Molecular assembly of measles and Nipah virus: specific lipid binding drives conformational change and matrix polymerization

2021 ◽  
Author(s):  
Michael J. Norris ◽  
Monica L. Husby ◽  
William B. Kiosses ◽  
Jieyun Yin ◽  
Linda J. Rennick ◽  
...  
Keyword(s):  
Measles Virus ◽  
Membrane Lipids ◽  
Nipah Virus ◽  
Disease Outbreaks ◽  
Molecular Assembly ◽  
Lipid Binding ◽  
M Protein ◽  
Clear Understanding ◽  
Virion Assembly ◽  
M Proteins

Measles virus, Nipah virus, and multiple other paramyxoviruses cause disease outbreaks in humans and animals worldwide. The paramyxovirus matrix (M) protein mediates virion assembly and budding from host cell membranes. M is thus a key target for antivirals, but few high-resolution structures of paramyxovirus M are available, and we lack the clear understanding of how viral M proteins interact with membrane lipids to mediate viral assembly and egress needed to guide antiviral design. Here, we reveal that M proteins associate with phosphatidylserine and phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) at the plasma membrane. Using X-ray crystallography, electron microscopy, and molecular dynamics we demonstrate that PI(4,5)P2 binding induces conformational and electrostatic changes in the M protein surface that trigger membrane deformation, matrix layer polymerization, and virion assembly.

scholarly journals How does temperature affect the dynamics of SARS-CoV-2 M proteins? Insights from Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Soumya Lipsa Rath ◽  
Madhusmita Tripathy ◽  
Nabanita Mandal
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Membrane Lipids ◽  
Membrane System ◽  
Host Cells ◽  
Coarse Grained ◽  
M Protein ◽  
Effect Of Temperature ◽  
M Proteins ◽  
Dynamics Simulations

Enveloped viruses, in general, have several transmembrane proteins and glycoproteins, which assist the virus in entry and attachment onto the host cells. These proteins also play a significant role in determining the shape and size of the newly formed virus particles. The lipid membrane and the embedded proteins affect each other in non-trivial ways during the course of the viral life cycle. Unravelling the nature of the protein-protein and protein-lipid interactions, under various environmental and physiological conditions, could therefore prove to be crucial in development of therapeutics. Here, we study the M protein of SARS-CoV-2 to understand the effect of temperature on the properties of the protein-membrane system. The membrane embedded dimeric M proteins were studied using atomistic and coarse-grained molecular dynamics simulations at temperatures ranging between 10 and 50 ˚C. While temperature induced fluctuations should be monotonic, we observe a steady rise in the protein dynamics up to 40 ˚C, beyond which it surprisingly reverts back to the low temperature behaviour. Detailed investigation reveals disordering of the membrane lipids in the presence of the protein, which induces additional curvature around the transmembrane region. Coarse-grained simulations indicate temperature dependent aggregation of M protein dimers. Our study clearly indicates that the dynamics of membrane lipids and integral M protein of SARS-CoV-2 enables it to better associate and aggregate only at a certain temperature range (i.e., ~30 to 40 ˚C). This can have important implications in the protein aggregation and subsequent viral budding/fission processes.   

scholarly journals Unification and extensive diversification of M/ORF3-related ion channel proteins in coronaviruses and other nidoviruses

2021 ◽  
Author(s):  
Yongjun Tan ◽  
Theresa Schneider ◽  
Prakash K Shukla ◽  
Mahesh B Chandrasekharan ◽  
L Aravind ◽  
...  
Keyword(s):  
Ion Channels ◽  
Ion Channel ◽  
M Protein ◽  
Detection Methods ◽  
Homology Detection ◽  
Virion Assembly ◽  
Wide Range ◽  
M Proteins ◽  
Slow Evolution ◽  
Membrane Budding

Abstract The coronavirus, SARS-CoV-2, responsible for the ongoing COVID-19 pandemic, has emphasized the need for a better understanding of the evolution of virus-host interactions. ORF3a in both SARS-CoV-1 and SARS-CoV-2 are ion channels (viroporins) implicated in virion assembly and membrane budding. Using sensitive profile-based homology detection methods, we unify the SARS-CoV ORF3a family with several families of viral proteins, including ORF5 from MERS-CoVs, proteins from beta-CoVs (ORF3c), alpha-CoVs (ORF3b), most importantly, the Matrix (M) proteins from CoVs, and more distant homologs from other nidoviruses. We present computational evidence that these viral families might utilize specific conserved polar residues to constitute an aqueous pore within the membrane-spanning region. We reconstruct an evolutionary history of these families and objectively establish the common origin of the M proteins of CoVs and Toroviruses. We also show that the divergent ORF3 clade (ORF3a/ORF3b/ORF3c/ORF5 families) represents a duplication stemming from the M protein in alpha- and beta-CoVs. By phyletic profiling of major structural components of primary nidoviruses, we present a hypothesis for their role in virion assembly of CoVs, ToroVs and Arteriviruses. The unification of diverse M/ORF3 ion channel families in a wide range of nidoviruses, especially the typical M protein in CoVs, reveal a conserved, previously under-appreciated role of ion channels in virion assembly and membrane budding. We show that M and ORF3 are under different evolutionary pressures; in contrast to the slow evolution of M as core structural component, the ORF3 clade is under selection for diversification, which suggests it might act at the interface with host molecules and/or immune attack.

scholarly journals Unification of the M/ORF3-related proteins points to a diversified role for ion conductance in pathogenesis of coronaviruses and other nidoviruses

2020 ◽  
Author(s):  
Yongjun Tan ◽  
Theresa Schneider ◽  
Prakash K. Shukla ◽  
Mahesh B. Chandrasekharan ◽  
L Aravind ◽  
...  
Keyword(s):  
Ion Channels ◽  
Ion Channel ◽  
M Protein ◽  
Homology Detection ◽  
Virion Assembly ◽  
Host Molecules ◽  
Wide Range ◽  
M Proteins ◽  
Immune Attack ◽  
Selection For

ABSTRACTThe new coronavirus, SARS-CoV-2, responsible for the COVID-19 pandemic has emphasized the need for a better understanding of the evolution of virus-host conflicts. ORF3a in both SARS-CoV-1 and SARS-CoV-2 are ion channels (viroporins) and involved in virion assembly and membrane budding. Using sensitive profile-based homology detection methods, we unify the SARS-CoV ORF3a family with several families of viral proteins, including ORF5 from MERS-CoVs, proteins from beta-CoVs (ORF3c), alpha-CoVs (ORF3b), most importantly, the Matrix (M) proteins from CoVs, and more distant homologs from other nidoviruses. By sequence analysis and structural modeling, we show that these viral families utilize specific conserved polar residues to constitute an ion-conducting pore in the membrane. We reconstruct the evolutionary history of these families, objectively establish the common origin of the M proteins of CoVs and Toroviruses. We show that the divergent ORF3a/ORF3b/ORF5 families represent a duplication stemming from the M protein in alpha- and beta-CoVs. By phyletic profiling of major structural components of primary nidoviruses, we present a model for their role in virion assembly of CoVs, ToroVs and Arteriviruses. The unification of diverse M/ORF3 ion channel families in a wide range of nidoviruses, especially the typical M protein in CoVs, reveal a conserved, previously under-appreciated role of ion channels in virion assembly, membrane fusion and budding. We show that the M and ORF3 are under differential evolutionary pressures; in contrast to the slow evolution of M as core structural component, the CoV-ORF3 clade is under selection for diversification, which indicates it is likely at the interface with host molecules and/or immune attack.IMPORTANCECoronaviruses (CoVs) have become a major threat to human welfare as the causative agents of several severe infectious diseases, namely Severe Acute Respiratory Syndrome (SARS), Middle Eastern Respiratory Syndrome (MERS), and the recently emerging human coronavirus disease 2019 (COVID-19). The rapid spread, severity of these diseases, as well as the potential re-emergence of other CoV-associated diseases have imposed a strong need for a thorough understanding of function and evolution of these CoVs. By utilizing robust domain-centric computational strategies, we have established homologous relationships between many divergent families of CoV proteins, including SARS-CoV/SARS-CoV-2 ORF3a, MERS-CoV ORF5, proteins from both beta-CoVs (ORF3c) and alpha-CoVs (ORF3b), the typical CoV Matrix proteins, and many distant homologs from other nidoviruses. We present evidence that they are active ion channel proteins, and the Cov-specific ORF3 clade proteins are under selection for rapid diversification, suggesting they might have been involved in interfering host molecules and/or immune attack.

scholarly journals Measles Virus: Identification in the M Protein Primary Sequence of a Potential Molecular Marker for Subacute Sclerosing Panencephalitis

2015 ◽  
Vol 2015 ◽  
pp. 1-12 ◽  
Author(s):  
Hasan Kweder ◽  
Michelle Ainouze ◽  
Joanna Brunel ◽  
Denis Gerlier ◽  
Evelyne Manet ◽  
...  
Keyword(s):  
Molecular Marker ◽  
Measles Virus ◽  
Subacute Sclerosing Panencephalitis ◽  
M Protein ◽  
Wild Type ◽  
Virus Identification ◽  
Viral Spread ◽  
M Proteins ◽  
Children And Young Adults ◽  
The Brain

Subacute Sclerosing Panencephalitis (SSPE), a rare lethal disease of children and young adults due to persistence of measles virus (MeV) in the brain, is caused by wild type (wt) MeV. Why MeV vaccine strains never cause SSPE is completely unknown. Hypothesizing that this phenotypic difference could potentially be represented by a molecular marker, we compared glycoprotein and matrix (M) genes from SSPE cases with those from the Moraten vaccine strain, searching for differential structural motifs. We observed that all known SSPE viruses have residues P64, E89, and A209 (PEA) in their M proteins whereas the equivalent residues for vaccine strains are either S64, K89, and T209 (SKT) as in Moraten or PKT. Through the construction of MeV recombinants, we have obtained evidence that the wt MeV-M protein PEA motif, in particular A209, is linked to increased viral spread. Importantly, for the 10 wt genotypes (of 23) that have had their M proteins sequenced, 9 have the PEA motif, the exception being B3, which has PET. Interestingly, cases of SSPE caused by genotype B3 have yet to be reported. In conclusion, our results strongly suggest that the PEA motif is a molecular marker for wt MeV at risk to cause SSPE.

MEASLES VIRUS ELIMINATION: RESOLVED ISSUES AND FUTURE CHALLENGES

2020 ◽  
pp. 83-88
Author(s):  
Kseniia Artemivna Veklych
Keyword(s):  
Measles Virus ◽  
Disease Outbreaks ◽  
Vaccination Schedule ◽  
Successful Implementation ◽  
Complete Elimination ◽  
Virus Elimination ◽  
Vaccination Programs ◽  
Future Challenges ◽  
The Moment ◽  
Measles Outbreaks

Measles is a highly contagious infectious disease caused by an RNA−containing virus of the family Paramyxoviridae and Morbillivirus genus. The most proper way to stop it is a total vaccination. At the moment, live attenuated strains of the Enders − Schwartz measles virus are used to conduct it. Although they were developed more than 50 years ago, the vaccines in use today are effective enough to create a proper immune protection that can defend against an infection for decades, if the vaccination schedule is followed. The vast majority of measles outbreaks that have been reported in Europe over the last seven years have been caused by a lack of an immune response resulting from the unprecedented coverage of the population with vaccination. The measles outbreak observed in the adult and child population of Ukraine since December 2018 indicates the need and urgency of additional efforts to curb the spread and complete elimination of the measles virus. It has been determined that more than 95 % of the population should be vaccinated to ensure an elimination of measles virus and prevent the disease outbreaks after the virus has been imported from the countries that are still endemic to measles. It is noted that as a result of successful implementation of vaccination programs, the public's attention to measles is diminished even among physicians who sometimes have a rather dubious understanding of the disease symptoms. Ensuring a complete elimination of the measles virus requires the development and implementation of additional laboratory tests for immunity, development and realization of new, more polyvalent vaccines that are more readily accepted by population, increased awareness on safety and necessity of vaccination, as well as regulation. Key words: measles, immunity, elimination, epidemiological control, vaccination.

scholarly journals Role of Small Envelope Protein in Sustaining the Intracellular and Extracellular Levels of Hepatitis B Virus Large and Middle Envelope Proteins

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 613
Author(s):  
Jing Zhang ◽  
Yongxiang Wang ◽  
Shuwen Fu ◽  
Quan Yuan ◽  
Qianru Wang ◽  
...  
Keyword(s):  
Envelope Proteins ◽  
Full Length ◽  
M Protein ◽  
Intracellular Level ◽  
S Protein ◽  
L Protein ◽  
M Proteins ◽  
B Virus ◽  
Subviral Particle ◽  
Genotype A

Hepatitis B virus (HBV) expresses co-terminal large (L), middle (M), and small (S) envelope proteins. S protein drives virion and subviral particle secretion, whereas L protein inhibits subviral particle secretion but coordinates virion morphogenesis. We previously found that preventing S protein expression from a subgenomic construct eliminated M protein. The present study further examined impact of S protein on L and M proteins. Mutations were introduced to subgenomic construct of genotype A or 1.1mer replication construct of genotype A or D, and viral proteins were analyzed from transfected Huh7 cells. Mutating S gene ATG to prevent expression of full-length S protein eliminated M protein, reduced intracellular level of L protein despite its blocked secretion, and generated a truncated S protein through translation initiation from a downstream ATG. Truncated S protein was secretion deficient and could inhibit secretion of L, M, S proteins from wild-type constructs. Providing full-length S protein in trans rescued L protein secretion and increased its intracellular level from mutants of lost S gene ATG. Lost core protein expression reduced all the three envelope proteins. In conclusion, full-length S protein could sustain intracellular and extracellular L and M proteins, while truncated S protein could block subviral particle secretion.

scholarly journals The SARS-CoV-2 nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shan Lu ◽  
Qiaozhen Ye ◽  
Digvijay Singh ◽  
Yong Cao ◽  
Jolene K. Diedrich ◽  
...  
Keyword(s):  
Phase Separation ◽  
Potential Role ◽  
Rna Binding ◽  
Stress Granule ◽  
M Protein ◽  
Rich Region ◽  
Virion Assembly ◽  
N Protein ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions

AbstractThe multifunctional nucleocapsid (N) protein in SARS-CoV-2 binds the ~30 kb viral RNA genome to aid its packaging into the 80–90 nm membrane-enveloped virion. The N protein is composed of N-terminal RNA-binding and C-terminal dimerization domains that are flanked by three intrinsically disordered regions. Here we demonstrate that the N protein’s central disordered domain drives phase separation with RNA, and that phosphorylation of an adjacent serine/arginine rich region modulates the physical properties of the resulting condensates. In cells, N forms condensates that recruit the stress granule protein G3BP1, highlighting a potential role for N in G3BP1 sequestration and stress granule inhibition. The SARS-CoV-2 membrane (M) protein independently induces N protein phase separation, and three-component mixtures of N + M + RNA form condensates with mutually exclusive compartments containing N + M or N + RNA, including annular structures in which the M protein coats the outside of an N + RNA condensate. These findings support a model in which phase separation of the SARS-CoV-2 N protein contributes both to suppression of the G3BP1-dependent host immune response and to packaging genomic RNA during virion assembly.

scholarly journals Structure and assembly of double-headed Sendai virus nucleocapsids

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Na Zhang ◽  
Hong Shan ◽  
Mingdong Liu ◽  
Tianhao Li ◽  
Rui Luo ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Measles Virus ◽  
Sendai Virus ◽  
Nipah Virus ◽  
Mumps Virus ◽  
Genome Replication ◽  
Direct Visualization ◽  
Closed State ◽  
Cryo Electron Microscopy ◽  
Negative Sense

AbstractParamyxoviruses, including the mumps virus, measles virus, Nipah virus and Sendai virus (SeV), have non-segmented single-stranded negative-sense RNA genomes which are encapsidated by nucleoproteins into helical nucleocapsids. Here, we reported a double-headed SeV nucleocapsid assembled in a tail-to-tail manner, and resolved its helical stems and clam-shaped joint at the respective resolutions of 2.9 and 3.9 Å, via cryo-electron microscopy. Our structures offer important insights into the mechanism of the helical polymerization, in particular via an unnoticed exchange of a N-terminal hole formed by three loops of nucleoproteins, and unveil the clam-shaped joint in a hyper-closed state for nucleocapsid dimerization. Direct visualization of the loop from the disordered C-terminal tail provides structural evidence that C-terminal tail is correlated to the curvature of nucleocapsid and links nucleocapsid condensation and genome replication and transcription with different assembly forms.

scholarly journals Two Overlapping Domains of a Lyssavirus Matrix Protein That Acts on Different Cell Death Pathways

2010 ◽  
Vol 84 (19) ◽  
pp. 9897-9906 ◽  
Author(s):  
Florence Larrous ◽  
Alireza Gholami ◽  
Shahul Mouhamad ◽  
Jérôme Estaquier ◽  
Hervé Bourhy
Keyword(s):  
Cell Death ◽  
Amino Acid ◽  
Matrix Protein ◽  
Full Length ◽  
M Protein ◽  
Genotype 3 ◽  
Cell Death Pathways ◽  
Acid Fragment ◽  
M Proteins ◽  
Cellular Apoptosis

ABSTRACT The lyssavirus matrix (M) protein induces apoptosis. The regions of the M protein that are essential for triggering cell death pathways are not yet clearly defined. We therefore compared the M proteins from two viruses that have contrasting characteristics in terms of cellular apoptosis: a genotype 3 lyssavirus, Mokola virus (MOK), and a genotype 1 rabies virus isolated from a dog from Thailand (THA). We identified a 20-amino-acid fragment (corresponding to positions 67 to 86) that retained the cell death activities of the full-length M protein from MOK via both the tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and inhibition of cytochrome c oxidase (CcO) activity. We found that the amino acids at positions 77 and 81 have an essential role in triggering these two cell death pathways. Directed mutagenesis demonstrated that the amino acid at position 77 affects CcO activity, whereas the amino acid at position 81 affects TRAIL-dependent apoptosis. Mutations in the full-length M protein that compromised induction of either of these two pathways resulted in delayed apoptosis compared with the time to apoptosis for the nonmutated control.

scholarly journals Cell tropism of wild-type measles virus is affected by amino acid substitutions in the P, V and M proteins, or by a truncation in the C protein

2004 ◽  
Vol 85 (10) ◽  
pp. 3001-3006 ◽  
Author(s):  
Naoko Miyajima ◽  
Makoto Takeda ◽  
Masato Tashiro ◽  
Koji Hashimoto ◽  
Yusuke Yanagi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Measles Virus ◽  
M Protein ◽  
Amino Acid Difference ◽  
Cell Tropism ◽  
Wild Type ◽  
M Gene ◽  
Nucleotide Difference ◽  
Virus Growth ◽  
C Protein

Two nucleotide differences in the P/C/V and M genes between B95a cell- and Vero cell-isolated wild-type measles viruses (MV) have previously been found from the same patient. The nucleotide difference in the P/C/V gene resulted in an amino acid difference (M175I) in the P and V proteins and a 19 aa deletion in the C protein. The nucleotide difference in the M gene resulted in an amino acid difference (P64H) in the M protein. To verify this result and to examine further whether the amino acid difference or truncation is important for MV cell tropism, recombinant MV strains containing one of the two nucleotide substitutions, or both, were generated. It was found that the P64H substitution in the M protein was important for efficient virus growth and dissemination in Vero cells and that the M175I substitution in the P and V protein or truncation of the C protein was required for optimal growth.

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