Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1998 Jul 1;26(13):3242–3246. doi: 10.1093/nar/26.13.3242

Long-range translational coupling in single-stranded RNA bacteriophages: an evolutionary analysis.

N Licis 1, J van Duin 1, Z Balklava 1, V Berzins 1
PMCID: PMC147662  PMID: 9628925

Abstract

In coliphage MS2 RNA a long-distance interaction (LDI) between an internal segment of the upstream coat gene and the start region of the replicase gene prevents initiation of replicase synthesis in the absence of coat gene translation. Elongating ribosomes break up the repressor LDI and thus activate the hidden initiation site. Expression studies on partial MS2 cDNA clones identified base pairing between 1427-1433 and 1738-1744, the so-called Min Jou (MJ) interaction, as the molecular basis for the long-range coupling mechanism. Here, we examine the biological significance of this interaction for the control of replicase gene translation. The LDI was disrupted by mutations in the 3'-side and the evolutionary adaptation was monitored upon phage passaging. Two categories of pseudorevertants emerged. The first type had restored the MJ interaction but not necessarily the native sequence. The pseudorevertants of the second type acquired a compensatory substitution some 80 nt downstream of the MJ interaction that stabilizes an adjacent LDI. In one examined case we confirmed that the second site mutations had restored coat-replicase translational coupling. Our results show the importance of translational control for fitness of the phage. They also reveal that the structure that buries the replicase start extends to structure elements bordering the MJ interaction.

Full Text

The Full Text of this article is available as a PDF (79.9 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Berkhout B., Schmidt B. F., van Strien A., van Boom J., van Westrenen J., van Duin J. Lysis gene of bacteriophage MS2 is activated by translation termination at the overlapping coat gene. J Mol Biol. 1987 Jun 5;195(3):517–524. doi: 10.1016/0022-2836(87)90180-x. [DOI] [PubMed] [Google Scholar]
  2. Berkhout B., de Smit M. H., Spanjaard R. A., Blom T., van Duin J. The amino terminal half of the MS2-coded lysis protein is dispensable for function: implications for our understanding of coding region overlaps. EMBO J. 1985 Dec 1;4(12):3315–3320. doi: 10.1002/j.1460-2075.1985.tb04082.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Berkhout B., van Duin J. Mechanism of translational coupling between coat protein and replicase genes of RNA bacteriophage MS2. Nucleic Acids Res. 1985 Oct 11;13(19):6955–6967. doi: 10.1093/nar/13.19.6955. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Domingo E., Martínez-Salas E., Sobrino F., de la Torre J. C., Portela A., Ortín J., López-Galindez C., Pérez-Breña P., Villanueva N., Nájera R. The quasispecies (extremely heterogeneous) nature of viral RNA genome populations: biological relevance--a review. Gene. 1985;40(1):1–8. doi: 10.1016/0378-1119(85)90017-4. [DOI] [PubMed] [Google Scholar]
  5. Gold L. Posttranscriptional regulatory mechanisms in Escherichia coli. Annu Rev Biochem. 1988;57:199–233. doi: 10.1146/annurev.bi.57.070188.001215. [DOI] [PubMed] [Google Scholar]
  6. Gualerzi C. O., Pon C. L. Initiation of mRNA translation in prokaryotes. Biochemistry. 1990 Jun 26;29(25):5881–5889. doi: 10.1021/bi00477a001. [DOI] [PubMed] [Google Scholar]
  7. Klovins J., Tsareva N. A., de Smit M. H., Berzins V., van Duin J. Rapid evolution of translational control mechanisms in RNA genomes. J Mol Biol. 1997 Jan 31;265(4):372–384. doi: 10.1006/jmbi.1996.0745. [DOI] [PubMed] [Google Scholar]
  8. Kolakofsky D., Weissmann C. Possible mechanism for transition of viral RNA from polysome to replication complex. Nat New Biol. 1971 May 12;231(19):42–46. doi: 10.1038/newbio231042a0. [DOI] [PubMed] [Google Scholar]
  9. Landweber L. F., Kreitman M. Producing single-stranded DNA in polymerase chain reaction for direct genomic sequencing. Methods Enzymol. 1993;218:17–26. doi: 10.1016/0076-6879(93)18004-v. [DOI] [PubMed] [Google Scholar]
  10. Min Jou W., Haegeman G., Ysebaert M., Fiers W. Nucleotide sequence of the gene coding for the bacteriophage MS2 coat protein. Nature. 1972 May 12;237(5350):82–88. doi: 10.1038/237082a0. [DOI] [PubMed] [Google Scholar]
  11. Olsthoorn R. C., 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. doi: 10.1002/j.1460-2075.1994.tb06556.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Poot R. A., Tsareva N. V., Boni I. V., van Duin J. RNA folding kinetics regulates translation of phage MS2 maturation gene. Proc Natl Acad Sci U S A. 1997 Sep 16;94(19):10110–10115. doi: 10.1073/pnas.94.19.10110. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Remaut E., Waele P. D., Marmenout A., Stanssens P., Fiers W. Functional expression of individual plasmid-coded RNA bacteriophage MS2 genes. EMBO J. 1982;1(2):205–209. doi: 10.1002/j.1460-2075.1982.tb01148.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Schmidt B. F., Berkhout B., Overbeek G. P., van Strien A., van Duin J. Determination of the RNA secondary structure that regulates lysis gene expression in bacteriophage MS2. J Mol Biol. 1987 Jun 5;195(3):505–516. doi: 10.1016/0022-2836(87)90179-3. [DOI] [PubMed] [Google Scholar]
  16. Skripkin E. A., Adhin M. R., de Smit M. H., van Duin J. Secondary structure of the central region of bacteriophage MS2 RNA. Conservation and biological significance. J Mol Biol. 1990 Jan 20;211(2):447–463. doi: 10.1016/0022-2836(90)90364-R. [DOI] [PubMed] [Google Scholar]
  17. Skripkin E. A., Jacobson A. B. A two-dimensional model at the nucleotide level for the central hairpin of coliphage Q beta RNA. J Mol Biol. 1993 Sep 20;233(2):245–260. doi: 10.1006/jmbi.1993.1503. [DOI] [PubMed] [Google Scholar]
  18. Witherell G. W., Gott J. M., Uhlenbeck O. C. Specific interaction between RNA phage coat proteins and RNA. Prog Nucleic Acid Res Mol Biol. 1991;40:185–220. doi: 10.1016/s0079-6603(08)60842-9. [DOI] [PubMed] [Google Scholar]
  19. Zuker M. On finding all suboptimal foldings of an RNA molecule. Science. 1989 Apr 7;244(4900):48–52. doi: 10.1126/science.2468181. [DOI] [PubMed] [Google Scholar]
  20. de Smit M. H., van Duin J. Control of prokaryotic translational initiation by mRNA secondary structure. Prog Nucleic Acid Res Mol Biol. 1990;38:1–35. doi: 10.1016/s0079-6603(08)60707-2. [DOI] [PubMed] [Google Scholar]
  21. van Himbergen J., van Geffen B., van Duin J. Translational control by a long range RNA-RNA interaction; a basepair substitution analysis. Nucleic Acids Res. 1993 Apr 25;21(8):1713–1717. doi: 10.1093/nar/21.8.1713. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES