# Arabidopsis Plastid-RNA Polymerase RPOTp Is Involved in Abiotic Stress Tolerance
## 1 Introduction  
The hypothesis that chloroplasts descend by endosymbiosis from erstwhile free-living, photosynthetically active cyanobacteria is currently widely accepted by the scientific community [1]. Nearly all the genes of the initially genetically autonomous endosymbiont were lost or relocated to the nucleus of the host cell. As a result, its activity was finally dependent on the functions provided by the host [2]. However, the endosymbiont retained part of the ancestral DNA, which eventually gave rise to the genomes of the different types of currently-existing plastids, including chloroplasts. Compared to the ancestral cyanobacteria from which they evolved, chloroplasts contain a very small genome (plastome) that typically ranges from 120 to 160 kb in size, and harbors only 90 to 100 genes, mostly involved in photosynthesis and plastid gene expression (PGE; [3]). PGE regulation can occur via the modulation of the number of copies of the plastome, or through mechanisms of transcriptional, post-transcriptional, translational or post-translational control [4]. The transcriptional control of PGE is highly complex. Along this line, the transcriptional machinery of the chloroplasts of land plants is more complex than that of prokaryotes. Accordingly, plastid genes are transcribed by two types of DNA-dependent RNA polymerases: PEP (Plastid-Encoded Polymerase), a bacterial-type polymerase encoded by the plastome, and NEP (Nuclear-Encoded Polymerase), a monomeric-type polymerase similar to that of T3/T7 phages, encoded by the nuclear genome [4]. PEP is a multimeric enzyme composed of subunits \(\alpha\), \(\beta\), \(\beta^{\prime}\) and \(\beta^{\prime\prime}\), which form the core of the enzyme (holoenzyme), and which are respectively encoded by plastome genes _rpoA_, _rpoB_, _rpoC1_ and _rpoC2_[5; 6; 7]. When isolated from photosynthetically active plastids, the PEP holoenzyme is usually associated with several nuclear-encoded proteins, such as sigma factors (SIG), which confer promoter recognition, and the PEP-associated proteins (PAP) required for plastid transcriptional regulation [8; 9; 10; 11]. In addition to PEP, the second level of the control of chloroplast transcription in land plants is represented by NEP polymerases. In monocots, a single NEP coded by the _RPOTp_ gene (RNA polymerase T3/T7 phage-type) has been hitherto identified, whereas two NEPs are present in dicots: RPOTp, targeted to plastids, and RPOTmp, dually targeted to plastids and mitochondria [12; 13; 14; 15]. Plastid RPOTp and RPOTmp polymerases most likely evolved from the duplication of an ancestral-nuclear gene encoding mitochondrial RPOTm polymerase [16]. Along these lines, the small _RPOT_ gene family in Arabidopsis comprises three members, that encode mitochondrial- (RPOTm), chloroplast- (RPOTp) and both organelle-targeted (RPOTmp) polymerases [12; 13; 14]. In stark contrast to PEP, NEP polymerases are single catalytic subunits that perform the entire transcription process, from promoter recognition to termination [17]. PEP is considered the predominant plant-RNA polymerase in green organs because it transcribes most plastid genes [18]. Notwithstanding, NEP remains essential for the expression of the chloroplast genes _rpoB_, _rpoC1_ and _rpoC2_ (which constitute an operon), and _rpoA_ and _accD_ (which encode the \(\beta\) subunit of acetyl-CoA carboxylase for lipid biosynthesis), in dicots [4]. Despite the proposal that _RPOTp_ and _RPOTmp_ display their highest levels of activity in different tissues and/or developmental stages in dicots, very few data currently support a distribution of functions between both RNA polymerases. In line with this, Arabidopsis RPOTmp activity has been reported in the non-photosynthetically and actively dividing cells of different organs, while that of RPOTp has been detected mainly in cells of green tissues [19]. Plant mutant analysis suggests the fundamental role of both PEP and NEP in chloroplast transcription, and, hence, in this organelle's biogenesis and function.