WO2018083128A3 - Microbial genome editing - Google Patents

Microbial genome editing Download PDF

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Publication number
WO2018083128A3
WO2018083128A3 PCT/EP2017/077975 EP2017077975W WO2018083128A3 WO 2018083128 A3 WO2018083128 A3 WO 2018083128A3 EP 2017077975 W EP2017077975 W EP 2017077975W WO 2018083128 A3 WO2018083128 A3 WO 2018083128A3
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WO
WIPO (PCT)
Prior art keywords
microbes
cas9 site
counter
nuclease activity
directed nuclease
Prior art date
Application number
PCT/EP2017/077975
Other languages
French (fr)
Other versions
WO2018083128A2 (en
Inventor
John Van Der Oost
Richard Van Kranenburg
Elleke Fenna BOSMA
Ioannis MOUGIAKOS
Original Assignee
Wageningen Universiteit
Stichting Voor De Technische Wetenschappen
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 Wageningen Universiteit, Stichting Voor De Technische Wetenschappen filed Critical Wageningen Universiteit
Publication of WO2018083128A2 publication Critical patent/WO2018083128A2/en
Publication of WO2018083128A3 publication Critical patent/WO2018083128A3/en

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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
    • C12N15/102—Mutagenizing nucleic acids
    • 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
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-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
    • 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
    • C12N15/87—Introduction of foreign genetic material using processes not otherwise provided for, e.g. co-transformation
    • C12N15/90—Stable introduction of foreign DNA into chromosome
    • C12N15/902—Stable introduction of foreign DNA into chromosome using homologous recombination
    • 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
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/20—Type of nucleic acid involving clustered regularly interspaced short palindromic repeats [CRISPRs]

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  • Genetics & Genomics (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Biomedical Technology (AREA)
  • Chemical & Material Sciences (AREA)
  • Wood Science & Technology (AREA)
  • Organic Chemistry (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • Plant Pathology (AREA)
  • Biophysics (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Mycology (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Enzymes And Modification Thereof (AREA)

Abstract

In an absence of efficient non-homologous end joining (NHEJ) repair mechanisms in the majority of microbes, double stranded DNA break (DSDB) typically leads to cell death. In methods of microbial gene editing using plasmid transformation, both homologous recombination and Cas9 site-specific gene editing events can be used together. Single or multiple plasmid approaches are used. In a method of counter-selection of microbes for a desired genetic change, a two-phase approach is used whereby a switch is made from a higher growth temperature phase favouring homologous recombination (HR) - as opposed to a Cas9 site-directed nuclease activity- to a lower growth temperature phase at which the Cas9 site directed nuclease activity takes place. This has the effect whereby the Cas9 site-directed nuclease activity has counter selecting activity, removing microbes which do not have a desired modification introduced beforehand by HR. The population of microbes surviving after the temperature switch counter selection is thereby enhanced for the desired modification.
PCT/EP2017/077975 2016-11-02 2017-11-01 Microbial genome editing WO2018083128A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
GB1618507.6 2016-11-02
GBGB1618507.6A GB201618507D0 (en) 2016-11-02 2016-11-02 Microbial genome editing

Publications (2)

Publication Number Publication Date
WO2018083128A2 WO2018083128A2 (en) 2018-05-11
WO2018083128A3 true WO2018083128A3 (en) 2019-02-14

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/EP2017/077975 WO2018083128A2 (en) 2016-11-02 2017-11-01 Microbial genome editing

Country Status (2)

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GB (1) GB201618507D0 (en)
WO (1) WO2018083128A2 (en)

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US9737604B2 (en) 2013-09-06 2017-08-22 President And Fellows Of Harvard College Use of cationic lipids to deliver CAS9
US9228207B2 (en) 2013-09-06 2016-01-05 President And Fellows Of Harvard College Switchable gRNAs comprising aptamers
US9322037B2 (en) 2013-09-06 2016-04-26 President And Fellows Of Harvard College Cas9-FokI fusion proteins and uses thereof
US20150166982A1 (en) 2013-12-12 2015-06-18 President And Fellows Of Harvard College Methods for correcting pi3k point mutations
US10077453B2 (en) 2014-07-30 2018-09-18 President And Fellows Of Harvard College CAS9 proteins including ligand-dependent inteins
IL294014B1 (en) 2015-10-23 2024-03-01 Harvard College Nucleobase editors and uses thereof
AU2017306676B2 (en) 2016-08-03 2024-02-22 President And Fellows Of Harvard College Adenosine nucleobase editors and uses thereof
CA3033327A1 (en) 2016-08-09 2018-02-15 President And Fellows Of Harvard College Programmable cas9-recombinase fusion proteins and uses thereof
WO2018039438A1 (en) 2016-08-24 2018-03-01 President And Fellows Of Harvard College Incorporation of unnatural amino acids into proteins using base editing
CN110214180A (en) 2016-10-14 2019-09-06 哈佛大学的校长及成员们 The AAV of nucleobase editing machine is delivered
WO2018119359A1 (en) 2016-12-23 2018-06-28 President And Fellows Of Harvard College Editing of ccr5 receptor gene to protect against hiv infection
US11898179B2 (en) 2017-03-09 2024-02-13 President And Fellows Of Harvard College Suppression of pain by gene editing
JP2020510439A (en) 2017-03-10 2020-04-09 プレジデント アンド フェローズ オブ ハーバード カレッジ Base-editing factor from cytosine to guanine
KR20190130613A (en) 2017-03-23 2019-11-22 프레지던트 앤드 펠로우즈 오브 하바드 칼리지 Nucleobase edits comprising nucleic acid programmable DNA binding proteins
WO2018209320A1 (en) 2017-05-12 2018-11-15 President And Fellows Of Harvard College Aptazyme-embedded guide rnas for use with crispr-cas9 in genome editing and transcriptional activation
WO2019023680A1 (en) 2017-07-28 2019-01-31 President And Fellows Of Harvard College Methods and compositions for evolving base editors using phage-assisted continuous evolution (pace)
US11319532B2 (en) 2017-08-30 2022-05-03 President And Fellows Of Harvard College High efficiency base editors comprising Gam
US11795443B2 (en) 2017-10-16 2023-10-24 The Broad Institute, Inc. Uses of adenosine base editors
CN109337904B (en) * 2018-11-02 2020-12-25 中国科学院动物研究所 Genome editing system and method based on C2C1 nuclease
WO2020185584A1 (en) * 2019-03-08 2020-09-17 Zymergen Inc. Pooled genome editing in microbes
EP3942040A1 (en) 2019-03-19 2022-01-26 The Broad Institute, Inc. Methods and compositions for editing nucleotide sequences
WO2021032180A1 (en) * 2019-08-21 2021-02-25 江南大学 Visualized screening method for multiple-targeted editing of recombinant aspergillus strains
CN115279898A (en) * 2019-10-23 2022-11-01 成对植物服务股份有限公司 Compositions and methods for RNA templated editing in plants
CN111235130B (en) * 2019-11-15 2022-11-25 武汉大学 II-type V-type CRISPR protein CeCas12a and application thereof in gene editing
MX2022014008A (en) 2020-05-08 2023-02-09 Broad Inst Inc Methods and compositions for simultaneous editing of both strands of a target double-stranded nucleotide sequence.
GB202015944D0 (en) 2020-10-08 2020-11-25 Univ Wageningen Universal riboswitch for inducible gene expression
US20240200059A1 (en) 2021-04-09 2024-06-20 Vor Biopharma Inc. Photocleavable guide rnas and methods of use thereof
CN113403294B (en) * 2021-06-04 2023-08-08 广州大学 Fusion protein, base editing tool and application thereof
WO2023283585A2 (en) 2021-07-06 2023-01-12 Vor Biopharma Inc. Inhibitor oligonucleotides and methods of use thereof
CA3228272A1 (en) 2021-08-02 2023-02-09 Vor Biopharma Inc. Compositions and methods for gene modification
WO2023049926A2 (en) 2021-09-27 2023-03-30 Vor Biopharma Inc. Fusion polypeptides for genetic editing and methods of use thereof
WO2023102393A1 (en) * 2021-11-30 2023-06-08 Pioneer Hi-Bred International, Inc. High efficiency large scale chromosomal genome manipulation
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WO2018083128A2 (en) 2018-05-11
GB201618507D0 (en) 2016-12-14

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