Underground gibberellin activity: differential gibberellin response in tomato shoots and roots
. New PhytologistNew PhytologistNew Phytol 2020
. Publisher's VersionAbstract
Abstract Plant organ growth is governed and modified by developmental programs and environmental cues. In most cases, these changes are mediated by the activity of phytohormones (Bradford Verma et al., 2016). Gibberellins (GAs) are growth promoting hormones that regulate many developmental processes, including organ growth and elongation (Davière Ueguchi-Tanaka et al., 2007).
Evolution of Abscisic Acid Signaling Module and Its Perception
. Frontiers in Plant Science 2020
, 934. Publisher's VersionAbstract
We hereby review the perception and responses to the stress hormone Abscisic acid (ABA), along the trajectory of 500M years of plant evolution, whose understanding may resolve how plants acquired this signaling pathway essential for the colonization of land. ABA levels rise in response to abiotic stresses, coordinating physiological and metabolic responses, helping plants survive stressful environments. In land plants, ABA signaling cascade leads to growth arrest and large-scale changes in transcript levels, required for coping with environmental stressors. This response is regulated by a PYRABACTIN RESISTANCE 1-like (PYL)–PROTEIN PHOSPHATASE 2C (PP2C)–SNF1-RELATED PROTEIN KINASE 2 (SnRK2) module, that initiates phosphor-activation of transcription factors and ion channels. The enzymatic portions of this module (phosphatase and kinase) are functionally conserved from streptophyte algae to angiosperms, whereas the regulatory component –the PYL receptors, putatively evolved in the common ancestor of Zygnematophyceae and embryophyte as a constitutive, ABA-independent protein, further evolving into a ligand-activated receptor at the embryophyta. This evolutionary process peaked with the appearance of the strictly ABA-dependent subfamily III stress-triggered angiosperms' dimeric PYL receptors. The emerging picture is that the ancestor of land plants and its predecessors synthesized ABA, as its biosynthetic pathway is conserved between ancestral and current day algae. Despite this ability, it was only the common ancestor of land plants which acquired the hormonal-modulation of PYL activity by ABA. This raises several questions regarding both ABA's function in ABA-non-responsive organisms, and the evolutionary aspects of the ABA signal transduction pathway.
Rapid starch degradation in the wood of olive trees under heat and drought is permitted by three stress-specific beta amylases
. New Phytologist 2020
. Publisher's VersionAbstract
Abstract Carbon reserve use is a major drought response in trees, enabling tree survival in conditions prohibiting photosynthesis. However, regulation of starch metabolism under drought at the whole-tree scale is still poorly understood. To this end, we combined measurements of nonstructural carbohydrates (NSC), tree physiology and gene expression. The experiment was conducted outside on olive trees in pots under 90 days of seasonal spring to summer warming. Half of the trees were also subjected to limited water conditions for 28 days. Photosynthesis decreased in dehydrating trees from 19 to 0.5 µmol m-2 s-1 during the drought period. Starch degradation and mannitol production were a major drought response, with mannitol increasing to 71% and 41% out of total NSC in shoots and roots, respectively. We identified the gene family members potentially relevant either to long-term or stress-induced carbon storage. Partitioning of expression patterns among β amylase and starch synthase family members was observed, with three β amylases possibly facilitating the rapid starch degradation under heat and drought. Our results suggest a group of stress-related, starch metabolism genes, correlated with NSC fluctuations during drought and recovery. The daily starch metabolism gene expression was different from the stress-mode starch metabolism pattern, where some genes are uniquely expressed during the stress-mode response.
Measuring the Hydraulic Conductivity of Grass Root Systems
. Current Protocols in Plant Biology 2020
e20110. Publisher's VersionAbstract
Abstract Root-system hydraulic conductivity (RSHC) is an important physiological characteristic that describes the inherent ability of roots to conduct water across a water-potential gradient between the root and the stem xylem. RSHC is commonly used as an indicator of plant functioning and adaptability to a given environment. A simple, fast, and easy-to-use protocol is described for the quantification of RSHC at the seedling stage in two important monocot species grown in hydroponic solution: Setaria viridis, a C4 model plant, and wheat, a C3 crop plant. This protocol can also be easily modified for use with almost any grass species and environmental treatments, such as salinity or hormone treatments. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Setaria hydrostatic root-system hydraulic conductivity Alternate Protocol: Measuring the root conductivity of young plants with soft stems
Environmental and genetic determinants of amphicarpy in Pisum fulvum, a wild relative of domesticated pea
. Plant Science 2020
, 110566. Publisher's VersionAbstract
Pisum fulvum is an annual legume native to Syria, Lebanon, Israel and Jordan. In certain locations, P. fulvum individuals were documented to display a reproductive dimorphism – amphicarpy, with both above and below ground flowers and pods. Herein we aimed to study the possible role of soil texture on amphicarpy in P. fulvum, to investigate the possible bio-climatic associations of P. fulvum amphicarpy and to identify genetic markers associated with this phenotype. A set of 127 germplasm accessions sampled across the Israeli distribution range of the species was phenotyped in two common garden nurseries. Land use and bioclimatic data were used to delineate the eco-geographic clustering of accession's sampling sites. Single nucleotide polymorphism (SNP) markers were employed in genome-wide association study to identify associated loci. Amphicarpy was subject to strong experimental site x genotype interaction with higher phenotypic expression in fine textured soil relative to sandy loam. Amphicarpy was more prevalent among accessions sampled in eastern Judea and Samaria and was weakly associated with early phenology and relatively modest above ground biomass production. Twelve SNP markers were significantly associated with amphicarpy, each explaining between 8 and 12 % of the phenotypic variation. In P. fulvum amphicarpy seems to be a polygenetic trait controlled by an array of genes that is likely to be affected by environmental stimuli. The probable selective advantage of the association between amphicarpy and early flowering is in line with its relative prevalence in drought prone territories subject to heavy grazing.
ACE2 Co-evolutionary Pattern Suggests Targets for Pharmaceutical Intervention in the COVID-19 Pandemic
. iScience 2020
, 101384. Publisher's VersionAbstract
Summary The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spillover infection in December 2019 has caused an unprecedented pandemic. SARS-CoV-2, as other coronaviruses, binds its target cells through the angiotensin-converting enzyme 2 (ACE2) receptor. Accordingly, this makes ACE2 research essential for understanding the zoonotic nature of coronaviruses and identifying novel drugs. Here we present a systematic analysis of the ACE2 conservation and co-evolution protein network across 1,671 eukaryotes, revealing an unexpected conservation pattern in specific metazoans, plants, fungi, and protists. We identified the co-evolved protein network and pinpointed a list of drugs that target this network by using data integration from different sources. Our computational analysis found widely used drugs such as nonsteroidal anti-inflammatory drugs and vasodilators. These drugs are expected to perturb the ACE2 network affecting infectivity as well as the pathophysiology of the disease.
Local auxin biosynthesis is required for root regeneration after wounding
. Nature Plant 2020
1020 - 1030. Publisher's VersionAbstract
The root meristem can regenerate following removal of its stem-cell niche by recruitment of remnant cells from the stump. Regeneration is initiated by rapid accumulation of auxin near the injury site but the source of this auxin is unknown. Here, we show that auxin accumulation arises from the activity of multiple auxin biosynthetic sources that are newly specified near the cut site and that their continuous activity is required for the regeneration process. Auxin synthesis is highly localized while PIN-mediated transport is dispensable for auxin accumulation and tip regeneration. Roots lacking the activity of the regeneration competence factor ERF115, or that are dissected at a zone of low regeneration potential, fail to activate local auxin sources. Remarkably, restoring auxin supply is sufficient to confer regeneration capacity to these recalcitrant tissues. We suggest that regeneration competence relies on the ability to specify new local auxin sources in a precise temporal pattern.
Genetic dissection of the auxin response network
. Nature Plant 2020
. Publisher's VersionAbstract
The expansion of gene families during evolution, which can generate functional overlap or specialization among their members, is a characteristic feature of signalling pathways in complex organisms. For example, families of transcriptional activators and repressors mediate responses to the plant hormone auxin. Although these regulators were identified more than 20 years ago, their overlapping functions and compensating negative feedbacks have hampered their functional analyses. Studies using loss-of-function approaches in basal land plants and gain-of-function approaches in angiosperms have in part overcome these issues but have still left an incomplete understanding. Here, we propose that renewed emphasis on genetic analysis of multiple mutants and species will shed light on the role of gene families in auxin response. Combining loss-of-function mutations in auxin-response activators and repressors can unravel complex outputs enabled by expanded gene families, such as fine-tuned developmental outcomes and robustness. Similar approaches and concepts may help to analyse other regulatory pathways whose components are also encoded by large gene families.
Nitrogen availability and genotype affect major nutritional quality parameters of tef grain grown under irrigation
. Scientific Reports 2020
, 14339. Publisher's VersionAbstract
Worldwide demand for tef (Eragrostis tef) as a functional food for human consumption is increasing, thanks to its nutritional benefits and gluten-free properties. As a result, tef in now grown outside its native environment in Ethiopia and thus information is required regarding plant nutrition demands in these areas, as well as resulting grain health-related composition. In the current work, two tef genotypes were grown in Israel under irrigation in two platforms, plots in the field and pots in a greenhouse, with four and five nitrogen treatments, respectively. Nutritional and health-related quality traits were analyzed, including mineral content, fatty acid composition, hydrophilic and lipophilic antioxidative capacity, total phenolic content and basic polyphenolic profile. Our results show that tef genotypes differ in their nutritional composition, e.g. higher phenolic contents in the brown compared to the white genotype. Additionally, nitrogen availability positively affected grain fatty acid composition and iron levels in both experiments, while negatively affecting total phenolics in the field trials. To conclude, nitrogen fertilization is crucial for crop growth and productivity, however it also implicates nutritional value of the grains as food. These effects should be considered when fertilizing tef with nitrogen, to optimize both crop productivity and nutritional effects.
A Telemetric, Gravimetric Platform for Real-Time Physiological Phenotyping of Plant–Environment Interactions
. J. Vis. Exp. 2020
, e61280. Publisher's VersionAbstract
Food security for the growing global population is a major concern. The data provided by genomic tools far exceeds the supply of phenotypic data, creating a knowledge gap. To meet the challenge of improving crops to feed the growing global population, this gap must be bridged.Physiological traits are considered key functional traits in the context of responsiveness or sensitivity to environmental conditions. Many recently introduced high-throughput (HTP) phenotyping techniques are based on remote sensing or imaging and are capable of directly measuring morphological traits, but measure physiological parameters mainly indirectly. This paper describes a method for direct physiological phenotyping that has several advantages for the functional phenotyping of plant–environment interactions. It helps users overcome the many challenges encountered in the use of load-cell gravimetric systems and pot experiments. The suggested techniques will enable users to distinguish between soil weight, plant weight and soil water content, providing a method for the continuous and simultaneous measurement of dynamic soil, plant and atmosphere conditions, alongside the measurement of key physiological traits. This method allows researchers to closely mimic field stress scenarios while taking into consideration the environment’s effects on the plants’ physiology. This method also minimizes pot effects, which are one of the major problems in pre-field phenotyping. It includes a feed-back fertigation system that enables a truly randomized experimental design at a field-like plant density. This system detects the soil-water-content limiting threshold (θ) and allows for the translation of data into knowledge through the use of a real-time analytic tool and an online statistical resource. This method for the rapid and direct measurement of the physiological responses of multiple plants to a dynamic environment has great potential for use in screening for beneficial traits associated with responses to abiotic stress, in the context of pre-field breeding and crop improvement.
The relation between crosstalk and gene regulation form revisited
. PLOS Computational Biology 2020
, 1-24. Publisher's VersionAbstract
Author summary Genes differ in the frequency at which they are expressed and in the form of regulation used to control their activity. The basic level of regulation is mediated by different types of DNA-binding proteins, where each type regulates particular gene(s). We distinguish between two basic forms of regulation: positive—if a gene is activated by the binding of its regulatory protein, and negative—if it is active unless bound by its regulatory protein. Due to the multitude of genes and regulators, spurious binding and unbinding events, called “crosstalk”, could occur. How does the form of regulation, positive or negative, affect the extent of regulatory crosstalk? To address this question, we used a mathematical model integrating many genes and many regulators. As intuition suggests, we found that in most of the parameter space, crosstalk increased with the availability of regulators. We propose, that crosstalk is usually reduced when networks are designed such that minimal regulation is needed, which we call the ‘idle’ design. In other words: a frequently needed gene will use negative regulation and conversely, a scarcely needed gene will employ positive regulation. In both cases, the requirement for the regulators is minimized. In addition, we demonstrate how crosstalk can be calculated from available datasets and discuss the technical challenges in such calculation, specifically data incompleteness.
Siliplant1 (Slp1) protein precipitates silica in sorghum silica cells
. Journal of Experimental Botany 2020
. Publisher's VersionAbstract
Silicon is absorbed by plant roots as silicic acid. The acid moves with the transpiration stream to the shoot, and mineralizes as silica. In grasses, leaf epidermal cells called silica cells deposit silica in most of their volume by unknown mechanism. Using bioinformatics tools, we identified a previously uncharacterized protein in sorghum (Sorghum bicolor), which we named Siliplant1 (Slp1). Slp1 is a basic protein with seven repeat units rich in proline, lysine, and glutamic acid. We found Slp1 RNA in sorghum immature leaf and immature inflorescence. In leaves, transcription was highest just before the active silicification zone (ASZ). There, Slp1 was localized specifically to developing silica cells, packed inside vesicles and scattered throughout the cytoplasm or near the cell boundary. These vesicles fused with the membrane, releasing their content in the apoplastic space. A short peptide that is repeated five times in Slp1 precipitated silica in vitro at a biologically relevant silicic acid concentration. Transient overexpression of Slp1 in sorghum resulted in ectopic silica deposition in all leaf epidermal cell-types. Our results show that Slp1 precipitates silica in sorghum silica cells.
Peptides from diatoms and grasses harness phosphate ion binding to silica to help regulate biomaterial structure
. Acta Biomaterialia 2020
. Publisher's VersionAbstract
Many life forms generate intricate submicron biosilica structures with various important biological functions. The formation of such structures, from the silicic acid in the waters and in the soil, is thought to be regulated by unique proteins with high repeats of specific amino acids and unusual sidechain modifications. Some silicifying proteins are characterized by high prevalence of basic amino acids in their primary structures. Lysine-rich domains are found, for instance, in diatom silaffin proteins and in the sorghum grass siliplant protein. These domains exhibit catalytic activity in silica chain condensation, owing to molecular interactions of the lysine amine groups with the forming mineral. The use of amine chemistry by two very remote organisms has motivated us to seek other molecular biosilicification processes that may be common to the two life forms. In diatom silaffins, domains rich in phosphoserine residues are thought to assist the assembly of silaffin molecules into an organic supra-structure which serves as a template for the silica to precipitate on. This mold, held by salt bridges between serine phosphates and lysine amines, dictates the shape of the silica particles formed. Yet, silica synthesized with the dephosphorylated silaffin in phosphate buffer showed similar morphology to the one prepared with the native protein, suggesting that a defined spatial arrangement of serine phosphates is not required to generate silica with the desired shape. Concurrently, free phosphates enhanced the activity of siliplant1 in silica formation. It is therefore beneficial to characterize the involvement of these anions as co-factors in regulated silicification by functional peptides from the two proteins and to understand whether they play similar molecular role in the mechanism of mineralization. Here we analyze the molecular interactions of free phosphate ions with silica and the silaffin peptide PL12 and separately with silica and siliplant1 peptide SLP1 in the two biomimetic silica products generated by the two peptides. MAS NMR measurements show that the phosphate ions interact with the peptides and at the same time may be forming bonds with the silica mineral. This bridging capability may add another avenue by which the structure of the silica material is influenced. A model for the molecular/ionic interactions at the bio-inorganic interface is described, which may have bearings for the role of phosphorylated residues beyond the function as intermolecular cross linkers or free phosphate ions as co-factors in regulation of silicification.
Regeneration of Grade 3 Ankle Sprain, Using the Recombinant Human Amelogenin Protein (rHAM+), in a Rat Model
. Journal of Orthopaedic Research 2020
. Publisher's VersionAbstract
Abstract Lateral ligament tears, also known as high-grade ankle sprains, are common, debilitating, and usually heal slowly. 10-30% of patients continue to suffer from chronic pain and ankle instability even after 3-9 months. Previously, we showed that the recombinant human amelogenin (rHAM+) induced regeneration of fully transected rat medial collateral ligament (MCL), a common proof-of-concept model. Our aim was to evaluate whether rHAM+ can regenerate torn ankle calcaneo-fibular ligament (CFL), an important component of the lateral ankle stabilizers. Right CFLs of Sabra rats were transected and treated with 0, 0.5 or 1µg/µl rHAM+ dissolved in propylene glycol alginate (PGA). Results were compared to the normal group, without surgery. Healing was evaluated 12 weeks after treatment by mechanical testing (ratio between the right and left, un-transected ligaments of the same rat), and histology including immunohistochemical staining of collagen I and S100. The mechanical properties, structure, and composition of transected ligaments treated with 0.5μg/μl rHAM+ (experimental) were similar to un-transected ligaments. PGA (control) treated ligaments were much weaker, lax and unorganized compared to un-transected ligaments. Treatment with 1μg/μl rHAM+ was not as efficient as 0.5μg/μl rHAM+. Normal arrangement of collagen I fibers and of proprioceptive nerve endings, parallel to the direction of the force, was detected in ligaments treated with 0.5μg/μl rHAM+, and scattered arrangement, resembling scar tissue, in control ligaments. In conclusion, we showed that rHAM+ induced significant mechanical and structural regeneration of torn rat CFLs, which might be translated into treatment for grade 2-3 ankle sprain injuries. This article is protected by copyright. All rights reserved.
A coherent feed forward loop drives vascular regeneration in damaged aerial organs growing in normal developmental-context
. Development 2020
Aerial organs of plants being highly prone to local injuries, require tissue restoration to ensure their survival. However, knowledge of the underlying mechanism is sparse. In this study, we mimicked natural injuries in growing leaf and stem to study the reunion between mechanically disconnected tissues. We show that ()/ () genes, which encodes stem cell promoting factors, are activated and contribute to vascular regeneration in response to these injuries. PLT proteins bind to and activate the CUC2 promoter. Both PLT and CUC2 regulate the transcription of the local auxin biosynthesis gene YUC4 in a coherent feed forward loop, and this process is necessary to drive vascular regeneration. In the absence of this PLT mediated regeneration response, leaf ground tissue cells can neither acquire early vascular identity marker ATHB8, nor properly polarize auxin transporters to specify new venation paths. The PLT-CUC2 module is required for vascular regeneration, but is dispensable for midvein formation in leaf. We reveal the mechanisms of vascular regeneration in plants and distinguishes the wound repair ability of the tissue from its formation during normal development.
High-density NGS-based map construction and genetic dissection of fruit shape and rind netting in Cucumis melo
. Theor Appl Genet 2020
Melon is an important crop that exhibits broad variation for fruit morphology traits that are the substrate for genetic mapping efforts. In the post-genomic era, the link between genetic maps and physical genome assemblies is key for leveraging QTL mapping results for gene cloning and breeding purposes. Here, using a population of 164 melon recombinant inbred lines (RILs) that were subjected to genotyping-by-sequencing, we constructed and compared high-density sequence- and linkage-based recombination maps that were aligned to the reference melon genome. These analyses reveal the genome-wide variation in recombination frequency and highlight regions of disrupted collinearity between our population and the reference genome. The population was phenotyped over 3 years for fruit size and shape as well as rind netting. Four QTLs were detected for fruit size, and they act in an additive manner, while significant epistatic interaction was found between two neutral loci for this trait. Fruit shape displayed transgressive segregation that was explained by the action of four QTLs, contributed by alleles from both parents. The complexity of rind netting was demonstrated on a collection of 177 diverse accessions. Further dissection of netting in our RILs population, which is derived from a cross of smooth and densely netted parents, confirmed the intricacy of this trait and the involvement of major locus and several other interacting QTLs. A major netting QTL on chromosome 2 co-localized with results from two additional populations, paving the way for future study toward identification of a causative gene for this trait.
Pharmaceuticals in treated wastewater induce a stress response in tomato plants
. Sci Rep 2020
Pharmaceuticals remain in treated wastewater used to irrigate agricultural crops. Their effect on terrestrial plants is practically unknown. Here we tested whether these compounds can be considered as plant stress inducers. Several features characterize the general stress response in plants: production of reactive oxygen species acting as stress-response signals, MAPKs signaling cascade inducing expression of defense genes, heat shock proteins preventing protein denaturation and degradation, and amino acids playing signaling roles and involved in osmoregulation. Tomato seedlings bathing in a cocktail of pharmaceuticals (Carbamazepine, Valporic acid, Phenytoin, Diazepam, Lamotrigine) or in Carbamazepine alone, at different concentrations and during different time-periods, were used to study the patterns of stress-related markers. The accumulation of the stress-related biomarkers in leaf and root tissues pointed to a cumulative stress response, mobilizing the cell protection machinery to avoid metabolic modifications and to restore homeostasis. The described approach is suitable for the investigation of stress response of different crop plants to various contaminants present in treated wastewater.
Upregulation of photosynthesis in mineral nutrition-deficient tomato plants by reduced source-to-sink ratio
. Plant Signal Behav 2020
Photosynthetic activity is affected by environmental factors and endogenous signals controlled by the source-sink relationship. We recently showed upregulated photosynthetic rate following partial defoliation under favorable environmental conditions. Here, we examined the influence of partial defoliation on the remaining leaves' function in tomato plants under nutrient deficiency. The effect of partial defoliation was more pronounced under limited mineral supply vs. favorable conditions. Reduced source-sink ratio resulted in increased stomatal conductance and transpiration rate, as well as higher photosystem II efficiency. Although chlorophyll concentration was significantly reduced under limited nutrient supply, the photosynthetic rate in the remaining leaf was similar to that measured under normal fertilization. Expression of genes involved in the phloem loading of assimilated sugars was downregulated in the remaining source leaf of unfertilized plants, 15 d after partial defoliation; in fertilized plants, these genes' expression was similar in control and partially defoliated plants. We propose that at early stage, the additional carbon assimilated in the remaining leaf is devoted to increasing source size rather than sink growth. The size increase of the remaining leaf in unfertilized plants was not sufficient to rebalance the source-sink ratio, resulting in inhibited sugar export and further carbohydrate allocation in the remaining leaf.
Root-shoot communication in tomato plants: cytokinin as a signal molecule modulating leaf photosynthetic activity
. Journal of experimental botany 2020
, 247-257. Publisher's VersionAbstract
Photosynthetic activity is affected by exogenous and endogenous inputs, including source-sink balance. Reducing the source to sink ratio by partial defoliation or heavy shading resulted in significant elevation of the photosynthetic rate in the remaining leaf of tomato plants within 3 d. The remaining leaf turned deep green, and its area increased by almost 3-fold within 7 d. Analyses of photosynthetic activity established up-regulation due to increased carbon fixation activity in the remaining leaf, rather than due to altered water balance. Moreover, senescence of the remaining leaf was significantly inhibited. As expected, carbohydrate concentration was lower in the remaining leaf than in the control leaves; however, expression of genes involved in sucrose export was significantly lower. These results suggest that the accumulated fixed carbohydrates were primarily devoted to increasing the size of the remaining leaf. Detailed analyses of the cytokinin content indicated that partial defoliation alters cytokinin biosynthesis in the roots, resulting in a higher concentration of trans-zeatin riboside, the major xylem-translocated molecule, and a higher concentration of total cytokinin in the remaining leaf. Together, our findings suggest that trans-zeatin riboside acts as a signal molecule that traffics from the root to the remaining leaf to alter gene expression and elevate photosynthetic activity. © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Experimental Biology.