Ubiquitin genes as a paradigm of concerted evolution of tandem repeats
Tóm tắt
Ubiquitin is remarkable for its ubiquitous distribution and its extreme protein sequence conservation. Ubiquitin genes comprise direct repeats of the ubiquitin coding unit with no spacers. The nucleotide sequences of several ubiquitin repeats from each of humans, chicken,Xenopus, Drosophila, barley, and yeast have recently been determined. By analysis of these data we show that ubiquitin is evolving more slowly than any other known protein, and that this (together with its gene organization) contributes to an ideal situation for the occurrence of concerted evolution of tandem repeats. By contrast, there is little evidence of between-cluster concerted evolution. We deduce that in ubiquitin genes, concerted evolution involves both unequal crossover and gene conversion, and that the average time since two repeated units within the polyubiquitin locus most recently shared a common ancestor is approximately 38 million years (Myr) in mammals, but perhaps only 11 Myr inDrosophila. The extreme conservatism of ubiquitin evolution also allows the inference that certain synonymous serine codons differing at the first two positions were probably mutated at single steps.
Tài liệu tham khảo
Arnheim N (1983) concerted evolution of multigene families. In: Nei M, Koehn RK (eds) Evolution of genes and proteins. Sinauer, Sunderland, MA, pp 38–61
Boguski MS, Elshourbagy N, Taylor JM, Gordon JI (1985) Comparative analysis of repeated sequences in rat apolipoproteins A-I, A-IV, and E. Proc Natl Acad Sci USA 82:992–996
Bond U, Schlesinger MJ (1985) Ubiquitin is a heat shock protein in chicken embryo fibroblasts. Mol Cell Biol 5:949–956
Ciechanover A, Finley D, Varshavsky A (1982) The ubiquitin-mediated proteolytic pathway and mechanisms of energy-dependent intracellular protein degradation. J Cell Biochem 24:27–53
Dayhoff MO (1972) Atlas of protein sequence and structure, vol 5. National Biomedical Research Foundation, Silver Spring, MD
Dickerson RE (1971) The structure of cytochrome c and the rates of molecular evolution. J Mol Evol 1:26–45
Dover GA (1982) Molecular drive: a cohesive mode of species evolution. Nature 299:111–117
Dworkin-Rastl E, Shrutkowski A, Dworkin MB (1984) Multiple ubiquitin mRNAs duringXenopus laevis development contain tandem repeats of the 76 amino acid coding sequence. Cell 39:321–325
Easteal S, Oakeshott JG (1985) Estimating divergence times ofDrosophila species from DNA sequence comparisons. Mol Biol Evol 2:87–91
Finley D, Varshavsky A (1985) The ubiquitin system: functions and mechanisms. Trends Biochem Sci 10:343–347
Fitch WM (1977) On the problem of discovering the most parsimonious tree. Am Nat 111:223–257
Fusauchi Y, Iwai K (1985)Tetrahymena ubiquitin-histone conjugate uH2A. Isolation and structural analysis. J Biochem 97:1467–1476
Gausing K, Barkardottir R (1986) Structure and expression of ubiquitin genes in higher plants. Eur J Biochem 158:57–62
Gavilanes JG, de Buitrago GG, Perez-Castells R, Rodriguez R (1982) Isolation, characterization, and amino acid sequence of a ubiquitin-like protein from insect eggs. J Biol Chem 257:10267–10270
GenBank Genetic Sequence Data Bank (1986) Release 42.0. Bolt, Beranek & Newman
Goldknopf IL, Busch H (1977) Isopeptide linkage between nonhistone and histone 2A polypeptides of chromosomal conjugate-protein A24. Proc Natl Acad Sci USA 74:864–868
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
Grantham R (1974) Amino acid difference formula to help explain protein evolution. Science 185:862–864
Hayashi H, Nomoto M, Iwai K (1984)Tetrahymena histone H4. Complete amino acid sequence of two variants. J Biochem 96:1449–1456
Izquierdo M, Arribas C, Galceran J, Burke J, Cabrera VM (1984) Characterization of aDrosophila repeat mapping at the earlyecdysone puff 63F and present in many eucaryotic genomes. Biochim Biophys Acta 783:114–121
Jacq C, Miller JR, Brownlee GG (1977) A pseudogene structure in 5S DNA ofXenopus laevis. Cell 12:109–120
Lamb BC (1984) The properties of meiotic gene conversion important in its effects on evolution. Heredity 53:113–138
Levinger L, Varshavsky A (1982) Selective arrangement of ubiquinated and D1 protein-containing nucleosomes within the Drosophila genome. Cell 28:375–385
Li W-H, Luo C-C, Wu C-I (1985a) Evolution of DNA sequences. In: MacIntyre RJ (ed) Molecular evolutionary genetics. Plenum, New York, pp 1–94
Li W-H, Wu C-I, Luo C-C (1985b) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol 2:150–174
Lund PK, Moats-Staats BM, Simmons JG, Hoyt E, D'Ercole AJ, Martin F, Van Wyck JJ (1985) Nucleotide sequence analysis of a cDNA encoding human ubiquitin reveals that ubiquitin is synthesized as a precursor. J Biol Chem 260:7609–7613
Luo C-C, Li W-H, Moore MN Chan L (1986) Structure and evolution of the apolipoprotein multigene family. J Mol Biol 187:325–340
Marx JL (1986) Ubiquitin moves to the cell surface. Science 231:796–797
Nagylaki T (1984) The evolution of multigene families under intrachromosomal gene conversion. Genetics 106:529–548
Ohta T (1980) Evolution and variation of multigene families. Springer-Verlag, Berlin
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, Solomon MJ, Varshavsky A (1987) The yeast ubiquitin genes: a family of natural gene fusions (in press)
Schlesinger DH, Goldstein G (1975) Molecular conservation of 74 amino acid sequence of ubiquitin between cattle and man. Nature 255:423–424
Schlesinger DH, Goldstein G, Niall HD (1975) The complete amino acid sequence of ubiquitin, an adenylate cyclase stimulating polypeptide probably universal in living cells. Biochemistry 14:2214–2218
Siegelman M, Bond MW, Gallatin WM, St. John T, Smith HT, Fried VA, Weissman IL (1986) Cell surface molecule associated with lymphocyte homing is a ubiquitinated branchedchain glycoprotein. Science 231:823–829
St. John T, Gallatin WM, Siegelman M, Smith HT, Fried VA, Weissman IL (1986) Expression cloning of a lymphocyte homing receptor cDNA: ubiquitin is the reactive species. Science 231:845–850
Vierstra RD, Langan SM, Schaller GE (1986) Complete amino acid sequence of ubiquitin from the higher plantAvena sativa. Biochemistry 25:3105–3108
Watson DC, Levy WB, Dixon GH (1975) Free ubiquitin is a non-histone protein of trout testis chromatin. Nature 276:196–198
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
Zimmer EA, Martin SL, Beverley SM, Kan YW, Wilson AC (1980) Rapid duplication and loss of genes coding for the alpha chains of hemoglobin. Proc Natl Acad Sci USA 77:2158–2162