Biology subjects

Rosenberg, S. M.

Publications and source records attributed to Rosenberg, S. M..

5 recordsLinked to original sources

bioRxiv2026

H2AX C-Terminal Dipeptide Truncation: A Master Switch of the DNA Damage Response.

Phosphorylation of histone H2AX at serine 139 ({gamma}H2AX) by ATM/ATR kinases is a central marker of the DNA damage response (DDR), widely used to detect DNA double-strand breaks. However, the molecular basis for tissue- and context-specific variation in {gamma}H2AX signaling remains poorly defined. Here we discover a post-translational truncation of H2AX, catalyzed by lysine demethylase 4A (KDM4A), which removes two C-terminal amino acids critical for ATM/ATR-dependent phosphorylation. This truncation renders H2AX refractory to {gamma}H2AX formation, effectively bypassing canonical DDR signaling. Truncated H2AX accumulates in select cell lines, primary cells, solid tumors, and normal tissues. Genetic knockdown or pharmacologic inhibition of KDM4A reduces H2AX truncation, restores {gamma}H2AX induction, and enhances DNA repair capacity. Conversely, KDM4A overexpression promotes H2AX truncation, impairs {gamma}H2AX signaling, and exacerbates DNA damage accumulation. This previously unrecognized regulatory axis implicates KDM4A catalyzed H2AX truncation as a superseding mechanism that represses the canonical DDR and disrupts the correlation between {gamma}H2AX and DNA damage. This dioxygenase-based protease mechanism represents a new class of proteases and is the first example of c-terminal dipeptide protein truncation. This discovery has broad implications in the basic science of genome maintenance, wound healing, cancer, combinatorial therapy, precision medicine, and technologies such as gene editing. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/723272v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@1b4050forg.highwire.dtl.DTLVardef@1b8333aorg.highwire.dtl.DTLVardef@2b27c5org.highwire.dtl.DTLVardef@13ff699_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2022

Interdependent progression of bidirectional sister replisomes in E. coli

Bidirectional DNA replication complexes initiated from the same origin remain colocalized in a factory configuration for part or all of their lifetimes. However, there is little evidence that sister replisomes are functionally interdependent, and the consequence of factory replication is unknown. Here, we investigated the functional relationship between sister replisomes in E. coli, which naturally exhibits both factory and solitary configurations in the same replication cycle. Using an inducible transcription factor roadblocking system, we found that blocking one replisome caused a significant decrease in overall progression and velocity of the sister replisome. Remarkably, progression was impaired only if the block occurred while sister replisomes were still in a factory configuration - blocking one fork had no significant effect on the other replisome when sister replisomes were physically separate. Disruption of factory replication also led to increased fork stalling and requirement of fork restart mechanisms. These results suggest that physical association between sister replisomes is important for establishing an efficient and uninterrupted replication program. We discuss the implications of our findings on mechanisms of replication factory structure and function, and cellular strategies of replicating problematic DNA such as highly transcribed segments.

genetics↗

bioRxiv2022

Starvation Response and RNA Polymerase Guide Antibiotic-induced Mutable Gambler Cells

Antibiotics can induce mutations that cause antibiotic resistance, triggered by stress responses. The identities of the stress-response activators reveal environmental cues that elicit mutagenesis, and are weak links in mutagenesis networks, inhibition of which could slow evolution of resistance during antibiotic therapies. Despite pivotal importance, few identities and fewer functions of stress responses in mutagenesis are clear. Here, we identify the stringent starvation response in fluoroquinolone-antibiotic ciprofloxacin (stress)-induced mutagenesis. We show its role in transient differentiation of a mutable "gambler" cell subpopulation. Stringent activity is induced by reactive oxygen and upregulates two small (s)RNAs that induce the general stress response, which allows mutagenic DNA-break repair. Surprisingly, RNA polymerase and response-activator nucleotide (p)ppGpp promote ciprofloxacin-induced DNA-damage signaling. We propose a model for their regulation of DNA-damage processing in transcribed regions. The data demonstrate a critical node in ciprofloxacin-induced mutagenesis, imply RNA-polymerase regulation of DNA-break repair, and identify promising targets for resistance-resisting drugs.

microbiology↗

bioRxiv2018

Gamblers: an Antibiotic-induced Evolvable Cell Subpopulation Differentiated by Reactive-oxygen-induced General Stress Response

Antibiotics can induce mutations that cause antibiotic resistance. Yet, despite their importance, mechanisms of antibiotic-promoted mutagenesis remain elusive. We report that the fluoroquinolone antibiotic ciprofloxacin (cipro) induces mutations that cause drug resistance by triggering differentiation of a mutant-generating cell subpopulation, using reactive oxygen species (ROS) to signal the sigma-S ({sigma}S) general-stress response. Cipro-generated DNA breaks activate the SOS DNA-damage response and error-prone DNA polymerases in all cells. However, mutagenesis is restricted to a cell subpopulation in which electron transfer and SOS induce ROS, which activate the {sigma}S response, allowing mutagenesis during DNA-break repair. When sorted, this small {sigma}S-response-\"on\" subpopulation produces most antibiotic cross-resistant mutants. An FDA-approved drug prevents {sigma}S induction specifically inhibiting antibiotic-promoted mutagenesis. Furthermore, SOS-inhibited cell division, causing multi-chromosome cells, is required for mutagenesis. The data support a model in which within-cell chromosome cooperation together with development of a \"gambler\" cell subpopulation promote resistance evolution without risking most cells.

microbiology↗

bioRxiv2018

Bacteria-to-human protein networks reveal origins of endogenous DNA damage

DNA damage provokes mutations and cancer, and results from external carcinogens or endogenous cellular processes. Yet, the intrinsic instigators of DNA damage are poorly understood. Here we identify proteins that promote endogenous DNA damage when overproduced: the DNA-damaging proteins (DDPs). We discover a large network of DDPs in Escherichia coli and deconvolute them into six DNA-damage-causing function clusters, demonstrating DDP mechanisms in three: reactive-oxygen increase by transmembrane transporters, chromosome loss by replisome binding, and replication stalling by transcription factors. Their 284 human homologs are over-represented among known cancer drivers, and their expression in tumors predicts heavy mutagenesis and poor prognosis. Half of tested human homologs, when overproduced in human cells, promote DNA damage and mutation, with DNA-damaging mechanisms like those in E. coli. Together, our work reveals DDP networks that provoke endogenous DNA damage and may indicate functions of many human known and newly implicated cancer-promoting proteins.

cancer biology↗