Real-time Assembly Landscape of Bacterial 30S Translation Initiation Complex

Overview

Journal Nat Struct Mol Biol

Specialties Cell Biology
Molecular Biology

Date 2012 May 8

PMID 22562136

Citations 58

Authors

Pohl Milon

Cristina Maracci

Liudmila Filonava

Claudio O Gualerzi

Marina V Rodnina

Affiliations

Soon will be listed here.

Abstract

Initiation factors guide the ribosome in the selection of mRNA and translational reading frame. We determined the kinetically favored assembly pathway of the 30S preinitiation complex (30S PIC), an early intermediate in 30S initiation complex formation in Escherichia coli. IF3 and IF2 are the first factors to arrive, forming an unstable 30S-IF2-IF3 complex. Subsequently, IF1 joins and locks the factors in a kinetically stable 30S PIC to which fMet-tRNA(fMet) is recruited. Binding of mRNA is independent of initiation factors and can take place at any time during 30S PIC assembly, depending on the cellular concentration of the mRNA and the structural determinants at the ribosome-binding site. The kinetic analysis shows both specific and cumulative effects of initiation factors as well as kinetic checkpoints of mRNA selection at the entry into translation.

Citing Articles

The translation inhibitors kasugamycin, edeine and GE81112 target distinct steps during 30S initiation complex formation.

Safdari H, Morici M, Sanchez-Castro A, Dallape A, Paternoga H, Giuliodori A Nat Commun. 2025; 16(1):2470.

PMID: 40075065 PMC: 11903750. DOI: 10.1038/s41467-025-57731-8.

Generation of ribosomal protein S1 mutants for improving of expression of difficult to translate mRNAs.

Niemela L, Pasztor A, Frey A Appl Microbiol Biotechnol. 2025; 109(1):20.

PMID: 39847144 PMC: 11759276. DOI: 10.1007/s00253-025-13406-4.

A binding site for the antibiotic GE81112 in the ribosomal mRNA channel.

Schedlbauer A, Han X, van Bakel W, Kaminishi T, Ochoa-Lizarralde B, Iturrioz I bioRxiv. 2024; .

PMID: 39386670 PMC: 11463416. DOI: 10.1101/2024.09.26.614503.

Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers.

Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H Chem Rev. 2024; 124(10):6444-6500.

PMID: 38688034 PMC: 11122139. DOI: 10.1021/acs.chemrev.3c00894.

Initiation at AUGUG and GUGUG sequences can lead to translation of overlapping reading frames in E. coli.

Kohl M, Kompatscher M, Clementi N, Holl L, Erlacher M Nucleic Acids Res. 2022; 51(1):271-289.

PMID: 36546769 PMC: 9841429. DOI: 10.1093/nar/gkac1175.

References

Qin D, Abdi N, Fredrick K . Characterization of 16S rRNA mutations that decrease the fidelity of translation initiation. RNA. 2007; 13(12):2348-55. PMC: 2080605. DOI: 10.1261/rna.715307. View

Rodnina M, Wintermeyer W . GTP consumption of elongation factor Tu during translation of heteropolymeric mRNAs. Proc Natl Acad Sci U S A. 1995; 92(6):1945-9. PMC: 42399. DOI: 10.1073/pnas.92.6.1945. View

Misselwitz R, Welfle K, Krafft C, Welfle H, Brandi L, Caserta E . The fMet-tRNA binding domain of translational initiation factor IF2: role and environment of its two Cys residues. FEBS Lett. 1999; 459(3):332-6. DOI: 10.1016/s0014-5793(99)01280-6. View

Peske F, Rodnina M, Wintermeyer W . Sequence of steps in ribosome recycling as defined by kinetic analysis. Mol Cell. 2005; 18(4):403-12. DOI: 10.1016/j.molcel.2005.04.009. View

Calogero R, Pon C, Canonaco M, Gualerzi C . Selection of the mRNA translation initiation region by Escherichia coli ribosomes. Proc Natl Acad Sci U S A. 1988; 85(17):6427-31. PMC: 281985. DOI: 10.1073/pnas.85.17.6427. View

Milon P, Carotti M, Konevega A, Wintermeyer W, Rodnina M, Gualerzi C . The ribosome-bound initiation factor 2 recruits initiator tRNA to the 30S initiation complex. EMBO Rep. 2010; 11(4):312-6. PMC: 2854590. DOI: 10.1038/embor.2010.12. View

Antoun A, Pavlov M, Lovmar M, Ehrenberg M . How initiation factors maximize the accuracy of tRNA selection in initiation of bacterial protein synthesis. Mol Cell. 2006; 23(2):183-93. DOI: 10.1016/j.molcel.2006.05.030. View

Kudla G, Murray A, Tollervey D, Plotkin J . Coding-sequence determinants of gene expression in Escherichia coli. Science. 2009; 324(5924):255-8. PMC: 3902468. DOI: 10.1126/science.1170160. View

Qin D, Fredrick K . Control of translation initiation involves a factor-induced rearrangement of helix 44 of 16S ribosomal RNA. Mol Microbiol. 2009; 71(5):1239-49. PMC: 3647337. DOI: 10.1111/j.1365-2958.2009.06598.x. View

10.

Carter A, Clemons Jr W, Brodersen D, Morgan-Warren R, Hartsch T, Wimberly B . Crystal structure of an initiation factor bound to the 30S ribosomal subunit. Science. 2001; 291(5503):498-501. DOI: 10.1126/science.1057766. View

11.

Surkov S, Nilsson H, Rasmussen L, Sperling-Petersen H, Isaksson L . Translation initiation region dependency of translation initiation in Escherichia coli by IF1 and kasugamycin. FEBS J. 2010; 277(11):2428-39. DOI: 10.1111/j.1742-4658.2010.07657.x. View

12.

Zucker F, Hershey J . Binding of Escherichia coli protein synthesis initiation factor IF1 to 30S ribosomal subunits measured by fluorescence polarization. Biochemistry. 1986; 25(12):3682-90. DOI: 10.1021/bi00360a031. View

13.

Celano B, Pawlik R, Gualerzi C . Interaction of Escherichia coli translation-initiation factor IF-1 with ribosomes. Eur J Biochem. 1988; 178(2):351-5. DOI: 10.1111/j.1432-1033.1988.tb14457.x. View

14.

Simonetti A, Marzi S, Jenner L, Myasnikov A, Romby P, Yusupova G . A structural view of translation initiation in bacteria. Cell Mol Life Sci. 2008; 66(3):423-36. PMC: 11131459. DOI: 10.1007/s00018-008-8416-4. View

15.

Studer S, Joseph S . Unfolding of mRNA secondary structure by the bacterial translation initiation complex. Mol Cell. 2006; 22(1):105-15. DOI: 10.1016/j.molcel.2006.02.014. View

16.

McCarthy J, GUALERZI C . Translational control of prokaryotic gene expression. Trends Genet. 1990; 6(3):78-85. DOI: 10.1016/0168-9525(90)90098-q. View

17.

Yusupova G, Jenner L, Rees B, Moras D, Yusupov M . Structural basis for messenger RNA movement on the ribosome. Nature. 2006; 444(7117):391-4. DOI: 10.1038/nature05281. View

18.

La Teana A, Gualerzi C, Brimacombe R . From stand-by to decoding site. Adjustment of the mRNA on the 30S ribosomal subunit under the influence of the initiation factors. RNA. 1995; 1(8):772-82. PMC: 1369318. View

19.

Kapralou S, Fabbretti A, Garulli C, Spurio R, Gualerzi C, Dahlberg A . Translation initiation factor IF1 of Bacillus stearothermophilus and Thermus thermophilus substitute for Escherichia coli IF1 in vivo and in vitro without a direct IF1-IF2 interaction. Mol Microbiol. 2008; 70(6):1368-77. PMC: 2614455. DOI: 10.1111/j.1365-2958.2008.06466.x. View

20.

Zuker M . Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003; 31(13):3406-15. PMC: 169194. DOI: 10.1093/nar/gkg595. View