Biopolym. Cell. 2001; 17(3):185-202.
Reviews
mRNA polyadenylation. 2. Formation of poly(A) tails in yeast, plant, prokaryote and virus mRNAs
- Institute of Molecular Biology and Genetics, NAS of Ukraine
150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680
Abstract
The present work is the last part of the review devoted to polyadenylation of pre mRNAs from different categories of organisms. The mechanisms of poly(A) tails formation in yeast, plant, prokaryote and virus mRNAs are under consideration. A model of formation of cleavage complex, assembled on the polyadenylation site of yeast pre mRNA, is proposed.
Full text: (PDF, in Russian)
References
[1]
Zarudnaya MI. mRNA polyadenylation. 1. 3'-end formation of vertebrates' mRNAs. Biopolym Cell. 2001; 17(2):93-108.
[2]
Keller W, Minvielle-Sebastia L. A comparison of mammalian and yeast pre-mRNA 3'-end processing. Curr Opin Cell Biol. 1997;9(3):329-36.
[3]
Preker PJ, Keller W. The HAT helix, a repetitive motif implicated in RNA processing. Trends Biochem Sci. 1998;23(1):15-6.
[4]
Kessler MM, Henry MF, Shen E, Zhao J, Gross S, Silver PA, Moore CL. Hrp1, a sequence-specific RNA-binding protein that shuttles between the nucleus and the cytoplasm, is required for mRNA 3'-end formation in yeast. Genes Dev. 1997;11(19):2545-56.
[5]
Minvielle-Sebastia L, Preker PJ, Keller W. RNA14 and RNA15 proteins as components of a yeast pre-mRNA 3'-end processing factor. Science. 1994;266(5191):1702-5.
[6]
Amrani N, Minet M, Le Gouar M, Lacroute F, Wyers F. Yeast Pab1 interacts with Rna15 and participates in the control of the poly(A) tail length in vitro. Mol Cell Biol. 1997;17(7):3694-701.
[7]
Zhao J, Kessler MM, Moore CL. Cleavage factor II of Saccharomyces cerevisiae contains homologues to subunits of the mammalian Cleavage/ polyadenylation specificity factor and exhibits sequence-specific, ATP-dependent interaction with precursor RNA. J Biol Chem. 1997;272(16):10831-8.
[8]
Barabino SM, H?bner W, Jenny A, Minvielle-Sebastia L, Keller W. The 30-kD subunit of mammalian cleavage and polyadenylation specificity factor and its yeast homolog are RNA-binding zinc finger proteins. Genes Dev. 1997;11(13):1703-16.
[9]
Zhelkovsky AM, Kessler MM, Moore CL. Structure-function relationships in the Saccharomyces cerevisiae poly(A) polymerase. Identification of a novel RNA binding site and a domain that interacts with specificity factor(s). J Biol Chem. 1995;270(44):26715-20.
[10]
Martin G, Keller W. Mutational analysis of mammalian poly(A) polymerase identifies a region for primer binding and catalytic domain, homologous to the family X polymerases, and to other nucleotidyltransferases. EMBO J. 1996;15(10):2593-603.
[11]
Sachs AB, Bond MW, Kornberg RD. A single gene from yeast for both nuclear and cytoplasmic polyadenylate-binding proteins: domain structure and expression. Cell. 1986;45(6):827-35.
[12]
Burd CG, Matunis EL, Dreyfuss G. The multiple RNA-binding domains of the mRNA poly(A)-binding protein have different RNA-binding activities. Mol Cell Biol. 1991;11(7):3419-24.
[13]
Barabino SM, Ohnacker M, Keller W. Distinct roles of two Yth1p domains in 3'-end cleavage and polyadenylation of yeast pre-mRNAs. EMBO J. 2000;19(14):3778-87.
[14]
Zhao J, Kessler M, Helmling S, O'Connor JP, Moore C. Pta1, a component of yeast CF II, is required for both cleavage and poly(A) addition of mRNA precursor. Mol Cell Biol. 1999;19(11):7733-40.
[15]
Jenny A, Minvielle-Sebastia L, Preker PJ, Keller W. Sequence similarity between the 73-kilodalton protein of mammalian CPSF and a subunit of yeast polyadenylation factor I. Science. 1996;274(5292):1514-7.
[16]
Preker PJ, Ohnacker M, Minvielle-Sebastia L, Keller W. A multisubunit 3' end processing factor from yeast containing poly(A) polymerase and homologues of the subunits of mammalian cleavage and polyadenylation specificity factor. EMBO J. 1997;16(15):4727-37.
[17]
Colgan DF, Manley JL. Mechanism and regulation of mRNA polyadenylation. Genes Dev. 1997;11(21):2755-66.
[18]
Wahle E, R?egsegger U. 3'-End processing of pre-mRNA in eukaryotes. FEMS Microbiol Rev. 1999;23(3):277-95.
[19]
Gunderson SI, Vagner S, Polycarpou-Schwarz M, Mattaj IW. Involvement of the carboxyl terminus of vertebrate poly(A) polymerase in U1A autoregulation and in the coupling of splicing and polyadenylation. Genes Dev. 1997;11(6):761-73.
[20]
Zhelkovsky A, Helmling S, Moore C. Processivity of the Saccharomyces cerevisiae poly(A) polymerase requires interactions at the carboxyl-terminal RNA binding domain. Mol Cell Biol. 1998;18(10):5942-51.
[21]
Williamson JR, Raghuraman MK, Cech TR. Monovalent cation-induced structure of telomeric DNA: the G-quartet model. Cell. 1989;59(5):871-80.
[22]
Takagaki Y, Manley JL. Complex protein interactions within the human polyadenylation machinery identify a novel component. Mol Cell Biol. 2000;20(5):1515-25.
[23]
Chen F, MacDonald CC, Wilusz J. Cleavage site determinants in the mammalian polyadenylation signal. Nucleic Acids Res. 1995;23(14):2614-20.
[24]
Graber JH, Cantor CR, Mohr SC, Smith TF. Genomic detection of new yeast pre-mRNA 3'-end-processing signals. Nucleic Acids Res. 1999;27(3):888-94.
[25]
Graber JH, Cantor CR, Mohr SC, Smith TF. In silico detection of control signals: mRNA 3'-end-processing sequences in diverse species. Proc Natl Acad Sci U S A. 1999;96(24):14055-60.
[27]
Manley JL, Takagaki Y. The end of the message--another link between yeast and mammals. Science. 1996;274(5292):1481-2.
[28]
Guo Z, Sherman F. Signals sufficient for 3'-end formation of yeast mRNA. Mol Cell Biol. 1996;16(6):2772-6.
[29]
Egli CM, Springer C, Braus GH. A complex unidirectional signal element mediates GCN4 mRNA 3' end formation in Saccharomyces cerevisiae. Mol Cell Biol. 1995;15(5):2466-73.
[30]
Minvielle-Sebastia L, Beyer K, Krecic AM, Hector RE, Swanson MS, Keller W. Control of cleavage site selection during mRNA 3' end formation by a yeast hnRNP. EMBO J. 1998;17(24):7454-68.
[31]
Chen S, Hyman LE. A specific RNA-protein interaction at yeast polyadenylation efficiency elements. Nucleic Acids Res. 1998;26(21):4965-74.
[32]
Russnak R, Nehrke KW, Platt T. REF2 encodes an RNA-binding protein directly involved in yeast mRNA 3'-end formation. Mol Cell Biol. 1995;15(3):1689-97.
[33]
Wahle E. Poly(A) tail length control is caused by termination of processive synthesis. J Biol Chem. 1995;270(6):2800-8.
[34]
Minvielle-Sebastia L, Preker PJ, Wiederkehr T, Strahm Y, Keller W. The major yeast poly(A)-binding protein is associated with cleavage factor IA and functions in premessenger RNA 3'-end formation. Proc Natl Acad Sci U S A. 1997;94(15):7897-902.
[35]
Afonina E, Stauber R, Pavlakis GN. The human poly(A)-binding protein 1 shuttles between the nucleus and the cytoplasm. J Biol Chem. 1998;273(21):13015-21.
[36]
Mangus DA, Amrani N, Jacobson A. Pbp1p, a factor interacting with Saccharomyces cerevisiae poly(A)-binding protein, regulates polyadenylation. Mol Cell Biol. 1998;18(12):7383-96.
[37]
Brown CE, Sachs AB. Poly(A) tail length control in Saccharomyces cerevisiae occurs by message-specific deadenylation. Mol Cell Biol. 1998;18(11):6548-59.
[38]
Russo P. Saccharomyces cerevisiae mRNA 3' end forming signals are also involved in transcription termination. Yeast. 1995;11(5):447-53.
[39]
Birse CE, Lee BA, Hansen K, Proudfoot NJ. Transcriptional termination signals for RNA polymerase II in fission yeast. EMBO J. 1997;16(12):3633-43.
[40]
Greger IH, Proudfoot NJ. Poly(A) signals control both transcriptional termination and initiation between the tandem GAL10 and GAL7 genes of Saccharomyces cerevisiae. EMBO J. 1998;17(16):4771-9.
[41]
Birse CE, Minvielle-Sebastia L, Lee BA, Keller W, Proudfoot NJ. Coupling termination of transcription to messenger RNA maturation in yeast. Science. 1998;280(5361):298-301.
[42]
Aranda A, P?rez-Ort?n JE, Moore C, del Olmo ML. Transcription termination downstream of the Saccharomyces cerevisiae FBP1 [changed from FPB1] poly(A) site does not depend on efficient 3'end processing. RNA. 1998;4(3):303-18. Erratum in: RNA 1998 Jul;4(7):870.
[43]
Rodriguez CR, Cho EJ, Keogh MC, Moore CL, Greenleaf AL, Buratowski S. Kin28, the TFIIH-associated carboxy-terminal domain kinase, facilitates the recruitment of mRNA processing machinery to RNA polymerase II. Mol Cell Biol. 2000;20(1):104-12.
[45]
Rothnie HM, Reid J, Hohn T. The contribution of AAUAAA and the upstream element UUUGUA to the efficiency of mRNA 3'-end formation in plants. EMBO J. 1994;13(9):2200-10.
[46]
Luehrsen KR, Walbot V. Intron creation and polyadenylation in maize are directed by AU-rich RNA. Genes Dev. 1994;8(9):1117-30.
[47]
Gallie DR. The cap and poly(A) tail function synergistically to regulate mRNA translational efficiency. Genes Dev. 1991;5(11):2108-16.
[48]
Le H, Tanguay RL, Balasta ML, Wei CC, Browning KS, Metz AM, Goss DJ, Gallie DR. Translation initiation factors eIF-iso4G and eIF-4B interact with the poly(A)-binding protein and increase its RNA binding activity. J Biol Chem. 1997;272(26):16247-55.
[49]
Wei CC, Balasta ML, Ren J, Goss DJ. Wheat germ poly(A) binding protein enhances the binding affinity of eukaryotic initiation factor 4F and (iso)4F for cap analogues. Biochemistry. 1998;37(7):1910-6.
[50]
Tarun SZ Jr, Sachs AB. Association of the yeast poly(A) tail binding protein with translation initiation factor eIF-4G. EMBO J. 1996;15(24):7168-77.
[51]
Sachs AB, Davis RW, Kornberg RD. A single domain of yeast poly(A)-binding protein is necessary and sufficient for RNA binding and cell viability. Mol Cell Biol. 1987;7(9):3268-76.
[52]
Caponigro G, Parker R. Multiple functions for the poly(A)-binding protein in mRNA decapping and deadenylation in yeast. Genes Dev. 1995;9(19):2421-32.
[53]
Sachs AB, Sarnow P, Hentze MW. Starting at the beginning, middle, and end: translation initiation in eukaryotes. Cell. 1997;89(6):831-8.
[54]
Muhlrad D, Decker CJ, Parker R. Deadenylation of the unstable mRNA encoded by the yeast MFA2 gene leads to decapping followed by 5'-->3' digestion of the transcript. Genes Dev. 1994;8(7):855-66.
[55]
Belostotsky DA, Meagher RB. A pollen-, ovule-, and early embryo-specific poly(A) binding protein from Arabidopsis complements essential functions in yeast. Plant Cell. 1996;8(8):1261-75.
[56]
Belostotsky DA, Meagher RB. Differential organ-specific expression of three poly(A)-binding-protein genes from Arabidopsis thaliana. Proc Natl Acad Sci U S A. 1993;90(14):6686-90.
[57]
Palanivelu R, Belostotsky DA, Meagher RB. Arabidopsis thaliana poly (A) binding protein 2 (PAB2) functions in yeast translational and mRNA decay processes. Plant J. 2000;22(3):187-98.
[58]
Gera JF, Baker EJ. Deadenylation-dependent and -independent decay pathways for alpha1-tubulin mRNA in Chlamydomonas reinhardtii. Mol Cell Biol. 1998;18(3):1498-505.
[59]
Yohn CB, Cohen A, Danon A, Mayfield SP. A poly(A) binding protein functions in the chloroplast as a message-specific translation factor. Proc Natl Acad Sci U S A. 1998;95(5):2238-43.
[60]
Yohn CB, Cohen A, Rosch C, Kuchka MR, Mayfield SP. Translation of the chloroplast psbA mRNA requires the nuclear-encoded poly(A)-binding protein, RB47. J Cell Biol. 1998;142(2):435-42.
[61]
Kudla J, Hayes R, Gruissem W. Polyadenylation accelerates degradation of chloroplast mRNA. EMBO J. 1996;15(24):7137-46.
[62]
Lisitsky I, Kotler A, Schuster G. The mechanism of preferential degradation of polyadenylated RNA in the chloroplast. The exoribonuclease 100RNP/polynucleotide phosphorylase displays high binding affinity for poly(A) sequence. J Biol Chem. 1997;272(28):17648-53.
[63]
Manley JL. Messenger RNA polyadenylylation: a universal modification. Proc Natl Acad Sci U S A. 1995;92(6):1800-1.
[65]
Xu F, Lin-Chao S, Cohen SN. 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 U S A. 1993;90(14):6756-60.
[66]
Sachs A, Wahle E. Poly(A) tail metabolism and function in eucaryotes. J Biol Chem. 1993;268(31):22955-8.
[68]
Yue D, Maizels N, Weiner AM. CCA-adding enzymes and poly(A) polymerases are all members of the same nucleotidyltransferase superfamily: characterization of the CCA-adding enzyme from the archaeal hyperthermophile Sulfolobus shibatae. RNA. 1996;2(9):895-908.
[69]
Yehudai-Resheff S, Schuster G. Characterization of the E.coli poly(A) polymerase: nucleotide specificity, RNA-binding affinities and RNA structure dependence. Nucleic Acids Res. 2000;28(5):1139-44.
[70]
Kalapos MP, Paulus H, Sarkar N. Identification of ribosomal protein S1 as a poly(A) binding protein in Escherichia coli. Biochimie. 1997;79(8):493-502.
[71]
Xu F, Cohen SN. RNA degradation in Escherichia coli regulated by 3' adenylation and 5' phosphorylation. Nature. 1995;374(6518):180-3.
[72]
Huang H, Liao J, Cohen SN. Poly(A)- and poly(U)-specific RNA 3' tail shortening by E. coli ribonuclease E. Nature. 1998;391(6662):99-102.
[73]
O'Hara EB, Chekanova JA, Ingle CA, Kushner ZR, Peters E, Kushner SR. Polyadenylylation helps regulate mRNA decay in Escherichia coli. Proc Natl Acad Sci U S A. 1995;92(6):1807-11.
[74]
Coburn GA, Mackie GA. Reconstitution of the degradation of the mRNA for ribosomal protein S20 with purified enzymes. J Mol Biol. 1998;279(5):1061-74.
[75]
Hajnsdorf E, R?gnier P. E. coli RpsO mRNA decay: RNase E processing at the beginning of the coding sequence stimulates poly(A)-dependent degradation of the mRNA. J Mol Biol. 1999;286(4):1033-43.
[76]
Hajnsdorf E, R?gnier P. Host factor Hfq of Escherichia coli stimulates elongation of poly(A) tails by poly(A) polymerase I. Proc Natl Acad Sci U S A. 2000;97(4):1501-5.
[77]
Virology. Ed. B N Fields, 1985 Raven Press. 1614 p.
[78]
Preiss T, Hentze MW. Dual function of the messenger RNA cap structure in poly(A)-tail-promoted translation in yeast. Nature. 1998;392(6675):516-20.
[79]
Poon LL, Pritlove DC, Sharps J, Brownlee GG. The RNA polymerase of influenza virus, bound to the 5' end of virion RNA, acts in cis to polyadenylate mRNA. J Virol. 1998;72(10):8214-9.
[80]
Poon LL, Pritlove DC, Fodor E, Brownlee GG. Direct evidence that the poly(A) tail of influenza A virus mRNA is synthesized by reiterative copying of a U track in the virion RNA template. J Virol. 1999;73(4):3473-6.
[81]
Poon LL, Fodor E, Brownlee GG. Polyuridylated mRNA synthesized by a recombinant influenza virus is defective in nuclear export. J Virol. 2000;74(1):418-27.
[82]
Plotch SJ, Bouloy M, Ulmanen I, Krug RM. A unique cap(m7GpppXm)-dependent influenza virion endonuclease cleaves capped RNAs to generate the primers that initiate viral RNA transcription. Cell. 1981;23(3):847-58.
[83]
Chen Z, Li Y, Krug RM. Influenza A virus NS1 protein targets poly(A)-binding protein II of the cellular 3'-end processing machinery. EMBO J. 1999;18(8):2273-83.
[84]
Hwang LN, Englund N, Pattnaik AK. Polyadenylation of vesicular stomatitis virus mRNA dictates efficient transcription termination at the intercistronic gene junctions. J Virol. 1998;72(3):1805-13.
[85]
Gershon PD, Ahn BY, Garfield M, Moss B. Poly(A) polymerase and a dissociable polyadenylation stimulatory factor encoded by vaccinia virus. Cell. 1991;66(6):1269-78.
[86]
Deng L, Johnson L, Neveu JM, Hardin S, Wang SM, Lane WS, Gershon PD. A polyadenylylation-specific RNA-contact site on the surface of the bifunctional vaccinia virus RNA modifying protein VP39 that is distinct from the mRNA 5' end-binding "cleft". J Mol Biol. 1999;285(4):1417-27.
[87]
Lu C, Bablanian R. Characterization of small nontranslated polyadenylylated RNAs in vaccinia virus-infected cells. Proc Natl Acad Sci U S A. 1996;93(5):2037-42.
[88]
Masison DC, Blanc A, Ribas JC, Carroll K, Sonenberg N, Wickner RB. Decoying the cap- mRNA degradation system by a double-stranded RNA virus and poly(A)- mRNA surveillance by a yeast antiviral system. Mol Cell Biol. 1995;15(5):2763-71.
[89]
Leathers V, Tanguay R, Kobayashi M, Gallie DR. A phylogenetically conserved sequence within viral 3' untranslated RNA pseudoknots regulates translation. Mol Cell Biol. 1993;13(9):5331-47.
[90]
Tsai CH, Cheng CP, Peng CW, Lin BY, Lin NS, Hsu YH. Sufficient length of a poly(A) tail for the formation of a potential pseudoknot is required for efficient replication of bamboo mosaic potexvirus RNA. J Virol. 1999;73(4):2703-9.
[91]
de Vries H, R?egsegger U, H?bner W, Friedlein A, Langen H, Keller W. Human pre-mRNA cleavage factor II(m) contains homologs of yeast proteins and bridges two other cleavage factors. EMBO J. 2000;19(21):5895-904.
[92]
Bai C, Tolias PP. Drosophila clipper/CPSF 30K is a post-transcriptionally regulated nuclear protein that binds RNA containing GC clusters. Nucleic Acids Res. 1998;26(7):1597-604.
[93]
Raynal LC, Carpousis AJ. Poly(A) polymerase I of Escherichia coli: characterization of the catalytic domain, an RNA binding site and regions for the interaction with proteins involved in mRNA degradation. Mol Microbiol. 1999;32(4):765-75.
[94]
Li QS, Gupta JD, Hunt AG. Polynucleotide phosphorylase is a component of a novel plant poly(A) polymerase. J Biol Chem. 1998;273(28):17539-43.