Flooding stress signaling through perturbations in oxygen, ethylene, nitric oxide and light

A grand challenge in the coming decades is to feed the rapidly growing world population. A second ‘Green Revolution’ is needed to further sustain and increase agricultural productivity in the face of global climate change. Climate projection models predict an increasingly wetter world with frequent and severe flooding events in major farming regions, especially in the tropics and Western Europe (Hirabayashi et al., 2013). Prolonged wet conditions hamper seedling establishment, growth, and reproduction of plants thereby negatively impacting yield (Bailey-Serres Voesenek Hattori et al., 2009). The elusive mechanism of O2 sensing involving Ethylene Response Transcription Factors of sub-clade group VII (ERF-VIIs) was unraveled (Gibbs et al., 2011; Licausi et al., 2011; Sasidharan van Veen et al., 2013). However, many breaches still exist in our knowledge of low-O2 sensing, signaling and downstream response networks. There are major challenges in understanding and improving aeration of roots, regulation of low-O2 metabolism and post-stress recovery. Considering the accelerated momentum in flooding research and the urgency of enhanced global food security, researchers with interests in flooding and low-O2 stress biology meet, discuss and update once every three years at a conference organized by the International Society of Plant Anaerobiosis (ISPA), and the most recent meeting was held in 2013. To enhance and synergize flooding research between ISPA meetings, and introduce new researchers to the community, an international New Phytologist Workshop on flooding biology was held in Ravenstein, the Netherlands in 2015. More than 20 leading scientists from 12 different countries met in the rustic former monastery Soeterbeeck in the rural south of the Netherlands. Several plant traits, either constitutively present or inducible, improve flooding tolerance. These traits are categorized as ‘Escape’ traits or ‘Quiescence’ traits. In the first category, anatomical and morphological features and modifications improves the access of flooded plant cells to O2 and CO2, thus impinging the energy and carbohydrate status of flooded plants. The latter class of traits involves a reorganization of a plant's metabolism and ultimately growth through which survival during flooding stress is perpetuated (Voesenek Tomé et al., 2014). These kinases are activated via phosphorylation under starvation conditions and subsequently activate S1 bZIP transcription factors involved in the activation of genes that stimulate catabolism to provide alternative carbon sources. Ming-Che Shih (Academia Sinica, Taipei, Taiwan) provided data demonstrating that an Arabidopsis SnRK1.1 dominant-negative mutant had reduced tolerance of submergence. A comparative phosphoproteomics survey of wildtype and mutant tissue of submerged plants identified a number of differentially phosphorylated proteins that range in function from sugar synthesis, glycolysis, osmotic regulation, ABA signaling, protein synthesis and ROS signaling. Linked to the regulation of energy homeostasis is the production of the metabolite trehalose-6-P from glucose-6-P and UDP-glucose (reviewed by Lawlor Weits et al., 2014). Two additional hypoxia-induced genes, LOB-DOMAIN-CONTAINING PROTEIN 41 (LBD41) and ABA REPRESSOR 1 (ABR1), are studied by Angelika Mustroph (University of Bayreuth, Germany). LBD41 is most likely a repressing transcription factor, whereas ABR1, induced primarily in shoot tissue, has a conserved Methionine-Cysteine conserved nitrogen (N)-terminal motif, which makes it a putative target for the N-end-rule pathway of protein degradation. This pathway is responsible for O2-dependent degradation of the ERF-VIIs (Gibbs et al., 2011; Licausi et al., 2011; Kosmacz et al., 2015). Another HRG is UNIVERSAL STRESS PROTEIN 1 (HRU1). Pierdomenico Perata (Scuola Superiore Sant'Anna, Pisa, Italy) presented evidence that HRU1 is induced by the ERF-VII transcription factor RELATED TO AP2.12 (RAP2.12) and that it modulates ROS production. It is proposed that HRU1 integrates the anaerobic response with the production of ROS under extreme O2 deprivation. A common observation of many researchers studying molecular mechanisms of sub-ambient O2 response in diverse plants are the strongly upregulated transcripts encoding non-symbiotic hemoglobins (Van Dongen Ng et al., 2013). An interesting question is whether the sensitivity of juvenile leaves to O2-deprivation or re-oxygenation relates to morphological distinctions, such as cuticular lipid composition or developmentally determined distinctions in cell growth and metabolism. An elegant demonstration of the role of O2 in developmental plasticity in Arabidopsis was made by Michael Holdsworth (University of Nottingham, UK). Work from his group demonstrated the ecological role of hypoxia in protecting the shoot stem cell niche through enhancement of the apical hook during early seedling growth. This hypocotyl curvature is regulated by the stabilization of the ERF-VIIs when O2 levels are below 12 kPa and NO levels are limited (Gibbs et al., 2014; Abbas et al., 2015; Voesenek & Bailey-Serres, 2015b). Progress in the field of flooding biology research is gaining rapid momentum. Breakthrough discoveries were made over the past years, such as the transcriptional regulation mediated by direct sensing of O2, necessary metabolic and growth reorganization via group ERF-VII transcription factors, their post translational regulation by means of the N-end rule of protein degradation, the importance of NO in regulating this protein degradation pathway and the function of hypoxia as an environmental cue in plant development. The small-scale workshop in Ravenstein stimulated interactions between flooding researchers and resulted in new collaborations and exchange of ideas and materials. In the final keynote, Julia Bailey-Serres summarized and linked together the main results of this event. We learned that short-term responses to hypoxia in plants are conserved and that small rather than big changes in metabolism distinguish tolerant plants from those that are intolerant. Moving beyond the mining of genetic variation in flooding tolerance in rice, evidence was provided that waterlogging tolerant maize can be established by introgression of gene(s) from a teosinte that enhance the barrier that prevents radial O2 loss. New discoveries were presented on the interactions between flooding and other stresses (heat, salt) and the functions of several conserved unknown HRGs were explored. Finally, the talks positioned phytoglobins as an important group of proteins that influence flooding tolerance most likely through their interaction with NO and the N-end rule pathway. In September 2016, ISPA will hold its next conference in Copenhagen, Denmark (http://www.is-pa.org). It will be a challenge to incorporate our fundamental knowledge into the development of flood tolerant crops to feed the expected nine billion people on our planet. The authors thank all participants of the workshop in Ravenstein for their contribution to the discussions and they thank Carla Brouwer, Elaine Yeung, Afke Vogelzang, Zeguang Liu and Sjon Hartman for practical assistance during the meeting. The authors also acknowledge the New Phytologist Trust for their generous financial contribution.