Long-SAGE (serial analysis of gene expression) for gene discovery and transcriptome profiling in the widespread marine coccolithophore Emiliania huxleyi

Applied and Environmental Microbiology, in press

Sonya T. Dyhrman¹, Sheean T. Haley¹, Shanda R. Birkeland², Louie L. Wurch¹, Michael J. Cipriano², and Andrew G. McArthur²

The abundant and widespread coccolithophore Emiliania huxleyi plays an important role in mediating CO₂ exchange between the ocean and the atmosphere through its impact on marine photosynthesis and calcification. Here, we use Long-SAGE (serial analysis of gene expression) to identify E. huxleyi genes responsive to nitrogen (N), or phosphorus (P) starvation. Long-SAGE is an elegant approach for examining quantitative, and comprehensive, gene expression patterns without a priori knowledge of gene sequences via the detection of 21 bp nucleotide sequence tags. E. huxleyi appears to have a robust, transcriptional level response to macronutrient deficiency with 42 tags uniquely present or up-regulated 2 fold or greater in the N starved library and 128 tags uniquely present or up-regulated 2 fold or greater in the P starved library. The expression patterns of several tags were validated with RT-PCR. Roughly 48% of these differentially expressed tags could be mapped to publicly available genomic or EST sequence data. For example, in the P starved library a number of the tags mapped to genes with a role in P scavenging including a putative phosphate repressible permease and a putative polyphosphate synthetase. In short, the Long-SAGE analyses have 1) identified many new differentially-regulated gene sequences, 2) assigned regulation data to EST sequences with no data-base homology and unknown function, and 3) highlighted previously uncharacterized aspects of E. huxleyi N and P physiology. To this end, our Long-SAGE libraries provide a new public resource for gene discovery and transcriptional analysis in this biogeochemically important marine organism.

¹Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA

²Marine Biological Laboratory, Woods Hole, MA