ISSN 1214-0287 (on-line)
ISSN 1214-021X (printed)

Volume 2 (2004), No 3, p 151-161

Nucleolins from different model organisms have conserved sequences reflecting the conservation of key cellular functions through evolution

Fernando Gonzalez-Camacho, Francisco Javier Medina

Address: Francisco Javier Medina Diaz, Centro de Investigaciones Biologicas (CSIC), Ramiro de Maeztu 9, E-28040 Madrid, Spain

Received 18th May 2004.
Published online 18th June 2004.

Full text article (pdf)

Sequences available in public protein databases belonging to nucleolin or nucleolin-like proteins have been aligned using public domain software, in order to obtain relevant data regarding the degree of their conservation, which could be a reflection of the degree of conservation of the functions currently attributed to this protein. Nucleolin is known to be a nucleolar multifunctional protein, involved in different steps of pre-rRNA transcription and processing. Three domains are constantly present in all nucleolins, namely a series of acidic/serin (Ac/Ser) sequences, a number of RNA recognition motifs (RRM) and a region rich in glycin and arginin (GAR). The number of motifs present in each one of the three domains is variable. Furthermore, we have characterized in all nucleolins the presence of a bipartite consensus nuclear localization sequence (NLS). The only cases in which this sequence with a definite structure was not totally evident were in the yeast S. pombe (a possible monopartite structure) and in the protozoan T. thermophyla, in which it appears to be absent. Finally, we have constructed the phylogenetic tree of the 15 species investigated, taking exclusively the data regarding this protein. Interestingly, the tree obtained closely resembles the organization of these taxonomic groups throughout evolution, as it is presently known. We conclude that nucleolin is a highly conserved protein, whose gene was already present in an ancestor eukaryotic species, at an early stage of the evolutionary process, from which it has evolved very slowly. This is a reflection of the fundamental functions carried out by this protein, which were already fixed in the ancestor species.

nucleolar protein; nuclear localization sequence; RNA recognition motifs; glycin-arginin-rich; phylogenetic study; evolution

Alvarez M, Quezada C, Navarro C, Molina A, Bouvet P, Krauskopf M, Vera MI: An increased expression of nucleolin is associated with a physiological nucleolar segregation. Biochem Biophys Res Commun 301:152-158, 2003.

Belenguer P, Caizergues-Ferrer M, Labbe JC, Doree M, Amalric F: Mitosis-specific phosphorylation of nucleolin by p34cdc2 protein kinase. Mol Cell Biol 10:3607-3618, 1990.

Bogre L, Jonak C, Mink M, Meskiene I, Traas J, Ha DTC, Swoboda I, Plank C, Wagner E, Heberle-Bors E, Hirt H: Developmental and cell cycle regulation of alfalfa nucMs1, a plant homolog of the yeast Nsr1 and mammalian nucleolin. Plant Cell 8:417-428, 1996.

Borer RA, Lehner CF, Eppenberger HM, Nigg EA: Major nucleolar proteins shuttle between nucleus and cytoplasm. Cell 56:379-390, 1989.

Bourbon HM, Amalric F: Nucleolin gene organization in rodents: highly conserved sequences within three of the 13 introns. Gene 88:187-196, 1990.

Bourbon HM, Lapeyre B, Amalric F: Structure of the mouse nucleolin gene: The complete sequence reveals that each RNA binding domain is encoded by two independent exons. J Mol Biol 200:627-638, 1988.

Caizergues-Ferrer M, Belenguer P, Lapeyre B, Amalric F, Wallace MO, Olson MOJ: Phosphorylation of nucleolin by a nuclear type NII protein kinase. Biochemistry 26:7876-7883, 1987.

Caizergues-Ferrer M, Mariottini P, Curie C, Lapeyre B, Gas N, Amalric F, Amaldi F: Nucleolin from Xenopus laevis: cDNA cloning and expression during development. Genes Dev 3:324-333, 1989.

Combet C, Blanchet C, Geourjon C, Deleage G: NPS@: network protein sequence analysis. Trends Biochem Sci 25:147-150, 2000.

De Carcer G, Cerdido A, Medina FJ: NopA64, a novel nucleolar phosphoprotein from proliferating onion cells, sharing immunological determinants with mammalian nucleolin. Planta 201:487-495, 1997.

Ghisolfi L, Kharrat A, Joseph G, Amalric F, Erard M: Concerted activities of the RNA recognition and the glycine- rich C-terminal domains of nucleolin are required for efficient complex formation with pre-ribosomal RNA. Eur J Biochem 209:541-548, 1992.

Ginisty H, Sicard H, Roger B, Bouvet P: Structure and functions of nucleolin. J Cell Sci 112:761-772, 1999.

Gonzalez-Camacho F, Medina FJ: Identification of specific plant nucleolar phosphoproteins in a functional proteomic analysis. Proteomics 4:407-417, 2004.

Gulli MP, Girard J-P, Zabetakis D, Lapeyre B, Melese T, Caizergues-Ferrer M: gar2 is a nucleolar protein from Schizosaccharomyces pombe required for 18S rRNA and 40S ribosomal subunit accumulation. Nucl Acids Res 23:1912-1918, 1995.

Kaneko T, Kato T, Sato S, Nakamura Y, Asamizu E, Tabata S: Sequence of Arabidopsis thaliana nucleolin-like protein. Protein Database EMBL/GenBank/DDBJ, 2000.

Lapeyre B, Bourbon HM, Amalric F: Nucleolin, the major nucleolar protein of growing eukaryotic cells: an unusual protein structure revealed by the nucleotide sequence. Proc Nat Acad Sci USA 84:1472-1476, 1987.

Lee WC, Xue Z, Melese T: The NSR1 gene encodes a protein that specifically binds nuclear localization sequences and has two RNA recognition motifs. J Cell Biol 113:1-12, 1991.

Leger-Silvestre I, Gulli MP, Noaillac-Depeyre J, Faubladier M, Sicard H, Caizergues-Ferrer M, Gas N: Ultrastructural changes in the Schizosaccharomyces pombe nucleolus following the disruption of the gar2+ gene, which encodes a nucleolar protein structurally related to nucleolin. Chromosoma 105:542-552, 1997.

Maeshima M, Matsuda N: Sequence of Nicotiana tabacum nucleolin-like protein. Protein Database EMBL/GenBank/DDBJ, 2002.

Maridor G, Krek W, Nigg EA: Structure and developmental expression of chicken nucleolin and NO38: coordinate expression of two abundant non-ribosomal nucleolar proteins. Biochim Biophys Acta 1049:126-133, 1990.

Martin M, Garcia-Fernandez LF, Moreno Diaz de la Espina S, Noaillac-Depeyre J, Gas N, Medina FJ: Identification and localization of a nucleolin homologue in onion nucleoli. Exp Cell Res 199:74-84, 1992.

McGrath KE, Smothers JF, Dadd CA, Madireddi MT, Gorovsky MA, Allis CD: An abundant nucleolar phosphoprotein is associated with ribosomal DNA in Tetrahymena macronuclei. Mol Biol Cell 8:97-108, 1997.

Medina FJ, Gonzalez-Camacho F, Cerdido A, De Carcer G: In situ localization of the onion nucleolar protein NopA64 is dependent on cell proliferation mechanisms and cell cycle phases. In Dini L and Catalano M (eds.): Proc. 5th Multinational Cong. Electron Microscopy. Rinton Press Inc., Princeton, New Jersey. 2001, pp. 197-207.

Olson MOJ: The role of proteins in nucleolar structure and function. In Strauss PR and Wilson SH (eds.): The eukaryotic nucleus. Molecular biochemistry and macromolecular assemblies. The Telford Press, Caldwell, New Jersey 1991, pp. 519-559.

Orrick L, Olson MOJ, Busch H: Comparison of nucleolar proteins of normal rat liver and Novikoff hepatoma ascites cells by two dimensional polyacrylamide gel electrophoresis. Proc Nat Acad Sci USA 70:1316-1320, 1973.

Peter M, Nakagawa J, Doree M, Labbe JC, Nigg EA: Identification of major nucleolar proteins as candidate mitotic substrates of cdc2 kinase. Cell 60:791-801, 1990.

Prestayko AW, Klomp GR, Schmoll DJ, Busch H: Comparison of proteins of ribosomal subunits and nucleolar preribosomal particles from Novikoff hepatoma ascites cells by two-dimensional polyacrylamide gel electrophoresis. Biochemistry 13:1945-1951, 1974.

Rankin ML, Heine MA, Xiao S, LeBlanc MD, Nelson JW, DiMario PJ: A complete nucleolin cDNA sequence from Xenopus laevis. Nucl Acids Res 21:169, 1993.

Rappsilber J, Ryder U, Lamond A, Mann M: Large-Scale proteomic analysis of the human spliceosome. Genome Res 12:1231-1245, 2002.

Schmidt-Zachmann MS, Nigg EA: Protein localization to the nucleolus: A search for targeting domains in nucleolin. J Cell Sci 105:799-806, 1993.

Srivastava M, McBride OW, Fleming PJ, Pollard HB, Burns AL: Genomic organization and chromosomal localization of the human nucleolin gene. J Biol Chem 265:14922-14935, 1990.

Tanaka KJ, Kawamuea H, Nishikata T: The transcript coding for an RNA-binding protein is localized in the anterior side of the ascidian 2-cell stage embryo. Dev Genes Evol 210:464-466, 2004.

Thompson JD, Higgins DG, Gibson TJ: Clustal-W, improving the sensitivity of progressive multiple alignment through sequence weighting. Nucl Acids Res 22:4673-4680, 1994.

Tong CG, Reichler S, Blumenthal S, Balk J, Hsieh HL, Roux SJ: Light regulation of the abundance of mRNA encoding a nucleolin-like protein localized in the nucleoli of pea nuclei. Plant Physiol 114:643-652, 1997.

Tuteja R, Tuteja N: Nucleolin: a multifunctional major nucleolar protein. CRC Crit Rev Biochem Mol Biol 33:407-436, 1998.

Sobol M, Gonzalez-Camacho F, Rodriguez-Vilarino V, Kordyum E, Medina FJ: Subnucleolar location of fibrillarin and NopA64 in Lepidium sativum root meristematic cells is changed in altered gravity. Protoplasma 228:209-219, 2006.

McCain J, Danzy L, Hamdi A, Dellafosse O, DiMario P: Tracking nucleolar dynamics with GFP-Nopp140 during Drosophila oogenesis and embryogenesis. Cell Tissue Res 323:105-115, 2006.