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.     

Lessons from seashells: silica mineralization via protein templating

Silica, the most abundant compound in the earth's crust, is also widespread in biological systems. Silica has many functions, including support and protection in single-celled organisms and in higher plants and animals alike. Despite this widespread occurrence and importance of function, little is known about biosilica and the mechanisms that produce controlled microscopic and macroscopic silica structures with nanoscale precision, exceeding present synthetic technological approaches. Here we highlight recent progress in identifying proteins, genes and the various environmental factors responsible for the controlled synthesis of silica by marine organisms. Examples of biomimetic approaches to biosilica formation using model peptides to control the formation of structures through manipulation of the processing environment are discussed.     

Silica in plants: biological, biochemical and chemical studies

BACKGROUND: The incorporation of silica within the plant cell wall has been well documented by botanists and materials scientists; however, the means by which plants are able to transport silicon and control its polymerization, together with the roles of silica in situ, are not fully understood. RECENT PROGRESS: Recent studies into the mechanisms by which silicification proceeds have identified the following: an energy-dependent Si transporter; Si as a biologically active element triggering natural defence mechanisms; and the means by which abiotic toxicities are alleviated by silica. A full understanding of silica formation in vivo still requires an elucidation of the role played by the environment in which silica formation occurs. Results from in-vitro studies of the effects of cell-wall components associated with polymerized silica on mineral formation illustrate the interactions occurring between the biomolecules and silica, and the effects their presence has on the mineralized structures so formed. SCOPE: This Botanical Briefing describes the uptake, storage and function of Si, and discusses the role biomolecules play when incorporated into model systems of silica polymerization as well as future directions for research in this field.     

Evidence for Fossilized Subsurface Microbial Communities at the TAG Hydrothermal Mound

Scanning electron microscope examinations have revealed fossilized cell-like structures randomly distributed in near-surface oxidized deposits of red and gray Fe-rich chert and Fe-Si oxyhydroxides of the Trans-Atlantic Geotraverse (TAG) hydrothermal mound, Mid-Atlantic Ridge at 26°08'N. Chemically, these structures are carbon-based with the morphology of half-spheroids that are 2 to 3 w m in diameter and are mostly arranged in the form of clusters and long thread-like cellular masses that resemble single-celled microorganisms. The wide range of intracrystalline silica concentration, which seems to replace the original chemistry, suggests that the microorganisms were subjected to various degrees of silica mineralization, which was probably controlled by the thermal development of this hydrothermal site.     

硅藻纳米技术

硅藻是一类微小的单细胞藻类,具有由无定形氧化硅组成的坚硬细胞壁(硅壳).硅壳具有精致的形态和结构,且随硅藻种类和生长条件不同而千变万化.目前估算的硅藻种类超过200 000种,其独特的纳米结构对光子结构、化学生物传感器、新纳米材料和器件的开发具有启发意义.同时硅藻形态形成学和分子生物学的研究,可以推动硅质材料的仿生合成...     

Biomineralization: Some complex crystallite-oriented skeletal structures

The present review focuses on some specific aspects of biomineralization with regard to the evolution of the first focused visioning systems in trilobites, the formation of molluscan shell architecture, dental enamel and its biomechanical properties and the structure of the calcified amniote egg, both fossil and recent. As an interdisciplinary field, biomineralization deals with the formation, structure and mechanical strength of mineralized skeletonized tissue secreted by organisms. Mineral matter formed in this way occurs in all three domains of life and consists of several mineral varieties, of which carbonates, phosphates and opaline silica are the most common. Animals and plants need mechanical support to counteract gravitational forces on land and hydrostatic pressure in the deep ocean, which is provided by a skeletonized framework. Skeleton architecture mainly consists of basic elements represented by small usually micrometer- to nanometer-sized crystallites of calcite and aragonite for carbonate systems and apatite crystallites for phosphatic ones, and then these building blocks develop into structured more complex frameworks. As selective pressures work towards optimizing stress and response, the orientation, morphology and structural arrangement of the crystallites indicates the distribution of the stress field of the biomineralized tissue. Large animals such as the dinosaurs have to deal with large gravitational forces, but in much smaller skeletonized organism such as the coccoliths, a few micrometer in diameter made up of even smaller individual crystallites, van der Waals forces play an increasingly important role and are at present poorly understood. Skeleton formation is dependent upon many factors including ambient water chemistry, temperature and environment. Ocean chemistry has played a vital role in the origins of skeletonization, 500 to 600 million years (ma) ago with the dominance of calcium carbonate as the principal skeleton-forming tissue and with phosphates and silica as important but secondary materials. The preservation of calcareous skeletons in deep time has resulted in providing interesting information: for example, the number of days in the Devonian year has been established on the basis of well-preserved lunar (annual) cycles, and isotope chemistry has led to an elaborate protocol for using O¹⁸/O¹⁶ stable isotopes for palaeotemperature measurements in the geological past. Stable isotopes of dental apatite have helped to establish ecological shifts (terrestrial to wholly marine) during the evolution of the Cetacea. Biomineralization as a field of specialization is still searching for its own independent identity, but gradually, its importance is being realized as a model for engineering applications especially at the nanometer scale.     

Pentalysine Clusters Mediate Silica Targeting of Silaffins in Thalassiosira pseudonana

The biological formation of inorganic materials (biomineralization) often occurs in specialized intracellular vesicles. Prominent examples are diatoms, a group of single-celled eukaryotic microalgae that produce their SiO₂ (silica)-based cell walls within intracellular silica deposition vesicles (SDVs). SDVs contain protein-based organic matrices that control silica formation, resulting in species specifically nanopatterned biosilica, an organic-inorganic composite material. So far no information is available regarding the molecular mechanisms of SDV biogenesis. Here we have investigated by fluorescence microscopy and subcellular membrane fractionation the intracellular transport of silaffin Sil3. Silaffins are a group of phosphoproteins constituting the main components of the organic matrix of diatom biosilica. We demonstrate that the N-terminal signal peptide of Sil3 mediates import into a specific subregion of the endoplasmic reticulum. Additional segments from the mature part of Sil3 are required to reach post-endoplasmic reticulum compartments. Further transport of Sil3 and incorporation into the biosilica (silica targeting) require protein segments that contain a high density of modified lysine residues and phosphoserines. Silica targeting of Sil3 is not dependent on a particular peptide sequence, yet a lysine-rich 12–14-amino acid peptide motif (pentalysine cluster), which is conserved in all silaffins, strongly promotes silica targeting. The results of the present work provide the first insight into the molecular mechanisms for biogenesis of mineral-forming vesicles from an eukaryotic organism.     

Cationic amino acids specific biomimetic silicification in ionic liquid: a quest to understand the formation of 3-D structures in diatoms

The intricate, hierarchical, highly reproducible, and exquisite biosilica structures formed by diatoms have generated great interest to understand biosilicification processes in nature. This curiosity is driven by the quest of researchers to understand nature's complexity, which might enable reproducing these elegant natural diatomaceous structures in our laboratories via biomimetics, which is currently beyond the capabilities of material scientists. To this end, significant understanding of the biomolecules involved in biosilicification has been gained, wherein cationic peptides and proteins are found to play a key role in the formation of these exquisite structures. Although biochemical factors responsible for silica formation in diatoms have been studied for decades, the challenge to mimic biosilica structures similar to those synthesized by diatoms in their natural habitats has not hitherto been successful. This has led to an increasingly interesting debate that physico-chemical environment surrounding diatoms might play an additional critical role towards the control of diatom morphologies. The current study demonstrates this proof of concept by using cationic amino acids as catalyst/template/scaffold towards attaining diatom-like silica morphologies under biomimetic conditions in ionic liquids.     

Catabolism of dimethylsulphoniopropionate: microorganisms, enzymes and genes

The compatible solute dimethylsulphoniopropionate (DMSP) has important roles in marine environments. It is an anti-stress compound made by many single-celled plankton, some seaweeds and a few land plants that live by the shore. Furthermore, in the oceans it is a major source of carbon and sulphur for marine bacteria that break it down to products such as dimethyl sulphide, which are important in their own right and have wide-ranging effects, from altering animal behaviour to seeding cloud formation. In this Review, we describe how recent genetic and genomic work on the ways in which several different bacteria, and some fungi, catabolize DMSP has provided new and surprising insights into the mechanisms, regulation and possible evolution of DMSP catabolism in microorganisms.     

Beyond micromachining: the potential of diatoms.

Diatoms are microscopic, single-celled algae that possess rigid cell walls (frustules) composed of amorphous silica. Depending on the species of diatom and the growth conditions, these frustules can display a wide range of different morphologies. It is possible to design and produce specific frustule morphologies that have potential applications in nanotechnology.     

Poly(vinyl amine)-silica composite nanoparticles: models of the silicic acid cytoplasmic pool and as a silica precursor for composite materials formation

The role of polymer (poly(vinylamine)) size (238-11000 units) on silicic acid condensation to yield soluble nanoparticles or composite precipitates has been explored by a combination of light scattering (static and dynamic), laser ablation combined with aerosol spectrometry, IR spectroscopy, and electron microscopy. Soluble nanoparticles or composite precipitates are formed according to the degree of polymerization of the organic polymer and pH. Nanoparticles prepared in the presence of the highest molecular weight polymers have core-shell like structures with dense silica cores. Composite particles formed in the presence of polymers with extent of polymerization below 1000 consist of associates of several polymer-silica nanoparticles. The mechanism of stabilization of the "soluble" silica particles in the tens of nanometer size range involves cooperative interactions with the polymer chains which varies according to chain length and pH. An example of the use of such polymer-poly(silicic acid) nanoparticles in the generation of composite polymeric materials is presented. The results obtained have relevance to the biomimetic design of new composite materials based on silica and polymers and to increasing our understanding of how silica may be manipulated (stored) in the biological environment prior to the formation of stable mineralized structures. We suspect that a similar method of storing silicic acid in an active state is used in silicifying organisms, at least in diatom algae.     

Separation and quantification of chicken and bovine growth plate cartilage matrix vesicle lipids by high-performance liquid chromatography using evaporative light scattering detection

Matrix vesicles (MV) are lipid bilayer-enclosed nanoscale structures that initiate extracellular mineral formation in most vertebrate species. Little attention has been given to differences between species in membrane lipid composition or to how new mineral is formed in MV. To explore more precisely the lipids of MV isolated from avian and bovine species, we developed a new high-performance liquid chromatography (HPLC) method used in combination with evaporative light scattering detection (ELSD) to quantify their lipid composition. HPLC analyses were performed on a Lichrosorb silica column using separate binary gradient elution systems for analyzing polar and nonpolar lipids. Standard mixtures of both phospholipids and nonpolar lipids were used to prepare calibration curves for each lipid, which were analyzed mathematically by polynomial regression for accurate quantitation. This new methodology provides high-resolution separations and quantitation of both the polar and the nonpolar lipids typically present in biological membranes, including lyso- (monoacyl-) phospholipids. We have applied this method to quantitate the phospholipid and nonpolar lipid composition of MV isolated from chicken and bovine growth plate cartilage. We also compared the ability of these MV to induce mineral formation. While the ability to induce mineralization and the lipid composition were generally similar, some significant differences between MV from these two disparate species were seen.     

Discussion on entrained droplets in fermenters used for the cultivation of single-celled mircoorganisms

The validity of regarding the liquid phase in vigorously agitated sparged fermenters during the cultivation of single-celled aerobic microorganisms as essentially homogeneous is examined. Droplet formation from bursting bubbles and physical effects of the spray environment on single-celled microorganisms are discussed. The implications of droplet removal from the head space of fermenters by collision with and drainage down the walls are considered, particularly factors concerned with wall growth above the liquid level in fermenters.     

Molecular product formation in the electron radiolysis of water.

The time dependence of the formation of a molecular product in radiation chemistry is linked to the yield of the product formed in scavenging experiments by a Laplace transform relationship. Kinetic modeling with deterministic methods is used to show that such a relationship can be used to describe the molecular product (H2 and H2O2) formation following the fast-electron radiolysis of water and of aqueous solutions. Experimental yields are fitted using an appropriate empirical function, and the time dependence of the yields of the molecular products in the absence of a scavenger is derived using the Laplace relationship.     

The Effect of Plants on Mineral Weathering

This paper is centered on the specific effects of plants on the soil weathering environment; we attempt to address how to quantify this component of the ecosystem and assess feedbacks between plants and weathering processes that influence the degree and rates of mineral weathering. The basic processes whereby plants directly influence the soil chemical environment is through the generation of weathering agents, biocycling of cations, and the production of biogenic minerals. Plants may indirectly influence soil processes through the alteration of regional hydrology and local soil hydrologic regime which determines the residence time of water available for weathering. We provide a brief review of the current state of knowledge regarding the effects of plants on mineral weathering and critical knowledge gaps are highlighted. We summarize approaches that may be used to help quantify the effects of plants on soil weathering such as state factor analyses, mass balance approaches, laboratory batch experiments and isotopic techniques. We assess the changes in the soil chemical environment along a tropical bioclimatic gradient and identify the possible effects of plant production on the soil mineralogical composition. We demonstrate that plants are important in the transfer of atmospheric carbon dioxide into the mineral weathering cycle and speculate how this may be related to ecosystem properties such as NPP. In the soils of Hawaiian rainforests subjected to deforestation, pasture grasses appear to change the proportion of non crystalline to crystalline minerals by altering the soil hydrologic regime or partitioning silica into more stable biogenic forms. A better understanding of the relationship between soil weathering processes and ecosystem productivity will assist in the construction predictive models capable of evaluating the sensitivity of biogeochemical cycles to perturbations.     

New insights into the complex architecture of siliceous copepod teeth

Copepods belong to the dominant marine zooplankton taxa and play an important role in particle and energy fluxes of the marine water column. Their mandibular gnathobases possess tooth-like structures, so-called teeth. In species feeding on large proportions of diatoms these teeth often contain silica, which is very probably the result of a coevolution with the siliceous diatom frustules. Detailed knowledge of the morphology and composition of the siliceous teeth is essential for understanding their functioning and their significance in the context of feeding interactions between copepods and diatoms. Based on analyses of the gnathobases of the Antarctic copepod Rhincalanus gigas, the present study clearly shows, for the first time, that the silica in the siliceous teeth features large proportions of crystalline silica that is consistent with the mineral α-cristobalite and is doped with aluminium. The siliceous structures have internal chitinous fibre networks, which are assumed to serve as scaffolds during the silicification process. The compact siliceous teeth of R. gigas are accompanied by structures with large proportions of the elastic protein resilin, likely reducing the mechanical damage of the teeth when the copepods feed on diatoms with very stable frustules. The results indicate that the coevolution with diatom frustules has resulted in gnathobases exhibiting highly sophisticated composite structures.     

Dynamics of silica cell wall morphogenesis in the diatom Cyclotella cryptica: Substructure formation and the role of microfilaments

Diatoms are unicellular algae that make cell walls out of silica with highly ornate features on the nano- to microscale. The complexity and variety of diatom cell wall structures exceeds those possible with synthetic materials chemistry approaches. Understanding the design and assembly processes involved in diatom silicification should provide insight into patterning on the unicellular level, and information for biomimetic approaches for materials synthesis. In this report we examine the formation of distinct cell wall structures (valves and girdle bands) in the diatom Cyclotella cryptica by high resolution imaging using SEM, AFM, and fluorescence microscopy. Special attention was paid to imaging structural intermediates, which provided insight into the underlying design and assembly principles involved. Distinct stages in valve formation were identified, indicating a transition from a fractally organized structure to a dynamic pathway-dependent process. Substructures in the valves appeared to be pre-positioned prior to complete silicification, suggesting that organics responsible for these structures were pre-assembled and put in place. Microtubules and microfilamentous actin play significant roles in the positioning process, and actin is also important in the pathway-dependent expansion of the front of silicification. Our results indicate that even though all silica structures in C. cryptica are made of assemblies of nanoparticulate silica, control of meso- and microscale structure occurs on a higher order. It is apparent that diatoms integrate bottom up and top down control and synthesis mechanisms to form the diversity of structures possible.     

Transient existence of life without a cell membrane: a novel strategy of siphonous seaweed for survival and propagation

Siphonous seaweeds, which constitute a vital component of coral reefs, are structurally simple, single-celled coenocytic macroscopic green algae. Kim et al.1 have recently shown the extraordinary wound-repair and propagation mechanism of one such siphonous green alga--Bryopsis plumosa. Nucleocytoplasmic aggregates, which are released after injury to this plant, are membraneless structures that can survive in seawater for 10-20 minutes, before they are surrounded by a gelatinous envelope. Subsequently, a cell membrane and cell wall are synthesized around each of these aggregates and the resulting individual cells, so formed, develop into new plants. This report represents a significant advance in our understanding of wound response and, more significantly, is probably the first example of transient survival of life without a cell membrane!     

Formation of nodular structures on the non-legumes Brassica napus,B. campestris,B. juncea and Arabidopsis thaliana with Bradyrhizobium and Rhizobium isolated from Parasponia spp. or legumes grown in tropical soils

Strains of Bradyrhizobium formed nodule-like structures on Arabidopsis and species of Brassica in pots with sandvermiculite and in glass tubes on a nitrogen-free mineral salts agar. Broad-host-range Rhizobium strains NGR234 from Lablab purpureus and NGR76 from Phaseolus vulgaris formed similar nodule-like structures on Brassica spp. The size of these structures on plants in pots were large, often reaching 10 mm in diameter.The frequency of inoculated Brassica plants in pots with nodule-like structures was 25–50%, depending on the inoculum strain. The inheritable nature of factors involved in the formation of the nodule-like structures was demonstrated when the structures occurred on 100% of inoculated B. napus seedlings derived from plants with the nodule-like structures.Nodule-like structures occurred without, but not with, the application of a cellulase-pectolyase-PEG treatment to the roots. Attempts to isolate Bradyrhizobium or Rhizobium from the nodule-like structures failed. Internal infection of these structures could not be detected using either the light or electron microscope. The inoculum strains of root-nodule bacteria were detected in high numbers in the rhizosphere of plants 5 months after inoculation. On agar plates bacterial colonies could be seen, with undiminished growth, over the surface of the agar extending to the root surface. However, ground root tissue of Brassica was toxic to Bradyrhizobium strains. This suggested that Bradyrhizobium strains would not survive after infecting the roots of Brassica spp. Nitrogen fixation was associated with high rhizosphere populations of Azospirillum and not with Bradyrhizobium induced nodule structures of Brassica spp.     

Improvement of hairy root cultures and plants by changing biosynthetic pathways leading to pharmaceutical metabolites: Strategies and applications

A plethora of bioactive plant metabolites has been explored for pharmaceutical, food chemistry and agricultural applications. The chemical synthesis of these structures is often difficult, so plants are favorably used as producers. While whole plants can serve as a source for secondary metabolites and can be also improved by metabolic engineering, more often cell or organ cultures of relevant plant species are of interest. It should be noted that only in few cases the production for commercial application in such cultures has been achieved. Their genetic manipulation is sometimes faster and the production of a specific metabolite is more reliable, because of less environmental influences. In addition, upscaling in bioreactors is nowadays possible for many of these cultures, so some are already used in industry. There are approaches to alter the profile of metabolites not only by using plant genes, but also by using bacterial genes encoding modifying enzymes. Also, strategies to cope with unwanted or even toxic compounds are available. The need for metabolic engineering of plant secondary metabolite pathways is increasing with the rising demand for (novel) compounds with new bioactive properties. Here, we give some examples of recent developments for the metabolic engineering of plants and organ cultures, which can be used in the production of metabolites with interesting properties.