Antisense RNA regulation in prokaryotes: Rapid RNA/RNA interaction facilitated by a general U-turn loop structure

Journal of Molecular Biology

Volumn 294, Issue 5, 1999, Pages 1115-1125

  Franch, Thomas ^a   Petersen, Michael ^a   Wagner, E Gerhart H ^b   Jacobsen, Jens Peter ^a   Gerdes, Kenn ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^b SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

Author keywords

Antisense RNA; hok mRNA; RNA RNA interaction; Sok RNA; U turn

Indexed keywords

COMPLEMENTARY RNA; ETHYLNITROSOUREA; MESSENGER RNA; PHOSPHATE; PURINE; PYRIMIDINE; TRANSFER RNA;

ANTICODON; ARTICLE; CONTROLLED STUDY; GENE CONTROL; GENE MUTATION; HYDROGEN BOND; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROKARYOTE; RNA STRUCTURE; STEREOCHEMISTRY;

EID: 0033579543     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3306     Document Type: Article

References (58)

1. Asano K., Niimi T., Yokoyama S., Mizobuchi K. Structural basis for binding of the plasmid ColIb-P9 antisense Inc RNA to its target RNA with the 5′-rUUGGCG-3′ motif in the loop sequence. J. Biol. Chem. 273:1998;11826-11838.
2. Ashraf S. S., Ansari G., Guenther R., Sochacka E., Malkiewicz A., Agris P. F. The uridine in "U-turn": contributions to tRNA-ribosomal binding. RNA. 5:1999;503-511.
3. Brantl S., Wagner E. G. H. Antisense RNA-mediated transcriptional attenuation occurs faster than stable antisense/target pairing: an in vitro study of plasmid IP501. EMBO J. 13:1994;3599-3607.
4. Brantl S., Wagner E. G. H. An unusually long-lived antisense RNA in plasmid copy number control: in vivo RNAs encoded by the Streptococcal plasmid pIP501. J. Mol. Biol. 255:1996;275-288.
5. phe. Biochemistry. 25:1986;6372-6378.
6. Citron M., Schuster H. The c4 repressors of bacteriophage P1 and P7 are antisense RNAs. Cell. 62:1990;591-598.
7. Craig M. E., Crothers D. M., Doty P. Relaxation kinetics of dimer formation by self-complementary oligonucleotides. J. Mol. Biol. 62:1971;383-401.
8. del Solar G., Acebo P., Espinosa M. Replication control of plasmid pLS1: the antisense RNAII and the compact rnaII region are involved in the translational regulation of the initiator RepB synthesis. Mol. Microbiol. 23:1997;95-108.
9. phe on the reaction with ribosomes. J. Biol. Chem. 261:1986;10112-10118.
10. Eguchi Y., Tomizawa J.-I. Complex formed by complementary RNA stem-loops and its stabilization by a protein: function of ColE1 Rom protein. Cell. 60:1990;199-209.
11. Eguchi Y., Tomizawa J.-I. Complexes formed by complementary RNA stem-loops. Their formations, structures and interactions with ColE1 Rom protein. J. Mol. Biol. 220:1991;831-842.
12. Eguchi Y., Itoh T., Tomizawa J.-I. Antisense RNA. Annu. Rev. Biochem. 60:1991;631-652.
13. phe. Nature New Biol. 231:1971;126-128.
14. Engdahl H. M., Hjalt T. Å., Wagner E. G. H. A two-unit antisense RNA casette system for silencing of target genes. Nucl. Acids Res. 25:1997;3218-3227.
15. Franch T., Gultyaev A. P., Gerdes K. Programmed cell death by hok/sok of plasmid R1: processing at the hok mRNA 3′ end triggers structural rearrangements that allow translation and antisense RNA binding. J. Mol. Biol. 273:1997;38-51.
16. Franch T., Thisted T., Gerdes K. Ribonuclease III processing of co-axiallly stacked RNA helices. J. Biol. Chem. 274:1999;26572-26578.
17. Fuller W., Hodgson A. Conformation of the anticodon loop of tRNA. Nature. 215:1967;817-821.
18. Gerdes K., Gultyaev A. P., Franch T., Pedersen K., Mikkelsen N. D. Antisense RNA-regulated programmed cell death. Annu. Rev. Genet. 31:1997;1-31.
19. Gregorian R. S., Crothers D. M. Determinants of RNA hairpin loop-loop complex stability. J. Mol. Biol. 248:1995;968-984.
20. Grosjean H., Söll D. G., Crothers D. M. Studies of the complex between transfer RNAs with complementary anticodons. J. Mol. Biol. 103:1976;499-519.
21. Gultyaev A. P., Franch T., Gerdes K. Programmed cell death by hok/sok of plasmid R1: coupled nucleotide co-variations reveal phylogenetically conserved folding pathway in the hok family of mRNAs. J. Mol. Biol. 273:1997;26-37.
22. phe. J. Mol. Biol. 124:1978;523-538.
23. Hjalt T. Å., Wagner E. G. H. Bulged-out nucleotides in an antisense RNA are required for rapid target RNA binding in vitro and inhibition in vivo. Nucl. Acids Res. 23:1995;580-587.
24. 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.
25. Kittle J. D., Simons R. W., Lee J., Kleckner N. Insertion sequence IS10 anti-sense pairing initiates by an interaction between the 5′ end of the target RNA and a loop in the anti-sense RNA. J. Mol. Biol. 210:1989;561-572.
26. Labuda D., Pörschke D. Multistep mechanism of codon recognition by trasnfer ribonucleic acid. Biochemistry. 19:1980;3799-3805.
27. Lacatena R. M., Cesareni G. Interaction between RNAI and the primer precursor in the regulation of ColE1 replication. J. Mol. Biol. 170:1983;635-650.
28. Le Chatelier E., Ehrlich S. D., Lanniere L. Countertranscript-driven attenuator system of the pAMβ1 repE gene. Mol. Microbiol. 20:1996;1099-1112.
29. Novick R. P., Iordanescu S., Projan S. J., Kornblum J., Edelman I. pT181 plasmid replication is regulated by a countertranscript-driven transcriptional attenuator. Cell. 59:1989;395-404.
30. Persson C., Wagner E. G. H., Nordström K. Control of replication of plasmid R1: kinetics of in vitro interaction between the antisense RNA, CopA, and its target, CopT. EMBO J. 7:1988;3279-3288.
31. Persson C., Wagner E. G. H., Nordström K. Control of replication of plasmid R1: formation of an initial transient complex is rate-limiting for antisense RNA-target RNA pairing. EMBO J. 9:1990;3777-3785.
32. Pley H. W., Flaherty K. M., McKay D. B. Three-dimensional structures of a hammerhead ribozyme. Nature. 372:1994;68-74.
33. Puglisi E. V., Puglisi J. D. HIV-1 A-rich RNA loop mimics the tRNA anticodon structure. Nature Struct. Biol. 5:1998;1033-1036.
34. Pörschke D. Elementary steps of base recognition and helix-coil transitions in nucleic acids. Mol. Biol. Biochem. Biophys. 24:1977;191-218.
35. Pörschke D., Eigen M. Co-operative non-enzymatic base recognition. J. Mol. Biol. 62:1971;361-381.
36. Quigley G. J., Rich A. Structural domains of transfer RNA molecules. Science. 194:1976;796-804.
37. Rittner K., Burmeister C., Szakiel G. In vitro selection of fast hybridizing and effective antisense RNAs directed against the human immunodeficiency virus type 1. Nucl. Acids Res. 21:1993;1381-1387.
38. val. J. Mol. Biol. 184:1985;107-118.
39. Saenger W. Principles of Nucleic Acid Structure. 1984;Springer-Verlag, New York.
40. Sambrook J., Fritsh E. J., Maniatis T. Molecular Cloning: A Laboratory Manual. 1989;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
41. Schaefer K. L., McClure W. R. Antisense RNA control of gene expresion in bacteriophage P22: II. Kinetic mechanism and cation specificity of the pairing reaction. RNA. 3:1997;157-174.
42. Schnitzer W., von Ahsen U. Identification of specific Rp-phosphate oxygens in the tRNA anticodon loop required for ribosomal P-site binding. Proc. Natl Acad. Sci. USA. 94:1997;12823-12828.
43. Siemering K. R., Praszkier J., Pittard A. J. Mechanism of binding of the antisense and target RNAs involved in the regulation of the IncB plasmid replication. J. Bacteriol. 176:1994;2677-2688.
44. Simons R. W., Kleckner N. Translational control of IS10 transposition. Cell. 34:1983;673-691.
45. Sprinzl M., Horn C., Ioudovitch A., Steinberg S. Compilation of tRNA sequences and sequences of tRNA genes. Nucl. Acids. Res. 26:1998;148-153.
46. Stallings S. C., Moore P. B. The structure of an essential splicing element: Stem loop IIa from yeast U2 snRNA. Structure. 5:1997;1173-1185.
47. Thisted T., Gerdes K. Mechanism of post-segregational killing by the hok/sok system of plasmid R1: Sok antisense RNA regulates hok gene expression indirectly through the overlapping mok gene. J. Mol. Biol. 223:1992;41-54.
48. Thisted T., Sørensen N. S., Wagner E. G. H., Gerdes K. Mechanism of post-segregational killing: Sok antisense RNA interacts with hok mRNA via its 5′-end singlestranded leader and competes with the 3′-end of hok mRNA for binding to the mok translational initiation region. EMBO J. 13:1994;1960-1968.
49. Tomizawa J.-I. Control of ColE1 plasmid replication: the process of binding of RNAI to the primer transcript. Cell. 38:1984;861-870.
50. Tomizawa J.-I. Evolution of functional RNA structures. Gesteland R. F., Atkins J. F. The RNA World. 1993;419-445 Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
51. Uhlenbeck O. C. Complementary oligonucleotide binding to transfer RNA. J. Mol. Biol. 65:1972;25-41.
52. van Biesen T., Söderbom F., Wagner E. G. H., Frost L. S. Structural and functional analysis of the FinOP antisense RNA system from the F-like conjugative plasmids. Mol. Microbiol. 10:1994;35-43.
53. Wagner E. G. H., Simons R. W. Antisense RNA control in bacteria, phages and plasmids. Annu. Rev. Microbiol. 48:1994;713-742.
54. Weaver K. E., Jensen K. D., Colwell A., Sriam S. L. Functional analysis of the enterococcus faecalis plasmid pAD1-encoded stability determinant par. Mol. Microbiol. 20:1996;53-63.
55. Westhof E., Dumas P., Moras D. Crystallographic refinement of yeast aspartic acid transfer RNA. J. Mol. Biol. 184:1985;119-145.
56. Vlassov V. V., Giege R., Ebel J. P. Tertiary structure of tRNAs in solution monitored by phosphodiester modification with ethylnitrosurea. Eur. J. Biochem. 119:1981;51-59.
57. Yoon K., Turner D. H., Tinoco I. Jr. The kinetics of codon-anticodon interaction in yeast phenylalanine transfer RNA. J. Mol. Biol. 99:1975;507-518.
58. Zeiler B. N., Simons R. W. Antisense RNA structure and function. Grunberg-Manago M., Simons R. W. RNA Structure and Function. 1997;437-464 Cold Spring Harbor Laboratory Press, Cold Spring Harbor.