CN114929873A - 使用靶向核酸酶调节微生物群的组成 - Google Patents

使用靶向核酸酶调节微生物群的组成 Download PDF

Info

Publication number
CN114929873A
CN114929873A CN202080083063.1A CN202080083063A CN114929873A CN 114929873 A CN114929873 A CN 114929873A CN 202080083063 A CN202080083063 A CN 202080083063A CN 114929873 A CN114929873 A CN 114929873A
Authority
CN
China
Prior art keywords
bacteroides
crispr
nucleic acid
nuclease
species
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
CN202080083063.1A
Other languages
English (en)
Chinese (zh)
Inventor
E·伊斯特伦德
Z·张
G·D·戴维斯
Z·W·贝勒
J·I·戈登
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.)
University of Washington
Sigma Aldrich Co LLC
Original Assignee
University of Washington
Sigma Aldrich Co LLC
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 University of Washington, Sigma Aldrich Co LLC filed Critical University of Washington
Publication of CN114929873A publication Critical patent/CN114929873A/zh
Pending legal-status Critical Current

Links

Images

Classifications

    • 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
    • C12N15/74Vectors or expression systems specially adapted for prokaryotic hosts other than E. coli, e.g. Lactobacillus, Micromonospora
    • 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
    • C12N15/11DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00Medicinal preparations containing organic active ingredients
    • A61K31/65Tetracyclines
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00Medicinal preparations containing organic active ingredients
    • A61K31/70Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088Compounds having three or more nucleosides or nucleotides
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00Medicinal preparations containing peptides
    • A61K38/16Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/43Enzymes; Proenzymes; Derivatives thereof
    • A61K38/46Hydrolases (3)
    • A61K38/465Hydrolases (3) acting on ester bonds (3.1), e.g. lipases, ribonucleases
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61PSPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/04Antibacterial agents
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61PSPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00Antineoplastic agents
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61PSPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00Drugs for immunological or allergic disorders
    • A61P37/02Immunomodulators
    • 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
    • C12N15/102Mutagenizing nucleic acids
    • 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
    • C12N15/11DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • 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
    • C12N15/87Introduction of foreign genetic material using processes not otherwise provided for, e.g. co-transformation
    • C12N15/90Stable introduction of foreign DNA into chromosome
    • C12N15/902Stable introduction of foreign DNA into chromosome using homologous recombination
    • 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
    • C12N15/87Introduction of foreign genetic material using processes not otherwise provided for, e.g. co-transformation
    • C12N15/90Stable introduction of foreign DNA into chromosome
    • C12N15/902Stable introduction of foreign DNA into chromosome using homologous recombination
    • C12N15/907Stable introduction of foreign DNA into chromosome using homologous recombination in mammalian cells
    • 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
    • C12N9/00Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14Hydrolases (3)
    • C12N9/16Hydrolases (3) acting on ester bonds (3.1)
    • C12N9/22Ribonucleases [RNase]; Deoxyribonucleases [DNase]
    • 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
    • C12N2310/00Structure or type of the nucleic acid
    • C12N2310/10Type of nucleic acid
    • C12N2310/20Type of nucleic acid involving clustered regularly interspaced short palindromic repeats [CRISPR]
    • 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
    • C12N2800/00Nucleic acids vectors
    • C12N2800/10Plasmid DNA
    • C12N2800/101Plasmid DNA for bacteria
    • 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
    • C12N2800/00Nucleic acids vectors
    • C12N2800/80Vectors containing sites for inducing double-stranded breaks, e.g. meganuclease restriction sites
    • 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
    • C12N2840/00Vectors comprising a special translation-regulating system
    • C12N2840/002Vectors comprising a special translation-regulating system controllable or inducible

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biomedical Technology (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Medicinal Chemistry (AREA)
  • Biophysics (AREA)
  • Plant Pathology (AREA)
  • Physics & Mathematics (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Veterinary Medicine (AREA)
  • Public Health (AREA)
  • Animal Behavior & Ethology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • General Chemical & Material Sciences (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Epidemiology (AREA)
  • Immunology (AREA)
  • Mycology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Oncology (AREA)
  • Communicable Diseases (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Gastroenterology & Hepatology (AREA)
  • Cell Biology (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Enzymes And Modification Thereof (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)
CN202080083063.1A 2019-09-30 2020-09-29 使用靶向核酸酶调节微生物群的组成 Pending CN114929873A (zh)

Applications Claiming Priority (7)

Application Number Priority Date Filing Date Title
US201962908130P 2019-09-30 2019-09-30
US62/908130 2019-09-30
US201962909078P 2019-10-01 2019-10-01
US62/909078 2019-10-01
US202063052825P 2020-07-16 2020-07-16
US63/052825 2020-07-16
PCT/US2020/053304 WO2021067291A1 (en) 2019-09-30 2020-09-29 Modulation of microbiota compositions using targeted nucleases

Publications (1)

Publication Number Publication Date
CN114929873A true CN114929873A (zh) 2022-08-19

Family

ID=72896108

Family Applications (1)

Application Number Title Priority Date Filing Date
CN202080083063.1A Pending CN114929873A (zh) 2019-09-30 2020-09-29 使用靶向核酸酶调节微生物群的组成

Country Status (10)

Country Link
US (1) US20210095273A1 (https=)
EP (1) EP4038185A1 (https=)
JP (2) JP2022549519A (https=)
KR (1) KR20220051259A (https=)
CN (1) CN114929873A (https=)
AU (1) AU2020357816A1 (https=)
BR (1) BR112022005831A2 (https=)
CA (1) CA3152931A1 (https=)
IL (1) IL291509A (https=)
WO (1) WO2021067291A1 (https=)

Families Citing this family (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2021127209A1 (en) * 2019-12-17 2021-06-24 Sigma-Aldrich Co. Llc Genome editing in bacteroides
CN116004688A (zh) * 2021-10-21 2023-04-25 中国科学院深圳先进技术研究院 肠道菌拟杆菌的基因编辑方法与应用
US20250034579A1 (en) * 2021-12-07 2025-01-30 Cornell University Methods and compositions for genetically modifying human gut microbes
KR20240172712A (ko) * 2023-05-31 2024-12-10 한국생명공학연구원 아커만시아 뮤시니필라 tars를 발현 및 분비하도록 설계된 프로바이오틱스 및 이의 제조를 위한 벡터

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN104854241A (zh) * 2012-05-25 2015-08-19 埃玛纽埃尔·沙尔庞捷 用于rna定向的靶dna修饰和用于rna定向的转录调节的方法和组合物
US20170240908A1 (en) * 2014-09-26 2017-08-24 Yale University Compositions and methods for biocontainment of microorganisms
US20180163216A1 (en) * 2015-06-10 2018-06-14 Massachusetts Institute Of Technology Gene expression in bacteroides

Family Cites Families (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU2002306849A1 (en) * 2001-03-21 2002-10-08 Elitra Pharmaceuticals, Inc. Identification of essential genes in microorganisms
JP5070051B2 (ja) * 2004-06-07 2012-11-07 クー バイオロジックス インク. 癌を治療するための細菌組成物
CA2682242A1 (en) * 2007-03-28 2008-10-02 Alimentary Health Limited Probiotic bifidobacterium longum strain
US20110281762A1 (en) * 2010-05-13 2011-11-17 Sonnenburg Justin L High throughput screening for anaerobic microorganisms
WO2015006294A2 (en) * 2013-07-10 2015-01-15 President And Fellows Of Harvard College Orthogonal cas9 proteins for rna-guided gene regulation and editing
WO2015148680A1 (en) * 2014-03-25 2015-10-01 Ginkgo Bioworks, Inc. Methods and genetic systems for cell engineering
CN107667173A (zh) * 2015-05-06 2018-02-06 斯尼普技术有限公司 改变微生物种群和改善微生物群
JP6886142B2 (ja) * 2017-01-04 2021-06-16 国立大学法人 新潟大学 腸内細菌叢改善剤及びその使用

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN104854241A (zh) * 2012-05-25 2015-08-19 埃玛纽埃尔·沙尔庞捷 用于rna定向的靶dna修饰和用于rna定向的转录调节的方法和组合物
US20170240908A1 (en) * 2014-09-26 2017-08-24 Yale University Compositions and methods for biocontainment of microorganisms
US20180163216A1 (en) * 2015-06-10 2018-06-14 Massachusetts Institute Of Technology Gene expression in bacteroides

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
MARK MIMEE ET AL.: "Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota", CELL SYST ., vol. 29, no. 1, 29 July 2015 (2015-07-29), pages 66 *
MEHRDAD TAJKARIMI ET AL.: "CRISPR-Cas Systems in Bacteroides fragilis, an Important Pathobiont in the Human Gut Microbiome", FRONT MICROBIOL ., vol. 8, 23 November 2017 (2017-11-23), pages 1 - 21 *

Also Published As

Publication number Publication date
BR112022005831A2 (pt) 2022-06-21
WO2021067291A1 (en) 2021-04-08
US20210095273A1 (en) 2021-04-01
CA3152931A1 (en) 2021-04-08
EP4038185A1 (en) 2022-08-10
KR20220051259A (ko) 2022-04-26
JP2022549519A (ja) 2022-11-25
AU2020357816A1 (en) 2022-04-14
IL291509A (en) 2022-05-01
JP2024116193A (ja) 2024-08-27

Similar Documents

Publication Publication Date Title
JP2021000092A (ja) 細胞工学のための方法および遺伝システム
CN107208070B (zh) 细菌基因的靶向消除
CN114929873A (zh) 使用靶向核酸酶调节微生物群的组成
EP4074330A1 (en) Tuning microbial populations with programmable nucleases
US20250354158A1 (en) Cis conjugative plasmid system
US20230287439A1 (en) Pathway integration and expression in host cells
US11591604B2 (en) Gene expression in Bacteroides
JP2021531039A (ja) 細菌接合システム及びその治療的使用
JP2024125308A (ja) バクテロイデスにおけるゲノム編集
US20230348877A1 (en) Base editing enzymes
JP2021509582A (ja) ブドウ球菌(Staphylococcus)属細菌の栄養要求株
Álvarez-Martín et al. Improved cloning vectors for bifidobacteria, based on the Bifidobacterium catenulatum pBC1 replicon
US20100003738A1 (en) Plasmid curing
Rodriguez et al. Targeted gene disruption in Francisella tularensis by group II introns
US20210071179A1 (en) Mobile-crispri plasmids and related methods
US20210093679A1 (en) Engineered gut microbes and uses thereof
Dangi Submitted to the
Shi et al. Engineering and characterization of a symbiotic selection-marker-free vector-host system for therapeutic plasmid production
JP2021524230A (ja) アッカーマンシア種の遺伝子操作のためのシステムおよび方法
CN1989255A (zh) 降低细胞中的自发突变率
WO2024096123A1 (ja) 遺伝子が改変された微生物およびその生産方法
Yang et al. Genomic integration and expression of the Aggregatibacter actinomycetemcomitans catalase gene in Aggregatibacter aphrophilus
Borah et al. Cloning and Expression of Arginase in E. coli
WO2025254183A1 (ja) CRISPR-Casベクター系、組成物、キット、標的DNAが修飾された原核生物の製造方法、および原核生物
Song et al. Establishment of a CRISPR interference (CRISPRi) system in Limosilactobacillus reuteri AR673

Legal Events

Date Code Title Description
PB01 Publication
PB01 Publication
SE01 Entry into force of request for substantive examination
SE01 Entry into force of request for substantive examination
WD01 Invention patent application deemed withdrawn after publication

Application publication date: 20220819

WD01 Invention patent application deemed withdrawn after publication