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

Abstract

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.

Computational modelling of diatom silicic acid transporters predicts a conserved fold with implications for their function and evolution

“…Frustule mineralization is an obligatory part of the lifecycle of many (but not all) of the thousands of extant diatom species [7]. A cadre of biomolecules have now been identified that seem to be dedicated to frustule formation [4,[8][9][10][11][12][13][14][15][16][17], and understanding the molecular basis of silicification remains an active area of study [18].…”

The molecular basis for pore pattern morphogenesis in diatom silica

“…2I, K, M, Supplementary Fig. 9B, D, 10G, 12G) 22 , and in dank2KO mutants the distal tubes are missing in all fultoportulae (Fig. 2L, Supplementary Fig.…”

“…In the past, the discovery of proteins involved in silica morphogenesis was severely hampered by the lack of a method for isolating SDVs. Therefore, biochemical analyses of diatom cell walls [19][20][21][22] and transcriptomics analyses of synchronized diatom cell cultures has been pursued 23,24 .…”

Mechanism of branching morphogenesis inspired by diatom silica formation

“…Once valve morphogenesis inside the SDV is complete, the new silica valve is exocytosed and integrated into the cell wall [12], [13]. In recent years, tremendous progress has been made in diatom research regarding sequencing and targeted manipulation of genomes [16], as well as the identification of candidate silica biogenesis proteins [17]- [19]. However, the physical principles that govern morphogenesis of the hierarchical silica patterns in diatoms are still enigmatic.…”