The 5e motif of eukaryotic signal recognition particle RNA contains a conserved adenosine for the binding of SRP72

RNA

Volumn 14, Issue 6, 2008, Pages 1143-1153

  Iakhiaeva, Elena ^a   Wower, Jacek ^b   Wower, Iwona K ^b   Zwieb, Christian ^a  

^a UNIVERSITY OF TEXAS HEALTH CENTER   (United States)

^b AUBURN UNIVERSITY   (United States)

Author keywords

Protein RNA interactions; RNP; Site directed mutagenesis

Indexed keywords

ADENOSINE; NUCLEOTIDE; RNA; SIGNAL RECOGNITION PARTICLE; SIGNAL RECOGNITION PARTICLE 72 PROTEIN;

ARTICLE; BINDING SITE; CHIMERA; CONTROLLED STUDY; METHANOCOCCUS JANNASCHII; MOLECULAR RECOGNITION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN MOTIF; PROTEIN RNA BINDING; RNA STRUCTURE;

ADENOSINE; BASE SEQUENCE; BINDING SITES; HUMANS; METHANOCOCCUS; NUCLEIC ACID CONFORMATION; RECOMBINANT FUSION PROTEINS; RNA, SMALL CYTOPLASMIC; SIGNAL RECOGNITION PARTICLE; SUBSTRATE SPECIFICITY;

ARCHAEA; EUKARYOTA; METHANOCALDOCOCCUS JANNASCHII;

EID: 44149103416     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.979508     Document Type: Article

References (41)

1. Andersen, E.S., Rosenblad, M.A., Larsen, N., Westergaard, J.C., Burks, J., Wower, I.K., Wower, J., Gorodkin, J., Samuelsson, T., and Zwieb, C. 2006. The tmRDB and SRPDB resources. Nucleic Acids Res. 34: D163-D168. doi: 10.1093/nar/gkj142.
2. Andrews, D.W., Walter, P., and Ottensmeyer, F.P. 1987. Evidence for an extended 7SL RNA structure in the signal recognition particle. EMBO J. 6: 3471-3477.
3. Batey, R.T., Rambo, R.P., Lucast, L., Rha, B., and Doudna, J.A. 2000. Crystal structure of the ribonucleoprotein core of the signal recognition particle. Science 287: 1232-1239.
4. Bhuiyan, S.H., Gowda, K., Hotokezaka, H., and Zwieb, C. 2000. Assembly of archaeal signal recognition particle from recombinant components. Nucleic Acids Res. 28: 1365-1373. doi: 10.1093/nar/28.6.1365.
5. Christiansen, J., Egebjerg, J., Larsen, N., and Garrett, R.A. (1990). Analysis of rRNA structure: Experimental and theoretical considerations. In Ribosomes and protein synthesis: A practical approach (ed. G. Speding), pp. 229-252. Oxford University Press, New York.
6. Diener, J.L. and Wilson, C. 2000. Role of SRP19 in assembly of the Archaeoglobus fulgidus signal recognition particle. Biochemistry 39: 12862-12874.
7. Doudna, J.A. and Batey, R.T. 2004. Structural insights into the signal recognition particle. Annu. Rev. Biochem. 73: 539-557.
8. Hainzl, T., Huang, S., and Sauer-Eriksson, A.E. 2002. Structure of the SRP19 RNA complex and implications for signal recognition particle assembly. Nature 417: 767-771.
9. Halic, M., Becker, T., Pool, M.R., Spahn, C.M., Grassucci, R.A., Frank, J., and Beckmann, R. 2004. Structure of the signal recognition particle interacting with the elongation-arrested ribosome. Nature 427: 808-814.
10. Halic, M. and Beckmann, R. 2005. The signal recognition particle and its interactions during protein targeting. Curr. Opin. Struct. Biol. 15: 116-125.
11. Henry, K.A., Zwieb, C., and Fried, H.M. 1997. Purification and biochemical characterization of the 19-kDa signal recognition particle RNA-binding protein expressed as a hexahistidine-tagged polypeptide in Escherichia coli. Protein Expr. Purif. 9: 15-26.
12. Iakhiaeva, E., Yin, J., and Zwieb, C. 2005. Identification of an RNA-binding domain in human SRP72. J. Mol. Biol. 345: 659-666.
13. Iakhiaeva, E., Bhuiyan, S.H., Yin, J., and Zwieb, C. 2006. Protein SRP68 of human signal recognition particle: Identification of the RNA and SRP72 binding domains. Protein Sci. 12: 467-468.
14. Kuglstatter, A., Oubridge, C., and Nagai, K. 2002. Induced structural changes of 7SL RNA during the assembly of human signal recognition particle. Nat. Struct. Biol. 9: 740-744.
15. Larsen, N. and Zwieb, C. 1991. SRP-RNA sequence alignment and secondary structure. Nucleic Acids Res. 19: 209-215.
16. Lütcke, H., Prehn, S., Ashford, A.J., Remus, M., Frank, R., and Dobberstein, B. 1993. Assembly of the 68- and 72-kDa proteins of signal recognition particle with 7S RNA. J. Cell Biol. 121: 977-985.
17. Menichelli, E., Isel, C., Oubridge, C., and Nagai, K. 2007. Protein-induced conformational changes of RNA during the assembly of human signal recognition particle. J. Mol. Biol. 367: 187-203.
18. Nagai, K., Oubridge, C., Kuglstatter, A., Menichelli, E., Isel, C., and Jovine, L. 2003. Structure, function and evolution of the signal recognition particle. EMBO J. 22: 3479-3485.
19. Oubridge, C., Kuglstatter, A., Jovine, L., and Nagai, K. 2002. Crystal structure of SRP19 in complex with the S domain of SRP RNA and its implication for the assembly of the signal recognition particle. Mol. Cell 9: 1251-1261.
20. Politz, J.C., Yarovoi, S., Kilroy, S.M., Gowda, K., Zwieb, C., and Pederson, T. 2000. Signal recognition particle components in the nucleolus. Proc. Natl. Acad. Sci. 97: 55-60.
21. Regalia, M., Rosenblad, M.A., and Samuelsson, T. 2002. Prediction of signal recognition particle RNA genes. Nucleic Acids Res. 30: 3368-3377. doi: 10.1093/nar/gkf468.
22. Rosendal, K.R., Wild, K., Montoya, G., and Sinning, I. 2003. Crystal structure of the complete core of archaeal signal recognition particle and implications for interdomain communication. Proc. Natl. Acad. Sci. 100: 14701-14706.
23. Samuelsson, T. 1992. A Mycoplasma protein homologous to mammalian SRP54 recognizes a highly conserved domain of SRP RNA. Nucleic Acids Res. 20: 5763-5770. doi: 10.1093/nar/20.21.5763.
24. Schneider, K.L., Pollard, K.S., Baertsch, R., Pohl, A., and Lowe, T.M. 2006. The UCSC Archaeal Genome Browser. Nucleic Acids Res. 34: D407-D410. doi: 10.1093/nar/gkj134.
25. Scoulica, E., Krause, E., Meese, K., and Dobberstein, B. 1987. Disassembly and domain structure of the proteins in the signal-recognition particle. Eur. J. Biochem. 163: 519-528.
26. Shan, S.O. and Walter, P. 2005. Co-translational protein targeting by the signal recognition particle. FEBS Lett. 579: 921-926.
27. Siegel, V. and Walter, P. 1988a. Each of the activities of signal recognition particle (SRP) is contained with a distinct domain: Analysis of biochemical mutants of SRP. Cell 52: 39-49.
28. Siegel, V. and Walter, P. 1988b. 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. 85: 1801-1805.
29. Siu, F.Y., Spanggord, R.J., and Doudna, J.A. 2007. SRP RNA provides the physiologically essential GTPase activation function in cotranslational protein targeting. RNA 13: 240-250.
30. Spanggord, R.J., Siu, F., Ke, A., and Doudna, J.A. 2005. RNA-mediated interaction between the peptide-binding and GTPase domains of the signal recognition particle. Nat. Struct. Mol. Biol. 12: 1116-1122.
31. Tozik, I., Huang, Q., Zwieb, C., and Eichler, J. 2002. Reconstitution of the signal recognition particle of the halophilic archaeon Haloferax volcanii. Nucleic Acids Res. 30: 4166-4175. doi: 10.1093/nar/gkf548.
32. Walter, P. and Blobel, G. 1983. Disassembly and reconstitution of signal recognition particle. Cell 34: 525-533.
33. Weichenrieder, O., Wild, K., Strub, K., and Cusack, S. 2000. Structure and assembly of the Alu domain of the mammalian signal recognition particle. Nature 408: 167-173.
34. Yin, J., Yang, C.H., and Zwieb, C. 2001. Assembly of human signal recognition particle (SRP): Overlap of regions required for binding of protein SRP54 and assembly control. RNA 7: 1389-1396.
35. Yin, J., Yang, C.H., and Zwieb, C. 2004. Two strategically placed base pairs in helix 8 of mammalian signal recognition particle RNA are crucial for the SPR19-dependent binding of protein SRP54. RNA 10: 574-580.
36. Yin, J., Iakhiaeva, E., Menichelli, E., and Zwieb, C. 2007. Identification of the RNA binding regions of SRP68/72 and SRP72 by systematic mutagenesis of human SRP RNA. RNA Biol. 4: 154-159.
37. Zwieb, C. 1991. Interaction of protein SRP19 with signal recognition particle RNA lacking individual RNA-helices. Nucleic Acids Res. 19: 2955-2960. doi: 10.1093/nar/19.11.2955.
38. Zwieb, C. 1992. Recognition of a tetranucleotide loop of signal recognition particle RNA by protein SRP19. J. Biol. Chem. 267: 15650-15656.
39. 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.
40. Zwieb, C. and Eichler, J. 2002. Getting on target: The archaeal signal recognition particle. Archaea 1: 27-34.
41. Zwieb, C., Van Nues, R.W., Rosenblad, M.A., Brown, J.D., and Samuelsson, T. 2005. A nomenclature for all signal recognition particle RNAs. RNA 11: 7-13.