Organic crystal lattices in the axial filament of silica spicules of Demospongiae

Natural hybrid silica/protein superstructure at atomic resolution

Formation of highly symmetric skeletal elements in demosponges, called spicules, follows a unique biomineralization mechanism in which polycondensation of an inherently disordered amorphous silica is guided by a highly ordered proteinaceous scaffold, the axial filament. The enzymatically active proteins, silicateins, are assembled into a slender hybrid silica/protein crystalline superstructure that directs the morphogenesis of the spicules. Furthermore, silicateins are known to catalyze the formation of a large variety of other technologically relevant organic and inorganic materials. However, despite the biological and biotechnological importance of this macromolecule, its tertiary structure was never determined. Here we report the atomic structure of silicatein and the entire mineral/organic hybrid assembly with a resolution of 2.4 Å. In this work, the serial X-ray crystallography method was successfully adopted to probe the 2-µm-thick filaments in situ, being embedded inside the skeletal elements. In combination with imaging and chemical analysis using high-resolution transmission electron microscopy, we provide detailed information on the enzymatic activity of silicatein, its crystallization, and the emergence of a functional three-dimensional silica/protein superstructure in vivo. Ultimately, we describe a naturally occurring mineral/protein crystalline assembly at atomic resolution.

Protein-driven biomineralization: Comparing silica formation in grass silica cells to other biomineralization processes

Biomineralization is a common strategy adopted by organisms to support their body structure. Plants practice significant silicon and calcium based biomineralization in which silicon is deposited as silica in cell walls and intracellularly in various cell-types, while calcium is deposited mostly as calcium oxalate in vacuoles of specialized cells. In this review, we compare cellular processes leading to protein-dependent mineralization in plants, diatoms and sponges (phylum Porifera). The mechanisms of biomineralization in these organisms are inherently different. The composite silica structure in diatoms forms inside the cytoplasm in a membrane bound vesicle, which after maturation is exocytosed to the cell surface. In sponges, separate vesicles with the mineral precursor (silicic acid), an inorganic template, and organic molecules, fuse together and are extruded to the extracellular space. In plants, calcium oxalate mineral precipitates in vacuolar crystal chambers containing a protein matrix which is never exocytosed. Silica deposition in grass silica cells takes place outside the cell membrane when the cells secrete the mineralizing protein into the apoplasm rich with silicic acid (the mineral precursor molecules). Our review infers that the organism complexity and precursor reactivity (calcium and oxalate versus silicic acid) are main driving forces for the evolution of varied mineralization mechanisms.

Silicatein expression in Haliclona indistincta (Phylum Porifera, Order Haplosclerida) at different developmental stages

Silicatein is the main protein responsible for the formation of spicules, tiny structures that constitute the silica skeleton of marine demosponges (Phylum Porifera). A unique innovation in Porifera that evolved from the cathepsin L family of proteins, it has been reported that two amino acids (S and H) are necessary to form the catalytic triad (SHN) to enable silica condensation. However, a diversity of silicatein sequence variants has since been reported with a variable pattern of presence/absence across sponge groups. Variants containing CHN or C/SQN at the active site appear more common in sponges from the Haplosclerida. Here, we report the expression levels of five silicatein variants through different developmental stages in the haplosclerid Haliclona indistincta. All five silicatein variants were expressed at low levels in the free-swimming larvae, which lack spicules and expression significantly increased at the two developmental phases in which spicules were visible. At these two phases, silicateins of CHN and C/SQN types were much more highly expressed than the SHN type indicating a possible ability of active sites with these alternative amino acids to condense silica and a more complex evolutionary story for spicule formation in marine demosponges than previously understood.

Structural studies on Demospongiae sponges from Gökçeada Island in the Northern Aegean Sea

The Demospongiae is the largest Class in the phylum Porifera (sponges). Most sponge species in the Class Demospongiae have a skeleton of siliceous spicules and/or protein spongin or both. The first aim of this study was to perform the morphological and structural characterization of the siliceous spicules of four species belonging to Class Demospongiae (Suberites domuncula, Axinella polypoides, Axinella damicornis and Agelas oroides) collected around Gökçeada Island-Turkey (Northern Aegean Sea). The characterizations were carried out using a combination of Scanning Electron Microscopy with Energy Dispersive X-ray Spectroscopy (SEM/EDX), Attenuated Total Reflection-Fourier Transform Infrared Spectroscopy (ATR-FTIR) and Small Angle X-ray Scattering (SAXS) techniques. The sponge Chondrosia reniformis (Porifera, Demospongiae) lacks a structural skeleton of spicules or the spongin. It consists mainly of a collagenous tissue. The collagen with sponge origin is an important source in biomedical and pharmaceutical applications. The second aim of this study was to provide more information on the molecular structure of collagen of outer (ectosome) and inner (choanosome) regions of the Chondrosia reniformis using ATR-FTIR spectroscopy. Hierarchical clustering analysis (HCA) was also used for the discrimination of ATR-FTIR spectra of species.

Shaping highly regular glass architectures: A lesson from nature

Demospongiae is a class of marine sponges that mineralize skeletal elements, the glass spicules, made of amorphous silica. The spicules exhibit a diversity of highly regular three-dimensional branched morphologies that are a paradigm example of symmetry in biological systems. Current glass shaping technology requires treatment at high temperatures. In this context, the mechanism by which glass architectures are formed by living organisms remains a mystery. We uncover the principles of spicule morphogenesis. During spicule formation, the process of silica deposition is templated by an organic filament. It is composed of enzymatically active proteins arranged in a mesoscopic hexagonal crystal-like structure. In analogy to synthetic inorganic nanocrystals that show high spatial regularity, we demonstrate that the branching of the filament follows specific crystallographic directions of the protein lattice. In correlation with the symmetry of the lattice, filament branching determines the highly regular morphology of the spicules on the macroscale.