A small ribozyme with dual-site kinase activity

Nucleic Acids Research

Volumn 40, Issue 15, 2012, Pages 7528-7540

  Biondi, Elisa ^a,b   Maxwell, Adam W R ^a   Burke, Donald H ^a  

^a University of Missouri   (United States)

^b FOUNDATION FOR APPLIED MOLECULAR EVOLUTION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FUNCTIONAL GROUP; NUCLEOTIDE; ORGANOMERCURY COMPOUND; PHOSPHORYL GROUP; POLYNUCLEOTIDE 5' HYDROXYL KINASE; RIBOZYME; RIBOZYME K28; RNA; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; ELECTROPHORETIC MOBILITY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME DEGRADATION; ENZYME KINETICS; ENZYME PHOSPHORYLATION; ENZYME STRUCTURE; ISOTOPE LABELING; MUTATIONAL ANALYSIS; PEPTIDE MAPPING; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE;

BINDING SITES; CATALYTIC DOMAIN; MUTATION; NUCLEIC ACID CONFORMATION; PHOSPHORYLATION; PHOSPHOTRANSFERASES; RNA, CATALYTIC;

EID: 84867322165     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks356     Document Type: Article

References (43)

1. Tsukiji, S., Pattnaik, S. and Suga, H. (2003) An alcohol dehydrogenase ribozyme. Nat. Struct. Biol., 10, 713-717.
2. Tsukiji, S., Pattnaik, S. and Suga, H. (2004) Reduction of an aldehyde by a NADH/Zn2+ -dependent redox active ribozyme. J. Am. Chem. Soc., 126, 5044-5045.
3. Nissen, P., Hansen, J., Ban, N., Moore, P. and Steitz, T. (2000) The structural basis of ribosome activity in peptide bond synthesis. Science, 289, 920-930.
4. Lohse, P. A. and Szostak, J. W. (1996) Ribozyme-catalyzed amino-acid transfer reactions. Nature, 381, 442-444.
5. Illangasekare, M., Sanchez, G., Nickels, T. and Yarus, M. (1995) Aminoacyl-RNA synthesis catalyzed by an RNA. Science, 267, 643-647.
6. Turk, R., Chumachenko, N. and Yarus, M. (2010) Multiple translational products from a five-nucleotide ribozyme. Proc. Natl. Acad. Sci. USA, 107, 4585-4589.
7. Chumachenko, N., Novikov, Y. and Yarus, M. (2009) Rapid and simple ribozymic aminoacylation using three conserved nucleotides. J. Am. Chem. Soc., 131, 5257-5263.
8. Landweber, L. F. and Pokrovskaya, I. D. (1999) Emergence of a dual-catalytic RNA with metal-specific cleavage and ligase activities: The spandrels of RNA evolution. Proc. Natl. Acad. Sci. USA, 96, 173-178.
9. Bartel, D. P. and Szostak, J. W. (1993) Isolation of new ribozymes from a large pool of random sequences. Science, 261, 1411-1418.
10. Ekland, E. H. and Bartel, D. P. (1996) RNA-catalysed RNA polymerization using nucleoside triphosphates. Nature, 382, 373-376.
11. Wochner, A., Attwater, J., Coulson, A. and Holliger, P. (2011) Ribozyme-catalyzed transcription of an active ribozyme. Science, 332, 209-212.
12. Hati, S., Boles, A. R., Zaborske, J. M., Bergman, B., Posto, A. L. and Burke, D. H. (2003) Nickel2+-mediated assembly of an RNA-amino acid complex. Chem. Biol., 10, 1129-1137.
13. Burke, D. H. (2004) Ribozyme-catalyzed genetics. In: Ribas de Pouplana, L. (ed.), The Genetic Code and the Origin of Life. Eurekah.com and Kluwer Academic/Plenum Publishers, Georgetown, TX, pp. 47-74.
14. Chen, X., Li, N. and Ellington, A. (2007) Ribozyme catalysis of metabolism in the RNA world. Chem. Biodivers., 4, 633-655.
15. Lorsch, J. R. and Szostak, J. W. (1995) Kinetic and thermodynamic characterization of the reaction catalyzed by a polynucleotide kinase ribozyme. Biochemistry, 34, 15315-15327.
16. Saran, D., Nickens, D. and Burke, D. (2005) A trans acting ribozyme that phosphorylates exogenous RNA. Biochemistry, 44, 15007-15016.
17. Saran, D., Held, D. and Burke, D. (2006) Multiple-turnover thio-ATP hydrolase and phospho-enzyme intermediate formation activities catalyzed by an RNA enzyme. Nucleic Acids Res., 34, 3201-3208.
18. Biondi, E., Nickens, D. G., Warren, S., Saran, D. and Burke, D. H. (2010) Convergent donor and acceptor substrate utilization among kinase ribozymes. Nucleic. Acids Res, 38, 6785-6795.
19. Curtis, E. and Bartel, D. (2005) New catalytic structures from an existing ribozyme. Nat. Struct. Mol. Biol., 12, 994-1000.
20. Lorsch, J. R. and Szostak, J. W. (1994) In vitro evolution of new ribozymes with polynucleotide kinase activity. Nature, 371, 31-36.
21. Li, Y. and Breaker, R. R. (1999) Phosphorylating DNA with DNA. Proc. Natl Acad. Sci USA, 96, 2746-2751.
22. Wang, W., Billen, L. P. and Li, Y. (2002) Sequence diversity, metal specificity, and catalytic proficiency of metal-dependent phosphorylating DNA enzymes. Chem. Biol., 9, 507-517.
23. Schlosser, K., Lam, J. and Li, Y. (2009) A genotype-to-phenotype map of in vitro selected RNA-cleaving DNAzymes: implications for accessing the target phenotype. Nucleic Acids Res., 37, 3545-3557.
24. Burke, D. and Rhee, S. (2010) Assembly and activation of a kinase ribozyme. RNA, 16, 2349-2359.
25. Cho, B. and Burke, D. (2006) Topological rearrangement yields structural stabilization and interhelical distance constraints in the Kin. 46 self-phosphorylating ribozyme. RNA, 12, 2118-2125.
26. Igloi, G. (1988) Interaction of tRNAs and of phosphorothioatesubstituted nucleic acids with an organomercurial. Probing the chemical environment of thiolated residues by affinity electrophoresis. Biochemistry, 27, 3842-3849.
27. Biondi, E. and Burke, D. (2012) Separating and analyzing sulfur-containing RNAs with organomercury gels. Methods Mol. Biol., 883, 111-120.
28. Rhee, S. and Burke, D. (2004) Tris (2-carboxyethyl) phosphine stabilization of RNA: comparison with dithiothreitol for use with nucleic acid and thiophosphoryl chemistry. Anal. Biochem., 325, 137-143.
29. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
30. Parisien, M. and Major, F. (2008) The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature, 452, 51-55.
31. Santoro, S. W. and Joyce, G. F. (1997) A general purpose RNAcleaving DNA enzyme. Proc. Natl Acad. Sci. USA, 94, 4262-4266.
32. Lorsch, J. R., Bartel, D. P. and Szostak, J. W. (1995) Reverse transcriptase reads through a 2'-5' linkage and a 2'-thiophosphate in a template. Nucleic Acids Res., 23, 2811-2814.
33. Patterson, J., Nickens, D. and Burke, D. (2006) HIV-1 reverse transcriptase pausing at bulky 2' adducts is relieved by deletion of the RNase H domain. RNA Biol., 3, 163-169.
34. Knapp, G. (1987) Enzymatic approaches to probing of RNA secondary and tertiary structure. Methods Enzymol., 180, 192-212.
35. Krol, A. and Carbon, P. (1987) A guide for probing native small nuclear RNA and ribonuclear structures. Methods Enzymol., 180, 212-227.
36. Chang, T., Horng, J. and Huang, H. (2008) RNALogo: a new approach to display structural RNA alignment. Nucleic Acids Res., 36, W91-W96.
37. Soukup, G. and Breaker, R. (1999) Relationship between internucleotide linkage geometry and the stability of RNA. RNA, 5, 1308-1325.
38. Pyle, A. (2010) The tertiary structure of group II introns: implications for biological function and evolution. Crit. Rev. Biochem. Mol. Biol., 45, 215-232.
39. Michel, F., Costa, M. and Westhof, E. (2009) The ribozyme core of group II introns: a structure in want of partners. Trends Biochem. Sci., 34, 189-199.
40. Dayie, K. and Padgett, R. (2008) A glimpse into the active site of a group II intron and maybe the spliceosome, too. RNA, 14, 1697-1703.
41. Vicens, Q. and Cech, T. (2006) Atomic level architecture of group I introns revealed. Trends Biochem. Sci., 31, 41-51.
42. Woodson, S. (2005) Structure and assembly of group I introns. Curr. Opin. Struct. Biol., 15, 324-330.
43. Westhof, E. (2002) Group I introns and RNA folding. Biochem. Soc. Trans., 30, 1149-1152.