bims-minimp 2021-12-05 papers

on Mitochondria, innate immunity, proteostasis

Issue of 2021–12–05
ten papers selected by
Hanna Salmonowicz, International Institute of Molecular Mechanisms and Machines of the Polish Academy of Sciences

ER-misfolded proteins become sequestered with mitochondria and impair mitochondrial function.
A Conserved Mitochondrial Chaperone-Protease Complex Involved in Protein Homeostasis.
Pathways shaping the mitochondrial inner membrane.
Age-related activation of cGAS-STING signaling in the auditory system is associated with presbycusis in C57BL/6J male mice.
Global mitochondrial protein import proteomics reveal distinct regulation by translation and translocation machinery.
Mitochondrial homeostasis is maintained in the absence of autophagy.
Mitochondrial TFAM as a Signaling Regulator between Cellular Organelles: A Perspective on Metabolic Diseases.
Malignancy and NF-κB signalling strengthen coordination between expression of mitochondrial and nuclear-encoded oxidative phosphorylation genes.
Ndufs4 knockout mouse models of Leigh syndrome: pathophysiology and intervention.
Substrate profiling of mitochondrial caseinolytic protease P via a site-specific photocrosslinking approach.

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
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
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
Neuroscience. 2021 Nov 27. pii: S0306-4522(21)00591-1. [Epub ahead of print]

Age-related activation of cGAS-STING signaling in the auditory system is associated with presbycusis in C57BL/6J male mice.

Jinlan Liu, Huiying Chen, Xiaoyu Lin, Jianqi Yi, Wanli Ye, Fangyu Wei, Xiaoting Zhu, Jialin Huang, Jiping Su.

  Presbycusis, or age-related hearing loss (ARHL), is primarily associated with sensory or transduction nerve cell degeneration in the peripheral and/or central auditory systems. During aging, the auditory system shows mitochondrial dysfunction and increased inflammatory responses. Mitochondrial dysfunction promotes leakage of mitochondrial DNA (mtDNA) into the cytosol, which activates the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway to induce type I interferon and inflammatory responses. However, whether this pathway is involved in the occurrence and development of ARHL is unknown. This study aimed to determine whether there are age-related changes in the levels of cytosolic mtDNA and cGAS-STING pathway activation in the auditory pathway and to explore their relationship with ARHL. The results showed that cGAS-positive immunoreactive cells were observed in the cochlea, inferior colliculus, and auditory cortex. Levels of cytosolic mtDNA, cGAS, STING, phosphorylated interferon regulatory factor 3, and cytokines were significantly increased in the cochlea, inferior colliculus, and auditory cortex of 6-, 9-, and 12-month-old mice compared with 3-month-old mice. These findings suggested that cytosolic mtDNA may play an important role in the pathogenesis of ARHL by activating cGAS-STING-mediated type I interferon and inflammatory responses.

Keywords:  age-related hearing loss; aging; cGAS–STING pathway; inflammation; mitochondrial DNA

DOI:  https://doi.org/10.1016/j.neuroscience.2021.11.031
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
Mol Cell Oncol. 2021 ;8(5): 1984162

Mitochondrial homeostasis is maintained in the absence of autophagy.

Christina G Towers.

  Autophagy is a central recycling process, and it plays a complex role in cancer. We discovered that when autophagy is blocked, cancer cells compensate by increasing mitochondrial-derived vesicles. However, there are many unanswered questions remaining, particularly in the context of the dual roles of autophagy in cancer.

Keywords:  Autophagy; cancer; mitochondria; mitochondrial derived vesicles; mitophagy

DOI:  https://doi.org/10.1080/23723556.2021.1984162
Diabetes Metab J. 2021 Nov;45(6): 853-865

Mitochondrial TFAM as a Signaling Regulator between Cellular Organelles: A Perspective on Metabolic Diseases.

Jin-Ho Koh, Yong-Woon Kim, Dae-Yun Seo, Tae-Seo Sohn.

  Tissues actively involved in energy metabolism are more likely to face metabolic challenges from bioenergetic substrates and are susceptible to mitochondrial dysfunction, leading to metabolic diseases. The mitochondria receive signals regarding the metabolic states in cells and transmit them to the nucleus or endoplasmic reticulum (ER) using calcium (Ca2+) for appropriate responses. Overflux of Ca2+ in the mitochondria or dysregulation of the signaling to the nucleus and ER could increase the incidence of metabolic diseases including insulin resistance and type 2 diabetes mellitus. Mitochondrial transcription factor A (Tfam) may regulate Ca2+ flux via changing the mitochondrial membrane potential and signals to other organelles such as the nucleus and ER. Since Tfam is involved in metabolic function in the mitochondria, here, we discuss the contribution of Tfam in coordinating mitochondria-ER activities for Ca2+ flux and describe the mechanisms by which Tfam affects mitochondrial Ca2+ flux in response to metabolic challenges.

Keywords:  Calcium; Cell nucleus; Diabetes mellitus, type 2; Endoplasmic reticulum; Mitochondria; TFAM protein

DOI:  https://doi.org/10.4093/dmj.2021.0138
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
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
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