The Archaeal Histone-Fold Protein HMf Organizes DNA into Bona Fide Chromatin Fibers

• Published in: Structure (London) Vol. 9; no. 12; pp. 1201 - 1211
• Main Authors: Tomschik, Miroslav, Karymov, Mikhail A, Zlatanova, Jordanka, Leuba, Sanford H
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.12.2001
• Subjects: Animals; Archaea; Archaea - chemistry; Archaea - ultrastructure; atomic force microscope; Chickens; Chromatin - chemistry; Chromatin - metabolism; Chromatin - ultrastructure; chromatin fibers; DNA - chemistry; Electrophoresis, Polyacrylamide Gel; Histones - chemistry; Histones - physiology; HMf; in vitro reconstitution; Microscopy, Atomic Force; Plasmids - metabolism; Protein Binding; Recombinant Proteins - metabolism; tetrasomes; HMf; atomic force microscope; tetrasomes; in vitro reconstitution; chromatin fibers; Archaea
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/S0969-2126(01)00682-7

Background: The discovery of histone-like proteins in Archaea urged studies into the possible organization of archaeal genomes in chromatin. Despite recent advances, a variety of structural questions remain unanswered. Results: We have used the atomic force microscope (AFM) with traditional nuclease digestion assays to compare the structure of nucleoprotein complexes reconstituted from tandemly repeated eukaryal nucleosome-positioning sequences and histone octamers, H3/H4 tetramers, and the histone-fold archaeal protein HMf. The data unequivocally show that HMf reconstitutes are indeed organized as chromatin fibers, morphologically indistinguishable from their eukaryal counterparts. The nuclease digestion patterns revealed a clear pattern of protection at regular intervals, again similar to the patterns observed with eukaryal chromatin fibers. In addition, we studied HMf reconstitutes on mononucleosome-sized DNA fragments and observed a great degree of similarity in the internal organization of these particles and those organized by H3/H4 tetramers. A difference in stability was observed at the level of mono-, di-, and triparticles between the HMf particles and canonical octamer-containing nucleosomes. Conclusions: The in vitro reconstituted HMf-nucleoprotein complexes can be considered as bona fide chromatin structures. The differences in stability at the monoparticle level should be due to structural differences between HMf and core histone H3/H4 tetramers, i.e., to the complete absence in HMf of histone tails beyond the histone fold. We speculate that the existence of core histone tails in eukaryotes may provide a greater stability to nucleosomal particles and also provide the additional ability of chromatin structure to regulate DNA function in eukaryotic cells by posttranslational histone tail modifications.