Skip to main content
PMC home page
The EMBO Journal logoLink to The EMBO Journal
. 1989 Nov;8(11):3501–3510. doi: 10.1002/j.1460-2075.1989.tb08515.x

Dual translational initiation sites control function of the lambda S gene.

U Bläsi 1, K Nam 1, D Hartz 1, L Gold 1, R Young 1
PMCID: PMC401507  PMID: 2531079

Abstract

Lysis gene S of phage lambda has a 107 codon reading frame beginning with the codons Met1-Lys2-Met3. Genetic data have suggested that translational initiation occurs at both Met1 and Met3, generating two polypeptides, S107 and S105 respectively. We have proposed a model in which the proper scheduling of lysis depends on the partition of translational initiations between the two start codons. Here, using in vitro methods, we show that two stem-loop structures, one immediately upstream of the reading frame and a second approximately 10 codons within the gene, control the partitioning event. Utilizing primer-extension inhibition or 'toeprinting', we show that the two S start codons are served by two adjacent Shine-Dalgarno sequences. Moreover, the timing of lysis supported by the wild-type and a number of mutant alleles in vivo can be correlated with the ratio of ternary complex formation over Met1 and Met3 in vitro. Thus the regulation of the S gene is unique in that the products of two adjacent in-frame initiation events have opposing function.

Full text

PDF
3505

Images in this article

3502Image
on p.3502
3503Image
on p.3503
3504Image
on p.3504
3505Image
on p.3505
3506Image
on p.3506

Selected References

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

  1. Altman E., Young K., Garrett J., Altman R., Young R. Subcellular localization of lethal lysis proteins of bacteriophages lambda and phiX174. J Virol. 1985 Mar;53(3):1008–1011. doi: 10.1128/jvi.53.3.1008-1011.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bienkowska-Szewczyk K., Lipinska B., Taylor A. The R gene product of bacteriophage lambda is the murein transglycosylase. Mol Gen Genet. 1981;184(1):111–114. doi: 10.1007/BF00271205. [DOI] [PubMed] [Google Scholar]
  3. Dunn J. J., Studier F. W. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. J Mol Biol. 1983 Jun 5;166(4):477–535. doi: 10.1016/s0022-2836(83)80282-4. [DOI] [PubMed] [Google Scholar]
  4. Freier S. M., Kierzek R., Jaeger J. A., Sugimoto N., Caruthers M. H., Neilson T., Turner D. H. Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci U S A. 1986 Dec;83(24):9373–9377. doi: 10.1073/pnas.83.24.9373. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Garrett J. M., Young R. Lethal action of bacteriophage lambda S gene. J Virol. 1982 Dec;44(3):886–892. doi: 10.1128/jvi.44.3.886-892.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. 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]
  7. Gold L., Pribnow D., Schneider T., Shinedling S., Singer B. S., Stormo G. Translational initiation in prokaryotes. Annu Rev Microbiol. 1981;35:365–403. doi: 10.1146/annurev.mi.35.100181.002053. [DOI] [PubMed] [Google Scholar]
  8. Grantham R., Gautier C., Gouy M. Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Res. 1980 May 10;8(9):1893–1912. doi: 10.1093/nar/8.9.1893. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Hall M. N., Gabay J., Débarbouillé M., Schwartz M. A role for mRNA secondary structure in the control of translation initiation. Nature. 1982 Feb 18;295(5850):616–618. doi: 10.1038/295616a0. [DOI] [PubMed] [Google Scholar]
  10. Halling S. M., Simons R. W., Way J. C., Walsh R. B., Kleckner N. DNA sequence organization of IS10-right of Tn10 and comparison with IS10-left. Proc Natl Acad Sci U S A. 1982 Apr;79(8):2608–2612. doi: 10.1073/pnas.79.8.2608. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hartz D., McPheeters D. S., Traut R., Gold L. Extension inhibition analysis of translation initiation complexes. Methods Enzymol. 1988;164:419–425. doi: 10.1016/s0076-6879(88)64058-4. [DOI] [PubMed] [Google Scholar]
  12. Herskowitz I., Hagen D. The lysis-lysogeny decision of phage lambda: explicit programming and responsiveness. Annu Rev Genet. 1980;14:399–445. doi: 10.1146/annurev.ge.14.120180.002151. [DOI] [PubMed] [Google Scholar]
  13. Itakura K., Hirose T., Crea R., Riggs A. D., Heyneker H. L., Bolivar F., Boyer H. W. Expression in Escherichia coli of a chemically synthesized gene for the hormone somatostatin. Science. 1977 Dec 9;198(4321):1056–1063. doi: 10.1126/science.412251. [DOI] [PubMed] [Google Scholar]
  14. Konigsberg W., Godson G. N. Evidence for use of rare codons in the dnaG gene and other regulatory genes of Escherichia coli. Proc Natl Acad Sci U S A. 1983 Feb;80(3):687–691. doi: 10.1073/pnas.80.3.687. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kunkel T. A., Roberts J. D., Zakour R. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol. 1987;154:367–382. doi: 10.1016/0076-6879(87)54085-x. [DOI] [PubMed] [Google Scholar]
  16. McPheeters D. S., Christensen A., Young E. T., Stormo G., Gold L. Translational regulation of expression of the bacteriophage T4 lysozyme gene. Nucleic Acids Res. 1986 Jul 25;14(14):5813–5826. doi: 10.1093/nar/14.14.5813. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. McPheeters D. S., Stormo G. D., Gold L. Autogenous regulatory site on the bacteriophage T4 gene 32 messenger RNA. J Mol Biol. 1988 Jun 5;201(3):517–535. doi: 10.1016/0022-2836(88)90634-1. [DOI] [PubMed] [Google Scholar]
  18. Messing J., Crea R., Seeburg P. H. A system for shotgun DNA sequencing. Nucleic Acids Res. 1981 Jan 24;9(2):309–321. doi: 10.1093/nar/9.2.309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Munson L. M., Stormo G. D., Niece R. L., Reznikoff W. S. lacZ translation initiation mutations. J Mol Biol. 1984 Aug 25;177(4):663–683. doi: 10.1016/0022-2836(84)90043-3. [DOI] [PubMed] [Google Scholar]
  20. Raab R., Neal G., Garrett J., Grimaila R., Fusselman R., Young R. Mutational analysis of bacteriophage lambda lysis gene S. J Bacteriol. 1986 Sep;167(3):1035–1042. doi: 10.1128/jb.167.3.1035-1042.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Raab R., Neal G., Sohaskey C., Smith J., Young R. Dominance in lambda S mutations and evidence for translational control. J Mol Biol. 1988 Jan 5;199(1):95–105. doi: 10.1016/0022-2836(88)90381-6. [DOI] [PubMed] [Google Scholar]
  22. Reader R. W., Siminovitch L. Lysis defective mutants of bacteriophage lambda: on the role of the S function in lysis. Virology. 1971 Mar;43(3):623–637. doi: 10.1016/0042-6822(71)90287-x. [DOI] [PubMed] [Google Scholar]
  23. Remaut E., Stanssens P., Fiers W. Plasmid vectors for high-efficiency expression controlled by the PL promoter of coliphage lambda. Gene. 1981 Oct;15(1):81–93. doi: 10.1016/0378-1119(81)90106-2. [DOI] [PubMed] [Google Scholar]
  24. Rennell D., Poteete A. R. Phage P22 lysis genes: nucleotide sequences and functional relationships with T4 and lambda genes. Virology. 1985 May;143(1):280–289. doi: 10.1016/0042-6822(85)90115-1. [DOI] [PubMed] [Google Scholar]
  25. Rothstein S. J., Jorgensen R. A., Postle K., Reznikoff W. S. The inverted repeats of Tn5 are functionally different. Cell. 1980 Mar;19(3):795–805. doi: 10.1016/s0092-8674(80)80055-9. [DOI] [PubMed] [Google Scholar]
  26. 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]
  27. Shapira S. K., Chou J., Richaud F. V., Casadaban M. J. New versatile plasmid vectors for expression of hybrid proteins coded by a cloned gene fused to lacZ gene sequences encoding an enzymatically active carboxy-terminal portion of beta-galactosidase. Gene. 1983 Nov;25(1):71–82. doi: 10.1016/0378-1119(83)90169-5. [DOI] [PubMed] [Google Scholar]
  28. Shine J., Dalgarno L. The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci U S A. 1974 Apr;71(4):1342–1346. doi: 10.1073/pnas.71.4.1342. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Smith R. A., Parkinson J. S. Overlapping genes at the cheA locus of Escherichia coli. Proc Natl Acad Sci U S A. 1980 Sep;77(9):5370–5374. doi: 10.1073/pnas.77.9.5370. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Stanssens P., Remaut E., Fiers W. Alterations upstream from the Shine-Dalgarno region and their effect on bacterial gene expression. Gene. 1985;36(3):211–223. doi: 10.1016/0378-1119(85)90176-3. [DOI] [PubMed] [Google Scholar]
  31. Wilson D. B. Effect of the lambda S gene product on properties of the Escherichia coli inner membrane. J Bacteriol. 1982 Sep;151(3):1403–1410. doi: 10.1128/jb.151.3.1403-1410.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Winter R. B., Morrissey L., Gauss P., Gold L., Hsu T., Karam J. Bacteriophage T4 regA protein binds to mRNAs and prevents translation initiation. Proc Natl Acad Sci U S A. 1987 Nov;84(22):7822–7826. doi: 10.1073/pnas.84.22.7822. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Young K. D., Young R. Lytic action of cloned phi X174 gene E. J Virol. 1982 Dec;44(3):993–1002. doi: 10.1128/jvi.44.3.993-1002.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Young R., Way J., Way S., Yin J., Syvanen M. Transposition mutagenesis of bacteriophage lambda: a new gene affecting cell lysis. J Mol Biol. 1979 Aug 15;132(3):307–322. doi: 10.1016/0022-2836(79)90262-6. [DOI] [PubMed] [Google Scholar]

Articles from The EMBO Journal are provided here courtesy of Nature Publishing Group

RESOURCES