Staphylococcus aureus protease. A probe of exposed, nonbasic histone sequences in nucleosomes

The digestion of histones in chicken erythrocyte nucleosome cores and chromatin by Staphylococcus aureus protease was examined. This protease cleaves specifically at acidic residues and prefers Glu-X bonds under the conditions used. Only 1 of 24 glutamic acids and 2 of 13 aspartic acids among all four core histones are located in basic, NH2-terminal tails; hence, the protease is a highly specific probe of exposed nonbasic sequences. The protease readily degraded H1, H5, and H3, moderately degraded H2b, and only slightly degraded H2a and H4 in nucleosomes and nucleosome cores. Electrophoresis of core histone fragments from limited digests showed that most glutamic acids were inaccessible, but at least five sites in nonbasic sequences were readily cleaved. Tentative assignments of these fragments based on comparisons with products from limited digests of pure histones suggested that most accessible sites in nucleosome cores occur in H3. The most probable sites of H3 cutting are glutamic acids at positions 51, 60, 73, 94, and 97. At least one site in H2b, probably the equivalent of glutamic acid 105 in the calf H2b sequence, was accessible. No sites in H2a and H4 appeared highly accessible. H5 was readily cleaved at a site near the NH2 terminus. These data substantiate other evidence that nonbasic core histone sequences are located primarily in the nucleosome interior, but that H3 binds to the ends of core DNA and thereby is partly exposed on the upper and lower surfaces of the disk-shaped core.