Research Themes

Investigating the interplay between genomic plasticity, evolutionary trade-offs, and synthetic biological systems.

Evolutionary Biology

Adaptive Fusion & Reproduction Trade-offs

Focusing on our work recently submitted to Nature Ecology & Evolution, we explore how cyclical sexual–asexual selection drives adaptive fusion in prm1∆ strains. We investigate the genetic assimilation and genomic changes that allow cells to bypass traditional fusion defects through complex reproduction trade-offs.

Single-Cell Genomics

Spatiotemporal Atlas of Sexual Development

Utilizing scRNA-seq, we are constructing a comprehensive transcriptomic atlas of sexual development in S. pombe. By correlating single-cell data with live-cell microscopy, we aim to decode the regulatory networks governing “developmentally primed mitosis” and cellular state transitions.

Lipidomics

Anaerobic Rescue & Membrane Remodeling

We investigate how environmental stressors, such as anaerobic conditions, can rescue cellular fusion defects. Our research focuses on the Sre1 and Sms1 signaling pathways and their impact on ergosterol-mediated membrane lipid composition during fusion events.

Automation & High-Throughput

Genome-wide Fluorescent Library Construction

We are automating the construction of a genome-wide library of fluorescently-tagged proteins in fission yeast. This platform enables the large-scale study of protein spatiotemporal dynamics and self-organization during meiosis and other physiological perturbations.

Genomic Plasticity

Gene Essentiality and Cellular Adaptation

Building on our findings in Cell, we study gene essentiality as a quantitative trait. By investigating how cells adapt to the deletion of supposedly essential genes, we uncover the fundamental principles of cellular evolvability and genomic robustness.

Synthetic Biology

Engineering Polyhydroxyalkanoate (PHA) Metabolism

We apply metabolic engineering and chimeric synthase design to optimize the production of biodegradable PHAs. Our projects include genomic insights into Priestia sp. metabolism and the creation of colorful, high-performance bioplastics in yeast hosts.

Gene essentiality is a quantitative trait

We screened ~1000 reported essential gene and found ~9% of them can be deleted from the genome without leading to lethality of the cell. We renamed these 88 genes as evolvable genes to distinguish them from non-essential genes and non-evolvable essential genes. Our finding revealed that gene essentiality is not a qualitative black/white trait but a quantitative trait linked to cellular evolvability.

Aneuploidy suggested adaptive mechanism

We analyzed more than 600 strains carried an evolvable gene deletion and discovered that the vast majority are aneuploid. These cells displayed different kinds of large scale genomic changes: whole genome duplication, disomy in haploids, monosomy in diploids, heterogeneous genome composition, etc. These observation suggested that these cells survived extreme stress- “essential gene deletion”- through aneuploidy.

Evolvable genes form a continuum in between non-evolvable essential genes and non-evolvable genes.

We analyzed the conservation score/ network topology properties of the three class of genes: non-essential genes, evolvable genes, non-evolvable essential genes. We found that evolvable genes always positioned in between the other two classes.

Evolvable genes were enriched in protein complexes involved in intracellular trafficking. Interestingly independently generated mutant strains carry the same gene deletion or deletion of genes involved in the
same protein complex carried specific set of aneuploidies, suggesting that aneuploidy could
function as an adaptive mutations and that cells respond to inactivation of different component of the same functional submodule in similar ways. Accordingly we showed that the presence of either specific aneuploidies or a specific gene on the aneuploid chromosome was required and sufficient to bypass the lethality of genes belonging to the same functional module.