A cellular mechanism to detect and alleviate reductive stress
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE155374 | GEO | 2020/07/30
REPOSITORIES: GEO
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Project description:A cellular mechanism to detect and alleviate reductive stress
| PRJNA649541 | ENA
Project description:Cells respond to mitochondrial energetic stress with rapid activation of the AMP-activated protein kinase (AMPK), which acutely inhibits anabolism and stimulates catabolism. AMPK also induces sustained transcriptional reprogramming of metabolism. The TFEB transcription factor is a major effector of AMPK signals, inducing lysosome genes following energetic stress. Yet the molecular mechanism underlying how AMPK activates TFEB remains unresolved. We demonstrate here that AMPK directly phosphorylates five conserved serine residues in FNIP1, which suppresses the function of the FLCN/FNIP1 RagC GAP complex, in turn controlling TFEB lysosomal localization. We demonstrate that FNIP1 phosphorylation is required for AMPK to induce nuclear translocation of TFEB, which is fully separable from AMPK control of canonical mTORC1 signaling. Using a non-phosphorylatable allele of FNIP1, we show that in parallel to lysosomal biogenesis, AMPK induces mitochondrial biogenesis via TFEB-dependent induction of PGC1a mRNA. This signaling from mitochondrial stress is also independent of amino-acid control of the Rags and TFEB, which still proceed normally in cells bearing the AMPK-non phosphorylatable allele of FNIP1. Taken together, mitochondrial energetic stress triggers AMPK/FNIP1-dependent TFEB nuclear translocation, inducing transcriptional waves of lysosomal and mitochondrial biogenesis.
2023-05-08 | GSE218827 | GEO
Project description:This experiment was conducted to identify FNIP1-dependent mRNA transcripts alteration in skeletal muscle. Mouse FNIP1 was specifically overexpressed in skeletal muscle in FNIP1-transgenic (FNIP1-Tg) mice. FNIP1-Tg mice were crossed with FNIP1-knockout (FNIP1-KO) mice to generate FNIP1-TgKO mice expressing FNIP1 only in skeletal muscle but not in other tissues. The muscle glycolytic-to-oxidative transformation is determined, largely in part, at the level of gene expression. To gain insight into the FNIP1-dependent regulation of skeletal muscle energy metabolism, transcriptome analysis was performed by whole-genome gene expression profiling experiments in gastrocnemius (GC) muscle from both FNIP1-KO and FNIP1-TGKO mice. We were particularly interested in the subset of genes that were regulated only in the FNIP1-KO mice but not in FNIP1-TGKO mice. Gene ontology (GO) analysis revealed that the primary FNIP1-regulated genes were mitochondrial metabolic genes. A broad array of genes involved in mitochondria was regulated FNIP1-KO muscle in a FNIP1-dependent manner. Together, the transcriptional profiling results indicate that a significant subset of FNIP1 target genes, were those involved in mitochondrial function.
2021-03-17 | GSE150193 | GEO
Project description:Activation of thermogenesis in brown and beige adipocytes upon activation by external stimuli burns fuel energy as heat. Owing to its remarkable benefits on metabolic health and its demonstrated presence in adult humans, beige adipocytes holds great promise to combat obesity and metabolic diseases. Folliculin interacting protein 1 (FNIP1) is an adaptor protein originally identified through its interaction with folliculin (FLCN) and AMPK. To investigate the physiological role of FNIP1 in adipose tissue in vivo, we generated adipocyte-specific FNIP1 deficient mice (referred to as FNIP1-AKO) by crossing mice bearing a conditional Fnip1 allele with introns 5 and 6 floxed (Fnip1 lox/lox) with the adiponectin promoter–driven Cre mice. We performed transcriptome analysis by whole-genome gene expression profiling experiments in inguinal white adipose tissue (iWAT) from both wild-type (WT) and FNIP1-AKO mice. We were particularly interested in the subset of genes that were up-regulated in the FNIP1-AKO mice. Gene ontology (GO) analysis revealed that the primary up-regulated genes were mitochondrial and lipid metabolism-related genes. Gene expression validation studies demonstrated that a broad array of genes involved in thermogenic and mitochondrial oxidative program was induced in FNIP1-AKO iWAT. Together, the transcriptional profiling results indicate that loss of FNIP1 activate thermogenic program in white adipocytes.
2022-02-26 | GSE185067 | GEO
Project description:This experiment was conducted to identify target genes of the microRNA-499 in skeletal muscle of transgenic mice that overexpressed miR-499. The following abstract from the submitted manuscript describes the major findings of this work. Coupling of mitochondrial function and skeletal muscle fiber type by a miR-499/Fnip1/AMPK circuit. Jing Liu, Xijun Liang, Danxia Zhou, Ling Lai, Tingting Fu, Yan Kong, Qian Zhou, Rick B. Vega, Min-Sheng Zhu, Daniel P. Kelly, Xiang Gao, and Zhenji Gan. Upon adaption of skeletal muscle to physiological and pathophysiological stimuli, muscle fiber type and mitochondrial function are coordinately regulated. Recent studies have identified pathways involved in control of contractile proteins of oxidative type fibers. However, the mechanism for coupling of mitochondrial function to muscle contractile machinery during fiber type transition remains unknown. Here, we show that the expression of the genes encoding type I myosins, Myh7/Myh7b and their intronic miR-208b/miR-499 parallels mitochondrial function during fiber type transitions. Using in vivo approaches in mice, we found that miR-499 drives a PGC-1a-dependent mitochondrial oxidative metabolism program to match shifts in slow-twitch muscle fiber composition. Mechanistically, miR-499 directly targets Fnip1, a known AMP-activated protein kinase (AMPK)-interacting protein that negatively regulates AMPK, a known activator of PGC-1a. Inhibition of Fnip1 reactivated AMPK/PGC-1a signaling and mitochondrial function in myocytes. Restoration of the expression of miR-499 in the mdx mouse model of Duchenne muscular dystrophy (DMD) reduced the severity of DMD. Thus, we have identified a miR-499/Fnip1/AMPK circuit that can serve as a mechanism to couple muscle fiber type and mitochondrial function. Keywords: muscle, contractile fiber type, mitochondrial function, microRNA, gene regulation RNA from three wild-type (non-transgenic (NTG)) and three miR-499 overexpressing (MCK-miR-499) mice was analyzed. three replicates of each are provided.
2016-09-03 | E-GEOD-72581 | biostudies-arrayexpress
Project description:Using muscle-specific FNIP1 (WT) and FNIP1 (S220A Tg) muscle tissues, we identified approximately 600 potential FNIP1 (WT) or FNIP1 (S220A) binding proteins in exercising muscle tissue of the corresponding mice by the CoIP-MS method, proteomic analysis showed that both FNIP1 (WT) and FNIP1 (S220A) interacted with major mitochondrial proteins, such as the respiratory complex subunits. Notably, FNIP1 (S220A) specifically interacted with additional mitochondrial subunits that were not observed for FNIP1 (WT), including protein involved in NADH metabolism and sulfur cluster binding. These data suggested that non-phosphorylated FNIP1 (S220A) could enhance its interaction with mitochondria.
2023-11-17 | PXD046977 | Pride
Project description:We have performred RNA-seq analysis of WT, ∆phoP and ∆sigH Mtb H37Rv under normal and redox (Diamide) stress, to investigate the role of PhoP and SigH in maintaning the redox homoeostasis of bacterium. RNA was extracted from exponentially growing mycobacterial cells in Middlebrook 7H9 media. Briefly, 25 ml of bacterial culture was grown to mid-log phase (OD600= 0.4 to 0.6) and combined with 40 ml of 5 M guanidinium thiocyanate solution containing 1% β-mercaptoethanol and 0.5% Tween 80. Cells were pelleted by centrifugation, and lysed by re-suspending in 1 ml Trizol (Ambion) in the presence of Lysing Matrix B (100 µm silica beads; MP Bio) using a FastPrep-24 bead beater (MP Bio) at a speed setting of 6.0 for 30 seconds. The procedure was repeated for 2-3 cycles with incubation on ice in between pulses. Next, cell lysates were centrifuged at 13000 rpm for 10 minutes; supernatant was collected and processed for RNA isolation using Direct-ZolTM RNA isolation kit (ZYMO) as per manufacturer’s recommendation. Following extraction, RNA was treated with DNAse I (Promega) to degrade contaminating DNA, and integrity was assessed using a Nanodrop (ND-1000, Spectrophotometer). RNA samples were further checked for intactness of 23S and 16S rRNA using formaldehyde-agarose gel electrophoresis, and Qubit fluoremeter (Invitrogen). RNA integrity was checked using Agilent 2200 Tape Station system (Agilent Technologies). Library construction, RNA-sequencing and data analysis have been carried out by Agrigenome Labs Private Limited (Cochin), India. The main purpose of this study is to understand how mycobacteria can sense numerous stress conditions and mount an appropriate stress response. Although recent evidence suggests that at low pH M. tuberculosis encounters reductive stress, the mechanism of integrated regulation of stress response remains unknown. Unexpectedly, we find that PhoP contributes to mycothiol level and a PhoP-depleted bacilli shows enhanced susceptibility to redox stress. Because SigH is known to control expression of redox inducible genes, we probed whether previously-reported PhoP-SigH interaction accounts for mycobacterial redox stress response. Our results suggest that while PhoP controls pH homeostasis via its interaction with SigE, SigH-dependent PhoP expression, but not PhoP -SigH interaction, and direct recruitment of SigH, but not PhoP controls expression of mycobacterial thioredoxin genes. Together, these results uncover novel stress-specific interaction events of sigma factors and PhoP or lack thereof, as the underlying mechanisms of an adaptive programme, which couples low pH conditions and mycobacterial thiol homeostasis. The main purpose of this study is to understand how mycobacteria can sense numerous stress conditions and mount an appropriate stress response. Although recent evidence suggests that at low pH M. tuberculosis encounters reductive stress, the mechanism of integrated regulation of stress response remains unknown. Unexpectedly, we find that PhoP contributes to mycothiol level and a PhoP-depleted bacilli shows enhanced susceptibility to redox stress. Because SigH is known to control expression of redox inducible genes, we probed whether previously-reported PhoP-SigH interaction accounts for mycobacterial redox stress response. Our results suggest that while PhoP controls pH homeostasis via its interaction with SigE, SigH-dependent PhoP expression, but not PhoP -SigH interaction, and direct recruitment of SigH, but not PhoP controls expression of mycobacterial thioredoxin genes. Together, these results uncover novel stress-specific interaction events of sigma factors and PhoP or lack thereof, as the underlying mechanisms of an adaptive programme, which couples low pH conditions and mycobacterial thiol homeostasis.
2022-04-09 | GSE171775 | GEO
Project description:Galactose catabolism in Aspergillus nidulans is regulated by at least two regulators, GalR and GalX. In Aspergillus niger only GalX is present, and its role in D-galactose catabolism in this fungus was investigated. Phenotypic and gene expression analysis of a wild type and a galX disruptant revealed that GalX does not substitute for the absence of GalR in A. niger, it regulates the D-galactose oxido-reductive pathway, but not the Leloir pathway. Four genes, including the recently characterized ladB (galactitol dehydrogenase) were found to have differencial expressions that are highly relevant to GalX , indicating a novel oxido-reductive pathway in A.niger .
2012-09-20 | GSE40219 | GEO
Project description:Precise regulation of stem cell activity is crucial for tissue homeostasis. In Drosophila, intestinal stem cells (ISCs) maintain the midgut epithelium and respond to oxidative challenges by increasing proliferation rates. However, the connection between intestinal homeostasis and redox signaling remains obscure. Here we identify Caliban (Clbn) as a novel mitochondrial protein involved in regulating the cellular redox state in enterocytes (ECs) and the proliferative activity of ISCs. We find that clbn knock-out flies lose the intestinal homeostasis characterized by increased ISCs proliferation, disrupted intestinal epithelial integrity, reduced viability in response to harmful stress and shortened lifespan. Mechanistically, Clbn is highly expressed and localized to mitochondria in ECs, and loss of clbn impairs mitochondrial morphology and functions, result in accumulation of reactive oxygen species, ECs damage and activation of JNK and JAK-STAT signaling pathways. Furthermore, loss of clbn promotes tumor growth in gut generated by activating Ras in intestinal progenitor cells. Our findings reveal the essential role of Clbn in maintaining intestinal homeostasis and may provide new insight into the functional link among mitochondrial redox modulation, tissue homeostasis and cancer.
2022-01-01 | GSE125032 | GEO
Project description:Galactose catabolism in Aspergillus nidulans is regulated by at least two regulators, GalR and GalX. In Aspergillus niger only GalX is present, and its role in D-galactose catabolism in this fungus was investigated. Phenotypic and gene expression analysis of a wild type and a galX disruptant revealed that GalX does not substitute for the absence of GalR in A. niger, it regulates the D-galactose oxido-reductive pathway, but not the Leloir pathway. Four genes, including the recently characterized ladB (galactitol dehydrogenase) were found to have differencial expressions that are highly relevant to GalX , indicating a novel oxido-reductive pathway in A.niger . We aim to discover differentially expressed genes in A.niger wild type strain N402 and M-NM-^TgalX mutant while growing on galactose as carbon source. Biological duplicates were made for both strains. The strains were grown O/N in complete medium with 2% frunctose and mycelium was then washed and transferred to minimal medium with 25 mM D-galactose and incubated for 2 hours. Affymetrix microarray experiments were performed RNA isolated from these samples.
2012-09-20 | E-GEOD-40219 | biostudies-arrayexpress