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At least 217 records · Page 12

Arsenic Accumulation in Microbial Biomass and the Interpretation of Signals of Early Arsenic‐Based Metabolisms

Carbonaceous particles that concentrate arsenic in microbialites as old as ~3.5 Ga are similar to As-rich organic globules in modern microbialites. The former particles have been interpreted as tracers of As cycling by early microbial metabolisms. However, it is unclear if arsenic accumulation is a consequence of biological activity or passive postmortem binding of arsenic by organic matter during diagenesis in volcanically influenced, As-rich environments. Here, we address this uncertainty by evaluating the concentrations, speciation, and detectability of As in active or heat-killed biofilms formed by cyanobacteria or anoxygenic photosynthetic microbes exposed to environmentally relevant concentrations of As(III) or As(V) (50 μM to 3 mM). The genomes or metagenomes of these biofilms contain genes involved in detoxifying or energy-yielding As metabolisms. Biomass accumulates As from the solution in a concentration-dependent manner and with a preference for oxidized As(V) over As(III). Autoclaved biomass accumulates As even more strongly than active biomass, likely because living biofilms actively detoxify As. Active biofilms oxidize and reduce As and accumulate both As(III) and As(V), whereas a small fraction of As(V) can be reduced in inactive biofilms that bind As during diagenesis. Arsenic enrichments in the biomass are detectable by X-ray based spectroscopy techniques (XRF, EPMA-WDS) that are commonly used to analyze geological materials. These findings enable the reconstruction of past active and passive interactions of microbial biomass with arsenic in fossilized microbial biofilms and microbialites from the early Earth.

Madrigal‐Trejo, David↗

Understanding metabolic alterations in space flight using quantitative models - Fluid and energy balance

The results of an integrated multidisciplinary and multiexperimental investigation, using data from the Skylab program, of metabolic adaptation to space flight are summarized and discussed. The effects of space flight on fluid-electrolyte regulation, mechanisms of hormone disturbances, energy balance, and the etiology of weight loss are emphasized. A composite picture of the fluid, electrolyte, and energy response to weightlessness, based primarily on data gathered from the nine Skylab crewmen, is presented.

Leonard, J. I.↗

Pyridoxal 5'-phosphate dependent reactions: Analyzing the mechanism of aspartate aminotransferase

Enzyme catalysis is the primary activity in energy and information metabolism and enzyme cofactors are key to the catalytic ability of most enzymes. Pyridoxal 5'-phosphate (PLP) cofactor, derived from Vitamin B6, is widely distributed in nature and has significant latitude in catalytic diversity. X-ray crystallography has revealed the structures of diverse PLP dependent enzymes from multiple families. But these structures are incomplete, lacking the positions of protons essential for understanding enzymatic mechanisms. Here, we review the diversity of PLP and discuss the use of neutron crystallography and joint X-ray/neutron refinement of Fold Type I aspartate aminotransferase to visualize the positions of protons in both the internal and external aldimine forms. Strategies used to prepare extremely large crystals required for neutron diffraction and the approach to data refinement including the PLP cofactor are discussed. The observed positions of protons, including one located in a previously unknown low-barrier hydrogen bond, have been used to create more accurate models for computational analysis. The results revealed a new mechanism for the transaminase reaction where hyperconjugation is key to reducing the energy barrier which finally provides a clear explanation of the Dunathan alignment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Elucidating regulatory processes of intense physical activity by multi-omics analysis

Abstract Background Physiological and biochemical processes across tissues of the body are regulated in response to the high demands of intense physical activity in several occupations, such as firefighting, law enforcement, military, and sports. A better understanding of such processes can ultimately help improve human performance and prevent illnesses in the work environment. Methods To study regulatory processes in intense physical activity simulating real-life conditions, we performed a multi-omics analysis of three biofluids (blood plasma, urine, and saliva) collected from 11 wildland firefighters before and after a 45 min, intense exercise regimen. Omics profiles post- versus pre-exercise were compared by Student’s t -test followed by pathway analysis and comparison between the different omics modalities. Results Our multi-omics analysis identified and quantified 3835 proteins, 730 lipids and 182 metabolites combining the 3 different types of samples. The blood plasma analysis revealed signatures of tissue damage and acute repair response accompanied by enhanced carbon metabolism to meet energy demands. The urine analysis showed a strong, concomitant regulation of 6 out of 8 identified proteins from the renin-angiotensin system supporting increased excretion of catabolites, reabsorption of nutrients and maintenance of fluid balance. In saliva, we observed a decrease in 3 pro-inflammatory cytokines and an increase in 8 antimicrobial peptides. A systematic literature review identified 6 papers that support an altered susceptibility to respiratory infection. Conclusion This study shows simultaneous regulatory signatures in biofluids indicative of homeostatic maintenance during intense physical activity with possible effects on increased infection susceptibility, suggesting that caution against respiratory diseases could benefit workers on highly physical demanding jobs.

59 BASIC BIOLOGICAL SCIENCES↗

Biogenic Iron Sulfide Nanoparticles to Enable Extracellular Electron Uptake in Sulfate‐Reducing Bacteria

Abstract Microbes synthesize cell‐associated nanoparticles (NPs) and utilize their physicochemical properties to produce energy under unfavorable metabolic conditions. Iron sulfide (FeS) NPs are ubiquitous and are predominantly biosynthesized by sulfate‐reducing bacteria (SRB). However, the biological role of FeS NPs in SRB remains understudied. Now, conductive FeS NPs function is demonstrated as an electron conduit enabling Desulfovibrio vulgaris Hildenborough, an SRB strain, to utilize solid‐state electron donors via direct electron uptake. After forming FeS NPs on the cell surface, D. vulgaris initiated current generation coupled with sulfate reduction on electrodes poised at −0.4 V versus standard hydrogen electrode. Single‐cell activity analysis showed that the electron uptake and metabolic rate via FeS NPs in D. vulgaris were about sevenfold higher than those via native cell‐surface proteins in other SRB.

Deng, Xiao↗

Biogenic Iron Sulfide Nanoparticles to Enable Extracellular Electron Uptake in Sulfate‐Reducing Bacteria

Abstract Microbes synthesize cell‐associated nanoparticles (NPs) and utilize their physicochemical properties to produce energy under unfavorable metabolic conditions. Iron sulfide (FeS) NPs are ubiquitous and are predominantly biosynthesized by sulfate‐reducing bacteria (SRB). However, the biological role of FeS NPs in SRB remains understudied. Now, conductive FeS NPs function is demonstrated as an electron conduit enabling Desulfovibrio vulgaris Hildenborough, an SRB strain, to utilize solid‐state electron donors via direct electron uptake. After forming FeS NPs on the cell surface, D. vulgaris initiated current generation coupled with sulfate reduction on electrodes poised at −0.4 V versus standard hydrogen electrode. Single‐cell activity analysis showed that the electron uptake and metabolic rate via FeS NPs in D. vulgaris were about sevenfold higher than those via native cell‐surface proteins in other SRB.

Deng, Xiao↗

Manganese-Rich Sandstones as an Indicator of Ancient Oxic Lake Water Conditions in Gale Crater, Mars

Manganese has been observed on Mars by the NASA Curiosity rover in a variety of contexts and is an important indicator of redox processes in hydrologic systems on Earth. Within the Murray formation, an ancient primarily fine-grained lacustrine sedimentary deposit in Gale crater, Mars, have observed up to 45× enrichment in manganese and up to 1.5× enrichment in iron within coarser grained bedrock targets compared to the mean Murray sediment composition. This enrichment in manganese coincides with the transition between two stratigraphic units within the Murray: Sutton Island, interpreted as a lake margin environment, and Blunts Point, interpreted as a lake environment. On Earth, lacustrine environments are common locations of manganese precipitation due to highly oxidizing conditions in the lakes. Here, we explore three mechanisms for ferromanganese oxide precipitation at this location: authigenic precipitation from lake water along a lake shore, authigenic precipitation from reduced groundwater discharging through porous sands along a lake shore, and early diagenetic precipitation from groundwater through porous sands. All three scenarios require highly oxidizing conditions and we discuss oxidants that may be responsible for the oxidation and precipitation of manganese oxides. This work has important implications for the habitability of Mars to microbes that could have used Mn redox reactions, owing to its multiple redox states, as an energy source for metabolism.

58 GEOSCIENCES↗

Design of diverse, functional mitochondrial targeting sequences across eukaryotic organisms using variational autoencoder

Mitochondria play a key role in energy production and metabolism, making them a promising target for metabolic engineering and disease treatment. However, despite the known influence of passenger proteins on localization efficiency, only a few protein-localization tags have been characterized for mitochondrial targeting. To address this limitation, we leverage a Variational Autoencoder to design novel mitochondrial targeting sequences. In silico analysis reveals that a high fraction of the generated peptides (90.14%) are functional and possess features important for mitochondrial targeting. We characterize artificial peptides in four eukaryotic organisms and, as a proof-of-concept, demonstrate their utility in increasing 3-hydroxypropionic acid titers through pathway compartmentalization and improving 5-aminolevulinate synthase delivery by 1.62-fold and 4.76-fold, respectively. Moreover, we employ latent space interpolation to shed light on the evolutionary origins of dual-targeting sequences. Overall, our work demonstrates the potential of generative artificial intelligence for both fundamental research and practical applications in mitochondrial biology.

59 BASIC BIOLOGICAL SCIENCES↗

Cyanobacterial circadian regulation enhances bioproduction under subjective nighttime through rewiring of carbon partitioning dynamics, redox balance orchestration, and cell cycle modulation

Abstract Background The industrial feasibility of photosynthetic bioproduction using cyanobacterial platforms remains challenging due to insufficient yields, particularly due to competition between product formation and cellular carbon demands across different temporal phases of growth. This study investigates how circadian clock regulation impacts carbon partitioning between storage, growth, and product synthesis in Synechococcus elongatus PCC 7942, and provides insights that suggest potential strategies for enhanced bioproduction. Results After entrainment to light-dark cycles, PCC 7942 cultures transitioned to constant light revealed distinct temporal patterns in sucrose production, exhibiting three-fold higher productivity during subjective night compared to subjective day despite moderate down-regulation of genes from the photosynthetic apparatus. This enhanced productivity coincided with reduced glycogen accumulation and halted cell division at subjective night time, suggesting temporal separation of competing processes. Transcriptome analysis revealed coordinated circadian clock-driven adjustment of the cell cycle and rewiring of energy and carbon metabolism, with over 300 genes showing differential expression across four time points. The subjective night was characterized by altered expression of cell division-related genes and reduced expression of genes involved in glycogen synthesis, while showing upregulation of glycogen degradation pathways, alternative electron flow components, the pentose phosphate pathway, and oxidative decarboxylation of pyruvate. These molecular changes created favorable conditions for product formation through enhanced availability of major sucrose precursors (glucose-1-phosphate and fructose-6-phosphate) and maintained redox balance through multiple mechanisms. Conclusions Our analysis of circadian regulatory rewiring of carbon metabolism and redox balancing suggests two potential approaches that could be developed for improving cyanobacterial bioproduction: leveraging natural circadian rhythms for optimizing cultivation conditions and timing of pathway induction, and engineering strains that mimic circadian-driven metabolic shifts through controlled carbon flux redistribution and redox rebalancing. While these strategies remain to be tested, they could theoretically improve the efficiency of photosynthetic bioproduction by enabling better temporal separation between cell growth, carbon storage accumulation, and product synthesis phases.

59 BASIC BIOLOGICAL SCIENCES↗

Data for "Design of Diverse, Functional Mitochondrial Targeting Sequences Across Eukaryotic Organisms Using Variational Autoencoder"

Mitochondria play a key role in energy production and metabolism, making them a promising target for metabolic engineering and disease treatment. However, despite the known influence of passenger proteins on localization efficiency, only a few protein-localization tags have been characterized for mitochondrial targeting. To address this limitation, we leverage a Variational Autoencoder to design novel mitochondrial targeting sequences. In silico analysis reveals that a high fraction of the generated peptides (90.14%) are functional and possess features important for mitochondrial targeting. We characterize artificial peptides in four eukaryotic organisms and, as a proof-of-concept, demonstrate their utility in increasing 3-hydroxypropionic acid titers through pathway compartmentalization and improving 5-aminolevulinate synthase delivery by 1.62-fold and 4.76-fold, respectively. Moreover, we employ latent space interpolation to shed light on the evolutionary origins of dual-targeting sequences. Overall, our work demonstrates the potential of generative artificial intelligence for both fundamental research and practical applications in mitochondrial biology.

AI/ML↗

Manganese-rich sandstones as an indicator of ancient oxic lake water conditions in Gale crater, Mars

Manganese has been observed on Mars by the NASA Curiosity rover in a variety of contexts and is an important indicator of redox processes in hydrologic systems on Earth. Within the Murray formation, an ancient primarily fine-grained lacustrine sedimentary deposit in Gale crater, Mars, have observed up to 45× enrichment in manganese and up to 1.5× enrichment in iron within coarser grained bedrock targets compared to the mean Murray sediment composition. This enrichment in manganese coincides with the transition between two stratigraphic units within the Murray: Sutton Island, interpreted as a lake margin environment, and Blunts Point, interpreted as a lake environment. On Earth, lacustrine environments are common locations of manganese precipitation due to highly oxidizing conditions in the lakes. Here, we explore three mechanisms for ferromanganese oxide precipitation at this location: authigenic precipitation from lake water along a lake shore, authigenic precipitation from reduced groundwater discharging through porous sands along a lake shore, and early diagenetic precipitation from groundwater through porous sands. All three scenarios require highly oxidizing conditions and we discuss oxidants that may be responsible for the oxidation and precipitation of manganese oxides. This work has important implications for the habitability of Mars to microbes that could have used Mn redox reactions, owing to its multiple redox states, as an energy source for metabolism.

58 GEOSCIENCES↗

PPI DataHub Project Data Package: S. elongatus PCC 7942 Circadian Control Bioproduction Transcriptomics (PB-DP3)

The purpose of this experiment was to evaluate how circadian clock regulation impacts carbon partitioning between storage, growth, and product synthesis in Synechococcus elongatus PCC 7942 in providing insights to strategies for enhanced bioproduction. Sample data was acquired using a Illumina HiSeq sequencer system and processed for RNA sequencing (RNA-Seq) expression analysis. Transcriptomic differential expression analysis revealed coordinated circadian clock-driven adjustment of the cell cycle and rewiring of energy and carbon metabolism. Processed RNA-Seq datasets are openly accessible from the PNNL DataHub project dataset download page and contain secondary processed RNA-seq results files and supporting metadata materials linked to relevant source code information supporting data transparency and reuse.

59 BASIC BIOLOGICAL SCIENCES↗

Experiment K-6-08. Biochemical and histochemical observations of vastus medialis

Muscles of the hindlimb in the rat have been used to demonstrate the effects of unloading in weightlessness and in animal models used to mimic weightlessness. The vastus medialis (VM) is discussed here. Samples were obtained from rats exposed to weightlessness for 12 days in Cosmos 1887 (Experiment K-6-08, coordinated by Dr. V.S. Oganov). The principal objective of this study was to ascertain if the vastus medialis responded to 12 days of microgravity exposure. The loss in muscle mass is greatest, -43 percent, when comparing F vs B, and least, -13 percent, when comparing F vs. V. Taken at face value these differences may be misleading. Due to the variability of the muscle weight in the basal group, these muscle mass losses may be exaggerated. In terms of percent water, there were no differences between the flight and the control groups. In spite of the limited sample, researchers conclude that muscle mass changes in the VM are not significant. Although some of the morphological parameters suggest a small degree of atrophy in the vastus medialis, the biochemical analyses (protein, RNA and DNA) suggest that these may be minimal and functionally nonsignificant. The relatively similar CS and LDH activities of VM from F and various control groups, as well as the lack of difference in LPL activity between F and S rats, suggests that there is little or no effect on the oxidative or glycolytic function of this muscle. Since the VM is chiefly a mixed fast twitch muscle, these metabolic indices of energy production are relatively unchanged. The results of VM studies are in agreement with previous observations of another type II fast twitch muscle, the EDL, from SL-3 rats which did not respond markedly to weightlessness and whole body suspension.

Musacchia, X. J.↗

Energy Requirements of Hydrogen-utilizing Microbes: A Boundary Condition for Subsurface Life

Microbial ecosystems based on the energy supplied by water-rock chemistry carry particular significance in the context of geo- and astrobiology. With no direct dependence on solar energy, lithotrophic microbes could conceivably penetrate a planetary crust to a depth limited only by temperature or pressure constraints (several kilometers or more). The deep lithospheric habitat is thereby potentially much greater in volume than its surface counterpart, and in addition offers a stable refuge against inhospitable surface conditions related to climatic or atmospheric evolution (e.g., Mars) or even high-energy impacts (e.g., early in Earth's history). The possibilities for a deep microbial biosphere are, however, greatly constrained by life s need to obtain energy at a certain minimum rate (the maintenance energy requirement) and of a certain minimum magnitude (the energy quantum requirement). The mere existence of these requirements implies that a significant fraction of the chemical free energy available in the subsurface environment cannot be exploited by life. Similar limits may also apply to the usefulness of light energy at very low intensities or long wavelengths. Quantification of these minimum energy requirements in terrestrial microbial ecosystems will help to establish a criterion of energetic habitability that can significantly constrain the prospects for life in Earth's subsurface, or on other bodies in the solar system. Our early work has focused on quantifying the biological energy quantum requirement for methanogenic archaea, as representatives of a plausible subsurface metabolism, in anoxic sediments (where energy availability is among the most limiting factors in microbial population growth). In both field and laboratory experiments utilizing these sediments, methanogens retain a remarkably consistent free energy intake, in the face of fluctuating environmental conditions that affect energy availability. The energy yields apparently required by methanogens in these sediment systems for sustained metabolism are about half that previously thought necessary. Lowered energy requirements would imply that a correspondingly greater proportion of the planetary subsurface could represent viable habitat for microorganisms.

Hoehler, Tori M.↗

Heat Production During Countermeasure Exercises Planned for the International Space Station

This investigation's purpose was to determine the amount of heat produced when performing aerobic and resistance exercises planned as part of the exercise countermeasures prescription for the ISS. These data will be used to determine thermal control requirements of the Node 1 and other modules where exercise hardware might reside. To determine heat production during resistive exercise, 6 subjects using the iRED performed 5 resistance exercises which form the core exercises of the current ISS resistive exercise countermeasures. Each exerciser performed a warm-up set at 50% effort, then 3 sets of increasing resistance. We measured oxygen consumption and work during each exercise. Heat loss was calculated as the difference between the gross energy expenditure (minus resting metabolism) and the work performed. To determine heat production during aerobic exercise, 14 subjects performed an interval, cycle exercise protocol and 7 subjects performed a continuous, treadmill protocol. Each 30-min. exercise is similar to exercises planned for ISS. Oxygen consumption monitored continuously during the exercises was used to calculate the gross energy expenditure. For cycle exercise, work performed was calculated based on the ergometer's resistance setting and pedaling frequency. For treadmill, total work was estimated by assuming 25% work efficiency and subtracting the calculated heat production and resting metabolic rate from the gross energy expenditure. This heat production needs to be considered when determining the location of exercise hardware on ISS and designing environmental control systems. These values reflect only the human subject s produced heat; heat produced by the exercise hardware also will contribute to the heat load.

Rapley, Michael G.↗

Assessing Habitability: Lessons from the Phoenix Mission

The Phoenix mission's key objective was to search for a habitable zone. The Phoenix lander carried a robotic arm with digging scoop to collect soil and icy material for analysis with an instrument payload that included volatile mineral and organic analysis(3) and soil ionic chemistry analysis (4). Results from Phoenix along with theoretical modeling and other previous mission results were used to evaluate the habitability of the landing site by considering four factors that characterize the environments ability to support life as we know it: the presence of liquid water, the presence of an energy source to support metabolism, the presence of nutrients containing the fundamental building blocks of life, and the absence of environmental conditions that are toxic to or preclude life. Phoenix observational evidence for the presence of liquid water (past or present) includes clean segregated ice, chemical etching of soil grains, calcite minerals in the soil and variable concentrations of soluble salts5. The maximum surface temperature measured was 260K so unfrozen water can form only in adsorbed films or saline brines but warmer climates occur cyclically on geologically short time scales due to variations in orbital parameters. During high obliquity periods, temperatures allowing metabolism extend nearly a meter into the subsurface. Phoenix discovered ~1%w/w perchlorate salt in the soil, a chemical energy source utilized by a wide range of microbes. Nutrient sources including C, H, N, O, P and S compounds are supplied by known atmospheric sources or global dust. Environmental conditions are within growth tolerance for terrestrial microbes. Summer daytime temperatures are sufficient for metabolic activity, the pH is 7.8 and is well buffered and the projected water activity of a wet soil will allow growth. In summary, martian permafrost in the north polar region is a viable location for modern life. Stoker et al. presented a formalism for comparing the habitability of various regions visited to date on Mars that involved computing a habitability probability, defined as the product of probabilities for the presence of liquid water (P(sub lw)), energy (P(sub e)), nutrients (P(sub ch)), and a benign environment (P(sub b)). Using this formalism, they argued that the Phoenix site was the most habitable of any site visited to date by landed missions and warranted a follow up mission to search for modern evidence of life. This paper will review that conclusion in view of more recent information from the Mars Exploration Rovers and Mars Science Lander missions.

Stoker, Carol R.↗

Rubisco regulation in response to altered carbon status in the cyanobacterium Synechococcus elongatus PCC 7942

Abstract Photosynthetic organisms possess a variety of mechanisms to achieve balance between absorbed light (source) and the capacity to metabolically utilize or dissipate this energy (sink). While regulatory processes that detect changes in metabolic status/balance are relatively well studied in plants, analogous pathways remain poorly characterized in photosynthetic microbes. Here, we explored systemic changes that result from alterations in carbon availability in the model cyanobacterium Synechococcus elongatus PCC 7942 by taking advantage of an engineered strain where influx/efflux of a central carbon metabolite, sucrose, can be regulated experimentally. We observed that induction of a high-flux sucrose export pathway leads to depletion of internal carbon storage pools (glycogen) and concurrent increases in estimates of photosynthetic activity. Further, a proteome-wide analysis and fluorescence reporter-based analysis revealed that upregulated factors following the activation of the metabolic sink are concentrated on ribulose-1,5-bisphosphate carboxylase-oxygenase (Rubisco) and auxiliary modules involved in Rubisco maturation. Carboxysome number and Rubisco activity also increased following engagement of sucrose secretion. Conversely, reversing the flux of sucrose by feeding exogenous sucrose through the heterologous transporter resulted in increased glycogen pools, decreased Rubisco abundance, and carboxysome reorganization. Our data suggest that Rubisco activity and organization are key variables connected to regulatory pathways involved in metabolic balancing in cyanobacteria.

Plant Sciences↗