PAP genes are tissue- and cell-specific markers of chloroplast development.

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CONCLUSION: Expression of PAP genes is strongly coordinated and represents a highly selective cell-specific marker associated with the development of chloroplasts in photosynthetically active organs of Arabidopsis seedlings and adult plants. Transcription in plastids of plants depends on the activity of phage-type single-subunit nuclear-encoded RNA polymerases (NEP) and a prokaryotic multi-subunit plastid-encoded RNA polymerase (PEP). PEP is comprised of the core subunits α, β, β' and β″ encoded by rpoA, rpoB/C1/C2 genes located on the plastome. This core enzyme needs to interact with nuclear-encoded sigma factors for proper promoter recognition. In chloroplasts, the core enzyme is surrounded by additional 12 nuclear-encoded subunits, all of eukaryotic origin. These PEP-associated proteins (PAPs) were found to be essential for chloroplast biogenesis as Arabidopsis inactivation mutants for each of them revealed albino or pale-green phenotypes. In silico analysis of transcriptomic data suggests that PAP genes represent a tightly controlled regulon, whereas wetlab data are sparse and correspond to the expression of individual genes mostly studied at the seedling stage. Using RT-PCR, transient, and stable expression assays of PAP promoter-GUS-constructs, we do provide, in this study, a comprehensive expression catalogue for PAP genes throughout the life cycle of Arabidopsis. We demonstrate a selective impact of light on PAP gene expression and uncover a high tissue specificity that is coupled to developmental progression especially during the transition from skotomorphogenesis to photomorphogenesis. Our data imply that PAP gene expression precedes the formation of chloroplasts rendering PAP genes a tissue- and cell-specific marker of chloroplast biogenesis.