Type-1 ribosome-inactivating protein from iris (Iris hollandica var. Professor Blaauw) binds specific genomic DNA fragments

The capacity of IRIP, a type-1 ribosome-inactivating protein (RIP) isolated from the bulbs of It-is hollandica, to bind specific DNA sequences from a mixture of approx. 200 bp (average length) fragments of total genomic DNA f rom Iris genome was studied. Fragments that were preferentially bound by IR IP were enriched by several cycles of affinity binding and PCR, and were cl oned and sequenced. The selected DNA fragments do not share conserved seque nces, indicating that IRIP does not bind DNA fragments in a strictly sequen ce-specific manner. According to sequence analysis, most IRIP-bound fragmen ts contain one or more possible free energy-stable hairpin structure(s) in their secondary structure, which may be the basis for recognition between I RIP and these DNA fragments. Some, but not all, DNA fragments moderately lo wer the RNA N-glycosidase activity of IRIP towards rabbit reticulocyte lysa te ribosomes. IRIP does not remove adenines from the binding fragments, whi ch implies that it does not act as a polynucleotide: adenosine glycosidase towards these DNA fragments. The selective binding of IRIP to conspecific D NA fragments is also discussed in view of the novel concept that RIPs may a ct as DNA-binding proteins with a regulatory activity on gene expression.