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Nucleic Acids Research Advance Access originally published online on April 4, 2007
Nucleic Acids Research 2007 35(8):2573-2583; doi:10.1093/nar/gkm165
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Nucleic Acids Research, 2007, Vol. 35, No. 8 2573-2583
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Molecular Biology

Concentration-dependent organization of DNA by the dinoflagellate histone-like protein HCc3

Yuk-Hang Chan and Joseph T. Y. Wong*

Department of Biology, Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, People's Republic of China

*To whom correspondence should be addressed. Tel: +86-852-2358-7343; Fax: + 86-852-2358-1559; Email: botin{at}ust.hk

Received February 10, 2007. Revised March 5, 2007. Accepted March 5, 2007.

The liquid crystalline chromosomes of dinoflagellates are the alternative to the nucleosome-based organization of chromosomes in the eukaryotes. These nucleosome-less chromosomes have to devise novel ways to maintain active parts of the genome. The dinoflagellate histone-like protein HCc3 has significant sequence identity with the bacterial DNA-binding protein HU. HCc3 also has a secondary structure resembling HU in silico. We have examined HCc3 in its recombinant form. Experiments on DNA-cellulose revealed its DNA-binding activity is on the C-terminal domain. The N-terminal domain is responsible for intermolecular oligomerization as demonstrated by cross-linking studies. However, HCc3 could not complement Escherichia coli HU-deficient mutants, suggesting functional differences. In ligation assays, HCc3-induced DNA concatenation but not ring closure as the DNA-bending HU does. The basic HCc3 was an efficient DNA condensing agent, but it did not behave like an ordinary polycationic compound. HCc3 also induced specific structures with DNA in a concentration-dependent manner, as demonstrated by atomic force microscopy (AFM). At moderate concentration of HCc3, DNA bridging and bundling were observed; at high concentrations, the complexes were even more condensed. These results are consistent with a biophysical role for HCc3 in maintaining extended DNA loops at the periphery of liquid crystalline chromosomes.


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