Decoding transcriptomic signatures of Cysteine String Protein alpha-mediated synapse maintenance
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE245339 | GEO | 2023/10/13
REPOSITORIES: GEO
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Project description:Decoding transcriptomic signatures of Cysteine String Protein alpha-mediated synapse maintenance
| PRJNA1027846 | ENA
Project description:Synapse maintenance is essential for generating functional circuitry and decrement in this process is a hallmark of neurodegenerative disease. While we are beginning to understand the basis of synapse formation, much less is known about synapse maintenance in vivo. Cysteine string protein α (CSPα), encoded by the Dnajc5 gene, is a synaptic vesicle chaperone that is necessary for synapse maintenance and linked to neurodegeneration. To investigate the transcriptional changes associated with synapse maintenance, we performed single nucleus transcriptomics on the cortex of young CSPα knockout (KO) mice and littermate controls. Through differential expression and gene ontology analysis, we observed that both neurons and glial cells exhibit unique signatures in CSPα KO brain. Significantly all neurons in CSPα KO brains show strong signatures of repression in synaptic pathways, while upregulating autophagy related genes. Through visualization of synapses and autophagosomes by electron microscopy, we confirmed these alterations especially in inhibitory synapses. By imputing cell-cell interactions, we found that neuron-glia interactions were specifically increased in CSPα KO mice. This was mediated by synaptogenic adhesion molecules, including the classical Neurexin1-Neuroligin 1 pair, suggesting that communication of glial cells with neurons is strengthened in CSPα KO mice in an attempt to achieve synapse maintenance. Together, this study reveals unique cellular and molecular transcriptional changes in CSPα KO cortex and provides new insights into synapse maintenance and neurodegeneration.
| S-EPMC10592922 | biostudies-literature
Project description:Synapse formation is critical for the wiring of neural circuits in the developing brain. The synaptic scaffolding protein S-SCAM/MAGI-2 has important roles in the assembly of signaling complexes at postsynaptic densities. However, the role of S-SCAM in establishing the entire synapse is not known. Here, we report significant effects of RNAi-induced S-SCAM knockdown on the number of synapses in early stages of network development in vitro. In vivo knockdown during the first three postnatal weeks reduced the number of dendritic spines in the rat brain neocortex. Knockdown of S-SCAM in cultured hippocampal neurons severely reduced the clustering of both pre- and postsynaptic components. This included synaptic vesicle proteins, pre- and postsynaptic scaffolding proteins, and cell adhesion molecules, suggesting that entire synapses fail to form. Correspondingly, functional and morphological characteristics of developing neurons were affected by reducing S-SCAM protein levels: neurons displayed severely impaired synaptic transmission and reduced dendritic arborization. A next generation sequencing approach showed normal expression of housekeeping genes, but changes of expression levels in 39 synaptic signaling molecules in cultured neurons. These results indicate that S-SCAM mediates the recruitment of all key classes of synaptic molecules during synapse assembly and is critical for the development of neural circuits in the developing brain.
2023-10-02 | GSE228093 | GEO
Project description:The enhanced green fluorescent protein (EGFP) is considered to be a harmless protein because the critical expression level that causes growth defects is higher than that of other proteins. Here we found that overexpression of EGFP, but not a glycolytic protein Gpm1, triggered the cell elongation phenotype in the budding yeast Saccharomyces cerevisiae. By the morphological analysis of the cell overexpressing each of five fluorescent proteins harboring different properties, we revealed that cysteine content was associated with the cell elongation phenotype. We further confirmed this finding by mutational analysis of an EGFP with additional cysteines, a cysteine-containing glycolytic enzyme Tpi1, and a cysteine-less glycolytic enzyme Gpm1. The abnormal cell morphology triggered by overexpression of EGFP was also observed in the fission yeast Schizosaccharomyces pombe. Overexpression of cysteine-containing protein was toxic, especially at high-temperature, while the toxicity could be modulated by additional protein characteristics. The morphological abnormality seemed to be triggered by the S-S bond-triggered protein aggregation, and by the interaction with a chaperone Ssa1 and the heat shock transcription factor Hsf1. Evolutionary analysis of duplicated genes showed that cysteine toxicity may be an evolutionary bias to exclude cysteine from highly expressed proteins. The overexpression of cysteine-less moxGFP, the least toxic protein revealed in this study, would be a good model system to understand the physiological state of protein burden triggered by ultimate overexpression of harmless proteins.
2022-03-31 | GSE178244 | GEO
Project description:First experiment: Cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM methionine + 0.1 mM cysteine (complete) or supplemented only with 0.1 mM methionine (cysteine-free). Cells were cultured in either medium for 42 h (Long + Cys; Long -Cys) or in cysteine-free medium for 36 h followed by 6 h in complete medium (Short +Cys) Second experiment: C3A/HepG2 cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM Met and 0.1 mM Cys (complete) or supplemented only with 0.1 mM Met (cysteine-devoid). Cells were cultured in complete medium for 42 h (Long +Cys) or in complete medium for 36 h followed by cysteine-devoid medium for 6 h (Short -Cys). Keywords: amino acid deprivation
2007-12-13 | GSE9517 | GEO
Project description:First experiment: Cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM methionine + 0.1 mM cysteine (complete) or supplemented only with 0.1 mM methionine (cysteine-free). Cells were cultured in either medium for 42 h (Long + Cys; Long -Cys) or in cysteine-free medium for 36 h followed by 6 h in complete medium (Short +Cys); Second experiment: C3A/HepG2 cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM Met and 0.1 mM Cys (complete) or supplemented only with 0.1 mM Met (cysteine-devoid). Cells were cultured in complete medium for 42 h (Long +Cys) or in complete medium for 36 h followed by cysteine-devoid medium for 6 h (Short -Cys). Experiment Overall Design: First experiment: Three plates of cells were cultured under each condition. Cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM methionine + 0.1 mM cysteine (complete) or supplemented only with 0.1 mM methionine (cysteine-free). Cells were cultured in either medium for 42 h (Long + Cys; Long -Cys) or in cysteine-free medium for 36 h followed by 6 h in complete medium (Short +Cys). Experiment Overall Design: Second experiment: C3A/HepG2 cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM Met and 0.1 mM Cys (complete) or supplemented only with 0.1 mM Met (cysteine-devoid). Cells were cultured in complete medium for 42 h (Long +Cys) or in complete medium for 36 h followed by cysteine-devoid medium for 6 h (Short -Cys).
2008-06-16 | E-GEOD-9517 | biostudies-arrayexpress
Project description:Excess cysteine (and cystine) is known to be toxic in organisms. Due to the absence of cysteine dioxygenase (involved in degradation of excess cysteine in humans and pathogenic fungi) in non pathogenic fungi such as S. cerevisiae, mechanism of cysteine (and cystine) tolerance is yet to be addressed.
2017-06-13 | GSE87794 | GEO
Project description:Cysteine occupies a central position in plant metabolism due to its biochemical functions. Arabidopsis thaliana cells contain different O-acetylserine(thiol)lyase (OASTL) enzymes that catalyze the biosynthesis of cysteine. Because they are localized in the cytosol, plastids and mitochondria, this results in multiple subcellular cysteine pools. Much progress has been made on the most abundant OASTL enzymes; however, information on the less abundant OASTL-like proteins has been scarce. To unequivocally establish the enzymatic reaction catalyzed by the minor cytosolic OASTL isoform CS-LIKE (AT5G28030), we expressed this enzyme in bacteria and characterized the purified recombinant protein. Our results demonstrate that CS-LIKE catalyzes the desulfuration of L-cysteine to sulfide plus ammonia and pyruvate. Thus, CS-LIKE is a novel L-cysteine desulfhydrase (EC 4.4.1.1), and we propose to designate it DES1. The impact and functionality of DES1 in cysteine metabolism was revealed by the phenotype of the T-DNA insertion mutants des1-1 and des1-2. Mutation of the DES1 gene leads to premature leaf senescence, as demonstrated by the increased expression of senescence-associated genes and transcription factors. Also, the absence of DES1 significantly reduces the total cysteine desulfuration activity in leaves, and there is a concomitant increase in the total cysteine content. As a consequence, the expression levels of sulfur-responsive genes are de-regulated, and the mutant plants show enhanced antioxidant defenses and tolerance to conditions that promote oxidative stress. Our results suggest that DES1 from Arabidopsis is an L-cysteine desulfhydrase involved in maintaining cysteine homeostasis, mainly at late developmental stages or under environmental perturbations. Using the Affymetrix ATH1 GeneChips, we performed a comparative transcriptomic analysis on leaves of the des1-1 and wild type plants grown on soil for three weeks. Three biological replicates were performed for each sample and hybridized to the chips. We made the comparison of des1-1 leaves versus wild-type leaves to classify the differently expressed genes in the mutant plant.
2011-11-23 | E-GEOD-19244 | biostudies-arrayexpress
Project description:Comparison of Clostridium difficile transcriptome of strain CD630E grown for 10 hours in PY (supplemented with mild concentration of cysteine) versus PYC (PY supplemented with 10 mM of cysteine). Experimental procedure was designed to investigate the influence of cysteine on toxins production and the regulatory network involved. two-conditions experiments, excess of cysteine vs mild concentration of cysteine, 4 biological replicates for each condition Description of the supplementary files: Main - Short description of the experiment Result_all - All significative genes Result_Gold* - High quality significative gene Result_Silver** - Medium quality significative gene All_Raw_data - All genes results significative and non significative Design_Genes-OUT - Genes not present in the platform Design_Genes-Oligos - Number of oligos design per gene * Gold : Nbr significative oligos = Nbr oligos designed for this gene ** Silver : Nbr significative oligos = Nbr oligos designed for this gene -1
2013-12-31 | E-GEOD-22423 | biostudies-arrayexpress
Project description:Cysteine occupies a central position in plant metabolism due to its biochemical functions. Arabidopsis thaliana cells contain different O-acetylserine(thiol)lyase (OASTL) enzymes that catalyze the biosynthesis of cysteine. Because they are localized in the cytosol, plastids and mitochondria, this results in multiple subcellular cysteine pools. Much progress has been made on the most abundant OASTL enzymes; however, information on the less abundant OASTL-like proteins has been scarce. To unequivocally establish the enzymatic reaction catalyzed by the minor cytosolic OASTL isoform CS-LIKE (AT5G28030), we expressed this enzyme in bacteria and characterized the purified recombinant protein. Our results demonstrate that CS-LIKE catalyzes the desulfuration of L-cysteine to sulfide plus ammonia and pyruvate. Thus, CS-LIKE is a novel L-cysteine desulfhydrase (EC 4.4.1.1), and we propose to designate it DES1. The impact and functionality of DES1 in cysteine metabolism was revealed by the phenotype of the T-DNA insertion mutants des1-1 and des1-2. Mutation of the DES1 gene leads to premature leaf senescence, as demonstrated by the increased expression of senescence-associated genes and transcription factors. Also, the absence of DES1 significantly reduces the total cysteine desulfuration activity in leaves, and there is a concomitant increase in the total cysteine content. As a consequence, the expression levels of sulfur-responsive genes are de-regulated, and the mutant plants show enhanced antioxidant defenses and tolerance to conditions that promote oxidative stress. Our results suggest that DES1 from Arabidopsis is an L-cysteine desulfhydrase involved in maintaining cysteine homeostasis, mainly at late developmental stages or under environmental perturbations.
2011-11-23 | GSE19244 | GEO