Alternative splicing of adeno-associated virus type 2 (AAV2) P19-generated pre-mRNAs generates the small Rep proteins Rep52 and Rep40, which differ in their carboxyl termini. Both proteins are required for optimal packaging of AAV2 genomes. AAV5 Rep-encoding P19-generated transcripts are primarily polyadenylated within the central intron and not efficiently spliced; however, surprisingly, AAV5 was found to generate high levels of a Rep40-like protein. The AAV5 Rep40-like protein was generated by internal initiation and has the same C terminus as Rep52. Although precluded from using alternative splicing to generate multiple Rep isoforms, AAV5 ensures the production of a Rep40-like protein by utilizing a novel internal translation initiation event.The adeno-associated virus type 2 (AAV2) P19 promoter generates pre-mRNAs that are alternatively spliced to yield the small nonstructural proteins Rep52 and Rep40 from unspliced and spliced mRNAs, respectively. These Rep proteins (as well as the overlapping large Rep proteins) share a common Walker-type domain common to the superfamily 3 (SF3)-type helicases (3, 4). Both small Rep proteins are required for efficient packaging of the AAV2 genome; Rep52 and Rep40 both possess 3Ј-to-5Ј helicase activity and are required for unwinding of the double-stranded replicative forms of AAV for insertion into preformed capsids (5). Rep52 and Rep40 possess some functional redundancy in their helicase activities, ATPase activities, and DNA binding activities; however, their precise mechanisms of action are different. Structural analyses have indicated that when bound to DNA, AAV2 Rep52 remains monomeric (14), while Rep40 assumes a hexameric ringlike structure (1, 4), which has been suggested to be important for its function. Although Rep52 and Rep40 both are capable of unwinding DNA substrates with single-stranded DNA ends in a 3Ј-to-5Ј fashion, Rep40, but not Rep52, efficiently unwinds double-stranded DNA (1). Therefore, it has been suggested that during AAV replication, the Rep40 hexamer may be necessary for the initial unwinding of the first few bases of the double-stranded DNA intermediate, and further unwinding may then be accomplished by Rep52 alone or by Rep52 in conjunction with Rep40 and other Rep proteins (1).In contrast to AAV2, pre-mRNA transcripts derived from the AAV5 and goat AAV P19 promoter are preferentially polyadenylated in the viral central intron and thus spliced at low efficiency (10-12). Thus, these viruses would not be expected to generate significant quantities of Rep40. However, immunoblot analyses have consistently demonstrated the presence of significant levels of a Rep40-like (but not a Rep 68-like) protein during AAV5 and goat AAV coinfection with adenovirus, as well as during transient transfection (7,8,11). This suggested that AAV5 may generate a Rep40-like protein using a mechanism distinct from the alternative splicing utilized by AAV2. Here we show that, unlike AAV2 Rep40, the AAV5 Rep40-like protein has the same C terminus as Rep52 and that these tw...