Skip to main content
NCBI home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1989 Jan;171(1):588–592. doi: 10.1128/jb.171.1.588-592.1989

Retroregulation of the bacteriophage lambda int gene: limited secondary degradation of the RNase III-processed transcript.

G Plunkett 3rd 1, H Echols 1
PMCID: PMC209629  PMID: 2521618

Abstract

Expression of the int gene of bacteriophage lambda from two promoters, pI and pL, is differentially regulated through RNA processing. Efficient Int protein synthesis from the pL RNA is inhibited by the action of sib, a cis-acting retroregulator downstream from the int gene. We have used mapping procedures with nuclease S1 to study the pL transcripts produced in vivo after phage lambda infection. We have found an RNase III-dependent processing site within the Int coding sequence, 387 nucleotides upstream from the site of the primary cleavage by RNase III at Sib. This secondary processing site is located at the most stable region of secondary structure in the sib int region, as predicted by computer analysis. We suggest that RNase III cleavage at the Sib site allows processive exonucleolytic degradation of the RNA to proceed to a region of secondary structure within the Int coding sequence, which protects the upstream region of the transcript from further degradation.

Full text

PDF
588

Images in this article

589Image
on p.589
590Image
on p.590

Selected References

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

  1. Barry G., Squires C., Squires C. L. Attenuation and processing of RNA from the rplJL--rpoBC transcription unit of Escherichia coli. Proc Natl Acad Sci U S A. 1980 Jun;77(6):3331–3335. doi: 10.1073/pnas.77.6.3331. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Belasco J. G., Beatty J. T., Adams C. W., von Gabain A., Cohen S. N. Differential expression of photosynthesis genes in R. capsulata results from segmental differences in stability within the polycistronic rxcA transcript. Cell. 1985 Jan;40(1):171–181. doi: 10.1016/0092-8674(85)90320-4. [DOI] [PubMed] [Google Scholar]
  3. Belfort M. The cII-independent expression of the phage lambda int gene in RNase III-defective E. coli. Gene. 1980 Oct;11(1-2):149–155. doi: 10.1016/0378-1119(80)90094-3. [DOI] [PubMed] [Google Scholar]
  4. Berk A. J., Sharp P. A. Spliced early mRNAs of simian virus 40. Proc Natl Acad Sci U S A. 1978 Mar;75(3):1274–1278. doi: 10.1073/pnas.75.3.1274. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Burton Z. F., Gross C. A., Watanabe K. K., Burgess R. R. The operon that encodes the sigma subunit of RNA polymerase also encodes ribosomal protein S21 and DNA primase in E. coli K12. Cell. 1983 Feb;32(2):335–349. doi: 10.1016/0092-8674(83)90453-1. [DOI] [PubMed] [Google Scholar]
  6. Cannistraro V. J., Subbarao M. N., Kennell D. Specific endonucleolytic cleavage sites for decay of Escherichia coli mRNA. J Mol Biol. 1986 Nov 20;192(2):257–274. doi: 10.1016/0022-2836(86)90363-3. [DOI] [PubMed] [Google Scholar]
  7. Court D., Huang T. F., Oppenheim A. B. Deletion analysis of the retroregulatory site for the lambda int gene. J Mol Biol. 1983 May 15;166(2):233–240. doi: 10.1016/s0022-2836(83)80010-2. [DOI] [PubMed] [Google Scholar]
  8. Donovan W. P., Kushner S. R. Polynucleotide phosphorylase and ribonuclease II are required for cell viability and mRNA turnover in Escherichia coli K-12. Proc Natl Acad Sci U S A. 1986 Jan;83(1):120–124. doi: 10.1073/pnas.83.1.120. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Epp C., Pearson M. L., Enquist L. Downstream regulation of int gene expression by the b2 region in phage lambda. Gene. 1981 May;13(4):327–337. doi: 10.1016/0378-1119(81)90012-3. [DOI] [PubMed] [Google Scholar]
  10. Gegenheimer P., Apirion D. Processing of procaryotic ribonucleic acid. Microbiol Rev. 1981 Dec;45(4):502–541. doi: 10.1128/mr.45.4.502-541.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Gottesman M., Oppenheim A., Court D. Retroregulation: control of gene expression from sites distal to the gene. Cell. 1982 Jul;29(3):727–728. doi: 10.1016/0092-8674(82)90434-2. [DOI] [PubMed] [Google Scholar]
  12. Guarneros G., Galindo J. M. The regulation of integrative recombination by the b2 region and the cII gene of bacteriophage lambda. Virology. 1979 May;95(1):119–126. doi: 10.1016/0042-6822(79)90406-9. [DOI] [PubMed] [Google Scholar]
  13. Guarneros G., Montañez C., Hernandez T., Court D. Posttranscriptional control of bacteriophage lambda gene expression from a site distal to the gene. Proc Natl Acad Sci U S A. 1982 Jan;79(2):238–242. doi: 10.1073/pnas.79.2.238. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Hyman H. C., Honigman A. Transcription termination and processing sites in the bacteriophage lambda pL operon. J Mol Biol. 1986 May 5;189(1):131–141. doi: 10.1016/0022-2836(86)90386-4. [DOI] [PubMed] [Google Scholar]
  15. King T. C., Sirdeskmukh R., Schlessinger D. Nucleolytic processing of ribonucleic acid transcripts in procaryotes. Microbiol Rev. 1986 Dec;50(4):428–451. doi: 10.1128/mr.50.4.428-451.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kinscherf T. G., Apirion D. Polynucleotide phosphorylase can participate in decay of mRNA in Escherichia coli in the absence of ribonuclease II. Mol Gen Genet. 1975 Sep 8;139(4):357–362. doi: 10.1007/BF00267975. [DOI] [PubMed] [Google Scholar]
  17. Klug G., Adams C. W., Belasco J., Doerge B., Cohen S. N. Biological consequences of segmental alterations in mRNA stability: effects of deletion of the intercistronic hairpin loop region of the Rhodobacter capsulatus puf operon. EMBO J. 1987 Nov;6(11):3515–3520. doi: 10.1002/j.1460-2075.1987.tb02677.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Lauer G., Pastrana R., Sherley J., Ptashne M. Construction of overproducers of the bacteriophage 434 repressor and cro proteins. J Mol Appl Genet. 1981;1(2):139–147. [PubMed] [Google Scholar]
  19. Martinez H. M. An RNA folding rule. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):323–334. doi: 10.1093/nar/12.1part1.323. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  21. Montañez C., Bueno J., Schmeissner U., Court D. L., Guarneros G. Mutations of bacteriophage lambda that define independent but overlapping RNA processing and transcription termination sites. J Mol Biol. 1986 Sep 5;191(1):29–37. doi: 10.1016/0022-2836(86)90420-1. [DOI] [PubMed] [Google Scholar]
  22. Mott J. E., Galloway J. L., Platt T. Maturation of Escherichia coli tryptophan operon mRNA: evidence for 3' exonucleolytic processing after rho-dependent termination. EMBO J. 1985 Jul;4(7):1887–1891. doi: 10.1002/j.1460-2075.1985.tb03865.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Newbury S. F., Smith N. H., Robinson E. C., Hiles I. D., Higgins C. F. Stabilization of translationally active mRNA by prokaryotic REP sequences. Cell. 1987 Jan 30;48(2):297–310. doi: 10.1016/0092-8674(87)90433-8. [DOI] [PubMed] [Google Scholar]
  24. Panayotatos N., Truong K. Cleavage within an RNase III site can control mRNA stability and protein synthesis in vivo. Nucleic Acids Res. 1985 Apr 11;13(7):2227–2240. doi: 10.1093/nar/13.7.2227. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Salser W., Gesteland R. F., Bolle A. In vitro synthesis of bacteriophage lysozyme. Nature. 1967 Aug 5;215(5101):588–591. doi: 10.1038/215588a0. [DOI] [PubMed] [Google Scholar]
  26. Schindler D., Echols H. Retroregulation of the int gene of bacteriophage lambda: control of translation completion. Proc Natl Acad Sci U S A. 1981 Jul;78(7):4475–4479. doi: 10.1073/pnas.78.7.4475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Schmeissner U., McKenney K., Rosenberg M., Court D. Removal of a terminator structure by RNA processing regulates int gene expression. J Mol Biol. 1984 Jun 15;176(1):39–53. doi: 10.1016/0022-2836(84)90381-4. [DOI] [PubMed] [Google Scholar]
  28. Sollner-Webb B., Reeder R. H. The nucleotide sequence of the initiation and termination sites for ribosomal RNA transcription in X. laevis. Cell. 1979 Oct;18(2):485–499. doi: 10.1016/0092-8674(79)90066-7. [DOI] [PubMed] [Google Scholar]
  29. Summers W. C. A simple method for extraction of RNA from E. coli utilizing diethyl pyrocarbonate. Anal Biochem. 1970 Feb;33(2):459–463. doi: 10.1016/0003-2697(70)90316-7. [DOI] [PubMed] [Google Scholar]
  30. Wong H. C., Chang S. Identification of a positive retroregulator that stabilizes mRNAs in bacteria. Proc Natl Acad Sci U S A. 1986 May;83(10):3233–3237. doi: 10.1073/pnas.83.10.3233. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Yousaf S. I., Carroll A. R., Clarke B. E. A new and improved method for 3'-end labelling DNA using [alpha-32P]ddATP. Gene. 1984 Mar;27(3):309–313. doi: 10.1016/0378-1119(84)90075-1. [DOI] [PubMed] [Google Scholar]
  32. Zaniewski R., Petkaitis E., Deutscher M. P. A multiple mutant of Escherichia coli lacking the exoribonucleases RNase II, RNase D, and RNase BN. J Biol Chem. 1984 Oct 10;259(19):11651–11653. [PubMed] [Google Scholar]
  33. Zuker M., Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981 Jan 10;9(1):133–148. doi: 10.1093/nar/9.1.133. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES