The serine-48 residue of nucleolar phosphoprotein nucleophosmin-1 plays critical role in subcellular localization and interaction with porcine circovirus type 3 capsid protein

hnRNP K regulates mitochondrial apoptosis induced by porcine circovirus type 3 capsid protein

Porcine circovirus type 3 (PCV3) is a globally emerging circovirus affecting pigs and other animals. The capsid protein (Cap) is the sole structural protein of PCV, with a crucial role in virus evolution and pathogenesis. Through interactions with host factors, Cap enables viral entry, transport, and replication while modifying various cellular processes. Cap protein-induced apoptosis has important implications for viral pathogenesis, but remains poorly defined. Herein, we demonstrated for the first time that PCV3 Cap induced cell cycle arrest of PK-15 cells in S-phase and initiated apoptosis via a mitochondrial Caspase-9-dependent pathway. Truncation analysis localized the apoptotic determinant to the N-terminal 1-34 aa of PCV3 Cap and heterogeneous nuclear ribonucleoprotein K (hnRNP K) was identified as a host protein that binds to PCV3 Cap. Overexpression of hnRNP K reduced PCV3 Cap-induced release of Cyt-c into the cytoplasm, implying a regulatory role in apoptosis. Based on structural modelling and molecular docking, amino acids at sites 24 and 27 of Cap from PCV3 variants, which define genotypes (PCV3a/b/c), affected binding with hnRNP K. Specifically, PCV3c Cap (V24/K27 and V24/R27) had higher affinity than PCV3a Cap (A24/R27) or PCV3b Cap (A24/K27), consistent with its superior apoptosis-inducing capacity compared to PCV3a/b variants, highlighting the importance of Cap interactions with hnRNP K. In summary, we identified novel molecular determinants of PCV3 pathogenesis that will inform development of vaccines and diagnostics.

DEAD-box RNA helicase 10 inhibits porcine circovirus type 3 replication by interacting with the viral capsid protein and activating interferon responses

Porcine circovirus type 3 (PCV3) is an emerging pathogen that causes porcine dermatitis and nephropathy syndrome-like symptoms, multisystemic inflammation, and reproductive failure. The PCV3 capsid (Cap) protein interacts with DEAD-box RNA helicase 10 (DDX10), a protein that functions primarily through regulating interferon (IFN)-β production to exert its antiviral activity. However, how the interaction between DDX10 and PCV3 Cap regulates viral replication remains unknown. We used Western blotting, interaction assays, and knockdown analyses to observe impaired PCV3 proliferation in transiently DDX10-overexpressing cells, as indicated by decreased viral protein expression levels and virus production. In contrast, PCV3 replication increased upon small interfering RNA-mediated DDX10 depletion. Furthermore, DDX10 positively regulated IFN-β production and interferon-stimulated gene expression, inhibiting PCV3 replication. Mechanistically, PCV3 Cap co-localized and interacted with DDX10, and the N-terminal nuclear localization signal of PCV3 Cap and the helicase domain of DDX10 were essential for the Cap-DDX10 interaction. Furthermore, PCV3 infection decreases DDX10 expression to antagonize its antiviral activity. These results show that DDX10 antagonizes PCV3 replication by interacting with the PCV3 Cap protein and activating IFN-β responses, which provides important insight into the prevention and control of PCV3 infection.IMPORTANCEClarifying how host factors contribute to infection with PCV3, a newly discovered pathogen associated with multiple clinicopathological signs in swine, helps elucidate viral pathogenesis. The PCV3 Cap protein has been shown to interact with DDX10, a crucial protein that regulates RNA virus replication. Herein, we further demonstrated that DDX10 expression is downregulated in PCV3-infected cells and antagonizes the replication of PCV3 and that DDX10 increases interferon-β and interferon-stimulated gene levels to inhibit PCV3 replication by binding to the PCV3 Cap. In addition, PCV3 infection decreases DDX10 expression to antagonize its antiviral activity. These results reveal a molecular mechanism by which DDX10 antagonizes PCV3 replication by binding to the PCV3 Cap protein and activating IFN signals, thereby providing important targets for preventing and controlling PCV3 infection.

Nucleophosmin 1 inhibits the replication of influenza A virus by competitively binding viral RNA with viral proteins

Influenza A viruses (IAVs) are single-stranded negative-sense RNA viruses that continually challenge animal and human health. In IAV-infected cells, host RNA-binding proteins play key roles in the life cycle of IAV by directly binding to viral RNA. Here, we examined the role of the host RNA-binding protein nucleophosmin-1 (NPM1) in IAV replication. We found that, as a nucleolar phosphoprotein, NPM1 directly binds to viral RNA (vRNA) and inhibits the replication of various subtypes of IAV. NPM1 binding to vRNA competitively reduces the assembly of the viral ribonucleoprotein complex and the viral polymerase activity, thereby reducing the generation of progeny viral RNA and virions. The RNA-binding activity of NPM1, with the key residues T199, T219, T234, and T237, is essential for its anti-influenza function. Taken together, our findings demonstrate that NPM1 acts as an RNA-binding protein and interacts with IAV vRNA to suppress viral replication.

DDX21 Promotes PCV3 Replication by Binding to Cap Protein and Inhibiting Interferon Responses

Porcine circovirus type 3 (PCV3) is an emerging pathogen that causes porcine dermatitis, nephropathy syndrome-like symptoms, multisystemic inflammation, and reproductive failure. The PCV3 capsid (Cap) protein interacts with DDX21, which functions mainly through controlling interferon (IFN)-β levels. However, how the interaction between DDX21 and PCV3 Cap regulates viral replication remains unknown. In the present study, upon shRNA-mediated DDX21 depletion in PK-15 cells, we observed impaired PCV3 proliferation via a lentivirus-delivered system, as indicated by reduced replicase (Rep) protein levels and viral titers. Furthermore, DDX21 negatively regulated IFN-β and interferon-stimulated gene (ISG) levels, promoting PCV3 replication. Mechanistically, PCV3 Cap co-localized and interacted with DDX21, and the nuclear localization signal (NLS) of PCV3 Cap and 763GSRSNRFQNK772 at the C-terminal domain (CTD) of DDX21 were indispensable to the interaction. Moreover, PCV3 infection prevented the repression of DDX21 to facilitate its pro-viral activity. Taken together, these results show that DDX21 promotes PCV3 replication by binding to the PCV3 Cap protein and prohibiting IFN-β response, which provides important insight on the prevention and control of PCV3 infection.

Nucleophosmin: A Nucleolar Phosphoprotein Orchestrating Cellular Stress Responses

Nucleophosmin (NPM1) is a key nucleolar protein released from the nucleolus in response to stress stimuli. NPM1 functions as a stress regulator with nucleic acid and protein chaperone activities, rapidly shuttling between the nucleus and cytoplasm. NPM1 is ubiquitously expressed in tissues and can be found in the nucleolus, nucleoplasm, cytoplasm, and extracellular environment. It plays a central role in various biological processes such as ribosome biogenesis, cell cycle regulation, cell proliferation, DNA damage repair, and apoptosis. In addition, it is highly expressed in cancer cells and solid tumors, and its mutation is a major cause of acute myeloid leukemia (AML). This review focuses on NPM1's structural features, functional diversity, subcellular distribution, and role in stress modulation.

DEAD-box RNA helicase 21 interacts with porcine circovirus type 2 Cap protein and facilitates viral replication

Porcine circovirus type 2 (PCV2) is the etiological agent of PCV2-associated diseases that pose a serious threat to the swine industry. PCV2 capsid (Cap) protein has been shown to interact with DEAD-box RNA helicase 21 (DDX21), an important protein that regulates RNA virus replication. However, whether the interaction between DDX21 and the PCV2 Cap regulates PCV2 replication remains unclear. Herein, by using western blotting, interaction assays, and knockdown analysis, we found that PCV2 infection induced the cytoplasmic relocation of DDX21 from the nucleolus in cultured PK-15 cells. Moreover, the nuclear localization signal (NLS) of PCV2 Cap interacted directly with DDX21. The NLS of PCV2 Cap and 763GSRSNRFQNK772 residues at the C-terminal domain (CTD) of DDX21 were essential for the dual interaction. Upon shRNA-mediated DDX21 depletion in PK-15 cells, we observed impaired PCV2 replication via a lentivirus-delivered system, as evidenced by decreased levels of viral protein expression and virus production. In contrast, the replication of PCV2 increased in transiently DDX21-overexpressing cells. Our results indicate that DDX21 interacts with PCV2 Cap and plays a crucial role in virus replication. These results provide a reference for developing novel potential targets for prevention and control of PCV2 infection.

Porcine Epidemic Diarrhea Virus: An Updated Overview of Virus Epidemiology, Virulence Variation Patterns and Virus-Host Interactions

The porcine epidemic diarrhea virus (PEDV) is a member of the coronavirus family, causing deadly watery diarrhea in newborn piglets. The global pandemic of PEDV, with significant morbidity and mortality, poses a huge threat to the swine industry. The currently developed vaccines and drugs are only effective against the classic GI strains that were prevalent before 2010, while there is no effective control against the GII variant strains that are currently a global pandemic. In this review, we summarize the latest progress in the biology of PEDV, including its transmission and origin, structure and function, evolution, and virus-host interaction, in an attempt to find the potential virulence factors influencing PEDV pathogenesis. We conclude with the mechanism by which PEDV components antagonize the immune responses of the virus, and the role of host factors in virus infection. Essentially, this review serves as a valuable reference for the development of attenuated virus vaccines and the potential of host factors as antiviral targets for the prevention and control of PEDV infection.

The Network of Interactions between the Porcine Epidemic Diarrhea Virus Nucleocapsid and Host Cellular Proteins

Host–virus protein interactions are critical for intracellular viral propagation. Understanding the interactions between cellular and viral proteins may help us develop new antiviral strategies. Porcine epidemic diarrhea virus (PEDV) is a highly contagious coronavirus that causes severe damage to the global swine industry. Here, we employed co-immunoprecipitation and liquid chromatography-mass spectrometry to characterize 426 unique PEDV nucleocapsid (N) protein-binding proteins in infected Vero cells. A protein–protein interaction network (PPI) was created, and gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) database analyses revealed that the PEDV N-bound proteins belong to different cellular pathways, such as nucleic acid binding, ribonucleoprotein complex binding, RNA methyltransferase, and polymerase activities. Interactions of the PEDV N protein with 11 putative proteins: tripartite motif containing 21, DEAD-box RNA helicase 24, G3BP stress granule assembly factor 1, heat shock protein family A member 8, heat shock protein 90 alpha family class B member 1, YTH domain containing 1, nucleolin, Y-box binding protein 1, vimentin, heterogeneous nuclear ribonucleoprotein A2/B1, and karyopherin subunit alpha 1, were further confirmed by in vitro co-immunoprecipitation assay. In summary, studying an interaction network can facilitate the identification of antiviral therapeutic strategies and novel targets for PEDV infection.

Structural basis for the recognition by 14-3-3 proteins of a conditional binding site within the oligomerization domain of human nucleophosmin

Nucleophosmin 1 (NPM1) is a multifunctional protein regulating ribosome biogenesis, centrosome duplication and chromatin remodeling. Being a major nucleolar protein, NPM1 can migrate to the nucleus and the cytoplasm, which is controlled by changes of NPM1 oligomerization and interaction with other cell factors. NPM1 forms a stable pentamer with its N-terminal structured domain, where two nuclear export signals and several phosphorylation sites reside. This domain undergoes dissociation and disordering upon Ser48 phosphorylation in the subunit interface. Recent studies indicated that Ser48 is important for NPM1 interaction with other proteins including 14-3-3, the well-known phosphoserine/phosphothreonine binders, but the structural basis for 14-3-3/NPM1 interaction remained unaddressed. By fusing human 14-3-3ζ with an NPM1 segment surrounding Ser48, which was phosphorylated inside Escherichia coli cells by co-expressed protein kinase A, here we obtained the desired protein/phosphopeptide complex and determined its crystal structure. While biochemical data indicated that the interaction is driven by Ser48 phosphorylation, the crystallographic 14-3-3/phosphopeptide interface reveals an NPM1 conformation distinctly different from that in the NPM1 pentamer. Given the canonical phosphopeptide-binding mode observed in our crystal structure, Ser48 emerges as a conditional binding site whose recognition by 14-3-3 proteins is enabled by NPM1 phosphorylation, disassembly and disordering under physiological circumstances.

Advances in Crosstalk between Porcine Circoviruses and Host

Porcine circoviruses (PCVs), including PCV1 to PCV4, are non-enveloped DNA viruses with a diameter of about 20 nm, belonging to the genus Circovirus in the family Circoviridae. PCV2 is an important causative agent of porcine circovirus disease or porcine circovirus-associated disease (PCVD/PCVAD), which is highly prevalent in pigs and seriously affects the swine industry globally. Furthermore, PCV2 mainly causes subclinical symptoms and immunosuppression, and PCV3 and PCV4 were detected in healthy pigs, sick pigs, and other animals. Although the pathogenicity of PCV3 and PCV4 in the field is still controversial, the infection rates of PCV3 and PCV4 in pigs are increasing. Moreover, PCV3 and PCV4 rescued from infected clones were pathogenic in vivo. It is worth noting that the interaction between virus and host is crucial to the infection and pathogenicity of the virus. This review discusses the latest research progress on the molecular mechanism of PCVs–host interaction, which may provide a scientific basis for disease prevention and control.

Interaction Network of Porcine Circovirus Type 3 and 4 Capsids with Host Proteins

An extensive understanding of the interactions between host cellular and viral proteins provides clues for studying novel antiviral strategies. Porcine circovirus type 3 (PCV3) and type 4 (PCV4) have recently been identified as viruses that can potentially damage the swine industry. Herein, 401 putative PCV3 Cap-binding and 484 putative PCV4 Cap-binding proteins were characterized using co-immunoprecipitation and liquid chromatography-mass spectrometry. Both PCV3 and PCV4 Caps shared 278 identical interacting proteins, but some putative interacting proteins (123 for PCV3 Cap and 206 for PCV4 Cap) differed. A protein-protein interaction network was constructed, and according to gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) database analyses, both PCV3 Cap- and PCV4 Cap-binding proteins participated mainly in ribosome biogenesis, nucleic acid binding, and ATP-dependent RNA helicase activities. Verification assays of eight putative interacting proteins indicated that nucleophosmin-1, nucleolin, DEAD-box RNA helicase 21, heterogeneous nuclear ribonucleoprotein A2/B1, YTH N6-methyladenosine RNA binding protein 1, and Y-box binding protein 1 bound directly to both PCV3 and PCV4 Caps, but ring finger protein 2 and signal transducer and activator of transcription 6 did not. Therefore, the interaction network provided helpful information to support further research into the underlying mechanisms of PCV3 and PCV4 infection.

Identification and genomic characterization of a novel porcine CRESS DNA virus from a pig suffering from diarrhea in China

The circular replication-associated protein (Rep)-encoding ssDNA (CRESS-DNA) viruses show high diversity and have a very wide range of hosts, including all three domains of cellular life. In the present study, a novel CRESS DNA virus, provisionally named "kirkovirus HNU-XX-2020" was discovered in a growing pig with watery diarrhea. The virus has a circular genome of 2961 nucleotides (nt) and three major putative open reading frames (ORFs), encoding a Rep protein (327 amino acids), a capsid protein (175 amino acids), and one protein (209 amino acids) of unknown function. The genome showed the highest sequence similarity (68.6% identity) to the genome of porcine circo-like virus 51 (JF713719), which was identified in pig faeces, and it showed very limited sequence similarity (less than 40% identity) to other virus genomes. Further phylogenetic analysis suggested that it could be a novel member in the proposed family "Kirkoviridae".

Contribution of DEAD-Box RNA Helicase 21 to the Nucleolar Localization of Porcine Circovirus Type 4 Capsid Protein

Porcine circovirus type 4 (PCV4) is a newly emerging pathogen which might be associated with diverse clinical signs, including respiratory and gastrointestinal distress, dermatitis, and various systemic inflammations. The host cellular proteins binding to PCV4 capsid (Cap) protein are still not clear. Herein, we found that the PCV4 Cap mediated translocation of DEAD-box RNA helicase 21 (DDX21) to the cytoplasm from the nucleolus and further verified that the nucleolar localization signal (NoLS) of the PCV4 Cap bound directly to the DDX21. The NoLS of PCV4 Cap and ⁷⁶³GSRSNRFQNK⁷⁷² residues at the C-terminal domain (CTD) of DDX21 were required for this PCV4 Cap/DDX21 interaction. Further studies indicated that the PCV4 Cap NoLS exploited DDX21 to facilitate its nucleolar localization. In summary, our results firstly demonstrated that DDX21 binds directly to the NoLS of the PCV4 Cap thereby contributing to the nucleolar localization of the PCV4 Cap protein.

The Nucleolar Localization Signal of Porcine Circovirus Type 4 Capsid Protein Is Essential for Interaction With Serine-48 Residue of Nucleolar Phosphoprotein Nucleophosmin-1

Porcine circovirus type 4 (PCV4) is an emerging etiological agent which was first detected in 2019. The nucleolar localization signal (NoLS) of PCV4 Cap protein and its binding host cellular proteins are still not elucidated. In the present study, we discovered a distinct novel NoLS of PCV4 Cap, which bound to the nucleolar phosphoprotein nucleophosmin-1 (NPM1). The NoLS of PCV4 Cap and serine-48 residue at the N-terminal oligomerization domain of NPM1 were necessary for PCV4 Cap/NPM1 interaction. Furthermore, the charge property of serine residue at position 48 of the NPM1 was crucial for its oligomerization and interaction with PCV4 Cap. In summary, our findings show for the first time that the PCV4 Cap NoLS and the NPM1 oligomerization determine the interaction of Cap/NPM1.

Nucleolar Phosphoprotein NPM1 Interacts With Porcine Circovirus Type 3 Cap Protein and Facilitates Viral Replication

Porcine circovirus type 3 (PCV3) is a recently discovered virus with potentially significant implications on the global swine industry. PCV3 replication involves the entry of the viral capsid (Cap) protein with nucleolar localization signals into the nucleus. Using liquid chromatography-mass spectrometry analysis, nucleolar phosphoprotein NPM1 was identified as one of the cellular proteins bound to PCV3 Cap. Co-immunoprecipitation demonstrated that PCV3 Cap interacts directly with NPM1, where the region binding with NPM1 is mapped to amino acid residues 1–38 of Cap. Upon co-transfection, the expression of Cap protein promoted the redistribution of NPM1, which translocated from the nucleus to the cytoplasm and colocalized with Cap in cultured PK15 cells. NPM1 expression was upregulated and translocated from the nucleus to the cytoplasm in PCV3-infected cells, upon siRNA-mediated depletion, or upon treatment with NPM1 inhibitor in PK15 cells with impaired PCV3 replication, as evidenced by decreased levels of viral DNA synthesis and protein expression. By contrast, the replication of PCV3 was enhanced in stably NPM1-expressing cells via a lentivirus-delivered system. Taken together, these findings indicate that NPM1 interacts with PCV3 Cap and plays a crucial role in PCV3 replication.