Regulatory Mechanisms of Low Oxygen Sensing and Response in Arabidopsis thaliana

Flooding is a major natural disaster that is responsible for significant crop loss worldwide. Ethylene accumulation and reduced oxygen availability are typical changes upon submergence in plant tissues. Researchers identified two antithetical strategies, `escape' and `quiescence', for survival of submergence. These are manifested in rice (Oryza sativa) through regulation of growth and carbohydrate consumption by group VII ETHYLENE RESPONSIVE FACTOR (ERF) transcription factors. The low oxygen response of Arabidopsis thaliana, a model dicot species, includes transcriptional regulation. Independent transcriptomic analyses using microarray technology identified about 50 core hypoxia-responsive genes, including over 25 encoding proteins of unknown function. In this study, in planta measurement of oxygen content revealed distinct dynamics in root and shoot tissues upon submergence. Microarray analysis was conducted to dissect the molecular response to submergence of these organs in rosettes and for comparison to that of roots and shoots of hypoxic seedlings. Studies of loss-of-function and gain-of-function mutants of HYPOXIA-RESPONSIVE UNKNOWN PROTEIN (HUP) genes identified conserved genes that contribute to low oxygen and submergence tolerance in Arabidopsis. Of these a previously uncharacterized protein was recognized as a negative transcriptional regulator of the hypoxia response. This protein, HYPOXIA RESPONSIVE ATTENUATOR1 (HRA1), contains a trihelix domain and functions as a transcriptional activator in yeast. Overexpression of HRA1 dampened transcription of core hypoxia-responsive genes in seedlings. Investigation of N-end rule pathway of targeted proteolysis (NERP) unveiled a mechanism of direct sensing of oxygen availability in Arabidopsis. Mutation of genes encoding NERP components resulted in constitutive expression of many core hypoxia-responsive genes. Five Arabidopsis group VII ERFs are positive regulators of transcription in response to hypoxia. One of these was shown to be unstable in seedlings maintained in air and stabilized upon transfer to low oxygen condition and in mutants lacking NERP activity. Thus, the observation that the mutation of the second amino acid of these proteins from cysteine to alanine, provides strong evidence that Arabidopsis group VII ERFs are substrates of NERP in an oxygen-dependent manner. This dissertation provides new insights into molecular mechanisms of low oxygen sensing and response in Arabidopsis, which may be conserved in other plant species