Determination of the DNA/RNA-Associated Subproteome from Chloroplasts and Other Plastid Types

Plastids of plant and algae cells are of endosymbiotic origin. They possess their own genome and a sophisticated protein machinery to express it. Studies over the recent years uncovered that the regulation of plastid gene expression is highly complex involving a multiplicity of regulatory protein factors that are mostly imported from the cytosol. Proper expression of the chloroplast genome in coordination with nuclear genome was found to be absolutely essential for efficient growth and development of plants especially during early steps of photomorphogenesis, but also at later stages of the plant life cycle. Protein factors being responsible for such essential steps, therefore, are highly interesting for fundamental science as well as for industrial applications targeting crop improvement and yield increase. Nevertheless, many proteins involved in regulation of plastid gene expression are still unidentified and/or uncharacterized. This asks for appropriate methods to analyze this special subproteome. Here, we describe suitable methods that proved to be successful in the analysis of the plastid subproteome of DNA/RNA-binding proteins.