Our previous studies have shown that targeting DNA vaccine-encoded major histocompatibility complex class I epitopes to the proteasome enhanced CD8؉ T-cell induction and protection against lymphocytic choriomeningitis virus (LCMV) challenge. Here, we expand these studies to evaluate CD4 ؉ T-cell responses induced by DNA immunization and describe a system for targeting proteins and minigenes to lysosomes. Full-length proteins can be targeted to the lysosomal compartment by covalent attachment to the 20-aminoacid C-terminal tail of lysosomal integral membrane protein-II (LIMP-II). Using minigenes encoding defined T-helper epitopes from lymphocytic choriomeningitis virus, we show that the CD4 ؉ T-cell response induced by the NP 309-328 epitope of LCMV was greatly enhanced by addition of the LIMP-II tail. However, the immunological consequence of lysosomal targeting is not invariably positive; the CD4 ؉ T-cell response induced by the GP 61-80 epitope was almost abolished when attached to the LIMP-II tail. We identify the mechanism which underlies this marked difference in outcome. The GP 61-80 epitope is highly susceptible to cleavage by cathepsin D, an aspartic endopeptidase found almost exclusively in lysosomes. We show, using mass spectrometry, that the GP 61-80 peptide is cleaved between residues F 74 and K 75 and that this destroys its ability to stimulate virus-specific CD4 ϩ T-cell induction by DNA vaccines. We have previously demonstrated that improving the degradation of endogenously expressed antigens in the proteasome enhanced the induction of CD8 ϩ T-cell responses; covalent linkage of the antigen to the cellular protein ubiquitin marked the fusion protein for rapid hydrolysis in the proteasome, improved class I-antigen presentation and enhanced the protection induced by the DNA vaccines in mice, both against a virus (27, 29) and an invasive melanoma (48). In this report we present a parallel strategy aimed at improving the CD4 ϩ responses induced by DNA immunization. Most CD4 ϩ T-cell responses are induced by proteins endocytosed from the extracellular milieu by specialized antigen-presenting cells (APCs) such as dendritic cells (DC); these proteins are then degraded in the acidic endosomal and lysosomal compartments, where they encounter major histocompatibility complex (MHC) class II molecules, leading to the eventual cell surface presentation of their encoded epitopes. However, although the underlying mechanisms are not fully understood, it has been clearly demonstrated that some proteins synthesized within an APC can be presented by MHC class II molecules and can induce CD4 ϩ T-cell responses (1,4,6,21,25,32). This observation suggested that a DNA vaccine could be designed which should direct endogenously synthesized proteins to the lysosomal compartment of APCs, thus enhancing the induction of CD4 ϩ T cells. To achieve our goal, we have used the lysosomal targeting signal of lysosomal integral membrane protein-II (LIMP-II) (41). Unlike other lysosomal proteins, which usually take an indirect route...