The nit-3 gene of Neurospora crassa encodes the enzyme nitrate reductase and is regulated by nitrogen catabolite repression and by specific induction with nitrate. The nit-3 gene was isolated from a cosmid-based genomic library by dual selection for benomyl resistance and for the ability to complement a nit-3 mutant strain using the siblingselection procedure. The nit-3 gene was subcloned as a 3.8-kilobase DNA fragment from a cosmid that carried an =40-kilobase N. crassa DNA insert. A restriction fragment length polymorphism analysis revealed that the cloned segment displayed tight linkage to two linkage-group-4 markers that flank the genomic location of nit-3. RNA gel blot analyses of RNA from wild-type and various mutant strains were carried out to examine the molecular mechanism for regulation of nit-3 gene expression. The nit-3 gene was transcribed to give a large mRNA of -3.4 kilobases, the expected size to encode nitrate reductase. The nit-3 gene was only expressed in wild-type cells subject to simultaneous nitrogen derepression and nitrate induction. A mutant of nit-2, the major nitrogen regulatory gene of Neurospora, did not have detectable levels of nit-3 gene transcripts under the exact conditions in which these transcripts were highly expressed in wild type. Similarly, a mutant of nit4, which defines a minor positive-acting nitrogen control gene, failed to express detectable levels of the nit-3 transcript. Nitrate reductase gene expression was partially resistant to nitrogen repression in a mutant of the nmr gene, which appears to be a regulatory gene with a direct role in nitrogen catabolite repression. Results are presented that suggest that the enzyme glutamine synthetase does not serve any regulatory role in controlling nitrate reductase gene expression.In the fungus Neurospora crassa the synthesis of enzymes in global areas of metabolism is subject to genetic regulation. Thus, Neurospora has been utilized as a model lower eukaryote to investigate complex regulatory circuits (1-3). The nitrogen control circuit of Neurospora has been studied extensively and is comprised of a set of genes that encode enzymes that enable this fungus to use various secondary nitrogen sources, e.g., nitrate, nitrite, purines, or amino acids, when preferred nitrogen sources such as ammonia or glutamine are unavailable (1). These nitrogen-related enzymes include nitrate and nitrite reductase, several purine catabolic enzymes, as well as various enzymes, including L-amino acid oxidase, a general amino acid permease, and an extracellular protease involved in the use of proteins and amino acids as nitrogen sources (1,(4)(5)(6)(7)(8). The various nitrogen-related structural genes of the nitrogen circuit are unlinked, yet their expression is controlled in a parallel fashion by major and minor control genes as well as metabolic inducers and repressors. The nit-2 gene is the major nitrogen regulatory gene; it appears to mediate nitrogen catabolite repression in Neurospora by turning on the various unlinked structural ge...