4.7 Article

Efficient CRISPR/Cas12a-Based Genome-Editing Toolbox for Metabolic Engineering in Methanococcus maripaludis

Journal

ACS SYNTHETIC BIOLOGY
Volume 11, Issue 7, Pages 2496-2503

Publisher

AMER CHEMICAL SOC
DOI: 10.1021/acssynbio.2c001372496

Keywords

Methanococcus maripaludis; methanogens; CRISPR/Cas12a; genome editing; metabolic engineering; synthetic biology

Funding

  1. Novo Nordisk Foundation [NNF19OC0054329, 326020]
  2. Academy of Finland
  3. Academy of Finland (AKA) [326020, 326020] Funding Source: Academy of Finland (AKA)

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This study developed a genome-editing toolbox using LbCas12a and the endogenous homology-directed repair machinery in M. maripaludis, enabling reliable and efficient genome editing in methanogens. The toolbox demonstrated successful deletion and replacement of target genes, and was applicable for metabolic engineering and flux balancing studies. This CRISPR/LbCas12a toolbox provides a reliable and quick method for genome editing in methanogens.
The rapid-growing and genetically tractable methanogen Methanococcus maripaludis is a promising host organism for the biotechnological conversion of carbon dioxide and renewable hydrogen to fuels and value-added products. Expansion of its product scope through metabolic engineering necessitates reliable and efficient genetic tools, particularly for genome edits that affect the primary metabolism and cell growth. Here, we have designed a genome-editing toolbox by utilizing Cas12a from Lachnospiraceae bacterium ND2006 (LbCas12a) in combination with the homology-directed repair machinery endogenously present in M. maripaludis. This toolbox can delete target genes with a success rate of up to 95%, despite the hyperpolyploidy of M. maripaludis. For the purpose of demonstrating a large deletion, the M. maripaludis flagellum operon (similar to 8.9 kbp) was replaced by the Escherichia coli beta-glucuronidase gene. To facilitate metabolic engineering and flux balancing in M. maripaludis, the relative strength of 15 different promoters was quantified in the presence of two common growth substrates, either formate or carbon dioxide and hydrogen. This CRISPR/LbCas12a toolbox can be regarded as a reliable and quick method for genome editing in a methanogen.

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