Programmed −1 Ribosomal Frameshifting in coronaviruses: A therapeutic target

Kelly, Jamie A.; Woodside, Michael T.; Dinman, Jonathan D.

doi:10.1016/j.virol.2020.12.010

Cited by 62 publications

(72 citation statements)

References 101 publications

(134 reference statements)

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“…The genome encodes 16 non-structural proteins (ORF1a → nsp1-11 and ORF1b → nsp12-16) from the left three-fourth of the genome, and 4-5 structural proteins (S, spike; E, envelope; M, membrane; N, nucleocapsid; HE, hemagglutinin esterase) and various number of accessory proteins (numbered boxes) from the right one-fourth of the genome cytoplasm as soon as the virus gets into a susceptible cell. Because ORF1a and ORF1b partially overlap and ORF1b is in the − 1 reading frame relative to ORF1a, expression of ORF1b requires a programed − 1 ribosomal frameshift, for which the mechanism is not fully understood [48]. Cleavage of the two polyproteins by two selfactivating viral proteases (Papain-like protease PLpro or nsp3 and 3-chymotrypsin-like protease 3CLpro or nsp5) produces 16 nsps.…”

Section: Sars-cov-2 Genome Structure and Expressionmentioning

confidence: 99%

SARS-CoV-2: from its discovery to genome structure, transcription, and replication

Tian²,

et al. 2021

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SARS-CoV-2 is an extremely contagious respiratory virus causing adult atypical pneumonia COVID-19 with severe acute respiratory syndrome (SARS). SARS-CoV-2 has a single-stranded, positive-sense RNA (+RNA) genome of ~ 29.9 kb and exhibits significant genetic shift from different isolates. After entering the susceptible cells expressing both ACE2 and TMPRSS2, the SARS-CoV-2 genome directly functions as an mRNA to translate two polyproteins from the ORF1a and ORF1b region, which are cleaved by two viral proteases into sixteen non-structural proteins (nsp1-16) to initiate viral genome replication and transcription. The SARS-CoV-2 genome also encodes four structural (S, E, M and N) and up to six accessory (3a, 6, 7a, 7b, 8, and 9b) proteins, but their translation requires newly synthesized individual subgenomic RNAs (sgRNA) in the infected cells. Synthesis of the full-length viral genomic RNA (gRNA) and sgRNAs are conducted inside double-membrane vesicles (DMVs) by the viral replication and transcription complex (RTC), which comprises nsp7, nsp8, nsp9, nsp12, nsp13 and a short RNA primer. To produce sgRNAs, RTC starts RNA synthesis from the highly structured gRNA 3' end and switches template at various transcription regulatory sequence (TRSB) sites along the gRNA body probably mediated by a long-distance RNA–RNA interaction. The TRS motif in the gRNA 5' leader (TRSL) is responsible for the RNA–RNA interaction with the TRSB upstream of each ORF and skipping of the viral genome in between them to produce individual sgRNAs. Abundance of individual sgRNAs and viral gRNA synthesized in the infected cells depend on the location and read-through efficiency of each TRSB. Although more studies are needed, the unprecedented COVID-19 pandemic has taught the world a painful lesson that is to invest and proactively prepare future emergence of other types of coronaviruses and any other possible biological horrors.

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Section: Sars-cov-2 Genome Structure and Expressionmentioning

confidence: 99%

SARS-CoV-2: from its discovery to genome structure, transcription, and replication

Tian²,

et al. 2021

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“…Given noted correlations between the conformational plasticity of the stimulatory element and the frameshifting efficiency, more complex pausing mechanisms may be involved than a simple “barrier”. 11 − 14 …”

Section: Introductionmentioning

confidence: 99%

“… 15 , 16 The FSE’s crucial role in viral protein synthesis makes it an excellent target for therapeutic intervention. 14 , 17 , 18 Indeed, small-molecule agents such as 1,4-diazepane derivative 10 (MTDB) (originally designed for SARS-CoV 13 , 15 , 19 ), fluoroquinolone antibacterial merafloxacin , 20 and a phenyl thiourea C5 16 were found to hamper SARS-CoV-2 frameshifting.…”

Section: Introductionmentioning

confidence: 99%

To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element

et al. 2021

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The SARS-CoV-2 frameshifting RNA element (FSE) is an excellent target for therapeutic intervention against Covid-19. This small gene element employs a shifting mechanism to pause and backtrack the ribosome during translation between Open Reading Frames 1a and 1b, which code for viral polyproteins. Any interference with this process has a profound effect on viral replication and propagation. Pinpointing the structures adapted by the FSE and associated structural transformations involved in frameshifting has been a challenge. Using our graph-theory-based modeling tools for representing RNA secondary structures, “RAG” (RNA-As-Graphs), and chemical structure probing experiments, we show that the 3-stem H-type pseudoknot (3_6 dual graph), long assumed to be the dominant structure, has a viable alternative, an HL-type 3-stem pseudoknot (3_3) for longer constructs. In addition, an unknotted 3-way junction RNA (3_5) emerges as a minor conformation. These three conformations share Stems 1 and 3, while the different Stem 2 may be involved in a conformational switch and possibly associations with the ribosome during translation. For full-length genomes, a stem-loop motif (2_2) may compete with these forms. These structural and mechanistic insights advance our understanding of the SARS-CoV-2 frameshifting process and concomitant virus life cycle, and point to three avenues of therapeutic intervention.

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“…Given noted correlations between the conformational plasticity of the stimulatory element and frameshifting efficiency, more complex pausing mechanisms may be involved than a simple “barrier”. 11–14…”

Section: Introductionmentioning

confidence: 99%

To knot or not to knot: Multiple conformations of the SARS-CoV-2 frameshifting RNA element

Schlick

Zhu

Dey

et al. 2021

Preprint

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The SARS-CoV-2 frameshifting RNA element (FSE) is an excellent target for therapeutic intervention against Covid-19. This small gene element employs a shifting mechanism to pause and backtrack the ribosome during translation between Open Reading Frames 1a and 1b, which code for viral polyproteins. Any interference with this process has profound effect on viral replication and propagation. Pinpointing the structures adapted by the FSE and associated structural transformations involved in frameshifting has been a challenge. Using our graph-theory-based modeling tools for representing RNA secondary structures, "RAG" (RNA-As-Graphs), and chemical structure probing experiments, we show that the 3-stem H-type pseudoknot (3_6 dual graph), long assumed to be the dominant structure, is replaced by a different, HL-type 3-stem pseudoknot (3_3) as more residues, in particular the slippery site's 7 residues, are considered. In addition, an unknotted 3-way junction RNA (3_5) emerges as a minor conformation. These three conformations share Stems 1 and 3, while the different Stem 2 may be involved in a conformational switch and possibly associations with the ribosome during translation. These structural and mechanistic insights advance our understanding of the SARS-CoV-2 frameshifting process and concomitant virus life cycle, and point to three avenues of therapeutic intervention.

show abstract

Programmed −1 Ribosomal Frameshifting in coronaviruses: A therapeutic target

Cited by 62 publications

References 101 publications

SARS-CoV-2: from its discovery to genome structure, transcription, and replication

SARS-CoV-2: from its discovery to genome structure, transcription, and replication

To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element

To knot or not to knot: Multiple conformations of the SARS-CoV-2 frameshifting RNA element

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