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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
NASA NTRS1992

Nucleotides as nucleophiles - Reactions of nucleotides with phosphoimidazolide activated guanosine

On the basis of recently discovered RNAs with catalytic capabilities resembling those of enzymes, it is postulated that an 'RNA world' may have played a determining role in prebiotic chemistry and led evolution from prebiological to biological systems. The advent of the RNA world thus postulated, however, entails the preexistence of ribomononucleotides, and presumes that their reactions resulted in templatelike oligonucleotides. Attention is presently given to the reaction of nucleoside monophosphates with the phosphoimidazolide-activated nucleosides that (1) have successfully been used in place of the natural nucleoside triphosphates and (2) for whose prebiotic existence there is now some evidence.

Kanavarioti, Anastassia↗
NASA NTRS1997

Isolation of novel ribozymes that ligate AMP-activated RNA substrates

BACKGROUND: The protein enzymes RNA ligase and DNA ligase catalyze the ligation of nucleic acids via an adenosine-5'-5'-pyrophosphate 'capped' RNA or DNA intermediate. The activation of nucleic acid substrates by adenosine 5'-monophosphate (AMP) may be a vestige of 'RNA world' catalysis. AMP-activated ligation seems ideally suited for catalysis by ribozymes (RNA enzymes), because an RNA motif capable of tightly and specifically binding AMP has previously been isolated. RESULTS: We used in vitro selection and directed evolution to explore the ability of ribozymes to catalyze the template-directed ligation of AMP-activated RNAs. We subjected a pool of 10(15) RNA molecules, each consisting of long random sequences flanking a mutagenized adenosine triphosphate (ATP) aptamer, to ten rounds of in vitro selection, including three rounds involving mutagenic polymerase chain reaction. Selection was for the ligation of an oligonucleotide to the 5'-capped active pool RNA species. Many different ligase ribozymes were isolated; these ribozymes had rates of reaction up to 0.4 ligations per hour, corresponding to rate accelerations of approximately 5 x10(5) over the templated, but otherwise uncatalyzed, background reaction rate. Three characterized ribozymes catalyzed the formation of 3'-5'-phosphodiester bonds and were highly specific for activation by AMP at the ligation site. CONCLUSIONS: The existence of a new class of ligase ribozymes is consistent with the hypothesis that the unusual mechanism of the biological ligases resulted from a conservation of mechanism during an evolutionary replacement of a primordial ribozyme ligase by a more modern protein enzyme. The newly isolated ligase ribozymes may also provide a starting point for the isolation of ribozymes that catalyze the polymerization of AMP-activated oligonucleotides or mononucleotides, which might have been the prebiotic analogs of nucleoside triphosphates.

NASA Discipline Exobiology↗
NASA NTRS1995

On the levels of enzymatic substrate specificity: Implications for the early evolution of metabolic pathways

The most frequently invoked explanation for the origin of metabolic pathways is the retrograde evolution hypothesis. In contrast, according to the so-called 'patchwork' theory, metabolism evolved by the recruitment of relatively inefficient small enzymes of broad specificity that could react with a wide range of chemically related substrates. In this paper it is argued that both sequence comparisons and experimental results on enzyme substrate specificity support the patchwork assembly theory. The available evidence supports previous suggestions that gene duplication events followed by a gradual neoDarwinian accumulation of mutations and other minute genetic changes lead to the narrowing and modification of enzyme function in at least some primordial metabolic pathways.

Lazcano, A.↗
NASA NTRS1980

From inanimate matter to living systems

Since the early part of this century, the Genesis account of the origin and evolution of life has been explained as an extrapolation of astronomical and geochemical processes. The essence of the answer to date is a protoreproductive protocell of much biochemical and cytophysical competance. The processes of its origin, molecular ordering, and its functions are described. A crucial understanding is that of the nonrandomness of evolutionary processes at all stages (with perhaps a minor statistical component). In this way, evolution conflicts with statistical randomness; the latter is a favorite assumption of both scientific and creationistic critics of the proteinoid theory. The principle contribution of the proteinoid theory to the understanding of general biology is to particularize the view that evolutionary direction is rooted in the shapes of molecules, in stereochemistry. After molecules of the right kind first assembled to protocells, life in its various stages of evolution was an inevitable consequence. It is molecules that continue to assemble as part of living process and, in the role of enzymes, continue to direct life cycle of the cell.

Fox, S. W.↗
NASA NTRS1980

Physical chemistry and evolution of salt tolerance in halobacteria

The cellular constituents of extremely halophilic bacteria not only tolerate high salt concentration, but in many cases require it for optical functioning. The characteristics affected by salt include enzyme activity, stability, allosteric regulation, conformation and subunit association. The salt effects are of two major kinds: electrostatic shielding of negative charges by cations at low salt concentration, and hydrophobic stabilization by salting-out type salts at high salt concentration. The composition of halobacterial proteins shows an excess of acidic amino acids and a deficiency of nonpolar amino acids, which accounts for these effects. Since the cohesive forces are weaker and the repulsing forces are stronger in these proteins, preventing aggregation in salt, these structures are no longer suited for functioning in the absence of high salt concentrations. Unlike these nonspecific effects, ribosomes in halobacteria show marked preference for potassium over sodium ions. To ensure the proper intracellular ionic composition, powerful ion transport systems have evolved in the halobacteria, resulting in the extrusion of sodium ions and their replacement by potassium. It is likely that such membrane transport system for ionic movements is a necessary requisite for salt tolerance.

Lanyi, J. K.↗
NASA NTRS1997

Attempted prebiotic synthesis of pseudouridine

Pseudouridine is a modified base found in all tRNA and rRNA. Hence, it is reasonable to think that pseudouridine was important in the early evolution, if not the origin, of life. Since uracil reacts rapidly with formaldehyde and other aldehydes at the C-5 position, it is plausible that pseudouridine could be synthesized in a similar way by the reaction of the C-5 of uracil with the C-1 of ribose. The determining factor is whether the ribose could react with the uracil faster than ribose decomposes. However, both rates are determined by the amount of free aldehyde in the ribose. Various plausible prebiotic reactions were investigated and none showed pseudouridine above the detection limit (<0.01%). Only unreacted uracil and ribose decomposition products could be observed. Thus the rate of addition of ribose to uracil is much slower than the decomposition of ribose under any reasonable prebiotic conditions. Unless efficient non-biological catalysts for any of these reactions exist, pseudouridine would not have been synthesized to any significant extent without the use of biologically produced enzymes.

NASA Discipline Exobiology↗
NASA NTRS1993

The RNA-world and co-evolution hypothesis and the origin of life: Implications, research strategies and perspectives

The applicability of the RNA-world and co-evolution hypothesis to the study of the very first stages of the origin of life is discussed. The discussion focuses on the basic differences between the two hypotheses and their implications, with regard to the reconstruction methodology, ribosome emergence, balance between ribozymes and protein enzymes, and their major difficultites. Additional complexities of the two hypotheses, such as membranes and the energy source of the first reactions, are not treated in the present work. A central element in the proposed experimental strategies is the study of the catalytic activites of very small peptides and RNA-like oligomers, according to existing, as well as to yet-to-be-invented scenarios of the two hypothesis under consideration. It is suggested that the novel directed molecular evolution technology, and molecular computational modeling, can be applied to this research. This strategy is assumed to be essential for the suggested goal of future studies of the origin of life, namely, the establishment of a `Primordial Darwinian entity'.

Lahav, Noam↗
NASA NTRS1989

Life sciences and space research XXIII(2): Planetary biology and origins of life; Proceedings of the Topical Meeting and Workshops XX, XXI and XXIII of the 27th COSPAR Plenary Meeting, Espoo, Finland, July 18-29, 1988

This volume includes chapters on exobiology in space, chemical and early biochemical evolution, life without oxygen, potential for chemical evolution in the early environment of Mars, planetary protection issues and sample return missions, and the modulation of biological evolution by astrophysical phenomena. Papers are presented on the results of spaceflight missions, the action of some factors of space medium on the abiogenic synthesis of nucleotides, early peptidic enzymes, microbiology and biochemistry of the methanogenic archaeobacteria, and present-day biogeochemical activities of anaerobic bacteria and their relevance to future exobiological investigations. Consideration is also given to the development of the Alba Patera volcano on Mars, biological nitrogen fixation under primordial Martian partial pressures of dinitrogen, the planetary protection issues in advance of human exploration of Mars, and the difficulty with astronomical explanations of periodic mass extinctions.

Schwartz, A. W.↗
NASA NTRS1998

Origin of the catalytic activity of bovine seminal ribonuclease against double-stranded RNA

Bovine seminal ribonuclease (RNase) binds, melts, and (in the case of RNA) catalyzes the hydrolysis of double-stranded nucleic acid 30-fold better under physiological conditions than its pancreatic homologue, the well-known RNase A. Reported here are site-directed mutagenesis experiments that identify the sequence determinants of this enhanced catalytic activity. These experiments have been guided in part by experimental reconstructions of ancestral RNases from extinct organisms that were intermediates in the evolution of the RNase superfamily. It is shown that the enhanced interactions between bovine seminal RNase and double-stranded nucleic acid do not arise from the increased number of basic residues carried by the seminal enzyme. Rather, a combination of a dimeric structure and the introduction of two glycine residues at positions 38 and 111 on the periphery of the active site confers the full catalytic activity of bovine seminal RNase against duplex RNA. A structural model is presented to explain these data, the use of evolutionary reconstructions to guide protein engineering experiments is discussed, and a new variant of RNase A, A(Q28L K31C S32C D38G E111G), which contains all of the elements identified in these experiments as being important for duplex activity, is prepared. This is the most powerful catalyst within this subfamily yet observed, some 46-fold more active against duplex RNA than RNase A.

Non-NASA Center↗
NASA NTRS1986

Evolution of thiol protective systems in prokaryotes

Biological thiols are essential elements in most aspects of cell function but undergo rapid oxidation to disulfides in the presence of oxygen. The evolution of systems to protect against such oxygen toxicity was essential to the emergence of aerobic life. The protection system used by eukaryotes is based upon glutathione (GSH) and GSH-dependent enzymes but many bacteria lack GSH and apparently use other mechanisms. The objective of this research is to elaborate the thiol protective mechanisms employed by prokaryotes of widely divergent evolutionary origin and to understand why GSH became the central thiol employed in essentially all higher organisms. Thiol-selective fluorescent labeling and HPLC analysis has been used to determine key monothiol components.

Fahey, R. C.↗
NASA NTRS1995

Unnatural selection in chemical systems

The theory of evolution through natural selection was proposed by Darwin and Wallace to explain how the characteristics of populations of animals change with time. An examination of their assumptions shows that the theory has much broader application than they originally envisaged. We now know that in appropriate environments RNA molecules or computer viruses, for example, can evolve. The adventure with which we are concerned is the quest for chemical systems that undergo processes analogous to Darwinian selection in the test tube. The search is not restricted to systems that are closely related to nucleic acids, although most of the available experimental evidence concerns such systems. A population of molecules satisfies all the requirements of the theory is there are different kinds of molecules in the population and if each individual molecule can direct the formation of copies of itself, then a population of molecules will adapt to a varying environment by changing its composition so as to maintain as high as possible a rate of replication. Sol Spiegelman is the inventor of 'unnatural selection'. He showed clearly that populations of RNA molecules evolve when replicated repeatedly by Q beta RNA polymerase under a chosen set of adverse reaction conditions. In the systems that he studied, the initial population was fairly homogeneous and much of the variation was created during the course of the experiment by mutation, that is, error of replication. The term 'unnatural selection' will be used loosely to describe evolution of nucleic acids or other replicatable polymers in vitro. The term 'Natural Selection' will be reserved for the evolution of living organisms and their viruses. Natural Section usually involves the coevolution of nucleic acids and proteins, while 'unnatural selection', as practiced so far, allows replicating nucleic acids to evolve but hold constant the enzymes that catalyze replication. It is widely believed that biology based on DNA, RNA, and proteins was preceded by the biology of an 'RNA world' in which enzymes were composed of RNA alone. The origin of RNA replication is thus the central puzzle of the origins of life. Consequently, RNA-catalyzed RNA replication is presently one of the main goals of experimental work on unnatural selection. However, there is also a more distant goal, namely, to achieve replication and selection in systems unrelated to RNA. These different systems are discussed in this article.

Orgel, Leslie E.↗
NASA NTRS1998

The prokaryote-to-eukaryote transition reflected in the evolution of the V/F/A-ATPase catalytic and proteolipid subunits

Changes in the primary and quarternary structure of vacuolar and archaeal type ATPases that accompany the prokaryote-to-eukaryote transition are analyzed. The gene encoding the vacuolar-type proteolipid of the V-ATPase from Giardia lamblia is reported. Giardia has a typical vacuolar ATPase as observed from the common motifs shared between its proteolipid subunit and other eukaryotic vacuolar ATPases, suggesting that the former enzyme works as a hydrolase in this primitive eukaryote. The phylogenetic analyses of the V-ATPase catalytic subunit and the front and back halves of the proteolipid subunit placed Giardia as the deepest branch within the eukaryotes. Our phylogenetic analysis indicated that at least two independent duplication and fusion events gave rise to the larger proteolipid type found in eukaryotes and in Methanococcus. The spatial distribution of the conserved residues among the vacuolar-type proteolipids suggest a zipper-type interaction among the transmembrane helices and surrounding subunits of the V-ATPase complex. Important residues involved in the function of the F-ATP synthase proteolipid have been replaced during evolution in the V-proteolipid, but in some cases retained in the archaeal A-ATPase. Their possible implication in the evolution of V/F/A-ATPases is discussed.

NASA Discipline Exobiology↗
NASA NTRS2000

Thermodynamics of Aqueous Organic Sulfur Compounds: A Key to the Organic Geochemistry of Hydrothermal Systems?

Hydrothermal environments are locations of varied geochemistry due to the disequilibrium between vent fluids and seawater. The disequilibrium geochemistry has been hypothesized to include reactions to synthesize organic compounds. Observations of the organic geochemistry of hydrothermal vent sites has received little attention. Experimental simulations of these environments, however, indicate that organic compounds may have difficulty forming in a purely aqueous environment. On the other hand, thiols. thioesters and disulfides have been implicated as reaction intermediates between CO or CO2 in experiments of carbon reduction in hydrothermal environments as well as in a variety of biological processes and other abiotic reactions (Wachtershauser, 1990, OLEB 20, 173; Heinen and Lauwers, 1996, OLEB 26, 13 1, Huber and Wachtershauser, 1997, Science 276, 245; Russell et al., 1998, in Thermophiles: The keys to molecular evolution and the origin of life?). The reduction of CO2 to thiols, for example, is observed using the FeS-H2S/FeS2 couple to provide the reducing power (see Schoonen et al., 1999, OLEB 29, 5). In addition, the enzyme involved in final stage of methanogenesis, coenzyme-M, is itself a thiol. Thus, organic sulfur compounds may hold the key to the organic chemistry leading to the origin of life at high temperatures. Understanding the biochemical processes of microorganisms that can live to temperatures at least as high as 113 C (Blochl et al., 1996, Extremophiles 1, 14) requires knowledge of the properties of the chemical reactions involved. In order to assess the role of aqueous organic sulfur compounds in hydrothermal organic geochemistry, we have been attempting to determine their thermodynamic properties. We have culled the literature to obtain the properties of organic sulfur compounds. We are able to calculate a number of essential properties, such as free energies of formation, from solubility data available in the literature together with standard properties of organic sulfur gases. However, a number of the properties for aqueous organic sulfur compounds have not been experimentally determined. Furthermore, most of thermodynamic data that are available are for 25 C and 1 bar. In order to determine reaction properties to temperatures and pressures appropriate to the hydrothermal conditions in which thermophilic organisms actually live, we use equations of state developed by Helgeson and co-workers (Helgeson et al., 1981, AJS 281, 1249). A key piece of information needed to go up in temperature is the partial molal heat capacity, which is one of the properties for which experimental data are unavailable for nearly all organic sulfur compounds. We have used correlation methods to determine the partial molal heat capacities and volumes of many organic solutes. These estimates allow us to asses the role of organic sulfur compounds during the reduction of carbon in hydrothermal settings. We will present these data, along with examples of the thermodynamic properties of reactions involving aqueous organic sulfur compounds.

Schulte, Mitchell↗
NASA NTRS1993

The evolution of energy-transducing systems: Studies with archaebacteria

N-ethylmaleimide (NEM) inhibits the ATPase of H. saccharovorum in a nucleotide protectable manner. The bulk of 14C-NEM is incorporated into subunit 1. Inhibition kinetics indicated a single binding site. To determine the sequence around this site, cyanogen bromide peptides of NEM-labeled ATPase enzyme were prepared and separated on Tris-Tricine gels. Autoradiography indicated that the NEM binding site is probably located in a fragment of Mr 10-12 K. This result will be confirmed by N-terminal sequencing of the peptide. Since the cysteinyl residue, to which NEM is bound, may be located at the C-terminal end, purification and proteolytic treatment of the 10 K peptide will be required. One inhibitor of V-type ATPases, fluoresceinisothiocyanate (FITC) inhibited also the ATPase of H. saccharovorum. Preliminary results indicated protection against inhibition by nucleotides. Localization of the binding sited to the major subunits is in progress. An extraction procedure for the membrane sector of the ATPase complex of H. saccharovorum yielded a preparation which was enriched in a peptide of Mr 5 500. Experiments to test the immunological crossreaction with subunit c from the Escherichia coli F-type ATPase and the labeling with 14C-DCCD are currently carried out. Polyclonal antiserum to the smaller of the major subunits of the ATPase from H. saccharovorum (subunit ll) reacts in Western blots strongly with the alpha and beta subunits of the F1 ATPase of E. coli, suggesting highly conserved regions on both types of ATPases. To elucidate further the regions of homology, cyanogen bromide peptides of the beta subunits were prepared for sequence analysis.

Stan-Lotter, Helga↗
NASA NTRS1972

Non-enzymic beta-decarboxylation of aspartic acid.

Study of the mechanism of nonenzymic beta-decarboxylation of aspartic acid in the presence of metal ions and pyridoxal. The results suggest that aspartic acid is first converted to oxalacetic acid by transamination with pyridoxal which in turn is converted to pyridoxamine. This is followed by decarboxylation of oxalacetic acid to form pyruvic acid which transaminates with pyridoxamine to form alanine. The possible significance of these results to prebiotic molecular evolution is briefly discussed.

Doctor, V. M.↗
NASA NTRS1995

Evolution of the biosynthesis of the branched-chain amino acids

The origins of the biosynthetic pathways for the branched-chain amino acids cannot be understood in terms of the backwards development of the present acetolactate pathway because it contains unstable intermediates. We propose that the first biosynthesis of the branched-chain amino acids was by the reductive carboxylation of short branched chain fatty acids giving keto acids which were then transaminated. Similar reaction sequences mediated by nonspecific enzymes would produce serine and threomine from the abundant prebiotic compounds glycolic and lactic acids. The aromatic amino acids may also have first been synthesized in this way, e.g. tryptophan from indole acetic acid. The next step would have been the biosynthesis of leucine from alpha-ketoisovalerc acid. The acetolactate pathway developed subsequently. The first version of the Krebs cycle, which was used for amino acid biosynthesis, would have been assembled by making use fo the reductive carboxylation and leucine biosynthesis enzymes, and completed with the development of a single new enzyme, succinate dehydrogenase. This evolutionary scheme suggests that there may be limitations to inferring the origins of metabolism by a simple back extrapolation of current pathways.

Keefe, Anthony D.↗
NASA NTRS1977

The evolution of the protein synthesis system. I - A model of a primitive protein synthesis system

A model is developed to describe the evolution of the protein synthesis system. The model is comprised of two independent autocatalytic systems, one including one gene (A-gene) and two activated amino acid polymerases (O and A-polymerases), and the other including the addition of another gene (N-gene) and a nucleotide polymerase. Simulation results have suggested that even a small enzymic activity and polymerase specificity could lead the system to the most accurate protein synthesis, as far as permitted by transitions to systems with higher accuracy.

Mizutani, H.↗