Isolation and Structural Analysis of DNA-binding proteins that are specific to chloroplast DNA

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We determined the nucleotide sequence of three cDNAs that encode PD1, PD2, and PD3. These proteins bind specifically to chloroplast DNA.1.PD1 (348 residues) contained 2 AT-hooks, but it was not homologous to other AT-hook proteins. A membrane-spanning region was also found in PD1. Immunoblot analysis detected bands at 50 kDa and 87 kDa in the chloroplast, as well as a 40 kDa band in the nucleus. Southern blot analysis indicated that PD1 is encoded by a multi gene family.2.PD2 (632 residues) was a bZIP protein, which contained 6 direct repeats of a sequence with 37 residues. It contained a membrane-spanning domain at its C-terminus. Immunoblot analysis suggested that PD2 was localized in the envelope membrane.3.PD3 (1629 residues) contained 5 AT-hook motifs and 8 CxxC motifs. Immunoblot analysis suggested that PD3 was localized in both envelope and nucleoid. PD3 was found to be cleaved within the chloroplast to yield two polypeptides.