Lineage-Specific Chromatin Signatures Reveal a Master Lipid Switch in Microalgae
ABSTRACT: Alga-derived lipids represent an attractive potential source of biofuels. However, lipid accumulation in algae is a stress response tightly coupled to growth arrest, thereby imposing a major limitation on productivity. To identify master regulators of lipid accumulation and decipher the regulation of lipid biosynthetic pathway, we performed an integrative chromatin signature and transcriptomic analysis in the alga Chlamydomonas reinhardtii. Genome-wide histone modification profiling revealed remarkable differences in functional chromatin states between algae and higher eukaryotes and uncovered regulatory components at the core of lipid accumulation pathways. We identified the transcription factor PSR1 as a pivotal master switch that triggers cytosolic lipid hyper-accumulation an order of magnitude higher than stress regimens have achieved. Dissection of the PSR1 target network corroborates its central role in coordinating multiple stress responses. The comprehensive maps of functional chromatin signatures in a major clade of eukaryotic life and the discovery of a central regulator of algal lipid metabolism will facilitate targeted engineering strategies in microalgae. 1. Genome-wide H3K4me3 time series profiling (at 0 hr, 10 min, 30 min, 1 hr, 2hr, 6 hr, 8 hr, 24 hr and 48 hr after nitrogen starvation) was performed to determine time point to capture maximal chromatin changes. 2. Genome-wide H3K4me3, H3K27ac, H3K9me3, H3K27me3, H3K36me3 and Pol II profiling were performed at 0 hr, 1 hr after nitrogen starvation and 1 hr after sulfur starvation to determine chromatin signatures. Genome-wide H3K4me2 profiling was performed at 0 hr before starvation. 3. Transcriptome time series profiling (at 0 hr, 10 min, 30 min, 1 hr, 2hr, 6 hr, 8 hr, 24 hr and 48 hr after nitrogen and sulfur starvation separately) for chromatin signature characterization and integrative analysis. 4. Genome-wide PSR1 binding profiling was performed with polyclonal antibody against PSR1 peptide A region and PSR1 peptide B region individually. (At 30 min and 1 hr after nitrogen starvation, and 1 hr, 2 hr and 6 hr after sulfur starvation.) Please note that the following reference genome and gene models used in these experiments are linked below; C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz reference_gene_model.gtf.gz These are based off Phytozome (http://www.phytozome.net/) which does not provide access to earlier version data.
Project description:This SuperSeries is composed of the following subset Series: GSE33039: replication experiment GSE33040: Sulfur starvation experiment in Chlamydomonas GSE33041: Chlamydomonas growth under nitrogen starvation Refer to individual Series
Project description:Nutrient-starvation induced lipid accumulation has been reported in diverse algae, including diatoms. Molecular mechanisms underlying lipid accumulation in nutrient-starved algae are of interest to inform genetic engineering strategies aimed at improving lipid productivity. Diatom cell walls are made of nanostructured silica which is a unique feature of the group and silicon deprivation induces both growth arrest and lipid accumulation. In this work, we report the whole cell transcript level response during silicon starvation induced lipid accumulation. Analyzed mRNA from cells after 0, 4, 8, 12, 18, and 24 hr of silicon starvation using the Affymetrix GeneChip whole genome tiling array. Initial analysis of gene level expression was performed using the Affymetrix Expression Console Software, version 1.1. No biological replicates were performed. 0 hr is used as a reference point.
Project description:C. reinhardtii cells exposed to abiotic stresses (e.g. iron-, nitrogen-, zinc- or phosphorus-deficiency) accumulate TAGs which are stored in lipid droplets. Here, we report that iron starvation leads to formation of lipids bodies and accumulation of TAGs. This occurs between 12 and 24 h of iron-starvation. C. reinhardtii cells deprived for iron have more saturated FA, due to the loss of functional FA desaturases, which are diiron enzymes. The abundance of a plastid ACP-acyl desaturase (FAB2) is significantly decreased to the same degree as observed for ferredoxin, which is a substrate of the desaturases. The increase in saturated FA (C16:0 and C18:0) is concomitant with the decrease in saturated FA (C16:4, C18:3 or C18:4). This pattern was observed for MGDG, DGTS or DGDG. When we monitored the absolute levels of glycerolipids, MGDG content dropped significantly after only 2 h of iron-starvation. On the other hand, DGTS and DGDG contents gradually decrease until a minimum is reached after 24-48 h of iron-deprivation. RNA-Seq analysis of iron-starved C. reinhardtii cells revealed significant changes in many transcripts coding for enzymes involved in FA metabolism. The mRNA abundances of genes coding for components involved in TAG accumulation (DGAT or MLDP) are increased. A more dramatic increase at the transcript level has been observed for many lipases, suggesting that a major remodeling of lipid membranes occurs during iron-starvation in C. reinhardtii. Sampling of Chlamydomonas CC-4532 (2137) cells cultivated photoheterotrophically (TAP) under iron-starvation condition (0 uM Fe-EDTA). Samples were collected from biological duplicates after washing in TAP medium lacking Fe at 0, 0.5, 1, 2, 4, 8, 12, 24 and 48 hours.
Project description:For the first time in Lactococcus lactis, amino acid starvation response was characterized. The natural imposition of isoleucine starvation, by its consumption during growth, associated to transcript profiling, allowed defining exhaustively this stress stimulon. It consisted of a general induction of nitrogen metabolism (amino acid biosynthesis and transport, proteolytic system and proteases), a strong repression of genes encoding major physiological activities (translation, transcription, carbon metabolism, purine and pyrimidine biosynthesis and fatty acid metabolism) and the induction of unexpected cross responses to acid, osmotic and oxidative stresses. Keywords: stress response, time course Isoleucine starvation was imposed by the consumption of this amino acid during the growth of Lactococcus lactis IL1403 on ILV0.1 medium (CDM with ten-fold reduced concentrations of isoleucine, leucine and valine) and under controlled conditions (30 °C, pH 6.6, nitrogen atmosphere). Cell samples were harvested in exponential phase and after 30 min, 1.7 h and 3.5 h of isoleucine starvation. Total RNA was extracted from these samples and radiolabelled cDNA were prepared and hybridized on nylon arrays. 2053 amplicons specific of Lactococcus lactis IL1403 genes were spotted twice on the array. The 4 time-points were analyzed simultaneously and 3 independent repetitions were performed.
Project description:Three acyltransferases, DGAT1, DGTT1, and PDAT1, are induced by nitrogen starvation and are likely to have a role in TAG accumulation based on their patterns of expression. Each gene also shows increased mRNA abundance in other TAG-accumulating conditions (-S, -P, -Zn, -Fe). Insertional mutants, pdat1-1 and pdat1-2, accumulate 25% less TAG compared to the parent strain, D66+, which demonstrates the relevance of the trans-acylation pathway in Chlamydomonas. The biochemical functions of DGTT1 and PDAT1 were validated by rescue of oleic acid sensitivity and restoration of TAG accumulation in a yeast strain lacking all acyltransferase activity. Time course analysis suggest than an SBP domain transcription factor protein, whose mRNA increases precede that of other genes like DGAT1, is a candidate regulator of the N-deficiency response. An insertional mutant, nrr1-1, accumulates only 50% of the TAG compared to the parental strain in N-starvation conditions and is unaffected by other nutrient stresses, suggesting the operation of multiple signaling pathways leading to stress-induced TAG accumulation. Sampling of Chlamydomonas 2137 cultivated in TAP, N-Free TAP or TAP with varying amounts of N.
Project description:The Chlamydomonas reinhardtii transcriptome was characterized from nutrient-replete and sulfur-depleted wild-type and snrk2.1 mutant cells; the mutant is null for the regulatory serine-threonine kinase SNRK2.1, which is required for acclimation to sulfur deprivation. The transcriptome analyses involved microarray hybridization and RNA-seq technology; RT-qPCR evaluation of the data obtained by these techniques showed that RNA-seq is significantly more quantitative than microarray hybridizations. Sulfur-deprivation-responsive transcripts included those encoding proteins involved in sulfur acquisition and assimilation, recycling of sulfur-containing amino acids, synthesis of reduced sulfur metabolites and cofactors, and modification of cellular structures such as the cell wall and complexes associated with the photosynthetic apparatus. Moreover, the data suggest that cells deprived of sulfur favors accumulation of proteins with fewer sulfur-containing amino acids. Most of these sulfur-deprivation responses are controlled by the SNRK2.1 kinase. Furthermore, the snrk2.1 mutant exhibits a set of unique responses during both sulfur-replete and sulfur-depleted conditions that are not observed in wild-type cells. Many of these responses are likely to be elicited by singlet O2 accumulation in the mutant cells. The transcriptome results for the wild-type and mutant cells strongly suggest the occurrence of massive changes in cellular physiology and metabolism as the cells become depleted for sulfur, and reveal aspects of acclimation that are likely critical for cell survival. The three supplementary files GSE17970_supplemental_table_*.xls below include results of the differential expression analysis (expression estimates, fold changes and p-values), and different clusters of functionally related genes. Chlamydomonas strains used for this study were D66 (wt strain; nit2 cw15 mt+), ars11 (snrk2.1cw15mt+), 21gr (wt strain; nit5 mt-) and sac1 (sac1mt+). The ars11 strain was designated as the snrk2.1 mutant throughout since the lesion is in the SNRK2.1 gene. Cells were cultured under continuous light of ~60 μmol photon m-2s-1 at 23ºC in liquid and on solid Tris-Acetate-Phosphate (TAP) medium. To impose S deprivation, cells in mid-logarithmic growth phase were washed twice with liquid TAP medium without S (TAP-S), and equal numbers of cells were resuspended in TAP or TAP-S. Cell aliquots were collected for RNA isolation just prior to and 6 h after being transferred to TAP and TAP-S medium. Total RNA from wt (D66) and snrk2.1 mutant cells after 0 and 6 h of being transferred to -S medium were submitted to Illumina for sequencing using their proprietary Genome Analyzer. cDNA libraries were assembled according to the manufacturer’s RNA-seq protocol, loaded and sequenced as 35-mers in a total of 11 Solexa lanes. Raw image files were collected by the sequencer and analyzed using the standard Solexa pipeline.
Project description:In this approach, changes in total transcript of a glnR deletion strain of Mycobacterium smegmatis due to nitrogen starvation were monitored. This is a control experiment for the comparison of wild type and glnR deletion strain resulting in putative nitrogen-related genes which are not controlled by GlnR. Two biological replicates were analyzed.
Project description:We have done next generation sequencing of optically thin, exponentialy growing Phaeodactylum tricornutum cultures grown with and without nitrogen source to improve our undestanding of the pathways regulation under conditions that promote lipid accumulation (N-starvation). 3 biologically independent exponentially growing culture of Phaeodactylum tricornutum were pelleted and washed several times with N-free media. Each culture was devided to 2 replicates with initial cell concentration of 2X105 cells/mL, one with NaNO3 as nitrogen source and the other without any nitrogen source. The cuture were bubbled foro 48 hours and sampled for transcriptome together with other physiological parameters and lipid analysis.
Project description:Testing for labeling efficiency and Replication effeciency of the microarray (Chlamydomonas cells grown for 24 h under sulfur starvation) Two-condition experiment, 3 Biological replicates