Biology subjects

Studt, L.

Publications and source records attributed to Studt, L..

2 recordsLinked to original sources

bioRxiv2025

Emergent Morphologies, Slow Dynamics, and Phase Behavior in Dps:DNA assemblies

The DNA-binding protein from starved cells (Dps) compacts bacterial DNA into stress-protective condensates, but the physical ingredients that are sufficient to produce the observed morphological and dynamical phenomenology remain unclear. Here we use Dps:DNA as the motivation for a broader soft-matter question: which properties govern the co-condensation of a semiflexible polymer with a binding co-solute, and how is the resulting condensate morphology selected? We combine coarse-grained Brownian dynamics (BD) simulations, in which DNA is a semiflexible bead-spring chain and Dps a spherical particle interacting through heterotypic attraction and homotypic repulsion, with a ternary Flory-Huggins free energy evolved under conserved Cahn-Hilliard-Cook dynamics. Both frameworks show that the condensate morphology is governed jointly by the heterotypic Dps:DNA attraction and by composition: attraction drives co-condensation, while at fixed attraction the relative abundance of the two species selects between extended, network-like structures and compact, droplet-like condensates. That two independent models, sampling different concentration regimes, both show composition-controlled morphology selection indicates it is a robust feature of the co-condensation thermodynamics. The simulations further reveal slow, heterogeneous dynamics: sub-diffusive Dps motion and a stretched-exponential collapse of chain dimensions, signatures of the dynamical arrest that accompanies compaction. The framework provides general, transferable principles for protein-nucleic-acid phase separation in soft and living matter.

biophysics↗

bioRxiv2020

Activation of silent secondary metabolite gene clusters by nucleosome map-guided positioning of the synthetic transcription factor VPR-dCas9

Current methods for forced expression of selected target genes are based on promoter exchange or on overexpressing native or hybrid transcriptional activators in which gene-specific DNA binding domains are coupled to strong activation domains. While these approaches are very useful for promoters with known or synthetically introduced transcription factor binding sites, they are not suitable to turn on genes in biosynthetic gene clusters which often lack pathway-specific activators. To expand the discovery toolbox, we designed a Cas9-based RNA guided synthetic transcription activation system for Aspergillus nidulans based on enzymatically disabled dCas9 fused to three consecutive activation domains (VPR-dCas9). Targeting two biosynthetic gene clusters involved in the production of secondary metabolites, we demonstrate the utility of the system. Especially in silent regions facultative heterochromatin and strictly positioned nucleosomes can constitute a relevant obstacle to the transcriptional machinery. To avoid this negative impact and to facilitate optimal positioning of RNA-guided VPR-dCas9 to our targeted promoters we have created a genome-wide nucleosome map to identify the cognate nucleosome-free-regions (NFRs). Based on these maps, different single-guide RNAs (sgRNA) were designed and tested for their targeting and activation potential. Our results demonstrate that the system can be used to activate silent BGCs in A. nidulans, partially to very high expression levels and also open the opportunity to stepwise turn on individual genes within a BGC that allows to decipher the correlated biosynthetic pathway.

bioengineering↗