The nuclear gene encoding the Rieske iron-sulfur protein of the cytochrome bc1 complex of the mitochondrial respiratory chain has been isolated and characterized from Saccharomyces cerevisiae. We used a segment of the iron-sulfur protein gene from Neurospora crassa (Harnisch, U., Weiss, H., and Sebald, W. (1985) Eur. J. Biochem. 149, 95-99) to detect the yeast gene by Southern analysis. Five different but overlapping clones were then isolated by probing a yeast genomic library carried on YEp 13 by colony lift hybridization. Several approaches confirmed that the isolated DNA contained the gene for the Rieske iron-sulfur protein. The yeast gene, which contains no introns, can be expressed in Escherichia coli. A 900-base pair HindIII-EcoRI fragment was subcloned into pUC19 and directed the synthesis of immunodetectable protein. The gene was also identified by disruption of its chromosomal copy by homologous integration. A 400 base pair PstI-EcoRI fragment cloned adjacent to a HIS3 marker in pUC18 was used as an integrating vector. HIS+ transformants were obtained which were unable to grow on the nonfermentable carbon source glycerol. Southern analysis of the respiration deficient (gly-) strains confirmed that the chromosomal copy of the gene was disrupted, and immunoblots of extracts of the transformants indicated a lack of iron-sulfur protein. A respiration-deficient integrant was transformed to GLY+ by a 2-kilobase pair HindIII-BglII fragment, including a complete copy of the gene, carried on a multicopy episomal vector. Immunoblots with monoclonal antibodies to the iron-sulfur protein indicated overproduction of the protein in the complemented strain and revealed expression of approximately equal amounts of mature iron-sulfur protein and of a protein approximately 3 kDa larger than the mature protein in the complemented strain. A 1.2-kilobase pair segment of DNA from the clone which complemented the disrupted strains was sequenced and found to contain an open reading frame of 645 nucleotides, capable of encoding a 21,946-dalton protein. The gene is flanked by consensus signal sequences for initiation and termination which are common in yeast and is preceded by a possible upstream activating sequence. Amino acid sequence analysis of the amino-terminal end of the mature iron-sulfur protein agreed exactly with that predicted by the nucleotide sequence starting at Lys-31.(ABSTRACT TRUNCATED AT 400 WORDS)