Assembly of complex viruses exemplified by a halophilic euryarchaeal virus

Optimal 3D angular sampling with applications to cryo-EM problems

The goal of cryo-EM experiments in the biological sciences is to determine the atomic structure of a molecule and deduce insights into its functions and mechanisms. Despite improvements in instrumentation for data collection and new software algorithms, in most cases, individual atoms are not resolved. Model building of proteins, nucleic acids, or molecules in general, is feasible from the experimentally determined density maps at resolutions up to the range of 3-4 Angstroms. For lower-resolution maps or parts of maps, fitting smaller structures obtained by modelling or experimental techniques with higher resolution is a way to resolve the issue. In practice, we have an atomic structure, generate its density map at a given resolution, and translate/rotate the map within a region of interest in the experimental map, computing a measure-of-fit score with the corresponding areas of the experimental map. This procedure is computationally intensive since we work in 6D space. An optimal ordered list of rotations will reduce the angular error and help to find the best-fitting positions faster for a coarse global search or a local refinement. It can be used for adaptive approaches to stop fitting algorithms earlier once the desired accuracy has been achieved. We demonstrate how the performance of some fitting algorithms can be improved by grouping sets of rotations. We present an approach to generate more efficient 3D angular sampling, and provide the computer code to generate lists of optimal orientations for single and grouped rotations and the lists themselves.

Hierarchical design of pseudosymmetric protein nanoparticles

Discrete protein assemblies ranging from hundreds of kilodaltons to hundreds of megadaltons in size are a ubiquitous feature of biological systems and perform highly specialized functions 1-3. Despite remarkable recent progress in accurately designing new self-assembling proteins, the size and complexity of these assemblies has been limited by a reliance on strict symmetry 4,5. Inspired by the pseudosymmetry observed in bacterial microcompartments and viral capsids, we developed a hierarchical computational method for designing large pseudosymmetric self-assembling protein nanomaterials. We computationally designed pseudosymmetric heterooligomeric components and used them to create discrete, cage-like protein assemblies with icosahedral symmetry containing 240, 540, and 960 subunits. At 49, 71, and 96 nm diameter, these nanoparticles are the largest bounded computationally designed protein assemblies generated to date. More broadly, by moving beyond strict symmetry, our work represents an important step towards the accurate design of arbitrary self-assembling nanoscale protein objects.

Local rules for the self-assembly of a non-quasi-equivalent viral capsid

The structures of many large bacteriophages, such as the P23-77 capsids, do not adhere strictly to the quasi-equivalence principle of viral architecture. Although the general architecture of the P23-77 capsids is classed as T=28d, it self-assembles from multiple copies of two types of coat protein subunits, and the resulting hexameric capsomers do not conform to the Caspar-Klug paradigm. There are two types of hexamers with distinct internal organization, that are located at specific positions in the capsid. It is an open problem which assembly mechanism can lead to such a complex capsid organization. Here we propose a simple set of local rules that can explain how such non-quasi-equivalent capsid structures can arise as a result of self-assembly.

Cellular homologs of the double jelly-roll major capsid proteins clarify the origins of an ancient virus kingdom

Viruses are the most abundant biological entities on Earth and ubiquitous parasites of cellular life forms. The general scenario for the origin of viruses involves evolution from nonviral replicators, such as plasmids and transposons, via recruitment of host proteins for virion formation. One of the most common virion core components, the double jelly-roll major capsid protein of a broad variety of viruses with double-stranded DNA genomes, so far has been thought to represent a virus innovation. However, we present evidence, obtained by protein structure comparison, that this type of virus capsid protein also evolved from a cellular ancestor, a distinct family of carbohydrate-active enzymes. These findings reinforce the chimeric scenario of virus origin.

Viruses are a distinct type of replicators that encode structural proteins encasing virus genomes in virions. For some of the widespread virus capsid proteins and other major components of virions, likely ancestors encoded by cellular life forms are identifiable. In particular, one of the most common capsid proteins, with the single jelly-roll (SJR) fold, appears to have evolved from a particular family of cellular carbohydrate-binding proteins. However, the double jelly-roll major capsid protein (DJR-MCP), the hallmark of the enormously diverse viruses of the kingdom Bamfordvirae within the realm Varidnaviria, which includes bacterial and archaeal icosahedral viruses as well as eukaryotic giant viruses, has been perceived as a virus innovation that evolved by duplication and fusion of the SJR capsid proteins. Here we employ protein structure comparison to show that the DJR fold is represented in several widespread families of cellular proteins, including several groups of carbohydrate-active enzymes. We show that DJR-MCPs share a common ancestry with a distinct family of bacterial DJR proteins (DUF2961) involved in carbohydrate metabolism. Based on this finding, we propose a scenario in which bamfordviruses evolved from nonviral replicators, in particular plasmids, by recruiting a host protein for capsid formation. This sequence of events appears to be the general route of virus origin. The results of this work indicate that virus kingdoms Bamfordvirae, with the DJR-MCPs, and Helvetiavirae that possess two SJR-MCPs, have distinct origins, suggesting a reappraisal of the realm Varidnaviria.

Superimposition of Viral Protein Structures: A Means to Decipher the Phylogenies of Viruses

Superimposition of protein structures is key in unravelling structural homology across proteins whose sequence similarity is lost. Structural comparison provides insights into protein function and evolution. Here, we review some of the original findings and thoughts that have led to the current established structure-based phylogeny of viruses: starting from the original observation that the major capsid proteins of plant and animal viruses possess similar folds, to the idea that each virus has an innate “self”. This latter idea fueled the conceptualization of the PRD1-adenovirus lineage whose members possess a major capsid protein (innate “self”) with a double jelly roll fold. Based on this approach, long-range viral evolutionary relationships can be detected allowing the virosphere to be classified in four structure-based lineages. However, this process is not without its challenges or limitations. As an example of these hurdles, we finally touch on the difficulty of establishing structural “self” traits for enveloped viruses showcasing the coronaviruses but also the power of structure-based analysis in the understanding of emerging viruses

Structure and assembly of archaeal viruses

Viruses of archaea represent one of the most enigmatic parts of the virosphere. Most of the characterized archaeal viruses infect extremophilic hosts and display remarkable diversity of virion morphotypes, many of which have never been observed among bacteriophages or viruses of eukaryotes. However, recent environmental studies have shown that archaeal viruses are widespread also in moderate ecosystems, where they play an important ecological role by influencing the turnover of microbial communities, with a global impact on the carbon and nitrogen cycles. In this review, we summarize recent advances in understanding the molecular details of virion organization and assembly of archaeal viruses. We start by briefly introducing the 20 officially recognized families of archaeal viruses and then outline the similarities and differences of archaeal virus assembly with the morphogenesis pathways used by bacterial and eukaryotic viruses, and discuss the evolutionary implications of these observations. Generally, the assembly of the icosahedral archaeal viruses closely follows the mechanisms employed by evolutionarily related bacterial and eukaryotic viruses with the HK97 fold and double jelly-roll major capsid proteins, emphasizing the overall conservation of these pathways over billions of years of evolution. By contrast, archaea-specific viruses employ unique virion assembly mechanisms. We also highlight some of the molecular adaptations underlying the stability of archaeal viruses in extreme environments. Despite considerable progress during the past few years, the archaeal virosphere continues to represent one of the least studied parts of the global virome, with many molecular features awaiting to be discovered and characterized.

Surface stresses in complex viral capsids and non-quasi-equivalent viral architectures

Many larger and more complex viruses deviate from the capsid layouts predicted in the seminal Caspar-Klug theory of icosahedral viruses. Instead of being built from one type of capsid protein (CP), they code for multiple distinct structural proteins that either break the local symmetry of the CP building blocks (capsomers) in specific positions or exhibit auxiliary proteins that stabilize the capsid shell. We investigate here the hypothesis that this occurs as a response to mechanical stress. For this, we construct a coarse-grained model of a viral capsid, derived from the experimentally determined atomistic positions of the CPs, that represents the basic features of protein organization in the viral capsid as described in Caspar-Klug theory. We focus here on viruses in the PRD1-adenovirus lineage. For T = 28 viruses in this lineage, which have capsids formed from two distinct structural proteins, we show that the tangential shear stress in the viral capsid concentrates at the sites of local symmetry breaking. In the T = 21, 25 and 27 capsids, we show that stabilizing proteins decrease the tangential stress. These results suggest that mechanical properties can act as selective pressures on the evolution of capsid components, offsetting the coding cost imposed by the need for such additional protein components.

The LUCA and its complex virome

The last universal cellular ancestor (LUCA) is the most recent population of organisms from which all cellular life on Earth descends. The reconstruction of the genome and phenotype of the LUCA is a major challenge in evolutionary biology. Given that all life forms are associated with viruses and/or other mobile genetic elements, there is no doubt that the LUCA was a host to viruses. Here, by projecting back in time using the extant distribution of viruses across the two primary domains of life, bacteria and archaea, and tracing the evolutionary histories of some key virus genes, we attempt a reconstruction of the LUCA virome. Even a conservative version of this reconstruction suggests a remarkably complex virome that already included the main groups of extant viruses of bacteria and archaea. We further present evidence of extensive virus evolution antedating the LUCA. The presence of a highly complex virome implies the substantial genomic and pan-genomic complexity of the LUCA itself.

Global Organization and Proposed Megataxonomy of the Virus World

Viruses and mobile genetic elements are molecular parasites or symbionts that coevolve with nearly all forms of cellular life. The route of virus replication and protein expression is determined by the viral genome type. Comparison of these routes led to the classification of viruses into seven "Baltimore classes" (BCs) that define the major features of virus reproduction. However, recent phylogenomic studies identified multiple evolutionary connections among viruses within each of the BCs as well as between different classes. Due to the modular organization of virus genomes, these relationships defy simple representation as lines of descent but rather form complex networks. Phylogenetic analyses of virus hallmark genes combined with analyses of gene-sharing networks show that replication modules of five BCs (three classes of RNA viruses and two classes of reverse-transcribing viruses) evolved from a common ancestor that encoded an RNA-directed RNA polymerase or a reverse transcriptase. Bona fide viruses evolved from this ancestor on multiple, independent occasions via the recruitment of distinct cellular proteins as capsid subunits and other structural components of virions. The single-stranded DNA (ssDNA) viruses are a polyphyletic class, with different groups evolving by recombination between rolling-circle-replicating plasmids, which contributed the replication protein, and positive-sense RNA viruses, which contributed the capsid protein. The double-stranded DNA (dsDNA) viruses are distributed among several large monophyletic groups and arose via the combination of distinct structural modules with equally diverse replication modules. Phylogenomic analyses reveal the finer structure of evolutionary connections among RNA viruses and reverse-transcribing viruses, ssDNA viruses, and large subsets of dsDNA viruses. Taken together, these analyses allow us to outline the global organization of the virus world. Here, we describe the key aspects of this organization and propose a comprehensive hierarchical taxonomy of viruses.

Cryo-electron microscopy for the study of virus assembly

Although viruses are extremely diverse in shape and size, evolution has led to a limited number of viral classes or lineages, which is probably linked to the assembly constraints of a viable capsid. Viral assembly mechanisms are restricted to two general pathways, (i) co-assembly of capsid proteins and single-stranded nucleic acids and (ii) a sequential mechanism in which scaffolding-mediated capsid precursor assembly is followed by genome packaging. Cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET), which are revolutionizing structural biology, are central to determining the high-resolution structures of many viral assemblies as well as those of assembly intermediates. This wealth of cryo-EM data has also led to the development and redesign of virus-based platforms for biomedical and biotechnological applications. In this Review, we will discuss recent viral assembly analyses by cryo-EM and cryo-ET showing how natural assembly mechanisms are used to encapsulate heterologous cargos including chemicals, enzymes, and/or nucleic acids for a variety of nanotechnological applications.

CryoEM reconstruction approaches to resolve asymmetric features

Although icosahedral viruses have highly symmetrical capsid features, asymmetric structural elements are also present since the genome and minor structural proteins are usually incorporated without adhering to icosahedral symmetry. Besides this inherent asymmetry, interactions with the host during the virus life cycle are also asymmetric. However, until recently it was impossible to resolve high resolution asymmetric features during single-particle cryoEM image processing. This review summarizes the current approaches that can be used to visualize asymmetric structural features. We have included examples of advanced structural strategies developed to reveal unique features and asymmetry in icosahedral viruses.

A packing for A-form DNA in an icosahedral virus

Studies on viruses infecting archaea living in the most extreme environments continue to show a remarkable diversity of structures, suggesting that the sampling continues to be very sparse. We have used electron cryo-microscopy to study at 3.7-Å resolution the structure of the Sulfolobus polyhedral virus 1 (SPV1), which was originally isolated from a hot, acidic spring in Beppu, Japan. The 2 capsid proteins with variant single jelly-roll folds form pentamers and hexamers which assemble into a T = 43 icosahedral shell. In contrast to tailed icosahedral double-stranded DNA (dsDNA) viruses infecting bacteria and archaea, and herpesviruses infecting animals and humans, where naked DNA is packed under very high pressure due to the repulsion between adjacent layers of DNA, the circular dsDNA in SPV1 is fully covered with a viral protein forming a nucleoprotein filament with attractive interactions between layers. Most strikingly, we have been able to show that the DNA is in an A-form, as it is in the filamentous viruses infecting hyperthermophilic acidophiles. Previous studies have suggested that DNA is in the B-form in bacteriophages, and our study is a direct visualization of the structure of DNA in an icosahedral virus.

Structures of enveloped virions determined by cryogenic electron microscopy and tomography

Enveloped viruses enclose their genomes inside a lipid bilayer which is decorated by membrane proteins that mediate virus entry. These viruses display a wide range of sizes, morphologies and symmetries. Spherical viruses are often isometric and their envelope proteins follow icosahedral symmetry. Filamentous and pleomorphic viruses lack such global symmetry but their surface proteins may display locally ordered assemblies. Determining the structures of enveloped viruses, including the envelope proteins and their protein-protein interactions on the viral surface, is of paramount importance. These structures can reveal how the virions are assembled and released by budding from the infected host cell, how the progeny virions infect new cells by membrane fusion, and how antibodies bind surface epitopes to block infection. In this chapter, we discuss the uses of cryogenic electron microscopy (cryo-EM) in elucidating structures of enveloped virions. Starting from a detailed outline of data collection and processing strategies, we highlight how cryo-EM has been successfully utilized to provide unique insights into enveloped virus entry, assembly, and neutralization.

Asymmetric analysis reveals novel virus capsid features

Cryo-electron microscopy and single-particle image analysis are frequently used methods for macromolecular structure determination. Conventional single-particle analysis, however, usually takes advantage of inherent sample symmetries which assist in the calculation of the structure of interest (such as viruses). Many viruses assemble an icosahedral capsid and often icosahedral symmetry is applied during structure determination. Symmetry imposition, however, results in the loss of asymmetric features of the virus. Here, we provide a brief overview of the methods used to investigate non-symmetric capsid features. These include the recently developed focussed classification as well as more conventional methods which simply do not impose any symmetry. Asymmetric single-particle image analysis can reveal novel aspects of virus structure. For example, the VP4 capsid spike of rotavirus is only present at partial occupancy, the bacteriophage MS2 capsid contains a single copy of a maturation protein and some viruses also encode portals or portal-like assemblies for the packaging and/or release of their genome upon infection. Advances in single-particle image reconstruction methods now permit novel discoveries from previous single-particle data sets which are expanding our understanding of fundamental aspects of virus biology such as viral entry and egress.