Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Nutrient-regulated transcriptional responses in the brown tide forming alga Aureococcus anophagefferens

ABSTRACT: Relatively little is known about the presence and regulation of pathways involved in nutrient acquisition in the brown tide forming alga, Aureococcus anophagefferens. In this study, Long-SAGE (Serial Analysis of Gene Expression) was used to profile the A. anophagefferens transcriptome under nutrient replete (control), and nitrogen (N) and phosphorus (P) deficiency with the goal of understanding how this organism responds at the transcriptional level to varying nutrient conditions. This approach has aided A. anophagefferens genome annotation efforts and identified a suite of genes up-regulated by N and P deficiency, some of which have known roles in nutrient metabolism. Genes up-regulated under N deficiency include an ammonium transporter, an acetamidase/formamidase, and two peptidases. This suggests an ability to utilize reduced N compounds and dissolved organic nitrogen, supporting the hypothesized importance of these N sources in A. anophagefferens bloom formation. There are also a broad suite of P-regulated genes, including an alkaline phosphatase, and two 5’-nucleotidases, suggesting A. anophagefferens may use dissolved organic phosphorus under low phosphate conditions. These N- and P-regulated genes may be important targets for exploring nutrient controls on bloom formation in field populations. Aureococcus anophagefferens CCMP 1984 was obtained from the Provasoli-Guillard Center for the Culture of Marine Phytoplankton (CCMP). The cultures were grown at 18C on a 14 h:10 h light:dark cycle (140 µmol quanta m-2 s-1). Nitrogen- and phosphate-replete (883 µM NO3- and 36.3 µM PO43-) cells, –N (40 µM NO3-) cells, and –P (1 µM PO43-) cells were grown in autoclaved L1 media with no Si (Guillard and Hargraves 1993), prepared using 0.2 µm filtered Vineyard Sound seawater. Vitamins (thiamine, biotin, and B12) were sterile filtered and added to the media after autoclaving. Replete cells were harvested during mid log phase of growth, while –N and –P cells were harvested at the onset of stationary phase when N or P was depleted.

ORGANISM(S): Aureococcus anophagefferens

SUBMITTER: Sonya Dyhrman

PROVIDER: E-GEOD-21465 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Nutrient-regulated transcriptional responses in the brown tide-forming alga Aureococcus anophagefferens.

Wurch Louie L LL Haley Sheean T ST Orchard Elizabeth D ED Gobler Christopher J CJ Dyhrman Sonya T ST

Environmental microbiology 20100930 2

Long-SAGE (serial analysis of gene expression) was used to profile the transcriptome of the brown tide-forming alga, Aureococcus anophagefferens, under nutrient replete (control), and nitrogen (N) and phosphorus (P) deficiency to understand how this organism responds at the transcriptional level to varying nutrient conditions. This approach has aided A. anophagefferens genome annotation efforts and identified a suite of genes upregulated by N and P deficiency, some of which have known roles in n ...[more]

PMID: 20880332

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Project description: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 serial analysis of gene expression (SAGE) 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 twofold or greater in the N-starved library and 128 tags uniquely present or up-regulated twofold or greater in the P-starved library. The expression patterns of several tags were validated with reverse transcriptase PCR. Roughly 48% of these differentially expressed tags could be mapped to publicly available genomic or expressed sequence tag (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 (i) identified many new differentially regulated gene sequences, (ii) assigned regulation data to EST sequences with no database homology and unknown function, and (iii) 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. Keywords: Emiliania, gene expression, nutrients, SAGE, phosphate, nitrogen Emiliania huxleyi CCMP 1516 was obtained from the Provasoli-Guillard Center for the Culture of Marine Phytoplankton, Bigelow Laboratories. Cultures were grown at 18°C on a 14 h:10 h light:dark cycle (140 µmol quanta m-2 s-1). Nitrogen and phosphate replete (Replete: 35 µM NO3- and 1.5 µM PO43-), low nitrogen (-N: 10 µM NO3-) and low phosphate (-P: 0 µM PO43-) cells were grown in f/50 medium without Si. Locally collected seawater was filtered (pore size, 0.2 µm) and autoclaved. Filter-sterilized inorganic nutrients, trace metals and vitamins (thiamin, biotin and B12) were added after autoclaving. The cells were grown in 8 L batch cultures. The growth of cultures was monitored daily by cell number counted on a hemacytometer, and by relative fluorescence using a Turner Designs AU Fluorometer. Replete cells were harvested in mid-log phase while –N and –P cells were harvested at the onset of stationary phase for SAGE analysis.

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Dataset Information

Nutrient-regulated transcriptional responses in the brown tide forming alga Aureococcus anophagefferens

Publications

Nutrient-regulated transcriptional responses in the brown tide-forming alga Aureococcus anophagefferens.

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