Simple Growth Conditions Improve Targeted Gene Deletion in Cryptococcus neoformans

Cryptococcus neoformans infections are a significant cause of morbidity and mortality among AIDS patients and the third most common invasive fungal infection in organ transplant recipients. The cryptococcal cell wall is very dynamic and can be modulated depending on growth conditions. It was reported that when C. neoformans is grown in unbuffered yeast nitrogen base (YNB) for 48 hours, the pH of the media drastically drops and the cells start to shed their cell walls. With this observation, we sought to determine if YNB-grown cells could be used directly for genetic transformation. To test this, we targeted ADE2 using TRACE (transient CRISPR–Cas9 coupled with electroporation) in YNB-grown or competent cells. Deletion of the ADE2 gene results in red-pigmented colonies allowing visual confirmation of disruption. We were able to successfully delete ADE2 in YNB-grown cells and with better efficiency compared to competent cells. Recently, it was shown that gene deletion can be accomplished using short (50 bp) homology arms in place of the normal long arms (∼1 kb). However, it was inefficient, leading to more insertions and gene disruption than gene deletions. We tested short homology with YNB-grown cells vs. competent cells and found gene deletion was significantly improved in YNB-grown cells, around 60%, compared to around 6% with the competent cells. This was also observed when we deleted LAC1 with the short arms. Altogether, using simple growth conditions, we have greatly improved the speed and efficiency of cryptococcal genetic transformations.