Genome mining of an endophytic natural yeast isolate Rhodotorula sp. Y090 and production of the antioxidant ergothioneine

Endophytic yeast strains are promising sources of various valuable bioactive compounds. However, studies on endophytic strains derived from lichen samples remains limited. In this study, we isolated and characterized Rhodotorula sp. Y090 from Usnea longissima and investigated its biosynthetic potential. Genome mining revealed distinct genetic features that differed from its closest relative strain R. graminis WP1. Ergothioneine (EGT) is a potent antioxidant and rare sulfur-containing histidine derivative. However, so far, the EGT biosynthetic enzymes by natural yeast strains have been limitedly studied. In this study, combining genome mining and transcriptomic analysis, genes encoding the potential enzymes for the production of EGT and xylose utilization were identified in Rhodotorula sp. Y090. Further studies demonstrated that Rhodotorula sp. Y090 was capable of producing EGT using xylose, glucose, glycerol, and sucrose as the sole carbon sources, and the highest titer reached 363.6   mg/L in shake flask culture, which is significantly higher than that of the most reported levels in the other natural yeasts. Rhodotorula sp. Y090 also exhibited a good ability of EGT export, which could facilitate cost-effective production. These findings suggest that the lichen-derived endophytic yeast Rhodotorula sp. Y090 represents a promising natural candidate for bio-production of the potent antioxidant.