Evolution-guided yeast complementation reveals functional differences in human PSPH variants

Area of Science:

• Evolutionary genomics
• Metabolic enzyme function
• Human genetics

Background:

• Understanding human genetic variants' impact on metabolic enzymes is crucial for evolutionary and clinical insights.
• Conserved metabolic enzymes play vital roles in cellular processes and disease pathogenesis.

Purpose of the Study:

• To investigate functional differences among human phosphoserine phosphatase (PSPH) variants using evolutionary genomics and experimental assays.
• To establish a framework linking ancient human genome data with functional validation of metabolic enzyme variants.

Main Methods:

• Sequence analyses of temporally stratified human genomes to identify regions of high nucleotide diversity in PSPH.
• Quantitative Saccharomyces cerevisiae complementation assay in a SER2 deletion strain to test PSPH variant function.
• Comparison of ancient-genome-prioritized variants (R27S, Q83H) with modern and disease-associated alleles (D32N, A35T) across various environmental conditions.

Main Results:

• Two PSPH exons showed elevated nucleotide diversity between ancient and modern humans.
• Human PSPH variants differentially complemented the yeast SER2 deletion mutant, affecting growth.
• The modern PSPH allele generally provided the strongest complementation, while ancient variants showed condition-dependent rescue, and disease-associated alleles exhibited the weakest complementation.

Conclusions:

• A scalable framework was established to integrate evolutionary genomics with functional assays for evaluating metabolic enzyme variants.
• Functional differences among PSPH alleles were identified, with context-dependent effects influenced by environmental conditions.
• This approach facilitates the identification and characterization of human metabolic enzyme variants with measurable in vivo effects.