The Origin of Life

The origin of life is in a sense a genetic problem, for, as H. J. Muller pointed out many years ago, the essential attribute that identifies living matter is its capacity to replicate itself and its variants (1). Because this uniquely biological property has its physical basis in proteins and nucleic acids, the goal of modern work on the origin of life is to discover the manner of origin of these polymers and of the interactions between them that constitute the genetic mechanism. In attempting to review this subject in a limited space, we cannot undertake an exhaustive treatment. Rather, we summarize work published principally since 1970 in the following areas, with emphasis on those aspects that are of greatest current interest: 1. precambrian paleontology, 2. chemical evolution of genetically important monomers, 3. prebiotic dehydration-condensation reactions, 4. organic compounds in meteorites and interstellar space, and 5. biological exploration of the planets. A large number of review articles (2-5), critical and theoretical discussions (6-8), books (9-16), and conference proceedings (17-21) dealing with the origin of have appeared in recent years. In addition, a new serial, the Journal of Molecular Evolution, publishing papers on this and related subjects, appeared in 1971; the journal Space Life Sciences has been renamed "Origins of Life," and a society, the International Society for the Study of the Origin of Life, was recently founded

Motility at the origin of life: Its characterization and a model

Due to recent advances in synthetic biology and artificial life, the origin of life is currently a hot topic of research. We review the literature and argue that the two traditionally competing "replicator-first" and "metabolism-first" approaches are merging into one integrated theory of individuation and evolution. We contribute to the maturation of this more inclusive approach by highlighting some problematic assumptions that still lead to an impoverished conception of the phenomenon of life. In particular, we argue that the new consensus has so far failed to consider the relevance of intermediate timescales. We propose that an adequate theory of life must account for the fact that all living beings are situated in at least four distinct timescales, which are typically associated with metabolism, motility, development, and evolution. On this view, self-movement, adaptive behavior and morphological changes could have already been present at the origin of life. In order to illustrate this possibility we analyze a minimal model of life-like phenomena, namely of precarious, individuated, dissipative structures that can be found in simple reaction-diffusion systems. Based on our analysis we suggest that processes in intermediate timescales could have already been operative in prebiotic systems. They may have facilitated and constrained changes occurring in the faster- and slower-paced timescales of chemical self-individuation and evolution by natural selection, respectively.Comment: 29 pages, 5 figures, Artificial Lif

Nonenzymatic formation of energy-rich lactoyl and glyceroyl thioesters from glyceraldehyde and a thiol

The energy rich thioester, N-acetyl-S-lactoylcysteine, is formed under anaerobic conditions from glyceraldehyde and N-acetylcysteine at ambient temperature in aqueous solutions of sodium phosphate (pH 7.0). The conversion occurs at a rate of about 0.4% per day in reactions with 10 millimoles (mM) glyceraldehyde, 10 mM thiol, and 500 mM sodium phosphate (pH 7.0). Thioester formation proceeds at an estimated efficiency of 76%. The formation of lactoyl thioester most likely occurs by the phosphate catalyzed dehydration of glyceraldehyde to give pyruvaldehyde, which combines with thiol to form a hemithioacetal that rearranges to the thioester. A second energy rich thioester, N-acetyl-S-glyceroylcysteine, is also produced from glyceraldehyde when these reactions are carried out in the presence of oxygen and to a limited extent in the absence of oxygen. In the presence of oxygen the formation of glyceroyl thioester continues until the thiol disappears completely by oxidation. The significance of these reactions to the energetics of the origin of life is discussed

DNA Renaturation at the Water-Phenol Interface

We study DNA adsorption and renaturation in a water-phenol two-phase system, with or without shaking. In very dilute solutions, single-stranded DNA is adsorbed at the interface in a salt-dependent manner. At high salt concentrations the adsorption is irreversible. The adsorption of the single-stranded DNA is specific to phenol and relies on stacking and hydrogen bonding. We establish the interfacial nature of a DNA renaturation at a high salt concentration. In the absence of shaking, this reaction involves an efficient surface diffusion of the single-stranded DNA chains. In the presence of a vigorous shaking, the bimolecular rate of the reaction exceeds the Smoluchowski limit for a three-dimensional diffusion-controlled reaction. DNA renaturation in these conditions is known as the Phenol Emulsion Reassociation Technique or PERT. Our results establish the interfacial nature of PERT. A comparison of this interfacial reaction with other approaches shows that PERT is the most efficient technique and reveals similarities between PERT and the renaturation performed by single-stranded nucleic acid binding proteins. Our results lead to a better understanding of the partitioning of nucleic acids in two-phase systems, and should help design improved extraction procedures for damaged nucleic acids. We present arguments in favor of a role of phenol and water-phenol interface in prebiotic chemistry. The most efficient renaturation reactions (in the presence of condensing agents or with PERT) occur in heterogeneous systems. This reveals the limitations of homogeneous approaches to the biochemistry of nucleic acids. We propose a heterogeneous approach to overcome the limitations of the homogeneous viewpoint

Oligoglyceric acid synthesis by autocondensation of glyceroyl thioester

The autocondensation of the glyceroyl thioester, S-glyceroyl-ethane-thiol, yielded olioglyceric acid. The rates of autocondensation and hydrolysis of the thioester increased from pH 6.5 to pH 7.5 in 2,6-lutidine and imidazole buffers. Autocondensation and hydrolysis were much more rapid in imidazole buffers as compared to 2,6-lutidine and phosphate buffers. The efficiency of ester bond synthesis was about 20% for 40 mM S-glyceroyl-ethane-thiol in 2,6-lutidine and imidazole buffers near neutral pH. The size and yield of the olioglyceric acid products increased when the concentration of the thioester was increased. The relationship of these results to prebiotic polymer synthesis is discussed

Nitrogen Oxide Concentrations in Natural Waters on Early Earth

A key challenge in origins-of-life studies is estimating the abundances of species relevant to the chemical pathways proposed to have contributed to the emergence of life on early Earth. Dissolved nitrogen oxide anions (NO$_{X}^{-}$), in particular nitrate (NO$_{3}^{-}$) and nitrite (NO$_{2}^{-}$), have been invoked in diverse origins-of-life chemistry, from the oligomerization of RNA to the emergence of protometabolism. Recent work has calculated the supply of NO$_{X}^{-}$ from the prebiotic atmosphere to the ocean, and reported steady-state [NO$_{X}^{-}$] to be high across all plausible parameter space. These findings rest on the assumption that NO$_{X}^{-}$ is stable in natural waters unless processed at a hydrothermal vent. Here, we show that NO$_{X}^{-}$ is unstable in the reducing environment of early Earth. Sinks due to UV photolysis and reactions with reduced iron (Fe$^{2+}$) suppress [NO$_{X}^{-}$] by several orders of magnitude relative to past predictions. For pH$=6.5-8$ and $T=0-50^\circ$C, we find that it is most probable that NO$_{X}^{-}$]$<1~\mu$M in the prebiotic ocean. On the other hand, prebiotic ponds with favorable drainage characteristics may have sustained [NO$_{X}^{-}$]$\geq 1~\mu$M. As on modern Earth, most NO$_{X}^{-}$ on prebiotic Earth should have been present as NO$_{3}^{-}$, due to its much greater stability. These findings inform the kind of prebiotic chemistries that would have been possible on early Earth. We discuss the implications for proposed prebiotic chemistries, and highlight the need for further studies of NO$_{X}^{-}$ kinetics to reduce the considerable uncertainties in predicting [NO$_{X}^{-}$] on early Earth.Comment: In review for publication at Geochemistry, Geophysics, and Geosystems (G-cubed). Comments, questions, and criticism solicited; please contact corresponding author at [email protected]. SI at: https://web-cert.mit.edu/sukrit/Public/nox_si.pdf. GitHub at: https://github.com/sukritranjan/no

Arabinoxylans, inulin and Lactobacillus reuteri 1063 repress the adherent-invasive Escherichia coli from mucus in a musosa-comprising gut model

The microbiota that colonises the intestinal mucus may particularly affect human health given its proximity to the epithelium. For instance, the presence of the adherent-invasive Escherichia coli (AIEC) in this mucosal microbiota has been correlated with Crohn's disease. Using short-term screening assays and a novel long-term dynamic gut model, which comprises a simulated mucosal environment (M-SHIME), we investigated how (potential) pro-and prebiotics may repress colonisation of AIEC from mucus. Despite that during the short-term screening assays, some of the investigated Lactobacillus strains adhered strongly to mucins, none of them competed with AIEC for mucin-adhesion. In contrast, AIEC survival and growth during co-culture batch incubations was decreased by Lactobacillus rhamnosus GG and L. reuteri 1063, which correlated with (undissociated) lactic acid and reuterin levels. Regarding the prebiotics, long-chain arabinoxylans (LC-AX) lowered the initial mucin-adhesion of AIEC, while both inulin (IN) and galacto-oligosaccharides (GOS) limited AIEC survival and growth during batch incubations. L. reuteri 1063, LC-AX and IN were thus retained for a long-term study with the M-SHIME. All treatments repressed AIEC from mucus without affecting AIEC numbers in the luminal content. As a possible explanation, L. reuteri 1063 treatment increased lactobacilli levels in mucus, while LC-AX and IN additionally increased mucosal bifidobacteria levels, thus leading to antimicrobial effects against AIEC in mucus. Overall, this study shows that pro-and prebiotics can beneficially modulate the in vitro mucosal microbiota, thus limiting occurrence of opportunistic pathogens among those mucosal microbes which may directly interact with the host given their proximity to the epithelium

Investigation Of Changes Of Structural-mechanical Properties Of Fatty Filling For Synbiotic Wafers

There was grounded the choice of functional ingredients for creating the synbiotic complex, consisted of immobilized bifidobacteria and inulin. There was demonstrated the necessity to realize the process of immobilization for “defending” bifidobacteria cells from the effect of unfavorable factors. There was determined the number of microorganisms\u27 cells and mass share of inulin for introducing in the recipe of a fatty filling. There was studied the influence of synbiotics on structural-mechanical properties of a fatty filling for wafers. The limit speed, that the high-quality filling can be received at, was established, according to experimental data. It was studied, that the decrease of the fat quantity in the mass and simultaneous increase of the solid phase leads to the increase of the filling firmness that allows to shorten of the process of wafer layers cooling.There was grounded the expedience of using the synbiotic complex in the technology of wafers fatty filling that allows to receive new wafer types of the functional directionality

Force for ancient and recent life: viral and stem-loop RNA consortia promote life.

Lytic viruses were thought to kill the most numerous host (i.e., kill the winner). But persisting viruses/defectives can also protect against viruses, especially in a ubiquitous virosphere. In 1991, Yarmolinsky et al. discovered the addiction modules of P1 phage, in which opposing toxic and protective functions stabilize persistence. Subsequently, I proposed that lytic and persisting cryptic virus also provide addiction modules that promote group identity. In eukaryotes (and the RNA world), a distinct RNA virus-host relationship exists. Retrovirurses/retroposons are major contributors to eukaryotic genomes. Eukaryotic complexity appears to be mostly mediated by regulatory complexity involving noncoding retroposon-derived RNA. RNA viruses evolve via quasispecies, which contain cooperating, minority, and even opposing RNA types. Quasispecies can also demonstrate group preclusion (e.g., hepatitis C). Stem-loop RNA domains are found in long terminal repeats (and viral RNA) and mediate viral regulation/identity. Thus, stem-loop RNAs may be ancestral regulators. I consider the RNA (ribozyme) world scenario from the perspective of addiction modules and cooperating quasispecies (i.e., subfunctional agents that establish group identity). Such an RNA collective resembles a "gang" but requires the simultaneous emergence of endonuclease, ligase, cooperative catalysis, group identity, and history markers (RNA). I call such a collective a gangen (pathway to gang) needed for life to emerge

Impact contribution of prebiotic reactants to Earth

It is proposed that the AIB amino acid at the K/T boundary were synthesized during entry of a comet. However, whether they were synthesized or supplied directly from space, the concentration of amino acids in the shallow K/T sea would have been about 10(exp -7) M. It is probable that clays were the dominant sinks for the amino acids in the K/T sea and in the primordial ocean. Because clay removed amino acids from sea water quickly, the amino acid contribution must be studied from individual comets in order to evaluate the effectiveness of comets for chemical evolution. Such an evaluation shows that comets would have produced amino acid concentration higher than equilibrium concentrations of amino acid from corona discharge at all times preceding the age of the oldest fossils. The perferred sites for chemical evolution of cometary amino acids are in cloud drops and tide pools where the concentration of amino acids would have been the highest. Life could have originated at the surface even during periods of intense bombardment of the earth before 3.8 billion years ago