HBV RNA pre-genome encodes specific motifs that mediate interactions with the viral core protein that promote nucleocapsid assembly

Patel, Nikesh; White, Simon; Thompson, Rebecca; Bingham, Richard J.; Weiß, Eva U.; Maskell, Daniel P.; Zlotnick, Adam; Dykeman, Eric C.; Tůma, Roman; Twarock, Reidun; Ranson, Neil A.; Stockley, Peter G.

doi:10.1038/nmicrobiol.2017.98

Cited by 75 publications

(146 citation statements)

References 60 publications

Supporting

Mentioning

140

Contrasting

Order By: Relevance

“…3F and 4G). This result demonstrates that few, if any, small conserved RNA structures exist in the P2 and P3 regions of the analyzed viruses that could accommodate the hypothesis of "multiple cryptic, sequence-degenerate, dispersed RNA packaging signals" (22). Manual inspection of structures conserved after synonymous recoding revealed that the majority of prevailing structures occurred over regions encoding amino acids that had reduced codon choice, such that selection of any possible synonymous codon would conserve the presence or absence of base-pairing.…”

Section: Resultsmentioning

confidence: 81%

“…Each conserved structure is represented by a rectangle that spans the range of the structure's position. (22). These hairpins, which are loosely conserved and carry common "assembly motifs," have been shown in in vitro experiments to promote RNA-dependent assembly of viral capsids, including elaborate structural rearrangements of capsid subunits (refs.…”

Section: Resultsmentioning

confidence: 99%

“…4I. We propose that the "cryptic, sequence-degenerate, dispersed RNA packaging signals" (22) provide a function in step II of morphogenesis. The cocondensation of genome with cognate CP, which have been characterized in genomes of RNA phage MS2 (19,21), of plant virus satellite tobacco necrosis virus (72), and of two human viruses (22,73,74), is to facilitate "cocondensation" (step II).…”

Section: Discussionmentioning

confidence: 99%

“…19-21 and references therein). This new model implies that the most important determinants for assembly specificity of +ssRNA viruses reside in dozens of genome-specific hairpins that have been described as "cryptic, sequence-degenerate, dispersed RNA packaging signals mapping throughout the genome" (22). We show that this model does not serve to explain PV morphogenesis.…”

mentioning

confidence: 89%

“…Variants P(1+2+3) SD (2,103/6,177) and P(2+3) SD (1,174/3,549), in which approximately every third nucleotide was changed, were debilitated but they still encapsidated their genomes. The combined data of (i) the excessive density of mutations in recoded domains of P2 and P3 variants, yet allowing replication and packaging; (ii) the known molecular steps of the PV replication and packaging cycle; and (iii) the superior assembly efficiency of DI particles (lacking the P1 domain) over WT PV, lead us to conclude that "multiple cryptic, sequence-degenerate, dispersed RNA packaging signals" (22) do not play a role in PV packaging specificity.…”

Section: Maxmentioning

confidence: 99%

See 4 more Smart Citations

Limits of variation, specific infectivity, and genome packaging of massively recoded poliovirus genomes

Song¹,

Gorbatsevych²,

Liu³

et al. 2017

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

View full text Add to dashboard Cite

Computer design and chemical synthesis generated viable variants of poliovirus type 1 (PV1), whose ORF (6,189 nucleotides) carried up to 1,297 "Max" mutations (excess of overrepresented synonymous codon pairs) or up to 2,104 "SD" mutations (randomly scrambled synonymous codons). "Min" variants (excess of underrepresented synonymous codon pairs) are nonviable except for P2 Min , a variant temperature-sensitive at 33 and 39.5 • C. Compared with WT PV1, P2 Min displayed a vastly reduced specific infectivity (si) (WT, 1 PFU/118 particles vs. P2 Min , 1 PFU/35,000 particles), a phenotype that will be discussed broadly. Si of haploid PV presents cellular infectivity of a single genotype. We performed a comprehensive analysis of sequence and structures of the PV genome to determine if evolutionary conserved cis-acting packaging signal(s) were preserved after recoding. We showed that conserved synonymous sites and/or local secondary structures that might play a role in determining packaging specificity do not survive codon pair recoding. This makes it unlikely that numerous "cryptic, poliovirus | genome recoding | packaging signal | specific infectivity T he capsid precursor P1 (881 amino acids) of type 1 poliovirus (PV), mapping to the N terminus of the polyprotein (PP) (Fig. 1A), can be encoded in 10 442 ways (1) due to the degenerate genetic code. The tiniest fraction of these possible sequences defines PV, the cause of poliomyelitis. PV occurs in three serotypes, of which the most neurovirulent type 1 Mahoney [PV1(M)], the main viral species analyzed in this study, was isolated in 1941 from pooled feces of three healthy children (2).Genome sequence (3, 4) and gene organization (3) of PV1(M) revealed highly complex structures in its 5'-terminal nontranslated region (5'-NTR), followed by a single ORF encoding the PP, followed by a complex 3'-heteropolymeric region and poly(A) tail (Fig. 1A) (5, 6). The PP (7) is an active molecule that cleaves itself into ∼29 polypeptides by two viral proteinases (2A pro and 3C pro /3CD pro ) and an enzyme-independent maturation cleavage (Fig. 1A) (5,6,8).Capsid domain P1 controls the identity of PV by determining virion structure (9), serotype identity (10), and interaction with the cellular receptor CD155 (10). Since PV replicates as quasispecies at an error rate of ∼10 −4 (11), the following questions arise: How conserved is its synonymous sequence given the astronomical number of alternative possibilities? What encoding could have coevolved that would be optimal to specify 881 capsid residues?If PV, a member of the genus Enterovirus of Picornaviridae, is an evolutionary descendant of C-cluster Coxsackie viruses (C-CAVs) (12), the evolution of PV nucleotide sequences was constrained as it adhered to the basic architecture of C-CAVs, its evolutionary parents (13). A second well-known restriction of sequence variability in ORFs is "codon bias" (14), the unequal use of synonymous codons. Encoding the PV1 P1 domain with an excess of "rarely used" (human) synonymous codons results in a ...

show abstract

Section: Resultsmentioning

confidence: 81%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 89%

Section: Maxmentioning

confidence: 99%

See 3 more Smart Citations

Limits of variation, specific infectivity, and genome packaging of massively recoded poliovirus genomes

Song¹,

Gorbatsevych²,

Liu³

et al. 2017

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

View full text Add to dashboard Cite

show abstract

Virus Assembly Pathways: Straying Away but Not Too Far

Bond

Tsvetkova

Wang

et al. 2020

Small

View full text Add to dashboard Cite

viruses, the CPs can self-assemble in vitro around a variety of non-genomic cargo, [6] forming shells that can be structurally identical to those of the wild type (wt) virus. However, wt virus assembly inside the heterogeneous, crowded environment of a host cell cytoplasm surprisingly leads to the large majority of virions being laden with genomic RNA. [7] The reason for non-specific encapsulation in vitro is relatively well understood. [5,8] The main driving force behind assembly at physiological ionic strengths are electrostatic interactions. [9] By comparison, the rate of empty capsids assembly, which can occur when electrostatic interactions are screened, is several orders of magnitude slower than co-assembly of coat proteins in presence of polyanionic species. [10] The question is then, how does a virus avoid production of virus-like particles that encapsulate many of the smaller, non-viral, transient RNAs and other polyions occurring in the cytoplasm? In attempting to answer this long-standing question we have studied the nature of chimeras which assemble out of small ssDNA oligonucleotides and viral coat protein. Cryo-electron microscopy (cryo-EM) and charge detection mass spectrometry (CDMS) analysis of in vitro assembly products suggest that CP shells do readily form around multiple oligonucleotides. However, these shells have specific, strained structures which easily split into large fragments. These may provide intermediates for correct, fast virion growth when cognate RNA, containing appropriate packaging signals becomes available. [11-13] 2. Results and Discussion In this work, virus-like particles (VLPs) were formed by mixing purified coat proteins of the brome mosaic virus (BMV) with two types of ssDNA oligonucleotides, both 52 nucleotides long. The two oligonucleotide fragments had different tertiary structures: the first one, hereafter called oligoB, originated from the BMV RNA genome sequence that interacts with the BMV CP N-terminal arm. [14,15] The second oligomer was a linear polyA polymer with no tertiary structure (see Figures S1 and S2, Supporting Information for assembly conditions, biochemical characterization, and transmission electron microscopy (TEM) characterization). To determine the masses of the VLPs formed, we employed charge detection mass spectrometry (CDMS). CDMS measures Non-enveloped RNA viruses pervade all domains of life. In a cell, they coassemble from viral RNA and capsid proteins. Virus-like particles can form in vitro where virtually any non-cognate polyanionic cargo can be packaged. How only viral RNA gets selected for packaging in vivo, in presence of myriad other polyanionic species, has been a puzzle. Through a combination of charge detection mass spectrometry and cryo-electron microscopy, it is determined that co-assembling brome mosaic virus (BMV) coat proteins and nucleic acid oligomers results in capsid structures and stoichiometries that differ from the icosahedral virion. These previously unknown shell structures are strained and less stable than the native ...

show abstract

Physical virology: From virus self‐assembly to particle mechanics

Buzón

Maity

Roos

2020

WIREs Nanomed Nanobiotechnol

View full text Add to dashboard Cite

Viruses are highly ordered supramolecular complexes that have evolved to propagate by hijacking the host cell's machinery. Although viruses are very diverse, spreading through cells of all kingdoms of life, they share common functions and properties. Next to the general interest in virology, fundamental viral mechanisms are of growing importance in other disciplines such as biomedicine and (bio)nanotechnology. However, in order to optimally make use of viruses and virus‐like particles, for instance as vehicle for targeted drug delivery or as building blocks in electronics, it is essential to understand their basic chemical and physical properties and characteristics. In this context, the number of studies addressing the mechanisms governing viral properties and processes has recently grown drastically. This review summarizes a specific part of these scientific achievements, particularly addressing physical virology approaches aimed to understand the self‐assembly of viruses and the mechanical properties of viral particles. Using a physicochemical perspective, we have focused on fundamental studies providing an overview of the molecular basis governing these key aspects of viral systems. This article is categorized under: Biology‐Inspired Nanomaterials > Protein and Virus‐Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology

show abstract

HBV RNA pre-genome encodes specific motifs that mediate interactions with the viral core protein that promote nucleocapsid assembly

Cited by 75 publications

References 60 publications

Limits of variation, specific infectivity, and genome packaging of massively recoded poliovirus genomes

Limits of variation, specific infectivity, and genome packaging of massively recoded poliovirus genomes

Virus Assembly Pathways: Straying Away but Not Too Far

Physical virology: From virus self‐assembly to particle mechanics

Contact Info

Product

Resources

About