Biology subjects

Ibarra, B.

Publications and source records attributed to Ibarra, B..

9 recordsLinked to original sources

bioRxiv2026

A dedicated motif in human polymerase gamma enables DNA synthesis through replication roadblocks

Mitochondrial DNA (mtDNA) maintenance is essential for cellular homeostasis, and defects in mtDNA replication are linked to a broad spectrum of mitochondrial diseases. During replication, DNA polymerase {gamma} (Pol{gamma}) must traverse duplex junctions and stable secondary structures, yet how the human enzyme overcomes these barriers remains incompletely understood. Here, cryo-electron microscopy structures of Pol{gamma} bound to forked DNA, G-quadruplex (G4)-containing DNA and DNA bound to mitochondrial single-stranded DNA-binding protein (mtSSB) reveal a common template-entry path along the catcher domain across distinct substrate and active-site configurations. Within this domain, an arginine-rich helix containing R1026, R1030 and R1034 constitutes a Template Stabilising Motif (TSM). Biochemical reconstitution and DNA-binding experiments show that disrupting the TSM selectively impairs strand displacement, RNA-DNA hybrid displacement and synthesis through G4-forming sequences, while largely preserving synthesis on unstructured templates. Single-molecule optical-tweezers experiments further show that mechanical destabilisation of the fork partially restores mutant strand-displacement activity, whereas force or mtSSB restores primer-extension kinetics on ssDNA templates. Together, these findings establish the role of the TSM in maintaining productive template engagement and identify template stabilisation as a common mechanism enabling Pol{gamma} to traverse structurally diverse barriers in mtDNA.

molecular biology↗

bioRxiv2026

Crowding on DNA modulates SSB protein binding mode kinetics

Single-stranded DNA-binding (SSB) proteins play a crucial role in DNA replication by binding to single-stranded DNA (ssDNA) in multiple binding modes, depending on conditions such as salt and protein concentrations. The coverage-dependent effects on the kinetics of these binding modes remain incompletely understood. In particular, the bimodal binding kinetics and the further SSB-ssDNA shortening observed when SSB is removed from the media. Here, we develop a kinetic model extending the Tonks-McGhee-von Hippel framework to incorporate ligand crowding and mode transformations, capturing the inhibition of SSB binding and transitions to higher binding modes as coverage increases. This model quantitatively reproduces experimental binding kinetics and coverage-dependent behaviors observed for human mitochondrial SSB (HmtSSB) and E. coli SSB (EcoSSB). Our findings elucidate the impact of ligand crowding on SSB-ssDNA interactions and provide a generalizable framework for studying multimode ligand binding to polymers, with implications for understanding genome maintenance mechanisms. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/736164v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@1dbd7a5org.highwire.dtl.DTLVardef@2aa614org.highwire.dtl.DTLVardef@1fd9530org.highwire.dtl.DTLVardef@14dbaba_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2024

Auto-regulation of the real-time kinetics of the human mitochondrial replicative helicase

The human mitochondrial replicative helicase, Twinkle, is essential for the replication and integrity of mitochondrial DNA (mtDNA). Therefore, investigating the real-time kinetics of Twinkles activities and their regulation is crucial for understanding mtDNA maintenance. Here, we combine biochemical and single-molecule manipulation and visualization techniques to investigate the loading of Twinkle onto the DNA fork, its real-time DNA unwinding and rewinding kinetics, and the regulation of these processes by the amino- (N) and carboxyl- (C) terminal ends of the helicase and the mitochondrial SSB protein (mtSSB). We observed that Twinkle rapidly diffuses along dsDNA scanning for the DNA fork, where it establishes specific interactions that halt further diffusion. Our results show that during DNA unwinding, the real-time kinetics of the helicase are downregulated by interactions of its N-terminal Zinc-binding domain (ZBD) with DNA and the control of the ATPase activity by the C-terminal tail. We found that binding of mtSSB to DNA likely outcompetes the ZBD-DNA interactions, alleviating the down regulatory effects of this domain. Furthermore, we show that ZBD-DNA interactions, together with the ATP binding, also control the real-time kinetics of the DNA rewinding events that follow helicase stalling. Our findings reveal that ZBD and C-terminal tail play a major role in regulation of Twinkles real-time kinetics. Their interplay constitutes an auto-regulatory mechanism that may be crucial for coordination of the mtDNA maintenance activities of the helicase.

biophysics↗

bioRxiv2023

Mesenchymal Wnts are required for morphogenetic movements of calvarial osteoblasts during apical expansion

Apical expansion of calvarial osteoblast progenitors from the cranial mesenchyme (CM) above the eye is integral for calvarial growth and enclosure of the brain. The cellular behaviors and signals underlying the morphogenetic process of calvarial expansion are unknown. During apical expansion, we found that mouse calvarial primordia have consistent cellular proliferation, density, and survival with complex tissue scale deformations, raising the possibility that morphogenetic movements underlie expansion. Time lapse light sheet imaging of mouse embryos revealed that calvarial progenitors intercalate in 3D to converge supraorbital arch mesenchyme mediolaterally and extend it apically. In contrast, progenitors located further apically exhibited protrusive and crawling activity. CM cells express non-canonical Wnt/Planar Cell Polarity (PCP) core components and calvarial osteoblasts are bidirectionally polarized. We found non-canonical ligand, Wnt5a-/- mutants have less dynamic cell rearrangements, protrusive activity, and a flattened head shape. Loss of cranial mesenchyme-restricted Wntless (CM-Wls), a gene required for secretion of all Wnt ligands, led to diminished apical expansion of OSX+ calvarial osteoblasts in the frontal bone primordia in a non-cell autonomous manner without perturbing proliferation or survival. Calvarial osteoblast polarization, progressive cell elongation and enrichment for actin cytoskeleton protein along the baso-apical axis were dependent on CM-Wnts. Thus, CM-Wnts regulate cellular behaviors during calvarial morphogenesis and provide tissue level cues for efficient apical expansion of calvarial osteoblasts. These findings also offer potential insights into the etiologies of calvarial dysplasias.

developmental biology↗

bioRxiv2022

Mechanism of strand displacement DNA synthesis by the coordinated activities of human mitochondrial DNA polymerase and SSB

Many replicative DNA polymerases couple DNA replication and unwinding activities to perform strand displacement DNA synthesis, a critical ability for DNA metabolism. Strand displacement is tightly regulated by partner proteins, such as single-stranded DNA (ssDNA) binding proteins (SSBs) by a poorly understood mechanism. Here, we use single-molecule optical tweezers and biochemical assays to elucidate the molecular mechanism of strand displacement DNA synthesis by the human mitochondrial DNA polymerase, Pol{gamma}, and its modulation by cognate and noncognate SSBs. We show that Pol{gamma} exhibits a robust DNA unwinding mechanism, which entails lowering the energy barrier for unwinding of the first base pair of the DNA fork junction, by [~]55%. However, the polymerase cannot prevent the reannealing of the parental strands efficiently, which limits by [~]30-fold its strand displacement activity. We demonstrate that SSBs stimulate the Pol{gamma} strand displacement activity through several mechanisms. SSB binding energy to ssDNA additionally increases the destabilization energy at the DNA junction, by [~]25%. Furthermore, SSB interactions with the displaced ssDNA reduce the DNA fork reannealing pressure on Pol{gamma}, in turn promoting the productive polymerization state by [~]3-fold. These stimulatory effects are enhanced by species-specific functional interactions and have significant implications in the replication of the human mitochondrial DNA.

biophysics↗

bioRxiv2021

Wnt-dependent activation of ERK mediates repression of chondrocyte fate during calvarial development.

Wnt signaling regulates cell fate decisions in diverse contexts during development, and loss of Wnt signaling in the cranial mesenchyme results in a robust and binary cell fate switch from cranial bone to ectopic cartilage. The Extracellular signal-regulated protein kinase 1 and 2 (ERK1/2) and Wnt signaling pathways are activated during calvarial osteoblast cell fate selection. Here, we test the hypothesis that ERK signaling is a mediator of Wnt-dependent cell fate decisions in the cranial mesenchyme. First, we show that loss of Erk1/2 in the cranial mesenchyme results in a diminished domain of osteoblast marker expression and increased expression of cartilage fate markers and ectopic cartilage formation in the frontal bone primordia. Second, we show that mesenchyme Wnt/{beta}-catenin signaling and Wntless are required for ERK activation in calvarial osteoblasts. Third, we demonstrate that Wnt and ERK signaling pathways function together to repress Sox9 expression in mouse cranial mesenchyme. Our results demonstrate a link between the Wnt and ERK signaling pathways in regulating lineage selection in a subset of calvarial cells and provide new insights into Wnt-dependent cell fate decisions.

developmental biology↗

bioRxiv2021

GTP and lipids control self-assembly and functional promiscuity of Dynamin2 molecular machinery

Dynamin2 GTPase (Dyn2) is a crucial player in clathrin-mediated endocytosis. Dyn2 is tetrameric in cytoplasm and self-assembles into functional units upon membrane binding. How the curvature activities and functionality of Dyn2 emerge during self-assembly and are regulated by lipids remains unknown. Here we reconstituted the Dyn2 self-assembly process using membrane nanotubes (NT) and vesicles and characterized it using single- molecule fluorescence microscopy, optical tweezers force spectroscopy and cryo-electron microscopy. On NTs, Dyn2 first forms small subhelical oligomers, which are already curvature active and display pronounced curvature sensing properties. Conical lipids and GTP promote their further self-assembly into helical machinery mediating the NT scission. In the presence of large unilamellar vesicles (LUVs), an alternative self- assembly pathway emerges where the subhelical oligomers form membrane tethering complexes mediating LUV-NT binding. Reconstitution of tethering in the LUV system revealed that lipid mixing is controlled by conical lipid species, divalents, GTP, and SH3 binding partners of Dyn2. In membranes with a high content of lipids with negative intrinsic curvature, cryo-EM revealed putative membrane contact sites made by Dyn2 clusters. On such membranes, with GTP lowered to 0.2 mM, both membrane fission and tethering activities become possible, indicating functional promiscuity of Dyn2. We conclude that GTP and lipids control both extent and topology of Dyn2 functional self-assembly. The function of Dyn2 oligomers evolves from curvature sensing, seen in subhelical Dyn2 oligomers, to curvature creation and fission, seen in Dyn2 helices. Under specific circumstances, such as downregulation of SH3 partners of Dyn2 and GTP depletion, membrane tethering activity can emerge in membrane systems enriched with conical lipids. Hence the Dyn2 functionality is actively adapted to lipidome, explaining its large habitat in the cells and tissues.

biophysics↗

bioRxiv2019

Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes

A-tracts are A:T rich DNA sequences that exhibit unique structural and mechanical properties associated with several functions in vivo. The crystallographic structure of A-tracts has been well characterized. However, their response to forces remains unknown and the variability of their flexibility reported for different length scales has precluded a comprehensive description of the mechanical properties of these molecules. Here, we rationalize the mechanical properties of A-tracts across multiple length scales using a combination of single-molecule experiments and theoretical polymer models applied to DNA sequences present in the C. elegans genome. Atomic Force Microscopy imaging shows that phased A-tracts induce long-range ([~]200 nm) bending. Moreover, the enhanced bending originates from an intrinsically bent structure rather than as a consequence of larger flexibility. In support of this, our data were well described with a theoretical model based on the worm-like chain model that includes intrinsic bending. Magnetic tweezers experiments confirm that the observed bent is intrinsic to the sequence and does not rely on particular ionic conditions. Using optical tweezers, we assess the local rigidity of A-tracts at high forces and unravel an unusually stiff character of these sequences, as quantified by their large stretch modulus. Our work rationalizes the complex multiscale flexibility of A-tracts, shedding light on the cryptic character of these sequences.

biophysics↗

bioRxiv2018

Dynamic constriction and fission of ER membranes by reticulon

The endoplasmic reticulum (ER) is a continuous cell-wide membrane network. Network formation has been widely associated with proteins producing membrane curvature and fusion, such as reticulons and atlastin. Regulated network fragmentation, occurring in different physiological contexts, is less understood. We found that the ER network has an embedded fragmentation mechanism based upon the ability of reticulons to produce fission of elongating network branches. In Drosophila, fission is counterbalanced by atlastin-driven fusion, with their imbalance leading to ER fragmentation. Live imaging of ER network dynamics upon ectopic expression of Drosophila reticulon linked fission to augmented membrane friction. Consistently, in vitro analysis revealed that purified reticulon produced velocity-dependent constriction and fission of lipid nanotubes pulled from a flat reservoir membrane. Fission occurred at elongation rates and pulling force ranges intrinsic to the ER network, thus suggesting a novel principle of organelle morphology regulation where the dynamic balance between fusion and fission is governed by membrane motility.

cell biology↗