Flooding is a widespread natural disaster that leads to oxygen (O(2)) and energy deficiency in terrestrial plants, thereby reducing their productivity. Rice is unusually tolerant to flooding, but the underlying mechanism for this tolerance has remained elusive. Here, we show that protein kinase CIPK15 [calcineurin B-like (CBL)-interacting protein kinase] plays a key role in O(2)-deficiency tolerance in rice. CIPK15 regulates the plant global energy and stress sensor SnRK1A (Snf1-related protein kinase 1) and links O(2)-deficiency signals to the SnRK1-dependent sugar-sensing cascade to regulate sugar and energy production and to enable rice growth under floodwater. Our studies contribute to understanding how rice grows under the conditions of O(2) deficiency necessary for growing rice in irrigated lowlands.

Expression of a-amylase genes during cereal grain germination and seedling growth is regulated negatively by sugar in embryos and positively by gibberellin (GA) in endosperm through the sugar response complex (SRC) and the GA response complex (GARC), respectively. We analyzed two a-amylase promoters, aAmy3 containing only SRC and aAmy8 containing overlapped SRC and GARC. aAmy3 was sugar-sensitive but GA-nonresponsive in both rice (Oryza sativa) embryos and endosperms, whereas aAmy8 was sugar-sensitive in embryos and GA-responsive in endosperms. Mutation of the GA response element (GARE) in the aAmy8 promoter impaired its GA response but enhanced sugar sensitivity, and insertion of GARE in the aAmy3 promoter rendered it GA-responsive but sugar-insensitive in endosperms. Expression of the GAREinteracting transcription factor MYBGA was induced by GA in endosperms, correlating with the endosperm-specific aAmy8 GA response. aAmy8 became sugar-sensitive in MYBGA knockout mutant endosperms, suggesting that the MYBGA-GARE interaction overrides the sugar sensitivity of aAmy8. In embryos overexpressing MYBGA, aAmy8 became sugar-insensitive, indicating that MYBGA affects sugar repression. a-Amylase promoters active in endosperms contain GARE, whereas those active in embryos may or may not contain GARE, confirming that the GARE and GA-induced MYBGA interaction prevents sugar feedback repression of endosperm a-amylase genes. We demonstrate that the MYBGA-GARE interaction affects sugar feedback control in balanced energy production during seedling growth and provide insight into the control mechanisms of tissue-specific regulation of a-amylase expression by sugar and GA signaling interference.

Germination is a unique developmental transition from metabolically quiescent seed to actively growing seedling that requires an ensemble of hydrolases for coordinated nutrient mobilization to support heterotrophic growth until autotrophic photosynthesis is established. This study reveals two crucial transcription factors, MYBS1 and MYBGA, present in rice (Oryza sativa) and barley (Hordeum vulgare), that function to integrate diverse nutrient starvation and gibberellin (GA) signaling pathways during germination of cereal grains. Sugar represses but sugar starvation induces MYBS1 synthesis and its nuclear translocation. GA antagonizes sugar repression by enhancing conuclear transport of the GA-inducible MYBGA with MYBS1 and the formation of a stable bipartite MYB-DNA complex to activate the a-amylase gene. We further discovered that not only sugar but also nitrogen and phosphate starvation signals converge and interconnect with GA to promote the conuclear import of MYBS1 and MYBGA, resulting in the expression of a large set of GA-inducible but functionally distinct hydrolases, transporters, and regulators associated with mobilization of the full complement of nutrients to support active seedling growth in cereals.

Rice is characterized by a broad range of metabolic and morphological adaptations to flooding, such as germination and mobilization of stored nutrients under submergence until seedlings reach the water surface to carry out photosynthesis, and sustainable growth of mature plants for long durations under partial submergence. The underlying mechanisms of the molecular basis of adaptation to anaerobic germination and seedling growth in rice are being uncovered. Induction of an ensemble of hydrolases to mobilize endosperm nutrient reserves is one of the key factors for successful germination and coleoptile elongation in rice under submergence. To compensate for reduced efficiency of Tricarboxylic Acid cycle and oxidative respiration in mitochondria under O2 deficient conditions, α-amylases play a central role in the hydrolysis of starch to provide sugar substrates for glycolysis and alcohol fermentation for generating ATP. We review the progress on the molecular mechanism regulating α-amylase expression that involves the integration of signals generated by the hormone gibberellin (GA), sugar starvation and O2 deprivation that results in germination and sustainable seedling growth in rice under anaerobic conditions. Comparisons are also made between dicots and monocots for the molecular mechanism of induction of genes involved in alcohol fermentation and sugar/O2 deficiency sensing system.

Expression of ␣-amylase genes in cereals is induced by both gibberellin (GA) and sugar starvation. In a transient expression assay, a 105-bp sugar response sequence (SRS) in the promoter of a sugar starvation highly inducible rice ␣-amylase gene, ␣Amy3, was shown previously to confer sugar response and to enhance the activity of the rice Act1 promoter in rice protoplasts. A 230-bp SRS-like sequence was also found in the promoter of another sugar starvation highly inducible rice ␣-amylase gene, ␣Amy8. The ␣Amy8 SRS contains a GA response sequence and was designated as ␣Amy8 SRS/ GARS. In the present study, a transgenic approach was employed to characterize the function of the ␣-amylase gene SRSs in rice. We found that the ␣Amy3 SRS significantly enhances the endogenous expression pattern of the Act1 promoter in various rice tissues throughout their developmental stages. By contrast, the ␣Amy8 SRS/ GARS significantly enhances Act1 promoter activity only in embryos and endosperms of germinating rice seeds. A minimal promoter fused to the ␣Amy8 SRS/ GARS is specifically active in rice embryo and endosperm and is subject to sugar repression and GA induction in rice embryos. This sugar repression was found to override GA induction of ␣Amy8 SRS/GARS activity. Our study demonstrates that the ␣-amylase transcriptional enhancers contain cis-acting elements capable of enhancing endogenous expression patterns or activating sugar-sensitive, hormone-responsive, tissue-specific, and developmental stage-dependent expression of promoters in transgenic rice. These enhancers may facilitate the design of highly active and tightly regulated composite promoters for monocot transformation and gene expression. Our study also reveals the existence of cross-talk between the sugar and GA signaling pathways in cereals and provides a system for analyzing the underlying molecular mechanisms involved.