Biology subjects

Abbondanzieri, E. A.

Publications and source records attributed to Abbondanzieri, E. A..

3 recordsLinked to original sources

bioRxiv2025

Genome-wide DNA bridging by H-NS reshapes the stationary phase nucleoid and transcriptional landscape

Bacterial nucleoid-associated proteins (NAPs) structure the chromosome and regulate gene expression, but how these two functions are related is unclear. H-NS is a well-studied NAP that acts as a global gene silencer capable of bridging and looping DNA in vitro. Here, using high-throughput chromosome conformation capture assays, we show that H-NS mediates genome-wide long-range DNA looping in the stationary-phase nucleoid of Escherichia coli. Chromatin immunoprecipitation assays demonstrate that high levels of H-NS are present at the base of DNA loops. Super-resolution imaging and single-particle tracking show that H-NS binds more tightly in stationary phase and compacts the nucleoid mesh. Transcriptomic analyses indicate H-NS represses gene expression more strongly in the looped nucleoid and enables higher expression of genes outside of H-NS-bound regions. Overall, our study demonstrates that H-NS bridges distal DNA regions along the genome upon nutrient limitation, causing reduced nucleoid accessibility, stronger transcriptional repression, and a shifted transcriptional landscape.

molecular biology↗

bioRxiv2025

Dps binds and protects DNA in starved Escherichia coli with minimal effect on chromosome accessibility, dynamics and organisation

Dps is the most abundant nucleoid-associated protein in starved Escherichia coli with [~]180,000 copies per cell. Dps binds DNA and oxidises iron, facilitating survival in harsh environments. Dps-DNA complexes can form crystalline structures, leading to the proposed model that Dps reorganises the starved E. coli nucleoid into a compact liquid crystal, slowing chromosome dynamics and limiting access of other proteins to DNA. In this work, we directly tested this model using live-cell super-resolution microscopy and Hi-C analysis. We found that after 96 h of starvation, Dps compacts the nucleoid and increases short-range DNA-DNA interactions, but does not affect chromosome accessibility to large protein nanocages or small restriction enzymes. We also report that chromosome dynamics and organisation are primarily impacted by the bacterial growth phase; the effect of Dps is relatively minor. Our work clarifies the role of Dps in modulating nucleoid properties, and we propose an updated model for Dps-DNA interactions in which Dps binds, protects and compacts DNA largely without influencing chromosome access, dynamics and organisation. Additionally, this work provides a general framework for assessing the impact of nucleoid-associated proteins on key aspects of chromosome function in live cells. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/673347v3_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1385efforg.highwire.dtl.DTLVardef@1e4cb76org.highwire.dtl.DTLVardef@1e9e43dorg.highwire.dtl.DTLVardef@8768f4_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2024

Engineered bacteria that self-assemble ''bioglass'' polysilicate coatings display enhanced light focusing

Photonic devices are cutting-edge optical materials that produce narrow, intense beams of light, but their synthesis typically requires toxic, complex methodology. Here we employ a synthetic biology approach to produce environmentally-friendly, living microlenses with tunable structural properties. We engineered Escherichia coli bacteria to display the silica biomineralization enzyme silicatein from aquatic sea sponges. Our silicatein-expressing bacteria can self-assemble a shell of polysilicate "bioglass" around themselves. Remarkably, the polysilicate-encapsulated bacteria can focus light into intense nanojets that are nearly an order of magnitude brighter than unmodified bacteria. Polysilicate-encapsulated bacteria are metabolically active for up to four months, potentially allowing them to sense and respond to stimuli over time. Our data demonstrate that engineered bacterial particles have the potential to revolutionize the development of multiple optical and photonic technologies. Significance StatementIn this work, we apply the principles of synthetic biology to create living optical devices. Utilizing the ability of sea sponges to polymerize bioglass from silica precursors in the ocean water using only a single enzyme, silicatein, we have fused this same enzyme to the surface of Escherichia coli bacterial cells. The modified bacteria can polymerize a layer of bioglass at their surface. This bioglass shell allows the bacteria to act as engineered optical devices that are able to scatter high intensity, focused light while also surviving for several months, opening the door to a wide range of sense-and-respond applications. ClassificationBiological Sciences, Applied Biological Sciences

synthetic biology↗