An mRNA-rRNA base-pairing mechanism for translation initiation in eukaryotes

Nature Structural and Molecular Biology

Volumn 13, Issue 1, 2006, Pages 30-34

  Dresios, John ^a   Chappell, Stephen A ^a   Zhou, Wei ^a   Mauro, Vincent P ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HOMEODOMAIN PROTEIN; MESSENGER RNA; RIBOSOME RNA;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; EUKARYOTE; MOLECULAR DYNAMICS; NONHUMAN; POINT MUTATION; PRIORITY JOURNAL; PROTEIN DOMAIN; RIBOSOME; RNA BINDING; RNA TRANSLATION; TRANSLATION INITIATION; YEAST;

ANIMALS; BASE PAIRING; BASE SEQUENCE; ENHANCER ELEMENTS (GENETICS); HOMEODOMAIN PROTEINS; MICE; MUTATION; PEPTIDE CHAIN INITIATION, TRANSLATIONAL; RNA, MESSENGER; RNA, RIBOSOMAL; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION FACTORS;

EUKARYOTA; PROKARYOTA;

EID: 30044446378     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb1031     Document Type: Article

References (31)

1. Mathews, M.B., Sonenberg, N. & Hershey, J.W. Origins and principles of translational control. in Translational Control of Gene Expression (eds. Sonenberg, N., Hershey, J.W. & Mathews, M.B.) Ch. 1, 1-31 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 2000).
2. Kapp, L.D. & Lorsch, J.R. The molecular mechanics of eukaryotic translation. Annu. Rev. Biochem. 73, 657-704 (2004).
3. Shine, J. & Dalgarno, L. The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc. Natl. Acad. Sci. USA 71, 1342-1346 (1974).
4. Steitz, J.A. & Jakes, K. How ribosomes select initiator regions in mRNA: base pair formation between the 3′ terminus of 16S rRNA and the mRNA during initiation of protein synthesis in Escherichia coli. Proc. Natl. Acad. Sci. USA 72, 4734-4738 (1975).
5. Hui, A. & De Boer, H.A. Specialized ribosome system: preferential translation of a single mRNA species by subpopulation of mutated ribosomes in Escherichia coli. Proc. Natl. Acad. Sci. USA 84, 4762-4766 (1987).
6. Vagner, S., Galy, B. & Pyronnet, S. Irresistible IRES: Attracting the translation machinery to internal ribosome entry sites. EMBO Rep. 2, 893-898 (2001).
7. Jackson, R.J. A comparative view of initiation site selection mechanisms. in Translational Control of Gene Expression (eds. Sonenberg, N., Hershey, J.W. & Mathews, M.B.) Ch. 4, 127-183 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 2000).
8. Matveeva, O.V. & Shabalina, S.A. Intermolecular mRNA-rRNA hybridization and the distribution of potential interaction regions in murine 18S rRNA. Nucleic Acids Res. 21, 1007-1011 (1993).
9. Nicholson, R., Pelletier, J., Le, S.-Y. & Sonenberg, N. Structural and functional analysis of the ribosome landing pad of poliovirus type 2: in vivo translation studies. J. Virol. 65, 5886-5894 (1991).
10. Scheper, G.C., Voorma, H.O. & Thomas, A.A. Base pairing with 18S ribosomal RNA in internal initiation ot translation. FEBS Lett. 352, 271-275 (1994).
11. Mauro, V.P. & Edelman, G.M. rRNA-like sequences occur in diverse primary transcripts: implications for the control of gene expression. Proc. Natl. Acad. Sci. USA 94, 422-427 (1997).
12. Tranque, P., Hu, M.C.-Y., Edelman, G.M. & Mauro, V.P. rRNA complementarity within mRNAs: A possible basis for mRNA-ribosome interactions and translational control. Proc. Natl. Acad. Sci. USA 95, 12238-12243 (1998).
13. Hu, M.C.-Y., Tranque, P., Edelman, G.M. & Mauro, V.P. rRNA-complementarity in the 5′ UTR of mRNA specifying the Gtx homeodomain protein: evidence that base-pairing to 18S rRNA affects translational efficiency. Proc. Natl. Acad. Sci. USA 96, 1339-1344 (1999).
14. Chappell, S.A., Edelman, G.M. & Mauro, V.P. A 9-nt segment of a cellular mRNA can function as an internal ribosome entry site (IRES) and when present in linked multiple copies greatly enhances IRES activity. Proc. Natl. Acad. Sci. USA 97, 1536-1541 (2000).
15. Owens, G.C., Chappell, S.A., Mauro, V.P. & Edelman, G.M. Identification of two short internal ribosome entry sites selected from libraries of random oligonucleotides. Proc. Natl. Acad. Sci. USA 98, 1471-1476 (2001).
16. Mauro, V.P. & Edelman, G.M. The ribosome filter hypothesis. Proc. Natl. Acad. Sci. USA 99, 12031-12036 (2002).
17. Mignone, F. & Pesole, G. rRNA-like sequences in human mRNAs. Appl. Bioinformatics 1, 145-154 (2002).
18. Chappell, S.A., Edelman, G.M. & Mauro, V.P. Biochemical and functional analysis of a 9-nucleotide RNA sequence that affects translation efficiency in eukaryotic cells. Proc. Natl. Acad. Sci. USA 101, 9590-9594 (2004).
19. Chappell, S.A. & Mauro, V.P. The internal ribosome entry site (IRES) contained within the RNA-binding motif protein 3 (Rbm3) mRNA is composed of functionally distinct elements. J. Biol. Chem. 278, 33793-33800 (2003).
20. Zeenko, V. & Gallie, D.R. Cap-independent translation of tobacco etch virus is conferred by an RNA pseudoknot in the 5′-leader. J. Biol. Chem. 280, 26813-26824 (2005).
21. Akbergenov, R. et al. ARC-1, a sequence element complementary to an internal 18S rRNA segment, enhances translation efficiency in plants when present in the leader or intercistronic region of mRNAs. Nucleic Acids Res. 32, 239-247 (2004).
22. Hellen, C.U. & Sarnow, P. Internal ribosome entry sites in eukaryotic mRNA molecules. Genes Dev. 15, 1593-1612 (2001).
23. Fux, C., Langer, D., Kelm, J.M., Weber, W. & Fussenegger, M. New-generation multicistronic expression platform: pTRIDENT vectors containing size-optimized IRES elements enable homing endonuclease-based cistron swapping into lentiviral expression vectors. Biotechnol. Bioeng. 86, 174-187 (2004).
24. Reiser, J., Lai, Z., Zhang, X.Y. & Brady, R.O. Development of multigene and regulated lentivirus vectors. J. Virol. 74, 10589-10599 (2000).
25. Thompson, J., Tapprich, W.E., Munger, C. & Dahlberg, A.E. Staphylococcus aureus domain V functions in Escherichia coli ribosomes provided a conserved interaction with domain IV is restored. RNA 7, 1076-1083 (2001).
26. Spann, C.M. et al. Structure of the 80S ribosome from Saccharomyces cerevisiae-tRNA-ribosome and subunit-subunit interactions. Cell 107, 373-386 (2001).
27. Wai, H.H., Vu, L., Oakes, M. & Nomura, M. Complete deletion of yeast chromosomal rDNA repeats and integration of a new rDNA repeat: use of rDNA deletion strains for functional analysis of rDNA promoter elements in vivo. Nucleic Acids Res. 28, 3524-3534 (2000).
28. Ausubel, F.M. et al. (eds.) Manipulation of plasmids from yeast cells. in Current Protocols in Molecular Biology Unit 13.9 (Wiley, Hoboken, New Jersey, USA, 2003).
29. Wimberly, B.T. et al. Structure of the 30S ribosomal subunit. Nature 407, 327-339 (2000).
30. Yusupova, G.Z., Yusupov, M.M., Cate, J.H. & Noller, H.F. The path of messenger RNA through the ribosome. Cell 106, 233-241 (2001).
31. Zhou, W., Edelman, G.M. & Mauro, V.P. Isolation and identification of short nucleotide sequences that affect translation initiation in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 100, 4457-4462 (2003).