Proteinaceous Amino Acids Research Articles

Regulation of nitrogen isotopic ratios of cellular components

This paper is an attempt to generalize the nitrogen isotope information of the molecules that make up the cell from our point of view. Nitrogen in the cell exists as 20 proteinaceous amino acids, nucleobases, hemes, chlorophylls, and others, and their composition is similar among organisms. Based on a physiologically simple autonomous system that maintains a balance between inputs and outputs, it is theoretically predicted that 15N is distributed to each cellular compound with a certain regularity, and thus a specific relationship in nitrogen isotopic ratios among compounds. Previous studies essentially confirm this. The nitrogen isotopic ratio of compound i constituting the cell can be generalized as δ15Ni = δ15Nplant + Δi (TP − 1) + γi, where TP represents the trophic position, and Δi and γi are the trophic discrimination factor and the intracellular 15N distribution of compound i, respectively. Knowing reliable values of Δi and γi will help us to better understand nitrogen dynamics in the biosphere and advance our understanding of the picture of the Earth’s environment through biogeochemistry.

Bile salt hydrolase acyltransferase activity expands bile acid diversity.

Bile acids (BAs) are steroid detergents in bile that contribute to the absorption of fats and fat-soluble vitamins while shaping the gut microbiome because of their antimicrobial properties1-4. Here we identify the enzyme responsible for a mechanism of BA metabolism by the gut microbiota involving amino acid conjugation to the acyl-site of BAs, thus producing a diverse suite of microbially conjugated bile acids (MCBAs). We show that this transformation is mediated by acyltransferase activity of bile salt hydrolase (bile salt hydrolase/transferase,BSH/T). Clostridium perfringens BSH/T rapidly performed acyl transfer when provided various amino acids and taurocholate, glycocholate or cholate, with an optimum at pH 5.3. Amino acid conjugation by C. perfringens BSH/T was diverse, including all proteinaceous amino acids except proline and aspartate. MCBA production was widespread among gut bacteria, with strain-specific amino acid use. Species with similar BSH/T amino acid sequences had similar conjugation profiles and several bsh/t alleles correlated with increased conjugation diversity. Tertiary structure mapping of BSH/T followed by mutagenesis experiments showed that active site structure affects amino acid selectivity. These MCBA products had antimicrobial properties, where greater amino acid hydrophobicity showed greater antimicrobial activity. Inhibitory concentrations of MCBAs reached those measured natively in the mammalian gut. MCBAs fed to mice entered enterohepatic circulation, in which liver and gallbladder concentrations varied depending on the conjugated amino acid. Quantifying MCBAs in human faecal samples showed that they reach concentrations equal to or greater than secondary and primary BAs and were reduced after bariatric surgery, thus supporting MCBAs as a significant component of the BA pool that can be altered by changes in gastrointestinal physiology. In conclusion, the inherent acyltransferase activity of BSH/T greatly diversifies BA chemistry, creating a set of previously underappreciated metabolites with the potential to affect the microbiome and human health.

Selenomethionine supplementation and expression of selenosugars, selenocysteine, and other selenometabolites in rat liver.

Selenomethionine (SeMet) as a methionine analog can be incorporated into protein. In turkeys, we recently found that selenium (Se) as selenite is not metabolized to SeMet but rather to selenosugars (seleno-N-acetyl galactosamine) bound to protein as well as to selenocysteine (Sec) in selenoproteins. To characterize the metabolism of SeMet, we fed rats graded levels of SeMet from 0 to 5µg Se/g in a Se-deficient diet for 4 wk, and investigated the fate and accumulation of liver Se using high pressure liquid chromatography (HPLC) coupled with Se-specific inductively coupled plasma mass spectrometry (ICP-MS) and molecule specific (Orbitrap MS/MS) detection. Up to 0.24µg Se/g (Se requirement for maximal glutathione peroxidase activity), Sec accounted for ∼40% of total liver Se whereas SeMet only accounted for 3-11%. Analysis of water-soluble extracts found negligible low molecular weight (LMW) Se species in rats fed 0 and 0.08µg Se/g, including no SeMet. At 0.24µg Se/g and above, SeMet accounted for only 10% of LMW Se species, whereas methyl- and glutathionyl-selenosugars accounted for 70% of LMW Se species. Above the Se requirement, SeMet was ∼30% of the proteinaceous amino acids, whereas Sec levels fell to 5% in rats fed 5µg Se/g as SeMet. Last, considerably less inorganic Se was bound to liver protein with high SeMet as compared to selenite in a parallel study. SeMet is efficiently metabolized and mixes with the common Se metabolite pool, where Se is preferentially incorporated into Sec and Sec-selenoproteins until selenoproteins plateau; with high SeMet intake, Se is increasingly accumulated as LMW selenosugars and as selenosugar-decorated proteins.

Precipitation-derived effects on the characteristics of proteinaceous soil organic matter across the continental United States

Proteinaceous amino acids composed up to 50% of microbial biomass, are a primary building block of soil organic nitrogen, and play a key role in soil organic N and C cycling. However, the large-scale drivers on these organic nitrogen pools is less explored. We hypothesized that the trends related to vegetation, soil mineralogy and climate will change the composition of hydrolyzable amino acids (HAAs), both within and between each horizon. Herein we report on the patterns of HAAs, and their dependence on soil (e.g., Al, Fe, pH) and climate (e.g., precipitation) factors between soil horizons across the continental U.S. It was found that the effect of vegetation type on HAAs was greater in the A horizon than in the C horizon, which was related to the different stages of the vegetation-associated decomposition and pedogenesis processes. A similar Leu-Phe-Ile-Gly co-occurrence structure was found in both soil horizons suggesting some similarity in processes that enrich organics in soil. Precipitation, but not temperature, showed significant associations with HAA composition. The chemical properties of the soil, including pH and mineral metals (Fe, Mn, Al, Ca), also influenced the HAAs’ characteristics. In particular, some specific HAAs (Glx, Asn, and Ala) mainly reflected the HAAs’ response to the environmental gradients in both horizons. The effect of precipitation on HAAs exhibits as a complex relationship mediated through organic matter, pH and minerals. To our knowledge, this is the first study to assess continental-wide descriptors of the largest soil organic N pool, showing that pH, Fe, Ca, precipitation and vegetation explain soil AA composition. The role played by each of these drivers in the accrual and turnover of organic matter over large regional scales deserve further scrutiny. The large surface and subsurface HAA data set from this study should help change the way micro-scale conceptual and mechanistic models describe the chemical interactions and source pools that drive soil organic nitrogen, and possibly soil organic matter composition over regional scales.

Analysis of the free amino acid content and profile of 129 peach (Prunus persica (L.) Batsch) germplasms using LC-MS/MS without derivatization

Free amino acids (FAAs) are essential for fruit flavor and function. In this study, mature fruits of 129 germplasms grown in China were employed to fully comprehend the variability in the FAA composition of peaches (Prunus persica (L.) Batsch). A brief sample preparation process, based on formic acid/water/methanol extraction, was performed. Using the HSS T3 column, 24 FAAs were successfully separated. These FAAs were analyzed using LC-MS/MS without derivatization. A total of 20 FAAs were detected in peaches. Asparagine was the most abundant FAA (368.04–6090.79 μg/g FW) in peach fruit, followed by aspartic acid (29.00–409.51 μg/g FW), glutamic acid (45.33–290.13 μg/g FW), alanine (22.39–805.21 μg/g FW), glutamine (12.05–322.62 μg/g FW), serine (17.81–323.35 μg/g FW), and threonine (10.9–109.04 μg/g FW). Other proteinaceous amino acids, including arginine, glycine, histidine, isoleucine, leucine, lysine, phenylalanine, proline, tryptophan, tyrosine, valine, cis-4-hydroxy-proline, and a specialized non-proteinaceous amino acid, γ-aminobutyric acid, were identified and quantified in the peach germplasm. By comparing the FAA content of various germplasms, middle- and late- maturing peaches were found to possess more asparagine, proline, and cis-4-hydroxy-proline than early-maturing peaches. These essential results could markedly augment peach breeding programs and provide a comprehensive understanding of the peach germplasm resources.

Targeted metabolomics and DIA proteomics-based analyses of proteinaceous amino acids and driving proteins in black tea during withering

Withering is a necessary step to improve the flavors during the manufacturing of black tea. Fresh tea leaves of Fuding Dabai were subjected to withering (kept for 0–28 h at room temperature of 25 °C) to observe corresponding morphological changes. In addition, dynamic changes in proteinaceous amino acids, especially taste-related proteinaceous amino acids and their corresponding driving proteins, were investigated using targeted metabolomics and data-independent acquisition (DIA) proteomics. The results indicated that tea leaves gradually withered and shrunk, and their color deepened with the extension of withering time. Furthermore, the contents of umami amino acids were always higher during the withering process. Sweet and bitter amino acids exhibited a significant cumulative effect at the middle and late withering stages. A total of 31 driving proteins were detected that were involved in the metabolic regulation of Ser, Thr, Phe, Trp, and His amino acids. The functional analysis of 776 differential expressed proteins revealed that the tea leaf cells maintained the maximum possible cellular activity during the withering process, and the toxins were decomposed at the end of withering. These findings can provide the metabolic basis for room temperature withering during black tea processing to further enhance the quality of tea.

Tracing carbon and nitrogen microbial assimilation in suspended particles in freshwaters

The dynamic interactions between dissolved organic matter (DOM) and particulate organic matter (POM) are central in nutrient cycling in freshwater ecosystems. However, the molecular-level mechanisms of such interactions are still poorly defined. Here, we study spatial differences in the chemical (i.e., individual proteinaceous amino acids) and microbial (i.e., 16S rRNA) composition of suspended sediments in the River Chew, UK. We then applied a compound-specific stable isotope probing (SIP) approach to test the potential assimilation of 13C,15N-glutamate (Glu) and 15N-NO3− into proteinaceous biomass by particle-associated microbial communities over a 72-h period. Our results demonstrate that the composition of suspended particles is strongly influenced by the effluent of sewage treatment works. Fluxes and percentages of assimilation of both isotopically labelled substrates into individual proteinaceous amino acids showed contrasting dynamics in processing at each site linked to primary biosynthetic metabolic pathways. Preferential assimilation of the organic molecule glutamate and evidence of its direct assimilation into newly synthesised biomass was obtained. Our approach provides quantitative molecular information on the mechanisms by which low molecular weight DOM is mineralised in the water column compared to an inorganic substrate. This is paramount for better understanding the processing and fate of organic matter in aquatic ecosystems.

Profiling of dynamic changes in non-volatile metabolites of shaken black tea during the manufacturing process using targeted and non-targeted metabolomics analysis

Shaken black tea (SBT) is a new type of black tea that combines the traditional black tea processing technology with the shaking process of oolong tea. In this study, non-targeted metabolomics analysis based on ultra-high-pressure liquid chromatography quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) was applied to comprehensively analyze the non-volatile metabolites of SBT during the manufacturing process. Using multivariate statistical analysis, 93 compounds were screened as differential compounds. During the whole process of SBT, amino acids, dipeptides, theaflavins and lipids contents showed significant increases, while that of catechins and procyanidin C1 significantly decreased. Compared with fresh leaves, the content of proteinaceous amino acids (PAAs) in the dried black tea increased 1.61-fold, and total catechins decreased to 7.25%. The results of hierarchical clustering analysis (HCA) showed that fermentation is the key process that causes the variations of these metabolites, followed by drying and shaking. The biosynthesis metabolism of amino acids, flavonoids and linoleic acid are abundant, mainly due to the stress response of fresh tea leaves to dehydration and mechanical damage during shaking processing. It is beneficial to explore the quality formation during the production of SBT through comprehensive analysis of the changes in metabolites.

ConCysFind: a pipeline tool to predict conserved amino acids of protein sequences across the plant kingdom

BackgroundPost-translational modifications (PTM) of amino acid (AA) side chains in peptides control protein structure and functionality. PTMs depend on the specific AA characteristics. The reactivity of cysteine thiol-based PTMs are unique among all proteinaceous AA. This pipeline aims to ease the identification of conserved AA of polypeptides or protein families based on the phylogenetic occurrence in the plant kingdom. The tool is customizable to include any species.The degree of AA conservation is taken as indicator for structural and functional significance, especially for PTM-based regulation. Further, this pipeline tool gives insight into the evolution of these potentially regulatory important peptides.ResultsThe web-based or stand-alone pipeline tool Conserved Cysteine Finder (ConCysFind) was developed to identify conserved AA such as cysteine, tryptophan, serine, threonine, tyrosin and methionine. ConCysFind evaluates multiple alignments considering the proteome of 21 plant species. This exemplar study focused on Cys as evolutionarily conserved target for multiple redox PTM. Phylogenetic trees and tables with the compressed results of the scoring algorithm are generated for each Cys in the query polypeptide. Analysis of 33 translation elongation and release factors alongside of known redox proteins from Arabidopsis thaliana for conserved Cys residues confirmed the suitability of the tool for identifying conserved and functional PTM sites. Exemplarily, the redox sensitivity of cysteines in the eukaryotic release factor 1-1 (eRF1-1) was experimentally validated.ConclusionConCysFind is a valuable tool for prediction of new potential protein PTM targets in a broad spectrum of species, based on conserved AA throughout the plant kingdom. The identified targets were successfully verified through protein biochemical assays. The pipeline is universally applicable to other phylogenetic branches by customization of the database.

Mutually stabilizing interactions between proto-peptides and RNA

The close synergy between peptides and nucleic acids in current biology is suggestive of a functional co-evolution between the two polymers. Here we show that cationic proto-peptides (depsipeptides and polyesters), either produced as mixtures from plausibly prebiotic dry-down reactions or synthetically prepared in pure form, can engage in direct interactions with RNA resulting in mutual stabilization. Cationic proto-peptides significantly increase the thermal stability of folded RNA structures. In turn, RNA increases the lifetime of a depsipeptide by >30-fold. Proto-peptides containing the proteinaceous amino acids Lys, Arg, or His adjacent to backbone ester bonds generally promote RNA duplex thermal stability to a greater magnitude than do analogous sequences containing non-proteinaceous residues. Our findings support a model in which tightly-intertwined biological dependencies of RNA and protein reflect a long co-evolutionary history that began with rudimentary, mutually-stabilizing interactions at early stages of polypeptide and nucleic acid co-existence.

Nonvolatile metabolism in postharvest tea (Camellia sinensis L.) leaves: Effects of different withering treatments on nonvolatile metabolites, gene expression levels, and enzyme activity

The influence mechanism of different withering methods (CK, indoor natural spreading; LTD, low-temperature plus dark; LTY, low-temperature plus yellow-light; LTCD, low-temperature plus CO2) on non-volatile compounds in postharvest tea leaves was investigated by UHPLC-Q‐TOF/MS-based non-targeted metabolomic and transcriptomic analyses. Compared with CK, low-temperature withering could slow down polyphenol oxidation by inhibiting polyphenol oxidase activity and keeping the expression of genes for flavanol synthesis. After withering, the proteinaceous amino acid content increased significantly, especially for LTCD and LTY, mainly due to increased peptidase activity and up-regulation of genes involved in the biosynthesis of valine, leucine, aspartic acid, glutamic acid, phenylalanine, and proline. Moreover, LTCD and LTY enhanced the synthesis of γ-aminobutyric acid and metabolism of phenylalanine-methyl salicylate and tryptophan-indole, respectively. Meanwhile, the transformation of theobromine to caffeine was accelerated under low-temperature withering. This research provides ageneticmetabolicbasis for the application of low-temperature withering to actual green tea processing.

Polyesters as a Model System for Building Primitive Biologies from Non-Biological Prebiotic Chemistry.

A variety of organic chemicals were likely available on prebiotic Earth. These derived from diverse processes including atmospheric and geochemical synthesis and extraterrestrial input, and were delivered to environments including oceans, lakes, and subaerial hot springs. Prebiotic chemistry generates both molecules used by modern organisms, such as proteinaceous amino acids, as well as many molecule types not used in biochemistry. As prebiotic chemical diversity was likely high, and the core of biochemistry uses a rather small set of common building blocks, the majority of prebiotically available organic compounds may not have been those used in modern biochemistry. Chemical evolution was unlikely to have been able to discriminate which molecules would eventually be used in biology, and instead, interactions among compounds were governed simply by abundance and chemical reactivity. Previous work has shown that likely prebiotically available α-hydroxy acids can combinatorially polymerize into polyesters that self-assemble to create new phases which are able to compartmentalize other molecule types. The unexpectedly rich complexity of hydroxy acid chemistry and the likely enormous structural diversity of prebiotic organic chemistry suggests chemical evolution could have been heavily influenced by molecules not used in contemporary biochemistry, and that there is a considerable amount of prebiotic chemistry which remains unexplored.

Enzymatic Reaction-Related Protein Degradation and Proteinaceous Amino Acid Metabolism during the Black Tea (Camellia sinensis) Manufacturing Process

Amino acids contribute to the nutritional value and quality of black tea. Fermentation is the most important stage of the black tea manufacturing process. In this study, we investigated protein degradation and proteinaceous amino acid metabolism associated with enzymatic reactions during fermentation in the black tea manufacturing process. The results showed that the concentrations of both protein and free amino acids decreased during fermentation. We also confirmed that proteins were broken down into free amino acids by artificially synthesized dipeptide benzyloxycarbonyl glutamyl-tyrosine (Z-Glu-Tyr). Metabolites of the amino acid metabolic pathway increased significantly during fermentation. Furthermore, we confirmed that free amino acids were degraded to volatile compounds in a tracer experiment with the isotope precursor. These results provide information that will help black tea manufacturers improve the quality of black tea.

Selective incorporation of proteinaceous over nonproteinaceous cationic amino acids in model prebiotic oligomerization reactions.

Numerous long-standing questions in origins-of-life research center on the history of biopolymers. For example, how and why did nature select the polypeptide backbone and proteinaceous side chains? Depsipeptides, containing both ester and amide linkages, have been proposed as ancestors of polypeptides. In this paper, we investigate cationic depsipeptides that form under mild dry-down reactions. We compare the oligomerization of various cationic amino acids, including the cationic proteinaceous amino acids (lysine, Lys; arginine, Arg; and histidine, His), along with nonproteinaceous analogs of Lys harboring fewer methylene groups in their side chains. These analogs, which have been discussed as potential prebiotic alternatives to Lys, are ornithine, 2,4-diaminobutyric acid, and 2,3-diaminopropionic acid (Orn, Dab, and Dpr). We observe that the proteinaceous amino acids condense more extensively than these nonproteinaceous amino acids. Orn and Dab readily cyclize into lactams, while Dab and Dpr condense less efficiently. Furthermore, the proteinaceous amino acids exhibit more selective oligomerization through their α-amines relative to their side-chain groups. This selectivity results in predominantly linear depsipeptides in which the amino acids are α-amine-linked, analogous to today's proteins. These results suggest a chemical basis for the selection of Lys, Arg, and His over other cationic amino acids for incorporation into proto-proteins on the early Earth. Given that electrostatics are key elements of protein-RNA and protein-DNA interactions in extant life, we hypothesize that cationic side chains incorporated into proto-peptides, as reported in this study, served in a variety of functions with ancestral nucleic acid polymers in the early stages of life.

Systematic characterization of position one variants within the lantibiotic nisin

Lantibiotics are a growing class of natural compounds, which possess antimicrobial activity against a broad range of Gram-positive bacteria. Their high potency against human pathogenic strains such as MRSA and VRE makes them excellent candidates as substitutes for classic antibiotics in times of increasing multidrug resistance of bacterial strains. New lantibiotics are detected in genomes and can be heterologously expressed. The functionality of these novel lantibiotics requires a systematic purification and characterization to benchmark them against for example the well-known lantibiotic nisin. Here, we used a standardized workflow to characterize lantibiotics consisting of six individual steps. The expression and secretion of the lantibiotic was performed employing the promiscuous nisin modification machinery. We mutated the first amino acid of nisin into all proteinaceous amino acids and compared their bactericidal potency against sensitive strains as well as strains expressing nisin resistance proteins. Interestingly, we can highlight four distinct groups based on the residual activity of nisin against sensitive as well as resistant L. lactis strains.

Red-Emitting Copper Nanoclusters: From Bulk-Scale Synthesis to Catalytic Reduction

A large-scale, easy synthesis of red fluorescent copper nanoclusters (CuNCs) from a cheap source copper acetate, monohydrate has been reported. A proteinaceous amino acid cysteine has been used to ...

Microbe-like inclusions in tree resins and implications for the fossil record of protists in amber.

During the past two decades, a plethora of fossil micro-organisms have been described from various Triassic to Miocene ambers. However, in addition to entrapped microbes, ambers commonly contain microscopic inclusions that sometimes resemble amoebae, ciliates, microfungi, and unicellular algae in size and shape, but do not provide further diagnostic features thereof. For a better assessment of the actual fossil record of unicellular eukaryotes in amber, we studied equivalent inclusions in modern resin of the Araucariaceae; this conifer family comprises important amber-producers in Earth history. Using time-of-flight secondary ion mass spectrometry (ToF-SIMS), we investigated the chemical nature of the inclusion matter and the resin matrix. Whereas the matrix, as expected, showed a more hydrocarbon/aromatic-dominated composition, the inclusions contain abundant salt ions and polar organics. However, the absence of signals characteristic for cellular biomass, namely distinctive proteinaceous amino acids and lipid moieties, indicates that the inclusions do not contain microbial cellular matter but salts and hydrophilic organic substances that probably derived from the plant itself. Rather than representing protists or their remains, these microbe-like inclusions, for which we propose the term 'pseudoinclusions', consist of compounds that are immiscible with the terpenoid resin matrix and were probably secreted in small amounts together with the actual resin by the plant tissue. Consequently, reports of protists from amber that are only based on the similarity of the overall shape and size to extant taxa, but do not provide relevant features at light-microscopical and ultrastructural level, cannot be accepted as unambiguous fossil evidence for these particular groups.

The transformation and renewal of soil amino acids induced by the availability of extraneous C and N

Developing an understanding of the transformation kinetics of amino acids in soil is of fundamental importance to probe into the stabilization and decomposition processes central to soil organic matter (SOM) cycling. Considering the transitional function of amino acids in SOM turnover, substrate availability controls the formation and decomposition of soil amino acids critically. However, compared to broad knowledge on free amino acid turnover, how the changing bio-availability of carbon (C) and nitrogen (N) influences the accumulation and turnover of proteinaceous amino acids in soil is not well understood. Therefore, a laboratory experiment was conducted in which soil samples were incubated and supplemented weekly with glucose and 15N-labeled inorganic N as either ammonium (NH4+) or nitrate (NO3−). The concentrations of soil amino acids, differentiated into the newly synthesized (15N-labeled) and endogenous (unlabeled) portion, were temporally quantified by an isotope-based high-performance liquid chromatography/mass spectrometric technique.During the incubation, extraneous substrates were rapidly immobilized into soil amino acids as important metabolic constituents. However, the dynamics and maintenance of soil amino acids were determined by changing C and N availability during microbial proliferation rather than static stoichiometry of available substrates. The significantly greater amount of de-novo synthesized amino acids in treatments with NH4+ addition than NO3− addition confirmed that microorganisms preferred the reduced N than the oxidized form due to significantly lower energy and C requirements. The decomposition of endogenous amino acids during the later stages of the incubation indicated that amino acids could partly meet microbial C and energy demand, but the capacity to get decomposed was independent on N species. Therefore, higher rate of extraneous N immobilization in glucose plus NH4+ treatment was closely associated with the net accumulation of amino acids; whereas the formation of new proteinaceous amino acids after weekly additions of glucose plus NO3− was eventually offset by the loss of the endogenous portion, resulting in apparently unchanged amounts of amino acids in the microcosms.Under the two incubation conditions with available C and N addition, both the intrinsic C percentage in molecules and the biosynthetic pathways have minor influence on the turnover pattern of HCl hydrolyzed amino acids. However, the transformation of individual amino acids was significantly correlated throughout the entire incubation. These findings suggested that the turnover of soil amino acids in proteinaceous form was critically interrelated instead of being controlled by the transformation pathways of different free amino acids. Compared to the NH4+ supply, the addition of NO3− enhanced the decomposition of glycogenic amino acid while reduced the degradation of most of ketogenic amino acids, possibly suggesting the important regulating strategy of energy yield on microbial speciation of the N forms.

The temperature effect on the glycine decomposition induced by 2 keV electron bombardment in space analog conditions

Glycine is the simplest proteinaceous amino acid that has been extensively detected in carbonaceous meteorites and was recently observed in the cometary samples returned to Earth by NASA’s Stardust spacecraft. In space, such species is exposed to several radiation fields at different temperatures. In aqueous solutions, this species appears mainly as zwitterionic glycine (+NH3CH2COO−) however, in solid phase, it may be found in amorphous or crystalline forms. Here, we present an experimental study on the destruction of two zwitterionic glycine crystals (α- and β-form) at two different temperatures (300 K and 14 K) by 2 keV electrons in an attempt to test the behavior and stability of this molecular species in different space environments. The samples were analyzed in situ by Fourier transform infrared spectrometry at electron fluences. The experiments were carried out under ultra-high vacuum conditions at the Molecular Physics Laboratory at the Open University at Milton Keynes, UK. The dissociation cross section of glycine is approximately 5 times higher for the 14 K samples when compared to the 300 K samples. In contrast, no significant differences emerged between the dissociation cross sections of α- and β-forms of glycine for fixed temperature experiments. We therefore conclude that the destruction cross section is more heavily dependent on temperature than the phase of the condensed glycine material. This may be associated with the opening of additional reaction routes in the frozen samples involving the trapped daughter species (e.g. CO2 and CO). The half-life of studied samples extrapolated to space conditions shows that glycine molecules on the surface of interstellar grains has less survivability and they are highly sensitive to ambient radiations, however, they can survive extended period of time in the solar system like environments. Survivability increases by a factor of 5 if the samples are at 300 K when compared to low temperature experiments at 14 K and is independent of the crystalline structure. In addition, this survival would increase if the molecular species were protected by several layers of other molecular species as trapped in comet mantles or embedded within regolith in asteroids/lunar surfaces. The understanding of the excitation and dissociation processes of organic compounds in space simulation is highly required to put constrains in the puzzle over the origin of life in the primitive Earth.

On an Early Gene for Membrane-Integral Inorganic Pyrophosphatase in the Genome of an Apparently Pre-LUCA Extremophile, the Archaeon Candidatus Korarchaeum cryptofilum

A gene for membrane-integral inorganic pyrophosphatase (miPPase) was found in the composite genome of the extremophile archaeon Candidatus Korarchaeum cryptofilum (CKc). This korarchaeal genome shows unusual partial similarity to both major archaeal phyla Crenarchaeota and Euryarchaeota. Thus this Korarchaeote might have retained features that represent an ancestral archaeal form, existing before the occurrence of the evolutionary bifurcation into Crenarchaeota and Euryarchaeota. In addition, CKc lacks five genes that are common to early genomes at the LUCA border. These two properties independently suggest a pre-LUCA evolutionary position of this extremophile. Our finding of the miPPase gene in the CKc genome points to a role for the enzyme in the energy conversion of this very early archaeon. The structural features of its miPPase indicate that it can pump protons through membranes. An miPPase from the extremophile bacterium Caldicellulosiruptor saccharolyticus also has a sequence indicating a proton pump. Recent analysis of the three-dimensional structure of the miPPase from Vigna radiata has resulted in the recognition of a strongly acidic substrate (orthophosphate: Pi, pyrophosphate: PPi) binding pocket, containing 11 Asp and one Glu residues. Asp (aspartic acid) is an evolutionarily very early proteinaceous amino acid as compared to the later appearing Glu (glutamic acid). All the Asp residues are conserved in the miPPase of CKc, V. radiata and other miPPases. The high proportion of Asp, as compared to Glu, seems to strengthen our argument that biological energy conversion with binding and activities of orthophosphate (Pi) and energy-rich pyrophosphate (PPi) in connection with the origin and early evolution of life may have started with similar or even more primitive acidic peptide funnels and/or pockets.