RNAseq Analysis of Transcriptomic Response to Zn Resupply in Chlamydomonas reinhardtii
Ontology highlight
ABSTRACT:
ORGANISM(S): Chlamydomonas reinhardtii
PROVIDER: GSE58786 | GEO | 2014/11/01
SECONDARY ACCESSION(S): PRJNA253485
REPOSITORIES: GEO
Similar Datasets
Project description:Zn-limited cells accumulate Cu in intracellular structures in a reversable manner. We used RNAseq analysis to monitor gene expression in Zn-limited cells, and during a time course (0 - 24 h) after Zn resupply. Comparison of Chlamydomonas reinhardtii gene expression when Zn deficient cells are resupplied with 2.5 M-BM-5M Zn. Time points 0 (before resupply), 1.5, 3, 4.5, 12, and 24 hours after resupply. Four biological replicates per condition.
2014-11-01 | E-GEOD-58786 | biostudies-arrayexpress
Project description:Zinc is an essential nutrient because of its role in catalysis and in stabilizing protein structure, but excess zinc can also be deleterious. Four nutritional zinc states have been identified in the alga Chlamydomonas reinhardtii: zinc toxic, zinc replete, zinc deficient and zinc limited. Growth is inhibited in zinc-limited and zinc toxic cells relative to zinc-replete cells, while zinc-deficiency is visually asymptomatic but distinguished by the accumulation of transcripts encoding ZIP family transporters. To identify targets of zinc deficiency and mechanisms of zinc acclimation, we used RNA-seq to probe zinc nutrition responsive changes in gene expression. We identified a subset of genes encoding zinc-handling components, including ZIP family transporters and candidate zinc chaperones. In addition, we noted an impact on two other regulatory pathways, the carbon concentrating mechanism (CCM) and the nutritional copper regulon. Targets of transcription factor Ccm1 and various CAH genes are up-regulated in zinc-deficiency, as a likely consequence of reduced carbonic anhydrase activity, which is validated by mass spectrometry and immunoblot analysis of Cah1, Cah3 and Cah4. Chlamydomonas is therefore not able to grow photoautotrophically in air in zinc limiting conditions, but supplementation with 1% CO2 restores growth to wild-type rates, suggesting that the inability to maintain CCM is a major consequence of zinc limitation. Surprisingly, we noted also that the Crr1 regulon, which responds to Cu limitation, is also turned on in zinc deficiency, and in fact, Crr1 is required for growth in zinc-limiting conditions. Zinc deficient cells are functionally copper deficient, as evidenced by reduced plastocyanin abundance, even though they hyperaccumulate copper up to 50-fold over normal levels. We suggest that zinc-deficient cells sequester Cu in a bio-unavailable form, perhaps to prevent mis-metallation of critical zinc sites. Zn-limited wild-type cells were generated by transfer of cells from the first round of growth in medium with no supplemental Zn into TAP medium supplemented or not with 2.5 µM Zn-EDTA The control samples for this study are represented in GSE25622
2013-05-03 | E-GEOD-41096 | biostudies-arrayexpress
Project description:RNAseq Analysis of Transcriptomic Response to Zn Resupply in Chlamydomonas reinhardtii
| PRJNA253485 | ENA
Project description:Abnormal metal accumulation is associated with Alzheimer’s disease (AD) and has a relevant role in affecting amyloid beta-peptide (Abeta) aggregation and neurotoxicity.In the present study, employing a microarray analysis of 35,129 genes, we analyzed gene expression profile changes due to exposure to Abeta-Zn or Abeta-Cu complexes in neuronal-like cells (SH-SY5Y). Microarray data indicated that Abeta-Zn or Abeta-Cu complexes selectively alter expression of genes mainly related to cell death, inflammatory responses, and apoptosis.Taken together these findings indicate that Abeta-Zn or Abeta-Cu show some commonalities in affecting AD-related target functions. The overall modulatory activity on these genes supports the idea of a possible net result leading to mechanisms that counteract toxic effects of Abeta-Zn or Abeta-Cu.
2012-05-01 | GSE37661 | GEO
Project description:Here, we report on the transcriptome of the organelles of the micro-alga, Chlamydomonas reinhardtii, sampled under a number of different conditions. The preparation of the RNA-Seq libraries and their analysis were performed using protocols optimized for organellar transcripts. Samples include growth in media +/– Fe, growth in media +/– Cu, diurnal growth samples collected in dark and light, and the sexual cycle.
2017-11-27 | GSE101944 | GEO
Project description:Using Illumina’s high-throughput small RNA sequencing and RNA sequencing, miRNAs and mRNAs differentially expressed under Zn deficiency and Zn resupply conditions were identified in shoots and roots of rice seedlings. A total of 68 miRNAs were identified to be differentially expressed under Zn deficiency and/or Zn resupply, and 38 of them were novel miRNAs. The Zn-responsive miRNAs were predicted to target a total of 799 genes. The transcriptome sequencing identified a total of 360 differentially expressed genes (DEGs) under Zn deficiency in shoots and roots, and 97 of them were recovered after Zn resupply treatment. Twelve DEGs were found to be potential targets genes of several Zn-responsive miRNAs like miR171g-5p, miR397b-5p, miR398a-5p, and miR528-5p.
2020-01-08 | GSE131003 | GEO
Project description:Using Illumina’s high-throughput small RNA sequencing and RNA sequencing, miRNAs and mRNAs differentially expressed under Zn deficiency and Zn resupply conditions were identified in shoots and roots of rice seedlings. A total of 68 miRNAs were identified to be differentially expressed under Zn deficiency and/or Zn resupply, and 38 of them were novel miRNAs. The Zn-responsive miRNAs were predicted to target a total of 799 genes. The transcriptome sequencing identified a total of 360 differentially expressed genes (DEGs) under Zn deficiency in shoots and roots, and 97 of them were recovered after Zn resupply treatment. Twelve DEGs were found to be potential targets genes of several Zn-responsive miRNAs like miR171g-5p, miR397b-5p, miR398a-5p, and miR528-5p.
2020-01-08 | GSE130980 | GEO
Project description:Zinc is an essential nutrient because of its role in catalysis and in stabilizing protein structure, but excess zinc can also be deleterious. Four nutritional zinc states have been identified in the alga Chlamydomonas reinhardtii: zinc toxic, zinc replete, zinc deficient and zinc limited. Growth is inhibited in zinc-limited and zinc toxic cells relative to zinc-replete cells, while zinc-deficiency is visually asymptomatic but distinguished by the accumulation of transcripts encoding ZIP family transporters. To identify targets of zinc deficiency and mechanisms of zinc acclimation, we used RNA-seq to probe zinc nutrition responsive changes in gene expression. We identified a subset of genes encoding zinc-handling components, including ZIP family transporters and candidate zinc chaperones. In addition, we noted an impact on two other regulatory pathways, the carbon concentrating mechanism (CCM) and the nutritional copper regulon. Targets of transcription factor Ccm1 and various CAH genes are up-regulated in zinc-deficiency, as a likely consequence of reduced carbonic anhydrase activity, which is validated by mass spectrometry and immunoblot analysis of Cah1, Cah3 and Cah4. Chlamydomonas is therefore not able to grow photoautotrophically in air in zinc limiting conditions, but supplementation with 1% CO2 restores growth to wild-type rates, suggesting that the inability to maintain CCM is a major consequence of zinc limitation. Surprisingly, we noted also that the Crr1 regulon, which responds to Cu limitation, is also turned on in zinc deficiency, and in fact, Crr1 is required for growth in zinc-limiting conditions. Zinc deficient cells are functionally copper deficient, as evidenced by reduced plastocyanin abundance, even though they hyperaccumulate copper up to 50-fold over normal levels. We suggest that zinc-deficient cells sequester Cu in a bio-unavailable form, perhaps to prevent mis-metallation of critical zinc sites.
2013-05-03 | GSE41096 | GEO
Project description:Understanding organisms’ environmental adaptation mechanisms is a fundamental question in ecology and evolution. The oyster Crassostrea gigas is able to accumulate high levels of zinc (Zn) and cadmium (Cd) without self-poisoning, and is thus widely used for pollution detection. However, the molecular mechanisms underlying such stress adaptation are largely unknown. Therefore, this study aimed to provide fundamental insights into the complex Zn/Cd-response regulatory networks.
2018-10-25 | PXD003290 | Pride
Project description:Systems analysis of Chlamydomonas Cu nutrition reveals connections between Cu and multiple O2-dependent metabolic steps
| PRJNA134525 | ENA