The nucleic acid binding activity of nucleolar protein B23.1 resides in its carboxyl-terminal end

Protein B23 is a major nucleolar phosphoprotein proposed to be a ribosome assembly factor. Protein B23 exists as two isoforms, B23.1 and B23.2, differing only in their carboxyl-terminal sequences. The interaction of recombinantly produced B23 isoforms with double-stranded DNA was studied using gel retardation and nitrocellulose filter disk assays. Protein B23.1 bound saturably to radiolabeled plasmid DNA. By competition assays protein B23.1 was also capable of binding RNA and single-stranded DNA. On the other hand, protein B23.2, the shorter of the two isoforms, was not capable of binding double-stranded DNA. The latter result suggested that the carboxyl-terminal end of B23.1 is essential for DNA binding activity. This was confirmed by partial digestion experiments using staphylococcal V8 protease which showed that a 5-kDa fragment, containing the carboxyl-terminal end of protein B23.1 retained DNA binding activity similar to that of the parent molecule. In contrast, a 19-kDa fragment from the amino-terminal half of B23.1 did not bind DNA. The sequence of the carboxyl-terminal 68 amino acids comprising the 5-kDa fragment showed little, if any, similarity to other proteins, suggesting that this segment contains a previously undiscovered nucleic acid binding motif.