Evolution of histone H4 and H3 genes in different ciliate lineages

Journal of Molecular Evolution

Volumn 46, Issue 3, 1998, Pages 344-354

  Bernhard, Detlef ^a   Schlegel, Martin ^a  

^a UNIVERSITY OF LEIPZIG   (Germany)

Author keywords

Ciliates; Evolution; Histone; Phylogeny

Indexed keywords

HISTONE;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; CILIATE; GENE INSERTION; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; SPECIES DIFFERENCE;

AMINO ACID SEQUENCE; ANIMALS; CILIOPHORA; EVOLUTION, MOLECULAR; GENE AMPLIFICATION; HISTONES; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT;

CILIOPHORA; EUKARYOTA; HETEROTRICHIDA; PROTOZOA;

EID: 0031936015     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006311     Document Type: Article

References (63)

1. Allis CD, Glover CVC, Gorovsky MA (1979) Micronuclei of Tetrahymena contain two types of histone H3. Proc Natl Acad Sci USA 76:4857-4861
2. Bannon GA, Calzone FJ, Bowen JK, Allis CD, Gorovsky MA (1983) Multiple, independently regulated, polyadenylated messages for histone H3 and H4 in Tetrahymena. Nucleic Acids Res 11:3903-3917
3. Bannon GA, Bowen JK, Yao M-C, Gorovsky MA (1984) Tetrahymena H4 genes: structure, evolution and organisation in macro- and micronuclei. Nucleic Acids Res 12:1961-1975
4. Bardele CF (1992) The ciliate tree turned upside down. J Protozool 39:11A
5. Baroin-Tourancheau A, Delgado P, Perasso R, Adoutte A (1992) A broad molecular phylogeny of cillates: identification of major evolutionary trends and radiations within the phylum. Proc Natl Acad Sci USA 89:9764-9768
6. Bender K, Betschart B, Schaller J, Kämpfer U, Hecker H (1992) Sequence differences between histones of procyclic Trypanosoma brucei brucei and higher eukaryotes. Parasitology 105:97-104
7. Bernhard D, Leipe D, Sogin ML, Schlegel M (1995) Phylogenetic relationships of the Nassulida within the phylum Ciliophora inferred from the complete small subunit rRNA gene sequences of Furgasonia blochmanni. Obertrumia georgiana, and Pseudomicrothorax dibius. J Euk Microbiol 42:126-131
8. Binder M, Ortner S, Plaimauer B, Födinger M, Wiedermann G, Scheiner O, Duchêne M (1995) Sequence and organization of an unusual histone H4 gene in the human parasite Entamoeba histolytica. Mol Biochem Parasitol 71:243-247
9. Brunk CF, Kahn RW, Sadler LA (1990) Phylogenetic relationships among Tetrahymena species determined using the polymerase chain reaction. J Mol Evol 30:290-297
10. Brunk CF, Sadler LA (1990) Characterization of the promotor region of Tetrahymena genes. Nucleic Acids Res 18:323-329
11. Butler AP, Laughlin TJ, Cadilla CL, Henry JM, Olins DE (1984) Physical structure of gene-sized chromatin from the protozoan Oxytricha. Nucleic Acids Res 12:3201-3217
12. Caplan EB (1977) Histones and other basic proteins in genetically active and genetically inactive nuclei of the ciliate, Oxytricha sp. Biochim Biophys Acta 479:214-279
13. Dayhoff MO (1979) Atlas of protein sequence and structure, vol 5, suppl 3, 1978. National Biomedical Research Foundation, Washington, DC
14. Durrin LK, Mann RK, Kayne PS, Grunstein M (1991) Yeast histone H4 N-terminal sequence is required for promoter activation in vivo. Cell 65:1023-1031
15. Eisler K (1992) Somatic kinetics or paroral membrane: which came first in ciliate evolution? Biosystems 26:239-254
16. Elsevier SM, Lipps HJ, Steinbrück G (1978) Histone genes in macronuclear DNA of the ciliate Stylonychia mytilus. Chromosoma 69:291-306
17. Felsenstein J (1985) Confidence intervals on phylogenies: an approach using the bootstrap. Evolution 39:783-791
18. Felsenstein J (1988) Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet 22:521-565
19. Felsenstein J (1993) PHYLIP (phylogeny inference package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle
20. Gajadhar AA, Marquardt WC, Hall R, Gunderson J, Ariztia-Carmona EV, Sogin ML (1991) Ribosomal RNA sequences of Sarococystis muris, Theileria annulata, and Cryptecodinium cohnii reveal evolutionary relationships among apicomplexans, dinoflagellates, and cillates. Mol Biochem Parasitol 45:147-154
21. Gorovsky MA, Keevert JB (1975) The absence of histone F1 in a mitotically dividing, genetically inactive nucleus. Proc Natl Acad Sci USA 72:2672-2676
22. Greenwood SJ, Schlegel M, Sogin ML, Lynn DH (1991) Phylogenetic relationships of Blepharisma americanum and Colpoda inflata within the phylum Ciliophora inferred from complete small subunit rRNA sequences. J Protozool 38:1-6
23. Hamana K, Iwai K (1971) Fractionation and characterization of Tetrahymena histone in comparison with mammalian histones. J Biochem 69:1097-1111
24. Hammerschmidt B, Schlegel M, Lynn DH, Leipe DD, Sogin ML, Raikov IB (1996) Insights into the evolution of nuclear dualism in the cillates revealed by phylogenetic analysis of rRNA sequences. J Euk Microbiol 43:225-230
25. Harper DS, Jahn CL (1989) Actin, tubulin and H4 histone genes in three species of hypotrichous ciliated protozoa. Gene 75:93-107
26. Hayashi H, Nomoto M, Iwai L (1984) Tetrahymena H4. Complete amino acid sequences of two variants. J Biochem (Tokyo) 96:1449-14456
27. Hecker H (1993) Man and sea urchin - more closely related than African and American trypanosomes. Parasitol Today 9:57
28. Herzog M, Soyer MO (1981) Distinctive features of dinoflagellate chromatin. Absence of nucleosomes in a primitive species Prorocentrum micans. Eur J Cell Biol 23:295-302
29. Higgins DG, Sharp PM (1988) CLUSTAL: a package for performing multiple sequence alignments on a microcomputer. Gene 73:237-244
30. Hirt RP, Dyal PL, Wilkinson M, Finlay BJ, Roberts DM, Embley TM (1995) Phylogenetic relationships among karyorelictids and heterotrichs inferred from small subunit rRNA sequences: resolution at the base of the ciliate tree. Mol Phylogenet Evol 4:77-87
31. Horowitz S, Bowen JK, Bannon GA, Gorovsky MA (1987) Unusual features of transcribed and translated regions of the histone H4 gene family of Tetrahymena thermophila. Nucleic Acids Res 15:141-160
32. Isenberg I (1979) Histones. Annu Rev Biochem 48:159-161
33. Johman CA, Gorovsky MA (1976) Purification and characterization of the histones associated with the macronucleus of Tetrahymena. Biochemistry 15:1249-1256
34. Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-120
35. Lawn RJ, Heumann SJ, Herrick G, Prescott DM (1978) The gene-sized DNA molecules of Oxytricha. Cold Spring Harb Symp Quant Biol 42:483-492
36. Leipe D, Bernhard D, Schlegel M, Sogin ML (1994) Evolution of the 16S-like ribosomal RNA genes in the ciliophoran taxa Litostomatea and Phyllopharyngea. Eur Protistol 30:354-361
37. Lipps HJ, Hantke KG (1975) Studies on the histones of the ciliate Stylonychia mytilus. Chromosoma 49:309-320
38. Lipps HJ, Morris NR (1977) Chromatin structure in the nuclei of the ciliate Stylonychia mytilus. Biochem Biophys Res Commun 74:230-234
39. Lynn DH (1996) Systematics of cillates. In: Hausmann K, Bradbury PC (eds) Cillates: cells as organisms. Gustav Fischer, Stuttgart, pp 51-72
40. Lynn DH, Small EB (1981) Protist kinetids: structural conservatism, kinetid structure and ancestral states. Biosystems 14:377-385
41. Marinets A, Müller M, Johnson PJ, Kulda J, Schreiner O, Wiedermann G, Dûchene M (1996) The sequence and organization of the core histone H3 and H4 genes in the early branching amitochondriate protist Trichomonas vaginalis. J Mol Evol 43:563-571
42. Megee PC, Morgan BA, Mittman BA, Smith MM (1990) Genetic analysis of histone H4: essential role of lysines subject to reversible acetylation. Science 247:841-845
43. Megee PC, Morgan BA, Smith MM (1995) Histone H4 and the maintenance of genome integrity. Genes Dev 9:1716-1727
44. Miller DJ, Harrison PL, Mahony TJ, McMillan JP, Miles A, Odorico DM, ten Lohuis MR (1993) Nucleotide sequence of the histone gene cluster in the coral Acropora formosa (Cnidaria; Scleractinia): features of histone gene structure and organisation are common to diploblastic and triploblastic metazoans. J Mol Evol 37:245-253
45. Müller K, Schmidt R (1988) Histone genes of Volvox carteri: DNA sequence and organisation of two H3-H4 gene loci. Nucleic Acid Res 16:4121-4136
46. Müller K, Lindauer A, Brüderlein M, Schmidt R (1990) Organization and transcription of Volvox histone-encoding genes: similarities between algal and animal genes. Gene 93:167-175
47. Nock A (1981) RNA and macronuclear transcription in the ciliate Stylonychia mytilus. Chromosoma 83:209-220
48. Prescott DM (1994) The DNA of ciliated protozoa. Microbiol Rev 58:233-267
49. Rizzo PJ (1981) Comparative aspects of basic chromatin proteins in dinoflagellates. Biosystems 14:433-444
50. Sadler LA, Brunk CF (1992) Phylogenetic relationships and unusual diversity in histone H4 proteins within the Tetrahymena pyriformis complex. Mol Biol Evol 9:70-84
51. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-424
52. Schlegel M (1991) Proust evolution and phylogeny as discerned from small subunit ribosomal RNA sequence comparisons. Eur J Protistol 27:207-219
53. Schlegel M (1994) Molecular phylogeny of eukaryotes. TREE 9:330-335
54. Schlegel M, Muller S, Ruder F, Büsen W (1990) Transcriptionally inactive micronuclei, macronuclear anlagen and transcriptionally active macronucleic differ in histone composition in the hypotrichous ciliate Stylonychia lemnae. Chromosoma 99:401-406
55. Schlegel M, Elwood HJ, Sogin ML (1991) Molecular evolution in hypotrichous cillates: sequence of the small subunit ribosomal RNA genes from Onychodromus quadricornutus and Oxytricha granulifera (Oxytrichidae, Hypotricha, Ciliophora). J Mol Evol 32:64-69
56. Smith MM, Andrésson ÓS (1983) DNA sequence of Yeast H3 and H4 Histone genes from two non-allelic gene sets encode identical H3 and H4 proteins. J Mol Biol 169:663-690
57. Sogin ML, Swanton MT, Gunderson JH, Elwood HJ (1986) Sequence of the small subunit ribosomal RNA gene from the hypotrichous ciliate Euplotes aediculatus. J Protozool 33:26-29
58. Steinbrück G, Schlegel M (1983) Characterization of two sibling species of the genus Stylonychia (Ciliata, Hypotricha) S. mytilus Ehrenberg, 1838 and S. lemnae n. sp. II. biochemical characterization. J Protozool 30:294-300
59. Thatcher TH, MacGaffey J, Bowen J, Horowitz S, Shapiro DL, Gorovsky MA (1994) Independent evolutionary origin of histone H3.3-like variants of animals and Tetrahymena. Nucleic Acids Res 22:180-186
60. Wefes I, Lipps HJ (1990) The two macronuclear histone H4 genes of the hypotrichous ciliate Stylonychia lemnae. DNA Seq J DNA Sea Mapp 1:25-32
61. Wells D, Brown D (1991) Histone and histone gene compilation and alignment update. Nucleic Acids Res 19 (Suppl):2173-2188
62. Wells D, McBride C (1989) A comprehensive compilation and alignment of histones and histone genes. Nucleic Acids Res 17(Suppl):r311-r346
63. Yu S-M, Horowitz S, Gorovsky MA (1987) A novel approach for studying gene expression in the cell cycle reveals coordinate and independent regulation of members of the H4 multigene family in cycling and in nongrowing Tetrahymena. Genes Dev 1:683-692