Biology subjects

Lao, S.

Publications and source records attributed to Lao, S..

3 recordsLinked to original sources

bioRxiv2026

Regulatory co-option of a homeobox gene drives parasitoid venom evolution

How gene regulatory networks are rewired to generate phenotypic and functional innovation remains a central question in evolutionary biology. Parasitoid wasp venoms provide a powerful system for addressing this question, as their repertoires evolve rapidly through extensive lineage-specific turnover, yet the regulatory principles underlying such flexibility are largely unknown. Here we integrate tissue-resolved transcriptomic, chromatin-accessibility and histone-modification profiling to reconstruct the venom regulatory network of the parasitoid wasp Pteromalus puparum. We show that venom expression is embedded in distinct chromatin states and shaped by regulatory elements associated with venom-gland transcription. Comparative and functional analyses support a general model in which regulators related to the endoplasmic reticulum stress and unfolded protein response pathways have been repeatedly recruited to venom regulation across venomous lineages. Unexpectedly, we identify the recently co-opted homeobox gene Lbx as a lineage-specific hub that regulates more than half of venom genes and is linked to enhancer evolution. These results reveal a nested model of venom regulatory evolution, in which an ancestral secretory programme provides a reusable regulatory backbone, while newly co-opted homeobox gene specify a lineage-specific venom expression. Our study highlights regulatory co-option as a mechanism by which conserved developmental genes can acquire new physiological functions during adaptive evolution.

evolutionary biology↗

bioRxiv2025

Accelerated evolution of whole gene clusters by an engineered lytic phage system in E. coli

Directed evolution excels at optimizing individual proteins, but simultaneous evolution of multiple genes remains a significant challenge. Here, we establish a robust phage-based system for accelerated evolution of large gene clusters of up to 39 kilobases. Lytic Selection and Evolution (LySE) selectively replicates and mutagenizes the target gene cluster, carried on a phagemid through alternating cycles of lysis and transduction in Escherichia coli. We engineered a hypermutagenic T7 DNA polymerase (T7 DNAP) that increases mutation rates of the replicating phagemid 7,000-fold during the lytic cycle. We further optimized the mutational spectrum by fusing the T7 DNAP to a dual adenine-cytosine deaminase to install all possible transition mutations at similar frequencies. LySE-mediated transduction enables selection for desired metabolic functions by coupling gene cluster expression to host fitness, while eliminating genomic off-target mutations by refreshing the host in each cycle. Using LySE, we evolved a 25-fold increase in tigecycline resistance in 5 cycles, and a 50.9% increase in end-point biomass of a bacterial strain that utilizes the PET monomer, ethylene glycol, as its sole carbon source.

synthetic biology↗

bioRxiv2020

A Proteomic Platform to Identify Off-Target Proteins Associated with Therapeutic Modalities that Induce Protein Degradation or Gene Silencing

Novel modalities such as Proteolysis Targeting Chimera (PROTAC) and RNA interference (RNAi) have a mechanism of action-based potential to alter the abundance of off-target proteins. The current in vitro secondary pharmacology assays, which evaluate off-target binding or activity of small molecules, do not fully assess the off-target effects of PROTAC and are not applicable to RNAi. To address this gap, we developed a proteomics-based platform to comprehensively evaluated abundance of off-target proteins. The first part of the manuscript describes the rationale and process through which the off-target proteins and cell lines were selected. The off-target proteins were selected from the entire human proteome based on genetics and pharmacology data (Deaton et al., 2018). The selection yielded 2,813 proteins, forming the nexus of a panel that we refer to as the "selected off-target proteome" (SOTP). An algorithm was then used to identify appropriate cell lines. Four human cell lines out of 932 were selected that, collectively, expressed ~ 80% of the SOTP based on transcriptome data. The second part of the manuscript describes the LC-MS/MS experimentation to quantify the intracellular and extracellular proteins of interest in the 4 selected cell lines. Among over 10,000 quantifiable proteins identified, 1,828 were part of the predefined SOTP. The SOTP was designed to be easily modified or expanded, owing rationale selection process developed and the label free LC-MS/MS approach chosen. This versatility inherent to our platform is essential to design fit-for-purpose studies that can address the dynamic questions faced in investigative toxicology.

pharmacology and toxicology↗