E.coli Apec growth experiment
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB18262 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1744137_1.fastq.gz | Fastqsanger.gz | |||
| ERR1744137_2.fastq.gz | Fastqsanger.gz | |||
| ERR2703300_1.fastq.gz | Fastqsanger.gz | |||
| ERR2703300_2.fastq.gz | Fastqsanger.gz | |||
| ERR2703301_1.fastq.gz | Fastqsanger.gz |
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Project description:Genes differentially expressed by exogenously supplied polyamines: putrescine, spermidine, spermine, thermospermine and cadaverine in Arabidopsis thaliana.
2020-08-25 | E-MTAB-9267 | biostudies-arrayexpress
Project description:Polyamines (putrescine, spermidine, and spermine) are major organic polycations essential for a wide spectrum of cellular processes. The cells require mechanisms to maintain homeostasis of intracellular polyamines to prevent otherwise severe adverse effects. We performed a detailed transcriptome profile analysis of P. aeruginosa in response to agmatine and putrescine with an emphasis in polyamine catabolism. Agmatine serves as precursor compound for putrescine (and hence spermidine and spermine), which was proposed to convert into GABA and succinate before entering the TCA cycle in support of cell growth as the sole source of carbon and nitrogen. Two acetylpolyamine amidohydrolases, AphA and AphB, were identified to be involved in the conversion of agmatine into putrescine. Enzymatic products of AphA were confirmed by mass spectrometry analysis. Interestingly, the alanine-pyruvate cycle was shown indispensable for polyamine utilization. The newly identified dadRAX locus, encoding the regulator, alanine transaminase and racemase respectively, coupled with SpuC, the major putrescine-pyruvate transaminase, were key components to maintain alanine homeostasis. Corresponding mutant strains were severely hampered in polyamine utilization. On the other hand, the alternative gamma-glutamylation pathway for the conversion of putrescine into GABA was also discussed. Subsequently, GabD, GabT and PA5313 were identified for GABA utilization. Growth defect of PA5313 gabT double mutant in GABA suggested the importance of these two transaminases. The succinic-semialdehyde dehydrogenase activity of GabD and its induction by GABA was also demonstrated in vitro. Polyamine utilization in general was proven independent of the PhoPQ two-component system even the expression of which was induced by polyamines. Multiple potent catabolic pathways as depicted in this study could serve pivotal roles in control of intracellular polyamine levels. Keywords: Metabolism, polyamines, agmatine, putrescine, glutamate, phoPQ.
2008-04-07 | GSE9926 | GEO
Project description:Polyamines play a pivotal role in plant growth and development by modulating metabolite levels and even regulating DNA methylation. To reveal novel insights into the intricate relationship among polyamines, metabolites and DNA methylation, the impact of exogenous putrescine on wheat was investigated at several levels. Since the outcome of putrescine treatment may vary depending on the light quality, the experiment was performed under both white and blue light. Metabolite profiling revealed distinct changes induced by blue light and/or putrescine. Blue light alone had increasing effects on several metabolites, but the effect of putrescine was dominant under blue light in most cases. Putrescine had a decreasing effect on some amino acids and the γ-glutamyl-cycle, while increasing effect on the TCA-cycle. Distinct changes in DNA methylation patterns were detected in response to blue light, putrescine or their combination. Blue light exerted strong effects on methylation, and putrescine application slightly could induce further changes. Putrescine had a higher impact under white as increased the leaf spermidine level, and parallel with this, a lower level of up-methylated genes involved in cellular processes, but a higher level of down-methylated genes involved in molecular function and biological processes occurred compared to the blue light.
2025-07-09 | GSE292105 | GEO
Project description:Polyamines (putrescine, spermidine, and spermine) are major organic polycations essential for a wide spectrum of cellular processes. The cells require mechanisms to maintain homeostasis of intracellular polyamines to prevent otherwise severe adverse effects. We performed a detailed transcriptome profile analysis of P. aeruginosa in response to agmatine and putrescine with an emphasis in polyamine catabolism. Agmatine serves as precursor compound for putrescine (and hence spermidine and spermine), which was proposed to convert into GABA and succinate before entering the TCA cycle in support of cell growth as the sole source of carbon and nitrogen. Two acetylpolyamine amidohydrolases, AphA and AphB, were identified to be involved in the conversion of agmatine into putrescine. Enzymatic products of AphA were confirmed by mass spectrometry analysis. Interestingly, the alanine-pyruvate cycle was shown indispensable for polyamine utilization. The newly identified dadRAX locus, encoding the regulator, alanine transaminase and racemase respectively, coupled with SpuC, the major putrescine-pyruvate transaminase, were key components to maintain alanine homeostasis. Corresponding mutant strains were severely hampered in polyamine utilization. On the other hand, the alternative gamma-glutamylation pathway for the conversion of putrescine into GABA was also discussed. Subsequently, GabD, GabT and PA5313 were identified for GABA utilization. Growth defect of PA5313 gabT double mutant in GABA suggested the importance of these two transaminases. The succinic-semialdehyde dehydrogenase activity of GabD and its induction by GABA was also demonstrated in vitro. Polyamine utilization in general was proven independent of the PhoPQ two-component system even the expression of which was induced by polyamines. Multiple potent catabolic pathways as depicted in this study could serve pivotal roles in control of intracellular polyamine levels. Experiment Overall Design: P. aeruginosa PAO1 was grown aerobically in minimal medium P with 350 rpm shaking at 37C, in the presence of L-glutamate alone or with the addition of putrescine, agmatine or GABA at 20 mM. Cells were harvested when the optical density at 600 nm reached 0.5~0.6 by centrifugation for 5 minutes at 4C. Total RNA samples were isolated by RNeasy purification kit following instructions of the manufacturer (Qiagen). Reverse transcription for cDNA synthesis, fragmentation by DNase I treatment, cDNA probe labeling and hybridization were performed according to the instructions of GeneChip manufacturer (Affymetrix). Data were processed by Microarray Suite 5.0 software normalizing the absolute expression signal values of all chips to a target intensity of 500. GeneSpring software (Silicon Genetics) was used for expression pattern analysis and comparison. Only genes showing consistent expression profiles in duplicates were selected for further analysis.
2008-06-16 | E-GEOD-9926 | biostudies-arrayexpress
Project description:Bacterial and mammalian cells are rich in putrescine, spermidine and spermine. Polyamines can be incorporated into proteins in vitro. Very few naturally occurring polyaminated proteins have been identified. Bovine albumin and the recombinant universal stress protein from Francisella tularensis were used as models for mass spectrometry analysis of polyaminated proteins. The proteins were covalently bound to putrescine, spermidine, or spermine by the action of carbodiimide or microbial transglutaminase. Tryptic peptides were subjected to liquid chromatography tandem mass spectrometry. Adducts were identified by Protein Prospector software. We describe the search parameters for identifying polyaminated peptides in Protein Prospector and show convincing MMS spectra for adducts with putrescine, spermidine, and spermine. Manual evaluation led us to recognize signature ions for polyamine adducts on Asp, Glu, and Gln. Manual evaluation recognized neutral loss from putrescine, spermidine and spermine during the fragmentation process. Mechanisms for formation of signature ions and neutral loss are presented. Manual evaluation recognized a false positive adduct which had been formed during trypsinolysis by rearrangement of a peptide sequence. Another false positive was a 71 Da added mass on cysteine, which was initially assumed to be putrescine, but was actually a propionamide adduct for a sample extracted from a polyacrylamide gel. The type of information presented in this report serves as a model for identifying naturally occurring polyaminated proteins.
2024-02-27 | PXD046396 | Pride
Project description:The naturally occurring polyamines putrescine, spermidine or spermine are ubiquitous in all cells. Although polyamines have prominent regulatory roles in cell division and growth, precise molecular and cellular functions are not well established in vivo. In this work we have performed a microarray experiment in a polyamine mutant (delta-spe3 delta-fms1) strain to investigate the responsiveness of yeast genes to supplementation with spermidine and spermine. Expression analysis identified genes responsive to the addition of either excess spermidine (10-5 M) or spermine (10-5 M) compared to a control culture containing 10-8 M spermidine. 247 genes were up-regulated >2-fold, and 11 genes were up-regulated more than 10-fold after spermidine addition. Functional categorization of the genes showed induction of transport related genes, and genes involved in methionine, arginine, lysine, NAD and biotin biosynthesis. 268 genes were down-regulated more than 2-fold, and 6 genes were down-regulated more than 8-fold after spermidine addition. A majority of the down-regulated genes are involved in nucleic acid metabolism and various stress responses. In contrast, only few genes (18) were significantly responsive to spermine. Thus, results from global gene expression profiling demonstrate a more major role for spermidine in modulating gene expression in yeast than spermine. Experiment Overall Design: 5 control replicates vs. 3 spermine (SP)-treated or 5 spermidine (SPD)-treated samples.
2009-09-05 | E-GEOD-15269 | biostudies-arrayexpress
Project description:Polyamines are aliphatic polycations that have emerged as important determinants of cell growth and viability in rapidly proliferating cells, including in the pathogenic protozoan parasite Leishmania donovani. In L. donovani, the polyamine spermidine is synthesized by the successive conversion of ornithine into putrescine (catalyzed by ornithine decarboxylase or ODC) and putrescine into spermidine (catalyzed by spermidine synthase or SPDSYN). Deletion of either ODC (del-odc) or SPDSYN (del-spdsyn) from the L. donovani genome renders these parasites auxotrophic for polyamines and these mutants are impaired in their ability to survive both in culture and within the mammalian host without the addition of exogenous polyamine supplementation. Significantly, del-odc parasites immediately cease proliferation after putrescine is removed from the culture media and perish within two weeks, while spermidine starved del-spdsyn mutants, which retain intracellular putrescine pools, show a slow-growth phenotype, and persist for several weeks in culture. To elucidate the key differences within the proteome of putrescine-starved del-odc cells and spermidine-starved del-spdsyn parasites, a shotgun quantitative proteomics approach was undertaken using TMT labeling and LC-MS/MS analysis. Briefly, three biological replicates each for mid-log phase del-odc and del-spdsyn promastigotes grown in the presence of exogenous putrescine (for del-odc) or spermidine (for del-spdsyn) supplementation were washed to remove the exogenous polyamine supplementation and incubated in polyamine-free media. At 24 and 48 h, cells from each biological replicate were isolated and prepared for tandem mass tag (TMT) labeling and downstream LC-MS/MS analyses. Peptides were identified using a database generated from the reference genome of L. donovani BPK282A1 strain. Changes in relative protein abundance for the polyamine-starved del-odc and del-spdsyn cell lines at 24 and 48 h were calculated by comparing aggregate total reporter ion intensities for each protein to that of the corresponding polyamine-supplemented 0-h timepoint.
2022-08-29 | PXD036349 | Pride
Project description:The naturally occurring polyamines putrescine, spermidine or spermine are ubiquitous in all cells. Although polyamines have prominent regulatory roles in cell division and growth, precise molecular and cellular functions are not well established in vivo. In this work we have performed a microarray experiment in a polyamine mutant (delta-spe3 delta-fms1) strain to investigate the responsiveness of yeast genes to supplementation with spermidine and spermine. Expression analysis identified genes responsive to the addition of either excess spermidine (10-5 M) or spermine (10-5 M) compared to a control culture containing 10-8 M spermidine. 247 genes were up-regulated >2-fold, and 11 genes were up-regulated more than 10-fold after spermidine addition. Functional categorization of the genes showed induction of transport related genes, and genes involved in methionine, arginine, lysine, NAD and biotin biosynthesis. 268 genes were down-regulated more than 2-fold, and 6 genes were down-regulated more than 8-fold after spermidine addition. A majority of the down-regulated genes are involved in nucleic acid metabolism and various stress responses. In contrast, only few genes (18) were significantly responsive to spermine. Thus, results from global gene expression profiling demonstrate a more major role for spermidine in modulating gene expression in yeast than spermine.
2009-08-20 | GSE15269 | GEO
Project description:Maintaining tissue homeostasis depends on a balance of cell proliferation, differentiation and apoptosis. Polyamine regulator, AMD1, is a crucial regulator of keratinocyte differentiation and AMD1 protein is upregulated on differentiation and highly expressed in the suprabasal layers of the human epidermis. During keratinocyte differentiation, elevated AMD1 promotes decreased putrescine and increased spermine levels. Inhibition of AMD1 results in reduced spermine levels and inhibition of keratinocyte differentiation. Supplementing AMD1 inhibited keratinocytes with exogenous spermidine/spermine rescued aberrant differentiation. Undifferentiated and differentiated keratinocytes that had been treated with and without AMD1 inhibitor EGBG in the presence or absence of spermidine/ spermine supplementation were subjected to microarray analysis. These data show that AMD1 up regulation is required for keratinocyte differentiation and that inhibition of AMD1 can be rescued by supplementation with the polyamines spermidine and spermine.
2021-01-15 | GSE164881 | GEO
Project description:Polyamines are absolutely required for cell growth and proliferation. While polyamine depletion results in reversible cell cycle arrest, the actual mechanism of growth inhibition is still obscure. This experiment aimed at determining the cellular processes elicited by re-addition of polyamines to polyamine-depleted (growth arrested) cells. In order to reveal the general transcriptional responses to polyamine re-addition, NIH3T3 mouse fibroblasts were first treated with 1mM L-Difluoromethylornithine (DFMO) for 96 hours and then growth stimulated by spermidine. Cells were collected at 0, 30, 60, 120, 240, 360, 480 and 600 min upon addition of spermidine to polyamine-depleted (growth arrested) cells. Total RNA was isolated, reverse-transcribed, fragmented, labeled and hybridized to Affymetrix MoGene 1.0 ST DNA array.
2012-09-11 | E-GEOD-36664 | biostudies-arrayexpress