Interplay of energy metabolism and autophagy

Macroautophagy/autophagy, is widely recognized for its crucial role in enabling cell survival and maintaining cellular energy homeostasis during starvation or energy stress. Its regulation is intricately linked to cellular energy status. In this review, covering yeast, mammals, and plants, we aim to provide a comprehensive overview of the understanding of the roles and mechanisms of carbon- or glucose-deprivation related autophagy, showing how cells effectively respond to such challenges for survival. Further investigation is needed to determine the specific degraded substrates by autophagy during glucose or energy deprivation and the diverse roles and mechanisms during varying durations of energy starvation.Abbreviations: ADP: adenosine diphosphate; AMP: adenosine monophosphate; AMPK: AMP-activated protein kinase; ATG: autophagy related; ATP: adenosine triphosphate; ER: endoplasmic reticulum; ESCRT: endosomal sorting complex required for transport; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GD: glucose deprivation; GFP: green fluorescent protein; GTPases: guanosine triphosphatases; HK2: hexokinase 2; K phaffii: Komagataella phaffii; LD: lipid droplet; MAP1LC3/LC3: microtubule-associated protein1 light chain 3; MAPK: mitogen-activated protein kinase; Mec1: mitosis entry checkpoint 1; MTOR: mechanistic target of rapamycin kinase; NAD (+): nicotinamide adenine dinucleotide; OGD: oxygen and glucose deprivation; PAS: phagophore assembly site; PCD: programmed cell death; PtdIns3K: class III phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate; ROS: reactive oxygen species; S. cerevisiae: Saccharomyces cerevisiae; SIRT1: sirtuin 1; Snf1: sucrose non-fermenting 1; STK11/LKB1: serine/threonine kinase 11; TFEB: transcription factor EB; TORC1: target of rapamycin complex 1; ULK1: unc-51 like kinase 1; Vps27: vacuolar protein sorting 27; Vps4: vacuolar protein sorting 4.

Identification and Potential Participation of Lipases in Autophagic Body Degradation in Embryonic Axes of Lupin (Lupinus spp.) Germinating Seeds

Autophagy is a fundamental process for plants that plays a crucial role in maintaining cellular homeostasis and promoting survival in response to various environmental stresses. One of the lesser-known stages of plant autophagy is the degradation of autophagic bodies in vacuoles. To this day, no plant vacuolar enzyme has been confirmed to be involved in this process. On the other hand, several enzymes have been described in yeast (Saccharomyces cerevisiae), including Atg15, that possess lipolytic activity. In this preliminary study, which was conducted on isolated embryonic axes of the white lupin (Lupinus albus L.) and Andean lupin (Lupinus mutabilis Sweet), the potential involvement of plant vacuolar lipases in the degradation of autophagic bodies was investigated. We identified in transcriptomes (using next-generation sequencing (NGS)) of white and Andean lupin embryonic axes 38 lipases with predicted vacuolar localization, and for three of them, similarities in amino acid sequences with yeast Atg15 were found. A comparative transcriptome analysis of lupin isolated embryonic axes cultured in vitro under different sucrose and asparagine nutrition, evaluating the relations in the levels of the transcripts of lipase genes, was also carried out. A clear decrease in lipase gene transcript levels caused by asparagine, a key amino acid in lupin seed metabolism which retards the degradation of autophagic bodies during sugar-starvation-induced autophagy in lupin embryonic axes, was detected. Although the question of whether lipases are involved in the degradation of autophagic bodies during plant autophagy is still open, our findings strongly support such a hypothesis.

Autophagy contributes to positive feedback regulation of SnRK1 signaling in plants

SnRK1 (SNF1-related protein kinase 1) is a plant ortholog of yeast Snf1 and mammalian adenosine monophosphate-activated protein kinase (AMPK) that acts as a positive regulator of macroautophagy/autophagy. However, whether and how the autophagy pathway modulates SnRK1 activity remains elusive. Recently, we identified a clade of plant-specific FLZ (FCS-like zinc finger) proteins as novel ATG8 (autophagy-related 8)-interacting partners in Arabidopsis thaliana. These AtFLZs, which mainly localize on the surface of mitochondria, can inhibit SnRK1 signaling by repressing the T-loop phosphorylation of its catalytic α subunits, thereby negatively regulating carbon starvation-induced autophagy and plant tolerance to energy deprivation. Upon energy starvation, autophagy is activated to mediate the degradation of these AtFLZs, thus relieving their repression of SnRK1. More importantly, the ATG8-FLZ-SnRK1 regulatory axis appears to be functionally conserved during seed plant evolution. These findings highlight the positive role of autophagy in SnRK1 signaling activation under energy-limiting conditions in plants.Abbreviations: ADS, AIMs docking site; AIM, ATG8-interacting motif; AMPK, adenosine monophosphate-activated protein kinase; ATG, autophagy-related; ESCRT, endosomal sorting complexes required for transport; FLZ, FCS-like zinc finger protein; FREE1, FYVE DOMAIN PROTEIN REQUIRED FOR ENDOSOMAL SORTING 1; RAPTOR, REGULATORY-ASSOCIATED PROTEIN OF TOR; Snf1, SUCROSE NON-FERMENTING 1; SnRK1, SNF1-related kinase 1; TOR, TARGET OF RAPAMYCIN.

The interplay between autophagy and chloroplast vesiculation pathways under dark-induced senescence

In cellular circumstances where carbohydrates are scarce, plants can use alternative substrates for cellular energetic maintenance. In plants, the main protein reserve is present in the chloroplast, which contains most of the total leaf proteins and represents a rich source of nitrogen and amino acids. Autophagy plays a key role in chloroplast breakdown, a well-recognised symptom of both natural and stress-induced plant senescence. Remarkably, an autophagic-independent route of chloroplast degradation associated with chloroplast vesiculation (CV) gene was previously demonstrated. During extended darkness, CV is highly induced in the absence of autophagy, contributing to the early senescence phenotype of atg mutants. To further investigate the role of CV under dark-induced senescence conditions, mutants with low expression of CV (amircv) and double mutants amircv1xatg5 were characterised. Following darkness treatment, no aberrant phenotypes were observed in amircv single mutants; however, amircv1xatg5 double mutants displayed early senescence and altered dismantling of chloroplast and membrane structures under these conditions. Metabolic characterisation revealed that the functional lack of both CV and autophagy leads to higher impairment of amino acid release and differential organic acid accumulation during starvation conditions. The data obtained are discussed in the context of the role of CV and autophagy, both in terms of cellular metabolism and the regulation of chloroplast degradation.

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.

Modeling the mechanisms of conifer mortality under seawater exposure

Relative sea level rise (SLR) increasingly impacts coastal ecosystems through the formation of ghost forests. To predict the future of coastal ecosystems under SLR and changing climate, it is important to understand the physiological mechanisms underlying coastal tree mortality and to integrate this knowledge into dynamic vegetation models. We incorporate the physiological effect of salinity and hypoxia in a dynamic vegetation model in the Earth system land model, and used the model to investigate the mechanisms of mortality of conifer forests on the west and east coast sites of USA, where trees experience different form of sea water exposure. Simulations suggest similar physiological mechanisms can result in different mortality patterns. At the east coast site that experienced severe increases in seawater exposure, trees loose photosynthetic capacity and roots rapidly, and both storage carbon and hydraulic conductance decrease significantly within a year. Over time, further consumption of storage carbon that leads to carbon starvation dominates mortality. At the west coast site that gradually exposed to seawater through SLR, hydraulic failure dominates mortality because root loss impacts on conductance are greater than the degree of storage carbon depletion. Measurements and modeling focused on understanding the physiological mechanisms of mortality is critical to reducing predictive uncertainty.

Drought-induced increase in tree mortality and corresponding decrease in the carbon sink capacity of Canada's boreal forests from 1970 to 2020

Canada's boreal forests, which occupy approximately 30% of boreal forests worldwide, play an important role in the global carbon budget. However, there is little quantitative information available regarding the spatiotemporal changes in the drought-induced tree mortality of Canada's boreal forests overall and their associated impacts on biomass carbon dynamics. Here, we develop spatiotemporally explicit estimates of drought-induced tree mortality and corresponding biomass carbon sink capacity changes in Canada's boreal forests from 1970 to 2020. We show that the average annual tree mortality rate is approximately 2.7%. Approximately 43% of Canada's boreal forests have experienced significantly increasing tree mortality trends (71% of which are located in the western region of the country), and these trends have accelerated since 2002. This increase in tree mortality has resulted in significant biomass carbon losses at an approximate rate of 1.51 ± 0.29 MgC ha^-1  year^-1 (95% confidence interval) with an approximate total loss of 0.46 ± 0.09 PgC year^-1 (95% confidence interval). Under the drought condition increases predicted for this century, the capacity of Canada's boreal forests to act as a carbon sink will be further reduced, potentially leading to a significant positive climate feedback effect.

Proteome Dynamics of Persulfidation in Leaf Tissue under Light/Dark Conditions and Carbon Deprivation

Hydrogen sulfide (H₂S) acts as a signaling molecule in plants, bacteria, and mammals, regulating various physiological and pathological processes. The molecular mechanism by which hydrogen sulfide exerts its action involves the posttranslational modification of cysteine residues to form a persulfidated thiol motif. This research aimed to study the regulation of protein persulfidation. We used a label-free quantitative approach to measure the protein persulfidation profile in leaves under different growth conditions such as light regimen and carbon deprivation. The proteomic analysis identified a total of 4599 differentially persulfidated proteins, of which 1115 were differentially persulfidated between light and dark conditions. The 544 proteins that were more persulfidated in the dark were analyzed, and showed significant enrichment in functions and pathways related to protein folding and processing in the endoplasmic reticulum. Under light conditions, the persulfidation profile changed, and the number of differentially persulfidated proteins increased up to 913, with the proteasome and ubiquitin-dependent and ubiquitin-independent catabolic processes being the most-affected biological processes. Under carbon starvation conditions, a cluster of 1405 proteins was affected by a reduction in their persulfidation, being involved in metabolic processes that provide primary metabolites to essential energy pathways and including enzymes involved in sulfur assimilation and sulfide production.

Denitrification by Bradyrhizobia under Feast and Famine and the Role of the bc1 Complex in Securing Electrons for N(2)O Reduction

Rhizobia living as microsymbionts inside nodules have stable access to carbon substrates, but also must survive as free-living bacteria in soil where they are starved for carbon and energy most of the time. Many rhizobia can denitrify, thus switch to anaerobic respiration under low O₂ tension using N-oxides as electron acceptors. The cellular machinery regulating this transition is relatively well known from studies under optimal laboratory conditions, while little is known about this regulation in starved organisms. It is, for example, not known if the strong preference for N₂O- over NO₃^- reduction in bradyrhizobia is retained under carbon limitation. Here, we show that starved cultures of a Bradyrhizobium strain with respiration rates 1 to 18% of well-fed cultures reduced all available N₂O before touching provided NO₃^-. These organisms, which carry out complete denitrification, have the periplasmic nitrate reductase NapA but lack the membrane-bound nitrate reductase NarG. Proteomics showed similar levels of NapA and NosZ (N₂O reductase), excluding that the lack of NO₃^- reduction was due to low NapA abundance. Instead, this points to a metabolic-level phenomenon where the bc1 complex, which channels electrons to NosZ via cytochromes, is a much stronger competitor for electrons from the quinol pool than the NapC enzyme, which provides electrons to NapA via NapB. The results contrast the general notion that NosZ activity diminishes under carbon limitation and suggest that bradyrhizobia carrying NosZ can act as strong sinks for N₂O under natural conditions, implying that this criterion should be considered in the development of biofertilizers. IMPORTANCE Legume cropped farmlands account for substantial N₂O emissions globally. Legumes are commonly inoculated with N₂-fixing bacteria, rhizobia, to improve crop yields. Rhizobia belonging to Bradyrhizobium, the microsymbionts of several economically important legumes, are generally capable of denitrification but many lack genes encoding N₂O reductase and will be N₂O sources. Bradyrhizobia with complete denitrification will instead act as sinks since N₂O-reduction efficiently competes for electrons over nitrate reduction in these organisms. This phenomenon has only been demonstrated under optimal conditions and it is not known how carbon substrate limitation, which is the common situation in most soils, affects the denitrification phenotype. Here, we demonstrate that bradyrhizobia retain their strong preference for N₂O under carbon starvation. The findings add basic knowledge about mechanisms controlling denitrification and support the potential for developing novel methods for greenhouse gas mitigation based on legume inoculants with the dual capacity to optimize N₂ fixation and minimize N₂O emission.

Arabidopsis flowering integrator SOC1 transcriptionally regulates autophagy in response to long-term carbon starvation

Autophagy is a highly conserved, self-digestion process that is essential for plant adaptations to various environmental stresses. Although the core components of autophagy in plants have been well established, the molecular basis for its transcriptional regulation remains to be fully characterized. In this study, we demonstrate that SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), a MADS-box family transcription factor that determines flowering transition in Arabidopsis, functions as a transcriptional repressor of autophagy. EMSAs, ChIP-qPCR assays, and dual-luciferase receptor assays showed that SOC1 can bind to the promoters of ATG4b, ATG7, and ATG18c via the conserved CArG box. qRT-PCR analysis showed that the three ATG genes ATG4b, ATG7, and ATG18c were up-regulated in the soc1-2 mutant. In line with this, the mutant also displayed enhanced autophagy activity, as revealed by increased autophagosome formation and elevated autophagic flux compared with the wild type. More importantly, SOC1 negatively affected the tolerance of plants to long-term carbon starvation, and this process requires a functional autophagy pathway. Finally, we found that SOC1 was repressed upon carbon starvation at both the transcriptional and protein levels. Overall, our study not only uncovers an important transcriptional mechanism that contributes to the regulation of plant autophagy in response to nutrient starvation, but also highlights novel cellular functions of the flowering integrator SOC1.

The plant circadian clock regulates autophagy rhythm through transcription factor LUX ARRHYTHMO

Autophagy is an evolutionarily conserved degradation pathway in eukaryotes; it plays a critical role in nutritional stress tolerance. The circadian clock is an endogenous timekeeping system that generates biological rhythms to adapt to daily changes in the environment. Accumulating evidence indicates that the circadian clock and autophagy are intimately interwoven in animals. However, the role of the circadian clock in regulating autophagy has been poorly elucidated in plants. Here, we show that autophagy exhibits a robust circadian rhythm in both light/dark cycle (LD) and in constant light (LL) in Arabidopsis. However, autophagy rhythm showed a different pattern with a phase-advance shift and a lower amplitude in LL compared to LD. Moreover, mutation of the transcription factor LUX ARRHYTHMO (LUX) removed autophagy rhythm in LL and led to an enhanced amplitude in LD. LUX represses expression of the core autophagy genes ATG2, ATG8a, and ATG11 by directly binding to their promoters. Phenotypic analysis revealed that LUX is responsible for improved resistance of plants to carbon starvation, which is dependent on moderate autophagy activity. Comprehensive transcriptomic analysis revealed that the autophagy rhythm is ubiquitous in plants. Taken together, our findings demonstrate that the LUX-mediated circadian clock regulates plant autophagy rhythms.

Processes and mechanisms of coastal woody-plant mortality

Observations of woody plant mortality in coastal ecosystems are globally widespread, but the overarching processes and underlying mechanisms are poorly understood. This knowledge deficiency, combined with rapidly changing water levels, storm surges, atmospheric CO₂ , and vapor pressure deficit, creates large predictive uncertainty regarding how coastal ecosystems will respond to global change. Here, we synthesize the literature on the mechanisms that underlie coastal woody-plant mortality, with the goal of producing a testable hypothesis framework. The key emergent mechanisms underlying mortality include hypoxic, osmotic, and ionic-driven reductions in whole-plant hydraulic conductance and photosynthesis that ultimately drive the coupled processes of hydraulic failure and carbon starvation. The relative importance of these processes in driving mortality, their order of progression, and their degree of coupling depends on the characteristics of the anomalous water exposure, on topographic effects, and on taxa-specific variation in traits and trait acclimation. Greater inundation exposure could accelerate mortality globally; however, the interaction of changing inundation exposure with elevated CO₂ , drought, and rising vapor pressure deficit could influence mortality likelihood. Models of coastal forests that incorporate the frequency and duration of inundation, the role of climatic drivers, and the processes of hydraulic failure and carbon starvation can yield improved estimates of inundation-induced woody-plant mortality.

Strategies of tree species to adapt to drought from leaf stomatal regulation and stem embolism resistance to root properties

Considerable evidences highlight the occurrence of increasing widespread tree mortality as a result of global climate change-associated droughts. However, knowledge about the mechanisms underlying divergent strategies of various tree species to adapt to drought has remained remarkably insufficient. Leaf stomatal regulation and embolism resistance of stem xylem serves as two important strategies for tree species to prevent hydraulic failure and carbon starvation, as comprising interconnected physiological mechanisms underlying drought-induced tree mortality. Hence, the physiological and anatomical determinants of leaf stomatal regulation and stems xylem embolism resistance are evaluated and discussed. In addition, root properties related to drought tolerance are also reviewed. Species with greater investment in leaves and stems tend to maintain stomatal opening and resist stem embolism under drought conditions. The coordination between stomatal regulation and stem embolism resistance are summarized and discussed. Previous studies showed that hydraulic safety margin (HSM, the difference between minimum water potential and that causing xylem dysfunction) is a significant predictor of tree species mortality under drought conditions. Compared with HSM, stomatal safety margin (the difference between water potential at stomatal closure and that causing xylem dysfunction) more directly merge stomatal regulation strategies with xylem hydraulic strategies, illustrating a comprehensive framework to characterize plant response to drought. A combination of plant traits reflecting species' response and adaptation to drought should be established in the future, and we propose four specific urgent issues as future research priorities.

The influence of increasing atmospheric CO2 , temperature, and vapor pressure deficit on seawater-induced tree mortality

Increasing seawater exposure is killing coastal trees globally, with expectations of accelerating mortality with rising sea levels. However, the impact of concomitant changes in atmospheric CO₂ concentration, temperature, and vapor pressure deficit (VPD) on seawater-induced tree mortality is uncertain. We examined the mechanisms of seawater-induced mortality under varying climate scenarios using a photosynthetic gain and hydraulic cost optimization model validated against observations in a mature stand of Sitka spruce (Picea sitchensis) trees in the Pacific Northwest, USA, that were dying from recent seawater exposure. The simulations matched well with observations of photosynthesis, transpiration, nonstructural carbohydrates concentrations, leaf water potential, the percentage loss of xylem conductivity, and stand-level mortality rates. The simulations suggest that seawater-induced mortality could decrease by c. 16.7% with increasing atmospheric CO₂ levels due to reduced risk of carbon starvation. Conversely, rising VPD could increase mortality by c. 5.6% because of increasing risk of hydraulic failure. Across all scenarios, seawater-induced mortality was driven by hydraulic failure in the first 2 yr after seawater exposure began, with carbon starvation becoming more important in subsequent years. Changing CO₂ and climate appear unlikely to have a significant impact on coastal tree mortality under rising sea levels.

Interaction of drought- and pathogen-induced mortality in Norway spruce and Scots pine

Pathogenic diseases frequently occur in drought-stressed trees. However, their contribution to the process of drought-induced mortality is poorly understood. We combined drought and stem inoculation treatments to study the physiological processes leading to drought-induced mortality in Norway spruce (Picea abies) and Scots pine (Pinus sylvestris) saplings infected with Heterobasidion annosum s.s. We analysed the saplings' water status, gas exchange, nonstructural carbohydrates (NSCs) and defence responses, and how they related to mortality. Saplings were followed for two growing seasons, including an artificially induced 3-month dormancy period. The combined drought and pathogen treatment significantly increased spruce mortality; however, no interaction between these stressors was observed in pine, although individually each stressor caused mortality. Our results suggest that pathogen infection decreased carbon reserves in spruce, reducing the capacity of saplings to cope with drought, resulting in increased mortality rates. Defoliation, relative water content and the starch concentration of needles were predictors of mortality in both species under drought and pathogen infection. Infection and drought stress create conflicting needs for carbon to compartmentalize the pathogen and to avoid turgor loss, respectively. Heterobasidion annosum reduces the functional sapwood area and shifts NSC allocation patterns, reducing the capacity of trees to cope with drought.

[Changes of non-structural carbohydrates and nitrogen contents of needles and twigs in Pinus sylvestris var. mongolica plantations along an aridity gradient]

With six Pinus sylvestris var. mongolica plantations (Huinan, Xifeng, Fujia, Zhanggutai, Naiman and Wulanaodu) along an aridity gradient in the Horqin sandy land, we examined the changes in non-structural carbohydrates (NSCs) and nitrogen (N) contents of current and one-year-old needles and twigs, to explore the carbon supply and demand status as well as the nutrient accumulation strategies of P. sylvestris var. mongolica under drought. The results showed that the contents of NSCs and soluble sugars in needles and twigs of P. sylvestris var. mongolica plantations significantly decreased with increasing aridity. From the most humid site (Huinan) to the most aridity site (Wulanaodu), the soluble sugar contents in current and one-year old needles of P. sylvestris var. mongolica decreased from 12.8% and 12.5% to 9.0% and 9.5%, respectively. The soluble sugar contents in current-year old twigs decreased from 15.6% to 9.2%. With increasing aridity, the starch contents in needles and twigs remained relatively stable, soluble sugars/starch ratio in current and one-year old needles decreased, the N contents in current and one-year old twigs significantly increased. The P. sylvestris var. mongolica plantations in the Horqin sandy land consumed soluble sugar storage under drought, resulting in a risk of mortality from 'carbon starvation'. P. sylvestris var. mongolica tended to maintain stable starch storage and accumulate N in twigs to cope with long-term drought stress.

Mutually inclusive mechanisms of drought-induced tree mortality

Unprecedented tree dieback across Central Europe caused by recent global change-type drought events highlights the need for a better mechanistic understanding of drought-induced tree mortality. Although numerous physiological risk factors have been identified, the importance of two principal mechanisms, hydraulic failure and carbon starvation, is still debated. It further remains largely unresolved how the local neighborhood composition affects individual mortality risk. We studied 9435 young trees of 12 temperate species planted in a diversity experiment in 2013 to assess how hydraulic traits, carbon dynamics, pest infestation, tree height and neighborhood competition influence individual mortality risk. Following the most extreme global change-type drought since record in 2018, one third of these trees died. Across species, hydraulic safety margins (HSMs) were negatively and a shift towards a higher sugar fraction in the non-structural carbohydrate (NSC) pool positively associated with mortality risk. Moreover, trees infested by bark beetles had a higher mortality risk, and taller trees a lower mortality risk. Most neighborhood interactions were beneficial, although neighborhood effects were highly species-specific. Species that suffered more from drought, especially Larix spp. and Betula spp., tended to increase the survival probability of their neighbors and vice versa. While severe tissue dehydration marks the final stage of drought-induced tree mortality, we show that hydraulic failure is interrelated with a series of other, mutually inclusive processes. These include shifts in NSC pools driven by osmotic adjustment and/or starch depletion as well as pest infestation and are modulated by the size and species identity of a tree and its neighbors. A more holistic view that accounts for multiple causes of drought-induced tree mortality is required to improve predictions of trends in global forest dynamics and to identify mutually beneficial species combinations.

Mutually inclusive mechanisms of drought-induced tree mortality

Unprecedented tree dieback across Central Europe caused by recent global change-type drought events highlights the need for a better mechanistic understanding of drought-induced tree mortality. Although numerous physiological risk factors have been identified, the importance of two principal mechanisms, hydraulic failure and carbon starvation, is still debated. It further remains largely unresolved how the local neighborhood composition affects individual mortality risk. We studied 9435 young trees of 12 temperate species planted in a diversity experiment in 2013 to assess how hydraulic traits, carbon dynamics, pest infestation, tree height and neighborhood competition influence individual mortality risk. Following the most extreme global change-type drought since record in 2018, one third of these trees died. Across species, hydraulic safety margins (HSMs) were negatively and a shift towards a higher sugar fraction in the non-structural carbohydrate (NSC) pool positively associated with mortality risk. Moreover, trees infested by bark beetles had a higher mortality risk, and taller trees a lower mortality risk. Most neighborhood interactions were beneficial, although neighborhood effects were highly species-specific. Species that suffered more from drought, especially Larix spp. and Betula spp., tended to increase the survival probability of their neighbors and vice versa. While severe tissue dehydration marks the final stage of drought-induced tree mortality, we show that hydraulic failure is interrelated with a series of other, mutually inclusive processes. These include shifts in NSC pools driven by osmotic adjustment and/or starch depletion as well as pest infestation and are modulated by the size and species identity of a tree and its neighbors. A more holistic view that accounts for multiple causes of drought-induced tree mortality is required to improve predictions of trends in global forest dynamics and to identify mutually beneficial species combinations.

Response of four evergreen savanna shrubs to an incidence of extreme drought: high embolism resistance, branch shedding and maintenance of nonstructural carbohydrates

Extreme drought events are becoming frequent globally, resulting in widespread plant mortality and forest dieback. Although savanna vegetation cover ~20% of the earth's land area, their responses to extreme drought have been less studied than that of forests. Herein, we quantified branch dieback, individual mortality and the associated physiological responses of four evergreen shrubs (Tarenna depauperate Hutch., Maytenus esquirolii (H. Lév.) C.Y. Cheng, Murraya exotica L., Jasminum nudiflorum Lindl.) in a savanna ecosystem in Southwest China to an incidence of extreme drought during 2019 and 2020. We found that 80-100% of the individuals of these species exhibited branch dieback, whereas individual mortality was only found in T. depauperate (4.5%). All species showed high resistance to stem embolism (P50, water potential at 50% loss of hydraulic conductivity ranged from -5.62 to -8.6 MPa), whereas the stem minimum water potentials reached -7.6 to ca -10.0 MPa during the drought. The low water potential caused high native embolism levels (percentage loss of hydraulic conductivity (PLC) 23-65%) in terminal branches, and the remaining stems maintained 15-35% PLC at the end of the drought. Large within-individual variations in stem vulnerability to embolism were detected, and shedding of vulnerable branches could be a mechanism for shrubs to reduce water and carbon consumption. Overall, the content of total nonstructural carbohydrates (NSC) and their components in the stem were generally comparable to or higher than those in the rainy season in three of the four species. Because the leaves were turgor-less for most time during the drought, high NSC levels during the drought could be due to recycling of NSC from dead branches or translocation from roots. Our results suggest high tolerance of savanna shrub species to extreme drought, which could be facilitated by high embolism resistance in some stems and shedding of vulnerable branches to maintain individual water and carbon balance.

Drought affects the fate of non-structural carbohydrates in hinoki cypress

Tree species that close stomata early in response to drought are likely to suffer from an imbalance between limited carbohydrate supply due to reduced photosynthesis and metabolic demand. Our objective was to clarify the dynamic responses of non-structural carbohydrates to drought in a water-saving species, the hinoki cypress (Chamaecyparis obtusa Sieb. et Zucc.). To this end, we pulse-labeled young trees with 13CO2 10 days after the beginning of the drought treatment. Trees were harvested 7 days later, early during drought progression, and 86 days later when they had suffered from a long and severe drought. The labeled carbon (C) was traced in phloem extract, in the organic matter and starch of all the organs, and in the soluble sugars (sucrose, glucose and fructose) of the most metabolically active organs (foliage, green branches and fine roots). No drought-related changes in labeled C partitioning between belowground and aboveground organs were observed. The C allocation between non-structural carbohydrates was altered early during drought progression: starch concentration was lower by half in the photosynthetic organs, while the concentration of almost all soluble sugars tended to increase. The preferential allocation of labeled C to glucose and fructose reflected an increased demand for soluble sugars for osmotic adjustment. After 3 months of a lethal drought, the concentrations of soluble sugars and starch were admittedly lower in drought-stressed trees than in the controls, but the pool of non-structural carbohydrates was far from completely depleted. However, the allocation to storage had been impaired by drought; photosynthesis and the sugar translocation rate had also been reduced by drought. Failure to maintain cell turgor through osmoregulation and to refill embolized xylem due to the depletion in soluble sugars in the roots could have resulted in tree mortality in hinoki cypress, though the total pool of carbohydrate was not completely depleted.

Melatonin delays dark-induced leaf senescence by inducing miR171b expression in tomato

Melatonin functions in multiple aspects of plant growth, development, and stress response. Nonetheless, the mechanism of melatonin in plant carbon metabolism remains largely unknown. In this study, we investigated the influence of melatonin on the degradation of starch in tomato leaves. Results showed that exogenous melatonin attenuated carbon starvation-induced chlorophyll degradation and leaf senescence. In addition, melatonin delayed leaf starch degradation and inhibited the transcription of starch-degrading enzymes after sunset. Interestingly, melatonin-alleviated symptoms of leaf senescence and starch degradation were compromised when the first key gene for starch degradation, α-glucan water dikinase (GWD), was overexpressed. Furthermore, exogenous melatonin significantly upregulated the transcript levels of several microRNAs, including miR171b. Crucially, the GWD gene was identified as a target of miR171b, and the overexpression of miR171b ameliorated the carbon starvation-induced degradation of chlorophyll and starch, and inhibited the expression of the GWD gene. Taken together, these results demonstrate that melatonin promotes plant tolerance against carbon starvation by upregulating the expression of miR171b, which can directly inhibit GWD expression in tomato leaves.

Tapping into the physiological responses to mistletoe infection during heat and drought stress

Mistletoes are important co-contributors to tree mortality globally, particularly during droughts. In Australia, mistletoe distributions are expanding in temperate woodlands, while their hosts have experienced unprecedented heat and drought stress in recent years. We investigated whether the excessive water use of mistletoes increased the probability of xylem emboli in a mature woodland during the recent record drought that was compounded by multiple heatwaves. We continuously recorded transpiration ($T_{SLA}$) of infected and uninfected branches from two eucalypt species over two summers, monitored stem and leaf water potentials ($\Psi $) and used hydraulic vulnerability curves to estimate percent loss in conductivity (PLC) for each species. Variations in weather (vapor pressure deficit, photosynthetically active radiation, soil water content), host species and % mistletoe foliage explained 78% of hourly $T_{SLA}$. While mistletoe acted as an uncontrollable sink for water in the host even during typical summer days, daily $T_{SLA}$ increased up to 4-fold in infected branches on hot days, highlighting the previously overlooked importance of temperature stress in amplifying water loss in mistletoes. The increased water use of mistletoes resulted in significantly decreased host $\Psi _{\rm{leaf}}$ and $\Psi _{\rm{trunk}}$. It further translated to an estimated increase of up to 11% PLC for infected hosts, confirming greater hydraulic dysfunction of infected trees that place them at higher risk of hydraulic failure. However, uninfected branches of Eucalyptus fibrosa F.Muell. had much tighter controls on water loss than uninfected branches of Eucalyptus moluccana Roxb., which shifted the risk of hydraulic failure towards an increased risk of carbon starvation for E. fibrosa. The contrasting mechanistic responses to heat and drought stress between both co-occurring species demonstrates the complexity of host-parasite interactions and highlights the challenge in predicting species-specific responses to biotic agents in a warmer and drier climate.

Tree hazards compounded by successive climate extremes after masting in a small endemic tree, Distylium lepidotum, on subtropical islands in Japan

Ongoing global warming increases the frequency and severity of tropical typhoons and prolonged drought, leading to forest degradation. Simultaneous and/or successive masting events and climatic extremes may thus occur frequently in the near future. If these climatic extremes occur immediately after mass seed reproduction, their effects on individual trees are expected to be very severe because mass reproduction decreases carbohydrate reserves. While the effects of either a single climate extreme or masting alone on tree resilience/growth have received past research attention, understanding the cumulative effects of such multiple events remains challenging and is crucial for predicting future forest changes. Here, we report tree hazards compound by two successive climate extremes, a tropical typhoon and prolonged drought, after mass reproduction in an endemic tree species (Distylium lepidotum Nakai) on oceanic islands. Across individual trees, the starch stored within the sapwood of branchlets significantly decreased with reproductive efforts (fruit mass/shoot mass ratio). Typhoon damage significantly decreased not only the total leaf area of apical shoots but also the maximum photosynthetic rates. During the 5-month period after the typhoon, the mortality of large branchlets (8-10-mm diameter) increased with decreasing stored starch when the typhoon hit. During the prolonged summer drought in the next year, the recovery of total leaf area, stored starch, and hydraulic conductivity was negatively correlated with the stored starch at the typhoon. These data indicate that the level of stored starch within branchlets is the driving factor determining tree regrowth or dieback, and the restoration of carbohydrates after mass reproduction is synergistically delayed by such climate extremes. Stored carbohydrates are the major cumulative factor affecting individual tree resilience, resulting in their historical effects. Because of highly variable carbohydrate levels among individual trees, the resultant impacts of such successive events on forest dieback will be fundamentally different among trees.

Storage of carbon reserves in spruce trees is prioritized over growth in the face of carbon limitation

Climate change is expected to pose a global threat to forest health by intensifying extreme events like drought and insect attacks. Carbon allocation is a fundamental process that determines the adaptive responses of long-lived late-maturing organisms like trees to such stresses. However, our mechanistic understanding of how trees coordinate and set allocation priorities among different sinks (e.g., growth and storage) under severe source limitation remains limited. Using flux measurements, isotopic tracing, targeted metabolomics, and transcriptomics, we investigated how limitation of source supply influences sink activity, particularly growth and carbon storage, and their relative regulation in Norway spruce (Picea abies) clones. During photosynthetic deprivation, absolute rates of respiration, growth, and allocation to storage all decline. When trees approach neutral carbon balance, i.e., daytime net carbon gain equals nighttime carbon loss, genes encoding major enzymes of metabolic pathways remain relatively unaffected. However, under negative carbon balance, photosynthesis and growth are down-regulated while sucrose and starch biosynthesis pathways are up-regulated, indicating that trees prioritize carbon allocation to storage over growth. Moreover, trees under negative carbon balance actively increase the turnover rate of starch, lipids, and amino acids, most likely to support respiration and mitigate stress. Our study provides molecular evidence that trees faced with severe photosynthetic limitation strategically regulate storage allocation and consumption at the expense of growth. Understanding such allocation strategies is crucial for predicting how trees may respond to extreme events involving steep declines in photosynthesis, like severe drought, or defoliation by heat waves, late frost, or insect attack.

Same Season and Carry-Over Effects of Source-Sink Adjustments on Grapevine Yields and Non-structural Carbohydrates

The grapevine (Vitis vinifera L.) is managed to balance the ratio of leaf area (source) to fruit mass (sink). Over cropping in the grapevine may reveal itself as spontaneous fruit abortion, delayed ripening, or as alternate bearing. The aim of this work was to study the same season and carry-over effects of manipulating source to sink ratios on grapevine phenology, leaf gas exchange, yield components, berry soluble solids accumulation, and reserve carbohydrate and soluble sugar concentration in roots. Cabernet Sauvignon grapevines were subjected to defoliation (33, 66, and 100% of the leaves retained) and fruit removal treatments (33, 66, and 100% of clusters retained) arranged in a factorial design. Results from two seasons of source-sink manipulations were substantially different. In both seasons defoliation treatments affected season-long net carbon assimilation (A _N ) and stomatal conductance (g _s ) where the less leaves were retained, the greater the A _N and g _s , and fruit removal had no impact on leaf gas exchange. In the first season, leaf area to fruit mass was hardly related to berry soluble solids and in the second season they were strongly correlated, suggesting a degree of acclimation. Defoliation treatments had great impacts on berry size, berries per cluster, and total soluble solids in both years. Fruit removal treatments only had effects on berry mass and berries per cluster in the first season, and only on berry soluble solids in the second. The predominant effect of defoliation (carbon starvation) cascaded onto reducing root starch content, root mass and delaying of veraison and leaf senescence, as well as harvest which was delayed up to 9 weeks with 33% of the leaves retained. In a third season, where grapevines grew without treatments, defoliation treatments had resultant carryover effects, including reduced leaf area, number of berries per cluster, clusters per vine, and yield, but not on leaf gas exchange dependent on previous seasons' severity of defoliation. Balancing source-to-sink ratio is crucial to obtain an adequate speed of ripening. However, this was the culmination of a more complex whole-plant regulation where the number of leaves (source strength) outweighed the effects of fruits (sink strength).

Shade-induced reduction of stem nonstructural carbohydrates increases xylem vulnerability to embolism and impedes hydraulic recovery in Populus nigra

Nonstructural carbohydrates (NSCs) have been suggested to affect xylem transport under fluctuating water availability, but conclusive evidence is still lacking. We tested the effect of shade-induced NSC depletion on xylem vulnerability to embolism and hydraulic recovery on Populus nigra saplings. Vulnerability was assessed in light-exposed (L) and shaded (S) plants with the hydraulic method, and in vivo with the optical method and X-ray micro-computed tomography. Plants were stressed to 80% loss of hydraulic conductance (PLC) and re-irrigated to check for possible recovery. We measured PLC, bark and wood NSC content, as well as xylem sap pH, surface tension (γ_sap ) and sugar concentration, before, during and after drought. Shading induced depletion of stem NSC (mainly starch) reserves. All methods converged in indicating higher xylem vulnerability in S than in L plants. This difference was not explained by xylem vessel and pit anatomy or by γ_sap . Shading impeded sap acidification and sugar accumulation during drought in S plants and prevented hydraulic recovery, which was observed in L plants. Our results highlight the importance of stem NSCs to sustain xylem hydraulic functioning during drought and suggest that light and/or adequate stem NSC thresholds are required to trigger xylem sap chemical changes involved in embolism recovery.

Temporal controls on crown nonstructural carbohydrates in southwestern US tree species

In trees, large uncertainties remain in how nonstructural carbohydrates (NSCs) respond to variation in water availability in natural, intact ecosystems. Variation in NSC pools reflects temporal fluctuations in supply and demand, as well as physiological coordination across tree organs in ways that differ across species and NSC fractions (e.g., soluble sugars vs starch). Using landscape-scale crown (leaves and twigs) NSC concentration measurements in three foundation tree species (Populus tremuloides, Pinus edulis, Juniperus osteosperma), we evaluated in situ, seasonal variation in NSC responses to moisture stress on three timescales: short-term (via predawn water potential), seasonal (via leaf δ13C) and annual (via current year's ring width index). Crown NSC responses to moisture stress appeared to depend on hydraulic strategy, where J. osteosperma appears to regulate osmotic potentials (via higher sugar concentrations), P. edulis NSC responses suggest respiratory depletion and P. tremuloides responses were consistent with direct sink limitations. We also show that overly simplistic models can mask seasonal and tissue variation in NSC responses, as well as strong interactions among moisture stress at different timescales. In general, our results suggest large seasonal variation in crown NSC concentrations reflecting the multiple cofunctions of NSCs in plant tissues, including storage, growth and osmotic regulation of hydraulically vulnerable leaves. We emphasize that crown NSC pool size cannot be viewed as a simple physiological metric of stress; in situ NSC dynamics are complex, varying temporally, across species, among NSC fractions and among tissue types.

Plant carbohydrate depletion impairs water relations and spreads via ectomycorrhizal networks

Under prolonged drought and reduced photosynthesis, plants consume stored nonstructural carbohydrates (NSCs). Stored NSC depletion may impair the regulation of plant water balance, but the underlying mechanisms are poorly understood, and whether such mechanisms are independent of plant water deficit is not known. If so, carbon costs of fungal symbionts could indirectly influence plant drought tolerance through stored NSC depletion. We connected well-watered Pinus ponderosa seedling pairs via ectomycorrhizal (EM) networks where one seedling was shaded (D) and the other kept illuminated (LD) and compared responses to seedling pairs in full light (L). We measured plant NSCs, osmotic and water potential, and transfer of ¹³ CO₂ through EM to explore mechanisms linking stored NSCs to plant water balance regulation and identify potential tradeoffs between plant water retention and EM fungi under carbon-limiting conditions. NSCs decreased from L to LD to D seedlings. Even without drought, NSC depletion impaired osmoregulation and turgor maintenance, both of which are critical for drought tolerance. Importantly, EM networks propagated NSC depletion and its negative effects on water retention from carbon stressed to nonstressed hosts. We demonstrate that NSC storage depletion influences turgor maintenance independently of plant water deficit and reveal carbon allocation tradeoffs between supporting fungal symbionts and retaining water.

An arabinose-induced enhancement of asexual reproduction and concomitant changes in metabolic state in the filamentous fungus Bipolaris maydis

l-Arabinose, a major constituent pentose of plant cell-wall polysaccharides, has been suggested to be a less preferred carbon source for fungi but to be a potential signalling molecule that can cause distinct genome-wide transcriptional changes in fungal cells. Here, we explore the possibility that this unique pentose influences the morphological characteristics of the phytopathogenic fungus Bipolaris maydis strain HITO7711. When grown on plate media under different sugar conditions, the mycelial dry weight of cultures on l-arabinose was as low as that with no sugar, suggesting that l-arabinose does not substantially contribute to vegetative growth. However, the intensity of conidiation on l-arabinose was comparable to or even higher than that on d-glucose and on d-xylose, in contrast to the poor conidiation under the no-sugar condition. To explore the physiological basis of the passive growth and active conidiation on l-arabinose, we next investigated cellular responses of the fungus to these sugar conditions. Transcriptional analysis of genes related to carbohydrate metabolism showed that l-arabinose stimulates carbohydrate utilization through the hexose monophosphate shunt (HMP shunt), a catabolic pathway parallel to glycolysis and which participates in the generation of the reducing agent NADPH (the reduced form of nicotinamide adenine dinucleotide phosphate). Then, the HMP shunt was impaired by disrupting the related gene BmZwf1, which encodes glucose-6-phosphate dehydrogenase in this fungus. The resulting mutants on l-arabinose showed remarkably decreased conidiation, but a conversely increased mycelial dry weight compared with the wild-type. Our study demonstrates that l-arabinose acts to enhance resource allocation to asexual reproduction in B. maydis HITO7711 at the cost of vegetative growth, and suggests that this is mediated by the concomitant stimulation of the HMP shunt.

Mortality predispositions of conifers across western USA

Conifer mortality rates are increasing in western North America, but the physiological mechanisms underlying this trend are not well understood. We examined tree-ring-based radial growth along with stable carbon (C) and oxygen (O) isotope composition (δ¹³ C and δ¹⁸ O, respectively) of dying and surviving conifers at eight old-growth forest sites across a strong moisture gradient in the western USA to retrospectively investigate mortality predispositions. Compared with surviving trees, lower growth of dying trees was detected at least one decade before mortality at seven of the eight sites. Intrinsic water-use efficiency increased over time in both dying and surviving trees, with a weaker increase in dying trees at five of the eight sites. C starvation was a strong correlate of conifer mortality based on a conceptual model incorporating growth, δ¹³ C, and δ¹⁸ O. However, this approach does not capture processes that occur in the final months of survival. Ultimately, C starvation may lead to increased mortality vulnerability, but hydraulic failure or biotic attack may dominate the process during the end stages of mortality in these conifers.

Vacuolar processing enzyme translocates to the vacuole through the autophagy pathway to induce programmed cell death

The caspase-like vacuolar processing enzyme (VPE) is a key factor in programmed cell death (PCD) associated with plant stress responses. Growth medium lacking a carbon source and dark conditions caused punctate labeling of 35S::VPE1-GFP (StVPE1-GFP) in potato leaves. Under conditions of carbon starvation, VPE activity and PCD symptoms strongly increased in BY-2 cells, but to a much lesser extent in VPE-RNAi BY-2 cells. During extended exposure to carbon starvation, VPE expression and activity levels peaked, with a gradual increase in BY-2 cell death. Histological analysis of StVPE1-GFP in BY-2 cells showed that carbon starvation induces its translocation from the endoplasmic reticulum to the central vacuole through tonoplast engulfment. Exposure of BY-2 culture to the macroautophagy/autophagy inhibitor concanamycin A led to, along with an accumulation of autophagic bodies, accumulation of StVPE1-GFP in the cell vacuole. This accumulation did not occur in the presence of 3-methyladenine, an inhibitor of early-stage autophagy. BY-2 cells constitutively expressing RFP-StATG8IL, an autophagosome marker, showed colocalization with the StVPE1-GFP protein in the cytoplasm and vacuole. RNAi silencing of the core autophagy component ATG4 in BY-2 cells reduced VPE activity and cell death. These results are the first to suggest that VPE translocates to the cell vacuole through the autophagy pathway, leading to PCD.Abbreviations: ATG: autophagy related; CLP: caspase-like protease; HR: hypersensitive response; PCD: programmed cell death; St: Solanum tuberosum; VPE: vacuolar processing enzyme.

EXO70D isoforms mediate selective autophagic degradation of type-A ARR proteins to regulate cytokinin sensitivity

The phytohormone cytokinin influences many aspects of plant growth and development, several of which also involve the cellular process of autophagy, including leaf senescence, nutrient remobilization, and developmental transitions. The Arabidopsis type-A response regulators (type-A ARR) are negative regulators of cytokinin signaling that are transcriptionally induced in response to cytokinin. Here, we describe a mechanistic link between cytokinin signaling and autophagy, demonstrating that plants modulate cytokinin sensitivity through autophagic regulation of type-A ARR proteins. Type-A ARR proteins were degraded by autophagy in an AUTOPHAGY-RELATED (ATG)5-dependent manner, and this degradation is promoted by phosphorylation on a conserved aspartate in the receiver domain of the type-A ARRs. EXO70D family members interacted with type-A ARR proteins, likely in a phosphorylation-dependent manner, and recruited them to autophagosomes via interaction of the EXO70D AIM with the core autophagy protein, ATG8. Consistently, loss-of-function exo70D1,2,3 mutants exhibited compromised targeting of type-A ARRs to autophagic vesicles, have elevated levels of type-A ARR proteins, and are hyposensitive to cytokinin. Disruption of both type-A ARRs and EXO70D1,2,3 compromised survival in carbon-deficient conditions, suggesting interaction between autophagy and cytokinin responsiveness in response to stress. These results indicate that the EXO70D proteins act as selective autophagy receptors to target type-A ARR cargos for autophagic degradation, demonstrating modulation of cytokinin signaling by selective autophagy.

Regulation of mRNA Stability During Bacterial Stress Responses

Bacteria have a remarkable ability to sense environmental changes, swiftly regulating their transcriptional and posttranscriptional machinery as a response. Under conditions that cause growth to slow or stop, bacteria typically stabilize their transcriptomes in what has been shown to be a conserved stress response. In recent years, diverse studies have elucidated many of the mechanisms underlying mRNA degradation, yet an understanding of the regulation of mRNA degradation under stress conditions remains elusive. In this review we discuss the diverse mechanisms that have been shown to affect mRNA stability in bacteria. While many of these mechanisms are transcript-specific, they provide insight into possible mechanisms of global mRNA stabilization. To that end, we have compiled information on how mRNA fate is affected by RNA secondary structures; interaction with ribosomes, RNA binding proteins, and small RNAs; RNA base modifications; the chemical nature of 5' ends; activity and concentration of RNases and other degradation proteins; mRNA and RNase localization; and the stringent response. We also provide an analysis of reported relationships between mRNA abundance and mRNA stability, and discuss the importance of stress-associated mRNA stabilization as a potential target for therapeutic development.

Molecular and physiological characterization of the monosaccharide transporters gene family in Medicago truncatula

Monosaccharide transporters (MSTs) represent key components of the carbon transport and partitioning mechanisms in plants, mediating the cell-to-cell and long-distance distribution of a wide variety of monosaccharides. In this study, we performed a thorough structural, molecular, and physiological characterization of the monosaccharide transporter gene family in the model legume Medicago truncatula. The complete set of MST family members was identified with a novel bioinformatic approach. Prolonged darkness was used as a test condition to identify the relevant transcriptomic and metabolic responses combining MST transcript profiling and metabolomic analysis. Our results suggest that MSTs play a pivotal role in the efficient partitioning and utilization of sugars, and possibly in the mechanisms of carbon remobilization in nodules upon photosynthate-limiting conditions, as nodules are forced to acquire a new role as a source of both C and N.

Genomewide Stabilization of mRNA during a "Feast-to-Famine" Growth Transition in Escherichia coli

The ability to rapidly respond to changing nutrients is crucial for E. coli to survive in many environments, including the gut. Reorganization of gene expression is the first step used by bacteria to adjust their metabolism accordingly. It involves fine-tuning of both transcription (transcriptional regulation) and mRNA stability (posttranscriptional regulation). While the forms of transcriptional regulation have been extensively studied, the role of mRNA stability during a metabolic switch is poorly understood. Investigating E. coli genomewide transcriptome and mRNA stability during metabolic transitions representative of the carbon source fluctuations in many environments, we have documented the role of mRNA stability in the response to nutrient changes. mRNAs are globally stabilized during carbon depletion. For a few genes, this leads directly to expression upregulation. As these genes are regulators of stress responses and metabolism, our work sheds new light on the likely importance of posttranscriptional regulations in response to environmental stress.

Bacteria have to continuously adjust to nutrient fluctuations from favorable to less-favorable conditions and in response to carbon starvation. The glucose-acetate transition followed by carbon starvation is representative of such carbon fluctuations observed in Escherichia coli in many environments. Regulation of gene expression through fine-tuning of mRNA pools constitutes one of the regulation levels required for such a metabolic adaptation. It results from both mRNA transcription and degradation controls. However, the contribution of transcript stability regulation in gene expression is poorly characterized. Using combined transcriptome and mRNA decay analyses, we investigated (i) how transcript stability changes in E. coli during the glucose-acetate-starvation transition and (ii) if these changes contribute to gene expression changes. Our work highlights that transcript stability increases with carbon depletion. Most of the stabilization occurs at the glucose-acetate transition when glucose is exhausted, and then stabilized mRNAs remain stable during acetate consumption and carbon starvation. Meanwhile, expression of most genes is downregulated and we observed three times less gene expression upregulation. Using control analysis theory on 375 genes, we show that most of gene expression regulation is driven by changes in transcription. Although mRNA stabilization is not the controlling phenomenon, it contributes to the emphasis or attenuation of transcriptional regulation. Moreover, upregulation of 18 genes (33% of our studied upregulated set) is governed mainly by transcript stabilization. Because these genes are associated with responses to nutrient changes and stress, this underscores a potentially important role of posttranscriptional regulation in bacterial responses to nutrient starvation.

IMPORTANCE The ability to rapidly respond to changing nutrients is crucial for E. coli to survive in many environments, including the gut. Reorganization of gene expression is the first step used by bacteria to adjust their metabolism accordingly. It involves fine-tuning of both transcription (transcriptional regulation) and mRNA stability (posttranscriptional regulation). While the forms of transcriptional regulation have been extensively studied, the role of mRNA stability during a metabolic switch is poorly understood. Investigating E. coli genomewide transcriptome and mRNA stability during metabolic transitions representative of the carbon source fluctuations in many environments, we have documented the role of mRNA stability in the response to nutrient changes. mRNAs are globally stabilized during carbon depletion. For a few genes, this leads directly to expression upregulation. As these genes are regulators of stress responses and metabolism, our work sheds new light on the likely importance of posttranscriptional regulations in response to environmental stress.

Cystoliths of Parietaria judaica can serve as an internal source of CO2 for photosynthetic assimilation when stomata are closed

The recently reported 'alarm photosynthesis' acts as a biochemical process that assimilates CO2 derived from the decomposition of calcium oxalate crystals. This study examined whether CaCO3 cystoliths could also serve as CO2 pools, fulfilling a similar role. Shoots of Parietaria judaica were subjected to carbon starvation, abscisic acid (ABA), or bicarbonate treatments, and the volume of cystoliths and the photochemical parameters of photosystem II (PSII) were determined. The size of cystoliths was reduced under carbon starvation or ABA treatments, whereas it was restored by xylem-provided bicarbonate. Under carbon starvation, ABA, or bicarbonate treatments, the photochemical efficiency of PSII was higher, while non-photochemical quenching, representing the safe dissipation of excess PSII energy due to lack of electron sinks, was lower in treated samples compared with controls. This observation suggests the involvement of ABA or other carbon starvation cues in the release of subsidiary CO2 for photosynthesis, inevitably from an internal source, which could be the cystoliths. Carbon remobilized from cystoliths can be photosynthetically assimilated, thus acting as a safety valve under stress. Together with alarm photosynthesis, these results show a tight link between leaf carbon deposits and photosynthesis.

Interaction of stomatal behaviour and vulnerability to xylem cavitation determines the drought response of three temperate tree species

How the mortality and growth of tree species vary with the iso-anisohydric continuum and xylem vulnerability is still being debated. We conducted a precipitation reduction experiment to create a mild drought condition in a forest in the Baotianman Mountains, China, a sub-humid region. Three main sub-canopy tree species in this region were examined. After rainfall reduction, Lindera obtusiloba showed severe dieback, but two other co-occurring species did not show dieback. The water potential at stomatal closure of Dendrobenthamia japonica, L. obtusiloba and Sorbus alnifolia was -1.70, -2.54 and -3.41 MPa, respectively, whereas the water potential at 88 % loss in hydraulic conductivity of the three species was -2.31, -2.11 and -7.01 MPa, respectively. Taken together, near-anisohydric L. obtusiloba with vulnerable xylem was highly susceptible to drought dieback. Anisohydric S. alnifolia had the most negative minimum water potential, and its xylem was the most resistant to cavitation. Isohydric D. japonica conserved water by rapidly closing its stomata. Ultimately, the hydraulic safety margin (HSM) of L. obtusiloba was the smallest among the three species, especially in precipitation-reduced plots. In terms of the stomatal safety margin (SSM), L. obtusiloba was negative, while S. alnifolia and D. japonica were positive. Of the two species without dieback, rainfall reduction decreased growth of D. japonica, but did not influence growth of S. Alnifolia; meanwhile, rainfall reduction led to a decrease of non-structural carbohydrates (NSCs) in D. japonica, but an increase in S. alnifolia. It is concluded that HSM as well as SSM allow interpreting the sensitivity of the three sub-canopy species to drought. The drought-induced dieback of L. obtusiloba is determined by the interaction of stomatal behaviour and xylem vulnerability, and the species could be sensitive to climate change-caused drought although still in sub-humid areas. The isohydric/anisohydric degree is associated with NSCs status and growth of plants.

[Changes of non-structural carbohydrates in Caryopteris mongolica seedlings during the process of drought-induced mortality]

The changes and distribution of non-structural carbohydrate (NSC, including soluble sugar and starch) content in different organs of one-year-old Caryopteris mongolica seedlings were investigated under suitable water condition (CK), slow-dying drought stress, and fast-dying drought stress. There was no significant difference in soluble sugar content of all organs between slow-dying drought stress and CK. With the extended duration of drought, the soluble sugar content in stem increased firstly and then decreased, while starch and NSC contents decreased. The soluble sugar content in coarse roots decreased, while starch and NSC contents increased. The soluble sugar content in leaves increased, while starch and NSC contents of leaves decreased. The NSC content of leaves, stems, coarse roots and fine roots were 6.2%, 7.8%, 8.3% and 7.4% at the death time (80 days), respectively. Under fast-dying drought stress, soluble sugar content in all organs was higher than that in CK, while starch and NSC contents were lower than that in CK. With the increasing time, soluble sugar content of roots decreased, while starch and NSC contents increased. The soluble sugar, starch and NSC contents in stems increased. The soluble sugar content of leaves increased, while starch and NSC contents decreased. The NSC content of leaves, stems, coarse roots and fine roots were 5.9%, 6.6%, 8.9% and 7.7% at lethal time (30 days), respectively. Under different drought stress, non-structural carbohydrates among different organs of C. mongolica seedlings showed different dynamics. Under slow-dying drought stress, NSC gave priority to allocate energy for maintaining physiological metabolism of organs. Under fast-dying drought stress, NSC mainly maintained plant metabolism in the form of soluble sugar, regulated osmotic potential, promoted water absorption, and coped with drastic drought stress.

Drought-induced mortality in Scots pine: opening the metabolic black box

Forests are sensitive to droughts, which increase the mortality rate of tree species. Various processes have been proposed to underlie drought-induced tree mortality, including hydraulic failure, carbon starvation and increased susceptibility to natural enemies. To give insights into these processes, we assessed the metabolic effects of a mortality-inducing drought on seedlings of Pinus sylvestris L. (Scots Pine), a widespread and important Eurasian species. We found divergence over time in the foliar metabolic composition of droughted vs well-watered seedlings, with the former showing increased abundance of aromatic amino acids and decreases in secondary metabolism associated with defence. We observed no significant differences amongst provenances in these effects: seedlings from drought-prone areas showed the same foliar metabolic changes under drought as seedlings from moist environments, although morphological effects of drought varied by provenance. Overall, our results demonstrate how severe drought prior to death may target particular primary and secondary metabolic pathways, weakening defences against natural enemies and contributing to the risk of drought-induced mortality in P. sylvestris.

Plant water content integrates hydraulics and carbon depletion to predict drought-induced seedling mortality

Widespread drought-induced forest mortality (DIM) is expected to increase with climate change and drought, and is expected to have major impacts on carbon and water cycles. For large-scale assessment and management, it is critical to identify variables that integrate the physiological mechanisms of DIM and signal risk of DIM. We tested whether plant water content, a variable that can be remotely sensed at large scales, is a useful indicator of DIM risk at the population level. We subjected Pinus ponderosa Douglas ex C. Lawson seedlings to experimental drought using a point of no return experimental design. Periodically during the drought, independent sets of seedlings were sampled to measure physiological state (volumetric water content (VWC), percent loss of conductivity (PLC) and non-structural carbohydrates) and to estimate population-level probability of mortality through re-watering. We show that plant VWC is a good predictor of population-level DIM risk and exhibits a threshold-type response that distinguishes plants at no risk from those at increasing risk of mortality. We also show that plant VWC integrates the mechanisms involved in individual tree death: hydraulic failure (PLC), carbon depletion across organs and their interaction. Our results are promising for landscape-level monitoring of DIM risk.

Identifying the relevant carbohydrate storage pools available for remobilization in aspen roots

Nonstructural carbohydrate (NSC) remobilization remains poorly understood in trees. In particular, it remains unclear (i) which tissues (e.g., living bark or xylem) and compounds (sugars or starch) in woody plants are the main sources of remobilized carbon, (ii) to what extent these NSC pools can be depleted and (iii) whether initial NSC mass or concentration is a better predictor of regrowth potential following disturbance. To address these questions, we collected root segments from a large mature trembling aspen stand; we then allowed them to resprout (sucker) in the dark and remobilize NSC until all sprouts had died. We found that initial starch mass, not concentration, was the best predictor of subsequent sprout mass. In total, more NSC mass (~4×) was remobilized from the living inner bark than the xylem of the roots. After resprouting, root starch was generally depleted to <0.6% w/w in both tissues. In contrast, a large portion of sugars appear unavailable for remobilization: sugar concentrations were only reduced to 12% w/w in the bark and 2% in the xylem. These findings suggest that in order to test whether plant processes like resprouting are limited by storage we need to (i) measure storage in the living bark, not just the xylem, (ii) consider storage pool size-not just concentration-and (iii) carefully determine which compounds are actually components of the storage pool.

mRNA Degradation Rates Are Coupled to Metabolic Status in Mycobacterium smegmatis

The logistics of tuberculosis therapy are difficult, requiring multiple drugs for many months. Mycobacterium tuberculosis survives in part by entering nongrowing states in which it is metabolically less active and thus less susceptible to antibiotics. Basic knowledge on how M. tuberculosis survives during these low-metabolism states is incomplete, and we hypothesize that optimized energy resource management is important. Here, we report that slowed mRNA turnover is a common feature of mycobacteria under energy stress but is not dependent on the mechanisms that have generally been postulated in the literature. Finally, we found that mRNA stability and growth status can be decoupled by a drug that causes growth arrest but increases metabolic activity, indicating that mRNA stability responds to metabolic status rather than to growth rate per se. Our findings suggest a need to reorient studies of global mRNA stabilization to identify novel mechanisms that are presumably responsible.

The success of Mycobacterium tuberculosis as a human pathogen is due in part to its ability to survive stress conditions, such as hypoxia or nutrient deprivation, by entering nongrowing states. In these low-metabolism states, M. tuberculosis can tolerate antibiotics and develop genetically encoded antibiotic resistance, making its metabolic adaptation to stress crucial for survival. Numerous bacteria, including M. tuberculosis, have been shown to reduce their rates of mRNA degradation under growth limitation and stress. While the existence of this response appears to be conserved across species, the underlying bacterial mRNA stabilization mechanisms remain unknown. To better understand the biology of nongrowing mycobacteria, we sought to identify the mechanistic basis of mRNA stabilization in the nonpathogenic model Mycobacterium smegmatis. We found that mRNA half-life was responsive to energy stress, with carbon starvation and hypoxia causing global mRNA stabilization. This global stabilization was rapidly reversed when hypoxia-adapted cultures were reexposed to oxygen, even in the absence of new transcription. The stringent response and RNase levels did not explain mRNA stabilization, nor did transcript abundance. This led us to hypothesize that metabolic changes during growth cessation impact the activities of degradation proteins, increasing mRNA stability. Indeed, bedaquiline and isoniazid, two drugs with opposing effects on cellular energy status, had opposite effects on mRNA half-lives in growth-arrested cells. Taken together, our results indicate that mRNA stability in mycobacteria is not directly regulated by growth status but rather is dependent on the status of energy metabolism.

Evidence of a seasonal trade-off between growth and starch storage in declining beeches: assessment through stem radial increment, non-structural carbohydrates and intra-ring δ13C

Forest decline is reported in recent decades all over the world. However, developing a clear vision of the associated tree dysfunctioning is still a challenge for plant physiologists. In this study, our aim was to examine the seasonal carbon adjustments of beech trees in the case of a long-term drought-induced decline. We compared healthy and declining trees in terms of stem radial growth, phloem sugar content and δ13C, together with xylem carbohydrates and intra-ring δ13C patterns. The radial growth of declining trees was clearly reduced by lower growth rates and shorter growing season length (44 days compared with healthy trees). The soluble sugar content was higher in the xylem of declining trees compared with the healthy ones, but similar in the phloem except at the end of their growth. Declining trees increased their levels of xylem starch content from budburst until the date of maximal growth rate. These reserve dynamics revealed an early trade-off between radial growth and starch storage that might be the result of an active or passive process. For declining trees, the slight decrease of intra-ring cellulose δ13C pattern during the early growing season was attributed to the synthesis of 13C enriched starch. For healthy trees, δ13C patterns were characterized by a progressive 13C increase along the ring, attributed to increased water-use efficiency (WUE) in response to decreased water availability. Individual variations of the crown area were negatively correlated to the intra-ring δ13C amplitude, which was ascribed to variations in canopy WUE and resource competition for healthy trees and partly to variations in the amount of reserves accumulated during spring for declining ones. Our study highlights the carbon physiological adjustment of declining trees towards reducing spring growth while storing starch, which can be reflected in the individual intra-ring cellulose δ13C patterns.

[Changes of non-structural carbohydrates of Pinus sylvestris var. mongolica seedlings in the process of drought-induced mortality]

To understand the distribution of non-structural carbohydrates (NSC) and adaptive mechanism in the process of drought-induced mortality, two-year-old Pinus sylvestris var. mongolica seedlings were grown under continuous natural drought condition. Needle water potential and the contents of soluble sugar, starch and total NSC in different organs (current-year-old needles, one-year-old needles, stems, coarse roots and fine roots) of the seedlings were measured when soil water content decreased to 60%, 40%, 30%, 20% and 15% of the soil field water capacity (SFC). The results showed that when the soil water content decreased from 40% SFC to 15% SFC, there was no significant change in needle water potential at predawn and midday. When soil water content decreased from 60% SFC to 30% SFC, the contents of soluble sugar, starch, total NSC and the ratio of soluble sugar and starch first decreased and then increased in all organs. When soil water content dropped from 30% SFC to 20% SFC, the soluble sugar, starch and total NSC contents decreased in the current-year-old needles, one-year-old needles, stems and fine roots. The soluble sugar content increased, but the starch and total NSC contents decreased in the coarse roots. When soil water content decreased from 20% SFC to 15% SFC, the contents of soluble sugar, starch and total NSC decreased in the current-year-old needles, one-year-old needles and stems, and the soluble sugar and total NSC contents decreased, but the starch content increased in the coarse roots, the soluble sugar content decreased, but the starch and total NSC contents increased in fine roots. The results indicated that NSC content in different organs of P. sylvestris var. mongolica seedlings varied in their adaptation to different degrees of drought. The contents of soluble sugar and total NSC in seedlings decreased under less than 30% of the soil field water capacity, with the starch being accumulated in the coarse roots and fine roots. The seedlings might be died due to carbon depletion.

JAZ repressors of metabolic defense promote growth and reproductive fitness in Arabidopsis

The plant hormone jasmonate promotes resistance to plant-eating organisms, ranging from pathogenic microbes to mammals. Jasmonate reprograms metabolism to fuel the production of diverse defense compounds and simultaneously inhibits plant growth. Understanding how growth is influenced across a range of defense levels remains unclear, but has important implications for optimizing crop productivity. Using a genetic approach to “tune” the jasmonate response, we assessed the physiological consequences of discrete levels of defense throughout the plant life cycle. Overactivation of jasmonate response led to carbon starvation, near loss of seed production and, under extreme conditions, lethality. Our findings explain the emergence of diverse strategies to keep jasmonate responses at bay and provide new insights into metabolic processes that underlie growth–defense trade-offs.

Plant immune responses mediated by the hormone jasmonoyl-l-isoleucine (JA-Ile) are metabolically costly and often linked to reduced growth. Although it is known that JA-Ile activates defense responses by triggering the degradation of JASMONATE ZIM DOMAIN (JAZ) transcriptional repressor proteins, expansion of the JAZ gene family in vascular plants has hampered efforts to understand how this hormone impacts growth and other physiological tasks over the course of ontogeny. Here, we combined mutations within the 13-member Arabidopsis JAZ gene family to investigate the effects of chronic JAZ deficiency on growth, defense, and reproductive output. A higher-order mutant (jaz decuple, jazD) defective in 10 JAZ genes (JAZ1–7, -9, -10, and -13) exhibited robust resistance to insect herbivores and fungal pathogens, which was accompanied by slow vegetative growth and poor reproductive performance. Metabolic phenotypes of jazD discerned from global transcript and protein profiling were indicative of elevated carbon partitioning to amino acid-, protein-, and endoplasmic reticulum body-based defenses controlled by the JA-Ile and ethylene branches of immunity. Resource allocation to a strong defense sink in jazD leaves was associated with increased respiration and hallmarks of carbon starvation but no overt changes in photosynthetic rate. Depletion of the remaining JAZ repressors in jazD further exaggerated growth stunting, nearly abolished seed production and, under extreme conditions, caused spreading necrotic lesions and tissue death. Our results demonstrate that JAZ proteins promote growth and reproductive success at least in part by preventing catastrophic metabolic effects of an unrestrained immune response.

To save or degrade: balancing proteasome homeostasis to maximize cell survival

Autophagic degradation of proteasomes (termed proteaphagy) is a conserved mechanism by which cells eliminate excess or damaged particles. This clearance is induced rapidly when organisms are starved for nitrogen and, because proteasomes are highly abundant, their breakdown likely makes an important contribution to the amino acid pools necessary for survival. By contrast, our recent studies found that proteasomes are not degraded in response to carbon starvation, even though bulk macroautophagy is similarly activated. Instead, carbon starvation induces sequestration of proteasomes into membrane-less cytoplasmic condensates previously termed proteasome storage granules (PSGs), which protect proteasomes from autophagic degradation. Preserving proteasomes in PSGs enhances the ability of yeast cells to recover from a variety of stresses, implying that rapid remobilization of stored proteasomes when conditions improve is advantageous to cell fitness. Consequently, the choice of whether to save or degrade proteasomes can profoundly impact cell survival.

[Ecological and physiological mechanisms of growth decline of Robinia pseudoacacia plantations in the Loess Plateau of China: A review.]

Robinia pseudoacacia has been widely planted in the Loess Plateau of China for soil and water conservation. The growth decline of R. pseudoacacia plantations has become a recently emerging challenge for the revegetation program and sustainable forest management in this region. As to the scientific definition, identified criteria and quantitative indices have not yet been comprehensively quantified, our current understanding of the ecological and physiological mechanisms for growth decline of R. pseudoacacia plantations is limited. The knowledge could enrich the basic theories of vegetation restoration and benefit the sustainable development of the afforestation project in the Loess Plateau. Through the comprehensive compilation of literatures on forest decline and tree mortality in the Loess Plateau and other regions across the world, this review summarized the mechanisms and recent research progress on growth decline for R. pseudoacacia plantations in the Loess Plateau, primarily demonstrated from ecological (e.g., climatic change, soil desiccation, the imbalance of community structure and the misconduct of forest management) and physiological (e.g., hydraulic failure, carbon starvation, genetic and molecular regulation) perspectives. Finally, we highlighted the research gap with regard to growth decline of R. pseudoacacia plantations in the Loess Plateau.

The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut

In the mammalian gut, bacteria compete for resources to maintain their populations, but the factors determining their success are poorly understood. We report that the human gut bacterium Bacteroides thetaiotaomicron relies on the stringent response, an intracellular signaling pathway that allocates resources away from growth, to survive carbon starvation and persist in the gut. Genome-scale transcriptomics, 13C-labeling, and metabolomics analyses reveal that B. thetaiotaomicron uses the alarmone (p)ppGpp to repress multiple biosynthetic pathways and upregulate tricarboxylic acid (TCA) cycle genes in these conditions. During carbon starvation, (p)ppGpp triggers accumulation of the metabolite alpha-ketoglutarate, which itself acts as a metabolic regulator; alpha-ketoglutarate supplementation restores viability to a (p)ppGpp-deficient strain. These studies uncover how commensal bacteria adapt to the gut by modulating central metabolism and reveal that halting rather than accelerating growth can be a determining factor for membership in the gut microbiome.

Living on next to nothing: tree seedlings can survive weeks with very low carbohydrate concentrations

The usage of nonstructural carbohydrates (NSCs) to indicate carbon (C) limitation in trees requires knowledge of the minimum tissue NSC concentrations at lethal C starvation, and the NSC dynamics during and after severe C limitation. We completely darkened and subsequently released seedlings of two deciduous and two evergreen temperate tree species for varying periods. NSCs were measured in all major organs, allowing assessment of whole-seedling NSC balances. NSCs decreased fast in darkness, but seedlings survived species-specific whole-seedling starch concentrations as low as 0.4-0.8% per dry matter (DM), and sugar (sucrose, glucose and fructose) concentrations as low as 0.5-2.0% DM. After re-illumination, the refilling of NSC pools began within 3 wk, while the resumption of growth was delayed or restricted. All seedlings had died after 12 wk of darkness, and starch and sugar concentrations in most tissues were lower than 1% DM. We conclude that under the applied conditions, tree seedlings can survive several weeks with very low NSC reserves probably also using alternative C sources like lipids, proteins or hemicelluloses; lethal C starvation cannot be assumed, if NSC concentrations are higher than the minimum concentrations found in surviving seedlings; and NSC reformation after re-illumination occurs preferentially over growth.