Silica in diatoms

Milligan, A., and Morel, F. (2002). A proton buffering role for silica in diatoms. Science 297, 1848-1850. 

Silicon, as silicate, has a large biochemistry in the plant kingdom, which is only beginning to be explored. Silicate appears to be transferred as the ester of a serine OH in the active site of a silicatein, an enzyme with sequence homology to cysteine proteinases, but with the crucial cysteine replaced by serine. "" Plant cell walls contain considerable amounts of silica - dry rice straw can contain 8wt% silica. Although deposition of silica in diatoms is mediated in the first instance by cationic proteins, a secondary role for a (1 ->3)-linked mannan has been suggested Figure 6.25. " ... 

Figure 19.2 Biogenic oxides, (a) Silica in diatom frustule (scale bar = 1 (im). (Reproduced with permission from Ref. [33]. Copyright 2003, Wiley-VCH Verlag GmbH, Weinheim.) (b) Iron oxide in magnetotactic bacteria (scale bar = 100 nm). (Reproduced with permission from...

Froelich, P. N., Blanc, V., Mortlock, R. A., Chillmd, S. N., Dunstan, W., Udomkit, A., and Peng, T. H. (1992). River fluxes of dissolved silica to the ocean were higher during glacials Ge/Si in diatoms, rivers, and oceans. Paleoceanography 7, 739-767. 

In contrast, such approaches have been much more developed with proteins, termed silicateins, that have been extracted from some silicified sponges [38]. The success of these approaches probably originates from the fact that the reactivity of these proteins towards silica precursors differs significantly from the processes occurring in diatoms. Whereas silaffins and poly-amines activate silica formation via electrostatic interactions due to the presence of positively-charged ammonium... 

Poulsen, N., Sumper, M. and Kroger, N. (2003) Silica formation in diatoms Characterization of native silaffin-2 and its role in silica morphogenesis. Proceedings of the National Academy of Sciences of the United States of America, 100, 12075-12080. 

Sumper, M. and Lehmann, G. (2006) Silica pattern formation in diatoms Species-specific polyamine biosynthesis. ChemBioChem, 7, 1419-1427. 

In each of these formulas additional free OH groups are available on the silicon so that it is possible to crosslink more than two polysaccharide chains. Silicon may function as a biological crosslinking agent in connective tissue. Silaffins, small polypeptides containing polyamine side chains of modified lysine residues, apparently initiate silica formation from silicic acid in diatoms.0... 

Possible explanations for the increase in silica in LRL at pH 4.7 include hydrologic differences, presence of a somewhat acid-tolerant diatom community, and the influence of another silica-utilizing community. Overall,... 

During silica deposition in diatoms a marked increase in protein concentration in cell walls is observed543 however, incorporation of carbohydrates increases only after Si-deposition. In addition, we have seen that there are consistent trends among specific amino acids in all analyzed species, while the sugars exhibit great variability. These two observations suggest that silicification is protein mediated548. ... 

Coombs, J., and Volcani, B. E. Studies on the biochemistry and fine structure of silica-shell formation in diatoms. Chemical changes in the wall of Navicula pelliculosa during its formation. Planta (Berl.) 82, 280-292 (1968). 

Preliminary calculations for the molecule, [ser-0-pSi(0CH3)3Nhis]-, result in a shift of -132 ppm.82 A transient resonance at -145 ppm lasting about 6 hours has been reported in diatom cultures that are actively synthesizing silica. This was a very weak peak indeed, but if it is accepted as an identifiable peak, one can say that the predicted value for the N-bearing pSi complex is within computational error of the observed value. 

In diatoms (unicellular algae), silica is a composite material containing glycoproteins. The walls are almost pure hydrated sihca with small amounts of A1 and Fe. 

Dissolved silicic acid is required for the growth of diatoms, which deposit opal (amorphous, hydrated silica) in their cell wall and dominate the production of opal in the modern-day ocean (Lisitzin, 1972). Silica (240 Tmol) is produced by diatoms in the surface ocean each year (Nelson et al., 1995 Treguer et al., 1995). Total inputs of... 

Because of the importance of diatoms in oceanic productivity, silicon is an important algal nutrient in seawater. A transporter of Si(OH)4 has been isolated and sequenced (Hildebrand et al, 1998 Hildebrand et al, 1997) and the physiology of silicon uptake has been well studied (Martin-Jezequel et al, 2000). Nonetheless, the molecular mechanism of Si(OH)4 transport and silica fmstule formation in diatoms are still largely mysterious. From indirect evidence, it appears possible that the Si(OH)4 transporter may contain zinc, coordinated to cysteines, as a metal center in the portion of the protein exposed to the outside of the cell (Hildebrand, 2000 Rueter and Morel, 1981). If true, this would be an unusual example of a transport protein functioning with a metal center. 

Biogenic silica, in the form of opal, makes up an important part of marine sediments, particularly in the southern and eastern equatorial oceans (Figure 15). These deposits are formed primarily from tests of diatoms that lived in the surface oceans. More than half of the opal formed in the... 

The isotopic composition of silicon in diatom opal has been investigated as a proxy for the degree of silicate utilization by diatoms, based on the fact that diatoms fractionate the silicon isotopes ( °Si and Si) during uptake (De La Rocha et al., 1997, 1998). This application is analogous to the use of nitrogen isotopes to study nitrate utilization, but with important differences. On the one hand, the upper ocean cycle is arguably simpler for silica than bio-available nitrogen, which bodes well for the silicon isotope system. 

Kroger N. and Sumper M. (2000) The biogeochemistry of silica formation in diatoms. In Biomineralization (ed. E. Baeuerlein). Wiley, Weinheim, Germany, pp. 151-170. 

---