*2.1. Transcription*

In plants, chloroplast gene transcription is conducted by two distinct types of RNA polymerases: Nucleus-encoded RNA polymerase (NEP) and plastid-encoded RNA polymerase (PEP) [32,33]. In mature chloroplasts, PEP represents the major transcriptional machinery, which transcribes >80% of all primary chloroplast transcripts, while NEP transcribes chloroplast housekeeping genes [34]. NEP is a phage-type RNA polymerase with a single subunit. In Arabidopsis (*Arabidopsis thaliana*), NEP is encoded by two nuclear genes, *rpoTp* and *rpoTmp* [35]. PEP is a bacteria-type RNA polymerase composed of four core enzyme subunits (α, β, β , and β") and a promoter-recognizing subunit (σ factor). The core enzyme subunits of PEP are encoded by a set of genes located in the plastid genome: *rpoA*, *rpoB*, *rpoC1*, and *rpoC2* [33]. By contrast, during evolution, genes for σ factors, which provide the necessary promoter specificity to PEP, were transferred to the nuclear genome, perhaps allowing the nucleus to regulate chloroplast gene transcription in response to environmental and developmental cues [36]. PEP and a set of polymerase-associated proteins (PAPs) form a huge protein complex required for transcription. All PAPs are encoded by genes in the nucleus, and most of them are the components of plastid transcriptionally active chromosome (pTAC) [37]. These PAPs are predicted to be involved in DNA and RNA metabolism (PAP1/pTAC3, PAP2/pTAC2, PAP3/pTAC10, PAP5/pTAC12, PAP7/pTAC14, and PAP12/pTAC7), redox regulation from photosynthesis (PAP6/FLN1, PAP10/TrxZ, and PAP12/pTAC7), and protecting the PEP complex from reactive oxygen species (PAP4/FSD3 and PAP9/FSD2) [38]. The transcriptional regulation of chloroplast genes is essential for the proper functioning of chloroplasts and for overall plant growth under both normal and adverse conditions.
