bims-cytox1 Biomed News
on Cytochrome oxidase subunit 1
Issue of 2021–12–05
ten papers selected by
Gavin McStay, Staffordshire University
  1. Pathways shaping the mitochondrial inner membrane.
  2. Global mitochondrial protein import proteomics reveal distinct regulation by translation and translocation machinery.
  3. Ndufs4 knockout mouse models of Leigh syndrome: pathophysiology and intervention.
  4. Spinal Nerve Roots Abnormalities on MRI in a Child with SURF1 Mitochondrial Disease.
  5. Functional studies of Plasmodium falciparum putative SURF1 in Saccharomyces cerevisiae.
  6. Malignancy and NF-κB signalling strengthen coordination between expression of mitochondrial and nuclear-encoded oxidative phosphorylation genes.
  7. A Conserved Mitochondrial Chaperone-Protease Complex Involved in Protein Homeostasis.
  8. ER-misfolded proteins become sequestered with mitochondria and impair mitochondrial function.
  9. Substrate profiling of mitochondrial caseinolytic protease P via a site-specific photocrosslinking approach.
  10. Effects of high-intensity interval training on mitochondrial supercomplex assembly and biogenesis, mitophagy, and the AMP-activated protein kinase pathway in the soleus muscle of aged female rats.
  1. Open Biol. 2021 Dec;11(12): 210238
    Pathways shaping the mitochondrial inner membrane.
    Till Klecker, Benedikt Westermann.
      Mitochondria are complex organelles with two membranes. Their architecture is determined by characteristic folds of the inner membrane, termed cristae. Recent studies in yeast and other organisms led to the identification of four major pathways that cooperate to shape cristae membranes. These include dimer formation of the mitochondrial ATP synthase, assembly of the mitochondrial contact site and cristae organizing system (MICOS), inner membrane remodelling by a dynamin-related GTPase (Mgm1/OPA1), and modulation of the mitochondrial lipid composition. In this review, we describe the function of the evolutionarily conserved machineries involved in mitochondrial cristae biogenesis with a focus on yeast and present current models to explain how their coordinated activities establish mitochondrial membrane architecture.
    Keywords:  ATP synthase; MICOS; Mgm1; Saccharomyces cerevisiae; cristae; mitochondrial lipids
    DOI:  https://doi.org/10.1098/rsob.210238
  2. Mol Cell. 2021 Nov 19. pii: S1097-2765(21)00954-0. [Epub ahead of print]
    Global mitochondrial protein import proteomics reveal distinct regulation by translation and translocation machinery.
    Jasmin Adriana Schäfer, Süleyman Bozkurt, Jonas Benjamin Michaelis, Kevin Klann, Christian Münch.
      Most mitochondrial proteins are translated in the cytosol and imported into mitochondria. Mutations in the mitochondrial protein import machinery cause human pathologies. However, a lack of suitable tools to measure protein uptake across the mitochondrial proteome has prevented the identification of specific proteins affected by import perturbation. Here, we introduce mePRODmt, a pulsed-SILAC based proteomics approach that includes a booster signal to increase the sensitivity for mitochondrial proteins selectively, enabling global dynamic analysis of endogenous mitochondrial protein uptake in cells. We applied mePRODmt to determine protein uptake kinetics and examined how inhibitors of mitochondrial import machineries affect protein uptake. Monitoring changes in translation and uptake upon mitochondrial membrane depolarization revealed that protein uptake was extensively modulated by the import and translation machineries via activation of the integrated stress response. Strikingly, uptake changes were not uniform, with subsets of proteins being unaffected or decreased due to changes in translation or import capacity.
    Keywords:  SILAC; TMT; disease; integrated stress response; mitochondria; protein translocation; proteomics; proteostasis; respiratory chain complexes; translation
    DOI:  https://doi.org/10.1016/j.molcel.2021.11.004
  3. Brain. 2021 Nov 29. pii: awab426. [Epub ahead of print]
    Ndufs4 knockout mouse models of Leigh syndrome: pathophysiology and intervention.
    Melissa van de Wal, Merel Adjobo-Hermans, Jaap Keijer, Tom Schirris, Judith Homberg, Mariusz R Wieckowski, Sander Grefte, Evert M van Schothorst, Clara van Karnebeek, Albert Quintana, Werner J H Koopman.
      Mitochondria are small cellular constituents that generate cellular energy (ATP) by oxidative phosphorylation (OXPHOS). Dysfunction of these organelles is linked to a heterogeneous group of multisystemic disorders, including diabetes, cancer, ageing-related pathologies and rare mitochondrial diseases (MDs). With respect to the latter, mutations in subunit-encoding genes and assembly factors of the first OXPHOS complex (CI) induce isolated CI deficiency and Leigh syndrome (LS). This syndrome is an early-onset, often fatal, encephalopathy with a variable clinical presentation and poor prognosis due to the lack of effective intervention strategies. Mutations in the nuclear DNA (nDNA)-encoded NDUFS4 gene, encoding the NADH: Ubiquinone oxidoreductase subunit S4 (NDUFS4) of CI induce "mitochondrial complex I deficiency, nuclear type 1" (MC1DN1) and LS in pediatric patients. A variety of (tissue-specific) Ndufs4 knockout mouse models were developed to study the LS pathomechanism and intervention testing. Here, we review and discuss the role of CI and NDUFS4 mutations in human MD, and review how the analysis of Ndufs4 knockout mouse models has generated new insights into the MC1ND1/LS pathomechanism and its therapeutic targeting.
    Keywords:  Leigh syndrome; intervention; mouse model; pathomechanism
    DOI:  https://doi.org/10.1093/brain/awab426
  4. Neuropediatrics. 2021 Dec 01.
    Spinal Nerve Roots Abnormalities on MRI in a Child with SURF1 Mitochondrial Disease.
    Alfonso Rubino, Giorgia Bruno, Federica Mazio, Maria Fulvia de Leva, Lucia Ruggiero, Filippo Maria Santorelli, Antonio Varone.
      Variants in SURF1, encoding an assembly factor of mitochondrial respiratory chain complex IV, cause Leigh syndrome (LS) and Charcot-Marie-Tooth type 4K in children and young adolescents. Magnetic resonance imaging (MRI) appearance of enlarged nerve roots with postcontrastographic enhancement is a distinctive feature of hypertrophic neuropathy caused by onion-bulb formation and it has rarely been described in mitochondrial diseases (MDs). Spinal nerve roots abnormalities on MRI are novel findings in LS associated with variants in SURF1. Here we report detailed neuroradiological and neurophysiologic findings in a child with LS and demyelinating neuropathy SURF1-related. Our case underlines the potential contributive role of spinal neuroimaging together with neurophysiological examination to identify the full spectrum of patterns in MDs. It remains to elucidate if these observations remain peculiar of SURF1 variants or potentially detectable in other MDs with peripheral nervous system involvement.
    DOI:  https://doi.org/10.1055/s-0041-1739135
  5. J Vector Borne Dis. 2020 Oct-Dec;57(4):57(4): 325-330
    Functional studies of Plasmodium falciparum putative SURF1 in Saccharomyces cerevisiae.
    Savitha Chellappan, Subarna Roy, Jyoti M Nagmoti, Wahida Tabassum, Raja Vukanti, S L Hoti, Mrinal Kanti Bhattacharyya, Praveen Balabaskaran Nina.
       BACKGROUND AND OBJECTIVES: The mitochondrial electron transport chain (mtETC) of Plasmodium falciparum is an important drug target. Identification and functional validation of putative mitochondrial proteins of the mtETC is critical for drug development. Many of the regulatory subunits and assembly factors of cytochrome c oxidase readily identifiable in humans and yeast are missing in P. falciparum. Here, we describe our efforts to identify and validate the function of putative Pfsurf1, a key assembly factor of complex IV of the mtETC.
    METHODS: Multiple sequence alignment of SURF 1/Shy 1 was carried out in Clustal X 2.1. Phylogenetic tree was constructed using "Draw tree" option in Clustal X, and was analyzed using interactive Tree of Life software. To identify the conserved sequences, domain search was done using Jalview version 2.8.2 (BLOSUM 62 scoring). The haploid Saccharomyces cerevisiae strain (BY4741) containing the null allele shy1 (Orf: YGR112w) (shy1::Kan) was complemented with putative Pfsurf1 to study its ability to rescue the growth defect.
    RESULTS: Similarity searches of PfSURF1-like protein in the Pfam shows statistically significant E = 4.7e-10 match to SURF1 family. Sequence alignment of PfSURF1 with other SURF1-like proteins reveals the conservation of transmembrane domains, α-helices and β-pleated sheets. Phylogenetic analysis clusters putative PfSURF1 with apicomplexan SURF1-like proteins. Yeast complementation studies show that Pfsurf1 can partially rescue the yeast shy1 mutant, YGR112w.
    INTERPRETATION & CONCLUSION: Bioinformatics and complementation studies in yeast show that P. falciparum's SURF1 is the functional ortholog of human SURF1 and yeast Shy1.
    Keywords:  Plasmodium falciparum; SURF1; Yeast complementation
    DOI:  https://doi.org/10.4103/0972-9062.311773
  6. Genome Biol. 2021 Dec 02. 22(1): 328
    Malignancy and NF-κB signalling strengthen coordination between expression of mitochondrial and nuclear-encoded oxidative phosphorylation genes.
    Marcos Francisco Perez, Peter Sarkies.
       BACKGROUND: Mitochondria are ancient endosymbiotic organelles crucial to eukaryotic growth and metabolism. The mammalian mitochondrial genome encodes for 13 mitochondrial proteins, and the remaining mitochondrial proteins are encoded by the nuclear genome. Little is known about how coordination between the expression of the two sets of genes is achieved.
    RESULTS: Correlation analysis of RNA-seq expression data from large publicly available datasets is a common method to leverage genetic diversity to infer gene co-expression modules. Here we use this method to investigate nuclear-mitochondrial gene expression coordination. We identify a pitfall in correlation analysis that results from the large variation in the proportion of transcripts from the mitochondrial genome in RNA-seq data. Commonly used normalisation techniques based on total read counts, such as FPKM or TPM, produce artefactual negative correlations between mitochondrial- and nuclear-encoded transcripts. This also results in artefactual correlations between pairs of nuclear-encoded genes, with important consequences for inferring co-expression modules beyond mitochondria. We show that these effects can be overcome by normalizing using the median-ratio normalisation (MRN) or trimmed mean of M values (TMM) methods. Using these normalisations, we find only weak and inconsistent correlations between mitochondrial and nuclear-encoded mitochondrial genes in the majority of healthy human tissues from the GTEx database.
    CONCLUSIONS: We show that a subset of healthy tissues with high expression of NF-κB show significant coordination, suggesting a role for NF-κB in ensuring balanced expression between mitochondrial and nuclear genes. Contrastingly, most cancer types show robust coordination of nuclear and mitochondrial OXPHOS gene expression, identifying this as a feature of gene regulation in cancer.
    DOI:  https://doi.org/10.1186/s13059-021-02541-6
  7. Front Mol Biosci. 2021 ;8 767088
    A Conserved Mitochondrial Chaperone-Protease Complex Involved in Protein Homeostasis.
    Mauro Serricchio, Peter Bütikofer.
      Mitochondria are essential organelles involved in cellular energy production. The inner mitochondrial membrane protein stomatin-like protein 2 (SLP-2) is a member of the SPFH (stomatin, prohibitin, flotilin, and HflK/C) superfamily and binds to the mitochondrial glycerophospholipid cardiolipin, forming cardiolipin-enriched membrane domains to promote the assembly and/or stabilization of protein complexes involved in oxidative phosphorylation. In addition, human SLP-2 anchors a mitochondrial processing complex required for proteolytic regulation of proteins involved in mitochondrial dynamics and quality control. We now show that deletion of the gene encoding the Trypanosoma brucei homolog TbSlp2 has no effect on respiratory protein complex stability and mitochondrial functions under normal culture conditions and is dispensable for growth of T. brucei parasites. In addition, we demonstrate that TbSlp2 binds to the metalloprotease TbYme1 and together they form a large mitochondrial protein complex. The two proteins negatively regulate each other's expression levels by accelerating protein turnover. Furthermore, we show that TbYme1 plays a role in heat-stress resistance, as TbYme1 knock-out parasites displayed mitochondrial fragmentation and loss of viability when cultured at elevated temperatures. Unbiased interaction studies uncovered putative TbYme1 substrates, some of which were differentially affected by the absence of TbYme1. Our results support emerging evidence for the presence of mitochondrial quality control pathways in this ancient eukaryote.
    Keywords:  Yme1; cardiolipin; membrane proteins; mitochondria; mitochondrial stress response; prohibitin; stomatin-like protein 2; trypanosoma
    DOI:  https://doi.org/10.3389/fmolb.2021.767088
  8. Commun Biol. 2021 Dec 02. 4(1): 1350
    ER-misfolded proteins become sequestered with mitochondria and impair mitochondrial function.
    Adrián Cortés Sanchón, Harshitha Santhosh Kumar, Matilde Mantovani, Ivan Osinnii, José María Mateos, Andres Kaech, Dimitri Shcherbakov, Rashid Akbergenov, Erik C Böttger.
      Proteostasis is a challenge for cellular organisms, as all known protein synthesis machineries are error-prone. Here we show by cell fractionation and microscopy studies that misfolded proteins formed in the endoplasmic reticulum can become associated with and partly transported into mitochondria, resulting in impaired mitochondrial function. Blocking the endoplasmic reticulum-mitochondria encounter structure (ERMES), but not the mitochondrial sorting and assembly machinery (SAM) or the mitochondrial surveillance pathway components Msp1 and Vms1, abrogated mitochondrial sequestration of ER-misfolded proteins. We term this mitochondria-associated proteostatic mechanism for ER-misfolded proteins ERAMS (ER-associated mitochondrial sequestration). We testify to the relevance of this pathway by using mutant α-1-antitrypsin as an example of a human disease-related misfolded ER protein, and we hypothesize that ERAMS plays a role in pathological features such as mitochondrial dysfunction.
    DOI:  https://doi.org/10.1038/s42003-021-02873-w
  9. Angew Chem Int Ed Engl. 2021 Nov 30.
    Substrate profiling of mitochondrial caseinolytic protease P via a site-specific photocrosslinking approach.
    Tuan-Anh Nguyen, Thomas Gronauer, Timon Nast-Kolb, Stephan Sieber, Kathrin Lang.
      Approaches for profiling protease substrates are critical for defining protease functions, but remain challenging tasks. Here we combine genetic code expansion, photocrosslinking and proteomics to identify substrates of the mitochondrial (mt) human caseinolytic protease P (hClpP). Site-specific incorporation of the diazirine-bearing amino acid DiazK into the inner proteolytic chamber of hClpP, followed by UV-irradiation of cells allows to covalently trap hClpP to substrate proteins and to substantiate hClpP's major involvement in maintaining overall mt homeostasis. In addition to confirming many of the previously annotated hClpP substrates, our approach adds a diverse set of new proteins to the hClpP interactome. Importantly, our workflow allows to identify substrate dynamics upon external cues in an unbiased manner. Identification of unique hClpP-substrate proteins upon induction of mt oxidative stress, suggests that hClpP counteracts oxidative stress by processing of proteins that are involved in respiratory chain complex synthesis and maturation as well as in catabolic pathways.
    Keywords:  Genetic code expansion; Proteomics; human caseinolytic protease P; photocrosslinking; protease profiling
    DOI:  https://doi.org/10.1002/anie.202111085
  10. Exp Gerontol. 2021 Nov 30. pii: S0531-5565(21)00430-7. [Epub ahead of print] 111648
    Effects of high-intensity interval training on mitochondrial supercomplex assembly and biogenesis, mitophagy, and the AMP-activated protein kinase pathway in the soleus muscle of aged female rats.
    Chong Han, Peng Lu, Shi-Zhan Yan.
       PURPOSE: Exercise helps improve mitochondrial function to combat sarcopenia. Certain parts of the mitochondrial respiratory chain complex can form a higher-order structure called "supercomplex" to reduce the production of reactive oxygen species and improve muscle mass. The effect of exercise on the assembly of the mitochondrial supercomplex is still unclear. The aim of this study was to investigate the effects of long-term high-intensity interval training (HIIT) on mitochondrial biogenesis, mitophagy, and mitochondrial supercomplexes (mitoSCs) assembly in aging soleus muscle.
    METHODS: Female Sprague-Dawley rats (n = 36) were randomly divided into four groups: young sedentary (Y-SED, 8 months old, n = 12), old sedentary (O-SED, 26 months old, n = 12), moderate-intensity continuous training (MICT, from 18 to 26 months old, n = 12), and HIIT (from 18 to 26 months old, n = 12). Rats in the MICT and HIIT groups were subjected to an 8-month training program. Real-time fluorescent quantitative polymerase chain reaction was used to measure the expression of the antioxidative factors, inflammatory factors, and mitochondrial fusion- and division-related genes. Western blotting was used to detect the expression of mitochondrial biogenesis and mitophagy markers and AMP-activated protein kinase (AMPK) pathway proteins. Enzyme-linked immunosorbent assays were used to determine serum irisin contents. Blue native polyacrylamide gel electrophoresis was used to assess the formation of mitochondrial supercomplexes.
    RESULTS: Compared with the Y-SED group, the soleus muscle and mitochondria in the O-SED group showed reduced expression of mitophagy- and mitochondrial biogenesis-related proteins. In the HIIT group, the expression of autophagy-related proteins in the soleus muscle and mitochondria was significantly increased compared with that in the MICT group. Serum irisin and mitochondrial fusion protein levels significantly decreased with age. Superoxide dismutase 2 protein levels and AMPK pathway protein expression were significantly increased in the HIIT group compared with those in the other groups. Additionally, the expression levels of mitoSCs and the mRNA levels of interleukin-15 and optical atrophy 1 increased in the HIIT group compared with that in the MICT group.
    CONCLUSION: Compared with MICT, HIIT activated the AMPK pathway to upregulate mitochondrial biogenesis- and mitophagy-related proteins, and promote the assembly and formation of mitoSCs to improve the mitochondrial function of aging soleus muscles.
    Keywords:  AMPK pathway; High-intensity interval training, aging; Mitochondrial supercomplex; Mitophagy
    DOI:  https://doi.org/10.1016/j.exger.2021.111648
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