JP2020524490A - Escherichia Coliを改良するためのHTPゲノム操作プラットフォーム - Google Patents

Escherichia Coliを改良するためのHTPゲノム操作プラットフォーム Download PDF

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JP2020524490A
JP2020524490A JP2019567283A JP2019567283A JP2020524490A JP 2020524490 A JP2020524490 A JP 2020524490A JP 2019567283 A JP2019567283 A JP 2019567283A JP 2019567283 A JP2019567283 A JP 2019567283A JP 2020524490 A JP2020524490 A JP 2020524490A
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coli
gene
library
coli strain
strain
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JP2020524490A5 (enExample
Inventor
マシュー デイビス,
マシュー デイビス,
クリスティー ウィスニュースキー,
クリスティー ウィスニュースキー,
パトリック ウエストフォール,
パトリック ウエストフォール,
ザック サーバー,
ザック サーバー,
エリック ジェデディア ディーン,
エリック ジェデディア ディーン,
ショーン マンチェスター,
ショーン マンチェスター,
キャサリン ゴラ,
キャサリン ゴラ,
エリン シェルマン,
エリン シェルマン,
アーロン キンボール,
アーロン キンボール,
ショーン シィジカ,
ショーン シィジカ,
バーバラ フレウェン,
バーバラ フレウェン,
トーマス トレイナー,
トーマス トレイナー,
マイケル フラッシュマン,
マイケル フラッシュマン,
ロバート ハウシャルター,
ロバート ハウシャルター,
ステイシー−アン モーガン,
ステイシー−アン モーガン,
マイケル ブレイズ,
マイケル ブレイズ,
プラバ ラマクリシュナン,
プラバ ラマクリシュナン,
カイル ロスチャイルド−マンチネッリ,
カイル ロスチャイルド−マンチネッリ,
ヨンニュン キム,
ヨンニュン キム,
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Zymergen Inc
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Zymergen Inc
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Publication of JP2020524490A5 publication Critical patent/JP2020524490A5/ja
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    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/10Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034Isolating an individual clone by screening libraries
    • C12N15/1058Directional evolution of libraries, e.g. evolution of libraries is achieved by mutagenesis and screening or selection of mixed population of organisms
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/10Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034Isolating an individual clone by screening libraries
    • C12N15/1079Screening libraries by altering the phenotype or phenotypic trait of the host
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/63Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/70Vectors or expression systems specially adapted for E. coli
    • C12N15/73Expression 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)
JP2019567283A 2017-06-06 2018-06-06 Escherichia Coliを改良するためのHTPゲノム操作プラットフォーム Pending JP2020524490A (ja)

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

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JP2020524490A true JP2020524490A (ja) 2020-08-20
JP2020524490A5 JP2020524490A5 (enExample) 2021-07-26

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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)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
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

Families Citing this family (25)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP7328695B2 (ja) * 2017-11-22 2023-08-17 国立大学法人神戸大学 安定で副作用の少ないゲノム編集用複合体及びそれをコードする核酸
MX2021005028A (es) 2018-10-31 2021-08-24 Zymergen Inc Ensamble determinista multiplexado de genotecas de adn.
KR20210136997A (ko) 2019-03-08 2021-11-17 지머젠 인코포레이티드 미생물에서 반복적 게놈 편집
US11053515B2 (en) 2019-03-08 2021-07-06 Zymergen Inc. Pooled 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
EP3987031A4 (en) * 2019-06-21 2023-06-07 Glycom A/S NUCLEIC ACID CONSTRUCT WITH 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
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
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
CN115820703A (zh) * 2022-12-20 2023-03-21 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
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
US824A (en) 1838-07-09 Construction of steam-engines
US72197A (en) 1867-12-17 Jesse h
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
US6117679A (en) * 1994-02-17 2000-09-12 Maxygen, Inc. Methods for generating polynucleotides having desired characteristics by iterative selection and recombination
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
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
AU743305C (en) * 1997-01-17 2006-03-30 Maxygen, Inc. 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
WO1998044151A1 (en) 1997-04-01 1998-10-08 Glaxo Group Limited Method of nucleic acid amplification
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
US6205404B1 (en) 1998-02-20 2001-03-20 George S. Michaels 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
CA2431308C (en) 2000-12-07 2010-04-13 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
MX2008015213A (es) 2006-05-30 2008-12-09 Dow Global Technologies Inc Metodo de optimizacion de codon.
CN101177454B (zh) * 2007-05-09 2010-09-22 郑骏年 Il-18突变体多肽及制备及用途
US8765403B2 (en) 2008-02-28 2014-07-01 The Regents Of The University Of California Use of synthetic scaffolds for the production of biosynthetic pathway products
AU2009266989B2 (en) * 2008-07-03 2013-05-02 Pfenex, Inc. High throughput screening method and use thereof to identify a production platform for a multifunctional binding protein
US8808986B2 (en) 2008-08-27 2014-08-19 Gen9, Inc. 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
WO2010094772A1 (en) 2009-02-20 2010-08-26 Febit Holding Gmbh 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
US20150368639A1 (en) * 2011-04-14 2015-12-24 Ryan T. Gill Compositions, methods and uses for multiplex protein sequence activity relationship mapping
PT2702160T (pt) * 2011-04-27 2020-07-30 Amyris Inc Métodos para modificação genómica
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
MY189533A (en) 2012-05-25 2022-02-16 Univ California Methods and compositions for rna-directed target dna modification and for rna-directed modulation of transcription
UA116639C2 (uk) 2012-10-09 2018-04-25 Рег'Юлес Терап'Ютікс Інк. Способи лікування синдрому альпорта
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
CN119752887A (zh) 2012-12-12 2025-04-04 布罗德研究所有限公司 用于序列操纵的系统、方法和优化的指导组合物的工程化
CA2894668A1 (en) 2012-12-12 2014-06-19 The Broad Institute, Inc. Crispr-cas systems and methods for altering expression of gene products in eukaryotic cells
EP2931898B1 (en) 2012-12-12 2016-03-09 The Broad Institute, Inc. Engineering and optimization of systems, methods and compositions for sequence manipulation with functional domains
US8697359B1 (en) 2012-12-12 2014-04-15 The Broad Institute, Inc. CRISPR-Cas systems and methods for altering expression of gene products
WO2014093694A1 (en) 2012-12-12 2014-06-19 The Broad Institute, Inc. Crispr-cas nickase systems, methods and compositions for sequence manipulation in eukaryotes
EP4481048A3 (en) 2012-12-17 2025-02-26 President and Fellows of Harvard College Rna-guided human genome engineering
PT3066201T (pt) 2013-11-07 2018-06-04 Massachusetts Inst Technology Métodos e composições relacionadas com crispr com arng reguladores
SG11201703472YA (en) 2014-11-05 2017-05-30 Illumina Inc Transposase compositions for reduction of insertion bias
KR102319192B1 (ko) 2015-01-28 2021-10-28 카리부 바이오사이언시스 인코포레이티드 Crispr 하이브리드 dna/rna 폴리뉴클레오티드 및 사용 방법
KR102697262B1 (ko) 2015-04-10 2024-08-20 펠단 바이오 인코포레이티드 표적 진핵세포의 세포질로의 폴리펩타이드 카고의 형질 도입 효과를 향상시키기 위한 폴리펩타이드계 셔틀제, 이의 용도, 방법 및 이에 관련된 키트
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
DK3350327T3 (en) 2015-10-23 2019-01-21 Caribou Biosciences Inc CONSTRUCTED CRISPR CLASS-2-NUCLEIC ACID TARGETING-NUCLEIC ACID
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
EP3858996B1 (en) * 2015-12-07 2022-08-03 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

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
BIOCHEMISTRY, 2003, VOL.42, PP.3798-3811, JPN6022021600, ISSN: 0004949462 *
GENE, 1991, VOL.97, PP.7-12, JPN6022021606, ISSN: 0004949460 *
THE EMBO JOURNAL, 1988, VOL.7, NO.9, PP.2919-2923, JPN6022021605, ISSN: 0004949461 *

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
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
JPWO2022124302A1 (enExample) * 2020-12-08 2022-06-16

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

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