The Origin of Life: Chemical Evolution of a Metabolic System in a Mineral Honeycomb?

For the RNA-world hypothesis to be ecologically feasible, selection mechanisms acting on replicator communities need to be invoked and the corresponding scenarios of molecular evolution specified. Complementing our previous models of chemical evolution on mineral surfaces, in which selection was the consequence of the limited mobility of macromolecules attached to the surface, here we offer an alternative realization of prebiotic group-level selection: the physical encapsulation of local replicator communities into the pores of the mineral substrate. Based on cellular automaton simulations we argue that the effect of group selection in a mineral honeycomb could have been efficient enough to keep prebiotic ribozymes of different specificities and replication rates coexistent, and their metabolic cooperation protected from extensive molecular parasitism. We suggest that mutants of the mild parasites persistent in the metabolic system can acquire useful functions such as replicase activity or the production of membrane components, thus opening the way for the evolution of the first autonomous protocells on Earth.     

Mineral interface in extreme habitats: a niche for primitive molecular evolution for the appearance of different forms of life on earth

Innumerable primitive membrane and protocell models in latter stages of chemical evolution are based on the properties of minerals' interfaces with primitive seawater. The ordering mechanism induced by mineral interfaces has been the basis of several prebiotic models of molecular complexification and compartmentalization towards the appearance and evolution of different forms of life. Since mineral-aqueous media interfaces have been considered as initial stages of prebiotic models dealing with the formation of energy-transducing systems, the interface formed by pyrite in the presence of artificial primitive seawater was chosen to show the functional richness of this special niche. Interfaces--especially sulphide interfaces--were proposed as suitable niches for a two-carbon extant metabolism, synthesis and polymerization of nucleotides--to form ancient RNA strands--and assembly of amino acids synthesized in its vicinity. Accumulation of precursors at sulphide interfaces could have avoided their dilution into the Hadean seas and provided a suitable geochemical environment for a variety of molecular interactions. In this essay, we present a short review of the proposed roles of mineral interfaces in chemical evolution towards the appearance of primitive membranes, which might have been relevant for the advent of cellular life before its divergent evolution and differentiation. This survey covers several previous studies on the early cycles of energy conservation and of the formation of molecules carrying genetic information.     

Molecular basis for microbial adhesion to geochemical surfaces: computer simulation of Pseudomonas aeruginosa adhesion to goethite

The adhesion of Pseudomonas aeruginosa to the goethite mineral is investigated using classical molecular simulation. A fragment model for goethite has been integrated into a fully atomistic membrane model. Properties for the resulting system are evaluated for a 1.5-ns simulation in the isothermal-isobaric ensemble. The response of the membrane to the presence of the mineral is investigated. Radial distribution functions are used to present an average picture of the hydrogen bonding. Orientational vectors, assigned to the saccharide groups, reveal the extent of the mineral's perturbations on the membrane. Significant structural changes were observed for the outermost saccharide groups, several of which rotate to form hydrogen bonds with the mineral surface. The structure of the inner core, and the corresponding integrity of the membrane, is maintained. The mineral surface dehydrates slightly in the presence of the membrane as saccharide hydroxyl groups compete with water molecules for hydrogen-bonding sites on its surface.     

Computer simulation on the cooperation of functional molecules during the early stages of evolution

It is very likely that life began with some RNA (or RNA-like) molecules, self-replicating by base-pairing and exhibiting enzyme-like functions that favored the self-replication. Different functional molecules may have emerged by favoring their own self-replication at different aspects. Then, a direct route towards complexity/efficiency may have been through the coexistence/cooperation of these molecules. However, the likelihood of this route remains quite unclear, especially because the molecules would be competing for limited common resources. By computer simulation using a Monte-Carlo model (with "micro-resolution" at the level of nucleotides and membrane components), we show that the coexistence/cooperation of these molecules can occur naturally, both in a naked form and in a protocell form. The results of the computer simulation also lead to quite a few deductions concerning the environment and history in the scenario. First, a naked stage (with functional molecules catalyzing template-replication and metabolism) may have occurred early in evolution but required high concentration and limited dispersal of the system (e.g., on some mineral surface); the emergence of protocells enabled a "habitat-shift" into bulk water. Second, the protocell stage started with a substage of "pseudo-protocells", with functional molecules catalyzing template-replication and metabolism, but still missing the function involved in the synthesis of membrane components, the emergence of which would lead to a subsequent "true-protocell" substage. Third, the initial unstable membrane, composed of prebiotically available fatty acids, should have been superseded quite early by a more stable membrane (e.g., composed of phospholipids, like modern cells). Additionally, the membrane-takeover probably occurred at the transition of the two substages of the protocells. The scenario described in the present study should correspond to an episode in early evolution, after the emergence of single "genes", but before the appearance of a "chromosome" with linked genes.     

The Combination of Salt Induced Peptide Formation Reaction and Clay Catalysis: A Way to Higher Peptides under Primitive Earth Conditions

Two reactions with suggested prebiotic relevance for peptide evolution, the saltinduced peptide formation reaction and the peptide chain elongation/stabilization on clay minerals have been combined in experimental series starting from dipeptides and dipeptide/amino acid mixtures. The results show that both reactions can take place simultaneously in the same reaction environment and that the presence of mineral catalysts favours the formation of higher oligopeptides. These findings lend further support to the relevance of these reactions for peptide evolution on the primitive earth. The detailed effects of the specific clay mineral depend both on the nature of the mineral and the reactants in solution.     

沉积型海底微生物燃料电池构建及其影响因素研究

海底微生物燃料电池具有底物丰富、可长期运行、维护成本低和环境友好等特点,具有很好的研究价值和广阔的发展前景。但由于其低的功率密度输出和长期运行的不稳定性,使海底微生物燃料电池尚未得到广泛地实际应用。选取海底沉积泥用于实验室构建的海底微生物燃料电池装置中,比较了在不同阳极材料、阴阳极面积比、阳极修饰、阳极泥下深度条件下海底微生物燃料电池的功率密度输出及其电化学性能,得出最佳的海底微生物燃料电池阳极材料为碳毡;阴极及电极最佳面积比为1∶1;最佳阳极修饰为氨水浸渍;最佳阳极泥下深度为2 cm。     

The Influence of Environmental Conditions,Lipid Composition,and Phase Behavior on the Origin of Cell Membranes

At some point in life’s development, membranes formed, providing barriers between the environment and the interior of the ‘cell.’ This paper evaluates the research to date on the prebiotic origin of cell membranes and highlights possible areas of continuing study. A careful review of the literature uncovered unexpected factors that influence membrane evolution. The major stages in primitive membrane formation and the transition to contemporary cell membranes appear to require an exacting relationship between environmental conditions and amphiphile composition and phase behavior. Also, environmental and compositional requirements for individual stages are in some instances incompatible with one another, potentially stultifying the pathway to contemporary membranes. Previous studies in membrane evolution have noted the effects composition and environment have on membrane formation but the crucial dependence and interdependence on these two factors has not been emphasized. This review makes clear the need to focus future investigations away from proof-of-principle studies towards developing a better understanding of the roles that environmental factors and lipid composition and polymorphic phase behavior played in the origin and evolution of cell membranes.     

The role of mineral surfaces in the origin of life

Adsorption of nucleoside phosphates on the surfaces of volcanic rocks has been studied. Differences in the adsorption of some nucleoside phosphates on the surface of basalt cinder have been found. Differences in the adsorption of similarmolecules on different mineral surfaces have also been shown. Different adsorptive capacities may have served as a mechanism for the selection of organic molecules during prebiotic evolution.     

The role of mineral surfaces in the origin of life.

Adsorption of nucleoside phosphates on the surfaces of volcanic rocks has been studied. Differences in the absorption of some nucleoside phosphates on the surface of basalt cinder have been found. Differences in the adsorption of similar molecules on different mineral surfaces have also been shown. Different adsorptive capacities may have served as a mechanism for the selection of organic molecules during prebiotic evolution.     

Energy Transduction Inside of Amphiphilic Vesicles: Encapsulation of Photochemically Active Semiconducting Particles

Amphiphilic bilayer membrane structures (vesicles) have been postulated to have been abiotically formed and spontaneously assemble on the prebiotic Earth, providing compartmentalization for the origin of life. These vesicles are similar to modern cellular membranes and can serve to contain water-soluble species, concentrate species, and have the potential to catalyze reactions. The origin of the use of photochemical energy in metabolism (i.e. energy transduction) is one of the central issues in the origin of life. This includes such questions as how energy transduction may have occurred before complex enzymatic systems, such as required by contemporary photosynthesis, had developed and how simple a photochemical system is possible. It has been postulated that vesicle structures developed the ability to capture and transduce light, providing energy for reactions. It has also been shown that pH gradients across the membrane surface can be photochemically created, but coupling these to drive chemical reactions has been difficult. Colloidal semiconducting mineral particles are known to photochemically drive redox chemistry. We propose that encapsulation of these particles has the potential to provide a source of energy transduction inside vesicles, and thereby drive protocellular chemistry, and represents a model system for early photosynthesis. In our experiments we show that TiO₂ particles, in the ~20 nm size range, can be incorporated into vesicles and retain their photoactivity through the dehydration/rehydration cycles that have been shown to concentrate species inside a vesicle.     

Translocation of precytochrome C2 into intracytoplasmic membrane vesicles of Rhodobacter capsulatus requires a peripheral membrane protein

Rhodobacter capsulatus is a member of the group α-purple bacteria which are closely related to the ancestral endosymbiont that gave rise to mitochondria. It has therefore been hypothesized that the molecular mechanisms governing protein export in α-purple bacteria have been conserved during the evolution of mitochondria. To enable analysis of protein export in α-purple bacteria we describe here the development of a homologous cell-free synthesis/export system consisting entirely of components of R. capsulatus. Translocation of precytochrome C₂ into intracytoplasmic membrane vesicles of this organism was found to require the proton-motive force and proceed at a significantly higher efficiency when membranes were present during protein synthesis. Furthermore, we show that, in this cell-free system, translocation depends on a preparation of peripheral membrane proteins Which do not possess detectable SecA- and SecB-like actvities.     

光系统Ⅱ的结构与功能以及光合膜对环境因素的响应机制

光合膜是地球上捕获、转换和利用太阳能的关键场所,光合膜的活动所提供的能源、粮食及氧气,是人类世界赖以生存的基础。经过35亿年的进化,光合膜已经进化成了一个高度精密的结构,色素分子高密度结合并合理排列,具有高精度的能级耦联网络和高效率的能量传递系统,这使得光合膜成为自然界中能够最高效地吸收和传递太阳能、并能在常温常压下高效地将太阳能转换成化学能和还原势的色素蛋白复合体体系。由于这一特性,光合膜被认为是最有潜力的固定太阳能的新材料,并为研究新型光电转换器件提供了新思路和新理论。因此,长期以来,光合膜的结构-功能关系研究及其功能模拟,特别是执行固定和转化太阳能第一步的光系统Ⅱ,在新能源的利用中吸引了大量的研究力量,取得了突飞猛进的进展。本文总结了近年来关于光系统Ⅱ的结构与功能,以及光合膜对环境的感应和功能调节机制等方面的研究进展。     

Mineral bridges in nacre

We confirm with high-resolution techniques the existence of mineral bridges between superposed nacre tablets. In the towered nacre of both gastropods and the cephalopod Nautilus there are large bridges aligned along the tower axes, corresponding to gaps (150–200 nm) in the interlamellar membranes. Gaps are produced by the interaction of the nascent tablets with a surface membrane that covers the nacre compartment. In the terraced nacre of bivalves bridges associated with elongated gaps in the interlamellar membrane (>100 nm) have mainly been found at or close to the edges of superposed parental tablets. To explain this placement, we hypothesize that the interlamellar membrane breaks due to differences in osmotic pressure across it when the interlamellar space below becomes reduced at an advanced stage of calcification. In no cases are the minor connections between superimposed tablets (<60 nm), earlier reported to be mineral bridges, found to be such.     

Three-Dimensional Cell Geometry Controls Excitable Membrane Signaling in Dictyostelium Cells

Phosphatidylinositol (3–5)-trisphosphate (PtdInsP3) is known to propagate as waves on the plasma membrane and is related to the membrane-protrusive activities in Dictyostelium and mammalian cells. Although there have been a few attempts to study the three-dimensional (3D) dynamics of these processes, most studies have focused on the dynamics extracted from single focal planes. However, the relation between the dynamics and 3D cell shape remains elusive because of the lack of signaling information about the unobserved part of the membrane. Here, we show that PtdInsP3 wave dynamics are directly regulated by the 3D geometry (i.e., size and shape) of the plasma membrane. By introducing an analysis method that extracts the 3D spatiotemporal activities on the entire cell membrane, we show that PtdInsP3 waves self-regulate their dynamics within the confined membrane area. This leads to changes in speed, orientation, and pattern evolution, following the underlying excitability of the signal transduction system. Our findings emphasize the role of the plasma membrane topology in reaction-diffusion-driven biological systems and indicate its importance in other mammalian systems.     

Biochemistry, physiology and pathophysiology of the extracellular calcium-sensing receptor

Calcium (Ca(2+)) has long been recognized as a physiologically indispensable ion owing to its numerous intra- and extracellular roles. More recently, it has become apparent that extracellular calcium (Ca(2+)(o)) also serves as an extracellular first messenger following the cloning of a Ca(2+)(o)-sensing receptor (CaR) that belongs to the superfamily of G protein-coupled receptors (GPCR). The CaR probably functions as a dimer in performing its central role of "sensing" minute alterations in Ca(2+)(o) and adjusting the secretion of parathyroid hormone (PTH) so as to normalize Ca(2+)(o) through the actions of PTH on the effector elements of the mineral ion homeostatic system (e.g., kidney, bone and intestine). Several inherited human conditions are caused by inactivating or activating mutations of this receptor, and mice have been generated with targeted disruption of the CaR gene. Characteristic changes in the functions of parathyroid and kidney in patients with these conditions and in CaR-deficient mice have proven the physiological importance of the CaR in mineral ion homeostasis. An accumulating body of evidence, however, suggests that the CaR also plays numerous roles outside the realm of systemic mineral ion homeostasis. The receptor regulates processes such as cellular proliferation and differentiation, secretion, membrane polarization and apoptosis in a variety of tissues/cells. Finally, the availability of specific "calcimimetic", allosteric CaR activators - which are currently in clinical trials - will probably have therapeutic implications for diseases caused by malfunction of the CaR in tissues not only within, but also outside, the mineral ion homeostatic system.     

Role of matrix vesicles in biomineralization

Background

Matrix vesicles have been implicated in the mineralization of calcified cartilage, bone and dentin for more than 40 years. During this period, their exact role, if any in the nucleation of hydroxyapatite mineral, and its subsequent association with the collagen fibrils in the organic matrix has been debated and remains controversial.

Scope of Review

This review summarizes studies spanning the whole history of matrix vesicles, but emphasizes recent findings and several hypotheses which have been recently introduced to explain in greater detail how matrix vesicles function in biomineralization.

Major Conclusions

It is now generally accepted that matrix vesicles have some role(s) in mineralization; that they are the initial site of mineral formation; that MV bud from the plasma membrane of mineral forming cells, but that they take with them only a subset of the materials found in the parent membrane; that the three proteins, alkaline phosphatase, nucleotide pyrophosphatase phosphodiesterase and annexin V have important roles in the process and that matrix vesicles participate in regulating the concentration of PPi in the matrix. In contrast, many open questions remain to be answered.

General Significance

Understanding the role of matrix vesicles in biomineralization will increase our knowledge of this important process.     

Gypsum and halite associated with the cyanobacterium Entophysalis

A study has been made on stalactite‐like structures formed by the cyanobacterium (blue‐green alga) En‐tophysalis major, growing on the roof of an undercut cliff facing the lagoon of Aldabra Atoll. The cyanobacterial cells grow in a rubbery, brown, gelatinous mucilage that contains some crystals; this mucilage surrounds a central region filled partly with gas and partly with further crystals. Halite is the predominant mineral in the mucilage, and gypsum the only mineral in the inner region. There is no evidence for a direct causal relationship between cyanobacterial metabolism and mineral crystallization, but the organic mucilage may have exerted an indirect physical control. A theory is suggested to explain the deposition of gypsum and halite, which depends on loss of water from the surface of the mucilage layer, and the layer as a whole acting as a semipermeable membrane. As the water volume decreases, gypsum will be deposited first, but subsequently, with increasing evaporation, there will be a mixture of gypsum and halite and finally halite only.     

Inhibitors of metalloendoproteases block spiculogenesis in sea urchin primary mesenchyme cells

Metalloendoproteases have been implicated in a variety of fusion processes including plasma membrane fusion and exocytosis. As a prerequisite to skeleton formation in the sea urchin embryo, primary mesenchyme cells undergo fusion via filopodia to form syncytia. The spicule is formed within the syncytial cable by matrix and mineral deposition. To investigate the potential involvement of a metalloendoprotease in spiculogenesis, the effect of inhibitors of this enzyme on skeleton formation was studied. Experiments with primary mesenchyme cells in vitro and in normal embryos revealed that skeleton formation was blocked by these inhibitors. These findings implicate a metalloendoprotease in spiculogenesis; such an enzyme has been demonstrated in homogenates of primary mesenchyme cells. The most likely site of action of the metalloendoprotease is at the cell membrane fusion stage and/or at subsequent events requiring membrane fusion.     

The origins of plastids

A new theory of plastid origins is presented in which only two symbiotic events are needed to explain the origin of the six fundamentally different types of plastid, which all probably originated in anteriorly biciliated phagotrophic cells. Four of them can be derived directly from a single endosymbiotic cyanophyte by the independent loss of different cyanophyte characters and the evolution of new characters in the immediate descendants of this primary endosymbiosis. Retention of the phagosomal membrane as well as the prokaryotic plasma and outer membrane could produce the dinozoan and euglenid plastids with three envelope membranes, whereas the loss of the phagosomal membrane could produce the two-membraned envelopes characteristic of the Biliphyta and Verdiplantae*. The phycobilins were retained essentially unaltered in the Biliphyta, but are modified or lost in the other lines. In the ancestor of the Euglenozoa and Verdiplantae they were replaced by chlorophyll b. In the ancestor of algae possessing chlorophyll c they were modified to the cryptophyte type, concomitantly with the evolution of chlorophyll c₂: one line of descent from this ancestor produced the dinozoan plastid by the complete loss of phycobilins, while the other was incorporated by endosymbiosis into another phagotrophic bibiliate to produce the cryptophyte plastid. The latter evolved into the chromophyte plastid by the loss of phycobilins and the evolution of chlorophyll c₂. The conversion of the endosymbiont into a plastid depended on the evolution of a system to transport proteins into it. I argue that this occurred by the modification of the pre-existing mitochondrial transport system, and that the major modifications needed to adjust this to plastids with more than two envelope membranes led to evolution of a new tubular or disc-like morphology for the mitochondrial cristae of these groups. This new cristal morphology is maintained by stabilizing selection even in species that have secondarily lost plastids.     

Tubular-vesicular transformation in the contractile vacuole system of Dictyostelium

The contractile vacuole complex of Dictyostelium is the paradigm of a membrane system that undergoes tubular-vesicular transitions during its regular cycle of activities. This system acts as an osmoregulatory organelle in freshwater amoebae and protozoa. It collects fluid in a network of tubules and cisternae, and pumps it out of the cell through transient pores in the plasma membrane. Tubules and vacuoles are interconvertible. The tubular channels are associated with the cortical actin network and are capable of moving and fusing. The contractile vacuole complex is separate from vesicles of the endosomal pathway and preserves its identity in a dispersed state during cell division. We outline techniques to visualize the contractile vacuole system by electron and light microscopy. Emphasis is placed on GFP-fusion proteins that allow visualization of the dynamics of the contractile vacuole network in living cells. Proteins that control activities of this specialized organelle in Dictyostelium have been conserved during evolution and also regulate membrane trafficking in man.