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Hypometabolism to survive the long polar night in the diatom Fragilariopsis cylindrus

ABSTRACT: Hypometabolism to survive the long polar night in the diatom Fragilariopsis cylindrus

PROVIDER: PRJNA902753 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22322200_1.fastq.gz	Fastqsanger.gz
	SRR22322200_2.fastq.gz	Fastqsanger.gz
	SRR22322204_1.fastq.gz	Fastqsanger.gz
	SRR22322204_2.fastq.gz	Fastqsanger.gz
	SRR22322205_1.fastq.gz	Fastqsanger.gz

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Hypometabolism to survive the long polar night in the diatom Fragilariopsis cylindrus

Project description:Diatoms, the major eukaryotic phytoplankton in polar regions, are essential to sustain food webs. As such, it is fundamental to understand the physiological mechanisms and associated molecular basis of resilience to polar night of diatoms. Here, we report an integrative approach that reveals that in prolonged darkness, the cell enters a state of hypometabolism associated with reduced transcriptional activity during which no cell division occurs. Minimal energy is provided by respiration via alternative oxidase and progressive degradation of protein, carbohydrate and lipid stores. We also report internal structural changes that manifest the morphological acclimation of cells to darkness. Our results further indicate that immediately after returning to light, the majority of cells were able to use photoprotective mechanisms and resume photosynthesis. Divisions of surviving cells resumed at rates similar to those before darkness. Our study demonstrates the robustness of this species to prolonged darkness at low temperatures.

2023-02-14 | GSE218215 | GEO

Fragilariopsis cylindrus

Project description:Fragilariopsis cylindrus overview

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Fragilariopsis Cylindrus dark survival experiment

Project description:The sea-ice dwelling diatom Fragilariopsis Cylindrus was cultured for 4 months under dark or light exposed conditions to mimic the effects of Antarctic winter growth conditions. Cells were harvested periodically and LFQ proteomics used to investigate the molecular mechanisms of dark survival.

2019-04-23 | PXD007098 | Pride

Fragilariopsis cylindrus CCMP1102 genome

Project description:Disentangling the genomic complexity of the Fragilariopsis cylindrus (CCMP1102) genome.

| PRJEB51975 | ENA

RNA-seq transcriptome profiling of the Southern Ocean diatom Fragilariopsis cylindrus under different experimental conditions, silica limitation and two different light spectra

Project description:The Southern Ocean diatom Fragilariopsis cylindrus was grown under half-saturating concentrations of silicate (0.3 uM) and in the blue (480 - 540 nm) and red (550 - 700 nm) light spectrum to investigate gene expression responses using RNA-seq relative to optimal growth conditions (deposited under accession E-MTAB-5024). RNA-seq was performed on three replicate samples for each experimental condition. Total RNA was extracted using a guanidinium thiocyanate-phenol-chloroform extraction protocol, followed by DNase I treatment and RNA purification (Quiagen). First strand cDNA synthesis was performed using random hexamers. Library preparation was performed using the RNA-seq Sample Prep Kit (Illumina) and sequencing was conducted according to the TruSeq RNA sequencing protocol (Illumina) All samples were sequenced together in one flowcell on one lane.

2020-12-31 | E-MTAB-5429 | biostudies-arrayexpress

Potential for the Production of Carotenoids of Interest in the Polar Diatom <i>Fragilariopsis cylindrus</i>.

Project description:Carotenoid xanthophyll pigments are receiving growing interest in various industrial fields due to their broad and diverse bioactive and health beneficial properties. Fucoxanthin (Fx) and the inter-convertible couple diadinoxanthin-diatoxanthin (Ddx+Dtx) are acknowledged as some of the most promising xanthophylls; they are mainly synthesized by diatoms (Bacillariophyta). While temperate strains of diatoms have been widely investigated, recent years showed a growing interest in using polar strains, which are better adapted to the natural growth conditions of Nordic countries. The aim of the present study was to explore the potential of the polar diatom Fragilariopsis cylindrus in producing Fx and Ddx+Dtx by means of the manipulation of the growth light climate (daylength, light intensity and spectrum) and temperature. We further compared its best capacity to the strongest xanthophyll production levels reported for temperate counterparts grown under comparable conditions. In our hands, the best growing conditions for F. cylindrus were a semi-continuous growth at 7 °C and under a 12 h light:12 h dark photoperiod of monochromatic blue light (445 nm) at a PUR of 11.7 μmol photons m-2 s-1. This allowed the highest Fx productivity of 43.80 µg L-1 day-1 and the highest Fx yield of 7.53 µg Wh-1, more than two times higher than under 'white' light. For Ddx+Dtx, the highest productivity (4.55 µg L-1 day-1) was reached under the same conditions of 'white light' and at 0 °C. Our results show that F. cylindrus, and potentially other polar diatom strains, are very well suited for Fx and Ddx+Dtx production under conditions of low temperature and light intensity, reaching similar productivity levels as model temperate counterparts such as Phaeodactylum tricornutum. The present work supports the possibility of using polar diatoms as an efficient cold and low light-adapted bioresource for xanthophyll pigments, especially usable in Nordic countries.

| S-EPMC9409807 | biostudies-literature

RNA-seq transcriptome profiling of the psychrophilic phytoplankton Fragilariopsis cylindrus under environmentally relevant growth limitations

Project description:We performed RNA-sequencing experiments to examine the differential regulation of genes in the genome of the Southern Ocean diatom Fragilariopsis cylindrus including diverged alleles. RNA-seq was performed on three replicate samples for each experimental condition. Phytoplankton cells were grown under six different experimental conditions including (1) optimal growth, (2) freezing temperatures, (3) elevated temperature, (4) elevated carbon dioxide concentrations, (5) low iron concentrations and (6) prolonged darkness. Total RNA was extracted using a guanidinium thiocyanate-phenol-chloroform extraction protocol, followed by DNase I treatment and RNA purification (Quiagen). First strand cDNA synthesis was performed using random hexamers. Library preparation was performed using the RNA-seq Sample Prep Kit (Illumina) and sequencing was conducted according to the TruSeq RNA sequencing protocol (Illumina) All samples were sequenced together in one flowcell on one lane.

2016-12-16 | E-MTAB-5024 | biostudies-arrayexpress

Genome-Scale Metabolic Reconstruction and in Silico Perturbation Analysis of the Polar Diatom Fragilariopsis cylindrus Predicts High Metabolic Robustness.

Project description:Diatoms are major primary producers in polar environments where they can actively grow under extremely variable conditions. Integrative modeling using a genome-scale model (GSM) is a powerful approach to decipher the complex interactions between components of diatom metabolism and can provide insights into metabolic mechanisms underlying their evolutionary success in polar ecosystems. We developed the first GSM for a polar diatom, Fragilariopsis cylindrus, which enabled us to study its metabolic robustness using sensitivity analysis. We find that the predicted growth rate was robust to changes in all model parameters (i.e., cell biochemical composition) except the carbon uptake rate. Constraints on total cellular carbon buffer the effect of changes in the input parameters on reaction fluxes and growth rate. We also show that single reaction deletion of 20% to 32% of active (nonzero flux) reactions and single gene deletion of 44% to 55% of genes associated with active reactions affected the growth rate, as well as the production fluxes of total protein, lipid, carbohydrate, DNA, RNA, and pigments by less than 1%, which was due to the activation of compensatory reactions (e.g., analogous enzymes and alternative pathways) with more highly connected metabolites involved in the reactions that were robust to deletion. Interestingly, including highly divergent alleles unique for F. cylindrus increased its metabolic robustness to cellular perturbations even more. Overall, our results underscore the high robustness of metabolism in F. cylindrus, a feature that likely helps to maintain cell homeostasis under polar conditions.

| S-EPMC7168318 | biostudies-literature

Building a locally diploid genome and transcriptome of the diatom Fragilariopsis cylindrus.

Project description:The genome of the cold-adapted diatom Fragilariopsis cylindrus is characterized by highly diverged haplotypes that intersperse its homozygous genome. Here, we describe how a combination of PacBio DNA and Illumina RNA sequencing can be used to resolve this complex genomic landscape locally into the highly diverged haplotypes, and how to map various environmentally controlled transcripts onto individual haplotypes. We assembled PacBio sequence data with the FALCON assembler and created a haplotype resolved annotation of the assembly using annotations of a Sanger sequenced F. cylindrus genome. RNA-seq datasets from six different growth conditions were used to resolve allele-specifc gene expression in F. cylindrus. This approach enables to study differential expression of alleles in a complex genomic landscape and provides a useful tool to study how diverged haplotypes in diploid organisms are used for adaptation and evolution to highly variable environments.

| S-EPMC5634323 | biostudies-literature

PacBio genome re-sequencing of the Fragilariopsis cylindrus genome

Project description:PacBio genome re-sequencing and assembly to confirm the haplotype and allelic divergence of the Fragilariopsis cylindrus genome

| PRJEB15040 | ENA

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