Transcriptome-Based Network Analysis on Gene Expression Regulated by CO2 Deprivation in Chlorella pyrenoidosa
Ontology highlight
ABSTRACT:
ORGANISM(S): Auxenochlorella pyrenoidosa
PROVIDER: GSE69816 | GEO | 2017/12/31
SECONDARY ACCESSION(S): PRJNA286860
REPOSITORIES: GEO
Similar Datasets
Project description:The understanding of molecular events occurring in Chlorella during heterotrophy to photoautotrophy transition as well as sudden light stress and glucose starvation, are still largely unknown. To well grasp its cellular metabolism, particularly the regulation of biosynthesis and degradation pathways of lipid, protein and carbohydrates, as well as the diverse trophic adaptation affecting carbon partitioning during heterotrophy to photoautotrophy transition process, we sequenced the transcriptome (RNA-seq) in six time points to discover how transcriptional changes in C. pyrenoidosa modulate metabolic flux trends leading to intracellular components dynamic reassortment.
2015-11-02 | GSE40028 | GEO
Project description:The understanding of molecular events occurring in Chlorella during heterotrophy to photoautotrophy transition as well as sudden light stress and glucose starvation, are still largely unknown. To well grasp its cellular metabolism, particularly the regulation of biosynthesis and degradation pathways of lipid, protein and carbohydrates, as well as the diverse trophic adaptation affecting carbon partitioning during heterotrophy to photoautotrophy transition process, we sequenced the transcriptome (RNA-seq) in six time points to discover how transcriptional changes in C. pyrenoidosa modulate metabolic flux trends leading to intracellular components dynamic reassortment. Three independent biological experiments (biological replicates) were carried out in the same batch. In total, eighteen samples collected at six time points (0-, 24-, 72-h from heterotrophic cells and 2-, 8-, 24-h from phototrophic cells) were used for mRNA-Seq library preparation and then submitted to Solexa GA-IIx (Illumina, USA) for sequencing.
2015-11-02 | E-GEOD-40028 | biostudies-arrayexpress
Project description:Chromochloris zofingiensis, featured by the capability of simultaneously synthesizing triacylglycerol (TAG) and astaxanthin, is emerging as a leading candidate alga for production uses. In order to better understand the oleaginous mechanism of this alga, we conducted a multi-omics analysis by systematically integrating the time-resolved transcriptomes, lipidomes, and metabolomes in response to nitrogen deprivation. The data analysis unraveled the distinct mechanism of TAG accumulation, which involved the coordinated stimulation of multiple biological processes including supply of energy and reductants, carbon reallocation from protein and starch, ‘pushing’ and ‘pulling’ carbon to TAG synthesis. Unlike in the model alga Chlamydomonas, the de novo fatty acid synthesis in C. zofingiensis was promoted, together with the enhanced turnover of both glycolipids and phospholipids, supporting the drastic need of acyls for TAG assembly. Moreover, genome-wide analysis identified many key functional enzymes and transcription factors with engineering potential for TAG modulation. Two genes encoding glycerol-3-phosphate acyltransferase (GPAT), the first committed enzyme for TAG assembly, were found in the genome of C. zofingiensis; in vivo functional characterization revealed that the extrachloroplastic GPAT instead of the chloroplastic one plays a central role in TAG synthesis. These findings illuminate distinct mechanism of oleaginousness of C. zofingiensis and pave a way toward rational manipulation of this alga as an emerging model for trait improvements.
2019-07-31 | GSE113802 | GEO
Project description:Commensal (symbiont) bacteria form communities in various regions of the bodies of vertebrates. Phylogenetic analysis of gut communities is advanced, but the relationships, especially at the trophic level, between commensals that share gut habitats of monogastric animals have not been investigated to any extent. Lactobacillus reuteri strain 100-23 and Lactobacillus johnsonii strain 100-33 cohabit in the forestomach of mice. According to the niche exclusion principle, this should not be possible because both strains utilise the two main fermentable carbohydrates present in the stomach digesta: glucose and maltose. We show, based on gene transcription analysis, in vitro physiological assays, and in vivo experiments that the two strains can co-exist in the forestomach habitat because L. reuteri 100-23 transports maltose into its cells more efficiently than does L. johnsonii 100-33. Conversely, strain 100-33 transports glucose more efficiently than 100-23. As a result, 100-23 shows a preference for growth using maltose, whereas 100-33 prefers glucose. Mutation of the maltose phosphorylase gene (malA) of strain 100-23 prevented its growth on maltose-containing culture medium, and resulted in the numerical dominance of 100-33 in the forestomach. The fundamental niche of L. reuteri 100-23 in the mouse forestomach can be defined in terms of glucose and maltose fermentation. Its realised niche when L. johnsonii 100-33 is present is maltose fermentation. Hence nutritional adaptations provided niche differentiation that enabled cohabitation by the two strains through resource partitioning in the mouse forestomach. This real life, trophic phenomenon conforms to a mathematical model. Analysis of the microarray data was obtained from two independent biological replicates. A dye swap was included in the analysis
2010-12-11 | E-GEOD-24472 | biostudies-arrayexpress
Project description:CO2 biofixation was investigated using tubular bioreactors (15 and 1.5 l) either in the presence of green algae Chlorella vulgaris or Nannochloropsis gaditana. The cultivation was carried out in the following conditions: temperature of 25 °C, inlet-CO2 of 4 and 8 vol%, and artificial light enhancing photosynthesis. Higher biofixation were observed in 8 vol% CO2 concentration for both microalgae cultures than in 4 vol%. Characteristic process parameters such as productivity, CO2 fixation, and kinetic rate coefficient were determined and discussed. Simplified and advanced methods for determination of CO2 fixation were compared. In a simplified method, it is assumed that 1 kg of produced biomass equals 1.88 kg recycled CO2. Advance method is based on empirical results of the present study (formula with carbon content in biomass). It was observed that application of the simplified method can generate large errors, especially if the biomass contains a relatively low amount of carbon. N. gaditana is the recommended species for CO2 removal due to a high biofixation rate-more than 1.7 g/l/day. On day 10 of cultivation, the cell concentration was more than 1.7 × 10(7) cells/ml. In the case of C. vulgaris, the maximal biofixation rate and cell concentration did not exceed 1.4 g/l/day and 1.3 × 10(7) cells/ml, respectively.
| S-EPMC4978769 | biostudies-literature
Project description:Commensal (symbiont) bacteria form communities in various regions of the bodies of vertebrates. Phylogenetic analysis of gut communities is advanced, but the relationships, especially at the trophic level, between commensals that share gut habitats of monogastric animals have not been investigated to any extent. Lactobacillus reuteri strain 100-23 and Lactobacillus johnsonii strain 100-33 cohabit in the forestomach of mice. According to the niche exclusion principle, this should not be possible because both strains utilise the two main fermentable carbohydrates present in the stomach digesta: glucose and maltose. We show, based on gene transcription analysis, in vitro physiological assays, and in vivo experiments that the two strains can co-exist in the forestomach habitat because L. reuteri 100-23 transports maltose into its cells more efficiently than does L. johnsonii 100-33. Conversely, strain 100-33 transports glucose more efficiently than 100-23. As a result, 100-23 shows a preference for growth using maltose, whereas 100-33 prefers glucose. Mutation of the maltose phosphorylase gene (malA) of strain 100-23 prevented its growth on maltose-containing culture medium, and resulted in the numerical dominance of 100-33 in the forestomach. The fundamental niche of L. reuteri 100-23 in the mouse forestomach can be defined in terms of glucose and maltose fermentation. Its realised niche when L. johnsonii 100-33 is present is maltose fermentation. Hence nutritional adaptations provided niche differentiation that enabled cohabitation by the two strains through resource partitioning in the mouse forestomach. This real life, trophic phenomenon conforms to a mathematical model.
2010-12-11 | GSE24472 | GEO
Project description:Genome assembly and annotation of the green alga Chlorella vulgaris
| PRJNA495479 | ENA
Project description:Background:The increasing emission of flue gas from industrial plants contributes to environmental pollution, global warming, and climate change. Microalgae have been considered excellent biological materials for flue gas removal, particularly CO2 mitigation. However, tolerance to high temperatures is also critical for outdoor microalgal mass cultivation. Therefore, flue gas- and thermo-tolerant mutants of Chlorella vulgaris ESP-31 were generated and characterized for their ability to grow under various conditions. Results:In this study, we obtained two CO2- and thermo-tolerant mutants of Chlorella vulgaris ESP-31, namely, 283 and 359, with enhanced CO2 tolerance and thermo-tolerance by using N-methyl-N-nitro-N-nitrosoguanidine (NTG) mutagenesis followed by screening at high temperature and under high CO2 conditions with the w-zipper pouch selection method. The two mutants exhibited higher photosynthetic activity and biomass productivity than that of the ESP-31 wild type. More importantly, the mutants were able to grow at high temperature (40 °C) and a high concentration of simulated flue gas (25% CO2, 80-90 ppm SO2, 90-100 ppm NO) and showed higher carbohydrate and lipid contents than did the ESP-31 wild type. Conclusions:The two thermo- and flue gas-tolerant mutants of Chlorella vulgaris ESP-31 were useful for CO2 mitigation from flue gas under heated conditions and for the production of carbohydrates and biodiesel directly using CO2 from flue gas.
| S-EPMC6800494 | biostudies-literature
Project description:Proteomics study in non-model alga Chlorella FC2 IITG (FC2) challenged with nitrogen starvation for 120 h. Three different nitrogen starvation time-points 40 h, 88 h and 120 h was compared with 0 h (nitrogen sufficient condition). Comparative proteomics analysis was performed using 4-plex isobaric tags for relative and absolute quantification (iTRAQ) labelling strategy, followed by chromatographic separation and final generation of tandem mass spectrometry (MS/MS) spectra of tryptic digested peptides on Q-TOF mass spectrometer.
2018-10-26 | PXD004712 | Pride