By using biochemical, immunological, and molecular strategies we have identified and cloned a cDNA encoding a protease from tomato (Lycopersicon esculentum) plants (P69B) that is part of a proteolytic system activated in the plant as a result of infection with citrus exocortis viroid. This new protease is closely related, in terms of amino acid sequence and structural organization, to the previously identified pathogenesis-related subtilisin-like protease (Tornero, P., Conejero, V., and Vera, P. (1996) Proc. Natl. Acad. Sci. U. S. A. 93, 6332-6337). The 745-residue amino acid sequence of P69B begins with a cleavable signal peptide, contains a prodomain and a 631-residue mature domain which is homologous to the catalytic modules of bacterial subtilisins and eukaryotic Kex2-like proteases. Within the catalytic domain, the essential Asp, His, and Ser residues that conform the catalytic triad of this family of proteases are conserved in P69B. Northern blot and reverse transcriptase-polymerase chain reaction analysis demonstrated widespread induced expression of the 2.5-kilobase hybridizing mRNA in plant tissues as a consequence of viroid infection. We propose that P69B is a member of a complex gene family of plant Kex2/subtilisin-like proteases presumably involved in a number of specific proteolytic events activated during pathogenesis in plants and that takes place in the extracellular matrix.Infection of plants with pathogens results in the induction of numerous host-specific biochemical responses, some of which are critical for the ability of the plant to withstand diseases (1). Physiological and pathological studies have examined diseased plants in the hope of uncovering the cause(s) of the pathogeninduced distress, and there is a plethora of studies describing the dramatic effect of pathogen infection upon different aspects of plant metabolism and catabolic disturbances (2-4). What is lacking, however, is a clear understanding of how different pathogens promote the often deleterious symptoms observed by switching on a common cascade of cellular events resulting in the disease syndrome and the accompanying resistant character to subsequent pathogenic attacks.Viroids are the smallest known plant infectious agents, made up of nude, circular, single-stranded RNA molecules of a few hundred nucleotides which do not code for any protein (5, 6), and thus they are an adequate model to analyze the physiological and molecular basis of plant responses to pathogen infection. This is more relevant if we consider that the viroid elicited responses resemble those resulting from infection by more complex type of pathogens or different kind of stresses (7,8).It has been shown previously (8) that plants infected with viroids produce de novo synthesis of a set of host-encoded proteins termed pathogenesis-related (PR) 1 proteins. The function of some PR proteins as hydrolytic enzymes (e.g. chitinases or -1,3-glucanases) has been demonstrated in many plant species irrespective of the nature of the attacking pathogen, and they appea...