Genotypic and phenotypic diversity among Komagataella species reveals a hidden pathway for xylose utilization

Abstract

AbstractBackgroundThe yeast genusKomagataellacurrently consists of seven methylotrophic species isolated from tree environments. Well-characterized strains ofK. phaffiiandK. pastorisare important hosts for biotechnological applications, but the potential of other species from the genus remains largely unexplored. In this study, we characterized 25 natural isolates from all seven describedKomagataellaspecies to identify interesting traits and provide a comprehensive overview of the genotypic and phenotypic diversity available within this genus.ResultsGrowth tests on different carbon sources and in the presence of stressors at two different temperatures allowed us to identify strains with differences in tolerance to high pH, high temperature, and growth on xylose. AsKomagataellaspecies are generally not considered xylose-utilizing yeasts, xylose assimilation was characterized in detail. Growth assays, enzyme activity measurements and13C labeling confirmed the ability ofK. phaffiito utilize D-xylose via the oxidoreductase pathway. In addition, we performed long-read whole-genome sequencing to generate genome assemblies of allKomagataellaspecies type strains and additionalK. phaffiiandK. pastorisisolates for comparative analysis. All sequenced genomes have a similar size and share 83–99% average sequence identity. Genome structure analysis showed thatK. pastorisandK. ulmishare the same rearrangements in difference toK. phaffii, while the genome structure ofK. kurtzmaniiis similar toK. phaffii. The genomes of the other, more distant species showed a larger number of structural differences. Moreover, we used the newly assembled genomes to identify putative orthologs of important xylose-related genes in the differentKomagataellaspecies.ConclusionsBy characterizing the phenotypes of 25 naturalKomagataellaisolates, we could identify strains with improved growth on different relevant carbon sources and stress conditions. Our data on the phenotypic and genotypic diversity will provide the basis for the use of so-far neglectedKomagataellastrains with interesting characteristics and the elucidation of the genetic determinants of improved growth and stress tolerance for targeted strain improvement.