Construction of protocellular structures under simulated primitive earth conditions

New Signatures of Bio-Molecular Complexity in the Hypervelocity Impact Ejecta of Icy Moon Analogues

Impact delivery of prebiotic compounds to the early Earth from an impacting comet is considered to be one of the possible ways by which prebiotic molecules arrived on the Earth. Given the ubiquity of impact features observed on all planetary bodies, bolide impacts may be a common source of organics on other planetary bodies both in our own and other solar systems. Biomolecules such as amino acids have been detected on comets and are known to be synthesized due to impact-induced shock processing. Here we report the results of a set of hypervelocity impact experiments where we shocked icy mixtures of amino acids mimicking the icy surface of planetary bodies with high-speed projectiles using a two-stage light gas gun and analyzed the ejecta material after impact. Electron microscopic observations of the ejecta have shown the presence of macroscale structures with long polypeptide chains revealed from LCMS analysis. These results suggest a pathway in which impact on cometary ices containing building blocks of life can lead to the synthesis of material architectures that could have played a role in the emergence of life on the Earth and which may be applied to other planetary bodies as well.

Scum of the Earth: A Hypothesis for Prebiotic Multi-Compartmentalised Environments

Compartmentalisation by bioenergetic membranes is a universal feature of life. The eventual compartmentalisation of prebiotic systems is therefore often argued to comprise a key step during the origin of life. Compartments may have been active participants in prebiotic chemistry, concentrating and spatially organising key reactants. However, most prebiotically plausible compartments are leaky or unstable, limiting their utility. Here, we develop a new hypothesis for an origin of life environment that capitalises upon, and mitigates the limitations of, prebiotic compartments: multi-compartmentalised layers in the near surface environment—a ’scum’. Scum-type environments benefit from many of the same ensemble-based advantages as microbial biofilms. In particular, scum layers mediate diffusion with the wider environments, favouring preservation and sharing of early informational molecules, along with the selective concentration of compatible prebiotic compounds. Biofilms are among the earliest traces imprinted by life in the rock record: we contend that prebiotic equivalents of these environments deserve future experimental investigation.

Spontaneous emergence of membrane-forming protoamphiphiles from a lipid-amino acid mixture under wet-dry cycles

Dynamic interplay between peptide synthesis and membrane assembly would have been crucial for the emergence of protocells on the prebiotic Earth. However, the effect of membrane-forming amphiphiles on peptide synthesis, under prebiotically plausible conditions, remains relatively unexplored. Here we discern the effect of a phospholipid on peptide synthesis using a non-activated amino acid, under wet-dry cycles. We report two competing processes simultaneously forming peptides and N-acyl amino acids (NAAs) in a single-pot reaction from a common set of reactants. NAA synthesis occurs via an ester-amide exchange, which is the first demonstration of this phenomenon in a lipid-amino acid system. Furthermore, NAAs self-assemble into vesicles at acidic pH, signifying their ability to form protocellular membranes under acidic geothermal conditions. Our work highlights the importance of exploring the co-evolutionary interactions between membrane assembly and peptide synthesis, having implications for the emergence of hitherto uncharacterized compounds of unknown prebiotic relevance.

Prebiotic Peptides: Molecular Hubs in the Origin of Life

The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.

Fatty acids' double role in the prebiotic formation of a hydrophobic dipeptide

In search of a connection between prebiotic peptide chemistry and lipid compartments, the reaction of a 5(4H)-oxazolone with leucinamide was extensively explored under buffered aqueous conditions, where diverse amphiphiles and surfactants could form supramolecular assemblies. Significant increases in yield and changes in stereoselectivity were observed when fatty acids exceeded their critical aggregation concentration, self-assembling into vesicles in particular. This effect does not take place below the fatty acid solubility limit, or when other anionic amphiphiles/surfactants are used. Data from fluorimetric and Langmuir trough assays, complementary to the main HPLC results reported here, demonstrate that the dipeptide product co-localizes with fatty acid bilayers and monolayers. Additional experiments in organic solvents suggest that acid-base catalysis operates at the water-aggregate interface, linked to the continuous proton exchange dynamics that fatty acids undergo at pH values around their effective pK_a. These simple amphiphiles could therefore play a dual role as enhancers of peptide chemistry under prebiotic conditions, providing soft and hydrophobic organic domains through self-assembly and actively inducing catalysis at their interface with the aqueous environment. Our results support a systems chemistry approach to life's origin.

Lipid-like self-assembling peptides

One important question in prebiotic chemistry is the search for simple structures that might have enclosed biological molecules in a cell-like space. Phospholipids, the components of biological membranes, are highly complex. Instead, we looked for molecules that might have been available on prebiotic Earth. Simple peptides with hydrophobic tails and hydrophilic heads that are made up of merely a combination of these robust, abiotically synthesized amino acids and could self-assemble into nanotubes or nanovesicles fulfilled our initial requirements. These molecules could provide a primitive enclosure for the earliest enzymes based on either RNA or peptides and other molecular structures with a variety of functions. We discovered and designed a class of these simple lipid-like peptides, which we describe in this Account. These peptides consist of natural amino acids (glycine, alanine, valine, isoleucine, leucine, aspartic acid, glutamic acid, lysine, and arginine) and exhibit lipid-like dynamic behaviors. These structures further undergo spontaneous assembly to form ordered arrangements including micelles, nanovesicles, and nanotubes with visible openings. Because of their simplicity and stability in water, such assemblies could provide examples of prebiotic molecular evolution that may predate the RNA world. These short and simple peptides have the potential to self-organize to form simple enclosures that stabilize other fragile molecules, to bring low concentration molecules into a local environment, and to enhance higher local concentration. As a result, these structures plausibly could not only accelerate the dehydration process for new chemical bond formation but also facilitate further self-organization and prebiotic evolution in a dynamic manner. We also expect that this class of lipid-like peptides will likely find a wide range of uses in the real world. Because of their favorable interactions with lipids, these lipid-like peptides have been used to solubilize and stabilize membrane proteins, both for scientific studies and for the fabrication of nanobiotechological devices. They can also increase the solubility of other water-insoluble molecules and increase long-term stability of some water-soluble proteins. Likewise, because of their lipophilicity, these structures can deliver molecular cargo, such as small molecules, siRNA, and DNA, in vivo for potential therapeutic applications.

Early self-reproduction, the emergence of division mechanisms in protocells

Synthetic Biology approaches are proposing model systems and providing experimental evidences that life can arise as spontaneous chemical self-assembly process where the ability to reproduce itself is an essential feature of the living system. The appearance of early cells has required an amphiphilic membrane compartment to confine molecular information against diffusion, and the ability to self-replicate the boundary layer and the genetic information. The initial spontaneous self-replication mechanisms based on thermodynamic instability would have evolved in a prebiotic and later biological catalysis. Early studies demonstrate that fatty acids spontaneously assemble into bilayer membranes, building vesicles able to grow by incorporation of free lipid molecules and divide. Early replication mechanisms may have seen inorganic molecules playing a role as the first catalysts. The emergence of a short ribozyme or short catalytic peptide may have initiated the first prebiotic membrane lipid synthesis required for vesicle growth. The evolution of early catalysts towards the simplest translation machine to deliver proteins from RNA sequences was likely to give early birth to one single enzyme controlling protocell membrane division. The cell replication process assisted by complex enzymes for lipid synthesis is the result of evolved pathways in early cells. Evolution from organic molecules to protocells and early cells, thus from chemistry to biology, may have occurred in and out of the boundary layer. Here we review recent experimental work describing membrane and vesicle division mechanisms based on chemico-physical spontaneous processes, inorganic early catalysis and enzyme based mechanisms controlling early protocell division and finally the feedback from minimal genome studies.

Collagen-based fibrillar multilayer films cross-linked by a natural agent

Surface functionalization plays an important role in the design of biomedical implants, especially when layer forming cells, such as endothelial or epithelial cells, are needed. In this study, we define a novel nanoscale surface coating composed of collagen/alginate polyelectrolyte multilayers and cross-linked for stability with genipin. This buildup follows an exponential growth regime versus the number of deposition cycles with a distinct nanofibrillar structure that is not damaged by the cross-linking step. Stability and cell compatibility of the cross-linked coatings were studied with human umbilical vein endothelial cells. The surface coating can be covered by a monolayer of vascular endothelial cells within 5 days. Genipin cross-linking renders the surface more suitable for cell attachment and proliferation compared to glutaraldehyde (more conventional cross-linker) cross-linked surfaces, where cell clumps in dispersed areas were observed. In summary, it is possible with the defined system to build fibrillar structures with a nanoscale control of film thickness, which would be useful for in vivo applications such as inner lining of lumens for vascular and tracheal implants.

Steps towards the formation of a protocell: the possible role of short peptides

The paper deals with molecular self-organization leading to formation of a protocell. Plausible steps towards a protocell include: polymerization of peptides and oligonucleotides on mineral surfaces; coevolution of peptides and oligonucleotides with formation of collectively autocatalytic sets; self-organization of short peptides into vesicles; entrapment of the peptide/oligonucleotide systems in mixed peptide and simple amphiphile membranes; and formation of functioning protocells with metabolism and cell division. The established propensity of short peptides to self-ordering and to formation of vesicles makes this sequence plausible. We further suggest that evolution of a protocell produced cellular ancestors of viruses as well as ancestors of cellular organisms.

From interstellar amino acids to prebiotic catalytic peptides: a review

Amino acids were most likely available on the primitive Earth, produced in the primitive atmosphere or in hydrothermal vents. Import of extraterrestrial amino acids may have represented the major supply, as suggested by micrometeorite collections and simulation experiments in space and in the laboratory. Selective condensation of amino acids in water has been achieved via N-carboxy anydrides. Homochiral peptides with an alternating sequence of hydrophobic and hydrophilic amino acids adopt stereoselective and thermostable beta-pleated sheet structures. Some of the homochiral beta-sheets strongly accelerate the hydrolysis of oligoribonucleotides. The beta-sheet-forming peptides have also been shown to protect their amino acids from racemization. Even if peptides are not able to self-replicate, i.e., to replicate a complete sequence from the mixture of amino acids, the accumulation of chemically active peptides on the primitive Earth appears plausible via thermostable and stereoselective beta-sheets made of alternating sequences.

Computational studies on conditions of the emergence of autopoietic protocells

It has been pointed out that the acquisition of self-maintaining protocells was one of the most important evolutionary steps in the earliest stage of life. However, there remains little evidence to show what the components of the protocells were and how they were acquired. A theoretical study to investigate the possible process of the emergence of protocells is therefore required. In this paper, we present a computational model that demonstrates the emergence and evolution of self-maintaining and self-reproducing structures to analyze conditions under which precellular autocatalytic molecules could evolve into self-reproducing protocells. We focused on the supply rates of molecular resources as environmental parameters and explored the pathways of evolution from molecular replication to cellular reproduction under various conditions. The results showed that the spontaneous organization of protocells from a random initial state takes place in a parameter region where the metabolism becomes difficult because of an insufficient supply of resources, but once cell structures are organized, they can survive in a wider range of environments. We investigated the evolution in temporally or spatially changing environments and found that the protocells can take over the precellular metabolic system after the transition. These results suggest a possible scenario for the evolution from precellular to cellular reproduction.

An overlooked riddle of life's origins: energy-dependent nucleic acid unzipping

The imposing progress in understanding contemporary life forms on Earth and in manipulating them has not been matched by a comparable progress in understanding the origins of life. This paper argues that a crucial problem of unzipping of the double helix molecule of nucleic acid during its replication has been underrated, if not plainly overlooked, in the theories of life's origin and evolution. A model is presented of how evolution may have solved the problem in its early phase. Similar to several previous models, the model envisages the existence of a protocell, in which osmotic disbalance is being created by accumulation of synthetic products resulting in expansion and division of the protocell. Novel in the model is the presence in the protocell of a double-stranded nucleic acid, with each of its two strands being affixed by its 3'-terminus to the opposite sides of the membrane of a protocell. In the course of the protocell expansion, osmotic force is utilized to pull the two strands longitudinally in opposite directions, unzipping the helix and partitioning the strands between the two daughter protocells. The model is also being used as a background for arguments of why life need operate in cycles. Many formal models of life's origin and evolution have not taken into account the fact that logical possibility does not equal thermodynamic feasibility. A system of self-replication has to consist of both replicators and replicants.

Self-maintenance and self-reproduction in an abstract cell model

Living cells must maintain their membranes by active metabolism. The membrane is not static but a dynamic structure that has evolved along with its internal reactions. When we reflect on the emergence and evolution of primitive cells, we should not forget the mutual dependency between membranes and metabolic cycles inside the cell. In this paper, we present a simple abstract model of the self-maintaining cell. A metabolic cycle will produce a self-assembling membrane that will enclose the metabolic cycle. We show that a self-maintaining cell has the potential to reproduce itself spontaneously. Further, we have demonstrated two different ways of cellular reproduction depending on the mobility of chemicals. In the first case, a cell releases autocatalytic chemicals that create new cells outside the mother cell. In the second case, a cell grows larger and divides itself into daughter cells by creating a new internal dividing membrane.

Origins of globular structure in proteins

Since natural proteins are the products of a long evolutionary process, the structural properties of present-day proteins should depend not only on physico-chemical constraints, but also on evolutionary constraints. Here we propose a model for protein evolution, in which membranes play a key role as a scaffold for supporting the gradual evolution from flexible polypeptides to well-folded proteins. We suggest that the folding process of present-day globular proteins is a relic of this putative evolutionary process. To test the hypothesis that membranes once acted as a cradle for the folding of globular proteins, extensive research on membrane proteins and the interactions of globular proteins with membranes will be required.

Contribution of temperature gradient to aggregation of thermal heterocopolymers of amino acids in aqueous milieu

We prepared thermal heterocopolymers of amino acids, aspartic acid and proline, and solubilized them in distilled water at boiling temperature. The resulting suspension was then cooled down while controlling the cooling rate. The maximum growth of phase-separated microspheres was found to occur at a finite, nonzero cooling rate. Temperature-gradient controlled growth of these microspheres indicates that aggregation of thermal heterocopolymers of amino acids in their aqueous milieu is irreversible. In view of the fact that evolutionary process is an indication of lasting physical irreversibility, thermal heterocopolymers of amino acids were shown to have an evolutionary significance in maintaining the capacity of irreversibility lasting over at least several hours.