Biology subjects

Bowman, G.

Publications and source records attributed to Bowman, G..

11 recordsLinked to original sources

bioRxiv2026

Chromatin architecture sets origin licensing capacity

Replication origin licensing enables complete and faithful genome duplication, yet how chromatin regulates this process in vivo remains unclear. Using MCM-ChEC-seq to track helicase loading from metaphase through G1 in budding yeast, we find that licensing occurs in a rapid, synchronous burst at mitotic exit and then reaches an early plateau despite continued permissive cell-cycle conditions and persistent ORC binding at origins. Here we show that this plateau is imposed by chromatin architecture at replication origins, which limits the extent of origin licensing. Histone H3K56 acetylation marks newly replicated chromatin and is removed at S-phase exit by the deacetylases Hst3 and Hst4. Persistent H3K56ac severely impairs MCM loading without affecting ORC occupancy, indicating that chromatin limits licensing at the helicase-loading step. Strikingly, deletion or catalytic inactivation of the chromatin remodeler Isw2 increases licensing by approximately 40% in wild-type cells and fully suppresses the licensing defect in hst3{Delta} hst4{Delta} mutants, identifying Isw2 as a physiological inhibitor of origin licensing. Isw2-dependent nucleosome repositioning narrows the origin nucleosome-depleted region and restricts helicase loading. Together, these findings show that chromatin architecture at replication origins sets licensing capacity. Newly replicated chromatin transiently adopts an Isw2-dependent inhibitory configuration that is relieved, but not completely eliminated, by post-replicative chromatin maturation. Genome-wide licensing thus reflects integration of chromatin-imposed licensing capacity with cell cycle-dependent control of licensing timing.

genetics↗

bioRxiv2026

cGAS bends unpaired DNA to form an unconventional structure that hyperactivates the innate immune response

cGAS is a pattern-recognition receptor for dsDNA and forms 2cGAS:2DNA dimers followed by oligomerization into phase-separated condensates when fully-complementary DNA is studied. However, many DNAs are not fully complementary. We report that DNA with unpaired regions such as those found during transcription, recombination or replication (designated as bubble-DNA, Bu-DNA) causes cGAS hyper-activation. Hyperactivation is observed by Bu-DNA embedded in linear DNA, circular DNA, plasmid DNA and mitochondria DNA. Bu-DNA binds significantly more tightly to the cGAS catalytic domain than paired-DNA but suppresses condensation. Cryo-EM and single-molecule FRET reveal that cGAS forms 2cGAS:1DNA complexes by bending Bu-DNA into a V-shape using the unpaired region as a hinge, limiting its oligomeric state. This uncovers a novel mode of cGAS activation attributed to pattern diversity within pattern ligands.

immunology↗

bioRxiv2026

On the predictability of progression-free survival in ovarian cancer from NanoString gene expression data

In the treatment of high grade serous ovarian cancer (HGSC), patients initially diagnosed with unresectable tumors are first treated with neoadjuvant chemotherapy (NACT) to reduce tumor burden prior to surgery. Analysis of matched pre- and post-NACT samples from the same patients enables the investigation of chemotherapy impacts and the biomarkers of progression. Although the tumor immune microenvironment (TIME) has increasingly been recognized as critical in shaping the development and progression of HGSC, we lack a comprehensive understanding of how chemotherapy remodels the TIME. Previous studies have found evidence for a general inflammatory response post-NACT, despite inconsistencies regarding which differentially expressed genes and pathways are implicated. We combine matched NanoString gene expression data from multiple sources to create a large dataset of matched pre- and post- NACT samples (N=83, with 29 novel to this study) and investigate reproducibility. Further, we use machine learning methods to investigate whether patient progression-free survival (PFS) can be predicted from the observed impact of chemotherapy on the TIME as represented by the comprehensive set of NanoString features. We find overall low predictability of PFS from all NanoString features, suggesting that previous results may have been limited by small sample size effects and that larger datasets are needed to identify more generalizable and translatable findings. We identify a set of differential expression features that are the most important for predicting patient outcomes that can be validated in future computational and biological studies. Author summaryA subset of patients with high grade serous ovarian cancer are treated with chemotherapy before surgery to reduce tumor burden. We investigate a large dataset of samples taken before and after chemotherapy. These matched samples enable an investigation of how the environment around tumors, for example immune cell infiltration, reacts to chemotherapy, providing insights into biomarkers for treatment response and treatments that could complement chemotherapy. This larger dataset only partially replicates results from previous studies, while also providing new insights. Machine learning models designed to predict the time to patient recurrence from available biomarkers indicate that they are not strongly predictive of patient outcomes, in contrast to past studies. These results suggest that larger datasets are needed. We identify a set of genes that change with chemotherapy and are indicative of and potentially useful for predicting time to disease recurrence and can be further investigated.

cancer biology↗

bioRxiv2025

Crowding does not suppress the opening of a cryptic pocket

Cryptic pockets are transient structural features that could provide new opportunities for drug design. However, their utility would be greatly diminished if the probability of pocket opening were universally suppressed in cells due to the excluded volume effects of crowding. As a first step to addressing this concern, we study the effect of the synthetic crowder Ficoll 70, which has been shown to mimic the excluded volume effects of biomolecular crowding well, on the opening of a cryptic pocket in the interferon inhibitory domain (IID) of Ebola viral protein 35 (VP35). We find that this synthetic crowder has a negligible effect on the probability of cryptic pocket opening, as measured by both thiol labeling and hydrogen-deuterium exchange mass spectrometry (HDX-MS). The probability that a specific pocket opens may still be altered by the soft, enthalpic interactions of crowding, which will vary between different cellular environments. However, our results demonstrate that excluded volume effects that are at play in all crowded environments do not pose a universal barrier to targeting cryptic pockets.

biophysics↗

bioRxiv2025

Microbial stem cells support productivity in dedicated factory cells in an asymmetrically dividing E. coli system

A major challenge for many bio-manufacturing operations is that cells are burdened by the high fitness cost of product synthesis, limiting their growth and productivity. A potential solution is to decouple cell reproduction from product synthesis by dividing these conflicting tasks between two differentiated cell types. This work describes the use of an asymmetrically inherited protein cue to differentiate an E. coli culture into reproductive stem cells and fully dedicated factory cells. Cell differentiation is based on the ability to accumulate two factors: a variant of phage-derived T7 RNA polymerase (T7RNAP) and GP2, a peptide that inhibits native host cell RNA polymerase. Activating these two factors in factory cells inhibited growth and focused them on T7RNAP-driven product synthesis. Preventing their accumulation in stem cells allowed this cell type to grow and divide asymmetrically, generating new factory cells in the process. These differentiating cell cultures generated over eight-fold higher target protein titers compared to factory cell-only controls. Because they include a mechanism for preventing leaky T7RNAP-driven gene expression in stem cells and pre-induction cultures, it was possible to generate strains with multiple plasmid-based copies of a cytotoxic target gene, whereas leaky expression made the same plasmid inviable in conventional protein expression strains. This versatile genetic system could be useful for generating higher product titers, particularly in cases where product synthesis causes cytotoxicity.

synthetic biology↗

bioRxiv2025

Pathogenic BRCA1 mutations disrupt allosteric control by BARD1

Mechanistic insight into biophysical perturbations caused by pathogenic missense mutations is highly valuable information for the rational design of therapeutics. For hereditary breast and ovarian cancer, multiple pathogenic mutations in the N-terminal domain of BRCA1 have been reported in patients. How exactly these mutations disrupt the catalytic activity of BRCA1, and thereby lead to oncogenesis, is unknown. Here, we posit that the mechanism of pathogenesis is tied to how binding of BARD1 activates BRCA1 for E3 ligase activity. We use atomistic molecular dynamics simulations and Markov state modeling to uncover how BARD1 selects for active conformational states of BRCA1. We show that the helix bundle, where BARD1 binds, is allosterically coupled to the E2 interface. Furthermore, we show that BARD1 selects for conformational states that are pre-organized for E3 activity. Lastly, we show that pathogenic mutations allosterically destabilize active states, whereas hyperactive mutations constitutively increase their likelihood. These results provide a concrete strategy supported by mechanistic insight for the design of restorative small molecules targeting BRCA1.

biophysics↗

bioRxiv2025

Native nucleosome-positioning elements for the investigation of nucleosome repositioning

Nucleosome repositioning is essential for establishing nucleosome-depleted regions (NDRs) to initiate transcription. This process has been extensively studied using structural, biochemical, and single-molecule approaches, which require homogenously positioned nucleosomes. This is often achieved using the Widom 601 sequence, a highly efficient nucleosome positioning element (NPE) selected for its unusually strong binding to the H3-H4 histone tetramer. Due to the artificial nature of 601, native NPEs are needed to explore the role of DNA sequence in nucleosome repositioning. Here, we characterize the position distributions and nucleosome formation free energy for a set of yeast native nucleosomes (YNNs) from Saccharomyces cerevisiae. We show these native NPEs can be used in biochemical studies of nucleosome repositioning by transcription factors (TFs) and the chromatin remodeler Chd1. TFs could directly reposition a fraction of nucleosomes containing native NPEs, but not 601-containing nucleosomes. In contrast, partial unwrapping was similar for 601 and native NPE sequences, and the rate of ATP-dependent remodeling by Chd1 was within the range of the fast and slow directions of the 601 nucleosomes. This set of native NPEs provides an alternative to the 601 NPE that can be used for probing the repositioning of nucleosomes that contain native DNA sequences.

molecular biology↗

bioRxiv2024

The G protein inhibitor YM-254890 is an allosteric glue

Given the prominence of G protein coupled receptors (GPCRs) as drug targets, targeting their immediate downstream effectors, G proteins, could be of immense therapeutic value. The discovery that the natural product YM-254890 (YM) can arrest uveal melanoma by specifically inhibiting constitutively active Gq/11without impacting other G protein families demonstrates the potential of this approach. However, efforts to find other G protein family-specific inhibitors have had limited success. Better understanding the mechanism of YM could facilitate efforts to develop other highly specific G protein inhibitors. We hypothesized that differences between the conformational distributions of various G proteins play an important role in determining he specificity of inhibitors like YM. To explore this hypothesis, we built Markov state models (MSMs) from molecular dynamics simulations of the G subunits of three different G proteins, as YM predominantly contacts G. We also modeled the heterotrimeric versions of these proteins where G is bound to the G{beta}{gamma} heterodimer. We find that YM-sensitive G proteins have a higher probability of adopting YM-bound-like conformations than insensitive variants. There is also strong allosteric coupling between the YM- and G{beta}{gamma}-binding interfaces of G. This allostery gives rise to positive cooperativity, wherein the presence of G{beta}{gamma} enhances preorganization for YM binding. We predict that YM acts as an "allosteric" glue that allosterically stabilizes the complex between G and G{beta}{gamma} despite the minimal contacts between YM and G{beta}{gamma}.

biophysics↗

bioRxiv2024

SGLT2 inhibitors activate pantothenate kinase in the human heart

Inhibitors of sodium glucose cotransporter-2 (SGLT2i) demonstrate strong symptomatic and mortality benefits in the treatment of heart failure but appear to do so independently of SGLT2. The relevant pharmacologic target of SGLT2i remains unclear. We show here that SGLT2i directly activate pantothenate kinase 1 (PANK1), the rate-limiting enzyme that initiates the conversion of pantothenate (vitamin B5) to coenzyme-A (CoA), an obligate co-factor for all major pathways of fuel use in the heart. Using stable-isotope infusion studies, we show that SGLT2i promote pantothenate consumption, activate CoA synthesis, rescue decreased levels of CoA in human failing hearts, and broadly stimulate fuel use in ex vivo perfused human cardiac blocks from patients with heart failure. Furthermore, we show that SGLT2i bind to PANK1 directly at physiological concentrations and promote PANK1 enzymatic activity in assays with purified components. Novel in silico dynamic modeling identified the site of SGLT2i binding on PANK1 and indicated a mechanism of activation involving prevention of allosteric inhibition of PANK1 by acyl-CoA species. Finally, we show that inhibition of PANK1 prevents SGLT2i-mediated increased contractility of isolated adult human cardiomyocytes. In summary, we demonstrate robust and specific off-target activation of PANK1 by SGLT2i, promoting CoA synthesis and efficient fuel use in human hearts, providing a likely explanation for the remarkable clinical benefits of SGLT2i.

biochemistry↗

bioRxiv2023

Homologous mutations in β, embryonic, and perinatal muscle myosins have divergent effects on molecular power generation

Mutations at a highly conserved homologous residue in three closely related muscle myosins cause three distinct diseases involving muscle defects: R671C in {beta}-cardiac myosin causes hypertrophic cardiomyopathy, R672C and R672H in embryonic skeletal myosin cause Freeman Sheldon syndrome, and R674Q in perinatal skeletal myosin causes trismus- pseudocamptodactyly syndrome. It is not known if their effects at the molecular level are similar to one another or correlate with disease phenotype and severity. To this end, we investigated the effects of the homologous mutations on key factors of molecular power production using recombinantly expressed human {beta}, embryonic, and perinatal myosin subfragment-1. We found large effects in the developmental myosins, with the most dramatic in perinatal, but minimal effects in {beta} myosin, and magnitude of changes correlated partially with clinical severity. The mutations in the developmental myosins dramatically decreased the step size and load-sensitive actin-detachment rate of single molecules measured by optical tweezers, in addition to decreasing ATPase cycle rate. In contrast, the only measured effect of R671C in {beta} myosin was a larger step size. Our measurements of step size and bound times predicted velocities consistent with those measured in an in vitro motility assay. Finally, molecular dynamics simulations predicted that the arginine to cysteine mutation in embryonic, but not {beta}, myosin may reduce pre-powerstroke lever arm priming and ADP pocket opening, providing a possible structural mechanism consistent with the experimental observations. This paper presents the first direct comparisons of homologous mutations in several different myosin isoforms, whose divergent functional effects are yet another testament to myosins highly allosteric nature.

biophysics↗

bioRxiv2022

Nucleosome sliding by the Chd1 chromatin remodeler relies on theintegrity of the DNA duplex

Chromatin remodelers use a helicase-type ATPase motor to shift DNA around the histone core. Although not directly reading out the DNA sequence, some chromatin remodelers are biased by DNA sequences, suggesting that they may be sensitive to properties of the DNA duplex. Here, we present a high-throughput method for determining nucleosome positioning in vitro using site-specific DNA cleavage coupled with next-generation sequencing. This method allowed us to systematically test how the introduction of poly(dA:dT) tracts and other perturbations affected the distribution of nucleosomes remodeled by the Chd1 remodeler. We found that Chd1 is sensitive to poly(dA:dT) tracts as short as 3 bp, and that its nucleosome sliding activity is severely perturbed by DNA mismatches and single-nucleotide insertions. These results suggest that remodelers rely on the integrity of duplex DNA for nucleosome sliding. We also discovered that DNA on the nucleosome can shift in the absence of a remodeler when multiple mismatches are placed at superhelix location 2 (SHL2). This DNA movement in response to a disruption of the double helix may explain why SHL2 is the preferred site of engagement by most chromatin remodelers.

biophysics↗