Biology subjects

Carmi, M.

Publications and source records attributed to Carmi, M..

4 recordsLinked to original sources

bioRxiv2026

Pex9 regulates TORC2 during the cellular response to oxidative stress

Peroxisomes are known for their detoxification role in cellular reactive oxygen species (ROS) homeostasis, yet their regulatory roles in cellular recovery from oxidative stress remain unclear. Here, using yeast, we systematically screened a panel of fluorescently tagged peroxisome-related proteins and identified widespread stress-induced changes in their localization. Notably, we discovered that the peroxisomal import receptor, Pex9, rapidly enters the nucleus upon H2O2 exposure, independently of the canonical oxidative stress regulators-Yap1 and Skn7, suggesting a non-canonical signaling function. We further show that Pex9 nuclear entry is modulated by Avo1, an essential Tor complex 2 (TORC2) subunit. In turn, Pex9 downregulates the essential TOR complexes kinase, Tor2, at both the transcriptional and protein levels. Finally, we show that this Pex9-TORC2 regulatory loop during oxidative stress is facilitated by the cellular envelope stress response. Our findings uncover an unexpected peroxisome-TORC2 signaling axis and highlight the importance of organelles in shaping global cellular responses to stress.

cell biology↗

bioRxiv2024

Massively Parallel Binding Assay (MPBA) reveals limited transcription factor binding cooperativity, challenging models of specificity

DNA binding domains (DBDs) within transcription factors (TFs) recognize short sequence motifs that are highly abundant in genomes. In vivo, TFs bind only a small subset of motif occurrences, which is often attributed to the cooperative binding of interacting TFs at proximal motifs. However, large-scale testing of this model is still lacking. Here, we describe a novel method allowing parallel measurement of TF binding to thousands of designed sequences within yeast cells and apply it to quantify the binding of dozens of TFs to libraries of regulatory regions containing clusters of binding motifs, systematically mutating all motif combinations. With few exceptions, TF occupancies were well explained by independent binding to individual motifs, with motif cooperation being of only limited effects. Our results challenge the general role of motif combinatorics in directing TF genomic binding and open new avenues for exploring the basis of protein-DNA interactions within cells.

systems biology↗

bioRxiv2024

Ordered and disordered regions of the Origin Recognition Complex (ORC) combine to direct in-vivo binding at symmetric and non-symmetric motif sequences.

The Origin Recognition Complex (ORC) seeds replication-fork formation by binding to DNA replication origins, which in budding yeast contain a 17bp DNA motif. High resolution structure of the ORC-DNA complex revealed two base-interacting elements: a disordered basic patch (Orc1-BP4) and an insertion helix (Orc4-IH). To define the ORC elements guiding its DNA binding in-vivo, we mapped genomic locations of 38 designed ORC mutants, revealing that different ORC elements guide binding at different sites. At silencing-associated sites lacking the motif, ORC binding and activity were fully explained by a BAH domain. Within replication origins, we reveal two dominating motif variants showing differential binding modes and symmetry: an asymmetric motif whose binding requires Orc1-BP4 and Orc4-IH, and a symmetric one where another basic patch, Orc1-BP3, can replace Orc4-IH. Disordered basic patches are therefore key for ORC-motif binding in-vivo, and we discuss how these conserved, minor-groove interacting elements can guide specific ORC-DNA recognition.

cell biology↗

bioRxiv2019

Resolving noise-control conflict by gene duplication

Gene duplication promotes adaptive evolution in two principle ways: allowing one duplicate to evolve a new function and resolving adaptive conflicts by splitting ancestral functions between the duplicates. In an apparent departure from both scenarios, low-expressing transcription factor (TF) duplicates commonly regulate similar sets of genes and act in overlapping conditions. To examine for possible benefits of such apparently redundant duplicates, we examined the budding yeast duplicated stress regulators Msn2 and Msn4. We show that Msn2,4 indeed function as one unit, inducing the same set of target genes in overlapping conditions, yet this two-factor composition allows its expression to be both environmental-responsive and with low-noise, thereby resolving an adaptive conflict that inherently limits expression of single genes. Our study exemplified a new model for evolution by gene duplication whereby duplicates provide adaptive benefit through cooperation, rather than functional divergence: attaining two-factor dynamics with beneficial properties that cannot be achieved by a single gene.

evolutionary biology↗