Silacidins: highly acidic phosphopeptides from diatom shells assist in silica precipitation in vitro

Characterization of an endoplasmic reticulum-associated silaffin kinase from the diatom Thalassiosira pseudonana

The formation of SiO(2)-based cell walls by diatoms (a large group of unicellular microalgae) is a well established model system for the study of molecular mechanisms of biological mineral morphogenesis (biomineralization). Diatom biomineralization involves highly phosphorylated proteins (silaffins and silacidins), analogous to other biomineralization systems, which also depend on diverse sets of phosphoproteins (e.g. mammalian teeth and bone, mollusk shells, and sponge silica). The phosphate moieties on biomineralization proteins play an essential role in mineral formation, yet the kinases catalyzing the phosphorylation of these proteins have remained poorly characterized. Recent functional genomics studies on the diatom Thalassiosira pseudonana have revealed >100 proteins potentially involved in diatom silica formation. Here we have characterized the biochemical properties and biological function of one of these proteins, tpSTK1. Multiple tpSTK1-like proteins are encoded in diatom genomes, all of which exhibit low but significant sequence similarity to kinases from other organisms. We show that tpSTK1 has serine/threonine kinase activity capable of phosphorylating silaffins but not silacidins. Cell biological and biochemical analysis demonstrated that tpSTK1 is an abundant component of the lumen of the endoplasmic reticulum. The present study provides the first molecular structure of a kinase that appears to catalyze phosphorylation of biomineral forming proteins in vivo.

Bioinspired control of colloidal silica in vitro by dual polymeric assemblies of zwitterionic phosphomethylated chitosan and polycations or polyanions

This paper focuses on the effects of biological and synthetic polymers on the formation of amorphous silica. A concise review of relevant literature related to biosilicification is presented. The importance of synergies between polyelectrolytes on the inhibition of silicic acid condensation is discussed. A specific example of a zwitterionic polymer phosphonomethylated chitosan (PCH) is further analyzed for its inhibitory activity. Specifically, the ability of PCH to retard silicic acid condensation at circumneutral pH in aqueous supersaturated solutions is explored. It was discovered that in short-term studies (0-8 h) the inhibitory activity is PCH dosage-independent, but for longer condensation times (>24 h) there is a clear increase in inhibition upon PCH dosage increase. Soluble silicic acid levels reach 300 ppm after 24 h in the presence of 160 ppm PCH. Furthermore, the effects of either purely cationic (polyethyleneimine, PEI) or purely anionic (carboxymethylinulin, CMI) polyelectrolytes on the inhibitory activity of PCH is systematically studied. It was found that the action of inhibitor blends is not cumulative. PCH/PEI blends stabilize the same level of silicic acid as PCH alone in both short-term (8 h) and long-term (72 h) experiments. PCH/CMI combinations on the other hand can only achieve short-term inhibition of silicic acid polymerization, but fail to extend this over the first 8 h. PCH and its combinations with PEI or CMI affect silica particle morphology, studied by SEM. Spherical particles and their aggregates, irregularly shaped particles and porous structures are obtained depending on additive or additive blend. It was demonstrated by FT-IR that PCH is trapped in the colloidal silica matrix.

Genome-wide transcriptome analyses of silicon metabolism in Phaeodactylum tricornutum reveal the multilevel regulation of silicic acid transporters

Background

Diatoms are largely responsible for production of biogenic silica in the global ocean. However, in surface seawater, Si(OH)₄ can be a major limiting factor for diatom productivity. Analyzing at the global scale the genes networks involved in Si transport and metabolism is critical in order to elucidate Si biomineralization, and to understand diatoms contribution to biogeochemical cycles.

Methodology/Principal Findings

Using whole genome expression analyses we evaluated the transcriptional response to Si availability for the model species Phaeodactylum tricornutum. Among the differentially regulated genes we found genes involved in glutamine-nitrogen pathways, encoding putative extracellular matrix components, or involved in iron regulation. Some of these compounds may be good candidates for intracellular intermediates involved in silicic acid storage and/or intracellular transport, which are very important processes that remain mysterious in diatoms. Expression analyses and localization studies gave the first picture of the spatial distribution of a silicic acid transporter in a diatom model species, and support the existence of transcriptional and post-transcriptional regulations.

Conclusions/Significance

Our global analyses revealed that about one fourth of the differentially expressed genes are organized in clusters, underlying a possible evolution of P. tricornutum genome, and perhaps other pennate diatoms, toward a better optimization of its response to variable environmental stimuli. High fitness and adaptation of diatoms to various Si levels in marine environments might arise in part by global regulations from gene (expression level) to genomic (organization in clusters, dosage compensation by gene duplication), and by post-transcriptional regulation and spatial distribution of SIT proteins.

The life of diatoms in the world's oceans

Marine diatoms rose to prominence about 100 million years ago and today generate most of the organic matter that serves as food for life in the sea. They exist in a dilute world where compounds essential for growth are recycled and shared, and they greatly influence global climate, atmospheric carbon dioxide concentration and marine ecosystem function. How these essential organisms will respond to the rapidly changing conditions in today's oceans is critical for the health of the environment and is being uncovered by studies of their genomes.

Kinetics of silica nucleation on carboxyl- and amine-terminated surfaces: insights for biomineralization

An in situ, atomic force microscopy- (AFM-)-based experimental approach is developed to directly measure the kinetics of silica nucleation on model biosubstrates under chemical conditions that mimic natural biosilica deposition environments. Relative contributions of thermodynamic and kinetic drivers to surface nucleation are quantified by use of amine-, carboxyl-, and hybrid NH(3)(+)/COO(-)-terminated surfaces as surrogates for charged and ionizable groups on silica-mineralizing organic matrices. The data show that amine-terminated surfaces do not promote silica nucleation, whereas carboxyl and hybrid NH(3)(+)/COO(-) substrates are active for silica deposition. The rate of silica nucleation is approximately 18x faster on the hybrid substrates than on carboxylated surfaces, but the free energy barriers to cluster formation are similar on both surface types. These findings suggest that surface nucleation rates are more sensitive to kinetic drivers than previously believed and that cooperative interactions between oppositely charged surface species play important roles in directing the onset of silica nucleation. Further experiments to test the importance of these cooperative interactions with patterned NH(3)(+)/COO(-) substrates, and aminated surfaces with solution-borne anionic species, confirm that silica nucleation is most rapid when oppositely charged species are proximal. By documenting the synergy that occurs between surface groups during silica formation, these findings demonstrate a new type of emergent behavior underlying the ability of self-assembled molecular templates to direct mineral formation.

3D imaging of diatoms with ion-abrasion scanning electron microscopy

Ion-abrasion scanning electron microscopy (IASEM) takes advantage of focused ion beams to abrade thin sections from the surface of bulk specimens, coupled with SEM to image the surface of each section, enabling 3D reconstructions of subcellular architecture at approximately 30nm resolution. Here, we report the first application of IASEM for imaging a biomineralizing organism, the marine diatom Thalassiosira pseudonana. Diatoms have highly patterned silica-based cell wall structures that are unique models for the study and application of directed nanomaterials synthesis by biological systems. Our study provides new insights into the architecture and assembly principles of both the "hard" (siliceous) and "soft" (organic) components of the cell. From 3D reconstructions of developmentally synchronized diatoms captured at different stages, we show that both micro- and nanoscale siliceous structures can be visualized at specific stages in their formation. We show that not only are structures visualized in a whole-cell context, but demonstrate that fragile, early-stage structures are visible, and that this can be combined with elemental mapping in the exposed slice. We demonstrate that the 3D architectures of silica structures, and the cellular components that mediate their creation and positioning can be visualized simultaneously, providing new opportunities to study and manipulate mineral nanostructures in a genetically tractable system.

Plasticity and robustness of pattern formation in the model diatom Phaeodactylum tricornutum

Understanding the morphogenesis of mineralized structures found in shells, bones, teeth, spicules and plant cell walls is difficult because of the complexities underlying biomineralization, and the requirement of accurate models for pattern formation. Here, we investigated the spatial and temporal development of siliceous structures found in a model diatom species, Phaeodactylum tricornutum, for which the entire genome has been sequenced and transformation is routine. Analyses of pattern formation revealed that the process of silicification starts from a 'pi-like' structure that controls the spatial organization of a sternum upon which regular instabilities are initiated and developed. Detailed analyses also demonstrate that morphogenesis of silica is nonuniform. We also tested the sensitivity of pattern formation to perturbation of proton pumps, and found that selective inhibitors of H(+)-V-ATPases affect silica biomineralization both quantitatively and qualitatively. Morphometric analyses of valves purified from isogenic populations of cells show that the morphometric noise of several traits is under exquisite regulation, explaining why the overall valve pattern is reproducibly maintained. Altogether our analyses demonstrate that silica morphogenesis is a robust but nonuniform process, and allow us to propose a model for the dynamic growth of materials within a spatially controlled geometry.

The Glass Menagerie: diatoms for novel applications in nanotechnology

Diatoms are unicellular, eukaryotic, photosynthetic algae that are found in aquatic environments. Diatoms have enormous ecological importance on this planet and display a diversity of patterns and structures at the nano- to millimetre scale. Diatom nanotechnology, a new interdisciplinary area, has spawned collaborations in biology, biochemistry, biotechnology, physics, chemistry, material science and engineering. We survey diatom nanotechnology since 2005, emphasizing recent advances in diatom biomineralization, biophotonics, photoluminescence, microfluidics, compustat domestication, multiscale porosity, silica sequestering of proteins, detection of trace gases, controlled drug delivery and computer design. Diatoms might become the first organisms for which the gap in our knowledge of the relationship between genotype and phenotype is closed.

Calcification and silicification: a comparative survey of the early stages of biomineralization

Most of the studies on biomineralization have focused on calcification and silicification, the two systems that predominate in nature in the construction of skeletal or integumental hard tissues. They have, however, been studied separately, as if they were completely distinct processes, in spite of their several points of contact, especially as far as the organic-inorganic relationships during the early mineralization stages are concerned. A very tight association of the inorganic substance with organic macromolecules, in fact, initially characterizes both systems. Although the mechanism of biomineralization remains elusive, a number of old and new findings, which have been taken into account in this review, support the view that, both in calcification and in silicification, genetically controlled organic macromolecules induce the formation of composite, organic-inorganic nanoparticles, behave as templates for the subsequent assemblage of the nanoparticles into micro- to macroarchitectures of complex pattern, and, eventually, are mostly reabsorbed. There are still many gaps left in our knowledge of this process. Comparative studies of the two biomineralization systems may help to fill them.

Templating silica nanostructures on rationally designed self-assembled peptide fibers

Nature presents exquisite examples of templating hard, functional inorganic materials on soft, self-assembled organic substrates. An ability to mimic and control similar processes in the laboratory would increase our understanding of fundamental science, and may lead to potential applications in the broad arena of bionanotechnology. Here we describe how self-assembled, alpha-helix-based peptide fibers of de novo design can promote and direct the deposition of silica from silicic acid solutions. The peptide substrate can be removed readily through proteolysis, or other facile means to render silica nanotubes. Furthermore, the resulting silica structures, which span the nanometer to micrometer range, can themselves be used to template the deposition of the cationic polyelectrolyte, poly-(diallyldimethylammonium chloride). Finally, the peptide-based substrates can be engineered prior to silicification to alter the morphology and mechanical properties of the resulting hybrid and tubular materials.

Silica biomineralization in diatoms: the model organism Thalassiosira pseudonana

After complete genome sequencing, the diatom Thalassiosira pseudonana has become an attractive model organism for silica biomineralization studies. Recent progress, especially with respect to intracellular silicic acid processing, as well as to the natures of the biomolecules involved in diatom cell wall formation, is described. On the one hand, considerable progress has been made with respect to silicon uptake by special proteins (SITs) from the surrounding water, as well as to the storage and processing of silicon before cell division. On the other hand, the discovery and characterisation of remarkable biomolecules such as silaffins, polyamines and--quite recently--of silacidins in the siliceous cell walls of diatoms strongly impacts the growing field of biomimetic materials synthesis.