Biosilicification: the role of the organic matrix in structure control

Silicon (although never in the elemental form) is present in all living organisms and is required for the production of structural materials in single-celled organisms through to higher plants and animals. Hydrated amorphous silica is a mineral of infinite functionality and yet it is formed into structures with microscopic and macroscopic form. Research into the mechanisms controlling the process have highlighted proteins and proteoglycans as possible control molecules. Such molecules are suggested to play a critical role in the catalysis of silica polycondensation reactions and in structure direction. This article reviews information on silica form and function, silica condensation chemistry, the role of macromolecules in structure control and in vitro studies of silica formation using biomolecules extracted from biological silicas. An understanding of the mechanisms by which biological organisms regulate mineral formation will assist in our understanding of the essentiality of silicon to life processes and in the generation of new materials with specific form and function for industrial application in the 21st century.     

Model studies of the precipitation of silica in the presence of aluminium; implications for biology and industry

The unique chemical affinity between the oxides of silicon and aluminium has been cited as a potential route for the amelioration of the detrimental effects of aluminium in the environment and in biological systems. A greater understanding of silicon-aluminium interactions may assist in this endeavour and also provide a means of overcoming silica fouling problems encountered by industry which are exacerbated by the presence of aluminium. It is also conceivable that this increased knowledge may demonstrate a positive use for aluminium in the processing of the silicon dioxide phase. In this study we report the effect of aluminium ions, derived from aluminium chloride, on silicic acid species obtained from potassium catecholato complexes of silicon at circumneutral pH at the molar ratios 1000Si:Al, 100Si:Al and 50Si:Al. Silica and low levels of aluminium-rich silica materials were formed with Si:Al ratios of about 3.5:1 comparable with the element ratios detected in senile plaques and aluminium-rich scale. A kinetic study showed that aluminium in the reaction medium slowed down the rate of formation of one of the silica species formed early in the condensation process, e.g. trimers, but increased the rate at which silicic acid was removed from sub 1 nm diameter particles. The materials precipitated in the presence of aluminium were composed of smaller particles and aggregates with smaller pores (Si100:Al and Si50:Al systems) or larger pores (Si1000:Al) compared to the control. The nature of the interactions responsible for these differences is discussed. The effects described here demonstrate the ability of silica and aluminium to interact under conditions such as those found in biological systems. That silica reacts with aluminium in the presence of catechol supports the protective role assigned to silicon.     

Biomolecular Self-assembly and its Relevance in Silica Biomineralization

Biomineralization, which means the formation of inorganic materials by biological processes, currently finds increasing research interest. It involves the synthesis of calcium-based minerals such as bones and teeth in vertebrates, and of shells. Silica biomineralization occurs, for example, in diatoms and silica sponges. Usually, biominerals are made up of amorphous compounds or small microcrystalline domains embedded into an amorphous matrix. Nevertheless, they exhibit very regular shapes and, as in the case of diatoms, intricate nanopatterns of amazing beauty. It is, therefore, commonly assumed that biominerals are formed under the structure-directing influence of templates. However, single molecules are by far too small to direct the formation of the observed shapes and patterns. Instead, supramolecular aggregates are shown to be involved in the formation of templating superstructures relevant in biomineralization. Specific biomolecules were identified in both diatoms and silica sponges, which elegantly combine two indispensable functions: on the one hand, the molecules are capable of inducing silica precipitation from precursor compounds. On the other hand, these molecules are capable of self-assembling into larger, structure-directing template aggregates. Such molecules are the silaffins in the case of diatoms and the silicateins in sponges. Long-chain polyamines of similar composition have meanwhile been discovered in both organisms. The present review is especially devoted to the discussion of the self-assembly behavior of these molecules. Physico-chemical studies on a model compound, poly(allylamine), are discussed in detail in order to elucidate the nature of the interactions responsible for self-assembly of long-chain polyamines and the parameters controlling this process. Numerous biomimetic silica synthesis experiments are discussed and evaluated with respect to the observations made on the aforementioned "natural" biomolecules.     

The role of the transmembrane domain of silicanin-1: Reconstitution of the full-length protein in artificial membranes

Biosilica formation in diatoms is a membrane-confined process that occurs in so-called silica deposition vesicles (SDVs). As SDVs have as yet not been successfully isolated, the impact of the SDV membrane on silica morphogenesis is not well understood. However, recently the first SDV transmembrane protein, silicanin-1 (Sin1) has been identified that appears to be involved in biosilica formation. In this study, we recombinantly expressed and isolated full-length Sin1 from E. coli and investigated its reconstitution behavior in artificial membranes. A reconstitution efficiency in vesicles of up to 80% was achieved by a co-micellization method. By using a chymotrypsin digest, the orientation of Sin1 in unilamellar vesicles was analyzed indicating a positioning of the large N-terminal domain to the outside of the vesicles. These proteoliposomes were capable of precipitating silica in the presence of long-chain polyamines. Supported lipid bilayers were produced by proteoliposome spreading on lipid monolayers to form continuous lipid bilayers with Sin1 confined to the membrane. Successful Sin1 reconstitution into these planar membranes was shown by means of immunostaining with purified primary anti-Sin1 and secondary fluorescent antibodies. The established planar model membrane system, amenable for surface sensitive and microscopy techniques, will pave the way to investigate SDV-membrane interactions with other SDV associated biomolecules and its role in silica biogenesis.     

Prescribing diatom morphology: toward genetic engineering of biological nanomaterials

The formation of inorganic materials with complex form is a widespread biological phenomenon (biomineralization). Among the most spectacular examples of biomineralization is the production by diatoms (a group of eukaryotic microalgae) of intricately nanopatterned to micropatterned cell walls made of silica (SiO2). Understanding the molecular mechanisms of diatom silica biomineralization is not only a fundamental biological problem, but also of great interest in materials engineering, as the biological self-assembly of three-dimensional (3D) inorganic nanomaterials has no man-made analog. Recently, insight into the molecular mechanism of diatom silica formation has been obtained by structural and functional analysis of biomolecules that are involved in this process. Furthermore, the rapid development of diatom molecular genetics has provided new tools for investigating the silica forming machinery of diatoms and for manipulating silica biogenesis. This has opened the door for the production, through genetic engineering, of unique 3D nanomaterials with designed structures and functionalities.     

Quartz fibers as templates for biopolymers

The polymerization of silica in water solution to form quartz fibers proceeds by a dehydration process, analogous to condensation polymerization in organic high-polymers, in which monomeric Si(OH)₄ groups unite through Si–O–Si bonds with the elimination of H₂O. The resulting fibers are structurally polar along the direction of elongation, are enantiomorphous, and generally shown stereospecific twisting around the direction of elongation. In these regards the fibers are analogues of biopolymers such as RNA and DNA. Quartz also possesses specific adsorptive relations to a wide range of organic substances including monomer amino acids, short-chain polypeptides, and proteins. These involve hydrogen-bonding between (OH) or silanoi groups on the surface of the quartz with active side-groups on the organic molecules and in part are epitaxial through dimensional coincidences in the interface.Geochemical evidence indicates that quartz was deposited in the early Precambrian ocean either by direct crystallization from seawater or by recrystallization of amorphous silica. What is of interest is the possible role of quartz fibers as a template and co-polymer in the passage of biomonomers in the pre-biotic ocean to the long-chain biopolymers such as nucleic acids and proteins that are involved in life processes.     

Silicon-augmented resistance of plants to herbivorous insects: a review

Silicon (Si) is one of the most abundant elements in the earth's crust, although its essentiality in plant growth is not clearly established. However, the importance of Si as an element that is particularly beneficial for plants under a range of abiotic and biotic stresses is now beyond doubt. This paper reviews progress in exploring the benefits at two‐ and three‐trophic levels and the underlying mechanism of Si in enhancing the resistance of host plants to herbivorous insects. Numerous studies have shown an enhanced resistance of plants to insect herbivores including folivores, borers, and phloem and xylem feeders. Silicon may act directly on insect herbivores leading to a reduction in insect performance and plant damage. Various indirect effects may also be caused, for example, by delaying herbivore establishment and thus an increased chance of exposure to natural enemies, adverse weather events or control measures that target exposed insects. A further indirect effect of Si may be to increase tolerance of plants to abiotic stresses, notably water stress, which can in turn lead to a reduction in insect numbers and plant damage. There are two mechanisms by which Si is likely to increase resistance to herbivore feeding. Increased physical resistance (constitutive), based on solid amorphous silica, has long been considered the major mechanism of Si‐mediated defences of plants, although there is recent evidence for induced physical defence. Physical resistance involves reduced digestibility and/or increased hardness and abrasiveness of plant tissues because of silica deposition, mainly as opaline phytoliths, in various tissues, including epidermal silica cells. Further, there is now evidence that soluble Si is involved in induced chemical defences to insect herbivore attack through the enhanced production of defensive enzymes or possibly the enhanced release of plant volatiles. However, only two studies have tested for the effect of Si on an insect herbivore and third trophic level effects on the herbivore's predators and parasitoids. One study showed no effect of Si on natural enemies, but the methods used were not favourable for the detection of semiochemical‐mediated effects. Work recently commenced in Australia is methodologically and conceptually more advanced and an effect of Si on the plants' ability to generate an induced response by acting at the third trophic level was observed. This paper provides the first overview of Si in insect herbivore resistance studies, and highlights novel, recent hypotheses and findings in this area of research. Finally, we make suggestions for future research efforts in the use of Si to enhance plant resistance to insect herbivores.     

Aluminium/silicon interactions in higher plants

Aluminium and silicon are usually abundant in soil mineral matter,but their availability for plant uptake is limited by low solubilityand, in the case of Al, high soil pH causes precipitation ofthe element in insoluble forms. Al toxicity is a major problemin naturally occurring acid soils and in soils affected by acidicprecipitation. Al has no known role in higher plants, and isgenerally known as a toxic element, whereas Si is generallyregarded as a beneficial element. Recently, it has been suggestedthat Al toxicity can be ameliorated by Si in a variety of animalsystems. In this review the evidence that amelioration of Altoxicity by Si can also occur in plants is assessed. At presentsuch amelioration has been shown in sorghum, barley, teosinte,and soybean, but not in rice, wheat, cotton, and pea. Plantspecies vary considerably in the amounts of Al and Si that theytransport into their tissues, and it seems that very high Siaccumulation and very high Al accumulation are mutually exclusive.The mechanisms considered for amelioration are: solution effects;codeposition of Al and Si within the plant; effects in the cytoplasmand on enzyme activity; and indirect effects. Key words: Aluminium, silicon, biomineralization, codeposition, toxicity, tolerance     

SILICON IN THE ROOTS OF HIGHER PLANTS

Silicon (Si) distribution in the roots of Sorghastrum nutans (L.) Nash and Sorghum bicolor (L.) Moench. was investigated by means of the electron-probe microanalyzer and scanning electron microscope. In both species, Si was confined to the inner tangential wall of the tertiary-phase endodermal cells in the form of nodular silica aggregates of similar morphology and X-ray intensity. The results are compared to those for six closely related genera, as well as to studies of Si in the roots of species of other tribes of the family Poaceae. The various types of root deposits occurring in the family are described, and their relationships discussed. It is concluded that the type of Si distribution exhibited is determined largely by the phylogenetic status of the genus, rather than by the basic pattern of root anatomy.     

Micromorphology of outer exospore coatings in Selaginella megaspores

Variability of Selaginella megaspore microsculpture is defined and illustrated by means of SEM and TEM. Additional EDX analyses demonstrated that microsculpture elements in the investigated specimens are mainly formed by silica which may be removed by hydrofluoric acid. Our observations suggest that different proportions of sporopollenin/silica are present in the outer coating of at least some Selaginella megaspore walls. Pattern formation mechanisms as well as implications for terminology are discussed. On the basis of this investigation and using data available from the literature, it is argued that the sporoderm layers of Isoetes and Selaginella megaspores are probably homologous, supporting the consensual view.     

Molecular aggregation of nucleotides and carbohydrates—their implication to prebiotic polymerization

Hydrogen bonding pattern of nucleotides and carbohydrates has been analysed using Cambridge database. An analysis on ribonucleotides shows the 3′ …5′ hydrogen bond mediated aggregation to be the most common alignment. The 2′ …5′ alignment, which occurs under special circumstances in nature, is found to be the second choice. An analysis on carbohydrates suggests that self assembly of these molecules is not conducive to the formation of polysaccharides of the type which are found in present day living organisms. Further, the role of water molecules in the polymerization of three important biomolecules, namely nucleotides, carbohydrates and amino acids, has been analysed. Implication of these results to prebiotic polymerization is discussed DCB contribution No. 804.     

The energetics of organic synthesis inside and outside the cell

Thermodynamic modelling of organic synthesis has largely been focused on deep-sea hydrothermal systems. When seawater mixes with hydrothermal fluids, redox gradients are established that serve as potential energy sources for the formation of organic compounds and biomolecules from inorganic starting materials. This energetic drive, which varies substantially depending on the type of host rock, is present and available both for abiotic (outside the cell) and biotic (inside the cell) processes. Here, we review and interpret a library of theoretical studies that target organic synthesis energetics. The biogeochemical scenarios evaluated include those in present-day hydrothermal systems and in putative early Earth environments. It is consistently and repeatedly shown in these studies that the formation of relatively simple organic compounds and biomolecules can be energy-yielding (exergonic) at conditions that occur in hydrothermal systems. Expanding on our ability to calculate biomass synthesis energetics, we also present here a new approach for estimating the energetics of polymerization reactions, specifically those associated with polypeptide formation from the requisite amino acids.     

Molecular mechanisms of the polymerization of fibrin and the formation of its three-dimensional network

The results of biochemical, immunochemical, and X-ray studies of the structures of fibrinogen and fibrin molecules were analyzed. The mechanisms of the successive formation of the fibrin three-dimensional network were described: the polymerization of monomeric molecules with the formation of bifilar protofibrils, the lateral association of protofibrils, and the embranchment of the forming fibrils. Data on the electron and confocal microscopy of the polymeric fibrin were considered. The role of the known polymerization centers of fibrin which participated in the formation of protofibrils and their lateral association was discussed. Data on the existence of the previously unknown polymerization centers were given. In particular, the experimental results demonstrated that one of such centers which participated in the formation of protofibrils was located in the Bβ12–46 fragment, and did not require the cleavage of fibrinopeptide B for its functioning. The results of the computer modeling of the spatial structure of the fibrin(ogen) molecule and the intermolecular interactions in the course of the fibrin polymerization were presented. The location of the αC domains in the fibrin(ogen) molecule and their role in the polymerization process were discussed. Information on the structure of the calciumbinding sites of fibrin(ogen) and the functional role of Ca²⁺ in fibrin polymerization was published. The structure of factor XIII(a) and the mechanisms of fibrin stabilization by this factor were briefly described.     

A general and efficient cantilever functionalization technique for AFM molecular recognition studies

Atomic force microscopy (AFM) is a versatile technique for the investigation of noncovalent molecular associations between ligand–substrate pairs. Surface modification of silicon nitride AFM cantilevers is most commonly achieved using organic trialkoxysilanes. However, susceptibility of the Si? O bond to hydrolysis and formation of polymeric aggregates diminishes attractiveness of this method for AFM studies. Attachment techniques that facilitate immobilization of a wide variety of organic and biological molecules via the stable Si? C bond on silicon nitride cantilevers would be of great value to the field of molecular recognition force spectroscopy. Here, we report (1) the formation of stable, highly oriented monolayers on the tip of silicon nitride cantilevers and (2) demonstrate their utility in the investigation of noncovalent protein–ligand interactions using molecular recognition force spectroscopy. The monolayers are formed through hydrosilylation of hydrogen‐terminated silicon nitride AFM probes using a protected α‐amino‐ω‐alkene. This approach facilitates the subsequent conjugation of biomolecules. The resulting biomolecules are bound to the tip by a strong Si? C bond, completely uniform with regard to both epitope density and substrate orientation, and highly suitable for force microscopy studies. We show that this attachment technique can be used to measure the unbinding profiles of tip‐immobilized lactose and surface‐immobilized galectin‐3. Overall, the proposed technique is general, operationally simple, and can be expanded to anchor a wide variety of epitopes to a silicon nitride cantilever using a stable Si? C bond. © 2012 Wiley Periodicals, Inc. Biopolymers 97: 761–765, 2012.     

The regulation of actin polymerization and cross-linking in Dictyostelium

It is clear that the polymerization and organization of actin filament networks plays a critical role in numerous cellular processes. Inhibition of actin polymerization by pharmacological agents will completely prevent chemotactic motility, macropinocytosis, endocytosis, and phagocytosis. Recently there has been great progress in understanding the mechanisms that control the assembly and structure of the actin cytoskeleton. Members of the Rho family of GTPases have been identified as major players in the signal transduction pathway leading from a cell surface signal to actin polymerization. The Arp2/3 complex has been added to the list of means by which new actin filaments can be nucleated. However, it is clear that actin polymerization by Arp2/3 complex is not the whole story. In principle, the final structures formed by actin filaments will depend on factors such as: the length of actin filaments, the degree of branching, how they are cross-linked and the tensions imparted on them. In addition, the means by which actin polymerization generates protrusion of membranes is still controversial. A phagosome, filopodium and a lamellipodium all require polymerization of new actin filaments, but each has a characteristic morphology and cytoskeletal structure. In the following chapter, we will discuss actin polymerization and filament organization, especially as it relates to the machinery of phagocytosis in Dictyostelium.     

Watershed land use alters riverine silica cycling

Recent research has highlighted that humans are perturbing the global silica (Si) cycle through land use change. Here we compare in-stream Si biogeochemistry across four rivers that lie along a gradient of land use change in New England, USA. Differences between basins were most notable during the late winter/early spring period when dissolved Si (DSi) concentrations declined significantly in all but the most urban site. Declines in DSi concentration could not be attributed to volumetric dilution by higher discharges, nor in-stream phytoplankton growth, as biogenic Si concentrations did not increase during this period. We provide evidence that uptake of Si by terrestrial vegetation, specifically trees, is responsible for the observed declines of in-stream DSi concentrations (a loss of 2.7 μM day^?1 at the most forested site). We hypothesize that sap flow during this late winter/early spring period is driving this accretion. We estimate that 68 kmol Si km^?2 is accreted annually by New England forests, falling well within the range of forest Si accretion rates found in published studies. This analysis increases our understanding of the mechanisms contributing to altered Si biogeochemistry in rivers draining watersheds with different land use.     

Quartz fibers as templates for biopolymers.

The polymerization of silica in water solution to form quartz fibers proceeds by a dehydration process, analogous to condensation polymerization in organic high-polymers, in which monomeric Si(OH)4 groups unite through Si--O--Si bonds with the elimination of H2O. The resulting fibers are structurally polar along the direction of elongation, are enantiomorphous, and generally show stereospecific twisting around the direction of elongation. In these regards the fibers are analogues of biopolymers such as RNA and DNA. Quartz also possesses specific adsorptive relations to a wide range of organic substances including monomer amino acids, short-chain polypeptides, and proteins. These involve hydrogen-bonding between (OH) or silanol groups on the surface of the quartz with active side-groups on the organic molecules, and in part are epitaxial through dimensional coincidences in the interface. Geochemical evidence indicates that quartz was deposited in the early Precambrian ocean either by direct crystallization from seawater or by recrystallization of amorphous silica. What is of interest is the possible role of quartz fibers as a template and co-polymer in the passage of biomonomers in the pre-biotic ocean to the long-chain biopolymers such as nucleic acids and proteins that are involved in life processes.     

Synthesis of novel porous magnetic silica microspheres as adsorbents for isolation of genomic DNA

An improved procedure is described for preparation of novel mesoporous microspheres consisting of magnetic nanoparticles homogeneously dispersed in a silica matrix. The method is based on a three-step process, involving (i) formation of hematite/silica composite microspheres by urea-formaldehyde polymerization, (ii) calcination of the composite particles to remove the organic constituents, and (iii) in situ transformation of the iron oxide in the composites by hydrogen reductive reaction. The as-synthesized magnetite/silica composite microspheres were nearly monodisperse, mesoporous, and magnetizable, with as typical values an average diameter of 3.5 microm, a surface area of 250 m(2)/g, a pore size of 6.03 nm, and a saturation magnetization of 9.82 emu/g. These magnetic particles were tested as adsorbents for isolation of genomic DNA from Saccharomyces cerevisiae cells and maize kernels. The results are quite encouraging as the magnetic particle based protocols lead to the extraction of genomic DNA with satisfactory integrity, yield, and purity. Being hydrophilic in nature, the porous magnetic silica microspheres are considered a good alternative to polystyrene-based magnetic particles for use in biomedical applications where nonspecific adsorption of biomolecules is to be minimized.