Evidence that the pathway of transferrin receptor mRNA degradation involves an endonucleolytic cleavage within the 3' UTR and does not involve poly(A) tail shortening. (original) (raw)

EMBO J. 1994 Apr 15; 13(8): 1969–1980.

Cell Biology and Metabolism Branch, NICHD, NIH, Bethesda, MD 20892.

Abstract

The stability of transferrin receptor (TfR) mRNA is regulated by iron availability. When a human plasma-cytoma cell line (ARH-77) is treated with an iron source (hemin), the TfR mRNA is destabilized and a shorter TfR RNA appears. A similar phenomenon is also observed in mouse fibroblasts expressing a previously characterized iron-regulated human TfR mRNA (TRS-1). In contrast, mouse cells expressing a constitutively unstable human TfR mRNA (TRS-4) display the shorter RNA irrespective of iron treatment. These shorter RNAs found in both the hemin-treated ARH-77 cells and in the mouse fibroblasts are shown to be the result of a truncation within the 3' untranslated regions of the mRNAs. The truncated RNA is generated by an endonuclease, as most clearly evidenced by the detection of the matching 3' endonuclease product. The cleavage site of the human TfR mRNA in the mouse fibroblasts has been mapped to single nucleotide resolution to a single-stranded region near one of the iron-responsive elements contained in the 3' UTR. Site-directed mutagenesis demonstrates that the sequence surrounding the mapped endonuclease cleavage site is required for both iron-regulated mRNA turnover and generation of the truncated degradation intermediate. The TfR mRNA does not undergo poly(A) tail shortening prior to rapid degradation since the length of the poly(A) tail does not decrease during iron-induced destabilization. Moreover, the 3' endonuclease cleavage product is apparently polyadenylated to the same extent as the full-length mRNA.

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Baker EJ, Diener DR, Rosenbaum JL. Accelerated poly(A) loss on alpha-tubulin mRNAs during protein synthesis inhibition in Chlamydomonas. J Mol Biol. 1989 Jun 20;207(4):771–781. [PubMed] [Google Scholar]
Bernstein P, Ross J. Poly(A), poly(A) binding protein and the regulation of mRNA stability. Trends Biochem Sci. 1989 Sep;14(9):373–377. [PubMed] [Google Scholar]
Bernstein PL, Herrick DJ, Prokipcak RD, Ross J. Control of c-myc mRNA half-life in vitro by a protein capable of binding to a coding region stability determinant. Genes Dev. 1992 Apr;6(4):642–654. [PubMed] [Google Scholar]
Binder R, Hwang SP, Ratnasabapathy R, Williams DL. Degradation of apolipoprotein II mRNA occurs via endonucleolytic cleavage at 5'-AAU-3'/5'-UAA-3' elements in single-stranded loop domains of the 3'-noncoding region. J Biol Chem. 1989 Oct 5;264(28):16910–16918. [PubMed] [Google Scholar]
Bohjanen PR, Petryniak B, June CH, Thompson CB, Lindsten T. An inducible cytoplasmic factor (AU-B) binds selectively to AUUUA multimers in the 3' untranslated region of lymphokine mRNA. Mol Cell Biol. 1991 Jun;11(6):3288–3295. [PMC free article] [PubMed] [Google Scholar]
Brewer G. An A + U-rich element RNA-binding factor regulates c-myc mRNA stability in vitro. Mol Cell Biol. 1991 May;11(5):2460–2466. [PMC free article] [PubMed] [Google Scholar]
Brewer G, Ross J. Poly(A) shortening and degradation of the 3' A+U-rich sequences of human c-myc mRNA in a cell-free system. Mol Cell Biol. 1988 Apr;8(4):1697–1708. [PMC free article] [PubMed] [Google Scholar]
Brown BD, Harland RM. Endonucleolytic cleavage of a maternal homeo box mRNA in Xenopus oocytes. Genes Dev. 1990 Nov;4(11):1925–1935. [PubMed] [Google Scholar]
Brown BD, Zipkin ID, Harland RM. Sequence-specific endonucleolytic cleavage and protection of mRNA in Xenopus and Drosophila. Genes Dev. 1993 Aug;7(8):1620–1631. [PubMed] [Google Scholar]
Casey JL, Di Jeso B, Rao K, Klausner RD, Harford JB. Two genetic loci participate in the regulation by iron of the gene for the human transferrin receptor. Proc Natl Acad Sci U S A. 1988 Mar;85(6):1787–1791. [PMC free article] [PubMed] [Google Scholar]
Casey JL, Hentze MW, Koeller DM, Caughman SW, Rouault TA, Klausner RD, Harford JB. Iron-responsive elements: regulatory RNA sequences that control mRNA levels and translation. Science. 1988 May 13;240(4854):924–928. [PubMed] [Google Scholar]
Casey JL, Koeller DM, Ramin VC, Klausner RD, Harford JB. Iron regulation of transferrin receptor mRNA levels requires iron-responsive elements and a rapid turnover determinant in the 3' untranslated region of the mRNA. EMBO J. 1989 Dec 1;8(12):3693–3699. [PMC free article] [PubMed] [Google Scholar]
Haile DJ, Hentze MW, Rouault TA, Harford JB, Klausner RD. Regulation of interaction of the iron-responsive element binding protein with iron-responsive RNA elements. Mol Cell Biol. 1989 Nov;9(11):5055–5061. [PMC free article] [PubMed] [Google Scholar]
Higuchi R, Krummel B, Saiki RK. A general method of in vitro preparation and specific mutagenesis of DNA fragments: study of protein and DNA interactions. Nucleic Acids Res. 1988 Aug 11;16(15):7351–7367. [PMC free article] [PubMed] [Google Scholar]
Horowitz JA, Harford JB. The secondary structure of the regulatory region of the transferrin receptor mRNA deduced by enzymatic cleavage. New Biol. 1992 Apr;4(4):330–338. [PubMed] [Google Scholar]
Jaffrey SR, Haile DJ, Klausner RD, Harford JB. The interaction between the iron-responsive element binding protein and its cognate RNA is highly dependent upon both RNA sequence and structure. Nucleic Acids Res. 1993 Sep 25;21(19):4627–4631. [PMC free article] [PubMed] [Google Scholar]
Klausner RD, Rouault TA, Harford JB. Regulating the fate of mRNA: the control of cellular iron metabolism. Cell. 1993 Jan 15;72(1):19–28. [PubMed] [Google Scholar]
Koeller DM, Casey JL, Hentze MW, Gerhardt EM, Chan LN, Klausner RD, Harford JB. A cytosolic protein binds to structural elements within the iron regulatory region of the transferrin receptor mRNA. Proc Natl Acad Sci U S A. 1989 May;86(10):3574–3578. [PMC free article] [PubMed] [Google Scholar]
Koeller DM, Horowitz JA, Casey JL, Klausner RD, Harford JB. Translation and the stability of mRNAs encoding the transferrin receptor and c-fos. Proc Natl Acad Sci U S A. 1991 Sep 1;88(17):7778–7782. [PMC free article] [PubMed] [Google Scholar]
Krol A, Carbon P. A guide for probing native small nuclear RNA and ribonucleoprotein structures. Methods Enzymol. 1989;180:212–227. [PubMed] [Google Scholar]
Laird-Offringa IA, de Wit CL, Elfferich P, van der Eb AJ. Poly(A) tail shortening is the translation-dependent step in c-myc mRNA degradation. Mol Cell Biol. 1990 Dec;10(12):6132–6140. [PMC free article] [PubMed] [Google Scholar]
Leibold EA, Guo B. Iron-dependent regulation of ferritin and transferrin receptor expression by the iron-responsive element binding protein. Annu Rev Nutr. 1992;12:345–368. [PubMed] [Google Scholar]
Liang HM, Jost JP. An estrogen-dependent polysomal protein binds to the 5' untranslated region of the chicken vitellogenin mRNA. Nucleic Acids Res. 1991 May 11;19(9):2289–2294. [PMC free article] [PubMed] [Google Scholar]
Lim SK, Sigmund CD, Gross KW, Maquat LE. Nonsense codons in human beta-globin mRNA result in the production of mRNA degradation products. Mol Cell Biol. 1992 Mar;12(3):1149–1161. [PMC free article] [PubMed] [Google Scholar]
Littauer UZ, Soreq H. The regulatory function of poly(A) and adjacent 3' sequences in translated RNA. Prog Nucleic Acid Res Mol Biol. 1982;27:53–83. [PubMed] [Google Scholar]
Lowell JE, Rudner DZ, Sachs AB. 3'-UTR-dependent deadenylation by the yeast poly(A) nuclease. Genes Dev. 1992 Nov;6(11):2088–2099. [PubMed] [Google Scholar]
Malter JS. Identification of an AUUUA-specific messenger RNA binding protein. Science. 1989 Nov 3;246(4930):664–666. [PubMed] [Google Scholar]
Maxam AM, Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. [PubMed] [Google Scholar]
Meinsma D, Holthuizen PE, Van den Brande JL, Sussenbach JS. Specific endonucleolytic cleavage of IGF-II mRNAs. Biochem Biophys Res Commun. 1991 Sep 30;179(3):1509–1516. [PubMed] [Google Scholar]
Müllner EW, Kühn LC. A stem-loop in the 3' untranslated region mediates iron-dependent regulation of transferrin receptor mRNA stability in the cytoplasm. Cell. 1988 Jun 3;53(5):815–825. [PubMed] [Google Scholar]
Myer VE, Lee SI, Steitz JA. Viral small nuclear ribonucleoproteins bind a protein implicated in messenger RNA destabilization. Proc Natl Acad Sci U S A. 1992 Feb 15;89(4):1296–1300. [PMC free article] [PubMed] [Google Scholar]
Neckers LM, Nordan R, Bauer S, Potter M. Studies on transferrin receptor expression in mouse plasmacytoma cells. Curr Top Microbiol Immunol. 1986;132:148–152. [PubMed] [Google Scholar]
Roberts KP, Griswold MD. Characterization of rat transferrin receptor cDNA: the regulation of transferrin receptor mRNA in testes and in Sertoli cells in culture. Mol Endocrinol. 1990 Apr;4(4):531–542. [PubMed] [Google Scholar]
Rosenthal ET, Tansey TR, Ruderman JV. Sequence-specific adenylations and deadenylations accompany changes in the translation of maternal messenger RNA after fertilization of Spisula oocytes. J Mol Biol. 1983 May 25;166(3):309–327. [PubMed] [Google Scholar]
Ross J, Peltz SW, Kobs G, Brewer G. Histone mRNA degradation in vivo: the first detectable step occurs at or near the 3' terminus. Mol Cell Biol. 1986 Dec;6(12):4362–4371. [PMC free article] [PubMed] [Google Scholar]
Rubin HN, Halim MN. Why, when and how does the poly(A) tail shorten during mRNA translation? Int J Biochem. 1993 Mar;25(3):287–295. [PubMed] [Google Scholar]
Sachs A. The role of poly(A) in the translation and stability of mRNA. Curr Opin Cell Biol. 1990 Dec;2(6):1092–1098. [PubMed] [Google Scholar]
Sachs AB. Messenger RNA degradation in eukaryotes. Cell. 1993 Aug 13;74(3):413–421. [PubMed] [Google Scholar]
Sachs AB, Davis RW. The poly(A) binding protein is required for poly(A) shortening and 60S ribosomal subunit-dependent translation initiation. Cell. 1989 Sep 8;58(5):857–867. [PubMed] [Google Scholar]
Sachs AB, Deardorff JA. Translation initiation requires the PAB-dependent poly(A) ribonuclease in yeast. Cell. 1992 Sep 18;70(6):961–973. [PubMed] [Google Scholar]
Schuler GD, Cole MD. GM-CSF and oncogene mRNA stabilities are independently regulated in trans in a mouse monocytic tumor. Cell. 1988 Dec 23;55(6):1115–1122. [PubMed] [Google Scholar]
Shaw G, Kamen R. A conserved AU sequence from the 3' untranslated region of GM-CSF mRNA mediates selective mRNA degradation. Cell. 1986 Aug 29;46(5):659–667. [PubMed] [Google Scholar]
Stern DB, Jones H, Gruissem W. Function of plastid mRNA 3' inverted repeats. RNA stabilization and gene-specific protein binding. J Biol Chem. 1989 Nov 5;264(31):18742–18750. [PubMed] [Google Scholar]
Stoeckle MY. Removal of a 3' non-coding sequence is an initial step in degradation of gro alpha mRNA and is regulated by interleukin-1. Nucleic Acids Res. 1992 Mar 11;20(5):1123–1127. [PMC free article] [PubMed] [Google Scholar]
Stoeckle MY, Hanafusa H. Processing of 9E3 mRNA and regulation of its stability in normal and Rous sarcoma virus-transformed cells. Mol Cell Biol. 1989 Nov;9(11):4738–4745. [PMC free article] [PubMed] [Google Scholar]
Uchida S, Kwon HM, Preston AS, Handler JS. Expression of Madin-Darby canine kidney cell Na(+)-and Cl(-)-dependent taurine transporter in Xenopus laevis oocytes. J Biol Chem. 1991 May 25;266(15):9605–9609. [PubMed] [Google Scholar]
Vakalopoulou E, Schaack J, Shenk T. A 32-kilodalton protein binds to AU-rich domains in the 3' untranslated regions of rapidly degraded mRNAs. Mol Cell Biol. 1991 Jun;11(6):3355–3364. [PMC free article] [PubMed] [Google Scholar]
Vreken P, Raué HA. The rate-limiting step in yeast PGK1 mRNA degradation is an endonucleolytic cleavage in the 3'-terminal part of the coding region. Mol Cell Biol. 1992 Jul;12(7):2986–2996. [PMC free article] [PubMed] [Google Scholar]
Weber B, Horiguchi J, Luebbers R, Sherman M, Kufe D. Posttranscriptional stabilization of c-fms mRNA by a labile protein during human monocytic differentiation. Mol Cell Biol. 1989 Feb;9(2):769–775. [PMC free article] [PubMed] [Google Scholar]
You Y, Chen CY, Shyu AB. U-rich sequence-binding proteins (URBPs) interacting with a 20-nucleotide U-rich sequence in the 3' untranslated region of c-fos mRNA may be involved in the first step of c-fos mRNA degradation. Mol Cell Biol. 1992 Jul;12(7):2931–2940. [PMC free article] [PubMed] [Google Scholar]

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