Endocytosed nanogold fiducials for improved in-situ cryo-electron tomography tilt-series alignment

Advances, challenges, and applications of cryo-electron tomography workflows for three-dimensional cellular imaging of infectious pathogens

Cryo-electron tomography (cryo-ET) has become a powerful tool for visualising cellular structures at sub-nanometer resolution in their near-native state, offering unique insights into the molecular architecture of diverse biological systems, including infectious agents and their interactions with host cells. This paper reviews key methodologies and recent advancements in cryo-ET, with a particular focus on sample preparation of protozoan parasites and host cells. Topics covered include photopatterning for cell positioning on EM grids, vitrification techniques, whole-cell imaging, and cryo-FIB milling followed by cryo-ET. The manuscript also addresses how these approaches are providing valuable structural information on pathogens and pathogen-host interactions, which are critical for understanding mechanisms of pathogenesis and the development of therapeutic strategies. Additionally, we examine the principles and practical considerations of the multistep workflow, highlighting innovations such as integrated fluorescence microscopy (iFLM) within cryo-FIB SEM systems for improved target identification and lamella positioning. Challenges such as ion beam damage, sample thickness constraints, and the need for greater workflow automation are also discussed as areas for future improvement. As cryo-ET continues to evolve and deliver transformative insights into the molecular architecture of life, it inspires great hope for the development of future therapies against infectious diseases. LAY DESCRIPTION: Cryo-electron tomography (cryo-ET) is a special type of microscopy that allows researchers to look at the inside of cells in 3D, almost as if a hologram of the cell in its natural state was generated. This technique reveals molecular structures inside cells, allowing scientists to better understand how molecules and cellular components work together. To obtain such detailed images, biological samples need to be thin and frozen very quickly so that they remain undamaged and close to their natural state. One recent breakthrough involves using a tool called cryo-focused ion beam scanning electron microscopy (cryo-FIB SEM), which allows a thin slice of a frozen sample to be collected and then analysed using cryo-ET. In addition, photopatterning of support surfaces are being used to place cells in a strategic position for cryo-FIB SEM, and improved plunge freezing and high-pressure freezing methods have been developed to better preserve samples. Together, these techniques make it easier to reproducibly prepare high-quality samples for cryo-ET. These innovations allow capturing clearer and detailed images of cells, tissues, and even entire small organisms. Cryo-ET has led to important discoveries in biology, such as how proteins and other molecules interact within cells at the sub-nanometre scale. This technique holds great promise for revealing how life works at a molecular level, understanding diseases, and discovering new drugs.

In situ and in vitro cryo-EM reveal structures of mycobacterial encapsulin assembly intermediates

Prokaryotes rely on proteinaceous compartments such as encapsulin to isolate harmful reactions. Encapsulin are widely expressed by bacteria, including the Mycobacteriaceae, which include the human pathogens Mycobacterium tuberculosis and Mycobacterium leprae. Structures of fully assembled encapsulin shells have been determined for several species, but encapsulin assembly and cargo encapsulation are still poorly characterised, because of the absence of encapsulin structures in intermediate assembly states. We combine in situ and in vitro structural electron microscopy to show that encapsulins are dynamic assemblies with intermediate states of cargo encapsulation and shell assembly. Using cryo-focused ion beam (FIB) lamella preparation and cryo-electron tomography (CET), we directly visualise encapsulins in Mycobacterium marinum, and observed ribbon-like attachments to the shell, encapsulin shells with and without cargoes, and encapsulin shells in partially assembled states. In vitro cryo-electron microscopy (EM) single-particle analysis of the Mycobacterium tuberculosis encapsulin was used to obtain three structures of the encapsulin shell in intermediate states, as well as a 2.3 Å structure of the fully assembled shell. Based on the analysis of the intermediate encapsulin shell structures, we propose a model of encapsulin self-assembly via the pairwise addition of monomers.

Structural glycobiology - from enzymes to organelles

Biological carbohydrate polymers represent some of the most complex molecules in life, enabling their participation in a huge range of physiological functions. The complexity of biological carbohydrates arises from an extensive enzymatic repertoire involved in their construction, deconstruction and modification. Over the past decades, structural studies of carbohydrate processing enzymes have driven major insights into their mechanisms, supporting associated applications across medicine and biotechnology. Despite these successes, our understanding of how multienzyme networks function to create complex polysaccharides is still limited. Emerging techniques such as super-resolution microscopy and cryo-electron tomography are now enabling the investigation of native biological systems at near molecular resolutions. Here, we review insights from classical in vitro studies of carbohydrate processing, alongside recent in situ studies of glycosylation-related processes. While considerable technical challenges remain, the integration of molecular mechanisms with true biological context promises to transform our understanding of carbohydrate regulation, shining light upon the processes driving functional complexity in these essential biomolecules.

ExoSloNano: Multi-Modal Nanogold Tags for identification of Macromolecules in Live Cells & Cryo-Electron Tomograms

In situ cryo-Electron Microscopy (cryo-EM) enables the direct interrogation of structure-function relationships by resolving macromolecular structures in their native cellular environment. Tremendous progress in sample preparation, imaging and data processing over the past decade has contributed to the identification and determination of large biomolecular complexes. However, the majority of proteins are of a size that still eludes identification in cellular cryo-EM data, and most proteins exist in low copy numbers. Therefore, novel tools are needed for cryo-EM to identify the vast majority of macromolecules across multiple size scales (from microns to nanometers). Here, we introduce and validate novel nanogold probes that enable the detection of specific proteins using cryo-ET (cryo-Electron Tomography) and resin-embedded correlated light and electron microscopy (CLEM). We demonstrate that these nanogold probes can be introduced into live cells, in a manner that preserves intact molecular networks and cell viability. We use this system to identify both cytoplasmic and nuclear proteins by room temperature EM, and resolve associated structures by cryo-ET. We further employ gold particles of different sizes to enable future multiplexed labeling and structural analysis. By providing high efficiency protein labeling in live cells and molecular specificity within cryo-ET tomograms, we establish a broadly enabling tool that significantly expands the proteome available to electron microscopy.

VitroJet: new features and case studies

Single-particle cryo-electron microscopy has become a widely adopted method in structural biology due to many recent technological advances in microscopes, detectors and image processing. Before being able to inspect a biological sample in an electron microscope, it needs to be deposited in a thin layer on a grid and rapidly frozen. The VitroJet was designed with this aim, as well as avoiding the delicate manual handling and transfer steps that occur during the conventional grid-preparation process. Since its creation, numerous technical developments have resulted in a device that is now widely utilized in multiple laboratories worldwide. It features plasma treatment, low-volume sample deposition through pin printing, optical ice-thickness measurement and cryofixation of pre-clipped Autogrids through jet vitrification. This paper presents recent technical improvements to the VitroJet and the benefits that it brings to the cryo-EM workflow. A wide variety of applications are shown: membrane proteins, nucleosomes, fatty-acid synthase, Tobacco mosaic virus, lipid nanoparticles, tick-borne encephalitis viruses and bacteriophages. These case studies illustrate the advancement of the VitroJet into an instrument that enables accurate control and reproducibility, demonstrating its suitability for time-efficient cryo-EM structure determination.

Bringing Structure to Cell Biology with Cryo-Electron Tomography

Recent advances in cryo-electron microscopy have marked only the beginning of the potential of this technique. To bring structure into cell biology, the modality of cryo-electron tomography has fast developed into a bona fide in situ structural biology technique where structures are determined in their native environment, the cell. Nearly every step of the cryo-focused ion beam-assisted electron tomography (cryo-FIB-ET) workflow has been improved upon in the past decade, since the first windows were carved into cells, unveiling macromolecular networks in near-native conditions. By bridging structural and cell biology, cryo-FIB-ET is advancing our understanding of structure-function relationships in their native environment and becoming a tool for discovering new biology.

Cryo-electron tomography on focused ion beam lamellae transforms structural cell biology

Cryogenic electron microscopy and data processing enable the determination of structures of isolated macromolecules to near-atomic resolution. However, these data do not provide structural information in the cellular environment where macromolecules perform their native functions, and vital molecular interactions can be lost during the isolation process. Cryogenic focused ion beam (FIB) fabrication generates thin lamellae of cellular samples and tissues, enabling structural studies on the near-native cellular interior and its surroundings by cryogenic electron tomography (cryo-ET). Cellular cryo-ET benefits from the technological developments in electron microscopes, detectors and data processing, and more in situ structures are being obtained and at increasingly higher resolution. In this Review, we discuss recent studies employing cryo-ET on FIB-generated lamellae and the technological developments in ultrarapid sample freezing, FIB fabrication of lamellae, tomography, data processing and correlative light and electron microscopy that have enabled these studies. Finally, we explore the future of cryo-ET in terms of both methods development and biological application.

Bimodal endocytic probe for three-dimensional correlative light and electron microscopy

We present a bimodal endocytic tracer, fluorescent BSA-gold (fBSA-Au), as a fiducial marker for 2D and 3D correlative light and electron microscopy (CLEM) applications. fBSA-Au consists of colloidal gold (Au) particles stabilized with fluorescent BSA. The conjugate is efficiently endocytosed and distributed throughout the 3D endolysosomal network of cells and has an excellent visibility in both fluorescence microscopy (FM) and electron microscopy (EM). We demonstrate that fBSA-Au facilitates rapid registration in several 2D and 3D CLEM applications using Tokuyasu cryosections, resin-embedded material, and cryoelectron microscopy (cryo-EM). Endocytosed fBSA-Au benefits from a homogeneous 3D distribution throughout the endosomal system within the cell, does not obscure any cellular ultrastructure, and enables accurate (50-150 nm) correlation of fluorescence to EM data. The broad applicability and visibility in both modalities makes fBSA-Au an excellent endocytic fiducial marker for 2D and 3D (cryo)CLEM applications.

Coming of Age: Cryo-Electron Tomography as a Versatile Tool to Generate High-Resolution Structures at Cellular/Biological Interfaces

Over the last few years, cryo electron microscopy has become the most important method in structural biology. While 80% of deposited maps are from single particle analysis, electron tomography has grown to become the second most important method. In particular sub-tomogram averaging has matured as a method, delivering structures between 2 and 5 Å from complexes in cells as well as in vitro complexes. While this resolution range is not standard, novel developments point toward a promising future. Here, we provide a guide for the workflow from sample to structure to gain insight into this emerging field.