Stable isotope analysis at the molecular level: a new approach for determining the origins of amino acids in the Murchison meteorite

Pyruvate utilization by a chemolithoautotrophic epsilonproteobacterial key player of pelagic Baltic Sea redoxclines

Pelagic redoxclines of the central Baltic Sea are dominated by the epsilonproteobacterial group Sulfurimonas GD17, considered to be the major driver of chemolithoautotrophic denitrification in this habitat. Autecological investigations of a recently isolated representative of this environmental group, Sulfurimonas gotlandica str. GD1(T), demonstrated that the bacterium grows best under sulfur-oxidizing, denitrifying conditions. However, in the presence of bicarbonate, this strain is able to use pyruvate as both an additional carbon source and an alternative electron donor. These observations suggested that the environmental group GD17 actively metabolizes organic substrates in situ. To examine this possibility, we used RNA-based stable isotope probing (RNA-SIP) on a natural redoxcline community provided with ¹³C-labeled pyruvate. While in this experiment, we were able to identify putative heterotrophic microorganisms, the uptake of ¹³C-pyruvate in GD17 nucleic acids could not be established. To resolve these contradictory findings, combined incorporation experiments with ¹⁴C- and ¹³C-labeled pyruvate were carried out in cells of strain GD1(T) cultivated under chemolithoautotrophic conditions, which favor pyruvate uptake rather than oxidation. An analysis of the labeled biomolecules revealed that pyruvate was mostly incorporated in cellular components such as amino acids, whose synthesis requires only minimal transformation. Carbon transfer into nucleic acids was not observed, explaining the inability of RNA-SIP to detect pyruvate incorporation by strain GD1(T) and the environmental group GD17. Together, these findings suggest that by integrating organic compounds such as pyruvate into cellular components S. gotlandica GD1(T) is able to replenish chemolithoautotrophic growth and thus ensure its survival in nutrient-limited habitats such as marine pelagic redoxclines.

Isotope fractionations in the biosynthesis of cell components by different fungi: a basis for environmental carbon flux studies

Abstract The isotope fractionation of carbon from substrates possessing different isotope ratios into fatty acids of polar lipids and amino acids was determined for four different fungi (Rhizopus arrhizus, Mortierella isabellina, Fusarium solani, Aspergillus niger). Carbon isotope ratios of fungi closely followed that of the substrates. Palmitic acid (C16:0), derived from phospholipids, did not display a large carbon isotope fractionation against the substrate. Stearic acid (C18:0), however, was depleted in (13)C against C16:0 in all strains. The desaturation of C18:0 to oleic acid (C18:1omega9) had little effect on the carbon isotope ratio. The subsequent desaturation of C18:1omega9 to linolic acid (C18:2omega6,9) enriched the resulting C18:2omega6,9 by +3.9 per thousand and varied little among strains. This result is important because C18:2omega6,9 is often used as a biomarker in environmental studies. Most amino acids were enriched in (13)C compared to the substrates, but isoleucine and lysine were close to the isotope ratio of the substrate and phenylalanine and leucine were depleted. Interestingly, the carbon isotope ratios of many amino acids differed significantly among different species. A discriminant analysis based on the isotope ratio of four amino acids (Thr, Ile, Phe, Val) resolved the two phyla in the first discriminant function and all four strains in the first two discriminant functions and confirmed a taxon-specific manner of isotope fractionation. The derived rules provide the basis for the use of stable isotopes in environmental studies to elucidate the role of fungi in the carbon flow in the environment.

Which amino acids should be used in prebiotic chemistry studies?

The adsorption of amino acids on minerals and their condensation under conditions that resemble those of prebiotic earth is a well studied subject. However, which amino acids should be used in these experiments is still an open question. The main goal of this review is to attempt to answer this question. There were two sources of amino acids for the prebiotic earth: (1) exogenous -- meaning that the amino acids were synthesized outside the earth and delivered to our planet by interplanetary dust particles (IDPs), meteorites, comets, etc. and (2) endogenous -- meaning that they were synthesized on earth in atmospheric mixtures, hydrothermal vents, etc. For prebiotic chemistry studies, the use of a mixture of amino acids from both endogenous and exogenous sources is suggested. The exogenous contribution of amino acids to this mixture is very different from the average composition of proteins, and contains several non-protein amino acids. On the other hand, the mixture of amino acids from endogenous sources is seems to more closely resemble the amino acid composition of terrestrial proteins.

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.

Identification of diamino acids in the Murchison meteorite

Amino acids identified in the Murchison chondritic meteorite by molecular and isotopic analysis are thought to have been delivered to the early Earth by asteroids, comets, and interplanetary dust particles where they may have triggered the appearance of life by assisting in the synthesis of proteins via prebiotic polycondensation reactions [Oró, J. (1961) Nature 190, 389-390; Chyba, C. F. & Sagan, C. (1992) Nature 355, 125-132]. We report the identification of diamino acids in the Murchison meteorite by new enantioselective GC-MS analyses. dl-2,3-diaminopropanoic acid, dl-2,4-diaminobutanoic acid, 4,4'-diaminoisopentanoic acid, 3,3'-diaminoisobutanoic acid, and 2,3-diaminobutanoic acid were detected in the parts per billion range after chemical transformation into N,N-diethoxycarbonyl ethyl ester derivatives. The chiral diamino acids show a racemic ratio. Laboratory data indicate that diamino acids support the formation of polypeptide structures under primitive Earth conditions [Brack, A. & Orgel, L. E. (1975) Nature 256, 383-387] and suggest polycondensation reactions of diamino acids into early peptide nucleic acid material as one feasible pathway for the prebiotic evolution of DNA and RNA genomes [Joyce, G. F. (2002) Nature 418, 214-221]. The results obtained in this study favor the assumption that not only amino acids (as the required monomers of proteins) form in interstellar/circumstellar environments, but also the family of diamino monocarboxylic acids, which might have been relevant in prebiotic chemistry.

High-Precision Position-Specific Isotope Analysis of 13C/12C in Leucine and Methionine Analogues

We report an automated method for high-precision position-specific isotope analysis (PSIA) of carbon in amino acid analogues. Carbon isotope ratios are measured for gas-phase pyrolysis fragments from multiple sources of 3-methylthiopropylamine (3MTP) and isoamylamine (IAA), the decarboxylated analogues of methionine and leucine, using a home-built gas chromatography (GC)-pyrolysis-GC preparation system coupled to a combustion-isotope ratio mass spectrometry system. Over a temperature range of 620-900 degrees C, the characteristic pyrolysis products for 3MTP were CH4, C2H6, HCN, and CH3CN and for IAA products were propylene, isobutylene, HCN, and CH3CN. Fragment origin was confirmed by 13C-labeling, and fragments used for isotope analysis were generated from unique moieties with > 95% structural fidelity. Isotope ratios for the fragments were determined with an average precision of SD(delta13C) < 0.3% per thousand, and relative isotope ratios of fragments from different sources were determined with an average precision of SD(delta(delta)13C) < 0.5% per thousand. Delta(delta)13C values of fragments were invariant over a range of pyrolysis temperatures. The delta(delta)13C of complementary fragments in IAA was within 0.8% per thousand of the delta(delta)13C of the parent compounds, indicating that pyrolysis-induced isotopic fractionation is effectively taken into account with this calibration procedure. Using delta(delta)13C values of fragments, delta(delta)13C values were determined for all four carbon positions of 3MTP and for C1, C2, and the propyl moiety of IAA, either directly or indirectly by mass balance. Large variations in position-specific isotope ratios were observed in samples from different commercial sources. Most dramatically, two 3MTP sources differed by 16.30% per thousand at C1, 48.33% per thousand at C2, 0.37% per thousand at C3, and 5.36% per thousand at C(methyl). These PSIA techniques are suitable for studying subtle changes in intramolecular isotope ratios due to natural processes.

Applied gas chromatography coupled to isotope ratio mass spectrometry

Compound-specific isotope analysis (CSIA) by isotope ratio mass spectrometry (IRMS) following on-line combustion (C) of compounds separated by gas chromatography (GC) is a relatively young analytical method. Due to its ability to measure isotope distribution at natural abundance level with great accuracy and high precision, GC-C-IRMS has increasingly become the method of choice in authenticity control of foodstuffs and determination of origin in archaeology, geochemistry, and environmental chemistry. In combination with stable isotope labelled compounds, GC-C-IRMS is also used more and more in biochemical and biomedical application as it offers a reliable and risk-free alternative to the use of radioactive tracers. The literature on these topics is reviewed from the advent of commercial GC-C-IRMS systems in 1990 up to the beginning of 1998. Demands on sample preparation and quality of GC separation for GC-C-IRMS are discussed also.