Abstract
Molecular biology, with its rapid advances in new techniques, has drastically influenced evolutionary investigations and a new field, molecular evolution, was recently established. In the previous period traditional evolutionary biologists based their investigations upon comparative anatomy, embryology and paleontology. The recognition of the enormous phylogenetic information in nucleotide (nt) and amino acid (aa) sequences directed the efforts of molecular evolutionists toward the extraction and analysis of that information. Comparative analysis of conserved genes (proteins) in different contemporary organisms provides information about ancient events in nature and greatly facilitates reconstruction of the biological history of the living world. The nature of the first common ancestor of all living organisms is one of the central, still unsolved problems in biology.
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References
Bachmair A, Finley D, Varshavsky A (1986) In vitro half-time of the protein is a function of its amino-terminal residue. Science 234: 179–186
Baker RT, Board PG (1987) The human ubiquitin gene family: structure of a gene and pseudogenes from the UB B subfamily. Nucleic Acids Res 15: 443–463
Baker RT, Tobias JW, Varshavsky A (1992) Ubiquitin specific proteases of Saccharomyces cerevisiae. J Biol Chem 267: 23364–23375
Biesalski HK, Doepner G, Tzimas G, Gamulin V, Schröder HC, Batel R, Nau H, Müller WEG (1992) Modulation of myb gene expression in sponges by retinoic acid. Oncogene 7: 1765–1774
Bond V, Schlesinger MJ (1986) The chicken ubiquitin gene contains a heat-shock promoter and expresses an unstable mRNA in heat-shocked cells. Mol Cell Biol 6: 4602–4610
Callis J, Carpenter T, Sun C-W, Vierstra RD (1995) Structure and evolution of genes encoding polyubiquitin and ubiquitin-like proteins in Arabidopsis thaliana ecotype Columbia. Genetics 139: 921–939
Cavalier-Smith T (1993) Kingdom Protozoa and its 18 phyla. Microbiol Rev 57: 953–994
De Laubenfels MW (1955) Archaeocyta and porifera. In: Moore RC (ed) Treatise on invertebrate paleontology, part E. Geological Society of American University of Kansas Press, Kansas, pp 22–122
Doherty F, Mayer RJ (1992) Intracellular protein degradation. IRL Press, Oxford University Press, New York
Dworkin-Rastl E, Shrutkowski A, Dworkin MB (1984) Multiple ubiquitin mRNAs during Xenopus laevis development contain tandem repeats of the 76 amino acid coding sequence. Cell 39: 321–325
Einspanier R, Sharma HS, Scheit KH (1987) An mRNA encoding polyubiquitin in porcine corpus luteum: identification by cDNA cloning and sequencing. DNA 6: 395–400
Eytan E, Ganoth A, Armon Y, Hershko A (1989) ATP-dependent incorporation of 20S protease into the 26S complex that degrades proteins conjugated to ubiquitin. Proc Natl Acad Sci USA 86: 7751–7755
Finley D, Chau V (1991) Ubiquitination. Annu Rev Cell Biol 7: 25–69
Finley D, Varshavsky A (1985) The ubiquitin system: functions and mechanisms. Trends Biochem Sci 10: 343–346
Finley D, Özkaynak E, Varshavsky A (1987) The yeast polyubiquitin gene is essential for resistance to high temperatures, starvation and other stresses. Cell 48: 1035–1046
Finley D, Bartel B, Varshavsky A (1989) The tails of ubiquitin precursors are ribosomal proteins whose fusion to ubiquitin facilitates ribosome biogenesis. Nature 338: 394–401
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. Biol Chem Hoppe Seyler 375: 583–588
Glotzer M, Murray AW, Kirschner MW (1991) Cyclin is degraded by the ubiquitin pathway. Nature 349: 132–138
Goebl MG, Yochem J, Jentsch S, McGrath JP, Varshavsky A, Byers B (1988) The yeast cell cycle gene CDC34 encodes a ubiquitin-conjugating enzyme. Science 241: 1331–1335
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. Proc Natl Acad Sci USA 72: 11–15
Graham RW, Jones D, Candido PM (1989) UbiA, the major polyubiquitin locus in Caenorhabditis elegans, has unusual structural features and is constitutively expressed. Mol Cell Biol 9: 268–277
Gramzow M, Schröder HC, Fritsche U, Kurelec B, Robitzki A, Zimmermann H, Friese K, Kreuter MH, Müller WEG (1989) Role of phospholipase A2 in the stimulation of sponge cell proliferation by the homologous lectin. Cell 59: 939–948
Gropper K, Brandt RA, Elias S, Bearer CF, Mayer A, Schwartz AL, Ciechanover A (1991) The ubiquitin activating enzyme, El, is required for stress-induced lysosomal degradation of cellular proteins. J Biol Chem 266: 3602–3610
Henkart P, Humphreys S, Humphreys T (1973) Characterization of sponge aggregation factor. A unique proteoglycan complex. Biochemistry 12: 3045–3050
Hershko A, Ciechanover A (1992) The ubiquitin system for protein degradation. Annu Rev Biochem 61: 761–807
Higgins DG, Sharp PM (1988) CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73: 237–244
Ikemura T (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol 2: 13–34
Jentsch S (1992) Ubiquitin dependent protein degradation: a cellular perspective. Trends Cell Biol 2: 98–103
Jentsch S, McGrath JP, Varshavsky A (1987) The DNA repair gene RAD6 encodes a ubiquitinconjugating enzyme. Nature 329: 131–134
Jentsch S, Seufert W, Hauser HP (1991) Genetic analysis of the ubiquitin system. Biochim Biophys Acta 1089: 127–139
Keeling PJ, Doolittle WF (1995) Concerted evolution in protists: recent homogenization of a polyubiquitin gene in Trichomonas vaginalis. J Mol Evol 41: 556–562
Kozak M (1984) Compilation analysis of sequences upstream from the translation start site in eukaryotic mRNA. Nucleic Acids Res 12: 857–872
Krebber H, Wöstmann C, Bakker-Grunwald T (1994) Evidence for the existence of a single ubiquitin gene in Giardia lamblia. FEBS Lett 343: 234–236
Laszlo L, Doherty FJ, Osborn NU, Mayer RJ (1990) Ubiquitinated protein conjugates are specifically enriched in the lysosomal system of fibroblasts. FEBS Lett 261: 365–368
Li W-H, Tanimura M, Sharp PM (1987) An evaluation of the molecular clock hypothesis using mammalian DNA sequences. J Mol Evol 25: 330–342
Mayer AN, Wilkinson KD (1989) Detection, resolution and nomenclature of multiple ubiquitin carboxyl-terminal esterases from bovine calf thymus. Biochemistry 28: 166–172
Mayer RJ, Arnold J, Laszlo L, Landon M, Lowe J (1991) Ubiquitin in health and disease. Biochim Biophys Acta 1089: 141–157
Müller WEG (1995) Molecular phylogeny of Metazoa (animals): monophyletic origin. Naturwissenschaften 82: 321–329
Müller WEG, Zahn RK (1973) Purification and characterization of a species-specific aggregation factor in sponges. Exp Cell Res 80: 95–104
Müller WEG, Diehl-Seifert B, Gramzow M, Friese U, Renneisen K, Schröder HC (1988) Interrelation between extracellular adhesion proteins and extracellular matrix in reaggregation of dissociated sponge cells. Int Rev Cytol 111: 211–229
Müller WEG, Ugarkovic D, Gamulin V, Weiler BE, Schröder HC (1990) Intracellular signal transduction pathways in sponges. Electron Microsc Rev 3: 97–114
Müller WEG, Schröder HC, Müller IM, Gamulin V (1994) Phylogenetic relationship of ubiquitin repeats of the polyubiquitin gene from the marine sponge Geodia cydonium. J Mol Evol 39: 369–377
Müller WEG, Müller IM, Schröder HC, Gamulin V (1995a) On the monophyletic evolution of the Metazoa. Braz J Med Biol Res 27: 2083–2097
Müller WEG, Müller IM, Rinkevich B, Gamulin V (1995b) Molecular evolution: evidence for the monophyletic origin of multicellular animals. Naturwissenschaften 82: 36–38
Nagylaki T (1984) The evolution of multigene families under intrachromosomal gene conversion. Genetics 106: 529–548
Neves A, Guerreiro P, Rodrigues-Pousada C (1990) Striking changes in polyubiquitin genes of Tetrahymena pyriformis. Nucleic Acids Res 18: 656
Nickel BE, Allis CD, Davie JR (1989) Ubiquitinated histone H2B is preferentially located in transcriptionally active chromatin. Biochemistry 28: 958–963
Ohmachi T, Giorda R, Shaw DR, Ennis HL (1989) Molecular organization of developmentally regulated Dictyostelium discoideum ubiquitin cDNAs. Biochemistry 28: 5226–5231
Ohta T (1980) Evolution and variation of mutligene families. Springer, Berlin Heidelberg New York
Ohta, T (1984) Some models of gene conversion for treating the evolution of multigene families. Genetics 106: 527–528
Ohta T, Dover GA (1983) Population genetics of multigene families that are dispersed into two or more chromosomes. Proc Natl Acad Sci USA 80: 4079–4083
Özkaynak E, Finley D, Varshavsky A (1984) The yeast ubiquitin gene: head-to-tail repeats encoding a polyubiquitin precursor protein. Nature 312: 663–666
Özkaynak E, Finley D, Varshavsky A (1987) The yeast ubiquitin genes: a family of natural gene fusions. EMBO J 6: 1429–1439
Pfeifer K, Frank W, Schröder HC, Gamulin V, Rinkevich B, Batel R, Müller IM, Müller WEG (1993a) Cloning of the polyubiquitin cDNA from the marine sponge Geodia cydonium and its preferential expression during reaggregation of cells. J Cell Sci 106: 545–554
Pfeifer K, Haasemann M, Gamulin V, Bretting H, Fahrenholz F, Müller WEG (1993b) S-type lectins occur also in invertebrates: high conservation of the carbohydrate recognition domain in the lectin genes from the marine sponge Geodia cydonium. Glycobiology 6: 179–184
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. Mol Membr Biol 11: 101–107
Schlesinger DH, Goldstein G (1975) Molecular conservation of 74 amino acid sequence of ubiquitin between cattle and man. Nature 255: 423–424
Schwartz LM, Myer A, Kosz L, Engelstein M, Maier C (1990) Activation of polyubiquitin gene expression during developmentally programmed cell death. Neuron 5: 411–419
Sharp PM, Li W-H (1987a) Molecular evolution of ubiquitin genes. Trends Ecol Evol 2: 328–332
Sharp PM, Li W-H (1987b) Ubiquitin genes as a paradigm of concerted evolution of tandem repeats. J Mol Evol 25: 58–64
Sharp PM, Li W-H (1987c) The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential application. Nucleic Acids Res 15: 1281–1295
Short JM, Fernandez J, Sorger JA, Huse WD, (1988) Lambda ZAP: a bacteriophage lambda expression vector with in vivo excision properties. Nucleic Acids Res 7583–7600
Swindle J, Ajioka J, Eisen H, Sanwal B, Jacquemot C, Browder Z, Buck G (1988) The genomic organization and transcription of the ubiquitin genes of Trypanosoma cruzi. EMBO J 7: 1121–1127
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 Res 22: 4673–4680
Vijay-Kumar S, Bugg CE, Cook WJ (1987a) Structure of ubiquitin refined at 1.8 Å resolution. J Mol Biol 194: 531–544
Vijay-Kumar S, Bugg CE, Wilkinson KD, Vierstra RD, Hatfield P (1987b) Comparison of the three-dimensional structures of human, yeast and oat ubiquitin. J Biol Chem 262: 6396–6399
Wiborg O, Pedersen MS, Wind A, Berglund LE, Marcker KA, Vuust J (1985) The human ubiquitin multigene family: some genes contain multiple directly repeated ubiquitin coding sequences. EMBO J 4: 755–759
Woese CR (1983) The primary lines of descent and universal ancestor. In: Bendall DS (ed) Evolution from molecules to man. Cambridge University Press, Cambridge, pp 209–233
Wöstmann C, Tannich E, Bakker-Grunwald T (1992) Ubiquitin of Entamoeba histolytica deviates in six amino acid residues from the consensus of all other known ubiquitins. FEBS Lett 308: 54–58
Wofl S, Lottspeich F, Baumeister W (1993) Ubiquitin in the archaebacterium Thermoplasma acidophilum. FEBS Lett 326: 42–44
Wöstmann C, Tannich E, Bakker-Grunwald T (1992) Ubiquitin of Entamoeba histolytica deviates in six amino acid residues from the consensus of all other known ubiquitins. FEBS Lett 308: 54–58
Wray CG, DeSalle R (1994) Phylogenetic utility of ubiquitin DNA sequence from 3 marine protest lineages. Mol Mar Biol Biotechnol 3: 13–22
Zarkower D, Stephenson P, Sheets M, Wickens M (1986) The AAUAAA sequence is required both for cleavage and for polyadenilation of Simian virus 40 pre-mRNA in vitro. Mol Cell Biol 6: 2317–2323
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Gamulin, V., Lukic, L. (1998). Structure and Evolution of Genes Encoding Polyubiquitin in Marine Sponges. In: Müller, W.E.G. (eds) Molecular Evolution: Towards the Origin of Metazoa. Progress in Molecular and Subcellular Biology, vol 21. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-72236-3_8
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DOI: https://doi.org/10.1007/978-3-642-72236-3_8
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