Packaged and Free Satellite Tobacco Mosaic Virus (STMV) RNA Genomes Adopt Distinct Conformational States

Larman, Bridget C.; Dethoff, Elizabeth A.; Weeks, Kevin M.

doi:10.1021/acs.biochem.6b01166

Cited by 28 publications

(39 citation statements)

References 23 publications

(111 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Although such interactions did not ensure efficient packaging of the full-length capsid genome on their own, several rounds of mutagenesis and screening afforded nucleocapsids with substantially higher loading capacity, greater specificity, and enhanced cargo protection. Consistent with suggestions that RNA architecture plays important roles in controlling the assembly of natural viruses (24,25,32), protein-protein and protein-RNA interactions were simultaneously optimized by coevolution of the circularly permuted capsid subunit with its encoding RNA. The resulting constructs are reminiscent of plant satellite viruses like satellite tobacco necrosis virus, which also have RNA genomes that encode only capsid protein and depend on cognate helper viruses to complement other aspects of the viral life cycle (33).…”

Section: Discussionsupporting

confidence: 58%

Laboratory evolution of virus-like nucleocapsids from nonviral protein cages

Terasaka

Azuma

Hilvert

2018

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

View full text Add to dashboard Cite

Viruses are remarkable nanomachines that efficiently hijack cellular functions to replicate and self-assemble their components within a complex biological environment. As all steps of the viral life cycle depend on formation of a protective proteinaceous shell that packages the DNA or RNA genome, bottom-up construction of virus-like nucleocapsids from nonviral materials could provide valuable insights into virion assembly and evolution. Such constructs could also serve as safe alternatives to natural viruses for diverse nano- and biotechnological applications. Here we show that artificial virus-like nucleocapsids can be generated-rapidly and surprisingly easily-by engineering and laboratory evolution of a nonviral protein cage formed by lumazine synthase (AaLS) and its encoding mRNA. Cationic peptides were appended to the engineered capsid proteins to enable specific recognition of packaging signals on cognate mRNAs, and subsequent evolutionary optimization afforded nucleocapsids with expanded spherical structures that encapsulate their own full-length RNA genome in vivo and protect the cargo molecules from nucleases. These findings provide strong experimental support for the hypothesis that subcellular protein-bounded compartments may have facilitated the emergence of ancient viruses.

show abstract

Section: Discussionsupporting

confidence: 58%

Laboratory evolution of virus-like nucleocapsids from nonviral protein cages

Terasaka

Azuma

Hilvert

2018

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

View full text Add to dashboard Cite

show abstract

“…Collectively, there is strong support, based on evolutionary pressure, secondary structure RINGs, or previous functional studies, for 22 of the 24 elements identified de novo as low-SHAPE/low-entropy elements ( Fig. 2 A and B, elements 1-9, 11-14, and [16][17][18][19][20][21][22][23][24].…”

Section: Conservation Of Secondary Structure Elements In Diverse Denv2mentioning

confidence: 79%

“…We recently developed a strategy called RING-MaP to detect nucleotides involved in through-space structural communication (10,16). Here RNA is modified by dimethyl sulfate such that each strand contains multiple structure-specific modifications.…”

Section: Nucleotide-resolution Structural Interrogation Of Authentic mentioning

confidence: 99%

Pervasive tertiary structure in the dengue virus RNA genome

Dethoff

Boerneke

Gokhale

et al. 2018

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

Self Cite

157

View full text Add to dashboard Cite

RNA virus genomes are efficient and compact carriers of biological information, encoding information required for replication both in their primary sequences and in higher-order RNA structures. However, the ubiquity of RNA elements with higher-order folds—in which helices pack together to form complex 3D structures—and the extent to which these elements affect viral fitness are largely unknown. Here we used single-molecule correlated chemical probing to define secondary and tertiary structures across the RNA genome of dengue virus serotype 2 (DENV2). Higher-order RNA structures are pervasive and involve more than one-third of nucleotides in the DENV2 genomic RNA. These 3D structures promote a compact overall architecture and contribute to viral fitness. Disrupting RNA regions with higher-order structures leads to stable, nonreverting mutants and could guide the development of vaccines based on attenuated RNA viruses. The existence of extensive regions of functional RNA elements with tertiary folds in viral RNAs, and likely many other messenger and noncoding RNAs, means that there are significant regions with pocket-containing surfaces that may serve as novel RNA-directed drug targets.

show abstract

“…The parallel development of computational methods for comparative and integrative analysis of probing data has made it possible to recover biological insights from data generated in these experiments ( 32 , 33 ). To date, large-scale structural information exists for three ssRNA positive sense viral genomes: hepatitis C virus (HCV) ( 34 ), human immunodeficiency virus ( 35 ), and tomato bushy stunt virus (TBSV) ( 36 ) as well as the satellite tobacco mosaic virus ( 37 , 38 ). By structurally characterizing large regions of viral genomes at once, potentially interesting structures can be discovered much more rapidly, and in the proper context.…”

Section: Introductionmentioning

confidence: 99%

Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements

Watters

Choudhary

Aviran

et al. 2017

Nucleic Acids Research

View full text Add to dashboard Cite

In single stranded (+)-sense RNA viruses, RNA structural elements (SEs) play essential roles in the infection process from replication to encapsidation. Using selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) and covariation analysis, we explore the structural features of the third genome segment of cucumber mosaic virus (CMV), RNA3 (2216 nt), both in vitro and in plant cell lysates. Comparing SHAPE-Seq and covariation analysis results revealed multiple SEs in the coat protein open reading frame and 3′ untranslated region. Four of these SEs were mutated and serially passaged in Nicotiana tabacum plants to identify biologically selected changes to the original mutated sequences. After passaging, loop mutants showed partial reversion to their wild-type sequence and SEs that were structurally disrupted by mutations were restored to wild-type-like structures via synonymous mutations in planta. These results support the existence and selection of virus open reading frame SEs in the host organism and provide a framework for further studies on the role of RNA structure in viral infection. Additionally, this work demonstrates the applicability of high-throughput chemical probing in plant cell lysates and presents a new method for calculating SHAPE reactivities from overlapping reverse transcriptase priming sites.

show abstract

Packaged and Free Satellite Tobacco Mosaic Virus (STMV) RNA Genomes Adopt Distinct Conformational States

Cited by 28 publications

References 23 publications

Laboratory evolution of virus-like nucleocapsids from nonviral protein cages

Laboratory evolution of virus-like nucleocapsids from nonviral protein cages

Pervasive tertiary structure in the dengue virus RNA genome

Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements

Contact Info

Product

Resources

About