Expressed sequence tag profiles from calcifying and non-calcifying cultures of Emiliania huxleyi

Wahlund, Thomas M.; Zhang, Xiaoyu; Read, Betsy

doi:10.2113/50.suppl_1.145

Cited by 20 publications

(23 citation statements)

References 51 publications

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“…Of the five tags most highly expressed in our long SAGE ϪP library (Table 4), none clearly map to the most prevalent ESTs in the calcifying library analyzed by Nguyen et al (22). Moreover, of the tags up-regulated or unique to the ϪP library, over 60 are orphan tags, which do not map to any of the genes identified to date in calcifying cells (22,40). Considering the sensitivity of the transcriptome to culture conditions and the differences between EST, suppressive subtractive hybridization, and long SAGE analyses, these inconsistencies are not surprising; rather, these data underscore the value of using multiple genomic approaches over a range of conditions to identify the genes involved in uncharacterized metabolic pathways such as calcification.…”

Section: Discussionmentioning

confidence: 77%

“…The high number of unique and up-regulated tags in the ϪP library suggests that we may be observing the up-regulation of genes involved in calcification or calcium homeostasis (e.g., tag 11952 [calmodulin]) in addition to those involved in P scavenging. Substantial efforts have been made to identify the genes involved in calcification, and the most recent approaches have compared E. huxleyi EST libraries (40) or used suppressive subtractive hybridization with calcifying and noncalcifying cells (22). Of the five tags most highly expressed in our long SAGE ϪP library (Table 4), none clearly map to the most prevalent ESTs in the calcifying library analyzed by Nguyen et al (22).…”

Section: Discussionmentioning

confidence: 97%

“…The material benefits of SAGE are its simplicity, low cost, and efficiency. Perhaps the most common approach to expression studies with eukaryotic marine algae involves expressed sequence tag (EST) sequencing (34,39,40). In contrast to EST sequencing, SAGE can provide a much deeper sampling of the transcriptome, is not subject to the difficulties involved in normalization, and is quantitative in nature.…”

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confidence: 99%

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Long Serial Analysis of Gene Expression for Gene Discovery and Transcriptome Profiling in the Widespread Marine Coccolithophore Emiliania huxleyi

Dyhrman

Haley

Birkeland

et al. 2006

Appl Environ Microbiol

121

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The abundant and widespread coccolithophore Emiliania huxleyi plays an important role in mediating CO 2 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.Coccolithophores are an abundant and widespread phytoplankton functional group responsible for significant amounts of calcification in the ocean. This group is intensively studied for its roles in the marine carbon and sulfur cycles, the production of alkenones, and marine calcification. The coccolithophore Emiliania huxleyi is the most abundant species of this functional group in the modern ocean, and it blooms in both coastal and open ocean regions (24). E. huxleyi both fixes CO 2 through photosynthesis and generates CO 2 through the biomineralization of calcium carbonate (calcification). Photosynthesis and calcification are important components of the global carbon (C) cycle. Ultimately, both the presence of E. huxleyi blooms and the ratio of photosynthesis to calcification within the population mediate exchange between atmospheric and oceanic CO 2 . As such, coccolithophores are being intensively studied for their role in the C cycle and their potential influence on global climate.Nitrogen (N) and phosphorus (P) are two critical macronutrients for E. huxleyi growth, and their availability can impact when and where E. huxleyi blooms are able to occur (20). Further, N and P starvation can influence CO 2 exchange by changing rates of photosynthesis and calcification (24). For example, P starvation typically increases calcifi...

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Section: Discussionmentioning

confidence: 77%

Section: Discussionmentioning

confidence: 97%

mentioning

confidence: 99%

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Long Serial Analysis of Gene Expression for Gene Discovery and Transcriptome Profiling in the Widespread Marine Coccolithophore Emiliania huxleyi

Dyhrman

Haley

Birkeland

et al. 2006

Appl Environ Microbiol

121

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“…Genes putatively related to calcification (e.g. calcium and inorganic carbon transport, H þ transport and carbonic anhydrases) have been identified via gene expression studies comparing calcifying and non-calcifying E. huxleyi cells [25][26][27][28][29], or in short-term experiments where calcification was regulated by limitation of ions needed for calcification (i.e. Ca 2þ , HCO 3 2 /CO 3 22 [26,30,31]).…”

Section: Introductionmentioning

confidence: 99%

Emiliania huxleyi increases calcification but not expression of calcification-related genes in long-term exposure to elevated temperature and p CO ₂

Benner

Diner

Lefebvre

et al. 2013

Phil. Trans. R. Soc. B

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Increased atmospheric p CO 2 is expected to render future oceans warmer and more acidic than they are at present. Calcifying organisms such as coccolithophores that fix and export carbon into the deep sea provide feedbacks to increasing atmospheric p CO 2 . Acclimation experiments suggest negative effects of warming and acidification on coccolithophore calcification, but the ability of these organisms to adapt to future environmental conditions is not well understood. Here, we tested the combined effect of p CO 2 and temperature on the coccolithophore Emiliania huxleyi over more than 700 generations. Cells increased inorganic carbon content and calcification rate under warm and acidified conditions compared with ambient conditions, whereas organic carbon content and primary production did not show any change. In contrast to findings from short-term experiments, our results suggest that long-term acclimation or adaptation could change, or even reverse, negative calcification responses in E. huxleyi and its feedback to the global carbon cycle. Genome-wide profiles of gene expression using RNA-seq revealed that genes thought to be essential for calcification are not those that are most strongly differentially expressed under long-term exposure to future ocean conditions. Rather, differentially expressed genes observed here represent new targets to study responses to ocean acidification and warming.

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“…Ecophysiological and environmental studies have related biomineralization to nutrient status, light, cell growth and division, and the life cycle of coccolithophorids (28). Biochemical analysis has led to the isolation of several macromolecules associated with the organic matrix (5,20,22,34), while more recently, expressed sequence tags (ESTs) have been used to catalog genes and proteins expressed during calcification (36,37). Despite these efforts, our understanding of the mechanisms governing biomineralization in coccolithophorids is very limited.…”

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confidence: 99%

Suppressive Subtractive Hybridization of and Differences in Gene Expression Content of Calcifying and Noncalcifying Cultures ofEmiliania huxleyiStrain 1516

Nguyen

Bowers

Wahlund

et al. 2005

Appl Environ Microbiol

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The marine coccolithophorid Emiliania huxleyi is a cosmopolitan alga intensely studied in relation to global carbon cycling, biogeochemistry, marine ecology, and biomineralization processes. The biomineralization capabilities of coccolithophorids have attracted the attention of scientists interested in exploiting this ability for the development of materials science and biomedical and biotechnological applications. Although it has been well documented that biomineralization in E. huxleyi is promoted by growth under phosphate-limited conditions, the genes and proteins that govern the processes of calcification and coccolithogenesis remain unknown. Suppressive subtractive hybridization (SSH) libraries were constructed from cultures grown in phosphate-limited and phosphate-replete media as tester and driver populations for reciprocal SSH procedures. Positive clones from each of the two libraries were randomly selected, and dot blotting was performed for the analysis of expression patterns. A total of 513 clones from the phosphate-replete library and 423 clones from the phosphate-limited library were sequenced, assembled, and compared to sequences in GenBank using BLASTX. Of the 103 differentially expressed gene fragments from the phosphate-replete library, 34% showed significant homology to other known proteins, while only 23% of the 65 differentially expressed gene fragments from the phosphate-limited library showed homology to other proteins. To further assess mRNA expression, real-time RT-PCR analysis was employed and expression profiles were generated over a 14-day time course for three clones from the phosphate-replete library and five clones from the phosphate-limited library. The fragments isolated provide the basis for future cloning of full-length genes and functional analysis.Coccolithophorids are unicellular marine algae that produce a wide variety of highly sculpted calcium carbonate cell coverings. Calcification in some coccolithophorids occurs intracellularly and is thought to begin with the conversion of calcium and bicarbonate ions into crystals of calcium carbonate that are deposited in a defined array in association with an organic matrix (35). A coccolith vesicle developing from the Golgi apparatus provides the microenvironment that promotes the formation of the crystallographically intricate coccolith structures, which are subsequently extruded from the cell to form the coccosphere (7,20). The coccolith vesicle fuses with the plasma membrane to release the individual coccoliths. While calcification and coccolithogenesis are presumed to occur in a genetically controlled manner, the functional significance and genetic control of these complex structures and the variation in crystal shape, orientation, order, and connectivity that occurs across species are poorly understood The size and morphology of the calcite structures are as diverse as the coccolithophorids that produce them. Some of the calcite elements are simple rhombohedral units, while others appear as ornate oval platelets, extended spic...

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Expressed sequence tag profiles from calcifying and non-calcifying cultures of Emiliania huxleyi

Cited by 20 publications

References 51 publications

Long Serial Analysis of Gene Expression for Gene Discovery and Transcriptome Profiling in the Widespread Marine Coccolithophore Emiliania huxleyi

Long Serial Analysis of Gene Expression for Gene Discovery and Transcriptome Profiling in the Widespread Marine Coccolithophore Emiliania huxleyi

Emiliania huxleyi increases calcification but not expression of calcification-related genes in long-term exposure to elevated temperature and p CO ₂

Suppressive Subtractive Hybridization of and Differences in Gene Expression Content of Calcifying and Noncalcifying Cultures ofEmiliania huxleyiStrain 1516

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Expressed sequence tag profiles from calcifying and non-calcifying cultures of Emiliania huxleyi

Cited by 20 publications

References 51 publications

Long Serial Analysis of Gene Expression for Gene Discovery and Transcriptome Profiling in the Widespread Marine Coccolithophore Emiliania huxleyi

Long Serial Analysis of Gene Expression for Gene Discovery and Transcriptome Profiling in the Widespread Marine Coccolithophore Emiliania huxleyi

Emiliania huxleyi increases calcification but not expression of calcification-related genes in long-term exposure to elevated temperature and p CO 2

Suppressive Subtractive Hybridization of and Differences in Gene Expression Content of Calcifying and Noncalcifying Cultures ofEmiliania huxleyiStrain 1516

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Emiliania huxleyi increases calcification but not expression of calcification-related genes in long-term exposure to elevated temperature and p CO ₂