An evolutionary perspective of AMPK-TOR signaling in the three domains of life

Feeding frequency does not interact with BPA exposure to influence metabolism or behaviour in zebrafish (Danio rerio)

Resource limitation can constrain energy (ATP) production, and thereby affect locomotion and behaviour such as exploration of novel environments and boldness. Consequently, ecological processes such as dispersal and interactions within and between species may be influenced by food availability. Energy metabolism, and behaviour are regulated by endocrine signalling, and may therefore be impacted by endocrine disrupting compounds (EDCs) including bisphenol A (BPA) derived from plastic manufacture and pollution. It is important to determine the impacts of these novel environmental contexts to understand how human activity alters individual physiology and behaviour and thereby populations. Our aim was to determine whether BPA exposure interacts with feeding frequency to alter metabolism and behaviour. In a fully factorial experiment, we show that low feeding frequency reduced zebrafish (Danio rerio) mass, condition, resting metabolic rates, total distance moved and speed in a novel arena, as well as anxiety indicated by the number of times fish returned to a dark shelter. However, feeding frequency did not significantly affect maximal metabolic rates, aerobic scope, swimming performance, latency to leave a shelter, or metabolic enzyme activities (citrate synthase and lactate dehydrogenase). Natural or anthropogenic fluctuation in food resources can therefore impact energetics and movement of animals with repercussions for ecological processes such as dispersal. BPA exposure reduced LDH activity and body mass, but did not interact with feeding frequency. Hence, behaviour of adult fish is relatively insensitive to disruption by BPA. However, alteration of LDH activity by BPA could disrupt lactate metabolism and signalling and together with reduction in body mass could affect size-dependent reproductive output. BPA released by plastic manufacture and pollution can thereby impact conservation and management of natural resources.

Frequent loss-of-function mutations in the AMPK-α2 catalytic subunit suggest a tumour suppressor role in human skin cancers

The AMP-activated protein kinase (AMPK) is a sensor of cellular energy status activated by increases in AMP or ADP relative to ATP. Once activated, it phosphorylates targets that promote ATP-generating catabolic pathways or inhibit ATP-consuming anabolic pathways, helping to restore cellular energy balance. Analysis of human cancer genome studies reveals that the PRKAA2 gene (encoding the α2 isoform of the catalytic subunit) is often subject to mis-sense mutations in cancer, particularly in melanoma and non-melanoma skin cancers, where up to 70 mis-sense mutations have been documented, often accompanied by loss of the tumour suppressor NF1. Recently it has been reported that knockout of PRKAA2 in NF1-deficient melanoma cells promoted anchorage-independent growth in vitro, as well as growth as xenografts in immunodeficient mice in vivo, suggesting that AMPK-α2 can act as a tumour suppressor in that context. However, very few of the mis-sense mutations in PRKAA2 that occur in human skin cancer and melanoma have been tested to see whether they cause loss-of-function. We have addressed this by making most of the reported mutations and testing their activity when expressed in AMPK knockout cells. Of 55 different mis-sense mutations (representing 75 cases), 9 (12%) appeared to cause a total loss of activity, 18 (24%) a partial loss, 11 (15%) an increase in phenformin-stimulated kinase activity, while just 37 (49%) had no clear effect on kinase activity. This supports the idea that AMPK-α2 acts as a tumour suppressor in the context of human skin cancer.

Oxygen and temperature affect cell sizes differently among tissues and between sexes of Drosophila melanogaster

Spatio-temporal gradients in thermal and oxygen conditions trigger evolutionary and developmental responses in ectotherms' body size and cell size, which are commonly interpreted as adaptive. However, the evidence for cell-size responses is fragmentary, as cell size is typically assessed in single tissues. In a laboratory experiment, we raised genotypes of Drosophila melanogaster at all combinations of two temperatures (16 °C or 25 °C) and two oxygen levels (10% or 22%) and measured body size and the sizes of cells in different tissues. For each sex, we measured epidermal cells in a wing and a leg and ommatidial cells of an eye. For males, we also measured epithelial cells of a Malpighian tubule and muscle cells of a flight muscle. On average, females emerged at a larger body size than did males, having larger cells in all tissues. Flies of either sex emerged at a smaller body size when raised under warm or hypoxic conditions. Development at 25 °C resulted in smaller cells in most tissues. Development under hypoxia resulted in smaller cells in some tissues, especially among females. Altogether, our results show thermal and oxygen conditions trigger shifts in adult size, coupled with the systemic orchestration of cell sizes throughout the body of a fly. The nature of these patterns supports a model in which an ectotherm adjusts its life-history traits and cellular composition to prevent severe hypoxia at the cellular level. However, our results revealed some inconsistencies linked to sex, cell type, and environmental parameters, which suggest caution in translating information obtained for single type of cells to the organism as a whole.

A Toxoplasma gondii putative arginine transporter localizes to the plant-like vacuolar compartment and controls parasite extracellular survival and stage differentiation

Toxoplasma gondii is a protozoan parasite that infects a broad spectrum of hosts and can colonize many organs and cell types. The ability to reside within a wide range of different niches requires substantial adaptability to diverse microenvironments. Very little is known about how this parasite senses various milieus and adapts its metabolism to survive, replicate during the acute stage, and then differentiate to the chronic stage. Most eukaryotes, from yeast to mammals, rely on a nutrient sensing machinery involving the TORC complex as master regulator of cell growth and cell cycle progression. The lysosome functions as a signaling hub where TORC complex assembles and is activated by transceptors, which both sense and transport amino acids, including the arginine transceptor SLC38A9. While most of the TORC components are lost in T. gondii , indicating the evolution of a distinct nutrient sensing mechanism, the parasite's lysosomal plant-like vacuolar compartment (PLVAC) may still serve as a sensory platform for controlling parasite growth and differentiation. Using SLC38A9 to query the T. gondii proteome, we identified four putative amino acid transporters, termed TgAAT1-4, that structurally resemble the SLC38A9 arginine transceptor. Assessing their expression and sub-cellular localization, we found that one of them, TgAAT1, localized to the PLVAC and is necessary for normal parasite extracellular survival and bradyzoite differentiation. Moreover, we show that TgAAT1 is involved in the PLVAC efflux of arginine, an amino acid playing a key role in T. gondii differentiation, further supporting the hypothesis that TgAAT1 might play a role in nutrient sensing.

IMPORTANCE

T. gondii is a highly successful parasite infecting a broad range of warm-blood organisms including about one third of all humans. Although Toxoplasma infections rarely result in symptomatic disease in individuals with a healthy immune system, the incredibly high number of persons infected along with the risk of severe infection in immunocompromised patients and the potential link of chronic infection to mental disorders make this infection a significant public health concern. As a result, there is a pressing need for new treatment approaches that are both effective and well-tolerated. The limitations in understanding how Toxoplasma gondii manages its metabolism to adapt to changing environments and triggers its transformation into bradyzoites have hindered the discovery of vulnerabilities in its metabolic pathways or nutrient acquisition mechanisms to identify new therapeutic targets. In this work, we have shown that the lysosome-like organelle PLVAC, acting through the putative arginine transporter TgAAT1, plays a pivotal role in regulating the parasite's extracellular survival and differentiation into bradyzoites.

Modulation of AMPK Significantly Alters Uveal Melanoma Tumor Cell Viability

INTRODUCTION

Uveal melanoma (UM) responds poorly to targeted therapies or immune checkpoint inhibitors. Adenosine monophosphate-activated protein kinase (AMPK) is a pivotal serine/threonine protein kinase that coordinates vital processes such as cell growth. Targeting AMPK pathway, which represents a critical mechanism mediating the survival of UM cells, may prove to be a novel treatment strategy for UM. We aimed to demonstrate the effects of AMPK modulation on UM cells.

METHODS

In silico analyses were performed to compare UM and normal melanocyte cells via Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Set Enrichment Analysis (GSEA). The effects of AMPK modulation on cell viability and proliferation in UM cell lines with different molecular profiles (i.e., 92-1, MP46, OMM2.5, and Mel270) were investigated via XTT cell viability and proliferation assays after treating the cells with varying concentrations of A-769662 (AMPK activator) or dorsomorphin (AMPK inhibitor).

RESULTS

KEGG/GSEA studies demonstrated that genes implicated in the AMPK signaling pathway were differentially regulated in UM. Gene sets comprising genes involved in AMPK signaling and genes involved in energy-dependent regulation of mammalian target of rapamycin by liver kinase B1-AMPK were downregulated in UM. We observed gradual decreases in the numbers of viable UM cells as the concentration of A-769662 treatment increased. All UM cells demonstrated statistically significant decreases in cell viability when treated with 200 µm A-769662. Moreover, the effects of AMPK inhibition on UM cells were potent, since low doses of dorsomorphin treatment resulted in significant decreases in viabilities of UM cells. The half maximal inhibitory concentration (IC50) values confirmed the potency of dorsomorphin treatment against UM in vitro.

CONCLUSION

AMPK may act like a friend or a foe in cancer depending on the context. As such, the current study contributes to the literature in determining the effects of therapeutic strategies targeting AMPK in several UM cells. We propose a new perspective in the treatment of UM. Targeting AMPK pathway may open up new avenues in developing novel therapeutic approaches to improve overall survival in UM.

The Case for the Target of Rapamycin Pathway as a Candidate Circadian Oscillator

The molecular mechanisms that drive circadian (24 h) rhythmicity have been investigated for many decades, but we still do not have a complete picture of eukaryotic circadian systems. Although the transcription/translation feedback loop (TTFL) model has been the primary focus of research, there are many examples of circadian rhythms that persist when TTFLs are not functioning, and we lack any good candidates for the non-TTFL oscillators driving these rhythms. In this hypothesis-driven review, the author brings together several lines of evidence pointing towards the Target of Rapamycin (TOR) signalling pathway as a good candidate for a non-TTFL oscillator. TOR is a ubiquitous regulator of metabolism in eukaryotes and recent focus in circadian research on connections between metabolism and rhythms makes TOR an attractive candidate oscillator. In this paper, the evidence for a role for TOR in regulating rhythmicity is reviewed, and the advantages of TOR as a potential oscillator are discussed. Evidence for extensive feedback regulation of TOR provides potential mechanisms for a TOR-driven oscillator. Comparison with ultradian yeast metabolic cycles provides an example of a potential TOR-driven self-sustained oscillation. Unanswered questions and problems to be addressed by future research are discussed.

Glucose Inhibits Yeast AMPK (Snf1) by Three Independent Mechanisms

Snf1, the fungal homologue of mammalian AMP-dependent kinase (AMPK), is a key protein kinase coordinating the response of cells to a shortage of glucose. In fungi, the response is to activate respiratory gene expression and metabolism. The major regulation of Snf1 activity has been extensively investigated: In the absence of glucose, it becomes activated by phosphorylation of its threonine at position 210. This modification can be erased by phosphatases when glucose is restored. In the past decade, two additional independent mechanisms of Snf1 regulation have been elucidated. In response to glucose (or, surprisingly, also to DNA damage), Snf1 is SUMOylated by Mms21 at lysine 549. This inactivates Snf1 and leads to Snf1 degradation. More recently, glucose-induced proton export has been found to result in Snf1 inhibition via a polyhistidine tract (13 consecutive histidine residues) at the N-terminus of the Snf1 protein. Interestingly, the polyhistidine tract plays also a central role in the response to iron scarcity. This review will present some of the glucose-sensing mechanisms of S. cerevisiae, how they interact, and how their interplay results in Snf1 inhibition by three different, and independent, mechanisms.

Systemic changes in cell size throughout the body of Drosophila melanogaster associated with mutations in molecular cell cycle regulators

Along with different life strategies, organisms have evolved dramatic cellular composition differences. Understanding the molecular basis and fitness effects of these differences is key to elucidating the fundamental characteristics of life. TOR/insulin pathways are key regulators of cell size, but whether their activity determines cell size in a systemic or tissue-specific manner awaits exploration. To that end, we measured cells in four tissues in genetically modified Drosophila melanogaster (rictor^Δ2 and Mnt¹) and corresponding controls. While rictor^Δ2 flies lacked the Rictor protein in TOR complex 2, downregulating the functions of this element in TOR/insulin pathways, Mnt¹ flies lacked the transcriptional regulator protein Mnt, weakening the suppression of downstream signalling from TOR/insulin pathways. rictor^Δ2 flies had smaller epidermal (leg and wing) and ommatidial cells and Mnt¹ flies had larger cells in these tissues than the controls. Females had consistently larger cells than males in the three tissue types. In contrast, dorsal longitudinal flight muscle cells (measured only in males) were not altered by mutations. We suggest that mutations in cell cycle control pathways drive the evolution of systemic changes in cell size throughout the body, but additional mechanisms shape the cellular composition of some tissues independent of these mutations.

Honokiol acts as an AMPK complex agonist therapeutic in non-alcoholic fatty liver disease and metabolic syndrome

BACKGROUND

Non-alcoholic fatty liver (NAFLD) and its related metabolic syndrome have become major threats to human health, but there is still a need for effective and safe drugs to treat these conditions. Here we aimed to identify potential drug candidates for NAFLD and the underlying molecular mechanisms.

METHODS

A drug repositioning strategy was used to screen an FDA-approved drug library with approximately 3000 compounds in an in vitro hepatocyte model of lipid accumulation, with honokiol identified as an effective anti-NAFLD candidate. We systematically examined the therapeutic effect of honokiol in NAFLD and metabolic syndrome in multiple in vitro and in vivo models. Transcriptomic examination and biotin-streptavidin binding assays were used to explore the underlying molecular mechanisms, confirmed by rescue experiments.

RESULTS

Honokiol significantly inhibited metabolic syndrome and NAFLD progression as evidenced by improved hepatic steatosis, liver fibrosis, adipose inflammation, and insulin resistance. Mechanistically, the beneficial effects of honokiol were largely through AMPK activation. Rather than acting on the classical upstream regulators of AMPK, honokiol directly bound to the AMPKγ1 subunit to robustly activate AMPK signaling. Mutation of honokiol-binding sites of AMPKγ1 largely abolished the protective capacity of honokiol against NAFLD.

CONCLUSION

These findings clearly demonstrate the beneficial effects of honokiol in multiple models and reveal a previously unappreciated signaling mechanism of honokiol in NAFLD and metabolic syndrome. This study also provides new insights into metabolic disease treatment by targeting AMPKγ1 subunit-mediated signaling activation.

Recent insights into metabolic and signalling events of directional root growth regulation and its implications for sustainable crop production systems

Roots are sensors evolved to simultaneously respond to manifold signals, which allow the plant to survive. Root growth responses, including the modulation of directional root growth, were shown to be differently regulated when the root is exposed to a combination of exogenous stimuli compared to an individual stress trigger. Several studies pointed especially to the impact of the negative phototropic response of roots, which interferes with the adaptation of directional root growth upon additional gravitropic, halotropic or mechanical triggers. This review will provide a general overview of known cellular, molecular and signalling mechanisms involved in directional root growth regulation upon exogenous stimuli. Furthermore, we summarise recent experimental approaches to dissect which root growth responses are regulated upon which individual trigger. Finally, we provide a general overview of how to implement the knowledge gained to improve plant breeding.

Systemic orchestration of cell size throughout the body: influence of sex and rapamycin exposure in Drosophila melanogaster

Along with differences in life histories, metazoans have also evolved vast differences in cellularity, involving changes in the molecular pathways controlling the cell cycle. The extent to which the signalling network systemically determines cellular composition throughout the body and whether tissue cellularity is organized locally to match tissue-specific functions are unclear. We cultured genetic lines of Drosophila melanogaster on food with and without rapamycin to manipulate the activity of target of rapamycin (TOR)/insulin pathways and evaluate cell-size changes in five types of adult cells: wing and leg epidermal cells, ommatidial cells, indirect flight muscle cells and Malpighian tubule epithelial cells. Rapamycin blocks TOR multiprotein complex 1, reducing cell growth, but this effect has been studied in single cell types. As adults, rapamycin-treated flies had smaller bodies and consistently smaller cells in all tissues. Regardless, females eclosed with larger bodies and larger cells in all tissues than males. Thus, differences in TOR activity and sex were associated with the orchestration of cell size throughout the body, leading to differences in body size. We postulate that the activity of TOR/insulin pathways and their effects on cellularity should be considered when investigating the origin of ecological and evolutionary patterns in life histories.

Ruminal tissue uptake of amino acids in Holstein cows when supply of nutrients within the rumen differs

Characterisation of amino acid (AA) use by the ruminal vein-drained viscera (RDV) has not been assessed in vivo in dairy cattle, and thus, the extent of ruminal AA use from arterial and postabsorptive blood supplies is unclear. Understanding the complete use of AA by the splanchnic bed may lead to alternative feeding programmes that maximise animal N efficiency. The objective of this work was to determine how different nutritional manipulations affect RDV net appearance and apparent affinity for arterial AA in lactating dairy cattle. Data from two arterio-venous (A-V) difference studies, that used a common set of multicatheterised lactating Holstein cows, assigned to different nutritional treatments, were used to assess ruminal metabolism. Study 1 consisted of three dietary treatments at calving [an alfalfa-glucogenic diet, a glucogenic diet (GLCG), or a ketogenic diet (KETO)] to investigate the effects of dietary nutrients and increasing intake postpartum on RDV metabolism of AA at -14, +4, +15, and +29 days relative to calving (DRTC). Study 2 consisted of two dietary levels of CP (17 or 13%) and three ruminal buffers (ammonia, butyrate, and control) to investigate the level of dietary CP and ruminal fermentation products on RDV metabolism of AA. Blood was collected at 9, 20, and 30 min after buffer administration. Regardless of dietary nutrients or fermentation products present in ruminal fluid, net RDV uptake was positive for most AA, excepting Asp, Cys, Glu, and Ser, which were consistently negative. The general positive net uptakes indicate that any AA potentially absorbed from the rumen were not adequate to meet apparent needs. Ruminal plasma flow and net RDV uptake of Trp, Ala, Gly, and Pro increased linearly with increased DRTC. Feeding KETO or GLCG diets increased ruminal plasma flow, and net RDV uptake of Thr and Gly. Feeding high CP diets increased ruminal uptake of Leu, Phe, and Val. The increased AA uptakes were partially driven by increased plasma flow, however, tissue affinity as reflected in clearance rates also increased or tended to for Met, Trp, Ala, Gly, Pro, and Tyr suggesting that changes in RDV uptake were regulated and not due solely to mass action. In conclusion, splanchnic tissue bed responses to dietary and washed rumen conditions were in part driven by changes in RDV nutrient demand and metabolic activity. The adaptive responses alter the fraction of absorbed AA utilised for non-productive purposes and thus the efficiency of conversion of those AA to product.

The rubber tree kinome: Genome-wide characterization and insights into coexpression patterns associated with abiotic stress responses

The protein kinase (PK) superfamily constitutes one of the largest and most conserved protein families in eukaryotic genomes, comprising core components of signaling pathways in cell regulation. Despite its remarkable relevance, only a few kinase families have been studied in Hevea brasiliensis. A comprehensive characterization and global expression analysis of the PK superfamily, however, is currently lacking. In this study, with the aim of providing novel inferences about the mechanisms associated with the stress response developed by PKs and retained throughout evolution, we identified and characterized the entire set of PKs, also known as the kinome, present in the Hevea genome. Different RNA-sequencing datasets were employed to identify tissue-specific expression patterns and potential correspondences between different rubber tree genotypes. In addition, coexpression networks under several abiotic stress conditions, such as cold, drought and latex overexploitation, were employed to elucidate associations between families and tissues/stresses. A total of 1,809 PK genes were identified using the current reference genome assembly at the scaffold level, and 1,379 PK genes were identified using the latest chromosome-level assembly and combined into a single set of 2,842 PKs. These proteins were further classified into 20 different groups and 122 families, exhibiting high compositional similarities among family members and with two phylogenetically close species Manihot esculenta and Ricinus communis. Through the joint investigation of tandemly duplicated kinases, transposable elements, gene expression patterns, and coexpression events, we provided insights into the understanding of the cell regulation mechanisms in response to several conditions, which can often lead to a significant reduction in rubber yield.

Energy sensor AMPK gamma regulates translation via phosphatase PPP6C independent of AMPK alpha

Maintenance of energy level to drive movements and material exchange with the environment is a basic principle of life. AMP-activated protein kinase (AMPK) senses energy level and is a major regulator of cellular energy responses. The gamma subunit of AMPK senses elevated ratio of AMP to ATP and allosterically activates the alpha catalytic subunit to phosphorylate downstream effectors. Here, we report that knockout of AMPKγ, but not AMPKα, suppressed phosphorylation of eukaryotic translation elongation factor 2 (eEF2) induced by energy starvation. We identified PPP6C as an AMPKγ-regulated phosphatase of eEF2. AMP-bound AMPKγ sequesters PPP6C, thereby blocking dephosphorylation of eEF2 and thus inhibiting translation elongation to preserve energy and to promote cell survival. Further phosphoproteomic analysis identified additional targets of PPP6C regulated by energy stress in an AMPKγ-dependent manner. Thus, AMPKγ senses cellular energy availability to regulate not only AMPKα kinase, but also PPP6C phosphatase and possibly other effectors.

The social network of target of rapamycin complex 1 in plants

Target of rapamycin complex 1 (TORC1) is a highly conserved serine-threonine protein kinase crucial for coordinating growth according to nutrient availability in eukaryotes. It works as a central integrator of multiple nutrient inputs such as sugar, nitrogen, and phosphate and promotes growth and biomass accumulation in response to nutrient sufficiency. Studies, especially in the past decade, have identified the central role of TORC1 in regulating growth through interaction with hormones, photoreceptors, and stress signaling machinery in plants. In this review, we comprehensively analyse the interactome and phosphoproteome of the Arabidopsis TORC1 signaling network. Our analysis highlights the role of TORC1 as a central hub kinase communicating with the transcriptional and translational apparatus, ribosomes, chaperones, protein kinases, metabolic enzymes, and autophagy and stress response machinery to orchestrate growth in response to nutrient signals. This analysis also suggests that along with the conserved downstream components shared with other eukaryotic lineages, plant TORC1 signaling underwent several evolutionary innovations and co-opted many lineage-specific components during. Based on the protein-protein interaction and phosphoproteome data, we also discuss several uncharacterized and unexplored components of the TORC1 signaling network, highlighting potential links for future studies.

The plant TOR kinase tunes autophagy and meristem activity for nutrient stress-induced developmental plasticity

Plants, unlike animals, respond to environmental challenges with comprehensive developmental transitions that allow them to cope with these stresses. Here we discovered that antagonistic activation of the Target of Rapamycin (TOR) kinase in Arabidopsis thaliana roots and shoots is essential for the nutrient deprivation-induced increase in the root-to-shoot ratio to improve foraging for mineral ions. We demonstrate that sulfate limitation-induced downregulation of TOR in shoots activates autophagy, resulting in enhanced carbon allocation to the root. The allocation of carbon to the roots is facilitated by the specific upregulation of the sucrose-transporter genes SWEET11/12 in shoots. SWEET11/12 activation is indispensable for enabling sucrose to act as a carbon source for growth and as a signal for tuning root apical meristem activity via glucose-TOR signaling. The sugar-stimulated TOR activity in the root suppresses autophagy and maintains root apical meristem activity to support root growth to enhance mining for new sulfate resources in the soil. We provide direct evidence that the organ-specific regulation of autophagy is essential for the increased root-to-shoot ratio in response to sulfur limitation. These findings uncover how sulfur limitation controls the central sensor kinase TOR to enable nutrient recycling for stress-induced morphological adaptation of the plant body.

Stress-responsive AMP Kinase like protein regulates encystation of Entamoeba invadens

Starvation is always accompanied by an increase in the ratio of AMP/ATP followed by activation of AMPK. It is one of the sensors for cellular energy status and is highly conserved across various species. Its role in the stage differentiation process of protozoan species like Giardia, Plasmodium, Trypanosome, and Toxoplasma has been reported. Since Entamoeba undergoes encystation in glucose-starved conditions; it intrigued us to investigate the existence and role of AMPK during the differentiation of trophozoites to the cyst. By employing in silico approaches, we have identified an AMPK homologue which is denominated here as EiAMPK (AMPK-like protein in Entamoeba invadens). Sequence and structural analysis indicate that EiAMPK is sequentially and structurally similar to the AMPK alpha subunit of other organisms. The recombinant form of EiAMPK was functionally active and in accordance, its activity was inhibited by an AMPK-specific inhibitor (eg. Compound C). The increased expression of EiAMPK during different stresses indicated that EiAMPK is a stress-responsive gene. To further investigate, whether EiAMPK has any role in encystation, we employed RNAi-mediated gene silencing that demonstrated its active involvement in encystation. It is known that Entamoeba maintains a flow of glucose from the glycolytic pathway to chitin synthesis for cyst wall formation during encystation. It is conceivable that EiAMPK might have a command over such glucose metabolism. As anticipated, the chitin synthesis was found greatly inhibited in both EiAMPK knockdown and Compound C treated cells, indicating that EiAMPK regulates the cyst wall chitin synthesis.

Roles of TOR signaling in nutrient deprivation and abiotic stress

In living organisms, nutrient, energy, and environmental stimuli sensing and signaling are considered as the most primordial regulatory networks governing growth and development. Target of Rapamycin (TOR) is a diversified Serine/Threonine protein kinase existing in all eukaryotes that regulates distinct salient growth and developmental signaling pathways. TOR signaling acts as a central hub in plants that allows a variety of nutrients, energy, hormones, and environmental stimuli to be integrated. TOR is activated by several nutrients and promotes energy-consuming processes such as cell division, protein translation, mRNA translation and ribosome biogenesis. We summarized the recent findings on the TOR function in regulating the dynamic networks of nutrients, including sugar, sulfur, nitrogen, carbon, phosphorus, potassium, and amino acids. TOR's role in abiotic stress was discussed, in which TOR orchestrating stress signaling, including heat, cold, salt, and osmotic stress, to regulate transcriptional and metabolic reprogramming, as well as growth and development. The interconnections between TOR and SnRK1 kinase were discussed in controlling nutrient deprivation and abiotic stress.

Bone morphogenetic protein signaling regulation of AMPK and PI3K in lung cancer cells and C. elegans

BACKGROUND

Bone morphogenetic protein (BMP) is a phylogenetically conserved signaling pathway required for development that is aberrantly expressed in several age-related diseases including cancer, Alzheimer's disease, obesity, and cardiovascular disease. Aberrant BMP signaling in mice leads to obesity, suggesting it may alter normal metabolism. The role of BMP signaling regulating cancer metabolism is not known.

METHODS

To examine BMP regulation of metabolism, C. elegans harboring BMP gain-of-function (gof) and loss-of-function (lof) mutations were examined for changes in activity of catabolic and anabolic metabolism utilizing Western blot analysis and fluorescent reporters. AMP activated kinase (AMPK) gof and lof mutants were used to examine AMPK regulation of BMP signaling. H1299 (LKB1 wild-type), A549 (LKB1 lof), and A549-LKB1 (LKB1 restored) lung cancer cell lines were used to study BMP regulation of catabolic and anabolic metabolism. Studies were done using recombinant BMP ligands to activate BMP signaling, and BMP receptor specific inhibitors and siRNA to inhibit signaling.

RESULTS

BMP signaling in both C. elegans and cancer cells is responsive to nutrient conditions. In both C. elegans and lung cancer cell lines BMP suppressed AMPK, the master regulator of catabolism, while activating PI3K, a regulator of anabolism. In lung cancer cells, inhibition of BMP signaling by siRNA or small molecules increased AMPK activity, and this increase was mediated by activation of LKB1. BMP2 ligand suppressed AMPK activation during starvation. BMP2 ligand decreased expression of TCA cycle intermediates and non-essential amino acids in H1299 cells. Furthermore, we show that BMP activation of PI3K is mediated through BMP type II receptor. We also observed feedback signaling, as AMPK suppressed BMP signaling, whereas PI3K increased BMP signaling.

CONCLUSION

These studies show that BMP signaling suppresses catabolic metabolism and stimulates anabolic metabolism. We identified feedback mechanisms where catabolic induced signaling mediated by AMPK negatively regulates BMP signaling, whereas anabolic signaling produces a positive feedback regulation of BMP signing through Akt. These mechanisms were conserved in both lung cancer cells and C. elegans. These studies suggest that aberrant BMP signaling causes dysregulation of metabolism that is a potential mechanism by which BMP promotes survival of cancer cells.

Evolution of plasticity: metabolic compensation for fluctuating energy demands at the origin of life

Phenotypic plasticity of physiological functions enables rapid responses to changing environments and may thereby increase the resilience of organisms to environmental change. Here, we argue that the principal hallmarks of life itself, self-replication and maintenance, are contingent on the plasticity of metabolic processes ('metabolic plasticity'). It is likely that the Last Universal Common Ancestor (LUCA), 4 billion years ago, already possessed energy-sensing molecules that could adjust energy (ATP) production to meet demand. The earliest manifestation of metabolic plasticity, switching cells from growth and storage (anabolism) to breakdown and ATP production (catabolism), coincides with the advent of Darwinian evolution. Darwinian evolution depends on reliable translation of information from information-carrying molecules, and on cell genealogy where information is accurately passed between cell generations. Both of these processes create fluctuating energy demands that necessitate metabolic plasticity to facilitate replication of genetic material and (proto)cell division. We propose that LUCA possessed rudimentary forms of these capabilities. Since LUCA, metabolic networks have increased in complexity. Generalist founder enzymes formed the basis of many derived networks, and complexity arose partly by recruiting novel pathways from the untapped pool of reactions that are present in cells but do not have current physiological functions (the so-called 'underground metabolism'). Complexity may thereby be specific to environmental contexts and phylogenetic lineages. We suggest that a Boolean network analysis could be useful to model the transition of metabolic networks over evolutionary time. Network analyses can be effective in modelling phenotypic plasticity in metabolic functions for different phylogenetic groups because they incorporate actual biochemical regulators that can be updated as new empirical insights are gained.

Coordinated resource allocation to plant growth-defense tradeoffs

Plant resource allocation patterns often reveal tradeoffs that favor growth (G) over defense (D), or vice versa. Ecologists most often explain G-D tradeoffs through principles of economic optimality, in which negative trait correlations are attributed to the reconciliation of fitness costs. Recently, researchers in molecular biology have developed 'big data' resources including multi-omic (e.g. transcriptomic, proteomic and metabolomic) studies that describe the cellular processes controlling gene expression in model species. In this synthesis, we bridge ecological theory with discoveries in multi-omics biology to better understand how selection has shaped the mechanisms of G-D tradeoffs. Multi-omic studies reveal strategically coordinated patterns in resource allocation that are enabled by phytohormone crosstalk and transcriptional signal cascades. Coordinated resource allocation justifies the framework of optimality theory, while providing mechanistic insight into the feedbacks and control hubs that calibrate G-D tradeoff commitments. We use the existing literature to describe the coordinated resource allocation hypothesis (CoRAH) that accounts for balanced cellular controls during the expression of G-D tradeoffs, while sustaining stored resource pools to buffer the impacts of future stresses. The integrative mechanisms of the CoRAH unify the supply- and demand-side perspectives of previous G-D tradeoff theories.

Tracing Eukaryotic Ribosome Biogenesis Factors Into the Archaeal Domain Sheds Light on the Evolution of Functional Complexity

Ribosome assembly is an essential and carefully choreographed cellular process. In eukaryotes, several 100 proteins, distributed across the nucleolus, nucleus, and cytoplasm, co-ordinate the step-wise assembly of four ribosomal RNAs (rRNAs) and approximately 80 ribosomal proteins (RPs) into the mature ribosomal subunits. Due to the inherent complexity of the assembly process, functional studies identifying ribosome biogenesis factors and, more importantly, their precise functions and interplay are confined to a few and very well-established model organisms. Although best characterized in yeast (Saccharomyces cerevisiae), emerging links to disease and the discovery of additional layers of regulation have recently encouraged deeper analysis of the pathway in human cells. In archaea, ribosome biogenesis is less well-understood. However, their simpler sub-cellular structure should allow a less elaborated assembly procedure, potentially providing insights into the functional essentials of ribosome biogenesis that evolved long before the diversification of archaea and eukaryotes. Here, we use a comprehensive phylogenetic profiling setup, integrating targeted ortholog searches with automated scoring of protein domain architecture similarities and an assessment of when search sensitivity becomes limiting, to trace 301 curated eukaryotic ribosome biogenesis factors across 982 taxa spanning the tree of life and including 727 archaea. We show that both factor loss and lineage-specific modifications of factor function modulate ribosome biogenesis, and we highlight that limited sensitivity of the ortholog search can confound evolutionary conclusions. Projecting into the archaeal domain, we find that only few factors are consistently present across the analyzed taxa, and lineage-specific loss is common. While members of the Asgard group are not special with respect to their inventory of ribosome biogenesis factors (RBFs), they unite the highest number of orthologs to eukaryotic RBFs in one taxon. Using large ribosomal subunit maturation as an example, we demonstrate that archaea pursue a simplified version of the corresponding steps in eukaryotes. Much of the complexity of this process evolved on the eukaryotic lineage by the duplication of ribosomal proteins and their subsequent functional diversification into ribosome biogenesis factors. This highlights that studying ribosome biogenesis in archaea provides fundamental information also for understanding the process in eukaryotes.

Evolution of opposing regulatory interactions underlies the emergence of eukaryotic cell cycle checkpoints

In eukaryotes the entry into mitosis is initiated by activation of cyclin-dependent kinases (CDKs), which in turn activate a large number of protein kinases to induce all mitotic processes. The general view is that kinases are active in mitosis and phosphatases turn them off in interphase. Kinases activate each other by cross- and self-phosphorylation, while phosphatases remove these phosphate groups to inactivate kinases. Crucial exceptions to this general rule are the interphase kinase Wee1 and the mitotic phosphatase Cdc25. Together they directly control CDK in an opposite way of the general rule of mitotic phosphorylation and interphase dephosphorylation. Here we investigate why this opposite system emerged and got fixed in almost all eukaryotes. Our results show that this reversed action of a kinase-phosphatase pair, Wee1 and Cdc25, on CDK is particularly suited to establish a stable G2 phase and to add checkpoints to the cell cycle. We show that all these regulators appeared together in LECA (Last Eukaryote Common Ancestor) and co-evolved in eukaryotes, suggesting that this twist in kinase-phosphatase regulation was a crucial step happening at the emergence of eukaryotes.

The tip of the iceberg: emerging roles of TORC1, and its regulatory functions in plant cells

Target of Rapamycin (TOR) is an evolutionarily conserved protein kinase that plays a central role in coordinating cell growth with light availability, the diurnal cycle, energy availability, and hormonal pathways. TOR Complex 1 (TORC1) controls cell proliferation, growth, metabolism, and defense in plants. Sugar availability is the main signal for activation of TOR in plants, as it also is in mammals and yeast. Specific regulators of the TOR kinase pathway in plants are inorganic compounds in the form of major nutrients in the soils, and light inputs via their impact on autotrophic metabolism. The lack of TOR is embryo-lethal in plants, whilst dysregulation of TOR signaling causes major alterations in growth and development. TOR exerts control as a regulator of protein translation via the action of proteins such as S6K, RPS6, and TAP46. Phytohormones are central players in the downstream systemic physiological TOR effects. TOR has recently been attributed to have roles in the control of DNA methylation, in the abundance of mRNA splicing variants, and in the variety of regulatory lncRNAs and miRNAs. In this review, we summarize recent discoveries in the plant TOR signaling pathway in the context of our current knowledge of mammalian and yeast cells, and highlight the most important gaps in our understanding of plants that need to be addressed in the future.

Constructing the constitutively active ribosomal protein S6 kinase 2 from Arabidopsis thaliana (AtRPS6K2) and testing its activity in vitro

Ribosomal protein S6 (RPS6) is the only phosphorylatable protein of the eukaryotic 40S ribosomal subunit. Ribosomes with phosphorylated RPS6 can selectively translate 5'TOP-(5'-terminal oligopyrimidine)-containing mRNAs that encode most proteins of the translation apparatus. The study of translational control of 5'TOP-mRNAs, which are preferentially translated when RPS6 is phosphorylated and cease to be translated when RPS6 is de-phosphorylated, is particularly important. In Arabidopsis thaliana, AtRPS6 is phosphorylated by kinase AtRPS6K2, which should in turn be phosphorylated by upper level kinases (AtPDK1 - at serine (S) 296, AtTOR - at threonine (T) 455 and S437) for full activation. We have cloned AtRPS6K2 cDNA gene and carried out in vitro mutagenesis replacing codons encoding S296, S437 and T455 by triplets of phosphomimetic glutamic acid (E). After the expression of both natural and mutated cDNAs in Escherichia coli cells, two recombinant proteins were isolated: native AtRPS6K2 and presumably constitutively active AtRPS6K2(S296E, S437E, T455E). The activity of these variants was tested in vitro. Both kinases could phosphorylate wheat (Triticum aestivum L.) TaRPS6 as part of 40S ribosomal subunits isolated from wheat embryos, though the non-mutated variant had less activity than phosphomimetic one. The ability of recombinant non-mutated kinase to phosphorylate TaRPS6 can be explained by its phosphorylation by bacterial kinases during the expression and isolation steps. The phosphomimetically mutated AtRPS6K2(S296E, S437E, T455E) can serve as a tool to investigate preferential translation of 5'TOP-mRNAs in wheat germ cell-free system, in which most of 40S ribosomal subunits have phosphorylated TaRPS6. Besides, such an approach has a biotechnological application in producing genetically modified plants with increased biomass and productivity through stimulation of cell growth and division.

The Protein Phosphatase PP2A Plays Multiple Roles in Plant Development by Regulation of Vesicle Traffic-Facts and Questions

The protein phosphatase PP2A is essential for the control of integrated eukaryotic cell functioning. Several cellular and developmental events, e.g., plant growth regulator (PGR) mediated signaling pathways are regulated by reversible phosphorylation of vesicle traffic proteins. Reviewing present knowledge on the relevant role of PP2A is timely. We discuss three aspects: (1) PP2A regulates microtubule-mediated vesicle delivery during cell plate assembly. PP2A dephosphorylates members of the microtubule associated protein family MAP65, promoting their binding to microtubules. Regulation of phosphatase activity leads to changes in microtubule organization, which affects vesicle traffic towards cell plate and vesicle fusion to build the new cell wall between dividing cells. (2) PP2A-mediated inhibition of target of rapamycin complex (TORC) dependent signaling pathways contributes to autophagy and this has possible connections to the brassinosteroid signaling pathway. (3) Transcytosis of vesicles transporting PIN auxin efflux carriers. PP2A regulates vesicle localization and recycling of PINs related to GNOM (a GTP-GDP exchange factor) mediated pathways. The proper intracellular traffic of PINs is essential for auxin distribution in the plant body, thus in whole plant development. Overall, PP2A has essential roles in membrane interactions of plant cell and it is crucial for plant development and stress responses.

The TOR-Auxin Connection Upstream of Root Hair Growth

Plant growth and productivity are orchestrated by a network of signaling cascades involved in balancing responses to perceived environmental changes with resource availability. Vascular plants are divided into the shoot, an aboveground organ where sugar is synthesized, and the underground located root. Continuous growth requires the generation of energy in the form of carbohydrates in the leaves upon photosynthesis and uptake of nutrients and water through root hairs. Root hair outgrowth depends on the overall condition of the plant and its energy level must be high enough to maintain root growth. TARGET OF RAPAMYCIN (TOR)-mediated signaling cascades serve as a hub to evaluate which resources are needed to respond to external stimuli and which are available to maintain proper plant adaptation. Root hair growth further requires appropriate distribution of the phytohormone auxin, which primes root hair cell fate and triggers root hair elongation. Auxin is transported in an active, directed manner by a plasma membrane located carrier. The auxin efflux carrier PIN-FORMED 2 is necessary to transport auxin to root hair cells, followed by subcellular rearrangements involved in root hair outgrowth. This review presents an overview of events upstream and downstream of PIN2 action, which are involved in root hair growth control.

Bioenergetic Evolution Explains Prevalence of Low Nephron Number at Birth: Risk Factor for CKD

There is greater than tenfold variation in nephron number of the human kidney at birth. Although low nephron number is a recognized risk factor for CKD, its determinants are poorly understood. Evolutionary medicine represents a new discipline that seeks evolutionary explanations for disease, broadening perspectives on research and public health initiatives. Evolution of the kidney, an organ rich in mitochondria, has been driven by natural selection for reproductive fitness constrained by energy availability. Over the past 2 million years, rapid growth of an energy-demanding brain in Homo sapiens enabled hominid adaptation to environmental extremes through selection for mutations in mitochondrial and nuclear DNA epigenetically regulated by allocation of energy to developing organs. Maternal undernutrition or hypoxia results in intrauterine growth restriction or preterm birth, resulting in low birth weight and low nephron number. Regulated through placental transfer, environmental oxygen and nutrients signal nephron progenitor cells to reprogram metabolism from glycolysis to oxidative phosphorylation. These processes are modulated by counterbalancing anabolic and catabolic metabolic pathways that evolved from prokaryote homologs and by hypoxia-driven and autophagy pathways that evolved in eukaryotes. Regulation of nephron differentiation by histone modifications and DNA methyltransferases provide epigenetic control of nephron number in response to energy available to the fetus. Developmental plasticity of nephrogenesis represents an evolved life history strategy that prioritizes energy to early brain growth with adequate kidney function through reproductive years, the trade-off being increasing prevalence of CKD delayed until later adulthood. The research implications of this evolutionary analysis are to identify regulatory pathways of energy allocation directing nephrogenesis while accounting for the different life history strategies of animal models such as the mouse. The clinical implications are to optimize nutrition and minimize hypoxic/toxic stressors in childbearing women and children in early postnatal development.

Importance of adipocyte browning in the evolution of endothermy

Endothermy changes the relationship between organisms and their environment fundamentally, and it is therefore of major ecological and evolutionary significance. Endothermy is characterized by non-shivering thermogenesis, that is metabolic heat production in the absence of muscular activity. In many eutherian mammals, brown adipose tissue (BAT) is an evolutionary innovation that facilitates non-shivering heat production in mitochondria by uncoupling food-derived substrate oxidation from chemical energy (ATP) production. Consequently, energy turnover is accelerated resulting in increased heat release. The defining characteristics of BAT are high contents of mitochondria and vascularization, and the presence of uncoupling protein 1. Recent insights, however, reveal that a range of stimuli such as exercise, diet and the immune system can cause the browning of white adipocytes, thereby increasing energy expenditure and heat production even in the absence of BAT. Here, we review the molecular mechanisms that cause browning of white adipose tissue, and their potential contribution to thermoregulation. The significance for palaeophysiology lies in the presence of adipose tissue and the mechanisms that cause its browning and uncoupling in all amniotes. Hence, adipocytes may have played a role in the evolution of endothermy beyond the more specific evolution of BAT in eutherians. This article is part of the theme issue 'Vertebrate palaeophysiology'.

The functional diversity of structural disorder in plant proteins

Structural disorder in proteins is a widespread feature distributed in all domains of life, particularly abundant in eukaryotes, including plants. In these organisms, intrinsically disordered proteins (IDPs) perform a diversity of functions, participating as integrators of signaling networks, in transcriptional and post-transcriptional regulation, in metabolic control, in stress responses and in the formation of biomolecular condensates by liquid-liquid phase separation. Their roles impact the perception, propagation and control of various developmental and environmental cues, as well as the plant defense against abiotic and biotic adverse conditions. In this review, we focus on primary processes to exhibit a broad perspective of the relevance of IDPs in plant cell functions. The information here might help to incorporate this knowledge into a more dynamic view of plant cells, as well as open more questions and promote new ideas for a better understanding of plant life.

Histone deacetylase activity mediates thermal plasticity in zebrafish (Danio rerio)

Regulatory mechanisms underlying thermal plasticity determine its evolution and potential to confer resilience to climate change. Here we show that class I and II histone deacetylases (HDAC) mediated thermal plasticity globally by shifting metabolomic profiles of cold acclimated zebrafish (Danio rerio) away from warm acclimated animals. HDAC activity promoted swimming performance, but reduced slow and fast myosin heavy chain content in cardiac and skeletal muscle. HDAC increased sarco-endoplasmic reticulum ATPase activity in cold-acclimated fish but not in warm-acclimated animals, and it promoted cardiac function (heart rate and relative stroke volume) in cold but not in warm-acclimated animals. HDAC are an evolutionarily ancient group of proteins, and our data show that they mediate the capacity for thermal plasticity, although the actual manifestation of plasticity is likely to be determined by interactions with other regulators such as AMP-activated protein kinase and thyroid hormone.

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.

SnRK1 and TOR: modulating growth-defense trade-offs in plant stress responses

The evolutionarily conserved protein kinase complexes SnRK1 and TOR are central metabolic regulators essential for plant growth, development, and stress responses. They are activated by opposite signals, and the outcome of their activation is, in global terms, antagonistic. Similarly to their yeast and animal counterparts, SnRK1 is activated by the energy deficit often associated with stress to restore homeostasis, while TOR is activated in nutrient-rich conditions to promote growth. Recent evidence suggests that SnRK1 represses TOR in plants, revealing evolutionary conservation also in their crosstalk. Given their importance for integrating environmental information into growth and developmental programs, these signaling pathways hold great promise for reducing the growth penalties caused by stress. Here we review the literature connecting SnRK1 and TOR to plant stress responses. Although SnRK1 and TOR emerge mostly as positive regulators of defense and growth, respectively, the outcome of their activities in plant growth and performance is not always straightforward. Manipulation of both pathways under similar experimental setups, as well as further biochemical and genetic analyses of their molecular and functional interaction, is essential to fully understand the mechanisms through which these two metabolic pathways contribute to stress responses, growth, and development.

Integration of nutrient, energy, light, and hormone signalling via TOR in plants

The multidomain target of rapamycin (TOR) is an atypical serine/threonine protein kinase resembling phosphatidylinositol lipid kinases, but retains high sequence identity and serves a remarkably conserved role as a master signalling integrator in yeasts, plants, and humans. TOR dynamically orchestrates cell metabolism, biogenesis, organ growth, and development transitions in response to nutrient, energy, hormone, and environmental cues. Here we review recent findings on the versatile and complex roles of TOR in transcriptome reprogramming, seedling, root, and shoot growth, and root hair production activated by sugar and energy signalling. We explore how co-ordination of TOR-mediated light and hormone signalling is involved in root and shoot apical meristem activation, proliferation of leaf primordia, cotyledon/leaf greening, and hypocotyl elongation. We also discuss the emerging TOR functions in response to sulfur assimilation and metabolism and consider potential molecular links and positive feedback loops between TOR, sugar, energy, and other essential macronutrients.

Genome-wide identification and characterization of CKIN/SnRK gene family in Chlamydomonas reinhardtii

The SnRK (Snf1-Related protein Kinase) gene family plays an important role in energy sensing and stress-adaptive responses in plant systems. In this study, Chlamydomonas CKIN family (SnRK in Arabidopsis) was defined after a genome-wide analysis of all sequenced Chlorophytes. Twenty-two sequences were defined as plant SnRK orthologs in Chlamydomonas and classified into two subfamilies: CKIN1 and CKIN2. While CKIN1 subfamily is reduced to one conserved member and a close protein (CKIN1L), a large CKIN2 subfamily clusters both plant-like and algae specific CKIN2s. The responsiveness of these genes to abiotic stress situations was tested by RT-qPCR. Results showed that almost all elements were sensitive to osmotic stress while showing different degrees of sensibility to other abiotic stresses, as occurs in land plants, revealing their specialization and the family pleiotropy for some elements. The regulatory pathway of this family may differ from land plants since these sequences shows unique regulatory features and some of them are sensitive to ABA, despite conserved ABA receptors (PYR/PYL/RCAR) and regulatory domains are not present in this species. Core Chlorophytes and land plant showed divergent stress signalling, but SnRKs/CKINs share the same role in cell survival and stress response and adaption including the accumulation of specific biomolecules. This fact places the CKIN family as well-suited target for bioengineering-based studies in microalgae (accumulation of sugars, lipids, secondary metabolites), while promising new findings in stress biology and specially in the evolution of ABA-signalling mechanisms.

The Arabidopsis THADA homologue modulates TOR activity and cold acclimation

Low temperature is one of the most important environmental factors that affect global survival of humans and animals and equally importantly the distribution of plants and crop productivity. Survival of metazoan cells under cold stress requires regulation of the sensor-kinase Target Of Rapamycin (TOR). TOR controls growth of eukaryotic cells by adjusting anabolic and catabolic metabolism. Previous studies identified the Thyroid Adenoma Associated (THADA) gene as the major effect locus by positive selection in the evolution of modern human adapted to cold. Here we investigate the role of THADA in TOR signaling and cold acclimation of plants. We applied BLAST searches and homology modeling to identify the AtTHADA (AT3G55160) in Arabidopsis thaliana as the highly probable orthologue protein. Reverse genetics approaches were combined with immunological detection of TOR activity and metabolite profiling to address the role of the TOR and THADA for growth regulation and cold acclimation. Depletion of the AtTHADA gene caused complete or partial loss of full-length mRNA, respectively, and significant retardation of growth under non-stressed conditions. Furthermore, depletion of AtTHADA caused hypersensitivity towards low-temperatures. Atthada displayed a lowered energy charge. This went along with decreased TOR activity, which offers a molecular explanation for the slow growth phenotype of Atthada. Finally, we used TOR RNAi lines to identify the de-regulation of TOR activity as one determinant for sensitivity towards low-temperatures. Taken together our results provide evidence for a conserved function of THADA in cold acclimation of eukaryotes and suggest that cold acclimation in plants requires regulation of TOR.

The effects of obesity on skeletal muscle contractile function

Obesity can cause a decline in contractile function of skeletal muscle, thereby reducing mobility and promoting obesity-associated health risks. We reviewed the literature to establish the current state-of-knowledge of how obesity affects skeletal muscle contraction and relaxation. At a cellular level, the dominant effects of obesity are disrupted calcium signalling and 5'-adenosine monophosphate-activated protein kinase (AMPK) activity. As a result, there is a shift from slow to fast muscle fibre types. Decreased AMPK activity promotes the class II histone deacetylase (HDAC)-mediated inhibition of the myocyte enhancer factor 2 (MEF2). MEF2 promotes slow fibre type expression, and its activity is stimulated by the calcium-dependent phosphatase calcineurin. Obesity-induced attenuation of calcium signalling via its effects on calcineurin, as well as on adiponectin and actinin affects excitation-contraction coupling and excitation-transcription coupling in the myocyte. These molecular changes affect muscle contractile function and phenotype, and thereby in vivo and in vitro muscle performance. In vivo, obesity can increase the absolute force and power produced by increasing the demand on weight-supporting muscle. However, when normalised to body mass, muscle performance of obese individuals is reduced. Isolated muscle preparations show that obesity often leads to a decrease in force produced per muscle cross-sectional area, and power produced per muscle mass. Obesity and ageing have similar physiological consequences. The synergistic effects of obesity and ageing on muscle function may exacerbate morbidity and mortality. Important future research directions include determining: the relationship between time course of weight gain and changes in muscle function; the relative effects of weight gain and high-fat diet feeding per se; the effects of obesity on muscle function during ageing; and if the effects of obesity on muscle function are reversible.

The FCS-like zinc finger scaffold of the kinase SnRK1 is formed by the coordinated actions of the FLZ domain and intrinsically disordered regions

The SNF1-related protein kinase 1 (SnRK1) is a heterotrimeric eukaryotic kinase that interacts with diverse proteins and regulates their activity in response to starvation and stress signals. Recently, the FCS-like zinc finger (FLZ) proteins were identified as a potential scaffold for SnRK1 in plants. However, the evolutionary and mechanistic aspect of this complex formation is currently unknown. Here, in silico analyses predicted that FLZ proteins possess conserved intrinsically disordered regions (IDRs) with a propensity for protein binding in the N and C termini across the plant lineage. We observed that the Arabidopsis FLZ proteins promiscuously interact with SnRK1 subunits, which formed different isoenzyme complexes. The FLZ domain was essential for mediating the interaction with SnRK1α subunits, whereas the IDRs in the N termini facilitated interactions with the β and βγ subunits of SnRK1. Furthermore, the IDRs in the N termini were important for mediating dimerization of different FLZ proteins. Of note, the interaction of FLZ with SnRK1 was confined to cytoplasmic foci, which colocalized with the endoplasmic reticulum. An evolutionary analysis revealed that in general, the IDR-rich regions are under more relaxed selection than the FLZ domain. In summary, the findings in our study reveal the structural details, origin, and evolution of a land plant-specific scaffold of SnRK1 formed by the coordinated actions of IDRs and structured regions in the FLZ proteins. We propose that the FLZ protein complex might be involved in providing flexibility, thus enhancing the binding repertoire of the SnRK1 hub in land plants.

The C/S1 bZIP Network: A Regulatory Hub Orchestrating Plant Energy Homeostasis

Sustaining energy homeostasis is crucial to every living being. To balance energy supply and demand, plants make use of an evolutionarily conserved management system consisting of two counteracting kinases, TOR (TARGET OF RAPAMYCIN) and SnRK1 (Snf1-RELATED PROTEIN KINASE 1). SnRK1 is involved in reorganizing enzymatic and transcriptional responses to survive energy-limiting conditions. Recently, members of the bZIP (basic leucine zipper) transcription factor family have been established as SnRK1 downstream mediators. We review here current knowledge on the functional impact of these group C and S₁ bZIPs, and analyze their regulation by environmental and endogenous cues. Given their specific homo- and heterodimerization, the so-called C/S₁ bZIP network is proposed to act as a signaling hub that coordinates plant development and stress responses.

Studying AMPK in an Evolutionary Context

The AMPK protein kinase forms the heart of a complex network controlling the metabolic activities in a eukaryotic cell. Unraveling the steps by which this pathway evolved from its primordial roots in the last eukaryotic common ancestor to its present status in contemporary species has the potential to shed light on the evolution of eukaryotes. A homolog search for the proteins interacting in this pathway is considerably straightforward. However, interpreting the results, when reconstructing the evolutionary history of the pathway over larger evolutionary distances, bears a number of pitfalls. With this in mind, we present a protocol to trace a metabolic pathway across contemporary species and backward in evolutionary time. Alongside the individual analysis steps, we provide guidelines for data interpretation generalizing beyond the analysis of AMPK.

Quantitative Phosphoproteomic and System-Level Analysis of TOR Inhibition Unravel Distinct Organellar Acclimation in Chlamydomonas reinhardtii

Rapamycin is an inhibitor of the evolutionary conserved Target of Rapamycin (TOR) kinase which promotes and coordinates translation with cell growth and division. In heterotrophic organisms, TOR regulation is based on intra- and extracellular stimuli such as amino acids level and insulin perception. However, how plant TOR pathways have evolved to integrate plastid endosymbiosis is a remaining question. Despite the close association of the TOR signaling with the coordination between protein turn-over and growth, proteome and phosphoproteome acclimation to a rapamycin treatment have not yet been thoroughly investigated in Chlamydomonas reinhardtii. In this study, we have used in vivo label-free phospho-proteomic analysis to profile both protein and phosphorylation changes at 0, 24, and 48 h in Chlamydomonas cells treated with rapamycin. Using multivariate statistics we highlight the impact of TOR inhibition on both the proteome and the phosphoproteome. Two-way ANOVA distinguished differential levels of proteins and phosphoproteins in response either to culture duration and rapamycin treatment or combined effects. Finally, protein-protein interaction networks and functional enrichment analysis underlined the relation between plastid and mitochondrial metabolism. Prominent changes of proteins involved in sulfur, cysteine, and methionine as well as nucleotide metabolism on the one hand, and changes in the TCA cycle on the other highlight the interplay of chloroplast and mitochondria metabolism. Furthermore, TOR inhibition revealed changes in the endomembrane trafficking system. Phosphoproteomics data, on the other hand, highlighted specific differentially regulated phosphorylation sites for calcium-regulated protein kinases as well as ATG7, S6K, and PP2C. To conclude we provide a first combined Chlamydomonas proteomics and phosphoproteomics dataset in response to TOR inhibition, which will support further investigations.

The evolution of metabolic regulation in animals

Energy metabolism is determined by a suite of regulatory mechanism, and their increasing complexity over evolutionary time provides the key to understanding the emergence of different metabolic phenotypes. Energy metabolism is at the core of biological processes because all organisms must maintain energy balance against thermodynamic gradients. Energy metabolism is regulated by a bewildering array of interacting molecular mechanisms, and much of what is known about metabolic regulation comes from the medical literature. However, ecology and evolutionary research would gain considerably by incorporating regulatory mechanisms more explicitly in research on topics such as the evolution of endothermy, metabolic plasticity, and energy balance. The purpose of this brief review is to summarise the main regulatory pathways of energy metabolism in animals and their evolutionary origins to make these complex interactions more accessible to researchers from a broad range of backgrounds. Some of the principal regulators of energy balance, such as the AMP-stimulated protein kinase, have an ancient prokaryotic origin. Most regulatory pathways (e.g. thyroid hormone, insulin, adipokines), however, are eukaryotic in origin and diversified substantially in metazoans and vertebrates. Diversification in vertebrates is at least partly due to genome duplications early in this lineage. The interaction between regulatory mechanisms permitted an increasingly sophisticated fine-tuning of energy balance and metabolism. Hence, regulatory complexity increased over evolutionary time, and taxa differ in their potential range of metabolic phenotypes. Choice of model organism therefore becomes important, and bacteria or even invertebrates are not good models for more derived vertebrates. Different metabolic phenotypes and their evolution, such as endothermy and metabolic plasticity, should be interpreted against this regulatory background.

Sulfur availability regulates plant growth via glucose-TOR signaling

Growth of eukaryotic cells is regulated by the target of rapamycin (TOR). The strongest activator of TOR in metazoa is amino acid availability. The established transducers of amino acid sensing to TOR in metazoa are absent in plants. Hence, a fundamental question is how amino acid sensing is achieved in photo-autotrophic organisms. Here we demonstrate that the plant Arabidopsis does not sense the sulfur-containing amino acid cysteine itself, but its biosynthetic precursors. We identify the kinase GCN2 as a sensor of the carbon/nitrogen precursor availability, whereas limitation of the sulfur precursor is transduced to TOR by downregulation of glucose metabolism. The downregulated TOR activity caused decreased translation, lowered meristematic activity, and elevated autophagy. Our results uncover a plant-specific adaptation of TOR function. In concert with GCN2, TOR allows photo-autotrophic eukaryotes to coordinate the fluxes of carbon, nitrogen, and sulfur for efficient cysteine biosynthesis under varying external nutrient supply.

Plants lack the amino acid sensors that regulate TOR in metazoans. Here Dong et al. show that Arabidopsis GCN2 senses carbon and nitrogen availability for cysteine synthesis while sulfur limitation activates TOR via glucose metabolism, providing a mechanism whereby plants control growth according to nutrient availability.

Redox state-dependent modulation of plant SnRK1 kinase activity differs from AMPK regulation in animals

The evolutionarily highly conserved SNF1‐related protein kinase (SnRK1) protein kinase is a metabolic master regulator in plants, balancing the critical energy consumption between growth‐ and stress response‐related metabolic pathways. While the regulation of the mammalian [AMP‐activated protein kinase (AMPK)] and yeast (SNF1) orthologues of SnRK1 is well‐characterised, the regulation of SnRK1 kinase activity in plants is still an open question. Here we report that the activity and T‐loop phosphorylation of AKIN10, the kinase subunit of the SnRK1 complex, is regulated by the redox status. Although this regulation is dependent on a conserved cysteine residue, the underlying mechanism is different to the redox regulation of animal AMPK and has functional implications for the regulation of the kinase complex in plants under stress conditions.

Shaping plant development through the SnRK1-TOR metabolic regulators

SnRK1 (Snf1-related protein kinase 1) and TOR (target of rapamycin) are evolutionarily conserved protein kinases that lie at the heart of energy sensing, playing central and antagonistic roles in the regulation of metabolism and gene expression. Increasing evidence links these metabolic regulators to numerous aspects of plant development, from germination to flowering and senescence. This prompts the hypothesis that SnRK1 and TOR modify developmental programs according to the metabolic status to adjust plant growth to a specific environment. The aim of this review is to provide support to this hypothesis and to incentivize further studies on this topic by summarizing the work that establishes a genetic connection between SnRK1-TOR and plant development.

Quantitative in vivo phosphoproteomics reveals reversible signaling processes during nitrogen starvation and recovery in the biofuel model organism Chlamydomonas reinhardtii

BACKGROUND

Nitrogen deprivation and replenishment induces massive changes at the physiological and molecular level in the green alga Chlamydomonas reinhardtii, including reversible starch and lipid accumulation. Stress signal perception and acclimation involves transient protein phosphorylation. This study aims to provide the first experimental phosphoprotein dataset for the adaptation of C. reinhardtii during nitrogen depletion and recovery growth phases and its impact on lipid accumulation.

RESULTS

To decipher the signaling pathways involved in this dynamic process, we applied a label-free in vivo shotgun phosphoproteomics analysis on nitrogen-depleted and recovered samples. 1227 phosphopeptides belonging to 732 phosphoproteins were identified and quantified. 470 phosphopeptides showed a significant change across the experimental set-up. Multivariate statistics revealed the reversible phosphorylation process and the time/condition-dependent dynamic rearrangement of the phosphoproteome. Protein-protein interaction analysis of differentially regulated phosphoproteins identified protein kinases and phosphatases, such as DYRKP and an AtGRIK1 orthologue, called CDPKK2, as central players in the coordination of translational, photosynthetic, proteomic and metabolomic activity. Phosphorylation of RPS6, ATG13, and NNK1 proteins points toward a specific regulation of the TOR pathway under nitrogen deprivation. Differential phosphorylation pattern of several eukaryotic initiation factor proteins (EIF) suggests a major control on protein translation and turnover.

CONCLUSION

This work provides the first phosphoproteomics dataset obtained for Chlamydomonas responses to nitrogen availability, revealing multifactorial signaling pathways and their regulatory function for biofuel production. The reproducibility of the experimental set-up allows direct comparison with proteomics and metabolomics datasets and refines therefore the current model of Chlamydomonas acclimation to various nitrogen levels. Integration of physiological, proteomics, metabolomics, and phosphoproteomics data reveals three phases of acclimation to N availability: (i) a rapid response triggering starch accumulation as well as energy metabolism while chloroplast structure is conserved followed by (ii) chloroplast degradation combined with cell autophagy and lipid accumulation and finally (iii) chloroplast regeneration and cell growth activation after nitrogen replenishment. Plastid development seems to be further interconnected with primary metabolism and energy stress signaling in order to coordinate cellular mechanism to nitrogen availability stress.