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2.A.32 The Silicon Transporter (SIT) Family

Marine diatoms such as Cylindrotheca fusiformis encode at least six silicon transport protein homologues which exhibit similar sizes (about 550 aas) and topologies (ten - twelve putative transmembrane α-helical spanners (TMSs)). The six homologues exhibit greater than 80% sequence identity with each other and therefore comprise a coherent family of closely related proteins. The six recognized SIT family members exhibit insufficient sequence similarity with other proteins in the databases to suggest homology. One characterized member of the family (Sit1) functions in the energy-dependent uptake of either silicic acid [Si(OH)4] or Silicate [Si(OH)3O-] by a Na+ symport mechanism. The system is found in marine diatoms which make their 'glass houses' out of silicon. Homologues of Sit1 are expressed at different levels and in different patterns. Multiple Sit1 homologues are found in all diatoms tested. Individual transporters probably play specific roles in silicon uptake. Thamatrakoln and Hildebrand (2005) have reviewed the evidence then available concerning SIT family members.  Members of the SIT family have been identified in plants, siliceous sponges and choanoflagellates (Marron et al. 2016).

Diatoms are a group of algae that produce intricate silicified cell walls (frustules). The complex process of silicification involves a set of transport proteins that actively transport the soluble precursor of biosilica, dissolved silicic acid. Full-length silicic acid transporters are found widely across the diatoms while homologous shorter proteins have now been identified in a range of other organisms. It appears that modern silicic acid transporters arose from the union of such partial sequences. Knight et al. 2022 presented a computational study of the silicic acid transporters and related transporter-like sequences to help understand the structures, functions and evolution of these porters. The AlphaFold software predicts that all of the protein sequences studied here share a common fold in the membrane domain which is entirely different from the predicted folds of non-homologous silicic acid transporters from plants. Substrate docking revealed how conserved polar residues could interact with silicic acid at a central solvent-accessible binding site, consistent with an alternating access mechanism of transport. 

The generalized transport reaction is:

Silicate (out) + nNa+ (out)  Silicate (in) + nNa+ (in)

References associated with 2.A.32 family:

Durak, G.M., A.R. Taylor, C.E. Walker, I. Probert, C. de Vargas, S. Audic, D. Schroeder, C. Brownlee, and G.L. Wheeler. (2016). A role for diatom-like silicon transporters in calcifying coccolithophores. Nat Commun 7: 10543. 26842659
Hildebrand, M., B.E. Volcani, W. Gassmann and J.I. Schroeder (1997). A gene family of silicon transporters. Nature 385: 688—689. 9034185
Hildebrand, M., K. Dahlin and B.E. Volcani (1998). Characterization of a silicon transporter gene family in Cylindrotheca fusiformis: sequences, expression analysis, and identification of homologs in other diatoms. Mol. Gen. Genet. 260: 480-486. 9894919
Knight, M.J., B.J. Hardy, G.L. Wheeler, and P. Curnow. (2022). Computational modelling of diatom silicic acid transporters predicts a conserved fold with implications for their function and evolution. Biochim. Biophys. Acta. Biomembr 184056. [Epub: Ahead of Print] 36191629
Marron, A.O., S. Ratcliffe, G.L. Wheeler, R.E. Goldstein, N. King, F. Not, C. de Vargas, and D.J. Richter. (2016). The Evolution of Silicon Transport in Eukaryotes. Mol Biol Evol. [Epub: Ahead of Print] 27729397
Shcherbakova, T.A., I.u.A. Masiukova, T.A. Safonova, D.P. Petrova, A.L. Vereshchagin, T.V. Minaeva, R.V. Adel''shin, T.I. Triboĭ, I.V. Stonik, N.A. Aĭzdaĭcher, M.V. Kozlov, E.V. Likhoshvaĭ, and M.A. Grachev. (2006). [Conservative motif CMLD in silicic acid transport proteins of diatom algae]. Mol Biol (Mosk) 39: 303-316. 15856954
Thamatrakoln, K., and M. Hildebrand. (2005). Approaches for functional characterization of diatom silicic acid transporters. J. Nanosci. Nanotechnol. 5: 158-166. 15762174