Did evolution select a nonrandom "alphabet" of amino acids?

The last universal common ancestor of contemporary biology (LUCA) used a precise set of 20 amino acids as a standard alphabet with which to build genetically encoded protein polymers. Considerable evidence indicates that some of these amino acids were present through nonbiological syntheses prior to the origin of life, while the rest evolved as inventions of early metabolism. However, the same evidence indicates that many alternatives were also available, which highlights the question: what factors led biological evolution on our planet to define its standard alphabet? One possibility is that natural selection favored a set of amino acids that exhibits clear, nonrandom properties-a set of especially useful building blocks. However, previous analysis that tested whether the standard alphabet comprises amino acids with unusually high variance in size, charge, and hydrophobicity (properties that govern what protein structures and functions can be constructed) failed to clearly distinguish evolution's choice from a sample of randomly chosen alternatives. Here, we demonstrate unambiguous support for a refined hypothesis: that an optimal set of amino acids would spread evenly across a broad range of values for each fundamental property. Specifically, we show that the standard set of 20 amino acids represents the possible spectra of size, charge, and hydrophobicity more broadly and more evenly than can be explained by chance alone.     

Biochemical constraints in a protobiotic earth devoid of basic amino acids: the "BAA(-) world"

It has been hypothesized in this journal and elsewhere, based on surveys of published data from prebiotic synthesis experiments and carbonaceous meteorite analyses, that basic amino acids such as lysine and arginine were not abundant on prebiotic Earth. If the basic amino acids were incorporated only rarely into the first peptides formed in that environment, it is important to understand what protobiotic chemistry is possible in their absence. As an initial test of the hypothesis that basic amino acid negative [BAA(-)] proteins could have performed at least a subset of protobiotic chemistry, the current work reports on a survey of 13 archaeal and 13 bacterial genomes that has identified 61 modern gene sequences coding for known or putative proteins not containing arginine or lysine. Eleven of the sequences found code for proteins whose functions are well known and important in the biochemistry of modern microbial life: lysine biosynthesis protein LysW, arginine cluster proteins, copper ion binding proteins, bacterial flagellar proteins, and PE or PPE family proteins. These data indicate that the lack of basic amino acids does not prevent peptides or proteins from serving useful structural and biochemical functions. However, as would be predicted from fundamental physicochemical principles, we see no fossil evidence of prebiotic BAA(-) peptide sequences capable of interacting directly with nucleic acids.     

Adsorption of amino acids (ALA, CYS, HIS, MET) on zeolites: fourier transform infrared and Raman spectroscopy investigations

Minerals adsorb more amino acids with charged R-groups than amino acids with uncharged R-groups. Thus, the peptides that form from the condensation of amino acids on the surface of minerals should be composed of amino acid residues that are more charged than uncharged. However, most of the amino acids (74%) in today's proteins have an uncharged R-group. One mechanism with which to solve this paradox is the use of organophilic minerals such as zeolites. Over the range of pH (pH 2.66-4.50) used in these experiments, the R-group of histidine (His) is positively charged and neutral for alanine (Ala), cysteine (Cys), and methionine (Met). In acidic hydrothermal environments, the pH could be even lower than those used in this study. For the pH range studied, the zeolites were negatively charged, and the overall charge of all amino acids was positive. The conditions used here approximate those of prebiotic Earth. The most important finding of this work is that the relative concentrations of each amino acid (X=His, Met, Cys) to alanine (X/Ala) are close to 1.00. This is an important result with regard to prebiotic chemistry because it could be a solution for the paradox stated above. Pore size did not affect the adsorption of Cys and Met on zeolites, and the Si/Al ratio did not affect the adsorption of Cys, His, and Met. ZSM-5 could be used for the purification of Cys from other amino acids (Student-Newman-Keuls test, p<0.05), and mordenite could be used for separation of amino acids from each other (Student-Newman-Keuls test, p<0.05). As shown by Fourier transform infrared (FT-IR) spectra, Ala interacts with zeolites through the [Formula: see text] group, and methionine-zeolite interactions involve the COO, [Formula: see text], and CH(3) groups. FT-IR spectra show that the interaction between the zeolites and His is weak. Cys showed higher adsorption on all zeolites; however, the hydrophobic Van der Waals interaction between zeolites and Cys is too weak to produce any structural changes in the Cys groups (amine, carboxylic, sulfhydryl, etc.); thus, the FT-IR and Raman spectra are the same as those of solid Cys.     

Survival of amino acids in micrometeorites during atmospheric entry

The delivery of amino acids by micrometeorites to the early Earth during the period of heavy bombardment could have been a significant source of the Earth's prebiotic amino acid inventory provided that these organic compounds survived atmospheric entry heating. To investigate the sublimation of amino acids from a micrometeorite analog at elevated temperature, grains from the CM-type carbonaceous chondrite Murchison were heated to 550 degrees C inside a glass sublimation apparatus (SA) under reduced pressure. The sublimed residue that had collected on the cold finger of the SA after heating was analyzed for amino acids by HPLC. We found that when the temperature of the meteorite reached approximately 150 degrees C, a large fraction of the amino acid glycine had vaporized from the meteorite, recondensed onto the end of the SA cold finger, and survived as the rest of the grains heated to 550 degrees C. alpha-Aminoisobutryic acid and isovaline, which are two of the most abundant non-protein amino acids in Murchison, did not sublime from the meteorite and were completely destroyed during the heating experiment. Our experimental results suggest that sublimation of glycine present in micrometeorite grains may provide a way for this amino acid to survive atmospheric entry heating at temperatures > 550 degrees C; all other amino acids apparently are destroyed.     

An examination of the carbon isotope effects associated with amino acid biosynthesis

Stable carbon isotope ratios (delta(13)C) were determined for alanine, proline, phenylalanine, valine, leucine, isoleucine, aspartate (aspartic acid and asparagine), glutamate (glutamic acid and glutamine), lysine, serine, glycine, and threonine from metabolically diverse microorganisms. The microorganisms examined included fermenting bacteria, organotrophic, chemolithotrophic, phototrophic, methylotrophic, methanogenic, acetogenic, acetotrophic, and naturally occurring cryptoendolithic communities from the Dry Valleys of Antarctica. Here we demonstrated that reactions involved in amino acid biosynthesis can be used to distinguish amino acids formed by life from those formed by nonbiological processes. The unique patterns of delta(13)C imprinted by life on amino acids produced a biological bias. We also showed that, by applying discriminant function analysis to the delta(13)C value of a pool of amino acids formed by biological activity, it was possible to identify key aspects of intermediary carbon metabolism in the microbial world. In fact, microorganisms examined in this study could be placed within one of three metabolic groups: (1) heterotrophs that grow by oxidizing compounds containing three or more carbon-to-carbon bonds (fermenters and organotrophs), (2) autotrophs that grow by taking up carbon dioxide (chemolitotrophs and phototrophs), and (3) acetoclastic microbes that grow by assimilation of formaldehyde or acetate (methylotrophs, methanogens, acetogens, and acetotrophs). Furthermore, we demonstrated that cryptoendolithic communities from Antarctica grouped most closely with the autotrophs, which indicates that the dominant metabolic pathways in these communities are likely those utilized for CO(2 )fixation. We propose that this technique can be used to determine the dominant metabolic types in a community and reveal the overall flow of carbon in a complex ecosystem.     

Analysis of underivatized amino acids in geological samples using ion-pairing liquid chromatography and electrospray tandem mass spectrometry

The capability of detecting biomarkers, such as amino acids, in chemically complex field samples is essential to establishing the knowledge required to search for chemical signatures of life in future planetary explorations. However, due to the complexities of in situ investigations, it is important to establish a new analytical scheme that utilizes a minimal amount of sample preparation. This paper reports the feasibility of a novel and sensitive technique, which has been established to quantitate amino acids in terrestrial crust samples directly without derivatization using volatile ion-pairing liquid chromatography and tandem mass spectrometry equipped with an electrospray ionization source. Adequate separation of 20 underivatized amino acids was achieved on a C(18) capillary column within 26 min with nonafluoropentanoic acid (NFPA) as ion-pairing reagent. Each amino acid was identified from its retention time as well as from its characteristic parent-to-daughter ion transition. Using tandem mass spectrometry as a detection technique allows co-elution of some amino acids, as it is more specific than traditional spectrophotometric methods. In the present study, terrestrial samples collected from 3 different locations were analyzed for their water-extractable free amino acid contents, following the removal of metal and organic interferences via ion exchange procedures. This is the first time that amino acids in geological samples were directly determined quantitatively without complicated derivatization steps. Depending on the amino acid, the detection limits varied from 0.02 to 5.7 pmol with the use of a 1 microl sample injection loop.     

Amino acid distribution in meteorites: diagenesis, extraction methods, and standard metrics in the search for extraterrestrial biosignatures

The relative abundance of the protein amino acids has been previously investigated as a potential marker for biogenicity in meteoritic samples. However, these investigations were executed without a quantitative metric to evaluate distribution variations, and they did not account for the possibility of interdisciplinary systematic error arising from inter-laboratory differences in extraction and detection techniques. Principal component analysis (PCA), hierarchical cluster analysis (HCA), and stochastic probabilistic artificial neural networks (ANNs) were used to compare the distributions for nine protein amino acids previously reported for the Murchison carbonaceous chondrite, Mars meteorites (ALH84001, Nakhla, and EETA79001), prebiotic synthesis experiments, and terrestrial biota and sediments. These techniques allowed us (1) to identify a shift in terrestrial amino acid distributions secondary to diagenesis; (2) to detect differences in terrestrial distributions that may be systematic differences between extraction and analysis techniques in biological and geological laboratories; and (3) to determine that distributions in meteoritic samples appear more similar to prebiotic chemistry samples than they do to the terrestrial unaltered or diagenetic samples. Both diagenesis and putative interdisciplinary differences in analysis complicate interpretation of meteoritic amino acid distributions. We propose that the analysis of future samples from such diverse sources as meteoritic influx, sample return missions, and in situ exploration of Mars would be less ambiguous with adoption of standardized assay techniques, systematic inclusion of assay standards, and the use of a quantitative, probabilistic metric. We present here one such metric determined by sequential feature extraction and normalization (PCA), information-driven automated exploration of classification possibilities (HCA), and prediction of classification accuracy (ANNs).     

Formation routes of interstellar glycine involving carboxylic acids: possible favoritism between gas and solid phase

Despite the extensive search for glycine (NH?CH?COOH) and other amino acids in molecular clouds associated with star-forming regions, only upper limits have been derived from radio observations. Nevertheless, two of glycine's precursors, formic acid and acetic acid, have been abundantly detected. Although both precursors may lead to glycine formation, the efficiency of reaction depends on their abundance and survival in the presence of a radiation field. These facts could promote some favoritism in the reaction pathways in the gas phase and solid phase (ice). Glycine and these two simplest carboxylic acids are found in many meteorites. Recently, glycine was also observed in cometary samples returned by the Stardust space probe. The goal of this work was to perform theoretical calculations for several interstellar reactions involving the simplest carboxylic acids as well as the carboxyl radical (COOH) in both gas and solid (ice) phase to understand which reactions could be the most favorable to produce glycine in interstellar regions fully illuminated by soft X-rays and UV, such as star-forming regions. The calculations were performed at four different levels for the gas phase (B3LYP/6-31G*, B3LYP/6-31++G**, MP2/6-31G*, and MP2/6-31++G**) and at MP2/6-31++G** level for the solid phase (ice). The current two-body reactions (thermochemical calculation) were combined with previous experimental data on the photodissociation of carboxylic acids to promote possible favoritism for glycine formation in the scenario involving formic and acetic acid in both gas and solid phase. Given that formic acid is destroyed more in the gas phase by soft X-rays than acetic acid is, we suggest that in the gas phase the most favorable reactions are acetic acid with NH or NH?OH. Another possible reaction involves NH?CH? and COOH, one of the most-produced radicals from the photodissociation of acetic acid. In the solid phase, we suggest that the reactions of formic acid with NH?CH or NH?CH?OH are the most favorable from the thermochemical point of view.     

Distribution and stable isotopic composition of amino acids from fungal peptaibiotics: assessing the potential for meteoritic contamination

The presence of nonprotein α-dialkyl-amino acids such as α-aminoisobutyric acid (α-AIB) and isovaline (Iva), which are considered to be relatively rare in the terrestrial biosphere, has long been used as an indication of the indigeneity of meteoritic amino acids. However, recent work showing the presence of α-AIB and Iva in peptides produced by a widespread group of filamentous fungi indicates the possibility of a terrestrial biotic source for the α-AIB observed in some meteorites. We measured the amino acid distribution and stable carbon and nitrogen isotopic composition of four α-AIB-containing fungal peptides and compared this data to similar meteoritic measurements. We show that the relatively simple distribution of the C(4) and C(5) amino acids in fungal peptides is distinct from the complex distribution observed in many carbonaceous chondrites. We also identify potentially diagnostic relationships between the stable isotopic compositions of pairs of amino acids from the fungal peptides that may aid in ruling out fungal contamination as a source of meteoritic amino acids.     

Investigation of low-energy proton effects on aptamer performance for astrobiological applications

Biochips are promising instruments for the search for organic molecules in planetary environments. Nucleic acid aptamers are powerful affinity receptors known for their high affinity and specificity, and therefore are of great interest for space biochip development. A wide variety of aptamers have already been selected toward targets of astrobiological interest (from amino acids to microorganisms). We present a first study to test the resistance of these receptors to the constraints of the space environment. The emphasis is on the effect of cosmic rays on the molecular recognition properties of DNA aptamers. Experiments on beam-line facilities have been conducted with 2 MeV protons and fluences much higher than expected for a typical mission to Mars. Our results show that this irradiation process did not affect the performances of DNA aptamers as molecular recognition tools.     

Analysis of carbonaceous biomarkers with the Mars Organic Analyzer microchip capillary electrophoresis system: carboxylic acids

The oxidizing surface chemistry on Mars argues that any comprehensive search for organic compounds indicative of life requires methods to analyze higher oxidation states of carbon with very low limits of detection. To address this goal, microchip capillary electrophoresis (μCE) methods were developed for analysis of carboxylic acids with the Mars Organic Analyzer (MOA). Fluorescent derivatization was achieved by activation with the water soluble 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) followed by reaction with Cascade Blue hydrazide in 30 mM borate, pH 3. A standard containing 12 carboxylic acids found in terrestrial life was successfully labeled and separated in 30 mM borate at pH 9.5, 20 °C by using the MOA CE system. Limits of detection were 5-10 nM for aliphatic monoacids, 20 nM for malic acid (diacid), and 230 nM for citric acid (triacid). Polyacid benzene derivatives containing 2, 3, 4, and 6 carboxyl groups were also analyzed. In particular, mellitic acid was successfully labeled and analyzed with a limit of detection of 300 nM (5 ppb). Analyses of carboxylic acids sampled from a lava tube cave and a hydrothermal area demonstrated the versatility and robustness of our method. This work establishes that the MOA can be used for sensitive analyses of a wide range of carboxylic acids in the search for extraterrestrial organic molecules.     

The reactions of nitrogen heterocycles with acrolein: scope and prebiotic significance

It has been suggested that life began with a self-replicating RNA molecule. However, after much research into the prebiotic synthesis of RNA, the difficulties encountered have lead some to hypothesize that RNA was preceded by a simpler molecule, one more easily synthesized prebiotically. Many of the proposed alternative molecules are based on acrolein, since it reacts readily with nucleophiles, such as the nucleobases, via Michael addition and is readily synthesized from formaldehyde and acetaldehyde. Reports regarding the reactions of nucleobases with concentrated acrolein solutions suggest that this is a plausible reaction mechanism, though there are also reports that the "incorrect" isomers are obtained. The scope and kinetics of the reaction of acrolein with various nitrogen heterocycles are reported here. Reactions of pyrimidines often give N(1) adducts as the major products. Reactions of purines often give N(9) adducts in good yield. The reactions are rapid under neutral to slightly alkaline conditions, and proceed at low temperatures and dilutions. The implications of these findings for the origin of life are discussed.     

An exit cavity was crucial to the polymerase activity of the early ribosome

The emergence of an RNA entity capable of synthesizing peptides was a key prebiotic development. It is hypothesized that a precursor of the modern ribosomal exit tunnel was associated with this RNA entity (e.g., "protoribosome" or "bonding entity") from the earliest time and played an essential role. Various compounds that can bind and activate amino acids, including extremely short RNA chains carrying amino acids, and possibly di- or tripeptides, would have associated with the internal cavity of the protoribosome. This cavity hosts the site for peptide bond formation and adjacent to it a relatively elongated feature that could have evolved to the modern ribosomal exit tunnel, as it is wide enough to allow passage of an oligopeptide. When two of the compounds carrying amino acids or di- or tripeptides (to which we refer, for simplicity, as small aminoacylated RNAs) were in proximity within the heart of the protoribosome, a peptide bond could form spontaneously. The growing peptide would enter the nearby cavity and would not disrupt the attachment of the substrates to the protoribosome or interfere with the subsequent attachment of additional small aminoacylated RNAs. Additionally, the presence of the peptide in the cavity would increase the lifetime of the oligopeptide in the protoribosome. Thus, subsequent addition of another amino acid would be more likely than detachment from the protoribosome, and synthesis could continue. The early ability to synthesize peptides may have resulted in an abbreviated RNA World.     

The origin and early evolution of membrane channels

The origin and early evolution of ion channels are considered from the point of view that the transmembrane segments of membrane proteins are structurally quite simple and do not require specific sequences to fold. We argue that the transport of solute species, especially ions, required an early evolution of efficient transport mechanisms, and that the emergence of simple ion channels was protobiologically plausible. We also argue that, despite their simple structure, such channels could possess properties that, at the first sight, appear to require markedly greater complexity. These properties can be subtly modulated by local modifications to the sequence rather than global changes in molecular architecture. In order to address the evolution and development of ion channels, we focus on identifying those protein domains that are commonly associated with ion channel proteins and are conserved throughout the three main domains of life (Eukarya, Bacteria, and Archaea). We discuss the potassium-sodium-calcium superfamily of voltage-gated ion channels, mechanosensitive channels, porins, and ABC-transporters and argue that these families of membrane channels have sufficiently universal architectures that they can readily adapt to the diverse functional demands arising during evolution.     

Many chemistries could be used to build living systems

It has been widely suggested that life based around carbon, hydrogen, oxygen, and nitrogen is the only plausible biochemistry, and specifically that terrestrial biochemistry of nucleic acids, proteins, and sugars is likely to be "universal." This is not an inevitable conclusion from our knowledge of chemistry. I argue that it is the nature of the liquid in which life evolves that defines the most appropriate chemistry. Fluids other than water could be abundant on a cosmic scale and could therefore be an environment in which non-terrestrial biochemistry could evolve. The chemical nature of these liquids could lead to quite different biochemistries, a hypothesis discussed in the context of the proposed "ammonochemistry" of the internal oceans of the Galilean satellites and a more speculative "silicon biochemistry" in liquid nitrogen. These different chemistries satisfy the thermodynamic drive for life through different mechanisms, and so will have different chemical signatures than terrestrial biochemistry.     

Amino acids from ion-irradiated nitrile-containing ices

Solid CH(3)CN and solid H(2)O + CH(3)CN were ion irradiated near 10 K to initiate chemical reactions thought to occur in extraterrestrial ices. The infrared spectra of these samples after irradiation revealed the synthesis of new molecules. After the irradiated ices were warmed to remove volatiles, the resulting residual material was extracted and analyzed. Both unhydrolyzed and acid-hydrolyzed residues were examined by both liquid and gas chromatographic-mass spectral methods and found to contain a rich mixture of products. The unhydrolyzed samples showed HCN, NH(3), acetaldehyde (formed by reaction with background and atmospheric H(2)O), alkyamines, and numerous other compounds, but no amino acids. However, reaction products in hydrolyzed residues contained a suite of amino acids that included some found in carbonaceous chondrite meteorites. Equal amounts of D- and L-enantiomers were found for each chiral amino acid detected. Extensive use was made of (13)C-labeled CH(3)CN to confirm amino acid identifications and discriminate against possible terrestrial contaminants. The results reported here show that ices exposed to cosmic rays can yield products that, after hydrolysis, form a set of primary amino acids equal in richness to those made by other methods, such as photochemistry.     

The role of mud volcanoes in the evolution of Hecate Tholus Volcano on the surface of Mars

Hecate Tholus Volcano has undergone numerous changes in its history of evolution. Further, the phenomena occurring on the surface of this volcano endow us with a remarkable perspective of recent martian geological changes. In the vicinity of this volcano cone, most of the lava is covered with a thick layer of loose sediments (probably clay). The presence of such sediments at the base of the volcano cone has led to the formation of several major landslides. Moreover, liquid water flow on the volcano cone has created a myriad of radial channels. The formation of such structures on the cone of a volcano is only plausible as a result of eruption of a mud volcano from its crater. Besides, the constant discharge of mud-like materials as well as hot water from the volcano paves the way for the growth and evolution of hydrothermal organisms.     

Fate of prebiotic adenine

Equilibrium adsorption isotherm data for the purine base adenine has been obtained on several prebiotically relevant minerals by frontal analysis using water as a mobile phase. Adenine is far displaced toward adsorption on pyrite (FeS2), quartz (SiO2), and pyrrhotite (FeS), but somewhat less for magnetite (Fe3O4) and forsterite (Mg2SiO4). The prebiotic prevalence of these minerals would have allowed them to act as a sink for adenine; removal from the aqueous phase would confer protection from hydrolysis as well, establishing a nonequilibrium thermodynamic framework for increased adenine synthesis. Our results provide evidence that adsorption phenomena may have been critical for the primordial genetic architecture.     

Effects of the diet on brain function.

The rates of synthesis by brain neurons of the neurotransmitters serotonin, acetylcholine, and the catecholamines depend on the brain levels of the respective precursor molecules. Brain levels of each precursor are influenced by their blood concentration, and for the amino acid precursors, by the blood levels of other amino acids as well. Since diet readily alters blood concentrations of each of these precursors, it thereby also influences the brain formation of their neurotransmitter products.     

平台自标定数据有效性评估方法研究

平台系统测量误差是构成导弹制导误差的主要成分,采用平台系统自标定技术是降低平台测量误差影响的有效手段;而自标定结果是否可信,用什么标准进行衡量判定,需要给出定量评估;本文探讨了采取与转台标定数据作相容性检验、对自标定数据有效性进行评估的方法,提出如果转台标定数据与自标定数据相容,则既能验证自标定数据的有效性,又能将两种数据融合,降低各误差系数均值的随机性,从而提高导弹的命中精度.