Biology subjects

Fakhri, N.

Publications and source records attributed to Fakhri, N..

5 recordsLinked to original sources

bioRxiv2024

Nonequilibrium phases of a biomolecular condensate facilitated by enzyme activity

Biomolecular condensates represent a frontier in cellular organization, existing as dynamic materials driven out of equilibrium by active cellular processes. Here we explore active mechanisms of condensate regulation by examining the interplay between DEAD-box helicase activity and RNA base-pairing interactions within ribonucleoprotein condensates. We demonstrate how the ATP-dependent activity of DEAD-box helicases--a key class of enzymes in condensate regulation--acts as a nonequilibrium driver of condensate properties through the continuous remodeling of RNA interactions. By combining the LAF-1 DEAD-box helicase with a designer RNA hairpin concatemer, we unveil a complex landscape of dynamic behaviors, including time-dependent alterations in RNA partitioning, evolving condensate morphologies, and shifting condensate dynamics. Importantly, we reveal an antagonistic relationship between RNA secondary structure and helicase activity which promotes condensate homogeneity via a nonequilibrium steady state. By elucidating these nonequilibrium mechanisms, we gain a deeper understanding of cellular organization and expand the potential for active synthetic condensate systems.

biophysics↗

bioRxiv2024

Sequence programmable nucleic acid coacervates

Nature uses bottom-up self-assembly to build structures with remarkable complexity and functionality. Understanding how molecular-scale interactions translate to macroscopic properties remains a major challenge and requires systems that effectively bridge these two scales. Here, we generate DNA and RNA liquids with exquisite programmability in their material properties. Nucleic acids are negatively charged, and in the presence of polycations, they may condense to a liquid-like state. Within these liquids, DNA and RNA retain sequence-specific hybridization abilities. We show that intermolecular hybridization in the condensed phase cross-links molecules and slows down chain dynamics. This reduced chain mobility is mirrored in the macroscopic properties of the condensates. Molecular diffusivity and material viscosity scale with the intermolecular hybridization energy, enabling precise sequence-based modulation of condensate properties over orders of magnitude. Our work offers a robust platform to create self-assembling programmable fluids and may help advance our understanding of liquid-like compartments in cells.

biophysics↗

bioRxiv2023

ATP-induced crosslinking of a biomolecular condensate

DEAD-box helicases are important regulators of biomolecular condensates. However, the mechanisms through which these enzymes affect the dynamics of biomolecular condensates have not been systematically explored. Here, we demonstrate the mechanism by which mutation of a DEAD-box helicases catalytic core alters ribonucleoprotein condensate dynamics in the presence of ATP. Through altering RNA length within the system, we are able to attribute the altered biomolecular dynamics and material properties to physical crosslinking of RNA facilitated by the mutant helicase. These results suggest the mutant condensates approach a gel transition when RNA length is increased to lengths comparable to eukaryotic mRNA. Lastly, we show that this crosslinking effect is tunable with ATP concentration, uncovering a system whose RNA mobility and material properties vary with enzyme activity. More generally, these findings point to a fundamental mechanism for modulating condensate dynamics and emergent material properties through nonequilibrium, molecular-scale interactions. SignificanceBiomolecular condensates are membraneless organelles which organize cellular biochemistry. These structures have a diversity of material properties and dynamics which are crucial to their function. How condensate properties are determined by biomolecular interactions and enzyme activity remain open questions. DEAD-box helicases have been identified as central regulators of many protein-RNA condensates, though their specific mechanistic roles are ill-defined. In this work, we demonstrate that a DEAD-box helicase mutation crosslinks condensate RNA in an ATP-dependent fashion via protein-RNA clamping. Protein and RNA diffusion can be tuned with ATP concentration, corresponding to an order of magnitude change in condensate viscosity. These findings expand our understanding of control points for cellular biomolecular condensates that have implications for medicine and bioengineering.

biophysics↗

bioRxiv2022

Active mechanics of sea star oocytes

Cell shape changes, driven by the contractile actomyosin cortex, are essential for multicellular organisms. Yet, how contractility and cell shape changes emerge from molecular scale interactions between proteins in the actomyosin cortex remains unclear. Oocytes of the bat star Patiria miniata exhibit a traveling wave of cellular deformation during meiosis, known as a surface contraction wave (SCW). Here, we exploit this highly stereotypical deformation to study how cortical properties are set by microscale processes. By pharmacologically modulating the levels of polymerized actin, we show that the wildtype composition maximizes the cellular deformation rate. To understand these results, we developed an active fluid model for shape changes that demonstrates that deformation rates are set by the ratio between cortical viscosity and active contractile stresses and provides a framework for deriving these two key material properties from coarse-grained molecular-scale interactions. In this model, the ratio of active stress to viscosity peaks at intermediate admixtures of passive crosslinkers. This explains the observations of the drug treatment experiments and makes additional predictions, namely that overexpression of either myosin or passive crosslinkers would decrease deformation rates, which we verified experimentally. Together, this shows that the interplay between cortical active stress and viscosity relies on balancing the ratio of myosin to passive crosslinkers on each filament, which can be modulated by actin density. Our results argue that changing the relative molecular compositions of cortical crosslinks and motors provides a mechanism that biological systems could exploit for robust and predictable control over both viscosity and active stresses.

biophysics↗

bioRxiv2021

Polarized Dishevelled dissolution and condensation drives embryonic axis specification in oocytes

The organismal body axes that are formed during embryogenesis are intimately linked to intrinsic asymmetries established at the cellular scale in oocytes [1]. Here, we report an axis-defining event in meiotic oocytes of the sea star Patiria miniata. Dishevelled is a cytoplasmic Wnt pathway effector required for axis development in diverse species [2-4], but the mechanisms governing its function and distribution remain poorly defined. Using time-lapse imaging, we find that Dishevelled localizes uniformly to puncta throughout the cell cortex in Prophase I-arrested oocytes, but becomes enriched at the vegetal pole following meiotic resumption through a dissolution-condensation mechanism. This process is driven by an initial disassembly phase of Dvl puncta, followed by selective reformation of Dvl assemblies at the vegetal pole. Rather than being driven by Wnt signaling, this localization behavior is coupled to meiotic cell cycle progression and influenced by Lamp1+ endosome association and Frizzled receptors pre-localized within the oocyte cortex. Our results reveal a cell cycle-linked mechanism by which maternal cellular polarity is transduced to the embryo through spatially-regulated Dishevelled dynamics.

cell biology↗