Update of the Diatom EST Database: a new tool for digital transcriptomics

Maheswari, G. Uma; Möck, Thomas; Armbrust, E. Virginia; Bowler, Chris

doi:10.1093/nar/gkn905

Cited by 73 publications

(52 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Thus, we can conclude that RedCAP and LHCF2 show a diurnal regulation of the gene expression at LL, which is not maintained in D or under ML illumination. This is in agreement with previous studies showing diurnal regulation of LHCF2 genes [36,38] and with the clustering of the P. tricornutum RedCAP gene with LHCF and LHCF-like genes in a hierarchical clustering analysis of diatom ESTs obtained from a range of different environmental conditions [39]. …”

Section: Resultssupporting

confidence: 93%

A novel type of light-harvesting antenna protein of red algal origin in algae with secondary plastids

et al. 2013

View full text Add to dashboard Cite

BackgroundLight, the driving force of photosynthesis, can be harmful when present in excess; therefore, any light harvesting system requires photoprotection. Members of the extended light-harvesting complex (LHC) protein superfamily are involved in light harvesting as well as in photoprotection and are found in the red and green plant lineages, with a complex distribution pattern of subfamilies in the different algal lineages.ResultsHere, we demonstrate that the recently discovered “red lineage chlorophyll a/b-binding-like proteins” (RedCAPs) form a monophyletic family within this protein superfamily. The occurrence of RedCAPs was found to be restricted to the red algal lineage, including red algae (with primary plastids) as well as cryptophytes, haptophytes and heterokontophytes (with secondary plastids of red algal origin). Expression of a full-length RedCAP:GFP fusion construct in the diatom Phaeodactylum tricornutum confirmed the predicted plastid localisation of RedCAPs. Furthermore, we observed that similarly to the fucoxanthin chlorophyll a/c-binding light-harvesting antenna proteins also RedCAP transcripts in diatoms were regulated in a diurnal way at standard light conditions and strongly repressed at high light intensities.ConclusionsThe absence of RedCAPs from the green lineage implies that RedCAPs evolved in the red lineage after separation from the the green lineage. During the evolution of secondary plastids, RedCAP genes therefore must have been transferred from the nucleus of the endocytobiotic alga to the nucleus of the host cell, a process that involved complementation with pre-sequences allowing import of the gene product into the secondary plastid bound by four membranes. Based on light-dependent transcription and on localisation data, we propose that RedCAPs might participate in the light (intensity and quality)-dependent structural or functional reorganisation of the light-harvesting antennae of the photosystems upon dark to light shifts as regularly experienced by diatoms in nature. Remarkably, in plastids of the red lineage as well as in green lineage plastids, the phycobilisome based cyanobacterial light harvesting system has been replaced by light harvesting systems that are based on members of the extended LHC protein superfamily, either for one of the photosystems (PS I of red algae) or for both (diatoms). In their proposed function, the RedCAP protein family may thus have played a role in the evolutionary structural remodelling of light-harvesting antennae in the red lineage.

show abstract

Section: Resultssupporting

confidence: 93%

A novel type of light-harvesting antenna protein of red algal origin in algae with secondary plastids

et al. 2013

View full text Add to dashboard Cite

show abstract

“…We also observed that methylation in the promoter (upstream 500 bp) of genes does not appear to impact transcription levels. We had previously estimated the degree of differential expression of P. tricornutum genes across 16 complementary DNA (cDNA) libraries by calculating the statistical significance of differential mRNA levels in specific conditions compared with random distribution (log likelihood ratio, R-value) 25,28 . Considering these criteria, constitutively expressed genes have low R-values (o12) while genes that are significantly overrepresented in specific growth conditions have high R-values (412).…”

Section: Resultsmentioning

confidence: 99%

Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum

et al. 2013

View full text Add to dashboard Cite

DNA cytosine methylation is a widely conserved epigenetic mark in eukaryotes that appears to have critical roles in the regulation of genome structure and transcription. Genome-wide methylation maps have so far only been established from the supergroups Archaeplastida and Unikont. Here we report the first whole-genome methylome from a stramenopile, the marine model diatom Phaeodactylum tricornutum. Around 6% of the genome is intermittently methylated in a mosaic pattern. We find extensive methylation in transposable elements. We also detect methylation in over 320 genes. Extensive gene methylation correlates strongly with transcriptional silencing and differential expression under specific conditions. By contrast, we find that genes with partial methylation tend to be constitutively expressed. These patterns contrast with those found previously in other eukaryotes. By going beyond plants, animals and fungi, this stramenopile methylome adds significantly to our understanding of the evolution of DNA methylation in eukaryotes.

show abstract

“…Studies in diatoms have benefited from developments in two model species, the centric diatom T. pseudonana (Coscinodiscophyceae) and the pennate diatom Phaeodactylum tricornutum (Bacillariophyceae), for which intense efforts have resulted in fully sequenced genomes (Armbrust et al, 2004;Bowler et al, 2008) and provided reference data for transcriptomic (Maheswari et al, , 2009Allen et al, 2008;Sapriel et al, 2009;Shrestha et al, 2012;Chauton et al, 2013) and whole-cell proteomic Nunn et al, 2009) analyses. P. tricornutum is pleiomorphic, with three major morphotypes (fusiform, triradiate, and oval).…”

mentioning

confidence: 99%

Membrane Glycerolipid Remodeling Triggered by Nitrogen and Phosphorus Starvation inPhaeodactylum tricornutum

et al. 2014

View full text Add to dashboard Cite

Diatoms constitute a major phylum of phytoplankton biodiversity in ocean water and freshwater ecosystems. They are known to respond to some chemical variations of the environment by the accumulation of triacylglycerol, but the relative changes occurring in membrane glycerolipids have not yet been studied. Our goal was first to define a reference for the glycerolipidome of the marine model diatom Phaeodactylum tricornutum, a necessary prerequisite to characterize and dissect the lipid metabolic routes that are orchestrated and regulated to build up each subcellular membrane compartment. By combining multiple analytical techniques, we determined the glycerolipid profile of P. tricornutum grown with various levels of nitrogen or phosphorus supplies. In different P. tricornutum accessions collected worldwide, a deprivation of either nutrient triggered an accumulation of triacylglycerol, but with different time scales and magnitudes. We investigated in depth the effect of nutrient starvation on the Pt1 strain (Culture Collection of Algae and Protozoa no. 1055/3). Nitrogen deprivation was the more severe stress, triggering thylakoid senescence and growth arrest. By contrast, phosphorus deprivation induced a stepwise adaptive response. The time scale of the glycerolipidome changes and the comparison with large-scale transcriptome studies were consistent with an exhaustion of unknown primary phosphorusstorage molecules (possibly polyphosphate) and a transcriptional control of some genes coding for specific lipid synthesis enzymes. We propose that phospholipids are secondary phosphorus-storage molecules broken down upon phosphorus deprivation, while nonphosphorus lipids are synthesized consistently with a phosphatidylglycerol-to-sulfolipid and a phosphatidycholine-to-betaine lipid replacement followed by a late accumulation of triacylglycerol.

show abstract

Update of the Diatom EST Database: a new tool for digital transcriptomics

Cited by 73 publications

References 32 publications

A novel type of light-harvesting antenna protein of red algal origin in algae with secondary plastids

A novel type of light-harvesting antenna protein of red algal origin in algae with secondary plastids

Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum

Membrane Glycerolipid Remodeling Triggered by Nitrogen and Phosphorus Starvation inPhaeodactylum tricornutum

Contact Info

Product

Resources

About