scholarly journals Small synthetic molecule-stabilized RNA pseudoknot as an activator for –1 ribosomal frameshifting

2018 ◽  
Vol 46 (16) ◽  
pp. 8079-8089 ◽  
Author(s):  
Saki Matsumoto ◽  
Neva Caliskan ◽  
Marina V Rodnina ◽  
Asako Murata ◽  
Kazuhiko Nakatani
Keyword(s):  
Ribosomal Frameshifting ◽  
Rna Pseudoknot ◽  
Synthetic Molecule

scholarly journals Characterization of an efficient coronavirus ribosomal frameshifting signal: Requirement for an RNA pseudoknot

Cell ◽  
1989 ◽  
Vol 57 (4) ◽  
pp. 537-547 ◽  
Author(s):  
Ian Brierley ◽  
Paul Digard ◽  
Stephen C. Inglis
Keyword(s):  
Ribosomal Frameshifting ◽  
Rna Pseudoknot

scholarly journals A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting

Nature ◽  
2006 ◽  
Vol 441 (7090) ◽  
pp. 244-247 ◽  
Author(s):  
Olivier Namy ◽  
Stephen J. Moran ◽  
David I. Stuart ◽  
Robert J. C. Gilbert ◽  
Ian Brierley
Keyword(s):  
Ribosomal Frameshifting ◽  
Mechanical Explanation ◽  
Rna Pseudoknot

scholarly journals An RNA pseudoknot stimulates HTLV-1 pro-pol programmed −1 ribosomal frameshifting

RNA ◽  
2020 ◽  
Vol 26 (4) ◽  
pp. 512-528
Author(s):  
Eliza Thulson ◽  
Erik W. Hartwick ◽  
Andrew Cooper-Sansone ◽  
Marcus A.C. Williams ◽  
Mary E. Soliman ◽  
...  
Keyword(s):  
Ribosomal Frameshifting ◽  
Rna Pseudoknot

scholarly journals Stem-loop structures can effectively substitute for an RNA pseudoknot in -1 ribosomal frameshifting

2011 ◽  
Vol 39 (20) ◽  
pp. 8952-8959 ◽  
Author(s):  
C.-H. Yu ◽  
M. H. Noteborn ◽  
C. W. A. Pleij ◽  
R. C. L. Olsthoorn
Keyword(s):  
Stem Loop ◽  
Ribosomal Frameshifting ◽  
Rna Pseudoknot

scholarly journals Regulators of Viral Frameshifting: More Than RNA Influences Translation Events

2020 ◽  
Vol 7 (1) ◽  
pp. 219-238
Author(s):  
Wesley D. Penn ◽  
Haley R. Harrington ◽  
Jonathan P. Schlebach ◽  
Suchetana Mukhopadhyay
Keyword(s):  
Messenger Rna ◽  
Protein Production ◽  
Productive Infection ◽  
Cis Elements ◽  
Stem Loop ◽  
Viral Translation ◽  
Ribosomal Frameshifting ◽  
Evolutionarily Conserved ◽  
Rna Pseudoknot ◽  
New Protein

Programmed ribosomal frameshifting (PRF) is a conserved translational recoding mechanism found in all branches of life and viruses. In bacteria, archaea, and eukaryotes PRF is used to downregulate protein production by inducing a premature termination of translation, which triggers messenger RNA (mRNA) decay. In viruses, PRF is used to drive the production of a new protein while downregulating the production of another protein, thus maintaining a stoichiometry optimal for productive infection. Traditionally, PRF motifs have been defined by the characteristics of two cis elements: a slippery heptanucleotide sequence followed by an RNA pseudoknot or stem-loop within the mRNA. Recently, additional cis and new trans elements have been identified that regulate PRF in both host and viral translation. These additional factors suggest PRF is an evolutionarily conserved process whose function and regulation we are just beginning to understand.

scholarly journals Modeling the structure of the frameshift stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers

2020 ◽  
Author(s):  
Sara Ibrahim Omar ◽  
Meng Zhao ◽  
Rohith Vedhthaanth Sekar ◽  
Sahar Arbabi Moghadam ◽  
Jack A. Tuszynski ◽  
...  
Keyword(s):  
Single Molecule ◽  
Structural Models ◽  
Viral Proteins ◽  
Single Molecule Force Spectroscopy ◽  
Ribosomal Frameshifting ◽  
Structural Prediction ◽  
Prediction Tools ◽  
Dynamics Simulations ◽  
Rna Pseudoknot ◽  
Stem Structure

The coronavirus causing the COVID-19 pandemic, SARS-CoV-2, uses −1 programmed ribosomal frameshifting (−1 PRF) to control the relative expression of viral proteins. As modulating −1 PRF can inhibit viral replication, the RNA pseudoknot stimulating −1 PRF may be a fruitful target for therapeutics treating COVID-19. We modeled the unusual 3-stem structure of the stimulatory pseudoknot of SARS-CoV-2 computationally, using multiple blind structural prediction tools followed by μs-long molecular dynamics simulations. The results were compared for consistency with nuclease-protection assays and single-molecule force spectroscopy measurements of the SARS-CoV-1 pseudoknot, to determine the most likely conformations. We found several possible conformations for the SARS-CoV-2 pseudoknot, all having an extended stem 3 but with different packing of stems 1 and 2. Several conformations featured rarely-seen threading of a single strand through the junction formed between two helices. These structural models may help interpret future experiments and support efforts to discover ligands inhibiting −1 PRF in SARS-CoV-2.

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