Information from comparative proteome analysis of Mycobacterium tuberculosis and Mycobacterium bovis bacillus Calmette-Guérin (BCG) principally allows prediction of potential vaccine candidates. Thirty-six M. tuberculosis DNA vaccine candidates identified by comparative proteome analysis were evaluated in the mouse model for protection against low-dose aerosol M. tuberculosis infection. We identified the DNA vaccine candidate Rv3407 as a protective antigen and analyzed putative major histocompatibility complex class I epitopes by computational predictions and gamma interferon Elispot assays. Importantly, we discovered that the DNA vaccine Rv3407 improved the efficacy of BCG vaccination in a heterologous prime-boost vaccination protocol. Our data demonstrate the rationale of a combination of proteomics, epitope prediction, and broad screening of putative antigens for identification of novel DNA vaccine candidates. Furthermore, our experiments show that heterologous prime-boost vaccination with a defined antigen boost "on top" of a BCG primer provides superior protection against tuberculosis over vaccination with BCG alone.Together with AIDS and malaria, tuberculosis remains a major health threat, particularly in developing countries (50). Frequently, chemotherapy with at least three drugs over a period of several months is hampered by insufficient compliance, resulting in dramatically increasing incidences of multidrug-resistant strains of Mycobacterium tuberculosis (9). The currently available vaccine, Mycobacterium bovis bacillus Calmette-Guérin (BCG), is the most widely used viable vaccine worldwide (2,11,12,43). BCG apparently fails to protect against the most common form of the disease, pulmonary tuberculosis in adults, but it prevents miliary tuberculosis in newborns and toddlers (11,25). This raises two issues: first, novel tuberculosis vaccine candidates, which protect against adulthood tuberculosis, are urgently needed (25, 38); second, BCG vaccination of newborns should be continued and not be given up prematurely. A solution which fulfills both requirements can be offered by heterologous prime-boost vaccination strategies comprised of priming with BCG and boosting with a novel vaccine candidate (4, 14).In preclinical trials, genetic immunization with naked DNA has proven to be a powerful antigen discovery tool and vaccination protocol (8, 16). DNA vaccines use episomal vectors expressing antigens under eukaryotic promoters in the vaccinated host and therefore can elicit potent humoral and cellular immune responses comprising both CD4 and CD8 T cells (8,16). Several mycobacterial DNA vaccines have been shown to elicit protective immune responses in mice (7,10,21,23,31,35,(45)(46)(47)(48). However, considerable amounts of DNA are required, particularly in nonhuman primates and humans. In clinical trials, multiple high doses of DNA were required for the induction of immune responses (5, 27, 49).Elucidation of the complete genome of M. tuberculosis has provided a blueprint for the search for novel vaccine ...