Conformational dynamics of the frameshift stimulatory structure in HIV-1

Ritchie, Dustin B.; Cappellano, Tonia R.; Tittle, Collin; Rezajooei, Negar; Rouleau, Logan; Sikkema, William K.A.; Woodside, Michael T.

doi:10.1261/rna.061655.117

Cited by 34 publications

(38 citation statements)

References 65 publications

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“…In contrast, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${{attC}}_{{\rm{bs}}}^{}$\end{document} and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${{\ attC}}_{{\rm{ts}}}^{}$\end{document} hairpins unfold at lower forces (<6 pN) via two consecutive events and show evidence of complex folding dynamics involving on-pathway intermediates. The partial unfolding of the hairpins into intermediate states (step 1, Figure 2E) occurred mostly at forces lower than the detection limit, similar to a recently reported case for the HIV-1 RNA hairpin with an unstable lower stem (28,29) or DNA hairpins with single base damages like 8-oxoguanine (30). The major unfolding event for attC hairpins was typically at forces around 5.5 pN.…”

Section: Discussionsupporting

confidence: 86%

Structural heterogeneity ofattCintegron recombination sites revealed by optical tweezers

Mukhortava

Pöge

Grieb

et al. 2018

Nucleic Acids Research

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A predominant tool for adaptation in Gram-negative bacteria is the functional genetic platform called integron. Integrons capture and rearrange promoterless gene cassettes in a unique recombination process involving the recognition of folded single-stranded DNA hairpins—so-called attC sites—with a strong preference for the attC bottom strand. While structural elements have been identified to promote this preference, their mechanistic action remains incomplete. Here, we used high-resolution single-molecule optical tweezers (OT) to characterize secondary structures formed by the attC bottom ( \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${{att}}{{{C}}_{{\rm{bs}}}}$\end{document} ) and top ( \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${{att}}{{{C}}_{{\rm{ts}}}}$\end{document} ) strands of the paradigmatic attC aadA7 site. We found for both sequences two structures—a straight, canonical hairpin and a kinked hairpin. Remarkably, the recombination-preferred \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${{att}}{{{C}}_{{\rm{bs}}}}$\end{document} predominantly formed the straight hairpin, while the \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${{att}}{{{C}}_{{\rm{ts}}}}$\end{document} preferentially adopted the kinked structure, which exposes only one complete recombinase binding box. By a mutational analysis, we identified three bases in the unpaired central spacer, which could invert the preferred conformations and increase the recombination frequency of the \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${{att}}{{{C}}_{{\rm{ts}}}}$\end{document} in vivo . A bioinformatics screen revealed structural bias toward a straight, canonical hairpin conformation in the bottom strand of many antibiotic resistance cassettes attC sites. Thus, we anticipate that structural fine tuning could be a mechanism in man...

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Section: Discussionsupporting

confidence: 86%

Structural heterogeneity ofattCintegron recombination sites revealed by optical tweezers

Mukhortava

Pöge

Grieb

et al. 2018

Nucleic Acids Research

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“…Do downstream stimulatory structures play active or passive roles in directing recoding? Numerous studies suggest that dynamic mRNA structural remodeling helps to physically “push” ribosomes to slip (Ritchie et al 2012; Tinoco et al 2013; Gupta and Bansal 2014; Ritchie et al 2014; Moomau et al 2016; Tsai et al 2016; Zhong et al 2016; Kendra et al 2017; Ritchie et al 2017). Coordination of base triples in both major and minor grooves provide mechanical resistance to pseudoknot unwinding, and stretches of adenosines confined along the minor groove of a helix prevent it from unwinding.…”

Section: Translational Recodingmentioning

confidence: 99%

Translation Elongation and Recoding in Eukaryotes

Dever

Dinman

Green

2018

Cold Spring Harb Perspect Biol

186

143

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In this review, we highlight the current understanding of translation elongation and recoding in eukaryotes. In addition to providing an overview of the process, recent advances in our understanding of the role of the factor eIF5A in both translation elongation and termination are discussed. We also highlight mechanisms of translation recoding with a focus on ribosomal frameshifting during elongation. We see that the balance between the basic steps in elongation and the less common recoding events is determined by the kinetics of the different processes as well as by specific sequence determinants.

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“…However, a survey of numerous different pseudoknots showed that the mechanical resistance was uncorrelated to −1 PRF efficiency; instead, −1 PRF efficiency was found to correlate with conformational plasticity or heterogeneity (16). This correlation was supported by subsequent work extending SMFS studies of −1 PRF to other pseudoknots (30), different types of stimulatory structures such as hairpins (31), and the effects of antiframeshifting ligands (32). Evidence supporting the importance of conformational plasticity has also been found from single-molecule fluorescence experiments of ribosomes translocating through pseudoknots (33) and ensemble structural studies of stimulatory structures using such methods as selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) (21,34).…”

mentioning

confidence: 97%

Complex dynamics under tension in a high-efficiency frameshift stimulatory structure

Halma

Ritchie

Cappellano

et al. 2019

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

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Specific structures in mRNA can stimulate programmed ribosomal frameshifting (PRF). PRF efficiency can vary enormously between different stimulatory structures, but the features that lead to efficient PRF stimulation remain uncertain. To address this question, we studied the structural dynamics of the frameshift signal from West Nile virus (WNV), which stimulates −1 PRF at very high levels and has been proposed to form several different structures, including mutually incompatible pseudoknots and a double hairpin. Using optical tweezers to apply tension to single mRNA molecules, mimicking the tension applied by the ribosome during PRF, we found that the WNV frameshift signal formed an unusually large number of different metastable structures, including all of those previously proposed. From force-extension curve measurements, we mapped 2 mutually exclusive pathways for the folding, each encompassing multiple intermediates. We identified the intermediates in each pathway from length changes and the effects of antisense oligomers blocking formation of specific contacts. Intriguingly, the number of transitions between the different conformers of the WNV frameshift signal was maximal in the range of forces applied by the ribosome during −1 PRF. Furthermore, the occupancy of the pseudoknotted conformations was far too low for static pseudoknots to account for the high levels of −1 PRF. These results support the hypothesis that conformational heterogeneity plays a key role in frameshifting and suggest that transitions between different conformers under tension are linked to efficient PRF stimulation.programmed ribosomal frameshifting | RNA folding | pseudoknots | force spectroscopy | West Nile virus

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Conformational dynamics of the frameshift stimulatory structure in HIV-1

Cited by 34 publications

References 65 publications

Structural heterogeneity ofattCintegron recombination sites revealed by optical tweezers

Structural heterogeneity ofattCintegron recombination sites revealed by optical tweezers

Translation Elongation and Recoding in Eukaryotes

Complex dynamics under tension in a high-efficiency frameshift stimulatory structure

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