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DOE OSTI2020

Regulatory interventions improve the biosynthesis of limiting amino acids from methanol carbon to improve synthetic methylotrophy in Escherichia coli

Synthetic methylotrophy aims to engineer methane and methanol utilization pathways in platform hosts like Escherichia coli for industrial bioprocessing of natural gas and biogas. While recent attempts to engineer synthetic methylotrophs have proved successful, autonomous methylotrophy, that is, the ability to utilize methane or methanol as sole carbon and energy substrates, has not yet been realized. Here, we address an important limitation of autonomous methylotrophy in E. coli: the inability of the organism to synthesize several amino acids when grown on methanol. We targeted global and local amino acid regulatory networks. Those include removal of amino acid allosteric feedback inhibition (argA H15Y , ilvA L447F , hisG E271K , leuA G462D , proB D107N , thrA S345F, trpE S40F ), knockouts of transcriptional repressors (ihfA, metJ); and overexpression of amino acid biosynthetic operons (hisGDCBHAFI, leuABCD, thrABC, trpEDCBA) and transcriptional regulators (crp, purR). Compared to the parent methylotrophic E. coli strain that was unable to synthesize these amino acids from methanol carbon, these strategies resulted in improved biosynthesis of limiting proteinogenic amino acids (histidine, leucine, lysine, methionine, phenylalanine, threonine, tyrosine) from methanol carbon. In several cases, improved amino acid biosynthesis from methanol carbon led to improvements in methylotrophic growth in methanol minimal medium supplemented with a small amount of yeast extract. Here, this study addresses a key limitation currently preventing autonomous methylotrophy in E. coli and possibly other synthetic methylotrophs and provides insight as to how this limitation can be alleviated via global and local regulatory modifications.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Quantitative Separation of Unknown Organic–Metal Complexes by Liquid Chromatography–Inductively Coupled Plasma-Mass Spectrometry

Dissolved organic matter (DOM) is widely recognized to control the solubility and reactivity of trace metals in the environment. However, the mechanisms that govern metal-DOM complexation remain elusive, primarily due to the analytical challenge of fractionating and quantifying metal–organic species within the complex mixture of organic compounds that comprise DOM. Here, we describe a quantitative method for fractionation and element-specific detection of organic–metal complexes using liquid chromatography with online inductively coupled plasma mass spectrometry (LC–ICP-MS). The method implements a post-column compensation gradient to stabilize ICP–MS elemental response across the LC solvent gradient, thereby overcoming a major barrier to achieving quantitative accuracy with LC–ICP-MS. With external calibration and internal standard correction, the method yields concentrations of organic–metal complexes that were consistently within 6% of their true values, regardless of the complex’s elution time. We used the method to evaluate the effects of four stationary phases (C18, phenyl, amide, and pentafluoroylphenyl propyl) on the recovery and separation of environmentally relevant trace metals (Mn, Fe, Co, Ni, Cu, Zn, Cd, and Pb) in Suwannee River Fulvic Acid and Suwannee River Natural Organic Matter. The C18, amide, and phenyl phases generally yielded optimal metal recoveries (>75% for all metals except Pb), with the phenyl phase separating polar species to a greater extent than C18 or amide. We also fractionated organic-bound Fe, Cu, and Ni in oxidized and reduced soils, revealing divergent metal-DOM speciation across soil redox environments. Finally, by enabling quantitative fractionation of DOM-bound metals, our method offers a means for advancing a mechanistic understanding of metal–organic complexation throughout the environment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRSDate not supplied

The Nature of Extraterrestrial Amino Acids in Carbonaceous Chondrites and Links to Their Parent Bodies

Meteorites and samples returned from asteroids and comets provide an important record of the physical and chemical processes that occurred in the early solar system and represent some of the oldest solid materials currently available for laboratory analyses. The delivery of organic matter by extraterrestrial material to the early Earth could have been an important source of complex prebiotic organic molecules available for the emergence of life. Analyses of primitive carbonaceous chondrites over the last five decades have revealed a major insoluble organic component [1,2], as well as a complex and highly diverse suite of soluble organic molecules of prebiotic importance [3,4] that includes carboxylic acids, N-heterocycles, sugars, amino acids, amines, and many other organic molecules that have not yet been identified [5]. Amino acids continue to be a primary focus of many soluble organic analyses in carbonaceous chondrites because (1) these molecules are essential components of life (as the monomers of proteins), (2) they have structural diversity (multiple possible isomers) that can be used to help constrain formation mechanisms and parent body conditions, and (3) most amino acids identified in carbonaceous chondrites are chiral, a property that can be used to distinguish between amino acids of extraterrestrial and terrestrial origins. The degree of parent body hydrothermal alteration has been shown to have a major influence on the formation and destruction of amino acids in carbonaceous meteorites as observed in the measured abundances and molecular distributions [6]. Aqueous alteration in primitive asteroids could have also led to the preferential enrichment of some left-handed amino acids over their right-handed forms, an astounding discovery that suggests that the origin of life on Earth or elsewhere was biased toward left-handed amino acid homochirality [7,8]. This talk will give an overview of what is known about the amino acid composition of carbonaceous chondrites, present some key unanswered questions, and discuss how the analysis of samples returned from asteroids Ryugu and Bennu will further advance our understanding of parent body chemistry and potential contributions from carbonaceous asteroids to the origin of life on Earth or elsewhere.

Daniel P. Glavin↗

NASA NTRS1971

The rapid evolution of complex systems from simple beginnings

Methods for the geological production of proteinous amino acids are examined. Particular attention was given to organic evolution and thermal polymerization. Also included are data on amino acid reactions after polymerization.

Fox, S. W.↗

NASA NTRS1997

Aqueous liquid feed organic fuel cell using solid polymer electrolyte membrane

A liquid organic fuel cell is provided which employs a solid electrolyte membrane. An organic fuel, such as a methanol/water mixture, is circulated past an anode of a cell while oxygen or air is circulated past a cathode of the cell. The cell solid electrolyte membrane is preferably fabricated from Nafion.TM.. Additionally, a method for improving the performance of carbon electrode structures for use in organic fuel cells is provided wherein a high surface-area carbon particle/Teflon.TM.-binder structure is immersed within a Nafion.TM./methanol bath to impregnate the electrode with Nafion.TM.. A method for fabricating an anode for use in a organic fuel cell is described wherein metal alloys are deposited onto the electrode in an electro-deposition solution containing perfluorooctanesulfonic acid. A fuel additive containing perfluorooctanesulfonic acid for use with fuel cells employing a sulfuric acid electrolyte is also disclosed. New organic fuels, namely, trimethoxymethane, dimethoxymethane, and trioxane are also described for use with either conventional or improved fuel cells.

Surampudi, Subbarao↗

NASA NTRS2001

Organic fuel cell methods and apparatus

Surampudi, Subbarao↗

NASA NTRS2004

Organic fuel cell methods and apparatus

A liquid organic, fuel cell is provided which employs a solid electrolyte membrane. An organic fuel, such as a methanol/water mixture, is circulated past an anode of a cell while oxygen or air is circulated past a cathode of the cell. The cell solid electrolyte membrane is preferably fabricated from Nafion.TM.. Additionally, a method for improving the performance of carbon electrode structures for use in organic fuel cells is provided wherein a high surface-area carbon particle/Teflon.TM.-binder structure is immersed within a Nafion.TM./methanol bath to impregnate the electrode with Nafion.TM.. A method for fabricating an anode for use in a organic fuel cell is described wherein metal alloys are deposited onto the electrode in an electro-deposition solution containing perfluorooctanesulfonic acid. A fuel additive containing perfluorooctanesulfonic acid for use with fuel cells employing a sulfuric acid electrolyte is also disclosed. New organic fuels, namely, trimethoxymethane, dimethoxymethane, and trioxane are also described for use with either conventional or improved fuel cells.

Surampudi, Subbarao↗

NASA NTRS2008

Organic fuel cell methods and apparatus

Vamos, Eugene↗

NASA NTRSDate not supplied

Apatite Nanoresponse to Acidic Dissolution

Phosphorus uptake by plants and organisms is one of the most important life-sustaining processes occurring in the critical zone (CZ). Because 95% of Earth’s reserves is relatively immobile in the form of apatite, plants and organisms rely on molecular scale solubilization process to extract available P. As the world experiences a global P shortage, influencing food production, it becomes increasingly important to understand apatite dissolution. The detailed study of chemically weathered apatite surfaces at the μm to nm-scale is key to understanding P solubilization and uptake in the CZ, allowing for better crop management and efficient fertilization. Apatite weathering is generally viewed in terms of a pH-dependent process where protons weaken atomic bonds, this leading to the disintegration of the apatite structure. A general feature of apatite weathering in acid and near neutral pH conditions is an apparent non-stoichiometric dissolution characterized by [Ca/P]aq > 1.66 in both fluorapatites (FAP) and hydroxyapatites (HAP). This process leads to the formation of a surface altered layer (SAL) with a different composition from the bulk, which many have argued is a Ca-depleted “leached layer.” We investigated apatite weathering at the nanoscale using FIB-prepared TEM-foils. Our preliminary results based on laboratory-altered FAP at ambient T and pH 3 show the formation of amorphous SALs with a maximum thickness of ~10 nm. High resolution chemical mapping and profiling using STEM-EELS and STEM-EDXS indicate that the SALs are generally, but not always, depleted in Ca and enriched in P. These results provide an alternate view of the mechanism of apatite dissolution with stoichiometric breakdown of the apatite structure, followed by the reprecipitation of an amorphous surface layer depleted in Ca. This mechanism can be described in terms of coupled interfacial dissolution-reprecipitation (CIDR), which is increasingly viewed as a universal mechanism of silicate mineral and glass dissolution. Our observation that apatite may dissolve similarly to silicates implies not only that apatite weathering may be more complex than originally thought, but also that the CIDR mechanism may extend beyond silicates.

mineralogy↗

DOE OSTI2022

Pressurized formic acid dehydrogenation: an entropic spring replaces hydrogen compression cost

Formic acid is unique among liquid organic hydrogen carriers (LOHCs), because its dehydrogenation is highly entropically driven. This enables the evolution of high-pressure hydrogen at mild temperatures that is difficult to achieve with other LOHCs, conceptually by releasing the “spring” of energy stored entropically in the liquid carrier. Applications calling for hydrogen-on-demand, such as vehicle filling, require pressurized H 2 . Hydrogen compression dominates the cost for such applications, yet there are very few reports of selective, catalytic dehydrogenation of formic acid at elevated pressure. Herein, we show that homogenous catalysts with various ligand frameworks, including Noyori-type tridentate (PNP, SNS, SNP, SNPO), bidentate chelates (pyridyl)NHC, (pyridyl)phosphine, (pyridyl)sulfonamide, and their metallic precursors, are suitable catalysts for the dehydrogenation of neat formic acid under self-pressurizing conditions. Quite surprisingly, we discovered that their structural differences can be related to performance differences in their respective structural families, with some tolerant or intolerant of pressure and others that are significantly advantaged by pressurized conditions. Here, we further find important roles for H 2 and CO in catalyst activation and speciation. In fact, for certain systems, CO behaves as a healing reagent when trapped in a pressurizing reactor system, enabling extended life from systems that would be otherwise deactivated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

dynamics of organic-mineral interactions at the metal oxide-solution interface as studied via binding energetics (Final report)

This project focused on addressing longstanding fundamental and experimental uncertainties on how dissolved organic substances (DOS) interact with metal oxide surface under environmentally relevant conditions. By leveraging a custom-built real-time, in-tandem flow adsorption microcalorimetry-UV-Vis/fluorescence spectroscopy platform, we characterized the binding energetics, kinetics and mechanistic pathways driving DOS-metal oxide interactions at temporal resolution on the order of 1-5 seconds. We studied a diverse suite of model organic compounds/substances – including monocarboxylates (e.g. acetate and benzoate), di-carboxylates (oxalate and succinate), amino acids, amino-based nanparticles and natural organic matter – interacting at the mineral-water interface of structurally- and/or chemically distinct metal oxides (including SiO2, boehmite, ferrihydrite, and γ-Al2O3). Our results indicated that DOS-metal oxide interactions are governed by multi-step reaction pathways, often switching between distinct, resolvable enthalpy- and entropy-driven non-electrostatic or electrostatic configurations. To quantify these interactions, we developed and implemented an analytical workflow that integrates peak deconvolution and Monte-Carlo based error propagation to determine site-specific thermodynamic and kinetic parameters for individual binding/debinding events. In addition to resolving apparent first-order rate constants of each event, we were able to quantify associated apparent equilibrium constants as well as free energy, enthalpy and entropy contribution to the activation and subsequent progression of the binding/debinding process across compounds, compound class and metal oxide surfaces. The kinetic-thermodynamic data produced in this study captured how the interplay between oxide surface reactivity and DOS molecular structure jointly drives binding-debinding dynamics. Notably, that at pH below PZC of the oxide surface, neutral species were heavily involved in monocarboxylate binding, while anionic species drove dicarboxylate binding. Also, that among amino acids 1) positional isomers show distinctive binding characteristics to each other while enantiomers show no significant differences in binding characteristics, 2) molecules that bind via outer-sphere complexation show a larger entropic shift between binding and debinding with no impact on oxide surface while 3) inner-sphere interactions increased anion exchange capacity of the oxide surface. The new insights and data from this work has great potential for improving predictive modeling of carbon dynamics and specifically organic-mineral interactions in environmental and industrial systems.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1993

A reexamination of amino acids in lunar soil

Amino acids in lunar soils provide an important indicator of the level of prebiotic organic compounds on the moon. The results provide insight into the chemistry of amino acid precursors, and furthermore, given the flux of carbonaceous material to the moon, we can evaluate the survival of organics upon impact. The amino acid contents of both hydrolyzed and unhydrolyzed hot-water extracts of Apollo 17 lunar soil were determined using ophthaldialdehyde/N-acetyl cysteine (OPA/NAC) derivatization followed by HPLC analysis. Previous studies of lunar amino acids were inconclusive, as the technique used (derivatization with ninhydrin followed by HPLC analysis) was unable to discriminate between cosmogenic amino acids and terrestrial contaminants. Cosmogenic amino acids are racemic, and many of the amino acids found in carbonaceous meteorites such as Murchison, i.e., alpha-amino-i-butyric acid (aib), are extremely rare on Earth. The ninhydrin method does not distinguish amino acid enantiomers, nor does it detect alpha-alkyl amino acids such as aib, whereas the OPA/NAC technique does both.

Brinton, K. L. F.↗

NASA NTRS1991

The relative importance of prebiotic synthesis on the Earth and input from comets and meteorites

The prebiotic synthesis of hydrogen cyanide and formaldehyde was studied by the action of electric discharges on various model primitive atmospheres containing CH4, CO, and CO2. Photochemical production rates would also have been important and were calculated for HCN and H2CO. A reasonable rate of synthesis of amino acids from these sources is about 10 n moles/(sq cm yr) or 0.10 moles/sq cm in 10(exp 7) yrs. This would give a concentration of 3 x 10(exp -4) M in an ocean of the present size (300 liters/sq cm). The amino acids cannot accumulate over a longer period because the entire ocean passes through the 350 C submarine vents in 10(exp 7) yrs, which decomposes all the organic compounds. A number of workers have calculated the influx of comets and meteorites on the primitive earth, both as a destructive process for organic compounds and for any life that was present, as well as a source of organic compounds. Some of the amino acids from the meteorite proposed to have hit the earth 65 x 10(exp 6) yrs ago were detected at the Cretaceous/Tertiary boundary sediments. The problem with proposing a large scale input of organic compounds from meteorites and comets is that they must survive passage through the atmosphere and impact. There are some processes that would allow survival such as showers of centimeter to meter sized meteorites and various aerodynamic braking processes for larger objects. Even if a significant amount of the organic material survived impact, the destructive processes in the hydrothermal vents would remove these compounds on the average in 10(exp 7) yrs or less. If it is assumed that the input rate was sufficient to overcome these destructive processes, then too much carbon and water, especially from comets, would have been added to the surface of the earth. It was concluded that while some organic material was added to the earth from comets and meteorites, the amount available from these sources at a given time was only a few percent of that from earth based syntheses.

Miller, S. L.↗

NASA NTRS1994

Evidence that the protocell was also a protoneuron

A blueprint for a protocell was presented in 1960 (Fox) as a consequence of the newly discovered self-ordering of amino acids and the self-organization of the resultant thermal proteins into cellular structures. The biofunctions of the laboratory protocells (proteinoid microspheres) have since been cataloged; they display roots of many phenomena of modern cells, e.g. synthesis of internucleotide and peptide bonds in aqueous media. These results are inconsistent with a popular assumption that DNA/RNA preceded protein in earliest molecular evolution. The necessity for synthetic research on molecules and cells to 'begin at the beginning' is being realized. Ivanov and Fortsch (1986) have described by analysis how the self-ordering mechanism of amino acids into informed thermal proteins was conserved in evolution from the earliest stage as modern (reverse) mechanisms assumed control. Tyagi and Ponnamperuma (1990) have negated assumptions corollary to DNA/RNA. Ponnamperuma has demonstrated the powerful effect of self-ordering of amino acids in polymerization of aminoacyl nucleotides and the irrelevance of mononucleotide residues. Excitable thermal proteins (Vaughan et al, 1987) are neurotrophic and antiaging when added to cultures of real neurons (Hefti et al, 1991) and are memory enhancers in mice (Fox and Flood, 1992). Proteinoid microspheres of dominant hydrophobic constitution form 'gap junctions', sprout axon-like outgrowths, and form dendritic networks spontaneously. In the latest studies, phenylalanine-rich equimolar proteinoid or the leucine analog (Ishima et al 1981), is found to produce electrical signals for several days when lecithin is included in the assembly with the thermal polymer.

Bi, YU↗

NASA NTRS2003

Determining D/L Ratios of Amino Acids Found in Ice Above Lake Vostok Using ESI/CIT Mass Spectroscopy

Astrobiology is an area where longevity of (micro) organisms is of great interest. Cryospheres are common phenomena in the solar system, particularly on satellites, comets and asteroids, as well as at least some of the planets. Recent data from the Mars Global Surveyor mission suggest the possibility of permafrost or perhaps even liquid water under the Martian surface [2]. These environments may be the areas in which the probability of finding life is the highest. This issue is of concern due to the probable evolution of planetary environments such as that of Mars from more hospitable to less hospitable conditions over the history of the solar system. In addition, evaluation of the possible transfer of living organisms between planets via impact ejecta [3] is dependent on knowledge of the maximum time periods over which microorganisms can remain dormant and subsequently revive and reproduce.Amino acid racemization dating, or aminostratigraphy, has been used for many years to date biological systems, and has been examined as a possible biosignature detection technique for Mars. We have suggested using amino acid racemization as one of the most indicative biosignatures [4]. Only life systems produce preferential synthesis of L-amino acids versus D-amino acids. Almost all amino acids in terrestrial organisms can be found only in the L-enantiomeric form.We studied the level of amino acid racemization, specifically of aspartic acid, in permafrost samples from eastern Siberia. Also we analyzed samples of ice from borehole drilled to lake Vostok, Antarctica.

A Tsapin↗

DOE OSTI2025

Tracing priming effects in palsa peat carbon dynamics using a stable isotope-assisted metabolomics approach

Introduction: Peatlands store up to a third of global soil carbon, and in high latitudes their litter inputs are increasing and changing in composition under climate change. Although litter significantly influences peatland carbon and nutrient dynamics by changing the overall lability of peatland organic matter, the physicochemical mechanisms of this impact—and thus its full scope—remain poorly understood. Methods: We applied multimodal metabolomics (UPLC-HRMS, 1 H NMR) paired with 13 C Stable Isotope-Assisted Metabolomics (SIAM) to track litter carbon and its potential priming effects on both existing soil organic matter and carbon gas emissions. Through this approach, we achieved molecule-specific tracking of carbon transformations at unprecedented detail. Results: Our analysis revealed several key findings about carbon dynamics in palsa peat. Microbes responded rapidly to litter addition, producing a short-term increase in CO 2 emissions, fueled nearly exclusively by transformations of litter carbon. Litter inputs significantly contributed to the organic nitrogen pool through amino acids and peptide derivatives, which served as readily accessible nutrient sources for microbial communities. We traced the fate of plant-derived polyphenols including flavonoids like rutin, finding evidence of their degradation through heterocyclic C-ring fission, while accumulation of some polyphenols suggested their role in limiting overall decomposition. The SIAM approach detected subtle molecular changes indicating minimal and transient priming activity that was undetectable through conventional gas measurements alone. This transient response was characterized by brief microbial stimulation followed by rapid return to baseline metabolism. Pre-existing peat organic matter remained relatively stable; significant priming of its consumption was not observed, nor was its structural alteration. Discussion: This suggests that while litter inputs temporarily increase CO 2 emissions, they don’t sustain long-term acceleration of stored carbon decomposition or substantially decrease peat’s carbon store capacity. Our findings demonstrate how technological advancements in analytical tools can provide a more detailed view of carbon cycling processes in complex soil systems.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Multisystem feedbacks from a changing climate: Do altered hydrological dynamics control vadose zone carbon nutrient cycling and storage in shallow aquifer systems?

The vadose zone, which extends from upper soils to the subsurface water table, consists of many distinct habitats (including the critical zone), each with its own physical characteristics. Upper soils are typically richer in organic carbon chemical diversity and concentration, while deeper portions near the water table have less labile carbon and a greater percentage of humic acids and other long-lived organics. The availability of carbon and oxygen constrain the habitability of these zones. Typically, microorganisms (bacteria, archaea, and fungi) extend throughout the vadose zone and potentially deeper into the bedrock, while higher eukaryotes (i.e., arthropods and plants) are limited to the surficial soils. An exception to this is deep taproots of some tree species that can extend tens of meters into the subsurface. In subsurface systems, microbial metabolisms are constrained by the availability of carbon (organic and inorganic) and electron acceptors.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Activity of Cannabidiol on Ex Vivo Amino Acid Fermentation by Bovine Rumen Microbiota

Amino-acid-fermenting bacteria are wasteful organisms within the rumens of beef cattle that remove dietary amino nitrogen by producing ammonia, which is then excreted renally. There are currently no on-label uses for the control of this microbial guild, but off-label use of broad-spectrum antimicrobials has shown efficacy, which contributes to antimicrobial resistance. Plant-derived antimicrobials supplemented into the diets of cattle may offer worthwhile alternatives. This study sought to investigate the role of cannabidiol (CBD) as a terpenophenolic antimicrobial. Ex vivo cell suspensions were harvested from the rumen fluid of Angus × Holstein steers in non-selective media with amino acid substrates. The suspensions were treated with five concentrations of CBD (860 μg mL−1–0.086 μg mL−1) and incubated (24 h), after which ammonia production and viable number of cells per substrate and treatment were measured. The data demonstrated a ~10–15 mM reduction in ammonia produced at the highest concentration of CBD and negligible changes in the viable number of amino-acid-fermenting bacteria. CBD does not appear to be a biologically or economically viable terpenophenolic candidate for the control of amino acid fermentation in beef cattle.

Biotechnology & Applied Microbiology↗