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DOE OSTI2023

Evidence of excited-state lifetime enhancement in dimyristoyl-phosphocholine nanodiscs by ultraviolet absorption spectroscopy

Ultraviolet absorption spectroscopy is an analytical tool that is commonly utilized to determine protein concentrations, primarily due to characteristic absorption of tryptophan and tyrosine at 280 nm. Accurate concentration determination is essential to the accuracy of many biophysical techniques, and ultraviolet absorption provides a convenient and rapid method to assess protein concentration. However, the widespread usage of this method assumes that ultraviolet absorption is the same for individual amino acids in aqueous solution (where the molar extinction coefficient was measured) as for the amino acid in the conformational environment of the protein of interest. We demonstrate that additional considerations may be necessary for the membrane scaffold protein in dimyristoyl-phosphocholine nanodiscs through ultraviolet absorption spectroscopy of nanodiscs, liposomes, the membrane scaffold protein, and a mixture of liposomes and the non-nanodisc-associated protein. The aromatic amino acids of the membrane scaffold protein absorb significantly less light at 280 nm when associated with lipids in a lipoprotein assembly, which we plausibly attribute to an enhancement of chromophore excited-state lifetimes due to reduced intramolecular motion in the nanodisc. We caution that using the molar absorptivity of the membrane scaffold protein alone to determine nanodisc concentrations may not yield accurate results. Instead, the molar absorptivity of each nanodisc formulation should be explored independently to account for the unique conformational environment of each nanodisc.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1995

Validation of Global Climatologies of Trace Gases Using NASA Global Tropospheric Experiment (GTE) Data

Methane is an important trace gas because it is a greenhouse gas that affects the oxidative capacity of the atmosphere. It is produced from biological and anthropogenic sources, and is increasing globally at a rate of approximately 0.6% per year [Climate Change 1992, IPCC]. By using National Oceanic and Atmospheric Administration/Climate Monitoring and Diagnostics Laboratory (NOAA/CMDL) ground station data, a global climatology of methane values was produced. Unfortunately, because the NOAA/CMDL ground stations are so sparse, the global climatology is low resolution. In order to compensate for this low resolution data, it was compared to in-situ flight data obtained from the NASA Global Tropospheric Experiment (GTE). The smoothed ground station data correlated well with the flight data. Thus, for the first time it is shown that the smoothing process used to make global contours of methane using the ground stations is a plausible way to approximate global atmospheric concentrations of the gas. These verified climatologies can be used for testing large-scale models of chemical production, destruction, and transport. This project develops the groundwork for further research in building global climatologies from sparse ground station data and studying the transport and distribution of trace gases.

Courchaine, Brian↗

DOE OSTI2020

Brachiopod δ 34 S CAS microanalyses indicate a dynamic, climate-influenced Permo-Carboniferous sulfur cycle

Early isotopic studies of sulfate in carbonate minerals (carbonate associated sulfate; CAS) suggested that carbonates can provide a reliable, well-dated archive of the marine sulfur cycle through time. However, subsequent research has shown that diagenetic alteration can impose highly heterogeneous CAS sulfur isotopic compositions (δ 34 S CAS ) among different carbonate phases within sediments. Such alteration necessitates targeted sampling of well-preserved, primary carbonate phases. Here, we present a new record of Carboniferous and Early Permian brachiopod δ 34 S CAS generated from over 130 measurements of microsampled brachiopod shells. Our record refines existing brachiopod δ 34 S CAS records and confirms a large, ~6.5‰ δ 34 S CAS decrease in the Early Carboniferous. Importantly, the record also features a novel 3–5‰ increase in δ 34 S CAS near the Serpukhovian-Bashkirian boundary (323.4 Ma) that coincides with carbonate δ 13 C and δ 18 O increases. Variability in δ 34 S CAS is minor both within (≤0.3‰) and among (≤2‰) individual co-depositional brachiopod specimens. A taxon-specific δ 34 S CAS offset is present one species (Composita subtilita) that also exhibits a δ 13 C offset, supporting the existence of biological “vital effects” on δ 34 S CAS . Geologic evidence and mathematical modeling of the Permo-Carboniferous carbon and sulfur cycles suggest that changes in the burial ratio of organic carbon to pyrite sulfur (R C:S ) are insufficient to explain the observed mid-Carboniferous δ 34 S CAS record. We find that changes in the 34 S depletion of pyrite relative to seawater sulfate ( 34 ε) or in the δ 34 S of the input to the ocean (δ 34 S in ) are also needed. Large additions of O 2 from organic carbon burial during the Permo-Carboniferous cannot be entirely compensated for with sulfur cycle changes; lower than modern late Visean pO 2 and/or additional O 2 sinks are needed to keep pO 2 at plausible levels. Based on the geologic context surrounding our record's mid-Carboniferous δ 34 S CAS increase, we advocate for simultaneous changes in pyrite burial, 34 ε, and δ 34 S in , driven by sea level or tectonically induced changes in environments of sulfur burial, as a viable mechanism to produce rapid seawater δ 34 S changes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Dirigent isoflavene-forming PsPTS2: 3D structure, stereochemical, and kinetic characterization comparison with pterocarpan-forming PsPTS1 homolog in pea

Pea (legume plant defense) phytoalexin pterocarpans (–)-maackiain and (+)-pisatin have opposite C6a and C11a configurations, but how this occurs biosynthetically is unknown. Herein, pea dirigent-protein (DP) PsPTS2, which generates 7,2'-dihydroxy-4',5'-methylenedioxyisoflav-3-ene (DMDIF), was investigated as regards stereoselectivity towards four possible 7,2'-dihydroxy-4',5'-methylenedioxyisoflavan-4-ol (DMDI) stereoisomers. Each DMDI stereoisomer configuration was determined using NMR spectroscopy, electronic circular dichroism, and molecular orbital analyses. PsPTS2 efficiently converted cis-(3R,4R)-DMDI into DMDIF, this being 20-fold faster than with the trans-(3R,4S)-isomer. The 4R-configured substrate’s near ß-axial OH orientation significantly enhanced its leaving group abilities in creating intermediate A-ring mono-quinone methide (QM), whereas the 4S-isomer’s 4-OH group α-equatorial orientation was a poorer leaving group. Substrate docking simulations also indicated that the 4R-configured ß-axial OH was closest to the Asp catalytic center, whereas the 4S-isomer’s α-equatorial OH was further away. Neither cis-(3S,4S)- nor trans-(3S, 4R)-DMDIs were substrates, even with the former having the same C3/C4 stereochemistry as (+)-pisatin. PsPTS2, assayed with cis-(3R,4R)-7,2'-dihydroxy-4'-methoxyisoflavan-4-ol [cis-(3R,4R)-DMI] and its C3/C4 stereoisomers, gave 2',7-dihydroxy-4'-methoxyisoflav-3-ene (DMIF), with the same substrate stereoselectivity. DP homologs may exist in licorice (Glycyrrhiza pallidiflora) and the tree legume Bolusanthus speciosus, as DMIF is found in both. PsPTS1 preferentially utilized cis-(3R,4R)-DMDI to give (–)-maackiain, this being 2200-fold more efficient than with cis-(3R,4R)-DMI. PsPTS1 also slowly converted trans-(3S,4R)-DMDI into (+)-maackiain, again reflecting the better 4R configured OH leaving group. Pea PsPTS2 and PsPTS1 provisionally provide a facile DP-engendered means to enable differing C6a and C11a configurations in (+)-pisatin and (–)-maackiain. Both DP transformations are considered to occur via DP-engendered generation of an identical mono-QM bound intermediate, which with PsPTS2 either re-aromatizes to give DMDIF or with PsPTS1 undergoes intramolecular cyclization to afford (–)-maackiain. Substrate docking simulations using PsPTS2 (2.5 Å resolution) and PsPTS1 (1.5 Å resolution) plausibly indicate that cis-(3R,4R)-DMDI binds in the anti-configuration in the PsPTS2 active site to afford DMDIF, and the syn-configuration in PsPTS1 to give maackiain.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2001

A stochastic differential equation model of diurnal cortisol patterns

Circadian modulation of episodic bursts is recognized as the normal physiological pattern of diurnal variation in plasma cortisol levels. The primary physiological factors underlying these diurnal patterns are the ultradian timing of secretory events, circadian modulation of the amplitude of secretory events, infusion of the hormone from the adrenal gland into the plasma, and clearance of the hormone from the plasma by the liver. Each measured plasma cortisol level has an error arising from the cortisol immunoassay. We demonstrate that all of these three physiological principles can be succinctly summarized in a single stochastic differential equation plus measurement error model and show that physiologically consistent ranges of the model parameters can be determined from published reports. We summarize the model parameters in terms of the multivariate Gaussian probability density and establish the plausibility of the model with a series of simulation studies. Our framework makes possible a sensitivity analysis in which all model parameters are allowed to vary simultaneously. The model offers an approach for simultaneously representing cortisol's ultradian, circadian, and kinetic properties. Our modeling paradigm provides a framework for simulation studies and data analysis that should be readily adaptable to the analysis of other endocrine hormone systems.

NASA Discipline Space Human Factors↗

NASA NTRS1997

A mathematical model of diurnal variations in human plasma melatonin levels

Studies in animals and humans suggest that the diurnal pattern in plasma melatonin levels is due to the hormone's rates of synthesis, circulatory infusion and clearance, circadian control of synthesis onset and offset, environmental lighting conditions, and error in the melatonin immunoassay. A two-dimensional linear differential equation model of the hormone is formulated and is used to analyze plasma melatonin levels in 18 normal healthy male subjects during a constant routine. Recently developed Bayesian statistical procedures are used to incorporate correctly the magnitude of the immunoassay error into the analysis. The estimated parameters [median (range)] were clearance half-life of 23.67 (14.79-59.93) min, synthesis onset time of 2206 (1940-0029), synthesis offset time of 0621 (0246-0817), and maximum N-acetyltransferase activity of 7.17(2.34-17.93) pmol x l(-1) x min(-1). All were in good agreement with values from previous reports. The difference between synthesis offset time and the phase of the core temperature minimum was 1 h 15 min (-4 h 38 min-2 h 43 min). The correlation between synthesis onset and the dim light melatonin onset was 0.93. Our model provides a more physiologically plausible estimate of the melatonin synthesis onset time than that given by the dim light melatonin onset and the first reliable means of estimating the phase of synthesis offset. Our analysis shows that the circadian and pharmacokinetics parameters of melatonin can be reliably estimated from a single model.

NASA Discipline Number 70-10↗

NASA NTRS2011

Carbonaceous Meteorites Contain a Wide Range of Extraterrestrial Nucleobases

All terrestrial organisms depend on nucleic acids (RNA and DNA), which use pyrimidine and purine nucleobases to encode genetic information. Carbon-rich meteorites may have been important sources of organic compounds required for the emergence of life on the early Earth; however, the origin and formation of nuc1eobases in meteorites has been debated for over 50 y. So far, the few nuc1eobases reported in meteorites are biologically common and lacked the structural diversity typical of other indigenous meteoritic organics. Here, we investigated the abundance and distribution of nucleobases and nucleobase analogs in formic acid extracts of 12 different meteorites by liquid chromatography-mass spectrometry. The Murchison and Lonewolf Nunataks 94102 meteorites contained a diverse suite of nucleobases, which included three unusual and terrestrially rare nucleobase analogs; purine, 2,6-diminopurine, and 6,8-diaminopurine. In a parallel experiment, we found an identical suite of nucleobases and nucleobase analogs generated in reactions of ammonium cyanide. Additionally, these nucleobase analoge were not detected above our parts-per-billion detection limits in any of the procedural blanks, control samples, a terrestrial soil sample, and an Antarctic ice sample. Our results demonstrate that the purines detected in meteorites are consistent with products of ammonium cyanide chemistry, which provides a plausible mechanism for their synthesis in the asteroid parent bodies, and strongly supports an extraterrestrial origin. The discovery of new nucleobase analogs in meteorites also expands the prebiotic molecular inventory available for constructing the first genetic molecules.

Callahan, Michael P.↗

DOE OSTI2022

Strengthening of enterococcal biofilms by Esp

Multidrug-resistant (MDR) Enterococcus faecalis are major causes of hospital-acquired infections. Numerous clinical strains of E . faecalis harbor a large pathogenicity island that encodes enterococcal surface protein (Esp), which is suggested to promote biofilm production and virulence, but this remains controversial. To resolve this issue, we characterized the Esp N-terminal region, the portion implicated in biofilm production. Small angle X-ray scattering indicated that the N-terminal region had a globular head, which consisted of two DEv-Ig domains as visualized by X-ray crystallography, followed by an extended tail. The N-terminal region was not required for biofilm production but instead significantly strengthened biofilms against mechanical or degradative disruption, greatly increasing retention of Enterococcus within biofilms. Biofilm strengthening required low pH, which resulted in Esp unfolding, aggregating, and forming amyloid-like structures. The pH threshold for biofilm strengthening depended on protein stability. A truncated fragment of the first DEv-Ig domain, plausibly generated by a host protease, was the least stable and sufficient to strengthen biofilms at pH ≤ 5.0, while the entire N-terminal region and intact Esp on the enterococcal surface was more stable and required a pH ≤ 4.3. These results suggested a virulence role of Esp in strengthening enterococcal biofilms in acidic abiotic or host environments.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2006

Degradation of Organics in a Glow Discharge Under Martian Conditions

The primary objective of this project is to understand the consequences of glow electrical discharges on the chemistry and biology of Mars. The possibility was raised some time ago that the absence of organic material and carbonaceous matter in the Martian soil samples studied by the VikinG Landers might be due in part to an intrinsic atmospheric mechanism such as glow discharge. The high probability for dust interactions during Martian dust storms and dust devils, combined with the cold, dry climate of Mars most likely results in airborne dust that is highly charged. Such high electrostatic potentials generated during dust storms on Earth are not permitted in the low-pressure CO2 environment on Mars; therefore electrostatic energy released in the form of glow discharges is a highly likely phenomenon. Since glow discharge methods are used for cleaning and sterilizing surfaces throughout industry, the idea that dust in the Martian atmosphere undergoes a cleaning action many times over geologic time scales appears to be a plausible one.

Hintze, P. E.↗

DOE OSTI2021

Genetic program activity delineates risk, relapse, and therapy responsiveness in multiple myeloma

Despite recent advancements in the treatment of multiple myeloma (MM), nearly all patients ultimately relapse and many become refractory to multiple lines of therapies. Therefore, we not only need the ability to predict which patients are at high risk for disease progression but also a means to understand the mechanisms underlying their risk. Here, we report a transcriptional regulatory network (TRN) for MM inferred from cross-sectional multi-omics data from 881 patients that predicts how 124 chromosomal abnormalities and somatic mutations causally perturb 392 transcription regulators of 8549 genes to manifest in distinct clinical phenotypes and outcomes. We identified 141 genetic programs whose activity profiles stratify patients into 25 distinct transcriptional states and proved to be more predictive of outcomes than did mutations. The coherence of these programs and accuracy of our network-based risk prediction was validated in two independent datasets. We observed subtype-specific vulnerabilities to interventions with existing drugs and revealed plausible mechanisms for relapse, including the establishment of an immunosuppressive microenvironment. Investigation of the t(4;14) clinical subtype using the TRN revealed that 16% of these patients exhibit an extreme-risk combination of genetic programs (median progression-free survival of 5 months) that create a distinct phenotype with targetable genes and pathways.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Likelihood-based docking of models into cryo-EM maps

Optimized docking of models into cryo-EM maps requires exploiting an understanding of the signal expected in the data to minimize the calculation time while maintaining sufficient signal. The likelihood-based rotation function used in crystallography can be employed to establish plausible orientations in a docking search. A phased likelihood translation function yields scores for the placement and rigid-body refinement of oriented models. Optimized strategies for choices of the resolution of data from the cryo-EM maps to use in the calculations and the size of search volumes are based on expected log-likelihood-gain scores computed in advance of the search calculation. Tests demonstrate that the new procedure is fast, robust and effective at placing models into even challenging cryo-EM maps.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1998

Gusev Crater Paleolake: Two-Billion Years of Martian Geologic, (and Biologic?) History

Ancient Martian lakes are sites where the climatological, chemical, and possibly biological history of the planet has been recorded. Their potential to keep this global information in their sedimentary deposits, potential only shared with the polar layered-deposits, designates them as the most promising targets for the ongoing exploration of Mars in terms of science return and global knowledge about Mars evolution. Many of the science priority objectives of the Surveyor Program can be met by exploring ancient Martian lake beds. Among martian paleolakes, lakes in impact craters represent probably the most favorable sites to explore. Though highly destructive events when they occur, impacts may have provided in time a significant energy source for life, by generating heat, and at the contact of water and/or ice, deep hydrothermal systems, which are considered as favorable environments for life. In addition, impact crater lakes are changing environments, from thermally driven systems at the very first stage of their formation, to cold ice-protected potential oases in the more recent Martian geological times. Thus, they are plausible sites to study the progression of diverse microbiologic communities.

Cabrol, N. A.↗

NASA NTRS2013

The Search for Nitrates on Mars by the Sample Analysis at Mars (SAM) Instrument

Planetary models suggest that nitrogen was abundant in the early Martian atmosphere as N2 but it was lost by sputtering and photochemical loss to space, impact erosion, and chemical oxidation to nitrates. A nitrogen cycle may exist on Mars where nitrates, produced early in Mars' history, may have been later decomposed back into N2 by the current impact flux. Nitrates are a fundamental source of nitrogen for terrestrial microorganisms, and they have evolved metabolic pathways to perform both oxidation and reduction to drive a complete biological nitrogen cycle. Therefore, the characterization of nitrogen in Martian soils is important to assess habitability of the Martian environment, particularly with respect to the presence of nitrates. The only previous mission that was designed to search for soil nitrates was the Phoenix mission but N-containing species were not detected by TEGA or the MECA WCL. Nitrates have been tentatively identified in Nakhla meteorites, and if nitrogen was oxidized on Mars, this has important implications for the habitability potential of Mars. Here we report the results from the Sample Analysis at Mars (SAM) instrument suite aboard the Curiosity rover during the first year of surface operations in Gale Crater. Samples from the Rocknest aeolian deposit and sedimentary rocks (John Klein) were heated to approx 835degC under helium flow and the evolved gases were analyzed by MS and GC-MS. Two and possibly three peaks may be associated with the release of m/z 30 at temperatures ranging from 180degC to 500degC. M/z 30 has been tentatively identified as NO; other plausible contributions include CH2O and an isotopologue of CO, 12C18O. NO, CH2O, and CO may be reaction products of reagents (MTBSTFA/DMF) carried from Earth for the wet chemical derivatization experiments with SAM and/or derived from indigenous soil nitrogenated organics. Laboratory analyses indicate that it is also possible that <550degC evolved NO is produced via reaction of HCl with nitrates arising from the decomposition of perchlorates. All sources of m/z 30 whether it be martian or terrestrial will be considered and their implications for Mars will be discussed.

Navarro-Gonzalez, Rafael↗

NASA NTRS1991

The chemistry and mineralogy of Mars soil and dust

A single geological unit consisting of fine, apparently weathered soil material is covering large portions of the surface of Mars. This soil material has been thoroughly homogenized by global dust storms and it is plausible to assume that Mars dust is strongly correlated with it. The chemical-elemental composition of the soil was directly measured by the Viking Landers. Positive detection of Si, Al, Fe, Mg, Ca, Ti, S, Cl, and Br was achieved. Analyses of the SNC meteorites, a group of meteorites that has been suggested to be ejected Martian rocks, supply additional elemental-concentration data, broadening considerably the chemical data-base on the surface materials. A composition model for Mars soil, giving selected average elemental concentrations of major and trace elements, was recently suggested. It was constructed by combining the Viking Lander data, the SNC meteorite analyses, and other analyses. The mineralogy of the surface materials on Mars has not been directly measured yet. By use of various indirect approaches, including chemical correspondence to the surface analyses, spectral analogies, simulations of Viking Lander experiments, analyses of the SNC meteorites and various modeling efforts, the mineralogical composition was constrained to some extent. No direct analyses of soil reactivity have been done yet. Indirect evidence, mostly from the Viking biology experimental results, suggests that the soil probably has a slightly acidic reaction and is generally oxidized. Unambiguous identification of the Mars soil minerals by direct mineralogical analyses, and non-disturbed or in-situ measurements of the soil's reactivity, are of primary importance in future Mars research.

Banin, A.↗

NASA NTRS2011

Exploring the Fate of Nitrogen Heterocycles in Complex Prebiotic Mixtures

A long standing question in the field of prebiotic chemistry is the origin of the genetic macromolecules DNA and RNA. DNA and RNA have very complex structures with repeating subunits of nucleotides, which are composed of nucleobases (nitrogen heterocycles) connected to sugar-phosphate. Due to the instability of some nucleobases (e.g. cytosine), difficulty of synthesis and instability of D-ribose, and the likely scarcity of polyphosphates necessary for the modern nucleotides, alternative nucleotides have been proposed for constructing the first genetic material. Thus, we have begun to investigate the chemistry of nitrogen heterocycles in plausible, complex prebiotic mixtures in an effort to identify robust reactions and potential alternative nucleotides. We have taken a complex prebiotic mixture produced by a spark discharge acting on a gas mixture of N2, CO2, CH4, and H2, and reacted it with four nitrogen heterocycles: uracil, 5-hydroxymethyluracil, guanine, and isoxanthopterin (2-amino-4,7-dihydroxypteridine). The products of the reaction between the spark mixture and each nitrogen heterocycle were characterized by liquid chromatography coupled to UV spectroscopy and Orbitrap mass spectrometry. We found that the reaction between the spark mixtUl'e and isoxanthopterin formed one major product, which was a cyanide adduct. 5-hydroxymethyluracil also reacted with the spark mixture to form a cyanide adduct, uracil-5-acetonitrile, which has been synthesized previously by reacting HCN with S-hydroxymethyluracil. Unlike isoxanthopterin, the chromatogram of the 5-hydroxymethyluracil reaction was much more complex with multiple products including spark-modified dimers. Additionally, we observed that HMU readily self-polymerizes in solution to a variety of oligomers consistent with those suggested by Cleaves. Guanine and uracil, the biological nucleobases, did not react with the spark mixture, even at high temperature (100 C). This suggests that there are alternative nucleobases which are more reactive under prebiotic conditions and may have been involved in producing precursor nucleotides.

Smith, Karen E.↗

NASA NTRS2011

Comets as Parent Bodies of CI1 Carbonaceous Meteorites and Possible Habitats of Ice-Microbiota

Recent studies of comets and cometary dust have confirmed the presence of biologically relevant organic molecules along with clay minerals and water ice. It is also now well established by deuterium/hydrogen ratios that the CI1 carbonaceous meteorites contain indigenous extraterrestrial water. The evidence of extensive aqueous alteration of the minerals in these meteorites led to the hypothesis that water-bearing asteroids or comets represent the parent bodies of the CI1 (and perhaps CM2) carbonaceous meteorites. These meteorites have also been shown to possess a diverse array of complex organics and chiral and morphological biomarkers. Stable isotope studies by numerous independent investigators have conclusively established that the complex organics found in these meteorites are both indigenous and extraterrestrial in nature. Although the origin of these organics is still unknown, some researchers have suggested that they originated by unknown abiotic mechanisms and may have played a role in the delivery of chiral biomolecules and the origin of life on Early Earth. In this paper we review these results and investigate the thermal history of comets. We show that permanent as well as transient domains of liquid water can be maintained on a comet under a plausible set of assumptions. With each perihelion passage of a comet volatiles are preferentially released, and during millions of such passages the comet could shed crustal debris that may survive transit through the Earth s atmosphere as a carbonaceous meteorite. We review the current state of knowledge of comets and carbonaceous meteorites. We also present the results of recent studies on the long-term viability of terrestrial ice-microbiota encased in ancient glacial ice and permafrost. We suggest that the conditions which have been observed to prevail on many comets do not preclude either survivability (or even the active metabolism and growth) of many types of eukaryotic and prokaryotic microbial extremophiles-including algae, cyanobacteria, bacteria and archaea. It is argued that the chemical and morphological biomarkers detected on comets and carbonaceous meteorites can be explained by ancient microbial activity without the need to invoke unknown abiotic production mechanisms.

Wickramasinghe, N. Chandra↗

NASA NTRS2011

Distinct Purine Distribution in Carbonaceous Chondrites

Carbonaceous chondrite meteorites are known to contain a diverse suite of organic compounds, many of which are essential components of biochemistry. Amino acids, which are the monomers of proteins, have been extensively studied in such meteorites (e.g. Botta and Bada 2002; Pizzarello et aI., 2006). The origin of amino acids in meteorites has been firmly established as extraterrestrial based on their detection typically as racemic mixtures of amino acids, the presence of many non-protein amino acids, and non-terrestrial values for compound-specific deuterium, carbon, and nitrogen isotopic measurements. In contrast to amino acids, nucleobases in meteorites have been far less studied. Nucleobases are substituted one-ring (pyrimidine) or two-ring (purine) nitrogen heterocyclic compounds and serve as the information carriers of nucleic acids and in numerous coenzymes. All of the purines (adenine, guanine, hypoxanthine, and xanthine) and pyrimidines (uracil) previously reported in meteorites are biologically common and could be interpreted as the result of terrestrial contamination (e.g. van del' Velden and Schwartz, 1974.) Unlike other meteoritic organics, there have been no observations of stochastic molecular diversity of purines and pyrimidines in meteorites, which has been a criterion for establishing extraterrestrial origin. Maltins et al. (2008) performed compound-specific stable carbon isotope measurements for uracil and xanthine in the Murchison meteorite. They assigned a non-terrestrial origin for these nucleobases; however, the possibility that interfering indigenous molecules (e.g. carboxylic acids) contributed to the 13C-enriched isotope values for these nucleobases cannot be completely ruled out. Thus, the origin of these meteoritic nucleobases has never been established unequivocally. Here we report on our investigation of extracts of II different carbonaceous chondrites covering various petrographic types (Cl, CM, and CR) and degrees of aqueous alteration (l, 2, and 3) and one ureilite. Analysis via liquid chromatography coupled with electrospray triple-stage mass spectrometry or orbitrap mass spectrometry employed a targeted approach for analysis focused on the five canonical RNA/DNA nucleobases as well as 14 non-canonical pyrimidines and purines, which have bcen observed under plausible prebiotic reactions.

Callahan, Michael P.↗

DOE OSTI2022

Trajectories for the evolution of bacterial CO 2 -concentrating mechanisms

Cyanobacteria rely on CO 2 -concentrating mechanisms (CCMs) to grow in today’s atmosphere (0.04% CO 2 ). These complex physiological adaptations require ≈15 genes to produce two types of protein complexes: inorganic carbon (Ci) transporters and 100+ nm carboxysome compartments that encapsulate rubisco with a carbonic anhydrase (CA) enzyme. Mutations disrupting any of these genes prohibit growth in ambient air. If any plausible ancestral form—i.e., lacking a single gene—cannot grow, how did the CCM evolve? Here, we test the hypothesis that evolution of the bacterial CCM was “catalyzed” by historically high CO 2 levels that decreased over geologic time. Using an E. coli reconstitution of a bacterial CCM, we constructed strains lacking one or more CCM components and evaluated their growth across CO 2 concentrations. We expected these experiments to demonstrate the importance of the carboxysome. Instead, we found that partial CCMs expressing CA or Ci uptake genes grew better than controls in intermediate CO 2 levels (≈1%) and observed similar phenotypes in two autotrophic bacteria, Halothiobacillus neapolitanus and Cupriavidus necator . To understand how CA and Ci uptake improve growth, we model autotrophy as colimited by CO 2 and HCO 3 − , as both are required to produce biomass. Our experiments and model delineated a viable trajectory for CCM evolution where decreasing atmospheric CO 2 induces an HCO 3 − deficiency that is alleviated by acquisition of CA or Ci uptake, thereby enabling the emergence of a modern CCM. This work underscores the importance of considering physiology and environmental context when studying the evolution of biological complexity.

Flamholz, Avi I.↗