Viruses

Editorial

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3 pages, 201 KiB

Open AccessEditorial

Advances in Structural Virology via Cryo-EM in 2022

by Guy Schoehn, Florian Chenavier and Thibaut Crépin

Viruses 2023, 15(6), 1315; https://doi.org/10.3390/v15061315 - 2 Jun 2023

Cited by 1 | Viewed by 1236

Abstract

In recent years, cryo-electron microscopy (cryo-EM) has emerged as an important standalone technique within structural biology [...] Full article

(This article belongs to the Special Issue Advances in Structural Virology via Cryo-EM 2022)

Research

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17 pages, 2350 KiB

Open AccessArticle

Multifunctional Protein A Is the Only Viral Protein Required for Nodavirus RNA Replication Crown Formation

by Johan A. den Boon, Hong Zhan, Nuruddin Unchwaniwala, Mark Horswill, Kailey Slavik, Janice Pennington, Amanda Navine and Paul Ahlquist

Viruses 2022, 14(12), 2711; https://doi.org/10.3390/v14122711 - 3 Dec 2022

Cited by 5 | Viewed by 1946

Abstract

Positive-strand RNA virus RNA genome replication occurs in membrane-associated RNA replication complexes (RCs). Nodavirus RCs are outer mitochondrial membrane invaginations whose necked openings to the cytosol are “crowned” by a 12-fold symmetrical proteinaceous ring that functions as the main engine of RNA replication. [...] Read more.

Positive-strand RNA virus RNA genome replication occurs in membrane-associated RNA replication complexes (RCs). Nodavirus RCs are outer mitochondrial membrane invaginations whose necked openings to the cytosol are “crowned” by a 12-fold symmetrical proteinaceous ring that functions as the main engine of RNA replication. Similar protein crowns recently visualized at the openings of alphavirus and coronavirus RCs highlight their broad conservation and functional importance. Using cryo-EM tomography, we earlier showed that the major nodavirus crown constituent is viral protein A, whose polymerase, RNA capping, membrane interaction and multimerization domains drive RC formation and function. Other viral proteins are strong candidates for unassigned EM density in the crown. RNA-binding RNAi inhibitor protein B2 co-immunoprecipitates with protein A and could form crown subdomains that protect nascent viral RNA and dsRNA templates. Capsid protein may interact with the crown since nodavirus virion assembly has spatial and other links to RNA replication. Using cryoelectron tomography and complementary approaches, we show that, even when formed in mammalian cells, nodavirus RC crowns generated without B2 and capsid proteins are functional and structurally indistinguishable from mature crowns in infected Drosophila cells expressing all viral proteins. Thus, the only nodaviral factors essential to form functional RCs and crowns are RNA replication protein A and an RNA template. We also resolve apparent conflicts in prior results on B2 localization in infected cells, revealing at least two distinguishable pools of B2. The results have significant implications for crown structure, assembly, function and control as an antiviral target. Full article

(This article belongs to the Special Issue Advances in Structural Virology via Cryo-EM 2022)

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11 pages, 1675 KiB

Open AccessArticle

Alphavirus Particles Can Assemble with an Alternate Triangulation Number

by Jason T. Kaelber, David Chmielewski, Wah Chiu and Albert J. Auguste

Viruses 2022, 14(12), 2650; https://doi.org/10.3390/v14122650 - 27 Nov 2022

Cited by 2 | Viewed by 1978

Abstract

Alphaviruses are spherical, enveloped RNA viruses primarily transmitted by mosquitoes, and cause significant arthritogenic and neurotropic disease in humans and livestock. Previous reports have shown that—in contrast to prototypical icosahedral viruses—alphaviruses incorporate frequent defects, and these may serve important functions in the viral [...] Read more.

Alphaviruses are spherical, enveloped RNA viruses primarily transmitted by mosquitoes, and cause significant arthritogenic and neurotropic disease in humans and livestock. Previous reports have shown that—in contrast to prototypical icosahedral viruses—alphaviruses incorporate frequent defects, and these may serve important functions in the viral life cycle. We confirm the genus-wide pleomorphism in live viral particles and extend our understanding of alphavirus assembly through the discovery of an alternate architecture of Eastern equine encephalitis virus (EEEV) particles. The alternate T = 3 icosahedral architecture differs in triangulation number from the classic T = 4 icosahedral organization that typifies alphaviruses, but the alternate architecture maintains the quasi-equivalence relationship of asymmetric units. The fusion spike glycoproteins are more loosely apposed in the T = 3 form with corresponding changes in the underlying capsid protein lattice. This alternate architecture could potentially be exploited in engineering alphavirus-based particles for delivery of alphaviral or other RNA. Full article

(This article belongs to the Special Issue Advances in Structural Virology via Cryo-EM 2022)

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13 pages, 2051 KiB

Open AccessArticle

A Capsid Structure of Ralstonia solanacearum podoviridae GP4 with a Triangulation Number T = 9

by Jing Zheng, Wenyuan Chen, Hao Xiao, Fan Yang, Xiaowu Li, Jingdong Song, Lingpeng Cheng and Hongrong Liu

Viruses 2022, 14(11), 2431; https://doi.org/10.3390/v14112431 - 1 Nov 2022

Cited by 2 | Viewed by 2041

Abstract

GP4, a new Ralstonia solanacearum phage, is a short-tailed phage. Few structures of Ralstonia solanacearum phages have been resolved to near-atomic resolution until now. Here, we present a 3.7 Å resolution structure of the GP4 head by cryo-electron microscopy (cryo-EM). The GP4 head [...] Read more.

GP4, a new Ralstonia solanacearum phage, is a short-tailed phage. Few structures of Ralstonia solanacearum phages have been resolved to near-atomic resolution until now. Here, we present a 3.7 Å resolution structure of the GP4 head by cryo-electron microscopy (cryo-EM). The GP4 head contains 540 copies of major capsid protein (MCP) gp2 and 540 copies of cement protein (CP) gp1 arranged in an icosahedral shell with a triangulation number T = 9. The structures of gp2 and gp1 show a canonical HK97-like fold and an Ig-like fold, respectively. The trimeric CPs stick on the surface of the head along the quasi-threefold axis of the icosahedron generating a sandwiched three-layer electrostatic complementary potential, thereby enhancing the head stability. The assembly pattern of the GP4 head provides a platform for the further exploration of the interaction between Ralstonia solanacearum and corresponding phages. Full article

(This article belongs to the Special Issue Advances in Structural Virology via Cryo-EM 2022)

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12 pages, 3861 KiB

Open AccessArticle

Structural Insights into Common and Host-Specific Receptor-Binding Mechanisms in Algal Picorna-like Viruses

by Han Wang, Anna Munke, Siqi Li, Yuji Tomaru and Kenta Okamoto

Viruses 2022, 14(11), 2369; https://doi.org/10.3390/v14112369 - 27 Oct 2022

Cited by 2 | Viewed by 1613

Abstract

Marnaviridae viruses are abundant algal viruses that regulate the dynamics of algal blooms in aquatic environments. They employ a narrow host range because they merely lyse their algal host species. This host-specific lysis is thought to correspond to the unique receptor-binding mechanism of [...] Read more.

Marnaviridae viruses are abundant algal viruses that regulate the dynamics of algal blooms in aquatic environments. They employ a narrow host range because they merely lyse their algal host species. This host-specific lysis is thought to correspond to the unique receptor-binding mechanism of the Marnaviridae viruses. Here, we present the atomic structures of the full and empty capsids of Chaetoceros socialis forma radians RNA virus 1 built-in 3.0 Å and 3.1 Å cryo-electron microscopy maps. The empty capsid structure and the structural variability provide insights into its assembly and uncoating intermediates. In conjunction with the previously reported atomic model of the Chaetoceros tenuissimus RNA virus type II capsid, we have identified the common and diverse structural features of the VP1 surface between the Marnaviridae viruses. We have also tested the potential usage of AlphaFold2 for structural prediction of the VP1s and a subsequent structural phylogeny for classifying Marnaviridae viruses by their hosts. These findings will be crucial for inferring the host-specific receptor-binding mechanism in Marnaviridae viruses. Full article

(This article belongs to the Special Issue Advances in Structural Virology via Cryo-EM 2022)

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18 pages, 4613 KiB

Open AccessArticle

The Vaccinia Virus DNA Helicase Structure from Combined Single-Particle Cryo-Electron Microscopy and AlphaFold2 Prediction

by Stephanie Hutin, Wai Li Ling, Nicolas Tarbouriech, Guy Schoehn, Clemens Grimm, Utz Fischer and Wim P. Burmeister

Viruses 2022, 14(10), 2206; https://doi.org/10.3390/v14102206 - 7 Oct 2022

Cited by 8 | Viewed by 2320

Abstract

Poxviruses are large DNA viruses with a linear double-stranded DNA genome circularized at the extremities. The helicase-primase D5, composed of six identical 90 kDa subunits, is required for DNA replication. D5 consists of a primase fragment flexibly attached to the hexameric C-terminal polypeptide [...] Read more.

Poxviruses are large DNA viruses with a linear double-stranded DNA genome circularized at the extremities. The helicase-primase D5, composed of six identical 90 kDa subunits, is required for DNA replication. D5 consists of a primase fragment flexibly attached to the hexameric C-terminal polypeptide (res. 323–785) with confirmed nucleotide hydrolase and DNA-binding activity but an elusive helicase activity. We determined its structure by single-particle cryo-electron microscopy. It displays an AAA+ helicase core flanked by N- and C-terminal domains. Model building was greatly helped by the predicted structure of D5 using AlphaFold2. The 3.9 Å structure of the N-terminal domain forms a well-defined tight ring while the resolution decreases towards the C-terminus, still allowing the fit of the predicted structure. The N-terminal domain is partially present in papillomavirus E1 and polyomavirus LTA helicases, as well as in a bacteriophage NrS-1 helicase domain, which is also closely related to the AAA+ helicase domain of D5. Using the Pfam domain database, a D5_N domain followed by DUF5906 and Pox_D5 domains could be assigned to the cryo-EM structure, providing the first 3D structures for D5_N and Pox_D5 domains. The same domain organization has been identified in a family of putative helicases from large DNA viruses, bacteriophages, and selfish DNA elements. Full article

(This article belongs to the Special Issue Advances in Structural Virology via Cryo-EM 2022)

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Review

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18 pages, 5199 KiB

Open AccessReview

CryoEM of Viral Ribonucleoproteins and Nucleocapsids of Single-Stranded RNA Viruses

by Andrea Modrego, Diego Carlero, Rocío Arranz and Jaime Martín-Benito

Viruses 2023, 15(3), 653; https://doi.org/10.3390/v15030653 - 28 Feb 2023

Cited by 4 | Viewed by 2262

Abstract

Single-stranded RNA viruses (ssRNAv) are characterized by their biological diversity and great adaptability to different hosts; traits which make them a major threat to human health due to their potential to cause zoonotic outbreaks. A detailed understanding of the mechanisms involved in viral [...] Read more.

Single-stranded RNA viruses (ssRNAv) are characterized by their biological diversity and great adaptability to different hosts; traits which make them a major threat to human health due to their potential to cause zoonotic outbreaks. A detailed understanding of the mechanisms involved in viral proliferation is essential to address the challenges posed by these pathogens. Key to these processes are ribonucleoproteins (RNPs), the genome-containing RNA-protein complexes whose function is to carry out viral transcription and replication. Structural determination of RNPs can provide crucial information on the molecular mechanisms of these processes, paving the way for the development of new, more effective strategies to control and prevent the spread of ssRNAv diseases. In this scenario, cryogenic electron microscopy (cryoEM), relying on the technical and methodological revolution it has undergone in recent years, can provide invaluable help in elucidating how these macromolecular complexes are organized, packaged within the virion, or the functional implications of these structures. In this review, we summarize some of the most prominent achievements by cryoEM in the study of RNP and nucleocapsid structures in lipid-enveloped ssRNAv. Full article

(This article belongs to the Special Issue Advances in Structural Virology via Cryo-EM 2022)

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18 pages, 3010 KiB

Open AccessReview

Viral Small Terminase: A Divergent Structural Framework for a Conserved Biological Function

by Ravi K. Lokareddy, Chun-Feng David Hou, Fenglin Li, Ruoyu Yang and Gino Cingolani

Viruses 2022, 14(10), 2215; https://doi.org/10.3390/v14102215 - 8 Oct 2022

Cited by 9 | Viewed by 2021

Abstract

The genome packaging motor of bacteriophages and herpesviruses is built by two terminase subunits, known as large (TerL) and small (TerS), both essential for viral genome packaging. TerL structure, composition, and assembly to an empty capsid, as well as the mechanisms of ATP-dependent [...] Read more.

The genome packaging motor of bacteriophages and herpesviruses is built by two terminase subunits, known as large (TerL) and small (TerS), both essential for viral genome packaging. TerL structure, composition, and assembly to an empty capsid, as well as the mechanisms of ATP-dependent DNA packaging, have been studied in depth, shedding light on the chemo-mechanical coupling between ATP hydrolysis and DNA translocation. Instead, significantly less is known about the small terminase subunit, TerS, which is dispensable or even inhibitory in vitro, but essential in vivo. By taking advantage of the recent revolution in cryo-electron microscopy (cryo-EM) and building upon a wealth of crystallographic structures of phage TerSs, in this review, we take an inventory of known TerSs studied to date. Our analysis suggests that TerS evolved and diversified into a flexible molecular framework that can conserve biological function with minimal sequence and quaternary structure conservation to fit different packaging strategies and environmental conditions. Full article

(This article belongs to the Special Issue Advances in Structural Virology via Cryo-EM 2022)

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39 pages, 30564 KiB

Open AccessReview

Revisiting Viral RNA-Dependent RNA Polymerases: Insights from Recent Structural Studies

by Kavitha Ramaswamy, Mariya Rashid, Selvarajan Ramasamy, Tamilselvan Jayavelu and Sangita Venkataraman

Viruses 2022, 14(10), 2200; https://doi.org/10.3390/v14102200 - 6 Oct 2022

Cited by 7 | Viewed by 2169

Abstract

RNA-dependent RNA polymerases (RdRPs) represent a distinctive yet versatile class of nucleic acid polymerases encoded by RNA viruses for the replication and transcription of their genome. The structure of the RdRP is comparable to that of a cupped right hand consisting of fingers, [...] Read more.

RNA-dependent RNA polymerases (RdRPs) represent a distinctive yet versatile class of nucleic acid polymerases encoded by RNA viruses for the replication and transcription of their genome. The structure of the RdRP is comparable to that of a cupped right hand consisting of fingers, palm, and thumb subdomains. Despite the presence of a common structural core, the RdRPs differ significantly in the mechanistic details of RNA binding and polymerization. The present review aims at exploring these incongruities in light of recent structural studies of RdRP complexes with diverse cofactors, RNA moieties, analogs, and inhibitors. Full article

(This article belongs to the Special Issue Advances in Structural Virology via Cryo-EM 2022)

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Other

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15 pages, 2883 KiB

Open AccessPerspective

SARS-CoV-2 S Glycoprotein Stabilization Strategies

by Borys Pedenko, Guidenn Sulbaran, Delphine Guilligay, Gregory Effantin and Winfried Weissenhorn

Viruses 2023, 15(2), 558; https://doi.org/10.3390/v15020558 - 17 Feb 2023

Cited by 1 | Viewed by 1992

Abstract

The SARS-CoV-2 pandemic has again shown that structural biology plays an important role in understanding biological mechanisms and exploiting structural data for therapeutic interventions. Notably, previous work on SARS-related glycoproteins has paved the way for the rapid structural determination of the SARS-CoV-2 S [...] Read more.

The SARS-CoV-2 pandemic has again shown that structural biology plays an important role in understanding biological mechanisms and exploiting structural data for therapeutic interventions. Notably, previous work on SARS-related glycoproteins has paved the way for the rapid structural determination of the SARS-CoV-2 S glycoprotein, which is the main target for neutralizing antibodies. Therefore, all vaccine approaches aimed to employ S as an immunogen to induce neutralizing antibodies. Like all enveloped virus glycoproteins, SARS-CoV-2 S native prefusion trimers are in a metastable conformation, which primes the glycoprotein for the entry process via membrane fusion. S-mediated entry is associated with major conformational changes in S, which can expose many off-target epitopes that deviate vaccination approaches from the major aim of inducing neutralizing antibodies, which mainly target the native prefusion trimer conformation. Here, we review the viral glycoprotein stabilization methods developed prior to SARS-CoV-2, and applied to SARS-CoV-2 S, in order to stabilize S in the prefusion conformation. The importance of structure-based approaches is highlighted by the benefits of employing stabilized S trimers versus non-stabilized S in vaccines with respect to their protective efficacy. Full article

(This article belongs to the Special Issue Advances in Structural Virology via Cryo-EM 2022)

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