Nucleocapsid protein structures from orthobunyaviruses reveal insight into ribonucleoprotein architecture and RNA polymerization

Ariza, Antonio; Tanner, S.J.; Walter, Cheryl T.; Dent, Kyle; Shepherd, Dale A.; Wu, Weining; Matthews, Susan V.; Hiscox, Julian A.; Green, Todd; Luo, Ming; Elliott, Richard M.; Fooks, Anthony R.; Ashcroft, Alison E.; Stonehouse, Nicola J.; Ranson, Neil A.; Barr, John N.; Edwards, Thomas A.

doi:10.1093/nar/gkt268

Cited by 72 publications

(91 citation statements)

References 64 publications

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“…Each NP subunit binds 11 nucleotides of RNA according to Niu et al, Reguera et al, and Ariza et al (4,5,7). Bound RNA is largely inaccessible, consistent with the observation that Orthobunyavirus NP-RNA complexes are generally resistant to RNase treatment (3-5, 7).…”

supporting

confidence: 54%

“…Each Orthobunyavirus NP folds into a compact structure that can be divided into four parts: the N-arm, N-terminal domain, C-terminal domain, and C-arm. The N-/C-terminal domains, formed by the N-/C-terminal halves of the polypeptide chain, comprise the NP structure core (3)(4)(5)(6)(7). The N-/C-arms are short sequences from the N/C termini, and they play important roles in mediating NP-NP interaction.…”

mentioning

confidence: 99%

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Genome encapsidation by orthobunyavirus nucleoproteins

Zheng¹,

Tao²

2013

Proc. Natl. Acad. Sci. U.S.A.

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supporting

confidence: 54%

mentioning

confidence: 99%

Genome encapsidation by orthobunyavirus nucleoproteins

Zheng¹,

Tao²

2013

Proc. Natl. Acad. Sci. U.S.A.

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“…The atomic structures of nucleocapsid-like particles (NLPs) have been reported for three NSV families: Rhabdoviridae, Paramyxoviridae (genus Pneumovirus), and Bunyaviridae (genera Phlebovirus and Orthobunyavirus) (11)(12)(13)(14)(27)(28)(29)(30)(31). A comparison of representative structures from each genus was performed.…”

Section: Resultsmentioning

confidence: 99%

Common Mechanism for RNA Encapsidation by Negative-Strand RNA Viruses

Green

Cox

Tsao

et al. 2014

J Virol

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The nucleocapsid of a negative-strand RNA virus is assembled with a single nucleocapsid protein and the viral genomic RNA. The nucleocapsid protein polymerizes along the length of the single-strand genomic RNA (viral RNA) or its cRNA. This process of encapsidation occurs concomitantly with genomic replication. Structural comparisons of several nucleocapsid-like particles show that the mechanism of RNA encapsidation in negative-strand RNA viruses has many common features. Fundamentally, there is a unifying mechanism to keep the capsid protein protomer monomeric prior to encapsidation of viral RNA. In the nucleocapsid, there is a cavity between two globular domains of the nucleocapsid protein where the viral RNA is sequestered. The viral RNA must be transiently released from the nucleocapsid in order to reveal the template RNA sequence for transcription/ replication. There are cross-molecular interactions among the protein subunits linearly along the nucleocapsid to stabilize its structure. Empty capsids can form in the absence of RNA. The common characteristics of RNA encapsidation not only delineate the evolutionary relationship of negative-strand RNA viruses but also provide insights into their mechanism of replication. IMPORTANCEWhat separates negative-strand RNA viruses (NSVs) from the rest of the virosphere is that the nucleocapsid of NSVs serves as the template for viral RNA synthesis. Their viral RNA-dependent RNA polymerase can induce local conformational changes in the nucleocapsid to temporarily release the RNA genome so that the viral RNA-dependent RNA polymerase can use it as the template for RNA synthesis during both transcription and replication. After RNA synthesis at the local region is completed, the viral RNA-dependent RNA polymerase processes downstream, and the RNA genome is restored in the nucleocapsid. We found that the nucleocapsid assembly of all NSVs shares three essential elements: a monomeric capsid protein protomer, parallel orientation of subunits in the linear nucleocapsid, and a (5H ؉ 3H) motif that forms a proper cavity for sequestration of the RNA. This observation also suggests that all NSVs evolved from a common ancestor that has this unique nucleocapsid.

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“…However, the two N domains may become more closed in other NSV N proteins, such as bunyaviruses (27)(28)(29)(30). The degree of openness of the two domains may not necessarily be related to the mode of RNA encapsidation by the N protein or the flexibility of the N protein core.…”

Section: Discussionmentioning

confidence: 99%

Releasing the Genomic RNA Sequestered in the Mumps Virus Nucleocapsid

Severin

Terrell

Zengel

et al. 2016

J Virol

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In a negative-strand RNA virus, the genomic RNA is sequestered inside the nucleocapsid when the viral RNA-dependent RNA polymerase uses it as the template for viral RNA synthesis. It must require a conformational change in the nucleocapsid protein (N) to make the RNA accessible to the viral polymerase during this process. The structure of an empty mumps virus (MuV) nucleocapsid-like particle was determined to 10.4-Å resolution by cryo-electron microscopy (cryo-EM) image reconstruction. By modeling the crystal structure of parainfluenza virus 5 into the density, it was shown that the ␣-helix close to the RNA became flexible when RNA was removed. Point mutations in this helix resulted in loss of polymerase activities. Since the core of N is rigid in the nucleocapsid, we suggest that interactions between this region of the mumps virus N and its polymerase, instead of large N domain rotations, lead to exposure of the sequestered genomic RNA. Some pathogens appear to reemerge in spite of available vaccines, such as mumps virus and measles virus (3-5). Effective controls are needed to combat these pathogens. In order to develop more effective countermeasures, the mechanism of NSV replication should be better understood. One of the unique features in NSVs is that the genomic RNA is sequestered in the nucleocapsid (6). During transcription and replication, the viral RNA-dependent RNA polymerase (vRdRp) must be able to gain access to the sequestered genomic RNA in order to use it as the template. For Rhabdoviridae and Paramyxoviridae, the virus encodes a single nucleocapsid protein (N) that polymerizes as a linear capsid to encapsidate the genomic RNA (7). The viral polymerase complex consists of the large protein (L) and the phosphoprotein (P). IMPORTANCE Mumps virus (MuVThe structure of the nucleocapsid or a nucleocapsid-like particle has been solved for several members of Rhabdoviridae and Paramyxoviridae by X-ray crystallography or cryo-electron microscopy (cryo-EM) three-dimensional (3D) reconstruction (8-12). The common features among various structures are that the N protein has an N-terminal domain and C-terminal domain in its core, composed mostly of ␣-helices. When the N subunits assemble into a polymeric capsid, they are aligned in parallel in a linear fashion (13). There are extensive side-by-side interactions between the neighboring domains and domain swaps of extended loops and long termini. The genomic RNA is encapsidated in a cavity formed between the two core domains. Most of the RNA bases are stacked, some of which face the exterior and some the interior of the N protein core. The tight assembly of the nucleocapsid clearly suggests that vRdRp must open the N protein core in order to unveil the genomic RNA. How this action is carried out remains to be discovered. The interaction of the polymerase cofactor P with the nucleocapsid may provide some insights on this subject. The C-terminal domain of vesicular stomatitis virus (VSV) P protein binds between the extended loops in the C-terminal domains ...

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Nucleocapsid protein structures from orthobunyaviruses reveal insight into ribonucleoprotein architecture and RNA polymerization

Cited by 72 publications

References 64 publications

Genome encapsidation by orthobunyavirus nucleoproteins

Genome encapsidation by orthobunyavirus nucleoproteins

Common Mechanism for RNA Encapsidation by Negative-Strand RNA Viruses

Releasing the Genomic RNA Sequestered in the Mumps Virus Nucleocapsid

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