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)



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.

Hildebrand, M., B.E. Volcani, W. Gassmann and J.I. Schroeder (1997). A gene family of silicon transporters. Nature 385: 688—689.

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.

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]

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]

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.

Thamatrakoln, K., and M. Hildebrand. (2005). Approaches for functional characterization of diatom silicic acid transporters. J. Nanosci. Nanotechnol. 5: 158-166.


TC#NameOrganismal TypeExample

Silicon transporter of 548 aas and 10 probable TMSs in a 2 + 3 + 2 + 3 TMS arrangement. It has a conserved aa motif, CMLD. Hydropathy profiles suggest that CMLD occupies a position between two TMSs. These two TMSs are candidates for a role of the channel through which transport of silicic acid occurs (Shcherbakova et al. 2006).

Marine diatoms

Sit1 of Cylindrotheca fusiformis (marine diatom)


Uncharacterized half transporter of 361 aas with 5 TMSs in a 2 + 3 TMS arrangement followed by a hydrophilic domain similar in sequence to those for 2.A.32.1.8 and 9.

UP of Ciona intestinalis (vase tunicate)


Silicon transporter-like 1, Sit-L, of 368 aas and 5 (2 + 3) TMSs followed by a hydrophilic domain.

Sit-L of Phaeodaria sp.


Uncharacterized protein of 225 aas and 5 TMSs in a 2 + 3 TMS arrangement.

UP of Cyanobium sp.


Uncharacterized protein of 222 aas and 5 TMSs in a 2 + 3 TMS arrangement.

UP of Synechococcus sp


Uncharacterized protein of 525 aas and 5 TMSs in a 2 + 3 TMS arrangement, with two moderately hydrophobic peaks preceeding these TMSs.

UP of Gammaproteobacteria bacterium (marine metagenome)


Putative silicon transporter of 1555 aas with ~30 TMSs including 6 repeats of the usual 2 + 3 TMS repeat, characteristic of this family.

Silicon transporter of Nitzschia inconspicua


Uncharacterized protein of 542 aas and 4 - 6 TMSs in a 2 + 2, 2 + 3 or 3 + 3 TMS arrangement. The first TMS of the first set of 3, and the last TMS in the second set of 3 show very weak hydrophobicity.

UP of Armatimonadetes bacterium (aquatic metagenome)


Silicon transporter, SIT1, of 546 aas and 10 probable TMSs in a 2  + 3 + 2 + 3 TMS arrangement.

SIT1 of Nitzschia alba (marine diatom)


Silicic acid transport protein, SIT, of 571 aas and 12 or 13 TMSs in a possible 1 + 2 + 3 + 2 + 3 +2 TMS arrangement.

SIT of Ulnaria acus


Silicic acid transporter, Sit1, of 503 aas and 10 TMSs in a 2 + 3 + 2 + 3 TMS arrangement (Durak et al. 2016).

Sit1 of Prymnesium neolepis


Silicon transporter alpha, Sit, of 527 aas and 10 TMSs in a 2 + 3 + 2 + 3 TMS arrangement.

Sit of Helgoeca nana


Putative silicon transporter of 225 aas, Sit, with proably 5 or 6 TMSs in a 2 + 3 or 2 + 3 + 1 TMS arrangement.  This sequence (which could be a fragment) shows about the same percent identity with both halves of the longer proteins listed in TC#s 2.A.32.1.1 - 1.5.

Sit of Fragilaria crotonensis


Silicon transporter, Sit, of 477 aas and 10 TMSs in a 2 + 3 + 2 + 3 TMS arrangement.

Sit of Ochromonas distigma


Uncharacterized protein of 407 aas with 5 TMSs in a 2 + 3 TMS arrangement (residues 1 - 210) followed by a 200 residue hydrophilic domain. Residues 1 - 210 show about equal sequence similarity with the two halves of all of the full length sequences (2.A.32.1.1 - 1.5 and 1.7). The N-terminal half of the protein seems to be a half transporter and may function as a dimer in the membrane.

UP of Styela clava


Uncharacterized protein of 352 aas and 5 N-terminal TMSs (residues 1 - 210) followed by a 150 residue hydrophilic domain, similar in sequence to that of TC# 2.A.32.1.8.

UP of Phallusia mammillata