LAUSR

The amoeba Paulinella chromatophora contains photosynthetic organelles, termed chromatophores, that evolved independently from plastids in plants and algae. At least one-third of the chromatophore proteome consists of nucleus-encoded proteins that are imported across the chromatophore double envelope membranes. Chromatophore-targeted proteins exceeding 250 amino acids carry a conserved N-terminal extension presumably involved in protein targeting, termed the chromatophore transit peptide'(crTP). Short imported proteins do not carry discernable targeting signals. To explore whether the import of proteins is accompanied by their N-terminal processing, here we identified N termini of 208 chromatophore-localized proteins by a mass spectrometry-based approach. Our study revealed extensive N-terminal acetylation and proteolytic processing in both nucleus- and chromatophore-encoded fractions of the chromatophore proteome. Mature N termini of 37 crTP-carrying proteins were identified, of which 30 were cleaved in a common processing region. Surprisingly, only the N-terminal ∼50 amino acids (part 1) become cleaved upon import. This part contains a conserved adaptor protein-1 (AP-1) complex-binding motif known to mediate protein sorting at the trans-Golgi network followed by a predicted transmembrane helix, implying that part 1 anchors the protein co-translationally in the endoplasmic reticulum and mediates trafficking to the chromatophore via the Golgi. The C-terminal part 2 contains conserved secondary structural elements, remains attached to the mature proteins, and might mediate translocation across the chromatophore inner membrane. Short imported proteins remain largely unprocessed. Finally, this work illuminates N-terminal processing of proteins encoded in an evolutionary-early-stage organelle and suggests host-derived post-translationally acting factors involved in regulation of the chromatophore-encoded chromatophore proteome.