Biology subjects

Heydari, S.

Publications and source records attributed to Heydari, S..

8 recordsLinked to original sources

bioRxiv2026

Dynamics and activation of the Legionella Type IV secretion system

Legionella pneumophila uses the Dot/Icm type IV secretion system (T4SS) to translocate hundreds of effector proteins into host cells, yet how this transenvelope machine assembles and becomes secretion competent remains poorly understood. Here, using cryo-electron tomography and in situ single-particle cryo-electron microscopy, we resolve distinct structural and functional states of the native Dot/Icm T4SS. Unexpectedly, the T4SS predominantly occupies a resting state containing the outer membrane core complex but lacking the inner-membrane complex, including DotA. Recruitment of inner-membrane components establishes a fully assembled but secretion-inactive primed state. A 3.6 [A] cryo-EM structure of the DotO-DotI-DotJ-IcmT complex, integrated with in situ reconstructions, reveals how membrane-associated components organize DotO into a hexamer of dimers ATPase platform. Upon host contact, the T4SS undergoes extensive conformational remodeling while preserving its transenvelope scaffold. Activation involves dilation of the DotG outer membrane gate and transformation of the DotA-IcmX protochannel into an open translocation conduit that extends beyond the bacterial surface. Substrate-associated state exhibit further channel expansion, revealing structural plasticity associated with effector translocation. During macrophage infection, the extracellular conduit bridges the bacterial and host membranes, establishing a direct pathway for effector delivery. Together, our findings reveal a stepwise mechanism of Dot/Icm T4SS channel assembly and activation, in which coordinated remodeling of the secretion channel converts a resting apparatus into a host-engaged translocation machine.

microbiology↗

bioRxiv2026

The pod components of the Shigella T3SS sorting platform accommodate multiple copies of Spa33 (SctQ)

The bacterial type III secretion system (T3SS) uses a membrane-embedded injectisome assembly to export effector proteins into host cells. While atomic-level structural details have been revealed for much of the T3SS apparatus, the model of the cytoplasmic sorting platform remains largely low-resolution. A central structural element of the sorting platform is the so-called "pod" protein, SctQ, which anchors the sorting platform to the inner membrane via interaction with the adaptor protein SctK, and connects to the central ATPase via the spoke protein SctL. SctQ proteins also interact with alternatively translated homodimers of their C-terminal SPOA2 domains. Low resolution electron density maps have provided an outline of the sorting platform architecture, and fluorescence microscopy studies have suggested a 1:4:2 SctK:SctQ:SctL stoichiometry. While there are experimental and AlphaFold structures of the individual components or complexes of sorting platform pod, there is currently no model for the pod structure that adequately fits the electron density or accounts for the proposed stoichiometry. Here we use AlphaFold to generate a model of the Shigella pod complex in which two copies of the SctQ protein, Spa33, bind the adaptor protein MxiK, with each copy of Spa33 bound to an alternately translated SPOA2-SPOA2 domain. We show through mutation of energetically critical interface residues, predicted by computational mutant scanning, that both Spa33 binding sites on MxiK are required for T3SS activity in Shigella flexneri, as well as binding of Spa33 to the SPOA2-SPOA2 homodimer. We find that this model fits well to the upper two-thirds of the pod electron density, albeit in a manner that places the protein components slightly closer to the inner membrane than traditionally presented. Further, cryogenic electron tomography of mutant injectisomes reveals the lack of a complete sorting platform and may suggest an alternative model featuring four copies of Spa33 that still fits the upper pod electron density but better explains unfilled density in the lower third of the pod.

biochemistry↗

bioRxiv2025

Assembly and glycosylation of Helicobacter pylori sheathed flagella

The bacterial flagellum is a complex nanomachine essential for motility, colonization, and invasion in diverse species. Helicobacter pylori has evolved elaborate sheathed flagella that enable migration through the highly viscous gastric mucus layer to reach its colonization niche on the gastric epithelium, yet the molecular basis for these unique adaptations has remained elusive. Here, we use in-situ single particle cryo-electron microscopy to determine near-atomic structures of the flagellar filament within the membranous sheath of H. pylori. The major flagellin FlaA constitutes the bulk of the filament, whereas the minor flagellin FlaB contributes critically to the hook-proximal region. Both FlaA and FlaB form a conserved core surrounded by variable surface-exposed domains. Our structures further reveal that pseudaminic-acid glycans decorate these domains, where they mediate inter- and intra-subunit contacts that stabilize the filament and confer a negatively charged surface. Together, these findings support a model in which the filament rotates independently of the membranous sheath to drive H. pylori motility and provide a molecular framework for understanding how the sheathed flagellum enables colonization and persistence within the gastric niche. Significance StatementWe present the first in-situ near-atomic structure of the sheathed flagellar filament in Helicobacter pylori, revealing distinctive adaptations that underpin the pathogens unique motility and persistent infection. Our in-situ structures show that the two flagellins, FlaA and FlaB, assemble into an extended and exceptionally stable filament through an extensive hydrogen-bonding network. Pseudaminic acid glycans decorate the surface-exposed domains, where they stabilize inter-subunit packing and render the surface negatively charged and hydrophilic. These findings, which provide insight into the assembly of the flagellar filament and its relationship to the surrounding sheath, provide a structural framework for developing strategies to disrupt H. pylori motility and infection.

microbiology↗

bioRxiv2025

In-situ structures of the Legionella Dot/Icm T4SS identify the DotA-IcmX complex as the gatekeeper for effector translocation

The Dot/Icm machine in Legionella pneumophila is one of the most versatile type IV secretion systems (T4SSs), with a remarkable capacity to translocate over 330 different effector proteins across the bacterial envelope into host cells. At least 27 Dot and Icm proteins are required for assembly and function of the system, yet the architecture and activation mechanism remain poorly understood at the molecular level. Here, we deploy cryo-electron microscopy to reveal in-situ structures of the Dot/Icm machine at near-atomic resolution. Importantly, two proteins essential for effector translocation, DotA and IcmX, form a pentameric protochannel at an inactive state. Upon activation, the DotA-IcmX protochannel undergoes extensive rearrangements to form an extended transenvelope passage capable of transporting effector proteins from the bacterial cytoplasm into host cells as revealed by cryo-electron tomography. Collectively, our findings suggest that the DotA-IcmX complex functions as the gatekeeper for effector translocation of the Dot/Icm T4SS.

molecular biology↗

bioRxiv2025

Tube feet dynamics drive adaptation in sea star locomotion

Sea stars use hundreds of tube feet on their oral surface to crawl, climb, and navigate complex environments--all without the coordination of a central brain. While the morphology of tube feet and their role as muscular hydrostats are well described, the dynamics underlying their locomotion remain poorly understood. To investigate these dynamics, we employed an optical imaging method based on frustrated total internal reflection to visualize and quantify tube foot adhesion in real time across individuals of Asterias rubens spanning a wide size range. Our results reveal an inverse relationship between crawling speed and the duration of tube foot contact with the substrate. This suggests that sea stars regulate locomotion by modulating foot-substrate interaction time in response to body load. To test this, we conducted perturbation experiments using 3D-printed backpacks that increased body mass by 25% and 50%, along with numerical simulations based on a mechanistic model incorporating decentralized feedback control of the tube feet. The added load significantly increased adhesion time, supporting the role of a load-dependent mechanical adaptation. We further investigated inverted locomotion, both experimentally and through simulation, and found that tube feet adjust their contact behavior when the animal is oriented upside down relative to gravity. Together, our findings demonstrate that sea stars adapt their locomotion to changing mechanical demands by modulating tube foot-substrate interactions, revealing a robust, decentralized strategy for navigating diverse and challenging terrains.

biophysics↗

bioRxiv2024

Soft skeletons transmit force with variable gearing

A hydrostatic skeleton allows a soft body to transmit muscular force via internal pressure. A humans tongue, an octopus arm, and a nematodes body illustrate the pervasive presence of hydrostatic skeletons among animals, which has inspired the design of soft engineered actuators. However, there is a need for a theoretical basis for understanding how hydrostatic skeletons apply mechanical work. We therefore model the shape change and mechanics of natural and engineered hydrostatic skeletons to determine their mechanical advantage (MA) and displacement advantage (DA). These models apply to a variety of biological structures, but we explicitly consider the tube feet of a sea star and the body segments of an earthworm, and contrast them with a hydraulic press and a McKibben actuator. A helical winding of stiff, elastic fibers around these soft actuators plays a critical role in their mechanics by maintaining a cylindrical shape, distributing forces throughout the structure, and storing elastic energy. In contrast to a single-joint lever system, soft hydrostats exhibit variable gearing with changes in MA generated by deformation in the skeleton. We found that this gearing is affected by the transmission efficiency of mechanical work (MA x DA) or, equivalently, the ratio of output to input work), which changes with the capacity to store elastic energy within helically wrapped fibers or associated musculature. This modeling offers a conceptual basis for understanding the relationship between the morphology of hydrostatic skeletons and their mechanical performance.

zoology↗

bioRxiv2024

Mapping Spatial Patterns to Energetic Benefits in Groups of Flow-coupled Swimmers

The coordinated motion of animal groups through fluids is thought to reduce the cost of locomotion to individuals in the group. However, the connection between the spatial patterns observed in collectively moving animals and the energetic benefits at each position within the group remains unclear. To address this knowledge gap, we study the spontaneous emergence of cohesive formations in groups of fish, modeled as flapping foils, all heading in the same direction. We show in pairwise formations and with increasing group size that (1) in side-by-side arrangements, the reciprocal nature of flow coupling results in an equal distribution of energy re-quirements among all members, with reduction in cost of locomotion for swimmers flapping inphase but an increase in cost for swimmers flapping antiphase, and (2) in inline arrangements, flow coupling is non-reciprocal for all flapping phase, with energetic savings in favor of trailing swimmers, but only up to a finite number of swimmers, beyond which school cohesion and energetic benefits are lost at once. We explain these findings mechanistically and we provide efficient diagnostic tools for identifying locations in the wake of single and multiple swimmers that offer op-portunities for hydrodynamic benefits to aspiring followers. Our results imply a connection between the resources generated by flow physics and social traits that influence greedy and cooperative group behavior.

biophysics↗

bioRxiv2023

Interpretable and Generalizable Strategies for Stably Following Hydrodynamic Trails

Aquatic animals offer compelling evidence that flow sensing alone, without vision, is sufficient to guide a swimming organism to the source of an unsteady hydrodynamic trail. However, the sensory feedback strategies that allow these remarkable trail tracking abilities remain opaque. Here, by integrating mechanistic flow simulations with reinforcement learning techniques, we discovered two simple and equally effective strategies for hydrodynamic trail following. Though not a priori obvious, these strategies possess parsimonious interpretations, analogous to Braitenbergs simplest vehicles, where the agent senses local flow signals and turns away from or toward the direction of stronger signals. A rigorous stability analysis shows that the effectiveness of these strategies in robustly tracking flow currents is independent of the type of sensor but depends on sensor placement and the traveling nature of the flow signal. Importantly, these results inform a suite of versatile strategies for hydrodynamic trail following applicable to both vortical and turbulent flows. These insights support the future design and implementation of adaptive real-time sensory feedback strategies for autonomous robots in dynamic flow environments.

biophysics↗