Alternate rRNA secondary structures as regulators of translation

Nature Structural and Molecular Biology

Volumn 18, Issue 2, 2011, Pages 169-177

  Feng, Shu ^a   Li, Heng ^a,c   Zhao, Jing ^a   Pervushin, Konstantin ^a   Lowenhaupt, Ky ^b   Schwartz, Thomas U ^b   Dröge, Peter ^a,c  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c Eli Lilly Singapore Pte Ltd   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

DNA Z; RIBOSOME RNA;

ARTICLE; ESCHERICHIA COLI; HUMAN; IN VITRO STUDY; IN VIVO STUDY; MAMMAL; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN PROCESSING; PROTEIN SECONDARY STRUCTURE; RIBOSOME; RNA EDITING; TRANSLATION REGULATION;

ADENOSINE DEAMINASE; CELL LINE; DNA, Z-FORM; ESCHERICHIA COLI; HUMANS; MODELS, MOLECULAR; MUTATION; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; PROTEIN BIOSYNTHESIS; PROTEIN STRUCTURE, TERTIARY; RIBOSOMES; RNA EDITING; RNA, BACTERIAL; RNA, RIBOSOMAL;

ESCHERICHIA COLI;

EID: 79551631613     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.1962     Document Type: Article

References (43)

1. Rich, A. & Zhang, S. Timeline: Z-DNA: the long road to biological function. Nat. Rev. Genet. 4, 566-572 (2003).
2. Rothenburg, S. et al. PKR-like eukaryotic initiation factor 2 α kinase from zebrafsh contains Z-DNA binding domains instead of dsRNA binding domains. Proc. Natl. Acad. Sci. USA 102, 1602-1607 (2005).
3. Bergan, V., Jagus, R., Lauksund, S., Kileng, Ø. & Robertsen, B. The Atlantic salmon Z-DNA binding protein kinase phosphorylates translation initiation factor 2 α and constitutes a unique orthologue to the mammalian dsRNA-activated protein kinase R. FEBS J. 275, 184-197 (2008).
4. Toth, A.M., Zhang, P., Das, S., George, C.X. & Samuel, C.E. Interferon action and the double-stranded RNA-dependent enzymes ADAR1 adenosine deaminase and PKR protein kinase. Prog. Nucleic Acid Res. Mol. Biol. 81, 369-434 (2006).
5. Kwon, J.A. & Rich, A. Biological function of the vaccinia virus Z-DNA-binding protein E3L: gene transactivation and antiapoptotic activity in HeLa cells. Proc. Natl. Acad. Sci. USA 102, 12759-12764 (2005).
6. Deng, L. et al. Vaccinia virus subverts a mitochondrial antiviral signaling protein-dependent innate immune response in keratinocytes through its double-stranded RNA binding protein, E3. J. Virol. 82, 10735-10746 (2008).
7. Schwartz, T., Rould, M.A., Lowenhaupt, K., Herbert, A. & Rich, A. Crystal structure of the Zα domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA. Science 284, 1841-1845 (1999).
8. Schwartz, T., Behlke, J., Lowenhaupt, K., Heinemann, U. & Rich, A. Structure of the DLM-1-Z-DNA complex reveals a conserved family of Z-DNA-binding proteins. Nat. Struct. Biol. 8, 761-765 (2001).
9. Ha, S.C. et al. The structures of non-CG-repeat Z-DNAs co-crystallized with the Z-DNA-binding domain, hZα (ADAR1). Nucleic Acids Res. 37, 629-637 (2009).
10. Placido, D., Brown, B.A., Lowenhaupt, K., Rich, A. & Athanasiadis, A. A left-handed RNA double helix bound by the Zα domain of the RNA-editing enzyme ADAR1. Structure 15, 395-404 (2007).
11. Wong, S.K., Sato, S. & Lazinski, D.W. Elevated activity of the large form of ADAR1 in vivo: very effcient RNA editing occurs in the cytoplasm. RNA 9, 586-598 (2003).
12. Koeris, M., Funke, L., Shrestha, J., Rich, A. & Maas, S. Modulation of ADAR1 editing activity by Z-RNA in vitro. Nucleic Acids Res. 33, 5362-5370 (2005).
13. Rothenburg, S., Schwartz, T., Koch-Nolte, F. & Haag, F. Complex regulation of the human gene for the Z-DNA binding protein DLM-1. Nucleic Acids Res. 30, 993-1000 (2002).
14. Takaoka, A. et al. DAI (DLM-1/ZBP1) is a cytosolic DNA sensor and an activator of innate immune response. Nature 448, 501-505 (2007).
15. Wang, Z. et al. Regulation of innate immune responses by DAI (DLM-1/ZBP1) and other DNA-sensing molecules. Proc. Natl. Acad. Sci. USA 105, 5477-5482 (2008).
16. Deigendesch, N., Koch-Nolte, F. & Rothenburg, S. ZBP1 subcellular localization and association with stress granules is controlled by its Z-DNA binding domains. Nucleic Acids Res. 34, 5007-5020 (2006).
17. Li, H. et al. Human genomic Z-DNA segments probed by the Zα domain of ADAR1. Nucleic Acids Res. 37, 2737-2746 (2009).
18. Schade, M. et al. The solution structure of the Zalpha domain of the human RNA editing enzyme ADAR1 reveals a prepositioned binding surface for Z-DNA. Proc. Natl. Acad. Sci. USA 96, 12465-12470 (1999).
19. Schuwirth, B.S. et al. Structures of the bacterial ribosome at 3.5 Å resolution. Science 310, 827-834 (2005).
20. Selmer, M. et al. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313, 1935-1942 (2006).
21. Korostelev, A., Trakhanov, S., Laurberg, M. & Noller, H.F. Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell 126, 1065-1077 (2006).
22. Hall, K., Cruz, P., Tinoco, I. Jr., Jovin, T.M. & Van de Sande, J.H. 'Z-RNA'- a left-handed RNA double helix. Nature 311, 584-586 (1984).
23. Steitz, T.A. A structural understanding of the dynamic ribosome machine. Nat. Rev. Mol. Cell Biol. 9, 242-253 (2008).
24. Schmeing, T.M. & Ramakrishnan, V. What recent ribosome structures have revealed about the mechanism of translation. Nature 461, 1234-1242 (2009).
25. Korostelev, A., Ermolenko, D.N. & Noller, H.F. Structural dynamics of the ribosome. Curr. Opin. Chem. Biol. 12, 674-683 (2008).
26. Schade, M., Turner, C.J., Lowenhaupt, K., Rich, A. & Herbert, A. Structure-function analysis of the Z-DNA-binding domain Zα of dsRNA adenosine deaminase type I reveals similarity to the (α + β) family of helix-turn-helix proteins. EMBO J. 18, 470-479 (1999).
27. Kahmann, J.D. et al. The solution structure of the N-terminal domain of E3L shows a tyrosine conformation that may explain its reduced affnity to Z-DNA in vitro. Proc. Natl. Acad. Sci. USA 101, 2712-2717 (2004).
28. Athanasiadis, A. et al. The crystal structure of the Zβ domain of the RNA-editing enzyme ADAR1 reveals distinct conserved surfaces among Z-domains. J. Mol. Biol. 351, 496-507 (2005).
29. Riazance, J.H. et al. Evidence for Z-form RNA by vacuum UV circular dichroism. Nucleic Acids Res. 13, 4983-4989 (1985).
30. Schade, M. et al. A 6 bp Z-DNA hairpin binds two Z α domains from the human RNA editing enzyme ADAR1. FEBS Lett. 458, 27-31 (1999).
31. Kang, Y.M. et al. NMR spectroscopic elucidation of the B-Z transition of a DNA double helix induced by the Z α domain of human ADAR1. J. Am. Chem. Soc. 13, 11485-11491 (2009).
32. Dröge, P. Protein tracking-induced supercoiling of DNA: A tool to regulate DNA transactions in vivo? Bioessays 16, 91-99 (1994).
33. Shachrai, I., Zaslaver, A., Alon, U. & Dekel, E. Cost of unneeded proteins in E. coli is reduced after several generations of exponential growth. Mol. Cell 38, 758-767 (2010).
34. Janeway, C.A. Jr. & Medzhitov, R. Innate immune recognition. Annu. Rev. Immunol. 20, 197-216 (2002).
35. Samuel, C.E. Innate immunity minireview series: making biochemical sense of nucleic acid sensors that trigger antiviral innate immunity. J. Biol. Chem. 282, 15313-15314 (2007).
36. Meylan, E., Tschopp, J. & Karin, M. Intracellular pattern recognition receptors in the host response. Nature 442, 39-44 (2006).
37. Williams, B.R. PKR; a sentinel kinase for cellular stress. Oncogene 18, 6112-6120 (1999).
38. Kumar, M. & Carmichael, G.G. Nuclear antisense RNA induces extensive adenosine modifcations and nuclear retention of target transcripts. Proc. Natl. Acad. Sci. USA 94, 3542-3547 (1997).
39. Cattaneo, R. et al. Biased hypermutation and other genetic changes in defective measles viruses in human brain infections. Cell 55, 255-265 (1988).
40. Cattaneo, R. Biased (A 3 I) hypermutation of animal RNA virus genomes. Curr. Opin. Genet. Dev. 4, 895-900 (1994).
41. Zarling, D.A., Calhoun, C.J., Feuerstein, B.G. & Sena, E.P. Cytoplasmic microinjection of immunoglobulin Gs recognizing RNA helices inhibits human cell growth. J. Mol. Biol. 211, 147-160 (1990).
42. Maas, S., Gerber, A.P. & Rich, A. Identifcation and characterization of a human tRNA-specifc adenosine deaminase related to the ADAR family of pre-mRNA editing enzymes. Proc. Natl. Acad. Sci. USA 96, 8895-8900 (1999).
43. Jan, E. & Sarnow, P. Factorless ribosome assembly on the internal ribosome entry site of cricket paralysis virus. J. Mol. Biol. 324, 889-902 (2002).