Maize β-amylase7 encodes 2 proteins using alternative transcriptional start sites: Nuclear BAM7 and plastidic BAM2

An unusual β-amylase7 (BAM7) gene in some angiosperms, including grasses such as maize (Zea mays), appears to encode 2 functionally distinct proteins: a nuclear-localized transcription factor (BAM7) and a plastid-localized starch hydrolase (BAM2). In Arabidopsis (Arabidopsis thaliana), these 2 proteins are encoded by separate genes on different chromosomes but their physiological functions are not well established. Using the maize BAM7 gene as a model, we detected 2 populations of transcripts by 5′-RACE which encode the predicted proteins. The 2 transcripts are apparently synthesized independently using separate core promoters about 1 kb apart, the second of which is located in the first intron of the full-length gene. The N-terminus of the shorter protein, ZmBAM7-S, begins near the 3′ end of the first intron of ZmBAM7-L and starts with a predicted chloroplast transit peptide. We previously showed that ZmBAM7-S is catalytically active with properties like those of AtBAM2. Here, we report that ZmBAM7-S targets green fluorescent protein to plastids. The transcript encoding the longer protein, ZmBAM7-L, encodes an additional DNA-binding domain containing a functional nuclear localization signal. This putative dual-function gene originated at least 400 Mya, prior to the emergence of ferns, and has persisted in some angiosperms that lack a separate BAM2 gene. It appears to have been duplicated and subfunctionalized in at least 4 lineages of land plants, resulting in 2 genes resembling Arabidopsis BAM2 and BAM7. Targeting of 2 products from a single gene to different subcellular locations is not uncommon in plants, but it is unusual when they are predicted to serve completely different functions in the 2 locations.