A cryo-tomography-based volumetric model of the actin core of mouse vestibular hair cell stereocilia lacking plastin 1

Untangling Irregular Actin Cytoskeleton Architectures in Tomograms of the Cell with Struwwel Tracer

In this work, we established, validated, and optimized a novel computational framework for tracing arbitrarily oriented actin filaments in cryo-electron tomography maps. Our approach was designed for highly complex intracellular architectures in which a long-range cytoskeleton network extends throughout the cell bodies and protrusions. The irregular organization of the actin network, as well as cryo-electron-tomography-specific noise, missing wedge artifacts, and map dimensions call for a specialized implementation that is both robust and efficient. Our proposed solution, Struwwel Tracer, accumulates densities along paths of a specific length in various directions, starting from locally determined seed points. The highest-density paths originating from the seed points form short linear candidate filament segments, which are further scrutinized and classified by users via inspection of a novel pruning map, which visualizes the likelihood of being a part of longer filaments. The pruned linear candidate filament segments are then iteratively fused into continuous, longer, and curved filaments based on their relative orientations, gap spacings, and extendibility. When applied to the simulated phantom tomograms of a Dictyostelium discoideum filopodium under experimental conditions, Struwwel Tracer demonstrated high efficacy, with F1-scores ranging from 0.85 to 0.90, depending on the noise level. Furthermore, when applied to a previously untraced experimental tomogram of mouse fibroblast lamellipodia, the filaments predicted by Struwwel Tracer exhibited a good visual agreement with the experimental map. The Struwwel Tracer framework is highly time efficient and can complete the tracing process in just a few minutes. The source code is publicly available with version 3.2 of the free and open-source Situs software package.

The actin cytoskeleton in hair bundle development and hearing loss

Inner ear hair cells assemble mechanosensitive hair bundles on their apical surface that transduce sounds and accelerations. Each hair bundle is comprised of ∼ 100 individual stereocilia that are arranged into rows of increasing height and width; their specific and precise architecture being necessary for mechanoelectrical transduction (MET). The actin cytoskeleton is fundamental to establishing this architecture, not only by forming the structural scaffold shaping each stereocilium, but also by composing rootlets and the cuticular plate that together provide a stable foundation supporting each stereocilium. In concert with the actin cytoskeleton, a large assortment of actin-binding proteins (ABPs) function to cross-link actin filaments into specific topologies, as well as control actin filament growth, severing, and capping. These processes are individually critical for sensory transduction and are all disrupted in hereditary forms of human hearing loss. In this review, we provide an overview of actin-based structures in the hair bundle and the molecules contributing to their assembly and functional properties. We also highlight recent advances in mechanisms driving stereocilia elongation and how these processes are tuned by MET.

Spaghetti Tracer: A Framework for Tracing Semiregular Filamentous Densities in 3D Tomograms

Within cells, cytoskeletal filaments are often arranged into loosely aligned bundles. These fibrous bundles are dense enough to exhibit a certain regularity and mean direction, however, their packing is not sufficient to impose a symmetry between—or specific shape on—individual filaments. This intermediate regularity is computationally difficult to handle because individual filaments have a certain directional freedom, however, the filament densities are not well segmented from each other (especially in the presence of noise, such as in cryo-electron tomography). In this paper, we develop a dynamic programming-based framework, Spaghetti Tracer, to characterizing the structural arrangement of filaments in the challenging 3D maps of subcellular components. Assuming that the tomogram can be rotated such that the filaments are oriented in a mean direction, the proposed framework first identifies local seed points for candidate filament segments, which are then grown from the seeds using a dynamic programming algorithm. We validate various algorithmic variations of our framework on simulated tomograms that closely mimic the noise and appearance of experimental maps. As we know the ground truth in the simulated tomograms, the statistical analysis consisting of precision, recall, and F1 scores allows us to optimize the performance of this new approach. We find that a bipyramidal accumulation scheme for path density is superior to straight-line accumulation. In addition, the multiplication of forward and backward path densities provides for an efficient filter that lifts the filament density above the noise level. Resulting from our tests is a robust method that can be expected to perform well (F1 scores 0.86–0.95) under experimental noise conditions.

Allosteric regulation controls actin-bundling properties of human plastins

Plastins/fimbrins are conserved actin-bundling proteins contributing to motility, cytokinesis and other cellular processes by organizing strikingly different actin assemblies as in aligned bundles and branched networks. We propose that this ability of human plastins stems from an allosteric communication between their actin-binding domains (ABD1/2) engaged in a tight spatial association. Here we show that ABD2 can bind actin three orders of magnitude stronger than ABD1, unless the domains are involved in an equally strong inhibitory engagement. A mutation mimicking physiologically relevant phosphorylation at the ABD1-ABD2 interface greatly weakened their association, dramatically potentiating actin cross-linking. Cryo-EM reconstruction revealed the ABD1-actin interface and enabled modeling of the plastin bridge and domain separation in parallel bundles. We predict that a strong and tunable allosteric inhibition between the domains allows plastins to modulate the cross-linking strength, contributing to remodeling of actin assemblies of different morphologies defining the unique place of plastins in actin organization.

ANKRD24 organizes TRIOBP to reinforce stereocilia insertion points

The stereocilia rootlet is a key structure in vertebrate hair cells, anchoring stereocilia firmly into the cell's cuticular plate and protecting them from overstimulation. Using superresolution microscopy, we show that the ankyrin-repeat protein ANKRD24 concentrates at the stereocilia insertion point, forming a ring at the junction between the lower and upper rootlets. Annular ANKRD24 continues into the lower rootlet, where it surrounds and binds TRIOBP-5, which itself bundles rootlet F-actin. TRIOBP-5 is mislocalized in Ankrd24KO/KO hair cells, and ANKRD24 no longer localizes with rootlets in mice lacking TRIOBP-5; exogenous DsRed-TRIOBP-5 restores endogenous ANKRD24 to rootlets in these mice. Ankrd24KO/KO mice show progressive hearing loss and diminished recovery of auditory function after noise damage, as well as increased susceptibility to overstimulation of the hair bundle. We propose that ANKRD24 bridges the apical plasma membrane with the lower rootlet, maintaining a normal distribution of TRIOBP-5. Together with TRIOBP-5, ANKRD24 organizes rootlets to enable hearing with long-term resilience.

Molecular structures and conformations of protocadherin-15 and its complexes on stereocilia elucidated by cryo-electron tomography

Mechanosensory transduction (MT), the conversion of mechanical stimuli into electrical signals, underpins hearing and balance and is carried out within hair cells in the inner ear. Hair cells harbor actin-filled stereocilia, arranged in rows of descending heights, where the tips of stereocilia are connected to their taller neighbors by a filament composed of protocadherin 15 (PCDH15) and cadherin 23 (CDH23), deemed the ‘tip link.’ Tension exerted on the tip link opens an ion channel at the tip of the shorter stereocilia, thus converting mechanical force into an electrical signal. While biochemical and structural studies have provided insights into the molecular composition and structure of isolated portions of the tip link, the architecture, location, and conformational states of intact tip links, on stereocilia, remains unknown. Here, we report in situ cryo-electron microscopy imaging of the tip link in mouse stereocilia. We observe individual PCDH15 molecules at the tip and shaft of stereocilia and determine their stoichiometry, conformational heterogeneity, and their complexes with other filamentous proteins, perhaps including CDH23. The PCDH15 complexes occur in clusters, frequently with more than one copy of PCDH15 at the tip of stereocilia, suggesting that tip links might consist of more than one copy of PCDH15 complexes and, by extension, might include multiple MT complexes.

TomoSim: Simulation of Filamentous Cryo-Electron Tomograms

As automated filament tracing algorithms in cryo-electron tomography (cryo-ET) continue to improve, the validation of these approaches has become more incumbent. Having a known ground truth on which to base predictions is crucial to reliably test predicted cytoskeletal filaments because the detailed structure of the filaments in experimental tomograms is obscured by a low resolution, as well as by noise and missing Fourier space wedge artifacts. We present a software tool for the realistic simulation of tomographic maps (TomoSim) based on a known filament trace. The parameters of the simulated map are automatically matched to those of a corresponding experimental map. We describe the computational details of the first prototype of our approach, which includes wedge masking in Fourier space, noise color, and signal-to-noise matching. We also discuss current and potential future applications of the approach in the validation of concurrent filament tracing methods in cryo-ET.

Tracing Filaments in Simulated 3D Cryo-Electron Tomography Maps Using a Fast Dynamic Programming Algorithm

We propose a fast, dynamic programming-based framework for tracing actin filaments in 3D maps of subcellular components in cryo-electron tomography. The approach can identify high-density filament segments in various orientations, but it takes advantage of the arrangement of actin filaments within cells into more or less tightly aligned bundles. Assuming that the tomogram can be rotated such that the filaments can be oriented to be directed in a dominant direction (i.e., the X, Y, or Z axis), the proposed framework first identifies local seed points that form the origin of candidate filament segments (CFSs), which are then grown from the seeds using a fast dynamic programming algorithm. The CFS length l can be tuned to the nominal resolution of the tomogram or the separation of desired features, or it can be used to restrict the curvature of filaments that deviate from the overall bundle direction. In subsequent steps, the CFSs are filtered based on backward tracing and path density analysis. Finally, neighboring CFSs are fused based on a collinearity criterion to bridge any noise artifacts in the 3D map that would otherwise fractionalize the tracing. We validate our proposed framework on simulated tomograms that closely mimic the features and appearance of experimental maps.

Correction of Missing-Wedge Artifacts in Filamentous Tomograms by Template-Based Constrained Deconvolution

Cryo-electron tomography maps often exhibit considerable noise and anisotropic resolution, due to the low-dose requirements and the missing wedge in Fourier space. These spurious features are visually unappealing and, more importantly, prevent an automated segmentation of geometric shapes, requiring a subjective and labor-intensive manual tracing. We developed a novel computational strategy for objectively denoising and correcting missing-wedge artifacts in homogeneous specimen areas of tomograms, where it is assumed that a template repeats itself across the volume under consideration, as happens in the case of filaments. In our deconvolution approach, we use a template and a map of corresponding template locations, allowing us to compensate for the information lost in the missing wedge. We applied the method to tomograms of actin-filament bundles of inner-ear stereocilia, which are critical for the senses of hearing and balance. In addition, we demonstrate that our method can be used for cell membrane detection.