Secondary metabolism, usually superfluous under laboratory conditions, is intrinsically elusive to genetic analysis of its regulation. We describe here a method of analyzing regulatory mutations affecting expression of secondary metabolic genes, with an Aspergillus nidulans penicillin structural gene (ipnA [encoding isopenicillin N-synthase]) as a model. The method is based on a targeted double integration of a lacZ fusion reporter gene in a chromosome different from that containing the penicillin gene cluster. The trans-acting regulatory mutations simultaneously affect lacZ expression and penicillin biosynthesis. One of these mutations (npeE1) has been analyzed in detail. This mutation is recessive, prevents penicillin production and ipnA::lacZ expression, and results in very low levels of the ipnA message at certain times of growth. This indicates that npeE positively controls ipnA transcription. We also show that this tandem reporter fusion allows genetic analysis of npeE1 by using the sexual and parasexual cycles and that lacZ expression is an easily scorable phenotype. Haploidization analysis established that npeE is located in chromosome IV, but npeE1 does not show meiotic linkage to a number of known chromosome IV markers. This method might be of general applicability to genetic analysis of regulation of other fungal secondary metabolic pathways.Secondary metabolism in microbes is often elusive to genetic analysis, because most, if not all, pathways classified in this category are dispensable under laboratory conditions. The penicillin biosynthetic pathway (22) is a prototype of such pathways in filamentous ascomycetes and has been extensively used as a model for at least four reasons. (i) It is a rather simple pathway, and only three enzymes are required to convert primary metabolites (three amino acids) into penicillin; (ii) the corresponding structural genes, which are clustered, have been cloned and characterized from several species; (iii) the end product can be sensitively detected with a bioassay; and (iv) it is of obvious biotechnological interest. As a consequence, a wealth of information about this pathway has been accumulated. In contrast, regulation of penicillin biosynthesis is largely unelucidated, possibly because the absence of a sexual cycle in Penicillium chrysogenum has hindered formal genetic analysis of the putative regulatory mechanisms. This problem has been circumvented by using Aspergillus nidulans (26), a closely related plectomycete amenable to formal genetic studies (9) and for which sophisticated molecular biology techniques are available (31).By using molecular techniques to analyze transcription of the A. nidulans ipnA gene (encoding isopenicillin N-synthase, a key enzyme catalyzing the central step in the pathway), we have described two modes of transcriptional regulation of a penicillin structural gene. Carbon regulation in response to the availability of a preferred carbon source modulates ipnA expression through the action of a yet undefined negative-acting regulatory ge...