Biomimetic and bioinspired silicifications: Recent advances for biomaterial design and applications

The rational design and controllable synthesis of functional silica-based materials have gained increased interest in a variety of biomedical and biotechnological applications due to their unique properties. The current review shows that marine organisms, such as siliceous sponges and diatoms, could be the inspiration for the fabrication of advanced biohybrid materials. Several biomolecules were involved in the molecular mechanism of biosilicification in vivo. Mimicking their behavior, functional silica-based biomaterials have been generated via biomimetic and bioinspired silicification in vitro. Additionally, several advanced technologies were developed for in vitro and in vivo immobilization of biomolecules with potential applications in biocatalysis, biosensors, bioimaging, and immunoassays. A thin silica layer could coat a single living cell or virus as a protective shell offering new opportunities in biotechnology and nanomedicine fields. Promising nanotechnologies have been developed for drug encapsulation and delivery in a targeted and controlled manner, in particular for poorly soluble hydrophobic drugs. Moreover, biomimetic silica, as a morphogenetically active biocompatible material, has been utilized in the field of bone regeneration and in the development of biomedical implantable devices. STATEMENT OF SIGNIFICANCE: In nature, silica-based biomaterials, such as diatom frustules and sponge spicules, with high mechanical and physical properties were created under biocompatible conditions. The fundamental knowledge underlying the molecular mechanisms of biosilica formation could inspire engineers and chemists to design novel hybrid biomaterials using molecular biomimetic strategies. The production of such biohybrid materials brings the biosilicification field closer to practical applications. This review starts with the biosilicification process of sponges and diatoms with recently updated researches. Then, this article covers recent advances in the design of silica-based biomaterials and their potential applications in the fields of biotechnology and nanomedicine, highlighting several promising technologies for encapsulation of functional proteins and living cells, drug delivery and the preparation of scaffolds for bone regeneration.

Identification of the Domains Involved in Promotion of Silica Formation in Glassin, a Protein Occluded in Hexactinellid Sponge Biosilica, for Development of a Tag for Purification and Immobilization of Recombinant Proteins

Glassin, a protein occluded in biosilica of the hexactinellid sponge Euplectela, promotes silica formation from silicic acid at room temperature and neutral pH and is characterized by its primary structure which consists of a tandem repeat carrying three distinct domains, histidine and aspartic acid-rich (HD) domain, proline-rich (P) domain, and histidine and threonine-rich (HT) domain. The present study aims to clarify the domain responsible for the promotion of silica formation and to demonstrate usefulness of glassin and its domain as a tag for purification and immobilization of recombinant proteins. When each domain was mixed with silicic acid at neutral pH, silica was formed with HD domain as well as glassin, or a single repeat, but not with P or HT domain. Neither of amino or carboxy-terminal half of HD domain induced silica formation. The amount of silica formed with HD domain was significantly lower than that of glassin or a single repeat. HD domain fused with HT domain raised the amount of silica formed, while a HD domain fused with P domain, a mixture of HD and P domains, or a mixture of HD and HT domains has little effect on the promotion of silica formation. Collectively, a minimum sequence for promotion of silica formation is HD domain, whose activity can be enhanced by HT domain through a topological effect. In addition, practicality of glassin and HD domain was demonstrated by fusion of these sequences to green fluorescent protein which was successfully purified with Ni affinity chromatography and immobilized on silica.

Evolution of the main skeleton-forming genes in sponges (phylum Porifera) with special focus on the marine Haplosclerida (class Demospongiae)

The skeletons of sponges (Phylum Porifera) are comprised of collagen, often embedded with small siliceous structures (spicules) arranged in various forms to provide strength and flexibility. The main proteins responsible for the formation of the spicules in demosponges are the silicateins, which are related to the cathepsins L of other animals. While the silicatein active site, necessary for the formation of biosilica crystals, is characterized by the amino acids SHN, different variants of the silicatein genes have been found, some that retain SHN at the active site and some that don't. As part of an effort to further understand skeleton formation in marine sponges of the order Haplosclerida, a search for all silicatein variants were made in Irish species representing the main clades of this large sponge group. For this task, transcriptomes were sequenced and de novo assembled from Haliclona oculata, H. simulans and H. indistincta. Silicatein genes were identified from these and all available genomes and transcriptomes from Porifera. These were analysed along with all complete silicateins from GenBank. Silicateins were only found in species belonging to the class Demospongiae but excluding Keratosa and Verongimorpha and there was significant duplication and diversity of these genes. Silicateins showing SHN at the active site were polyphyletic. Indeed silicatein sequences were divided into six major clades (CHNI, CHNII, CHNIII, SHNI, SHNII and C/SQN). In those clades where haplosclerids were well represented the silicatein phylogeny reflected previous ribosomal and mitochondrial topologies. The most basal silicatein clade (CHNI) contained sequences only from marine haplosclerids and freshwater sponges while one silicatein from H. indistincta was more related to cathepsins L (outgroup) than to the overall silicatein clade indicating the presence of an old silicatein or an intermediary form. This data could suggest that marine haplosclerids were one of the first groups of extant demosponges to acquire silicatein genes. Furthermore, we suggest that the paucity of spicule types in this group may be due to their single copy of SHNI variants, and the lack of a silintaphin gene.

Identifying N-terminal peptides by a combination of the edman procedures with a bromine isotope tag: Application to the silicateins

Silicateins are proteins found within spicules of siliceous sponges. They are analogs of proteinases cathepsins; they catalyze the transformation of silicic acid esters into biogenic silica (SiO2 ·nH2 O), and are believed to take part in the processes of silicification in marine and freshwater sponges. Earlier studies by Kalyuzhnaya et al. revealed that the Baikal Sponge Lubomirskia baicalensis Pallas, 1773 (L. baicalensis) contains a gene 1988 bp long, which hosts four sequences that encode four mRNAs giving rise to silicateins α1, α2, α3 and α4 (SILα1, SILα2, SILα3, SILα4) whose predicted amino acid sequences are similar to those of the predicted sequences of marine sponge silicateins. However, the sequences of mature silicateins of L. baicalensis remained unknown, since their N-terminal peptides were not identified. We found the sequences of these N-terminal peptides using a combination of the Edman procedure, which involved reaction with phenylisothiocyanate, treatment with trifluoroacetic acid and trypsinolysis followed by treatment with 4-bromine-phenylisothiocyanate performed directly within polyacrylamide gel bands, and subsequent mass spectrometry. The N-terminal peptides are YAESIDWR (SILα1), YVDSIDWR (SILα2 and α4), and YADSLDWR (SILα3). All mature silicateins of L. baicalensis had a length 217 amino acid residues.

Glassin, a histidine-rich protein from the siliceous skeletal system of the marine sponge Euplectella, directs silica polycondensation

The hexactinellids are a diverse group of predominantly deep sea sponges that synthesize elaborate fibrous skeletal systems of amorphous hydrated silica. As a representative example, members of the genus Euplectella have proved to be useful model systems for investigating structure-function relationships in these hierarchically ordered siliceous network-like composites. Despite recent advances in understanding the mechanistic origins of damage tolerance in these complex skeletal systems, the details of their synthesis have remained largely unexplored. Here, we describe a previously unidentified protein, named "glassin," the main constituent in the water-soluble fraction of the demineralized skeletal elements of Euplectella. When combined with silicic acid solutions, glassin rapidly accelerates silica polycondensation over a pH range of 6-8. Glassin is characterized by high histidine content, and cDNA sequence analysis reveals that glassin shares no significant similarity with any other known proteins. The deduced amino acid sequence reveals that glassin consists of two similar histidine-rich domains and a connecting domain. Each of the histidine-rich domains is composed of three segments: an amino-terminal histidine and aspartic acid-rich sequence, a proline-rich sequence in the middle, and a histidine and threonine-rich sequence at the carboxyl terminus. Histidine always forms HX or HHX repeats, in which most of X positions are occupied by glycine, aspartic acid, or threonine. Recombinant glassin reproduces the silica precipitation activity observed in the native proteins. The highly modular composition of glassin, composed of imidazole, acidic, and hydroxyl residues, favors silica polycondensation and provides insights into the molecular mechanisms of skeletal formation in hexactinellid sponges.

Where's the glass? Biomarkers, molecular clocks, and microRNAs suggest a 200-Myr missing Precambrian fossil record of siliceous sponge spicules

The earliest evidence for animal life comes from the fossil record of 24-isopropylcholestane, a sterane found in Cryogenian deposits, and whose precursors are found in modern demosponges, but not choanoflagellates, calcareans, hexactinellids, or eumetazoans. However, many modern demosponges are also characterized by the presence of siliceous spicules, and there are no convincing demosponge spicules in strata older than the Cambrian. This temporal disparity highlights a problem with our understanding of the Precambrian fossil record--either these supposed demosponge-specific biomarkers were derived from the sterols of some other organism and are simply retained in modern demosponges, or spicules do not primitively characterize crown-group demosponges. Resolving this issue requires resolving the phylogenetic placement of another group of sponges, the hexactinellids, which not only make a spicule thought to be homologous to the spicules of demosponges, but also make their first appearance near the Precambrian/Cambrian boundary. Using two independent analytical approaches and data sets--traditional molecular phylogenetic analyses and the presence or absence of specific microRNA genes--we show that demosponges are monophyletic, and that hexactinellids are their sister group (together forming the Silicea). Thus, spicules must have evolved before the last common ancestor of all living siliceans, suggesting the presence of a significant gap in the silicean spicule fossil record. Molecular divergence estimates date the origin of this last common ancestor well within the Cryogenian, consistent with the biomarker record, and strongly suggests that siliceous spicules were present during the Precambrian but were not preserved.