The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism

Interior modification of Macrobrachium rosenbergii nodavirus-like particle enhances encapsulation of VP37-dsRNA against shrimp white spot syndrome infection

BACKGROUND

Application of a virus-like particle (VLP) as a nanocontainer to encapsulate double stranded (ds)RNA to control viral infection in shrimp aquaculture has been extensively reported. In this study, we aimed at improving VLP's encapsulation efficiency which should lead to a superior fighting weapon with disastrous viruses.

RESULTS

We constructed 2 variants of chimeric Macrobrachium rosenbergii nodavirus (MrNV)-like particles (V1- and V2-MrN-VLPs) and tested their efficiency to encapsulate VP37 double stranded RNA as well as WSSV protection in P. vannamei. Two types of short peptides, RNA-binding domain (RBD) and deca-arginine (10R) were successfully engineered into the interior surface of VLP, the site where the contact with VP37-dsRNA occurs. TEM and dynamic light scattering (DLS) analyses revealed that the chimeric VLPs remained their assembling property to be an icosahedral symmetric particle with a diameter of about 30 nm, similar to the original MrN-VLP particle. The superior encapsulation efficiency of VP37-dsRNA into V2-MrN-VLP was achieved, which was slightly better than that of V1-MrN-VLP but far better (1.4-fold) than its parental V0-MrN-VLP which the mole ratio of 7.5-10.5 for all VLP variants. The protection effect against challenging WSSV (as gauged from the level of VP37 gene and the remaining viral copy number in shrimp) was significantly improved in both V1- and V2-MrN-VLP compared with an original V0-MrN-VLP template.

CONCLUSION

MrN-VLP (V0-) were re-engineered interiorly with RBD (V1-) and 10R (V2-) peptides which had an improved VP37-dsRNA encapsulation capability. The protection effect against WSSV infection through shrimp administration with dsRNA + V1-/V2-MrN VLPs was experimentally evident.

On the space of SARS-CoV-2 genetic sequence variants

The coronavirus pandemic caused by the SARS-CoV-2 virus, which humanity resisted using the latest advances in science, left behind, among other things, extensive genetic data. Every day since the end of 2019, samples of the virus genomes have been collected around the world, which makes it possible to trace its evolution in detail from its emergence to the present. The accumulated statistics of testing results showed that the number of confirmed cases of SARS-CoV-2 infection was at least 767.5 million (9.5 % of the current world population, excluding asymptomatic people), and the number of sequenced virus genomes is more than 15.7 million (which is over 2 % of the total number of infected people). These new data potentially contain information about the mechanisms of the variability and spread of the virus, its interaction with the human immune system, the main parameters characterizing the mechanisms of the development of a pandemic, and much more. In this article, we analyze the space of possible variants of SARS-CoV-2 genetic sequences both from a mathematical point of view and taking into account the biological limitations inherent in this system, known both from general biological knowledge and from the consideration of the characteristics of this particular virus. We have developed software capable of loading and analyzing SARS-CoV-2 nucleotide sequences in FASTA format, determining the 5' and 3' UTR positions, the number and location of unidentified nucleotides ("N"), performing alignment with the reference sequence by calling the program designed for this, determining mutations, deletions and insertions, as well as calculating various characteristics of virus genomes with a given time step (days, weeks, months, etc.). The data obtained indicate that, despite the apparent mathematical diversity of possible options for changing the virus over time, the corridor of the evolutionary trajectory that the coronavirus has passed through seems to be quite narrow. Thus it can be assumed that it is determined to some extent, which allows us to hope for a possibility of modeling the evolution of the coronavirus.

Structures of honeybee-infecting Lake Sinai virus reveal domain functions and capsid assembly with dynamic motions

Understanding the structural diversity of honeybee-infecting viruses is critical to maintain pollinator health and manage the spread of diseases in ecology and agriculture. We determine cryo-EM structures of T = 4 and T = 3 capsids of virus-like particles (VLPs) of Lake Sinai virus (LSV) 2 and delta-N48 LSV1, belonging to tetraviruses, at resolutions of 2.3-2.6 Å in various pH environments. Structural analysis shows that the LSV2 capsid protein (CP) structural features, particularly the protruding domain and C-arm, differ from those of other tetraviruses. The anchor loop on the central β-barrel domain interacts with the neighboring subunit to stabilize homo-trimeric capsomeres during assembly. Delta-N48 LSV1 CP interacts with ssRNA via the rigid helix α1', α1'-α1 loop, β-barrel domain, and C-arm. Cryo-EM reconstructions, combined with X-ray crystallographic and small-angle scattering analyses, indicate that pH affects capsid conformations by regulating reversible dynamic particle motions and sizes of LSV2 VLPs. C-arms exist in all LSV2 and delta-N48 LSV1 VLPs across varied pH conditions, indicating that autoproteolysis cleavage is not required for LSV maturation. The observed linear domino-scaffold structures of various lengths, made up of trapezoid-shape capsomeres, provide a basis for icosahedral T = 4 and T = 3 architecture assemblies. These findings advance understanding of honeybee-infecting viruses that can cause Colony Collapse Disorder.

Chimeric virus-like particles (VLPs) designed from shrimp nodavirus (MrNV) capsid protein specifically target EGFR-positive human colorectal cancer cells

Recombinant MrNV capsid protein has been shown to effectively deliver plasmid DNA and dsRNA into Sf9 insect cells and shrimp tissues. To extend its application to cancer cell-targeting drug delivery, we created three different types of chimeric MrNV virus-like particles (VLPs) (R-MrNV, I-MrNV, and E-MrNV) that have specificity toward the epidermal growth factor receptor (EGFR), a cancer cell biomarker, by incorporating the EGFR-specific GE11 peptide at 3 different locations within the host cell recognition site of the capsid. All three chimeric MrNV-VLPs preserved the ability to form a mulberry-like VLP structure and to encapsulate EGFP DNA plasmid with an efficiency comparable to that previously reported for normal MrNV (N-MrNV). Compared to N-MrNV, the chimeric R-MrNV and E-MrNV carrying the exposed GE-11 peptide showed a significantly enhanced binding and internalization abilities that were specific towards EGFR expression in colorectal cancer cells (SW480). Specific targeting of chimeric MrNV to EGFR was proven by both EGFR silencing with siRNA vector and a competition with excess GE-11 peptide as well as the use of EGFR-negative colorectal cells (SW620) and breast cancer cells (MCF7). We demonstrated here that both chimeric R-MrNV and E-MrNV could be used to encapsulate cargo such as exogenous DNA and deliver it specifically to EGFR-positive cells. Our study presents the potential use of surface-modified VLPs of shrimp virus origin as nanocontainers for targeted cancer drug delivery.

Innate immune responses against viral pathogens in Macrobrachium

Some members of genus Macrobrachium are important economically prawns and valuable objects for studying the innate immune defense mechanism of crustaceans. Studies have focused on immune responses against bacterial and fungal infections and have expanded to include antiviral immunity over the past two decades. Similar to all living organisms, prawns are exposed to viruses, including white spot syndrome virus, Macrobrachium rosenbergii nodavirus, and Decapod iridescent virus 1 and develop effective defense mechanisms. Here, we review current understanding of the antiviral host defense in two species of Macrobrachium. The main antiviral defense of Macrobrachium is the activation of intracellular signaling cascades, leading to the activation of cellular responses (apoptosis) and humoral responses (immune-related signaling pathways, antimicrobial and antiviral peptides, lectins, and prophenoloxidase-activating system).

Ancient gene duplications in RNA viruses revealed by protein tertiary structure comparisons

To date only a handful of duplicated genes have been described in RNA viruses. This shortage can be attributed to different factors, including the RNA viruses with high mutation rate that would make a large genome more prone to acquire deleterious mutations. This may explain why sequence-based approaches have only found duplications in their most recent evolutionary history. To detect earlier duplications, we performed protein tertiary structure comparisons for every RNA virus family represented in the Protein Data Bank. We present a list of thirty pairs of possible paralogs with <30 per cent sequence identity. It is argued that these pairs are the outcome of six duplication events. These include the α and β subunits of the fungal toxin KP6 present in the dsRNA Ustilago maydis virus (family Totiviridae), the SARS-CoV (Coronaviridae) nsp3 domains SUD-N, SUD-M and X-domain, the Picornavirales (families Picornaviridae, Dicistroviridae, Iflaviridae and Secoviridae) capsid proteins VP1, VP2 and VP3, and the Enterovirus (family Picornaviridae) 3C and 2A cysteine-proteases. Protein tertiary structure comparisons may reveal more duplication events as more three-dimensional protein structures are determined and suggests that, although still rare, gene duplications may be more frequent in RNA viruses than previously thought. Keywords: gene duplications; RNA viruses.

Immunological Analysis of the Hepatitis B Virus "a" Determinant Displayed on Chimeric Virus-Like Particles of Macrobrachium rosenbergii Nodavirus Capsid Protein Produced in Sf9 Cells

Chimeric virus-like particles (VLPs) have been widely exploited for various purposes including their use as vaccine candidates, particularly due to their ability to induce stronger immune responses than VLPs consisting of single viral proteins. In the present study, VLPs of the Macrobrachium rosenbergii nodavirus (MrNV) capsid protein (Nc) displaying the hepatitis B virus “a” determinant (aD) were produced in Spodoptera frugiperda (Sf9) insect cells. BALB/c mice immunised with the purified chimeric Nc-aD VLPs elicited a sustained titre of anti-aD antibody, which was significantly higher than that elicited by a commercially available hepatitis B vaccine and Escherichia coli-produced Nc-aD VLPs. Immunophenotyping showed that the Sf9-produced Nc-aD VLPs induced proliferation of cytotoxic T-lymphocytes and NK1.1 natural killer cells. Furthermore, enzyme-linked immunospot (ELISPOT)analysis showed the presence of antibody-secreting memory B cells in the mice splenocytes stimulated with the synthetic aD peptide. The significant humoral, natural killer cell and memory B cell immune responses induced by the Sf9-produced Nc-aD VLPs suggest that they present good prospects for use as a hepatitis B vaccine candidate.

Characterization of Dimeric Interactions within Protrusion-Domain Interfaces of Parallel and X-Shaped Conformations of Macrobrachium rosenbergii Nodavirus: A Theoretical Study Using the DFT Method along with QTAIM and NBO Analyses

The protrusion domain (P-domain; MrNVPd) of Macrobrachium rosenbergii nodavirus (MrNV) exists in two conformations, parallel and X-shaped. We have performed a theoretical study to gain insight into the nature of the dimeric interactions involving the dimeric interfaces within parallel and X-shaped conformations of MrNVPd by applying the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses in the framework of the density functional theory (DFT) approach. The results reveal that the dimer-dimer interfaces of MrNVPd have hydrogen bonds of common types. Leu255-Lys287, Tyr257-Lys287, Lys287-Ser253, Met294-Cys328, Asp295-Lys327, Ser298-Ser324, Ile326-Asp295, and Cys328-Met294 are the key residue pairs of the dimer-dimer interfaces to maintain the dimer-dimer structures of MrNVPd through charge-charge, charge-dipole, dipole-dipole, hydrophobic, and hydrogen bonding interactions. The strengths of these intermolecular dimer-dimer interactions in the parallel conformation are much greater than those in the X-shaped conformation. The parallel trimeric interface is held basically by electrostatic and hydrophobic interactions. The electrostatic interactions accompanying a strong hydrogen bond of Oγ1-Hγ1···Oγ1 in the Thr276 A-Thr276 D pair maintain the intermolecular interface of two X-shaped MrNVPd dimers.

Noncrystallographic symmetry-constrained map obtained by direct density optimization

Noncrystallographic symmetry (NCS) averaging following molecular-replacement phasing is generally the major technique used to solve a structure with several molecules in one asymmetric unit, such as a spherical icosahedral viral particle. As an alternative method to NCS averaging, a new approach to optimize or to refine the electron density directly under NCS constraints is proposed. This method has the same effect as the conventional NCS-averaging method but does not include the process of Fourier synthesis to generate the electron density from amplitudes and the corresponding phases. It has great merit for the solution of structures with limited data that are either twinned or incomplete at low resolution. This method was applied to the case of the T = 1 shell-domain subviral particle of Penaeus vannamei nodavirus with data affected by twinning using the REFMAC5 refinement software.