A family of silicon transporter structural genes in a pennate diatom Synedra ulna subsp. danica (Kütz.) Skabitsch.

Artyom M Marchenkov,Alexey A Morozov,Yulia R Zakharova,Alexander A Bondar,Michael A Grachev,Darya P Petrova

doi:10.1371/journal.pone.0203161

Abstract

Silicon transporters (SIT) are the proteins, which capture silicic acid in the aquatic environment and direct it across the plasmalemma to the cytoplasm of diatoms. Diatoms utilize silicic acid to build species-specific ornamented exoskeletons and make a significant contribution to the global silica cycle, estimated at 240 ±40 Tmol a year. Recently SaSIT genes of the freshwater araphid pennate diatom Synedra acus subsp. radians are found to be present in the genome as a cluster of two structural genes (SaSIT-TD and SaSIT-TRI) encoding several concatenated copies of a SIT protein each. These structural genes could potentially be transformed into “mature” SIT proteins by means of posttranslational proteolytic cleavage. In the present study, we discovered three similar structural SuSIT genes in the genome of a closely related freshwater diatom Synedra ulna subsp. danica. Structural gene SuSIT1 is identical to structural gene SuSIT2, and the two are connected by a non-coding nucleotide DNA sequence. All the putative “mature” SITs contain conserved amino acid motifs, which are believed to be important in silicon transport. The data obtained suggest that the predicted “mature” SIT proteins may be the minimal units necessary for the transport of silicon is S. ulna subsp. danica. The comparative analysis of all available multi-SITs has allowed us to detect two conservative motifs YQXDXVYL and DXDID, located between the “mature” proteins. Aspartic acid-rich DXDID motif can, in our opinion, serve as a proteolysis site during the multi-SIT cleavage. The narrow distribution of the distances between CMLD and DXDID motifs can serve as additional evidence to the conservation of their function.

Highlights

Silicon is the second most abundant element on the planet, amounting to 28% of Earth’s crust by mass [1]
The cells were cultivated for four weeks at 16 ̊C with intermittent mixing under a natural day-night biorhythm in 20-L glass bottles filled with Diatom Medium (DM) [42]
As a direct primer (UniCMLD F), we chose the sequence of the sense DNA chain encoding CMLD and its context, taking into account codon degeneracy and persistence of nucleotide positions

Summary

Introduction

Silicon (after oxygen) is the second most abundant element on the planet, amounting to 28% of Earth’s crust by mass [1]. In this work we have sequenced three multi-SIT genes, as well as 50- and 30-ends of their mRNAs, in a freshwater araphid pennate diatom Synedra ulna subsp. The comparative analysis of the multi-SIT sequences from a range of diatoms has allowed us to detect aspartaterich conservative motifs (DXDID) which, in our opinion, can serve as the proteolysis sites necessary for processing a multi-SIT into multiple “mature” proteins SIT, each capable of transporting silicic acid.

Results

Conclusion