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Organization, Function, and Therapeutic Targeting of the Morbillivirus RNA-Dependent RNA Polymerase Complex

View Article: PubMed Central - PubMed

ABSTRACT

The morbillivirus genus comprises major human and animal pathogens, including the highly contagious measles virus. Morbilliviruses feature single stranded negative sense RNA genomes that are wrapped by a plasma membrane-derived lipid envelope. Genomes are encapsidated by the viral nucleocapsid protein forming ribonucleoprotein complexes, and only the encapsidated RNA is transcribed and replicated by the viral RNA-dependent RNA polymerase (RdRp). In this review, we discuss recent breakthroughs towards the structural and functional understanding of the morbillivirus polymerase complex. Considering the clinical burden imposed by members of the morbillivirus genus, the development of novel antiviral therapeutics is urgently needed. The viral polymerase complex presents unique structural and enzymatic properties that can serve as attractive candidates for druggable targets. We evaluate distinct strategies for therapeutic intervention and examine how high-resolution insight into the organization of the polymerase complex may pave the path towards the structure-based design and optimization of next-generation RdRp inhibitors.

No MeSH data available.


Related in: MedlinePlus

Model of the interaction between L, N, and P in the paramyxovirus RNA dependent RNA polymerase RdRp complex. (A) P binds L via its C-terminal domain. The P-L complex is recruited to the nucleocapsid through the interaction of the N-terminal domain of P (black and sand) with the N-CTD in the Ncore. Transient docking of P-XD (orange) and the MoRE in the Ntail (salmon) reduces the frequency of premature separation of the advancing polymerase complex from the RNP template. The P interaction with Ncore, possibly involving docking of the soyouz1 motif (sand) of P to N-CTD, locally opens the nucleocapsid and exposes the encapsidated RNA at the leading edge of the RdRp complex; (B) Ribbon representation of the crystal structure of a chimeric protein comprising PXD (dark orange, residues 457–507) and N (residues 477–505) (PDB code 1T6O) [48]. The α-MoRE of N has an alpha helical conformation spanning residues 487–503 and interacts with the second and third helixes of P-XD.
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viruses-08-00251-f004: Model of the interaction between L, N, and P in the paramyxovirus RNA dependent RNA polymerase RdRp complex. (A) P binds L via its C-terminal domain. The P-L complex is recruited to the nucleocapsid through the interaction of the N-terminal domain of P (black and sand) with the N-CTD in the Ncore. Transient docking of P-XD (orange) and the MoRE in the Ntail (salmon) reduces the frequency of premature separation of the advancing polymerase complex from the RNP template. The P interaction with Ncore, possibly involving docking of the soyouz1 motif (sand) of P to N-CTD, locally opens the nucleocapsid and exposes the encapsidated RNA at the leading edge of the RdRp complex; (B) Ribbon representation of the crystal structure of a chimeric protein comprising PXD (dark orange, residues 457–507) and N (residues 477–505) (PDB code 1T6O) [48]. The α-MoRE of N has an alpha helical conformation spanning residues 487–503 and interacts with the second and third helixes of P-XD.

Mentions: Although the most heterogeneous across different pathogens of the morbillivirus genus, the Ntail region contains three clusters of conserved residues, designated boxes 1 (400–420), 2 (489–506), and 3 (517–525) [30]. Overall, Ntail is mainly structurally disordered and residues (450–525) are thought to extend outward from the assembled nucleocapsid [43]. Its role in viral replication is not well understood; it was first proposed that Ntail is necessary for the recruitment of the RdRp complex to the nucleocapsid. Indeed, it has been shown in early studies of Sendai virus (SeV) that deletion of a fragment of Ntail leads to a significant loss of RdRp activity [44], and a C-terminal truncation of residues 495–525 of the MeV Ntail, which contain boxes 2 and 3, was found in subsequent work to cause a dramatic loss in RdRp activity in MeV minireplicon assays [45]. This observation appeared consistent with a role of Ntail in RdRp recruitment to the nucleocapsid, since box 2 contains a binding site for the P protein, the Molecular Recognition Element (MoRE), which specifically interacts with an X domain in the P protein (P-XD) that is located close to the C-terminus of the protein. MoRE assumes a molten globule conformation that transiently folds into short alpha helical structures, which are thought to establish the initial contact with P-XD. Subsequently, full conversion into a helical conformation is proposed to stabilize the interaction [46,47]. An X-ray structure of a recombinant MeV P-XD fused to a box 2-derived peptide provides high-resolution insight into this interaction [48] (Figure 4). Rather strikingly, however, further truncation of Ntail upstream of box 2 up to an additional 40 residues progressively restored RdRp activity in the MeV minireplicon system [49]. Expanding the reporter construct to full genome length in this study reduced transcription success, resulting in the current view that the MoRE P-XD interaction is, in fact, dispensable for RdRp recruitment to the genome. Rather, loading of the MeV RdRp complex onto the RNP template must be mediated by a direct interaction between P-L and Ncore in assembled nucleocapsids. Likely, truncating only the C-terminal region of the Ntails as done in the earlier studies masks access to Ncore, since the unstructured central Ntail regions are still present but cannot be ordered by the RdRp complex through interaction of P-XD with MoRE [49]. Once the polymerase is loaded on the template, MoRE P-XD binding is not mechanistically required for polymerization but appears to contribute to preventing premature separation of the advancing polymerase from the template through cycles of temporary binding and release (Figure 4A,B).


Organization, Function, and Therapeutic Targeting of the Morbillivirus RNA-Dependent RNA Polymerase Complex
Model of the interaction between L, N, and P in the paramyxovirus RNA dependent RNA polymerase RdRp complex. (A) P binds L via its C-terminal domain. The P-L complex is recruited to the nucleocapsid through the interaction of the N-terminal domain of P (black and sand) with the N-CTD in the Ncore. Transient docking of P-XD (orange) and the MoRE in the Ntail (salmon) reduces the frequency of premature separation of the advancing polymerase complex from the RNP template. The P interaction with Ncore, possibly involving docking of the soyouz1 motif (sand) of P to N-CTD, locally opens the nucleocapsid and exposes the encapsidated RNA at the leading edge of the RdRp complex; (B) Ribbon representation of the crystal structure of a chimeric protein comprising PXD (dark orange, residues 457–507) and N (residues 477–505) (PDB code 1T6O) [48]. The α-MoRE of N has an alpha helical conformation spanning residues 487–503 and interacts with the second and third helixes of P-XD.
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Related In: Results  -  Collection

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Show All Figures
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viruses-08-00251-f004: Model of the interaction between L, N, and P in the paramyxovirus RNA dependent RNA polymerase RdRp complex. (A) P binds L via its C-terminal domain. The P-L complex is recruited to the nucleocapsid through the interaction of the N-terminal domain of P (black and sand) with the N-CTD in the Ncore. Transient docking of P-XD (orange) and the MoRE in the Ntail (salmon) reduces the frequency of premature separation of the advancing polymerase complex from the RNP template. The P interaction with Ncore, possibly involving docking of the soyouz1 motif (sand) of P to N-CTD, locally opens the nucleocapsid and exposes the encapsidated RNA at the leading edge of the RdRp complex; (B) Ribbon representation of the crystal structure of a chimeric protein comprising PXD (dark orange, residues 457–507) and N (residues 477–505) (PDB code 1T6O) [48]. The α-MoRE of N has an alpha helical conformation spanning residues 487–503 and interacts with the second and third helixes of P-XD.
Mentions: Although the most heterogeneous across different pathogens of the morbillivirus genus, the Ntail region contains three clusters of conserved residues, designated boxes 1 (400–420), 2 (489–506), and 3 (517–525) [30]. Overall, Ntail is mainly structurally disordered and residues (450–525) are thought to extend outward from the assembled nucleocapsid [43]. Its role in viral replication is not well understood; it was first proposed that Ntail is necessary for the recruitment of the RdRp complex to the nucleocapsid. Indeed, it has been shown in early studies of Sendai virus (SeV) that deletion of a fragment of Ntail leads to a significant loss of RdRp activity [44], and a C-terminal truncation of residues 495–525 of the MeV Ntail, which contain boxes 2 and 3, was found in subsequent work to cause a dramatic loss in RdRp activity in MeV minireplicon assays [45]. This observation appeared consistent with a role of Ntail in RdRp recruitment to the nucleocapsid, since box 2 contains a binding site for the P protein, the Molecular Recognition Element (MoRE), which specifically interacts with an X domain in the P protein (P-XD) that is located close to the C-terminus of the protein. MoRE assumes a molten globule conformation that transiently folds into short alpha helical structures, which are thought to establish the initial contact with P-XD. Subsequently, full conversion into a helical conformation is proposed to stabilize the interaction [46,47]. An X-ray structure of a recombinant MeV P-XD fused to a box 2-derived peptide provides high-resolution insight into this interaction [48] (Figure 4). Rather strikingly, however, further truncation of Ntail upstream of box 2 up to an additional 40 residues progressively restored RdRp activity in the MeV minireplicon system [49]. Expanding the reporter construct to full genome length in this study reduced transcription success, resulting in the current view that the MoRE P-XD interaction is, in fact, dispensable for RdRp recruitment to the genome. Rather, loading of the MeV RdRp complex onto the RNP template must be mediated by a direct interaction between P-L and Ncore in assembled nucleocapsids. Likely, truncating only the C-terminal region of the Ntails as done in the earlier studies masks access to Ncore, since the unstructured central Ntail regions are still present but cannot be ordered by the RdRp complex through interaction of P-XD with MoRE [49]. Once the polymerase is loaded on the template, MoRE P-XD binding is not mechanistically required for polymerization but appears to contribute to preventing premature separation of the advancing polymerase from the template through cycles of temporary binding and release (Figure 4A,B).

View Article: PubMed Central - PubMed

ABSTRACT

The morbillivirus genus comprises major human and animal pathogens, including the highly contagious measles virus. Morbilliviruses feature single stranded negative sense RNA genomes that are wrapped by a plasma membrane-derived lipid envelope. Genomes are encapsidated by the viral nucleocapsid protein forming ribonucleoprotein complexes, and only the encapsidated RNA is transcribed and replicated by the viral RNA-dependent RNA polymerase (RdRp). In this review, we discuss recent breakthroughs towards the structural and functional understanding of the morbillivirus polymerase complex. Considering the clinical burden imposed by members of the morbillivirus genus, the development of novel antiviral therapeutics is urgently needed. The viral polymerase complex presents unique structural and enzymatic properties that can serve as attractive candidates for druggable targets. We evaluate distinct strategies for therapeutic intervention and examine how high-resolution insight into the organization of the polymerase complex may pave the path towards the structure-based design and optimization of next-generation RdRp inhibitors.

No MeSH data available.


Related in: MedlinePlus