For almost 200 years scientists have been fascinated by the ornate cell walls of the diatoms. These structures are made of amorphous silica, exhibiting species-specific, mostly porous patterns in the nano-to micrometer range. Recently, from the diatom Cylindrotheca fusiformis unusual phosphoproteins (termed silaffins) and long chain polyamines have been identified and implicated in biosilica formation. However, analysis of the role of silaffins in morphogenesis of species-specific silica structures has so far been hampered by the difficulty of obtaining structural data from these extremely complex proteins. In the present study, the five major silaffins from the diatom Thalassiosira pseudonana (tpSil1H, -1L, -2H, -2L, and -3) have been isolated, functionally analyzed, and structurally characterized, making use of the recently available genome data from this organism. Surprisingly, the silaffins of T. pseudonana and C. fusiformis share no sequence homology but are similar regarding amino acid composition and posttranslational modifications. Silaffins tpSil1H and -2H are higher molecular mass isoforms of tpSil1L and -2L, respectively, generated in vivo by alternative processing of the same precursor polypeptides. Interestingly, only tpSil1H and -2H but not tpSil1L and -2L induce the formation of porous silica patterns in vitro, suggesting that the alternative processing event is an important step in morphogenesis of T. pseudonana biosilica.During evolution many organisms (e.g. diatoms, sponges, radiolaria) have acquired the ability to use the ubiquitous monosilicic acid Si(OH) 4 for the formation of species specifically structured, silica-based exo-or endoskeletons (1). This interesting biomineralization phenomenon is mediated by cellular organic (macro-) molecules that accelerate silicic acid polycondensation and control morphogenesis of the forming silica (2). Diatoms are an extremely large group (Ͼ10,000 species) of unicellular eukaryotic algae that play a major role in biological silica cycling. Within the last few years diatom biosilica-associated proteins (termed silaffins) and long chain polyamines (LCPA) 1 have been identified and hypothesized to represent key components of the diatom biosilica-forming machinery. Silaffins and LCPA exhibit the remarkable ability to induce rapid silica deposition in vitro and to control the nanostructure of the forming silica (3). Therefore, unraveling the correlations between chemical structures, physical properties, and silica-forming activities of silaffins and LCPA will be important for understanding the molecular mechanism of species-specific biosilica nanopatterning. So far, silaffins have only been characterized from the diatom Cylindrotheca fusiformis. They are highly modified proteins/peptides rich in hydroxyamino acids (serine, threonine, hydroxyproline) and lysine residues. Silaffins natSil1A and -1B are O-phosphorylated at numerous sites and contain polyamine-modified lysine residues, features that enable these peptides to rapidly form silica nanospheres in vitr...