Shedding light on silica biomineralization by comparative analysis of the silica‐associated proteomes from three diatom species

• Published in: The Plant journal : for cell and molecular biology 2022-06, Vol.110 (6), p.1700-1716
• Main Authors: Skeffington, Alastair W., Gentzel, Marc, Ohara, Andre, Milentyev, Alexander, Heintze, Christoph, Böttcher, Lorenz, Görlich, Stefan, Shevchenko, Andrej, Poulsen, Nicole, Kröger, Nils
• Format: Article
• Language: English
• Subjects: Bioinformatics; biosilica; Cell walls; Comparative analysis; Coupled walls; Demineralization; Demineralizing; frustule; fultoportula; GFP‐tagging; Homology; intrinsically disordered proteins; Liquid chromatography; Localization; Marine microorganisms; Mass spectrometry; Mass spectroscopy; Mineralization; Morphogenesis; Plankton; Proteins; Proteomes; silaffins; Silica; silica morphogenesis; Silicon dioxide; Species; Thalassiosira oceanica and Cyclotella cryptica; Thalassiosira pseudonana
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/tpj.15765

SUMMARY Morphogenesis of the intricate patterns of diatom silica cell walls is a protein‐guided process, yet to date only very few such silica biomineralization proteins have been identified. Therefore, it is currently unknown whether all diatoms share conserved proteins of a basal silica forming machinery, and whether unique proteins are responsible for the morphogenesis of species‐specific silica patterns. To answer these questions, we extracted proteins from the silica of three diatom species (Thalassiosira pseudonana, Thalassiosira oceanica, and Cyclotella cryptica) by complete demineralization of the cell walls. Liquid chromatography coupled with tandem mass spectrometry (LC‐MS/MS) analysis of the extracts identified 92 proteins that we name ‘soluble silicome proteins’ (SSPs). Surprisingly, no SSPs are common to all three species, and most SSPs showed very low similarity to one another in sequence alignments. In‐depth bioinformatics analyses revealed that SSPs could be grouped into distinct classes based on short unconventional sequence motifs whose functions are yet unknown. The results from the in vivo localization of selected SSPs indicates that proteins, which lack sequence homology but share unconventional sequence motifs may exert similar functions in the morphogenesis of the diatom silica cell wall. Significance Statement This comprehensive analysis of silica‐associated diatom proteins employs a combination of proteomics, bioinformatics, and protein localization studies to identify candidate proteins involved in silica biogenesis. Through in‐depth statistical analysis and phylogenomics, we show that these proteins are dominated by intrinsically disordered domains, are enriched in unconventional sequence motifs, and identify potential members of the basal silica biomineralization machinery as well as proteins that probably exert species‐specific functions in this process.