Silaffins are involved in the formation of the cell walls of diatoms. It is known that silaffins can precipitate silica in vitro, forming nano- and micro-particles in the shape of spheres and plates containing many pores. It is important to note that the deposition of silica and the particle morphology in the presence of silaffins affects chemical and physical agents (e.g., peptides, polyamines, phosphate, nitrogen, and the mechanical changes of the reaction mixture). It is believed that silaffins act as an organic matrix for silica-genesis and that silica pore size should reflect the pattern of a matrix. Here, biotechnology related to silaffins is discussed in the context of “a hypothesis of silaffin matrix” and “the LCPA-phosphate model”. We discuss the most promising area of silaffin biotechnology—the development of production methods for silicon structures with desired shapes and nanostructural properties that can be used to create biocompatible materials.

We discuss, from the aspect of phylogeny, the interrelationships of the phytolith types in plants from the main taxonomical groups (algae, lichens, horsetails, gymnosperms, and floral plants) with homologues of known proteins of biomineralization. Phytolith morphotypes in various phylogenetic plant domains have different shapes. We found that, in ancient types of plants (algae, horsetails, and gymnosperms), there are fewer different phytolith morphotypes compared to more modern plants (floral plants). The phytolith morphotypes in primitive plants are generally larger than the morphotypes in more highly organized plants. We found that the irregular ruminate and irregular smooth morphotypes are the two most frequently encountered phytolith morphotypes in the tested plants (from algae to floral plants). These two morphotypes probably have a universal role. Silacidins, silicon transporters, silicateins, silaffins, and silicase homologues are often found in the major taxonomic groups of plants. Red algae had the smallest number of homologues of the biomineralization proteins (70–80), Monocotyledonous: 142, Coniferous: 166, Mosses: 227, and Dicotyledones: 336.

The taxonomic affiliation (in the systematisation of viruses, and biological domains) of known peptides and proteins of biomineralization (silicateins, silaffins, silacidins and silicase) and their primary structure homologues were analyzed (methods in silico; using Uniprot database). The total number of known peptides and proteins of biosilicification was counted. The data of the quantitative distribution of the detected homologues found in nature are presented. The similarity of the primary structures of silaffins, silacidins, silicateins, silicase, and their homologues was 21–94%, 45–98%, 39–50%, and 28–40%, respectively. These homologues are found in many organisms, from the Protista to the higher plants and animals, including humans, as well as in bacteria and extracellular agents, and they perform a variety of biological functions, such as biologically controlled mineralisation. The provisional classification of these biomineralization proteins is presented. The interrelation of the origin of the first organic polymers and biomineralization is discussed.

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