Visualizing cellular processes at the molecular level by cryo-electron tomography

Strategies for the Viral Exploitation of Nuclear Pore Transport Pathways

Viruses frequently exploit the host's nucleocytoplasmic trafficking machinery to facilitate their replication and evade immune defenses. By encoding specialized proteins and other components, they strategically target host nuclear transport receptors (NTRs) and nucleoporins within the spiderweb-like inner channel of the nuclear pore complex (NPC), enabling efficient access to the host nucleus. This review explores the intricate mechanisms governing the nuclear import and export of viral components, with a focus on the interplay between viral factors and host determinants that are essential for these processes. Given the pivotal role of nucleocytoplasmic shuttling in the viral life cycle, we also examine therapeutic strategies aimed at disrupting the host's nuclear transport pathways. This includes evaluating the efficacy of pharmacological inhibitors in impairing viral replication and assessing their potential as antiviral treatments. Furthermore, we emphasize the need for continued research to develop targeted therapies that leverage vulnerabilities in nucleocytoplasmic trafficking. Emerging high-resolution techniques, such as advanced imaging and computational modeling, are transforming our understanding of the dynamic interactions between viruses and the NPC. These cutting-edge tools are driving progress in identifying novel therapeutic opportunities and uncovering deeper insights into viral pathogenesis. This review highlights the importance of these advancements in paving the way for innovative antiviral strategies.

Recognition of necroptosis: From molecular mechanisms to detection methods

Necroptosis is a crucial modality of programmed cell death characterized by distinct morphological and biochemical hallmarks, including cell membrane rupture, organelle swelling, cytoplasmic and nuclear disintegration, cellular contents leakage, and release of damage-associated molecular patterns (DAMPs), accompanied by the inflammatory responses. Studies have shown that necroptosis is involved in the etiology and evolution of a variety of pathologies including organ damage, inflammation disorders, and cancer. Despite its significance, the field of necroptosis research grapples with the challenge of non-standardized detection methodologies. In this review, we introduce the fundamental concepts and molecular mechanisms of necroptosis and critically appraise the principles, merits, and inherent limitations of current detection technologies. This endeavor seeks to establish a methodological framework for necroptosis detection, thereby propelling deeper insights into the research of cell necroptosis.

Filament assembly of the C. elegans lamin in the absence of helix 1A

Lamins are the major constituent of the nuclear lamina, a protein meshwork underlying the inner nuclear membrane. Nuclear lamins are type V intermediate filaments that assemble into ~3.5 nm thick filaments. To date, only the conditions for the in vitro assembly of Caenorhabditis elegans lamin (Ce-lamin) are known. Here, we investigated the assembly of Ce-lamin filaments by cryo-electron microscopy and tomography. We show that Ce-lamin is composed of ~3.5 nm protofilaments that further interact in vitro and are often seen as 6–8 nm thick filaments. We show that the assembly of lamin filaments is undisturbed by the removal of flexible domains, that is, the intrinsically unstructured head and tail domains. In contrast, much of the coiled-coil domains are scaffold elements that are essential for filament assembly. Moreover, our results suggest that Ce-lamin helix 1A has a minor scaffolding role but is important to the lateral assembly regulation of lamin protofilaments.

Progress of tubulin polymerization activity detection methods

Tubulin, an important target in tumor therapy, is one of the hotspots in the field of antineoplastic drugs in recent years, and it is of great significance to design and screen new inhibitors for this target. Natural products and chemical synthetic drugs are the main sources of tubulin inhibitors. However, due to the variety of compound structure types, it has always been difficult for researchers to screen out polymerization inhibitors with simple operation, high efficiency and low cost. A large number of articles have reported the screening methods of tubulin inhibitors and their biological activity. In this article, the biological activity detection methods of tubulin polymerization inhibitors are reviewed. Thus, it provides a theoretical basis for the further study of tubulin polymerization inhibitors and the selection of methods for tubulin inhibitors.

The molecular architecture of engulfment during Bacillus subtilis sporulation

The study of bacterial cell biology is limited by difficulties in visualizing cellular structures at high spatial resolution within their native milieu. Here, we visualize Bacillus subtilis sporulation using cryo-electron tomography coupled with cryo-focused ion beam milling, allowing the reconstruction of native-state cellular sections at molecular resolution. During sporulation, an asymmetrically-positioned septum generates a larger mother cell and a smaller forespore. Subsequently, the mother cell engulfs the forespore. We show that the septal peptidoglycan is not completely degraded at the onset of engulfment. Instead, the septum is uniformly and only slightly thinned as it curves towards the mother cell. Then, the mother cell membrane migrates around the forespore in tiny finger-like projections, whose formation requires the mother cell SpoIIDMP protein complex. We propose that a limited number of SpoIIDMP complexes tether to and degrade the peptidoglycan ahead of the engulfing membrane, generating an irregular membrane front.

Feature Decomposition Based Saliency Detection in Electron Cryo-Tomograms

Electron Cryo-Tomography (ECT) allows 3D visualization of subcellular structures at the submolecular resolution in close to the native state. However, due to the high degree of structural complexity and imaging limits, the automatic segmentation of cellular components from ECT images is very difficult. To complement and speed up existing segmentation methods, it is desirable to develop a generic cell component segmentation method that is 1) not specific to particular types of cellular components, 2) able to segment unknown cellular components, 3) fully unsupervised and does not rely on the availability of training data. As an important step towards this goal, in this paper, we propose a saliency detection method that computes the likelihood that a subregion in a tomogram stands out from the background. Our method consists of four steps: supervoxel over-segmentation, feature extraction, feature matrix decomposition, and computation of saliency. The method produces a distribution map that represents the regions' saliency in tomograms. Our experiments show that our method can successfully label most salient regions detected by a human observer, and able to filter out regions not containing cellular components. Therefore, our method can remove the majority of the background region, and significantly speed up the subsequent processing of segmentation and recognition of cellular components captured by ECT.

Microtubule structure by cryo-EM: snapshots of dynamic instability

The development of cryo-electron microscopy (cryo-EM) allowed microtubules to be captured in their solution-like state, enabling decades of insight into their dynamic mechanisms and interactions with binding partners. Cryo-EM micrographs provide 2D visualization of microtubules, and these 2D images can also be used to reconstruct the 3D structure of the polymer and any associated binding partners. In this way, the binding sites for numerous components of the microtubule cytoskeleton-including motor domains from many kinesin motors, and the microtubule-binding domains of dynein motors and an expanding collection of microtubule associated proteins-have been determined. The effects of various microtubule-binding drugs have also been studied. High-resolution cryo-EM structures have also been used to probe the molecular basis of microtubule dynamic instability, driven by the GTPase activity of β-tubulin. These studies have shown the conformational changes in lattice-confined tubulin dimers in response to steps in the tubulin GTPase cycle, most notably lattice compaction at the longitudinal inter-dimer interface. Although work is ongoing to define a complete structural model of dynamic instability, attention has focused on the role of gradual destabilization of lateral contacts between tubulin protofilaments, particularly at the microtubule seam. Furthermore, lower resolution cryo-electron tomography 3D structures are shedding light on the heterogeneity of microtubule ends and how their 3D organization contributes to dynamic instability. The snapshots of these polymers captured using cryo-EM will continue to provide critical insights into their dynamics, interactions with cellular components, and the way microtubules contribute to cellular functions in diverse physiological contexts.

From Atoms to Cells: Using Mesoscale Landscapes to Construct Visual Narratives

Modeling and visualization of the cellular mesoscale, bridging the nanometer scale of molecules to the micrometer scale of cells, is being studied by an integrative approach. Data from structural biology, proteomics, and microscopy are combined to simulate the molecular structure of living cells. These cellular landscapes are used as research tools for hypothesis generation and testing, and to present visual narratives of the cellular context of molecular biology for dissemination, education, and outreach.

An updated look at actin dynamics in filopodia

Cells dynamically interact with and probe their environment by growing finger-like structures named filopodia. The dynamics of filopodia are mainly caused by the actin rich core or shaft which sits inside the filopodial membrane and continuously undergoes changes like growth, shrinking, bending, and rotation. Recent experiments combining advanced imaging and manipulation tools have provided detailed quantitative data on the correlation between mechanical properties of filopodia, their molecular composition, and the dynamic architecture of the actin structure. These experiments have revealed how retrograde flow and twisting of the actin shaft within filopodia can generate traction on external substrates. Previously, the mechanism behind filopodial pulling was mainly attributed to retrograde flow of actin, but recent experiments have shown that rotational dynamics can also contribute to the traction force. Although force measurements have indicated a step-like behavior in filopodial pulling, no direct evidence has been provided to link this behavior to a molecular motor like myosin. Therefore, the underlying biochemical and mechanical mechanisms behind filopodial force generation still remain to be resolved.

Imaging Cytoskeleton Components by Electron Microscopy

The cytoskeleton is a complex of detergent-insoluble components of the cytoplasm playing critical roles in cell motility, shape generation, and mechanical properties of a cell. Fibrillar polymers-actin filaments, microtubules, and intermediate filaments-are major constituents of the cytoskeleton, which constantly change their organization during cellular activities. The actin cytoskeleton is especially polymorphic, as actin filaments can form multiple higher order assemblies performing different functions. Structural information about cytoskeleton organization is critical for understanding its functions and mechanisms underlying various forms of cellular activity. Because of the nanometer-scale thickness of cytoskeletal fibers, electron microscopy (EM) is a key tool to determine the structure of the cytoskeleton. This article describes application of rotary shadowing (or metal replica) EM for visualization of the cytoskeleton. The procedure is applicable to thin cultured cells growing on glass coverslips and consists of detergent extraction of cells to expose their cytoskeleton, chemical fixation to provide stability, ethanol dehydration and critical point drying to preserve three-dimensionality, rotary shadowing with platinum to create contrast, and carbon coating to stabilize replicas. This technique provides easily interpretable three-dimensional images, in which individual cytoskeletal fibers are clearly resolved, and individual proteins can be identified by immunogold labeling. More importantly, replica EM is easily compatible with live cell imaging, so that one can correlate the dynamics of a cell or its components, e.g., expressed fluorescent proteins, with high resolution structural organization of the cytoskeleton in the same cell.

Cellular structural biology as revealed by cryo-electron tomography

Understanding the function of cellular machines requires a thorough analysis of the structural elements that underline their function. Electron microscopy (EM) has been pivotal in providing information about cellular ultrastructure, as well as macromolecular organization. Biological materials can be physically fixed by vitrification and imaged with cryo-electron tomography (cryo-ET) in a close-to-native condition. Using this technique, one can acquire three-dimensional (3D) information about the macromolecular architecture of cells, depict unique cellular states and reconstruct molecular networks. Technical advances over the last few years, such as improved sample preparation and electron detection methods, have been instrumental in obtaining data with unprecedented structural details. This presents an exciting opportunity to explore the molecular architecture of both individual cells and multicellular organisms at nanometer to subnanometer resolution. In this Commentary, we focus on the recent developments and in situ applications of cryo-ET to cell and structural biology.

Dynamic buckling of actin within filopodia

Filopodia are active tubular structures protruding from the cell surface which allow the cell to sense and interact with the surrounding environment through repetitive elongation-retraction cycles. The mechanical behavior of filopodia has been studied by measuring the traction forces exerted on external substrates.¹ These studies have revealed that internal actin flow can transduce a force across the cell surface through transmembrane linkers like integrins. In addition to the elongation-retraction behavior filopodia also exhibit a buckling and rotational behavior. Filopodial buckling in conjunction with rotation enables the cell to explore a much larger 3-dimensional space and allows for more complex, and possibly stronger, interactions with the external environment.² Here we focus on how bending of the filopodial actin dynamically correlates with pulling on an optically trapped microsphere which acts like an external substrate attached to the filopodial tip. There is a clear correlation between presence of actin near the tip and exertion of a traction force, thus demonstrating that the traction force is transduced along the actin shaft inside the filopodium. By extending a filopodium and holding it while measuring the cellular response, we also monitor and analyze the waiting times for the first buckle observed in the fluorescently labeled actin shaft.

Dictionary-learning-based reconstruction method for electron tomography

Electron tomography usually suffers from so-called “missing wedge” artifacts caused by limited tilt angle range. An equally sloped tomography (EST) acquisition scheme (which should be called the linogram sampling scheme) was recently applied to achieve 2.4-angstrom resolution. On the other hand, a compressive sensing inspired reconstruction algorithm, known as adaptive dictionary based statistical iterative reconstruction (ADSIR), has been reported for X-ray computed tomography. In this paper, we evaluate the EST, ADSIR, and an ordered-subset simultaneous algebraic reconstruction technique (OS-SART), and compare the ES and equally angled (EA) data acquisition modes. Our results show that OS-SART is comparable to EST, and the ADSIR outperforms EST and OS-SART. Furthermore, the equally sloped projection data acquisition mode has no advantage over the conventional equally angled mode in this context.

Structural analysis of supramolecular assemblies by cryo-electron tomography

Structural analysis of macromolecular assemblies in their physiological environment is a challenging task that is instrumental in answering fundamental questions in cellular and molecular structural biology. The continuous development of computational and analytical tools for cryo-electron tomography (cryo-ET) enables the study of these assemblies at a resolution of a few nanometers. Through the implementation of thinning procedures, cryo-ET can now be applied to the reconstruction of macromolecular structures located inside thick regions of vitrified cells and tissues, thus becoming a central tool for structural determinations in various biological disciplines. Here, we focus on the successful in situ applications of cryo-ET to reveal structures of macromolecular complexes within eukaryotic cells.

Plasma membrane--cortical cytoskeleton interactions: a cell biology approach with biophysical considerations

From a biophysical standpoint, the interface between the cell membrane and the cytoskeleton is an intriguing site where a "two-dimensional fluid" interacts with an exceedingly complex three-dimensional protein meshwork. The membrane is a key regulator of the cytoskeleton, which not only provides docking sites for cytoskeletal elements through transmembrane proteins, lipid binding-based, and electrostatic interactions, but also serves as the source of the signaling events and molecules that control cytoskeletal organization and remolding. Conversely, the cytoskeleton is a key determinant of the biophysical and biochemical properties of the membrane, including its shape, tension, movement, composition, as well as the mobility, partitioning, and recycling of its constituents. From a cell biological standpoint, the membrane-cytoskeleton interplay underlies--as a central executor and/or regulator--a multitude of complex processes including chemical and mechanical signal transduction, motility/migration, endo-/exo-/phagocytosis, and other forms of membrane traffic, cell-cell, and cell-matrix adhesion. The aim of this article is to provide an overview of the tight structural and functional coupling between the membrane and the cytoskeleton. As biophysical approaches, both theoretical and experimental, proved to be instrumental for our understanding of the membrane/cytoskeleton interplay, this review will "oscillate" between the cell biological phenomena and the corresponding biophysical principles and considerations. After describing the types of connections between the membrane and the cytoskeleton, we will focus on a few key physical parameters and processes (force generation, curvature, tension, and surface charge) and will discuss how these contribute to a variety of fundamental cell biological functions.

How filopodia pull: what we know about the mechanics and dynamics of filopodia

In recent years, the dynamic, hair-like cell protrusions called filopodia have attracted considerable attention. They have been found in a multitude of different cell types and are often called "sensory organelles," since they seem to sense the mechanical and chemical environment of a cell. Once formed, filopodia can exhibit complex behavior, they can grow and retract, push or pull, and transform into distinct structures. They are often found to make first adhesive contact with the extracellular matrix, pathogens or with adjacent cells, and to subsequently exert pulling forces. Much is known about the cytoskeletal players involved in filopodia formation, but only recently have we started to explore the mechanics of filopodia together with the related cytoskeletal dynamics. This review summarizes current advancements in our understanding of the mechanics and dynamics of filopodia, with a focus on the molecular mechanisms behind filopodial force exertion.

Correlative cryo-electron tomography and optical microscopy of cells

The biological processes occurring in a cell are complex and dynamic, and to achieve a comprehensive understanding of the molecular mechanisms underlying these processes, both temporal and spatial information is required. While cryo-electron tomography (cryoET) provides three-dimensional (3D) still pictures of near-native state cells and organelles at molecular resolution, fluorescence light microscopy (fLM) offers movies of dynamic cellular processes in living cells. Combining and integrating these two commonly used imaging modalities (termed correlative microscopy) provides a powerful means to not only expand the imaging scale and resolution but also to complement the dynamic information available from optical microscopy with the molecular-level, 3D ultrastructure detail provided by cryoET. As such, a correlative approach performed on a given specimen can provide high resolution snapshots of dynamic cellular events. In this article, I review recent advances in correlative light microscopy and cryoET and discuss major findings made available by applying this method.

Ultrastructure of protrusive actin filament arrays

The actin cytoskeleton is the major force-generating machinery in the cell, which can produce pushing, pulling, and resistance forces. To accomplish these diverse functions, actin filaments, with help of numerous accessory proteins, form higher order ensembles, networks and bundles, adapted to specific tasks. Moreover, dynamic properties of the actin cytoskeleton allow a cell to constantly build, renew, and redesign actin structures according to its changing needs. High resolution architecture of actin filament arrays provides key information for understanding mechanisms of force generation. To generate pushing force, cells use coordinated polymerization of multiple actin filaments organized into branched (dendritic) networks or parallel bundles. This review summarizes our current knowledge of the structural organization of these two actin filament arrays.

Advances in cryogenic transmission electron microscopy for the characterization of dynamic self-assembling nanostructures

Elucidating the structural information of nanoscale materials in their solvent-exposed state is crucial, as a result, cryogenic transmission electron microscopy (cryo-TEM) has become an increasingly popular technique in the materials science, chemistry, and biology communities. Cryo-TEM provides a method to directly visualize the specimen structure in a solution-state through a thin film of vitrified solvent. This technique complements X-ray, neutron, and light scattering methods that probe the statistical average of all species present; furthermore, cryo-TEM can be used to observe changes in structure over time. In the area of self-assembly, this tool has been particularly powerful for the characterization of natural and synthetic small molecule assemblies, as well as hybrid organic-inorganic composites. In this review, we discuss recent advances in cryogenic TEM in the context of self-assembling systems with emphasis on characterization of transitions observed in response to external stimuli.

Single versus dual-axis cryo-electron tomography of microtubules assembled in vitro: limits and perspectives

Single-axis cryo-electron tomography of vitrified specimens has become a method of choice to reconstruct in three dimensions macromolecular assemblies in their cellular context or prepared from purified components. Here, we asked how a dual-axis acquisition scheme would improve three-dimensional reconstructions of microtubules assembled in vitro. We show that in single-axis tomograms, microtubules oriented close to the perpendicular of the tilt axis display diminished contrast, and ultimately transform into sets of parallel lines oriented in the direction of the electron beam when observed in cross-section. Analysis of their three-dimensional Fourier transform indicates that this imaging artifact is due to a decrease in the angular sampling of their equatorial components. Although the second orthogonal series does not fully complement the first one at the specimen level due to increased radiation damage, it still allows elongated features oriented in any directions to be correctly reconstructed, which might be essential for highly heterogeneous specimens such as cells.

Vitrification of thick samples for soft X-ray cryo-tomography by high pressure freezing

Soft X-ray cryo-microscopy (cryo-XT) offers an ideal complement to electron cryo-microscopy (cryo-EM). Cryo-XT is applicable to samples more than an order of magnitude thicker than cryo-EM, albeit at a more modest resolution of tens of nanometers. Furthermore, the natural contrast obtained in the "water-window" by differential absorption by organic matter vs water yields detailed images of organelles, membranes, protein complexes, and other cellular components. Cryo-XT is thus ideally suited for tomography of eukaryotic cells. The increase in sample thickness places more stringent demands on sample preparation, however. The standard method for cryo-EM, i.e., plunging to a cryogenic fluid such as liquid ethane, is no longer ideally suited to obtain vitrification of thick samples for cryo-XT. High pressure freezing is an alternative approach, most closely associated with freeze-substitution and embedding, or with electron cryo-microscopy of vitreous sections (CEMOVIS). We show here that high pressure freezing can be adapted to soft X-ray tomography of whole vitrified samples, yielding a highly reliable method that avoids crystallization artifacts and potentially offers improved imaging conditions in samples not amenable to plunge-freezing.

Perspective on the metazoan nuclear pore complex

Fusing the inner and outer membranes of the nucleus, the nuclear pore complex (NPC) forms a selective portal which serves as the sole gateway of the nucleus. These aqueous translocation channels allow free diffusion of small molecules and ions, as well as receptor-mediated transport of large macromolecules. Over the last several years major progress has been made in both structural determination of individual nucleopurins (Nups) and their complexes by X-ray crystallography and in structural analysis of the entire assembly by means of cryo-electron tomography. By combining cryo-electron tomography with advanced image processing techniques, the metazoan NPC structure from Xenopus oocytes was resolved to medium resolution, revealing novel details. Here, we discuss new features of the Xenopus NPC and consider future perspectives that will eventually allow resolution of the structure and function of NPCs with high accuracy.

The human nuclear pore complex as revealed by cryo-electron tomography

Nuclear pore complexes (NPCs) are the sole passage through the nuclear envelope, connecting the cytoplasm to the nucleoplasm. These gigantic molecular machines, over 100 MDa in molecular weight, allow free diffusion of small molecules and ions while mediating selective energy-dependent nucleocytoplasmic transport of large macromolecules. Here, we applied cryo-electron tomography to human fibroblast cells, reconstructing their nuclear envelopes without applying any purification steps. From these reconstructions, we extracted subtomograms containing individual NPCs and utilized in silico subtomogram averaging procedures to determine the structure of the mammalian pore complex at a resolution of ∼6.6 nm. Beyond revealing the canonical features of the human NPC, our analysis identified inner lateral channels and fusing bridge-like structures, suggesting alternative routes of peripheral nuclear passage. Finally, we concluded from our structural analysis that the human NPC is structurally distinct from that of lower eukaryotes in terms of dimension and organization but resembles its amphibian (frog) counterpart.

Computational separation of conformational heterogeneity using cryo-electron tomography and 3D sub-volume averaging

We have previously used cryo-electron tomography combined with sub-volume averaging and classification to obtain 3D structures of macromolecular assemblies in cases where a single dominant species was present, and applied these methods to the analysis of a variety of trimeric HIV-1 and SIV envelope glycoproteins (Env). Here, we extend these studies by demonstrating automated, iterative, missing wedge-corrected 3D image alignment and classification methods to distinguish multiple conformations that are present simultaneously. We present a method for measuring the spatial distribution of the vector elements representing distinct conformational states of Env. We identify data processing strategies that allow clear separation of the previously characterized closed and open conformations, as well as unliganded and antibody-liganded states of Env when they are present in mixtures. We show that identifying and removing spikes with the lowest signal-to-noise ratios improves the overall accuracy of alignment between individual Env sub-volumes, and that alignment accuracy, in turn, determines the success of image classification in assessing conformational heterogeneity in heterogeneous mixtures. We validate these procedures for computational separation by successfully separating and reconstructing distinct 3D structures for unliganded and antibody-liganded as well as open and closed conformations of Env present simultaneously in mixtures.

Transmission electron microscopy studies of cellular responses to entry of virions: one kind of natural nanobiomaterial

Virions are one kind of nanoscale pathogen and are able to infect living cells of animals, plants, and bacteria. The infection is an intrinsic property of the virions, and the biological process provides a good model for studying how these nanoparticles enter into cells. During the infection, the viruses employ different strategies to which the cells have developed respective responses. For this paper, we chose Bombyx mori cypovirus 1 (BmCPV-1) interactions with midgut cells from silkworm, and severe acute respiratory syndrome (SARS) associated coronavirus interactions with Vero E6 cells, as examples to demonstrate the response of eukaryotic cells to two different types of virus from our previous studies. The bacteriophage-bacteria interactions are also introduced to elucidate how the bacteriophage conquers the barrier of cell walls in the prokaryotic cells to transport genome into the host.

[The rebirth of the ultrastructure of cilia and flagella]

The sensory and motility functions of eukaryotic cilia and flagella are essential for cell survival in protozoans and for cell differentiation and homoeostasis in metazoans. Ciliary biology has benefited early on from the input of electron microscopy. Over the last decade, the visualization of cellular structures has greatly progressed, thus it becomes timely to review the ultrastructure of cilia and flagella. Briefly touching upon the typical features of a 9+2 axoneme, we dwell extensively on the transition zone, the singlet zone, the ciliary necklace, cap and crown. The relation of the singlet zone to sensory and/or motile function, the link of the ciliary cap to microtubule dynamics and to ciliary beat, the involvement of the ciliary crown in ovocyte and mucosal propulsion, and the role of the transition zone/the ciliary necklace in axonemal stabilization, autotomy and as a diffusion barrier will all be discussed.

The structure of cell-matrix adhesions: the new frontier

Adhesions between the cell and the extracellular matrix (ECM) are mechanosensitive multi-protein assemblies that transmit force across the cell membrane and regulate biochemical signals in response to the chemical and mechanical environment. These combined functions in force transduction, signaling and mechanosensing contribute to cellular phenotypes that span development, homeostasis and disease. These adhesions form, mature and disassemble in response to actin organization and physical forces that originate from endogenous myosin activity or external forces by the extracellular matrix. Despite advances in our understanding of the protein composition, interactions and regulation, our understanding of matrix adhesion structure and organization, how forces affect this organization, and how these changes dictate specific signaling events is limited. Insights across multiple structural levels are acutely needed to elucidate adhesion structure and ultimately the molecular basis of signaling and mechanotransduction. Here we describe the challenges and recent advances and prospects for unraveling the structure of cell-matrix adhesions and their response to force.

D-CAT: Density and Clustering Annotation Tool for three dimensional electron microscopic volumes

Three dimensional (3D) electron microscopy techniques have become valuable tools for investigating cellular architecture and the processes that govern it. A vast amount of information is available in every 3D tomogram but the options for presenting this information in a clear and visually appealing way are limited. To address this, we developed D-CAT; a MatLab-application to accurately visualize the distribution of membrane proteins and/or membrane-bound structures. Presence (density) and distribution (clustering, depletion) are presented as color-coded areas on membranes. By using IMOD models both as input and output format, we ensure that the application fits within workflows common in the field of 3D electron microscopy.

Cryo electron tomography of herpes simplex virus during axonal transport and secondary envelopment in primary neurons

During herpes simplex virus 1 (HSV1) egress in neurons, viral particles travel from the neuronal cell body along the axon towards the synapse. Whether HSV1 particles are transported as enveloped virions as proposed by the ‘married’ model or as non-enveloped capsids suggested by the ‘separate’ model is controversial. Specific viral proteins may form a recruitment platform for microtubule motors that catalyze such transport. However, their subviral location has remained elusive. Here we established a system to analyze herpesvirus egress by cryo electron tomography. At 16 h post infection, we observed intra-axonal transport of progeny HSV1 viral particles in dissociated hippocampal neurons by live-cell fluorescence microscopy. Cryo electron tomography of frozen-hydrated neurons revealed that most egressing capsids were transported independently of the viral envelope. Unexpectedly, we found not only DNA-containing capsids (cytosolic C-capsids), but also capsids lacking DNA (cytosolic A-/B-capsids) in mid-axon regions. Subvolume averaging revealed lower amounts of tegument on cytosolic A-/B-capsids than on C-capsids. Nevertheless, all capsid types underwent active axonal transport. Therefore, even few tegument proteins on the capsid vertices seemed to suffice for transport. Secondary envelopment of capsids was observed at axon terminals. On their luminal face, the enveloping vesicles were studded with typical glycoprotein-like spikes. Furthermore, we noted an accretion of tegument density at the concave cytosolic face of the vesicle membrane in close proximity to the capsids. Three-dimensional analysis revealed that these assembly sites lacked cytoskeletal elements, but that filamentous actin surrounded them and formed an assembly compartment. Our data support the ‘separate model’ for HSV1 egress, i.e. progeny herpes viruses being transported along axons as subassemblies and not as complete virions within transport vesicles.

Herpes simplex virus 1 (HSV1) establishes lifelong latent infections in the peripheral nervous system. After reactivation, progeny viral particles travel within sensory neurons towards sites of initial infection. There are conflicting reports what type of viral structures are transported: some studies observed non-enveloped capsids traveling while others reported transport of fully enveloped viruses within vesicles. Here, we used cryo electron tomography to analyze the three-dimensional architecture of HSV1 in axons of hippocampal neurons. In mid-axonal regions we found predominantly non-enveloped capsids. Interestingly, we observed both genome-containing and empty capsids that differed significantly in the amount of bound proteins. Viral protein recruitment thus varied between the different cytosolic capsid types, but effective transport occurred despite these differences. Furthermore, we observed three-dimensional snapshots of secondary capsid envelopment in axon terminals. Altogether, this study provides valuable structural detail on axonal HSV1 particles supporting the notion that viral subassemblies are conveyed along the axons to be assembled only after axonal transport.

Putting structure into context: fitting of atomic models into electron microscopic and electron tomographic reconstructions

A complete understanding of complex dynamic cellular processes such as cell migration or cell adhesion requires the integration of atomic level structural information into the larger cellular context. While direct atomic-level information at the cellular level remains inaccessible, electron microscopy, electron tomography and their associated computational image processing approaches have now matured to a point where sub-cellular structures can be imaged in three dimensions at the nanometer scale. Atomic-resolution information obtained by other means can be combined with this data to obtain three-dimensional models of large macromolecular assemblies in their cellular context. This article summarizes some recent advances in this field.

Assembly and breakdown of microtubules within the midbody

In animal cells, cell division concludes with the separation of two daughter cells during a process called cytokinesis. Abscission, the termination of cytokinesis, is performed through formation of the midbody, a vis-á-vis microtubule (MT)-rich structure bridging the daughter cells. Disassembly of the midbody is the final stage of daughter cell separation and occurs in parallel to membrane fusion in this area. To shed light on this process and to better understand MT organization within the dense area of the midbody structure, an integrative fluorescence microscopy and cryo-electron tomography (cryo-ET) approach was taken.1 These efforts led to a resolving of MT architecture at single-fiber resolution, resulting in a refined model of abscission.

Peptidoglycan remodeling and conversion of an inner membrane into an outer membrane during sporulation

Two hallmarks of the Firmicute phylum, which includes the Bacilli and Clostridia classes, are their ability to form endospores and their "Gram-positive" single-membraned, thick-cell-wall envelope structure. Acetonema longum is part of a lesser-known family (the Veillonellaceae) of Clostridia that form endospores but that are surprisingly "Gram negative," possessing both an inner and outer membrane and a thin cell wall. Here, we present macromolecular resolution, 3D electron cryotomographic images of vegetative, sporulating, and germinating A. longum cells showing that during the sporulation process, the inner membrane of the mother cell is inverted and transformed to become the outer membrane of the germinating cell. Peptidoglycan persists throughout, leading to a revised, "continuous" model of its role in the process. Coupled with genomic analyses, these results point to sporulation as a mechanism by which the bacterial outer membrane may have arisen and A. longum as a potential "missing link" between single- and double-membraned bacteria.

Ultrastructure of cilia and flagella - back to the future!

Eukaryotic cilia and flagella perform motility and sensory functions which are essential for cell survival in protozoans, and to organism development and homoeostasis in metazoans. Their ultrastructure has been studied from the early beginnings of electron microscopy, and these studies continue to contribute to much of our understanding about ciliary biology. In the light of the progress made in the visualization of cellular structures over the last decade, we revisit the ultrastructure of cilia and flagella. We briefly describe the typical features of a 9+2 axoneme before focusing extensively on the transition zone, the ciliary necklace, the singlet zone, the ciliary cap and the ciliary crown. We discuss how the singlet zone is linked to sensory and/or motile function, the contribution of the ciliary crown to ovocyte and mucosal propulsion, and the relationship between the ciliary cap and microtubule growth and shortening, and its relation to ciliary beat. We further examine the involvement of the transition zone/the ciliary necklace in axonemal stabilization, autotomy and as a diffusion barrier.

New insights into HTLV-1 particle structure, assembly, and Gag-Gag interactions in living cells

Human T-cell leukemia virus type 1 (HTLV-1) has a reputation for being extremely difficult to study in cell culture. The challenges in propagating HTLV-1 has prevented a rigorous analysis of how these viruses replicate in cells, including the detailed steps involved in virus assembly. The details for how retrovirus particle assembly occurs are poorly understood, even for other more tractable retroviral systems. Recent studies on HTLV-1 using state-of-the-art cryo-electron microscopy and fluorescence-based biophysical approaches explored questions related to HTLV-1 particle size, Gag stoichiometry in virions, and Gag-Gag interactions in living cells. These results provided new and exciting insights into fundamental aspects of HTLV-1 particle assembly-which are distinct from those of other retroviruses, including HIV-1. The application of these and other novel biophysical approaches promise to provide exciting new insights into HTLV-1 replication.

Investigating a macromolecular complex: the toolkit of methods

Structural biologists studying macromolecular complexes spend considerable effort doing strictly "non-structural" work: investigating the physiological relevance and biochemical properties of a complex, preparing homogeneous samples for structural analysis, and experimentally validating structure-based hypotheses regarding function or mechanism. Familiarity with the diverse perspectives and techniques available for studying complexes helps in the critical assessment of non-structural data, expedites the pre-structural characterization of a complex and facilitates the investigation of function. Here we survey the approaches and techniques used to study macromolecular complexes from various viewpoints, including genetics, cell and molecular biology, biochemistry/biophysics, structural biology, and systems biology/bioinformatics. The aim of this overview is to heighten awareness of the diversity of perspectives and experimental tools available for investigating complexes and of their usefulness for the structural biologist.

Electron tomography of plant thylakoid membranes

For more than half a century, electron microscopy has been a main tool for investigating the complex ultrastructure and organization of chloroplast thylakoid membranes, but, even today, the three-dimensional relationship between stroma and grana thylakoids, and the arrangement of the membrane protein complexes within them are not fully understood. Electron cryo-tomography (cryo-ET) is a powerful new technique for visualizing cellular structures, especially membranes, in three dimensions. By this technique, large membrane protein complexes, such as the photosystem II supercomplex or the chloroplast ATP synthase, can be visualized directly in the thylakoid membrane at molecular (4-5 nm) resolution. This short review compares recent advances by cryo-ET of plant thylakoid membranes with earlier results obtained by conventional electron microscopy.

Exploring the spatial and temporal organization of a cell's proteome

To increase our current understanding of cellular processes, such as cell signaling and division, knowledge is needed about the spatial and temporal organization of the proteome at different organizational levels. These levels cover a wide range of length and time scales: from the atomic structures of macromolecules for inferring their molecular function, to the quantitative description of their abundance, and spatial distribution in the cell. Emerging new experimental technologies are greatly increasing the availability of such spatial information on the molecular organization in living cells. This review addresses three fields that have significantly contributed to our understanding of the proteome's spatial and temporal organization: first, methods for the structure determination of individual macromolecular assemblies, specifically the fitting of atomic structures into density maps generated from electron microscopy techniques; second, research that visualizes the spatial distributions of these complexes within the cellular context using cryo electron tomography techniques combined with computational image processing; and third, methods for the spatial modeling of the dynamic organization of the proteome, specifically those methods for simulating reaction and diffusion of proteins and complexes in crowded intracellular fluids. The long-term goal is to integrate the varied data about a proteome's organization into a spatially explicit, predictive model of cellular processes.

Tomography of actin cytoskeletal networks

Structural biology research is increasingly focusing on unraveling structural variations at the micro-, meso-, and macroscale aiming at interpreting dynamic biological processes and pathways. Toward this goal, high-resolution transmission cryoelectron microscopy (cryo-EM) and cryoelectron tomography (cryo-ET) are indispensable, as these provide the ability to determine 3D structures of large, dynamic macromolecular assemblies in their native, fully hydrated state in situ. Underlying such analyses is the implicit assumption that specific structural states yield specific cellular outputs. The dependence on this structure-function paradigm is not unique to studies pertaining a particular pathway or biological process but it sets the foundation for all cell biological analyses of macromolecular assemblies. Yet, the paradigm still awaits formal proof. The field of high-resolution electron microscopy (HREM) is in dire need of establishing approaches and technologies to systematic and quantitative determining structure-function correlates in physiologically relevant environment. Here, using the actin cytoskeletal networks as an example, we will provide snapshots of current advances in defining the structures of these highly dynamic networks in situ. We will further detail some of the major stumbling blocks on the way to quantitatively correlate the dynamic state to network morphology in the same window of time and space.

Methods for segmentation and interpretation of electron tomographic reconstructions

Electron tomography has become a powerful tool for revealing the molecular architecture of biological cells and tissues. In principle, electron tomography can provide high-resolution mapping of entire proteomes. The achievable resolution (3-8 nm) is capable of bridging the gap between live-cell imaging and atomic resolution structures. However, the relevant information is not readily accessible from the data and needs to be identified, extracted, and processed before it can be used. Because electron tomography imaging and image acquisition technologies have enjoyed major advances in the last few years and continue to increase data throughput, the need for approaches that allow automatic and objective interpretation of electron tomograms becomes more and more urgent. This chapter provides an overview of the state of the art in this field and attempts to identify the major bottlenecks that prevent approaches for interpreting electron tomography data to develop their full potential.