Mechanism of tRNA-mediated +1 ribosomal frameshifting

Hong, Sung Il; Sunita, S.; Maehigashi, Tatsuya; Hoffer, Eric D.; Dunkle, J.A.; Dunham, C.M.

doi:10.1073/pnas.1809319115

Cited by 44 publications

(65 citation statements)

References 60 publications

(78 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, biochemical and structural studies of ASL CGG Pro lacking the modification revealed that this four-nucleotide interaction does not occur in the A site during decoding (30,31). Additionally, the mRNA is positioned in the unshifted or zero frame, indicating that the frameshift event occurs post-decoding, consistent with recent structures (32). Interestingly, the absence of the methylation at G37 causes a distortion of the tRNA on the opposite side of the anticodon loop at nucleotide U32 (31), leading to the disruption of interactions with A38.…”

supporting

confidence: 82%

“…Kinetic analyses of tRNA GGG Pro movement through the ribosome reveal that the shift can occur at two distinct stages: a fast mechanism during translocation of the tRNA-mRNA pairs to the P site and a slower mechanism when tRNA GGG Pro is stalled in the P site while waiting for A-site tRNA delivery (28). A recent structure of ASL SufA6 bound to a ϩ1 codon in the P site demonstrates the ASL alone is sufficient for the ϩ1 mRNA frameshift consistent with the slow mechanism presented above (32). Another possibility is what is also observed in the structure of ASL CGG Pro lacking the m 1 G37 modification in the A site (31): the 3Ј anticodon stem is destabilized, which, in turn, may influence how elongation factor G (EF-G) recognizes the tRNA in the A site to initiate translocation.…”

Section: Asl Elements That Ensure Accurate Trna Cgg Pro Decodingsupporting

confidence: 60%

See 1 more Smart Citation

Importance of a tRNA anticodon loop modification and a conserved, noncanonical anticodon stem pairing in tRNACGGPro for decoding

Nguyen

Hoffer

Dunham

2019

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

Edited by Karin Musier-Forsyth Modification of anticodon nucleotides allows tRNAs to decode multiple codons, expanding the genetic code. Additionally, modifications located in the anticodon loop, but outside the anticodon itself, stabilize tRNA-codon interactions, increasing decoding fidelity. Anticodon loop nucleotide 37 is 3 to the anticodon and, in tRNA CGG Pro , is methylated at the N1 position in its nucleobase (m 1 G37). The m 1 G37 modification in tRNA CGG Pro stabilizes its interaction with the codon and maintains the mRNA frame. However, it is unclear how m 1 G37 affects binding at the decoding center to both cognate and ؉1 slippery codons. Here, we show that the tRNA CGG Pro m 1 G37 modification is important for the association step during binding to a cognate CCG codon. In contrast, m 1 G37 prevented association with a slippery CCC-U or ؉1 codon. Similar analyses of frameshift suppressor tRNA SufA6 , a tRNA CGG Pro derivative containing an extra nucleotide in its anticodon loop that undergoes ؉1 frameshifting, reveal that m 1 G37 destabilizes interactions with both the cognate CCG and slippery codons. One reason for this destabilization is the disruption of a conserved U32⅐A38 nucleotide pairing in the anticodon stem through insertion of G37.5. Restoring the tRNA SufA6 U32⅐A37.5 pairing results in a high-affinity association on the slippery CCC-U codon. Further, an X-ray crystal structure of the 70S ribosome bound to tRNA SufA6 U32⅐A37.5 at 3.6 Å resolution shows a reordering of the anticodon loop consistent with the findings from the high-affinity measurements. Our results reveal how the tRNA modification at nucleotide 37 stabilizes interactions with the mRNA codon to preserve the mRNA frame. Protein synthesis is performed by the ribosome, a conserved protein-RNA macromolecular machine where mRNA, tRNAs, and translation factors read the genetic information as presented on mRNA into proteins. There are four defined stages of protein synthesis: initiation, elongation, termination, and recycling (reviewed in Ref. 1). During elongation, three nucleotides of the mRNA codon are read (or decoded) by three anticodon nucleotides of a tRNA in the ribosomal aminoacyl site (A site) 2 on the small 30S subunit. The three-nucleotide code on the mRNA defines a single amino acid delivered by the corresponding tRNA. The regulation of the mRNA frame is critically important to maintain the correct sequential addition of amino acids to the nascent chain (2). Despite the importance of accurate protein expression for cell viability, the molecular basis for how the ribosome maintains this three-nucleotide mRNA frame is not well-understood. Because tRNAs decode mRNAs, these RNA molecules probably play a role in mRNA frame maintenance. tRNAs are ϳ76-90 nucleotides in length and adopt an L-shaped tertiary structure allowing them to fit into ribosome-binding sites that span both subunits (Fig. 1). tRNAs undergo extensive posttranscriptional modifications important for the correct tertiary fold of the tRNA, including the conforma...

show abstract

supporting

confidence: 82%

Section: Asl Elements That Ensure Accurate Trna Cgg Pro Decodingsupporting

confidence: 60%

Importance of a tRNA anticodon loop modification and a conserved, noncanonical anticodon stem pairing in tRNACGGPro for decoding

Nguyen

Hoffer

Dunham

2019

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

show abstract

“…A recent ribosome structure by Dunham and coworkers (54) shows that binding of a frameshift-inducing tRNA containing an eight-nucleotide anticodon loop can also lead to a spontaneous large-scale rotation of the 30S subunit head. In this structure, containing a single tRNA bound in the e*/E state, A1503 is not intercalated within the mRNA, suggesting a possible role for this base in reading-frame maintenance.…”

Section: Discussionmentioning

confidence: 99%

Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state

Zhou

Lancaster

Donohue

et al. 2019

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

View full text Add to dashboard Cite

show abstract

“…Our proposed bound model of four L7/L12 proteins is a snapshot of the variable complexes that the multimer can adopt to probe aa-tRNAs, and therefore only a subset of cross-linking data is satisfied. The flexibility of the 30S-50S interface is further highlighted by five additional violated cross-links that are mapped on L5, S9 and S10, which are all known to be involved in tRNA binding [54] and frameshifting [55]. An exercise to finally fit all derived cross-links in a single static model or in snapshots is impossible, and highlights the fact that the ribosome, even in its single, purified state, probes a significantly large and complex conformational landscape.…”

Section: Discussionmentioning

confidence: 99%

Structural Analysis of 70S Ribosomes by Cross-Linking/Mass Spectrometry Reveals Conformational Plasticity

Tüting

Iacobucci

Ihling

et al. 2020

Preprint

View full text Add to dashboard Cite

The ribosome is not only a highly complex molecular machine that executes translation according to the central dogma of molecular biology, but also an exceptional specimen for testing and optimizing cross-linking/mass spectrometry (XL-MS) workflows. Due to its high abundance, ribosomal proteins are frequently identified in proteome-wide XL-MS studies of cells or cell extracts. Here, we performed in-depth cross-linking of the E. coli ribosome using the amine-reactive cross-linker diacetyl dibutyric urea (DSAU). We analyzed 143 E. coli ribosomal structures, mapping a total of 10,771 intramolecular distances for 126 cross-linkpairs and 3,405 intermolecular distances for 97 protein pairs. Remarkably, 44% of intermolecular cross-links covered regions that have not been resolved in any high-resolution E. coli ribosome structure and point to a plasticity of cross-linked regions. We systematically characterized all cross-links and discovered flexible regions, conformational changes, and stoichiometric variations in bound ribosomal proteins, and ultimately remodeled 2,057 residues (15,794 atoms) in total. Our working model explains more than 95% of all crosslinks, resulting in an optimized E. coli ribosome structure based on the cross-linking data obtained. Our study might serve as benchmark for conducting biochemical experiments on newly modeled protein regions, guided by XL-MS. Data are available via ProteomeXchange with identifier PXD018935.

show abstract

Mechanism of tRNA-mediated +1 ribosomal frameshifting

Cited by 44 publications

References 60 publications

Importance of a tRNA anticodon loop modification and a conserved, noncanonical anticodon stem pairing in tRNACGGPro for decoding

Importance of a tRNA anticodon loop modification and a conserved, noncanonical anticodon stem pairing in tRNACGGPro for decoding

Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state

Structural Analysis of 70S Ribosomes by Cross-Linking/Mass Spectrometry Reveals Conformational Plasticity

Contact Info

Product

Resources

About