Ribosomal Translocation: One Step Closer to the Molecular Mechanism

Overview

Journal ACS Chem Biol

Publisher American Chemical Society

Specialties Biochemistry
Biology

Date 2009 Jan 29

PMID 19173642

Citations 48

Authors

Shinichiro Shoji

Sarah E Walker

Kurt Fredrick

Affiliations

Soon will be listed here.

Abstract

Protein synthesis occurs in ribosomes, the targets of numerous antibiotics. How these large and complex machines read and move along mRNA have proven to be challenging questions. In this Review, we focus on translocation, the last step of the elongation cycle in which movement of tRNA and mRNA is catalyzed by elongation factor G. Translocation entails large-scale movements of the tRNAs and conformational changes in the ribosome that require numerous tertiary contacts to be disrupted and reformed. We highlight recent progress toward elucidating the molecular basis of translocation and how various antibiotics influence tRNA-mRNA movement.

Citing Articles

Alternate conformational trajectories in ribosome translocation.

Alejo J, Girodat D, Hammerling M, Willi J, Jewett M, Engelhart A PLoS Comput Biol. 2024; 20(8):e1012319.

PMID: 39141679 PMC: 11346969. DOI: 10.1371/journal.pcbi.1012319.

Dysregulated ribosome quality control in human diseases.

McGirr T, Onar O, Jafarnejad S FEBS J. 2024; 292(5):936-959.

PMID: 38949989 PMC: 11880988. DOI: 10.1111/febs.17217.

On the response of elongating ribosomes to forces opposing translocation.

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Efficient fluorescent recognition of ATP/GTP by a water-soluble bisquinolinium pyridine-2,6-dicarboxamide compound. Crystal structures, spectroscopic studies and interaction mode with DNA.

Viviano-Posadas A, Romero-Mendoza U, Bazany-Rodriguez I, Velazquez-Castillo R, Martinez-Otero D, Bautista-Renedo J RSC Adv. 2022; 12(43):27826-27838.

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A Ribosome Interaction Surface Sensitive to mRNA GCN Periodicity.

Scopino K, Williams E, Elsayed A, Barr W, Krizanc D, Thayer K Biomolecules. 2020; 10(6).

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References

March P, Inouye M . Characterization of the lep operon of Escherichia coli. Identification of the promoter and the gene upstream of the signal peptidase I gene. J Biol Chem. 1985; 260(12):7206-13. View

Tai P, Davis B . Triphasic concentration effects of gentamicin on activity and misreading in protein synthesis. Biochemistry. 1979; 18(1):193-8. DOI: 10.1021/bi00568a029. View

Cornish P, Ermolenko D, Noller H, Ha T . Spontaneous intersubunit rotation in single ribosomes. Mol Cell. 2008; 30(5):578-88. PMC: 2491453. DOI: 10.1016/j.molcel.2008.05.004. View

Konevega A, Fischer N, Semenkov Y, Stark H, Wintermeyer W, Rodnina M . Spontaneous reverse movement of mRNA-bound tRNA through the ribosome. Nat Struct Mol Biol. 2007; 14(4):318-24. DOI: 10.1038/nsmb1221. View

Berk V, Zhang W, Pai R, Cate J, Cate J . Structural basis for mRNA and tRNA positioning on the ribosome. Proc Natl Acad Sci U S A. 2006; 103(43):15830-4. PMC: 1635088. DOI: 10.1073/pnas.0607541103. View

Abdi N, Fredrick K . Contribution of 16S rRNA nucleotides forming the 30S subunit A and P sites to translation in Escherichia coli. RNA. 2005; 11(11):1624-32. PMC: 1370848. DOI: 10.1261/rna.2118105. View

Noller H . RNA structure: reading the ribosome. Science. 2005; 309(5740):1508-14. DOI: 10.1126/science.1111771. View

Gromadski K, Rodnina M . Kinetic determinants of high-fidelity tRNA discrimination on the ribosome. Mol Cell. 2004; 13(2):191-200. DOI: 10.1016/s1097-2765(04)00005-x. View

Nechifor R, Murataliev M, Wilson K . Functional interactions between the G' subdomain of bacterial translation factor EF-G and ribosomal protein L7/L12. J Biol Chem. 2007; 282(51):36998-7005. DOI: 10.1074/jbc.M707179200. View

10.

Qin Y, Polacek N, Vesper O, Staub E, Einfeldt E, Wilson D . The highly conserved LepA is a ribosomal elongation factor that back-translocates the ribosome. Cell. 2006; 127(4):721-33. DOI: 10.1016/j.cell.2006.09.037. View

11.

Wintermeyer W, Peske F, Beringer M, Gromadski K, Savelsbergh A, Rodnina M . Mechanisms of elongation on the ribosome: dynamics of a macromolecular machine. Biochem Soc Trans. 2004; 32(Pt 5):733-7. DOI: 10.1042/BST0320733. View

12.

Connell S, Takemoto C, Wilson D, Wang H, Murayama K, Terada T . Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors. Mol Cell. 2007; 25(5):751-64. DOI: 10.1016/j.molcel.2007.01.027. View

13.

Cukras A, Southworth D, Brunelle J, Culver G, Green R . Ribosomal proteins S12 and S13 function as control elements for translocation of the mRNA:tRNA complex. Mol Cell. 2003; 12(2):321-8. DOI: 10.1016/s1097-2765(03)00275-2. View

14.

Spahn C, Gomez-Lorenzo M, Grassucci R, Jorgensen R, Andersen G, Beckmann R . Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation. EMBO J. 2004; 23(5):1008-19. PMC: 380967. DOI: 10.1038/sj.emboj.7600102. View

15.

Noller H, Yusupov M, Yusupova G, Baucom A, Cate J . Translocation of tRNA during protein synthesis. FEBS Lett. 2002; 514(1):11-6. DOI: 10.1016/s0014-5793(02)02327-x. View

16.

Palade G . A small particulate component of the cytoplasm. J Biophys Biochem Cytol. 1955; 1(1):59-68. PMC: 2223592. DOI: 10.1083/jcb.1.1.59. View

17.

Bergemann K, Nierhaus K . Spontaneous, elongation factor G independent translocation of Escherichia coli ribosomes. J Biol Chem. 1983; 258(24):15105-13. View

18.

Selmer M, Dunham C, Murphy 4th F, Weixlbaumer A, Petry S, Kelley A . Structure of the 70S ribosome complexed with mRNA and tRNA. Science. 2006; 313(5795):1935-42. DOI: 10.1126/science.1131127. View

19.

Wimberly B, Brodersen D, Clemons Jr W, Morgan-Warren R, Carter A, Vonrhein C . Structure of the 30S ribosomal subunit. Nature. 2000; 407(6802):327-39. DOI: 10.1038/35030006. View

20.

Agirrezabala X, Lei J, Brunelle J, Ortiz-Meoz R, Green R, Frank J . Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome. Mol Cell. 2008; 32(2):190-7. PMC: 2614368. DOI: 10.1016/j.molcel.2008.10.001. View