Silicon-responsive cDNA clones isolated from the marine diatom Cylindrotheca fusiformis

Linking extreme seasonality and gene expression in Arctic marine protists

At high latitudes, strong seasonal differences in light availability affect marine organisms and regulate the timing of ecosystem processes. Marine protists are key players in Arctic aquatic ecosystems, yet little is known about their ecological roles over yearly cycles. This is especially true for the dark polar night period, which up until recently was assumed to be devoid of biological activity. A 12 million transcripts catalogue was built from 0.45 to 10 μm protist assemblages sampled over 13 months in a time series station in an Arctic fjord in Svalbard. Community gene expression was correlated with seasonality, with light as the main driving factor. Transcript diversity and evenness were higher during polar night compared to polar day. Light-dependent functions had higher relative expression during polar day, except phototransduction. 64% of the most expressed genes could not be functionally annotated, yet up to 78% were identified in Arctic samples from Tara Oceans, suggesting that Arctic marine assemblages are distinct from those from other oceans. Our study increases understanding of the links between extreme seasonality and biological processes in pico- and nanoplanktonic protists. Our results set the ground for future monitoring studies investigating the seasonal impact of climate change on the communities of microbial eukaryotes in the High Arctic.

Computational modelling of diatom silicic acid transporters predicts a conserved fold with implications for their function and evolution

Diatoms are an important group of algae that can produce intricate silicified cell walls (frustules). The complex process of silicification involves a set of enigmatic integral membrane proteins that are thought to actively transport the soluble precursor of biosilica, dissolved silicic acid. Full-length silicic acid transporters are found widely across the diatoms while homologous shorter proteins have now been identified in a range of other organisms. It has been suggested that modern silicic acid transporters arose from the union of such partial sequences. Here, we present a computational study of the silicic acid transporters and related transporter-like sequences to help understand the structure, function and evolution of this class of membrane protein. The AlphaFold software predicts that all of the protein sequences studied here share a common fold in the membrane domain which is entirely different from the predicted folds of non-homologous silicic acid transporters from plants. Substrate docking reveals how conserved polar residues could interact with silicic acid at a central solvent-accessible binding site, consistent with an alternating access mechanism of transport. The structural conservation between these proteins supports a model where modern silicon transporters evolved from smaller ancestral proteins by gene fusion.

Genome-wide identification and functional analysis of silicon transporter family genes in moso bamboo (Phyllostachys edulis)

Silicon (Si) has crucial effects on plant development and stress resistance. Silicon transporters regulate Si absorption, transport, and distribution in plants. In this study, we identified and characterized the Si transporter gene family of moso bamboo (Phyllostachys edulis) and cloned seven putative Si transporter genes. Moso bamboo Si transporters contain conserved functional domains that mediate the accumulation of considerable amounts of Si. The analysis of gene duplication patterns and divergence times suggested that the expansion of the moso bamboo Si transporter family was mainly due to segmental duplications. The expression of moso bamboo Si transporter genes, which varied among organs, was significantly modulated by Si treatments. The subcellular localization analysis showed that Si transporters are plasma membrane proteins. The Si content increased in transgenic Arabidopsis overexpressing PeLsi1-1 or PeLsi1-2, which affected vegetative and reproductive growth. Our single-particle tracking analysis revealed the four diffusion modes of PeLsi1-1 on the plasma membrane. Moreover, the particle velocity, dwell time, and motion range of PeLsi1-1 decreased in response to Si treatments. The results of this study will further clarify the molecular mechanisms underlying Si absorption and accumulation in bamboo plants.

Identification of a mammalian silicon transporter

Silicon (Si) has long been known to play a major physiological and structural role in certain organisms, including diatoms, sponges, and many higher plants, leading to the recent identification of multiple proteins responsible for Si transport in a range of algal and plant species. In mammals, despite several convincing studies suggesting that silicon is an important factor in bone development and connective tissue health, there is a critical lack of understanding about the biochemical pathways that enable Si homeostasis. Here we report the identification of a mammalian efflux Si transporter, namely Slc34a2 (also termed NaPiIIb), a known sodium-phosphate cotransporter, which was upregulated in rat kidney following chronic dietary Si deprivation. Normal rat renal epithelium demonstrated punctate expression of Slc34a2, and when the protein was heterologously expressed in Xenopus laevis oocytes, Si efflux activity (i.e., movement of Si out of cells) was induced and was quantitatively similar to that induced by the known plant Si transporter OsLsi2 in the same expression system. Interestingly, Si efflux appeared saturable over time, but it did not vary as a function of extracellular HPO42− or Na⁺ concentration, suggesting that Slc34a2 harbors a functionally independent transport site for Si operating in the reverse direction to the site for phosphate. Indeed, in rats with dietary Si depletion-induced upregulation of transporter expression, there was increased urinary phosphate excretion. This is the first evidence of an active Si transport protein in mammals and points towards an important role for Si in vertebrates and explains interactions between dietary phosphate and silicon.

Direct evidence of the molecular basis for biological silicon transport

Diatoms are an important group of eukaryotic algae with a curious evolutionary innovation: they sheath themselves in a cell wall made largely of silica. The cellular machinery responsible for silicification includes a family of membrane permeases that recognize and actively transport the soluble precursor of biosilica, silicic acid. However, the molecular basis of silicic acid transport remains obscure. Here, we identify experimentally tractable diatom silicic acid transporter (SIT) homologues and study their structure and function in vitro, enabled by the development of a new fluorescence method for studying substrate transport kinetics. We show that recombinant SITs are Na⁺/silicic acid symporters with a 1:1 protein: substrate stoichiometry and K_M for silicic acid of 20 μM. Protein mutagenesis supports the long-standing hypothesis that four conserved GXQ amino acid motifs are important in SIT function. This marks a step towards a detailed understanding of silicon transport with implications for biogeochemistry and bioinspired materials.

Diatoms sheath themselves in a self-made casing of silica, which requires the function of silicic acid transporters. Here, the authors identify versions of these transporters that are experimentally tractable, and develop a fluorescence method to study silicic acid transport in vitro.

Aquaporins Mediate Silicon Transport in Humans

In animals, silicon is an abundant and differentially distributed trace element that is believed to play important biological functions. One would thus expect silicon concentrations in body fluids to be regulated by silicon transporters at the surface of many cell types. Curiously, however, and even though they exist in plants and algae, no such transporters have been identified to date in vertebrates. Here, we show for the first time that the human aquaglyceroporins, i.e., AQP3, AQP7, AQP9 and AQP10 can act as silicon transporters in both Xenopus laevis oocytes and HEK-293 cells. In particular, heterologously expressed AQP7, AQP9 and AQP10 are all able to induce robust, saturable, phloretin-sensitive silicon transport activity in the range that was observed for low silicon rice 1 (lsi1), a silicon transporter in plant. Furthermore, we show that the aquaglyceroporins appear as relevant silicon permeation pathways in both mice and humans based on 1) the kinetics of substrate transport, 2) their presence in tissues where silicon is presumed to play key roles and 3) their transcriptional responses to changes in dietary silicon. Taken together, our data provide new evidence that silicon is a potentially important biological element in animals and that its body distribution is regulated. They should open up original areas of investigations aimed at deciphering the true physiological role of silicon in vertebrates.

Diatom silica biomineralization: Parallel development of approaches and understanding

Diatom silica cell walls present an intriguing application of biomineralization in a single celled organism. The ability of diatoms to make an enormous variety of silica structures on the nano- to micro-scale is unparalleled in nature. The process is a whole-cell endeavor, involving diverse cellular components that coordinate "bottom up" and "top down" structure formation processes to reproducibly convert genetic information into physical structure. The study of silicification has been similarly all encompassing, involving the application of diverse analytical techniques to examine different aspects of the process. This review highlights the application of different approaches used to study silicification and the insights they have provided, and documents the progress that has been made. The current status offers the possibility of major breakthroughs in our understanding, by enabling a more widespread identification of genes involved, and direct testing of the role these genes play by genetic manipulation.

A family of diatom-like silicon transporters in the siliceous loricate choanoflagellates

Biosilicification is widespread across the eukaryotes and requires concentration of silicon in intracellular vesicles. Knowledge of the molecular mechanisms underlying this process remains limited, with unrelated silicon-transporting proteins found in the eukaryotic clades previously studied. Here, we report the identification of silicon transporter (SIT)-type genes from the siliceous loricate choanoflagellates Stephanoeca diplocostata and Diaphanoeca grandis. Until now, the SIT gene family has been identified only in diatoms and other siliceous stramenopiles, which are distantly related to choanoflagellates among the eukaryotes. This is the first evidence of similarity between SITs from different eukaryotic supergroups. Phylogenetic analysis indicates that choanoflagellate and stramenopile SITs form distinct monophyletic groups. The absence of putative SIT genes in any other eukaryotic groups, including non-siliceous choanoflagellates, leads us to propose that SIT genes underwent a lateral gene transfer event between stramenopiles and loricate choanoflagellates. We suggest that the incorporation of a foreign SIT gene into the stramenopile or choanoflagellate genome resulted in a major metabolic change: the acquisition of biomineralized silica structures. This hypothesis implies that biosilicification has evolved multiple times independently in the eukaryotes, and paves the way for a better understanding of the biochemical basis of silicon transport through identification of conserved sequence motifs.

Preparation and in vitro evaluation of plasma-sprayed Mg(2)SiO(4) coating on titanium alloy

In this paper, chemically synthesized Mg(2)SiO(4) (MS) powder was plasma-sprayed onto a titanium alloy substrate to evaluate its application potentials in biomedicine. The phase composition and surface morphology of the MS coating were analyzed. Results showed that the MS coating was composed mainly of Mg(2)SiO(4) phase, with a small amount of MgO and glass phases. Mechanical testing showed that the coating exhibited good adhesion strength to the substrate due to the close thermal expansion coefficient between the MS ceramic and the titanium alloy substrate. The measured bonding strength was as high as 41.5+/-5.3MPa, which is much higher than the traditional HA coating. In vitro cytocompatibility evaluation of the MS coating was performed using canine bone marrow stem cells (MSCs). The MSCs exhibited good adhesion, proliferation and differentiation behavior on the MS coating surface, which can be explained by the high protein adsorption capability of the MS coating, as well as the stimulatory effects of Mg and Si ions released from the coating. The proliferation rate of the MSCs on MS coating was very close to that on the hydroxylapatite (HA) coating. Alkaline phosphatase (ALP) activity analysis demonstrated that the ALP level of the MSCs on the MS coating remained high even after 21days, implying that the surface characteristics of the coating are beneficial for the differentiation of MSCs. In summary, our results suggest that MS coating might be a new approach to prepare bone implants.

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.

An efflux transporter of silicon in rice

Silicon is an important nutrient for the optimal growth and sustainable production of rice. Rice accumulates up to 10% silicon in the shoot, and this high accumulation is required to protect the plant from multiple abiotic and biotic stresses. A gene, Lsi1, that encodes a silicon influx transporter has been identified in rice. Here we describe a previously uncharacterized gene, low silicon rice 2 (Lsi2), which has no similarity to Lsi1. This gene is constitutively expressed in the roots. The protein encoded by this gene is localized, like Lsi1, on the plasma membrane of cells in both the exodermis and the endodermis, but in contrast to Lsi1, which is localized on the distal side, Lsi2 is localized on the proximal side of the same cells. Expression of Lsi2 in Xenopus oocytes did not result in influx transport activity for silicon, but preloading of the oocytes with silicon resulted in a release of silicon, indicating that Lsi2 is a silicon efflux transporter. The identification of this silicon transporter revealed a unique mechanism of nutrient transport in plants: having an influx transporter on one side and an efflux transporter on the other side of the cell to permit the effective transcellular transport of the nutrients.

Human osteoblast response to silicon-substituted hydroxyapatite

Human osteoblasts were cultured on hydroxyapatite (HA), 0.8 wt % silicon substituted hydroxyapatite (Si-HA) and 1.5 wt % Si-HA discs. The influence of these substrates on cell behaviour in vitro was assessed by measuring total protein in the cell lysate and the production of several phenotypic markers: collagen type I (COL I), alkaline phosphatase (ALP), osteocalcin (OC), and the formation of bone mineral. After 7 days, beta-glycerophosphate and physiological levels of hydrocortisone were added to the culture medium to stimulate cell differentiation and mineral production. There was a significantly higher production of ALP on 1.5 wt % Si-HA at day 7 following which, the addition of hydrocortisone promoted the differentiation of cells on the other two substrates. Hydrocortisone addition also decreased the production of OC. During the period, when hydrocortisone was present, no significant difference in behavior was seen between cells on Si-HA and HA; however, following removal of hydrocortisone, cells responded to 0.8 wt % Si-HA with a significant increase in protein production. Using fluorescence microscopy, nodular structures labeled with tetracycline were observed on the surface of all substrates after 21 days. These structures were deposited on areas of high cell density but were not related to the presence or level of silicon in the substrate. These results indicate that human osteoblasts are affected by the presence of silicon in the HA substrate and that the timing of these effects may be dependent upon the level of silicon substitution.

Silicon uptake and accumulation in higher plants

Silicon (Si) accumulation differs greatly between plant species because of differences in Si uptake by the roots. Recently, a gene encoding a Si uptake transporter in rice, a typical Si-accumulating plant, was isolated. The beneficial effects of Si are mainly associated with its high deposition in plant tissues, enhancing their strength and rigidity. However, Si might play an active role in enhancing host resistance to plant diseases by stimulating defense reaction mechanisms. Because many plants are not able to accumulate Si at high enough levels to be beneficial, genetically manipulating the Si uptake capacity of the root might help plants to accumulate more Si and, hence, improve their ability to overcome biotic and abiotic stresses.

A silicon transporter in rice

Silicon is beneficial to plant growth and helps plants to overcome abiotic and biotic stresses by preventing lodging (falling over) and increasing resistance to pests and diseases, as well as other stresses. Silicon is essential for high and sustainable production of rice, but the molecular mechanism responsible for the uptake of silicon is unknown. Here we describe the Low silicon rice 1 (Lsi1) gene, which controls silicon accumulation in rice, a typical silicon-accumulating plant. This gene belongs to the aquaporin family and is constitutively expressed in the roots. Lsi1 is localized on the plasma membrane of the distal side of both exodermis and endodermis cells, where casparian strips are located. Suppression of Lsi1 expression resulted in reduced silicon uptake. Furthermore, expression of Lsi1 in Xenopus oocytes showed transport activity for silicon only. The identification of a silicon transporter provides both an insight into the silicon uptake system in plants, and a new strategy for producing crops with high resistance to multiple stresses by genetic modification of the root's silicon uptake capacity.

Early apatite deposition and osteoblast growth on plasma-sprayed dicalcium silicate coating

Dicalcium silicate coating was deposited onto a Ti-6Al-4V substrate using plasma-spraying technology. The coating was immersed in simulated body fluid (SBF) for 1, 3, 6, 12, 24, and 48 h to investigate early apatite formation on the coating. Osteoblasts were also seeded onto the surface of the dicalcium silicate coating to evaluate its biocompatibility. Cold field-emission scanning electron microscopy and energy-dispersive X-ray spectrometry were used to evaluate the morphologies and determine the chemical composition of the coatings. The surface structural changes caused by immersion in SBF were analyzed using thin-film X-ray diffraction. After the dicalcium silicate coating was soaked in SBF solution 1-6 h, two types of particles containing calcium and phosphorus were formed on the surface. One type consisted of relatively larger particles (P1) precipitated on the surface of the coating from the precursor cluster formed in the SBF solution. The second type was composed of particles (P2) nucleated on the surface of the coating. With increasing immersion time, the particles coalesced to form a surface Ca-P layer. The Ca-P layer was composed of amorphous calcium phosphate that was not transformed to crystalline apatite until the immersion time in SBF exceeded 24 h. The formation mechanism of the Ca-P layer and apatite on the surface of the coating is believed to be involved in the formation of the Si 3-ring active surface site with negative charge. The cell-seeding test revealed that osteoblasts grew and proliferated very well on the surface of the dicalcium silicate coating.

Characterization of the silicon uptake system and molecular mapping of the silicon transporter gene in rice

Rice (Oryza sativa L. cv Oochikara) is a typical silicon-accumulating plant, but the mechanism responsible for the high silicon uptake by the roots is poorly understood. We characterized the silicon uptake system in rice roots by using a low-silicon rice mutant (lsi1) and wild-type rice. A kinetic study showed that the concentration of silicon in the root symplastic solution increased with increasing silicon concentrations in the external solution but saturated at a higher concentration in both lines. There were no differences in the silicon concentration of the symplastic solution between the wild-type rice and the mutant. The form of soluble silicon in the root, xylem, and leaf identified by (29)Si-NMR was also the same in the two lines. However, the concentration of silicon in the xylem sap was much higher in the wild type than in the mutant. These results indicate that at least two transporters are involved in silicon transport from the external solution to the xylem and that the low-silicon rice mutant is defective in loading silicon into xylem rather than silicon uptake from external solution to cortical cells. To map the responsible gene, we performed a bulked segregant analysis by using both microsatellite and expressed sequence tag-based PCR markers. As a result, the gene was mapped to chromosome 2, flanked by microsatellite marker RM5303 and expressed sequence tag-based PCR marker E60168.

A rice mutant defective in Si uptake

Rice (Oryza sativa) accumulates silicon (Si) in the tops to levels up to 10.0% of shoot dry weight, but the mechanism responsible for high Si uptake by rice roots is not understood. We isolated a rice mutant (GR1) that is defective in active Si uptake by screening M(2) seeds (64,000) of rice cv Oochikara that were treated with 10(-3) M sodium azide for 6 h at 25 degrees C. There were no phenotypic differences between wild type (WT) and GR1 except that the leaf blade of GR1 remained droopy when Si was supplied. Uptake experiments showed that Si uptake by GR1 was significantly lower than that by WT at both low and high Si concentrations. However, there was no difference in the uptake of other nutrients such as phosphorus and potassium. Si concentration in the xylem sap of WT was 33-fold that of the external solution, but that of GR1 was 3-fold higher than the external solution at 0.15 mM Si. Si uptake by WT was inhibited by metabolic inhibitors including NaCN and 2,4-dinitrophenol and by low temperature, whereas Si uptake by GR1 was not inhibited by these agents. These results suggest that an active transport system for Si uptake is disrupted in GR1. Analysis of F(2) populations between GR1 and WT showed that roots with high Si uptake and roots with low Si uptake segregated at a 3:1 ratio, suggesting that GR1 is a recessive mutant of Si uptake.

Plasma sprayed wollastonite/TiO2 composite coatings on titanium alloys

Wollastonite/TiO2 composite coatings were prepared using plasma spraying technology onto Ti-6Al-4V substrate. The composite coatings exhibit obvious lamellar structure with alternating wollastonite coating and TiO2 coating. No obvious cracks exist on the interface between coatings and substrate. In the case of composite coatings, the primarily crystalline phases of the coatings are wollastonite and rutile, indicating wollastonite and TiO2 did not react during plasma spraying process. Some of rutile in the powders transforms into anatase due to plasma spraying. The mean bond strength of the composite coatings is higher than 30 MPa. The Vickers microhardness of coatings increase with the increase in the content of TiO2. Wollastonite/TiO2 composite coatings were soaked in simulated body fluid to examine their bioactivity. Carbonate-containing hydroxyapatite (CHA) layer was formed on the surface of the wollastonite and W7T3 coatings soaked in simulated body fluid, while was not formed on the surface of the TiO2 and W3T7 coatings after immersion. In addition, a rich-silica layer appeared at the interface of CHA and wollastonite and W7T3 coatings. In order to investigate the cytocompatibility of the coatings, osteoblast was seeded onto the surface of the coatings. The scanning electron microscopy observation showed that the addition of wollastonite promote the proliferation of osteoblast. It is enough to prove that the wollastonite and wollastonite/TiO2 composite coatings possess excellent cytocompatibility.

SILICON

Silicon is present in plants in amounts equivalent to those of such macronutrient elements as calcium, magnesium, and phosphorus, and in grasses often at higher levels than any other inorganic constituent. Yet except for certain algae, including prominently the diatoms, and the Equisetaceae (horsetails or scouring rushes), it is not considered an essential element for plants. As a result it is routinely omitted from formulations of culture solutions and considered a nonentity in much of plant physiological research. But silicon-deprived plants grown in conventional nutrient solutions to which silicon has not been added are in many ways experimental artifacts. They are often structurally weaker than silicon-replete plants, abnormal in growth, development, viability, and reproduction, more susceptible to such abiotic stresses as metal toxicities, and easier prey to disease organisms and to herbivores ranging from phytophagous insects to mammals. Many of these same conditions afflict plants in silicon-poor soils-and there are such. Taken together, the evidence is overwhelming that silicon should be included among the elements having a major bearing on plant life.

Supplementation of calves with stabilized orthosilicic acid. Effect on the Si, Ca, Mg, and P concentrations in serum and the collagen concentration in skin and cartilage

The bioavailability of silicon in stabilized orthosilicic acid was investigated in a double blind, placebo controlled supplementation study of calves maintained on a normal diet. The total dietary Si intake was increased by 4.9% in the form of stabilized orthosilicic acid. After 23 wk of Si supplementation, the serum Si concentration increased (p = 0.0001, n = 29) by 70% compared to control animals in spite of the low Si dose administered and the Si adequate diet. The individually administered Si dose was significantly associated with the serum Si concentration (r = 0.44, p = 0.016, n = 29). The collagen concentration in dermis was significantly higher (p = 0.019, n = 4) in the Si group and a positive correlation (r = 0.72, p = 0.018, n = 9) was found between the Si concentration in serum and the collagen concentration in cartilage. The calcium (Ca) and phosphorus (P) concentrations in serum were marginally higher for animals supplemented with Si compared to control animals. In serum, a significant linear relationship was found between the Si and the Ca concentration (r = 0.31, p = 0.019, n = 59), whereas the magnesium concentration correlated marginally with the Si concentration (r = 0.25, p = 0.068, n = 59). In summary, increasing the total dietary Si intake by 4.9% in the form of stabilized orthosilicic acid resulted in a 70% higher Si concentration in serum indicating a high bioavailability of Si in this supplement. The positive correlation between the serum Si concentration and the collagen concentration in cartilage and the serum Ca concentration, respectively, suggest the involvement of Si both in the formation of extracellular matrix components and in Ca metabolism.