'Summary'	57	
I.	'Introduction'	58	
II.	'Root acclimations that promote root aeration'	60	
III.	'Regulating reaeration by active emergence in Rumex palustris and Oryza sativa'	62	
IV.	'Limiting O2 starvation with gas films and underwater photosynthesis'	64	
V.	'Key metabolic acclimations to flooding and low-O2 stress and their control'	65	
VI.	'Managing quiescence in growth during submergence'	67	
VII.	'After the deluge'	68	
VIII.	'Perspective'	69	
 	'Acknowledgements'	69	
 	References	69	


Summary
Unanticipated flooding challenges plant growth and fitness in natural and agricultural ecosystems. Here we describe mechanisms of developmental plasticity and metabolic modulation that underpin adaptive traits and acclimation responses to waterlogging of root systems and submergence of aerial tissues. This includes insights into processes that enhance ventilation of submerged organs. At the intersection between metabolism and growth, submergence survival strategies have evolved involving an ethylene-driven and gibberellin-enhanced module that regulates growth of submerged organs. Opposing regulation of this pathway is facilitated by a subgroup of ethylene-response transcription factors (ERFs), which include members that require low O2 or low nitric oxide (NO) conditions for their stabilization. These transcription factors control genes encoding enzymes required for anaerobic metabolism as well as proteins that fine-tune their function in transcription and turnover. Other mechanisms that control metabolism and growth at seed, seedling and mature stages under flooding conditions are reviewed, as well as findings demonstrating that true endurance of submergence includes an ability to restore growth following the deluge. Finally, we highlight molecular insights obtained from natural variation of domesticated and wild species that occupy different hydrological niches, emphasizing the value of understanding natural flooding survival strategies in efforts to stabilize crop yields in flood-prone environments.

https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/nph.13209

Flood adaptive traits and processes: an overview

Dynamic environmental changes such as extreme temperature, water scarcity and high salinity affect plant growth, survival, and reproduction. Plants have evolved sophisticated regulatory mechanisms to adapt to these unfavorable conditions, many of which interface with plant hormone signaling pathways. Abiotic stresses alter the production and distribution of phytohormones that in turn mediate stress responses at least in part through hormone- and stress-responsive transcription factors. Among these, the APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) family transcription factors (AP2/ERFs) have emerged as key regulators of various stress responses, in which they also respond to hormones with improved plant survival during stress conditions. Apart from participation in specific stresses, AP2/ERFs are involved in a wide range of stress tolerance, enabling them to form an interconnected stress regulatory network. Additionally, many AP2/ERFs respond to the plant hormones abscisic acid (ABA) and ethylene (ET) to help activate ABA and ET dependent and independent stress-responsive genes. While some AP2/ERFs are implicated in growth and developmental processes mediated by gibberellins (GAs), cytokinins (CTK), and brassinosteroids (BRs). The involvement of AP2/ERFs in hormone signaling adds the complexity of stress regulatory network. In this review, we summarize recent studies on AP2/ERF transcription factors in hormonal and abiotic stress responses with an emphasis on selected family members in Arabidopsis. In addition, we leverage publically available Arabidopsis gene networks and transcriptome data to investigate AP2/ERF regulatory networks, providing context and important clues about the roles of diverse AP2/ERFs in controlling hormone and stress responses.

/pdf/ap2-erf-transcription-factor-regulatory-networks-in-hormone-5efuzvwy46.pdf

AP2/ERF Transcription Factor Regulatory Networks in Hormone and Abiotic Stress Responses in Arabidopsis.

https://www.cell.com/molecular-plant/pdf/S1674-2052(14)00046-X.pdf

Nitric Oxide: A Multitasked Signaling Gas in Plants

Adventitious roots are plant roots that form from any nonroot tissue and are produced both during normal development (crown roots on cereals and nodal roots on strawberry [Fragaria spp.]) and in response to stress conditions, such as flooding, nutrient deprivation, and wounding. They are important economically (for cuttings and food production), ecologically (environmental stress response), and for human existence (food production). To improve sustainable food production under environmentally extreme conditions, it is important to understand the adventitious root development of crops both in normal and stressed conditions. Therefore, understanding the regulation and physiology of adventitious root formation is critical for breeding programs. Recent work shows that different adventitious root types are regulated differently, and here, we propose clear definitions of these classes. We use three case studies to summarize the physiology of adventitious root development in response to flooding (case study 1), nutrient deficiency (case study 2), and wounding (case study 3).

/pdf/the-physiology-of-adventitious-roots-3r2z0z7lmu.pdf

The Physiology of Adventitious Roots.

The protein ubiquitin is a covalent modifier of proteins, including itself. The ubiquitin system encompasses the enzymes required for catalysing attachment of ubiquitin to substrates as well as proteins that bind to ubiquitinated proteins leading them to their final fate. Also included are activities that remove ubiquitin independent of, or in concert with, proteolysis of the substrate, either by the proteasome or proteases in the vacuole. In addition to ubiquitin encoded by a family of fusion proteins, there are proteins with ubiquitin-like domains, likely forming ubiquitin's β-grasp fold, but incapable of covalent modification. However, they serve as protein-protein interaction platforms within the ubiquitin system. Multi-gene families encode all of these types of activities. Within the ubiquitination machinery “half” of the ubiquitin system are redundant, partially redundant, and unique components affecting diverse developmental and environmental responses in plants. Notably, multiple aspects of biotic...

https://bioone.org/journals/the-arabidopsis-book/volume-2014/issue-12/tab.0174/The-Ubiquitination-Machinery-of-the-Ubiquitin-System/10.1199/tab.0174.pdf

The Ubiquitination Machinery of the Ubiquitin System

http://wrap.warwick.ac.uk/59286/1/WRAP_PIIS1097276513009301.pdf

Nitric oxide sensing in plants is mediated by proteolytic control of group VII ERF transcription factors

https://nottingham-repository.worktribe.com/preview/750325/MJH73.pdf

Oxygen Sensing Coordinates Photomorphogenesis to Facilitate Seedling Survival

The N-end rule pathway is a highly conserved mechanism present in all eukaryotes. It targets specific proteins based on the recognition of the substrate's N-terminal amino acid by E3-ligase for degradation via ubiquitin-proteasome pathway in the cell. In A.thaliana, the Group VII ERFs transcription factors are substrates of N-end rule pathway that begin with ‘Met-Cys. In presence of oxygen and nitric oxide, cysteine is oxidized and arginylated and recognized by the E3-ligase PROTEOLYSIS 6 (PRT6). Previous studies on prt6 mutant endosperm containing promABI5::GUS showed that the ABI5 5’UTR region that contains 2 EBP boxes (GCCGCC) mediate regulation via Group VII ERFs. Whereas, expression was inhibited when two EBP boxes were absent. Hence, suggesting that genes containing EBP boxes as similar as ABI5 might also be regulated through the N-end rule pathway. In this project fourteen genes containing two copies of GCCGCC in the 5’UTR/promoter were identified as potential candidate genes to be regulated by Group VII ERFs, similarly to ABI5. Successful amplification of the promoter region of five of these genes [AT4G01026 (PYL7), AT1G14810, AT3G54510 (ERD4), At3G13440 and AT5G44420 (PDF1.2)] was followed by cloning into a GUS-reporter plasmid and transformation into Arabidopsis wild type (Col-0) and prt6-1 plants. Leaves and flowers of transgenic plants were analysed by GUS staining to reveal promoter activity. This analysis has shown that these promoters enhanced GUS expression in prt6 in comparison to Col-0, suggesting that genes are regulated by the Group VII ERFs. Analysis of in-vivo binding of ERFs to selected promoters was done by Chromatin Immuno- precipitation (ChIP). To confirm the hypothesis that promoters carrying GCCGCC binding sites are bound in-vivo by Group VII ERFs. Future work involves analysis of mutant combinations of prt6 with genes such as PYL7 and ERD4 for ABA assay.

Jorge Vicente Conde

Papers

Nitric oxide sensing in plants is mediated by proteolytic control of group VII ERF transcription factors

Oxygen Sensing Coordinates Photomorphogenesis to Facilitate Seedling Survival

To Investigate the Relationship between Substrates of the N-end Rule Pathway and Genes Regulated by EBP Binding Sites (GCCGCC) in Arabidopsis thaliana