Search bioRxiv⌕ Search

Biology subjects

Al-Zuhairi, H.

Publications and source records attributed to Al-Zuhairi, H..

2 recordsLinked to original sources

A dual-function regulatory element couples ParB expression and DNA substrate specificity

Chromosome segregation is essential for cell survival. Most bacteria encode the chromosome partitioning ParABS system. Although even small changes in ParA or ParB levels disrupt genome maintenance, the mechanisms that control their abundance have remained unresolved. Using Caulobacter crescentus, we provide the first mechanistic evidence that ParB levels are regulated post-transcriptionally. Through single-nucleotide substitutions and compensatory mutation analyses, we identify an mRNA secondary structure at the 5' end of the parB transcript that enhances ParB cellular abundance. Loss of this regulatory mechanism sensitizes cells to modest increases in ParA levels, causing cell death. Additionally, we demonstrate that ParB substrate specificity is not determined solely by the central helix-turn-helix domain that interacts with parS but is unexpectedly modulated by the N-terminal domain. Together, our findings reveal an uncharacterized layer of chromosome segregation control and highlight post-transcriptional regulation of ParB abundance as a potential mechanism for maintaining the precise ParA-ParB balance required for bacterial viability.

microbiology↗

Probing the effect of PEG-DNA interactions and buffer viscosity on tethered DNA in shear flow

DNA flow-stretching is a widely employed, powerful technique for investigating the mechanisms of DNA-binding proteins involved in compacting and organizing chromosomal DNA. We combine single-molecule DNA flow-stretching experiments with Brownian dynamics simulations to study the effect of the crowding agent polyethylene glycol (PEG) in these experiments. PEG interacts with DNA by an excluded volume effect, resulting in compaction of single, free DNA molecules in PEG solutions. In addition, PEG increases the viscosity of the buffer solution. By stretching surface-tethered bacteriophage lambda DNA in a flow cell and tracking the positions of a quantum dot labeled at the free DNA end using total internal reflection fluorescence (TIRF) microscopy, we find that higher PEG concentrations result in increased end-to-end length of flow-stretched DNA and decreased fluctuations of the free DNA end. To better understand our experimental results, we perform Brownian dynamics simulations of a bead-spring chain model of flow-stretched DNA in a viscous buffer that models the excluded volume effect of PEG by an effective attractive interaction between DNA segments. We find quantitative agreement between our model and the experimental results for suitable PEG-DNA interaction parameters.

biophysics↗