Is Boron a Prebiotic Element? A Mini-review of the Essentiality of Boron for the Appearance of Life on Earth

Boron is probably a prebiotic element with special importance in the so-called "sugars world". Boron is not present on Earth in its elemental form. It is found only in compounds, e.g., borax, boric acid, kernite, ulexite, colemanite and other borates. Volcanic spring waters sometimes contain boron-based acids (e.g., boric, metaboric, tetraboric and pyroboric acid). Borates influence the formation of ribofuranose from formaldehyde that feeds the "prebiotic metabolic cycle". The importance of boron in the living world is strongly related to its implications in the prebiotic origins of genetic material; consequently, we believe that throughout the evolution of life, the primary role of boron has been to provide thermal and chemical stability in hostile environments. The complexation of boric acid and borates with organic cis-diols remains the most probable chemical mechanism for the role of this element in the evolution of the living world. Because borates can stabilize ribose and form borate ester nucleotides, boron may have provided an essential contribution to the "pre-RNA world".     

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.     

The Effects of Borate Minerals on the Synthesis of Nucleic Acid Bases,Amino Acids and Biogenic Carboxylic Acids from Formamide

The thermal condensation of formamide in the presence of mineral borates is reported. The products afforded are precursors of nucleic acids, amino acids derivatives and carboxylic acids. The efficiency and the selectivity of the reaction was studied in relation to the elemental composition of the 18 minerals analyzed. The possibility of synthesizing at the same time building blocks of both genetic and metabolic apparatuses, along with the production of amino acids, highlights the interest of the formamide/borate system in prebiotic chemistry.     

Boron Enrichment in Martian Clay

We have detected a concentration of boron in martian clay far in excess of that in any previously reported extra-terrestrial object. This enrichment indicates that the chemistry necessary for the formation of ribose, a key component of RNA, could have existed on Mars since the formation of early clay deposits, contemporary to the emergence of life on Earth. Given the greater similarity of Earth and Mars early in their geological history, and the extensive disruption of Earth''s earliest mineralogy by plate tectonics, we suggest that the conditions for prebiotic ribose synthesis may be better understood by further Mars exploration.     

Amount of leachant and water absorption levels of wood treated with borates and water repellents

Wood protection efficacy of borates against biological agents, flame retardancy, and suitability to the environment is well known. Since borates can be applied to timber as water based solutions, they are preferred economically as well. Even though they are highly mobile in wood, boron compounds are widely used in timber preservation. Borates migrate in liquid and increase the hygroscopicity of wood in damp conditions. This study deals with the physical restriction of water access in wood by impregnating water repellent agents into wood to limit amount of leachant and water absorption levels of wood after boron treatment. Borates were incorporated with polyethylene glycol-400 (PEG-400) their bulking effect in wood was considered. Results indicated that the amount of leachates from wood treated with borates in PEG-400 was remarkably higher compared to those of wood treated with the aqueous solutions of borates. Water absorption (WA) levels of wood treated with aqueous solutions of borates were higher than those of their treated samples with the solutions in PEG-400. Secondary treatments of wood with the water repellent (WR) chemicals following borate impregnation reduced the leaching of chemicals from wood in water and also WA of the specimens were less than those of the wood treated with only borates from aqueous and PEG solutions. Styrene (St) was the most effective monomer among the other agents used in terms of immobility effect on borates and WA.     

Faunal correlation of Wadi Moghara, Egypt: implications for the age of Prohylobates tandyi

Wadi Moghara, Egypt, is an early Miocene fossil locality with a mammalian fauna that includes Prohylobates tandyi, one of the earliest known representatives of the Cercopithecoidea. Faunal correlations were conducted between Moghara, Gebel Zelten (Libya) and a series of East African fossil sites with established radiometric dates in order to estimate the age of the Moghara mammals, including P. tandyi. Results confirm hypotheses proposed in some previous studies that: (1) Moghara is about 18-17 Ma, approximately the same age as the Hiwegi fauna from Rusinga Island (Kenya); (2) Moghara is slightly older than Gebel Zelten (Libya) (17-15 Ma); and (3) the cercopithecoid tooth presently identified as Victoriapithecus sp. from Napak V (ca. 19 Ma) is currently the oldest known record of a fossil Old World monkey, followed by P. tandyi from Moghara (Egypt) (18-17 Ma) and Prohylobates sp. from Buluk (Kenya) (>17.2 Ma), P. simonsi from Gebel Zelten (Libya) (ca. 17-15 Ma), and V. macinnesi from Maboko (Kenya) (ca. 16-14.7 Ma).     

Development of the East Asian summer monsoon: Evidence from the sediment record in the South China Sea since 8.5 Ma

128 samples from Ocean Drilling Program (ODP) Site 1143 in the southern South China Sea were analyzed for grain size, clay minerals, biogenic opal content and quartz in order to reconstruct changes in East Asian monsoon climate since 8.5 Ma. An abrupt change of terrigenous mass accumulation rate (MAR), clay mineral assemblage, median grain size and biogenic opal MAR about 5.2 Ma suggests that between 8.5-5.2 Ma the source of terrigenous sediment was mainly in the region of surface uplift and basaltic volcanism in southern Vietnam. A simple model of East Asian summer monsoon evolution was based on the clay/feldspar ratio, kaolinite/chlorite ratio and biogenic opal MAR. The summer monsoon has two periods of maximum strength at 8.5-7.6 Ma and 7.1-6.2 Ma. Subsequently, there was a relatively stable period at 6.2-3.5 Ma, continued intensification about 3.5-2.5 Ma, and gradually weakening after 2.5 Ma. Since 1 Ma the monsoon has intensified, with remarkable high-frequency and amplitude variability. Simultaneous increase in sedimentation rates at ODP Sites 1143, 1146 and 1148, as well as in MAR of terrigenous materials, quartz, feldspar and clay minerals at ODP Site 1143 at 3.5-2.5 Ma, may be the erosional response to both global climatic deterioration and the strengthening of the East Asian summer monsoon after about 3-4 Ma.     

A new hypothesis for the origin of life

This hypothesis suggests that calcium chelating sugars, and especially ribose, have determined the nature of the first molecular systems. The self-organization capacities of these molecules enabled them to form regular arrays with certain salts. These arrays then evolved to form polysaccharides. In this first step, ribose and particularly -D-ribofuranose predominated over other prebiotic components. In a second step, the purines invaded these polysaccharides (3–5-polyribophosphodiester). The purines best suited for this were adenine and deoxyguanine, arising from the polymerization of HCN. Just as the polysaccharides reacted with purines, so the purines reacted with other small molecules and in particular, certain alkylating agents and water. After several methylation and oxidation reactions, adenine and deoxyguanine evolved to adenine, methylguanine, cytosine, uracil and thymine. Slow evolution of the prebiotic components gradually brought about a transition from a ribose world to an RNA world. The environment of this prebiotic RNA was different from that of modern RNA. For example, interaction of prebiotic RNA with water, calcium salts and certain zwitterionic molecules like the amino acids glycine and alanine was unavoidable. The interaction of these two small amino acids with calcium evolved to form transient anhydride bonds that quickly reverted to the initial state, or transformed to a peptide bond or to a more stable activated state, the oxazolone ring. The formation of this ring in double-stranded prebiotic RNA is the critical event that allowed the synthesis of new -L-amino acids. The positioning of the lateral sides of the amino acids inside the RNA suggests a stereochemical relationship that could explain the origin of the genetic code.     

A Possible Path to the RNA World: Enantioselective and Diastereoselective Purification of Ribose

A theoretical mechanism resulting in the prebiotic appearance of enantiopure ribose, which would be needed for the origin of RNA and the “RNA world” is proposed. The mechanism simultaneously explains the emergence of biological homochirality and could answer the question of why nucleic acids are based on ribose rather than another sugar. Cleavage of certain non-chiral mineral crystals is known to lead to formation of chiral surfaces. In a chromatography-like process a mixture of racemic carbohydrates originating from the formose reaction is proposed to have been separated on such a chiral surface. Monosaccharides interact with surfaces through their hydroxyl groups, either by hydrogen bond formation or complex formation with metal ions. α-Ribopyranose, which has all hydroxyl groups on one side of the ring, is known to interact more strongly than other sugars with surfaces, as corroborated by certain chromatographic and electrophoresis data. A similar scenario leading to enantiopure ribose is separation on a flat, but not necessarily chiral surface in the presence of a strong electric field capable of orienting highly polar derivatives of sugars. Portions of this work were presented to Mid-Atlantic Regional Meeting of ACS, Hershey, PA, USA, June 05, 2006.     

Prebiotic ribose synthesis: A critical analysis

The discovery of catalytic ability in RNA has given fresh impetus to speculations that RNA played a critical role in the origin of life. This question must rest on the plausibility of prebiotic oligonucleotide synthesis, rather than on the properties of the final product. Many cliams have been published to support the idea that the components of RNA were readily available on the prebiotic earth. In this article, the literature cited in support of the prebiotic availability of one subunit, D-ribose, is reviewed to determine whether it justifies the claim.Polymerization of formaldehyde (the formose reaction) has been the single reaction cited for prebiotic ribose synthesis. It has been conducted with different catalysts: numerous basic substances, neutral clays and heat, and various types of radiation. Ribose has been identified (yields are uncertain, but unlikely to be greater than 1%) in reactions run with concentrated (0.15 M or greater) formaldehyde. It has been claimed in reactions run at lower concentration, but characterization has been inadequate, and experimental details have not been provided.The complex sugar mixture produced in the formose reaction is rapidly destroyed under the reaction conditions. Nitrogenous substances (needed for prebiotic base synthesis) would interfere with the formose reaction by reacting with formaldehyde, the intermediates, and sugar products in undesirable ways.The evidence that is currently available does not support the availability of ribose on the prebiotic earth, except perhaps for brief periods of time, in low concentration as part of a complex mixture, and under conditions unsuitable for nucleoside synthesis.     

Chemistry and biology of boron.

Boron is an essential nutrient for certain organisms, notably vascular plants and diatoms. Cyanobacteria require boron for formation of nitrogen-fixing heterocysts and boron may be beneficial to animals. Boron deficiency in plants produces manifold symptoms: many functions have been postulated. Deficiency symptoms first appear at growing points, within hours in root tips and within minutes or seconds in pollen tube tips, and are characterized by cell wall abnormalities. Boron-deficient tissues are brittle or fragile, while plants grown on high boron levels may have unusually flexible or resilient tissues. Borate forms cyclic diesters with appropriate diols or polyols. The most stable are formed with cis-diols on a furanoid ring. Two compounds have this structure physiologically: ribose in ribonucleotides and RNA, and apiose in the plant cell wall. Germanium can substitute for boron in carrot cell cultures. Both boron and germanium are localized primarily in the cell wall. We postulate that borate-apiofuranose ester cross-links are the auxin-sensitive acid-growth link in vascular plants, that the cyanobacterial heterocyst envelope depends on borate cross-linking of mannopyranose and/or galactopyranose residues in a polysaccharide-lipid environment, and that boron in diatoms forms ester cross-links in the polysaccharide cell wall matrix rather than boron-silicon interactions. Complexing of ribonucleotides is probably a factor in boron toxicity.     

Comparative toxicology of borates

Inorganic borates, including boric acid, Na, ammonium, K, and Zn borates generally display low acute toxicity orally, dermally, and by inhalation. They are either not irritant or mild skin and eye irritants. Exceptions owing to physiochemical properties do occur. Longer-term toxicological studies have been reported mainly on boric acid or borax where the properties are generally similar on an equivalent boron (B) basis. The critical effects in several species are male reproductive toxicity and developmental toxicity. The doses that cause these effects are far higher than any levels to which the human population could be exposed. Humans would need to consume daily some 3.3 g of boric acid (or 5.0 g borax) to ingest the same dose level as the lowest animal NOAEL. No effects on fertility were seen in a population of workers exposed to borates or to a population exposed to high environmental borate levels. There is remarkable similarity in the toxicological effects of boric acid and borax across different species. Other inorganic borates that simply dissociate to boric acid are expected to display similar toxicity, whereas those that do not dissociate simply to boric acid may display a different toxicological profile.     

Intramolecular RNA replicase: Possibly the first self-replicating molecule in the RNA world

Although there is more and more evidence suggested the existence of an RNA World during the origin of life, the scenario concerning the origin of the RNA World remains blurry. Usually it is speculated that it originated from a prebiotic nucleotide pool, during which a self-replicating RNA synthesis ribozyme may have emerged as the first ribozyme – the RNA replicase. However, there is yet no ersuasive supposition for the mechanism for the self-favouring feature of the replicase, thus the speculation remains unconvincing. Here we suggest that intramolecular catalysis is a possible solution. Two RNA synthesis ribozymes may be integrated into one RNA molecule, as two functional domains which could catalyze the copy of each other. Thus the RNA molecule could self-replicate and be referred to as “intramolecular replicase“ here. Computational simulation to get insight into the dynamic mechanism of emergence of the intramolecular replicase from a nucleotide pool is valuable and would be included in a following work of our group.     

Effects of Chronic Boron Exposure on Semen Profile

The possible changes in semen quality were studied in men living in a boron mining area. The subjects in the boron group had exposure to boron at an average level of 6.5 mg/day, as determined by urinary analysis. The results obtained by the boron group were compared to those obtained for the control group whose subjects were living in the same geographical area but away from the boron region; average exposure level was 1.4 mg/day for this group. The semen samples were analyzed according to the recommendations of the World Health Organization. Boron levels were established in the water samples obtained from various locations in the study region. In the boron mining fields where the subjects in the boron group live, water samples contained boron in the range of 1.4–6.5 mg/L, while the values were <0.01 mg/L for the water samples obtained from the region where the subjects of the control group reside. No negative effects were found in the sperm samples obtained from the subjects of the boron group.     

Molecular Modelling of the Mechanism of Action of Borate Retarders on Hydrating Cements at High Temperature

Abstract

We consider the class of borate additives in an attempt to understand, on the basis of molecular modelling techniques, why they are effective high temperature cement setting retarder aids. Borates are known to act as cement retarders under ambient conditions, for which the Billingham-Coveney clock reaction scheme [1] based on a gel → crystalline ettringite transformation provides the basic model. Under conditions of high temperature (above ca. 80°C) ettringite is known to be unstable, so that a modification to this mechanism is then required. However, conceptually (and mathematically) the kinetic scheme remains unchanged: we are concerned with a gel → crystalline silicate transition, which can be inhibited by suitable retarders. Thus the proposed mechanism for the high temperature retardation of hydrating cements by borates is that the latter prevent the growth of polymeric or crystalline calcium silicate hydrates such as tobermorite from the initially formed C ? S ? H gel.

The mechanism which we propose in this paper, which is based on chemisorption of borate species, explains some experimentally observed phenomena relating to the retarding action of both monomeric and polymeric borates in solution. On the basis of this work, we are able to predict vibrational frequencies for the cyclic borosilicate species which is formed, observation of which would confirm the validity of the mechanism proposed here. We can also use our work to explain the effectiveness of different borates. We conclude by suggesting a novel boronate retarder which might be expected to be more potent than those currently in use.     

Prebiotic Chemistry and the Origin of the RNA World

The demonstration that ribosomal peptide synthesis is a ribozyme-catalyzed reaction makes it almost certain that there was once an RNA World. The central problem for origin-of-life studies, therefore, is to understand how a protein-free RNA World became established on the primitive Earth. We first review the literature on the prebiotic synthesis of the nucleotides, the nonenzymatic synthesis and copying of polynucleotides, and the selection of ribozyme catalysts of a kind that might have facilitated polynucleotide replication. This leads to a brief outline of the Molecular Biologists' Dream, an optimistic scenario for the origin of the RNA World. In the second part of the review we point out the many unresolved problems presented by the Molecular Biologists' Dream. This in turn leads to a discussion of genetic systems simpler than RNA that might have “invented” RNA. Finally, we review studies of prebiotic membrane formation.     

Xylonucleic acid: synthesis,structure, and orthogonal pairing properties

There is a common interest for studying xeno-nucleic acid systems in the fields of synthetic biology and the origin of life, in particular, those with an engineered backbone and possessing novel properties. Along this line, we have investigated xylonucleic acid (XyloNA) containing a potentially prebiotic xylose sugar (a 3′-epimer of ribose) in its backbone. Herein, we report for the first time the synthesis of four XyloNA nucleotide building blocks and the assembly of XyloNA oligonucleotides containing all the natural nucleobases. A detailed investigation of pairing and structural properties of XyloNAs in comparison to DNA/RNA has been performed by thermal UV-melting, CD, and solution state NMR spectroscopic studies. XyloNA has been shown to be an orthogonal self-pairing system which adopts a slightly right-handed extended helical geometry. Our study on one hand, provides understanding for superior structure-function (-pairing) properties of DNA/RNA over XyloNA for selection as an informational polymer in the prebiotic context, while on the other hand, finds potential of XyloNA as an orthogonal genetic system for application in synthetic biology.     

Nucleotide analogs based on pentaerythritol — An hypothesis

The synthesis of ribose and ribose-based nucleotides under reasonable prebiotic conditions has not been achieved. Glycerol has been suggested as a structural unit that might have preceded ribose in the evolutionary emergence of RNA. Template-directed oligomerizations of nucleotide analogs based on glycerol, however, have been only partially successful. Recent studies on the effect of ultraviolet irradiation of formaldehyde solutions have shown that the reduced sugar pentaerythritol is formed with great specificity. I argue that pentaerythritol is potentially capable of being converted by simple chemistry into a series of nucleoside analogs related to barbituric acid. These analogs may be able to take part in nucleic acid-like interactions and could therefore be of potential interest as a new class of candidates as RNA precursors.     

The isotopic composition of anthropogenic boron and its potential impact on the environment

The present study investigates the isotopic composition of anthropogenic boron (B) and its potential affects on the environment. The isotopic ratios of B in synthetic products from the main ores in the world have been measured by negative thermal ionization mass spectrometry. The data show that the isotopic compositions of Na-borate products and washing powders overlap with those of natural Na-borate minerals. In contrast, the¹¹B/¹⁰B ratios of synthetic Ca-borate and Na/Ca borate products are significantly lower (by 15 permil) and overlap with those of the natural Ca-borate minerals. Consequently, the original isotopic signature of natural borate minerals is not modified during the manufacturing process of synthetic products. The B isotopic composition of domestic wastewater from Israel and Riverside, California suggests that B in sewage is derived from Na-borate components used in detergents. Since B, like other inorganic ions, is not removed during conventional sewage treatment, it accumulates in domestic wastewater. Although the B concentration in pristine groundwaters is generally low (<0.05 mg/L), contaminant sources (e.g., wastewater) are relatively enriched in B (0.5–1 mg/L). The isotopically distinguished signature of borate compounds is used to trace groundwater contamination.     

Prebiotic chemistry and the origin of the RNA world

The demonstration that ribosomal peptide synthesis is a ribozyme-catalyzed reaction makes it almost certain that there was once an RNA World. The central problem for origin-of-life studies, therefore, is to understand how a protein-free RNA World became established on the primitive Earth. We first review the literature on the prebiotic synthesis of the nucleotides, the nonenzymatic synthesis and copying of polynucleotides, and the selection of ribozyme catalysts of a kind that might have facilitated polynucleotide replication. This leads to a brief outline of the Molecular Biologists' Dream, an optimistic scenario for the origin of the RNA World. In the second part of the review we point out the many unresolved problems presented by the Molecular Biologists' Dream. This in turn leads to a discussion of genetic systems simpler than RNA that might have "invented" RNA. Finally, we review studies of prebiotic membrane formation.