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PubMed2002

A selected ribozyme catalyzing diverse dipeptide synthesis.

The sequence of events by which protein, RNA, and DNA emerged during early biological evolution is one of the most profound questions regarding the origin of life. The contemporary role of aminoacyl-adenylates as intermediates in both ribosomal and nonribosomal peptide synthesis suggests that they may have served as substrates for uncoded peptide synthesis during early evolution. We report a highly active peptidyl transferase ribozyme family, isolated by in vitro selection, that efficiently catalyzes dipeptide synthesis by using an aminoacyl-adenylate substrate. It was characterized by sequence and structural analysis and kinetic studies. Remarkably, the ribozyme catalyzed the formation of 30 different dipeptides, the majority of rates being within 5-fold that of the Met-Phe dipeptide required by the selection. The isolation of this synthetic ribozyme fosters speculation that ribozyme-mediated uncoded peptide synthesis may have preceded coded peptide synthesis.

Adenosine Monophosphate↗
PubMed2003

Sequence-universal recognition of duplex DNA by oligonucleotides via pseudocomplementarity and helix invasion.

The well-known Watson-Crick complementarity rules, which were discovered 50 years ago, elegantly direct the specific pairing of two DNA single strands. On the contrary, once formed, the double-stranded (ds) DNA lacks such a simple and sequence-universal recognition principle, since most of the characteristic chemical groups of nucleobases are now buried deep inside the double helix, the major DNA form. We report a promising versatile approach for highly selective recognition of designated sites within dsDNA featuring considerable practical potential for a variety of molecular-biological, biotechnological, gene-therapeutic, and diagnostic applications. It may also have implications for prebiotic evolution of genetic machinery at the primordial stages of the origin of life. Our design synergistically employs the robust helix-invasion ability of recently developed DNA mimics and analogs, pseudocomplementary peptide nucleic acids and pseudocomplementary oligonucleotides, thus enabling the sequence-unrestricted recognition of chosen DNA duplexes by nucleobase oligomers. Using this basically general approach, we selectively tagged a unique mixed-base site on the target dsDNA fragment with streptavidin and/or multiply labeled this site with fluorophores via the primer-extension reaction.

DNA↗
PubMed1997

The chemical end-ligation of homopyrimidine oligodeoxyribonucleotides within a DNA triple helix.

BACKGROUND: Triple-helical nucleic acids, first reported in the late 1950s, are receiving attention for their possible involvement in controlling gene expression. Certain sequences of DNA are believed to form local triple-helical structures (H-form DNA), although this has not been directly observed in vivo. Studies carried out in our laboratories have suggested that self-replicating oligonucleotides could have been involved in chemical evolution via triple-helical intermediates. In addition to self-replication mechanisms, elucidating processes for the nonenzymatic elongation of biologically relevant polymers remains an important challenge in understanding the origin of life. To this end, we have studied a novel ligation of oligodeoxyribonucleotides that lie within a triple helix. RESULTS: The chemical end-ligation of homopyrimidine oligodeoxyribonucleotides on a triple helix is reported. This selective process, induced by cyanoimidazole, is facilitated by a template effect of the DNA aggregate and occurs between the 3' end (hydroxyl) of the third minor-groove-bound strand and the 5' end (phosphate) of the antiparallel oligopyrimidine strand. CONCLUSIONS: Double-helical homopurine/homopyrimidine DNA can serve as a template for the elongation of oligonucleotides in a manner that has not been described previously. The end-ligation of homopyrimidine oligomers, a nonenzymatic process, proceeds via a requisite triple-helical intermediate and constitutes an efficient and selective method for the template-directed elongation of nucleic acids. Such a process could conceivably have been involved in the elongation of primordial information-bearing biopolymers.

DNA↗
PubMed1998

Peptidyl-transferase ribozymes: trans reactions, structural characterization and ribosomal RNA-like features.

BACKGROUND: One of the most significant questions in understanding the origin of life concerns the order of appearance of DNA, RNA and protein during early biological evolution. If an 'RNA world' was a precursor to extant life, RNA must be able not only to catalyze RNA replication but also to direct peptide synthesis. Iterative RNA selection previously identified catalytic RNAs (ribozymes) that form amide bonds between RNA and an amino acid or between two amino acids. RESULTS: We characterized peptidyl-transferase reactions catalyzed by two different families of ribozymes that use substrates that mimic A site and P site tRNAs. The family II ribozyme secondary structure was modeled using chemical modification, enzymatic digestion and mutational analysis. Two regions resemble the peptidyl-transferase region of 23S ribosomal RNA in sequence and structural context; these regions are important for peptide-bond formation. A shortened form of this ribozyme was engineered to catalyze intermolecular ('trans') peptide-bond formation, with the two amino-acid substrates binding through an attached AMP or oligonucleotide moiety. CONCLUSIONS: An in vitro-selected ribozyme can catalyze the same type of peptide-bond formation as a ribosome; the ribozyme resembles the ribosome because a very specific RNA structure is required for substrate binding and catalysis, and both amino acids are attached to nucleotides. It is intriguing that, although there are many different possible peptidyl-transferase ribozymes, the sequence and secondary structure of one is strikingly similar to the 'helical wheel' portion of 23S rRNA implicated in ribosomal peptidyl-transferase activity.

Adenosine Monophosphate↗
PubMed2002

Approaching exponential growth with a self-replicating peptide.

Self-replicating peptide systems hold great promise for a wide range of technological applications, as well as to address fundamental questions pertaining to the molecular origins of life. The development of self-replicating compounds capable of high efficiency, however, has remained elusive. Here we disclose a successful strategy whereby modulation of coiled-coil stability results in remarkable catalytic efficiency for self-replication. By shortening the peptide to the minimum length necessary for coiled-coil formation a highly efficient self-replicating system was obtained due to very low background reaction rates, bringing the efficiency close to naturally occurring enzymes.

Amino Acid Sequence↗
PubMed2003

Sequence- and regioselectivity in the montmorillonite-catalyzed synthesis of RNA.

The possible role of catalysis in forming a limited number of RNAs from activated monomers is investigated by examining the sequence- and regioselectivity in the montmorillonite-catalyzed formation of RNA dimers and trimers. The reactivity of A was similar to that of G, and C was comparable in reactivity to U. Yet the reactivity of the purine nucleotides differed from that of the pyrimidines. In the reaction of nucleotides (pN) with activated monomers (ImpN), the sequence- and regioselectivity was Pu(3')Py > Pu(3')Pu = Pu(2')Py > Pu(2')Pu. The 5'-pyrimidine initiated dimers formed less efficiently than the 5'-purine initiated dimers. Trimer formation was investigated by the synthesis of 8 dimers (pNpN) and measuring the yields of trimers formed in the reaction of each dimer with a mixture of equal molar amounts of four activated monomers. The reactivity of the dimers depended on the nucleotide attached to the 3'-end of the RNA and the regiochemistry of the phosphodiester bond. Rules based on these studies are proposed to predict the sequence- and regioselectivity of the RNAs formed in montmorillonite-catalyzed reactions. These rules are consistent with the structures of the 2-5-mers formed in the reaction of equimolar amounts of ImpA and ImpC. This research establishes that the montmorillonite catalyst limits the number of RNA oligomer isomers formed. The potential significance of these findings to the origins of life is discussed.

Bentonite↗
PubMed2003

Glycine on a wet pyrite surface at extreme conditions.

We present ab initio molecular dynamics (MD) simulations of the simplest amino acid, glycine, at the water/pyrite interface under extreme pressure/temperature conditions. These simulations are aimed to contribute to the discussion of the "iron-sulfur world" (ISW) scenario, an intriguing proposal in the controversial field of "Origin of Life" research. The simulations show that glycine easily desorbs from a water/pyrite interface through hydrogen-bond assistance. The retention time is only of the order of a picosecond, and the surface bonding is best understood as a relatively weak electrostatic interaction. However, we have found indications of glycine activation due to the interaction with the surface, and thus for a possible reaction with a suitable anchor molecule.

Journal Article↗
PubMed2006

The peptide formation mediated by cyanate revisited. N-carboxyanhydrides as accessible intermediates in the decomposition of N-carbamoylamino acids.

Similar to many ureas, N-carbamoylamino acids were shown to be hydrolyzed in aqueous solution through elimination mechanisms at close to neutral pH, the nucleophilic attack of water being a minor process. Two competing elimination mechanisms can take place involving either cyanate or isocyanate transient intermediates. Peptide formation was observed and attributed to the latter pathway through the intermediacy of amino acid N-carboxyanhydride (NCA). Eventually, cyanate and its precursors (including urea) unexpectedly behave as amino acid activating agents because of their ability in amino acid carbamoylation. Owing to its ability to generate a background prebiotic production of NCAs on the primitive Earth, this reaction is suggested to have contributed to the origin of life process.

Amino Acids↗
PubMed2003

Activity difference between alpha-COOH and beta-COOH in N-phosphorylaspartic acids.

N-phosphorylamino acids are chemically active species that have many biomimic activities. alpha-COOH in amino acids and peptides behaviors rather differently than beta-COOH in many biochemical processes and takes a more important role in the origin of life. Activity differences between alpha-COOH and beta-COOH in the peptide formation of phosphoryl amino acids are studied by 1D, 2D NMR techniques and by ab initio and density functional theory (DFT) calculations in this paper. Phosphoryl dipeptide is formed directly from phosphoryl aspartic acids without any coupling reagents. Only the alpha-dipeptide ester is observed by 1D (1)H, (13)C, and (31)P NMR and 2D NMR. In the ab initio and DFT calculations, the pentacoordinate phosphorane intermediates containing five-membered rings are predicted to be more favored than those with six-membered rings. Both the experimental results and the theoretical calculations suggest that only the alpha-COOH group is activated by N-phosphorylation in N-phosphorylaspartic acid under mild conditions.

Aspartic Acid↗
PubMed2005

RNA selectively interacts with vesicles depending on their size.

RNA and vesicles are two important molecular classes in the origin of life and early evolution, but they are not generally considered as interacting partners. The present paper reports about the interaction between tRNA (Esherichia coli) and vesicles made of the zwitterionic surfactant POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine), partially positively charged with small molar fractions (max 10%) of the single-chained CTAB (cetyltrimethylammonium bromide). CTAB is capable to insert efficiently in POPC vesicles (as determined by zeta-potential measurements), and the binding of tRNA to such charged vesicles operates a strong selection being critically dependent upon the vesicle size. The binding of tRNA to the vesicles is size-selective as it induces a strongly pronounced process of aggregation of large vesicles (ca. 160-nm diameter) but not of small ones (ca. 80-nm diameter) that are stable against vesicle aggregation (as followed by dynamic light-scattering and optical density measurements). The aggregation of the large vesicles is fully reversible upon the addition of RNase A. The selective behavior of tRNA with respect to differently sized vesicles is observable in separated samples as well as in a mixture of both populations. In the latter case, the fraction of large vesicles readily aggregates in the presence of the small ones that remain unaltered in the mixture. This kind of discrimination capability of RNA might have been of importance in the early phases of the formation of the protocells.

Cetrimonium↗
PubMed1997

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.

Deoxyribose↗
PubMed2002

Primordial coding of amino acids by adsorbed purine bases.

Scanning tunneling microscopy and chromatography experiments exploring the potential templating properties of nucleic acid bases adsorbed to the surface of crystalline graphite, revealed that the interactions of amino acids with the bare crystal surface are significantly modulated by the prior adsorption of adenine and hypoxanthine. These bases are the coding elements of a putative purine-only genetic alphabet and the observed effects are different for each of the bases. Such mapping between bases and amino acids provides a coding mechanism. These observations demonstrate that a simple pre-RNA amino acid discrimination mechanism could have existed on the prebiotic Earth providing critical functionality for the origin of life.

Adenine↗
PubMed2002

D-amino acids in living higher organisms.

The homochirality of biological amino acids (L-amino acids) and of the RNA/DNA backbone (D-ribose) might have become established before the origin of life. It has been considered that D-amino acids and L-sugars were eliminated on the primitive Earth. Therefore, the presence and function of D-amino acids in living organisms have not been studied except for D-amino acids in the cell walls of microorganisms. However, D-amino acids were recently found in various living higher organisms in the form of free amino acids, peptides, and proteins. Free D-aspartate and D-serine are present and may have important physiological functions in mammals. D-amino acids in peptides are well known as opioid peptides and neuropeptides. In protein, D-aspartate residues increase during aging. This review deals with recent advances in the study of D-amino acids in higher organisms.

Amino Acid Sequence↗
PubMed2002

Comments on 'concentration by evaporation and the prebiotic synthesis of cytosine'.

The claim by Nelson et al. (2001) that the reaction of cyanoacetaldehyde and urea provides 'an efficient prebiotic synthesis' of cytosine is disputed. The authors have not dealt with the important points presented in a criticism of this reaction (Shapiro, 1999): (1) The reactants undergo side reactions with common nucleophiles that appear to proceed more rapidly than cytosine formation, and (2) No reactions have been described thus far that would produce cytosine at a rate sufficient to compensate for its decomposition by deamination, and permit accumulation over extended periods of time. Instead, Nelson et al. have conducted 'drying-down' experiments, in an effort to simulate evaporations on the early Earth, but the design of these experiments is flawed. The initial reactant concentrations are much higher than might be expected in a natural setting, and potentially interfering substances such as glycine, cyanide and thiols have been excluded. 'Drying beaches and drying lagoons' have been invoked as sites for such a reaction but no effort has been made to describe the characteristics of such sites or to estimate their frequency with reference to the present Earth. In the absence of contradictory data, the conclusion put forward in Shapiro (1999) remains valid: 'It was quite unlikely that cytosine played a role in the origin of life'.

Cytosine↗
PubMed2002

Unexpected differences between D- and L- tyrosine lead to chiral enhancement in racemic mixtures.

We report here an unexpected difference in the solubilities of D- and L-tyrosine in water, which could be discerned by their rate of crystallization and the resulting concentrations of their saturated solutions. A supersaturated solution of 10 mM L-tyrosine at 20 degrees C crystallized much more slowly than that of D-tyrosine under the same conditions, and the saturated solution of L-tyrosine was more concentrated than that of D-tyrosine. Supersaturated solutions of 10 mM DL-tyrosine in water formed precipitates of predominantly D-tyrosine and DL-tyrosine, resulting in an excess of L-tyrosine in the saturated solution. The experimental setups were monitored independently by UV-absorption, radioactivity tracing, optical rotation and X-ray diffraction. The process of nucleation and crystallization of D- and L-tyrosine is characterized by an exceptionally high cooperativity. It is possible that minute energy differences between D- and L-tyrosine, originating from parity violation or other non-conservative chiral discriminatory rules, could account for the observations. The physical process that initiated chiral selection in biological systems remains a challenging problem in understanding the origin of life, and it is possible that chiral compounds were concentrated from supersaturated racemic mixtures by preferential crystallization.

Crystallization↗
PubMed2003

Origin of sex revisited.

Why did sex ever arise in the first place? Why it does not disappear in view of the greater efficiency of asexuals? These are clearly two different questions, and we suggest here that the solution for the origin of sex does not necessarily come from theoretical considerations based on currently existing genetic systems. Thus, while we agree with a number of authors in that the emergence of sex (understood as the exchange of genetic material between genomes) is deeply rooted in the origin of life and happened during the very early stages in the transition from individual genes ('replicators') to bacteria-like cells ('reproducers'), we challenge the idea that recombinational repair was the major selective force for the emergence of sex. Taking the stochastic corrector model as a starting point, we provide arguments that question the putative costs of redundancy in primitive protocells. In addition, if genes that cause intragenomic conflict (i.e., parasites) are taken into account, it is certainly wrong to suggest that cellular fusion would be beneficial at the population level (although this strong claim needs some qualifications). However, when a continuous input of deleterious mutations that impair the fitness of the protocell as a whole is considered in the model (in the realistic range in which stable mutant distributions of quasi-species within compartments are established), there are circumstances when sex could be beneficial as a side effect of the dynamic equilibrium between cellular fusion-mutation-selection. The scenario we have explored numerically is fully consistent with the idea that the universal ancestor was not a discrete entity but an ensemble of proto-organisms that exchanged much genetic information.

Biological Evolution↗
PubMed2004

Monte Carlo simulations of vesicles and fluid membranes transformations.

The appearance of compartmentalization is recognized as a key step in biogenesis. The study of the dynamical behaviour of amphiphilic close membranes at equilibrium or under some external stress (osmotic pressure or dehydration process) can be useful in order to better elucidate the role of vesicles in the origin of life and to get insight into the molecular and membrane properties that bring to a spontaneous vesicle division. A Monte Carlo approach to simulate the evolution of close membranes under an external stress will be presented. This approach is mainly based on the accepted surface energy model introduced by Helfrich (1973) and Seifert (1997a). Some preliminary results will be also illustrated and possible developments and limits of this method discussed.

Membranes, Artificial↗
PubMed1998

Alteration processes in volcanic soils and identification of exobiologically important weathering products on Mars using remote sensing.

Determining the mineralogy of the Martian surface material provides information about the past and present environments on Mars which are an integral aspect of whether or not Mars was suitable for the origin of life. Mineral identification on Mars will most likely be achieved through visible-infrared remote sensing in combination with other analyses on landed missions. Therefore, understanding the visible and infrared spectral properties of terrestrial samples formed via processes similar to those thought to have occurred on Mars is essential to this effort and will facilitate site selection for future exobiology missions to Mars. Visible to infrared reflectance spectra are presented here for the fine-grained fractions of altered tephra/lava from the Haleakala summit basin on Maui, the Tarawera volcanic complex on the northern island of New Zealand, and the Greek Santorini island group. These samples exhibit a range of chemical and mineralogical compositions, where the primary minerals typically include plagioclase, pyroxene, hematite, and magnetite. The kind and abundance of weathering products varied substantially for these three sites due, in part, to the climate and weathering environment. The moist environments at Santorini and Tarawera are more consistent with postulated past environments on Mars, while the dry climate at the top of Haleakala is more consistent with the current Martian environment. Weathering of these tephra is evaluated by assessing changes in the leachable and immobile elements, and through detection of phyllosilicates and iron oxide/oxyhydroxide minerals. Identifying regions on Mars where phyllosilicates and many kinds of iron oxides/oxyhydroxides are present would imply the presence of water during alteration of the surface material. Tephra samples altered in the vicinity of cinder cones and steam vents contain higher abundances of phyllosilicates, iron oxides, and sulfates and may be interesting sites for exobiology.

Evolution, Planetary↗