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Nucleocapsid protein captures DDX5 and RNMT facilitating viral RNA synthesis and viral protein translation for coronavirus replication

ABSTRACT: Coronaviruses (CoVs) hijack host RNA-binding proteins (RBPs) to facilitate their replication, but the viral proteins and host RBDs that participate in the synthesis of viral RNA and protein are unclear. In this study, we revealed that DEAD-box helicase (DDX5) and staphylococcal nuclease domain-containing protein (SND1) facilitate viral RNA synthesis, and that RNA guanine-7 methyltransferase (RNMT) enhances viral protein translation to promote viral replication via coronaviral subgenomic RNA-protein interactomes. DDX5 and SND1 positively regulate PEDV replication by promoting viral RNA synthesis via the binding of DDX5 to positive-sense viral RNA, whereas SND1 specifically detects negative-sense viral RNA. The interaction of DDX5/SND1 and N/nsp9/nsp12 promotes the formation of replication-transcription complexes for viral RNA synthesis to facilitate viral replication. We found that RNMT captures the host protein translation system to cyclize viral mRNA to assist in viral protein translation to promote viral replication. We also found that DDX5 broadly interacts with the N protein of CoVs and promotes the RNA synthesis of bovine coronavirus and porcine delta-coronavirus to promote viral replication. These results indicate that CoVs use host proteins to assist in the synthesis of viral RNA and protein to facilitate viral replication.

INSTRUMENT(S):

ORGANISM(S): Chlorocebus Sabaeus Sus Scrofa (pig)

TISSUE(S): Vero Cell, Llc-pk1 Cell

SUBMITTER: Liu Yuchang

LAB HEAD: Tongling Shan

PROVIDER: PXD067906 | Pride | 2026-01-21

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	Co-IP_PEDV_Flag-CTRL.zip	Other
	Co-IP_PEDV_Flag-DDX5.zip	Other
	Heavy-chain_amino_acids-MS.zip	Other
	RNA_pull_down_Chlorocebus_sabaeus.zip	Other
	RNA_pull_down_Sus_scrofa.zip	Other

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Project description:Heldt2012 - Influenza Virus Replication The model describes the life cycle of influenza A virus in a mammalian cell including the following steps: attachment of parental virions to the cell membrane, receptor-mediated endocytosis, fusion of the virus envelope with the endosomal membrane, nuclear import of vRNPs, viral transcription and replication, translation of the structural viral proteins, nuclear export of progeny vRNPs and budding of new virions. It also explicitly accounts for the stabilization of cRNA by viral polymerases and NP and the inhibition of vRNP activity by M1 protein binding. In short, the model focuses on the molecular mechanism that controls viral transcription and replication. This model is described in the article: Modeling the intracellular dynamics of influenza virus replication to understand the control of viral RNA synthesis. Heldt FS, Frensing T, Reichl U. J Virol. Abstract: Influenza viruses transcribe and replicate their negative-sense RNA genome inside the nucleus of host cells via three viral RNA species. In the course of an infection, these RNAs show distinct dynamics, suggesting that differential regulation takes place. To investigate this regulation in a systematic way, we developed a mathematical model of influenza virus infection at the level of a single mammalian cell. It accounts for key steps of the viral life cycle, from virus entry to progeny virion release, while focusing in particular on the molecular mechanisms that control viral transcription and replication. We therefore explicitly consider the nuclear export of viral genome copies (vRNPs) and a recent hypothesis proposing that replicative intermediates (cRNA) are stabilized by the viral polymerase complex and the nucleoprotein (NP). Together, both mechanisms allow the model to capture a variety of published data sets at an unprecedented level of detail. Our findings provide theoretical support for an early regulation of replication by cRNA stabilization. However, they also suggest that the matrix protein 1 (M1) controls viral RNA levels in the late phase of infection as part of its role during the nuclear export of viral genome copies. Moreover, simulations show an accumulation of viral proteins and RNA toward the end of infection, indicating that transport processes or budding limits virion release. Thus, our mathematical model provides an ideal platform for a systematic and quantitative evaluation of influenza virus replication and its complex regulation. With the current parameter set, the model reproduces an infection at a multiplicity of infection (MOI) of 10. Figure 2A of the paper is reproduced here, with parameters kDegRnp and kSynP changed to zeros. Initial conditions and parameter changes that were used to obtain specific figures in the article can be found in Table A2. The model has the correct value for kAttLo as 4.55e-04. The value of this parameter mentioned as 4.55e-02 in Table 1 of the paper is incorrect. This is checked with the author. This model is hosted on BioModels Database and identified by: MODEL1307270000 . To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models . To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

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Nucleocapsid protein captures DDX5 and RNMT facilitating viral RNA synthesis and viral protein translation for coronavirus replication

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