Genomic structure of the human p47-phox (NCF1) Gene

The cytosolic factor p47-phox, encoded by the NCF1 gene, is an essential co mponent of the phagocyte NADPH-oxidase system. Upon activation of this mult icomponent system, p47-phox translocates to the membrane and participates i n the electron transfer from NADPH to molecular oxygen. A deficiency or abs ence of p47-phox is the most common autosomal form of chronic granulomatous disease (CGD). We have cloned and characterized the NCF1 gene from four ba cteriophage clones, a P1 clone and genomic DNA from normal individuals. The gene is 15,236 base pairs long and includes 11 exons. It is 98.6% homologo us in sequence to at least one pseudogene that maps to the same region of c hromosome 7q11.23. Slightly more than half (50.37%) of the wild-type NCF1 g ene consists of repetitive elements. In particular, the density of Alu sequ ences is high (1.4 Alu/kb); there are 21 Alu repeats interspersed through 1 0 introns. These findings are consistent with the observation that recombin ation events between the wild-type gene and its highly homologous pseudogen es account for the majority of potentially lethal mutations in p47-phox-def icient chronic granulomatous disease. Analysis of 1.96 kb of sequence 5' of the start of translation revealed a high homology (99.6%) between wild-typ e and pseudogene clones. Characterization of NCF1 establishes a foundation for detailed molecular analysis of p47-phox-deficient CGD patients as well as for the study of the regulation of the NCF1 gene and pseudogenes, both o f which are present as full-length transcripts in normal individuals.