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At least 19 records

Proteomic characterization of Mycobacterium tuberculosis subjected to carbon starvation

ABSTRACT Mycobacterium tuberculosis(Mtb) is the causative agent of tuberculosis (TB), the leading cause of infectious disease-related deaths worldwide. TB infections present on a spectrum from active to latent disease. In the human host,Mtbfaces hostile environments, such as nutrient deprivation, hypoxia, and low pH. Under these conditions,Mtbcan enter a dormant, but viable, state characterized by a lack of cell replication and increased resistance to antibiotics. DormantMtbposes a major challenge to curing infections and eradicating TB globally. We subjectedMtbmc 2 6020 (ΔlysAand ΔpanCD), a double auxotrophic strain, to carbon starvation (CS), a culture condition that induces growth stasis and mimics environmental conditions associated with dormancyin vivo. We provide a detailed analysis of the proteome in CS compared to replicating samples. We observed extensive proteomic reprogramming, with 36% of identified proteins significantly altered in CS. Many enzymes involved in oxidative phosphorylation and lipid metabolism were retained or more abundant in CS. The cell wall biosynthetic machinery was present in CS, although numerous changes in the abundance of peptidoglycan, arabinogalactan, and mycolic acid biosynthetic enzymes likely result in pronounced remodeling of the cell wall. Many clinically approved anti-TB drugs target cell wall biosynthesis, and we found that these enzymes were largely retained in CS. Lastly, we compared our results to those of other dormancy models and propose that CS produces a physiologically distinct state of stasis compared to hypoxia inMtb. IMPORTANCE Tuberculosis is a devastating human disease that kills over 1.2 million people a year. This disease is caused by the bacterial pathogenMycobacterium tuberculosis(Mtb).Mtbexcels at surviving in the human host by entering a non-replicating, dormant state. The current work investigated the proteomic changes thatMtbundergoes in response to carbon starvation, a culture condition that models dormancy. The authors found broad effects of carbon starvation on the proteome, with the relative abundance of 37% of proteins significantly altered. Protein changes related to cell wall biosynthesis, metabolism, and drug susceptibility are discussed. Proteins associated with a carbon starvation phenotype are identified, and results are compared to other dormancy models, including hypoxia.

Microbiology↗

Severe declines in hydraulic capacity and associated carbon starvation drive mortality in seawater exposed Sitka-spruce (Picea sitchensis) trees

Abstract Sea-level rise is causing widespread tree mortality of coastal forests, with large consequences on the Earth system as a result of these forests’ importance in carbon and nutrient export. The mechanisms of mortality under these conditions are, however, poorly tested. We used wood anatomy traits, wood δ 13 C, and tree radial growth to retrospectively assess the physiological process of seawater effects on whole tree xylem hydraulic capacity, gas exchange, and radial growth. During the latter stages of mortality (2018–2019), we directly measured metrics of water use and carbon metabolism across trees having crowns ranging from fully foliated to completely defoliated to investigate mortality processes at the sub-annual scale. Upon seawater exposure, soil salinity increased and allocation to hydraulic function declined, resulting in a dramatic reduction in water supply to the crown, increased crown-level water stress, and subsequent crown foliage loss. Simultaneously, leaf-level photosynthetic capacity declined steeply with increasing salinity. The combined loss of crown foliage area and photosynthetic rates per unit leaf area promoted carbon starvation, while no evidence of hydraulic failure was observed. These results elucidate mechanisms of coastal forest death under seawater exposure, enabling more accurate modeling in the future.

54 ENVIRONMENTAL SCIENCES↗

Adapted laboratory evolution of Thermotoga sp. strain RQ7 under carbon starvation

Abstract Objective Adaptive laboratory evolution (ALE) is an effective approach to study the evolution behavior of bacterial cultures and to select for strains with desired metabolic features. In this study, we explored the possibility of evolving Thermotoga sp. strain RQ7 for cellulose-degrading abilities. Results Wild type RQ7 strain was subject to a series of transfers over six and half years with cellulose filter paper as the main and eventually the sole carbon source. Each transfer was accompanied with the addition of 50 μg of Caldicellulosiruptor saccharolyticus DSM 8903 genomic DNA. A total of 331 transfers were completed. No cellulose degradation was observed with the RQ7 cultures. Thirty three (33) isolates from six time points were sampled and sequenced. Nineteen (19) of the 33 isolates were unique, and the rest were duplicated clones. None of the isolates acquired C. saccharolyticus DNA, but all accumulated small-scale mutations throughout their genomes. Sequence analyses revealed 35 mutations that were preserved throughout the generations and another 15 mutations emerged near the end of the study. Many of the affected genes participate in phosphate metabolism, substrate transport, stress response, sensory transduction, and gene regulation.

54 ENVIRONMENTAL SCIENCES↗

Carbon starvation is absent regardless of season of burn in Liquidambar styraciflua L.

In the Southeastern United States, the function and stability of pine ecosystems depends on frequent low intensity fires. One of the critical effects of frequent fire is the inhibition of hardwood competition by removing above-ground stems (top-kill). Previous long-term studies have correlated early growing season burns with higher understory mortality when compared to dormant season burns. Seasonal differences in mortality from insufficient carbon reserves in roots after leaf flush were posited as the mechanism but this was never explicitly tested. In this experiment, we burned two-year-old pot-grown sweetgums (Liquidambar styraciflua L.) in the dormant season (February), growing season (May), and compared their physiological responses to plants that were unburned. By the end of the first post-burn growing season, mortality was higher after the dormant season burn than the growing season burn and unburned trees had nearly twice the mass of either the burned treatments. Tissue starch concentrations were similar across all treatments highlighting the resiliency of sweetgum carbon stocks to recover from above-ground stem removal regardless of season. We showed the critical importance of top-killing stems regardless of season of burn. Our findings further suggest that dormant season fires can be more lethal to young sweetgum, possibly due to susceptibility of tender new shoots to freezing damage.

54 ENVIRONMENTAL SCIENCES↗

Climate warming causes photobiont degradation and carbon starvation in a boreal climate sentinel lichen

The long-term potential for acclimation by lichens to changing climates is poorly known, despite their prominent roles in forested ecosystems. Although often considered “extremophiles,” lichens may not readily acclimate to novel climates well beyond historical norms. In a previous study, Evernia mesomorpha transplants in a whole-ecosystem climate change experiment showed drastic mass loss after 1 yr of warming and drying; however, the causes of this mass loss were not addressed. We examined the causes of this warming-induced mass loss by measuring physiological, functional, and reproductive attributes of lichen transplants. Severe loss of mass and physiological function occurred above +2°C of experimental warming. Loss of algal symbionts (“bleaching”) and turnover in algal community compositions increased with temperature and were the clearest impacts of experimental warming. Enhanced CO 2 had no significant physiological or symbiont composition effects. The functional loss of algal photobionts led to significant loss of mass and specific thallus mass (STM), which in turn reduced water-holding capacity (WHC). Although algal genotypes remained detectable in thalli exposed to higher stress, within-thallus photobiont communities shifted in composition toward greater diversity. The strong negative impacts of warming and/or lower humidity on Evernia mesomorpha were driven by a loss of photobiont activity. Analogous to the effects of climate change on corals, the balance of symbiont carbon metabolism in lichens is central to their resilience to changing conditions.

54 ENVIRONMENTAL SCIENCES↗

Context-dependent coordination of TOR and SnRK1 signaling under carbon and nitrogen perturbations

Target of rapamycin (TOR) and sucrose non-fermenting 1–related protein kinase 1 (SnRK1) are conserved regulators of plant growth and metabolism and are often portrayed as functionally antagonistic under nutrient limitation. However, how this relationship operates across different nutrient contexts remains poorly defined. Here, we generated an Arabidopsis dual-reporter line that enables simultaneous monitoring of TOR and SnRK1 activities and profiled their dynamics under carbon and nitrogen perturbations. We found that TOR and SnRK1 activities overall exhibit a negative relationship during the transition from carbon starvation to carbon abundance; however, their temporal dynamics during that transition do not support a strictly inverse correlation. Under dark conditions, TOR activity is gradually repressed, while SnRK1 is initially repressed in the early hours and subsequently activated during extended darkness. During nitrogen starvation, TOR activity is progressively repressed, whereas SnRK1 is activated during early hours and then becomes repressed. In vitro , recombinant SnRK1α1 directly inhibits the activity of immunoprecipitated TOR (IP-TOR), whereas IP-TOR does not directly affect SnRK1α1 activity. Together, these results support a nutrient-dependent model in which TOR and SnRK1 are coordinated primarily by cellular metabolic status.

59 BASIC BIOLOGICAL SCIENCES↗

Changes in carbon and nitrogen metabolism during seawater-induced mortality of Picea sitchensis trees

Abstract Increasing seawater exposure is causing mortality of coastal forests, yet the physiological response associated with seawater-induced tree mortality, particularly in non-halophytes, is poorly understood. We investigated the shifts in carbon and nitrogen (N) metabolism of mature Sitka-spruce trees that were dying after an ecosystem-scale manipulation of tidal seawater exposure. Soil porewater salinity and foliar ion concentrations increased after seawater exposure and were strongly correlated with the percentage of live foliated crown (PLFC; e.g., crown ‘greenness’, a measure of progression to death). Co-occurring with decreasing PLFC was decreasing photosynthetic capacity, N-investment into photosynthesis, N-resorption efficiency and non-structural carbohydrate (soluble sugars and starch) concentrations, with the starch reserves depleted to near zero when PLFC dropped below 5%. Combined with declining PLFC, these changes subsequently decreased total carbon gain and thus exacerbated the carbon starvation process. This study suggests that an impairment in carbon and N metabolism during the mortality process after seawater exposure is associated with the process of carbon starvation, and provides critical knowledge necessary to predict sea-level rise impacts on coastal forests.

Li, Weibin↗

The influence of increasing atmospheric CO 2 , temperature, and vapor pressure deficit on seawater-induced tree mortality

We report 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 CO 2 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 ~16.7% with increasing atmospheric CO 2 levels due to reduced risk of carbon starvation. Conversely, rising VPD could increase mortality by ~5.6% because of increasing risk of hydraulic failure. Across all scenarios, seawater-induced mortality was driven by hydraulic failure in the first two years after seawater exposure began, with carbon starvation becoming more important in subsequent years. Changing CO 2 and climate appear unlikely to have a significant impact on coastal tree mortality under rising sea levels.

54 ENVIRONMENTAL SCIENCES↗

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 CO 2 , 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 CO 2 , 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.

salinity↗

The role of height–driven constraints and compensations on tree vulnerability to drought

Frequent observations of higher mortality in larger trees than in smaller ones during droughts have sparked an increasing interest in size–dependent drought–induced mortality. However, the underlying physiological mechanisms are not well understood, with height–associated hydraulic constraints often being implied as the potential mechanism driving increased drought vulnerability. Here we performed a quantitative synthesis on how key traits that drive plant water and carbon economy change with tree height within species and assessed the implications that the different constraints and compensations may have on the interacting mechanisms (hydraulic failure, carbon starvation and/or biotic–agent attacks) affecting tree vulnerability to drought. While xylem tension increases with tree height, taller trees present a range of structural and functional adjustments, including more efficient water use and transport and greater water uptake and storage capacity, that mitigate the path–length–associated drop in water potential. These adaptations allow taller trees to withstand episodic water stress. Conclusive evidence for height–dependent increased vulnerability to hydraulic failure and carbon starvation, and their coupling to defence mechanisms and pest and pathogen dynamics, is still lacking. Further research is needed, particularly at the intraspecific level, to ascertain the specific conditions and thresholds above which height hinders tree survival under drought.

54 ENVIRONMENTAL SCIENCES↗

Modeling the mechanisms of conifer mortality under seawater exposure

Summary 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.

59 BASIC BIOLOGICAL SCIENCES↗

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. Additionally, 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.

59 BASIC BIOLOGICAL SCIENCES↗

Chemoproteomic Elucidation of β-Lactam Drug Targets in Mycobacterium abscessus

The pathogen Mycobacterium abscessus (Mab) can cause severe and difficult-to-treat chronic lung infections. Despite the rising incidence and clinical concern of Mab infections, treatment options are limited and often ineffective. Treatment is complicated by Mab’s ability to persist in a nonreplicating, drug-resistant state. Several β-lactam antibiotics are potently bactericidal against Mab but are underutilized because their molecular mechanisms of action against Mab are incompletely understood. In the current study, we used β-lactam-derived activity-based probes and chemoproteomics to report the first comprehensive list of Mab enzymes targeted by β-lactams. We compared β-lactam targets across two Mab subspecies in actively replicating and nonreplicating cultures, using a new carbon starvation model of persistence. We identified 17 targets that were active in every condition tested, seven of which were previously unknown to bind β-lactams. Lastly, we characterized the β-lactamase activity and β-lactam inhibition profiles of nine Mab enzymes, demonstrating that imipenem inhibits these targets more effectively than cefoxitin. These findings demonstrate β-lactam target engagement in persistent Mab and provide clarity on the mechanisms of action of clinically relevant β-lactams in Mab, crucial steps toward fully realizing their potential for treating infections caused by this opportunistic pathogen.

Mycobacterium abscessus↗

Mechanisms of woody-plant mortality under rising drought, CO 2 and vapour pressure deficit

Drought-associated woody plant mortality may have increased over the past several decades, and is projected to increase in the future, impacting terrestrial climate forcing, biodiversity, and resource availability. The mechanisms underlying such mortality, however, are debated owing to interactions between multiple drivers and mechanisms. In this work, we synthesize knowledge of drought-related tree mortality under a warming and drying atmosphere with rising atmospheric CO 2 . Drought-associated mortality results from the depletion of pools of water and carbon within a plant and declines in their fluxes relative to demand by living tissues. These pools and fluxes are interdependent and underlay plant defenses against biotic agents. Death via failure to maintain a positive water balance is particularly dependent on soil-to-root conductance, capacitance, vulnerability to hydraulic failure, cuticular water losses, and dehydration tolerance, all of which could be exacerbated by reduced carbon supply rates to support cellular survival e.g. the carbon starvation process. The depletion of plant water and carbon pools accelerates under rising vapor pressure deficit; however, increasing CO 2 can mitigate these impacts. Advancing knowledge and reducing predictive uncertainties requires studies that integrate carbon, water, and defensive processes, and utilize a range of experimental and modeling approaches.

54 ENVIRONMENTAL SCIENCES↗

Declining carbohydrate content of Sitka-spruce treesdying from seawater exposure

Abstract Increasing sea levels associated with climate change threaten the survival of coastal forests, yet the mechanisms by which seawater exposure causes tree death remain poorly understood. Despite the potentially crucial role of nonstructural carbohydrate (NSC) reserves in tree survival, their dynamics in the process of death under seawater exposure are unknown. Here we monitored progressive tree mortality and associated NSC storage in Sitka-spruce (Picea sitchensis) trees dying under ecosystem-scale increases in seawater exposure in western Washington, USA. All trees exposed to seawater, because of monthly tidal intrusion, experienced declining crown foliage during the sampling period, and individuals with a lower percentage of live foliated crown (PLFC) died faster. Tree PLFC was strongly correlated with subsurface salinity and needle ion contents. Total NSC concentrations in trees declined remarkably with crown decline, and reached extremely low levels at tree death (2.4% and 1.6% in leaves and branches, respectively, and 0.4% in stems and roots). Starch in all tissues was almost completely consumed, while sugars remained at a homeostatic level in foliage. The decreasing NSC with closer proximity to death and near zero starch at death are evidences that carbon starvation occurred during Sitka-spruce mortality during seawater exposure. Our results highlight the importance of carbon storage as an indicator of tree mortality risks under seawater exposure.

59 BASIC BIOLOGICAL SCIENCES↗

Tree crown damage and its effects on forest carbon cycling in a tropical forest

Abstract Crown damage can account for over 23% of canopy biomass turnover in tropical forests and is a strong predictor of tree mortality; yet, it is not typically represented in vegetation models. We incorporate crown damage into the Functionally Assembled Terrestrial Ecosystem Simulator (FATES), to evaluate how lags between damage and tree recovery or death alter demographic rates and patterns of carbon turnover. We represent crown damage as a reduction in a tree's crown area and leaf and branch biomass, and allow associated variation in the ratio of aboveground to belowground plant tissue. We compare simulations with crown damage to simulations with equivalent instant increases in mortality and benchmark results against data from Barro Colorado Island (BCI), Panama. In FATES, crown damage causes decreases in growth rates that match observations from BCI. Crown damage leads to increases in carbon starvation mortality in FATES, but only in configurations with high root respiration and decreases in carbon storage following damage. Crown damage also alters competitive dynamics, as plant functional types that can recover from crown damage outcompete those that cannot. This is a first exploration of the trade‐off between the additional complexity of the novel crown damage module and improved predictive capabilities. At BCI, a tropical forest that does not experience high levels of disturbance, both the crown damage simulations and simulations with equivalent increases in mortality does a reasonable job of capturing observations. The crown damage module provides functionality for exploring dynamics in forests with more extreme disturbances such as cyclones and for capturing the synergistic effects of disturbances that overlap in space and time.

Needham, Jessica F.↗

Hot droughts in the Amazon provide a window to a future hypertropical climate

Tropical forests represent the warmest and wettest of Earth’s biomes, but with continued anthropogenic warming, they will be pushed to climate states with no current analogue. Droughts in the tropics are already becoming more intense as they occur at successively higher temperatures. Here, in this study, we synthesize multiple datasets to assess the effects of hot droughts on a central Amazon forest. First, a more than 30-year record of annually resolved forest demographic data from a selective logging experiment showed higher tree mortality during intense droughts, particularly among fast-growing pioneer species with low wood density. Second, analysis of ecophysiological field measurements from the 2015 and 2023 El Niño droughts identified a soil moisture threshold beyond which transpiration rates rapidly declined. As rainless days beyond this threshold continued, drought conditions intensified, increasing the potential for tree mortality from hydraulic failure and carbon starvation. Third, analyses from the Coupled Model Intercomparison Project Phase 6 demonstrated that under high-emission scenarios, a large area of tropical forest will shift to a hotter ‘hypertropical’ climate by 2100. Last, under a hypertropical climate, temperature and moisture conditions during typical dry season months will more frequently exceed identified drought mortality thresholds, elevating the risk of forest dieback. Present-day hot droughts are harbingers of this emerging climate, offering a window for studying tropical forests under expected extreme future conditions.

drought↗

Genome reduction improves octanoic acid production in scale down bioreactors

Microorganisms in large-scale bioreactors are exposed to heterogeneous environmental conditions due to physical mixing constraints. Nutritional gradients can lead to transient expression of energetically wasteful stress responses and as a result, can reduce the titres, rates and yields of a bioprocess at larger scales. To what extent these process parameters are impacted is often unknown and therefore bioprocess scale-up comes with major risk. Designing platform strains to account for these intermittent stresses before introducing synthesis pathways is one strategy for de-risking bioprocess development. For example, Escherichia coli strain RM214 is a derivative of wild-type MG1655 that has had several genes and whole operons removed from its genome based on their metabolic cost. In this study, we engineered E. coli strain RM214 (referred to as WG02) to produce octanoic acid from glycerol in batch-flask and fed-batch bioreactor cultivations and compared it to an octanoic acid-producing E. coli MG1655 (WG01). In batch flask cultivations, the two strains performed similarly. However, in carbon limited fed-batch bioreactor cultivations, WG02 provided a greater than 22% boost to biomass compared to WG01 while maintaining similar titres of octanoic acid. Reducing the biomass accumulation of WG02 with nitrogen limited fed-batch cultivation resulted in a 16% improvement in octanoic acid titre over WG01. Finally, in a scale-down system consisting of a stirred tank reactor (representing a well-mixed zone) and plug flow reactor (representing an intermittent carbon starvation zone), WG02 again improved octanoic acid titre by almost 18% while maintaining similar biomass concentrations as WG01.

59 BASIC BIOLOGICAL SCIENCES↗