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Seys FM, Humphreys CM, Tomi-Andrino C, Li Q, Millat T, Yang S, Minton NP. Base editing enables duplex point mutagenesis in Clostridium autoethanogenum at the price of numerous off-target mutations. Front Bioeng Biotechnol 2023; 11:1211197. [PMID: 37496853 PMCID: PMC10366002 DOI: 10.3389/fbioe.2023.1211197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/06/2023] [Indexed: 07/28/2023] Open
Abstract
Base editors are recent multiplex gene editing tools derived from the Cas9 nuclease of Streptomyces pyogenes. They can target and modify a single nucleotide in the genome without inducing double-strand breaks (DSB) of the DNA helix. As such, they hold great potential for the engineering of microbes that lack effective DSB repair pathways such as homologous recombination (HR) or non-homologous end-joining (NHEJ). However, few applications of base editors have been reported in prokaryotes to date, and their advantages and drawbacks have not been systematically reported. Here, we used the base editors Target-AID and Target-AID-NG to introduce nonsense mutations into four different coding sequences of the industrially relevant Gram-positive bacterium Clostridium autoethanogenum. While up to two loci could be edited simultaneously using a variety of multiplexing strategies, most colonies exhibited mixed genotypes and most available protospacers led to undesired mutations within the targeted editing window. Additionally, fifteen off-target mutations were detected by sequencing the genome of the resulting strain, among them seven single-nucleotide polymorphisms (SNP) in or near loci bearing some similarity with the targeted protospacers, one 15 nt duplication, and one 12 kb deletion which removed uracil DNA glycosylase (UDG), a key DNA repair enzyme thought to be an obstacle to base editing mutagenesis. A strategy to process prokaryotic single-guide RNA arrays by exploiting tRNA maturation mechanisms is also illustrated.
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Affiliation(s)
- François M. Seys
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Christopher M. Humphreys
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Claudio Tomi-Andrino
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
- Centre for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
- Nottingham BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Qi Li
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Thomas Millat
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Nigel P. Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
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Veillet F, Perrot L, Guyon-Debast A, Kermarrec MP, Chauvin L, Chauvin JE, Gallois JL, Mazier M, Nogué F. Expanding the CRISPR Toolbox in P. patens Using SpCas9-NG Variant and Application for Gene and Base Editing in Solanaceae Crops. Int J Mol Sci 2020; 21:ijms21031024. [PMID: 32033083 PMCID: PMC7036883 DOI: 10.3390/ijms21031024] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/29/2020] [Accepted: 02/01/2020] [Indexed: 11/16/2022] Open
Abstract
Genome editing has become a major tool for both functional studies and plant breeding in several species. Besides generating knockouts through the classical CRISPR-Cas9 system, recent development of CRISPR base editing holds great and exciting opportunities for the production of gain-of-function mutants. The PAM requirement is a strong limitation for CRISPR technologies such as base editing, because the base substitution mainly occurs in a small edition window. As precise single amino-acid substitution can be responsible for functions associated to some domains or agronomic traits, development of Cas9 variants with relaxed PAM recognition is of upmost importance for gene function analysis and plant breeding. Recently, the SpCas9-NG variant that recognizes the NGN PAM has been successfully tested in plants, mainly in monocotyledon species. In this work, we studied the efficiency of SpCas9-NG in the model moss Physcomitrellapatens and two Solanaceae crops (Solanum lycopersicum and Solanum tuberosum) for both classical CRISPR-generated gene knock-out and cytosine base editing. We showed that the SpCas9-NG greatly expands the scope of genome editing by allowing the targeting of non-canonical NGT and NGA PAMs. The CRISPR toolbox developed in our study opens up new gene function analysis and plant breeding perspectives for model and crop plants.
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Affiliation(s)
- Florian Veillet
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, F-29260 Ploudaniel, France; (M.-P.K.); (L.C.); (J.-E.C.)
- Germicopa Breeding, Kerguivarch, 29520 Chateauneuf Du Faou, France
- Correspondence: (F.V.); (F.N.)
| | - Laura Perrot
- INRAE, GAFL, F-84143 Montfavet, France; (L.P.); (J.-L.G.); (M.M.)
| | - Anouchka Guyon-Debast
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France;
| | - Marie-Paule Kermarrec
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, F-29260 Ploudaniel, France; (M.-P.K.); (L.C.); (J.-E.C.)
| | - Laura Chauvin
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, F-29260 Ploudaniel, France; (M.-P.K.); (L.C.); (J.-E.C.)
| | - Jean-Eric Chauvin
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, F-29260 Ploudaniel, France; (M.-P.K.); (L.C.); (J.-E.C.)
| | - Jean-Luc Gallois
- INRAE, GAFL, F-84143 Montfavet, France; (L.P.); (J.-L.G.); (M.M.)
| | - Marianne Mazier
- INRAE, GAFL, F-84143 Montfavet, France; (L.P.); (J.-L.G.); (M.M.)
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France;
- Correspondence: (F.V.); (F.N.)
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