Locking and Unlocking of Ribosomal Motions

Valle, Mikel; Zavialov, Andrey V.; Sengupta, Jayati; Rawat, U.; Ehrenberg, Måms; Frank, Joachim

doi:10.1142/9789813234864_0034

Cited by 34 publications

(58 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…After peptidyl transfer, the ribosome becomes 'unlocked' as small subunit counterclockwise rotation, coupled with backwards tilting, facilitates temporary withdrawal of rRNA 'codon gating' and mRNA: tRNA translocation across the ribosomal sites. Ribosome-tRNA and tRNA-mRNA interactions are weaker at that stage before clockwise rotation back and relocking (574,575). Even in standard decoding there is fluctuation in the unlocked state (576)(577)(578).…”

Section: Stimulator Effects On Ribosome Excursions Classical Pausingmentioning

confidence: 99%

Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use

Atkins¹,

Loughran²,

Bhatt³

et al. 2016

Nucleic Acids Res

251

367

View full text Add to dashboard Cite

Genetic decoding is not ‘frozen’ as was earlier thought, but dynamic. One facet of this is frameshifting that often results in synthesis of a C-terminal region encoded by a new frame. Ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational ‘correction’ of problem or ‘savior’ indels. Utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. One class of regulatory frameshifting of stable chromosomal genes governs cellular polyamine levels from yeasts to humans. In many cases of productively utilized frameshifting, the proportion of ribosomes that frameshift at a shift-prone site is enhanced by specific nascent peptide or mRNA context features. Such mRNA signals, which can be 5′ or 3′ of the shift site or both, can act by pairing with ribosomal RNA or as stem loops or pseudoknots even with one component being 4 kb 3′ from the shift site. Transcriptional realignment at slippage-prone sequences also generates productively utilized products encoded trans-frame with respect to the genomic sequence. This too can be enhanced by nucleic acid structure. Together with dynamic codon redefinition, frameshifting is one of the forms of recoding that enriches gene expression.

show abstract

Section: Stimulator Effects On Ribosome Excursions Classical Pausingmentioning

confidence: 99%

Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use

Atkins¹,

Loughran²,

Bhatt³

et al. 2016

Nucleic Acids Res

251

367

View full text Add to dashboard Cite

show abstract

“…Translocation is accomplished via multistep large-scale conformational changes catalyzed by elongation factor-G (EF-G) (13)(14)(15)(16). Spontaneous ribosomal conformational changes include rotation of the ribosomal subunits (50S, 30S) relative to each other, L1 stalk closure and formation of hybrid tRNAs (15)(16)(17)(18)(19)(20). In the hybrid state, the anticodon stem loops of the two tRNAs are located at the P-and A-sites in the 30S small subunit while their acceptor arms are located at the E-and P-sites in the 50S large subunit (P/E, A/P).…”

Section: Introductionmentioning

confidence: 99%

EF-G catalyzed translocation dynamics in the presence of ribosomal frameshifting stimulatory signals

Kim

Tinoco

2016

Nucleic Acids Res

View full text Add to dashboard Cite

Programmed -1 ribosomal frameshifting (-1PRF) is tightly regulated by messenger RNA (mRNA) sequences and structures in expressing two or more proteins with precise ratios from a single mRNA. Using single-molecule fluorescence resonance energy transfer (smFRET) between (Cy5)EF-G and (Cy3)tRNALys, we studied the translational elongation dynamics of -1PRF in the Escherichia coli dnaX gene, which contains three frameshifting signals: a slippery sequence (A AAA AAG), a Shine-Dalgarno (SD) sequence and a downstream hairpin. The frameshift promoting signals mostly impair the EF-G-catalyzed translocation step of the two tRNALys and the slippery codons from the A- and P- sites. The hairpin acts as a road block slowing the translocation rate. The upstream SD sequence together with the hairpin promotes dissociation of futile EF-G and thus causes multiple EF-G driven translocation attempts. A slippery sequence also helps dissociation of the EF-G by providing alternative base-pairing options. These results indicate that frameshifting takes place during the repetitive ribosomal conformational changes associated with EF-G dissociation upon unsuccessful translocation attempts of the second slippage codon from the A- to the P- sites.

show abstract

“…Following peptidyl transfer, the small ribosomal subunit undergoes a rapid (∼48 s −1 ) counterclockwise rotation of 3–10° with respect to the large subunit [Fig. (A)], resulting in a so‐called rotated state conformation . The tRNAs also transitions from the classical (P/P, A/A) to the hybrid (P/E, A/E) state [Fig.…”

Section: Translocation: Ribosome As a Molecular Motormentioning

confidence: 99%

Dynamic basis of fidelity and speed in translation: Coordinated multistep mechanisms of elongation and termination

Prabhakar

Choi²,

Wang

et al. 2017

Protein Science

View full text Add to dashboard Cite

As the universal machine that transfers genetic information from RNA to protein, the ribosome synthesizes proteins with remarkably high fidelity and speed. This is a result of the accurate and efficient decoding of mRNA codons via multistep mechanisms during elongation and termination stages of translation. These mechanisms control how the correct sense codon is recognized by a tRNA for peptide elongation, how the next codon is presented to the decoding center without change of frame during translocation, and how the stop codon is discriminated for timely release of the nascent peptide. These processes occur efficiently through coupling of chemical energy expenditure, ligand interactions, and conformational changes. Understanding this coupling in detail required integration of many techniques that were developed in the past two decades. This multidisciplinary approach has revealed the dynamic nature of translational control and uncovered how external cellular factors such as tRNA abundance and mRNA modifications affect the synthesis of the protein product. Insights from these studies will aid synthetic biology and therapeutic approaches to translation.

show abstract

Locking and Unlocking of Ribosomal Motions

Cited by 34 publications

References 0 publications

Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use

Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use

EF-G catalyzed translocation dynamics in the presence of ribosomal frameshifting stimulatory signals

Dynamic basis of fidelity and speed in translation: Coordinated multistep mechanisms of elongation and termination

Contact Info

Product

Resources

About