Transcriptome analysis of Paracoccus denitrificans during Cu-limitation
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Agilent-026900 Paracoccus denitrificans
ORGANISM(S): Paracoccus denitrificans PD1222
SUBMITTER: 
Matthew John Sullivan
SECONDARY ACCESSION(S): PRJNA210735
REPOSITORIES: GEO
Similar Datasets
Project description:Transcriptional profiling of Paracoccus denitrificans PD1222 wild type grown to mid-exponential phase in minimal media with either 13 uM (Cu-H) or 0.5 uM (Cu-L) Cu regimes. The goal was to define the effects of Cu-limitation on denitrification genes Two growth conditions, three biological replicates of each condition. Each sample hybridised in a two-channel hybridization against Paracoccus denitrificans genomic DNA as the comparator/reference, which also acted as a control for spot quality. Cu-concentration 13 uM (Cu-H) versus 0.5 uM Cu (Cu-L) in anaerobic growth conditions.
2013-11-18 | E-GEOD-48577 | ArrayExpress
Project description:Transcriptional profiling of Paracoccus denitrificans PD1222 wild type incubated in continuous culture (continuous culture (CSTR)) in minimal media with aerobic or anaerobic conditions. The goal was to define the core respiratory genes. Overall design: Two growth conditions, three biological replicates of each condition. Each sample hybridised in a two-channel hybridization against Paracoccus denitrificans genomic DNA as the comparator/reference, which also acted as a control for spot quality.
| GSE97959 | GEO
Project description:We used digital gene expression (NlaIII sequence tags) and RNA-Seq to compare the transcriptomes of Cu-replete vs. Cu–deficient Chlamydomonas wild-type cells to reveal dozens of mRNAs whose abundance is modified. Half of the corresponding genes are targets of CRR1, a master regulator of nutritional copper sensing, and are associated with candidate CRR1 binding sites. The targets include many plastid-localized proteins, like FDX5 encoding a ferredoxin isoform, and CGL78, encoding a protein conserved in the green lineage, indicative of modified plastid metabolism. Immunoblot analysis and proteome profiles recapitulate the transcriptome profiles. New evidence for Cu sparing is suggested by up-regulation of AOF1 encoding a copper-independent but flavin-dependent amine oxidase and down-regulation of two metal- binding proteins. Genes encoding redox proteins, many of which function in lipid metabolism, are over-represented, which is compatible with the role of Cu in biology. Lipid profiles indicate a CRR1-dependent increase in Cu-deficient cells in the proportion of unsaturated (16:2, 16:3, 16:4, 18:2) fatty acids at the expense of the more saturated (16:0, 16:1, 18:0) precursors, especially on plastid galactolipids, which validates the increased expression of acyl-ACP and plastid-localized w-6 desaturases. CRR1-independent changes in the transcriptome suggest a role for Cu in oxygen sensing in Chlamydomonas. Sampling of Chlamydomonas CC-1021 (2137) and crr1-2, crr1:CRR1 mutant cells (the mutant is knock-down for the transcription factor crr1, which plays a key role in the transcriptional response to copper levels) cultivated in TAP or minimal medium under Cu-sufficient (control) and Cu-defficient conditions. poly-A purification, NlaIII digestion/random fragmentation
2011-10-23 | E-GEOD-25124 | ArrayExpress
Project description:We used digital gene expression (NlaIII sequence tags) and RNA-Seq to compare the transcriptomes of Cu-replete vs. Cu–deficient Chlamydomonas wild-type cells to reveal dozens of mRNAs whose abundance is modified. Half of the corresponding genes are targets of CRR1, a master regulator of nutritional copper sensing, and are associated with candidate CRR1 binding sites. The targets include many plastid-localized proteins, like FDX5 encoding a ferredoxin isoform, and CGL78, encoding a protein conserved in the green lineage, indicative of modified plastid metabolism. Immunoblot analysis and proteome profiles recapitulate the transcriptome profiles. New evidence for Cu sparing is suggested by up-regulation of AOF1 encoding a copper-independent but flavin-dependent amine oxidase and down-regulation of two metal- binding proteins. Genes encoding redox proteins, many of which function in lipid metabolism, are over-represented, which is compatible with the role of Cu in biology. Lipid profiles indicate a CRR1-dependent increase in Cu-deficient cells in the proportion of unsaturated (16:2, 16:3, 16:4, 18:2) fatty acids at the expense of the more saturated (16:0, 16:1, 18:0) precursors, especially on plastid galactolipids, which validates the increased expression of acyl-ACP and plastid-localized w-6 desaturases. CRR1-independent changes in the transcriptome suggest a role for Cu in oxygen sensing in Chlamydomonas. Overall design: Sampling of Chlamydomonas CC-1021 (2137) and crr1-2, crr1:CRR1 mutant cells (the mutant is knock-down for the transcription factor crr1, which plays a key role in the transcriptional response to copper levels) cultivated in TAP or minimal medium under Cu-sufficient (control) and Cu-defficient conditions. poly-A purification, NlaIII digestion/random fragmentation
2011-10-24 | GSE25124 | GEO
Project description:In this work, the denitrification process carried out by Paracoccus denitrificans PD1222 has been followed up by a quantitative proteomic analysis.
2018-06-14 | PXD006821 | Pride
Project description:Background: MicroRNAs (miRNAs) are a class of single-stranded non-coding small RNAs (sRNAs) that are 20-24 nucleotides (nt) in length. Extensive studies have indicated that miRNAs play important roles in plant growth, development, and stress responses. With more copper (Cu) and copper-containing compounds used as bactericides and fungicides in viticulture, Cu stress has become one of the serious environmental problems that affect plant growth and development. In order to uncover the hidden response mechanisms of Cu stress, many Cu-responsive miRNAs have been detected in several plant species. However, there have been few reports about the grapevine miRNAs in response to Cu. Results: Here, two small RNA libraries were constructed from Cu-treated and water-treated (control) leaves of 'Summer Black' grapevine. Following high-throughput sequencing and filtering, 158 known vvi-miRNAs and 98 novel vvi-miRNAs were identified in the two libraries. Among these, 24 could only be detected in the treatment, and 63 were only detected in the control. Additionally, 100 known vvi-miRNAs were found to be clearly responsive to Cu, among which 96 were down-regulated and four were up-regulated; 47 novel vvi-miRNAs were found to be clearly responsive to Cu, among which 35 were down-regulated and 12 were up-regulated. Subsequently, expression patterns of a set of Cu-responsive vvi-miRNAs were validated by quantitative real-time PCR (qRT-PCR). There existed some consistency in expression levels of Cu-responsive vvi-miRNAs between high-throughput sequencing and qRT-PCR assays. In addition, 92 putative targets for 79 known vvi-miRNAs and 51 putative targets for 22 novel vvi-miRNAs were predicted, and most of the targets are involved in multiple biological processes including transcriptional regulation and response to biotic and abiotic stresses. Conclusions: In this study, 147 Cu-responsive vvi-miRNAs were identified using high-throughput sequencing, and their target genes were predicted, which will be helpful to understanding the molecular mechanisms of miRNAs in response to Cu stress. Furthermore, this work can also provide a foundation for further study of the networks of miRNAs involved in grapevine plant growth and breeding some Cu-tolerant grapevine cultivars. Mixed 'Summer Black' grapevine young leaves (2 weeks old), large leaves (5 weeks old), and old leaves (9 week old) in randomly-selected plants from both the Cu-treated and control groups were collected for high-throughput sequencing. Subsequently, we carried out the analysis of Solexa sequencing data, and performed the research of regulatory modes of grapevine miRNAs on their target genes during Cu stress.
2016-02-20 | E-GEOD-78133 | ArrayExpress
Project description:Beller, H. R., T. E. Letain, A. Chakicherla, S. R. Kane, T. C. Legler, and M. A. Coleman. 2006. Whole-genome transcriptional analysis of chemolithoautotrophic thiosulfate oxidation by Thiobacillus denitrificans under aerobic vs. denitrifying conditions. Journal of Bacteriology 188:7005-7015. Thiobacillus denitrificans is one of the few known obligate chemolithoautotrophic bacteria capable of energetically coupling thiosulfate oxidation to denitrification as well as aerobic respiration. As very little is known about the differential expression of genes associated with key chemolithoautotrophic functions (such as sulfur-compound oxidation and CO2 fixation) under aerobic versus denitrifying conditions, we conducted whole-genome, cDNA microarray studies to explore this topic systematically. The microarrays identified 277 genes (approximately ten percent of the genome) as differentially expressed using Robust Multi-array Average statistical analysis and a 2-fold cutoff. Genes upregulated (ca. 6- to 150-fold) under aerobic conditions included a cluster of genes associated with iron acquisition (e.g., siderophore-related genes), a cluster of cytochrome cbb3 oxidase genes, cbbL and cbbS (encoding the large and small subunits of form I ribulose 1,5-bisphosphate carboxylase/oxygenase, or RubisCO), and multiple molecular chaperone genes. Genes upregulated (ca. 4- to 95-fold) under denitrifying conditions included nar, nir, and nor genes (associated respectively with nitrate reductase, nitrite reductase, and nitric oxide reductase, which catalyze successive steps of denitrification), cbbM (encoding form II RubisCO), and genes involved with sulfur-compound oxidation (including two physically separated but highly similar copies of sulfide:quinone oxidoreductase and of dsrC, associated with dissimilatory sulfite reductase). Among genes associated with denitrification, relative expression levels (i.e., degree of upregulation with nitrate) tended to decrease in the order nar > nir > nor > nos. Reverse transcription, quantitative PCR analysis was used to validate these trends. Keywords: bacterial metabolism Overall design: After growth under either aerobic or denitrifying conditions (at least two successive transfers) with thiosulfate as the electron donor, triplicate cultures were harvested for RNA extraction. The specific rates of thiosulfate oxidation were assessed in all cultures immediately before the harvesting of cells and were comparable under aerobic and denitrifying conditions.
2006-10-06 | GSE5256 | GEO
Project description:Iron (Fe) and copper (Cu) are essential metal micronutrients that are necessary for many redox reactions. The uptake of these metals is tightly regulated in plants. Some redox processes can alternatively use Fe-containing proteins or Cu-containing proteins, depending on nutritional status. Copper deficiency can rescue a Cucumis melo Fe uptake deficient mutant, and Fe deficiency can result in increased accumulation of Cu. However, the system responsible for Fe-deficiency-regulated Cu-uptake is unknown. To understand the genes and gene networks associated with Fe-deficiency regulated Cu uptake and Fe-Cu cross-talk, we conducted transcriptomic profiling of roots and rosettes of spl7 (a Cu uptake deficient mutant in arabidopsis) and Col-0 (WT) grown under Fe, Cu and simultaneous Fe and Cu deficiency conditions. Overall design: We conducted transcriptomic profiling of roots and rosettes of spl7 (a Cu uptake deficient mutant in arabidopsis) and Col-0 (WT) grown under Fe, Cu and simultaneous Fe and Cu deficiency conditions mRNA deep sequencing
| GSE104916 | GEO
Project description:Despite the increased utilization of nanoparticles, the behavior and effect in the environment is largely unknown and few resources are available for health and environmental effect studies. Enchytraeids are extensively used in studies of soil ecotoxicology and recently, a cDNA microarray for Enchytraeus albidus was developed, allowing also toxicogenomic studies in this species. These organisms are ecologically relevant small worms that indirectly contribute to the regulation and degradation of organic matter. In this study we compared the gene expression profiles of E. albidus when exposed to copper-salt (CuCl2) and copper nanoparticles (Cu-NP) spiked soil. The worms were exposed for 48 hours in soil to a range of concentrations. Microarray hybridizations revealed different response patterns between copper-salt and copper nanoparticles exposed organisms, these differences are mainly related with transcripts involved in the energy metabolism of the organisms. Despite unknown gene function in the data-set there are indications that Cu-salt and Cu-NP exposure induced specific gene level responses. Fluorescently labelled cDNA, from enchytraeids exposed during 2 days to control soil (from Hygum site in Denmark) and to the different exposure conditions (Cy5), was synthesized for microarray analysis and hybridizations were performed. After scanning, spots were identified and ratios quantified using the QuantArray (Packard Biochip Technologies). Statistical analysis of the microarrays was performed using limmaGUI package (1.18.0) (Smyth, 2005) in the R (2.8.0) software environment (http://www.R-project.org/). After being submitted to local background subtraction, microarrays were normalized using global loess method. To statistically evaluate the differential gene expression between the different conditions, a gene-per-gene linear model (limma – linear model for microarray analysis) and empirical Bayes methods were applied. The results were then corrected for multiple testing using the Benjamini-Hochberg’s method (adjusted p<0.05 was considered significant) (Benjamini and Hochberg, 1995).
2011-09-07 | E-GEOD-26331 | ArrayExpress
Project description:Drought and salinity reduce plant growth and grain yield in wheat. To explain the role of Cu and Fe NPs in the improvement of growth and yield of wheat varieties, gel-free proteomic technique was used. Spike length, number of grains per spike, and 100 grain weight were increased at 25 ppm Cu and Fe NPs in high yielding galaxy-13, drought tolerant Pakistan-13, and salinity tolerant NARC-11. A total of 86, 131, and 30 proteins were significantly changed in abundance under Cu and Fe NPs exposure. The number of proteins related to stress, proteins, and glycolysis were mainly changed by Cu and Fe NPs exposure. By Cu NPs, in galaxy-13 starch degradation and glycolysis pathway were increased, while decreased in Pakistan-13 and NARC-11. Furthermore, by Fe NPs, only in galaxy-13 tricarboxylic acid cycle was increased while did not change glycolysis and starch degradation. Uptake of Cu NPs increased at 25 ppm in galaxy-13, Pakistan-13 and NARC-11 while Fe NPs uptake increased only at 35 and 40 ppm in NARC-11.
2016-10-12 | PXD003671 | Pride