# Arabidopsis Plastid-RNA Polymerase RPOTp Is Involved in Abiotic Stress Tolerance
## 3 Discussion
Besides, the GO terms associated with the response to different abiotic stresses were also significantly over-represented in this set of under-expressed genes, which falls in line with the stress phenotypes of the _sca3-2_ mutant. Consequently, the stress hypersensitivity of the _sca3_-2 mutant might be due to the down-regulation of these genes, at least in part. Chloroplast genome expression is under dual genetic control, and changes in the activity of plastid-RNA polymerases, due to endogenous or external cues, can seriously affect chloroplast function. As such, we studied the effect of continuous exposure to moderate salt stress or ABA on the expression of NEP genes. Our results showed that the transcript levels of NEP genes significantly increased in response to salinity, albeit to different extents, because the mRNAs of genes _RPOTmp_ and _RPOTp_ respectively accumulated nearly three- and twofold more than those of _RPOTm_. In line with this, [PERSON] et al. [50] reported a higher level of expression of the _RPOTmp_ vs. _RPOTp_ genes under heat stress in Arabidopsis. Interestingly, NEP up-regulation by salt stress was not found in genes _mTERF5_ or _mTERF6_, which suggests a differential effect of salinity on the expression of the nuclear components of the plastid gene expression machinery. It is worth noting the enhanced expression of NEP genes in salt-stressed seedlings, which did not result in a significant up-regulation of plastid genes solely transcribed by NEP. This result somehow resembles the effect of heat stress on PEP and NEP expression, as reported by [PERSON] et al. [50]. These authors proposed heat stress causing PEP deficiency, which, in turn, would result in a compensatory increase in NEP expression at the mRNA level. Our findings fall in line with the activation of this compensatory mechanism--also in response to salinity--for maintaining chloroplast functionality. Along these lines, increased NEP transcript levels have been reported in mutants defective in PEP [21] or PAP [51] function. Reduced PEP activity by salt would account for the significant down-regulation of PEP-dependent PSII gene _psbA_, but it did not noticeably affect the expression of genes PSI _psaA_ and _psaB_, also transcribed by PEP. A differential effect on the expression of plastid genes PSI and PSII has been reported in response to heat stress, which might be due to the different mechanisms governing the expression of these PS genes [50]. The effect of salinity on the accumulation and activity of NEP proteins remains to be elucidated. We have focused on the study of the steady-state levels of NEP mRNAs in response to salt stress. However, we cannot exclude that NEP up-regulation could be the consequence of impaired NEP activity by salinity, which still results in lower levels of NEP activity than under control conditions. As transcripts of RPOTm, which is solely targeted to mitochondria, also accumulated in response to 100 mM NaCl, salinity also affected mitochondria activity. _RPOTm_ up-regulation could be interpreted as an attempt to provide energy and to maintain metabolism under stress. Consistently with this, we found that the _AOX1A_ gene was overexpressed in salt-grown seedlings, which agrees with the reported activation of the AOX pathway in response to impaired mitochondrial function [34]. We found that all the NEP and PEP genes herein investigated were down-regulated by the externally applied ABA. Hence the lower transcript levels of the NEP-dependent-plastid genes could be due to the lowered RPOTp activity in response to ABA. The inhibitory effect of ABA on the expression of chloroplast and NEP genes has been previously described. Accordingly, [PERSON] et al. [52] reported that exogenously applied ABA represses Arabidopsis plastid transcription by both PEP and NEP. Besides, ABA also reduces _RPOTp_ transcript accumulation to about 50% of the control levels, whereas those of _RPOTmp_ remain unaffected [52]. The same authors obtained similar results in barley leaves [53]. In line with this, [PERSON] et al.