Ontology highlight
ABSTRACT:
PROVIDER: PRJEB29668 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Here, we investigated marine thraustochytrid Schizochytrium limacinum SR21 for its ability to convert waste oil, mixture of commercial oils (mCOs) and volatile fatty acids i.e., acetic acid and butyric acid into ω-3 fatty acid; docosahexaenoic acid (DHA). Metabolic insights through whole cell transcriptomic aid in tracing the route of substrate assimilation.
2024-04-10 | GSE252403 | GEO
Project description:16S rRNA raw data of Penaeus monodon fed Schizochytrium limacinum
| PRJNA632684 | ENA
Project description:Carotenoids have been demonstrated to be indispensable plant secondary metabolites that are involved in photosynthesis, antioxidation, and phytohormone biosynthesis. Carotenoids are likely involved in other biological functions that have yet to be discovered. In this study, we utilized genomic expression investigation to gain a deep insight into the carotenoid-related biological processes in the citrus calli overexpressing CrtB.
2014-09-23 | GSE61633 | GEO
Project description:QN Orange scallops is new strain with carotenoid deposition in orange adductor muscle, which provided suitable model for studying carotenoid accumulation. The present study was conducted to further understand the role of VPS29 in carotenoids deposition process via RNA interference (RNAi) of VPS29. Transcriptomic analysis revealed 534 differentially expressed genes (DEGs) between the groups without and with RNAi, among which were 288 upregulated and 246 were downregulated. Among these DGEs, genes related to carotenoids biosynthesis decrease in the expression of low-density lipoprotein receptor domain class (LDLR), cytochrome P450 (CYP 450), Niemann Pick C1-like 1 (NPC1L1) and ATP binding cassette transporter (ABC transporter) were identified. These results indicated that VPS29 played a vital role on carotenoids deposition by regulating other genes.
2019-10-09 | GSE138590 | GEO
Project description:Xanthophyllomyces dendrorhous is a basidiomycete yeast that produces carotenoids, mainly astaxanthin. Astaxanthin is an organic pigment of commercial interest due to its antioxidant and coloring properties. X. dendrorhous has a functional Sterol Regulatory Element-Binding Protein (SREBP) pathway, and the Sre1 protein is the SREBP homolog in this yeast. However, how Sre1 is promoting the biosynthesis of sterols and carotenoids in X. dendrorhous is unknown. In this work, comparative RNA-seq analysis between modified X. dendrorhous strains that have an active Sre1 protein and the wild-type was performed to identify Sre1-dependent genes. In addition, Sre1 direct target genes were identified through chromatin immunoprecipitation combined with lambda exonuclease digestion (ChIP-exo) assays. SRE motifs were detected in the promoter regions of several Sre1 direct target genes and were consistent with the SREs described in other yeast species. Sre1 directly regulates genes related to ergosterol biosynthesis as well as genes related to the mevalonate pathway, which synthesizes the building blocks of isoprenoids, including carotenoids. Two carotenogenic genes, crtE and crtR, were also identified as Sre1 direct target genes. Thus, carotenogenesis in X. dendrorhous is regulated by Sre1 through the regulation of the mevalonate pathway and the regulation of the crtE and crtR genes. As the crtR gene encodes a cytochrome P450 reductase, Sre1 regulates pathways that include cytochrome P450 enzymes, such as the biosynthesis of carotenoids and sterols. These results demonstrate that Sre1 is a sterol master regulator that is conserved in X. dendrorhous.
2020-09-29 | GSE152739 | GEO
Project description:During senescence of detached rice leaves, tryptophan (Trp) and Trp-derived secondary metabolites such as serotonin and 4-coumaroylserotonin accumulated in concert with methanol (MeOH) production. This senescence-induced MeOH induction was closely associated with levels of pectin methylesterase (PME)1 mRNA and PME enzyme activity. Exogenous challenge of detached rice leaves with 1% MeOH accelerated Trp and serotonin biosynthesis with induction of the corresponding genes. No other solvents including ethanol resulted in a Trp-inducing effect. This MeOH-induced Trp synthesis was positively regulated by abscisic acid but negatively regulated by cytokinin, suggesting hormonal involvement on the action of MeOH. Endogenous overproduction or suppression of MeOH either by PME1 overexpression or RNAi gene silencing revealed that PME1 overexpressing lines produced twofold higher Trp levels with elevated Trp biosynthetic gene expression, whereas RNAi lines showed twofold reduction in Trp level in healthy control rice leaves, suggesting that MeOH acts as an endogenous elicitor to enhance Trp biosynthesis. Among many transcription factors induced following MeOH treatment, the WRKY family showed significant induction patterns of which WRKY14 appeared to play a key regulatory role in MeOH-induced Trp and Trp-derived secondary metabolite biosynthesis. Total RNAs were extracted from the detached rice leaves with 1% MeOH or distilled water for 1 d, and gene expression was compared between the two groups with two replicates. DW, detached leaves in distilled water for 1 day; MeOH (2-replications), methanol treated detached leaves at the same time point as control. 2 sets of separately normalized data; DW-MeOH(1) and MeOH(2).
2011-01-03 | E-GEOD-26387 | biostudies-arrayexpress
Project description:We investigated gene expression during the bench-scale batch fermentation phase, glycerol feed phase, glycerol-methanol mixture feed (GM) phase, and at different time points following methanol induction using RNA-Seq. We report that the addition of the GM phase may help to alleviate the adverse effects of methanol addition (alone) on P. pastoris cells. Secondly, enhanced upregulation of the mitogen-activated protein kinase (MAPK) signaling pathway was observed in P. pastoris following methanol induction. The MAPK signaling pathway may be related to P. pastoris cell growth, and may regulate the AOX1 promoter via regulatory factors activated by methanol-mediated stimulation. Thirdly, the unfolded protein response (UPR) and ER-associated degradation (ERAD) pathways were not significantly upregulated during the methanol induction period. These results imply that the presence of unfolded or misfolded phytase protein did not represent a serious problem in our study. Finally, the upregulation of the autophagy pathway during the methanol induction phase may be related to the degradation of damaged peroxisomes but not to the production of phytase. This work describes the metabolic characteristics of P. pastoris during heterologous protein production under high-cell-density fed-batch cultivation. We believe that the results of this study will aid further in-depth studies of P. pastoris protein expression, regulation, and secretory mechanisms.
2019-12-20 | GSE142326 | GEO
Project description:Chlorophyll a synthase (ChlG) is the enzyme responsible for attaching either a geranygeranyl or phytyl group to the chlorophyllide macrocycle during chlorophyll biosynthesis. Previous co-immunoprecipitation assays using FLAG-tagged ChlG identified the high light inducible protein HliD and the photosystem II assembly factor Ycf39 among the interaction partners. Non-protein components of this complex are the carotenoids zeaxanthin and myxoxanthophyll. To elucidate the function of these carotenoids in the association of ChlG/HliD/Ycf39, knockout strains of Synechocystis were produced to disrupt carotenoid biosynthesis. The abundances of HliD and Ycf39 relative to FLAG-tagged ChlG were compared in the different strains by proteomic analysis.
2022-08-18 | PXD020471 | Pride