PRJNA378177: Understanding lipid metabolism in high-lipid-producing Chlorella vulgaris mutants at the genome-wide level
概要: In this study, physical and chemical mutagenesis methods were applied to enhance lipid productivity in Chlorella vulgaris. Then, de novo RNA-seq was performed to observe lipid metabolism changes at the genome-wide level. Characterization of two mutants, UV-715 and EMS-25, showed marked increases in lipid contents, i.e., 42% and 45%, respectively. In addition, the biomass productivity of the UV-715 cells was 9% higher than that of wild-type cells. Furthermore, gas chromatography-mass spectrophotometry analysis showed that both mutants have higher fatty acid methyl ester (FAME) contents than wild-type cells. To understand the effect of mutations that caused yield changes in UV-715 and EMS-25 cells at a genome-wide level, we carried out de novo RNA-seq. As expected, the transcriptional levels of the lipid biosynthesis genes were up-regulated, while the transcriptional levels of genes involved in lipid catabolism were down-regulated. Surprisingly, the transcriptional levels of the genes involved in nitrate assimilation and detoxification of reactive oxygen species (ROS) were significantly increased in the mutants. The genome-wide analysis results highlight the importance of nitrate metabolism and detoxification of ROS for high biomass and lipid productivity.
项目整体设计: mRNA profiles of wild type and mutant (UV-715 and EMS-25) Chlorella vulgaris SAG 211-12 cells were generated at stationary phase cell culture by deep sequencing, in two biological replicates, using Illumina MiSeq platform.
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Chlorella vulgaris (SAG 211-12) was obtained from the collection of algal cultures at the University of Göttingen, Germany. The inoculum was grown in Bold’s Basal medium consisting of (per liter): 0.25 g NaNO3, 0.075 g MgSO4.7H2O, 0.075 g K2HPO4, 0.175 g KH2PO4, 0.025 g NaCl, 0.025 g CaCl2.2H2O, 8.82 mg ZnSO4.7H2O, 0.44 mg MnCl2.4H2O, 0.71 mg MoO3, 1.57 mg CuSO4.5H2O, 0.49 mg CoCl2.6H2O, 11.42 mg H3BO3, 50 mg EDTA, 31 mg KOH, 4.98 mg feSO4.7H2O. Cultures were maintained at 25◦C under continuous illumination by four fluorescent lamps |
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250 µl culture of C. vulgaris with the cell count of 4×10e8 cells/ml was spread on solid Bold’s basal media and then exposed to UV irradiation (254 nm) with an intensity of 2.9 ×10-2 W/cm2 for 0.5 to 10 minutes at a distance of 15 cm. UVX Digital Radiometer (UVP, USA) was used to measure the UV-light intensity. The UV-irradiated plates were kept in dark for 24 h to prevent light-induced repair. The plates were then maintained under normal light for 2 weeks. Single colonies appearing on plates were selected and transferred individually into 2 ml Bold’s basal medium. After 10 days of culturing, the cell densities were determined by measuring OD at 680 nm. |
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Total RNA was extracted from 14-days old stationary phase reached (OD680=5) 5 ml cell culture using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions. Briefly, after quality and quantity measurement using 2100 BioAnalyzer (Agilent, USA), it was treated with RNase-free DNase I (Thermo Scientific, USA) at a concentration of 1 U/µg to remove residual genomic DNA. Then, RNA-seq library preparation was performed using TruSeq mRNA Sample Preparation Kit (Illumina, USA) according to the manufacturer’s instructions. mRNAs were purified from the 1 µg of total RNA using oligo (dT) magnetic beads and fragmented using fragmentation buffer. Afterthat, the cleaved short RNA fragments were used for first-strand cDNA synthesis using first strand synthesis mix, and the second strand was synthesized using second strand marking master mix. The double strand cDNAs were purified with AMPure XP beads (Beckman Coulter, USA) and eluted with resuspension buffer followed by 3’end adenine nucleotide addition. Finally, sequencing adaptors were ligated to the fragments and cDNA fragments were enriched by PCR amplification. |
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Enriched cDNA libraries were used for cluster generation and sequencing. 75x2 paired-end sequencing of three cDNA libraries (WT, UV-715 and EMS-25) with two biological replicates were performed using the Illumina MiSeq sequencing platform (Illumina, USA). All sequence data are PE 2x75 bp. Image processing, base calling, and quality calue calculation were performed by the Illumina data processing pipeline (v1.5). High quality reads were saved in FASTQ format. |
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polyA(+) RNA |
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Illumina MiSeq |
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Unspecific; Specific |
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