Introduction

The transition from skotomorphogenesis to photomorphogenesis is an extremely rapid and complex process. Several developmental changes occur: decrease in the rate of the stem elongation, apical hook straightening, and the initiation of the synthesis of the chlorophyll pigments. In angiosperm, the cotyledons are white until they reached the sunlight to be coloured in green by chlorophylls while in the gymnosperm, cotyledons are capable of greening in the dark (Solymosi and Schoefs, 2010). Obviously, this step of greening in angiosperm is regulated by a transduction signal that allows the activation of genes. Recent research has shown that genes from the nucleus and from the plastid have an impact on this transition (Pfannschmidt, et al.) and the development of the chloroplast. Yet the mechanism is poorly understood, we already know what the essential element for this transition are.  The shift from plastid state to the complex chloroplast state is regulated by a plastid-encoded RNA polymerase (PEP). The PEP core works with 12 small PEP-associated proteins (PAP).
Conforming to their functional and structural units, we can hypothesize that PAPs can be divided into three major groups. Group 1 comprises PAPs involved in DNA/RNA metabolism (PAP1, 2, 3, 5, and 7), group 2 includes proteins involved in redox regulation (PAP6 and 10) and ROS protection (PAP4 and 9) and group 3 includes proteins with unknown function (PAP8, 11, and 12) (Steiner et al. 2011; Kindgren and Strand 2015; Pfannschmidt et al. 2015).
The understanding of this system required the isolation and accurate work on each parts of the complex.
Here we focus on the purification and amplification of the PAP 1, 2, 3 and 11 genes. In this article, we will however only explain in detail the steps needed to obtain PAP1 and use those results to discuss the efficiency of this difficult process.