Skip to main content
Molecular and Cellular Biology logoLink to Molecular and Cellular Biology
. 1995 Nov;15(11):5983–5990. doi: 10.1128/mcb.15.11.5983

3'-end-forming signals of yeast mRNA.

Z Guo 1, F Sherman 1
PMCID: PMC230850  PMID: 7565751

Abstract

It was previously shown that three distinct but interdependent elements are required for 3' end formation of mRNA in the yeast Saccharomyces cerevisiae: (i) the efficiency element TATATA and related sequences, which function by enhancing the efficiency of positioning elements; (ii) positioning elements, such as TTAAGAAC and AAGAA, which position the poly(A) site; and (iii) the actual site of polyadenylation. In this study, we have shown that several A-rich sequences, including the vertebrate poly(A) signal AATAAA, are also positioning elements. Saturated mutagenesis revealed that optimum sequences of the positioning element were AATAAA and AAAAAA and that this element can tolerate various extents of replacements. However, the GATAAA sequence was completely ineffective. The major cleavage sites determined in vitro corresponded to the major poly(A) sites observed in vivo. Our findings support the assumption that some components of the basic polyadenylation machinery could have been conserved among yeasts, plants, and mammals, although 3' end formation in yeasts is clearly distinct from that of higher eukaryotes.

Full Text

The Full Text of this article is available as a PDF (468.7 KB).

Selected References

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

  1. Abe A., Hiraoka Y., Fukasawa T. Signal sequence for generation of mRNA 3' end in the Saccharomyces cerevisiae GAL7 gene. EMBO J. 1990 Nov;9(11):3691–3697. doi: 10.1002/j.1460-2075.1990.tb07581.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bennetzen J. L., Hall B. D. The primary structure of the Saccharomyces cerevisiae gene for alcohol dehydrogenase. J Biol Chem. 1982 Mar 25;257(6):3018–3025. [PubMed] [Google Scholar]
  3. Brown P. H., Tiley L. S., Cullen B. R. Efficient polyadenylation within the human immunodeficiency virus type 1 long terminal repeat requires flanking U3-specific sequences. J Virol. 1991 Jun;65(6):3340–3343. doi: 10.1128/jvi.65.6.3340-3343.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Butler J. S., Platt T. RNA processing generates the mature 3' end of yeast CYC1 messenger RNA in vitro. Science. 1988 Dec 2;242(4883):1270–1274. doi: 10.1126/science.2848317. [DOI] [PubMed] [Google Scholar]
  5. Butler J. S., Sadhale P. P., Platt T. RNA processing in vitro produces mature 3' ends of a variety of Saccharomyces cerevisiae mRNAs. Mol Cell Biol. 1990 Jun;10(6):2599–2605. doi: 10.1128/mcb.10.6.2599. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Carswell S., Alwine J. C. Efficiency of utilization of the simian virus 40 late polyadenylation site: effects of upstream sequences. Mol Cell Biol. 1989 Oct;9(10):4248–4258. doi: 10.1128/mcb.9.10.4248. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Chelly J., Montarras D., Pinset C., Berwald-Netter Y., Kaplan J. C., Kahn A. Quantitative estimation of minor mRNAs by cDNA-polymerase chain reaction. Application to dystrophin mRNA in cultured myogenic and brain cells. Eur J Biochem. 1990 Feb 14;187(3):691–698. doi: 10.1111/j.1432-1033.1990.tb15355.x. [DOI] [PubMed] [Google Scholar]
  8. DeZazzo J. D., Falck-Pedersen E., Imperiale M. J. Sequences regulating temporal poly(A) site switching in the adenovirus major late transcription unit. Mol Cell Biol. 1991 Dec;11(12):5977–5984. doi: 10.1128/mcb.11.12.5977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. DeZazzo J. D., Imperiale M. J. Sequences upstream of AAUAAA influence poly(A) site selection in a complex transcription unit. Mol Cell Biol. 1989 Nov;9(11):4951–4961. doi: 10.1128/mcb.9.11.4951. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Egli C. M., Springer C., Braus G. H. A complex unidirectional signal element mediates GCN4 mRNA 3' end formation in Saccharomyces cerevisiae. Mol Cell Biol. 1995 May;15(5):2466–2473. doi: 10.1128/mcb.15.5.2466. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Gilmartin G. M., Fleming E. S., Oetjen J. Activation of HIV-1 pre-mRNA 3' processing in vitro requires both an upstream element and TAR. EMBO J. 1992 Dec;11(12):4419–4428. doi: 10.1002/j.1460-2075.1992.tb05542.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Gilmartin G. M., Fleming E. S., Oetjen J., Graveley B. R. CPSF recognition of an HIV-1 mRNA 3'-processing enhancer: multiple sequence contacts involved in poly(A) site definition. Genes Dev. 1995 Jan 1;9(1):72–83. doi: 10.1101/gad.9.1.72. [DOI] [PubMed] [Google Scholar]
  13. Guo Z., Russo P., Yun D. F., Butler J. S., Sherman F. Redundant 3' end-forming signals for the yeast CYC1 mRNA. Proc Natl Acad Sci U S A. 1995 May 9;92(10):4211–4214. doi: 10.1073/pnas.92.10.4211. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Heidmann S., Obermaier B., Vogel K., Domdey H. Identification of pre-mRNA polyadenylation sites in Saccharomyces cerevisiae. Mol Cell Biol. 1992 Sep;12(9):4215–4229. doi: 10.1128/mcb.12.9.4215. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Heidmann S., Schindewolf C., Stumpf G., Domdey H. Flexibility and interchangeability of polyadenylation signals in Saccharomyces cerevisiae. Mol Cell Biol. 1994 Jul;14(7):4633–4642. doi: 10.1128/mcb.14.7.4633. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Henikoff S., Cohen E. H. Sequences responsible for transcription termination on a gene segment in Saccharomyces cerevisiae. Mol Cell Biol. 1984 Aug;4(8):1515–1520. doi: 10.1128/mcb.4.8.1515. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Henikoff S., Kelly J. D., Cohen E. H. Transcription terminates in yeast distal to a control sequence. Cell. 1983 Jun;33(2):607–614. doi: 10.1016/0092-8674(83)90441-5. [DOI] [PubMed] [Google Scholar]
  18. Hyman L. E., Moore C. L. Termination and pausing of RNA polymerase II downstream of yeast polyadenylation sites. Mol Cell Biol. 1993 Sep;13(9):5159–5167. doi: 10.1128/mcb.13.9.5159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Hyman L. E., Seiler S. H., Whoriskey J., Moore C. L. Point mutations upstream of the yeast ADH2 poly(A) site significantly reduce the efficiency of 3'-end formation. Mol Cell Biol. 1991 Apr;11(4):2004–2012. doi: 10.1128/mcb.11.4.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Irniger S., Braus G. H. Saturation mutagenesis of a polyadenylation signal reveals a hexanucleotide element essential for mRNA 3' end formation in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1994 Jan 4;91(1):257–261. doi: 10.1073/pnas.91.1.257. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Irniger S., Egli C. M., Braus G. H. Different classes of polyadenylation sites in the yeast Saccharomyces cerevisiae. Mol Cell Biol. 1991 Jun;11(6):3060–3069. doi: 10.1128/mcb.11.6.3060. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Irniger S., Sanfaçon H., Egli C. M., Braus G. H. Different sequence elements are required for function of the cauliflower mosaic virus polyadenylation site in Saccharomyces cerevisiae compared with in plants. Mol Cell Biol. 1992 May;12(5):2322–2330. doi: 10.1128/mcb.12.5.2322. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. 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]
  24. Li W. Z., Sherman F. Two types of TATA elements for the CYC1 gene of the yeast Saccharomyces cerevisiae. Mol Cell Biol. 1991 Feb;11(2):666–676. doi: 10.1128/mcb.11.2.666. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Osborne B. I., Guarente L. Mutational analysis of a yeast transcriptional terminator. Proc Natl Acad Sci U S A. 1989 Jun;86(11):4097–4101. doi: 10.1073/pnas.86.11.4097. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Osborne B. I., Guarente L. Transcription by RNA polymerase II induces changes of DNA topology in yeast. Genes Dev. 1988 Jun;2(6):766–772. doi: 10.1101/gad.2.6.766. [DOI] [PubMed] [Google Scholar]
  27. Peterson J. A., Myers A. M. Functional analysis of mRNA 3' end formation signals in the convergent and overlapping transcription units of the S. cerevisiae genes RHO1 and MRP2. Nucleic Acids Res. 1993 Nov 25;21(23):5500–5508. doi: 10.1093/nar/21.23.5500. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Preker P. J., Lingner J., Minvielle-Sebastia L., Keller W. The FIP1 gene encodes a component of a yeast pre-mRNA polyadenylation factor that directly interacts with poly(A) polymerase. Cell. 1995 May 5;81(3):379–389. doi: 10.1016/0092-8674(95)90391-7. [DOI] [PubMed] [Google Scholar]
  29. Russnak R., Ganem D. Sequences 5' to the polyadenylation signal mediate differential poly(A) site use in hepatitis B viruses. Genes Dev. 1990 May;4(5):764–776. doi: 10.1101/gad.4.5.764. [DOI] [PubMed] [Google Scholar]
  30. Russo P., Li W. Z., Guo Z., Sherman F. Signals that produce 3' termini in CYC1 mRNA of the yeast Saccharomyces cerevisiae. Mol Cell Biol. 1993 Dec;13(12):7836–7849. doi: 10.1128/mcb.13.12.7836. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Russo P., Li W. Z., Hampsey D. M., Zaret K. S., Sherman F. Distinct cis-acting signals enhance 3' endpoint formation of CYC1 mRNA in the yeast Saccharomyces cerevisiae. EMBO J. 1991 Mar;10(3):563–571. doi: 10.1002/j.1460-2075.1991.tb07983.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Russo P. Saccharomyces cerevisiae mRNA 3' end forming signals are also involved in transcription termination. Yeast. 1995 Apr 30;11(5):447–453. doi: 10.1002/yea.320110507. [DOI] [PubMed] [Google Scholar]
  33. Russo P., Sherman F. Transcription terminates near the poly(A) site in the CYC1 gene of the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1989 Nov;86(21):8348–8352. doi: 10.1073/pnas.86.21.8348. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Sadhale P. P., Sapolsky R., Davis R. W., Butler J. S., Platt T. Polymerase chain reaction mapping of yeast GAL7 mRNA polyadenylation sites demonstrates that 3' end processing in vitro faithfully reproduces the 3' ends observed in vivo. Nucleic Acids Res. 1991 Jul 11;19(13):3683–3688. doi: 10.1093/nar/19.13.3683. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Sanfaçon H., Brodmann P., Hohn T. A dissection of the cauliflower mosaic virus polyadenylation signal. Genes Dev. 1991 Jan;5(1):141–149. doi: 10.1101/gad.5.1.141. [DOI] [PubMed] [Google Scholar]
  36. Schek N., Cooke C., Alwine J. C. Definition of the upstream efficiency element of the simian virus 40 late polyadenylation signal by using in vitro analyses. Mol Cell Biol. 1992 Dec;12(12):5386–5393. doi: 10.1128/mcb.12.12.5386. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Sheets M. D., Ogg S. C., Wickens M. P. Point mutations in AAUAAA and the poly (A) addition site: effects on the accuracy and efficiency of cleavage and polyadenylation in vitro. Nucleic Acids Res. 1990 Oct 11;18(19):5799–5805. doi: 10.1093/nar/18.19.5799. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Valsamakis A., Schek N., Alwine J. C. Elements upstream of the AAUAAA within the human immunodeficiency virus polyadenylation signal are required for efficient polyadenylation in vitro. Mol Cell Biol. 1992 Sep;12(9):3699–3705. doi: 10.1128/mcb.12.9.3699. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Valsamakis A., Zeichner S., Carswell S., Alwine J. C. The human immunodeficiency virus type 1 polyadenylylation signal: a 3' long terminal repeat element upstream of the AAUAAA necessary for efficient polyadenylylation. Proc Natl Acad Sci U S A. 1991 Mar 15;88(6):2108–2112. doi: 10.1073/pnas.88.6.2108. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Wahle E., Keller W. The biochemistry of 3'-end cleavage and polyadenylation of messenger RNA precursors. Annu Rev Biochem. 1992;61:419–440. doi: 10.1146/annurev.bi.61.070192.002223. [DOI] [PubMed] [Google Scholar]
  41. Yu K., Elder R. T. Some of the signals for 3'-end formation in transcription of the Saccharomyces cerevisiae Ty-D15 element are immediately downstream of the initiation site. Mol Cell Biol. 1989 Jun;9(6):2431–2444. doi: 10.1128/mcb.9.6.2431. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Zaret K. S., Sherman F. DNA sequence required for efficient transcription termination in yeast. Cell. 1982 Mar;28(3):563–573. doi: 10.1016/0092-8674(82)90211-2. [DOI] [PubMed] [Google Scholar]

Articles from Molecular and Cellular Biology are provided here courtesy of Taylor & Francis

RESOURCES