Noriyoshi
Arai
*a,
Yuki
Yoshimoto
a,
Kenji
Yasuoka
b and
Toshikazu
Ebisuzaki
c
aDepartment of Mechanical Engineering, Kindai University, Higashiosaka, Osaka, Japan. E-mail: arai@mech.kindai.ac.jp; Fax: +81 6 6727 2024; Tel: +81 6 4307 3483
bDepartment of Mechanical Engineering, Keio University, Yokohama, Japan
cComputational Astrophysics Laboratory, RIKEN, Wako, Saitama, Japan
First published on 29th June 2016
Researchers have studied the origin of life and the process of evolution on early Earth for decades. However, we lack a comprehensive understanding of biogenesis, because there are many stages in the formation and growth of the first cell. We investigate the self-replication processes of coacervate protocells using computer simulations of single-chain lipid and phospholipid aqueous mixtures. Based on a morphological phase diagram, we develop a model of prebiotic self-replication driven by only environmental factors (i.e. temperature and lipid concentrations) without any external force. Moreover, we investigate high concentration structures during the process of self-replication. These structures have an advantage in fusion and repair of cell membranes. Therefore, lipid hot spots may have existed in primordial soup.
Sutherland's group discovered that pyrimidine nucleotides can be readily synthesized from ribose, a simple prebiotic molecule, bypassing the more difficult routes.2 This discovery offers persuasive support for the RNA world hypothesis.3 It was a significant step to explain how a complex molecule like a ribonucleic acid (RNA) was formed on the primitive Earth. Alternative models of prebiotic evolution include the peptide nucleic acid (PNA) world hypothesis,4 protein world hypothesis,5 and panspermia hypothesis.6,7
We focus on the self-replication processes of primitive coacervate cells in the primordial soup. All cells are wrapped in membranes that consist mainly of lipids. Cell membranes collect cellular constituents together and prevent the free penetration of large molecules. Modern cell membranes are composed of lipids, cholesterols, and functional proteins. Some proteins are capable of selective water transport,8–10 and have a function of constructing and repairing membranes.11,12 On the other hand, the primitive protocell can accomplish these tasks without proteins. Moreover, it has metabolic and self-replicative functionality. The earliest life may have been simple fatty acid membranes self-replicating in water. Protocells would compete against each other by proliferating, and then adapt to their surroundings. Growth and division are two processes necessary for protocell proliferation.
The study of the fatty acid may lead to the elucidation of the origin of terrestrial life. In the 1990s, Luisi et al.13 added fatty acids to a vesicular solution. These workers observed that when a fatty acid is introduced to the vesicle membrane, the surface area and volume increase. Chen et al.14,15 carried out an experiment on the control of the concentration in a vesicular solution. When a concentration gradient arises across the interior and exterior of a vesicle, water molecules intrude into the vesicle by an osmotic pressure to equalize the concentration between the interior and exterior, and then, tension of the membrane increases. To decrease its membrane tension, the high-tension vesicle grows by competing with nearby vesicles for additional fatty acids.
The nearby vesicles losing their fatty acids shrink and disappear. Zhu et al.16,17 found that spherical vesicles form filament-like shapes with their growth. The filament-like vesicle is fragile; by weak external force, it disaggregates into smaller vesicles, which are spherical protocells. Szostak et al. argued that these processes facilitated many rounds of self-replication.
Self-assembled structures such as micelles, vesicles and bi-layer membranes have already been reported.18–21 Recent studies use functional molecules or heterogeneous lipid mixtures to control self-assembled structures. Morrow et al.19 used a molecular dynamics method to simulate pH-sensitive surfactant solutions. These authors demonstrated pH-dependent morphologies including the formation of a gel-state bilayer at low and intermediate pH, and a spherical micelle at high pH. Chen and Hao20 performed molecular simulations to determine a phase diagram of self-assembly in cationic–anionic surfactant mixtures. This simulation result indicated that the aggregation number, shape, and composition respond to changes in the surfactant ratio. Hu21 used dissipative particle dynamics simulations to investigate the self-assembly in lipid and dendritic molecule mixtures at varying hydrophilic/hydrophobic ratios. Structures characteristic of different mixing ratios include the high-genus vesicle, toroidal vesicle, oblate vesicle, and perforated vesicle. However, the self-assembly behaviour of the fatty acid itself has not been investigated fully.22–24
We investigate the potential for oleic acid and dipalmitoylphosphatidylcholine to have been primitive biomolecules. We present a detailed phase diagram at different vol% of molecules and temperature, using coarse-grained molecular simulations. Based on the result, we discuss the morphological features of a mechanism of self-replication proposed by Szostak et al.14–17
The motions of DPD particles obey Newton's equations of motion,
![]() | (1) |
![]() | (2) |
![]() | (3) |
![]() | (4) |
The dissipative force and the random force are linked by the fluctuation–dissipation theorem,27 thereby one of the two weight functions appearing in eqn (3) and (4) can be chosen arbitrarily with a relation between the amplitude and kBT,
σ2 = 2γkBT, | (5) |
![]() | (6) |
H1 | H2 | H3 | T1 | T2 | W | |
---|---|---|---|---|---|---|
H1 | 147.71 | 148.58 | 147.73 | 195.84 | 187.21 | 155.24 |
H2 | 148.58 | 147.71 | 148.89 | 209.66 | 199.82 | 150.98 |
H3 | 147.73 | 148.89 | 147.71 | 193.75 | 185.32 | 156.09 |
T1 | 195.84 | 209.66 | 193.75 | 147.71 | 148.13 | 241.43 |
T2 | 187.21 | 199.82 | 185.32 | 148.13 | 147.71 | 229.22 |
W | 155.24 | 150.98 | 156.09 | 241.43 | 229.22 | 147.71 |
We can convert the reduced length unit to SI units by examining the membrane thickness. Usually, the thickness of a DPPC bilayer is about 4.7 nm in vitro.38 Considering that the thickness is about 4.4rc in our simulations, we can yield rc ∼ 1.06 nm.
Two series of computer simulations are carried out in this study. The first series simulates OA solutions and the second series simulates DPPC solutions. To illustrate the phase diagram, we select the concentration c and temperature T as axes. Each initial configuration is random, and the equilibrated systems are simulated in constant-volume and constant-temperature ensembles. A periodic boundary condition is adopted for all directions of the simulation cells. We used cell length (L) values of 15.9, 21.2, 26.5, 31.8, and 42.4 nm. For each L and molecular model, we performed 80 simulations, i.e. four different temperatures ranging from 0.5 to 2.0 kBT and 20 different concentrations ranging from 2.5 to 100%.
To give an estimate of the values of the reduced temperatures T* in terms of physical temperatures T, we have mapped T* onto T according to the linear relation,39i.e. T = aT* + b. The values of the coefficients a and b were obtained using the reduced and physical values of the melting point, and the OA vesicle disruption temperatures.40 The resulting values are a = 21.7 °C and b = 4.3 °C. For the DPPC lipid, we found that a and b are 8.6 °C and 32.6 °C, respectively.
As expected, some micelles are formed at very low concentration (c ≤ 20%). Randomly dispersed OA molecules aggregated into several isolated spherical micelles for a short time period. After that the spherical micelles collided with each other, and fused together if they overcame an energy barrier. Eventually, the micelles transitioned to other shapes, depending on the aggregation number. When T ≥ 25 °C, collisions and fusions of micelles occurred frequently. A spherical vesicle (Fig. 2b) is formed at c ∼ 10%. As T increased beyond 45 °C, a tube-like vesicle appeared. The tube-like vesicle was also observed as a filamentous vesicle in vitro.15 On the other hand, at lower T, the collision of micelles occurred rarely. Moreover, the curvature of the aggregated structure decreased at low temperature.41,42 Each micelle had low mean aggregation and low flexibility; accordingly, the vesicle could not form even at c ∼ 20%; however, a disk like micelle emerged (Fig. 2a). As c increased to ∼30%, a cell membrane is formed (Fig. 2c). The membrane stemmed from an opened vesicle, which became more stable than the closed vesicle as c increased.
With further increasing c, a threadlike micelle or a filamentous vesicle composed of excess OAs budded from the membrane, and a bi-layer with a column structure was observed (Fig. 2d). The bud grew up thicker and wider as c increased. A cross bi-layer, which is two bi-layers crossed perpendicularly, emerged at c ∼ 55% (Fig. 2f). However, when the temperature was high (T = 45 °C), the membrane fluctuated rapidly. The column did not develop, but a double bi-layer is formed (Fig. 2e). When c was higher than 60%, the bi-layers intricately intertwined, forming a complex network structure (Fig. 2f). As c increased further, several water domains emerged separately, and a sponge-like phase (Fig. 2h) emerged in the range of 70% < c < 90%. When water was almost exhausted from the system, a gyroid (Fig. 2i) or hexagonal phases emerged at low temperature; at high temperatures, the ordered structure was broken up, and a phase-separated morphology emerged (Fig. 2k).
To confirm the reproducibility of our observations, we carried out five independent simulations for some conditions. Our replicate simulations included conditions for forming a vesicle, bi-layer, and bi-layer with a column. Each simulation was begun with randomized initial parameters; the final morphologies were nearly the same, regardless of the initial parameters.
From low c through moderate c, micelles (Fig. 3a), vesicles (Fig. 3b), and bi-layers (Fig. 3c and d) formed as easily from DPPC as they formed from OA. The bi-layer of DPPC is slightly thicker than that of OA because of the size of the molecule. Whereas the vesicle emerged at T ≥ 25 °C in the OA solution, it emerged at T ≥ 35 °C in the DPPC solution. As c increased to 40%, a bi-layer with a column (Fig. 3d) formed. With further increasing c, water molecules were wrapped in the column, and then it grew thicker. As c continued to increase, the mixture exhibited a network morphology (Fig. 3e), followed by a sponge morphology (Fig. 3f). At c ∼ 85% and T ≤ 45 °C, the body centred cubic (BCC) structure (Fig. 3g) emerged. Eventually, at c ∼ 95%, a disordered and phase-separated morphology emerged at all temperatures (Fig. 3h).
The fluctuations of each lipid increase naturally if the temperature increases. The excess part, such as a tube-like vesicle, is divided from the membrane (Fig. 2d and 3d) when temperature of the aqueous solution increases. After that, the divided parts aggregate to form a spherical vesicle (vesiculation); the exposed hydrophobic groups are surrounded by water, and consequently become a new protocell (Fig. 4).
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Fig. 4 A schematic depicting concentration-dependent transitions in protocell morphology. Red and blue arrows represent increasing and decreasing concentration, respectively. Points are early experimental conditions as follows. Square: The data reported by Zhu et al.,17 circle: the data reported by Budin et al.,51 triangle: the data reported by Zhu et al.16 (CMC: critical micelle concentration and CMC for oleic acid = 0.03%53). |
First, fatty acids (or lipids) collected in a puddle on the early Earth. They gathered mutually by a chemical interaction, and as a result, many micelles and vesicles formed (as modelled by the coacervate theory). During the dry season, the concentration of the lipid would increase due to evaporation from the puddle. Accordingly, micelles and vesicles would merge into giant vesicles, which do not have local curvatures, and can be regarded as a flat membrane locally (Fig. 2c). With further increasing concentration, tube-like vesicles would bud from the membranes. After that, as the temperature increased (due to seasonality or a local heat source), bud fission would occur. Then during the rainy season, concentration and temperature would decrease, and the fission products would have become new protocells. This sequence would be repeated over a long period of time.
It is known that morphological phase boundaries depend on the size of the lipid–water system. For example, the simulational concentration (c) of about 30% yields a periodic bilayer when the system size is 15.93 nm3. However, this bilayer forms at c ∼ 18% when the system size is 42.43 nm3. In other words, the concentration at which a particular morphology is observed decreases exponentially with the increasing system size. We used five simulation box sizes to investigate the effect of size on morphology, and estimated a scaling factor for the concentration in our simulations (see the ESI†). The concentration at which the bilayer membrane is formed decreases exponentially with the increasing length of a side of the cubic simulation box. The data are fitted to the function of f(x) = AxB, where A and B are constant. Next, we estimated the scaled physical concentration (cs) on the early Earth by fitting with an actual size by those curves. As a result, in our simulation, the vesicle appears in the cs range of about 0.1–0.8%, consistent with in vitro observations of, 0.28–0.85%.15,17 Actually, the early processes of cell division and growth are thought to be functions of the giant sizes (1 μm order) at which many vesicles probably existed.46,47 If the system sizes were set to 103 μm3, we calculate that the lipid concentrations necessary for bilayer and budding bilayer formation would be 0.55% and 1.05%, respectively. In light of the estimated error arising from our use of a power function fit to five values, the lipid concentration necessary to form a bilayer ranges from 0.48% to 0.62%. Therefore, coacervates proliferate if concentrations change by more than 1% (e.g., due to seasons).
Next, we consider the physical meaning of the fitted curve's constant in Fig. S1 (ESI†). The concentration (CBL) at which the bilayer is formed is attenuated with the box length L (slope factor −0.58). However, the slope factor of CBL for L is generally −1.0. The explanation is as follows. The concentration CBL, density ρ, and area density of the membrane ρa are given by Nl/N, N/L3, and Nl/L2, respectively. Here, Nl is the number of lipid molecules. The concentration can be expressed as
![]() | (7) |
![]() | (8) |
As shown in Fig. 4, due to slight changes in concentration, various self-assembly structures or phases arise. For that reason, when the concentration of OA is more than 1.05% in the dry-season (concentration-increasing processes), the tubes budding from the bi-layers grow, leading to the cross bi-layer (Fig. 2f) and network (Fig. 2g) morphologies. These structures have many small chambers (water domains separated by a bi-layer). We can regard each small chamber as a small vesicle separated by cell membranes. This transition corresponds to the processes of vesicle fusion. In this state, since the volume of a cell membrane is relatively low, the rate of chemical interaction for a nucleotide and its precursors phosphoric acid, sugar, and amino acid would be enhanced. It is expected that were these materials to have different concentrations between neighbouring chambers, osmolality gaps would facilitate the exchange of chemicals across membranes. Also, these chambers constantly fuse and divide due to thermal fluctuation. In other words, it is expected that self-replication is achieved without external stimuli, for example, shear or electric forces.17,48 Moreover, in this study, to investigate basic processes of cell division, we employed the primitive biomolecule, OA, and simulated simple OA solutions. However, in modern cell membranes, not only a primary lipid, but also steroids, cholesterols, and proteins coexist.49 They have complex structures and functions, and diffuse throughout the modern cell membrane. Therefore, in high-concentration phases (network and sponge), when membrane is damaged, lipids or proteins are easily exchanged for membrane from a neighbouring chamber by translational and flip-flop motions.
To represent the origin of life, several experiments using an oleic acid vesicle have been carried out in recent years.16,17,50,51 The Szostak group proposes that vesicle replication is mediated through cycles of growth and division of vesicles. Zhu et al.16 prepared unilamellar fatty acid vesicles using the dehydration/rehydration method, and applied various shear rates to the solution. As a result, many spherical (daughter) vesicles were formed from long filamentous vesicles with modest shear forces. These authors mention that vesicle pearling and division have important implications for understanding the origin of cellular life.
Budin et al.51 investigated the concentration dependence of fatty acid aggregation. They observed different phases in the fatty acid solutions, including soluble monomers, micelles, and lamellar vesicles, depending on concentration and pH. The micelle–vesicle equilibrium is changed by the concentration: lower concentrations favour smaller micellar aggregates, and higher concentrations favour larger vesicle aggregates. They reported that the micelle–vesicle equilibrium can be used to drive the growth of vesicles upon increasing the amphiphile concentration. Based on this experimental result, they proposed a model for a driven cell cycle.
Zhu et al.17 described an alternative process for protocell division based on simple chemical mechanisms. In their model, protocell division is facilitated by thiol-rich surface environments featuring UV-absorbing polycyclic aromatic hydrocarbons. They suggested that the control of the timing of cell division by the thiol redox state is a mechanism by which an initial dependence on environmental fluctuations could have transitioned to an internally controlled process. The temperature and monomer concentration conditions reported for these in vitro experiments (plotted in Fig. 4) are consistent with the phase boundaries that we observe in silico. This result strongly supports our discussion.
At low OA or DPPC concentrations, a similar vesicle, bi-layer, and bi-layer with column morphologies arise depending on the concentration. However, these self-assembled structures are observed at DPPC concentrations slightly higher than their OA counterparts, because the molecular structure of DPPC is more complex than that of OA. Also, since the 41.3 °C melting temperature of DPPC52 is relatively high, the temperature at which DPPC vesicles form is slightly higher than that for OA vesicles. Therefore, for a modern lipid, prebiotic proliferation proceeds via changing the concentration and temperature, similar to the primitive molecule but at slightly elevated concentrations and temperatures. This observation suggests that the process we report is common to biomolecules, though morphological phase boundary concentrations and temperatures depend on the molecular participants.
High-concentration structures correspond to states when vesicles are quite close, or in the middle of fusion. These structures have an advantage in the fusion and repair of cell membranes. Hence, during the process of self-replication, locally high concentrations of lipid hot spots may have existed in the primordial soup.
Footnote |
† Electronic supplementary information (ESI) available. See DOI: 10.1039/c6cp02380k |
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