Expression Profile Analysis of Hypoxia Responses in Arabidopsis Roots and Shoots

Abstract

Physiological and molecular adaptation mechanisms enable plants to improve their survival under harsh conditions, including low oxygen levels caused by flooding. When Arabidopsis was exposed to hypoxia, we observed hyponastic response, shoot elongation, leaf chlorosis, and inhibited growth. To understand this response, we used a specialized complementary DNA microarray from our laboratory to examine the time-dependent profiles of gene expression in Arabidopsis roots and shoots. From this, we identified 282 hypoxia-responsive genes. These included novel genes for a zinc finger protein, WRKY family transcription factor, and glycosyl hydrolase as well as those previously identified as hypoxia-related genes including alcohol dehydrogenase (ADH), pyruvate decarboxylase (PDC), and phosphofructokinase. Cluster analysis of these profiles suggested that the hypoxia response occurs in two distinctive phases: early and late. The early response to imposed stress (hours 1, 3, and 8) includes increased expression of fermentation-related genes and transcription factors, such as by members of the C 2 H 2 zinc finger family and WRKY family. The late response (hours 24 and 72) involves the down-regulation of genes that function in secondary metabolic pathways and up-regulation of transcription factors that are mostly related to the ethylene-responsive element binding protein family. Mutants of Arabidopsis defective in sucrose synthase1 (SUS1), the At1g05060 gene (with unknown function), ADH, and the WRKY33 were more sensitive to hypoxic stress, evidence of the importance of these genes in that response. The genes presented here allow us to deepen our understanding of the mechanism for this stress response and, eventually, will aid in the development of more flood-tolerant crops.

Long-Term Waterlogging as Factor Contributing to Hypoxia Stress Tolerance Enhancement in Cucumber: Comparative Transcriptome Analysis of Waterlogging Sensitive and Tolerant Accessions

“…NAD + regeneration from NADH is considered to be the most important function of the alcoholic fermentation pathway under oxygen restricted conditions [ 98 ]. An increased expression level of adh under hypoxic stress was also demonstrated in the roots of radish [ 99 ], poplar [ 63 ], and the cucumber genotype Zaoer, which has a high level of tolerance to flooding stress [ 52 ]. Relative expression levels of adh obtained for both cucumber accessions by qRT-PCR correspond to RNA-Seq results.…”

Group VII Ethylene Response Factors in Arabidopsis: Regulation and Physiological Roles

“…MPK3/6 act in retrograde signaling following mitochondrial ROS stress during hypoxia (Chang et al, 2012) and activate ERF6 (a hub of immunity, ROS, and hormone responses; Huang et al, 2016) upon B. cinerea attack or ROS treatment (Meng et al, 2013). WRKY33 contributes to Arabidopsis resistance to B. cinerea (Liu et al, 2015) and submergence tolerance (Hwang et al, 2011).…”

WRKY33 interacts with WRKY12 protein to up‐regulate RAP2.2 during submergence induced hypoxia response in Arabidopsis thaliana

“…However, still little is known of WRKY genes’ involvement in submergence tolerance in the model plant Arabidopsis thaliana to date, although several studies have indicated that hypoxia could change the expression of some WRKY genes and mutation of some WRKY genes can change the hypoxia sensitivity. For example, submergence can induce expression of WRKY22 , thereby enhancing disease resistance in Arabidopsis (Hsu et al ., 2013), while WRKY33 is reportedly induced after hypoxia treatment in Arabidopsis roots (Klok et al ., 2002) and the wrky33 mutant is hypersensitive to hypoxia stress treatment (Hwang et al ., 2011).…”