Hendrickson, B. G. | Search bioRxiv

bioRxiv2025

Pathway Sculptor for Compact and Versatile Combinatorial Genetic Perturbation

The Transforming Growth Factor beta (TGF-{beta}) superfamily, like other biological pathways, relies on families of co-expressed, partially redundant protein components, such as receptor subunits. The inability to systematically modulate multi-gene component expression profiles has made it difficult to understand how components and sets of components collectively process information. To overcome this, we developed Pathway Sculptor, a dCas12a-based epigenetic editing system that achieves simultaneous same-cell knockdown of at least twelve target genes. Programming TGF-{beta} receptor profiles, by knocking down different receptor subsets, revealed functional interactions between the canonical BMP and TGF-{beta} pathway branches. Unexpectedly, signaling within each branch depended on receptors in the opposite branch. Further, different receptor subsets played distinct roles: ACVR-class receptors modulated signaling magnitude, whereas BMPRs and TGFBRs discriminated among ligand variants. These results show how the two branches of the TGF-{beta} superfamily collaboratively process signals, and establish Pathway Sculptor as a general platform for high-order combinatorial perturbation.

synthetic biology↗

bioRxiv2023

A diet of oxidative stress-adapted bacteria improves stress resistance and lifespan in C. elegans via p38-MAPK.

Organisms across taxa are exposed to stresses such as variable temperature, redox imbalance, and xenobiotics. Successfully responding to stress and restoring homeostasis is crucial for viability of the organism. During aging, the ability to effectively respond to stress declines, contributing to development of disease. In many multicellular animals, aging also coincides with changes in the microbiome that can contribute to disease-states. Because animals and their microbiota coexist in the same broad environment, they each must adapt to similar stresses. However, the short generation time of microbes leads to faster evolution, allowing the possibility that microbial stress adaptation may influence host physiology. Here we leverage a simplified model involving the nematode C. elegans and its bacterial diet. Our work highlights how bacterial adaptation to oxidative stress impacts the hosts lifespan and response to stress. Intriguingly, our findings reveal that worms fed with bacteria adapted to withstand oxidative stress exhibit enhanced stress resistance and an extended lifespan. Through whole genome sequencing, genetic assays, and metabolic analysis, this study underscores the pivotal role of the bacterial iron-sulfur pathway in governing host stress resistance and lifespan. We further find that iron in the stress-evolved bacteria boost the worms stress resistance and lifespan through activation of the mitogen-activated protein kinase (MAPK) pathway. In conclusion, this study provides evidence that understanding the evolutionary path of microbial adaptation during stress could be leveraged to slow aging and mitigate age-related decline in health.

molecular biology↗