Extensive and intimate association of the cytoskeleton with forming silica in diatoms: control over patterning on the meso- and micro-scale

The actin cytoskeleton plays multiple roles in structural colour formation in butterfly wing scales

Vivid structural colours in butterflies are caused by photonic nanostructures scattering light. Structural colours evolved for numerous biological signalling functions and have important technological applications. Optically, such structures are well understood, however insight into their development in vivo remains scarce. We show that actin is intimately involved in structural colour formation in butterfly wing scales. Using comparisons between iridescent (structurally coloured) and non-iridescent scales in adult and developing H. sara, we show that iridescent scales have more densely packed actin bundles leading to an increased density of reflective ridges. Super-resolution microscopy across three distantly related butterfly species reveals that actin is repeatedly re-arranged during scale development and crucially when the optical nanostructures are forming. Furthermore, actin perturbation experiments at these later developmental stages resulted in near total loss of structural colour in H. sara. Overall, this shows that actin plays a vital and direct templating role during structural colour formation in butterfly scales, providing ridge patterning mechanisms that are likely universal across lepidoptera.

ROCK and the actomyosin network control biomineral growth and morphology during sea urchin skeletogenesis

Biomineralization had apparently evolved independently in different phyla, using distinct minerals, organic scaffolds, and gene regulatory networks (GRNs). However, diverse eukaryotes from unicellular organisms, through echinoderms to vertebrates, use the actomyosin network during biomineralization. Specifically, the actomyosin remodeling protein, Rho-associated coiled-coil kinase (ROCK) regulates cell differentiation and gene expression in vertebrates' biomineralizing cells, yet, little is known on ROCK's role in invertebrates' biomineralization. Here, we reveal that ROCK controls the formation, growth, and morphology of the calcite spicules in the sea urchin larva. ROCK expression is elevated in the sea urchin skeletogenic cells downstream of the Vascular Endothelial Growth Factor (VEGF) signaling. ROCK inhibition leads to skeletal loss and disrupts skeletogenic gene expression. ROCK inhibition after spicule formation reduces the spicule elongation rate and induces ectopic spicule branching. Similar skeletogenic phenotypes are observed when ROCK is inhibited in a skeletogenic cell culture, indicating that these phenotypes are due to ROCK activity specifically in the skeletogenic cells. Reduced skeletal growth and enhanced branching are also observed under direct perturbations of the actomyosin network. We propose that ROCK and the actomyosin machinery were employed independently, downstream of distinct GRNs, to regulate biomineral growth and morphology in Eukaryotes.

Transcriptional responses to salinity-induced changes in cell wall morphology of the euryhaline diatom Pleurosira laevis

Diatoms are unicellular algae with morphologically diverse silica cell walls, which are called frustules. The mechanism of frustule morphogenesis has attracted attention in biology and nanomaterials engineering. However, the genetic regulation of the morphology remains unclear. We therefore used transcriptome sequencing to search for genes involved in frustule morphology in the centric diatom Pleurosira laevis, which exhibits morphological plasticity between flat and domed valve faces in salinity 2 and 7, respectively. We observed differential expression of transposable elements (TEs) and transporters, likely due to osmotic response. Up-regulation of mechanosensitive ion channels and down-regulation of Ca2+-ATPases in cells with flat valves suggested that cytosolic Ca2+ levels were changed between the morphologies. Calcium signaling could be a mechanism for detecting osmotic pressure changes and triggering morphological shifts. We also observed an up-regulation of ARPC1 and annexin, involved in the regulation of actin filament dynamics known to affect frustule morphology, as well as the up-regulation of genes encoding frustule-related proteins such as BacSETs and frustulin. Taken together, we propose a model in which salinity-induced morphogenetic changes are driven by upstream responses, such as the regulation of cytosolic Ca2+ levels, and downstream responses, such as Ca2+-dependent regulation of actin dynamics and frustule-related proteins. This study highlights the sensitivity of euryhaline diatoms to environmental salinity and the role of active cellular processes in controlling gross valve morphology under different osmotic pressures.

Mechanism of branching morphogenesis inspired by diatom silica formation

The silica-based cell walls of diatoms are prime examples of genetically controlled, species-specific mineral architectures. The physical principles underlying morphogenesis of their hierarchically structured silica patterns are not understood, yet such insight could indicate novel routes toward synthesizing functional inorganic materials. Recent advances in imaging nascent diatom silica allow rationalizing possible mechanisms of their pattern formation. Here, we combine theory and experiments on the model diatom Thalassiosira pseudonana to put forward a minimal model of branched rib patterns-a fundamental feature of the silica cell wall. We quantitatively recapitulate the time course of rib pattern morphogenesis by accounting for silica biochemistry with autocatalytic formation of diffusible silica precursors followed by conversion into solid silica. We propose that silica deposition releases an inhibitor that slows down up-stream precursor conversion, thereby implementing a self-replicating reaction-diffusion system different from a classical Turing mechanism. The proposed mechanism highlights the role of geometrical cues for guided self-organization, rationalizing the instructive role for the single initial pattern seed known as the primary silicification site. The mechanism of branching morphogenesis that we characterize here is possibly generic and may apply also in other biological systems.

Hierarchical morphogenesis of swallowtail butterfly wing scale nanostructures

The study of color patterns in the animal integument is a fundamental question in biology, with many lepidopteran species being exemplary models in this endeavor due to their relative simplicity and elegance. While significant advances have been made in unraveling the cellular and molecular basis of lepidopteran pigmentary coloration, the morphogenesis of wing scale nanostructures involved in structural color production is not well understood. Contemporary research on this topic largely focuses on a few nymphalid model taxa (e.g., Bicyclus, Heliconius), despite an overwhelming diversity in the hierarchical nanostructural organization of lepidopteran wing scales. Here, we present a time-resolved, comparative developmental study of hierarchical scale nanostructures in Parides eurimedes and five other papilionid species. Our results uphold the putative conserved role of F-actin bundles in acting as spacers between developing ridges, as previously documented in several nymphalid species. Interestingly, while ridges are developing in P. eurimedes, plasma membrane manifests irregular mesh-like crossribs characteristic of Papilionidae, which delineate the accretion of cuticle into rows of planar disks in between ridges. Once the ridges have grown, disintegrating F-actin bundles appear to reorganize into a network that supports the invagination of plasma membrane underlying the disks, subsequently forming an extruded honeycomb lattice. Our results uncover a previously undocumented role for F-actin in the morphogenesis of complex wing scale nanostructures, likely specific to Papilionidae.

Enhancement of hemostatic properties of Cyclotella cryptica frustule through genetic manipulation

BACKGROUND

The silicified cell wall of diatoms, also known as frustule, shows huge potential as an outstanding bio-nanomaterial for hemostatic applications due to its high hemostatic efficiency, good biocompatibility, and ready availability. As the architectural features of the frustule determine its hemostatic performance, it is of great interest to develop an effective method to modify the frustule morphology into desired patterns to further improve hemostatic efficiency.

RESULTS

In this study, the gene encoding Silicalemma Associated Protein 2 (a silicalemma-spanning protein) of Cyclotella cryptica (CcSAP2) was identified as a key gene in frustule morphogenesis. Thus, it was overexpressed and knocked down, respectively. The frustule of the overexpress lines showed no obvious alteration in morphology compared to the wild type (WT), while the size, specific surface area (BET), pore volume, and pore diameter of the knockdown strains changed greatly. Particularly, the knockdown frustules achieved a more pronounced coagulation effect and in vivo hemostatic performance than the WT strains. Such observations suggested that silicalemma proteins are ideal genetic encoding targets for manipulating frustule morphology associated hemostatic properties. Furthermore, the Mantel test was adopted to identify the key morphologies associated with C. cryptica bleeding control. Finally, based on our results and recent advances, the mechanism of frustule morphogenesis was discussed.

CONCLUSION

This study explores a new strategy for enhancing the hemostatic efficiency of the frustule based on genetic morphology modification and may provide insights into a better understanding of the frustule morphogenesis mechanism.

Analysis of Predicted Amino Acid Sequences of Diatom Microtubule Center Components

Diatoms synthesize species-specific exoskeletons inside cells under the control of the cytoskeleton and microtubule center. Previous studies have been conducted with the visualization of the microtubule center; however, its composition has not been studied and reliably established. In the present study, several components of MTOC in diatoms, GCP (gamma complex proteins), Aurora A, and centrins have been identified. Analysis of the predicted amino acid sequences of these proteins revealed structural features typical for diatoms. We analyzed the conserved amino acids and the motives necessary for the functioning of proteins. Phylogenetic analysis of GCP showed that all major groups of diatoms are distributed over phylogenetic trees according to their systematic position. This work is a theoretical study; however, it allows drawing some conclusions about the functioning of the studied components and possible ways to regulate them.

Removal of the Basic and Diazo Dyes from Aqueous Solution by the Frustules of Halamphora cf. salinicola (Bacillariophyta)

Industrial wastes with hazardous dyes serve as a major source of water pollution, which is considered to have an enormous impact on public health. In this study, an eco-friendly adsorbent, the porous siliceous frustules extracted from the diatom species Halamphora cf. salinicola, grown under laboratory conditions, has been identified. The porous architecture and negative surface charge under a pH of 7, provided by the various functional groups via Si-O, N-H, and O-H on these surfaces, revealed by SEM, the N₂ adsorption/desorption isotherm, Zeta-potential measurement, and ATR-FTIR, respectively, made the frustules an efficient mean of removal of the diazo and basic dyes from the aqueous solutions, 74.9%, 94.02%, and 99.81% against Congo Red (CR), Crystal Violet (CV), and Malachite Green (MG), respectively. The maximum adsorption capacities were calculated from isotherms, as follows: 13.04 mg g^-1, 41.97 mg g^-1, and 33.19 mg g^-1 against CR, CV, and MG, respectively. Kinetic and isotherm models showed a higher correlation to Pore diffusion and Sips models for CR, and Pseudo-Second Order and Freundlich models for CV and MG. Therefore, the cleaned frustules of the thermal spring-originated diatom strain Halamphora cf. salinicola could be used as a novel adsorbent of a biological origin against anionic and basic dyes.

Exocytosis of the silicified cell wall of diatoms involves extensive membrane disintegration

Diatoms are unicellular algae characterized by silica cell walls. These silica elements are known to be formed intracellularly in membrane-bound silica deposition vesicles and exocytosed after completion. How diatoms maintain membrane homeostasis during the exocytosis of these large and rigid silica elements remains unknown. Here we study the membrane dynamics during cell wall formation and exocytosis in two model diatom species, using live-cell confocal microscopy, transmission electron microscopy and cryo-electron tomography. Our results show that during its formation, the mineral phase is in tight association with the silica deposition vesicle membranes, which form a precise mold of the delicate geometrical patterns. We find that during exocytosis, the distal silica deposition vesicle membrane and the plasma membrane gradually detach from the mineral and disintegrate in the extracellular space, without any noticeable endocytic retrieval or extracellular repurposing. We demonstrate that within the cell, the proximal silica deposition vesicle membrane becomes the new barrier between the cell and its environment, and assumes the role of a new plasma membrane. These results provide direct structural observations of diatom silica exocytosis, and point to an extraordinary mechanism in which membrane homeostasis is maintained by discarding, rather than recycling, significant membrane patches.

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.

The molecular basis for pore pattern morphogenesis in diatom silica

Biomineral-forming organisms produce inorganic materials with complex, genetically encoded morphologies that are unmatched by current synthetic chemistry. It is poorly understood which genes are involved in biomineral morphogenesis and how the encoded proteins guide this process. We addressed these questions using diatoms, which are paradigms for the self-assembly of hierarchically meso- and macroporous silica under mild reaction conditions. Proteomics analysis of the intracellular organelle for silica biosynthesis led to the identification of new biomineralization proteins. Three of these, coined dAnk1-3, contain a common protein-protein interaction domain (ankyrin repeats), indicating a role in coordinating assembly of the silica biomineralization machinery. Knocking out individual dank genes led to aberrations in silica biogenesis that are consistent with liquid-liquid phase separation as underlying mechanism for pore pattern morphogenesis. Our work provides an unprecedented path for the synthesis of tailored mesoporous silica materials using synthetic biology.

Morphological plasticity in response to salinity change in the euryhaline diatom Pleurosira laevis (Bacillariophyta)

Pleurosira laevis is a salt-tolerant diatom distributed around the world. The valve of P. laevis has distinct structures called ocelli, which are sharply defined areas with fine, densely packed pores. Two formae of this diatom, P. laevis f. laevis and P. laevis f. polymorpha, are distinguished from each other by their flat or dome-shaped valve faces and degree of elevation of the ocelli, respectively. In this study, we established 4 strains of P. laevis isolated from freshwaters or coastal areas in Japan and the United States, and tracked the formation of newly formed valves with the fluorescent SDV-specific dye PDMPO in culture under several salinity conditions. The result clearly demonstrated the morphological plasticity of the valves, controlled by environmental salinity. The laevis form and polymorpha form valves were produced at salinities of 2 and 7, respectively. The salinity thresholds dictating the morphological plasticity of the valve were consistent in all 4 strains. A similar morphology to the polymorpha form was reproduced in a freshwater medium with the addition of sorbitol, suggesting that osmotic pressure plays a key role in this morphological plasticity. The highly reproducible and easily manipulated change in morphology makes this diatom an ideal model for lab experiments focusing on the molecular and genetic factors involved with valve morphogenesis.

Geometrical frustration of phase-separated domains in Coscinodiscus diatom frustules

Diatoms are microalgae with intricate cell walls made of glass. These structures feature micro- and nanoscale hierarchical patterns that cannot be produced with existing synthetic methods. At the same time, manufacturing the cell wall requires little energy and is powered by the sun. Diatoms can thus inspire and inform approaches to sustainable materials processing. Here, we focus on the large-scale organization of micrometer-scale pores in diatom cell walls, which possess an unusual combination of periodicity and radial alignment. While we are not aware of other examples of this organization in nature, it is common in the traditional craft of crochet. Our experiments further show that the competing tendencies of alignment and crystallinity are driven by distinct biological processes.

Diatoms are single-celled organisms with a cell wall made of silica, called the frustule. Even though their elaborate patterns have fascinated scientists for years, little is known about the biological and physical mechanisms underlying their organization. In this work, we take a top-down approach and examine the micrometer-scale organization of diatoms from the Coscinodiscus family. We find two competing tendencies of organization, which appear to be controlled by distinct biological pathways. On one hand, micrometer-scale pores organize locally on a triangular lattice. On the other hand, lattice vectors tend to point globally toward a center of symmetry. This competition results in a frustrated triangular lattice, populated with geometrically necessary defects whose density increases near the center.

Arrested in Glass: Actin within Sophisticated Architectures of Biosilica in Sponges

Actin is a fundamental member of an ancient superfamily of structural intracellular proteins and plays a crucial role in cytoskeleton dynamics, ciliogenesis, phagocytosis, and force generation in both prokaryotes and eukaryotes. It is shown that actin has another function in metazoans: patterning biosilica deposition, a role that has spanned over 500 million years. Species of glass sponges (Hexactinellida) and demosponges (Demospongiae), representatives of the first metazoans, with a broad diversity of skeletal structures with hierarchical architecture unchanged since the late Precambrian, are studied. By etching their skeletons, organic templates dominated by individual F-actin filaments, including branched fibers and the longest, thickest actin fiber bundles ever reported, are isolated. It is proposed that these actin-rich filaments are not the primary site of biosilicification, but this highly sophisticated and multi-scale form of biomineralization in metazoans is ptterned.

Molecular Evolution of Tubulins in Diatoms

Microtubules are formed by α- and β-tubulin heterodimers nucleated with γ-tubulin. Tubulins are conserved eukaryotic proteins. Previously, it was shown that microtubules are involved in diatom silica frustule morphogenesis. Diatom frustules are varied, and their morphology is species-specific. Despite the attractiveness of the problem of elucidating the molecular mechanisms of genetically programmed morphogenesis, the structure and evolution of diatom tubulins have not been studied previously. Based on available genomic and transcriptome data, we analyzed the phylogeny of the predicted amino acid sequences of diatom α-, β- and γ-tubulins and identified five groups for α-tubulins, six for β-tubulins and four for γ-tubulins. We identified characteristic amino acids of each of these groups and also analyzed possible posttranslational modification sites of diatom tubulins. According to our results, we assumed what changes occurred in the diatom tubulin structures during their evolution. We also identified which tubulin groups are inherent in large diatom taxa. The similarity between the evolution of diatom tubulins and the evolution of diatoms suggests that molecular changes in α-, β- and γ-tubulins could be one of the factors in the formation of a high morphological diversity of diatoms.

Solid-State NMR Investigations of Extracellular Matrixes and Cell Walls of Algae, Bacteria, Fungi, and Plants

Extracellular matrixes (ECMs), such as the cell walls and biofilms, are important for supporting cell integrity and function and regulating intercellular communication. These biomaterials are also of significant interest to the production of biofuels and the development of antimicrobial treatment. Solid-state nuclear magnetic resonance (ssNMR) and magic-angle spinning-dynamic nuclear polarization (MAS-DNP) are uniquely powerful for understanding the conformational structure, dynamical characteristics, and supramolecular assemblies of carbohydrates and other biomolecules in ECMs. This review highlights the recent high-resolution investigations of intact ECMs and native cells in many organisms spanning across plants, bacteria, fungi, and algae. We spotlight the structural principles identified in ECMs, discuss the current technical limitation and underexplored biochemical topics, and point out the promising opportunities enabled by the recent advances of the rapidly evolving ssNMR technology.

Phylogeny and structural peculiarities of the EB proteins of diatoms

The end-binding proteins are a family of microtubule-associated proteins; this family belongs to plus-end-tracking proteins (+TIPs) that regulate microtubule growth and stabilisation. Although the genes encoding EB proteins are found in all eukaryotic genomes, most studies of them have centred on one or another taxonomic group, without a broad comparative analysis. Here, we present a first phylogenetic analysis and a comparative analysis of domain structures of diatom EB proteins in comparison with other phyla of Chromista, red and green algae, as well as model organisms A. thaliana and H. sapiens. Phylogenetically, diatom EB proteins are separated into six clades, generally corresponding to the phylogeny of their respective organisms. The domain structure of this family is highly variable, but the CH and EBH domains responsible for binding tubulin and other MAPs are mostly conserved. Homologous modelling of the F. cylindrus EB protein shows that conserved motifs of the CH domain are positioned on the protein surface, which is necessary for their functioning. We hypothesise that high variance of the diatom C-terminal domain is caused by previously unknown interactions with a CAP-GLY motif of dynactin subunit p150. Our findings contribute to wider possibilities for further investigations of the cytoskeleton in diatoms.

Mini-Review: Potential of Diatom-Derived Silica for Biomedical Applications

Diatoms are unicellular eukaryotic microalgae widely distributed in aquatic environments, possessing a porous silica cell wall known as frustule. Diatom frustules are considered as a sustainable source for several industrial applications because of their high biocompatibility and the easiness of surface functionalisation, which make frustules suitable for regenerative medicine and as drug carriers. Frustules are made of hydrated silica, and can be extracted and purified both from living and fossil diatoms using acid treatments or high temperatures. Biosilica frustules have proved to be suitable for biomedical applications, but, unfortunately, they are not officially recognised as safe by governmental food and medical agencies yet. In the present review, we highlight the frustule formation process, the most common purification techniques, as well as advantages and bottlenecks related to the employment of diatom-derived silica for medical purposes, suggesting possible solutions for a large-scale biosilica production.

A biomimetic peptide has no effect on the isotopic fractionation during in vitro silica precipitation

The stable isotopic composition of diatom silica is used as a proxy for nutrient utilisation in natural waters. This approach provides essential insight into the current and historic links between biological production, carbon cycling and climate. However, estimates of isotopic fractionation during diatom silica production from both laboratory and field studies are variable, and the biochemical pathways responsible remain unknown. Here, we investigate silicon isotopic fractionation through a series of chemical precipitation experiments that are analogous to the first stages of intracellular silica formation within the diatom silicon deposition vesicle. The novelty of our experiment is the inclusion of the R5 peptide, which is closely related to a natural biomolecule known to play a role in diatom silicification. Our results suggest that the presence of R5 induces a systematic but non-significant difference in fractionation behaviour. It thus appears that silicon isotopic fractionation in vitro is largely driven by an early kinetic fractionation during rapid precipitation that correlates with the initial amount of dissolved silica in the system. Our findings raise the question of how environmental changes might impact silicon isotopic fractionation in diatoms, and whether frustule archives record information in addition to silica consumption in surface water.

Comparative Structural and Functional Analyses of the Fusiform, Oval, and Triradiate Morphotypes of Phaeodactylum tricornutum Pt3 Strain

The diatom Phaeodactylum tricornutum is a marine unicellular microalga that exists under three main morphotypes: oval, fusiform, and triradiate. Previous works have demonstrated that the oval morphotype of P. tricornutum Pt3 strain presents specific metabolic features. Here, we compared the cellular organization of the main morphotypes of the diatom P. tricornutum Pt3 strain through transmission electron and advanced light microscopies. The three morphotypes share similarities including spectral characteristics of the plastid, the location of the nucleus, the organization of mitochondria around the plastid as well as the existence of both a F-actin cortex, and an intracellular network of F-actin. In contrast, compared to fusiform and triradiate cells, oval cells spontaneously release proteins more rapidly. In addition, comparison of whole transcriptomes of oval versus fusiform or triradiate cells revealed numerous differential expression of positive and negative regulators belonging to the complex dynamic secretory machinery. This study highlights the specificities occurring within the oval morphotype underlying that the oval cells secrete proteins more rapidly.

Diatoms constrain forensic burial timelines: case study with DB Cooper money

Diatoms are found universally in waters around the world. Some diatom species such as Asterionella formosa have a broad variation in seasonal abundance leading to the possibility that diatoms could constrain the time of year when an object was immersed in water. Here we apply this technique to the cold case of DB Cooper’s money. Nine years after the crime, six thousand dollars in three bundles were found on the shore of the Columbia River near Portland, Oregon. This burial site was ~30 km from his reported jump location which gave no apparent reason for the money to end up there. This study found diatoms on a recovered bill which indicates that the money was immersed before burial. The species mix found on the bills was compared to a test bill submerged in the Columbia River in November which was the timeframe for the crime. The Cooper bill contained diatoms from summer bloom species suggesting that the money was not directly buried dry and the immersion happened months after the late November hijacking. This finding rules out of a majority of current theories related to the crime and proposes diatoms as a feasible methodology to constrain seasonal timelines in forensics.

An intimate view into the silica deposition vesicles of diatoms

Diatoms are single-celled microalgae that produce silica-based cell walls with intricate nano- and micropatterns. Biogenesis of diatom biosilica is a bottom-up process that occurs in large intracellular compartments termed silica deposition vesicles (SDVs). Investigating the mechanisms of silica morphogenesis has so far been severely limited by the lack of methods for imaging the entire volume of an SDV with high spatial resolution during all stages of development. Here we have developed a method that allows for rapid identification and electron microscopy imaging of many different, full sized SDVs that are in the process of producing biosilica valves. This enabled visualizing the development of characteristic morphological biosilica features with unprecedented spatio-temporal resolution. During early to mid-term development, valve SDVs contained ~ 20 nm sized particles that were primarily associated with the radially expanding rib-like biosilica structures. The results from electron dispersive X-ray analysis suggests that the immature biosilica patterns are silica-organic composites. This supports the hypothesis that silica morphogenesis is dependent on organic biomolecules inside the SDV lumen.

Ontogenetic analysis of siliceous cell wall formation in Triparma laevis f. inornata (Parmales, Stramenopiles)

Triparma laevis f. inornata is a unicellular alga belonging to the Bolidophyceae, which is most closely related to diatoms. Like diatoms, T. laevis f. inornata has a siliceous cell wall. The cell wall of T. laevis f. inornata consists of four round plates (three shields and one ventral plate) and one dorsal and three girdle plates. But, unlike diatoms, T. laevis f. inornata cells can grow when concentrations of silica are depleted. We took advantage of this ability, using TEM to study the ontogeny of the siliceous plate, pattern center formation, and development. Two types of pattern centers (annulus and sternum) were observed in the early and middle stage of plate formation. During their formation, the annuli were initially crescent-shaped but eventually their ends fused to make a ring. Only outward silica deposition of the branching ribs occurred on the growing annulus until it became a ring, resulting in an unfilled circle inside the annulus. The pattern center of the shield plate was always an annulus, but in ventral plates both annulus and sternum were observed. The annuli and sterna in T. laevis f. inornata round plates were very similar to the annuli and sterna in diatom valves. These results suggested that the round plates of Parmales are homologous to diatom valves. This information on the plate ontogeny of T. laevis f. inornata provides new insights into the evolution of the siliceous cell wall in the Parmales and diatoms.

Fast Fourier infrared spectroscopy to characterize the biochemical composition in diatoms

Diatoms are photosynthetic unicellular microalgae and are nature's hidden source of several biosynthetic metabolites with their use in biofuel, food and drug industries. They mainly contain various lipids, sterols, isoprenoids and toxins with their use in apoptotic, fertility controlling and cancer drugs. Chemical studies on diatoms are limited due to various limitations such as variation of nutrients, contaminants and change in seasonal factors in the environment. To overcome these limitations, we obtained axenic cultures of 12 fresh-water diatom strains on the 22nd day of inoculation having a dry weight of 1 mg each and performed their Fourier transform infrared (FTIR) study for the detection of functional groups responsible for their chemical moiety. The spectral mapping showed a varied level of polyunsaturated fatty acids, amides, amines, ketone bodies and esters for their applications in various pharmacological, food and biofuel industries in the exponential phase of their growth in f/2 media. The FTIR study of the 12 diatom strains showed various similarities in the form of some common peak patterns ranging from 3000 to 3600 cm^-1 for v^O-H absorption. The symmetric stretching vibration frequency of Diadesmis confervaceae (V2) type species showed different behaviour than others in the spectral region starting from 1600 to 1700 cm^-1. The absorption between 1500 and 1575 cm-1 reflects the presence of the -N-H group. Infrared (IR) absorptions falling between 1600 and 1700 cm^-1 reflect the presence of amide's v^C=O in all species. Placoneis elginensis (V8) type species showed an additional absorption band which is centred around 1735-1750 cm^-1 which perhaps reflects the presence of ester's v^C=O. Diadesmis confervaceae (V2), Nitzschia palea (V4), Placoneis elginensis (V8), Nitzschia palea var. debilis (V6), Nitzschia inconspicua (V10), Gomphonema parvulum (V11) and Sellaphora (V12) showed distinct structural features with important key functionalities that can make them essential drug markers in the pharmaceutical industry.

Anomalies in the valve morphogenesis of the centric diatom alga Aulacoseira islandica caused by microtubule inhibitors

Of all unicellular organisms possessing a cell wall, diatoms are the most adept at micro- and nanoscale embellishment of their frustules. Elements of their cell walls are formed inside the cell under cytoskeletal control. In this work, we used laser scanning microscopy and electron microscopy to describe the major stages of cell wall formation in the centric diatom algae Aulacoseira islandica and to study the effect of various microtubule inhibitors on the morphogenesis of frustule elements. Our results show that colchicine inhibits karyokinesis and cytokinesis in A. islandica colonies. In contrast, valve morphogenesis is changed, rather than inhibited altogether. In normal cells, this process starts simultaneously in both daughter cells, beginning with the formation of two adjacent discs that later become valve faces and connecting spines. Under colchicine treatment, however, the cleavage furrow is blocked and a single lateral valve forms on the side of the cylindrical frustule. As a result, a single hollow pipe forms instead of two separate drinking glass-shaped frustules; such pipes can form up to 35% of all forming frustules. Colchicine inhibits the formation of connecting spines, whereas paclitaxel causes spines to form a complex, branching shape. At the same time, inhibitors do not affect the formation of areolae (openings) in the frustule. We discuss the possibility that various processes of the diatom frustule morphogenesis are controlled by two different mechanisms: membrane-related micromorphogenesis and cytoskeleton-mediated macromorphogenesis.

Frustule morphogenesis of raphid pennate diatom Encyonema ventricosum (Agardh) Grunow

Diatoms stand out among other microalgae due to the high diversity of species-specific silica frustules whose components (valves and girdle bands) are formed within the cell in special organelles called silica deposition vesicles (SDVs). Research on cell structure and morphogenesis of frustule elements in diatoms of different taxonomic groups has been carried out since the 1950s but is still relevant today. Here, cytological features and valve morphogenesis in the freshwater raphid pennate diatom Encyonema ventricosum (Agardh) Grunow have been studied using light and transmission electron microscopy of cleaned frustules and ultrathin sections of cells, and scanning electron and atomic force microscopy of the frustule surface. Data have been obtained on chloroplast structure: the pyrenoid is spherical, penetrated by a lamella (a stack of two thylakoids); the girdle lamella consists of several short lamellae. The basic stages of frustule morphogenesis characteristic of raphid pennate diatoms have been traced, with the presence of cytoskeletal elements near SDVs being observed throughout this process. Degradation of the plasmalemma and silicalemma is shown to take place when the newly formed valve is released into the space between sister cells. The role of vesicular transport and exocytosis in the gliding of pennate diatoms is discussed.

The role of the cytoskeleton in biomineralisation in haptophyte algae

The production of calcium carbonate by coccolithophores (haptophytes) contributes significantly to global biogeochemical cycling. The recent identification of a silicifying haptophyte, Prymnesium neolepis, has provided new insight into the evolution of biomineralisation in this lineage. However, the cellular mechanisms of biomineralisation in both calcifying and silicifying haptophytes remain poorly understood. To look for commonalities between these two biomineralisation systems in haptophytes, we have determined the role of actin and tubulin in the formation of intracellular biomineralised scales in the coccolithophore, Coccolithus braarudii and in P. neolepis. We find that disruption of the actin network interferes with secretion of the biomineralised elements in both C. braarudii and P. neolepis. In contrast, disruption of the microtubule network does not prevent secretion of the silica scales in P. neolepis but results in production of abnormally small silica scales and also results in the increased formation of malformed coccoliths in C. braarudii. We conclude that the cytoskeleton plays a crucial role in biomineralisation in both silicifying and calcifying haptophytes. There are some important similarities in the contribution of the cytoskeleton to these different forms of biomineralisation, suggesting that common cellular mechanisms may have been recruited to perform similar roles in both lineages.

Novel subfamilies of actin-regulating proteins

Ability of actin to polymerise and depolymerise makes it essential to key functions of eukaryotic cell. The functioning of actin is controlled by a host of regulatory proteins, the repertoire of which in diatoms is known to remarkably differ from other organisms. We have performed a phylogenetic analysis of 521 actin and actin-related proteins' aminoacid sequences, as well as 190 sequences of gelsolin family proteins from various genomic and transcriptomic datasets. Based on the results of this analysis, as well as on the presence of clade-specific indels in some of the actin-related proteins, we describe a novel ARP subfamily, dubbed ARP12, which is specific to heterokonts and related organisms. We also describe two novel diatom-specific subfamilies, dGRC1 and dGRC2, among short gelsolin repeat-containing proteins.

Characterization of a New Protein Family Associated With the Silica Deposition Vesicle Membrane Enables Genetic Manipulation of Diatom Silica

Diatoms are known for their intricate, silicified cell walls (frustules). Silica polymerization occurs in a compartment called the silica deposition vesicle (SDV) and it was proposed that the cytoskeleton influences silica patterning through the SDV membrane (silicalemma) via interactions with transmembrane proteins. In this work we identify a family of proteins associated with the silicalemma, named SAPs for Silicalemma Associated Proteins. The T. pseudonana SAPs (TpSAPs) are characterized by their motif organization; each contains a transmembrane domain, serine rich region and a conserved cytoplasmic domain. Fluorescent tagging demonstrated that two of the TpSAPs were localized to the silicalemma and that the intralumenal region of TpSAP3 remained embedded in the silica while the cytoplasmic region was cleaved. Knockdown lines of TpSAP1 and 3 displayed malformed valves; which confirmed their roles in frustule morphogenesis. This study provides the first demonstration of altering silica structure through manipulation of a single gene.

Nitrate Reductase Knockout Uncouples Nitrate Transport from Nitrate Assimilation and Drives Repartitioning of Carbon Flux in a Model Pennate Diatom

The ecological prominence of diatoms in the ocean environment largely results from their superior competitive ability for dissolved nitrate (NO3-). To investigate the cellular and genetic basis of diatom NO3- assimilation, we generated a knockout in the nitrate reductase gene (NR-KO) of the model pennate diatom Phaeodactylum tricornutum In NR-KO cells, N-assimilation was abolished although NO3- transport remained intact. Unassimilated NO3- accumulated in NR-KO cells, resulting in swelling and associated changes in biochemical composition and physiology. Elevated expression of genes encoding putative vacuolar NO3- chloride channel transporters plus electron micrographs indicating enlarged vacuoles suggested vacuolar storage of NO3- Triacylglycerol concentrations in the NR-KO cells increased immediately following the addition of NO3-, and these increases coincided with elevated gene expression of key triacylglycerol biosynthesis components. Simultaneously, induction of transcripts encoding proteins involved in thylakoid membrane lipid recycling suggested more abrupt repartitioning of carbon resources in NR-KO cells compared with the wild type. Conversely, ribosomal structure and photosystem genes were immediately deactivated in NR-KO cells following NO3- addition, followed within hours by deactivation of genes encoding enzymes for chlorophyll biosynthesis and carbon fixation and metabolism. N-assimilation pathway genes respond uniquely, apparently induced simultaneously by both NO3- replete and deplete conditions.

Silicanin-1 is a conserved diatom membrane protein involved in silica biomineralization

BACKGROUND

Biological mineral formation (biomineralization) proceeds in specialized compartments often bounded by a lipid bilayer membrane. Currently, the role of membranes in biomineralization is hardly understood.

RESULTS

Investigating biomineralization of SiO₂ (silica) in diatoms we identified Silicanin-1 (Sin1) as a conserved diatom membrane protein present in silica deposition vesicles (SDVs) of Thalassiosira pseudonana. Fluorescence microscopy of GFP-tagged Sin1 enabled, for the first time, to follow the intracellular locations of a biomineralization protein during silica biogenesis in vivo. The analysis revealed incorporation of the N-terminal domain of Sin1 into the biosilica via association with the organic matrix inside the SDVs. In vitro experiments showed that the recombinant N-terminal domain of Sin1 undergoes pH-triggered assembly into large clusters, and promotes silica formation by synergistic interaction with long-chain polyamines.

CONCLUSIONS

Sin1 is the first identified SDV transmembrane protein, and is highly conserved throughout the diatom realm, which suggests a fundamental role in the biomineralization of diatom silica. Through interaction with long-chain polyamines, Sin1 could serve as a molecular link by which the SDV membrane exerts control on the assembly of biosilica-forming organic matrices in the SDV lumen.

Dynamic responses to silicon in Thalasiossira pseudonana - Identification, characterisation and classification of signature genes and their corresponding protein motifs

The diatom cell wall, or frustule, is a highly complex, three-dimensional structure consisting of nanopatterned silica as well as proteins and other organic components. While some key components have been identified, knowledge on frustule biosynthesis is still fragmented. The model diatom Thalassiosira pseudonana was subjected to silicon (Si) shift-up and shift-down situations. Cellular and molecular signatures, dynamic changes and co-regulated clusters representing the hallmarks of cellular and molecular responses to changing Si availabilities were characterised. Ten new proteins with silaffin-like motifs, two kinases and a novel family of putatively frustule-associated transmembrane proteins induced by Si shift-up with a possible role in frustule biosynthesis were identified. A separate cluster analysis performed on all significantly regulated silaffin-like proteins (SFLPs), as well as silaffin-like motifs, resulted in the classification of silaffins, cingulins and SFLPs into distinct clusters. A majority of the genes in the Si-responsive clusters are highly divergent, but positive selection does not seem to be the driver behind this variability. This study provides a high-resolution map over transcriptional responses to changes in Si availability in T. pseudonana. Hallmark Si-responsive genes are identified, characteristic motifs and domains are classified, and taxonomic and evolutionary implications outlined and discussed.

All New Faces of Diatoms: Potential Source of Nanomaterials and Beyond

Nature's silicon marvel, the diatoms have lately astounded the scientific community with its intricate designs and lasting durability. Diatoms are a major group of phytoplanktons involved in the biogeochemical cycling of silica and are virtually inherent in every environment ranging from water to ice to soil. The usage of diatoms has proved prudently cost effective and its handling neither requires costly materials nor sophisticated instruments. Diatoms can easily be acquired from the environment, their culture requires ambient condition and does not involve any costly media or expensive instruments, besides, they can be transported in small quantities and proliferated to a desirable confluence from that scratch, thus are excellent cost effective industrial raw material. Naturally occurring diatom frustules are a source of nanomaterials. Their silica bio-shells have raised curiosity among nanotechnologists who hope that diatoms will facilitate tailoring minuscule structures which are beyond the capabilities of material scientists. Additionally, there is a colossal diversity in the dimensions of diatoms as the frustule shape differs from species to species; this provides a scope for the choice of a particular species of diatom to be tailored to an exacting requisite, thus paving the way to create desired three dimensional nanocomposites. The present article explores the use of diatoms in various arenas of science, may it be in nanotechnology, biotechnology, environmental science, biophysics or biochemistry and summarizes facets of diatom biology under one umbrella. Special emphasis has been given to biosilicification, biomineralization and use of diatoms as nanomaterials', drug delivery vehicles, optical and immune-biosensors, filters, immunodiagnostics, aquaculture feeds, lab-on-a-chip, metabolites, and biofuels.

Non-model model organisms

Model organisms are widely used in research as accessible and convenient systems to study a particular area or question in biology. Traditionally only a handful of organisms have been widely studied, but modern research tools are enabling researchers to extend the set of model organisms to include less-studied and more unusual systems. This Forum highlights a range of 'non-model model organisms' as emerging systems for tackling questions across the whole spectrum of biology (and beyond), the opportunities and challenges, and the outlook for the future.

The Diatom Staurosirella pinnata for Photoactive Material Production

A native isolate of the colonial benthic diatom Staurosirella pinnata was cultivated for biosilica production. The silicified cell walls (frustules) were used as a source of homogeneous and structurally predictable porous biosilica for dye trapping and random laser applications. This was coupled with the extraction of lipids from biomass showing potential to fabricate photoactive composite materials sustainably. The strain was selected for its ease of growth in culture and harvesting. Biosilica and lipids were obtained at the end of growth in indoor photobioreactors. Frustules were structurally characterized microscopically and their chemistry analyzed with Fourier Transform Infrared Spectroscopy. Frustule capacity of binding laser dyes was evaluated on a set of frustules/Rhodamine B (Rho B) solutions and with respect to silicon dioxide and diatomite by Fluorescence Spectroscopy demonstrating a high affinity for the organic dye. The effect of dye trapping property in conveying Rho B emission to frustules, with enhancement of scattering events, was analyzed on Rho B doped polyacrylamide gels filled or not with frustules. Amplified spontaneous emission was recorded at increasing pump power indicating the onset of a random laser effect in frustule filled gels at lower power threshold compared to unfilled matrices.

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.

Silaffins in Silica Biomineralization and Biomimetic Silica Precipitation

Biomineralization processes leading to complex solid structures of inorganic material in biological systems are constantly gaining attention in biotechnology and biomedical research. An outstanding example for biomineral morphogenesis is the formation of highly elaborate, nano-patterned silica shells by diatoms. Among the organic macromolecules that have been closely linked to the tightly controlled precipitation of silica in diatoms, silaffins play an extraordinary role. These peptides typically occur as complex posttranslationally modified variants and are directly involved in the silica deposition process in diatoms. However, even in vitro silaffin-based peptides alone, with and without posttranslational modifications, can efficiently mediate biomimetic silica precipitation leading to silica material with different properties as well as with encapsulated cargo molecules of a large size range. In this review, the biomineralization process of silica in diatoms is summarized with a specific focus on silaffins and their in vitro silica precipitation properties. Applications in the area of bio- and nanotechnology as well as in diagnostics and therapy are discussed.

Ultrastructure and Membrane Traffic During Cell Division in the Marine Pennate Diatom Phaeodactylum tricornutum

The marine pennate diatom Phaeodactylum tricornutum has become a model for diatom biology, due to its ease of culture and accessibility to reverse genetics approaches. While several features underlying the molecular mechanisms of cell division have been described, morphological analyses are less advanced than they are in other diatoms. We therefore examined cell ultrastructure changes prior to and during cytokinesis. Following chloroplast division, cleavage furrows are formed at both longitudinal ends of the cell and are accompanied by significant vesicle transport. Although neither spindle nor microtubules were observed, the nucleus appeared to be split by the furrow after duplication of the Golgi apparatus. Finally, centripetal cytokinesis was completed by fusion of the furrows. Additionally, F-actin formed a ring structure and its diameter became smaller, accompanying the ingrowing furrows. To further analyse vesicular transport during cytokinesis, we generated transgenic cells expressing yellow fluorescent protein (YFP) fusions with putative diatom orthologs of small GTPase Sec4 and t-SNARE protein SyntaxinA. Time-lapse observations revealed that SyntaxinA-YFP localization expands from both cell tips toward the center, whereas Sec4-YFP was found in the Golgi and subsequently relocalizes to the future division plane. This work provides fundamental new information about cell replication processes in P. tricornutum.

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.

Judging diatoms by their cover: variability in local elasticity of Lithodesmium undulatum undergoing cell division

Unique features of diatoms are their intricate cell covers (frustules) made out of hydrated, amorphous silica. The frustule defines and maintains cell shape and protects cells against grazers and pathogens, yet it must allow for cell expansion during growth and division. Other siliceous structures have also evolved in some chain-forming species as means for holding neighboring cells together. Characterization and quantification of mechanical properties of these structures are crucial for the understanding of the relationship between form and function in diatoms, but thus far only a handful of studies have addressed this issue. We conducted micro-indentation experiments, using atomic force microscopy (AFM), to examine local variations in elastic (Young's) moduli of cells and linking structures in the marine, chain-forming diatom Lithodesmium undulatum. Using a fluorescent tracer that is incorporated into new cell wall components we tested the hypothesis that new siliceous structures differ in elastic modulus from their older counterparts. Results show that the local elastic modulus is a highly dynamic property. Elastic modulus of stained regions was significantly lower than that of unstained regions, suggesting that newly formed cell wall components are generally softer than the ones inherited from the parent cells. This study provides the first evidence of differentiation in local elastic properties in the course of the cell cycle. Hardening of newly formed regions may involve incorporation of additional, possibly organic, material but further studies are needed to elucidate the processes that regulate mechanical properties of the frustule during the cell cycle.

Self-Assembly in Biosilicification and Biotemplated Silica Materials

During evolution, living organisms have learned to design biomolecules exhibiting self-assembly properties to build-up materials with complex organizations. This is particularly evidenced by the delicate siliceous structures of diatoms and sponges. These structures have been considered as inspiration sources for the preparation of nanoscale and nanostructured silica-based materials templated by the self-assembled natural or biomimetic molecules. These templates range from short peptides to large viruses, leading to biohybrid objects with a wide variety of dimensions, shapes and organization. A more recent strategy based on the integration of biological self-assembly as the driving force of silica nanoparticles organization offers new perspectives to elaborate highly-tunable, biofunctional nanocomposites.

Identification of a frustule-associated protein of the marine pennate diatom Fistulifera sp. strain JPCC DA0580

Among the proteins localized on the cell wall (frustule) of diatoms (frustule-associated proteins), several proteins tightly associated with the cell wall have been implicated in frustule formation. These proteins include diatom-specific unique serine- and lysine-rich sequences represented by silaffins. Taking advantage of available genome information, we used a recently described bioinformatics approach to screen silaffin-like proteins rich in serine and lysine from the genome of the marine pennate diatom Fistulifera sp. strain JPCC DA0580 and identified 7 proteins. All of the proteins shared a sequence motif called the XGXG domain, which was also confirmed in a silaffin-like protein identified in other diatoms. In vivo localization analysis revealed that one of the identified proteins, G7408, occurs throughout the frustule with a slightly uneven distribution. This novel frustule-associated protein could be a useful tool to elucidate the mechanism of biosilica formation in diatoms and to functionalize this strain for future biotechnological applications.

Brown algal morphogenesis: atomic force microscopy as a tool to study the role of mechanical forces

Over the last few years, a growing interest has been directed toward the use of macroalgae as a source of energy, food and molecules for the cosmetic and pharmaceutical industries. Besides this, macroalgal development remains poorly understood compared to other multicellular organisms. Brown algae (Phaeophyceae) form a monophyletic lineage of usually large multicellular algae which evolved independently from land plants. In their environment, they are subjected to strong mechanical forces (current, waves, and tide), in response to which they modify rapidly and reversibly their morphology. Because of their specific cellular features (cell wall composition, cytoskeleton organization), deciphering how they cope with these forces might help discover new control mechanisms of cell wall softening and cellulose synthesis. Despite the current scarcity in knowledge on brown algal cell wall dynamics and protein composition, we will illustrate, in the light of methods adapted to Ectocarpus siliculosus, to what extent atomic force microscopy can contribute to advance this field of investigation.