids
US8574835B2 (en) 2009-05-29 2013-11-05 Life Technologies Corporation Scaffolded nucleic acid polymer particles and methods of making and using
EP2395087A1 (en) 2010-06-11 2011-12-14 Icon Genetics GmbH System and method of modular cloning
MY173933A (en) * 2010-12-21 2020-02-27 Cj Cheiljedang Corp Modified polypeptide having homoserine acetyltransferase activity and microorganism expressing the same
WO2012142591A2 (en) * 2011-04-14 2012-10-18 The Regents Of The University Of Colorado Compositions, methods and uses for multiplex protein sequence activity relationship mapping
CA2834375C (en) * 2011-04-27 2020-07-14 Amyris, Inc. Methods for genomic modification
CN102352337B (zh) * 2011-08-03 2014-04-23 中国人民解放军军事医学科学院生物工程研究所 利用异源启动子控制大肠杆菌基因组n-乙酰基转移酶表达重组菌及应用
US9637739B2 (en) 2012-03-20 2017-05-02 Vilnius University RNA-directed DNA cleavage by the Cas9-crRNA complex
ES2728782T3 (es) 2012-05-25 2019-10-28 Univ California Métodos y composiciones para la modificación de ADN objetivo dirigida por ARN y para la modulación de la transcripción dirigida por ARN
UA116639C2 (uk) 2012-10-09 2018-04-25 Рег'Юлес Терап'Ютікс Інк. Способи лікування синдрому альпорта
WO2014093694A1 (en) 2012-12-12 2014-06-19 The Broad Institute, Inc. Crispr-cas nickase systems, methods and compositions for sequence manipulation in eukaryotes
CN105209621B (zh) 2012-12-12 2021-05-25 布罗德研究所有限公司 对用于序列操纵的改进的系统、方法和酶组合物进行的工程化和优化
US8697359B1 (en) 2012-12-12 2014-04-15 The Broad Institute, Inc. CRISPR-Cas systems and methods for altering expression of gene products
KR102955556B1 (ko) 2012-12-12 2026-04-22 더 브로드 인스티튜트, 인코퍼레이티드 서열 조작을 위한 crispr-cas 성분 시스템, 방법 및 조성물
MX380562B (es) 2012-12-12 2025-03-12 Broad Inst Inc Modificaciones de sistemas, métodos y composiciones guía optimizadas para la manipulación de secuencias.
PT2931898E (pt) 2012-12-12 2016-06-16 Harvard College Manipulação e otimização de sistemas, métodos e composições para manipulação de sequências com domínios funcionais
IL308158A (en) 2012-12-17 2023-12-01 Harvard College Rna-guided human genome engineering
CN111218447B (zh) 2013-11-07 2024-10-11 爱迪塔斯医药有限公司 使用统治型gRNA的CRISPR相关方法和组合物
CA2965995A1 (en) 2014-11-05 2016-05-12 Illumina, Inc. Transposase compositions for reduction of insertion bias
AU2016211517B2 (en) 2015-01-28 2021-05-13 Caribou Biosciences, Inc. CRISPR hybrid DNA/RNA polynucleotides and methods of use
CA3149413C (en) 2015-04-10 2025-07-08 Feldan Bio Inc. Polypeptide-based carrier agents to improve the transduction efficiency of polypeptide cargo to cytosol in target eukaryotic cells and their uses, methods, and related kits
US9790490B2 (en) 2015-06-18 2017-10-17 The Broad Institute Inc. CRISPR enzymes and systems
KR102356072B1 (ko) 2015-09-10 2022-01-27 에스케이하이닉스 주식회사 메모리 시스템 및 그 동작 방법
EP3350327B1 (en) 2015-10-23 2018-09-26 Caribou Biosciences, Inc. Engineered crispr class 2 cross-type nucleic-acid targeting nucleic acids
US11151497B2 (en) * 2016-04-27 2021-10-19 Zymergen Inc. Microbial strain design system and methods for improved large-scale production of engineered nucleotide sequences
US9988624B2 (en) * 2015-12-07 2018-06-05 Zymergen Inc. Microbial strain improvement by a HTP genomic engineering platform
JP6821598B2 (ja) * 2015-12-07 2021-01-27 ザイマージェン インコーポレイテッド Corynebacterium glutamicum由来のプロモーター
CA3007840C (en) * 2015-12-07 2020-09-15 Zymergen Inc. Microbial strain improvement by a htp genomic engineering platform
US9896696B2 (en) 2016-02-15 2018-02-20 Benson Hill Biosystems, Inc. Compositions and methods for modifying genomes

Also Published As

Publication number Publication date
EP3485013A1 (en) 2019-05-22
WO2018226880A1 (en) 2018-12-13
EP3485013B1 (en) 2021-03-24
CN110945125A (zh) 2020-03-31
ES2875579T3 (es) 2021-11-10
KR20200026874A (ko) 2020-03-11
US20200370058A1 (en) 2020-11-26
JP2020524490A (ja) 2020-08-20
EP3878961A1 (en) 2021-09-15

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Effective date: 20231206