The use of cytosine deaminase (CD) in conjunction with 5-fluorocytosine (5-FC) has been studied for cancer gene therapy as a means of achieving tumor-specific generation of the toxic metabolite 5-fluorouracil (5-FU). Since 5-FC is frequently used as an antifungal agent, and because it has little or no efficacy as an antibacterial agent, we hypothesized that yeast CD (YCD) might be more efficient at utilizing 5-FC as a substrate and hence be a better choice for a CD/5-FC gene therapy strategy than the typically utilized bacterial CD (BCD). To that end Saccharomyces cerevisiae CD was cloned from yeast genomic DNA and expressed in vitro. Functional analysis of BCD and YCD expressed in COS-1 cells indicated that BCD and YCD both utilized cytosine with equal efficacy; however, 5-FC was an extremely poor substrate for BCD, with an apparent catalytic efficiency 280-fold lower than that observed for YCD. Retroviral infection of tumor cell lines in vitro indicated that the IC50 of 5-FC was 30-fold lower in YCD-infected cultures as compared with cultures infected with BCD retrovirus. In addition, when SCCVII murine squamous cell carcinoma cells were infected in vitro at low rates of infection (< or =10%) there was no significant cytotoxicity toward BCD-expressing cells while there was potent cytotoxicity to both YCD-expressing cells and "bystander cells" even at this low level of expression. Finally, stable BCD- or YCD-expressing SCCVII clones were developed and used in an orthotopic immune-competent model of head and neck cancer. Subsequent treatment with 5-FC followed by monitoring of tumor growth by noninvasive magnetic resonance imaging (MRI) and survival of animals indicated a growth delay during the course of 5-FC treatment for BCD-expressing tumors, which quickly regrew at the end of treatment. In contrast, YCD-expressing tumors exhibited not only a growth delay, which was of longer duration, but also in some cases frank tumor regression and complete cures occurred.