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Results for “competition for substrate”

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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Assessing the impact of substrate-level enzyme regulations limiting ethanol titer in Clostridium thermocellum using a core kinetic model

Clostridium thermocellum is a promising candidate for consolidated bioprocessing because it can directly ferment cellulose to ethanol. Despite significant efforts, achieved yields and titers fall below industrially relevant targets. This implies that there still exist unknown enzymatic, regulatory, and/or possibly thermodynamic bottlenecks that can throttle back metabolic flow. By (i) elucidating internal metabolic fluxes in wild-type C. thermocellum grown on cellobiose via 13 C-metabolic flux analysis ( 13 C-MFA), (ii) parameterizing a core kinetic model, and (iii) subsequently deploying an ensemble-docking workflow for discovering substrate-level regulations, this paper aims to reveal some of these factors and expand our knowledgebase governing C. thermocellum metabolism. Generated 13 C labeling data were used with 13 C-MFA to generate a wild-type flux distribution for the metabolic network. Notably, flux elucidation through MFA alluded to serine generation via the mercaptopyruvate pathway. Using the elucidated flux distributions in conjunction with batch fermentation process yield data for various mutant strains, we constructed a kinetic model of C. thermocellum core metabolism (i.e. k-ctherm138). Subsequently, we used the parameterized kinetic model to explore the effect of removing substrate-level regulations on ethanol yield and titer. Upon exploring all possible simultaneous (up to four) regulation removals we identified combinations that lead to many-fold model predicted improvement in ethanol titer. In addition, by coupling a systematic method for identifying putative competitive inhibitory mechanisms using K-FIT kinetic parameterization with the ensemble-docking workflow, we flagged 67 putative substrate-level inhibition mechanisms across central carbon metabolism supported by both kinetic formalism and docking analysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A Discrete Dendrite Dynamics Model for Epitaxial Columnar Grain Growth in Metal Additive Manufacturing with Application to Inconel

Epitaxial columnar grain growth is a prevalent microstructural feature in the additive manufacturing (AM) of metal components such as Inconel, with cubic unit cell crystal lattice structure (face centered cubic (FCC) or body centered cubic (BCC)). These columnar grains evolve from the partly molten grains in the substrate or the solidified metal. This work proposes an efficient model to simulate the competitive growth of epitaxial columnar dendritic grains. The proposed model tracks the dynamic changes in the dendrites emanating from discrete points along the solid/liquid interface of a quasi-steady melt pool (MP). These dynamic changes include convergence and divergence of growing dendrites. The model is extended to predict the microstructure of large 3D parts and experimentally validated by comparing the simulation results for laser powder bed fusion (L-PBF) and wire-arc additive manufacturing (WAAM) processes. The microstructure and pole figures are predicted for Inconel 718 samples produced by L-PBF and Inconel 740H samples produced by WAAM processes. Finally, the model predictions compare well with the observed microstructure and pole figures results for both the L-PBF and WAAM processes.

20 FOSSIL-FUELED POWER PLANTS↗
DOE OSTI2020

Area-selective atomic layer deposition enabled by competitive adsorption

In this work, we investigate the atomic layer deposition (ALD) of ZrO2 thin films on Cu and SiO2 substrates, using Zr[N(C2H5CH3)]4 as the thin-film precursor, and H2O or O2 as the coreactants. Here, we introduce 3-hexyne as a coadsorbate molecule during the thin-film precursor half-cycle and examine its effect on the selectivity of growth. We find that 3-hexyne strongly inhibits growth on Cu, while having essentially no effect on the growth on SiO2. Calculations using dispersion-inclusive density functional theory verify that 3-hexyne undergoes sp → sp2 rehybridization on Cu, which results in strong chemisorption on the metal surface, while only binding weakly to SiO2 via nonbonded van der Waals/dispersion interactions. After 10 cycles of ALD using 3-hexyne as the coadsorbate, we observed the deposition of ∼1.5 nm of ZrO2 on SiO2. On a Cu substrate, we only detected <0.15 nm of ZrO2 after the same number of cycles of ALD. At this point in the process, we find evidence of the formation of cuprous oxide (Cu2O) from in situ x-ray photoelectron spectroscopy and a significant increase in the roughness of the Cu substrate. We conclude that both factors likely contribute to the loss of selectivity due to the formation of sites (e.g., Cu2O) that bind 3-hexyne less strongly and/or an increase in the density of highly reactive sites (e.g., steps, kinks) that promote dissociative chemisorption of the thin-film precursor.

Suh, Taewon (ORCID:0000000163823811)↗
DOE OSTI2025

Electric Drive Technologies Consortium (EDTC)/ Cost competitive, high-Performance, highly Reliable (CPR) Power Devices on 4H-SiC (Final Report)

4H-Silicon carbide (4H-SiC) is a wide bandgap semiconductor that offers superior material properties over silicon, including higher critical electric field, thermal conductivity, and electron saturation velocity. These advantages make 4H-SiC highly attractive for high-voltage, high-efficiency power electronics. However, realizing the full potential of SiC requires device technologies that are not only high-performing but also manufacturable and reliable under real-world operating conditions. This report summarizes the outcomes of a five-year R&D effort funded by the U.S. Department of Energy (DOE) under the Electric Drive Technologies Consortium (EDTC), focused on developing cost-competitive, high-performance, and highly reliable (CPR) power devices on 4H-SiC substrates. The program targeted scalable and manufacturable 1.2 kV-class SiC MOSFETs optimized for next-generation electric vehicles, renewable energy systems, and industrial power conversion. The project delivered transformative advancements in SiC power device performance and ruggedness. Particularly, Specific on-resistance (R on,sp ) was reduced by up to 37%, from ~4.0 m$\Omega \cdot$cm 2 in earlier designs to an industry-leading 2.40 m$\Omega \cdot$cm 2 , driven by optimized doping, refined JFET widths, and layout engineering. Breakdown voltages (BV) exceeded 1600 V, marking improvement over legacy baselines, and demonstrating the robustness of newly implemented junction profiles and edge terminations. Short-circuit withstand time (SCWT) saw a remarkable 4$\times$ increase, from ~2 $\mu$s to over 8 $\mu$s, achieved through the successful deployment of deep P-well structures (~1.8–2.0 $\mu$m) via channeling implantation. This innovative process breakthrough enabled precise junction formation without MeV-class implantation tools, reduced leakage under high field stress, and allowed even the shortest-channel devices (down to 0.3 $\mu$m) to achieve both high BV and excellent ruggedness—breaking the traditional trade-off between conduction efficiency and blocking capability. Several novel architectures pushed the performance envelope further. JBSFETs—featuring embedded Schottky portions—eliminated bipolar degradation and drastically reduced third-quadrant leakage, while Ladder MOSFETs introduced a clever orthogonal conduction path that achieved a 15.4% reduction in R on,sp over standard linear designs. Switching performance reached new benchmarks: short-channel devices showed a 31% reduction in total switching energy compared to 0.5 $\mu$m counterparts, while maintaining manageable gate drive requirements. Layout-optimized structures not only improved transconductance but also accelerated switching transitions, pointing to real-world benefits in converter-level efficiency. The devices also passed rigorous reliability validation. Stress-tested across TDDB, HTGB, HTRB, HVP, and burn-in, the devices screened under 30 V/10 hr and 43 V/1 s protocols consistently exhibited tighter lifetime distributions and long-term oxide robustness. These screening techniques proved effective in identifying latent defects and ensuring deployment-grade reliability. Meanwhile, advanced 3D TCAD simulations revealed and resolved electric field hotspots—particularly in HEXFET corners—where fields exceeding 4.8 MV/cm were mitigated through geometry-aware layout corrections. Overall, the results of this project demonstrate a manufacturable and scalable SiC power device platform that addresses key DOE performance targets for efficient, robust, and reliable 1.2kV 4H-SiC Power Devices. The developed technologies represent a meaningful step forward in the commercial readiness of high-voltage SiC solutions and provide a strong foundation for continued advancement in wide bandgap power electronics.

42 ENGINEERING↗
NASA NTRS1974

Effect of pollutant gases on ozone production by simulated solar radiation

The present investigation provides some information related to the problem of ozone destruction by nitric oxide emission from high flying vehicles. It is found that CO and H2O can counteract NO destruction of O3 in laboratory simulations. The addition of CO and H2O to aircraft exhausts could be a practical means of reducing the damage of the UV-filtering ozone layer. It is also discovered that NO is not regenerated as it destroys ozone, except at low stratospheric pressures. It is believed that the presence of H2O and CO gives rise to a series of reactions which provide a kinetically competitive pathway for the NO, causing it to go into NO2 production via these substrates rather than via O3.

Wong, E. L.↗
DOE OSTI2020

The role of iron in magnetic damping of Mg(Al,Fe) 2 O 4 spinel ferrite thin films

© 2020 Author(s). We have investigated magnesium aluminum ferrite thin films with a range of iron concentrations and identified the optimal iron content to obtain high crystalline quality thin films with the low magnetic damping required for spin current-based applications. Epitaxial MgAl 2-x FexO4 films with 0.8 < x < 2.0 were grown by pulsed laser deposition on single crystal MgAl2O4 substrates and were characterized structurally and magnetically. We find that the x = 1.5 composition minimizes the room-temperature magnetic damping with a typical Gilbert damping parameter of α eff = 1.8 × 10-3. This minimized damping is governed by a competition between the more robust magnetic ordering with increased iron content, x, and the more defective structure due to larger film-substrate lattice mismatch with increased iron content. The temperature-dependent magnetization curves indicate that Tc is suppressed below room temperature for iron content x ≤ 1.2 and eventually suppressed entirely for x = 0.8. X-ray magnetic circular dichroism results indicate that for all x the magnetic moment is dominated by Fe 3 + cations distributed in a 60:40 ratio on the octahedral and tetrahedral sites, with minimal contribution from Fe 2 + cations. Films with x = 1.4-1.6 exhibit very strong ferromagnetic resonance and low Gilbert damping with α eff = (1.8-6) × 10-3, making them ideal candidates for microwave and spintronic applications.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Inhibition of the C1s Protease and the Classical Complement Pathway by 6-(4-Phenylpiperazin-1-yl)Pyridine-3-Carboximidamide and Chemical Analogs

Abstract The classical pathway (CP) is a potent mechanism for initiating complement activity and is a driver of pathology in many complement-mediated diseases. The CP is initiated via activation of complement component C1, which consists of the pattern recognition molecule C1q bound to a tetrameric assembly of proteases C1r and C1s. Enzymatically active C1s provides the catalytic basis for cleavage of the downstream CP components, C4 and C2, and is therefore an attractive target for therapeutic intervention in CP-driven diseases. Although an anti-C1s mAb has been Food and Drug Administration approved, identifying small-molecule C1s inhibitors remains a priority. In this study, we describe 6-(4-phenylpiperazin-1-yl)pyridine-3-carboximidamide (A1) as a selective, competitive inhibitor of C1s. A1 was identified through a virtual screen for small molecules that interact with the C1s substrate recognition site. Subsequent functional studies revealed that A1 dose-dependently inhibits CP activation by heparin-induced immune complexes, CP-driven lysis of Ab-sensitized sheep erythrocytes, CP activation in a pathway-specific ELISA, and cleavage of C2 by C1s. Biochemical experiments demonstrated that A1 binds directly to C1s with a K d of ∼9.8 μM and competitively inhibits its activity with an inhibition constant (K i) of ∼5.8 μM. A 1.8-Å-resolution crystal structure revealed the physical basis for C1s inhibition by A1 and provided information on the structure–activity relationship of the A1 scaffold, which was supported by evaluating a panel of A1 analogs. Taken together, our work identifies A1 as a new class of small-molecule C1s inhibitor and lays the foundation for development of increasingly potent and selective A1 analogs for both research and therapeutic purposes.

Immunology↗
DOE OSTI2020

Soil aminopeptidase induction is unaffected by inorganic nitrogen availability

Soil microbes release a variety of aminopeptidase enzymes to degrade proteins into their constituent amino acid monomers, thereby increasing amino acid availability in the near-cell environment. In this work we investigated how inorganic N availability controls the substrate induction response of aminopeptidase enzymes by conducting protein amendment experiments via gelatin addition to fertilized and unfertilized soil from a long-term N addition study. Protein addition triggered a measurable increase in enzyme activity, which we interpreted as an induction response, in all five of the aminopeptidase enzymes we investigated. The magnitude of these induction responses did not differ by fertilization regime even when unamended aminopeptidase activity differed between long-term fertilization treatments. Though soil microbes are thought to release aminopeptidase enzymes as a means of cellular N acquisition at steady-state concentrations, our results suggest that they use the same enzymes to access protein-derived C as an energetic resource at non-steady-state conditions, such as those triggered by the substrate induction response. The substrate induction response of aminopeptidase enzymes is therefore best viewed as a means of microbial competition for the substantial energetic resources available in protein subsidies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Microwave-assisted C–H oxidation of methylpyridylheteroarenes via a Kornblum-Type reaction

Expansion of the operational capacity of soft-Lewis basic complexant scaffolds towards improved physical properties for the chemoselective sequestration of minor actinides from the electronically similar lanthanides necessitates rapid access to synthons for efficient complexant construction for downstream employment in separations assays. Pursuant to the aforementioned, we were interested in exploring the potential utility of advanced, unsymmetric heteroarene constructs for separations which required access to pyridyl carbaldehydes. Limited commercial availability of synthetic precursors inspired our effort to define a chemoselective, microwave assisted, Kornblum-type reaction via C–H functionalization. This efficient reaction sequence uses I 2 as a mild oxidant without acidic or basic additives, in concert with DMSO as the solvent and putative oxygen source to afford a diverse array of heteroaryl products devoid of competitive remote methyl group oxidation, or degradation of the heteroaryl N atom. Finally, method development, substrate scope, and a preliminary mechanistic hypothesis supported by Density Functional Theory are presented herein.

1,2,4-triazine↗
DOE OSTI2020

Fungal Community, Not Substrate Quality, Drives Soil Microbial Function in Northeastern U.S. Temperate Forests

Mycorrhizal fungi can affect soil organic matter cycling through several mechanisms including priming, nutrient competition, and direct enzyme production. Differences in nutrient foraging strategies between ectomycorrhizal (EcM) and arbuscular mycorrhizal (AM) fungi produce divergent belowground dynamics: where EcM can take up organic nitrogen and directly break down soil organic matter (SOM) by producing enzymes, AM fungi are limited to scavenging mineral N. EcM-associated tree species also have leaf litter with relatively higher ratios of carbon to nitrogen (C:N), and belowground saprotrophic communities more dominated by fungi. Consequently, free-living microbes in EcM-dominated soils should experience nitrogen limitation, with subsequent increases in enzyme production and decreased carbon use efficiency (CUE). However, the relative importance of the effects of substrate quality and fungal community composition on enzyme production and CUE are unclear. To assess this distinction, we sampled the organic horizon and 10 cm of the mineral horizon in northern temperate forest soils along a gradient of EcM dominance. We characterized fungal community composition by measuring EcM relative abundances from extracted fungal DNA and the fungal to bacterial (F:B) ratios from phospholipid fatty acid (PLFA) analysis. We assessed soil substrate quality as the soil C:N ratio. Soil microbial functions were measured as potential activities of five hydrolytic and two oxidative enzymes, and microbial CUE. We found that the fungal community, represented by either the F:B ratio, EcM relative abundance, or both, affected CUE and six measured enzyme activities, while the C:N ratio affected only oxidative and chitin-targeting extracellular enzyme activities. Our results highlight the use of EcM relative dominance as a predictor of soil microbial community composition and function independent of substrate quality.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Carbonate Minerals and Dissimilatory Iron-Reducing Organisms Trigger Synergistic Abiotic and Biotic Chain Reactions under Elevated CO 2 Concentration

Increasing CO 2 emission has resulted in pressing climate and environmental issues. While abiotic and biotic processes mediating the fate of CO 2 have been studied separately, their interactions and combined effects have been poorly understood. To explore this knowledge gap, an iron-reducing organism, Orenia metallireducens, was cultured under 18 conditions that systematically varied in headspace CO 2 concentrations, ferric oxide loading, and dolomite (CaMg(CO 3 ) 2 ) availability. The results showed that abiotic and biotic processes interactively mediate CO 2 acidification and sequestration through "chain reactions", with pH being the dominant variable. Specifically, dolomite alleviated CO 2 stress on microbial activity, possibly via pH control that transforms the inhibitory CO 2 to the more benign bicarbonate species. The microbial iron reduction further impacted pH via the competition between proton (H + ) consumption during iron reduction and H + generation from oxidization of the organic substrate. Under Fe(III)-rich conditions, microbial iron reduction increased pH, driving dissolved CO 2 to form bicarbonate. Spectroscopic and microscopic analyses showed enhanced formation of siderite (FeCO 3 ) under elevated CO 2 , supporting its incorporation into solids. In conclusion, the results of these CO 2 -microbe-mineral experiments provide insights into the synergistic abiotic and biotic processes that alleviate CO 2 acidification and favor its sequestration, which can be instructive for practical applications (e.g., acidification remediation, CO 2 sequestration, and modeling of carbon flux).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics

Marinobacter spp. are cosmopolitan in saline environments, displaying a diverse set of metabolisms that allow them to competitively occupy these environments, some of which can be extreme in both salinity and temperature. Here, we introduce a distinct cluster of Marinobacter genomes, composed of novel isolates and in silico assembled genomes obtained from subzero, hypersaline cryopeg brines, relic seawater-derived liquid habitats within permafrost sampled near Utqiaġvik, Alaska. Using these new genomes and 45 representative publicly available genomes of Marinobacter spp. from other settings, we assembled a pangenome to examine how the new extremophile members fit evolutionarily and ecologically, based on genetic potential and environmental source. This first genus-wide genomic analysis revealed that Marinobacter spp. in general encode metabolic pathways that are thermodynamically favored at low temperature, cover a broad range of organic compounds, and optimize protein usage, e.g., the Entner–Doudoroff pathway, the glyoxylate shunt, and amino acid metabolism. The new isolates contributed to a distinct clade of subzero brine-dwelling Marinobacter spp. that diverged genotypically and phylogenetically from all other Marinobacter members. The subzero brine clade displays genomic characteristics that may explain competitive adaptations to the extreme environments they inhabit, including more abundant membrane transport systems (e.g., for organic substrates, compatible solutes, and ions) and stress-induced transcriptional regulatory mechanisms (e.g., for cold and salt stress) than in the other Marinobacter clades. We also identified more abundant signatures of potential horizontal transfer of genes involved in transcription, the mobilome, and a variety of metabolite exchange systems, which led to considering the importance of this evolutionary mechanism in an extreme environment where adaptation via vertical evolution is physiologically rate limited. Assessing these new extremophile genomes in a pangenomic context has provided a unique view into the ecological and evolutionary history of the genus Marinobacter , particularly with regard to its remarkable diversity and its opportunism in extremely cold and saline environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Graphene nanoribbons for quantum electronics

Graphene nanoribbons (GNRs) are a family of one-dimensional (1D) materials with a graphitic lattice structure. GNRs possess high mobility and current-carrying capability, sizeable bandgap and versatile electronic properties, which make them promising candidates for quantum electronic applications. In the past 5 years, progress has been made towards atomically precise bottom-up synthesis of GNRs and heterojunctions that provide an ideal platform for functional molecular devices, as well as successful production of semiconducting GNR arrays on insulating substrates potentially useful for large-scale digital circuits. With further development, GNRs can be envisioned as a competitive candidate material in future quantum information sciences. In this Perspective, we discuss recent progress in GNR research and identify key challenges and new directions likely to develop in the near future.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Zero-Carbon Biofuels: An Optimized Two-Stage System for High Productivity Conversion of CO2 to Liquid Fuels

In MIT’s Zero-Carbon Biofuels work, under ARPAe’s EcoSynBio funding, we capitalized on our previously developed technology of the oleaginous yeast, Yarrowia lipolytica, engineered to produce high titer biodiesel-like lipids and alkanes, and set out to reduce or eliminate CO 2 generation during lipid production. We set out to do this by both engineering Y. lipolytica with the necessary enzymes to allow the generation of reducing equivalents from H 2 , formic acid, or methanol, and, in parallel, installing the non-oxidative glycolysis (NOG) pathway. The goal was that combination of these two would enable stoichiometric conversion of glucose and acetate to biodiesel products. Furthermore, our ARPAe Electrofuels funded research, yielded a very innovative two-stage system where gases comprising CO 2 and H 2 are used for the production of liquid fuels. Acetate is produced from CO 2 and H 2 , via acetogenic fermentation, in the first stage as the intermediary product, then fed to Y. lipolytica in the second stage, for conversion to lipids and alkanes. To increase the commercial competitiveness of the two-stage system, by improvement to the overall productivity, we recently showed that synergistic substrate co-feeding drastically enhances CO 2 fixation rates and set out to explore additional co-substrate pairs, including methanol and formic acid, in order to maximize acetate productivity. Finally, given the attractiveness as a biofuel, we also set out to attempt an important increase in the production of alkanes over lipids in Yarrowia.

10 SYNTHETIC FUELS↗
NASA NTRS2004

Utility of Thin-Film Solar Cells on Flexible Substrates for Space Power

The thin-film solar cell program at NASA GRC is developing solar cell technologies for space applications which address two critical metrics: specific power (power per unit mass) and launch stowed volume. To be competitive for many space applications, an array using thin film solar cells must significantly increase specific power while reducing stowed volume when compared to the present baseline technology utilizing crystalline solar cells. The NASA GRC program is developing two approaches. Since the vast majority of the mass of a thin film solar cell is in the substrate, a thin film solar cell on a very lightweight flexible substrate (polymer or metal films) is being developed as the first approach. The second approach is the development of multijunction thin film solar cells. Total cell efficiency can be increased by stacking multiple cells having bandgaps tuned to convert the spectrum passing through the upper cells to the lower cells. Once developed, the two approaches will be merged to yield a multijunction, thin film solar cell on a very lightweight, flexible substrate. The ultimate utility of such solar cells in space require the development of monolithic interconnections, lightweight array structures, and ultra-lightweight support and deployment techniques.

Dickman, J. E.↗
DOE OSTI2022

Controlling the Balance between Remote, Pinhole, and van der Waals Epitaxy of Heusler Films on Graphene/Sapphire

Remote epitaxy is promising for the synthesis of lattice-mismatched materials, exfoliation of membranes, and reuse of expensive substrates. However, clear experimental evidence of a remote mechanism remains elusive. Alternative mechanisms such as pinhole-seeded epitaxy or van der Waals epitaxy can often explain the resulting films. Here, in this study, we show that growth of the Heusler compound GdPtSb on clean graphene/sapphire produces a 30° rotated (R30) superstructure that cannot be explained by pinhole epitaxy. With decreasing temperature, the fraction of this R30 domain increases, compared to the direct epitaxial R0 domain, which can be explained by a competition between remote versus pinhole epitaxy. Careful graphene/substrate annealing and consideration of the relative lattice mismatches are required to obtain epitaxy to the underlying substrate across a series of other Heusler films, including LaPtSb and GdAuGe. The R30 superstructure provides a possible experimental fingerprint of remote epitaxy, since it is inconsistent with the leading alternative mechanisms.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics

Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable successional dynamics on complex, natural organic matter, functionally redundant bacteria can coexist by partitioning low-concentration substrates even though they compete for one simple, dominant substrate. We allowed ocean microbial communities to self-assemble on leachates of the brown seaweed Fucus vesiculosus and then analyzed the competition among 10 taxonomically diverse isolates representing two distinct stages of the succession. All, but two isolates, exhibited an average of 90% ± 6% pairwise overlap in resource use, and functional redundancy of isolates from the same assembly stage was higher than that from between assembly stages, leading us to construct a simpler four-isolate community with two isolates from each of the early and late stages. We found that, although the short-term dynamics of the four-isolate communities in F. vesiculosus leachate was dependent on initial isolate ratios, in the long term, the four isolates stably coexist in F. vesiculosus leachate, albeit with some strains at low abundance. We therefore explored the potential for nonredundant substrate use by genomic content analysis and RNA expression patterns. This analysis revealed that the four isolates mainly differed in peripheral metabolic pathways, such as the ability to degrade pyrimidine, leucine, and tyrosine, as well as aromatic substrates. These results highlight the importance of fine-scale differences in metabolic strategies for supporting the frequently observed coexistence of large numbers of rare organisms in natural microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1998

The N-end rule pathway catalyzes a major fraction of the protein degradation in skeletal muscle

In skeletal muscle, overall protein degradation involves the ubiquitin-proteasome system. One property of a protein that leads to rapid ubiquitin-dependent degradation is the presence of a basic, acidic, or bulky hydrophobic residue at its N terminus. However, in normal cells, substrates for this N-end rule pathway, which involves ubiquitin carrier protein (E2) E214k and ubiquitin-protein ligase (E3) E3alpha, have remained unclear. Surprisingly, in soluble extracts of rabbit muscle, we found that competitive inhibitors of E3alpha markedly inhibited the 125I-ubiquitin conjugation and ATP-dependent degradation of endogenous proteins. These inhibitors appear to selectively inhibit E3alpha, since they blocked degradation of 125I-lysozyme, a model N-end rule substrate, but did not affect the degradation of proteins whose ubiquitination involved other E3s. The addition of several E2s or E3alpha to the muscle extracts stimulated overall proteolysis and ubiquitination, but only the stimulation by E3alpha or E214k was sensitive to these inhibitors. A similar general inhibition of ubiquitin conjugation to endogenous proteins was observed with a dominant negative inhibitor of E214k. Certain substrates of the N-end rule pathway are degraded after their tRNA-dependent arginylation. We found that adding RNase A to muscle extracts reduced the ATP-dependent proteolysis of endogenous proteins, and supplying tRNA partially restored this process. Finally, although in muscle extracts the N-end rule pathway catalyzes most ubiquitin conjugation, it makes only a minor contribution to overall protein ubiquitination in HeLa cell extracts.

Non-NASA Center↗