The present invention relates to a method for engineering a protein in a host cell, comprising the following steps: identifying a protein of interest and introducing the coding sequence of the protein of interest into the genome of the host cell; screening for hotspots for amino acid mutations in the protein of interest; generating a set of specific guide RNAs and libraries of homologous recombination template that generate mutations at the desired sites within the protein coding region; introducing the guide RNA and the library of homologous recombination template into the host cell, thereby producing mutated protein coding regions; screening to select for cells that express the protein of interest with desired activity and/or property from the mutated protein coding regions, thereby providing an engineered protein.
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