Plant ribosomal DNA external spacer binding factors: a novel protein binds specifically to a sequence close to the primary pre-rRNA processing site.

Sequence analyses of the ribosomal DNA (rDNA) external spacer region revealed a peculiar structure around the primary pre-rRNA processing site in radish. Using the electrophoretic mobility shift assay, DNAse I footprinting and methylation interference analysis, we have identified in radish extracts a novel nuclear factor, NF B, that recognises this region. NF B binds to a unique CGATTTTGCCCCTGA sequence located 164 bp downstream of the transcription initiation site and immediately upstream of the pre-rRNA processing site. Interestingly, this motif is flanked by four homologous sequences, including the primary pre-rRNA processing site, which are not recognised by NF B. Based on these data and the prediction that alternative hairpin loops can be formed in this region of the nascent pre-rRNA, a putative role for NF B as a factor coupling transcription and pre-rRNA processing is discussed. NF B is unique among plant and animal rDNA-binding proteins and it differs from a previously described radish factor and from other proteins that bind to plant rDNA promoters.