Adaptive evolution of the histone fold domain in centromeric histones

Molecular Biology and Evolution

Volumn 21, Issue 9, 2004, Pages 1712-1718

  Cooper, Jennifer L ^a   Henikoff, Steven ^a  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Adaptive evolution; Arabidopsis; Brassicaceae; Centromere; Histone

Indexed keywords

GENOMIC DNA; HISTONE; HISTONE H3; REPETITIVE DNA; STRUCTURAL PROTEIN;

ADAPTATION; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARABIDOPSIS; ARABIDOPSIS ARENOSA; ARTICLE; BRASSICA; CELL DIVISION; CENTROMERE; CHROMOSOME STRUCTURE; CONFORMATIONAL TRANSITION; DNA SEQUENCE; DROSOPHILA; GENETIC ANALYSIS; GENETIC SELECTION; GENETIC VARIABILITY; HETEROCHROMATIN; MOLECULAR CLONING; MOLECULAR EVOLUTION; MOLECULAR INTERACTION; NONHUMAN; NUCLEOSOME; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROTEIN DOMAIN; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; TECHNIQUE;

AMINO ACID SEQUENCE; ANIMALS; ARABIDOPSIS; ARABIDOPSIS PROTEINS; BASE SEQUENCE; BRASSICACEAE; CENTROMERE; DNA, PLANT; DROSOPHILA; DROSOPHILA PROTEINS; EVOLUTION, MOLECULAR; HISTONES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANT PROTEINS; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE HOMOLOGY, AMINO ACID;

ARABIDOPSIS; ARABIDOPSIS ARENOSA; ARABIDOPSIS THALIANA; ARACHNIDA; BRASSICA; BRASSICACEAE; HEXAPODA;

EID: 4143071290     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msh179     Document Type: Article

References (27)

1. Chen, Y., R. E. Baker, K. C. Keith, K. Harris, S. Stoler, and M. Fitzgerald-Hayes. 2000. The N terminus of the centromere H3-like protein Cse4p performs an essential function distinct from that of the histone fold domain. Mol. Cell. Biol. 20:7037-7048.
2. Chenna, R., H. Sugawara, T. Koike, R. Lopez, T. J. Gibson, D. G. Higgins, and J. D. Thompson. 2003. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31:3497-3500.
3. Comai, L., A. P. Tyagi, K. Winter, R. Holmes-Davis, S. H. Reynolds, Y. Stevens, and B. Byers. 2000. Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids. Plant Cell 12:1551-1568.
4. Comeron, J. M. 1999. K-Estimator: calculation of the number of nucleotide substitutions per site and the confidence intervals. Bioinformatics 15:763-764.
5. Daniel, A. 2002. 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. 111:450-452.
6. Davey, C. A., D. F. Sargent, K. Luger, A. W. Maeder, and T. J. Richmond. 2002. Solvent mediated interactions in the structure of the nucleosome core partical at 1.9 Å resolution. J. Mol. Biol., 319:1097-1113.
7. Hebsgaard, S. M., P. G. Korning, N. Tolstrup, J. Engelbrecht, P. Rouze, and S. Brunak. 1996. Splice site prediction in Arabidopsis thaliana pre-mDNA by combining local and global sequence information. Nucleic Acids Res. 24:3439-3452.
8. Henikoff, S., K. Ahmad, and H. S. Malik. 2001. The centromere paradox: stable inheritance with rapidly evolving DNA. Science 293:1098-1102.
9. Howman, E. V., K. J. Fowler, A. J. Newson, S. Redward, A. C. MacDonald, P. Kalitsis, and K. H. A. Choo. 2000. Early disruption of centromereic chromatin organization in centromere protein A (Cenpa) null mice. Proc. Natl. Acad. Sci. U S A. 97:1148-1153.
10. Janin, J. 1999. Wet and dry interfaces: the role of solvent in protein-protein and protein-DNA recognition. Structure Fold Des. 7:R277-R279.
11. Lo, A. W., J. M. Craig, R. Saffery, P. Kalitsis, D. V. Irvine, E. Earle, D. J. Magliano, and K. H. Choo. 2001. A 330 kb CENP-A binding domain and altered replication timing at a human neocentromere. EMBO J. 20:2087-2096.
12. Luger, K., A. W. Mader, R. K. Richmond, D. F. Sargent, and T. J. Richmond. 1997. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389:251-260.
13. Malik, H. S., and S. Henikoff. 2001. Adaptive evolution of Cid, a centromere-specific histone in Drosophila. Genetics 157:1293-1298.
14. Malik, H. S., and S. Henikoff. 2003. Phylogenomics of the nucleosome. Nat. Struct. Biol. 10:882-891.
15. Malik, H. S., D. Vermaak, and S. Henikoff. 2002. Recurrent evolution of DNA-binding motifs in the Drosophila centromeric histone. Proc. Natl. Acad. Sci. U S A. 99:1449-1454.
16. Moore, L. L., and M. B. Roth. 2001. HCP-4, a CENP-C-like protein in Caenorhabditis elegans, is required for resolution of sister centromeres. J. Cell. Biol. 153:1199-1208.
17. Nagaki, K., Z. Cheng, S. Ouyang, P. B. Talbert, M. Kim, K. M. Jones, S. Henikoff, C. R. Buell, and J. Jiang. 2004. Sequencing of a rice centromere uncovers active genes. Nat. Genet. 36:138-145.
18. Palmer, D. K., K. O'Day, and R. L. Margolis. 1990. The centromere specific histone CENP-A is selectively retained in discrete foci in mammalian sperm nuclei. Chromosoma 100:32-36.
19. Pardo-Manuel de Villena, F., and C. Sapienza. 2001. Transmission ratio distortion in offspring of heterozygous female carriers of Robertsonian translocations. Hum. Genet. 108: 31-36.
20. Rose, T. M., E. R. Schultz, J. G. Henikoff, S. Pietrokovski, C. M. McCallum, and S. Henikoff. 1998. Consensus degenerate hybrid oligonucleotide primers for amplification of distantly related sequences. Nucleic Acids Res. 26:1628-1635.
21. Saffery, R., H. Sumer, S. Hassan, L. H. Wong, J. M. Craig, K. Todokoro, M. Anderson, A. Stafford, and K. H. Choo. 2003. Transcription within a functional human centromere. Mol. Cell 12:509-516.
22. Saitou, N., and M. Nei. 1987. The Neighbor-Joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
23. Schwabe, J. W. 1997. The role of water in protein-DNA interactions. Curr. Opin. Struct. Biol. 7:126-134.
24. Swofford, D. L. 2000. PAUP: Phylogenetic analysis using parsimony (and other methods). Sinauer, Sunderland, Mass.
25. Talbert, P. B., R. Masuelli, A. P. Tyagi, L. Comai, and S. Henikoff. 2002. Centromeric localization and adaptive evolution of an Arabidopsis histone H3 variant. Plant Cell 14:1053-1066.
26. Vermaak, D., H. S. Hayden, and S. Henikoff. 2002. A centromere targeting element within the histone fold domain of Cid. Mol. Cell. Biol. 22:7553-7561.
27. Yang, Z. 1997. PAML, a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.