COMPARATIVE SEQUENCE ANALYSIS OF DIATOM SILICON TRANSPORTERS: TOWARD A MECHANISTIC MODEL OF SILICON TRANSPORT¹

Abstract

Silicon is an important element in biology, for organisms ranging from unicellular algae to humans. It acts as a structural material for both plants and animals, but can also function as a metabolite or regulator of gene expression, affecting a wide range of cellular processes. Molecular details of biological interaction with silicon are poorly understood. Diatoms, the largest group of silicifying organisms, are a good model system for studying this interaction. The first proteins shown to directly interact with silicon were diatom silicon transporters (SITs). Because the basis for substrate recognition lies within the primary sequence of a protein, identification of conserved amino acid residues would provide insight into the mechanism of SIT function. Lack of SIT sequences from a diversity of diatoms and high sequence conservation in known SITs has precluded identification of such residues. In this study, PCR was used to amplify partial SIT sequences from eight diverse diatom species. Multiple gene copies were prevalent in each species, and phylogenetic analysis showed that SITs generally group according to species. In addition to partial SIT sequences, full-length SIT genes were identified from the pennate diatom, Nitzschia alba (Lewin and Lewin), and the centric diatom Skeletonema costatum (Greville) Cleve. Comparing these SITs with previously identified SITs showed structural differences between SITs of centrics and pennates, suggesting differences in transport mechanism or regulation. Comparative amino acid analysis identified conserved regions that may be important for silicon transport, including repeats of the motif GXQ. A model for silicon uptake and efflux is presented that is consistent with known aspects of transport.

A family of diatom-like silicon transporters in the siliceous loricate choanoflagellates

“…The two pairs of GXQ-containing motifs have been noted previously, the first in TMDs 2 and 3, the second located in TMDs 7 and 8, but symmetrically orientated with respect to the membrane polarity [13]. In our alignment, the C-terminal motifs of the pair contained GRQ, apart from one CRQ motif (Shionodiscus ritscheri).…”

“…The TMDs predicted for choanoflagellate and diatom SITs overlap to some degree; however, the location of TMD 4 is considerably different. The COILS software found no evidence for putative coiled-coil motifs in the SdSIT sequences, unlike pennate diatom SITs which contain prominent C-terminal coiled-coil motifs [13].…”

“…The 156 significant PSI-BLAST hits to SdSITa were aligned against the choanoflagellate SIT sequences (see the electronic supplementary material). Choanoflagellate and stramenopile SITs were compared to identify conserved motifs, charged residues and hydroxylated residues (following [13]). Features were noted if they were conserved across all SITs.…”

“…Within each transporter type, only a few silicon transport-related protein motifs have been identified, the GXQ amino acid motifs in SITs [13] and arginine/aromatic selectivity filter of silicon-related NIPs [14]. This lack of homology has hindered research into silicon biochemistry and prevented the identification of other silicon-interacting protein features.…”

The relationship between light intensity and nutrient uptake kinetics in six freshwater diatoms

“…The affinity differences in Si uptake can be influenced by various types of silicic acid transporter (SIT) genes and the synthesis of higher affinity transporters (Martin-Jézéquel et al, 2000). Thamatrakoln et al (2006) pointed that there were structural differences of SITs between centrics and pennates. The incorporation of Si is mainly linked to cell wall synthesis phase (Martin-Jézéquel et al, …”