Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

The genomic foundation of heterotrophy to photoautotrophy transition in Oleaginous Chlorella

ABSTRACT: 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.

ORGANISM(S): Chlorella pyrenoidosa

SUBMITTER: Jianhua Fan

PROVIDER: E-GEOD-40028 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Genomic Foundation of Starch-to-Lipid Switch in Oleaginous Chlorella spp.

Fan Jianhua J Ning Kang K Zeng Xiaowei X Luo Yuanchan Y Wang Dongmei D Hu Jianqiang J Li Jing J Xu Hui H Huang Jianke J Wan Minxi M Wang Weiliang W Zhang Daojing D Shen Guomin G Run Conglin C Liao Junjie J Fang Lei L Huang Shi S Jing Xiaoyan X Su Xiaoquan X Wang Anhui A Bai Lili L Hu Zanmin Z Xu Jian J Li Yuanguang Y

Plant physiology 20151020 4

The ability to rapidly switch the intracellular energy storage form from starch to lipids is an advantageous trait for microalgae feedstock. To probe this mechanism, we sequenced the 56.8-Mbp genome of Chlorella pyrenoidosa FACHB-9, an industrial production strain for protein, starch, and lipids. The genome exhibits positive selection and gene family expansion in lipid and carbohydrate metabolism and genes related to cell cycle and stress response. Moreover, 10 lipid metabolism genes might be or ...[more]

PMID: 26486592

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Project description:Paramecium bursaria chlorella virus (PBCV-1), a member of the family Phycodnaviridae, is a large dsDNA, plaque-forming virus that infects the unicellular green alga Chlorella NC64A. The 331 kb PBCV-1 genome is predicted to encode 365 proteins and 11 tRNAs. To follow global transcription during PBCV-1 replication, a microarray containing 50-mer probes to the PBCV-1 365 protein-encoding genes (CDS) was constructed. Competitive hybridization experiments were conducted employing cDNA from poly A-containing RNA obtained from cells at seven time points after virus infection. The results led to the following conclusions: i) the PBCV-1 replication cycle is temporally programmed and regulated; ii) 360 (99%) of the arrayed PBCV-1 CDSs are expressed at some time in the virus life cycle in the laboratory; iii) 227 (62%) of the CDSs are expressed before virus DNA synthesis begins; iv) these 227 CDSs were grouped into two classes: 127 transcripts disappear prior to initiation of virus DNA synthesis (considered early) and 100 transcripts are still detected after virus DNA synthesis begins (considered early/late); v) 133 (36%) of the CDSs are expressed after virus DNA synthesis begins (considered late); vi) expression of most late CDSs is inhibited by adding the DNA replication inhibitor aphidicolin prior to virus infection. This study provides the first comprehensive evaluation of virus gene expression during the PBCV-1 lifecycle. Time course analysis of chlorella virus PBCV-1: cDNAs from poly A-containing RNAs isolated from cells at seven times after PBCV-1 infection (20, 40, 60, 90, 120, 240, 360 min p.i.) were competitively hybridized against a reference sample on the microarrays. Three independent biological replica, four technical replica of the genome per array. Time course analysis of chlorella virus PBCV-1 gene expression in the presence of aphidicolin: cDNAs from poly A-containing RNAs isolated from aphidicolin-treated cells at seven times after PBCV-1 infection (20, 40, 60, 90, 120, 240, 360 min p.i.) were competitively hybridized against non-treated, infected samples from the same time points. Three independent biological replica, four technical replica of the genome per array.

Project description:Chlorella has been reported to have various physiological activities, including antiarteriosclerotic, cholesterol-lowering, anti-inflammatory, and immunoregulatory effects. However, there has been no report on the long-term effects of chlorella ingestion on immunity. In the present study, 4- to 10-week-old (young) and 4- to 50-week-old (old) female BALB/c mice were sensitized or not with ovalbumin (OVA), and given basic diet containing chlorella powder at 2% or basic diet alone. The effects of chlorella ingestion on immunity were investigated by measurement of splenic cytokines and immunoglobulin (Ig), analysis of T- and B-cells in the spleen and small intestine by flow cytometry, and analysis of the liver by DNA microarray. Results were compared between the young and old, OVA-sensitized and -nonsensitized, and chlorella and non-chlorella ingestion groups. Production of interferon-γ (IFN-γ) was maintained in the nonsensitized old groups, and ratios of T-helper type 1 (Th1) to T-helper type 2 (Th2) cells were similar in the young and old groups. In addition, overproduction of OVA-specific Igs due to OVA sensitization was strongly suppressed, and significant immunotolerance was exhibited irrespective of age. In addition, suppression of T-cell decreases in the spleen due to aging and suppression of changes in T- and B-cells due to OVA sensitization in the small intestinal lymph were demonstrated on flow cytometric analyses. On DNA microarray analysis, immune-related terms including IL11 and major histocompatibility complex (MHC) class 1 were detected, and expression of genes was shown, which were related to IL1-linked genes and complex involving macrophages from the pathways of cytokines and inflammatory response. In addition, suppressions of declined lipid metabolism and energy production were also suggested. Although how the ingredients in chlorella were involved in these changes is unclear, our findings suggest that prevention of decrease in acquired immunity by aging and induction of strong immunotolerance occurred following chlorella ingestion. The Young Control group and Old Control group were fed normal food, and the Old Chlorella intake group was fed food including 2.0% Chlorella powder. The total RNA was isolated from liver and samples was pooled for each group (n = 6 for each group). A table of normalized log2 ratios (where numerator is sample expression data, and denominator is all sample median data) is linked below as a supplementary file.

Dataset Information

The genomic foundation of heterotrophy to photoautotrophy transition in Oleaginous Chlorella

Publications

Genomic Foundation of Starch-to-Lipid Switch in Oleaginous Chlorella spp.

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