We describe the isolation and characterization of cDNAs encoding two DNases that may be involved in the programmed death of plant cells: a 35-kDa nuclease of barley, which had been reported to be secreted from the aleurone layer into the endosperm during germination and may be responsible for the digestion of nuclear DNA in the course of degradation (cell death) of endosperm, and a 43-kDa nuclease of zinnia, which appears transiently in association with differentiation to tracheary elements and is likely to participate in the autolysis at the final step of the differentiation. Genes for these nucleases of barley and zinnia were designated BEN1 and ZEN1, respectively. The amino acid sequence of BEN1 protein deduced from the nucleotide sequence of BEN1 cDNA consisted of 288 residues with a putative signal sequence of 23 residues. RNA gel blot analysis revealed that BEN1 mRNA increased in the embryo-less half seeds of barley in response to the application of gibberellic acid. The deduced amino acid sequence of ZEN1 protein consisted of 303 residues with a putative signal sequence of 25 residues. Temporal accumulation of ZEN1 mRNA was detected during transdifferentiation of zinnia mesophyll cells into tracheary elements. Significant similarities were found among the amino acid sequences of BEN1, ZEN1, nuclease S1 from Aspergillus oryzae, and two other S1-type nucleases.