Michael James Van Oosten

Quantitative phosphoproteomics identifies SnRK2 protein kinase substrates and reveals the effectors of abscisic acid action

Sucrose nonfermenting 1 (SNF1)-related protein kinase 2s (SnRK2s) are central components of abscisic acid (ABA) signaling pathways. The snrk2.2/2.3/2.6 triple-mutant plants are nearly completely insensitive to ABA, suggesting that most of the molecular actions of ABA are triggered by the SnRK2s-mediated phosphorylation of substrate proteins. Only a few substrate proteins of the SnRK2s are known. To identify additional substrate proteins of the SnRK2s and provide insight into the molecular actions of ABA, we used quantitative phosphoproteomics to compare the global changes in phosphopeptides in WT and snrk2.2/2.3/2.6 triple mutant seedlings in response to ABA treatment. Among the 5,386 unique phosphorylated peptides identified in this study, we found that ABA can increase the phosphorylation of 166 peptides and decrease the phosphorylation of 117 peptides in WT seedlings. In the snrk2.2/2.3/2.6 triple mutant, 84 of the 166 peptides, representing 58 proteins, could not be phosphorylated, or phosphorylation was not increased under ABA treatment. In vitro kinase assays suggest that most of the 58 proteins can serve as substrates of the SnRK2s. The SnRK2 substrates include proteins involved in flowering time regulation, RNA and DNA binding, miRNA and epigenetic regulation, signal transduction, chloroplast function, and many other cellular processes. Consistent with the SnRK2 phosphorylation of flowering time regulators, the snrk2.2/2.3/2.6 triple mutant flowered significantly earlier than WT. These results shed new light on the role of the SnRK2 protein kinases and on the downstream effectors of ABA action, and improve our understanding of plant responses to adverse environments.

The Salt Overly Sensitive (SOS) Pathway: Established and Emerging Roles

Soil salinity is a growing problem around the world with special relevance in farmlands. The ability to sense and respond to environmental stimuli is among the most fundamental processes that enable plants to survive. At the cellular level, the Salt Overly Sensitive (SOS) signaling pathway that comprises SOS3, SOS2, and SOS1 has been proposed to mediate cellular signaling under salt stress, to maintain ion homeostasis. Less well known is how cellularly heterogenous organs couple the salt signals to homeostasis maintenance of different types of cells and to appropriate growth of the entire organ and plant. Recent evidence strongly indicates that different regulatory mechanisms are adopted by roots and shoots in response to salt stress. Several reports have stated that, in roots, the SOS proteins may have novel roles in addition to their functions in sodium homeostasis. SOS3 plays a critical role in plastic development of lateral roots through modulation of auxin gradients and maxima in roots under mild salt conditions. The SOS proteins also play a role in the dynamics of cytoskeleton under stress. These results imply a high complexity of the regulatory networks involved in plant response to salinity. This review focuses on the emerging complexity of the SOS signaling and SOS protein functions, and highlights recent understanding on how the SOS proteins contribute to different responses to salt stress besides ion homeostasis.

Transcriptomic Changes Drive Physiological Responses to Progressive Drought Stress and Rehydration in Tomato

Tomato is a major crop in the Mediterranean basin, where the cultivation in the open field is often vulnerable to drought. In order to adapt and survive to naturally occurring cycles of drought stress and recovery, plants employ a coordinated array of physiological, biochemical, and molecular responses. Transcriptomic studies on tomato responses to drought and subsequent recovery are few in number. As the search for novel traits to improve the genetic tolerance to drought increases, a better understanding of these responses is required. To address this need we designed a study in which we induced two cycles of prolonged drought stress and a single recovery by rewatering in tomato. In order to dissect the complexity of plant responses to drought, we analyzed the physiological responses (stomatal conductance, CO2 assimilation, and chlorophyll fluorescence), abscisic acid (ABA), and proline contents. In addition to the physiological and metabolite assays, we generated transcriptomes for multiple points during the stress and recovery cycles. Cluster analysis of differentially expressed genes (DEGs) between the conditions has revealed potential novel components in stress response. The observed reduction in leaf gas exchanges and efficiency of the photosystem PSII was concomitant with a general down-regulation of genes belonging to the photosynthesis, light harvesting, and photosystem I and II category induced by drought stress. Gene ontology (GO) categories such as cell proliferation and cell cycle were also significantly enriched in the down-regulated fraction of genes upon drought stress, which may contribute to explain the observed growth reduction. Several histone variants were also repressed during drought stress, indicating that chromatin associated processes are also affected by drought. As expected, ABA accumulated after prolonged water deficit, driving the observed enrichment of stress related GOs in the up-regulated gene fractions, which included transcripts putatively involved in stomatal movements. This transcriptomic study has yielded promising candidate genes that merit further functional studies to confirm their involvement in drought tolerance and recovery. Together, our results contribute to a better understanding of the coordinated responses taking place under drought stress and recovery in adult plants of tomato.

The role of biostimulants and bioeffectors as alleviators of abiotic stress in crop plants

The use of bioeffectors, formally known as plant biostimulants, has become common practice in agriculture and provides a number of benefits in stimulating growth and protecting against stress. A biostimulant is loosely defined as an organic material and/or microorganism that is applied to enhance nutrient uptake, stimulate growth, enhance stress tolerance or crop quality. This review is intended to provide a broad overview of known effects of biostimulants and their ability to improve tolerance to abiotic stresses. Inoculation or application of extracts from algae or other plants have beneficial effects on growth and stress adaptation. Algal extracts, protein hydrolysates, humic and fulvic acids, and other compounded mixtures have properties beyond basic nutrition, often enhancing growth and stress tolerance. Non-pathogenic bacteria capable of colonizing roots and the rhizosphere also have a number of positive effects. These effects include higher yield, enhanced nutrient uptake and utilization, increased photosynthetic activity, and resistance to both biotic and abiotic stresses. While most biostimulants have numerous and diverse effects on plant growth, this review focuses on the bioprotective effects against abiotic stress. Agricultural biostimulants may contribute to make agriculture more sustainable and resilient and offer an alternative to synthetic protectants which have increasingly falling out of favour with consumers. An extensive review of the literature shows a clear role for a diverse number of biostimulants that have protective effects against abiotic stress but also reveals the urgent need to address the underlying mechanisms responsible for these effects.Graphical abstractBiostimulants have protective effects against abiotic stress.

The Role of the Epigenome in Gene Expression Control and the Epimark Changes in Response to the Environment

Our knowledge base involving the biochemical participants of epigenetic control has expanded greatly over the last decade. The role of epigenetic marks to DNA and histones controlled by non-coding RNAs is one of the most intensely studied areas of biology today. This review covers many of the mechanisms that non-coding RNAs and other molecules use to control gene expression and eventually affect responses to the environment. In the first part of the review, we discuss the array of covalent modifications to the genome that constitute the epigenome, which consists of the histone variants, covalent modifications, and post-translational modifications that result in gene expression changes. How the histone variants and post-translational modifications including, acetylation, methylation, phosphorylation, ubiquitination and sumoylation help form the epigenome is also summarized. Our eventual understanding of how the environment controls these modifications will open incredible opportunities in agriculture, medicine and the development of practical tools for biology. In the second part of this review we discuss the growing list of environmentally-mediated epigenetic modifications, and examples of transgenerational epigenetic inheritance events, that may begin to change our views of adaptive responses to the environment and evolution.

Genetics of Drought Stress Tolerance in Crop Plants

Drought is the single abiotic stress with the biggest impact on global crop yields, thus improving crop performance under water-limiting conditions is essential to global food security. This chapter is intended to cover a broad overview of traits and mechanisms known to play a role in drought tolerance in crop plants. Although traditional breeding has largely focused on improving yield under stress-free conditions, a number of mechanisms exist that may be exploited to improve drought tolerance; these include the ABA signaling network for regulation of stomatal movements and root architecture modifications. This chapter reviews the biochemical and molecular modifications induced by water deficit. Stress-induced regulatory genes, specifically involved in marshaling survival responses in metabolism and development, are covered. Traits and genes from tolerant varieties, landraces, and wild relatives, known to contribute to drought tolerance from major crops are also addressed. As our understanding of signaling pathways improves based on studies in models, new traits and opportunities for genetic improvement emerge. Developing varieties that have high yields and are yield-stable in dry environments requires progress in both understanding and applying of genetic and physiological processes. This chapter covers the key traits and genes that have the greatest potential for improving drought tolerance in crop species.

Asg1 is a stress-inducible gene which increases stomatal resistance in salt stressed potato

The identification of critical components in plant salt stress adaptation has greatly benefitted, in the last two decades, from fundamental discoveries in Arabidopsis and close model systems. Nevertheless, this approach has also highlighted a non-complete overlap between stress tolerance mechanisms in Arabidopsis and agricultural crops. Within a long-running research program aimed at identifying salt stress genetic determinants in potato by functional screening in Escherichia coli, we isolated Asg1, a stress-related gene with an unknown function. Asg1 is induced by salt stress in both potato and Arabidopsis and by abscisic acid in Arabidopsis. Asg1 is actively transcribed in all plant tissues. Furthermore, Asg1 promoter analysis confirmed its ubiquitous expression, which was remarkable in pollen, a plant tissue that undergoes drastic dehydration/hydration processes. Fusion of Asg1 with green fluorescent protein showed that the encoded protein is localized close to the plasma membrane with a non-continuous pattern of distribution. In addition, Arabidopsis knockout asg1 mutants were insensitive to both NaCl and sugar hyperosmotic environments during seed germination. Transgenic potato plants over-expressing the Asg1 gene revealed a stomatal hypersensitivity to NaCl stress which, however, did not result in a significantly improved tuber yield in stress conditions. Altogether, these data suggest that Asg1 might interfere with components of the stress signaling pathway by promoting stomatal closure and participating in stress adaptation.

A Benzimidazole Proton Pump Inhibitor Increases Growth and Tolerance to Salt Stress in Tomato

Pre-treatment of tomato plants with micromolar concentrations of omeprazole (OP), a benzimidazole proton pump inhibitor in mammalian systems, improves plant growth in terms of fresh weight of shoot and roots by 49 and 55% and dry weight by 54 and 105% under salt stress conditions (200 mM NaCl), respectively. Assessment of gas exchange, ion distribution, and gene expression profile in different organs strongly indicates that OP interferes with key components of the stress adaptation machinery, including hormonal control of root development (improving length and branching), protection of the photosynthetic system (improving quantum yield of photosystem II) and regulation of ion homeostasis (improving the K+:Na+ ratio in leaves and roots). To our knowledge OP is one of the few known molecules that at micromolar concentrations manifests a dual function as growth enhancer and salt stress protectant. Therefore, OP can be used as new inducer of stress tolerance to better understand molecular and physiological stress adaptation paths in plants and to design new products to improve crop performance under suboptimal growth conditions. Highlight: Omeprazole enhances growth of tomato and increases tolerance to salinity stress through alterations of gene expression and ion uptake and transport.