Plant Core Environmental Stress Response Genes Are Systemically Coordinated during Abiotic Stresses

Abstract

Studying plant stress responses is an important issue in a world threatened by global warming. Unfortunately, comparative analyses are hampered by varying experimental setups. In contrast, the AtGenExpress abiotic stress experiment displays intercomparability. Importantly, six of the nine stresses (wounding, genotoxic, oxidative, UV-B light, osmotic and salt) can be examined for their capacity to generate systemic signals between the shoot and root, which might be essential to regain homeostasis in Arabidopsis thaliana. We classified the systemic responses into two groups: genes that are regulated in the non-treated tissue only are defined as type I responsive and, accordingly, genes that react in both tissues are termed type II responsive. Analysis of type I and II systemic responses suggest distinct functionalities, but also significant overlap between different stresses. Comparison with salicylic acid (SA) and methyl-jasmonate (MeJA) responsive genes implies that MeJA is involved in the systemic stress response. Certain genes are predominantly responding in only one of the categories, e.g., WRKY genes respond mainly non-systemically. Instead, genes of the plant core environmental stress response (PCESR), e.g., ZAT10, ZAT12, ERD9 or MES9, are part of different response types. Moreover, several PCESR genes switch between the categories in a stress-specific manner.

The ROS Wheel: Refining ROS Transcriptional Footprints

“…1) were defined in each profile, resulting in a number of DEGs ranging from 6,430 to only two per profile (specified in Supplemental Table S1). The lowest number of DEGs was found in a 1-h methyl viologen treatment of the experiments performed by the AtGenExpress consortium and is consistent with the relatively low number of DEGs reported previously for this treatment (Hahn et al, 2013). A large majority of transcriptional profiles (149 out of 157) yielded more than 50 DEGs.…”

“…Both the O 3 study (Booker et al, 2012) and the UV-B studies of the AtGenExpress consortium (Hahn et al, 2013) contained transcriptional profiles of earlier time points that were also present in cluster V, which, as noted above, was the largest ROS cluster. This suggests that cluster V represents transcriptional changes that occur upstream of those present in cluster VIII.…”

“…In total, 17 high-light (HL) profiles were gathered from studies in which plants were shifted from low to high light intensities, and data also were included from analyses of the effect of irradiation with short wavelengths, such as UV-B (290-320 nm; 16 profiles) and g-rays (less than 10 211 nm; five profiles). For the single g-ray (Culligan et al, 2006) and three UV-B irradiation studies (Ulm et al, 2004;Oravecz et al, 2006;Hahn et al, 2013), a short 15-min irradiation was followed by a recovery in which later time points were sampled. In contrast, two other UV-B studies exposed plants continuously for 1 h, 6 h (Favory et al, 2009), or 24 h (Kusano et al, 2011).…”

“…Early osmotic and salt stress time points from the AtGenExpress consortium were retrieved (Hahn et al, 2013). Both abiotic stresses had been considered to display a common plant core environmental stress response (PCESR; Hahn et al, 2013). Representative PCESR genes were defined as 56 genes that were differentially expressed in UV-B, osmotic, salt, and wounding stress (Hahn et al, 2013).…”

“…S6). Early osmotic and salt stress time points from the AtGenExpress consortium were retrieved (Hahn et al, 2013). Both abiotic stresses had been considered to display a common plant core environmental stress response (PCESR; Hahn et al, 2013).…”