Comparative analysis of tertiary structure elements in signal recognition particle RNA

Folding and Design

Volumn 1, Issue 4, 1996, Pages 315-324

  Zwieb, Christian ^a   Müller, Florian ^b   Larsen, Niels ^c  

^a UNIVERSITY OF TEXAS AT TYLER   (United States)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^c Michigan State University ^*  (United States)

Author keywords

Comparative sequence analysis; Pseudoknot; RNA folding; RNA tetraloop; RNA protein interactions; Tertiary interaction; Translation

Indexed keywords

RNA; SIGNAL RECOGNITION PARTICLE;

ANIMAL; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; CONFORMATION; GENETICS; HUMAN; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE;

ANIMALS; BASE SEQUENCE; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; NUCLEIC ACID CONFORMATION; RNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SIGNAL RECOGNITION PARTICLE; SPECIES SPECIFICITY;

EID: 0030342517     PISSN: 13590278     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1359-0278(96)00044-2     Document Type: Article

References (42)

1. Lütcke, H. (1995). Signal recognition particle (SRP), a ubiquitous initiator of protein translocation. Eur. J. Biochem. 228, 531-550.
2. Walter, P. & Blobel, G. (1983). Disassembly and reconstitution of the signal recognition particle. Cell 34, 525-533.
3. Römisch, K., et al., & Dobberstein, B. (1989). Homology of 54K protein of signal-recognition particle, docking protein and two E. coli proteins with putative GTP-binding domains. Nature 340, 478-482.
4. Bernstein, H., Poritz, M., Strub, K., Hoben, P.J., Brenner, S. & Walter, P. (1989). Model for signal sequence recognition from amino-acid sequence of 54K subunit of signal recognition particle. Nature 340, 482-486.
5. Andrews, D., Walter, P. & Ottensmeyer, F. (1985). Structure of signal recognition particle by electron microscopy. Proc. Natl. Acad. Sci. USA 82, 785-789.
6. Andrews, D., Walter P. & Ottensmeyer, F. (1987). Evidence for an extended 7SL RNA structure in the signal recognition particle. EMBO J. 6, 3471-3477.
7. Zwieb, C. & Schüler, D. (1989). Low resolution three-dimensional models of the 7SL RNA of the signal recognition particle, based on an intramolecular cross-link introduced by mild irradiation with ultraviolet light. Biochem. Cell Biol. 67, 434-442.
8. Larsen, N. & Zwieb, C. (1991). SRP-RNA sequence alignment and secondary structure. Nucleic Acids Res. 19, 209-215.
9. Larsen, N. & Zwieb, C. (1996). The signal recognition particle database (SRPDB). Nucleic Acids Res. 24, 80-81.
10. Larsen, N. (1992). Higher order interactions in 23s rRNA. Proc. Natl. Acad. Sci. USA 89, 5044-5048.
11. Müller, F., et al., & Brimacombe, R. (1995). Getting closer to an understanding of the three-dimensional structure of ribosomal RNA. Biochem. Cell Biol. 73, 767-773.
12. Zwieb, C. (1989). Structure and function of signal recognition particle RNA. Prog. Nucleic Acid Res. Mol. Biol. 37, 207-234.
13. Gundelfinger, E.D., Krause, E., Melli, M. & Dobberstein, B. (1983). The organization of the 7SL RNA in the signal recognition particle. Nucleic Acids Res. 11, 7363-7374.
14. Walter, A., et al., & Zuker, M. (1994). Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc. Natl. Acad. Sci. USA 91, 9218-9222.
15. Gundelfinger, E.D., DiCarlo, M., Zopf, D. & Melli, M. (1984). Structure and evolution of the 7SL RNA component of the signal recognition particle. EMBO J. 3, 2325-2332.
16. Strub, K., Moss, J. & Walter, P. (1991 ). Binding sites of the 9- and 14-kilodalton heterodimeric protein subunit of the signal recognition particle (SRP) are contained exclusively in the Alu domain of SRP RNA and contain a sequence motif that is conserved in evolution. Mol. Cell. Biol. 11, 3949-3959.
17. Andreazzoli, M. & Gerbi, S.A. (1991). Changes in 7SL RNA conformation during the signal recognition particle cycle. EMBO J. 10, 767-777.
18. Davis, J.P., Janjic, N., Pribnow, D. &. Zichi, D.A. (1995). Alignment editing and identification of consensus secondary structures for nucleic acid sequences: interactive use of dot matrix representations. Nucleic Acids Res. 23, 4471-4479.
19. Woese, C.R., Winker, S. & Gutell, R.R. (1990). Architecture of riboso-mal RNA: constraints on the sequence of 'tetra-loops'. Proc. Natl. Acad. Sci. USA 87, 8467-8471.
20. Cheong, C., Varani, G. & Tinoco, I.J. (1990). Solution structure of an unusually stable RNA hairpin, 5′GGAC(UUCG)GUCC. Nature 346, 680-682.
21. Heus, H.A. & Pardi, A. (1991). Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science 253, 191-194.
22. Jucker, F. & Pardi, A. (1995). GNRA tetraloops make a U-turn. RNA 1, 219-222.
23. Quigley, G. & Rich, A. (1976). Structural domains of transfer RNA molecules. The ribose 2 hydroxyl which distinguishes RNA from DNA plays a key role in stabilizing tRNA structure. Science 194, 796-806.
24. Lentzen, G., Dobberstein, B. & Wintermeyer, W. (1994). Formation of SRP-like particles induces a conformational change in E. coli 4.5S RNA. FEBS Lett. 348, 233-238.
25. Walker, P., Black, S. & Zwieb, C. (1995). Cooperative assembly of signal recognition particle RNA with protein SRP19. Biochemistry 34, 11989-11997.
26. Zwieb, C. (1991). Interaction of protein SRP19 with signal recognition particle RNA lacking individual RNA helices. Nucleic Acids Res. 19, 2955-2960.
27. Zwieb, C. (1992). Recognition of a tetranucleotide loop of signal recognition particle RNA by protein SRP19. J. Biol. Chem. 267, 15650-15656.
28. Zwieb, C. (1994). Site-directed mutagenesis of signal recognition particle RNA: identification of the nucleotides in helix 8 required for interaction with protein SRP19. Eur. J. Biochem. 222, 885-890.
29. Czarnota, G., Andrews, D., Farrow, N. & Ottensmeyer, F. (1994). A structure for the signal sequence binding protein SRP54: 3D reconstruction from STEM images of single molecules. J. Struct. Biol. 113, 35-46.
30. Samuelsson, T. (1992). A Mycoplasma protein homologous to mammalian SRP54 recognizes a highly conserved domain of SRP RNA. Nucleic Acids Res. 20, 5763-5770.
31. Siegel, V. & Walter, P. (1988). Binding sites of the 19-kDa and 68/72-kDa signal recognition particle (SRP) proteins on SRP RNA as determined in protein-RNA 'footprinting'. Proc. Natl. Acad. Sci. USA 85, 1801-1805.
32. Römisch, K., Webb, J., Lingelbach, K., Gausepohl, H. & Dobberstein, B. (1990). The 54-kD protein of signal recognition particle contains a methionine-rich RNA binding domain. J. Cell Biol. 111, 1793-1802.
33. Zopf, D., Bernstein, H.D., Johnson, A.E. & Walter, P. (1990). The methionine-rich domain of the 54 kd protein subunit of the signal recognition particle contains an RNA binding site and can be crosslinked to a signal sequence. EMBO J. 9, 4511-4517.
34. Krolkiewicz, S., Sänger, H. & Niesbach-Klösgen, U. (1994). Structural and functional characterisation of the signal recognition particle-specific 54-kD protein (SRP54) of tomato. Mol. Gen. Genet. 245, 565-576.
35. Zwieb, C. & Ullu, E. (1986). Identification of dynamic sequences in the central domain of 7SL RNA. Nucleic Acids Res. 14, 4639-4657.
36. Gast, F. & Hagerman, P. (1991). Electrophoretic and hydrodynamic properties of duplex ribonucleic acid molecules transcribed in vitro: evidence that A-tracts do not generate curvature in RNA. Biochemistry 30, 4268-4277.
37. Tang, R. & Draper, D. (1994). Bend and helical twist associated with a symmetric internal loop from 5S ribosomal RNA. Biochemistry 33, 10089-10093.
38. Weeks, K. & Cech, T. (1996). Assembly of a ribonucleoprotein catalyst by tertiary structure capture. Science 271, 345-348.
39. Bernstein, F., et al., & Tasumi, M. (1977). The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
40. Levitt, M. (1969). Detailed molecular model for transfer ribonucleic acid. Nature 224, 759-763.
41. Fox, G. & Woese, C. (1975). 5S RNA secondary structure. Nature 256, 505-507.
42. Massire, C., Gaspin, C. & Westhof, E. (1994). DRAWNA: a program for drawing schematic views of nucleic acids. J. Mol. Graphics 12, 201-206.