Fast and efficient CRISPR-mediated genome editing in Aureobasidium pullulans using Cas9 ribonucleoproteins

Aureobasidium pullulans is a ubiquitous, polyextremotolerant, "yeast-like" ascomycete used for the industrial production of pullulan and other products and as biocontrol agent in the agriculture. Its application potential and its wide-spread occurrence make A. pullulans an interesting study object. The availability of a fast and efficient genome editing method is an obvious advantage for future basic and applied research on A. pullulans. In this study, we describe the development of a CRISPR/Cas9-based genome editing method using ribonucleoproteins (RNPs). We demonstrate that this method can be used for single and multiplex genome editing using only RNPs by targeting ura3 (encoding for orotidine-5'-phosphate decarboxylase), praics (encoding for phosphoribosyl aminoimidazole-succinocarboxamide synthase) and asl (encoding for arginine succinate lyase). We demonstrate the applicability of Trichoderma reesei pyr4 and Aspergillus fumigatus pyrG to complement the ura3 deficiency. Further, we show that the usage of RNPs can boost the homologous recombination rate up to nearly 100%, even when using only 20bp long homologous flanks. Therefore, the repair cassettes can be constructed by a single PCR, abolishing the need for laborious and time-consuming cloning. The here presented method allows fast and efficient genome editing for gene deletions, modifications, and insertions in A. pullulans.