Rethinking early Earth phosphorus geochemistry

From the RNA world to the RNA/protein world: contribution of some riboswitch-binding species?

Some amino acids and their formal derivatives, currently riboswitch-binding species, could have interacted with polyribonucletides in prebiotic environments, leading to the peptide formation. If the resulting compounds had led to a sustainable polymerization of amino acids and the new structures had catalytic activity, such would have been an important contribution to the transition from the RNA world to the RNA/Protein world.

Redox chemistry in the phosphorus biogeochemical cycle

The element phosphorus (P) controls growth in many ecosystems as the limiting nutrient, where it is broadly considered to reside as pentavalent P in phosphate minerals and organic esters. Exceptions to pentavalent P include phosphine--PH3--a trace atmospheric gas, and phosphite and hypophosphite, P anions that have been detected recently in lightning strikes, eutrophic lakes, geothermal springs, and termite hindguts. Reduced oxidation state P compounds include the phosphonates, characterized by C-P bonds, which bear up to 25% of total organic dissolved phosphorus. Reduced P compounds have been considered to be rare; however, the microbial ability to use reduced P compounds as sole P sources is ubiquitous. Here we show that between 10% and 20% of dissolved P bears a redox state of less than +5 in water samples from central Florida, on average, with some samples bearing almost as much reduced P as phosphate. If the quantity of reduced P observed in the water samples from Florida studied here is broadly characteristic of similar environments on the global scale, it accounts well for the concentration of atmospheric phosphine and provides a rationale for the ubiquity of phosphite utilization genes in nature. Phosphine is generated at a quantity consistent with thermodynamic equilibrium established by the disproportionation reaction of reduced P species. Comprising 10-20% of the total dissolved P inventory in Florida environments, reduced P compounds could hence be a critical part of the phosphorus biogeochemical cycle, and in turn may impact global carbon cycling and methanogenesis.

Glasses as sources of condensed phosphates on the early earth

Procedures for the analysis of phosphorus in geological material normally aims for the determination of the total amount of P expressed as orthophosphate [Formula: see text] or the differentiation between inorganic and organic P. This is probably due to analytical difficulties but also to the prevalent opinion that the chemistry of phosphorus in geological environments is almost entirely restricted to the mineral apatite. Because of the low solubility of apatite it is, therefore, commonly argued that little P was around for prebiotic chemistry and that pre-biological processes would essentially have had to do without this indispensable element unless it was provided by alternative sources or mechanisms (such as reduction and activation by lightning or delivery to Earth by celestial bodies). It is a paradox that the potential existence of reactive phosphorus compounds, such as the mineral schreibersite - iron phosphide, in geological material on Earth is seldom considered although we are aware of the existence of such compounds in meteorite material. The content of Al2O3 in rocks appears to be important for the speciation of phosphorus and for how strongly it binds to silicates. In general, low alumina seems to promote the existence of isolated charge-balanced phosphorus complexes.

Crystal structure of PhnZ in complex with substrate reveals a di-iron oxygenase mechanism for catabolism of organophosphonates

The enzymes PhnY and PhnZ comprise an oxidative catabolic pathway that enables marine bacteria to use 2-aminoethylphosphonic acid as a source of inorganic phosphate. PhnZ is notable for catalyzing the oxidative cleavage of a carbon-phosphorus bond using Fe(II) and dioxygen, despite belonging to a large family of hydrolytic enzymes, the HD-phosphohydrolase superfamily. We have determined high-resolution structures of PhnZ bound to its substrate, (R)-2-amino-1-hydroxyethylphosphonate (2.1 Å), and a buffer additive, l-tartrate (1.7 Å). The structures reveal PhnZ to have an active site containing two Fe ions coordinated by four histidines and two aspartates that is strikingly similar to the carbon-carbon bond cleaving enzyme, myo-inositol-oxygenase. The exception is Y24, which forms a transient ligand interaction at the dioxygen binding site of Fe2. Site-directed mutagenesis and kinetic analysis with substrate analogs revealed the roles of key active site residues. A fifth histidine that is conserved in the PhnZ subclade, H62, specifically interacts with the substrate 1-hydroxyl. The structures also revealed that Y24 and E27 mediate a unique induced-fit mechanism whereby E27 specifically recognizes the 2-amino group of the bound substrate and toggles the release of Y24 from the active site, thereby creating space for molecular oxygen to bind to Fe2. Structural comparisons of PhnZ reveal an evolutionary connection between Fe(II)-dependent hydrolysis of phosphate esters and oxidative carbon-phosphorus or carbon-carbon bond cleavage, thus uniting the diverse chemistries that are found in the HD superfamily.

Borophosphates and silicophosphates as plausible contributors to the emergence of life

Scientific explanations for the origin of life are incomplete and may differ on some issues. Here, we argue that some prebiological steps have occurred in environments with borophosphates and/or silicophosphates in the form of hydrogels, on the basis of their chemical groups and structural properties. These could have decreased the diffusion rate of some prebiotic molecules, stabilized molecules with vicinal cis-diol groups, reduced the hydrolytic activity of water and inserted catalytic metal ions into their networks. Additionally, these hydrogels could have acted as reaction media, supplied a phosphate source for phosphorylations and produced crystals that may have permitted enantiomeric enrichment of prebiotic molecules, thus providing conditions for the emergence of protocells.

Prebiotic phosphate ester syntheses in a deep eutectic solvent

We report a route to synthesize a wide range of organophosphates of biological significance in a deep eutectic solvent (2:1 urea and choline chloride), utilizing various orthophosphate sources. Heating an organic alcohol in the solvent along with a soluble phosphorus source yields phosphorus esters of choline as well as that of the added organic in yields between 15 to 99 %. In addition, phosphite analogs of biological phosphates and peptides were also formed by the simple mixing of reagents and heating at 60-70 °C in the deep eutectic solvent. The presented dehydration reactions are relevant to prebiotic and green chemistry in alternative solvents.

The origin of RNA and "my grandfather's axe"

The origin of RNA is one of the most formidable problems facing prebiotic chemists. We consider RNA as a product of evolution, as opposed to the more conventional view of RNA as originally being the product of abiotic processes. We have come to accept that life's informational polymers have changed in chemical structure since their emergence, which presents a quandary similar to the paradox of "My Grandfather's Axe". Here, we discuss reasons why all contemporary components of RNA--the nucleobases, ribose, and phosphate--are not likely the original components of the first informational polymer(s) of life. We also evaluate three distinct models put forth as pathways for how the earliest informational polymers might have assembled. We see the quest to uncover the ancestors of RNA as an exciting scientific journey, one that is already providing additional chemical constraints on the origin of life and one that has the potential to produce self-assembling materials, novel catalysis, and bioactive compounds.

Oxygen isotope signature of UV degradation of glyphosate and phosphonoacetate: tracing sources and cycling of phosphonates

The degradation of phosphonates in the natural environment constitutes a major route by which orthophosphate (Pi) is regenerated from organic phosphorus and recently implicated in marine methane production, with ramifications to environmental pollution issues and global climate change concerns. This work explores the application of stable oxygen isotope analysis in elucidating the CP bond cleavage mechanism(s) of phosphonates by UV photo-oxidation and for tracing their sources in the environment. The two model phosphonates used, glyphosate and phosphonoacetic acid were effectively degraded after exposure to UV irradiation. The isotope results indicate the involvement of both ambient water and atmospheric oxygen in the CP bond cleavage and generally consistent with previously posited mechanisms of UV-photon excitation reactions. A model developed to calculate the oxygen isotopic composition of the original phosphonate P-moiety, shows both synthetic phosphonates having distinctly lower values compared to naturally derived organophosphorus compounds. Such mechanistic models, based on O-isotope probing, are useful for tracing the sources and reactions of phosphonates in the environment.

Applicability of anaerobic nitrate-dependent Fe(II) oxidation to microbial enhanced oil recovery (MEOR)

Microbial processes that produce solid-phase minerals could be judiciously applied to modify rock porosity with subsequent alteration and improvement of floodwater sweep in petroleum reservoirs. However, there has been little investigation of the application of this to enhanced oil recovery (EOR). Here, we investigate a unique approach of altering reservoir petrology through the biogenesis of authigenic rock minerals. This process is mediated by anaerobic chemolithotrophic nitrate-dependent Fe(II)-oxidizing microorganisms that precipitate iron minerals from the metabolism of soluble ferrous iron (Fe(2+)) coupled to the reduction of nitrate. This mineral biogenesis can result in pore restriction and reduced pore throat diameter. Advantageously and unlike biomass plugs, these biominerals are not susceptible to pressure or thermal degradation. Furthermore, they do not require continual substrate addition for maintenance. Our studies demonstrate that the biogenesis of insoluble iron minerals in packed-bed columns results in effective hydrology alteration and homogenization of heterogeneous flowpaths upon stimulated microbial Fe(2+) biooxidation. We also demonstrate almost 100% improvement in oil recovery from hydrocarbon-saturated packed-bed columns as a result of this metabolism. These studies represent a novel departure from traditional microbial EOR approaches and indicate the potential for nitrate-dependent Fe(2+) biooxidation to improve volumetric sweep efficiency and enhance both the quality and quantity of oil recovered.

Phosphite in sedimentary interstitial water of Lake Taihu, a large eutrophic shallow lake in China

The seasonal occurrence and distribution of phosphite (HPO3(2-), P) in sedimentary interstitial water from Lake Taihu was monitored from 2011 to 2012 to better understand its possible link to P cycle in the eutrophic shallow lake. Phosphite concentrations ranged from < MDL to 14.32 ± 0.19 μg P/kg with a mean concentration of 1.58 ± 0.33 μg P/kg, which accounts for 5.51% total soluble P (TSP(s)) in surficial sediments (0-20 cm). Spatially, the concentrations of sedimentary phosphite in the lake's northern areas were relatively higher than those in the southern areas. Higher phosphite concentrations were always observed in seriously polluted sites. Generally, phosphite in the deeper layers (20-40 cm and 40-60 cm) showed minor fluctuations compared to that in the surficial sediments, which may be associated with the frequent exchange at the sediment-water interface. Phosphite concentrations in surficial or core sediments decreased as spring > autumn > summer > winter. Higher phosphite levels occurred in the areas with lower redox (Eh), higher P contents, and particularly when metal bonded with P to form Al-P(s) and Ca-P(s). Phosphite may be an important media in the P biogeochemical cycle in Lake Taihu and contribute to its internal P transportation.

Evidence for reactive reduced phosphorus species in the early Archean ocean

It has been hypothesized that before the emergence of modern DNA-RNA-protein life, biology evolved from an "RNA world." However, synthesizing RNA and other organophosphates under plausible early Earth conditions has proved difficult, with the incorporation of phosphorus (P) causing a particular problem because phosphate, where most environmental P resides, is relatively insoluble and unreactive. Recently, it has been proposed that during the Hadean-Archean heavy bombardment by extraterrestrial impactors, meteorites would have provided reactive P in the form of the iron-nickel phosphide mineral schreibersite. This reacts in water, releasing soluble and reactive reduced P species, such as phosphite, that could then be readily incorporated into prebiotic molecules. Here, we report the occurrence of phosphite in early Archean marine carbonates at levels indicating that this was an abundant dissolved species in the ocean before 3.5 Ga. Additionally, we show that schreibersite readily reacts with an aqueous solution of glycerol to generate phosphite and the membrane biomolecule glycerol-phosphate under mild thermal conditions, with this synthesis using a mineral source of P. Phosphite derived from schreibersite was, hence, a plausible reagent in the prebiotic synthesis of phosphorylated biomolecules and was also present on the early Earth in quantities large enough to have affected the redox state of P in the ocean. Phosphorylated biomolecules like RNA may, thus, have first formed from the reaction of reduced P species with the prebiotic organic milieu on the early Earth.

Is struvite a prebiotic mineral?

The prebiotic relevance of mineral struvite, MgNH4PO4·6H2O, was studied experimentally as a phosphorylating reagent and, theoretically, to understand the geochemical requirements for its formation. The effectiveness of phosphorylation by the phosphate mineral, monetite, CaHPO4, was also studied to compare to the efficiency of struvite. The experiments focused on the phosphorylation reactions of the minerals with organic compounds, such as nucleosides, glycerol and choline chloride, and heat at 75 °C for about 7-8 days and showed up to 28% phosphorylation of glycerol. In contrast, the compositional requirements for the precipitation of struvite are high ammonium and phosphate concentrations, as well as a little Ca2+ dissolved in the water. Combined, these requirements suggest that it is not likely that struvite was present in excess on the early Earth to carry out phosphorylation reactions. The present study focuses on the thermodynamic aspects of struvite formation, complementing the results given by Orgel and Handschuh (1973), which were based on the kinetic effects.

Determination of phosphite in a eutrophic freshwater lake by suppressed conductivity ion chromatography

The establishment of a sensitive and specific method for the detection of reduced phosphorus (P) is crucial for understanding P cycle. This paper presents the quantitative evidence of phosphite (P, +3) from the freshwater matrix correspondent to the typically eutrophic Lake Taihu in China. By ion chromatography coupled with gradient elution procedure, efficient separation of micromolar levels of phosphite is possible in the presence of millimolar levels of interfering ions, such as chloride, sulfate, and hydrogen carbonate in freshwater lakes. Optimal suppressed ion chromatography conditions include the use of 500 μL injection volumes and an AS11 HC analytical column heated to 30 °C. The method detection limit of 0.002 μM for phosphite was successfully applied for phosphite determination in natural water samples with recoveries ranging from 90.7 ± 3.2% to 108 ± 1.5%. Phosphite in the freshwater matrix was also verified using a two-dimensional capillary ion chromatography and ion chromatography coupled with mass spectrometry. Results confirmed the presence of phosphite in Lake Taihu ranging from 0.01 ± 0.01 to 0.17 ± 0.01 μM, which correlated to 1-10% of the phosphate. Phosphite is an important component of P and may influence biogeochemical P cycle in lakes.

Engineering phosphorus metabolism in plants to produce a dual fertilization and weed control system

High crop yields depend on the continuous input of orthophosphate (PO(4)(−3))-based fertilizers and herbicides. Two major challenges for agriculture are that phosphorus is a nonrenewable resource and that weeds have developed broad herbicide resistance. One strategy to overcome both problems is to engineer plants to outcompete weeds and microorganisms for limiting resources, thereby reducing the requirement for both fertilizers and herbicides. Plants and most microorganisms are unable to metabolize phosphite (PO(3)(−3)), so we developed a dual fertilization and weed control system by generating transgenic plants that can use phosphite as a sole phosphorus source. Under greenhouse conditions, these transgenic plants require 30–50% less phosphorus input when fertilized with phosphite to achieve similar productivity to that obtained by the same plants using orthophosphate fertilizer and, when in competition with weeds, accumulate 2–10 times greater biomass than when fertilized with orthophosphate.

The significance of Mg in prebiotic geochemistry

Magnesium plays a special role in biochemistry because of its ability to coordinate six oxygen atoms efficiently in its first coordination shell. Such oxygen atoms may be part of one or two charged oxyanions, which means that Mg²⁺ can, for instance, tie together two different phosphate groups that are located at distance from each other in a macromolecule, and in this way be responsible for the folding of molecules like RNA. This property of Mg²⁺ also helps the stabilization of diphosphate and triphosphate groups of nucleotides, as well as promoting the condensation of orthophosphate to oligophosphates, like pyrophosphate and trimetaphosphate. Borates, on the other hand, are known to promote the formation of nucleobases and carbohydrates, ribose in particular, which is yet another constituent of nucleotides. The oldest borate minerals that we find on Earth today are magnesium borates. Dissolved borate stabilizes pentose sugars by forming complexes with cis-hydroxyl groups. In the furanose form of ribose, the preferential binding occurs to the 2 and 3 carbon, leaving the 5 carbon free for phosphorylation. The central role of Mg²⁺ in the function of ribozymes and its 'archaic' position in ribosomes, and the fact that magnesium generally has coordination properties different from other cations, suggests that the inorganic chemistry of magnesium had a key position in the first chemical processes leading to the origin and early evolution of life.

Acidification of Europa's subsurface ocean as a consequence of oxidant delivery

Oxidants are formed at the surface of Europa and may be delivered to the subsurface ocean, possibly in great quantities. Whether these substances would be available for biological metabolism is uncertain, because they may react with sulfides and other compounds to generate sulfuric and other acids. If this process has been active on Europa for much of its age, then not only would it rob the ocean of life-supporting oxidants but the subsurface ocean could have a pH of ~2.6, which is so acidic as to present an environmental challenge for life, unless organisms consume or sequester the oxidants fast enough to ameliorate the acidification.

Theory of the origin, evolution, and nature of life

Life is an inordinately complex unsolved puzzle. Despite significant theoretical progress, experimental anomalies, paradoxes, and enigmas have revealed paradigmatic limitations. Thus, the advancement of scientific understanding requires new models that resolve fundamental problems. Here, I present a theoretical framework that economically fits evidence accumulated from examinations of life. This theory is based upon a straightforward and non-mathematical core model and proposes unique yet empirically consistent explanations for major phenomena including, but not limited to, quantum gravity, phase transitions of water, why living systems are predominantly CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur), homochirality of sugars and amino acids, homeoviscous adaptation, triplet code, and DNA mutations. The theoretical framework unifies the macrocosmic and microcosmic realms, validates predicted laws of nature, and solves the puzzle of the origin and evolution of cellular life in the universe.

Phosphorus sorption on marine carbonate sediment: phosphonate as model organic compounds

Organophosphonate, characterized by the presence of a stable, covalent, carbon to phosphorus (C-P) bond, is a group of synthetic or biogenic organophosphorus compounds. The fate of these organic phosphorus compounds in the environment is not well studied. This study presents the first investigation on the sorption of phosphorus (P) in the presence of two model phosphonate compounds, 2-aminothylphosphonoic acid (2-AEP) and phosphonoformic acid (PFA), on marine carbonate sediments. In contrast to other organic P compounds, no significant inorganic phosphate exchange was observed in seawater. P was found to adsorb on the sediment only in the presence of PFA, not 2-AEP. This indicated that sorption of P from phosphonate on marine sediment was compound specific. Compared with inorganic phosphate sorption on the same sediments, P sorption from organic phosphorus is much less in the marine environment. Further study is needed to understand the potential role of the organophosphonate compounds in biogeochemical cycle of phosphorus in the environment.

Physiological and biochemical responses of Microcystis aeruginosa to phosphite

Phosphorus (P) is a key biological element and limiting nutrient in aquatic environments. Phosphate (+5) is traditionally associated with the P nutrient supply. However, phosphite (+3) has recently generated a great deal of interest, because of the possibility that it is a P source based on recognition of its vital role in the original life of the early earth. This study investigated whether phosphite can be an alternative P source for Microcystis aeruginosa PCC 7806, one of the predominant bloom species in freshwater systems. The results indicated that M. aeruginosa could not utilize phosphite as a sole P-nutrient directly for cell growth at any concentration, but that phosphite could boost cell numbers and chlorophyll a (Chl-a) content as long as phosphate was provided simultaneously. Specifically, Chl-a production increased sharply when 5.44 mg PL(-1) phosphite was added to 0.54 mg PL(-1) phosphate medium. Analysis of the maximum yield of PSII indicated that phosphite may stimulate the photosynthesis process of cells in phosphate-phosphite medium. In addition, phosphite failed to support cell growth, even though it more readily permeated the cells in P-deficient medium than in P-sufficient medium. Alkaline phosphatase activity (APA) analysis indicated that, unlike organic P, phosphite inhibits the response of cells to deficient P status, especially under P-deprived conditions.

Phosphite utilization by the marine picocyanobacterium Prochlorococcus MIT9301

Primary productivity in the ocean's oligotrophic regions is often limited by phosphorus (P) availability. In low phosphate environments, the prevalence of many genes involved in P acquisition is elevated, suggesting that the ability to effectively access diverse P sources is advantageous for organisms inhabiting these regions. Prochlorococcus, the numerically dominant primary producer in the oligotrophic ocean, encodes high-affinity P transporters, P regulatory proteins and enzymes for organic phosphate utilization, but its ability to use reduced P compounds has not been previously demonstrated. Because Prochlorococcus strain MIT9301 encodes genes similar to phnY and phnZ, which constitute a novel marine bacterial 2-aminoethylphosphonate (2-AEPn) utilization pathway, it has been suggested that this organism might use 2-AEPn as an alternative P source. We show here that although MIT9301 was unable to use 2-AEPn as a sole P source under standard culture conditions, it was able to use phosphite. Phosphite utilization by MIT9301 appears to be mediated by an NAD-dependent phosphite dehydrogenase encoded by ptxD. We show that phosphite utilization genes are present in diverse marine microbes and that their abundance is higher in low-P waters. These results strongly suggest that phosphite represents a previously unrecognized component of the marine P cycle.

Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisome

Background

Volutin granules appear to be universally distributed and are morphologically and chemically identical to acidocalcisomes, which are electron-dense granular organelles rich in calcium and phosphate, whose functions include storage of phosphorus and various metal ions, metabolism of polyphosphate, maintenance of intracellular pH, osmoregulation and calcium homeostasis. Prokaryotes are thought to differ from eukaryotes in that they lack membrane-bounded organelles. However, it has been demonstrated that as in acidocalcisomes, the calcium and polyphosphate-rich intracellular "volutin granules (polyphosphate bodies)" in two bacterial species, Agrobacterium tumefaciens, and Rhodospirillum rubrum, are membrane bound and that the vacuolar proton-translocating pyrophosphatases (V-H⁺PPases) are present in their surrounding membranes. Volutin granules and acidocalcisomes have been found in organisms as diverse as bacteria and humans.

Results

Here, we show volutin granules also occur in Archaea and are, therefore, present in the three superkingdoms of life (Archaea, Bacteria and Eukarya). Molecular analyses of V-H⁺PPase pumps, which acidify the acidocalcisome lumen and are diagnostic proteins of the organelle, also reveal the presence of this enzyme in all three superkingdoms suggesting it is ancient and universal. Since V-H⁺PPase sequences contained limited phylogenetic signal to fully resolve the ancestral nodes of the tree, we investigated the divergence of protein domains in the V-H⁺PPase molecules. Using Protein family (Pfam) database, we found a domain in the protein, PF03030. The domain is shared by 31 species in Eukarya, 231 in Bacteria, and 17 in Archaea. The universal distribution of the V-H⁺PPase PF03030 domain, which is associated with the V-H⁺PPase function, suggests the domain and the enzyme were already present in the Last Universal Common Ancestor (LUCA).

Conclusion

The importance of the V-H⁺PPase function and the evolutionary dynamics of these domains support the early origin of the acidocalcisome organelle. In particular, the universality of volutin granules and presence of a functional V-H⁺PPase domain in the three superkingdoms of life reveals that the acidocalcisomes may have appeared earlier than the divergence of the superkingdoms. This result is remarkable and highlights the possibility that a high degree of cellular compartmentalization could already have been present in the LUCA.

Reviewers

This article was reviewed by Anthony Poole, Lakshminarayan Iyer and Daniel Kahn

Reactivity of alanylalanine diastereoisomers in neutral and acid aqueous solutions: a versatile stereoselectivity

A good comprehension of the reactivity of peptides in aqueous solution is fundamental in prebiotic chemistry, namely for understanding their stability and behavior in primitive oceans. Relying on the stereoselectivity of the involved reactions, there is a huge interest in amino acid derivatives for explaining the spontaneous emergence of homochirality on primitive Earth. The corresponding kinetic and thermodynamic parameters are however still poorly known in the literature. We studied the reactivity of alanylalanine in acidic to neutral conditions as a model system. The hydrolysis into amino acids, the epimerization of the N-terminal residue, and the cyclization into diketopiperazine could be successfully identified and studied. This kinetic investigation highlighted interesting behaviors. Complex mechanisms were observed in very acidic conditions. The relative kinetic stability of the diastereoisomers of the dipeptide is highly dependent of the pH, with the possibility to dynamically destabilize the thermodynamically more stable diastereoisomers. The existence of the cyclization of dipeptides adds complexity to the system. On one hand it brings additional stereoselectivities; on the other hand fast racemization of heterochiral dipeptides is obtained.

Links between hydrothermal environments, pyrophosphate, na(+), and early evolution

The discovery that photosynthetic bacterial membrane-bound inorganic pyrophosphatase (PPase) catalyzed light-induced phosphorylation of orthophosphate (Pi) to pyrophosphate (PPi) and the capability of PPi to drive energy requiring dark reactions supported PPi as a possible early alternative to ATP. Like the proton-pumping ATPase, the corresponding membrane-bound PPase also is a H⁺-pump, and like the Na⁺-pumping ATPase, it can be a Na⁺-pump, both in archaeal and bacterial membranes. We suggest that PPi and Na⁺ transport preceded ATP and H⁺ transport in association with geochemistry of the Earth at the time of the origin and early evolution of life. Life may have started in connection with early plate tectonic processes coupled to alkaline hydrothermal activity. A hydrothermal environment in which Na⁺ is abundant exists in sediment-starved subduction zones, like the Mariana forearc in the W Pacific Ocean. It is considered to mimic the Archean Earth. The forearc pore fluids have a pH up to 12.6, a Na⁺-concentration of 0.7 mol/kg seawater. PPi could have been formed during early subduction of oceanic lithosphere by dehydration of protonated orthophosphates. A key to PPi formation in these geological environments is a low local activity of water.

Primitive genetic polymers

Since the structure of DNA was elucidated more than 50 years ago, Watson-Crick base pairing has been widely speculated to be the likely mode of both information storage and transfer in the earliest genetic polymers. The discovery of catalytic RNA molecules subsequently provided support for the hypothesis that RNA was perhaps even the first polymer of life. However, the de novo synthesis of RNA using only plausible prebiotic chemistry has proven difficult, to say the least. Experimental investigations, made possible by the application of synthetic and physical organic chemistry, have now provided evidence that the nucleobases (A, G, C, and T/U), the trifunctional moiety ([deoxy]ribose), and the linkage chemistry (phosphate esters) of contemporary nucleic acids may be optimally suited for their present roles-a situation that suggests refinement by evolution. Here, we consider studies of variations in these three distinct components of nucleic acids with regard to the question: Is RNA, as is generally acknowledged of DNA, the product of evolution? If so, what chemical and structural features might have been more likely and advantageous for a proto-RNA?

Genotypic variation in element concentrations in brown rice from Yunnan landraces in China

The mineral elements present in brown rice play an important physiological role in global human health. We investigated genotypic variation of eight of these elements (P, K, Ca, Mg, Fe, Zn, Cu, and Mn) in 11 different grades of brown rice on the basis of the number and distance coefficients of 282 alleles for 20 simple sequence repeat (SSR) markers. Six-hundred and twenty-eight landraces from the same field in Yunnan Province, one of the largest centers of genetic diversity of rice (Oryza sativa L.) in the world, formed our core collection. The mean concentrations (mg kg(-1)) of the eight elements in brown rice for these landraces were P (3,480) > K (2,540) > Mg (1,480) > Ca (157) > Zn (32.8) > Fe (32.0) > Cu (13.6) > Mn (13.2). Mean P concentrations in brown rice were 6.56 times total soil P, so the grains are important in tissue storage of P, but total soil K is 7.82 times mean K concentrations in brown rice. The concentrations of the eight elements in some grades of brown rice, on the basis of the number and distance coefficients of alleles for 20 SSR markers for the landraces, were significantly different (P < 0.05), and further understanding of the relationship between mineral elements and gene diversity is needed. There was large variation in element concentrations in brown rice, ranging from 2,160 to 5,500 mg P kg(-1), from 1,130 to 3,830 mg K kg(-1), from 61.8 to 488 mg Ca kg(-1), from 864 to 2,020 mg Mg kg(-1), from 0.40 to 147 mg Fe kg(-1), from 15.1 to 124 mg Zn kg(-1), from 0.10 to 59.1 mg Cu kg(-1), and from 6.7 to 26.6 mg Mn kg(-1). Therefore, germplasm evaluations for Ca, Fe, and Zn concentrations in rice grains have detected up to sevenfold genotypic differences, suggesting that selection for high levels of Ca, Fe, and Zn in breeding for mass production is a feasible approach. Increasing the concentrations of Ca, Fe, and Zn in rice grains will help alleviate chronic Ca, Zn, and Fe deficiencies in many areas of the world.

Detection of geothermal phosphite using high-performance liquid chromatography

Little is known about the prebiotic mechanisms that initiated the bioavailability of phosphorus, an element essential to life. A better understanding of phosphorus speciation in modern earth environments representative of early earth may help to elucidate the origins of bioavailable phosphorus. This paper presents the first quantitative measurements of phosphite in a pristine geothermal pool representative of early earth. Phosphite and phosphate were initially identified and quantified in geothermal pool and stream samples at Hot Creek Gorge near Mammoth Lakes, California, using suppressed conductivity ion chromatography. Results confirmed the presence of 0.06 +/- 0.02 microM of phosphite and 0.05 +/- 0.01 microM of phosphate in a geothermal pool. In the stream, phosphite concentrations were below detection limit (0.04 microM) and phosphate was measured at 1.06 +/- 0.36 microM. The presence of phosphite in the geothermal pool was confirmed using both chemical oxidation and ion chromatography/mass spectrometry.

On the origin of life in the zinc world: 1. Photosynthesizing, porous edifices built of hydrothermally precipitated zinc sulfide as cradles of life on Earth

BACKGROUND

The complexity of the problem of the origin of life has spawned a large number of possible evolutionary scenarios. Their number, however, can be dramatically reduced by the simultaneous consideration of various bioenergetic, physical, and geological constraints.

RESULTS

This work puts forward an evolutionary scenario that satisfies the known constraints by proposing that life on Earth emerged, powered by UV-rich solar radiation, at photosynthetically active porous edifices made of precipitated zinc sulfide (ZnS) similar to those found around modern deep-sea hydrothermal vents. Under the high pressure of the primeval, carbon dioxide-dominated atmosphere ZnS could precipitate at the surface of the first continents, within reach of solar light. It is suggested that the ZnS surfaces (1) used the solar radiation to drive carbon dioxide reduction, yielding the building blocks for the first biopolymers, (2) served as templates for the synthesis of longer biopolymers from simpler building blocks, and (3) prevented the first biopolymers from photo-dissociation, by absorbing from them the excess radiation. In addition, the UV light may have favoured the selective enrichment of photostable, RNA-like polymers. Falsification tests of this hypothesis are described in the accompanying article (A.Y. Mulkidjanian, M.Y. Galperin, Biology Direct 2009, 4:27).

CONCLUSION

The suggested "Zn world" scenario identifies the geological conditions under which photosynthesizing ZnS edifices of hydrothermal origin could emerge and persist on primordial Earth, includes a mechanism of the transient storage and utilization of solar light for the production of diverse organic compounds, and identifies the driving forces and selective factors that could have promoted the transition from the first simple, photostable polymers to more complex living organisms.