Respiratory supercomplexes provide metabolic efficiency in zebrafish
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ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE133487 | GEO | 2020/05/03
REPOSITORIES: GEO
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Project description:Respiratory supercomplexes provide metabolic efficiency in zebrafish
| PRJNA551601 | ENA
Project description:Assembly factors play a critical role in the biogenesis of mitochondrial respiratory chain complexes I-IV where they assist in the membrane insertion of subunits, attachment of co-factors, and stabilization of assembly intermediates. The major fraction of complexes I, III and IV are present together in large molecular structures known as respiratory chain supercomplexes. A number of assembly factors have been proposed as required for supercomplex assembly, including the hypoxia inducible gene 1 domain family member HIGD2A. Using gene-edited human cell lines and extensive steady state, translation and affinity enrichment proteomics techniques we show that loss of HIGD2A leads to defects in the de novo biogenesis of mtDNA-encoded COX3, subsequent accumulation of complex IV intermediates and turnover of COX3 partner proteins. Deletion of HIGD2A also leads to defective complex IV activity. The impact of HIGD2A loss on complex IV was not altered by growth under hypoxic conditions, consistent with its role being in basal complex IV assembly. While in the absence of HIGD2A we show that mitochondria do contain an altered supercomplex assembly, we demonstrate it to harbor a crippled complex IV lacking COX3. Our results redefine HIGD2A as a classical assembly factor required for building the COX3 module of complex IV.
2020-04-22 | PXD016864 | Pride
Project description:The existence of respiratory supercomplexes (SCs) has been well acknowledged especially with the development of cryo-EM in the past few years, but their physiological relevance remains elusive. Dynamics of OXPHOS complexes is tightly correlated to cell fate switch, but whether SCs involve in this process is unknown. During C2C12 myogenesis, CIII2 and CIV as well as the subunits of CIII and CIV were slightly increasing, while SC III2+IV was decreasing, which indicates that SC reorganization may regulate myogenesis. Knockdown Cox7a2l decreased SCs III2+IV, I+III2+IV2 and I+III2+IV3, but had little effect on I+III2+IV. Transcriptome and quantitative-proteome analysis indicated that Cox7a2l silence activated myogenic gene expression and repressed cell cycle-associated gene expression. Besides, knockdown of Cox7a2l decreased CII abundance and accumulated succinate, which in turn suppressed certain key transcription factors, such as HMGA1 which is important for stemness maintenance. Our results indicated that respiratory supercomplex reorganization changed succinate homeostasis and myogenesis related gene expression profiles, thus switching cell fate.
2021-11-01 | GSE178547 | GEO
Project description:To identify protein composition of photosystem II (PSII) supercomplexes separated from spruce seedlings using sucrose gradient centrifugation. These supercomplexes represent mainly so called C2S2 PSII supercomplex as revealed by high-resolution cryo-EM.
2023-07-19 | PXD035272 | Pride
Project description:Short chain enoyl-CoA hydratase 1 (ECHS1) is involved in the second step of mitochondrial fatty acid β-oxidation (FAO), catalysing the hydration of short chain enoyl-CoA esters to short chain 3-hyroxyl-CoA esters. Genetic deficiency in ECHS1 (ECHS1D) is associated with a specific subset of Leigh Syndrome, a disease typically caused by defects in oxidative phosphorylation (OXPHOS). Here, we examined the molecular pathogenesis of ECHS1D using a CRISPR/Cas9 edited human cell ‘knockout’ model and fibroblasts from ECHS1D patients. Transcriptome analysis of ECHS1 ‘knockout’ cells showed reductions in key mitochondrial pathways, including the TCA cycle, receptor mediated mitophagy and nucleotide biosynthesis. Subsequent proteomic analyses confirmed these reductions and revealed additional defects in mitochondrial oxidoreductase activity and fatty acid β-oxidation. Functional analysis of ECHS1 ‘knockout’ cells showed reduced mitochondrial oxygen consumption rates when metabolising glucose or OXPHOS complex I-linked substrates, as well as decreased complex I and complex IV enzyme activities. ECHS1 ‘knockout’ cells also exhibited decreased OXPHOS protein complex steady-state levels (complex I, complex III2, complex IV, complex V and supercomplexes CIII2/CIV and CI/CIII2/CIV). Patient fibroblasts exhibit varied reduction of mature OXPHOS complex steady-state levels, with defects detected in CIII2, CIV, CV and the CI/CIII2/CIV supercomplex. Overall, these findings highlight the contribution of defective OXPHOS function, in particular complex I deficiency, to the molecular pathogenesis of ECHS1D.
2022-04-10 | GSE200252 | GEO
Project description:It is now accepted that mitochondrial respiratory complex subunits assemble in supercomplexes. However, studying supercomplexes has typically relied upon antibody-based protein quantification, often limited to a single subunit per respiratory complex. To provide a deeper insight into mitochondrial plasticity and supercomplex formation, we combined Blue Native Polyacrylamide Gel Electrophoresis (BN-PAGE) and high-resolution mass spectrometry-based proteomics in sedentary and exercise-trained skeletal muscle. We quantified 422 mitochondrial proteins within ten bands. Our analyses revealed the often-unaccounted presence of complex II and V subunits within the majority of supercomplexes. Upon exercise-induced mitochondrial biogenesis, non-stoichiometric changes in subunits and their incorporation into supercomplexes were apparent. Finally, we uncovered the dynamics of supercomplex-related assembly proteins and mtDNA-encoded subunits within supercomplexes, as well as the high-molecular mass complexes of ubiquinone biosynthesis enzymes and Lactb, a mitochondrial-localized obesogenic polymer. Thus, combining BN-PAGE and mass spectrometry to comprehensively analyze respiratory supercomplexes illuminates previously undetectable complexity in mitochondrial plasticity.
2021-05-17 | PXD016289 | Pride
Project description:Photosystem II (PSII) complexes are organized into large supercomplexes with variable amounts of light-harvesting proteins (Lhcb). A typical PSII supercomplex in plants is formed by four trimers of Lhcb proteins (LHCII trimers), which are bound to the PSII core dimer via monomeric antenna proteins. However, the architecture of PSII supercomplexes in Norway spruce (Picea abies (L.) Karst.) is different, most likely due to a lack of two Lhcb proteins, Lhcb6 and Lhcb3. Interestingly, the spruce PSII supercomplex shares similar structural features with its counterpart in the green alga Chlamydomonas reinhardtii (Kouřil et al.: New Phytol. 210, 808-814, 2016). Here we present a single-particle electron microscopy study of isolated PSII supercomplexes from Norway spruce that revealed binding of a variable amount of LHCII trimers to the PSII core dimer at positions that have never been observed in any other plant species so far. The largest spruce PSII supercomplex, which was found to bind 8 LHCII trimers, is even larger than the current largest known PSII supercomplex from Chlamydomonas reinhardtii. We have also shown that the spruce PSII supercomplexes can form various types of PSII megacomplexes, which were also identified in intact grana membranes. Some of these large PSII supercomplexes and megacomplexes were identified also in Pinus sylvestris, another representative of Pinaceae family. The structural variability and complexity of LHCII organization in Pinaceae seems to be related to the absence of Lhcb6 and Lhcb3 in this family and may be beneficial for the optimization of light-harvesting under varying environmental conditions.
2021-09-09 | PXD020138 | Pride
Project description:Mitochondrial supercomplexes are functionally important, but how supercomplexes being assembled is not known. Mitochondrial Complex I has an important role in the assembly of supercomplex. In this study, we generated a series of cell model with shRNA mediated gene silencing or CRISPR-Cas9 gene knockout technology. We performed a series of mitochondrial proteome analyses in different cell lines with disruption of gene that encodes subunit of Complex I. Also, we performed Co-IP of exogenous TIMMDC1, which was an assembly factor of Complex I.
2021-01-08 | PXD023474 | iProX
Project description:Mitochondrial complex III (CIII2) and complex IV (CIV) which can associate into a higher-order supercomplex (SC III2 IV) play key roles in respiration. However, structures of these plant complexes remain unknown. We present atomic models of CIII2, CIV and SC III2 IV from Vigna radiata determined by single-particle cryoEM. The structures reveal plant-specific differences in the MPP domain of CIII2 and define the subunit composition of CIV. Conformational heterogeneity analysis of CIII2 revealed long-range, coordinated movements across the complex as well as the motion of CIII2s iron-sulfur head domain. The CIV structure suggests that, in plants, proton translocation does not occur via the H-channel. The supercomplex interface differs significantly from that in yeast and bacteria in its interacting subunits angle of approach and limited interactions in the mitochondrial matrix. These structures challenge long-standing assumptions about the plant complexes, generate new mechanistic hypotheses and allow for the generation of more selective agricultural inhibitors.
2020-10-05 | MSV000086237 | MassIVE
Project description:We report the ability of the Drosha null/conditional-null mouse model to enable the identification of pri-miRNA transcripts. The conditional-null allele of Drosha phenocopies the null allele both in mESC and in mice, upon conversion to the null state with Cre.
2015-02-09 | GSE55735 | GEO