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

Info

Publication number
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
Authority
JP
Japan
Prior art keywords
coli
gene
library
coli strain
strain
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.)
Pending
Application number
JP2019567283A
Other languages
English (en)
Japanese (ja)
Other versions
JP2020524490A5 (https=
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，
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 JP2020524490A publication Critical patent/JP2020524490A/ja
Publication of JP2020524490A5 publication Critical patent/JP2020524490A5/ja
Pending legal-status Critical Current

Links

Classifications

    • 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

Landscapes

  • 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

Publications (2)

Publication Number Publication Date
JP2020524490A true JP2020524490A (ja) 2020-08-20
JP2020524490A5 JP2020524490A5 (https=) 2021-07-26

Family

ID=62751581

Family Applications (1)

Application Number Title Priority Date Filing Date
JP2019567283A Pending JP2020524490A (ja) 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

Country Status (8)

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

Cited By (1)

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

Families Citing this family (25)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN111615557B (zh) * 2017-11-22 2025-04-18 国立大学法人神户大学 稳定且副作用少的基因组编辑用复合物和编码该复合物的核酸
SG11202104409YA (en) 2018-10-31 2021-05-28 Zymergen Inc Multiplexed deterministic assembly of dna libraries
CN113728106A (zh) * 2019-03-08 2021-11-30 齐默尔根公司 微生物中的迭代基因组编辑
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
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
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
KR20250069469A (ko) * 2023-11-10 2025-05-19 한국과학기술원 TdT(Terminal deoxynucleotidyl transferase) 및 dNTP를 이용한 비번역영역 (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
KR100570935B1 (ko) * 1997-01-17 2006-04-13 맥시겐, 인크. 반복적 서열 재조합에 의한 전세포 및 유기체의 개량 방법
US6326204B1 (en) * 1997-01-17 2001-12-04 Maxygen, Inc. Evolution of whole cells and organisms by recursive sequence recombination
JP2002503954A (ja) 1997-04-01 2002-02-05 グラクソ、グループ、リミテッド 核酸増幅法
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
KR20010041088A (ko) 1998-02-20 2001-05-15 게놈 다이내믹스 인코포레이티드 아연-핑거 클래스의 ｄｎａ-결합 단백질의 디자인 방법
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
AU2002228841C1 (en) 2000-12-07 2006-11-23 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
EP2021489A2 (en) 2006-05-30 2009-02-11 Dow Global Technologies Inc. Codon optimization method
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
CA2729839A1 (en) * 2008-07-03 2010-01-07 Diane Retallack 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
PL2657250T3 (pl) * 2010-12-21 2018-02-28 Cj Cheiljedang Corporation Odmiana polipeptydu posiadającego aktywność acetylotransferazy homoseryny oraz mikroorganizm wyrażający to samo
US20150368639A1 (en) * 2011-04-14 2015-12-24 Ryan T. Gill Compositions, methods and uses for multiplex protein sequence activity relationship mapping
AU2012249390B2 (en) * 2011-04-27 2017-03-30 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
AU2013266968B2 (en) 2012-05-25 2017-06-29 Emmanuelle CHARPENTIER 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
CN113355357B (zh) 2012-12-12 2024-12-03 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
EP2840140B2 (en) 2012-12-12 2023-02-22 The Broad Institute, Inc. Crispr-Cas based method for mutation of prokaryotic cells
US8697359B1 (en) 2012-12-12 2014-04-15 The Broad Institute, Inc. CRISPR-Cas systems and methods for altering expression of gene products
US20140310830A1 (en) 2012-12-12 2014-10-16 Feng Zhang CRISPR-Cas Nickase Systems, Methods And Compositions For Sequence Manipulation in Eukaryotes
IL239344B2 (en) 2012-12-12 2024-06-01 Broad Inst Inc Systems engineering, methods and optimal guiding components for sequence manipulation
WO2014093655A2 (en) 2012-12-12 2014-06-19 The Broad Institute, Inc. Engineering and optimization of systems, methods and compositions for sequence manipulation with functional domains
DK2931891T3 (da) 2012-12-17 2019-08-19 Harvard College Rna-styret modificering af menneskelige genomer
CN106459995B (zh) 2013-11-07 2020-02-21 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
US10815478B2 (en) 2014-11-05 2020-10-27 Illumina, Inc. Method of sequential tagmentation with transposase compositions for reduction of insertion bias
US9650617B2 (en) 2015-01-28 2017-05-16 Pioneer Hi-Bred International. Inc. CRISPR hybrid DNA/RNA polynucleotides and methods of use
CA2981716C (en) 2015-04-10 2022-04-12 Feldan Bio Inc. Polypeptide-based shuttle agents for improving the transduction efficiency of polypeptide cargos to the cytosol of target eukaryotic cells, uses thereof, methods and kits relating to same
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
WO2017070598A1 (en) 2015-10-23 2017-04-27 Caribou Biosciences, Inc. Engineered crispr class 2 cross-type nucleic-acid targeting nucleic acids
BR112018011503A2 (pt) * 2015-12-07 2018-12-04 Zymergen Inc promotores da corynebacterium glutamicum
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
KR20190090081A (ko) * 2015-12-07 2019-07-31 지머젠 인코포레이티드 Htp 게놈 공학 플랫폼에 의한 미생물 균주 개량
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
JPWO2022124302A1 (https=) * 2020-12-08 2022-06-16
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

Also Published As

Publication number Publication date
CA3064612A1 (en) 2018-12-13
CN110945125A (zh) 2020-03-31
ES2875579T3 (es) 2021-11-10
EP3485013B1 (en) 2021-03-24
EP3485013A1 (en) 2019-05-22
US20200370058A1 (en) 2020-11-26
EP3878961A1 (en) 2021-09-15
WO2018226880A1 (en) 2018-12-13
KR20200026874A (ko) 2020-03-11

Similar Documents

Publication Publication Date Title
EP3485013B1 (en) A htp genomic engineering platform for improving escherichia coli
US11352621B2 (en) HTP genomic engineering platform
JP6715374B2 (ja) Ｈｔｐゲノム操作プラットフォームによる微生物株の改良
US11208649B2 (en) HTP genomic engineering platform
US20200102554A1 (en) High throughput transposon mutagenesis
HK40017912A (en) A htp genomic engineering platform for improving escherichia coli
HK1262289B (en) Microbial strain improvement by a htp genomic engineering platform

Legal Events

Date Code Title Description
A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20210524

A621 Written request for application examination

Free format text: JAPANESE INTERMEDIATE CODE: A621

Effective date: 20210524

A131 Notification of reasons for refusal

Free format text: JAPANESE INTERMEDIATE CODE: A131

Effective date: 20220531

A02 Decision of refusal

Free format text: JAPANESE INTERMEDIATE CODE: A02

Effective date: 20221221