Expression of the chloroplast genome: Modern concepts and experimental approaches

Abstract

A unique feature of plants is the presence of two extra-nuclear genomes of chloroplasts and mitochondria. The chloroplast (cp) genome is relatively small and contains only 100–120 genes, which encode less than 5% of all proteins required for plastid to function. Expression of the cpDNA retains certain prokaryotic features, such as gene cotranscription within the operon, bacteria-like RNA polymerases and promoters, and 70S ribosomes. However, eukaryotic features also appear in this process, such as the uncoupling of transcription and translation, the involvement of phage-type RNA polymerases, RNA editing, and splicing of the primary transcripts. The interaction between the nucleus (nuclear genome) and cytoplasm (plastid and mitochondrial genomes) during plant development is necessary for proper development and adaptation to the environment. The aim of this review is to disclose the peculiarities of plastid genome expression. The way how the genetic information in chloroplasts is used (transcription, editing, splicing, polyadenylation, and translation) is consequently described. Furthermore, the importance of all expression machinery components in plant life is discussed. Modern approaches for RNA pool studies are described, and the critical points of the nuclear-cytoplasmic interactions in the chloroplast function are revealed. Information about the most important factors of nuclear-cytoplasmic signaling in higher plants (sigma factors and PPR proteins encoded by the nucleus) are reviewed. Thus, the multilevelness and viability of regulating the plastid genome expression in plant cells and the interdependence of the processes in different compartments is proved. A summary of the latest studies of the expression of plastid genome using genetic chips (microarrays and macroarrays) is described. The original results are presented.