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ReScribe: An Unrestrained Tool Combining Multiplex Recombineering and Minimal-PAM ScCas9 for Genome Recoding Pseudomonas putida

[Image: see text] Genome recoding enables incorporating new functions into the DNA of microorganisms. By reassigning codons to noncanonical amino acids, the generation of new-to-nature proteins offers countless opportunities for bioproduction and biocontainment in industrial chassis. A key bottlenec...

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Autores principales: Asin-Garcia, Enrique, Martin-Pascual, Maria, Garcia-Morales, Luis, van Kranenburg, Richard, Martins dos Santos, Vitor A. P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2021
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8524654/
https://www.ncbi.nlm.nih.gov/pubmed/34547891
http://dx.doi.org/10.1021/acssynbio.1c00297
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author Asin-Garcia, Enrique
Martin-Pascual, Maria
Garcia-Morales, Luis
van Kranenburg, Richard
Martins dos Santos, Vitor A. P.
author_facet Asin-Garcia, Enrique
Martin-Pascual, Maria
Garcia-Morales, Luis
van Kranenburg, Richard
Martins dos Santos, Vitor A. P.
author_sort Asin-Garcia, Enrique
collection PubMed
description [Image: see text] Genome recoding enables incorporating new functions into the DNA of microorganisms. By reassigning codons to noncanonical amino acids, the generation of new-to-nature proteins offers countless opportunities for bioproduction and biocontainment in industrial chassis. A key bottleneck in genome recoding efforts, however, is the low efficiency of recombineering, which hinders large-scale applications at acceptable speed and cost. To relieve this bottleneck, we developed ReScribe, a highly optimized recombineering tool enhanced by CRISPR-Cas9-mediated counterselection built upon the minimal PAM 5′-NNG-3′ of the Streptococcus canis Cas9 (ScCas9). As a proof of concept, we used ReScribe to generate a minimally recoded strain of the industrial chassis Pseudomonas putida by replacing TAG stop codons (functioning as PAMs) of essential metabolic genes with the synonymous TAA. We showed that ReScribe enables nearly 100% engineering efficiency of multiple loci in P. putida, opening promising avenues for genome editing and applications thereof in this bacterium and beyond.
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spelling pubmed-85246542021-10-20 ReScribe: An Unrestrained Tool Combining Multiplex Recombineering and Minimal-PAM ScCas9 for Genome Recoding Pseudomonas putida Asin-Garcia, Enrique Martin-Pascual, Maria Garcia-Morales, Luis van Kranenburg, Richard Martins dos Santos, Vitor A. P. ACS Synth Biol [Image: see text] Genome recoding enables incorporating new functions into the DNA of microorganisms. By reassigning codons to noncanonical amino acids, the generation of new-to-nature proteins offers countless opportunities for bioproduction and biocontainment in industrial chassis. A key bottleneck in genome recoding efforts, however, is the low efficiency of recombineering, which hinders large-scale applications at acceptable speed and cost. To relieve this bottleneck, we developed ReScribe, a highly optimized recombineering tool enhanced by CRISPR-Cas9-mediated counterselection built upon the minimal PAM 5′-NNG-3′ of the Streptococcus canis Cas9 (ScCas9). As a proof of concept, we used ReScribe to generate a minimally recoded strain of the industrial chassis Pseudomonas putida by replacing TAG stop codons (functioning as PAMs) of essential metabolic genes with the synonymous TAA. We showed that ReScribe enables nearly 100% engineering efficiency of multiple loci in P. putida, opening promising avenues for genome editing and applications thereof in this bacterium and beyond. American Chemical Society 2021-09-22 2021-10-15 /pmc/articles/PMC8524654/ /pubmed/34547891 http://dx.doi.org/10.1021/acssynbio.1c00297 Text en © 2021 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by-nc-nd/4.0/Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works (https://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Asin-Garcia, Enrique
Martin-Pascual, Maria
Garcia-Morales, Luis
van Kranenburg, Richard
Martins dos Santos, Vitor A. P.
ReScribe: An Unrestrained Tool Combining Multiplex Recombineering and Minimal-PAM ScCas9 for Genome Recoding Pseudomonas putida
title ReScribe: An Unrestrained Tool Combining Multiplex Recombineering and Minimal-PAM ScCas9 for Genome Recoding Pseudomonas putida
title_full ReScribe: An Unrestrained Tool Combining Multiplex Recombineering and Minimal-PAM ScCas9 for Genome Recoding Pseudomonas putida
title_fullStr ReScribe: An Unrestrained Tool Combining Multiplex Recombineering and Minimal-PAM ScCas9 for Genome Recoding Pseudomonas putida
title_full_unstemmed ReScribe: An Unrestrained Tool Combining Multiplex Recombineering and Minimal-PAM ScCas9 for Genome Recoding Pseudomonas putida
title_short ReScribe: An Unrestrained Tool Combining Multiplex Recombineering and Minimal-PAM ScCas9 for Genome Recoding Pseudomonas putida
title_sort rescribe: an unrestrained tool combining multiplex recombineering and minimal-pam sccas9 for genome recoding pseudomonas putida
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8524654/
https://www.ncbi.nlm.nih.gov/pubmed/34547891
http://dx.doi.org/10.1021/acssynbio.1c00297
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