'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

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

Nitric Oxide: A Multitasked Signaling Gas in Plants

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

Plant survival depends on seed germination and progression through post-germinative developmental checkpoints. These processes are controlled by the stress phytohormone abscisic acid (ABA). ABA regulates the basic leucine zipper transcriptional factor ABI5, a central hub of growth repression, while the reactive nitrogen molecule nitric oxide (NO) counteracts ABA during seed germination. However, the molecular mechanisms by which seeds sense more favourable conditions and start germinating have remained elusive. Here we show that ABI5 promotes growth via NO, and that ABI5 accumulation is altered in genetic backgrounds with impaired NO homeostasis. S-nitrosylation of ABI5 at cysteine-153 facilitates its degradation through CULLIN4-based and KEEP ON GOING E3 ligases, and promotes seed germination. Conversely, mutation of ABI5 at cysteine-153 deregulates protein stability and inhibition of seed germination by NO depletion. These findings suggest an inverse molecular link between NO and ABA hormone signalling through distinct posttranslational modifications of ABI5 during early seedling development.

/pdf/s-nitrosylation-triggers-abi5-degradation-to-promote-seed-3jzn7kxljj.pdf

S-nitrosylation triggers ABI5 degradation to promote seed germination and seedling growth.

Plants are exposed to an ever-changing environment to which they have to adjust accordingly. Their response is tightly regulated by complex signaling pathways that all start with stimulus perception. Here, we give an overview of the latest developments in the perception of various abiotic stresses, including drought, salinity, flooding, and temperature stress. We discuss whether proposed perception mechanisms are true sensors, which is well established for some abiotic factors but not yet fully elucidated for others. In addition, we review the downstream cellular responses, many of which are shared by various stresses but result in stress-specific physiological and developmental output. New sensing mechanisms have been identified, including heat sensing by the photoreceptor phytochrome B, salt sensing by glycosylinositol phosphorylceramide sphingolipids, and drought sensing by the specific calcium influx channel OSCA1. The simultaneous occurrence of multiple stress conditions shows characteristic downstream signaling signatures that were previously considered general signaling responses. The integration of sensing of multiple stress conditions and subsequent signaling responses is a promising venue for future research to improve the understanding of plant abiotic stress perception.

/pdf/how-plants-sense-and-respond-to-stressful-environments-591q1yqaej.pdf

How plants sense and respond to stressful environments

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

Many regulatory circuits in plants contain steps of targeted proteolysis, with the ubiquitin proteasome system (UPS) as the mediator of these proteolytic events. In order to decrease ubiquitin-dependent proteolysis, we inducibly expressed a ubiquitin variant with Arg at position 48 instead of Lys (ubK48R). This variant acts as an inhibitor of proteolysis via the UPS, and allowed us to uncover processes that are particularly sensitive to UPS perturbation.Expression of ubK48R during germination leads to seedling death. We analyzed the seedling transcriptome, proteome and metabolome 24 h post ubK48R induction and confirmed defects in chloroplast development. We found that mutations in single genes can suppress seedling lethality, indicating that a single process in seedlings is critically sensitive to decreased performance of the UPS. Suppressor mutations in phototropin 2 (PHOT2) suggest that a contribution of PHOT2 to chloroplast protection is compromised by proteolysis inhibition.Overall, the results reveal protein turnover as an integral part of a signal transduction chain that protects chloroplasts during development. 

/pdf/transcriptome-metabolome-and-suppressor-analysis-reveal-an-2dvtfl0n.pdf

Transcriptome, metabolome and suppressor analysis reveal an essential role for the ubiquitin-proteasome system in seedling chloroplast development

/pdf/transcriptome-metabolome-and-suppressor-analysis-reveal-an-1eaf95x8.pdf

Bulut Hamali

Papers

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

Transcriptome, metabolome and suppressor analysis reveal an essential role for the ubiquitin-proteasome system in seedling chloroplast development

Transcriptome, metabolome and suppressor analysis reveal an essential role for the ubiquitin-proteasome system in seedling chloroplast development