Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Poly(A)- and poly(U)-specific RNA 3′ tail shortening by E. coli ribonuclease E

Nature volume 391, pages 99–102 (1998)Cite this article

Abstract

Ribonuclease (RNase) E is an extensively studied enzyme from Escherichia coli whose site-specific endoribonuclease activity on single-stranded RNA has a central role in the processing of ribosomal RNA, the degradation of messenger RNA and the control of replication of ColE1-type plasmids (for recent reviews, see 1–3). Here we report a previously undetected activity of RNase E: the ability to shorten 3′ poly(A)- and poly(U)-homopolymer tails on RNA molecules. This activity, which leaves a 6-nucleotide adenylate or a 1-nucleotide uridylate remnant on primary transcripts, resides in the amino-terminal region of RNase E and does not require other protein cofactors. Addition of a 3′-terminal phosphate group prevents both removal of the poly(A) tail and endonucleolytic cleavage within primary transcripts, but has no effect on the cleavage of transcripts with tails that have already been truncated. The ability of RNase E to shorten poly(A) tails, together with the effect of tail length on endonucleolytic cleavage within primary transcripts, suggests a mechanism by which RNase E may exercise overall control over RNA decay.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Purification of RNase E.
Figure 2: Poly(A)- and poly(U)-specific exonucleolytic activity of purified RNase E.
Figure 3: Elimination of both poly(A)-tail removal and endonucleolytic activity of N-Rne by 3′ terminal addition of [32P]AP to RNAI-40A.

Similar content being viewed by others

References

  1. Cohen, S. N. & McDowall, K. J. RNase E: still a wonderfully mysterious enzyme. Mol. Microbiol. 23, 1099–1106 (1996).

    Article  Google Scholar 

  2. Ehretsmann, C. P., Carpousis, A. J. & Krisch, H. M. mRNA degradation in procaryotes. FASEB J. 6, 3186–3192 (1992).

    Article  CAS  Google Scholar 

  3. Melefors, O., Lundberg, U. & von Gabain, A. in Control of Messenger RNA Stability (eds Belasco, J. & Brawerman, G.) 53–70 (Academic, San Diego, (1993)).

    Book  Google Scholar 

  4. Tomcsanyi, T. & Apirion, D. Processing enzyme ribonuclease E specifically cleaves RNA I: an inhibitor of primer formation in plasmid DNA synthesis. J. Mol. Biol. 185, 713–720 (1985).

    Article  CAS  Google Scholar 

  5. Lin-Chao, S. & Cohen, S. N. The rate of processing and degradation of antisense RNAI regulates the replication of ColE-1 type plasmids in vivo. Cell 65, 1233–1242 (1991).

    Article  CAS  Google Scholar 

  6. Littauer, U. Z. & Soreq, H. Polynucleotide phosphorylase. The Enzymes XV, 517–553 (1982).

    Article  Google Scholar 

  7. Singer, M. F. & Tolbert, G. Purification and properties of a potassium-activated phosphodiesterase (RNase II) from Escherichia coli. Biochemistry 4, 1319–1330 (1965).

    Article  CAS  Google Scholar 

  8. Nossal, N. G. & Singer, M. F. The processive degradation of individual polyribonucleotide chains. J. Biol. Chem. 243, 913–922 (1968).

    CAS  PubMed  Google Scholar 

  9. Klee, C. B. & Singer, M. F. The processive degradation of individual polyribonucleotide chains. J. Biol. Chem. 243, 923–927 (1968).

    CAS  PubMed  Google Scholar 

  10. McDowall, K. J. & Cohen, S. N. The N-terminal domain of the rne gene product has RNase E activity and is non-overlapping with the arginine-rich RNA-bindign motif. J. Mol. Biol. 255, 349–355 (1996).

    Article  CAS  Google Scholar 

  11. Kido, M., Yamanaka, K., Mitani, T., Niki, H., Ogura, T. & Hiraga, S. RNase E polypeptides lacking a carboxyl-terminal half suppress a mukB mutation in Escherichia coli. J. Bacteriol. 178, 3917–3925 (1996).

    Article  CAS  Google Scholar 

  12. Helmer-Citterich, M., Anceschi, M. M., Banner, D. W. & Cesareni, G. Control of ColE1 replication: low affinity specific binding of Rop (Rom) to RNAI and RNAII. EMBO J. 7, 557–566 (1988).

    Article  CAS  Google Scholar 

  13. Xu, F. & Cohen, S. N. RNA degradation in Escherichia coli regulated by 3′ adenylation and 5′ phosphorylation. Nature 374, 180–183 (1995).

    Article  ADS  CAS  Google Scholar 

  14. Xu, F., Lin-Chao, S. & Cohen, S. N. 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. USA 90, 6756–6760 (1993).

    Article  ADS  CAS  Google Scholar 

  15. Claverie-Martin, F., Wang, M. & Cohen, S. N. Ard-1 cDNA from human cells encodes a site-specific single strand endoribonuclease that functionally resembles Escherichia coli RNase E. J. Biol. Chem. 272, 13823–13828 (1997).

    Article  CAS  Google Scholar 

  16. Kaberdin, V.. R., Chao, Y.-H. & Lin-Chao, S. RNase E cleaves at multiple sites in bubble region of RNAI stem-loops yielding products and dissociate differentially from the enzyme. J. Biol. Chem. 271, 13103–13109 (1996).

    Article  CAS  Google Scholar 

  17. Caponigro, G. & Parker, R. Mechanisms and control of mRNA turnover in Saccharomyces cerevisiae. Microbiol. Rev. 60, 233–249 ((1996)).

    Article  CAS  Google Scholar 

  18. Cohen, S. N. Surprises at the 3′ end of prokaryotic RNA. Cell 80, 829–832 (1995).

    Article  CAS  Google Scholar 

  19. Sarkar, N. Polyadenylation of mRNA in bacteria. Microbiology 142, 3125–3133 (1996).

    Article  CAS  Google Scholar 

  20. Hajnsdorf, E., Braun, F., Haugel-Nielsen, J. & Regnier, P. Polyadenylation destabilizes the rpsO mRNA of Escherichia coli. Proc. Natl Acad. Sci. USA 92, 3973–3977 (1995).

    Article  ADS  CAS  Google Scholar 

  21. Coburn, G. A. & Mackie, G. A. Overexpression, purification, and properties of Escherichia coli ribonuclease II. J. Biol. Chem. 271, 1048–1053 (1996).

    Article  CAS  Google Scholar 

  22. Py, B., Higgins, C. F., Krisch, H. M. & Carpousis, A. J. ADEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature 381, 169–172 (1996).

    Article  ADS  CAS  Google Scholar 

  23. Carpousis, A. J., Van Houwe, G., Ehretsmann, G. & Krisch, H. M. Copurification of E. coli RNase E and PNPase: evidence for a specific association between two enzymes important in RNA processing and degradation. Cell 76, 889–900 (1994).

    Article  CAS  Google Scholar 

  24. Miczak, A., Kaberdin, V. R., Wei, C. L. & Lin-Chao, S. Proteins associated with RNase E in a multicomponent ribonucleolytic complex. Proc. Natl Acad. Sci. USA 93, 3865–3869 (1996).

    Article  ADS  CAS  Google Scholar 

  25. Py, B., Causton, H., Mudd, E. A. & Higgins, C. F. Aprotein complex mediating mRNA degradation in Escherichia coli. Mol. Microbiol. 14, 717–799 (1994).

    Article  CAS  Google Scholar 

  26. Razzell, W. E. & Khorana, H. G. Studies on polynucleotides. III. Enzymatic degradation. Substrate specificity and properties of snake venom phosphodiesterase. J. Biol. Chem. 234, 2105–2113 (1959).

    CAS  PubMed  Google Scholar 

  27. Jacobson, A. Poly(A) metabolism and translation: The closed-loop model.in Cold Spring Harbor Monogr. Ser. 30, 451–480 (1996).

    CAS  Google Scholar 

  28. Hochuli, E., Dobeli, H. & Schacher, A. New metal chelate adsorbent selective for proteins and peptides containing neighboring histidine residues. J. Chromatogr. 411, 177–184 (1987).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

These studies were supported by a grant for mthe US NIH. We thank Y. Feng for his-tagged PAP I constructs, and J. Belasco, R. Lehman and C. Higgins for comments on this manuscript.

Author information

Authors and Affiliations

  1. Departments of Genetics Stanford University School of Medicine, Stanford, 94305-5120, California, USA

    Hongjin Huang & Stanley, N. Cohen

  2. Departments of Medicine, Stanford University School of Medicine, Stanford, 94305-5120, California, USA

    Jian Liao & Stanley, N. Cohen

Authors
  1. Hongjin Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jian Liao
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Stanley, N. Cohen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Stanley, N. Cohen.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Huang, H., Liao, J. & Cohen, S. Poly(A)- and poly(U)-specific RNA 3′ tail shortening by E. coli ribonuclease E. Nature 391, 99–102 (1998). https://doi.org/10.1038/34219

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/34219

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing