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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,135 records · Page 63
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

A bacterial surface layer protein exploits multistep crystallization for rapid self-assembly

Surface layers (S-layers) are crystalline protein coats surrounding microbial cells. S-layer proteins (SLPs) regulate their extracellular self-assembly by crystallizing when exposed to an environmental trigger. However, molecular mechanisms governing rapid protein crystallization in vivo or in vitro are largely unknown. Here, we demonstrate that the Caulobacter crescentus SLP readily crystallizes into sheets in vitro via a calcium-triggered multistep assembly pathway. This pathway involves 2 domains serving distinct functions in assembly. The C-terminal crystallization domain forms the physiological 2-dimensional (2D) crystal lattice, but full-length protein crystallizes multiple orders of magnitude faster due to the N-terminal nucleation domain. Observing crystallization using a time course of electron cryo-microscopy (Cryo-EM) imaging reveals a crystalline intermediate wherein N-terminal nucleation domains exhibit motional dynamics with respect to rigid lattice-forming crystallization domains. Dynamic flexibility between the 2 domains rationalizes efficient S-layer crystal nucleation on the curved cellular surface. Rate enhancement of protein crystallization by a discrete nucleation domain may enable engineering of kinetically controllable self-assembling 2D macromolecular nanomaterials.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A synthetic promoter system for well-controlled protein expression with different carbon sources in Saccharomyces cerevisiae

Saccharomyces cerevisiae is an important synthetic biology chassis for microbial production of valuable molecules. Promoter engineering has been frequently applied to generate more synthetic promoters with a variety of defined characteristics in order to achieve a well-regulated genetic network for high production efficiency. Galactose-inducible (GAL) expression systems, composed of GAL promoters and multiple GAL regulators, have been widely used for protein overexpression and pathway construction in S. cerevisiae. However, the function of each element in synthetic promoters and how they interact with GAL regulators are not well known. Here, a library of synthetic GAL promoters demonstrate that upstream activating sequences (UASs) and core promoters have a synergistic relationship that determines the performance of each promoter under different carbon sources. We found that the strengths of synthetic GAL promoters could be fine-tuned by manipulating the sequence, number, and substitution of UASs. Core promoter replacement generated synthetic promoters with a twofold strength improvement compared with the GAL1 promoter under multiple different carbon sources in a strain with GAL1 and GAL80 engineering. These results represent an expansion of the classic GAL expression system with an increased dynamic range and a good tolerance of different carbon sources. In this study, the effect of each element on synthetic GAL promoters has been evaluated and a series of well-controlled synthetic promoters are constructed. By studying the interaction of synthetic promoters and GAL regulators, synthetic promoters with an increased dynamic range under different carbon sources are created.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Systematic investigations on iron cycling in phosphorus/siderophore systems: Synergism or antagonism?

Synergisms between microbial exudates on Fe (hydr)oxide dissolution as an effective Fe acquisition pathway have been recently addressed and vigorously debated. However, Fe liberation mechanisms and where siderophores and phosphorus (P) coexist received little attentions. Current study systematically investigated ferrihydrite dissolution in the presence of desferrioxamine B (DFOB) (a kind of fungally-derived siderophores) and inorganic/organic phosphorus (orthophosphate, Pi; myo-inositol hexaphosphate, IHP), as a function of solute pH, reaction time and reagent content. Reacted solids were characterized by N 2 -BET adsorption, zeta (ζ) potential analysis, sequential extraction analysis (SEDEX), field emission scanning electron microscopy (FESEM), high-resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), micro Raman spectroscopy and attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR). Our results indicate that upon reaction with P-only or (DFOB + P) systems, interfacial complexation partially switched from monolayer bidentate-binuclear surface complexes to ternary complexes, or laterally transformed into amorphous Fe–P precipitates. The Fe-Pi complex precipitated more readily under acidic conditions, and Fe-IHP complex preferentially nucleated in neutral-alkaline environments. Phosphorus slightly promoted Fe release from minerals and fixation to the leached layer or interfacial liquid zone initially, but subsequently prevented further attacks from protons and DFOB. The co-effects of P and DFOB likely correspond to two successive scenarios: 1) DFOB is preferentially attracted toward ferrihydrite surfaces by negative electrical fields induced by adsorbed phosphorus and can act synergistically with labile P–Fe complexes, resulting in intensive temporal dissolution of Fh; 2) subsequent Fe shuttling to DFOB can be prohibited by stabilized, passive P/Fe–P layers. Finally, our results emphasize the antagonism between P compounds and siderophores (i.e., DFOB here) on ferrihydrite dissolution to improve understanding of the biologically-mediated Fe cycling in natural systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

The importance of sourcing enzymes from non-conventional fungi for metabolic engineering and biomass breakdown

A wealth of fungal enzymes has been identified from nature, which continue to drive strain engineering and bioprocessing for a range of industries. However, while a number of clades have been investigated, the vast majority of the fungal kingdom remains unexplored for industrial applications. In this study, we discuss selected classes of fungal enzymes that are currently in biotechnological use, and explore more basal, non-conventional fungi and their underexploited biomass-degrading mechanisms as promising agents in the transition towards a bio-based society. Of special interest are anaerobic fungi like the Neocallimastigomycota, which were recently found to harbor the largest diversity of biomass-degrading enzymes among the fungal kingdom. Enzymes sourced from these basal fungi have been used to metabolically engineer substrate utilization in yeast, and may offer new paths to lignin breakdown and tunneled biocatalysis. We also contrast classic enzymology approaches with emerging ‘omics’-based tools to decipher function within novel fungal isolates and identify new promising enzymes. Recent developments in genome editing are expected to accelerate discovery and metabolic engineering within these systems, yet are still limited by a lack of high-resolution genomes, gene regulatory regions, and even appropriate culture conditions. Lastly, we present new opportunities to harness the biomass-degrading potential of undercharacterized fungi via heterologous expression and engineered microbial consortia.

09 BIOMASS FUELS↗
DOE OSTI2019

Global ecotypes in the ubiquitous marine clade SAR86

SAR86 is an abundant and ubiquitous heterotroph in the surface ocean that plays a central role in the function of marine ecosystems. We hypothesized that despite its ubiquity, different SAR86 subgroups may be endemic to specific ocean regions and functionally specialized for unique marine environments. However, the global biogeographical distributions of SAR86 genes, and the manner in which these distributions correlate with marine environments, have not been investigated. We quantified SAR86 gene content across globally distributed metagenomic samples and modeled these gene distributions as a function of 51 environmental variables. We identified five distinct clusters of genes within the SAR86 pangenome, each with a unique geographic distribution associated with specific environmental characteristics. Gene clusters are characterized by the strong taxonomic enrichment of distinct SAR86 genomes and partial assemblies, as well as differential enrichment of certain functional groups, suggesting differing functional and ecological roles of SAR86 ecotypes. We then leveraged our models and high-resolution, remote sensing-derived environmental data to predict the distributions of SAR86 gene clusters across the world's oceans, creating global maps of SAR86 ecotype distributions. Finally, our results reveal that SAR86 exhibits previously unknown, complex biogeography, and provide a framework for exploring geographic distributions of genetic diversity from other microbial clades.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Non-growing season plant nutrient uptake controls Arctic tundra vegetation composition under future climate

Abstract Plant growth and distribution in high-latitude tundra ecosystems is strongly limited by nutrient availability and is critical for quantifying centennial-scale carbon-climate interactions. However, land model representations of plant–nutrient interactions are uncertain, leading to poor comparisons with high-latitude observations. Although it has been recognized for decades in the observational community that plants continue to acquire nutrients well past when aboveground activity has ceased, most large-scale land models ignore this process. Here we address the role tundra plant nutrient acquisition during the non-growing season (NGS) has on centennial-scale vegetation growth and dynamics, with a focus on shrub expansion. We apply a well-tested mechanistic model of coupled plant, microbial, hydrological, and thermal dynamics that explicitly represents nutrient acquisition based on plant and microbial traits, thereby allowing a prognostic assessment of NGS nutrient uptake. We first show that the model accurately represents observed seasonality of NGS plant nutrient uptake in a northern Alaskan tundra site. Applying the model across the North America tundra indicates that NGS nutrient uptake is consistent with observations and ranges between ∼5% and 50% of annual uptake, with large spatial variability and dependence on plant functional type. We show that NGS plant nutrient acquisition strongly enhances modeled 21 st century tundra shrub growth and expansion rates. Our results suggest that without NGS nutrient uptake, total shrub aboveground dominance would be ∼50% lower, limited primarily by their inability to grow tall enough to maximize their inherent capacity for light competition. Evergreen shrubs would be more strongly affected because of their relatively lower capacity for nutrient remobilization and acquisition compared to deciduous shrubs. Our results highlight the importance of NGS plant and soil processes on high-latitude biogeochemistry and vegetation dynamics and motivate new observations and model structures to represent these dynamics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

The universal suppressor mutation restores membrane budding defects in the HSV-1 nuclear egress complex by stabilizing the oligomeric lattice

Nuclear egress is an essential process in herpesvirus replication whereby nascent capsids translocate from the nucleus to the cytoplasm. This initial step of nuclear egress–budding at the inner nuclear membrane–is coordinated by the nuclear egress complex (NEC). Composed of the viral proteins UL31 and UL34, NEC deforms the membrane around the capsid as the latter buds into the perinuclear space. NEC oligomerization into a hexagonal membrane-bound lattice is essential for budding because NEC mutants designed to perturb lattice interfaces reduce its budding ability. Previously, we identified an NEC suppressor mutation capable of restoring budding to a mutant with a weakened hexagonal lattice. Using an established in-vitro budding assay and HSV-1 infected cell experiments, we show that the suppressor mutation can restore budding to a broad range of budding-deficient NEC mutants thereby acting as a universal suppressor. Cryogenic electron tomography of the suppressor NEC mutant lattice revealed a hexagonal lattice reminiscent of wild-type NEC lattice instead of an alternative lattice. Further investigation using x-ray crystallography showed that the suppressor mutation promoted the formation of new contacts between the NEC hexamers that, ostensibly, stabilized the hexagonal lattice. This stabilization strategy is powerful enough to override the otherwise deleterious effects of mutations that destabilize the NEC lattice by different mechanisms, resulting in a functional NEC hexagonal lattice and restoration of membrane budding.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Tapping the treasure trove of atypical phages

With advancements in genomics technologies, a vast diversity of ‘atypical’ phages, that is, with single-stranded DNA or RNA genomes, are being uncovered from different ecosystems. Though these efforts have revealed the existence and prevalence of these nonmodel phages, computational approaches often fail to associate these phages with their specific bacterial host(s), while the lack of methods to isolate these phages has limited our ability to characterize infectivity pathways and new gene function. In this review, we call for the development of generalizable experimental methods to better capture this understudied viral diversity via isolation and study them through gene-level characterization and engineering. Establishing a diverse set of new ‘atypical’ phage model systems has the potential to provide many new biotechnologies, including potential uses of these atypical phages in halting the spread of antibiotic resistance and engineering of microbial communities for beneficial outcomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Putative Mixotrophic Nitrifying-Denitrifying Gammaproteobacteria Implicated in Nitrogen Cycling Within the Ammonia/Oxygen Transition Zone of an Oil Sands Pit Lake

Anthropogenically-impacted environments offer the opportunity to discover novel microbial species and metabolisms, which may be undetectable in natural systems. Here, a combined metagenomic and geochemical study in Base Mine Lake, Alberta, Canada, which is the only oil sands end pit lake to date, revealed that nitrification was performed by members from Nitrosomonadaceae, Chloroflexi and unclassified Gammaproteobacteria "MBAE14." While Nitrosomonadaceae and Chloroflexi groups were relatively abundant in the upper oxygenated zones, MBAE14 dominated the hypoxic hypolimnetic zones (approximately 30% of total microbial communities); MBAE14 was not detected in the underlying anoxic tailings. Replication rate analyses indicate that MBAE14 grew in metalimnetic and hypolimnetic water cap regions, most actively at the metalimnetic, ammonia/oxygen transition zone consistent with it putatively conducting nitrification. Detailed genomic analyses of MBAE14 evidenced both ammonia oxidation and denitrification into dinitrogen capabilities. However, the absence of known CO 2 -fixation genes suggests a heterotrophic denitrifying metabolism. Functional marker genes of ammonia oxidation ( amo and hao ) in the MBAE14 genome are homologous with those conserved in autotrophic nitrifiers, but not with those of known heterotrophic nitrifiers. We propose that this novel MBAE14 inhabits the specific ammonia-rich, oxygen and labile organic matter-limited conditions occurring in Base Mine Lake which selectively favors mixotrophic coupled nitrifier denitrification metabolism. Our results highlight the opportunities to better constrain biogeochemical cycles from the application of metagenomics to engineered systems associated with extractive resource sectors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Data for “Fast-decaying plant litter enhances soil carbon in temperate forests, but not through microbial physiological traits”

This data package contains data and code used in the paper “Fast-decaying plant litter enhances soil carbon in temperate forests, but not through microbial physiological traits”. This paper details results from two studies: 1) a laboratory leaf litter incubation experiment (lab experiment) and 2) a multi-site observational field study (field study). Both studies were designed to test the relationships among litter quality, microbial physiological traits, and mineral-associated soil carbon (C). In the lab experiment, we incubated 16 temperate tree litters of differing chemical quality with isotopically distinct soil, measuring microbial physiological traits and the flow of litter-derived C into the mineral-associated soil C pool. In the field study, we sampled soils (0-5 cm) across six eastern US temperate forests, measuring microbial physiological traits, soil abiotic properties, and leaf litter chemistry. The analysis data are provided in two .csv files corresponding to either the lab experiment or field study. Both files contain data on litter chemistry, microbial physiological traits (growth and turnover rates, and carbon use efficiency [CUE]), and the mineral-associated soil C pool. The lab experiment dataset additionally contains litter-derived versus soil-derived soil C, respiration, and litter decomposition parameters. The field study dataset additionally contains site-level climatic information, ectomycorrhizal dominance of plots, and plot-level soil properties. Also provided is the R code and output reproducing the results in the related publication. Analyses were originally performed using R version 3.6.1 using the package "lavaan" and the packages listed on lines 5-7 in the file "data.R".

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Autogenic succession and deterministic recovery following disturbance in soil bacterial communities

The response of bacterial communities to environmental change may affect local to global nutrient cycles; however the dynamics of these communities following disturbance are poorly understood, and are generally attributed to abiotic factors. Here, we subjected soil microcosms to a heat disturbance and followed the community composition of active bacteria over 50 days of recovery. Phylogenetic turnover patterns indicated that biotic interactions shaped the community during recovery, and that the disturbance imposed a strong selective pressure that persisted for up to 10 days, after which the importance of stochastic processes increased. Three successional stages were detected: a primary response (1-4 days after disturbance) in which surviving taxa increased in abundance; a secondary response phase (10-29 days), during which community dynamics slowed down, and a stability phase (after 29 days), during which the community tended towards its original composition. Furthermore, soil bacterial communities, despite their extreme diversity and functional redundancy, respond to disturbances like many macroecological systems and exhibit path-dependent, autogenic dynamics during secondary succession.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater

While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analysis comparing archaeal and bacterial communities in disconnected fracture fluids of the Fennoscandian Shield in Europe. Leveraging a dataset that combines metagenomes, single cell genomes, and metatranscriptomes, we show that groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common core microbiome. Functional expression analysis highlights that these deep groundwater ecosystems foster diverse, yet cooperative communities adapted to this setting. We suggest that these communities stimulate cooperation by expression of functions related to ecological traits, such as aggregate or biofilm formation, while alleviating the burden on microorganisms producing compounds or functions that provide a collective benefit by facilitating reciprocal promiscuous metabolic partnerships with other members of the community. We hypothesize that an episodic lifestyle enabled by reversible bacteriostatic functions ensures the subsistence of the oligotrophic deep groundwater microbiome.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Biochar-compost-based controlled-release nitrogen fertilizer intended for an active microbial community

Nitrogen (N) fertilizers in agriculture suffer losses by volatilization of N to the air, surface runoff and leaching into the soil, resulting in low N use efficiency (NUE) (< 50%) and raising severe environmental pollutions. Controlled- release nitrogen fertilizers (CRNFs) can control the release of N nutrients to NUE in crop production. Different methods were used to develop new CRNFs. However, different CRNF technologies are still underdeveloped due to inadequate controlling on N releasing time and/or unsustainable diffusion. The study on the influences of CRNF processing parameters on microbial conditions are lacking when the CRNFs composed of various bio-ingredients such as biochar, composts, and biowaste. The complexity of processing methods, material biodegradability, and other physical properties make current CRNFs of questionable value in agricultural production. This research aims to develop a novel biochar-compost-based controlled-release urea fertilizer (BCRUF) to preserve microbial properties carried by the compost. The BCRUF was synthesized by pelletizing the 50:50 (dry, wt/wt) mixture of biochar and compost. BCRUF was loaded with urea and then spray-coated with polylactic acid (PLA). The releasing time of two types of BCRUFs, coated and uncoated with PLA, for 80% of N release in water was up to 6 h at three different temperatures (4, 23, and 40 °C), compared to conventional urea fertilizer and commercial environmentally smart N (ESN) fertilizer. The releasing time of coated BCRUF for 80% N release in soil was up to 192 h (8 days). Fourier-transform infrared spectroscopy (FTIR) analysis revealed that no new functional groups were found in the release solution, indicating no new chemical hazards generated. The differential scanning calorimetry (DSC) tests also verified that its thermal stability could be up to 160 °C. The microbe populations in the BCRUF pellets were reduced after the pelleting and drying processes in BCRUF fabrication, but a few bacteria can endure in the air-drying process. BCRUF pellets soaked in water for 4 days retained some bacteria. The BCRUF showed very promising characteristics to improve NUE and sustainability in agricultural production.

58 GEOSCIENCES↗
DOE OSTI2018

Exposure to traffic-related air pollution and the composition of the gut microbiota in overweight and obese adolescents

Highlights: • Traffic-related air pollution (TRAP) was positively correlated with fasting glucose. • TRAP exposure was correlated with specific gut microbial taxa. • These taxa partially explained the correlation between TRAP and fasting glucose. • TRAP exposure may negatively impact metabolic health via the gut microbiota. Traffic-related air pollution (TRAP) exposure has been linked to type 2 diabetes and metabolic dysfunction in humans. Animal studies suggest that air pollutants may alter the composition of the gut microbiota, which may negatively impact metabolic health through changes in the composition and/or function of the gut microbiome.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

ClusterCAD 2.0: an updated computational platform for chimeric type I polyketide synthase and nonribosomal peptide synthetase design

Abstract Megasynthase enzymes such as type I modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) play a central role in microbial chemical warfare because they can evolve rapidly by shuffling parts (catalytic domains) to produce novel chemicals. If we can understand the design rules to reshuffle these parts, PKSs and NRPSs will provide a systematic and modular way to synthesize millions of molecules including pharmaceuticals, biomaterials, and biofuels. However, PKS and NRPS engineering remains difficult due to a limited understanding of the determinants of PKS and NRPS fold and function. We developed ClusterCAD to streamline and simplify the process of designing and testing engineered PKS variants. Here, we present the highly improved ClusterCAD 2.0 release, available at https://clustercad.jbei.org. ClusterCAD 2.0 boasts support for PKS-NRPS hybrid and NRPS clusters in addition to PKS clusters; a vastly enlarged database of curated PKS, PKS-NRPS hybrid, and NRPS clusters; a diverse set of chemical ‘starters’ and loading modules; the new Domain Architecture Cluster Search Tool; and an offline Jupyter Notebook workspace, among other improvements. Together these features massively expand the chemical space that can be accessed by enzymes engineered with ClusterCAD.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

2D reactive transport model of shale chemical weathering and biogeochemical fluxes along a mountainous hillslope, East River Watershed, Colorado: Input files and simulation results

This data package contains input files and simulation results for a two-dimensional (2D) reactive transport model used to quantitatively analyze the coupled hydrological and biogeochemical processes governing shale weathering and associated biogeochemical fluxes under realistic environmental conditions in the high-elevation East River Watershed. These data support the conclusions presented in Stolze et al. (Water Resources Research, under review), "Model-based interpretation of solute exports and carbon partitioning during shale weathering in a mountainous hillslope". The model simulates atmospheric-subsurface gas exchange, subsurface water flow, and shale weathering processes under dynamic, year-scale conditions along a shale-underlain hillslope located in the East River watershed. The simulations were performed using the PFLOTRAN flow and reactive transport code and executed on the Perlmutter supercomputer to leverage its large-scale parallel computing capabilities. The data package contains two zipped folders, "model_input_files" and "simulation_results", and one readme.txt file. "model_input_files" contains the necessary input files to run the calibrated base-base model presented in Stolze et al. (Water Resources Research, under review). "simulation_results" contains a single hdf5 file ("Output_2D_hillslope_model.h5") which includes the results of simulation performed using the base-case model. This file can be opened with HDFView 3.1.4, Python, or MATLAB. "readme.txt" contains relevant information about the base-case model and provides guidelines on how to run the associated input files provided in the folder "model_input_files". Furthermore, readme.txt provides information regarding the model results provided in "Output_2D_hillslope_model.h5" such as matrix dimensionality and output units. Field datasets used to evaluate model performance were collected at three monitoring wells located along a hillslope transect (PLM1, PLM2, and PLM3). Dissolved ion concentration data were collected from November 2016 to October 2021 for Ca, Mg, DIC, Na, K, SO4 (Dong et al., 2025 - dic_npoc_data_2014_2024.zip - DOI:10.15485/1660459; Williams et al., 2025 - anion_data_2014_2024.zip - DOI:10.15485/1668054; Dong et al., 2025 - cation_data_2014_2024.zip - DOI:10.15485/1668055). Note that we used the files named er_PLM1_xx_yy, er_PLM2_xx_yy, and er_PLM3_xx_yy where xx stands for the name of the aqueous species and yy stands for the depth where the measurements were performed. Soil water content ([0 - 1] m) and water table depth were collected from November 2016 to October 2021 (Wan et al., 2024 - Dynamic_water_table__depthsFig2b.csv and Soil_water_content_Fig4e.csv - DOI:10.15485/2322567). Gaseous CO2 concentration were collected from October 2020 to December 2021(Wan et al., 2024 - Soil_CO2_concentrations_Fig4h.csv - DOI:10.15485/2322567) Gaseous CO2 flux from the subsurface to the atmosphere were collected in the vicinity of PLM2 from October 2019 to May 2022 (Wu et al., 2025). Soil microbial biomass concentration was measured from August 2016 to June 2017 (Sorensen et al., 2019 - 2017_East_River_Pumphouse_Microbial_Biomass__1_.csv - DOI:10.15485/1577267) All field data are published as CSV files compatible with Microsoft Excel, MATLAB, and Python, or as text files. The coordinates of the monitoring wells and the CO2(g) flux sensor in the coordinate system WGS84 are: -PLM1: [38.9197710 ; -106.9492750] -PLM2: [38.9201580 ; -106.9487170] -PLM3: [38.9207843 ; -106.9483668] -PLM4: 38.9210060 ; -106.9479528] -CO2(g) flux sensor: [38.9199180 ; -106.9489906] ------------------------------------------------------------------------------------------- This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. This research used resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility using NERSC award BER-ERCAP 23980, BER-ERCAP 28550, and BER-ERCAP 33789.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Binding site for coenzyme A revealed in the structure of pyruvate:ferredoxin oxidoreductase from Moorella thermoacetica

Pyruvate:ferredoxin oxidoreductase (PFOR) is a microbial enzyme that uses thiamine pyrophosphate (TPP), three [4Fe-4S] clusters, and coenzyme A (CoA) in the reversible oxidation of pyruvate to generate acetyl-CoA and carbon dioxide. The two electrons that are generated as a result of pyruvate decarboxylation are used in the reduction of low potential ferredoxins, which provide reducing equivalents for central metabolism, including the Wood–Ljungdahl pathway. PFOR is a member of the 2-oxoacid:ferredoxin oxidoreductase (OFOR) superfamily, which plays major roles in both microbial redox reactions and carbon dioxide fixation. Here, we present a set of crystallographic snapshots of the best-studied member of this superfamily, the PFOR from Moorella thermoacetica ( Mt PFOR). These snapshots include the native structure, those of lactyl-TPP and acetyl-TPP reaction intermediates, and the first of an OFOR with CoA bound. These structural data reveal the binding site of CoA as domain III, the function of which in OFORs was previously unknown, and establish sequence motifs for CoA binding in the OFOR superfamily. Mt PFOR structures further show that domain III undergoes a conformational change upon CoA binding that seals off the active site and positions the thiolate of CoA directly adjacent to the TPP cofactor. Finally, these structural findings provide a molecular basis for the experimental observation that CoA binding accelerates catalysis by 10 5 -fold.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Effects of microbiota-directed foods in gnotobiotic animals and undernourished children

To examine the contributions of impaired gut microbial community development to childhood undernutrition, we combined metabolomic and proteomic analyses of plasma samples with metagenomic analyses of fecal samples to characterize the biological state of Bangladeshi children with severe acute malnutrition (SAM) as they transitioned, after standard treatment, to moderate acute malnutrition (MAM) with persistent microbiota immaturity. Host and microbial effects of microbiota-directed complementary food (MDCF) prototypes targeting weaning-phase bacterial taxa underrepresented in SAM and MAM microbiota were characterized in gnotobiotic mice and gnotobiotic piglets colonized with age- and growth-discriminatory bacteria. A randomized, double-blind controlled feeding study identified a lead MDCF that changes the abundances of targeted bacteria and increases plasma biomarkers and mediators of growth, bone formation, neurodevelopment, and immune function in children with MAM.

59 BASIC BIOLOGICAL SCIENCES↗