Ubiquitins (polyubiquitin and ubiquitin extension protein) in marine sponges: cDNA sequence and phylogenetic analysis

Biological Journal of the Linnean Society

Volumn 67, Issue 1, 1999, Pages 43-56

  Wiens, Matthias ^a   Lukic, Lada ^b   Müller, Werner E G ^a   Gamulin, Vera ^b  

^a JOHANNES GUTENBERG UNIVERSITY   (Germany)

^b RUDER BO KOVI INSTITUTE   (Croatia)

Author keywords

Metazoa; Phylogeny; Porifera; Ribosomal protein

Indexed keywords

ANIMALIA; CALCAREA; DEMOSPONGIAE; EUKARYOTA; GEODIA CYDONIUM; INVERTEBRATA; METAZOA; PORIFERA; RAPHANUS; RAPHANUS SATIVUS; SCYPHA; SCYPHA RAPHANUS; SUBERITES DOMUNCULA;

EID: 0033010198     PISSN: 00244066     EISSN: None     Source Type: Journal    
DOI: 10.1006/bijl.1998.0286     Document Type: Article

References (51)

1. Ausubel FM, Brent R, Kingston RE, Moore DD, Smith JA, Seidmann JG, Struhl K. 1995. Current Protocols in Molecular Biology. New York: John Wiley and Sons.
2. Baker RT, Tobias JW, Varshavsky A. 1992. Ubiquitin specific proteases of Saccharomyces cerevisiae. Journal of Biological Chemistry 267: 23364-23375.
3. Baldauf SI, Palmer JD. 1993. Animals and fungi are each other's closest relatives: congruent evidence from multiple proteins. Proceedings of the National Academy of Sciences USA 90: 11558-11562.
4. Bishoff ST, Schwartz LM. 1990. Characterization of a ubiquitin-fusion gene from the tobacco hawkmoth, Manduca sexta. Nucleic Acids Research 18: 6039-6043.
5. Callis J, Raasch JA, Vierstra RD. 1990. Ubiquitin extension proteins of Arabidopsis thaliana: Structure, localization and expression of their promotors in transgenic tobacco. Journal of Biological Chemistry 265: 12486-12493.
6. Chan YL, Suzuki K, Wool IG. 1995. The carboxyl extensions of two rat ubiquitin fusion proteins are ribosomal proteins S27a and L40. Biochemical Biophysical Research Communications 215: 682-690.
7. Chevalier C, Le Querrec F, Raymond P. 1996. Sugar levels regulate the expression of ribosomal protein genes encoding protein S28 and ubiquitin-fused protein S27a in maize root tips. Plant Science 117: 95-105.
8. Dayhoff MO, Schwartz RM, Orcutt BC. 1978. A model of evolutionary change in protein. In: Dayhoff MO ed. Atlas of Protein Sequence and Structure Vol. 5 suppl. 3. Washington, DC, National Biomedical Research Foundation, 345-352.
9. Felsenstein J. 1993. PHYLIP, ver. 3.5. University of Washington, Seattle.
10. Gamulin V, Lukic L. 1998. Structure and evolution of genes encoding polyubiquitin in marine sponges. In: Müller WEG ed. Molecular Evolution: Towards the Origin of Metazoa. Progress in Molecular and Subcellular Biology Vol 21. Springer-Verlag, Heidelberg, 157-181.
11. Gamulin V, Rinkevich B, Schäcke H, Kruse M, Müller IM, Müller WEG. 1994. Cell adhesion receptors and nuclear receptors are highly conserved from the lowest Metazoa (marine sponges) to vertebrates. Biological Chemistry Hoppe-Seyler 375: 583-588.
12. Garbarino JE, Belknap WR. 1994. Isolation of a ubiquitin-ribosomal protein gene (ubi3) from potato and expression of its promoter in transgenic plants. Plant Molecular Biology 24: 119-127.
13. Goldstein G, Scheid M, Hammerling U, Boyse EA, Schlesinger DH, Niall HD. 1975. Isolation of a polypeptide that has lymphocyte-differentiating properties and is probably represented universally in living cells. Proceedings of the National Academy of Sciences USA 72: 11-15.
14. Hauser LJ, Roberson AE, Olins DE. 1991. Structure of the polyubiquitin gene in Euplotes. Chromosoma 100: 386-394.
15. Hershko A. 1996. Lessons from the discovery of the ubiquitin system. Trends in Biochemical Sciences 21: 445-449.
16. Hershko A, Ciechanover A. 1992. The ubiquitin system for protein degradation. Annual Review of Biochemistry 61: 761-807.
17. Hoffman NE, Ko K, Milkowski D, Pichersky E. 1991. Isolation and characterization of tomato cDNA and genomic clones encoding the ubiquitin gene ubi3. Plant Molecular Biology 17: 1189-1201.
18. Jentsch S, Seufert W, Hauser HP. 1991. Genetic analysis of the ubiquitin system. Biochimica Biophysica Acta 1089: 127-139.
19. Jones D, Candido PM. 1993. Novel ubiquitin-like ribosomal protein fusion genes from the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. Journal of Biological Chemistry 268: 19545-19551.
20. Kalderon D, Roberts BL, Richardson WD, Smith AE. 1984. A short amino acid sequence able to specify nuclear location. Cell 39: 499-509.
21. Keeling PJ, Doolittle WF. 1995. Concerted evolution in protists: recent homogenization of a polyubiquitin gene in Trichomonas vaginalis. Journal of Molecular Evolution 41: 556-562.
22. Kim HU, Yun CH, Cho WS, Kang SK, Chung TY. 1995. Nucleotide sequence of rice cDNA that encodes a ubiquitin protein and a 79-amino acid protein. Plant Physiology 108: 865.
23. Klug A, Rhodes D. 1987. 'Zinc finger': a novel protein motif for nucleic acid recognition. Trends in Biochemical Sciences 12: 464-469.
24. Krebber H, Wöstmann C, Bakker-Grunwald T. 1994. Evidence for the existence of a single ubiquitin gene in Giardia lamblia. FEBS Letters 343: 234-236.
25. Kruse M, Müller IM, Müller WEG. 1997. Early evolution of metazoan serine/threonine-and tyosine kinases: identification of selected kinases in marine sponges. Molecular Biology and Evolution 14: 1326-1334.
26. Lee H, Simon JA, Lis JT. 1988. Structure and expression of ubiquitin genes of Drosophila melanogaster. Molecular Cell Biology 8: 4727-4735.
27. Li C-W, Chen J-Y, Hua T-E. 1998. Precambrian sponges with cellular structures. Science 279: 879-882.
28. Lund PK, Moats-Staats BM, Simmons JG, Hoyt ED, Ercole AJ, Martin F, Van Wyk JJ. 1985. Nucleotide sequence analysis of a cDNA encoding human ubiquitin reveals that ubiquitin is synthesized as a precursor. Journal of Biological Chemistry 260: 7609-7613.
29. Mayer AN, Wilkinson KD. 1989. Detection, resolution and nomenclature of multiple ubiquitin carboxyl-terminal esterases from bovine calf thymus. Biochemistry 28: 166-172.
30. Mezguita J, Pau M, Mezguita C. 1997. Characterization and expression of two chicken cDNAs encoding ubiquitin fused to ribosomal proteins of 52 and 80 amino acids. Gene 195: 313-319.
31. Müller WEG. 1995. Molecular phylogeny of Metazoa (animals): monophyletic origin. Naturwissenschaften 82: 321-329.
32. Müller WEG, Schröder HC, Müller IM, Gamulin V. 1994. Phylogenetic relationship of ubiquitin repeats in the polyubiquitin gene from the marine sponge Geodia cydonium. Journal of Molecular Evolution 39: 369-377.
33. Müller WEG, Müller IM, Rinkevich B, Gamulin V. 1995. Molecular evolution: evidence for the monophyletic origin of multicellular animals. Naturwissenschaften 82: 36-38.
34. Neves AM, Guerreiro P, Miquerol L, Rodrigues-Pousada C. 1991. Molecular cloning and expression of a Tetrahymena pyriformis ubiquitin fusion gene coding for 53 amino acid extension. Molecular Gene Genetics 230: 186-192.
35. Nicholas KB, Nicholas HB Jr. 1996. GeneDoc version 1.1.004.
36. Ohmachi T, Giorda R, Shaw DR, Ennis HL. 1989. Molecular organization of developmentally regulated Dictyostelium discoideum ubiquitin cDNAs. Biochemistry 28: 5226-5231.
37. Özkaynak E, Finley D, Solomon MJ, Varshavsky A. 1987. The yeast ubiquitin gene: a family of natural gene fusions. EMBO Journal 6: 1429-1439.
38. Park SM, Kim JH, Lee YK, Pyee JH, Cheon CI, Hong CB. 1997. Nucleotide sequence of a ubiquitin-extension protein gene in Nicotiana tabacum and its expression pattern upon heat shock. Molecules and Cells 7: 125-130.
39. Pfeifer K, Frank W, Schröder HC, Gamulin V, Rinkevich B, Batel R, Müller IM, Müller WEG. 1993. Cloning of the polyubiquitin cDNA from the marine sponge Geodia cydonium and its preferential expression during reaggregation of cells. Journal of Cell Science 106: 545-554.
40. Saitou N, Nei M. 1987. The neighbour-joining method: a new method for reconstructing phylogenetic trees. Molecular Biological & Evolution 4: 406-425.
41. Sambrook J, Fritsch EF, Maniatis T. 1989. Mulecular Cloning: A Laboratory Manual. Cold Spring Harbour Laboratory Press, New York.
42. Sanger F, Nicklen S, Coulson AR. 1977. DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences USA 74: 5463-5467.
43. Schäcke H, Schröder HC, Gamulin V, Rinkevich B, Müller IM, Müller WEG. 1994. Molecular cloning of a receptor tyrosine kinase from the marine sponge Geodia cydonium: a new member of the receptor tyrosine kinase class II family in invertebrates. Molecular Membrane Biology 11: 101-107.
44. Schlesinger DH, Goldstein G. 1975. Molecular conservation of 74 amino acid sequence of ubiquitin between cattle and man. Nature 255: 423-424.
45. Sharp PM, Li W-H. 1987a. Molecular evolution of ubiquitin genes. Trends in Ecology and Evolution 2: 328-332.
46. Sharp PM, Li W-H. 1987b. Ubiquitin genes as a paradigm of concerted evolution of tandem repeats. Journal of Molecular Evolution 25: 58-64.
47. Short JM, Fernandez J, Sorger JA, Huse WD. 1988. Lambda ZAP: a bacteriophage lambda expression vector with in vivo excision properties. Nucleic Acids Research 16: 7583-7600.
48. Taccioli GE, Grotewold E, Aisemberg GO, Judewicz ND. 1991. The cDNA sequence and expression of an ubiquitin-tail gene fusion in Neurospora crassa. Gene 102: 133-137.
49. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673-4680.
50. Vijay-Kumar S, Bugg CE, Cook WJ. 1987. Structure of ubiquitin refined at 1.8 A resolution. Journal of Molecular Biology 194: 531-544.
51. Xiao S, Zhang Y, Knoll AH. 1998. Three-dimensional preservation of algae and animal embryos in a Neoproterozoic phosphorite. Nature 391: 553-558.