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J. Biol. Chem., Vol. 277, Issue 11, 9293-9301, March 15, 2002

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Both DNA and Histone Fold Sequences Contribute to Archaeal Nucleosome Stability^*

Kathryn A. Bailey, Frédéric Marc, Kathleen Sandman, and John N. Reeve^§

From the Department of Microbiology, Ohio State University, Columbus, Ohio 43210

The roles and interdependence of DNA sequence and archaeal histone fold structure in determining archaeal nucleosome stability and positioning have been determined and quantitated. The presence of four tandem copies of TTTAAAGCCG in the polylinker region of pLITMUS28 resulted in a DNA molecule with increased affinity (G of ~700 cal mol¹) for the archaeal histone HMfB relative to the polylinker sequence, and the dominant, quantitative contribution of the helical repeats of the dinucleotide TA to this increased affinity has been established. The rotational and translational positioning of archaeal nucleosomes assembled on the (TTTAAAGCCG)₄ sequence and on DNA molecules selectively incorporated into archaeal nucleosomes by HMfB have been determined. Alternating A/T- and G/C-rich regions were located where the minor and major grooves, respectively, sequentially faced the archaeal nucleosome core, and identical positioning results were obtained using HMfA, a closely related archaeal histone also from Methanothermus fervidus. However, HMfA did not have similarly high affinities for the HMfB-selected DNA molecules, and domain-swap experiments have shown that this difference in affinity is determined by residue differences in the C-terminal region of -helix 3 of the histone fold, a region that is not expected to directly interact with DNA. Rather this region is thought to participate in forming the histone dimer:dimer interface at the center of an archaeal nucleosome histone tetramer core. If differences in this interface do result in archaeal histone cores with different sequence preferences, then the assembly of alternative archaeal nucleosome tetramer cores could provide an unanticipated and novel structural mechanism to regulate gene expression.

This article has been cited by other articles:

				Y. Xie and J. N. Reeve Transcription by an Archaeal RNA Polymerase Is Slowed but Not Blocked by an Archaeal Nucleosome J. Bacteriol., June 1, 2004; 186(11): 3492 - 3498. [Abstract] [Full Text] [PDF]

				D. J. Soares, F. Marc, and J. N. Reeve Conserved Eukaryotic Histone-Fold Residues Substituted into an Archaeal Histone Increase DNA Affinity but Reduce Complex Flexibility J. Bacteriol., June 1, 2003; 185(11): 3453 - 3457. [Abstract] [Full Text] [PDF]

				F. Marc, K. Sandman, R. Lurz, and J. N. Reeve Archaeal Histone Tetramerization Determines DNA Affinity and the Direction of DNA Supercoiling J. Biol. Chem., August 16, 2002; 277(34): 30879 - 30886. [Abstract] [Full Text] [PDF]