Extraterrestrial ribose and other sugars in primitive meteorites

Polycyclic aromatics in the Chang'E 5 lunar soils

Polycyclic aromatics are ubiquitous in the interstellar medium and meteorites, yet the search for lunar polycyclic aromatics remains a significant challenge. Here, we analyze Chang'E-5 lunar soil samples, revealing polycyclic aromatic concentrations of 5.0-9.2 µg/g (average: 7.4 ± 1.4 µg/g). Their aromatic structures are highly condensed, comparable to ~4 nm graphene sheets, and distinct from terrestrial analogs, such as wood char, soot and kerogen. While meteorite impacts are the most likely sources, the stable carbon isotope composition of polycyclic aromatics in Chang'E-5 lunar soil (δ13C: -5.0 ± 0.6‰ to +3.6 ± 1.3‰) is more enriched in 13C compared to that in meteorites. This enrichment suggests a de novo formation mechanism during meteorite impacts, involving the conversion of non-aromatic organic matter-which is more enriched in δ13C-into polycyclic aromatics. This process may play a significant role in carbon accretion in lunar regolith, as the resulting polycyclic aromatics are more stable and resistant to degradation compared to smaller organic molecules (e.g., amino acids), which are largely destroyed during impact events.

Abiotic formation of hexoses and disaccharides in aqueous microdroplets

Understanding the chemical reactions that led to the origin of life is a fundamental challenge of chemistry. The formose reaction, an abiotic pathway to monosaccharides, provides a mechanism of sugar formation from simple aldehydes and ketones. However, the reaction requires the addition of base, metal catalysts, and is prone to side reactions, leaving questions about how such processes could have occurred on a primitive Earth. The abiotic formation of more complex sugars, such as disaccharides also require catalysts, and remains underexplored compared to other classes of biomolecules. This study investigates the role of microdroplets in the formation of hexoses and their subsequent condensation reactions to produce disaccharides, without the need for catalysts. The microdroplet-mediated synthesis of fructose and sorbose from glyceraldehyde or dihydroxyacetone, as well as that of disaccharides from various pentoses or hexoses, was monitored via mass spectrometery. Products were confirmed by high resolution mass spectrometry and tandem mass spectrometry. The product distribution of glucose disaccharides was determined by matching the relative intensities of product ions to a mixture of six disaccharide and showed a maximum yield of 9.4% or 1.7 µg min-1 emitter. This study demonstrates the abiotic formation of monosaccharides and disaccharides, such as xylobiose and maltose, providing a possible link between prebiotic sugar synthesis and extant carbohydrate biochemistry. Hexose formation and disaccharide synthesis are driven by the unique air water interface of microdroplets, where partial solvation, pH extremes, and fast mass transfer kinetics enable abiotic transformations.

Low-Temperature Aqueous Alteration of Chondrites

Chondritic meteorites (chondrites) contain evidence for the interaction of liquid water with the interiors of small bodies early in Solar System history. Here we review the processes, products and timings of the low-temperature aqueous alteration reactions in CR, CM, CI and ungrouped carbonaceous chondrites, the asteroids Ryugu and Bennu, and hydrated dark clasts in different types of meteorites. We first consider the nature of chondritic lithologies and the insights that they provide into alteration conditions, subdivided by the mineralogy and petrology of hydrated chondrites, the mineralogy of hydrated dark clasts, the effects of alteration on presolar grains, and the evolution of organic matter. We then describe the properties of the aqueous fluids and how they reacted with accreted material as revealed by physicochemical modelling and hydrothermal experiments, the analysis of fluid inclusions in aqueously formed minerals, and isotope tracers. Lastly, we outline the chronology of aqueous alteration reactions as determined using the 53Mn-53Cr and 129I-129Xe systems.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11214-024-01132-8.

Reciprocating thermochemical mediator of pre-biotic polymer decomposition on mineral surfaces

A continuing frustration for origin of life scientists is that abiotic and, by extension, pre-biotic attempts to develop self-sustaining, evolving molecular systems tend to produce more dead-end substances than macromolecular products with the necessary potential for biostructure and function - the so-called 'tar problem'. Nevertheless primordial life somehow emerged despite that presumed handicap. A resolution of this problem is important in emergence-of-life science because it would provide valuable guidance in choosing subsequent paths of investigation, such as identifying pre-biotic patterns on Mars. To study the problem we set up a simple non-equilibrium flow dynamical model for the coupled temperature and mass dynamics of the decomposition of a polymeric carbohydrate adsorbed on a mineral surface, with incident stochastic thermal fluctuations. Results show that the model system behaves as a reciprocating thermochemical oscillator. The output fluctuation distribution is bimodal, with a right-weighted component that guarantees a bias towards detachment and desorption of monomeric species such as ribose, even while tar is formed concomitantly. This fluctuating thermochemical reciprocator may ensure that non-performing polymers can be fractionated into a refractory carbon reservoir and active monomers which may be reincorporated into better-performing polymers with less vulnerability towards adsorptive tarring.

The second wave of formose research

This review article highlights key developments in the second wave of formose research (from approximately 2000), summarizing approximately 100 relevant studies. Section 1 introduces the basics of formose reaction and its historical context. Section 2 provides a brief overview of the pioneering works from the first wave of formose research (from 1970 to 1990). Section 3 then overviews the second wave of formose research, in which formose reactions under various conditions, mechanistic studies of the formose reaction, formose reactions and the origin of life, and applications of formose reactions are described. Finally, Section 4 offers summary and outlook.

Hypothesis for Molecular Evolution in the Pre-Cellular Stage of the Origin of Life

Life was originated from inorganic world and had experienced a long period of evolution in about 3.8 billion years. The time for emergence of the pioneer creations on Earth is debatable nowadays, and how the scenario for the prebiotic molecular interactions is still mysterious. Before the spreading of cellular organisms, chemical evolution was perhaps prevailing for millions of years, in which inorganic biosynthesis was ultimately replaced by biochemical reactions. Understanding the major molecular players and their interactions toward cellular life is fundamental for current medical science and extraterrestrial life exploration. In this review, we propose a road map for the primordial molecular evolution in early Earth, which probably occurred adjacent to hydrothermal vents with a strong gradient of organic molecules, temperature, and metal contents. Natural selection of the macromolecules with strong secondary structures and catalytic centers is associated with decreasing of overall entropy of the biopolymers. Our review may shed lights into the important selection of gene-coding RNA with secondary structures from large amounts of random biopolymers and formation of ancient ribosomes with biological machines supporting the basic life processes. Integration of the free environmental ribosomes by the early cellular life as symbiotic molecular machines is probably the earliest symbiosis on Earth.

Interstellar formation of lactaldehyde, a key intermediate in the methylglyoxal pathway

Aldehydes are ubiquitous in star-forming regions and carbonaceous chondrites, serving as essential intermediates in metabolic pathways and molecular mass growth processes to vital biomolecules necessary for the origins of life. However, their interstellar formation mechanisms have remained largely elusive. Here, we unveil the formation of lactaldehyde (CH3CH(OH)CHO) by barrierless recombination of formyl (HĊO) and 1-hydroxyethyl (CH3ĊHOH) radicals in interstellar ice analogs composed of carbon monoxide (CO) and ethanol (CH3CH2OH). Lactaldehyde and its isomers 3-hydroxypropanal (HOCH2CH2CHO), ethyl formate (CH3CH2OCHO), and 1,3-propenediol (HOCH2CHCHOH) are identified in the gas phase utilizing isomer-selective photoionization reflectron time-of-flight mass spectrometry and isotopic substitution studies. These findings reveal fundamental formation pathways for complex, biologically relevant aldehydes through non-equilibrium reactions in interstellar environments. Once synthesized, lactaldehyde can act as a key precursor to critical biomolecules such as sugars, sugar acids, and amino acids in deep space.

The HOMO-LUMO Gap as Discriminator of Biotic from Abiotic Chemistries

Low-molecular-mass organic chemicals are widely discussed as potential indicators of life in extraterrestrial habitats. However, demarcation lines between biotic chemicals and abiotic chemicals have been difficult to define. Here, we have analyzed the potential utility of the quantum chemical property, HOMO-LUMO gap (HLG), as a novel proxy variable of life, since a significant trend towards incrementally smaller HLGs has been described in the genetically encoded amino acids. The HLG is a zeroth-order predictor of chemical reactivity. Comparing a set of 134 abiotic organic molecules recovered from meteorites, with 570 microbial and plant secondary metabolites thought to be exclusively biotic, we found that the average HLG of biotic molecules was significantly narrower (-10.4 ± 0.9 eV versus -12.4 ± 1.6 eV), with an effect size of g = 1.87. Limitation to hydrophilic molecules (XlogP < 2) improved the separation of biotic from abiotic compounds (g = 2.52). The "hydrophilic reactivity" quadrant defined by |HLG| < 11.25 eV and XlogP < 2 was populated exclusively by 183 biotic compounds and 6 abiotic compounds, 5 of which were nucleobases. We conclude that hydrophilic molecules with small HLGs represent valuable indicators of biotic activity, and we discuss the evolutionary plausibility of this inference.

Interstellar Formation of Nitrogen Heteroaromatics [Indole, C8H7N; Pyrrole, C4H5N; Aniline, C6H5NH2]: Key Precursors to Amino Acids and Nucleobases

Nitrogen-substituted polycyclic aromatic hydrocarbons (NPAHs) are not only fundamental building blocks in the prebiotic synthesis of vital biomolecules such as amino acids and nucleobases of DNA and RNA but also a potential source of the prominent unidentified 6.2 μm interstellar absorption band. Although NPAHs have been detected in meteorites and are believed to be ubiquitous in the universe, their formation mechanisms in deep space have remained largely elusive. Here, we report the first bottom-up formation pathways to the simplest prototype of NPAHs, indole (C8H7N), along with its building blocks pyrrole (C4H5N) and aniline (C6H5NH2) in low-temperature model interstellar ices composed of acetylene (C2H2) and ammonia (NH3). Utilizing the isomer-selective techniques of resonance-enhanced multiphoton ionization and tunable vacuum ultraviolet photoionization reflectron time-of-flight mass spectrometry, indole, pyrrole, and aniline were identified in the gas phase, suggesting that they are promising candidates for future astronomical searches in star-forming regions. Our laboratory experiments utilizing infrared spectroscopy and mass spectrometry in tandem with electronic structure calculations reveal critical insights into the reaction pathways toward NPAHs and their precursors, thus advancing our fundamental understanding of the interstellar formation of aromatic proteinogenic amino acids and nucleobases, key classes of molecules central to the Origins of Life.

Formation of methylglyoxal (CH3C(O)CHO) in interstellar analog ices - a key intermediate in cellular metabolism

Ketoaldehydes are key intermediates in biochemical processes including carbohydrate, lipid, and amino acid metabolism. Despite their crucial role in the interstellar synthesis of essential biomolecules necessary for the Origins of Life, their formation mechanisms have largely remained elusive. Here, we report the first bottom-up formation of methylglyoxal (CH3C(O)CHO)-the simplest ketoaldehyde-through the barrierless recombination of the formyl (HĊO) radical with the acetyl (CH3ĊO) radical in low-temperature interstellar ice analogs upon exposure to energetic irradiation as proxies of galactic cosmic rays. Utilizing vacuum ultraviolet photoionization reflectron time-of-flight mass spectrometry and isotopic substitution studies, methylglyoxal and its enol tautomer 2-hydroxypropenone (CH3C(OH)CO) were identified in the gas phase during the temperature-programmed desorption of irradiated carbon monoxide-acetaldehyde (CO-CH3CHO) ices, suggesting their potential as promising candidates for future astronomical searches. Once synthesized in cold molecular clouds, methylglyoxal can serve as a key precursor to sugars, sugar acids, and amino acids. Furthermore, this work provides the first experimental evidence for tautomerization of a ketoaldehyde in interstellar ice analogs, advancing our fundamental knowledge of how ketoaldehydes and their enol tautomers can be synthesized in deep space.

Stable carbon isotope evolution of formaldehyde on early Mars

Organic matter in the Martian sediments may provide a key to understanding the prebiotic chemistry and habitability of early Mars. The Curiosity rover has measured highly variable and 13C-depleted carbon isotopic values in early Martian organic matter whose origin is uncertain. One hypothesis suggests the deposition of simple organic molecules generated from 13C-depleted CO derived from CO2 photochemical reduction in the atmosphere. Here, we present a coupled photochemistry-climate evolution model incorporating carbon isotope fractionation processes induced by CO2 photolysis, carbon escape, and volcanic outgassing in an early Martian atmosphere of 0.5-2 bar, composed mainly of CO2, CO, and H2 to track the evolution of the carbon isotopic composition of C-bearing species. The calculated carbon isotopic ratio in formaldehyde (H2CO) can be highly depleted in 13C due to CO2-photolysis-induced fractionation and is variable with changes in atmospheric CO/CO2 ratio, surface pressure, albedo, and H2 outgassing rate. Conversely, CO2 becomes enriched in 13C, as estimated from the carbonates preserved in ALH84001 meteorite. Complex organic matter formed by the polymerization of such H2CO could explain the strong depletion in 13C observed in the Martian organic matter. Mixing with other sources of organic matter would account for its unique variable carbon isotopic values.

Kinetics and coexistence of autocatalytic reaction cycles

Biological reproduction rests ultimately on chemical autocatalysis. Autocatalytic chemical cycles are thought to have played an important role in the chemical complexification en route to life. There are two, related issues: what chemical transformations allow such cycles to form, and at what speed they are operating. Here we investigate the latter question for solitary as well as competitive autocatalytic cycles in resource-unlimited batch and resource-limited chemostat systems. The speed of growth tends to decrease with the length of a cycle. Reversibility of the reproductive step results in parabolic growth that is conducive to competitive coexistence. Reversibility of resource uptake also slows down growth. Unilateral help by a cycle of its competitor tends to favour the competitor (in effect a parasite on the helper), rendering coexistence unlikely. We also show that deep learning is able to predict the outcome of competition just from the topology and the kinetic rate constants, provided the training set is large enough. These investigations pave the way for studying autocatalytic cycles with more complicated coupling, such as mutual catalysis.

The Origin of RNA and the Formose-Ribose-RNA Pathway

Prebiotic pre-Darwinian reactions continued throughout biochemical or Darwinian evolution. Early chemical processes could have occurred on Earth between 4.5 and 3.6 billion years ago when cellular life was about to come into being. Pre-Darwinian evolution assumes the development of hereditary elements but does not regard them as self-organizing processes. The presence of biochemical self-organization after the pre-Darwinian evolution did not justify distinguishing between different types of evolution. From the many possible solutions, evolution selected from among those stable reactions that led to catalytic networks, and under gradually changing external conditions produced a reproducible, yet constantly evolving and adaptable, living system. Major abiotic factors included sunlight, precipitation, air, minerals, soil and the Earth's atmosphere, hydrosphere and lithosphere. Abiotic sources of chemicals contributed to the formation of prebiotic RNA, the development of genetic RNA, the RNA World and the initial life forms on Earth and the transition of genRNA to the DNA Empire, and eventually to the multitude of life forms today. The transition from the RNA World to the DNA Empire generated new processes such as oxygenic photosynthesis and the hierarchical arrangement of processes involved in the transfer of genetic information. The objective of this work is to unite earlier work dealing with the formose, the origin and synthesis of ribose and RNA reactions that were published as a series of independent reactions. These reactions are now regarded as the first metabolic pathway.

Proton Transfer Processes in 2-Butenenitrile Dimer Cation Studied by Mass-Selective Infrared Spectroscopy

2-Butenenitrile (2-Bu) is a recently discovered crucial interstellar molecule. Herein, an abnormal NH band was observed in the infrared spectrum of the 2-Bu dimer cation, suggestive of a proton transfer reaction within the cluster. Through a comprehensive theoretical analysis of the IR spectrum of (2-Bu)2+, we discovered not only the formation of a new C-N bond through the attachment of one 2-Bu to another but also the occurrence of a proton transfer reaction in the cluster. This proton was identified as originating from the methyl group of the attaching 2-Bu in the cluster based on the analysis of IR spectra of (2-Bu)+ and [2-Bu-acrylonitrile (AN)]+. Furthermore, the detailed reaction process of this ion-molecule reaction is examined with theoretical calculation. This finding contributes significantly to our deeper understanding of ion-molecule reactions in the gas phase and the formation of nitrogen-containing prebiotic molecules in the interstellar medium.

Unveiling the role of inorganic nanoparticles in Earth's biochemical evolution through electron transfer dynamics

This article explores the intricate interplay between inorganic nanoparticles and Earth's biochemical history, with a focus on their electron transfer properties. It reveals how iron oxide and sulfide nanoparticles, as examples of inorganic nanoparticles, exhibit oxidoreductase activity similar to proteins. Termed "life fossil oxidoreductases," these inorganic enzymes influence redox reactions, detoxification processes, and nutrient cycling in early Earth environments. By emphasizing the structural configuration of nanoparticles and their electron conformation, including oxygen defects and metal vacancies, especially electron hopping, the article provides a foundation for understanding inorganic enzyme mechanisms. This approach, rooted in physics, underscores that life's origin and evolution are governed by electron transfer principles within the framework of chemical equilibrium. Today, these nanoparticles serve as vital biocatalysts in natural ecosystems, participating in critical reactions for ecosystem health. The research highlights their enduring impact on Earth's history, shaping ecosystems and interacting with protein metal centers through shared electron transfer dynamics, offering insights into early life processes and adaptations.

The enol of isobutyric acid

We present the gas-phase synthesis of 2-methyl-prop-1-ene-1,1-diol, an unreported higher energy tautomer of isobutyric acid. The enol was captured in an argon matrix at 3.5 K, characterized spectroscopically and by DFT computations. The enol rearranges likely photochemically to isobutyric acid and dimethylketene. We also identified propene, likely photochemically formed from dimethylketene.

Resolution and quantification of carbohydrates by enantioselective comprehensive two-dimensional gas chromatography

Carbohydrates, in particular the d-enantiomers of ribose, 2-deoxyribose, and glucose, are essential to life's informational biopolymers (RNA/DNA) and for supplying energy to living cells through glycolysis. Considered to be potential biosignatures in the search of past or present life, our capacity to detect and quantify these essential sugars is crucial for future space missions to the Moon, Mars or Titan as well as for sample-return missions. However, the enantioselective analysis of carbohydrates is challenging and both research and routine applications, are lacking efficient methods that combine highly sensitive and reproducible detection with baseline enantioselective resolution and reliable enantiomeric excess (ee) measurements. Here, we present four different derivatization strategies in combination with multidimensional gas chromatography coupled to a reflectron time-of-flight mass spectrometer (GC×GC-TOF-MS) for the enantioselective resolution of C3 to C6 carbohydrates potentially suitable for sample-return analyses. Full mass spectral interpretation and calibration curves for one single-step (cyclic boronate derivatives) and three two-step derivatization protocols (aldononitrile-acetate, hemiacetalization-trifluoroacetylation, and hemiacetalization-permethylation) are presented for concentrations ranging from 1 to 50 pmol μL⁻1 with correlation coefficients R2 > 0.94. We compared several analytical parameters including reproducibility, sensitivity (LOD and LOQ), overall separation, chiral resolution (RS), mass spectrum selectivity, stability during long term storage, and reliability of ee measurements to guide the application-dependent selection of optimal separation and quantification performance.

Abiotic Ribose Synthesis Under Aqueous Environments with Various Chemical Conditions

Ribose is the defining sugar in ribonucleic acid (RNA), which is often proposed to have carried the genetic information and catalyzed the biological reactions of the first life on Earth. Thus, abiological processes that yield ribose under prebiotic conditions have been studied for decades. However, aqueous environments required for the formation of ribose from materials available in quantity under geologically reasonable models, where the ribose formed is not immediately destroyed, remain unclear. This is due in large part to the challenge of analysis of carbohydrates formed under a wide range of aqueous conditions. Thus, the formation of ribose on prebiotic Earth has sometimes been questioned. We investigated the quantitative effects of pH, temperature, cation, and the concentrations of formaldehyde and glycolaldehyde on the synthesis of diverse sugars, including ribose. The results suggest a range of conditions that produce ribose and that ribose could have formed in constrained aquifers on prebiotic Earth.

Prebiotic Vitamin B3 Synthesis in Carbonaceous Planetesimals

Aqueous chemistry within carbonaceous planetesimals is promising for synthesizing prebiotic organic matter essential to all life. Meteorites derived from these planetesimals delivered these life building blocks to the early Earth, potentially facilitating the origins of life. Here, we studied the formation of vitamin B3 as it is an important precursor of the coenzyme NAD(P)(H), which is essential for the metabolism of all life as we know it. We propose a new reaction mechanism based on known experiments in the literature that explains the synthesis of vitamin B3. It combines the sugar precursors glyceraldehyde or dihydroxyacetone with the amino acids aspartic acid or asparagine in aqueous solution without oxygen or other oxidizing agents. We performed thermochemical equilibrium calculations to test the thermodynamic favorability. The predicted vitamin B3 abundances resulting from this new pathway were compared with measured values in asteroids and meteorites. We conclude that competition for reactants and decomposition by hydrolysis are necessary to explain the prebiotic content of meteorites. In sum, our model fits well into the complex network of chemical pathways active in this environment.

Infrared Spectroscopy of RNA Nucleosides in a Wide Range of Temperatures

The RNA world hypothesis suggests that early cellular ancestors relied solely on RNA molecules for both genetic information storage and cellular functions. RNA, composed of four nucleosides-adenosine, guanosine, cytidine, and uridine-forms the basis of this theory. These nucleosides consist of purine nucleobases, adenine and guanine, and pyrimidine nucleobases, cytosine and uracil, bonded to ribose sugar. Notably, carbonaceous chondrite meteorites have revealed the presence of these bases and sugar, hinting at the potential existence of nucleosides in space. This study aims to present the infrared spectra of four RNA nucleosides commonly found in terrestrial biochemistry, facilitating their detection in space, especially in astrobiological and astrochemical contexts. Laboratory measurements involved obtaining mid- and far-IR spectra at three temperatures (-180 °C, room temperature, and +180 °C), followed by calculating molar extinction coefficients (ε) and integrated molar absorptivities (ψ) for corresponding bands. These spectral data, along with ε and ψ values, serve to provide quantitative insights into the presence and relative abundance of nucleosides in space and aid in their detection.

Interstellar formation of glyceric acid [HOCH2CH(OH)COOH]-The simplest sugar acid

Glyceric acid [HOCH2CH(OH)COOH]-the simplest sugar acid-represents a key molecule in biochemical processes vital for metabolism in living organisms such as glycolysis. Although critically linked to the origins of life and identified in carbonaceous meteorites with abundances comparable to amino acids, the underlying mechanisms of its formation have remained elusive. Here, we report the very first abiotic synthesis of racemic glyceric acid via the barrierless radical-radical reaction of the hydroxycarbonyl radical (HOĊO) with 1,2-dihydroxyethyl (HOĊHCH2OH) radical in low-temperature carbon dioxide (CO2) and ethylene glycol (HOCH2CH2OH) ices. Using isomer-selective vacuum ultraviolet photoionization reflectron time-of-flight mass spectrometry, glyceric acid was identified in the gas phase based on the adiabatic ionization energies and isotopic substitution studies. This work reveals the key reaction pathways for glyceric acid synthesis through nonequilibrium reactions from ubiquitous precursor molecules, advancing our fundamental knowledge of the formation pathways of key biorelevant organics-sugar acids-in deep space.

Chapter 4: A Geological and Chemical Context for the Origins of Life on Early Earth

Within the first billion years of Earth's history, the planet transformed from a hot, barren, and inhospitable landscape to an environment conducive to the emergence and persistence of life. This chapter will review the state of knowledge concerning early Earth's (Hadean/Eoarchean) geochemical environment, including the origin and composition of the planet's moon, crust, oceans, atmosphere, and organic content. It will also discuss abiotic geochemical cycling of the CHONPS elements and how these species could have been converted to biologically relevant building blocks, polymers, and chemical networks. Proposed environments for abiogenesis events are also described and evaluated. An understanding of the geochemical processes under which life may have emerged can better inform our assessment of the habitability of other worlds, the potential complexity that abiotic chemistry can achieve (which has implications for putative biosignatures), and the possibility for biochemistries that are vastly different from those on Earth.

Atmospheric formaldehyde production on early Mars leading to a potential formation of bio-important molecules

Formaldehyde (H2CO) is a critical precursor for the abiotic formation of biomolecules, including amino acids and sugars, which are the building blocks of proteins and RNA. Geomorphological and geochemical evidence on Mars indicates a temperate environment compatible with the existence of surface liquid water during its early history at 3.8-3.6 billion years ago (Ga), which was maintained by the warming effect of reducing gases, such as H2. However, it remains uncertain whether such a temperate and weakly reducing surface environment on early Mars was suitable for producing H2CO. In this study, we investigated the atmospheric production of H2CO on early Mars using a 1-D photochemical model assuming a thick CO2-dominated atmosphere with H2 and CO. Our results show that a continuous supply of atmospheric H2CO can be used to form various organic compounds, including amino acids and sugars. This could be a possible origin for the organic matter observed on the Martian surface. Given the previously reported conversion rate from H2CO into ribose, the calculated H2CO deposition flux suggests a continuous supply of bio-important sugars on early Mars, particularly during the Noachian and early Hesperian periods.

High-spatial resolution functional chemistry of nitrogen compounds in the observed UK meteorite fall Winchcombe

Organic matter in extraterrestrial samples is a complex material that might have played an important role in the delivery of prebiotic molecules to the early Earth. We report here on the identification of nitrogen-containing compounds such as amino acids and N-heterocycles within the recent observed meteorite fall Winchcombe by high-spatial resolution spectroscopy techniques. Although nitrogen contents of Winchcombe organic matter are low (N/C ~ 1-3%), we were able to detect the presence of these compounds using a low-noise direct electron detector. These biologically relevant molecules have therefore been tentatively found within a fresh, minimally processed meteorite sample by high spatial resolution techniques conserving the overall petrographic context. Carbon functional chemistry investigations show that sizes of aromatic domains are small and that abundances of carboxylic functional groups are low. Our observations demonstrate that Winchcombe represents an important addition to the collection of carbonaceous chondrites and still preserves pristine extraterrestrial organic matter.

Hexose phosphorylation for a non-enzymatic glycolysis and pentose phosphate pathway on early Earth

Glycolysis and pentose phosphate pathways play essential roles in cellular processes and are assumed to be among the most ancient metabolic pathways. Non-enzymatic metabolism-like reactions might have occurred on the prebiotic Earth and been inherited by the biological reactions. Previous research has identified a part of the non-enzymatic glycolysis and the non-enzymatic pentose phosphate pathway from glucose 6-phosphate and 6-phosphogluconate, which are intermediates of these reactions. However, how these phosphorylated molecules were formed on the prebiotic Earth remains unclear. Herein, we demonstrate the synthesis of glucose and gluconate from simple aldehydes in alkaline solutions and the formation of glucose 6-phosphate and 6-phosphogluconate with borate using thermal evaporation. These results imply that the initial stages of glycolysis-like and pentose phosphate pathway-like reactions were achieved in borate-rich evaporative environments on prebiotic Earth, suggesting that non-enzymatic metabolism provided biomolecules and their precursors on prebiotic Earth.

Synthesis and chemical transformations of glycol nucleic acid (GNA) nucleosides

Xeno nucleic acids (XNA) are an increasingly important class of hypermodified nucleic acids with great potential in bioorganic chemistry and synthetic biology. Glycol nucleic acid (GNA) is constructed from a three-carbon 1,2-propanediol (propylene glycol) backbone attached to a nucleobase entity, representing the simplest known XNA. This review is intended to present GNA nucleosides from a synthetic chemistry perspective-a perspective that serves as a starting point for biological studies. Therefore this account focuses on synthetic methods for GNA nucleoside synthesis, as well as their postsynthetic chemical transformations. The properties and biological activity of GNA constituents are also highlighted. A literature survey shows four major approaches toward GNA nucleoside scaffold synthesis. These approaches pertain to glycidol ring-opening, Mitsunobu, SN2, and dihydroxylation reactions. The general arsenal of reactions used in GNA chemistry is versatile and encompasses the Sonogashira reaction, Michael addition, silyl-Hilbert-Johnson reaction, halogenation, alkylation, cyclization, Rh-catalyzed N-allylation, Sharpless catalytic dihydroxylation, and Yb(OTf)3-catalyzed etherification. Additionally, various phosphorylation reactions have enabled the synthesis of diverse types of GNA nucleotides, dinucleoside phosphates, phosphordiamidites, and oligos. Furthermore, recent advances in GNA chemistry have resulted in the synthesis of previously unknown redox-active (ferrocenyl) and luminescent (pyrenyl and phenanthrenyl) GNA nucleosides, which are also covered in this review.

Xeno Amino Acids: A Look into Biochemistry as We Do Not Know It

Would another origin of life resemble Earth's biochemical use of amino acids? Here, we review current knowledge at three levels: (1) Could other classes of chemical structure serve as building blocks for biopolymer structure and catalysis? Amino acids now seem both readily available to, and a plausible chemical attractor for, life as we do not know it. Amino acids thus remain important and tractable targets for astrobiological research. (2) If amino acids are used, would we expect the same L-alpha-structural subclass used by life? Despite numerous ideas, it is not clear why life favors L-enantiomers. It seems clearer, however, why life on Earth uses the shortest possible (alpha-) amino acid backbone, and why each carries only one side chain. However, assertions that other backbones are physicochemically impossible have relaxed into arguments that they are disadvantageous. (3) Would we expect a similar set of side chains to those within the genetic code? Many plausible alternatives exist. Furthermore, evidence exists for both evolutionary advantage and physicochemical constraint as explanatory factors for those encoded by life. Overall, as focus shifts from amino acids as a chemical class to specific side chains used by post-LUCA biology, the probable role of physicochemical constraint diminishes relative to that of biological evolution. Exciting opportunities now present themselves for laboratory work and computing to explore how changing the amino acid alphabet alters the universe of protein folds. Near-term milestones include: (a) expanding evidence about amino acids as attractors within chemical evolution; (b) extending characterization of other backbones relative to biological proteins; and (c) merging computing and laboratory explorations of structures and functions unlocked by xeno peptides.

Epistemology of synthetic biology: a new theoretical framework based on its potential objects and objectives

Synthetic biology is a new research field which attempts to understand, modify, and create new biological entities by adopting a modular and systemic conception of the living organisms. The development of synthetic biology has generated a pluralism of different approaches, bringing together a set of heterogeneous practices and conceptualizations from various disciplines, which can lead to confusion within the synthetic biology community as well as with other biological disciplines. I present in this manuscript an epistemological analysis of synthetic biology in order to better define this new discipline in terms of objects of study and specific objectives. First, I present and analyze the principal research projects developed at the foundation of synthetic biology, in order to establish an overview of the practices in this new emerging discipline. Then, I analyze an important scientometric study on synthetic biology to complete this overview. Afterwards, considering this analysis, I suggest a three-level classification of the object of study for synthetic biology (which are different kinds of living entities that can be built in the laboratory), based on three successive criteria: structural hierarchy, structural origin, functional origin. Finally, I propose three successively linked objectives in which synthetic biology can contribute (where the achievement of one objective led to the development of the other): interdisciplinarity collaboration (between natural, artificial, and theoretical sciences), knowledge of natural living entities (past, present, future, and alternative), pragmatic definition of the concept of "living" (that can be used by biologists in different contexts). Considering this new theoretical framework, based on its potential objects and objectives, I take the position that synthetic biology has not only the potential to develop its own new approach (which includes methods, objects, and objectives), distinct from other subdisciplines in biology, but also the ability to develop new knowledge on living entities.

A Comparative Study of Methods for Detecting Extraterrestrial Life in Exploration Missions to Mars and the Solar System II: Targeted Characteristics, Detection Techniques, and Their Combination for Survey, Detection, and Analysis

We present a comparative study of the methods used in the search for extraterrestrial microorganism life, including a summary table where different life-detection techniques can be easily compared as an aid to mission and instrument design aimed at life detection. This is an extension of previous study, where detection techniques for a series of target characteristics and molecules that could constitute a positive life detection were evaluated. This comparison has been extended with a particular consideration to sources of false positives, the causes of negative detection, the results of detection techniques when presented regarding terrestrial life, and additional science objectives that could be achieved outside the primary aim of detecting life. These additions address both the scientific and programmatic side of exploration mission design, where a successful proposal must demonstrate probable outcomes and be able to return valuable results even if no life is found. The applicability of the life detection techniques is considered for Earth life, Earth-independent life (life emerging independently from that on Earth,) and Earth-kin life (sharing a common ancestor with life on Earth), and techniques effective in detecting Earth life should also be useful in the detection of Earth-kin life. However, their applicability is not guaranteed for Earth-independent life. As found in our previous study, there exists no realistic single detection method that can conclusively determine the discovery of extraterrestrial life, and no method is superior to all others. In this study, we further consider combinations of detection techniques and identify imaging as a valuable addition to molecule detection methods, even in cases where there is insufficient resolution to observe the detailed morphology of a microbial cell. The search for extraterrestrial life is further divided into a survey-and-detection and analysis-and-conclusion step. These steps benefit from different detection techniques, but imaging is necessary for both parts.

The enol of propionic acid

We demonstrate the gas-phase synthesis of prop-1-ene-1,1-diol, the hitherto unreported higher energy tautomer of propionic acid. The enol was trapped in an argon matrix and characterized by IR and UV/Vis spectroscopy in combination with density functional theory computations. Upon photolysis, the enol rearranges to propionic acid and methylketene.

Carbonyl Migration in Uronates Affords a Potential Prebiotic Pathway for Pentose Production

Carbohydrate biosynthesis is fundamental to modern terrestrial biochemistry, but how this collection of metabolic pathways originated remains an open question. Prebiotic sugar synthesis has focused primarily on the formose reaction and Kiliani-Fischer homologation; however, how they can transition to extant biochemical pathways has not been studied. Herein, a nonenzymatic pathway for pentose production with similar chemical transformations as those of the pentose phosphate pathway is demonstrated. Starting from a C6 aldonate, namely, gluconate, nonselective chemical oxidation yields a mixture of 2-oxo-, 4-oxo-, 5-oxo-, and 6-oxo-uronate regioisomers. Regardless at which carbinol the oxidation takes place, carbonyl migration enables β-decarboxylation to yield pentoses. In comparison, the pentose phosphate pathway selectively oxidizes 6-phosphogluconate to afford the 3-oxo-uronate derivative, which undergoes facile subsequent β-decarboxylation and carbonyl migration to afford ribose 5-phosphate. The similarities between these two pathways and the potential implications for prebiotic chemistry and protometabolism are discussed.

Molecular Crowding Facilitates Ribozyme-Catalyzed RNA Assembly

Catalytic RNAs or ribozymes are considered to be central to primordial biology. Most ribozymes require moderate to high concentrations of divalent cations such as Mg2+ to fold into their catalytically competent structures and perform catalysis. However, undesirable effects of Mg2+ such as hydrolysis of reactive RNA building blocks and degradation of RNA structures are likely to undermine its beneficial roles in ribozyme catalysis. Further, prebiotic cell-like compartments bounded by fatty acid membranes are destabilized in the presence of Mg2+, making ribozyme function inside prebiotically relevant protocells a significant challenge. Therefore, we sought to identify conditions that would enable ribozymes to retain activity at low concentrations of Mg2+. Inspired by the ability of ribozymes to function inside crowded cellular environments with <1 mM free Mg2+, we tested molecular crowding as a potential mechanism to lower the Mg2+ concentration required for ribozyme-catalyzed RNA assembly. Here, we show that the ribozyme-catalyzed ligation of phosphorimidazolide RNA substrates is significantly enhanced in the presence of the artificial crowding agent polyethylene glycol. We also found that molecular crowding preserves ligase activity under denaturing conditions such as alkaline pH and the presence of urea. Additionally, we show that crowding-induced stimulation of RNA-catalyzed RNA assembly is not limited to phosphorimidazolide ligation but extends to the RNA-catalyzed polymerization of nucleoside triphosphates. RNA-catalyzed RNA ligation is also stimulated by the presence of prebiotically relevant small molecules such as ethylene glycol, ribose, and amino acids, consistent with a role for molecular crowding in primordial ribozyme function and more generally in the emergence of RNA-based cellular life.

Electron transport chains as a window into the earliest stages of evolution

The origin and early evolution of life is generally studied under two different paradigms: bottom up and top down. Prebiotic chemistry and early Earth geochemistry allow researchers to explore possible origin of life scenarios. But for these "bottom-up" approaches, even successful experiments only amount to a proof of principle. On the other hand, "top-down" research on early evolutionary history is able to provide a historical account about ancient organisms, but is unable to investigate stages that occurred during and just after the origin of life. Here, we consider ancient electron transport chains (ETCs) as a potential bridge between early evolutionary history and a protocellular stage that preceded it. Current phylogenetic evidence suggests that ancestors of several extant ETC components were present at least as late as the last universal common ancestor of life. In addition, recent experiments have shown that some aspects of modern ETCs can be replicated by minerals, protocells, or organic cofactors in the absence of biological proteins. Here, we discuss the diversity of ETCs and other forms of chemiosmotic energy conservation, describe current work on the early evolution of membrane bioenergetics, and advocate for several lines of research to enhance this understanding by pairing top-down and bottom-up approaches.

Metal-Organic Frameworks as Formose Reaction Catalysts with Enhanced Selectivity

The formose reaction is an autocatalytic series of aldol condensations that allows one to obtain monosaccharides from formaldehyde. The formose reaction suffers from a lack of selectivity, which hinders practical applications at the industrial level. Over the years, many attempts have been made to overcome this selectivity issue, with modest results. Heterogeneous porous catalysts with acid-base properties, such as Metal-Organic Frameworks (MOFs), can offer advantages compared to homogeneous strong bases (e.g., calcium hydroxide) for increasing the selectivity of this important reaction. For the very first time, four different Zeolite Imidazolate Frameworks are presented in this work as catalysts for the formose reaction in liquid phase, and their catalytic performances were compared with those of the typical homogeneous catalyst (i.e., calcium hydroxide). The heterogeneous nature of the catalysis, the possible contribution of leached metal or linkers to the solution, and the stability of the materials were investigated. The porous structure of these solids and their mild basicity make them suitable for obtaining enhanced selectivity at 30% formaldehyde conversion. Most of the MOFs tested showed low structural stability under reaction conditions, thereby indicating the need to search for new MOF families with higher robustness. However, this important result opens the path for future research on porous heterogeneous basic catalysts for the formose reaction.

Organic Matter in the Asteroid Ryugu: What We Know So Far

The Hayabusa2 mission was tasked with returning samples from the C-complex asteroid Ryugu (1999 JU3), in order to shed light on the formation, evolution and composition of such asteroids. One of the main science objectives was to understand whether such bodies could have supplied the organic matter required for the origin of life on Earth. Here, a review of the studies concerning the organic matter within the Ryugu samples is presented. This review will inform the reader about the Hayabusa2 mission, the nature of the organic matter analyzed and the various interpretations concerning the analytical findings including those concerning the origin and evolution of organic matter from Ryugu. Finally, the review puts the findings and individual interpretations in the context of the current theories surrounding the formation and evolution of Ryugu. Overall, the summary provided here will help to inform those operating in a wide range of interdisciplinary fields, including planetary science, astrobiology, the origin of life and astronomy, about the most recent developments concerning the organic matter in the Ryugu return samples and their relevance to understanding our solar system and beyond. The review also outlines the issues that still remain to be solved and highlights potential areas for future work.

Distributions of CHN compounds in meteorites record organic syntheses in the early solar system

Carbonaceous meteorites contain diverse soluble organic compounds. These compounds formed in the early solar system from volatiles accreted on tiny dust particles. However, the difference in the organic synthesis on respective dust particles in the early solar system remains unclear. We found micrometer-scale heterogeneous distributions of diverse CHN_1-2 and CHN_1-2O compounds in two primitive meteorites: the Murchison and NWA 801, using a surface-assisted laser desorption/ionization system connected to a high mass resolution mass spectrometer. These compounds contained mutual relationships of ± H₂, ± CH₂, ± H₂O, and ± CH₂O and showed highly similar distributions, indicating that they are the products of series reactions. The heterogeneity was caused by the micro-scale difference in the abundance of these compounds and the extent of the series reactions, indicating that these compounds formed on respective dust particles before asteroid accretion. The results of the present study provide evidence of heterogeneous volatile compositions and the extent of organic reactions among the dust particles that formed carbonaceous asteroids. The compositions of diverse small organic compounds associated with respective dust particles in meteorites are useful to understand different histories of volatile evolution in the early solar system.

Evaluating the abiotic synthesis potential and the stability of building blocks of life beneath an impact-induced steam atmosphere

A prerequisite for prebiotic chemistry is the accumulation of critical building blocks of life. Some studies argue that more frequent impact events on the primitive Earth could have induced a more reducing steam atmosphere and thus favor widespread and more efficient synthesis of life building blocks. However, elevated temperature is also proposed to threaten the stability of organics and whether life building blocks could accumulate to appreciable levels in the reducing yet hot surface seawater beneath the steam atmosphere is still poorly examined. Here, we used a thermodynamic tool to examine the synthesis affinity of various life building blocks using inorganic gasses as reactants at elevated temperatures and corresponding steam pressures relevant with the steam-seawater interface. Our calculations show that although the synthesis affinity of all life building blocks decreases when temperature increases, many organics, including methane, methanol, and carboxylic acids, have positive synthesis affinity over a wide range of temperatures, implying that these species were favorable to form (>10-6 molal) in the surface seawater. However, cyanide and formaldehyde have overall negative affinities, suggesting that these critical compounds would tend to undergo hydrolysis in the surface seawaters. Most of the 18 investigated amino acids have positive affinities at temperature <220°C and their synthesis affinity increases under more alkaline conditions. Sugars, ribose, and nucleobases have overall negative synthesis affinities at the investigated range of temperatures. Synthesis affinities are shown to be sensitive to the hydrogen fugacity. Higher hydrogen fugacity (in equilibrium with FQI or IW) favors the synthesis and accumulation of nearly all the investigated compounds, except for HCN and its derivate products. In summary, our results suggest that reducing conditions induced by primitive impacts could indeed favor the synthesis/accumulation of some life building blocks, but some critical species, particularly HCN and nucleosides, were still unfavorable to accumulate to appreciable levels. Our results can provide helpful guidance for future efforts to search for or understand the stability of biomolecules on other planets like Mars and icy moons. We advocate examining craters formed by more reducing impactors to look for the preservation of prebiotic materials.

Biochar-Mediated Control of Metabolites and Other Physiological Responses in Water-Stressed Leptocohloa fusca

We investigated biochar-induced drought tolerance in Leptocohloa fusca (Kallar grass) by exploring the plant defense system at physiological level. L. fusca plants were exposed to drought stress (100%, 70%, and 30% field capacity), and biochar (BC), as an organic soil amendment was applied in two concentrations (15 and 30 mg kg-1 soil) to induce drought tolerance. Our results demonstrated that drought restricted the growth of L. fusca by inhibiting shoot and root (fresh and dry) weight, total chlorophyll content and photosynthetic rate. Under drought stress, the uptake of essential nutrients was also limited due to lower water supply, which ultimately affected metabolites including amino and organic acids, and soluble sugars. In addition, drought stress induced oxidative stress, which is evidenced by the higher production of reactive oxygen species (ROS) including hydrogen peroxide (H2O2), superoxide ion (O2-), hydroxyl ion (OH-), and malondialdehyde (MDA). The current study revealed that stress-induced oxidative injury is not a linear path, since the excessive production of lipid peroxidation led to the accumulation of methylglyoxal (MG), a member of reactive carbonyl species (RCS), which ultimately caused cell injury. As a consequence of oxidative-stress induction, the ascorbate-glutathione (AsA-GSH) pathway, followed by a series of reactions, was activated by the plants to reduce ROS-induced oxidative damage. Furthermore, biochar considerably improved plant growth and development by mediating metabolites and soil physio-chemical status.

Prebiotic Synthesis of ATP: A Terrestrial Volcanism-Dependent Pathway

Adenosine triphosphate (ATP) is a multifunctional small molecule, necessary for all modern Earth life, which must be a component of the last universal common ancestor (LUCA). However, the relatively complex structure of ATP causes doubts about its accessibility on prebiotic Earth. In this paper, based on previous studies on the synthesis of ATP components, a plausible prebiotic pathway yielding this key molecule is constructed, which relies on terrestrial volcanism to provide the required materials and suitable conditions.

Gnawing pressure led to the expansion of JAZ genes in angiosperms

A long-standing problem in evolutionary biology is why some populations differentiate into many species while the majority do not. Angiosperms is an excellent group for investigating this problem because their diversity is unevenly distributed in space and phylogeny. Plant hormone participates in growth, development and defense. However, jasmonic acid (JA) was the only hormone response to bites. We first searched jasmonate ZIM-domain (JAZ), AUXIN/INDOLE ACETIC ACID (IAA / aux), PYR/PYL/RCAR (PYL), DELLA, and SUPPRESSOR OF MAX2 1-like (SMAX) in 272 plant species. We found the gene number change trends were consistent with origination rates and species numbers of angiosperms. So, 26 representative species were selected as an example for further analysis. The results showed JAZ had experienced two lineage-specific gene expansion events in angiosperms, which coincided with increases in mammalian body size and dental diversity. The proliferation of large herbivores as a results of mammalian prosperity after dinosaur extinction may be related to angiosperm evolution and bursting. The proliferation of large herbivores as the result of mammalian prosperity after the extinction of the dinosaurs was related to angiosperm evolution and bursting. Overall, our study uncovered a previously unknown co-evolution mechanism in terrestrial plants exposed to extreme environmental conditions.

The mammalian purine salvage pathway as an exploitable route for cerebral bioenergetic support after brain injury

Purine-based molecules play ancient, fundamental, and evolutionarily-conserved roles across life on Earth, ranging from DNA and RNA, to the universal energy currency, ATP. In mammals, the two primary routes for the synthesis of the adenine nucleotides ATP, ADP and AMP, and, as a consequence, the major bioactive metabolite adenosine, are the de novo purine biosynthesis (DNPB) pathway, and the purine salvage pathway (PSP). Of the two, the PSP dominates in both the mammalian brain and heart. This is because the PSP utilizes the breakdown products of ATP, occasioned by the high energy demands of these organs, to rapidly regenerate adenine nucleotides. This resynthesis route, while efficient and energetically favourable, leaves these organs vulnerable to loss of salvageable metabolites, with the potential for protracted depletion of the means to synthesize ATP, and the ability to deploy neuro- and cardioprotective adenosine. Having previously shown that hippocampal cellular ATP and adenosine release can be increased by supplying substrates for the PSP (d-ribose and adenine), we now explore the expression of DNPB and PSP enzymes in hippocampal neurons and astrocytes based on available transcriptomic data. We find that key enzymes of the PSP are expressed at higher levels than those in the DNPB pathway, and that PSP enzymes are expressed at higher levels in neurons than in astrocytes. These data reflect the importance of the PSP in the mammalian brain and imply that pharmacological targeting of the PSP may be particularly beneficial to neurons at times of metabolic stress. This article is part of the Special Issue on 'Purinergic Signaling: 50 years'.

Industrial Biotechnology Conservation Processes: Similarities with Natural Long-Term Preservation of Biological Organisms

Cryopreservation and lyophilization processes are widely used for conservation purposes in the pharmaceutical, biotechnological, and food industries or in medical transplantation. Such processes deal with extremely low temperatures (e.g., -196 °C) and multiple physical states of water, a universal and essential molecule for many biological lifeforms. This study firstly considers the controlled laboratory/industrial artificial conditions used to favor specific water phase transitions during cellular material cryopreservation and lyophilization under the Swiss progenitor cell transplantation program. Both biotechnological tools are successfully used for the long-term storage of biological samples and products, with reversible quasi-arrest of metabolic activities (e.g., cryogenic storage in liquid nitrogen). Secondly, similarities are outlined between such artificial localized environment modifications and some natural ecological niches known to favor metabolic rate modifications (e.g., cryptobiosis) in biological organisms. Specifically, examples of survival to extreme physical parameters by small multi-cellular animals (e.g., tardigrades) are discussed, opening further considerations about the possibility to reversibly slow or temporarily arrest the metabolic activity rates of defined complex organisms in controlled conditions. Key examples of biological organism adaptation capabilities to extreme environmental parameters finally enabled a discussion about the emergence of early primordial biological lifeforms, from natural biotechnology and evolutionary points of view. Overall, the provided examples/similarities confirm the interest in further transposing natural processes and phenomena to controlled laboratory settings with the ultimate goal of gaining better control and modulation capacities over the metabolic activities of complex biological organisms.

Preferential formation of specific hexose and heptose in the formose reaction under microwave irradiation

To realize sustainable societies, the production of organic compounds not based on fossil resources should be developed. Thus, C1 chemistry, utilizing one-carbon compounds as starting materials, has been of increasing importance. In particular, the formose reaction is promising because the reaction produces sugars (monosaccharides) from formaldehyde under basic conditions. On the other hand, since microwave (MW) induces the rotational motion of molecules, MW irradiation often improves the selectivity and efficiency of reactions. In this study, the formose reaction under MW irradiation was thus investigated under various conditions. The formose reaction proceeded very fast using 1.0 mol per kg formaldehyde and 55 mmol per kg calcium hydroxide (Ca(OH)₂) as a catalyst at a high set temperature (150 °C) for a short time (1 min) to form preferentially specific hexose and heptose. The major products were isolated by thin layer chromatography and characterized by mass spectroscopy and NMR. These characterization data elucidated that the hexose and heptose were 2-hydroxymethyl-1,2,4,5-tetrahydroxy-3-pentanone (C6*) and 2,4-bis(hydroxymethyl)-1,2,4,5-tetrahydroxy-3-pentanone (C7*), respectively. On the basis of these observations, as well as density functional theory calculations, a plausible reaction pathway was also discussed; once 1,3-dihydroxyacetone is formed, consecutive aldol reactions favorably occur to form C6* and C7*.

Setting the geological scene for the origin of life and continuing open questions about its emergence

The origin of life is one of the most fundamental questions of humanity. It has been and is still being addressed by a wide range of researchers from different fields, with different approaches and ideas as to how it came about. What is still incomplete is constrained information about the environment and the conditions reigning on the Hadean Earth, particularly on the inorganic ingredients available, and the stability and longevity of the various environments suggested as locations for the emergence of life, as well as on the kinetics and rates of the prebiotic steps leading to life. This contribution reviews our current understanding of the geological scene in which life originated on Earth, zooming in specifically on details regarding the environments and timescales available for prebiotic reactions, with the aim of providing experimenters with more specific constraints. Having set the scene, we evoke the still open questions about the origin of life: did life start organically or in mineralogical form? If organically, what was the origin of the organic constituents of life? What came first, metabolism or replication? What was the time-scale for the emergence of life? We conclude that the way forward for prebiotic chemistry is an approach merging geology and chemistry, i.e., far-from-equilibrium, wet-dry cycling (either subaerial exposure or dehydration through chelation to mineral surfaces) of organic reactions occurring repeatedly and iteratively at mineral surfaces under hydrothermal-like conditions.

Quantification of disaccharides in solution using isomer-selective ultraviolet photodissociation of hydrogen-bonded clusters in the gas phase

Chemical properties of gas-phase hydrogen-bonded clusters were investigated as a model for interstellar molecular clouds. Cold gas-phase hydrogen-bonded clusters of tryptophan (Trp) enantiomers and disaccharide isomers, including d-maltose and d-cellobiose, were generated by electrospray ionization and collisional cooling in an ion trap at 8 K. Product ion spectra in the 265-290 nm wavelength range were obtained using tandem mass spectrometry. NH₂CHCOOH loss via the C_α-C_β bond cleavage of Trp occurred frequently in homochiral H⁺(d-Trp)(d-maltose) compared with heterochiral H⁺(l-Trp)(d-maltose) at 278 nm, indicating that an enantiomeric excess of l-Trp was formed via the enantiomer-selective photodissociation. The photoreactivity differed between the enantiomers and isomers contained in the clusters at the photoexcitation of 278 nm. A calibration curve for the quantification of disaccharide isomers in solution was constructed by photoexcitation of the hydrogen-bonded clusters of disaccharide isomers with H⁺(l-Trp) at 278 nm. A linear relationship between the natural logarithm of the relative product ion abundance and the mole fraction of d-maltose to d-cellobiose ratio in the solution was obtained, indicating that the mole fraction could be determined from a single product ion spectrum. A calibration curve, for quantification of Trp enantiomers, was also obtained using d-maltose as a chiral auxiliary.

Photorespiration - Rubisco's repair crew

The photorespiratory repair pathway (photorespiration in short) was set up from ancient metabolic modules about three billion years ago in cyanobacteria, the later ancestors of chloroplasts. These prokaryotes developed the capacity for oxygenic photosynthesis, i.e. the use of water as a source of electrons and protons (with O₂ as a by-product) for the sunlight-driven synthesis of ATP and NADPH for CO₂ fixation in the Calvin cycle. However, the CO₂-binding enzyme, ribulose 1,5-bisphosphate carboxylase (known under the acronym Rubisco), is not absolutely selective for CO₂ and can also use O₂ in a side reaction. It then produces 2-phosphoglycolate (2PG), the accumulation of which would inhibit and potentially stop the Calvin cycle and subsequently photosynthetic electron transport. Photorespiration removes the 2-PG and in this way prevents oxygenic photosynthesis from poisoning itself. In plants, the core of photorespiration consists of ten enzymes distributed over three different types of organelles, requiring interorganellar transport and interaction with several auxiliary enzymes. It goes together with the release and to some extent loss of freshly fixed CO₂. This disadvantageous feature can be suppressed by CO₂-concentrating mechanisms, such as those that evolved in C₄ plants thirty million years ago, which enhance CO₂ fixation and reduce 2PG synthesis. Photorespiration itself provided a pioneer variant of such mechanisms in the predecessors of C₄ plants, C₃-C₄ intermediate plants. This article is a review and update particularly on the enzyme components of plant photorespiration and their catalytic mechanisms, on the interaction of photorespiration with other metabolism and on its impact on the evolution of photosynthesis. This focus was chosen because a better knowledge of the enzymes involved and how they are embedded in overall plant metabolism can facilitate the targeted use of the now highly advanced methods of metabolic network modelling and flux analysis. Understanding photorespiration more than before as a process that enables, rather than reduces, plant photosynthesis, will help develop rational strategies for crop improvement.

How Did Life Emerge in Chemically Complex Messy Environments?

One of the problems that make it difficult to solve the mystery of the origin of life is determining how life emerged in chemically complex messy environments on primitive Earth. In this article, the “chemically complex messy environments” that are focused on are a mixed state of various organic compounds produced via prebiotic means and accumulated on primitive earth. The five factors described below are thought to have contributed to opening the way for the emergence of life: (1) A characteristic inherent in [GADV]-amino acids, which are easily produced via prebiotic means. [GADV] stands for four amino acids, Gly [G], Ala [A], Asp [D] and Val [V], which are indicated by a one-letter symbol. (2) The protein 0th-order structure or a [GADV]-amino acid composition generating water-soluble globular protein with some flexibility, which can be produced even by the random joining of [GADV]-amino acids. (3) The formation of versatile [GADV]-microspheres, which can grow, divide and proliferate even without a genetic system, was the emergence of proto-life. (4) The [GADV]-microspheres with a higher proliferation ability than others were able to be selected. Proto-Darwin evolution made it possible to proceed forward to the creation of a core life system composed of the (GNC)_n gene, anticodon stem-loop tRNA or AntiC-SL tRNA (GNC genetic code), and [GADV]-protein. (5) Eventually, the first genuine life with a core life system emerged. Thus, the formation processes of [GADV]-protein and the (GNC)_n gene in chemically complex messy environments were the steps to the emergence of genuine life.

Nucleobases in Meteorites to Nucleobases in RNA and DNA?

Nucleic acids likely played a foundational role in the origin of life. However, the prebiotic chemistry of nucleoside and nucleotide synthesis has proved challenging on a number of fronts. The recent discovery of both pyrimidine and purine nucleobases in carbonaceous chondrite meteorites has garnered much attention from both the popular press and the scientific community. Here, we discuss these findings in the context of nucleoside/nucleotide prebiotic chemistry. We consider that the main challenge of prebiotic nucleoside synthesis, that of nucleosidic bond formation, is not addressed by the identification nucleobases in meteorites. We further discuss issues of selection that arise from the observation that such meteorites contain both canonical and non-canonical nucleobases. In sum, we argue that, despite the major analytical achievement of identifying and characterizing nucleobases in meteorites, this observation does little to advance our understanding of the prebiotic chemistry that could have led to the first genetic molecules that gave rise to us.

Exploitation of Synchrotron Radiation Photoionization Mass Spectrometry in the Analysis of Complex Organics in Interstellar Model Ices

Unravelling the generation of complex organic molecules (COMs) on interstellar nanoparticles (grains) is essential in establishing predictive astrochemical reaction networks and recognizing evolution stages of molecular clouds and star-forming regions. The formation of COMs has been associated with the irradiation of interstellar ices by ultraviolet photons and galactic cosmic rays. Herein, we pioneer the first incorporation of synchrotron vacuum ultraviolet photoionization reflectron time-of-flight mass spectrometry (SVUV-PI-ReTOF-MS) in laboratory astrophysics simulation experiments to afford an isomer-selective identification of key COMs (ketene (H₂C═CO); acetaldehyde (CH₃CHO); vinyl alcohol (H₂C═CHOH)) based on photoionization efficiency (PIE) curves of molecules desorbing from exposed carbon monoxide-methane (CO-CH₄) ices. Our results demonstrate that the SVUV-PI-ReTOF-MS approach represents a versatile, rapid methodology for a comprehensive identification and explicit understanding of the complex organics produced in space simulation experiments. This methodology is expected to significantly improve the predictive nature of astrochemical models of complex organic molecules formed abiotically in deep space, including biorelated species linked to the origins-of-life topic.

Do Soluble Phosphates Direct the Formose Reaction towards Pentose Sugars?

The formose reaction has been a leading hypothesis for the prebiotic synthesis of sugars such as ribose for many decades but tends to produce complex mixtures of sugars and often tars. Channeling the formose reaction towards the synthesis of biologically useful sugars such as ribose has been a holy grail of origins-of-life research. Here, we tested the hypothesis that a simple, prebiotically plausible phosphorylating agent, acetyl phosphate, could direct the formose reaction towards ribose through phosphorylation of intermediates in a manner resembling gluconeogenesis and the pentose phosphate pathway. We did indeed find that addition of acetyl phosphate to a developing formose reaction stabilized pentoses, including ribose, such that after 5 h of reaction about 10-fold more ribose remained compared with control runs. But mechanistic analyses using liquid chromatography-mass spectrometry showed that, far from being directed towards ribose by phosphorylation, the formose reaction was halted by the precipitation of Ca²⁺ ions as phosphate minerals such as apatite and hydroxyapatite. Adding orthophosphate had the same effect. Phosphorylated sugars were only detected below the limit of quantification when adding acetyl phosphate. Nonetheless, our findings are not strictly negative. The sensitivity of the formose reaction to geochemically reasonable conditions, combined with the apparent stability of ribose under these conditions, serves as a valuable constraint on possible pathways of sugar synthesis at the origin of life.