Comparative characterization of aluminum responsive transcriptome in Arabidopsis roots: comparison with other rhizotoxic ions at different stress intensities

Under abiotic stress conditions, plants actively modify the transcriptome either for activation of stress tolerance mechanisms or adjustment of biological processes for adaptation to the stress. Comparative analysis of transcriptome data under different stressors and stress intensities is useful to understand how plants balance growth and survival under stress conditions. In this study, the transcriptome of Arabidopsis roots was investigated in response to four rhizotoxic stressors, namely aluminum (Al³⁺), cadmium (Cd²⁺), and copper (Cu²⁺) ions and sodium chloride (NaCl), under mild stress (50% inhibition of root elongation compared with the control) and severe stress (>90% inhibition of root elongation). Only Al treatment showed similar transcriptome responses between the stress intensities. The shared Al-specific up-regulated genes included known Al-tolerance genes and downstream genes of SENSITIVE TO PROTON1 (STOP1) such as ALUMINUM ACTIVATED MALATE TRANSPORTER1 and malic enzymes, suggesting that Al-defense mechanisms regulated by STOP1 might be activated over a broader range of Al stress intensities. The sulfur metabolism pathway was activated only under severe Al stress, suggesting that rapid activation of sulfur metabolism is crucial for survival of root cells in the early stage of severe Al stress. A large number of genes associated with the response mechanism to reactive oxygen species production were up-regulated by Cd and Cu treatment under both severe and mild stress, but the members of the genes sets differed between the stress severities. The results indicated that Cd and Cu stress trigger common transcriptional responses, but the responses are likely associated with the stress severity. The transcriptional response to mild NaCl stress was relatively smaller compared with those to the other stressors, suggesting that in Arabidopsis different mechanisms other than rapid transcriptomic responses are involved in the response to NaCl stress. Comparison between Al and the other stressors indicated that the STOP1 regulation system and central metabolic pathways contribute to the similarity of the transcriptional response to different intensities of Al stress. The results suggest that robustness of transcriptionally regulated Al tolerance systems to different stress intensities is important for both of growth and survival in plant roots under Al stress.