Devarajan, M. | bioRxiv Science

bioRxiv2026

ATGL-catalyzed lipid catabolism promotes DNA repair

An imbalance of DNA damage over DNA repair contributes to the genomic instability that drives aging and numerous age-related diseases. While numerous DNA repair mechanisms have been elucidated over decades of study, little is known about the contribution of metabolism to genomic stability. We report that adipose triglyceride lipase (ATGL), a lipolytic enzyme, promotes DNA repair. We show that lipid droplets (LDs) accumulate in response to DNA damage and that inhibition of LD biogenesis before genotoxic stress increases the persistence of DNA damage. Overexpression of ATGL, which increases lipolysis, reduces DNA damage following etoposide and ionizing radiation, thereby promoting genomic stability. Further, ATGL expression prior to DNA damage attenuates the long-term consequences of DNA damage, reducing senescence and enhancing viability. Mechanistically, ATGL promotes double-strand break repair via NHEJ and HR to mitigate DNA damage. Overall, these studies reveal a novel role for LDs and their proteins in DNA damage and repair, thereby unveiling a mechanism by which lipid metabolism contributes to genomic stability.

biochemistry↗

bioRxiv2022

A gene expression control technology for cell-free systems and synthetic cells via targeted gene silencing and transfection

Cell-free transcription-translation (TXTL) is an in vitro protein expression platform. In synthetic biology, TXTL is utilized for a variety of technologies, such as genetic circuit construction, metabolic pathway optimization, and building prototypes of synthetic cells. For all these purposes, the ability to precisely control gene expression is essential. Various strategies to control gene expression in TXTL have been developed; however, further advancements on gene-specific and straightforward regulation methods are still demanded. Here, we designed a novel method to control gene expression in TXTL, called a "silencing oligo." The silencing oligo is a short oligonucleotide that binds to the target mRNA. We demonstrated that addition of the silencing oligo inhibits eGFP expression in TXTL in a sequence-dependent manner. We investigated one of the silencing oligos inhibitory mechanisms and confirmed that silencing is associated with RNase H activity in bacterial TXTL reactions. We also engineered a transfection system that can be used in synthetic cells. We screened two dozen different commercially available transfection reagents to identify the one that works most robustly in our system. Finally, we combined the silencing oligo with the transfection technology, demonstrating that we can control the gene expression by transfecting silencing oligo-containing liposomes into the synthetic cells.

synthetic biology↗