A Central Fragment of Ribosomal Protein S26 Containing the Eukaryote-specific Motif YxxPKxYxK is a Key Component of the Ribosomal Binding Site of MRNA Region 5' of the E Site Codon

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2011 Dec 15

PMID 22167470

Citations 9

Authors

Dmitri Sharifulin

Yulia Khairulina

Anton Ivanov

Maria Meschaninova

Aliya Venyaminova

Dmitri Graifer

Galina Karpova

Affiliations

Soon will be listed here.

Abstract

The eukaryotic ribosomal protein S26e (rpS26e) lacking eubacterial counterparts is a key component of the ribosomal binding site of mRNA region 5' of the codon positioned at the exit site. Here, we determined the rpS26e oligopeptide neighboring mRNA on the human 80S ribosome using mRNA analogues bearing perfluorophenyl azide-derivatized nucleotides at designed locations. The protein was cross-linked to mRNA analogues in specific ribosomal complexes, in which the derivatized nucleotide was located at positions -3 to -9. Digestion of cross-linked rpS26e with various specific proteolytic agents followed by identification of the resulting modified oligopeptides made it possible to map the cross-links to fragment 60-71. This fragment contains the motif YxxPKxYxK conserved in eukaryotic but not in archaeal rpS26e. Analysis of X-ray structure of the Tetrahymena thermophila 40S subunit showed that this motif is not implicated in the intraribosomal interactions, implying its involvement in translation process in a eukaryote-specific manner. Comparison of the results obtained with data on positioning of ribosomal ligands on the 40S subunit lead us to suggest that this motif is involved in interaction with both the 5'-untranslated region of mRNA and the initiation factor eIF3 specific for eukaryotes, providing new insights into molecular mechanisms of translation in eukaryotes.

Citing Articles

Structures of Saccharolobus solfataricus initiation complexes with leaderless mRNAs highlight archaeal features and eukaryotic proximity.

Bourgeois G, Coureux P, Lazennec-Schurdevin C, Madru C, Gaillard T, Duchateau M Nat Commun. 2025; 16(1):348.

PMID: 39753558 PMC: 11698992. DOI: 10.1038/s41467-024-55718-5.

HELZ2: a new, interferon-regulated, human 3'-5' exoribonuclease of the RNB family is expressed from a non-canonical initiation codon.

Huntzinger E, Sinteff J, Morlet B, Seraphin B Nucleic Acids Res. 2023; 51(17):9279-9293.

PMID: 37602378 PMC: 10516660. DOI: 10.1093/nar/gkad673.

Two "Edges" in Our Knowledge on the Functions of Ribosomal Proteins: The Revealed Contributions of Their Regions to Translation Mechanisms and the Issues of Their Extracellular Transport by Exosomes.

Ochkasova A, Arbuzov G, Malygin A, Graifer D Int J Mol Sci. 2023; 24(14).

PMID: 37511213 PMC: 10380927. DOI: 10.3390/ijms241411458.

, a 40S Ribosomal Protein Subunit, Regulates the Growth and Pathogenicity of f. sp. .

Wang B, Song N, Tang C, Ma J, Wang N, Sun Y Front Microbiol. 2019; 10:968.

PMID: 31134016 PMC: 6523408. DOI: 10.3389/fmicb.2019.00968.

Loss of oocyte Rps26 in mice arrests oocyte growth and causes premature ovarian failure.

Liu X, Yan M, Ji S, Sha Q, Huang T, Zhao H Cell Death Dis. 2018; 9(12):1144.

PMID: 30451825 PMC: 6242890. DOI: 10.1038/s41419-018-1196-3.

References

Stahl J, Kobetz N . Affinity labelling of rat liver ribosomal protein S26 by heptauridylate containing a 5'-terminal alkylating group. Mol Biol Rep. 1984; 9(4):219-22. DOI: 10.1007/BF00775350. View

Pisarev A, Kolupaeva V, Pisareva V, Merrick W, Hellen C, Pestova T . Specific functional interactions of nucleotides at key -3 and +4 positions flanking the initiation codon with components of the mammalian 48S translation initiation complex. Genes Dev. 2006; 20(5):624-36. PMC: 1410799. DOI: 10.1101/gad.1397906. View

Matasova N, Myltseva S, Zenkova M, Graifer D, Vladimirov S, Karpova G . Isolation of ribosomal subunits containing intact rRNA from human placenta: estimation of functional activity of 80S ribosomes. Anal Biochem. 1991; 198(2):219-23. DOI: 10.1016/0003-2697(91)90416-q. View

Pisarev A, Kolupaeva V, Yusupov M, Hellen C, Pestova T . Ribosomal position and contacts of mRNA in eukaryotic translation initiation complexes. EMBO J. 2008; 27(11):1609-21. PMC: 2426728. DOI: 10.1038/emboj.2008.90. View

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

Demeshkina N, Laletina E, Meshchaninova M, Repkova M, Veniaminova A, Graifer D . [The mRNA codon environment at the P and E sites of human ribosomes deduced from photo crosslinking with pUUUGUU]. Mol Biol (Mosk). 2003; 37(1):147-55. View

Rodnina M, Wintermeyer W . Recent mechanistic insights into eukaryotic ribosomes. Curr Opin Cell Biol. 2009; 21(3):435-43. DOI: 10.1016/j.ceb.2009.01.023. View

Stahl J, Karpova G . Investigations on the messenger RNA binding site of eukaryotic ribosomes by using reactive oligo(U) derivatives. Biomed Biochim Acta. 1985; 44(7-8):1057-64. View

Malygin A, Baranovskaya O, Ivanov A, Karpova G . Expression and purification of human ribosomal proteins S3, S5, S10, S19, and S26. Protein Expr Purif. 2003; 28(1):57-62. DOI: 10.1016/s1046-5928(02)00652-6. View

10.

Louie D, Resing K, Lewis T, Ahn N . Mass spectrometric analysis of 40 S ribosomal proteins from Rat-1 fibroblasts. J Biol Chem. 1996; 271(45):28189-98. DOI: 10.1074/jbc.271.45.28189. View

11.

Yusupova G, Yusupov M, Cate J, Noller H . The path of messenger RNA through the ribosome. Cell. 2001; 106(2):233-41. DOI: 10.1016/s0092-8674(01)00435-4. View

12.

Ben-Shem A, Jenner L, Yusupova G, Yusupov M . Crystal structure of the eukaryotic ribosome. Science. 2010; 330(6008):1203-9. DOI: 10.1126/science.1194294. View

13.

Molotkov M, Graifer D, Demeshkna N, Repkova M, Venyaminova A, Karpova G . Arrangement of mRNA 3' of the A site codon on the human 80S ribosome. RNA Biol. 2006; 2(2):63-9. DOI: 10.4161/rna.2.2.1756. View

14.

Yusupov M, Yusupova G, Baucom A, Lieberman K, Earnest T, Cate J . Crystal structure of the ribosome at 5.5 A resolution. Science. 2001; 292(5518):883-96. DOI: 10.1126/science.1060089. View

15.

Hardy S, Kurland C, Voynow P, Mora G . The ribosomal proteins of Escherichia coli. I. Purification of the 30S ribosomal proteins. Biochemistry. 1969; 8(7):2897-905. DOI: 10.1021/bi00835a031. View

16.

Graifer D, Molotkov M, Styazhkina V, Demeshkina N, Bulygin K, Eremina A . Variable and conserved elements of human ribosomes surrounding the mRNA at the decoding and upstream sites. Nucleic Acids Res. 2004; 32(11):3282-93. PMC: 443533. DOI: 10.1093/nar/gkh657. View

17.

Chandramouli P, Topf M, Menetret J, Eswar N, Cannone J, Gutell R . Structure of the mammalian 80S ribosome at 8.7 A resolution. Structure. 2008; 16(4):535-48. PMC: 2775484. DOI: 10.1016/j.str.2008.01.007. View

18.

Steitz T . A structural understanding of the dynamic ribosome machine. Nat Rev Mol Cell Biol. 2008; 9(3):242-53. DOI: 10.1038/nrm2352. View

19.

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

20.

Ramakrishnan V . Ribosome structure and the mechanism of translation. Cell. 2002; 108(4):557-72. DOI: 10.1016/s0092-8674(02)00619-0. View