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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

MeV L protein architecture. (A) Organization of three conserved domains (LD I–III) separated by two variable regions in the morbillivirus L protein (linker I: residues 607–649, linker II: residues 1695–1717) [29,78]. Six, conserved regions (CRs) present in all mononegavirales L proteins are numbered I to VI: residues 217–408, residues 495–599, residues 653–876, residues 927–1092, residues 1129–1376, and residues 1754–1831 respectively [83]. Color coding of the functional domain organization based on VSV L [97]: RdRp domain in blue, residues 1–924, capping domain in green, residues 925–1416, connector domain in yellow, residues 1439–1634, methyltransferase domain in orange, residues 1680–2018 and C-terminal residues 2019–2184. Specific conserved motifs involved in enzymatic activity are highlighted: GDNQ (residues 772–775), RdRp activity [76,98]; GxxT … HR (residues G1214, T1217, H1288, R1289, putative polyribonucleotidyl-transferase activity [95,99]; GxGxG (residues G1788, G1790, G1792), putative S-adenosyl-l-methionine binding site [100]; K-D-K-E (residues K1766, D1881, K1917, E1954), putative methyltransferase activity [91,92]; K-K-G (residues K2169 K2173 G2176), putative guanylyltransferase activity [88]; (B) Left: Ribbon representation of the cryo-EM structure of the VSV L protein [97]. Functional domains are rendered with the same color pattern. Right: homology model of the MeV L protein (derived from the Edmonston strain) rendered using the Swiss model server on the basis of the density maps released for VSV L [101]; (C) Mapping of the resistance mutations of the allosteric morbillivirus polymerase blocker ERDRP-0519 class [18,102]. Close-up view of the VSV L (left) and MeV L (right) polymerase catalytic site. The GDNQ tetrad is rendered in red. VSV L residues corresponding to resistance hotspots in MeV or canine distemper virus (CDV) L are rendered in yellow (MeV residue S768A), blue (CDV residues T751I, H816L, and G835R) and green (MeV and CDV residues H589Y and T776A) [102]. Corresponding residues on VSV L are rendered using the same color pattern.
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viruses-08-00251-f006: MeV L protein architecture. (A) Organization of three conserved domains (LD I–III) separated by two variable regions in the morbillivirus L protein (linker I: residues 607–649, linker II: residues 1695–1717) [29,78]. Six, conserved regions (CRs) present in all mononegavirales L proteins are numbered I to VI: residues 217–408, residues 495–599, residues 653–876, residues 927–1092, residues 1129–1376, and residues 1754–1831 respectively [83]. Color coding of the functional domain organization based on VSV L [97]: RdRp domain in blue, residues 1–924, capping domain in green, residues 925–1416, connector domain in yellow, residues 1439–1634, methyltransferase domain in orange, residues 1680–2018 and C-terminal residues 2019–2184. Specific conserved motifs involved in enzymatic activity are highlighted: GDNQ (residues 772–775), RdRp activity [76,98]; GxxT … HR (residues G1214, T1217, H1288, R1289, putative polyribonucleotidyl-transferase activity [95,99]; GxGxG (residues G1788, G1790, G1792), putative S-adenosyl-l-methionine binding site [100]; K-D-K-E (residues K1766, D1881, K1917, E1954), putative methyltransferase activity [91,92]; K-K-G (residues K2169 K2173 G2176), putative guanylyltransferase activity [88]; (B) Left: Ribbon representation of the cryo-EM structure of the VSV L protein [97]. Functional domains are rendered with the same color pattern. Right: homology model of the MeV L protein (derived from the Edmonston strain) rendered using the Swiss model server on the basis of the density maps released for VSV L [101]; (C) Mapping of the resistance mutations of the allosteric morbillivirus polymerase blocker ERDRP-0519 class [18,102]. Close-up view of the VSV L (left) and MeV L (right) polymerase catalytic site. The GDNQ tetrad is rendered in red. VSV L residues corresponding to resistance hotspots in MeV or canine distemper virus (CDV) L are rendered in yellow (MeV residue S768A), blue (CDV residues T751I, H816L, and G835R) and green (MeV and CDV residues H589Y and T776A) [102]. Corresponding residues on VSV L are rendered using the same color pattern.

Mentions: Alignments of the L proteins from different members of the mononegavirales furthermore highlighted six conserved regions (CR I–VI) in the linear sequence of L [83,84] (Figure 6). Based on sequence data and structural analyses, most of the conserved regions were assigned a functional role in the RdRp complex. CR I (MeV 217–408) has been shown to be involved in the interaction with MeV and RPV P [62,64,68,85], and it was also proposed to mediate a putative homo-oligomerization [85]. CR II (MeV 495–599) and III (MeV 653–876) contain subdomains shared by all L polymerases [83]. In particular, a GDN tripeptide motif located in CR III is extremely conserved and is considered part of the catalytic center for phosphodiester bond formation [68,86]. CR V (MeV 1129–1376) and VI (MeV 1754–1831) are required for the cap synthesis and methylation of viral mRNAs. All paramyxoviruses replicate in the cytosol, which necessitates mRNA capping and cap methylation activities of the polymerase complex to ensure the synthesis of functional mRNAs and protect them from innate immunity. In mammalian cells, this post-translational step relies on distinct and sequential enzymatic activities: (i) RNA TriPhosphatase (RTPase) activity removes the 5′ phosphate of pre-mRNA; (ii) Guanylyl Transferase (GTase) activity uses a guanylyl triphosphate to transfer a guanylyl monophosphate on pre-mRNA (iii) Guanine-N7-MethylTransferase (GN7-MTase) followed by 2′O MethylTransferase (2′O MTase) fully methylates the new cap. RPV L has been shown to carry a GTase activity [87], that might involve a conserved C-terminal K-K-G motif [88], and an RTPase activity has been recently described [89,90]. Fragment (717–2183) has shown detectable GN7-MTase activity [91] and multiple sequence alignments also revealed the presence of K-D-K-E and GxGxG motifs described as involved in 2′O MTase activity [83,92,93]. Furthermore, a domain near the C-terminus of the L protein of human parainfluenzavirus type 2 shares homology with cellular GTases and was shown to be required for viral mRNA synthesis [94]. Nevertheless, the necessity for the L protein of morbilliviruses to carry its own enzymatic activities opens the alternative possibility that viral cap synthesis and methylation may diverge from the cellular pathway, since morbillivirus L also contain residues characteristic of an unconventional polyribonucleotidyl-transferase (PRNTase)-driven capping mechanism found in rhabdoviruses [95]. Further investigation is required to fully appreciate the morbillivirus capping mechanism.


Organization, Function, and Therapeutic Targeting of the Morbillivirus RNA-Dependent RNA Polymerase Complex
MeV L protein architecture. (A) Organization of three conserved domains (LD I–III) separated by two variable regions in the morbillivirus L protein (linker I: residues 607–649, linker II: residues 1695–1717) [29,78]. Six, conserved regions (CRs) present in all mononegavirales L proteins are numbered I to VI: residues 217–408, residues 495–599, residues 653–876, residues 927–1092, residues 1129–1376, and residues 1754–1831 respectively [83]. Color coding of the functional domain organization based on VSV L [97]: RdRp domain in blue, residues 1–924, capping domain in green, residues 925–1416, connector domain in yellow, residues 1439–1634, methyltransferase domain in orange, residues 1680–2018 and C-terminal residues 2019–2184. Specific conserved motifs involved in enzymatic activity are highlighted: GDNQ (residues 772–775), RdRp activity [76,98]; GxxT … HR (residues G1214, T1217, H1288, R1289, putative polyribonucleotidyl-transferase activity [95,99]; GxGxG (residues G1788, G1790, G1792), putative S-adenosyl-l-methionine binding site [100]; K-D-K-E (residues K1766, D1881, K1917, E1954), putative methyltransferase activity [91,92]; K-K-G (residues K2169 K2173 G2176), putative guanylyltransferase activity [88]; (B) Left: Ribbon representation of the cryo-EM structure of the VSV L protein [97]. Functional domains are rendered with the same color pattern. Right: homology model of the MeV L protein (derived from the Edmonston strain) rendered using the Swiss model server on the basis of the density maps released for VSV L [101]; (C) Mapping of the resistance mutations of the allosteric morbillivirus polymerase blocker ERDRP-0519 class [18,102]. Close-up view of the VSV L (left) and MeV L (right) polymerase catalytic site. The GDNQ tetrad is rendered in red. VSV L residues corresponding to resistance hotspots in MeV or canine distemper virus (CDV) L are rendered in yellow (MeV residue S768A), blue (CDV residues T751I, H816L, and G835R) and green (MeV and CDV residues H589Y and T776A) [102]. Corresponding residues on VSV L are rendered using the same color pattern.
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Related In: Results  -  Collection

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viruses-08-00251-f006: MeV L protein architecture. (A) Organization of three conserved domains (LD I–III) separated by two variable regions in the morbillivirus L protein (linker I: residues 607–649, linker II: residues 1695–1717) [29,78]. Six, conserved regions (CRs) present in all mononegavirales L proteins are numbered I to VI: residues 217–408, residues 495–599, residues 653–876, residues 927–1092, residues 1129–1376, and residues 1754–1831 respectively [83]. Color coding of the functional domain organization based on VSV L [97]: RdRp domain in blue, residues 1–924, capping domain in green, residues 925–1416, connector domain in yellow, residues 1439–1634, methyltransferase domain in orange, residues 1680–2018 and C-terminal residues 2019–2184. Specific conserved motifs involved in enzymatic activity are highlighted: GDNQ (residues 772–775), RdRp activity [76,98]; GxxT … HR (residues G1214, T1217, H1288, R1289, putative polyribonucleotidyl-transferase activity [95,99]; GxGxG (residues G1788, G1790, G1792), putative S-adenosyl-l-methionine binding site [100]; K-D-K-E (residues K1766, D1881, K1917, E1954), putative methyltransferase activity [91,92]; K-K-G (residues K2169 K2173 G2176), putative guanylyltransferase activity [88]; (B) Left: Ribbon representation of the cryo-EM structure of the VSV L protein [97]. Functional domains are rendered with the same color pattern. Right: homology model of the MeV L protein (derived from the Edmonston strain) rendered using the Swiss model server on the basis of the density maps released for VSV L [101]; (C) Mapping of the resistance mutations of the allosteric morbillivirus polymerase blocker ERDRP-0519 class [18,102]. Close-up view of the VSV L (left) and MeV L (right) polymerase catalytic site. The GDNQ tetrad is rendered in red. VSV L residues corresponding to resistance hotspots in MeV or canine distemper virus (CDV) L are rendered in yellow (MeV residue S768A), blue (CDV residues T751I, H816L, and G835R) and green (MeV and CDV residues H589Y and T776A) [102]. Corresponding residues on VSV L are rendered using the same color pattern.
Mentions: Alignments of the L proteins from different members of the mononegavirales furthermore highlighted six conserved regions (CR I–VI) in the linear sequence of L [83,84] (Figure 6). Based on sequence data and structural analyses, most of the conserved regions were assigned a functional role in the RdRp complex. CR I (MeV 217–408) has been shown to be involved in the interaction with MeV and RPV P [62,64,68,85], and it was also proposed to mediate a putative homo-oligomerization [85]. CR II (MeV 495–599) and III (MeV 653–876) contain subdomains shared by all L polymerases [83]. In particular, a GDN tripeptide motif located in CR III is extremely conserved and is considered part of the catalytic center for phosphodiester bond formation [68,86]. CR V (MeV 1129–1376) and VI (MeV 1754–1831) are required for the cap synthesis and methylation of viral mRNAs. All paramyxoviruses replicate in the cytosol, which necessitates mRNA capping and cap methylation activities of the polymerase complex to ensure the synthesis of functional mRNAs and protect them from innate immunity. In mammalian cells, this post-translational step relies on distinct and sequential enzymatic activities: (i) RNA TriPhosphatase (RTPase) activity removes the 5′ phosphate of pre-mRNA; (ii) Guanylyl Transferase (GTase) activity uses a guanylyl triphosphate to transfer a guanylyl monophosphate on pre-mRNA (iii) Guanine-N7-MethylTransferase (GN7-MTase) followed by 2′O MethylTransferase (2′O MTase) fully methylates the new cap. RPV L has been shown to carry a GTase activity [87], that might involve a conserved C-terminal K-K-G motif [88], and an RTPase activity has been recently described [89,90]. Fragment (717–2183) has shown detectable GN7-MTase activity [91] and multiple sequence alignments also revealed the presence of K-D-K-E and GxGxG motifs described as involved in 2′O MTase activity [83,92,93]. Furthermore, a domain near the C-terminus of the L protein of human parainfluenzavirus type 2 shares homology with cellular GTases and was shown to be required for viral mRNA synthesis [94]. Nevertheless, the necessity for the L protein of morbilliviruses to carry its own enzymatic activities opens the alternative possibility that viral cap synthesis and methylation may diverge from the cellular pathway, since morbillivirus L also contain residues characteristic of an unconventional polyribonucleotidyl-transferase (PRNTase)-driven capping mechanism found in rhabdoviruses [95]. Further investigation is required to fully appreciate the morbillivirus capping mechanism.

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