Pneumocystis carinii forma specialis carinii has a unique locus called the UCS, which controls surface antigen variation by acting as the expression site for a family of genes encoding isoforms of the major surface glycoprotein (MSG). Every MSG mRNA begins with 380 nucleotides copied from the UCS locus. This UCS leader sequence is necessary for initiation of translation and for protein processing. Given the UCS's importance in P. carinii f. sp. carinii, it was of interest to examine the UCS locus in the related P. carinii f. sp. ratti. The first 380 nucleotides of P. carinii f. sp. ratti MSG mRNAs were 59% identical to the P. carinii f. sp. carinii UCS. However, the DNA encoding the P. carinii f. sp. ratti UCS was not unique in the genome. Instead, only the first 97 nucleotides came from a unique locus and the remainder from >/=7 loci. These data suggest that the two organisms may use different mechanisms to generate surface variation.