Abstract
The first processing step of precursor ribosomal RNA (pre-rRNA) involves a cleavage within the 5' external transcribed spacer. This processing requires sequences downstream of the cleavage site which are perfectly conserved among human, mouse and Xenopus and also several small nucleolar RNAs (snoRNAs): U3, U14, U17 and E3. In this study, we show that nucleolin, one of the major RNA-binding proteins of the nucleolus, is involved in the early cleavage of pre-rRNA. Nucleolin interacts with the pre-rRNA substrate, and we demonstrate that this interaction is required for the processing reaction in vitro. Furthermore, we show that nucleolin interacts with the U3 snoRNP. Increased levels of nucleolin, in the presence of the U3 snoRNA, activate the processing activity of a S100 cell extract. Our results suggest that the interaction of nucleolin with the pre-rRNA substrate might be a limiting step in the primary processing reaction. Nucleolin is the first identified metazoan proteinaceous factor that interacts directly with the rRNA substrate and that is required for the processing reaction. Potential roles for nucleolin in the primary processing reaction and in ribosome biogenesis are discussed.
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- Bach R., Grummt I., Allet B. The nucleotide sequence of the initiation region of the ribosomal transcription unit from mouse. Nucleic Acids Res. 1981 Apr 10;9(7):1559–1569. doi: 10.1093/nar/9.7.1559. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Belenguer P., Baldin V., Mathieu C., Prats H., Bensaid M., Bouche G., Amalric F. Protein kinase NII and the regulation of rDNA transcription in mammalian cells. Nucleic Acids Res. 1989 Aug 25;17(16):6625–6636. doi: 10.1093/nar/17.16.6625. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Belenguer P., Caizergues-Ferrer M., Labbé J. C., Dorée M., Amalric F. Mitosis-specific phosphorylation of nucleolin by p34cdc2 protein kinase. Mol Cell Biol. 1990 Jul;10(7):3607–3618. doi: 10.1128/mcb.10.7.3607. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Beltrame M., Tollervey D. Identification and functional analysis of two U3 binding sites on yeast pre-ribosomal RNA. EMBO J. 1992 Apr;11(4):1531–1542. doi: 10.1002/j.1460-2075.1992.tb05198.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bharti A. K., Olson M. O., Kufe D. W., Rubin E. H. Identification of a nucleolin binding site in human topoisomerase I. J Biol Chem. 1996 Jan 26;271(4):1993–1997. doi: 10.1074/jbc.271.4.1993. [DOI] [PubMed] [Google Scholar]
- Blum B., Pierron G., Seebeck T., Braun R. Processing in the external transcribed spacer of ribosomal RNA from Physarum polycephalum. Nucleic Acids Res. 1986 Apr 25;14(8):3153–3166. doi: 10.1093/nar/14.8.3153. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bouche G., Baldin V., Belenguer P., Prats H., Amalric F. Activation of rDNA transcription by FGF-2: key role of protein kinase CKII. Cell Mol Biol Res. 1994;40(5-6):547–554. [PubMed] [Google Scholar]
- Bouche G., Caizergues-Ferrer M., Bugler B., Amalric F. Interrelations between the maturation of a 100 kDa nucleolar protein and pre rRNA synthesis in CHO cells. Nucleic Acids Res. 1984 Apr 11;12(7):3025–3035. doi: 10.1093/nar/12.7.3025. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bourbon H. M., Bugler B., Caizergues-Ferrer M., Amalric F., Zalta J. P. Maturation of a 100 kDa protein associated with preribosomes in Chinese hamster ovary cells. Mol Biol Rep. 1983 May;9(1-2):39–47. doi: 10.1007/BF00777472. [DOI] [PubMed] [Google Scholar]
- Bourbon H., Bugler B., Caizergues-Ferrer M., Amalric F. Role of phosphorylation on the maturation pathways of a 100 kDa nucleolar protein. FEBS Lett. 1983 May 8;155(2):218–222. doi: 10.1016/0014-5793(82)80606-6. [DOI] [PubMed] [Google Scholar]
- Bourquin J. P., Stagljar I., Meier P., Moosmann P., Silke J., Baechi T., Georgiev O., Schaffner W. A serine/arginine-rich nuclear matrix cyclophilin interacts with the C-terminal domain of RNA polymerase II. Nucleic Acids Res. 1997 Jun 1;25(11):2055–2061. doi: 10.1093/nar/25.11.2055. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bouvet P., Jain C., Belasco J. G., Amalric F., Erard M. RNA recognition by the joint action of two nucleolin RNA-binding domains: genetic analysis and structural modeling. EMBO J. 1997 Sep 1;16(17):5235–5246. doi: 10.1093/emboj/16.17.5235. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bugler B., Bourbon H., Lapeyre B., Wallace M. O., Chang J. H., Amalric F., Olson M. O. RNA binding fragments from nucleolin contain the ribonucleoprotein consensus sequence. J Biol Chem. 1987 Aug 15;262(23):10922–10925. [PubMed] [Google Scholar]
- Bugler B., Caizergues-Ferrer M., Bouche G., Bourbon H., Amalric F. Detection and localization of a class of proteins immunologically related to a 100-kDa nucleolar protein. Eur J Biochem. 1982 Nov 15;128(2-3):475–480. doi: 10.1111/j.1432-1033.1982.tb06989.x. [DOI] [PubMed] [Google Scholar]
- Caizergues-Ferrer M., Belenguer P., Lapeyre B., Amalric F., Wallace M. O., Olson M. O. Phosphorylation of nucleolin by a nucleolar type NII protein kinase. Biochemistry. 1987 Dec 1;26(24):7876–7883. doi: 10.1021/bi00398a051. [DOI] [PubMed] [Google Scholar]
- Craig N., Kass S., Sollner-Webb B. Nucleotide sequence determining the first cleavage site in the processing of mouse precursor rRNA. Proc Natl Acad Sci U S A. 1987 Feb;84(3):629–633. doi: 10.1073/pnas.84.3.629. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Craig N., Kass S., Sollner-Webb B. Sequence organization and RNA structural motifs directing the mouse primary rRNA-processing event. Mol Cell Biol. 1991 Jan;11(1):458–467. doi: 10.1128/mcb.11.1.458. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Egyhazi E., Pigon A., Chang J. H., Ghaffari S. H., Dreesen T. D., Wellman S. E., Case S. T., Olson M. O. Effects of anti-C23 (nucleolin) antibody on transcription of ribosomal DNA in Chironomus salivary gland cells. Exp Cell Res. 1988 Oct;178(2):264–272. doi: 10.1016/0014-4827(88)90397-7. [DOI] [PubMed] [Google Scholar]
- Eichler D. C., Craig N. Processing of eukaryotic ribosomal RNA. Prog Nucleic Acid Res Mol Biol. 1994;49:197–239. doi: 10.1016/s0079-6603(08)60051-3. [DOI] [PubMed] [Google Scholar]
- Eichler D. C., Eales S. J. Isolation and characterization of a single-stranded specific endoribonuclease from Ehrlich cell nucleoli. J Biol Chem. 1982 Dec 10;257(23):14384–14389. [PubMed] [Google Scholar]
- Elela S. A., Igel H., Ares M., Jr RNase III cleaves eukaryotic preribosomal RNA at a U3 snoRNP-dependent site. Cell. 1996 Apr 5;85(1):115–124. doi: 10.1016/s0092-8674(00)81087-9. [DOI] [PubMed] [Google Scholar]
- Enright C. A., Maxwell E. S., Eliceiri G. L., Sollner-Webb B. 5'ETS rRNA processing facilitated by four small RNAs: U14, E3, U17, and U3. RNA. 1996 Nov;2(11):1094–1099. [PMC free article] [PubMed] [Google Scholar]
- Erard M. S., Belenguer P., Caizergues-Ferrer M., Pantaloni A., Amalric F. A major nucleolar protein, nucleolin, induces chromatin decondensation by binding to histone H1. Eur J Biochem. 1988 Aug 15;175(3):525–530. doi: 10.1111/j.1432-1033.1988.tb14224.x. [DOI] [PubMed] [Google Scholar]
- Escande-Géraud M. L., Azum M. C., Tichadou J. L., Gas N. Correlation between rDNA transcription and distribution of a 100 kD nucleolar protein in CHO cells. Exp Cell Res. 1985 Dec;161(2):353–363. doi: 10.1016/0014-4827(85)90092-8. [DOI] [PubMed] [Google Scholar]
- Ghisolfi-Nieto L., Joseph G., Puvion-Dutilleul F., Amalric F., Bouvet P. Nucleolin is a sequence-specific RNA-binding protein: characterization of targets on pre-ribosomal RNA. J Mol Biol. 1996 Jul 5;260(1):34–53. doi: 10.1006/jmbi.1996.0380. [DOI] [PubMed] [Google Scholar]
- Gurney T., Jr Characterization of mouse 45S ribosomal RNA subspecies suggests that the first processing cleavage occurs 600 +/- 100 nucleotides from the 5' end and the second 500 +/- 100 nucleotides from the 3' end of a 13.9 kb precursor. Nucleic Acids Res. 1985 Jul 11;13(13):4905–4919. doi: 10.1093/nar/13.13.4905. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hanakahi L. A., Dempsey L. A., Li M. J., Maizels N. Nucleolin is one component of the B cell-specific transcription factor and switch region binding protein, LR1. Proc Natl Acad Sci U S A. 1997 Apr 15;94(8):3605–3610. doi: 10.1073/pnas.94.8.3605. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Herrera A. H., Olson M. O. Association of protein C23 with rapidly labeled nucleolar RNA. Biochemistry. 1986 Oct 7;25(20):6258–6264. doi: 10.1021/bi00368a063. [DOI] [PubMed] [Google Scholar]
- Hughes J. M., Ares M., Jr Depletion of U3 small nucleolar RNA inhibits cleavage in the 5' external transcribed spacer of yeast pre-ribosomal RNA and impairs formation of 18S ribosomal RNA. EMBO J. 1991 Dec;10(13):4231–4239. doi: 10.1002/j.1460-2075.1991.tb05001.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kass S., Craig N., Sollner-Webb B. Primary processing of mammalian rRNA involves two adjacent cleavages and is not species specific. Mol Cell Biol. 1987 Aug;7(8):2891–2898. doi: 10.1128/mcb.7.8.2891. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kass S., Sollner-Webb B. The first pre-rRNA-processing event occurs in a large complex: analysis by gel retardation, sedimentation, and UV cross-linking. Mol Cell Biol. 1990 Sep;10(9):4920–4931. doi: 10.1128/mcb.10.9.4920. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kass S., Tyc K., Steitz J. A., Sollner-Webb B. The U3 small nucleolar ribonucleoprotein functions in the first step of preribosomal RNA processing. Cell. 1990 Mar 23;60(6):897–908. doi: 10.1016/0092-8674(90)90338-f. [DOI] [PubMed] [Google Scholar]
- Kharrat A., Derancourt J., Dorée M., Amalric F., Erard M. Synergistic effect of histone H1 and nucleolin on chromatin condensation in mitosis: role of a phosphorylated heteromer. Biochemistry. 1991 Oct 22;30(42):10329–10336. doi: 10.1021/bi00106a034. [DOI] [PubMed] [Google Scholar]
- Kim E., Du L., Bregman D. B., Warren S. L. Splicing factors associate with hyperphosphorylated RNA polymerase II in the absence of pre-mRNA. J Cell Biol. 1997 Jan 13;136(1):19–28. doi: 10.1083/jcb.136.1.19. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lübben B., Marshallsay C., Rottmann N., Lührmann R. Isolation of U3 snoRNP from CHO cells: a novel 55 kDa protein binds to the central part of U3 snoRNA. Nucleic Acids Res. 1993 Nov 25;21(23):5377–5385. doi: 10.1093/nar/21.23.5377. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Maden B. E. The numerous modified nucleotides in eukaryotic ribosomal RNA. Prog Nucleic Acid Res Mol Biol. 1990;39:241–303. doi: 10.1016/s0079-6603(08)60629-7. [DOI] [PubMed] [Google Scholar]
- Maser R. L., Calvet J. P. U3 small nuclear RNA can be psoralen-cross-linked in vivo to the 5' external transcribed spacer of pre-ribosomal-RNA. Proc Natl Acad Sci U S A. 1989 Sep;86(17):6523–6527. doi: 10.1073/pnas.86.17.6523. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Maxwell E. S., Fournier M. J. The small nucleolar RNAs. Annu Rev Biochem. 1995;64:897–934. doi: 10.1146/annurev.bi.64.070195.004341. [DOI] [PubMed] [Google Scholar]
- McCracken S., Fong N., Yankulov K., Ballantyne S., Pan G., Greenblatt J., Patterson S. D., Wickens M., Bentley D. L. The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature. 1997 Jan 23;385(6614):357–361. doi: 10.1038/385357a0. [DOI] [PubMed] [Google Scholar]
- Michot B., Bachellerie J. P. Secondary structure of the 5' external transcribed spacer of vertebrate pre-rRNA. Presence of phylogenetically conserved features. Eur J Biochem. 1991 Feb 14;195(3):601–609. doi: 10.1111/j.1432-1033.1991.tb15743.x. [DOI] [PubMed] [Google Scholar]
- Miesfeld R., Arnheim N. Identification of the in vivo and in vitro origin of transcription in human rDNA. Nucleic Acids Res. 1982 Jul 10;10(13):3933–3949. doi: 10.1093/nar/10.13.3933. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Miller K. G., Sollner-Webb B. Transcription of mouse rRNA genes by RNA polymerase I: in vitro and in vivo initiation and processing sites. Cell. 1981 Nov;27(1 Pt 2):165–174. doi: 10.1016/0092-8674(81)90370-6. [DOI] [PubMed] [Google Scholar]
- Miller O. L., Jr, Bakken A. H. Morphological studies of transcription. Acta Endocrinol Suppl (Copenh) 1972;168:155–177. doi: 10.1530/acta.0.071s155. [DOI] [PubMed] [Google Scholar]
- Miller O. L., Jr, Beatty B. R. Visualization of nucleolar genes. Science. 1969 May 23;164(3882):955–957. doi: 10.1126/science.164.3882.955. [DOI] [PubMed] [Google Scholar]
- Mougey E. B., O'Reilly M., Osheim Y., Miller O. L., Jr, Beyer A., Sollner-Webb B. The terminal balls characteristic of eukaryotic rRNA transcription units in chromatin spreads are rRNA processing complexes. Genes Dev. 1993 Aug;7(8):1609–1619. doi: 10.1101/gad.7.8.1609. [DOI] [PubMed] [Google Scholar]
- Mougey E. B., Pape L. K., Sollner-Webb B. A U3 small nuclear ribonucleoprotein-requiring processing event in the 5' external transcribed spacer of Xenopus precursor rRNA. Mol Cell Biol. 1993 Oct;13(10):5990–5998. doi: 10.1128/mcb.13.10.5990. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ohmori H., Murakami T., Furutani A., Higashi K., Hirano H., Gotoh S., Kuroiwa A., Masui A., Nakamura T., Amalric F. Simultaneous activation of heat shock protein (hsp 70) and nucleolin genes during in vivo and in vitro prereplicative stages of rat hepatocytes. Exp Cell Res. 1990 Aug;189(2):227–232. doi: 10.1016/0014-4827(90)90240-b. [DOI] [PubMed] [Google Scholar]
- Olson M. O., Rivers Z. M., Thompson B. A., Kao W. Y., Case S. T. Interaction of nucleolar phosphoprotein C23 with cloned segments of rat ribosomal deoxyribonucleic acid. Biochemistry. 1983 Jul 5;22(14):3345–3351. doi: 10.1021/bi00283a007. [DOI] [PubMed] [Google Scholar]
- Parker K. A., Steitz J. A. Structural analysis of the human U3 ribonucleoprotein particle reveal a conserved sequence available for base pairing with pre-rRNA. Mol Cell Biol. 1987 Aug;7(8):2899–2913. doi: 10.1128/mcb.7.8.2899. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Peter M., Nakagawa J., Dorée M., Labbé J. C., Nigg E. A. Identification of major nucleolar proteins as candidate mitotic substrates of cdc2 kinase. Cell. 1990 Mar 9;60(5):791–801. doi: 10.1016/0092-8674(90)90093-t. [DOI] [PubMed] [Google Scholar]
- Savino R., Gerbi S. A. Preribosomal RNA processing in Xenopus oocytes does not include cleavage within the external transcribed spacer as an early step. Biochimie. 1991 Jun;73(6):805–812. doi: 10.1016/0300-9084(91)90060-e. [DOI] [PubMed] [Google Scholar]
- Scheer U., Benavente R. Functional and dynamic aspects of the mammalian nucleolus. Bioessays. 1990 Jan;12(1):14–21. doi: 10.1002/bies.950120104. [DOI] [PubMed] [Google Scholar]
- Serin G., Joseph G., Faucher C., Ghisolfi L., Bouche G., Amalric F., Bouvet P. Localization of nucleolin binding sites on human and mouse pre-ribosomal RNA. Biochimie. 1996;78(6):530–538. doi: 10.1016/0300-9084(96)84759-6. [DOI] [PubMed] [Google Scholar]
- Serin G., Joseph G., Ghisolfi L., Bauzan M., Erard M., Amalric F., Bouvet P. Two RNA-binding domains determine the RNA-binding specificity of nucleolin. J Biol Chem. 1997 May 16;272(20):13109–13116. doi: 10.1074/jbc.272.20.13109. [DOI] [PubMed] [Google Scholar]
- Shumard C. M., Eichler D. C. Ribosomal RNA processing. Limited cleavages of mouse preribosomal RNA by a nucleolar endoribonuclease include the early +650 processing site. J Biol Chem. 1988 Dec 25;263(36):19346–19352. [PubMed] [Google Scholar]
- Sirri V., Roussel P., Trerè D., Derenzini M., Hernandez-Verdun D. Amount variability of total and individual Ag-NOR proteins in cells stimulated to proliferate. J Histochem Cytochem. 1995 Sep;43(9):887–893. doi: 10.1177/43.9.7642962. [DOI] [PubMed] [Google Scholar]
- Stroke I. L., Weiner A. M. The 5' end of U3 snRNA can be crosslinked in vivo to the external transcribed spacer of rat ribosomal RNA precursors. J Mol Biol. 1989 Dec 5;210(3):497–512. doi: 10.1016/0022-2836(89)90126-5. [DOI] [PubMed] [Google Scholar]
- Suzuki N., Matsui H., Hosoya T. Effects of androgen and polyamines on the phosphorylation of nucleolar proteins from rat ventral prostates with particular reference to 110-kDa phosphoprotein. J Biol Chem. 1985 Jul 5;260(13):8050–8055. [PubMed] [Google Scholar]
- Tollervey D. Trans-acting factors in ribosome synthesis. Exp Cell Res. 1996 Dec 15;229(2):226–232. doi: 10.1006/excr.1996.0364. [DOI] [PubMed] [Google Scholar]
- Tyc K., Steitz J. A. A new interaction between the mouse 5' external transcribed spacer of pre-rRNA and U3 snRNA detected by psoralen crosslinking. Nucleic Acids Res. 1992 Oct 25;20(20):5375–5382. doi: 10.1093/nar/20.20.5375. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Urano Y., Kominami R., Mishima Y., Muramatsu M. The nucleotide sequence of the putative transcription initiation site of a cloned ribosomal RNA gene of the mouse. Nucleic Acids Res. 1980 Dec 20;8(24):6043–6058. doi: 10.1093/nar/8.24.6043. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Warrener P., Petryshyn R. Phosphorylation and proteolytic degradation of nucleolin from 3T3-F442A cells. Biochem Biophys Res Commun. 1991 Oct 31;180(2):716–723. doi: 10.1016/s0006-291x(05)81124-6. [DOI] [PubMed] [Google Scholar]
- Yang T. H., Tsai W. H., Lee Y. M., Lei H. Y., Lai M. Y., Chen D. S., Yeh N. H., Lee S. C. Purification and characterization of nucleolin and its identification as a transcription repressor. Mol Cell Biol. 1994 Sep;14(9):6068–6074. doi: 10.1128/mcb.14.9.6068. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Yuryev A., Patturajan M., Litingtung Y., Joshi R. V., Gentile C., Gebara M., Corden J. L. The C-terminal domain of the largest subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteins. Proc Natl Acad Sci U S A. 1996 Jul 9;93(14):6975–6980. doi: 10.1073/pnas.93.14.6975. [DOI] [PMC free article] [PubMed] [Google Scholar]