tmRNA on its way through the ribosome

Fu, Jie; Hashem, Yaser; Wower, Jacek; Frank, Joachim

doi:10.4161/rna.8.4.15585

Cited by 5 publications

(2 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Docking of the known tmRNA bound 70S models of Ec and Tth in our map enabled us to identify that our trans-translation state represents the resumed state with tRNA bound at A-site and tmRNA-SmpB complex at P-site (Fig. 3a,b ) 12 , 15 , 31 , 32 . It is possible that due to the abundance of leaderless mRNA (about one fourth of total mRNA) 33 , which might result in higher level of translational stalling because of the incorrect translation initiation of these classes of transcripts, trans-translation state plays significant role during translation in Mycobacteria which would need further investigations.…”

Section: Resultsmentioning

confidence: 99%

Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA

Mishra

Ahmed

Tyagi

et al. 2018

Sci Rep

View full text Add to dashboard Cite

Ribosomes are the dynamic protein synthesis machineries of the cell. They may exist in different functional states in the cell. Therefore, it is essential to have structural information on these different functional states of ribosomes to understand their mechanism of action. Here, we present single particle cryo-EM reconstructions of the Mycobacterium smegmatis 70S ribosomes in the hibernating state (with HPF), trans-translating state (with tmRNA), and the P/P state (with P-tRNA) resolved to 4.1, 12.5, and 3.4 Å, respectively. A comparison of the P/P state with the hibernating state provides possible functional insights about the Mycobacteria-specific helix H54a rRNA segment. Interestingly, densities for all the four OB domains of bS1 protein is visible in the hibernating 70S ribosome displaying the molecular details of bS1-70S interactions. Our structural data shows a Mycobacteria-specific H54a-bS1 interaction which seems to prevent subunit dissociation and degradation during hibernation without the formation of 100S dimer. This indicates a new role of bS1 protein in 70S protection during hibernation in Mycobacteria in addition to its conserved function during translation initiation.

show abstract

Section: Resultsmentioning

confidence: 99%

Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA

Mishra

Ahmed

Tyagi

et al. 2018

Sci Rep

View full text Add to dashboard Cite

show abstract

“…While tmRNA maintains its overall structure during translocation from the A to the P site, the region encompassing helices 2a-2d (hp2a-2d) and pk1 undergoes significant conformational changes. Molecular modeling suggests that pk1 unfolds, at least partially, as the TLD is translocated to the E site [ 21 ]. This suggestion is consistent with our earlier studies demonstrating that pk1 could be reduced to a hairpin without affecting tmRNA’s tagging activity [ 22 ].…”

Section: Introductionmentioning

confidence: 99%

Requirements for resuming translation in chimeric transfer-messenger RNAs of Escherichia coli and Mycobacterium tuberculosis

2014

Self Cite

View full text Add to dashboard Cite

BackgroundTrans-translation is catalyzed by ribonucleprotein complexes composed of SmpB protein and transfer-messenger RNA. They release stalled ribosomes from truncated mRNAs and tag defective proteins for proteolytic degradation. Comparative sequence analysis of bacterial tmRNAs provides considerable insights into their secondary structures in which a tRNA-like domain and an mRNA-like region are connected by a variable number of pseudoknots. Progress toward understanding the molecular mechanism of trans-translation is hampered by our limited knowledge about the structure of tmRNA:SmpB complexes.ResultsComplexes consisting of M. tuberculosis tmRNA and E. coli SmpB tag truncated proteins poorly in E. coli. In contrast, the tagging activity of E. coli tmRNA is well supported by M. tuberculosis SmpB that is expressed in E. coli. To investigate this incompatibility, we constructed 12 chimeric tmRNA molecules composed of structural features derived from both E. coli and M. tuberculosis. Our studies demonstrate that replacing the hp5-pk2-pk3-pk4 segment of E. coli tmRNA with the equivalent segment of M. tuberculosis tmRNA has no significant effect on the tagging efficiency of chimeric tmRNAs in the presence of E. coli SmpB. Replacing either helices 2b-2d, the single-stranded part of the ORF, pk1, or residues 79–89 of E. coli tmRNA with the equivalent features of M. tuberculosis tmRNA yields chimeric tmRNAs that are tagged at 68 to 88 percent of what is observed with E. coli tmRNA. Exchanging segments composed of either pk1 and the single-stranded segment upstream of the ORF or helices 2b-2d and pk1 results in markedly impaired tagging activity.ConclusionOur observations demonstrate the existence of functionally important but as yet uncharacterized structural constraints in the segment of tmRNA that connects its TLD to the ORF used for resuming translation. As trans-translation is important for the survival of M. tuberculosis, our work provides a new target for pharmacological intervention against multidrug-resistant tuberculosis.

show abstract

Joachim Frank's Binding with the Ribosome

Agrawal

2019

Structure

View full text Add to dashboard Cite

With recent technological advancements, single-particle cryogenic electron microscopy (cryo-EM) is now the technique of choice to study structure and function of biological macromolecules at near-atomic resolution. Many single-particle EM reconstruction methods necessary for these advances were pioneered by Joachim Frank, and were optimized using the ribosome as a benchmark specimen. In doing so, he made several landmark contributions to the understanding of the structure and function of ribosomes. These include the first 3D visualization of ribosome-bound transfer RNAs, the first experimentally derived structures of the primary complexes formed during the bacterial translation elongation cycle, and the critical ribosomal conformational transitions required for translation. Over the years, his laboratory studied many important functional complexes of the ribosome from both eubacterial and eukaryotic systems, including ribosomes from pathogenic organisms. This article presents a brief account of the contributions made by Joachim Frank to the ribosome field.

show abstract

tmRNA on its way through the ribosome

Cited by 5 publications

References 39 publications

Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA

Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA

Requirements for resuming translation in chimeric transfer-messenger RNAs of Escherichia coli and Mycobacterium tuberculosis

Joachim Frank's Binding with the Ribosome

Contact Info

Product

Resources

About