In vivo determination of RNA structure-function relationships: Analysis of the 790 loop in ribosomal RNA

Journal of Molecular Biology

Volumn 269, Issue 5, 1997, Pages 732-743

  Lee, Kangseok ^a   Varma, Shikha ^a   SantaLucia Jr , John ^a   Cunningham, Philip R ^a  

^a WAYNE STATE UNIVERSITY   (United States)

Author keywords

790 loop; Instant evolution; Mutation; NMR; Ribosomal RNA

Indexed keywords

RIBOSOME RNA; RNA 16S;

ARTICLE; ESCHERICHIA COLI; GENETIC CONSERVATION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN SYNTHESIS; RIBOSOME; RNA STRUCTURE; SITE DIRECTED MUTAGENESIS; STRUCTURE ACTIVITY RELATION; THERMODYNAMICS;

EID: 0031588021     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1092     Document Type: Article

References (58)

1. Barta A., Steiner G., Brosius J., Noller H. F., Kuechler E. Identification of a site on 23S ribosomal RNA located at the peptidyl transferase center. Proc. Natl Acad. Sci. USA. 81:1984;3607-3611.
2. Brosius J., Ullrich A., Raker M. A., Gray A., Dull T. J., Gutell R. R., Noller H. F. Construction and fine mapping of recombinant plasmids containing the rrn B ribosomal RNA operon of E. coli. Plasmid. 6:1981;112-118.
3. Brow D. A., Noller H. F. Protection of ribosomal RNA from kethoxal in polyribosomes. Implication of specific sites in ribosome function. J. Mol. Biol. 163:1983;27-46.
4. Brown T., Leonard G. A., Booth E. D., Kneale G. Influence of pH on the conformation and stability of mismatch base-pairs in DNA. J. Mol. Biol. 212:1990;437-440.
5. Burns D. K., Crowl R. M. In vitro mutagenesis of chloramphenicol acetyl transferase to investigate structure/function relationships. Protein Struct. Fold. Des. 2:1987;375-384.
6. Calos M. P. DNA sequence for a low-level promoter of the lac repressor gene and 'up' promoter mutation. Nature. 274:1978;762-769.
7. Capaldi D., Reese C. Use of the 1-(2-fluorophenyl)-4-methoxypiperidin-4-yl (Fpmp) and related protecting groups in oligoribonucleotide synthesis: stability of internucleotide linkages to aqueous acid. Nucl. Acids Res. 22:1994;2209-2216.
8. Chapman N. M. Protection of specific sites in 16S RNA from chemical modification by association of 30 S and 50 S ribosomes. J. Mol. Biol. 109:1977;131-149.
9. Cundliffe E. Involvement of specific portions of ribosomal RNA in defined ribosomal functions: a study utilizing antibiotics. Structure, Function and Genetics of Ribosomes. 1986;Springer-Verlag, New York.
10. Cunningham P. R., Weitzman C. J., Nègre D., Sinning J., Nurse K., Ofengand J. G1401: A keystone nucleotide at the decoding site of Escherichia coli 30S ribosomes. Biochemistry. 31:1992;7629-7637.
11. Cunningham P. R., Nurse K., Weitzmann C., Ofengand J. Functional effects of base changes which further define the decoding center of Eshcerichia coli 16 S ribosomal RNA: Mutation of C1404, G1405, C1496, G1497 and U1498. Biochemistry. 32:1993;7172-7180.
12. Dahlberg A. E. The functional role of ribosomal RNA in protein synthesis. Cell. 57:1989;525-529.
13. de Boer H. A., Comstock L. J., Vasser M. The tac promoter: a functional hybrid derived from the trp and lac promoters. Proc. Natl Acad. Sci. USA. 80:1983;21-25.
14. de Stasio E. A., Göringer H. U., Tapprich W. E., Dahlberg A. E. Probing ribosome function through mutagenesis of ribosomal RNA. Tuite M. F., Picard M., Bolotin-Fukuhara M. Genetics of Translation. 1988;Springer-Verlag, Berlin.
15. Dower W. J., Miller J. F., Ragsdale C. W. High efficiency transformation of E. coli by high voltage electroporation. Nucl. Acids Res. 16:1988;6127.
16. Fourmy D., Recht M. I., Blanchard S. C., Puglisi J. D. Structure of the A site of Escherichia coli 16 S ribosomal RNA complexed with an aminoglycoside antibiotic. Science. 274:1996;1367-1371.
17. Gutell R. R. Collection of small subunit (16 S- and 16 S-like) ribosomal RNA structures: 1994. Nucl. Acids Res. 22(17):1994;3502-3507.
18. Hanahan D. Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 166:1983;557-580.
19. He L., Kierzek R., SantaLucia J., John, Walter A. E., Turner D. H. Nearest-neighbor parameters for G·U mismatches. Biochemistry. 30:1991;11124-11132.
20. Herr W., Chapman N., Noller H. Mechanism of ribosomal subunit association: discrimination of specific sites in 16S RNA essential for association activity. J. Mol. Biol. 130:1979;433-449.
21. Higuchi R. Using PCR to engineer DNA. Erlich H. A. PCR Technology. 1989;Stockton Press, New York.
22. Huang S., Wang Y. X., Draper D. E. Structure of a hexanucleotide RNA hairpin loop conserved in ribosomal RNAs. J. Mol. Biol. 258:1996;308-321.
23. Hui A. S., de Boer H. A. Specialized ribosome system: preferential translation of a single mRNA species by a subpopulation of mutated ribosomes in Escherichia coli. Proc. Natl Acad. Sci. USA. 84:1987;4762-4766.
24. Hui A., Jhurani P., de Boer H. A. Directing ribosomes to a single mRNA species: A method to study ribosomal RNA mutations and their effects on translation of a single messsenger in Escherichia coli. Methods Enzymol. 153:1987;432-452.
25. Hunter W. N., Brown T., Anand N. N., Kennard O. Structure of an adenine-cytosine base pair in DNA and its implications for mismatch repair. Nature. 320:1986;552-555.
26. Lata R., Agrawal R., Penczek P., Grassucci R., Zhu J., Frank J. Three-dimensional reconstruction of the Escherichia coli 30 S ribosomal subunit in ice. J. Mol. Biol. 262:1996;43-52.
27. Lee K., Holland-Staley C. A., Cunningham P. R. Genetic analysis of the Shine-Dalgarno interaction: selection of alternative functional mRNA-rRNA combinations. RNA. 2:1996;1270-1285.
28. Lippens G., Dhalluin C., Wieruszeski J.-M. Use of a water flip-back pulse in the homonuclear NOESY experiment. J. Biomol. NMR. 5:1995;327-331.
29. Lodmell J. S., Gutell R. R., Dahlberg A. E. Genetic and comparative analyses reveal an alternative secondary structure in the region of nt 912 of Escherichia coli 16 S rRNA. Proc. Natl Acad. Sci. USA. 92:1995;10555-10559.
30. Lu M., Draper D. E. On the role of rRNA tertiary structure in recognition of ribosomal protein L11 and thiostrepton. Nucl. Acids Res. 23:1995;3426-3433.
31. Luria S. E., Burrous J. W. Hybridization between Escherichia coli and Shigella. J. Bacteriol. 74:1957;461-476.
32. 2by two-dimensional NMR and simulated anealing. Biochemistry. 35:1996;14077-14089.
33. Maidak B. L., Olsen G. J., Larsen N., Overbeek R., McCaughey M. J., Woese C. R. The ribosomal database project (RDP). Nucl. Acids Res. 24:1996;82-85.
34. Miller J. H. Procedures for working with lac. Miller J. H. A Short Course in Bacterial Genetics. 1992;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
35. Moazed D., Noller H. F. Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes. Cell. 47:1986;985-994.
36. Moazed D., Van Stolk B. J., Douthwaite S., Noller H. F. Interconversion of active and inactive 30 S ribosomal subunits is accompanied by a conformational change in the decoding region of 16 S rRNA. J. Mol. Biol. 191:1986;483-493.
37. Moazed D., Samaha R. R., Gualerzi C., Noller H. F. Specific protection of 16 S rRNA by translational initiation factors. J. Mol. Biol. 248:1995;207-210.
38. Moine H., Dahlberg A. E. Mutations in helix 34 of Escherichia coli 16 S ribosomal RNA have multiple effects on ribosome function and synthesis. J. Mol. Biol. 243:1994;402-412.
39. Muralikrishna P., Wickstrom E. Escherichia coli initiation factor 3 protein binding to 30 S ribosomal subunits alters the accessibility of nucleotides within the conserved central region of 16S rRNA. Biochemistry. 28:1989;7505-7510.
40. Nielsen D. A., Chang T., Shapiro D. J. A highly sensitive, mixed-phase assay for chloramphenicol acetyltransferase activity in transfected cells. Anal. Biochem. 179:1989;19-23.
41. Noller H. F. Ribosomal RNA and translation. Annu. Rev. Biochem. 60:1991;191-227.
42. Noller H. F., Hoffarth V., Zimniak L. Unusual resistance of peptidyl transferase to protein extraction procedures. Science. 256:1992;1416-1419.
43. Piotto M., Saudek V., Sklenar V. Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. J. Biomol. NMR. 2:1992;661-665.
44. Powers T., Noller H. F. A functional pseudoknot in 16S ribosomal RNA. EMBO J. 10:1991;2203-2214.
45. Ryan P. C., Draper D. E. Detection of a key tertiary interaction in the highly conserved GTPase center of large subunit ribosomal RNA. Proc. Natl Acad. Sci. USA. 88:1991;6308-6312.
46. SantaLucia J. Jr, Kierzek R., Turner D. H. Stabilities of consecutive A·C, C·:C, G·G, U·C, and U·U mismatches in RNA internal loops: evidence for stable hydrogen-bonded U·U and C·C+ pairs. Biochemistry. 30:1991;8242-8251.
47. SantaLucia J., Allawi H. T., Seneviratne P. A. Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry. 35:1996;3555-3562.
48. Santer M., Shane S. Area of 16 S ribonucleic acid at or near the interface between the 30 S and 50 S ribosomes ofEscherichia coli. J. Bacteriol. 130:1977;900-910.
49. Serra M. J., Lyttle M. H., Axenson T. J., Schadt C. A., Turner D. H. RNA hairpin loop stability depends on closing base pair. Nucl. Acids Res. 21:1993;3845-3849.
50. Shine J., Dalgarno L. The 3′-terminal sequence of E. coli 16 S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc. Natl Acad. Sci. USA. 71:1974;1342-1346.
51. Sigmund C. D., Ettayebi M., Borden A., Morgan E. A. Antibiotic resistance mutations in ribosomal RNA genes of Escherichia coli. Methods Enzymol. 164:1988;673-689.
52. Szewczak A. A., Moore P. B. The sarcin/ricin loop, a modular RNA. J. Mol. Biol. 247:1995;81-98.
53. 1H correlation spectroscopy with spin-echo and gradient pulses. FEBS Letters. 327:1993;261-264.
54. Tapprich W., Hill W. Involvement of bases 787-795 of Escherichia coli 16 S ribosomal RNA in ribosomal subunit association. Proc. Natl Acad. Sci. USA. 83:1986;556-560.
55. Tapprich W. E., Goss D. J., Dahlberg A. E. Mutation at position 791 in Escherichia coli 16 S ribosomal RNA affects processes involved in the initiation of protein synthesis. Proc. Natl Acad. Sci. USA. 86:1989;4927-4931.
56. Triman K., Becker E., Dammel C., Katz J., Mori H., Douthwaite S., Yapijakis C., Yoast S., Noller H. F. Isolation of temperature-sensitive mutants of 16 S rRNA in E. coli. J. Mol. Biol. 209:1989;643-653.
57. 1H correlated experiments. J. Am. Chem. Soc. 113:1991;9349-9354.
58. Zimmermann R. A., Dahlberg A. E. Ribosomal RNA. 1996;CRC Press, Boca Raton.