The UBA domain of SnRK1 promotes activation and maintains catalytic activity

A maize WAK-SnRK1α2-WRKY module regulates nutrient availability to defend against head smut disease

Obligate biotrophs depend on living hosts for nutrient acquisition to complete their life cycle, yet the mechanisms by which hosts restrict nutrient availability to pathogens remain largely unknown. The fungal pathogen Sporisorium reilianum infects maize seedlings and causes head smut disease in inflorescences at maturity, while a cell wall-associated kinase, ZmWAK, provides quantitative resistance against it. In this study, we demonstrate that S. reilianum can rapidly activate ZmWAK kinase activity, which is sustained by the 407th threonine residue in the juxtamembrane domain, enabling it to interact with and phosphorylate ZmSnRK1α2, a conserved sucrose non-fermenting-related kinase α subunit. The activated ZmSnRK1α2 translocates from the cytoplasm to the nucleus, where it phosphorylates and destabilizes the transcription factor ZmWRKY53. The reduced ZmWRKY53 abundance leads to the downregulation of genes involved in transmembrane transport and carbohydrate metabolism, resulting in nutrient starvation for S. reilianum in the apoplast. Collectively, our study uncovers a WAK-SnRK1α2-WRKY53 signaling module in maize that conveys phosphorylation cascades from the plasma membrane to the nucleus to confer plant resistance against head smut in maize, offering new insights and potential targets for crop disease management.

Bioinformatic insights into sugar signaling pathways in sugarcane growth

The SnRK1, hexokinase, and TORC1 (TOR, LST8, RAPTOR) are three pivotal kinases at the core of sugar level sensing, significantly impacting plant metabolism and development. We retrieved and analyzed protein sequences of these three kinase pathways from seven sugarcane transcriptome and genome datasets, identifying protein domains, phylogenetic relationships, sequence ancestry, and in silico expression levels. Additionally, we predicted HXK subcellular localization and assessed its enzymatic activity in sugarcane leaves and culms along development in the field. We retrieved 11 TOR, 23 RAPTOR, 55 LST8, 95 SnRK1α, 98 HXK, and 14 HXK-like putative full-length sequences containing all the conserved domains. Most of these transcripts seem to share a common origin with the three ancestral species of sugarcane: Saccharum officinarum, Saccharum spontaneum, and Saccharum barberi. We accessed the expression profile of sequences from one sugarcane transcriptome. We found the highest enzymatic activity of HXK in culms in the first month, which, at this stage, provides carbon (sucrose) and nitrogen (amino acids) for initial plant development. Our approach places novel sugar sensing sequences that work as a guideline for further research into the underlying signaling mechanisms and biotechnology applications in sugarcane.

Phosphoregulation in the N-terminus of NRT2.1 affects nitrate uptake by controlling the interaction of NRT2.1 with NAR2.1 and kinase HPCAL1 in Arabidopsis

NRT2.1, the major high affinity nitrate transporter in roots, can be phosphorylated at five different sites within the N- and the C-terminus. Here, we characterized the functional relationship of two N-terminal phosphorylation sites, S21 and S28, in Arabidopsis. Based on a site-specific correlation network, we identified a receptor kinase (HPCAL1, AT5G49770), phosphorylating NRT2.1 at S21 and resulting in active nitrate uptake. HPCAL1 itself was regulated by phosphorylation at S839 and S870 within its kinase domain. In the active state, when S839 was dephosphorylated and S870 was phosphorylated, HPCAL1 was found to interact with the N-terminus of NRT2.1, mainly when S28 was dephosphorylated. Phosphorylation of NRT2.1 at S21 resulted in a reduced interaction of NRT2.1 with its activator NAR2.1, but nitrate transport activity remained. By contrast, phosphorylated NRT2.1 at S28 enhanced the interaction with NAR2.1, but reduced the interaction with HPCAL1. Here we identified HPCAL1 as the kinase affecting this phospho-switch through phosphorylation of NRT2.1 at S21.

Identification of Ossnrk1a-1 Regulated Genes Associated with Rice Immunity and Seed Set

Sucrose non-fermenting-1-related protein kinase-1 (SnRK1) is a highly conserved serine-threonine kinase complex regulating plants' energy metabolisms and resistance to various types of stresses. However, the downstream genes regulated by SnRK1 in these plant physiological processes still need to be explored. In this study, we found that the knockout of OsSnRK1a resulted in no obvious defects in rice growth but notably decreased the seed setting rate. The ossnrk1a mutants were more sensitive to blast fungus (Magnaporthe oryzae) infection and showed compromised immune responses. Transcriptome analyses revealed that SnRK1a was an important intermediate in the energy metabolism and response to biotic stress. Further investigation confirmed that the transcription levels of OsNADH-GOGAT2, which positively controls rice yield, and the defense-related gene pathogenesis-related protein 1b (OsPR1b) were remarkably decreased in the ossnrk1a mutant. Moreover, we found that OsSnRK1a directly interacted with the regulatory subunits OsSnRK1β1 and OsSnRK1β3, which responded specifically to blast fungus infection and starvation stresses, respectively. Taken together, our findings provide an insight into the mechanism of OsSnRK1a, which forms a complex with specific β subunits, contributing to rice seed set and resistance by regulating the transcription of related genes.

A Soybean Sucrose Non-Fermenting Protein Kinase 1 Gene, GmSNF1, Positively Regulates Plant Response to Salt and Salt-Alkali Stress in Transgenic Plants

Soybean is one of the most widely grown oilseed crops worldwide. Several unfavorable factors, including salt and salt-alkali stress caused by soil salinization, affect soybean yield and quality. Therefore, exploring the molecular basis of salt tolerance in plants and developing genetic resources for genetic breeding is important. Sucrose non-fermentable protein kinase 1 (SnRK1) belongs to a class of Ser/Thr protein kinases that are evolutionarily highly conserved direct homologs of yeast SNF1 and animal AMPKs and are involved in various abiotic stresses in plants. The GmPKS4 gene was experimentally shown to be involved with salinity tolerance. First, using the yeast two-hybrid technique and bimolecular fluorescence complementation (BiFC) technique, the GmSNF1 protein was shown to interact with the GmPKS4 protein. Second, the GmSNF1 gene responded positively to salt and salt-alkali stress according to qRT-PCR analysis, and the GmSNF1 protein was localized in the nucleus and cytoplasm using subcellular localization assay. The GmSNF1 gene was then heterologously expressed in yeast, and the GmSNF1 gene was tentatively identified as having salt and salt-alkali tolerance function. Finally, the salt-alkali tolerance function of the GmSNF1 gene was demonstrated by transgenic Arabidopsis thaliana, soybean hairy root complex plants overexpressing GmSNF1 and GmSNF1 gene-silenced soybean using VIGS. These results indicated that GmSNF1 might be useful in genetic engineering to improve plant salt and salt-alkali tolerance.

A positive feedback regulation of SnRK1 signaling by autophagy in plants

SnRK1, an evolutionarily conserved heterotrimeric kinase complex that acts as a key metabolic sensor in maintaining energy homeostasis in plants, is an important upstream activator of autophagy that serves as a cellular degradation mechanism for the healthy growth of plants. However, whether and how the autophagy pathway is involved in regulating SnRK1 activity remains unknown. In this study, we identified a clade of plant-specific and mitochondria-localized FCS-like zinc finger (FLZ) proteins as currently unknown ATG8-interacting partners that actively inhibit SnRK1 signaling by repressing the T-loop phosphorylation of the catalytic α subunits of SnRK1, thereby negatively modulating autophagy and plant tolerance to energy deprivation caused by long-term carbon starvation. Interestingly, these AtFLZs are transcriptionally repressed by low-energy stress, and AtFLZ proteins undergo a selective autophagy-dependent pathway to be delivered to the vacuole for degradation, thereby constituting a positive feedback regulation to relieve their repression of SnRK1 signaling. Bioinformatic analyses show that the ATG8-FLZ-SnRK1 regulatory axis first appears in gymnosperms and seems to be highly conserved during the evolution of seed plants. Consistent with this, depletion of ATG8-interacting ZmFLZ14 confers enhanced tolerance, whereas overexpression of ZmFLZ14 leads to reduced tolerance to energy deprivation in maize. Collectively, our study reveals a previously unknown mechanism by which autophagy contributes to the positive feedback regulation of SnRK1 signaling, thereby enabling plants to better adapt to stressful environments.

The Role of GmSnRK1-GmNodH Module in Regulating Soybean Nodulation Capacity

SnRK1 protein kinase plays hub roles in plant carbon and nitrogen metabolism. However, the function of SnRK1 in legume nodulation and symbiotic nitrogen fixation is still elusive. In this study, we identified GmNodH, a putative sulfotransferase, as an interacting protein of GmSnRK1 by yeast two-hybrid screen. The qRT-PCR assays indicate that GmNodH gene is highly expressed in soybean roots and could be induced by rhizobial infection and nitrate stress. Fluorescence microscopic analyses showed that GmNodH was colocalized with GsSnRK1 on plasma membrane. The physical interaction between GmNodH and GmSnRK1 was further verified by using split-luciferase complementary assay and pull-down approaches. In vitro phosphorylation assay showed that GmSnRK1 could phosphorylate GmNodH at Ser193. To dissect the function and genetic relationship of GmSnRK1 and GmNodH in soybean, we co-expressed the wild-type and mutated GmSnRK1 and GmNodH genes in soybean hairy roots and found that co-expression of GmSnRK1/GmNodH genes significantly promoted soybean nodulation rates and the expression levels of nodulation-related GmNF5α and GmNSP1 genes. Taken together, this study provides the first biological evidence that GmSnRK1 may interact with and phosphorylate GmNodH to synergistically regulate soybean nodulation.

Compartmentalization, a key mechanism controlling the multitasking role of the SnRK1 complex

SNF1-related protein kinase 1 (SnRK1), the plant ortholog of mammalian AMP-activated protein kinase/fungal (yeast) Sucrose Non-Fermenting 1 (AMPK/SNF1), plays a central role in metabolic responses to reduced energy levels in response to nutritional and environmental stresses. SnRK1 functions as a heterotrimeric complex composed of a catalytic α- and regulatory β- and βγ-subunits. SnRK1 is a multitasking protein involved in regulating various cellular functions, including growth, autophagy, stress response, stomatal development, pollen maturation, hormone signaling, and gene expression. However, little is known about the mechanism whereby SnRK1 ensures differential execution of downstream functions. Compartmentalization has been recently proposed as a new key mechanism for regulating SnRK1 signaling in response to stimuli. In this review, we discuss the multitasking role of SnRK1 signaling associated with different subcellular compartments.

SlSnRK2.3 interacts with SlSUI1 to modulate high temperature tolerance via Abscisic acid (ABA) controlling stomatal movement in tomato

Tomato is often exposed to high temperature stress during summer cultivation. Stomatal movement plays important roles in photosynthesis and transpiration which restricts the quality and yield of tomato under environmental stress. To elucidate the mechanism of stomatal movement in high temperature tolerance, SlSnRK2s (sucrose non-fermenting 1-related protein kinases) silenced plants were generated in tomato with CRISPR-Cas 9 gene editing techniques. Through the observation of stomatal parameters, SlSnRK2.3 regulated stomatal closure which was responded to ABA (abscisic acid) and activated signaling pathway of ROS (reactive oxygen species) in high temperature stress. Based on the positive functions of SlSnRK2.3, the cDNA library was generated to investigate interaction proteins of SlSnRK2s. The interaction between SlSnRK2.3 and SlSUI1 (protein translation factor SUI1 homolog) was employed by Yeast two hybrid assay (Y2H), Luciferase (LUC), and Bimolecular fluorescence complementation (BiFC). Finally, the specific interactive sites between SlSnRK2.3 and SlSUI1 were verified by site-directed mutagenesis. The consistent mechanism of SlSnRK2.3 and SlSUI1 in stomatal movement, indicating that SlSUI1 interacted with SlSnRK2.3 through ABA-dependent signaling pathway in high temperature stress. Our results provided evidence for improving the photosynthetic capacity of tomato under high temperature stress, and support the breeding and genetic engineering of tomato over summer facility cultivation.

A negative feedback loop of TOR signaling balances growth and stress-response trade-offs in plants

TOR kinase is a central coordinator of nutrient-dependent growth in eukaryotes. Maintaining optimal TOR signaling is critical for the normal development of organisms. In this study, we describe a negative feedback loop of TOR signaling helping in the adaptability of plants in changing environmental conditions. Using an interdisciplinary approach, we show that the plant-specific zinc finger protein FLZ8 acts as a regulator of TOR signaling in Arabidopsis. In sugar sufficiency, TOR-dependent and -independent histone modifications upregulate the expression of FLZ8. FLZ8 negatively regulates TOR signaling by promoting antagonistic SnRK1α1 signaling and bridging the interaction of SnRK1α1 with RAPTOR1B, a crucial accessory protein of TOR. This negative feedback loop moderates the TOR-growth signaling axis in the favorable condition and helps in the activation of stress signaling in unfavorable conditions, establishing its importance in the adaptability of plants.

SNF1-related protein kinase 1: the many-faced signaling hub regulating developmental plasticity in plants

The Snf1-related protein kinase 1 (SnRK1) is the plant homolog of the heterotrimeric AMP-activated protein kinase/sucrose non-fermenting 1 (AMPK/Snf1), which works as a major regulator of growth under nutrient-limiting conditions in eukaryotes. Along with its conserved role as a master regulator of sugar starvation responses, SnRK1 is involved in controlling the developmental plasticity and resilience under diverse environmental conditions in plants. In this review, through mining and analyzing the interactome and phosphoproteome data of SnRK1, we are highlighting its role in fundamental cellular processes such as gene regulation, protein synthesis, primary metabolism, protein trafficking, nutrient homeostasis, and autophagy. Along with the well-characterized molecular interaction in SnRK1 signaling, our analysis highlights several unchartered regions of SnRK1 signaling in plants such as its possible communication with chromatin remodelers, histone modifiers, and inositol phosphate signaling. We also discuss potential reciprocal interactions of SnRK1 signaling with other signaling pathways and cellular processes, which could be involved in maintaining flexibility and homeostasis under different environmental conditions. Overall, this review provides a comprehensive overview of the SnRK1 signaling network in plants and suggests many novel directions for future research.

Kinase SnRK1.1 regulates nitrate channel SLAH3 engaged in nitrate-dependent alleviation of ammonium toxicity

Nitrate (NO3-) and ammonium (NH4+) are major inorganic nitrogen (N) supplies for plants, but NH4+ as the sole or dominant N source causes growth inhibition in many plants, known as ammonium toxicity. Small amounts of NO3- can significantly mitigate ammonium toxicity, and the anion channel SLAC1 homolog 3 (SLAH3) is involved in this process, but the mechanistic detail of how SLAH3 regulates nitrate-dependent alleviation of ammonium toxicity is still largely unknown. In this study, we identified SnRK1.1, a central regulator involved in energy homeostasis, and various stress responses, as a SLAH3 interactor in Arabidopsis (Arabidopsis thaliana). Our results suggest that SNF1-related protein kinase 1 (SnRK1.1) functions as a negative regulator of SLAH3. Kinase assays indicate SnRK1.1 strongly phosphorylates the C-terminal of SLAH3 at the site S601. Under high-NH4+/low-pH condition, phospho-mimetic and phospho-dead mutations in SLAH3 S601 result in barely rescued phenotypes and fully complemented phenotypes in slah3. Furthermore, SnRK1.1 migrates from cytoplasm to nucleus under high-NH4+/low-pH conditions. The translocation of SnRK1.1 from cytosol to nucleus under high-ammonium stress releases the inhibition on SLAH3, which allows SLAH3-mediated NO3- efflux leading to alleviation of high-NH4+/low-pH stress. Our study reveals that the C-terminal phosphorylation also plays important role in SLAH3 regulation and provides additional insights into nitrate-dependent alleviation of ammonium toxicity in plants.

Lessons from Comparison of Hypoxia Signaling in Plants and Mammals

Hypoxia is an important stress for organisms, including plants and mammals. In plants, hypoxia can be the consequence of flooding and causes important crop losses worldwide. In mammals, hypoxia stress may be the result of pathological conditions. Understanding the regulation of responses to hypoxia offers insights into novel approaches for crop improvement, particularly for the development of flooding-tolerant crops and for producing better therapeutics for hypoxia-related diseases such as inflammation and cancer. Despite their evolutionary distance, plants and mammals deploy strikingly similar mechanisms to sense and respond to the different aspects of hypoxia-related stress, including low oxygen levels and the resulting energy crisis, nutrient depletion, and oxidative stress. Over the last two decades, the ubiquitin/proteasome system and the ubiquitin-like protein SUMO have been identified as key regulators that act in concert to regulate core aspects of responses to hypoxia in plants and mammals. Here, we review ubiquitin and SUMO-dependent mechanisms underlying the regulation of hypoxia response in plants and mammals. By comparing and contrasting these mechanisms in plants and mammals, this review seeks to pinpoint conceptually similar mechanisms but also highlight future avenues of research at the junction between different fields of research.

SnRK1 and trehalose 6-phosphate - two ancient pathways converge to regulate plant metabolism and growth

SUCROSE-NON-FERMENTING1-RELATED KINASE1 (SnRK1) belongs to a family of protein kinases that originated in the earliest eukaryotes and plays a central role in energy and metabolic homeostasis. Trehalose 6-phosphate (Tre6P) is the intermediate of trehalose biosynthesis, and has even more ancient roots, being found in all three domains of life - Archaea, Bacteria and Eukarya. In plants, the function of SnRK1 has diverged from its orthologues in fungi and animals, evolving new roles in signalling of nutrient status and abiotic stress. Tre6P has also acquired a novel function in plants as a signal and homeostatic regulator of sucrose, the dominant sugar in plant metabolism. These two ancient pathways have converged in a unique way in plants, enabling them to coordinate their metabolism, growth, and development with their environment, which is essential for their autotrophic and sessile lifestyle.

Review: How do SnRK1 protein kinases truly work?

The AMPK/SNF1/SnRK1 family of protein kinases is involved in cellular responses to energy stress. They also interact with molecules of other signaling pathways to regulate many aspects of growth and development. The biochemical, genetic and molecular knowledge of SnRK1 in plants lags behind that of AMPK and SNF1 and is freely extrapolated such that, in many cases, it is assumed that plant enzymes behave in the same way as homologs in other organisms. In this review, we present data that support the evidence that the structural characteristics of the SnRK1 subunits determine the functional properties of the complex. We also discuss results suggesting that the SnRK1 subunits participate in the assembly of different complexes and that not all combinations are equally important. The activity of SnRK1 is dependent on the phosphorylation of SnRK1α^Thr175 found in the activation loop of the catalytic domain. However, we propose that the phosphorylation of sites close to SnRK1α^Thr175 might contribute to the fine-tuned regulation of SnRK1 activity and thus requires further evaluation. Finally, we also call attention to the interaction of the SnRK1α with regulatory proteins that are not typically identified as putative substrates. The additional functions of the SnRK1 subunits, in addition to those of the active complex, may be necessary for the cell to respond to the complicated conditions presented by energy stress.

SnRK1 activation, signaling, and networking for energy homeostasis

The SnRK1 kinases are key regulators of the plant energy balance, but how their activity is regulated by metabolic status is still unclear. While the heterotrimeric kinase complex is well conserved among plants, fungi, and animals, plants appear to have modified its regulation to better fit their unique physiology and lifestyle. The SnRK1 kinases control metabolism, growth, and development, and stress tolerance by direct phosphorylation of metabolic enzymes and regulatory proteins and by extensive transcriptional regulation. Diverse types of transcription factors have already been implicated, with a well-studied role for the heterodimerizing group C and group S1 bZIPs. SnRK1 is also part of a more elaborate metabolic and stress signaling network, which includes the TOR kinase and the ABA-signaling SnRK2 kinases.

Evolution of TOR-SnRK dynamics in green plants and its integration with phytohormone signaling networks

The target of rapamycin (TOR)-sucrose non-fermenting 1 (SNF1)-related protein kinase 1 (SnRK1) signaling is an ancient regulatory mechanism that originated in eukaryotes to regulate nutrient-dependent growth. Although the TOR-SnRK1 signaling cascade shows highly conserved functions among eukaryotes, studies in the past two decades have identified many important plant-specific innovations in this pathway. Plants also possess SnRK2 and SnRK3 kinases, which originated from the ancient SnRK1-related kinases and have specialized roles in controlling growth, stress responses and nutrient homeostasis in plants. Recently, an integrative picture has started to emerge in which different SnRKs and TOR kinase are highly interconnected to control nutrient and stress responses of plants. Further, these kinases are intimately involved with phytohormone signaling networks that originated at different stages of plant evolution. In this review, we highlight the evolution and divergence of TOR-SnRK signaling components in plants and their communication with each other as well as phytohormone signaling to fine-tune growth and stress responses in plants.