Search NASA⌕ Search

SEARCH · Search NASA

Results for “machinery”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Biological upgrading of pyrolysis-derived wastewater: Engineering Pseudomonas putida for alkylphenol, furfural, and acetone catabolism and (methyl)muconic acid production

While biomass-derived carbohydrates have been predominant substrates for biological production of renewable fuels, chemicals, and materials, organic waste streams are growing in prominence as potential alternative feedstocks to improve the sustainability of manufacturing processes. Catalytic fast pyrolysis (CFP) is a promising approach to generate biofuels from lignocellulosic biomass, but it generates a complex, carbon-rich, and toxic wastewater stream that is challenging to process catalytically but could be biologically upgraded to valuable co-products. Here, we implemented modular, heterologous catabolic pathways in the Pseudomonas putida KT2440-derived EM42 strain along with the overexpression of native toxicity tolerance machinery to enable utilization of 89% (w/w) of carbon in CFP wastewater. The dmp monooxygenase and meta-cleavage pathway from Pseudomonas putida CF600 were constitutively expressed to enable utilization of phenol, cresols, 2- and 3-ethyl phenol, and methyl catechols, and the native chaperones clpB, groES, and groEL were overexpressed to improve toxicity tolerance to diverse aromatic substrates. Next, heterologous furfural and acetone utilization pathways were incorporated, and a native alcohol dehydrogenase was overexpressed to improve methanol utilization, generating reducing equivalents. All pathways (encoded by genes totaling ~30 kilobases of DNA) were combined into a single strain that can catabolize a mock CFP wastewater stream as a sole carbon source. Further engineering enabled conversion of all aromatic compounds in the mock wastewater stream to (methyl)muconates with a ~90% (mol/mol) yield. Biological upgrading of CFP wastewater as outlined in this work provides a roadmap for future applications in valorizing other heterogeneous waste streams.

(methyl)muconates↗
DOE OSTI2024

Structural Studies of Inhibitors with Clinically Relevant Influenza Endonuclease Variants

Vital to the treatment of influenza is the use of antivirals such as Oseltamivir (Tamiflu) and Zanamivir (Relenza); however, antiviral resistance is becoming an increasing problem for these therapeutics. The RNA-dependent RNA polymerase acidic N-terminal (PA N ) endonuclease, a critical component of influenza viral replication machinery, is an antiviral target that was recently validated with the approval of Baloxavir Marboxil (BXM). Despite its clinical success, BXM has demonstrated susceptibility to resistance mutations, specifically the I38T, E23K, and A36 V mutants of PAN. To better understand the effects of these mutations on BXM resistance and improve the design of more robust therapeutics, this study examines key differences in protein–inhibitor interactions with two inhibitors and the I38T, E23K, and A36 V mutants. Differences in inhibitor binding were evaluated by measuring changes in binding to PA N using two biophysical methods. The binding mode of two distinct inhibitors was determined crystallographically with both wild-type and mutant forms of PA N . Collectively, these studies give some insight into the mechanism of antiviral resistance of these mutants.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Role of Ribosomal Protein bS1 in Orthogonal mRNA Start Codon Selection

In many bacteria, the location of the mRNA start codon is determined by a short ribosome binding site sequence that base pairs with the 3'-end of 16S rRNA (rRNA) in the 30S subunit. Many groups have changed these short sequences, termed the Shine-Dalgarno (SD) sequence in the mRNA and the anti-Shine-Dalgarno (ASD) sequence in 16S rRNA, to create "orthogonal" ribosomes to enable the synthesis of orthogonal polymers in the presence of the endogenous translation machinery. However, orthogonal ribosomes are prone to SD-independent translation. Ribosomal protein bS1, which binds to the 30S ribosomal subunit, is thought to promote translation initiation by shuttling the mRNA to the ribosome. Thus, a better understanding of how the SD and bS1 contribute to start codon selection could help efforts to improve the orthogonality of ribosomes. Here, we engineered the Escherichia coli ribosome to prevent binding of bS1 to the 30S subunit and separate the activity of bS1 binding to the ribosome from the role of the mRNA SD sequence in start codon selection. We find that ribosomes lacking bS1 are slightly less active than wild-type ribosomes in vitro. Furthermore, orthogonal 30S subunits lacking bS1 do not have an improved orthogonality. Our findings suggest that mRNA features outside the SD sequence and independent of binding of bS1 to the ribosome likely contribute to start codon selection and the lack of orthogonality of present orthogonal ribosomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting

Recent advances in cryo-electron microscopy (cryo-EM) have enabled modeling macromolecular complexes that are essential components of the cellular machinery. The density maps derived from cryo-EM experiments are often integrated with manual, knowledge or artificial intelligence driven, and physics-guided computational methods to build, fit, and refine molecular structures. Going beyond a single stationary- structure determination scheme, it is becoming more common to interpret the experimental data with an ensemble of models, which contributes to an average observation. Hence, there is a need to decide on the quality of an ensemble of protein structures on-the-fly, while refining them against the density maps. Here, we introduce such an adaptive decision making scheme during the molecular dynamics flexible fitting (MDFF) of biomolecules. Using RADICAL-Cybertools, and the new RADICAL augmented MDFF implementation (R-MDFF) is examined in high-performance computing environments for refinement of two protein systems, Adenylate Kinase and Carbon Monoxide Dehydrogenase. For the test cases, use of multiple replicas in flexible fitting with adaptive decision making in R-MDFF improves the overall correlation to the density by 40% relative to the refinements of the brute-force MDFF. The improvements are particularly significant at high, 2 - 3 Å, map resolutions. More importantly, the ensemble model captures key features of biologically relevant molecular dynamics that is inaccessible to a single-model interpretation. Finally, the pipeline is applicable to systems of growing sizes, which is demonstrated using ensemble refinement of capsid proteins from Chimpanzee adenovirus. The overhead for decision making remaining low and robust to computing environments. The software is publicly available on GitHub and includes a short user guide to install the R-MDFF on different computing environments, from local Linux based workstations to High Performance Computing (HPC) environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Structure-Based Analysis of Semisynthetic Anti-TB Rufomycin Analogues

This study employed structural information from cocrystals of rufomycin 4 (1a) and caseinolytic protein C1 (ClpC1)-NTD-wt to guide design and semisynthesis of rufomycin analogues, evaluate their antituberculosis (TB) biological profiles, and establish structure–activity relationships (SAR). Covering three regions of interest (ROIs, A–C) as modification sites, 14 of the 30 semisynthetic analogues (2–31) showed similar or improved MICs relative to the main natural precursors, rufomycins 4/6 (1a/b). Compounds 5 and 27 exhibited up to 10-fold enhanced potency against Mycobacterium tuberculosis (Mtb) in vitro, with MIC values of 1.9 and 1.4 nM, respectively. Evaluation of ClpC1-binding properties used existing ClpC1-NTD complexes with rufomycin 4 (PDB: 6cn8) and ecumicin (PDB: 6pbs) as references. The newly reported X-ray ClpC1-NTD cocrystal structure of 11 (syn. But4-Cl) revealed significant conformational effects involving the side chains of certain amino acids of the heptapeptide and confirmed the importance of ROIs A–C for medicinal chemistry efforts. Observed interactions of the N-terminal tail of ClpC1 with the rufomycin analogues vs ecumicin explains their different modes of inactivating the ClpC1/P1/P2 homeostatic machinery. Collectively, the observations inform further SAR optimization strategies for the rufomycin class of antibiotics and complement our understanding of their mode of action.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Human Coronavirus 229E Infection Alters Histone Proteoforms

Viruses rely on host machinery to replicate, and growing evidence demonstrates that they utilize host epigenetic regulation, including histone modification, to modulate host gene expression for their benefit. Herein, we employed top-down proteomics to quantify histone proteoforms in a model human lung cell line following human coronavirus 229E (HCoV-229E) infection and compared them to mock-infected controls. A total of 572 proteoforms from mock-infected and HCoV-229E infected human lung fibroblast (MRC5) cells (N = 5 per condition) were identified; this included 461 histone proteoforms that were assigned to H2A, H2B, H3, or H4. 200 histone proteoforms were quantifiable, and differential abundance analysis revealed several statistically significant changes in both reversible post-translational modifications (e.g. phosphorylation, acetylation) and the truncation states of core histones. Notably, we found decreased abundance of C-terminally truncated histone H2A and N-terminally truncated histone H3 in HCoV-229E-infected samples. These findings underscore the power of top-down proteomics to resolve unique truncation states of proteoforms and support the hypothesis that viruses alter histone length (removing regulatory sites) to influence host gene expression.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Valence Effects of Fe Impurity for Recovered LiNi 0.6 Co 0.2 Mn 0.2 O 2 Cathode Materials

Iron impurities are generally included in the obtained leaching liquor solution during the hydrometallurgical recycling method of spent lithium-ion batteries (LIBs) due to the usage of iron in battery casings and machinery parts of recycling equipment, which would definitely affect the physical and electrochemical features of the recovered active materials. In this paper, the effects of iron impurity with different valence states (Fe 2+ and Fe 3+ ) and gradient concentrations (0.2, 1.0, and 5.0 at. %) for the obtained LiNi 0.6 Co 0.2 Mn 0.2 O 2 (NCM622) cathodes are fully studied. It is found that Fe3+ impurity could easily lower the tap density and average size of NCM622 particles and even introduce some impurity phases in the NCM622 structure at high concentration (5.0 at. %), leading to much lower specific capacity, worse rate capability, and cycling performance of the Fe 3+ -based NCM622 cathode. On contrast, with certain concentrations of Fe 2+ impurity (0.2 and 1.0 at. %), the NCM622 cathode material exhibits comparable and much better electrochemical properties compared with the virgin NCM622 materials. Based on these results, the valence of Fe impurity should be considered and controlled as well as its concentration during the recycling process design for spent LIBs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Copper–Carbon Nanotube Composites Enabled by Electrospinning for Advanced Conductors

The power losses associated with the electrical resistance of copper (Cu) have generated considerable interest in the development of advanced conductors that incorporate carbon nanotubes (CNTs) into the Cu matrix—ultraconductive Cu (UCC) composites—to increase energy efficiency in various industrial and residential applications, ranging from electric power transmission and rotating machinery to electronic devices. To meet this demand, we describe an electrospinning-based polymer nanofiber templating strategy for the fabrication of UCC composites with electrical and mechanical performance exceeding that of Cu. Our approach involves electrospinning of polyvinylpyrrolidone (PVP)-based solutions containing CNTs into aligned PVP/CNT nanofibers onto Cu foil substrates, followed by vacuum-assisted thermal removal of organic solvent/polymer from the CNT matrix to achieve a uniformly distributed CNT layer on the Cu surface. Following additional Cu deposition, the Cu–CNT–Cu composites demonstrated similar electrical conductivity, higher current carrying capacity, and improved mechanical properties compared with those obtained from reference Cu. Importantly, after the heat treatment, Raman analysis of the CNT network displayed an increased metallic character that supports the enhanced electrical properties of the UCC composites. Thus, we believe that these performance characteristics together with the commercial viability of the present approach could open new possibilities in designing advanced conductors for a broad range of electrical systems and industrial applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Multilayered Cu-Carbon Nanotube Composites for Advanced Conductors

Improving the efficiency of electrical components is critical in reducing energy consumption for various industrial and residential applications, ranging from rotating machinery to all electric devices and electric vehicle (EV) components to power grid systems. Substituting Cu wires with reduced resistance conductors that incorporate carbon nanotubes (CNTs) into Cu─ultraconductive Cu (UCC) composites─has recently been considered a promising strategy to improve energy efficiency, power density, and/or performance across various applications. Here, in this study, we created stable material formulations [CNT-containing polyvinylpyrrolidone (PVP) in dimethylformamide (DMF) solution] and utilized commercially viable fabrication approaches (electrospinning and magnetron sputtering) that produced high-performance multilayered tape-based UCC composite architectures. Increasing the CNT volume fraction by sequential layering of the structure with additional Cu-CNT layers showed a nearly stepwise improved performance in electrical and mechanical properties. This study also provides valuable insight into the effectiveness of nitrogen doping in modifying the conductivity of the CNT matrix. Fabricated prototypes demonstrated a >10% increase in current carrying capacity and >10% improvement in mechanical strength compared to those obtained on pure Cu. We believe that the properties demonstrated here, combined with the scalable manufacturing pathway of our approach, pave the way in designing future advanced conductors for diverse energy efficient and high-performance electrical systems and applications.

Carbon nanotubes↗
DOE OSTI2025

Thioesters Support Efficient Protein Biosynthesis by the Ribosome

Thioesters are critical chemical intermediates in numerous extant biochemical reactions and are invoked as key reagents during prebiotic peptide synthesis on an evolving Earth. Here we asked if a thioester could replace the native oxo-ester in acyl-tRNA substrates during protein biosynthesis by the ribosome. We prepared 3'-thio-3'-deoxyadenosine triphosphate in 10 steps from xylose and demonstrated that it is an effective substrate for the Escherichia coli CCA-adding enzyme, which appends 3'-thio-3'-deoxyadenosine to truncated tRNAs ending with 3'-CC. Using a variety of aminoacyl-tRNA synthetases, flexizymes, or a direct thioester exchange reaction, we prepared a suite of 3'-thio-tRNAs acylated with α- and non-α-amino acids. All were recognized and utilized by wild-type E. coli ribosomes during in vitro translation reactions to generate oligopeptides in yields commensurate with native oxo-ester tRNAs. These results indicate that thioester intermediates widely used in Nature can be co-opted to support the incorporation of natural α-amino acids as well as noncanonical monomers by the extant translational machinery for sequence-defined polymer synthesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

High Temperature Acclimation of Leaf Gas Exchange, Photochemistry, and Metabolomic Profiles in Populus trichocarpa

High temperatures alter the thermal sensitivities of numerous physiological and biochemical processes that impact tree growth and productivity. Foliar and root applications of methanol have been implicated in plant acclimation to high temperature via the C 1 pathway. Here, we characterized temperature acclimation at 35°C of leaf gas exchange, chlorophyll fluorescence and extractable metabolites of potted Populus trichocarpa saplings and examined potential influences of mM concentrations of methanol added during soil watering over a two-month period. Relative to plants grown under the low growth temperature (LGT), high growth temperature (HGT) plants showed a suppression of leaf water use and carbon cycling including transpiration (E), net photosynthesis (P n ), an estimate of photorespiration (R p ), and dark respiration (R d ), attributed to reductions in stomatal conductance and direct negative effects on gas exchange and photosynthetic machinery. In contrast, HGT plants showed an upregulation of non-photochemical quenching (NPQ t ), the optimum temperature for ETR, and leaf isoprene emissions at 40°C. A large number of metabolites (867) were induced under HGT, many implicated in flavonoid biosynthesis highlighting a potentially protective role for these compounds. Methanol application did not significantly alter leaf gas exchange but slightly reduced the suppression of R d and R p by the high growth temperature while slightly impairing ETR, Fv’/Fm’, and q p . However, we were unable to determine if soil methanol was sufficiently taken up by the plant to have a direct effect on foliar processes. A small number of extracted leaf tissue metabolites (55 out of 10,015) showed significantly altered abundances under LGT and methanol treatments relative to water controls, and this increased in compound number (222) at the HGT. The results demonstrate the large physiological and biochemical impacts of high growth temperature on poplar seedlings and highlights the enhancement of the optimum temperature of ETR as a rapid thermal acclimation mechanism. Finally, although no large effect on leaf physiology was observed, the results are consistent with methanol both impairing photochemistry of the light reactions via formaldehyde toxicity, and stimulating photosynthesis and dark respiration through formate oxidation to CO 2 .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Marine Toxicity, Biodegradability, and Rolling-Sliding Tribological Performance of Ionic Liquid-Enhanced Environmentally-Acceptable Lubricants for Tidal Turbomachinery

Environmentally acceptable lubricants (EALs) are increasingly being recognized in many fields including waterpower, hydraulics, water transport, agricultural machinery, offshore wind turbines, etc. Specifically, high-performance EALs are demanded for tidal turbomachinery to ensure high efficiency and reliability and avoid the significant risk of direct contamination of the marine ecosystem upon leaks. Here we report a new development of ionic liquid (IL)-enhanced EALs for tidal energy. One short-chain phosphonium phosphate and one short-chain ammonium phosphate ILs were used as the candidate additives and the IL-containing EALs demonstrated significantly improved lubricating performance, much lower toxicity, and increased biodegradability compared with commercial baselines. Specifically, in a rolling-sliding test simulating the operation of a model tidal turbine gearbox bearing, an EAL containing the ILs at a 0.5 wt % concentration demonstrated 40% lower friction, 45% less wear loss, substantially reduced rolling contact fatigue-induced surface damage, and one order of magnitude lower vibration noise compared with a commercial gear oil. In an EPA standard toxicity test, 90 and 70% survival of marine biota was observed when exposed to an EAL containing 5 wt % of the short-chain phosphonium phosphate and ammonium phosphate ILs, respectively, while the selected commercial gear oil and bioderived additive killed all marine biota. In a standard biodegradability test, 2 wt % addition of the phosphonium phosphate IL not only retained the EAL’s ready biodegradability but further boosted the oil decomposition from a range of 60–80% to a higher level of 80–95%. Conversely, adding the commercial bioderived additive downgraded the EAL from readily to inherently biodegradable. Furthermore, this work offers scientific insights for development of ILs as potential EAL additives for marine energy and broader applications.

additives↗
DOE OSTI2025

Cell-Free-Based Thermophilic Biocatalyst for the Synthesis of Amino Acids from One-Carbon Feedstocks

Bioproduction from one-carbon compounds, such as formate, is an attractive prospect due to reduced energy requirements and the possibility for using CO 2 as a sustainable feedstock. Formate-fixing pathways engineered using Escherichia coli lysate-based cell-free expression (CFE) biocatalysts have the potential to route 100% of feedstock carbon toward chemical synthesis but are undermined by siphoning of in-pathway metabolites and cofactors by the CFE background metabolism. To address this limitation, we engineer a CFE-based thermophilic multienzyme biocatalyst for the synthesis of serine and glycine from formate, bicarbonate, and ammonia. After expression of the thermophilic formate-to-serine pathway in a one-pot reaction, the mesophilic E. coli CFE background machinery is removed by simple heat denaturation, eliminating the siphoning of cofactors, inpathway metabolites, and products. After bioprocess optimization, including pathway gene expression duration and chemical synthesis temperature, we achieve near stoichiometric conversion of formate and bicarbonate to serine and glycine, reaching 97% of stoichiometric yield. The use of a moderately thermophilic biocatalyst allowed chemical synthesis to take place at mesophilic temperatures, enabling the balance of optimal enzyme activity with minimal metabolite/cofactor thermal degradation. In a fed-batch experiment, the biocatalyst shows sustained chemical synthesis rates for 8 h, paving the way toward a continuous bioprocess. Finally, a sensitivity analysis of cofactor usage revealed that the most expensive cofactors, THF and NADPH, can be reduced by 5-fold without significantly lowering product yields. To the best of our knowledge, this is the first instance of expressing a thermophilic pathway in an E. coli lysate-based CFE system to generate a thermophilic biocatalyst for use at mesophilic temperatures. The CFEbased thermophilic formate-to-serine biocatalyst triples the combined serine and glycine yield previously obtained by a CFE-based mesophilic formate-to-serine biocatalyst (30%), and quadruple the yield obtained by a purified enzyme system (22%). Ultimately, this work opens the door to using E. coli lysate-based CFE for thermophilic biocatalyst generation to achieve high chemical synthesis yields.

bacteria↗
DOE OSTI2026

Quantitative Dissection of Agrobacterium Virulence to Generate a Synthetic Ti Plasmid

Agrobacterium is not only a costly plant pathogen but is also an essential tool for plant transformation. Though Agrobacterium-mediated transformation (AMT) has been heavily studied, its polygenic nature and complex transcriptional regulation make identification of the genetic basis of transformational efficiency difficult through traditional genetic and bioinformatic approaches. Here, we use a bottom-up synthetic approach to systematically engineer the tumor-inducing plasmid (pTi), wherein the majority of virulence machinery is encoded. Using a validated toolkit to control Agrobacterium gene expression in planta, we perform a quantitative dissection of AMT to investigate the contributions of critical vir-genes at different expression levels. We construct a synthetic pTi capable of transient plant and stable fungal transformation and characterize bottlenecks and solutions for complex polygenic synthetic pTi designs. Our reductionist approach demonstrates how bottom-up engineering can be used to dissect and elucidate the genetic underpinnings of complex biological traits, laying the foundation for future engineering to establish full synthetic control over the critical process of AMT.

Agrobacterium-mediated transformation↗
DOE OSTI2022

Assembly and Evolution of Artificial Metalloenzymes within E. coli Nissle 1917 for Enantioselective and Site-Selective Functionalization of C–H and C=C Bonds

The potential applications afforded by the generation and reactivity of artificial metalloenzymes (ArMs) in microorganisms are vast. Here we show that a non-pathogenic E. coli strain, Nissle 1917 (EcN), is a suitable host for the creation of ArMs from cytochrome P450s and artificial heme cofactors. An outer-membrane receptor in EcN transports an iridium porphyrin into the cell, and the Ir-CYP119 (CYP119 containing iridium porphyrin) assembled in vivo catalyzes carbene insertions into benzylic C-H bonds enantioselectively and site-selectively. The application of EcN as a whole-cell screening platform eliminates the need for laborious processing procedures, drastically increases the ease and throughput of screening, and accelerates the development of Ir-CYP119 with improved catalytic properties. Studies to identify the transport machinery suggest that a transporter different from the previously assumed ChuA receptor serves to usher the iridium porphyrin into the cytoplasm.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

AI Improves the Accuracy, Reliability, and Economic Value of Continental‐Scale Flood Predictions

Accurate flood early warnings are critical to minimize damage and loss of life. Current large‐scale operational forecasting systems, however, have limited accuracy, description of uncertainty, and computational efficiency. While Artificial intelligence (AI) can address these limitations in principle, the accuracy and reliability of AI forecasts have thus far proven insufficient. Here we present a novel hybrid framework that integrates AI‐based machinery termed Errorcastnet (ECN) with the National Water Model (NWM) to showcase the potential of ensemble AI flood forecasts over the contiguous U.S. ECN boosts prediction accuracy four‐ to six‐fold across lead times of 1–10 days, while providing uncertainty quantification. It also outperforms Google's state‐of‐the‐art global AI model. ECN‐based forecasts offer superior economic value (up to four‐fold) for decision‐making as compared to those from NWM alone. ECN performs well in varied ecoregions, physiography, and land management conditions. The framework is computationally efficient, enabling national‐scale ensemble forecasts in minutes.

artificial intelligence↗
DOE OSTI2022

Soils and sediments host Thermoplasmata archaea encoding novel copper membrane monooxygenases (CuMMOs)

Copper membrane monooxygenases (CuMMOs) play critical roles in the global carbon and nitrogen cycles. Organisms harboring these enzymes perform the first, and rate limiting, step in aerobic oxidation of ammonia, methane, or other simple hydrocarbons. Within archaea, only organisms in the order Nitrososphaerales (Thaumarchaeota) encode CuMMOs, which function exclusively as ammonia monooxygenases. From grassland and hillslope soils and aquifer sediments, we identified 20 genomes from distinct archaeal species encoding divergent CuMMO sequences. These archaea are phylogenetically clustered in a previously unnamed Thermoplasmatota order, herein named the Ca. Angelarchaeales. The CuMMO proteins in Ca. Angelarchaeales are more similar in structure to those in Nitrososphaerales than those of bacteria, and contain all functional residues required for general monooxygenase activity. Ca. Angelarchaeales genomes are significantly enriched in blue copper proteins (BCPs) relative to sibling lineages, including plastocyanin-like electron carriers and divergent nitrite reductase-like (nirk) 2-domain cupredoxin proteins co-located with electron transport machinery. Ca. Angelarchaeales also encode significant capacity for peptide/amino acid uptake and degradation and share numerous electron transport mechanisms with the Nitrososphaerales. Ca. Angelarchaeales are detected at high relative abundance in some of the environments where their genomes originated from. While the exact substrate specificities of the novel CuMMOs identified here have yet to be determined, activity on ammonia is possible given their metabolic and ecological context. The identification of an archaeal CuMMO outside of the Nitrososphaerales significantly expands the known diversity of CuMMO enzymes in archaea and suggests previously unaccounted organisms contribute to critical global nitrogen and/or carbon cycling functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structural asymmetry governs the assembly and GTPase activity of McrBC restriction complexes

Abstract McrBC complexes are motor-driven nucleases functioning in bacterial self-defense by cleaving foreign DNA. The GTP-specific AAA + protein McrB powers translocation along DNA and its hydrolysis activity is stimulated by its partner nuclease McrC. Here, we report cryo-EM structures of Thermococcus gammatolerans McrB and McrBC, and E. coli McrBC. The McrB hexamers, containing the necessary catalytic machinery for basal GTP hydrolysis, are intrinsically asymmetric. This asymmetry directs McrC binding so that it engages a single active site, where it then uses an arginine/lysine-mediated hydrogen-bonding network to reposition the asparagine in the McrB signature motif for optimal catalytic function. While the two McrBC complexes use different DNA-binding domains, these contribute to the same general GTP-recognition mechanism employed by all G proteins. Asymmetry also induces distinct inter-subunit interactions around the ring, suggesting a coordinated and directional GTP-hydrolysis cycle. Our data provide insights into the conserved molecular mechanisms governing McrB family AAA + motors.

59 BASIC BIOLOGICAL SCIENCES↗