Biology subjects

Bialek, W.

Publications and source records attributed to Bialek, W..

3 recordsLinked to original sources

bioRxiv2025

Arsenic-sensing domain controls ACR3 transporter trafficking and function in Marchantia polymorpha

Arsenic, a toxic and carcinogenic metalloid, is a pervasive environmental contaminant that threatens human health through contaminated water and food. The efflux of As(III) via ACR3 transporters is an ancient detoxification mechanism conserved across prokaryotes, fungi, and plants, with the notable exception of angiosperms. Despite their evolutionary significance, plant ACR3s remain largely uncharacterized. Here, we demonstrate that MpACR3, the ACR3 orthologue from the liverwort Marchantia polymorpha, functions as a metalloid/proton antiporter, conferring resistance to arsenicals and moderate tolerance to antimony. Additionally, we uncover an arsenic-sensing domain within MpACR3 that regulates its intracellular trafficking. Under normal conditions, MpACR3 sorting to the plasma membrane is delayed, resulting in its retention within Golgi bodies. However, As(III) binding to three cysteine residues in the N-terminal cytosolic domain induces a conformational change that facilitates MpACR3 trafficking to the plasma membrane. Furthermore, mutational analysis of a conserved arginine-based motif reveals that the N-terminal domain not only controls MpACR3 accumulation at the plasma membrane but also modulates its transport activity. Importantly, this arsenic-sensing domain is conserved among plant ACR3 transporters, suggesting a plant-specific adaptation to arsenic toxicity.

plant biology↗

bioRxiv2025

Searching for Sequence Features that Control DNA Cyclizability

The mechanical properties of DNA molecules are crucial in many biological processes, from DNA packaging to transcription regulation. While the mechanics of long DNA typically follow the worm-like chain polymer model, multiple studies have shown that the mechanics of short DNA - at the length scale of DNA-protein interactions - depend strongly on its sequence content. Motivated by recent high-throughput measurements of sequence-dependent DNA cyclizability - the DNAs tendency to mechanically bend and form a loop, we developed a statistical mechanics approach to systematically explore how cyclizability depends on interactions between individual nucleotides in the sequence. By applying this method to datasets of randomly generated and biologically derived sequences, we identified characteristic sequence features that control DNA cyclizability and extracted the most and least cyclizable sequences, the behavior of which we validated through all-atom molecular dynamics simulations. We found that while highly cyclizable sequences share the same periodic features across datasets, distinct sequence patterns can result in low cyclizability. This work contributes to our understanding of the sequence dependence of DNA mechanics and its role in various biological processes, and has implications for the growing field of DNA nanofabrication.

biophysics↗

bioRxiv2023

Replication stress response in fission yeast differentially depends on maintaining proper levels of Srs2 helicase and Rrp1, Rrp2 DNA translocases.

Homologous recombination is a key process that governs the stability of eukaryotic genomes during DNA replication and repair. Multiple auxiliary factors regulate the choice of homologous recombination pathway in response to different types of replication stress. Using Schizosaccharomyces pombe we have previously suggested the role of DNA translocases Rrp1 and Rrp2, together with Srs2 helicase, in the common synthesis dependent strand annealing sub-pathway of homologous recombination. Here we show that all three proteins are important for completion of replication after hydroxyurea exposure and provide data comparing the effect of overproduction of Srs2 with Rrp1 and Rrp2. Upregulation of Srs2 protein levels leads to enhanced replication stress, chromosome instability and viability loss, as previously reported for Rrp1 and Rrp2. Interestingly, our data suggests that dysregulation of Srs2, Rrp1 and Rrp2 protein levels differentially affects checkpoint response. Overproduction of Srs2 activates simultaneously DNA damage and replication stress response checkpoints, while cells overproducing Rrp1 mainly launch DNA damage checkpoint. Upregulation of Rrp2 primarily leads to replication stress response checkpoint activation. Overall, we propose that Srs2, Rrp1 and Rrp2 have important and independent functions for maintenance of distinct difficult to replicate regions of the genome.

cell biology↗