# Arabidopsis Plastid-RNA Polymerase RPOTp Is Involved in Abiotic Stress Tolerance
## 3 Discussion  
This work investigated the role of Arabidopsis plastid-RNA polymerase RPOTp in tolerance to abiotic stress. To this end, the germination and seedling establishment of strong loss-of-function mutants _sca3-2_ and _sca3-3_, affected in the _RPOTp_ gene, were studied under different abiotic stress conditions. _sca3_ mutants were hypersensitive to NaCl, mannitol and ABA during germination and seedling establishment, and _sca3-2_ was more sensitive to stress than _sca3_-3. This is consistent with the location of the T-DNA insertions in the _RPOTp_ gene in these mutants (intron 3 and exon 18 in _sca3-2_ and _sca3-3_, respectively [23]). Along these lines, it has been reported that the _sca3-2_ mutant exhibits enhanced sensitivity to cold in the seedling stage [23]. We consider that the hypersensitivity to stress displayed by the _sca3_ mutants is due to impaired RPOTp function, and does not result from a delayed germination caused by the stress treatments. Consistent with this, other chloroplast-defective mutants, such as _mterf9_ [which also shows, like _sca3_ plants, stunted growth and impaired chloroplast biogenesis, and is morphologically very similar to _sca3_ (both mutations even interact synergistically)], display enhanced tolerance to abiotic stress [31; 42]. As such, these results suggest that _RPOTp_ promotes tolerance to environmental stress during germination and seedling establishment. Later in development, RPOTp would act differently, because the _sca3-2_ and _sca3-3_ roots were less sensitive than Col-0 to NaCl. However, we cannot rule out that this deviating response to stress could be due to the different activities of RPOTp and RPOTmp in tissues and developmental stages [4], because _RPOTmp_ and _RPOTp_ expressions were detected mainly in the non-green cells of different organs and in photosynthetically active tissues, respectively [43]. Alternatively, the lesser reduction in root length of _sca3_ plants exposed to salt stress, compared to the wild-type, might result from the _sca3-2_ and _sca3-3_ roots being closer to a growth limit situation (Figure S1). Altered sensitivity to salt stress has been reported for other Arabidopsis mutants defective in genes involved in PGE [26; 42; 44; 45]. Noteworthy among these genes, _mTERF5_, _mTERF6_ and _SIGMA FACTOR5_ (_SIG5_) regulate chloroplast transcription. Accordingly, mTERF5 acts as a PEP transcriptional pausing factor that specifically modulates the transcription of plastid _psbEFLJ_ polycistron [32], whereas mTERF6 promotes the transcription termination of plastid _rpoA_ polycistron [46]. As for _sca3_ mutants, _sig5_-2 germination is hypersensitive to salinity, and _SIG5_ expression, unlike the remaining _SIG_ genes, is induced in response to salinity and other abiotic stresses [47]. [PERSON] et al. [47] suggested SIG5 is involved in protecting chloroplasts under abiotic stress by promoting the repair of the PSII reaction center. Recently, [PERSON] et al. [48] obtained transgenic lines overexpressing _SIG5_, which showed increased tolerance to salinity. As such, as these results show that both RPOTp- and PEP-mediated plastid transcription are involved in plant salt tolerance, we consider it feasible that PGE alteration at the transcriptional level may account for the abiotic stress phenotype of mutants _sca3_, _mterf_ and _sig5_-2. Consistently with this, _sca3-2_ synergistically interacts with mutations _mterf6_-5 and _mterf9_[31; 49]. Our enrichment analysis of GO terms, which used the complete sets of under- and over-expressed genes in the _sca3-2_ mutant, revealed that most of the enriched GO terms belonged to the 'biological processes' and 'cellular components' sub-ontologies, and matched the expected function of RPOTp as a plastid-RNA polymerase. Accordingly, the GO terms related to photosynthesis or chloroplasts were significantly enriched in the set of down-regulated genes in _sca3_-2 plants.