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Hallmarks of the dynamic responses to silica in Thalassiosira pseudonana - Identification, characterization and classification of signature genes and their corresponding motifs

ABSTRACT: The diatom cell wall, or frustule, is a highly complex, three-dimensional structure consisting of nanopatterned silica as well as proteins and other organic components. While some key components have been identified, knowledge on frustule biosynthesis is still fragmented. The model diatom Thalassiosira pseudonana was subjected to silicon (Si) shift-up and shift-down situations. Cellular and molecular signatures, dynamic changes and co-regulated clusters representing the hallmarks of cellular and molecular responses to changing Si availabilities were characterised. 62 silaffin-like proteins (SFLPs), two kinases and a novel family of putatively frustule-associated transmembrane proteins induced by Si shift-up and a possible role in frustule biosynthesis were identified. A separate cluster analysis performed on all significantly regulated SFLPs, as well as fourteen new proteins with silaffin-like motifs, resulted in the classification of silaffins, cingulins and SFLPs into distinct clusters. The genes in the Si-responsive clusters are in general highly divergent, but positive selection does not seem to be the driver behind this variability. This study provides a high-resolution map over transcriptional responses to changes in Si availability in T. pseudonana. Hallmark Si-responsive genes are identified, characteristic motifs and domains are classified, and taxonomic and evolutionary implications outlined and discussed.

ORGANISM(S): Thalassiosira pseudonana Thalassiosira pseudonana CCMP1335

PROVIDER: GSE94329 | GEO | 2017/05/31

SECONDARY ACCESSION(S): PRJNA369386

REPOSITORIES: GEO

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