Permeation of aldopentoses and nucleosides through fatty acid and phospholipid membranes: implications to the origins of life

The fats of the matter: Lipids in prebiotic chemistry and in origin of life studies

The unique biophysical and biochemical properties of lipids render them crucial in most models of the origin of life (OoL). Many studies have attempted to delineate the prebiotic pathways by which lipids were formed, how micelles and vesicles were generated, and how these micelles and vesicles became selectively permeable towards the chemical precursors required to initiate and support biochemistry and inheritance. Our analysis of a number of such studies highlights the extremely narrow and limited range of conditions by which an experiment is considered to have successfully modeled a role for lipids in an OoL experiment. This is in line with a recent proposal that bias is introduced into OoL studies by the extent and the kind of human intervention. It is self-evident that OoL studies can only be performed by human intervention, and we now discuss the possibility that some assumptions and simplifications inherent in such experimental approaches do not permit determination of mechanistic insight into the roles of lipids in the OoL. With these limitations in mind, we suggest that more nuanced experimental approaches than those currently pursued may be required to elucidate the generation and function of lipids, micelles and vesicles in the OoL.

The Origin(s) of Cell(s): Pre-Darwinian Evolution from FUCAs to LUCA : To Carl Woese (1928-2012), for his Conceptual Breakthrough of Cellular Evolution

The coming of the Last Universal Cellular Ancestor (LUCA) was the singular watershed event in the making of the biotic world. If the coming of LUCA marked the crossing of the "Darwinian Threshold", then pre-LUCA evolution must have been Pre-Darwinian and at least partly non-Darwinian. But how did Pre-Darwinian evolution before LUCA actually operate? I broaden our understanding of the central mechanism of biological evolution (i.e., variation-selection-inheritance) and then extend this broadened understanding to its natural starting point: the origin(s) of the First Universal Cellular Ancestors (FUCAs) before LUCA. My hypothesis centers upon vesicles' making-and-remaking as variation and competition as selection. More specifically, I argue that vesicles' acquisition and merger, via breaking-and-repacking, proto-endocytosis, proto-endosymbiosis, and other similar processes had been a central force of both variation and selection in the pre-Darwinian epoch. These new perspectives shed important new light upon the origin of FUCAs and their subsequent evolution into LUCA.

A Step toward Molecular Evolution of RNA: Ribose Binds to Prebiotic Fatty Acid Membranes, and Nucleosides Bind Better than Individual Bases Do

A major challenge in understanding how biological cells arose on the early Earth is explaining how RNA and membranes originally colocalized. We propose that the building blocks of RNA (nucleobases and ribose) bound to self-assembled prebiotic membranes. We have previously demonstrated that the bases bind to membranes composed of a prebiotic fatty acid, but evidence for the binding of sugars has remained a technical challenge. Here, we used pulsed-field gradient NMR spectroscopy to demonstrate that ribose and other sugars bind to membranes of decanoic acid. Moreover, the binding of some bases is strongly enhanced when they are linked to ribose to form a nucleoside or - with the addition of phosphate - a nucleotide. This enhanced binding could have played a role in the molecular evolution leading to the production of RNA.

Macrophage-driven nutrient delivery to phagosomal Staphylococcus aureus supports bacterial growth

Staphylococcus aureus is a notorious pathogen causing significant morbidity and mortality worldwide. The ability of S. aureus to survive and replicate within phagocytes such as macrophages represents an important facet of immune evasion and contributes to pathogenesis. The mechanisms by which S. aureus acquires nutrients within host cells to support growth remain poorly characterized. Here, we demonstrate that macrophages infected with S. aureus maintain their dynamic ruffling behavior and consume macromolecules from the extracellular milieu. To support the notion that fluid-phase uptake by macrophages can provide S. aureus with nutrients, we utilized the pharmacological inhibitors PIK-III and Dynasore to impair uptake of extracellular macromolecules. Inhibitor treatment also impaired S. aureus replication within macrophages. Finally, using a mutant of S. aureus that is defective in purine biosynthesis we show that intracellular growth is inhibited unless the macrophage culture medium is supplemented with the metabolite inosine monophosphate. This growth rescue can be impaired by inhibition of fluid-phase uptake. In summary, through consumption of the extracellular environment macrophages deliver nutrients to phagolysosomal S. aureus to promote bacterial growth.

Purines: From Diagnostic Biomarkers to Therapeutic Agents in Brain Injury

The purines constitute a family of inter-related compounds that serve a broad range of important intracellular and extracellular biological functions. In particular, adenosine triphosphate (ATP) and its metabolite and precursor, adenosine, regulate a wide variety of cellular and systems-level physiological processes extending from ATP acting as the cellular energy currency, to the adenosine arising from the depletion of cellular ATP and responding to reduce energy demand and hence to preserve ATP during times of metabolic stress. This inter-relationship provides opportunities for both the diagnosis of energy depletion during conditions such as stroke, and the replenishment of ATP after such events. In this review we address these opportunities and the broad potential of purines as diagnostics and restorative agents.

Hydrothermal Chemistry and the Origin of Cellular Life

Two processes required for life's origin are condensation reactions that produce essential biopolymers by a nonenzymatic reaction, and self-assembly of membranous compartments that encapsulate the polymers into populations of protocells. Because life today thrives not just in the temperate ocean and lakes but also in extreme conditions of temperature, salinity, and pH, there is a general assumption that any form of liquid water would be sufficient to support the origin of life as long as there are sources of chemical energy and simple organic compounds. We argue here that the first forms of life would be physically and chemically fragile and would be strongly affected by ionic solutes and pH. A hypothesis emerges from this statement that hot springs associated with volcanic land masses have an ionic composition more conducive to self-assembly and polymerization than seawater. Here we have compared the ionic solutes of seawater with those of terrestrial hot springs. We then describe preliminary experimental results that show how the hypothesis can be tested in a prebiotic analog environment.

Weak Acid Permeation in Synthetic Lipid Vesicles and Across the Yeast Plasma Membrane

We present a fluorescence-based approach for determination of the permeability of small molecules across the membranes of lipid vesicles and living cells. With properly designed experiments, the method allows us to assess the membrane physical properties both in vitro and in vivo. We find that the permeability of weak acids increases in the order of benzoic > acetic > formic > lactic, both in synthetic lipid vesicles and the plasma membrane of Saccharomyces cerevisiae, but the permeability is much lower in yeast (one to two orders of magnitude). We observe a relation between the molecule permeability and the saturation of the lipid acyl chain (i.e., lipid packing) in the synthetic lipid vesicles. By analyzing wild-type yeast and a manifold knockout strain lacking all putative lactic acid transporters, we conclude that the yeast plasma membrane is impermeable to lactic acid on timescales up to ∼2.5 h.

The Purine Salvage Pathway and the Restoration of Cerebral ATP: Implications for Brain Slice Physiology and Brain Injury

Brain slices have been the workhorse for many neuroscience labs since the pioneering work of Henry McIlwain in the 1950s. Their utility is undisputed and their acceptance as appropriate models for the central nervous system is widespread, if not universal. However, the skeleton in the closet is that ATP levels in brain slices are lower than those found in vivo, which may have important implications for cellular physiology and plasticity. Far from this being a disadvantage, the ATP-impoverished slice can serve as a useful and experimentally-tractable surrogate for the injured brain, which experiences similar depletion of cellular ATP. We have shown that the restoration of cellular ATP in brain slices to in vivo values is possible with a simple combination of D-ribose and adenine (RibAde), two substrates for ATP synthesis. Restoration of ATP in slices to physiological levels has implications for synaptic transmission and plasticity, whilst in the injured brain in vivo RibAde shows encouraging positive results. Given that ribose, adenine, and a third compound, allopurinol, are all separately in use in man, their combined application after acute brain injury, in accelerating ATP synthesis and increasing the reservoir of the neuroprotective metabolite, adenosine, may help reduce the morbidity associated with stroke and traumatic brain injury.

A hypothesis about the origin of biology

It is proposed that processes characteristic of biology today, autocatalysis, selection of molecules for linkage by their electrical shape, and evolution by survival selection were also the processes that initiated biology. A reconnaissance is made of both paradoxes and potential questions. It is argued that the minimal requirement for initiating Darwinian evolution is not a molecule copying process, but a linkage copying process. Survival selection evolution does not require a heterocatalytic polymer and a separate replicase process until there is uncertainty where molecular additions will occur. It is argued that a linkage directing process will be found for a lipid membrane (though this needs to be verified) and may in the right environment result in initial evolution, including initiation of α-helices, the development of a single chirality and NTPs. The system has at this point become sufficiently complex that higher precision copying is needed. However it seems likely that this state is able to generate the first miniature ribozymes and their replicases, and so satisfies the prior requirement. With the proposed requirements, it is likely that the development of polymers was within membranes.

Towards co-evolution of membrane proteins and metabolism

Primordial metabolism co-evolved with the earliest membrane peptides to produce more environmentally fit progeny. Here, we map a continuous, evolutionary path that connects nascent biochemistry with simple, membrane-bound oligopeptides, ion channels and, further, membrane proteins capable of energy transduction and utilization of energy for active transport.

Nucleobases bind to and stabilize aggregates of a prebiotic amphiphile, providing a viable mechanism for the emergence of protocells

Primordial cells presumably combined RNAs, which functioned as catalysts and carriers of genetic information, with an encapsulating membrane of aggregated amphiphilic molecules. Major questions regarding this hypothesis include how the four bases and the sugar in RNA were selected from a mixture of prebiotic compounds and colocalized with such membranes, and how the membranes were stabilized against flocculation in salt water. To address these questions, we explored the possibility that aggregates of decanoic acid, a prebiotic amphiphile, interact with the bases and sugar found in RNA. We found that these bases, as well as some but not all related bases, bind to decanoic acid aggregates. Moreover, both the bases and ribose inhibit flocculation of decanoic acid by salt. The extent of inhibition by the bases correlates with the extent of their binding, and ribose inhibits to a greater extent than three similar sugars. Finally, the stabilizing effects of a base and ribose are additive. Thus, aggregates of a prebiotic amphiphile bind certain heterocyclic bases and sugars, including those found in RNA, and this binding stabilizes the aggregates against salt. These mutually reinforcing mechanisms might have driven the emergence of protocells.