Whole Transcriptome Analysis of the Silicon Response of the Diatom Thalassiosira pseudonana

Diatom cell walls, made of nanostructured silica, are of interest in diverse areas ranging from cellular structure, to hierarchical organization in biomineralization, to nanotechnology. Thus far, only cell surface proteins and proteins tightly associated with silica matrix have been characterized, and essential components of the silica deposition vesicle (SDV) are unknown, including components of the SDV membrane, cytoskeletal-interacting proteins, and proteins involved in trafficking associated with the SDV. Thus, an understanding of most of the molecular components and the dynamics of cellular processes involved in cell wall synthesis is lacking. In this work we report the first whole-cell response analysis using whole genome microarrays to identify genes potentially involved in diverse aspects of diatom cell division or cell wall synthesis. Thalassiosira pseudonana transcript profiles from precise time points, known to be associated with specific cell wall formation processes in cell-cycle synchronized cultures, suggests that this gene set includes extracellular proteins, silica matrix proteins, and proteins involved in signal transduction, vesicle trafficking, and transport. Protein localization experiments further confirm the first discovery of proteins associated with the SDV membrane. We propose that these proteins provide the interface between extra-SDV organization by the cytoskeleton and intra-SDV organization of silica polymerization determinants, which lead to the higher order organization of diatom silica structure. Analyzed mRNA from 0, 2, 4, 7, 8 and 9 hr of synchronized cell cycle using the Affymetrix GeneChip whole genome tiling array. Initial analysis of gene level expression was performed using Affymetrix Expression Console Software, version 1.1. No biological replicates were performed. 0 hr is used as reference point.