Raw data for mass spectrometry analysis of the effects of hypoxia on mitochondrial protein composition
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Hela Cell
DISEASE(S): Cervix Carcinoma
SUBMITTER: 
Tianshu Hao
LAB HEAD: Zhiyin Song
PROVIDER: PXD034375 | Pride | 2023-10-24
REPOSITORIES: Pride
Dataset's files
Publications
Hypoxia-reprogramed megamitochondrion contacts and engulfs lysosome to mediate mitochondrial self-digestion.
Hao Tianshu T Yu Jianglong J Wu Zhida Z Jiang Jie J Gong Longlong L Wang Bingjun B Guo Hanze H Zhao Huabin H Lu Bin B Engelender Simone S He He H Song Zhiyin Z
Nature communications 20230711 1
Mitochondria are the key organelles for sensing oxygen, which is consumed by oxidative phosphorylation to generate ATP. Lysosomes contain hydrolytic enzymes that degrade misfolded proteins and damaged organelles to maintain cellular homeostasis. Mitochondria physically and functionally interact with lysosomes to regulate cellular metabolism. However, the mode and biological functions of mitochondria-lysosome communication remain largely unknown. Here, we show that hypoxia remodels normal tubular ...[more]
Similar Datasets
Project description:Intermittent hypoxia is a common stressor in estuarine and coastal habitats due to the diurnal and tidal cycles of oxygen availability. Oxygen deficiency results in energy stress by limiting aerobic ATP production, while reoxygenation may lead to oxidative injury due to the excessive production of reactive oxygen species (ROS) in mitochondria. Mitochondria are a key intracellular target of hypoxia-reoxygenation (H/R) stress due to their central role in ATP production, ROS generation and stress signaling. Marine intertidal bivalves such as the Pacific oyster Crassostrea gigas are adapted to frequent H/R cycles in the intertidal zone and maintain mitochondrial integrity and aerobic function despite frequent oxygen fluctuations. To gain insight into the molecular responses of mitochondria of the hypoxia-tolerant Pacific oyster to H/R stress, we studied changes in oxidative phosphorylation (OXPHOS) capacity, proton leak and activity of the electron transport system enzymes (ETS) in gill mitochondria of C. gigas. We furthermore investigated shifts in mitochondrial proteome and phosphoproteome after 24 h of hypoxia and 1 h of post-hypoxic recovery. Oyster mitochondria maintained normal ETS and OXPHOS capacity during H/R stress, despite a slight but significant decline in cytochrome c oxidase (Complex IV) activity after reoxygenation. Fifty total proteins and 36 phosphoproteins were differentially abundant in mitochondria of H/R exposed oysters compared with the controls. Rearrangements of the mitochondrial (phospho)proteome during H/R stress involved upregulation of mitochondrial ETS (most notably Complexes I and IV) and iron-binding proteins (frataxin and ferrochelatase) as well as suppression of the metabolic pathways that channel electrons to ubiquinone, possibly as a mechanism to limit ROS production due to the iron overload and reverse flow of electrons through ETS. H/R stress also led to upregulation of a mitophagic activator serine/threonine protein phosphatase PGAM5 and dephosphorylation of metalloendopeptidase OMA1 indicating stimulation of mitochondrial quality control mechanisms during reoxygenation. Changes in the overall abundance and phosphorylation levels of several key proteins involved in the mitochondrial protein homeostasis (including subunits of the mitochondrial ribosome, mitochondrial inner membrane translocase and elongation factor G) are consistent with the suppression of the protein synthesis during hypoxia, likely as an energy-saving mechanism. Overall, our study indicates that shifts in the mitochondrial (phospho-)proteome play an important role in responses of oysters to H/R stress and might complement adaptations of anaerobic metabolism and metabolic rate depression in ensuring hypoxic survival and rapid recovery in this hypoxia-tolerant intertidal species.
2021-11-04 | PXD011365 | Pride
Project description:The human mitochondrial genome comprises a distinct genetic system transcribed as precursor polycistronic transcripts that are subsequently cleaved to generate individual mRNAs, tRNAs and rRNAs. Here we provide a comprehensive analysis of the human mitochondrial transcriptome across multiple cell lines and tissues. Using directional deep sequencing and parallel analysis of RNA ends, we demonstrate wide variation in mitochondrial transcript abundance, and precisely resolve transcript processing and maturation events. We identify novel transcripts, including small RNAs, and observe the enrichment of several nuclear RNAs in mitochondria. Using high-throughput in vivo DNaseI footprinting, we establish the global profile of DNA-binding protein occupancy across the mitochondrial genome at single nucleotide resolution, revealing novel regulatory features at mitochondrial transcription initiation sites and functional insights into disease-associated variants. Together, this integrated analysis of the mitochondrial transcriptome reveals unexpected complexity in the regulation, expression, and processing of mitochondrial RNA, and itM-CM-^BM-BM- provides a resource for the future study of mitochondrial function (accessed at mitochondria.matticklab.com). Examination of the mitochondiral transcriptome by long and small RNA sequencing, PARE sequencing and DNAseI hypersensitivity mapping.
2011-07-20 | E-GEOD-30772 | biostudies-arrayexpress
Project description:Mitochondria are vital in providing cellular energy via their oxidative phosphorylation system, which requires the coordinated expression of genes encoded by both the nuclear and mitochondrial genomes (mtDNA). Transcription of the circular mammalian mtDNA depends on a single mitochondrial RNA polymerase (POLRMT). Although the transcription initiation process is well understood, it remains highly controversial if POLRMT also serves as the primase for initiation of mtDNA replication. In the nucleus, the RNA polymerases needed for gene expression have no such role. Conditional knockout of Polrmt in heart results in severe mitochondrial dysfunction causing dilated cardiomyopathy in young mice. We further studied the molecular consequences of different expression levels of POLRMT and found that POLRMT is essential for primer synthesis to initiate mtDNA replication in vivo. Furthermore, transcription initiation for primer formation has priority over gene expression. Surprisingly, mitochondrial transcription factor A (TFAM) exists in an mtDNA-free pool in the Polrmt knockout mice. TFAM levels remain unchanged despite strong mtDNA depletion and TFAM is thus protected from degradation of the AAA+ Lon protease in absence of POLRMT. Lastly, mitochondrial transcription elongation factor (TEFM) can compensate for a partial depletion of POLRMT in heterozygous Polrmt knockout mice, indicating a direct regulatory role for this factor in transcription. In conclusion, we present here the first in vivo evidence that POLRMT has a key regulatory role in replication of mammalian mtDNA and is part of a mechanism that provides a switch between RNA primer formation for mtDNA replication and mtDNA expression. Isolated heart mitochondria from three control mice (L/L) and three Polrmt knockout mice (L/L, cre), aged 3-4 weeks, were sequenced and analyzed for differential expression.
2016-08-05 | E-GEOD-83368 | biostudies-arrayexpress
Project description:There is a paucity of data regarding what proteins localize to the mitochondria in the social amoeba Dictyostelium discoideum. Therefore, here, we utilized high-throughput tandem mass tag (TMT)-based protein quantitation to identify proteins in the whole-cell lysate, as well as in crude and purified mitochondrial samples. We then calculated the ratio of a protein’s abundance in the mitochondria isolates, both crude and highly purified, versus its abundance in the whole-cell lysate. The resulting value, indicating its enrichment in mitochondrial preparations, was further normalized to the average enrichment ratio of 47 reference mitochondrial proteins, to compute the relative enrichment ratio. Using this approach, we identified 908 putative mitochondrial proteins. We ultimately combined proteomic and in silico analyses to yield a comprehensive mitochondrial protein compendium. Our compendium lays the foundation for future studies to understand the functions of conserved mitochondrial proteins in health and diseases using D. discoideum as the model. It also provides an entry to study many fascinating mitochondrial processes that are unique in protists. Additionally, through comparative genomics, our compendium will complement mitochondrial protein discovery in other organisms and may shed light on the evolution of mitochondrial proteomes and processes.
2022-06-06 | PXD029101 | Pride
Project description:Hypoxia is a hallmark of solid tumors. Mitochondria play essential roles in cellular adaptation to hypoxia, but the underlying mechanisms are not fully understood. Through mitochondrial proteomic profiling, we find that the prolyl hydroxylase EglN1 accumulates on mitochondria under hypoxia. EglN1 substrate binding region 23 loop is responsible for its mitochondrial translocation and contributes to tumor growth. Furthermore, we identify AMPK as an EglN1 substrate on mitochondria. The EglN1-AMPK interaction is essential for their mutual mitochondrial translocation. EglN1 prolyl-hydroxylates AMPK under normoxia, then they rapidly dissociate following prolyl-hydroxylation, leading to their immediate release from mitochondria. While hypoxia results in constant EglN1-AMPK interaction and accumulation on mitochondria, leading to the formation of CaMKK2-EglN1-AMPK complex to activate AMPK phosphorylation, consequently ensuring metabolic homeostasis and tumor growth. Our findings demonstrate EglN1 as an oxygen-sensitive metabolic checkpoint signaling hypoxic stress to mitochondria through its 23 loop, revealing a therapeutic target for solid tumors.
2023-08-29 | PXD041653 | Pride
Project description:Mitochondria are essential organelles involved in critical biological processes such as energy metabolism and cell survival. Their dysfunction is linked to numerous human pathologies that often manifest in a tissue-specific manner. Accordingly, mitochondria fitness depends on versatile proteomes specialized to meet diverse tissue-specific requirements. Furthermore, increasing evidence suggests that phosphorylation may also play an important role in regulating tissue-specific mitochondrial functions and pathophysiology. We hypothesized that recent advances in mass spectrometry (MS)-based proteomics would now enable in-depth measurement toof quantitatively profile mitochondrial proteomes along with their matching phosphoproteomes across tissues. We isolated mitochondria from mouse heart, skeletal muscle, brown adipose tissue, kidney, liver, brain, and spleen by differential centrifugation followed by separation on Percoll gradients and high resolution MS analysis of the proteomes and phosphoproteomes. This in-depth map substantially quantifies known and predicted mitochondrial proteins and provides a resource of core and tissue modulated mitochondrial proteins (mitophos.biochem.mpg.de). We also uncover tissue-specific repertoires of dozens of kinases and phosphatases. Predicting kinase substrate associations for different mitochondrial compartments indicates tissue-specific regulation at the phosphoproteome level. Illustrating the functional value of our resource, we reproduce mitochondrial phosphorylation events on DRP1 responsible for its mitochondrial recruitment and fission imitation initationinitiation and describe phosphorylation clusters on MIGA2 linked to mitochondrial fusion.
2023-11-03 | PXD030062 | Pride
Project description:Hypoxia is a characteristic feature of marine environments and a major stressor for marine organisms inhabiting benthic and intertidal zones. Several studies have explored the responses of these organisms to hypoxic stress at the whole organism level with a focus on energy metabolism and mitochondrial response, but the instrinsic mitochondrial responses that support the organelle’s function under hypoxia and reoxygenation (H/R) stress are not well understood. We studied the effects of acute H/R stress (10 min anoxia followed by 15 min reoxygenation) on mitochondrial respiration, production of reactive oxygen species (ROS) and posttranslational modifications (PTM) of the proteome in a marine facultative anaerobe, the blue mussel Mytilus edulis. The mussels’ mitochondria showed increased OXPHOS respiration and suppressed proton leak resulting in a higher coupling efficiency after H/R stress. ROS production decreased in both the resting (LEAK) and phosphorylating (OXPHOS) state indicating that M. edulis is able to prevent oxidative stress and mitochondrial damage during reoxygenation. Hypoxia did not stimulate the rearrangement of the mitochondrial supercomplexes but impacted the mitochondrial phosphoproteome including the proteins involved in OXPHOS, amino acid and fatty acid catabolism, and protein quality control. This study indicates that mussels’ mitochondria possess intrinsic mechanisms (including regulation via PTM mechanisms such as reversible protein phosphorylation) that ensure high respiratory flux and mitigate oxidative damage during H/R stress and contribute to the hypoxia-tolerant mitochondrial phenotype of this metabolically plastic species.
2021-11-25 | PXD027955 | Pride
Project description:Background: Developments in DNA resequencing microarrays include mitochondrial DNA (mtDNA) sequencing and mutation detection. During automated analysis to sequence mtDNA, bases can be identified as wildtype, variant, or there may be a failure to assign a base (N-call) when compared to the mtDNA reference sequence (rCRS). The purpose of our study was to re-examine the N-call distribution of mtDNA samples, based on the hypothesis that N-calls may represent insertions or deletions in mtDNA. Findings: We analysed mtDNA from 16 patient samples (8 blood/bone marrow origin and 8 from cultured fibroblasts) using the Affymetrix MitoChip v.2.0 which has 2 probe areas, one for sequencing compared to the rCRS and one for 500 common haplotypes. N-calls by the proprietary GSEQ software were significantly reduced when the freeware on-line algorithm M-bM-^@M-^XsPROFILERM-bM-^@M-^Y was utilized. Interestingly, this decrease in N-calls, in both sections of the MitoChip, had no effect on the homoplasmic or heteroplasmic mutation levels compared to GSEQ software. We then used conventional DNA sequencing to analyse continuous N-call stretches identified by sPROFILER, ranging from 2 to 22 bases, to identify changes resulting in base calling failures. Conclusions: Our study is the first to analyse N-calls produced from GSEQ software for the MitoChip v2.0. We found that by narrowing the focus to stretches of N-calls revealed by sPROFILER, conventional sequencing was able to identify unique deletions and insertions. This study also appeared to support the contention that the GSEQ is more capable of assigning bases when used in conjunction with sPROFILER. mtDNA from 16 patient samples were analysed using Mitochip v2.0. Eight samples were DNA extractions directly from blood/bone marrow. The other eight samples were DNA extractions from primary cultured fibroblasts. Results were generated in GSEQ and reanalysed in sPROFILER for comparison.
2012-05-17 | E-GEOD-29550 | biostudies-arrayexpress
Project description:Mitochondria are known to be functional organelles, but their role as a signaling unit is increasingly being appreciated. The recent identification of a short open reading frame (sORF) in the mitochondrial DNA (mtDNA) that encodes a signaling peptide, humanin, suggests the possible existence of additional sORFs in the mtDNA that yield bioactive peptides. Here we report the identification of a sORF within the mitochondrial 12S rRNA encoding a 16-amino-acid peptide named MOTS-c (mitochondrial open-reading-frame of the twelve S rRNA -c) that regulates insulin sensitivity and metabolic homeostasis. MOTS-c is detected in various tissues and in circulation in an age-dependent manner. Its primary target organ appears to be the skeletal muscle and its cellular actions inhibit the folate cycle and its tethered de novo purine biosynthesis, causing a significant accumulation of AICAR levels concomitantly with AMPK activation. MOTS-c treatment in mice prevented age-dependent and high-fat diet-induced insulin resistance, as well as diet-induced obesity. These results suggest that mitochondria may be more actively engaged in regulating metabolic homeostasis than previously recognized, through the production of peptides encoded within its genome that act at the cellular and organismal level. Human embryonic kidney cells (HEK293 cell line) were cultured in 10-cm dishes in 7 mL of phenol-free DMEM supplemented with 10% FBS and incubated with water (controls) or the 16-amino-acid peptide mitochondrial open-reading-frame of the twelve S rRNA-c (MOTS-c, 10 uM) for 4 or 72 hours prior to RNA extraction.
2015-03-07 | E-GEOD-65068 | biostudies-arrayexpress
Project description:The mitochondrial subcompartment proteomes revealed by quantitative MS.
2017-08-24 | PXD005463 | Pride