• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of rnaThe RNA SocietyeTOC AlertsSubscriptionsJournal HomeCSHL PressRNA
RNA. Aug 1998; 4(8): 948–957.
PMCID: PMC1369672

A long-range interaction in Qbeta RNA that bridges the thousand nucleotides between the M-site and the 3' end is required for replication.


The genome of the positive strand RNA bacteriophage Qbeta folds into a number of structural domains, defined by long-distance interactions. The RNA within each domain is ordered in arrays of three- and four-way junctions that confer rigidity to the chain. One such domain, RD2, is about 1,000-nt long and covers most of the replicase gene. Its downstream border is the 3' untranslated region, whereas upstream the major binding site for Qbeta replicase, the M-site, is located. Replication of Qbeta RNA has always been puzzling because the binding site for the enzyme lies some 1,500-nt away from the 3' terminus. We present evidence that the long-range interaction defining RD2 exists and positions the 3' terminus in the vicinity of the replicase binding site. The model is based on several observations. First, mutations destabilizing the long-range interaction are virtually lethal to the phage, whereas base pair substitutions have little effect. Secondly, in vitro analysis shows that destabilizing the long-range pairing abolishes replication of the plus strand. Thirdly, passaging of nearly inactive mutant phages results in the selection of second-site suppressor mutations that restore both long-range base pairing and replication. The data are interpreted to mean that the 3D organization of this part of Qbeta RNA is essential to its replication. We propose that, when replicase is bound to the internal recognition site, the 3' terminus of the template is juxtaposed to the enzyme's active site.

Full Text

The Full Text of this article is available as a PDF (309K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Barrera I, Schuppli D, Sogo JM, Weber H. Different mechanisms of recognition of bacteriophage Q beta plus and minus strand RNAs by Q beta replicase. J Mol Biol. 1993 Jul 20;232(2):512–521. [PubMed]
  • Beekwilder J, Nieuwenhuizen R, Poot R, van Duin J. Secondary structure model for the first three domains of Q beta RNA. Control of A-protein synthesis. J Mol Biol. 1996 Feb 16;256(1):8–19. [PubMed]
  • Beekwilder MJ, Nieuwenhuizen R, van Duin J. Secondary structure model for the last two domains of single-stranded RNA phage Q beta. J Mol Biol. 1995 Apr 14;247(5):903–917. [PubMed]
  • Biebricher CK, Luce R. In vitro recombination and terminal elongation of RNA by Q beta replicase. EMBO J. 1992 Dec;11(13):5129–5135. [PMC free article] [PubMed]
  • Blumenthal T, Carmichael GG. RNA replication: function and structure of Qbeta-replicase. Annu Rev Biochem. 1979;48:525–548. [PubMed]
  • Boni IV, Isaeva DM, Musychenko ML, Tzareva NV. Ribosome-messenger recognition: mRNA target sites for ribosomal protein S1. Nucleic Acids Res. 1991 Jan 11;19(1):155–162. [PMC free article] [PubMed]
  • Brown L, Elliott T. Mutations that increase expression of the rpoS gene and decrease its dependence on hfq function in Salmonella typhimurium. J Bacteriol. 1997 Feb;179(3):656–662. [PMC free article] [PubMed]
  • Brown D, Gold L. RNA replication by Q beta replicase: a working model. Proc Natl Acad Sci U S A. 1996 Oct 15;93(21):11558–11562. [PMC free article] [PubMed]
  • Bycroft M, Hubbard TJ, Proctor M, Freund SM, Murzin AG. The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold. Cell. 1997 Jan 24;88(2):235–242. [PubMed]
  • Haugel-Nielsen J, Hajnsdorf E, Regnier P. The rpsO mRNA of Escherichia coli is polyadenylated at multiple sites resulting from endonucleolytic processing and exonucleolytic degradation. EMBO J. 1996 Jun 17;15(12):3144–3152. [PMC free article] [PubMed]
  • Ho SN, Hunt HD, Horton RM, Pullen JK, Pease LR. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene. 1989 Apr 15;77(1):51–59. [PubMed]
  • Jacobson AB. Secondary structure of coliphage Q beta RNA. Analysis by electron microscopy. J Mol Biol. 1991 Sep 20;221(2):557–570. [PubMed]
  • Jacobson AB, Zuker M. Structural analysis by energy dot plot of a large mRNA. J Mol Biol. 1993 Sep 20;233(2):261–269. [PubMed]
  • Klovins J, van Duin J, Olsthoorn RC. Rescue of the RNA phage genome from RNase III cleavage. Nucleic Acids Res. 1997 Nov 1;25(21):4201–4208. [PMC free article] [PubMed]
  • Mans RM, Pleij CW, Bosch L. tRNA-like structures. Structure, function and evolutionary significance. Eur J Biochem. 1991 Oct 15;201(2):303–324. [PubMed]
  • Meyer F, Weber H, Weissmann C. Interactions of Q beta replicase with Q beta RNA. J Mol Biol. 1981 Dec 15;153(3):631–660. [PubMed]
  • Miranda G, Schuppli D, Barrera I, Hausherr C, Sogo JM, Weber H. Recognition of bacteriophage Qbeta plus strand RNA as a template by Qbeta replicase: role of RNA interactions mediated by ribosomal proteins S1 and host factor. J Mol Biol. 1997 Apr 18;267(5):1089–1103. [PubMed]
  • Muffler A, Traulsen DD, Fischer D, Lange R, Hengge-Aronis R. The RNA-binding protein HF-I plays a global regulatory role which is largely, but not exclusively, due to its role in expression of the sigmaS subunit of RNA polymerase in Escherichia coli. J Bacteriol. 1997 Jan;179(1):297–300. [PMC free article] [PubMed]
  • Olsthoorn RC, Licis N, van Duin J. Leeway and constraints in the forced evolution of a regulatory RNA helix. EMBO J. 1994 Jun 1;13(11):2660–2668. [PMC free article] [PubMed]
  • Olsthoorn RC, van Duin J. Random removal of inserts from an RNA genome: selection against single-stranded RNA. J Virol. 1996 Feb;70(2):729–736. [PMC free article] [PubMed]
  • Schuppli D, Miranda G, Tsui HC, Winkler ME, Sogo JM, Weber H. Altered 3'-terminal RNA structure in phage Qbeta adapted to host factor-less Escherichia coli. Proc Natl Acad Sci U S A. 1997 Sep 16;94(19):10239–10242. [PMC free article] [PubMed]
  • Subramanian AR. Structure and functions of ribosomal protein S1. Prog Nucleic Acid Res Mol Biol. 1983;28:101–142. [PubMed]
  • Taniguchi T, Palmieri M, Weissmann C. QB DNA-containing hybrid plasmids giving rise to QB phage formation in the bacterial host. Nature. 1978 Jul 20;274(5668):223–228. [PubMed]
  • Tsui HC, Leung HC, Winkler ME. Characterization of broadly pleiotropic phenotypes caused by an hfq insertion mutation in Escherichia coli K-12. Mol Microbiol. 1994 Jul;13(1):35–49. [PubMed]
  • van Rossum CM, Brederode FT, Neeleman L, Bol JF. Functional equivalence of common and unique sequences in the 3' untranslated regions of alfalfa mosaic virus RNAs 1, 2, and 3. J Virol. 1997 May;71(5):3811–3816. [PMC free article] [PubMed]
  • Weber H, Billeter MA, Kahane S, Weissmann C, Hindley J, Porter A. Molecular basis for repressor activity of Q replicase. Nat New Biol. 1972 Jun 7;237(75):166–170. [PubMed]
  • Xu F, Lin-Chao S, Cohen SN. The Escherichia coli pcnB gene promotes adenylylation of antisense RNAI of ColE1-type plasmids in vivo and degradation of RNAI decay intermediates. Proc Natl Acad Sci U S A. 1993 Jul 15;90(14):6756–6760. [PMC free article] [PubMed]
  • Yonesaki T, Furuse K, Haruna I, Watanabe I. Relationships among four groups of RNA coliphages based on the template specificity of GA replicase. Virology. 1982 Jan 15;116(1):379–381. [PubMed]

Articles from RNA are provided here courtesy of The RNA Society


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


  • PubMed
    PubMed citations for these articles

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...