Genome-wide transcriptome analyses of silicon metabolism in Phaeodactylum tricornutum reveal the multilevel regulation of silicic acid transporters

PLoS One. 2009 Oct 14;4(10):e7458. doi: 10.1371/journal.pone.0007458.


Background: Diatoms are largely responsible for production of biogenic silica in the global ocean. However, in surface seawater, Si(OH)(4) can be a major limiting factor for diatom productivity. Analyzing at the global scale the genes networks involved in Si transport and metabolism is critical in order to elucidate Si biomineralization, and to understand diatoms contribution to biogeochemical cycles.

Methodology/principal findings: Using whole genome expression analyses we evaluated the transcriptional response to Si availability for the model species Phaeodactylum tricornutum. Among the differentially regulated genes we found genes involved in glutamine-nitrogen pathways, encoding putative extracellular matrix components, or involved in iron regulation. Some of these compounds may be good candidates for intracellular intermediates involved in silicic acid storage and/or intracellular transport, which are very important processes that remain mysterious in diatoms. Expression analyses and localization studies gave the first picture of the spatial distribution of a silicic acid transporter in a diatom model species, and support the existence of transcriptional and post-transcriptional regulations.

Conclusions/significance: Our global analyses revealed that about one fourth of the differentially expressed genes are organized in clusters, underlying a possible evolution of P. tricornutum genome, and perhaps other pennate diatoms, toward a better optimization of its response to variable environmental stimuli. High fitness and adaptation of diatoms to various Si levels in marine environments might arise in part by global regulations from gene (expression level) to genomic (organization in clusters, dosage compensation by gene duplication), and by post-transcriptional regulation and spatial distribution of SIT proteins.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Biological Transport*
  • Cluster Analysis
  • Diatoms / metabolism*
  • Gene Expression Profiling*
  • Gene Expression Regulation*
  • Genome*
  • Genome-Wide Association Study
  • Models, Biological
  • Molecular Sequence Data
  • Open Reading Frames
  • Sequence Homology, Amino Acid
  • Silicic Acid / metabolism*
  • Silicon / chemistry
  • Silicon / metabolism*


  • Silicic Acid
  • Silicon

Grant support

The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. GS was supported by the European Framework V project (MARGENES, QLRT-2001-01226). PJL is supported in part by the EU Sixth Framework Programme (Diatomics; LSHG-CT-2004-512035), the EU Network of Ecellence (Marine Genomics Europe) and the Centre National de la Recherche Scientifique (CNRS; France).