Comparative Genomics and Heterologous Complementation Reveal Sequence and Structural Divergence of Selected Transcription Factors From <i>Spathaspora passalidarum</i>

ABSTRACT The yeast Spathaspora passalidarum is considered promising for domestication and use in second‐generation ethanol production because it ferments xylose and glucose with yields above 70%. However, successful domestication requires not only efficient sugar utilization but also enhanced tolerance to the stresses associated with industrial fermentation, particularly ethanol accumulation, osmotic pressure, and oxidative conditions. To investigate stress responses in Sp. passalidarum , its repertoire of transcription factors and over 300 stress‐related proteins were predicted and compared to orthologs in Saccharomyces cerevisiae . While most stress‐related proteins were conserved between the two species, more than 70% of Sp. passalidarum transcription factors showed less than 30% sequence identity, lacked recognizable domains, or diverged within functional domains. Gene complementation assays showed that the Sp. passalidarum YAP1 and MSN‐like genes showed limited or incomplete complementation of oxidative stress tolerance in S. cerevisiae mutant strains compared with the corresponding native genes. Together, these findings support functional divergence of the analyzed transcription factors in the heterologous S. cerevisiae system and suggest that regulatory divergence may contribute to stress‐response differences between Spathaspora passalidarum and Saccharomyces cerevisiae .