In vitro selection of RNA aptamers that bind special elongation factor SelB, a protein with multiple RNA-binding sites, reveals one major interaction domain at the carboxyl terminus

RNA

Volumn 5, Issue 9, 1999, Pages 1180-1190

  Klug, Stefanie J ^a   Hüttenhofer, Alexander ^b   Famulok, Michael ^a,c  

^a UNIVERSITY OF MUNICH   (Germany)

^b UNIVERSITY OF MÜNSTER   (Germany)

^c UNIVERSITY OF BONN   (Germany)

Author keywords

Aptamers; Elongation factor EF Tu; Selenocysteine; SELEX; Special elongation factor SelB

Indexed keywords

AMINOACYL TRANSFER RNA; ELONGATION FACTOR; ELONGATION FACTOR SELB; MESSENGER RNA; OXIDOREDUCTASE; RIBOSOME PROTEIN; RIBOSOME RNA; RNA; SELENOCYSTEINE; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; BINDING COMPETITION; BINDING SITE; CARBOXY TERMINAL SEQUENCE; CONSENSUS SEQUENCE; CONTROLLED STUDY; ESCHERICHIA COLI; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; PEPTIDE MAPPING; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; REACTION ANALYSIS; RNA ANALYSIS; RNA CONFORMATION; SEQUENCE ANALYSIS;

BACTERIAL PROTEINS; BASE SEQUENCE; DNA; DNA-DIRECTED RNA POLYMERASES; GENE LIBRARY; KINETICS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PEPTIDE ELONGATION FACTOR TU; RNA; RNA, RIBOSOMAL; RNA, TRANSFER; SEQUENCE ANALYSIS, RNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 0344564163     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S135583829999088X     Document Type: Article

References (37)

1. Baron C, Heider J, Böck A. 1993. Interaction of translation factor SELB with the formiate dehydrogenase H selenopeptide mRNA. Proc Natl Acad Sci USA 90:4181-4185.
2. Bartel DP, Zapp ML, Green MR, Szostak JW. 1991. HIV-1 Rev regulation involves recognition of non-Watson-Crick base pairs in viral RNA. Cell 67:529-536.
3. Berry MJ, Banu L, Chen YY, Mandel SJ, Kieffer JD, Harney JW, Larsen PR. 1991a. Recognition of UGA as a selenocysteine codon in type I deiodinase requires sequences in the 3′ untranslated region. Nature 353:273-276.
4. Berry MJ, Banu L, Larsen PR. 1991b. Type I iodothyronine deiodinase is a selenocysteine containing enzyme. Nature 349:438-440.
5. Böck A, Hilgenfeld R, Tormay P, Wilting R, Kromayer M. 1997. Domain structure of the selenocysteine-specific translation factor SelB in prokaryotes. Biomed Environ Sci 10:125-128.
6. Carey J, Uhlenbeck OC. 1983. Sequence-specific interaction of R17 coat protein with its ribonucleic acid binding site. Biochemistry 22:2601-2610.
7. Chambers I, Goldfarb P, Hampton J, Affara N, McBain W, Harrison P. 1986. The structure of the mouse glutathion peroxidase gene: The selenocysteine in the active site is encoded by the "termination" codon, TGA. EMBO J 5:1121-1127.
8. Fitzwater T, Polisky B. 1996. A SELEX primer. Methods Enzymol 267:275-301.
9. Forchhammer K, Leinfelder W, Böck A. 1989. Identification of a novel translation factor necessary for the incorporation of selenocysteine into protein. Nature 342:453-456.
10. Geiger A, Burgstaller P, Von der Eltz H, Roeder A, Famulok M. 1996. RNA aptamers that bind L-arginine with sub-micromolar dissociation constants and high enatioselectivity. Nucleic Acids Res 24:1029-1036.
11. Ghetti A, Company M, Abelson J. 1995. Specificity of PrP24 binding to RNA: A role for PrP24 in the dynamic interaction of U4 and U6 snRNAs. RNA 1:132-145.
12. Gold L, Polisky B, Uhlenbeck O, Yarus M. 1995. Diversity of oligonucleotide function. Annu Rev Biochem 64:763-797.
13. Hill KE, Lloyd RS, Yang JG, Read R, Burk RF. 1991. The cDNA for rat selenoprotein P contains 10 TGA codons in the open reading frame. J Biol Chem 266:10050-10053.
14. Hornung V, Hofmann HP, Sprinzl M. 1998. In vitro selected RNA molecules that bind to elongation factor Tu. Biochemistry 37: 7260-7267.
15. Hüttenhofer A, Bock A. 1998a. RNA structures involved in selenoprotein synthesis. In: Simons RW, Grunberg-Manago M, eds. RNA structure and function. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, pp 603-639.
16. Hüttenhofer A, Böck A. 1998b. Selenocysteine inserting RNA elements modulate GTP hydrolysis of elongation factor SelB. Biochemistry 37:885-890.
17. Hüttenhofer A, Westhof E, Böck A. 1996. Solution structure of mRNA hairpins promoting selenocysteine incorporation in Escherichia coli and their base-specific interaction with special elongation factor SELB. RNA 2:354-366.
18. Irvine D, Tuerk C, Gold L. 1991. SELEXION: Systematic evolution of ligands by exponential enrichment with integrated optimization by non-linear analysis. J Mol Biol 222:739-761.
19. Jenne A, Famulok M. 1998. Oligonucleotide libraries - variatio delectat. Curr Opin Chem Biol 2:320-327.
20. Klug SJ, Famulok M. 1994. All you wanted to know about SELEX. Mol Biol Rep 20:97-107.
21. Klug SJ, Hüttenhofer A, Kromayer M, Famulok M. 1997. In vitro and in vivo characterization of novel mRNA motifs that bind special elongation factor SelB. Proc Natl Acad Sci USA 94:6676-6681.
22. Kromayer M, Wilting R, Tormay P, Böck A. 1996. Domain structure of the prokaryotic selenocysteine-specific elongation factor SelB. J Mol Biol 262:413-420.
23. Leinfelder W, Zehelein E, Mandrand-Berthelot MA, Böck A. 1988. Gene of a novel tRNA species that cotranslationally inserts selenocysteine. Nature 331:723-725.
24. Liu Z, Reches M, Grolsman I, Engelberg-Kulka H. 1998. The nature of the minimal "selenocysteine insertion sequence" (SECIS) in Escherichia coli. Nucleic Acids Res 26:896-902.
25. Moazed D, Robertson JM, Noller HF. 1988. Interaction of elongation factors EF-G and EF-Tu with a conserved loop in 23S rRNA. Nature 334:362-364.
26. Narazenko IA, Uhlenbeck OC. 1995. Defining a smaller RNA substrate for elongation factor Tu. Biochemistry 43:2545-2552.
27. Osborne SE, Ellington AD. 1997. Nucleic acid selection and the challenge of combinatorial chemistry. Chem Rev 97:349-370.
28. Schneider D, Tuerk C, Gold L. 1992. Selection of high affinity RNA ligands to the bacteriophage R17 coat protein. J Mol Biol 228: 862-869.
29. Shannon KW, Guthrie C. 1991. Suppressors of a U4 snRNA mutation define a novel U6 snRNP protein with RNA binding motifs. Genes & Dev 5:773-785.
30. Stadtmann TC. 1990. Selenium biochemistry. Annu Rev Biochem 59:111-128.
31. Stern S, Moazed D, Noller HF. 1988. Analysis of RNA structure using chemical or enzymatic probing monitored by primer extension. Methods Enzymol 164:481-489.
32. Sturchler C, Carbon P, Krol A. 1995. Selenium, selenoproteins: An alternate reading of the genetic code. Med/Sci 11:1081-1088.
33. Tuerk C, Gold L 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505-510.
34. Walczak R, Westhof E, Carbon P, Krol A. 1996. A novel RNA structural motif in the selenocysteine insertion element of eukaryotic selenoprotein mRNAs. RNA 2:367-379.
35. Zinoni F, Birkmann A, Stadtmann T, Böck A. 1986. Cotranslational insertion of selenocysteine into formiate dehydrogenase from Escherichia coli directed by an UGA codon. Proc Natl Acad Sci USA 83:4560-4564.
36. Zinoni F, Heider J, Böck A. 1990. Features of the formiate dehydrogenase mRNA necessary for decoding of the UGA codon as selenocysteine. Proc Natl Acad Sci USA 87:4660-4664.
37. Zuker M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244:48-52.