Defining the enzyme binding domain of a ribonuclease III processing signal. Ethylation interference and hydroxyl radical footprinting using catalytically inactive RNase III mutants

EMBO Journal

Volumn 15, Issue 6, 1996, Pages 1421-1433

  Li, Honglin ^a,b   Nicholson, Allen W ^a  

^a WAYNE STATE UNIVERSITY   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

Author keywords

dsRBM; dsRNA; Ethylation interference; Hydroxyl radical footprinting; Ribonuclease III

Indexed keywords

CALCIUM ION; GLUTAMIC ACID; HYDROXYL RADICAL; LYSINE; MAGNESIUM ION; RIBONUCLEASE III;

AMINO ACID SUBSTITUTION; ARTICLE; BACTERIOPHAGE T7; BINDING AFFINITY; CONTROLLED STUDY; ENZYME BINDING; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN MODIFICATION; RNA CLEAVAGE;

ESCHERICHIA COLI;

EID: 0029976320     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1002/j.1460-2075.1996.tb00484.x     Document Type: Article

References (40)

1. Beese, L.S. and Steitz, T.A. (1991). Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism. EMBO J., 10, 25-33.
2. Bram, R.J., Young, R.A. and Steitz, J.A. (1980) The ribonuclease III site flanking 23S sequences in the 30S ribosomal precursor RNA of E.coli. Cell, 19, 393-401.
3. Bycroft, M., Grunert, S., Murzin, A.G., Proctor, M. and St Johnston, D. (1995) NMR solution structure of a dsRNA binding domain from Drosophila staufen protein reveals homology to the N-terminal domain of ribosomal protein S5. EMBO J., 14, 3563-3571.
4. Carey, J , Cameron, V., deHaseth, P.L. and Uhlenbeck, O.C. (1983) Sequence-specific interaction of R17 coat protein with its ribonucleic acid binding site. Biochemistry, 22, 2601-2610.
5. Chelladurai, B.S., Li, H and Nicholson, A.W. (1991) A conserved sequence element in ribonuclease III processing signals is not required for accurate in vitro enzymatic cleavage. Nucleic Acids Res., 19, 1759-1766.
6. Chelladurai, B.S., Li, H., Zhang, K. and Nicholson, A.W. (1993) Mutational analysis of a ribonuclease III processing signal. Biochemistry, 32, 7549-7558.
7. Clarke, P.A. and Mathews, M.B. (1995) Interactions between the double-stranded RNA binding motif and RNA: definition of the binding site for the interferon-induced protein kinase DAI (PKR) on adenovirus VA RNA. RNA, 1, 7-20.
8. Court, D. (1993) RNA processing and degradation by RNase III. In Belasco, J.G. and Brawerman, G. (eds), Control of Messenger RNA Stability. Academic Press, New York pp. 71-116.
9. Dunn, J.J. (1982) Ribonuclease III. In Boyer, P. (ed.), The Enzymes. Vol 15. Academic Press, New York, pp 485-499.
10. Dunn, J.J. and Studier, F.W. (1983) Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. J. Mol. Biol., 166, 477-535.
11. Fersht, A. (1985) Enzyme Structure and Mechanism. W H. Freeman and Co , New York.
12. Gott, J.M., Pan, T., LeCuyer, K. and Uhlenbeck, O.C. (1993) Using circular permutation analysis to redefine the R17 coat protein binding site. Biochemistry, 32, 13399-13404.
13. Grodberg, J and Dunn, J.J. (1990) OmpT encodes the Escherichia coli outer membrane protease that cleaves T7 RNA polymerase during purification. J. Bacteriol., 170, 1245-1253.
14. Hertzberg, R.P. and Dervan, P.B. (1984) Cleavage of DNA with methidiumpropyl-EDTA-iron(II): reaction conditions and product analysis. Biochemistry, 23, 3934-3945.
15. +, whose overexpression inhibits sexual development, encodes a ribonuclease III-like RNase. EMBO J., 10, 221-226.
16. Inada, T., Kawakami, K., Chen, S.-M., Takiff, H.E., Court, D.L. and Nakamura, Y. (1989) Temperature-sensitive lethal mutant of Era, a G protein in Escherichia coli. J. Bacteriol., 171, 5017-5024.
17. Katayanagi, K., Miyagawa, M., Matsushima, M., Ishikawa, M., Kanaya, S., Ikehara, M., Matsuzaki, T. and Morikawa, K. (1990) Three-dimensional structure of ribonuclease H from E.coli. Nature, 347, 306-309
18. Kharrat, A., Macia, M.J., Gibson, T.J., Nilges, M. and Pastore, A (1995) Structure of the dsRNA binding domain of E.coli RNase III. EMBO J., 14, 3572-3584.
19. Krinke, L. and Wulff, D.L. (1990) The cleavage specificity of RNase III. Nucleic Acids Res., 18, 4809-4815.
20. Latham, J.A. and Cech, T.R. (1989) Defining the inside and outside of a catalytic RNA molecule. Science, 245, 276-282.
21. Li, H., Chelladurai, B.S., Zhang, K. and Nicholson, A.W. (1993) Ribonuclease III cleavage of a bacteriophage T7 processing signal. Divalent cation specificity, and specific anion effects. Nucleic Acids Res., 21, 1919-1925.
22. March, P.E. and Gonzalez, M. (1990) Characterization of the biochemical properties of recombinant ribonuclease III. Nucleic Acids Res., 18, 3293-3298
23. Meegan, J.M. and Marcus, P.I. (1989) Double-stranded ribonuclease coinduced with interferon. Science, 244, 1089-1091.
24. Mitra, S. and Bechhofer, D.H. (1994) Substrate specificity of an RNase III-like activity from Bacillus subtilis. J. Biol. Chem., 269, 31450-31456.
25. Montesano, L., Cawley, D., and Herschman, H.R. (1982) Disuccinimidyl suberate cross-linked ricin does not inhibit cell-free protein synthesis Biochem. Biophys. Res. Commun., 109, 7-13.
26. Nicholson, A.W. (1992) Accurate enzymatic cleavage in vitro of a 2′-deoxyribose-substituted ribonuclease III processing signal. Biochim. Biophys. Acta, 1129, 318-322.
27. Nicholson, A.W (1995) Structure, reactivity and biology of double-stranded RNA. Progr. Nucleic Acids Res. Mol. Biol., 52, 1-65.
28. Nicholson, A.W., Niebling, K.R., McOsker, P. and Robertson, H.D. (1988) Accurate in vitro cleavage by RNase III of phosphorothioate-substituted RNA processing signals in bacteriophage T7 early mRNA. Nucleic Acids Res., 16, 1577-1591.
29. Perrin, S. and Gilliland, G. (1990) Site-specific mutagenesis using asymmetric polymerase chain reaction and a single mutant primer. Nucleic Acids Res., 18, 7433-7438.
30. Robertson, H.D. (1982) Escherichia coli ribonuclease III cleavage sites. Cell, 30, 669-672.
31. 4 and the antibiotic thiostrepton interact with overlapping regions of the 23S rRNA backbone in the ribosomal GTPase centre J. Mol. Biol., 234, 1013-1020.
32. St Johnston, D., Brown, N.H., Gall, J.G. and Jantsch, M. (1992) A conserved double-stranded RNA-binding domain. Proc. Natl Acad. Sci. USA, 89, 10979-10983.
33. Schweisguth, D.C., Chelladurai, B.S., Nicholson, A.W. and Moore, P B. (1994) Structural characterization of a ribonuclease III processing signal. Nucleic Acids Res., 22, 604-612.
34. Smith, R.J., Capaldi, R.A., Muchmore, D. and Dahlquist, F. (1978) Cross-linking of ubiquinone cytochrome c reductase (Complex III) with periodate-cleavable bifunctional reagents. Biochemistry, 17, 3719-3723.
35. Studier, F.W. (1973) Analysis of bactenophage T7 early RNAs and proteins on slab gels. J. Mol. Biol., 79, 237-248.
36. Vlassov, V.V., Giegé, R and Ebel, J.-P. (1981) Tertiary structure of tRNAs in solution monitored by phosphodiester modification with ethylnitrosourea. Eur. J. Biochem., 119, 51-59.
37. Wagner, E.G.H. and Simons, R.W. (1994) Antisense RNA control in bacteria, phages and plasmids. Annu. Rev. Biochem., 48, 713-742.
38. Winkler, F.K. et al. (1993) The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J., 12, 1781-1795.
39. Yang, W., Hendrickson, W.A., Crouch, R.J. and Satow, Y. (1990) Structure of ribonuclease H phased at 2 Å resolution by MAD analysis of the selenomethionyl protein. Science, 249, 1398-1405.
40. Zuber, M., Hoover, T A , Powell, B.S. and Court, D.L. (1994) Analysis of the rnc locus of Coxiella burnetii. Mol. Microbiol., 14, 291-300.