Adaptive evolution of centromere proteins in plants and animals

Journal of Biology

Volumn 3, Issue 4, 2004, Pages

  Talbert, Paul B ^a   Bryson, Terri D ^a   Henikoff, Steven ^a  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CENTROMERE PROTEIN C; DNA; NUCLEAR PROTEIN; UNCLASSIFIED DRUG; AUTOANTIGEN; CENTROMERE PROTEIN A; DNA BINDING PROTEIN; MIF2 PROTEIN, S CEREVISIAE; NONHISTONE PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN; VEGETABLE PROTEIN;

AMINO TERMINAL SEQUENCE; ARABIDOPSIS; ARTICLE; CARBOXY TERMINAL SEQUENCE; CENTROMERE; CHROMOSOME SEGREGATION; DNA BINDING; DROSOPHILA; FUNGUS; GENETIC LINKAGE; NONHUMAN; PLANT; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN MOTIF; ADAPTATION; AMINO ACID SEQUENCE; ANIMAL; CHEMISTRY; EXON; GENETICS; MEIOSIS; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MOUSE; NUCLEOTIDE SEQUENCE; POACEAE; RAT; SEQUENCE ALIGNMENT;

ANIMALIA; ARABIDOPSIS; FUNGI; MAMMALIA; POACEAE;

ADAPTATION, PHYSIOLOGICAL; AMINO ACID SEQUENCE; ANIMALS; AUTOANTIGENS; BASE SEQUENCE; CENTROMERE; CHROMOSOMAL PROTEINS, NON-HISTONE; DNA-BINDING PROTEINS; EVOLUTION, MOLECULAR; EXONS; MEIOSIS; MICE; MOLECULAR SEQUENCE DATA; PLANT PROTEINS; POACEAE; RATS; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE ALIGNMENT;

EID: 27744470402     PISSN: 14785854     EISSN: 14754924     Source Type: Journal    
DOI: None     Document Type: Article

References (77)

1. Henikoff S, Ahmad K, Malik HS: The centromere paradox: stable inheritance with rapidly evolving DNA. Science 2001, 293:1098-1102.
2. Schueler MG, Higgins AW, Rudd MK, Gustashaw K, Willard HF: Genomic and genetic definition of a functional human centromere. Science 2001, 294:109-115.
3. Lohe A, Roberts P: Evolution of satellite DNA sequences in Drosophila. In Heterochromatin, Molecular and Structural Aspects. Edited by Verma RS. Cambridge: Cambridge University Press; 1988:148-186.
4. Haaf T, Willard HF: Chromosome-specific alpha-satellite DNA from the centromere of chimpanzee chromosome 4. Chromosoma 1997, 106:226-232.
5. Heslop-Harrison JS, Brandes A, Schwarzacher T: Tandemly repeated DNA sequences and centromeric chromosomal regions of Arabidopsis species. Chromosome Res 2003, 11:241-253.
6. Choo KH: Domain organization at the centromere and neocentromere. Dev Cell 2001, 1:165-177.
7. Palmer DK, O'Day K, Wener MH, Andrews BS, Margolis RL: A 17-kD centromere protein (CENP-A) copurifies with nucleosome core particles and with histones. J Cell Biol 1987, 104:805-815.
8. Yoda K, Ando S, Morishita S, Houmura K, Hashimoto K, Takeyasu K, Okazaki T: Human centromere protein A (CENP-A) can replace histone 3 in nucleosome reconstitution in vitro. Proc Natl Acad Sci USA 2000, 97:7266-7271.
9. Malik HS, Henikoff S: Adaptive evolution of Cid, a centromere-specific histone in Drosophila. Genetics 2001, 157:1293-1298.
10. Talbert PB, Masuelli R, Tyagi AP, Comai L, Henikoff S: Centromeric localization and adaptive evolution of an Arabidopsis histone H3 variant. Plant Cell 2002, 14:1053-1066.
11. Cooper JL, Henikoff S: Adaptive evolution of the histone fold domain in centromeric histories. Mol Biol Evol 2004, 21:1712-1718.
12. Malik HS, Vermaak D, Henikoff S: Recurrent evolution of DNA-binding motifs in the Drosophila centromeric histone. Proc Natl Acad Sci USA 2002, 99:1449-1454.
13. Saitoh H, Tomkiel J, Cooke CA, Ratrie H, Maurer M, Rothfield NF, Earnshaw WC: CENP-C, an autoantigen in scleroderma, is a component of the human inner kinetochore plate. Cell 1992, 70:115-125.
14. McKay S, Thomson E, Cooke H: Sequence homologies and linkage group conservation of the human and mouse Cenpc genes. Genomics 1994, 22:36-40.
15. Burkin DJ, Jones C, Burkin HR, McGrew JA, Broad TE: Sheep CENPB and CENPC genes show a high level of sequence similarity and conserved synteny with their human homologs. Cytogenet Cell Genet 1996, 74:86-89.
16. Fukagawa T, Brown WR: Efficient conditional mutation of the vertebrate CENP-C gene. Hum Mol Genet 1997, 6:2301-2308.
17. Sugimoto K, Kuriyama K, Shibata A, Himeno M: Characterization of internal DNA-binding and C-terminal dimerization domains of human centromere/kinetochore autoantigen CENP-C in vitro: role of DNA-binding and self-associating activities in kinetochore organization. Chromosome Res 1997, 5:132-141.
18. Sugimoto K, Yata H, Muro Y, Himeno M: Human centromere protein C (CENP-C) is a DNA-binding protein which possesses a novel DNA-binding motif. J Biochem 1994, 116:877-881.
19. Yang CH, Tomkiel J, Saitoh H, Johnson DH, Earnshaw WC: Identification of overlapping DNA-binding and centromere-targeting domains in the human kinetochore protein CENP-C. Mol Cell Biol 1996, 16:3576-3586.
20. Politi V, Perini G, Trazzi S, Pliss A, Raska I, Earnshaw WC, Della Valle G: CENP-C binds the alpha-satellite DNA in vivo at specific centromere domains. J Cell Sci 2002, 115:2317-2327.
21. Trazzi S, Bernardoni R, Diolaiti D, Politi V, Earnshaw WC, Perini G, Della Valle G: In vivo functional dissection of human inner kinetochore protein CENP-C. J Struct Biol 2002, 140:39-48.
22. Brown MT: Sequence similarities between the yeast chromosome segregation protein Mif2 and the mammalian centromere protein CENP-C. Gene 1995, 160:111-116.
23. Meluh PB, Koshland D: Evidence that the MIF2 gene of Saccharomyces cerevisiae encodes a centromere protein with homology to the mammalian centromere protein CENP-C. Mol Biol Cell 1995, 6:793-807.
24. Moore LL, Roth MB: HCP-4, a CENP-C-like protein in Caenorhabditis elegans, is required for resolution of sister centromeres. J Cell Biol 2001, 153:1199-1208.
25. Dawe RK, Reed LM, Yu HG, Muszynski MG, Hiatt EN: A maize homolog of mammalian CENPC is a constitutive component of the inner kinetochore. Plant Cell 1999, 11:1227-1238.
26. Brown MT, Goetsch L, Hartwell LH: MIF2 is required for mitotic spindle integrity during anaphase spindle elongation in Saccharomyces cerevisiae. J Cell Biol 1993, 123:387-403.
27. Tomkiel J, Cooke CA, Saitoh H, Bernat RL, Earnshaw WC: CENP-C is required for maintaining proper kinetochore size and for a timely transition to anaphase. J Cell Biol 1994, 125:531-545.
28. Kalitsis P, Fowler KJ, Earle E, Hill J, Choo KH: Targeted disruption of mouse centromere protein C gene leads to mitotic disarray and early embryo death. Proc Natl Acad Sci USA 1998, 95:1136-1141.
29. Kalitsis P, MacDonald AC, Newson AJ, Hudson DF, Choo KH: Gene structure and sequence analysis of mouse centromere proteins A and C. Genomics 1998, 47:108-114.
30. NCBI High-throughput genomic sequences [http://www.ncbi.nlm.nih.gov/HTGS/ index.html]
31. Comeron JM: K-Estimator: calculation of the number of nucleotide substitutions per site and the confidence intervals. Bioinform 1999, 15:763-764.
32. Figueroa J, Pendon C, Valdivia MM: Molecular cloning and sequence analysis of hamster CENP-A cDNA. BMC Genomics 2002, 3:11.
33. Sullivan KF, Hechenberger M, Masri K: Human CENP-A contains a histone H3 related histone fold that is required for targeting to the centromere. J Cell Biol 1994, 127:581-592.
34. Chimpanzee Genome [http://www.genome.wustl.edu/projects/chimp]
35. NCBI BLAST [http://www.ncbi.nlm.nih.gov/BLAST]
36. Zhong CX, Marshall JB, Topp C, Mroczek R, Kato A, Nagaki K, Birchler JA, Jiang J, Dawe RK: Centromeric retroelements and satellites interact with maize kinetochore protein CENH3. Plant Cell 2002, 14:2825-2836.
37. Vettore AL, da Silva FR, Kemper EL, Souza GM, da Silva AM, Ferro MI, Henrique-Silva F, Giglioti EA, Lemos MV, Coutinho LL et al: Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane. Genome Res 2003, 13:2725-2735.
38. Miller JT, Jackson SA, Nasuda S, Gill BS, Wing RA, Jiang J: Cloning and characterization of centromere specific DNA element from Sorghum bicolor. Theor Appl Genet 1998, 96:832-839.
39. Xie Y, Heng HH: FISH mapping of centromere protein C (CENPC) on human chromosome 4q31-q21. Cytogenet Cell Genet 1996, 74:192-193.
40. Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 1997, 13:555-556.
41. Suzuki N, Nakano M, Nozaki N, Egashira S, Okazaki T, Masumoto H: CENP-B interacts with CENP-C domains containing MifZ regions responsible for centromere localization. J Biol Chem 2004, 279:5934-5946.
42. Song K, Gronemeyer B, Lu W, Eugster E, Tomkiel JE: Mutational analysis of the central centromere targeting domain of human centromere protein C, (CENP-C). Exp Cell Res 2002, 275:81-91.
43. Lanini L, McKeon F: Domains required for CENP-C assembly at the kinetochore. Mol Biol Cell 1995, 6:1049-1059.
44. Vermaak D, Hayden HS, Henikoff S: Centromere targeting element within the histone fold domain of Cid. Mol Cell Biol 2002, 22:7553-7561.
45. Goshima G, Kiyomitsu T, Yoda K, Yanagida M: Human centromere chromatin protein hMis12, essential for equal segregation, is independent of CENP-A loading pathway. J Cell Biol 2003, 160:25-39.
46. Howman EV, Fowler KJ. Newson AJ, Redward S, MacDonald AC, Kalitsis P, Choo KH: Early disruption of centromeric chromatin organization in centromere protein A (CenpA) null mice. Proc Natl Acad Sci USA 2000, 97:1148-1153.
47. Oegema K, Desai A, Rybina S, Kirkham M, Hyman AA: Functional analysis of kinetochore assembly in Caenorhabditis elegans. J Cell Biol 2001, 153:1209-1226.
48. Van Hooser AA, Ouspenski II, Gregson HC, Starr DA, Yen TJ, Goldberg ML, Yokomori K, Earnshaw WC, Sullivan KF, Brinkley BR: Specification of kinetochore-forming chromatin by the histone H3 variant CENP-A. J Cell Sci 2001, 114:3529-3542.
49. Westermann S, Cheeseman IM, Anderson S, Yates JR 3rd, Drubin DG, Barnes G: Architecture of the budding yeast kinetochore reveals a conserved molecular core. J Cell Biol 2003, 163:215-222.
50. Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ: Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 1997, 389:251-260.
51. Okamura A, Pendon C, Valdivia MM, Ikemura T, Fukagawa T: Gene structure, chromosomal localization and immunolocalization of chicken centromere proteins CENP-C and ZW10. Gene 2001, 262:283-290.
52. Shibata F, Murata M: Differential localization of the centromere-specific proteins in the major centromeric satellite of Arabidopsis thaliana. J Cell Sci 2004, 117:2963-2970.
53. Messier W, Stewart CB: Episodic adaptive evolution of primate lysozymes. Nature 1997, 385:151-154.
54. Yang Z: Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol 1998, 15:568-573.
55. Kellis M, Patterson N, Endrizzi M, Birren B, Under ES: Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 2003, 423:241-254.
56. Pardo-Manuel de Villena F, Sapienza C: Nonrandom segregation during meiosis: the unfairness of females. Mamm Genome 2001, 12:331-339.
57. Wieland G, Orthaus S, Ohndorf S, Diekmann S, Hemmerich P: Functional complementation of human centromere protein A (CENP-A) by Cse4p from Saccharomyces cerevisiae. Mol Cell Biol 2004, 24:6620-6630.
58. Daniel A: Distortion of female meiotic segregation and reduced male fertility in human Robertsonian translocations: consistent with the centromere model of co-evolving centromere DNA/centromeric histone (CENP-A). Am J Med Genet 2002, 111:450-452.
59. Pardo-Manuel de Villena F, Sapienza C: Female meiosis drives karyotypic evolution in mammals. Genetics 2001, 159:1179-1189.
60. Palestis BG, Burt A, Jones RN, Trivers R: B chromosomes are more frequent in mammals with acrocentric karyotypes: support for the theory of centromeric drive. Proc R Soc Lond B Biol Sci 2004, 271:S22-S24.
61. Sainz A, Wilder JA, Wolf M, Hollocher H: Drosophila melanogaster and D. simulans rescue strains produce fit offspring, despite divergent centromere-specific histone alleles. Heredity 2003, 91:28-35.
62. Coyne JA, Orr HA: Speciation. Sunderland: Sinauer; 2004.
63. Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuveglise C, Talla E et al.: Genome evolution in yeasts. Nature 2004, 430:35-44.
64. Henikoff S, Comai U A DNA methyltransferase homolog with a chromodomain exists in multiple forms in Arabidopsis. Genetics 1998, 149:307-318.
65. Rozen S, Skaletsky H: Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 2000, 132:365-386.
66. Gene Codes Corporation [http://www.genecodes.com]
67. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
68. Gramene [http://www.gramene.org]
69. TIGR Gene Indices [http://www.tigr.org/tdb/tgi]
70. Stothard P: The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques 2000, 28:1102-1104.
71. Translate [http://www.ualberta.ca/~stothard/javascript/translate.html]
72. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680.
73. EMBL/EBI ClustalW [http://www.ebi.ac.uk/clustalw]
74. Pietrokovski S: Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res 1996, 24:3836-3845.
75. Blocks WWW Server [http://blocks.fhcrc.org]
76. Hebsgaard SM, Korning PG, Tolstrup N, Engelbrecht J, Rouze P, Brunak S: Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. Nudeic Acids Res 1996, 24:3439-3452.
77. NetGene2 Server [http://www.cbs.dtu.dk/services/NetGene2]