An unusual structure formed by antisense-target rna binding involves an extended kissing complex with a four-way junction and a side-by-side helical alignment

RNA

Volumn 6, Issue 3, 2000, Pages 311-324

  Kolb, Fabrice A ^a   Malmgren, Charlotta ^c   Westhof, Eric ^a   Ehresmann, Chantal ^a   Ehresmann, Bernard ^a   Wagner, E Gerhart H ^b   Romby, Pascale ^a  

^a INSTITUT DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

^b SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^c UPPSALA UNIVERSITY   (Sweden)

Author keywords

Antisense RNA; Chemical mapping; RNA modeling; RNA structure; RNA RNA interaction

Indexed keywords

COMPLEMENTARY RNA;

ARTICLE; COMPLEX FORMATION; COMPUTER MODEL; MOLECULAR INTERACTION; MUTATION; PRIORITY JOURNAL; RNA BINDING; RNA CONFORMATION; RNA STRUCTURE; STRUCTURE ANALYSIS;

BACTERIAL PROTEINS; BASE PAIRING; BASE SEQUENCE; BINDING SITES; CATIONS, DIVALENT; COMPUTER SIMULATION; METALS, HEAVY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA STABILITY; RNA, ANTISENSE; RNA, DOUBLE-STRANDED; RNA, MESSENGER; RNA, SPLICED LEADER;

EID: 0034106753     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S135583820099215X     Document Type: Article

References (49)

1. Asano K, Mizobuchi K. 1998. An RNA pseudoknot as the molecular switch for translation of the repZ gene encoding the replication initiator of the Inclα plasmid Collb-P9. J Biol Chem 273:11815-11825.
2. Asano K, Niimi T, Yokoyama S, Mizobuchi K. 1998. Structural basis for binding of the plasmid Collb-P9 antisense Inc RNA to its target RNA with the 5′-rUUGGCG-3′ motif in the loop sequence. J Biol Chem 273:11826-11838.
3. Blomberg P, Engdahl HM, Malmgren C, Romby P, Wagner EGH. 1994. Replication control of plasmid R1:Disruption of an inhibitory RNA structure that sequesters the repA ribosome binding site permits tap-independent RepA synthesis. Mol Microbiol 12: 49-60.
4. Blomberg P, Nordström K, Wagner EGH. 1992. Replication control of plasmid R1:RepA synthesis is regulated by CopA RNA through inhibition of leader peptide translation. EMBO J 11:2675-2683.
5. Blomberg P, Wagner EGH, Nordström K. 1990. Control of replication of plasmid R1:The duplex between the antisense RNA, CopA, and its target, CopT, is processed specifically in vivo and in vitro by RNase III. EMBO J 9:2331-2340.
6. Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Kundrot GE, Cech TR, Doudna J. 1996. Crystal structure of a group 1 ribozyme domain:Principles of RNA packing. Science 273:1678-1685.
7. Chen X, Woodson SA, Burrows CJ, Rokita SE. 1993. A highly sensitive probe for guanine N7 in folded structures of RNA:Application to tRNA-Phe and Tetrahymena group I intron. Biochemistry 32:7610-7616.
8. Donis-Keller H, Maxam AM, Gilbert W. 1977. Mapping adenines, guanines, and pyrimidines in RNA. Nucleic Acids Res 4:2527-2538.
9. Duckett DR, Murchie AIH, Bhattacharyya A, Clegg RM, Diekmann S, Kitzing E, Lilley DMJ. 1992. The structure of DNA junctions and their interaction with enzymes. Eur J Biochem 207:285-295.
10. Earnshaw DJ, Masquida B, Müller S, Sigurdsson STh, Eckstein F, Westhof E, Gait M. 1997 Inter-domain cross-linking and molecular modeling of the hairpin ribozyme. J Mol Biol 274:197-212.
11. Eguchi Y, Itoh T, Tomizawa J. 1991. Antisense RNA. Annu Rev Biochem 60:631-652.
12. Eguchi Y, Tomizawa J. 1991. Complexes formed by complementary RNA stem-loops. Their formations, structures and interactions with ColE1 Rom protein. J Mol Biol 220:831-842.
13. Ehresmann C, Baudin F, Mougel M, Romby P, Ebel JP, Ehresmann B. 1987. Probing the structure of RNAs in solution. Nucleic Acids Res 16:9109-9128.
14. England TE, Uhlenbeck OC. 1978. 3′-terminal labeling of RNA with T4 RNA ligase. Nature 275:560-561.
15. Hermann T, Westhof E. 1998. Exploration of metal ion binding sites in RNA folds by Brownian-dynamics simulations. Structure 15: 1303-1314.
16. Hjalt T, Wagner EGH. 1992. The effect of loop size in antisense and target RNAs on the efficiency of antisense RNA control. Nucleic Acids Res 20:6723-6732.
17. Hjalt T, Wagner EGH. 1995. Bulged-out nucleotides in an antisense RNA are required for rapid target RNA binding in vitro and inhibition in vivo. Nucleic Acids Res 23:571-579.
18. Kittle JD, Simons RW, Lee Y, Kleckner N. 1989. Insertion sequence IS10 antisense pairing initiates by an interaction between the 5′ end of the target RNA and a loop in the antisense RNA. J Mol Biol 210:561-572.
19. Krol A, Westhof E, Bach M, Lührmann R, Ebel JP, Carbon P. 1990. Solution structure of human U1 snRNA:Derivation of a possible three-dimensional model. Nucleic Acids Res 18:3803-3811.
20. Latham JA, Cech TR. 1989. Defining the inside and outside of a catalytic RNA molecule. Science 245:276-282.
21. Lee AJ, Crothers DM. 1998. The solution structure of an RNA loop-loop complex:The ColE1 inverted loop sequence. Structure 6:993-1005.
22. Malmgren C, Engdahl H, Romby P, Wagner EGH. 1996. An antisense/ target RNA duplex or a strong intramolecular RNA structure 5′ of a translation initiation signal blocks ribosome binding:The case of plasmid R1. RNA 2:1022-1032.
23. Malmgren C, Wagner EGH, Ehresmann C, Ehresmann B, Romby P. 1997. Antisense RNA control of plasmid R1 replication:The dominant product of the antisense RNA-mRNA binding is not a full RNA duplex. J Biol Chem 19:12508-12512.
24. Maniatis T, Fritsch EF, Sambrook J. 1982. Molecular cloning:A laboratory manual. Cold Spring Harbor, New York:Cold Spring Harbor Laboratory Press.
25. Marino JP, Gregorian RS, Csankovski G, Crothers DM. 1995. Bent helix formation between RNA hairpins with complementary loops. Science 268:1448-1454.
26. Massire C, Gaspin C, Westhof E. 1994. A program for drawing schematic views of nucleic acids. J Mol Graph 12:201-206.
27. Massire C, Westhof E. 1998. MANIP:An interactive tool for the modeling of ribonucleic acids. J Mol Graph 16:197-205.
28. Nowakowski J, Shim PJ, Prasad GS, Stout CD, Joyce GF 1999. Crystal structure of an 82-nucleotide RNA-DNA complex formed by the 10-23 DNA enzyme. Nat Struct Biol 6:151-156.
29. Öhman M, Wagner EGH. 1989. Secondary structure analysis of the RepA mRNA leader transcript involved in control of plasmid R1. Nucleic Acids Res 17:2557-2579.
30. Pan T, Long DM, Uhlenbeck OC. 1993. Divalent metal ions in RNA folding and catalysis. In:Gesteland RF, Atkins JF, eds. The RNA world. Cold Spring Harbor, New York:Cold Spring Harbor Laboratory Press, pp 271-302.
31. Peattie DA, Gilbert W. 1980. Chemical probes for higher-order structure in RNA. Proc Natl Acad Sci USA 77:4679-4682.
32. Persson C, Wagner EGH, Nordström K. 1988. Control of replication of plasmid R1:Kinetics of in vitro interaction between the antisense RNA, CopA, and its target, CopT. EMBO J 7:3279-3288.
33. Persson C, Wagner EGH, Nordström K. 1990a. Control of replication of plasmid R1:Structures and sequences of the antisense RNA, CopA, required for its binding to the target RNA, CopT. EMBO J 9:3767-3775.
34. Persson C, Wagner EGH, Nordström K. 1990b. Control of replication of plasmid R1:Formation of an initial transient complex is rate-limiting for antisense RNA-target RNA pairing. EMBO J 9:3777-3785.
35. Serganov A, Rak A, Garber M, Reinbolt J, Ehresmann B, Ehresmann C, Grunberg-Manago M, Portier C. 1997. Ribosomal protein S15 from Thermus thermophilus:Cloning, sequencing, overexpression of the gene and RNA-binding properties of the protein. Eur J Biochem 246:291-300.
36. Siemering KR, Praszkier J, Pittard AJ. 1994. Mechanism of binding of the antisense and target RNAs involved in the regulation of IncB plasmid replication. J Bacteriol 176:2677-2688.
37. Söderbom F, Binnie U, Masters M, Wagner EGH. 1997. Regulation of plasmid R1 replication:PcnB and RNase E expedite the decay of the antisense RNA, CopA. Mol Microbiol 26:493-504.
38. Thisted T, Sørensen NS, Wagner EGH, Gerdes K. 1994. Mechanism of post-segregational killing:Sok antisense RNA interacts with Hok mRNA via its 5′-end single-stranded leader and competes with the 3′ end of Hok mRNA for binding to the mok translational initiation region. EMBO J 73:1960-1968.
39. Tomizawa J. 1990. Control of ColE1 plasmid replication. Interaction of Rom protein with an unstable complex formed by RNA I and RNA II. J Mol Biol 272:695-708.
40. Wagner EGH, Blomberg P, Nordström K. 1992. Replication control in plasmid R1:Duplex formation between the antisense RNA, CopA, and its target, CopT, is not required for inhibition of RepA synthesis. EMBO J 11:1195-1203.
41. Wagner EGH, Brantl S. 1998. Kissing and RNA stability in antisense control of plasmid replication. Trends Biochem Sci 23:451-454.
42. Wagner EGH, Simons RW. 1994. Antisense RNA control in bacteria, phages, and plasmids. Annu Rev Microbiol 48:713-742.
43. Walter F, Murchie AIH, Lilley DMJ. 1998a. Folding of the four-way RNA junction of the hairpin ribozyme. Biochemistry 37:17629-17636.
44. Walter F, Murchie AIH, Thomson JB, Lilley DMJ. 1998b. Structure and activity of the hairpin ribozyme in its natural junction conformation:Effect of metal ions. Biochemistry 37:14195-14203.
45. Weeks KM, Crothers DM. 1993. Major groove accessibility of RNA. Science 261:1574-1577.
46. Westhof E. 1993. Modeling the three-dimensional structure of ribonucleic acids. J Mol Struct 286:203-211.
47. Westhof E, Romby P, Romaniuk PR, Ebel JP, Ehresmann C, Ehresmann B. 1989. Computer modeling from solution data of spinach chloroplast and X. laevis somatic and oocyte 5S rRNAs. J Mol Biol 207:417-431.
48. Wilson IW, Praszkier J, Pittard AJ. 1993. Mutations affecting pseudo-knot control of the replication of B group plasmids. J Bacteriol 175:6476-6483.
49. Zeiler BN, Simons RW. 1998. Antisense RNA structure and function. In:Simons RW, Grunberg-Manago M, eds. RNA structure and function. Cold Spring Harbor, New York:Cold Spring Harbor Laboratory Press. pp 437-464.