# Arabidopsis Plastid-RNA Polymerase RPOTp Is Involved in Abiotic Stress Tolerance
## 2 Results
### Analysis of Gene Ontologies in the Transcriptome of the _sca3_-2 Mutant  
A microarray analysis of the transcriptome of the _sca3_-2 mutant, previously performed using total RNA extracted from 3-week-old plants, revealed 301 differentially expressed (DE) nuclear genes, 198 and 103 down- and up-regulated, respectively, compared to Col-0 [23]. No  
Figure 3: Box plots for sensitivity to ABA and NaCl of _sca3_ plants. Individuals were transplanted at 7 DAS from the non-supplemented growth media to the media supplemented with either 125 or 150 mM NaCl, or 5 or 10 \(\upmu\)M ABA. Seven days after the transfer, the root lengths of the plants transferred to the NaCl- (**) or ABA- (**) supplemented media were determined and referred to those of the same genotypes transferred to the non-supplemented media. These values are represented as percentages of root length of the plants transferred to the non-supplemented media. Dark horizontal lines represent the median, (\(\times\)) denotes the mean, the box represents the 25 th and 75 th percentiles, whiskers represent the 1.5 IQR (Inter-Quartile Range) limits and outliers are shown by dots (n \(\geq\) 15). Values significantly differed from Col-0 at * \(p\) \(<\) 0.05 or ** \(p\) \(<\) 0.01, according to a Student’s t-test. present in the array. We decided to examine the set of DE in _sca3-2_ to identify functions related to abiotic stress response. To this end, we carried out an analysis of gene ontologies (GO) using the Singular Enrichment Analysis (SEA) online tool, accessed through agriGO v2.0 [29]. This allowed us to find which GO terms are enriched, that is, over-represented (or under-represented), using annotations for a given gene set. Enriched GO terms appear, statistically, more (or less) frequently than would be expected just by chance when analyzing the list of annotated terms for the set of input genes. We performed the GO enrichment analysis on the sets of 198 under-expressed and 103 over-expressed genes separately. For the under-expressed genes, we found 95 terms significantly enriched (all of them over-represented), of which 48, 38 and 9 terms belonged to the 'biological process', 'cellular component' and'molecular function' sub-ontologies, respectively (Table S2). Interestingly, we identified numerous GO terms that were associated with environmental stress, and which were significantly enriched in the set of under-expressed genes in the _sca3-2_ mutant. The most significantly enriched term in the 'biological process' was'response to a low light intensity stimulus' (GO:0009645), as 26.35% of the genes containing this term in the background set of genes were DE in _sca3-2_ (Table S2). Interestingly, most of the identified terms in this sub-ontology were associated with the response to external stimuli, with different types of stresses:'response to water deprivation' (GO:0009414),'response to oxidative stress' (GO:0006979),'response to abiotic stimulus' (GO:0009628),'response to cold' (GO:0009409),'response to osmotic stress' (GO:0006970) or'response to stress' (GO:0006950). Another group of terms significantly enriched in this ontology were those related to photosynthesis, such as 'photosynthesis, light harvesting' (GO:0009765), 'photorespiration' (GO:0009853) or 'photosynthesis, light reaction' (GO:0019684) (Table S2). For the'molecular function' sub-ontology, the most significantly enriched term was 'pigment binding' (GO:0031409), as 22.72% of the genes in the background set of genes containing this term were DE in _sca3-2_. Consistent with this, other significantly enriched terms were 'chlorophyll binding' (GO:0016168), 'tetrapyrrole binding' (GO:0046906) and 'catalytic activity' (GO:0003824) (Table S2).